Prerpints.org logo
Preprint
Article

Leaf Proteomic Analysis in Two Maize Landraces With Different Tolerance to Boron Toxicity

Altmetrics

Downloads

159

Views

69

Comments

0

A peer-reviewed article of this preprint also exists.

supplementary.xlsx (4.14MB )

Submitted:

04 May 2023

Posted:

05 May 2023

You are already at the latest version

Alerts
Abstract
Boron (B) toxicity is an important stress that negatively affects maize yield and quality production. The excessive B content in agricultural lands is a growing problem due to the increase in arid and semi-arid areas because of climate change. Recently, two Peruvian maize landraces, Sama and Pachía, were physiologically characterized based on their tolerance to B toxicity, the former being more tolerant to B excess than Pachía. However, many aspects regarding the molecular mechanisms of these two maize landraces against B toxicity are still unknown. In this study, a leaf proteomic analysis of Sama and Pachía was performed. Out of a total of 2793 proteins identified only 303 proteins were differentially accumulated. Functional analysis indicated that many of these proteins are involved in transcription and translation processes, amino acids metabolism, photosynthesis, carbohydrate metabolism, protein degradation, and protein stabilization and folding. Compared to Sama, Pachía had a higher number of differentially expressed proteins related to protein degradation, and transcription and translation processes under B toxicity conditions, which might reflect the greater protein damage caused by B toxicity in Pachía. Our results suggest that higher tolerance to B toxicity of Sama can be attributed to more stable photosynthesis that would avoid damage caused by stromal over-reduction under this stress condition.
Keywords: 
Subject: Biology and Life Sciences  -   Plant Sciences

1. Introduction

Boron (B) is an essential element for plants being well known its structural role in both cell walls and membranes [1,2,3,4,5]. Actually, B establishes diester bonds between apiose residues of two rhamnogalacturonan-II (RGII) molecules forming RGII-B complexes that stabilize the pectin network of the cell wall [6,7,8]. Furthermore, B contributes to the preservation of plasmalemma integrity and function [9], likely through the formation of B complexes with membrane components that contain cis-diol groups [10,11]. Thereby, B forms complexes with major constituents of membrane lipid rafts, such a as glycosyl inositol phosphoryl ceramides (GIPCs) [12]. Moreover, B participates in the formation of GIPCs-B-RGII complexes, which connect the plasmalemma to the cell wall [13]. Besides these structural roles, B is also involved in plant development participating in root and shoot elongation, pollen-tube growth, flowering, and fruiting [14,15,16]. In addition, B has been reported to participate in several physiological processes, such as photosynthesis, nucleic acid synthesis, phenolic, nitrogen and polyamines metabolisms, proteins stabilization and biosynthesis, and gene expression, among others [16,17,18,19,20,21,22].
Since B is a micronutrient, the range between its deficient, optimal, and toxic concentrations for plants is very narrow [23]. Therefore, it is common to find soils with inadequate B content for optimal plant development. Soils with high B contents predominantly occurs in arid and semi-arid countries, where this micronutrient accumulates in the topsoil mainly owing to high evapotranspiration and tiny leaching caused by low rainfall, a situation that is often aggravated by irrigation with B-enriched water [22,23]. Additionally, excess B is also found in lands close to coastal areas due to the hydraulic connection between their coastal aquifers and seawater [24] or in regions with recurrent geothermal activities [2]. Climate change is another factor that is contributing to the B increase in soils. Increasing temperatures and decreasing rainfall are predicted in the coming years, which will lead to an increase in agricultural areas with excessive B levels [3,25].
Excessive B contents in soils cause adverse effects such as chlorosis and necrosis in leaves, damages to stems and buds, and misshapen fruits [17,22]. Furthermore, an excess of B provokes DNA damages, inhibition of protein folding, impairment of protein functions and activities, and alterations in photosynthesis and nitrogen and carbon metabolisms, among other processes [2,22,26]. In fact, several photosynthetic parameters, such as CO2 assimilation (PN), photosynthetic electron transport rate (ETR), maximum quantum yield of chlorophyll fluorescence (Fv/Fm), and CO2 use efficiency decreased under B toxicity conditions [22,27]. Because of the aforementioned effects of B toxicity in plant physiology, elevated B contents in agricultural lands reduce crop growth, yield, and quality [22,28]. In fact, a noteworthy decrease in the yield of several main crops subjected to B toxicity has been reported [28]. Despite the large number of effects caused by B toxicity in plants, it is not well known how B produces these alterations. However, it has been suggested that the ability of B to form bonds with molecules containing mono-, di- and poly-hydroxyl groups could be the chemical basis by which B toxicity could trigger morphophysiological alterations [29].
Maize is an important crop that provides approximately half of the calories consumed worldwide being, in addition, one of the principal genetic model plants for crop improvement and food security [30,31,32]. However, maize production is seriously constrained by abiotic and biotic stresses [33]. In particular, B toxicity causes a decrease in maize production as well as in other cereals [28,34,35]. Therefore, the search and molecular characterization of new maize varieties with improved tolerance to B toxicity has become an interesting research topic. In a recent work, two Peruvian maize landraces (Pachía and Sama) were tested for tolerance to high B. The Sama landrace had greater tolerance to B excess than Pachía [27]. In this work, a comparative proteomic characterization of these two maize landraces with different tolerance to B toxicity was performed to improve our molecular knowledge about which proteins are involved in B-toxicity tolerance.

2. Results

A total of 2793 proteins were identified in at least one of the biological replicates of a landrace (Sama or Pachía) and a B treatment analyzed (Table S1a). In addition, the number of proteins detected in both Pachía and Sama in each of the B treatments studied was similar being close to 1100 proteins (Table 1).
Table S1a shows the dataset of the identified proteins indicating their gene ontology (GO) biological processes (GOBP), GO molecular functions (GOMF), and GO cellular compartments (GOCC), and Table S1b summarizes the statistical analysis and fold changes of the proteins. To study the differentially accumulated proteins in Pachía and Sama in both B treatments, four comparison groups were established: 1) Sama and Pachía seedlings subjected to the control B condition (S0.05/P0.05), 2) Sama and Pachía treated with 10 mM B (S10/P10), 3) Sama subjected to 10 mM and 0.05 mM B (S10/S0.05), and 4) Pachía treated with 10 mM and 0.05 mM B (P10/P0.05). A total of 303 proteins had statistically significant differential expression (P ≤ 0.05) in the above groups (Table S2). The S0.05/P0.05 and S10/P10 groups contain those proteins that were differentially expressed between Sama and Pachía in 0.05 mM or 10 mM B, respectively. In media with 0.05 mM B, more proteins were up- and down-accumulated between Sama and Pachía than in 10 mM B (Figure 1 and Table 1). In addition, the S10/S0.05 and P10/P0.05 comparison groups included proteins that were differentially expressed in response to B toxicity in Sama or Pachía, respectively. Pachía had a higher number of proteins induced and repressed by B toxicity than Sama, thus 98 proteins were up-expressed in Pachía in 10 mM B while only 38 in Sama and 51 proteins were down-expressed in Pachía under B toxicity versus 28 in Sama (Figure 1).

2.1. Classification into several functional categories of differentially accumulated proteins in both maize landraces and B treatments

All significant differentially expressed proteins in the four comparison groups described above were functionally classified into 26 categories using several databases (Table S2). The functional categories that included the largest number of differentially accumulated proteins were transcription and translation processes (57), photosynthesis (25), amino acid metabolism (24), protein degradation (23), carbohydrate metabolism (20), and protein stabilization and folding (18) (Figure 2 and Table S2). These main categories together contained more than 50% of the total differentially expressed proteins.

2.2. Differentially expressed proteins in Sama and Pachía in response to B toxicity

Considering that the major aim of this work was to analyze the changes provoked by B toxicity on protein expressions in Pachía and Sama, we will now focus on the proteins that were differentially expressed by B toxicity in these landraces. Thus, 66 and 149 proteins were differentially expressed in response to B toxicity in Sama and Pachía, respectively (Table 1). The main functional categories containing the highest number of differentially expressed proteins under B toxicity in both Sama and Pachía were transcription and translation, photosynthesis, amino acid metabolism, protein degradation, protein stabilization and folding, and reactive oxygen species (ROS) (Figure 3 and Figure 4). Interestingly, most of the proteins belonging to the transcription and translation category were induced in response to B toxicity in both Sama and Pachía, the number of differentially induced proteins being remarkably higher in Pachía (Figure 3 and Figure 4). However, almost all proteins included in the photosynthesis category were repressed in 10 mM B, the number of down-accumulated proteins being also higher in Pachía than in Sama (Figure 4 and Table S2). Regarding protein degradation, and protein stabilization and folding, most of the differentially expressed proteins in 10 mM B were found in Pachía, suggesting that B toxicity would alter the structure and folding of proteins in this landrace. In addition, many of the proteins in the ROS category were induced by B toxicity in both landraces (Figure 4 and Table S2). Although the groups of carbon assimilation and metabolism, lipid metabolism, and respiration included a smaller number of proteins that those mentioned above, nevertheless, a larger number of differentially expressed proteins were found in Pachía under B toxicity (Figure 4 and Table S2). Other interesting categories were cell death, cell division, cell wall, ribosome biogenesis, and RNA binding and processing which, despite having a very small number of proteins regulated by B toxicity, had an interesting distribution in both landraces and B treatments. In fact, in the cell death and cell wall categories, only proteins whose expressions were induced by B toxicity were found in Pachía, however, the cell division, ribosome biogenesis, and RNA binding and processing categories also contained proteins with higher accumulation in 10 mM B but in both landraces (Figure 4 and Table S2).
A total of 18 proteins were commonly expressed (repressed or induced) in both landraces in response to B toxicity, with the amino acid metabolism and photosynthesis categories having the highest number of proteins (Table 2). All proteins of the amino acid metabolism group were up-accumulated under B toxicity conditions, with these inductions being slightly greater in Pachía than in Sama. Interestingly, however, all commonly expressed proteins from the photosynthesis category were repressed by B toxicity, these repressions being remarkably higher in Pachía than in Sama (Table 2).
Table 3 and Table 4 list the most strongly differentially expressed proteins that were up- or down-regulated more than twofold by B toxicity in Pachía and Sama, respectively. In Pachía, 105 proteins had strong differential expression under B toxicity, while only 27 were found in Sama. Photosynthesis was the functional category containing the highest number of proteins whose expressions were strongly down-accumulated in response to B toxicity in both Pachía and Sama, however, interestingly, both minor number of repressed and very strongly repressed (FC <0.33) proteins were observed in Sama (Tables 3,4, and S2). Different subunits of the NDH complex (NDHS, B1, B2, J, and H) were strongly repressed by B toxicity in Pachía but not in Sama (Tables 3, 4, and S2). In addition, only in Pachía were detected proteins related to protein degradation processes whose expressions were mainly induced by B toxicity suggesting that enhanced damage would be provoked by 10 mM B in Pachía proteins (Table 3). Furthermore, B toxicity markedly induced a larger number (15) of proteins in Pachía belonging to the transcription and translation category (Table 3).
Table 5 shows the proteins that were strongly up- or down-accumulated when protein expressions of Sama were compared to those of Pachía in media with 10 mM B. Sama had a remarkable up-accumulation of four proteins involved in photosynthesis (ZmPIFI and OEE2-1), chlorophyll biosynthesis (ChlH1), and secondary metabolism (PAO1) being, in addition, this last protein strongly induced in response to B toxicity (Table 4 and Table 5). However, in Pachía several proteins were detected with a strong accumulation in 10 mM B when compared with Sama (shown in Table 5 as strongly down-accumulated proteins in Sama) highlighting, among them, histone H1 and ribosomal protein S7 which, besides, were strongly induced by B toxicity (Table 3 and Table 5).
Finally, in both Pachía and Sama, proteins exclusively detected in one of these landraces were found, among them, Nfc103a and eIF3a, which were only identified in Pachía in 10 mM B (Table 6).

3. Discussion

Although 2793 proteins were detected in this proteomic analysis, only 303 proteins were differentially accumulated (Tables S1a and S2), which were classified into 26 functional categories. Functional analysis indicated that pathways involved in transcription and translation processes, amino acids metabolism, photosynthesis, carbohydrate metabolism, protein degradation, and protein stabilization and folding were highly enriched categories in both landraces (Figure 2). Remarkably, the expression levels of proteins related to these enriched processes were significantly different between Pachía and Sama.

3.1. Several proteases and translation-related proteins would allow Pachía to survive in media with B excess

Pachía is a B-sensitive maize cultivar described by Mamani-Huarcaya et al. [27]. Interestingly, the highest number of differentially accumulated proteins (DAPs) was found in the comparison group P10/P0.05 (Figure 1) suggesting that the B toxicity damage caused in Pachía could be partially relieved by these proteins. A remarkable number of these DAPs included in the categories of protein degradation (11), and transcription and translation (15) were strongly overexpressed in Pachía (Table S2 and 3). However, only four proteins of the transcription and translation group were markedly induced by 10 mM B in Sama (Table 4). The B-sensitive Citrus grandis had a higher number of proteins involved in protein degradation that was also overexpressed under B toxicity conditions in comparison with B-tolerant Citrus sinensis [36]. These authors concluded that B toxicity caused greater protein damage and proteolysis in C. grandis. Therefore, the high number of protein degradation-related proteins that were overexpressed in Pachía in 10 mM B would suggest that B toxicity would cause greater damage in Pachía proteins than in those of Sama leading to increased proteolysis in B-sensitive Pachía. Proteins related to protein degradation strongly overexpressed in Pachía included, among others, cysteine protease14 and four serine proteases (Table 3). Proteases have been implicated in plant acclimation to abiotic stress, playing a major role in the degradation of damaged and misfolded proteins, thus contributing to cell survival. In fact, cysteine and serine proteases are involved in degradation of misfolded proteins and protection against abiotic stresses [37,38,39,40]. Hence, these five proteases could have a main role in the degradation of damaged and misfolded proteins in Pachía under excess B, contributing to maintaining the correct conformation of Pachía proteins and, therefore, to the survival of this landrace under this stressful condition. In addition, a noteworthy number of proteins involved in transcription and translation processes were overexpressed at 10 mM B in Pachía, namely, 30 in contrast to only nine of Sama (Table S2). Proteomic analysis performed with dehydration, salt, and temperature stresses in cereals also displayed alterations in the levels of translation-related proteins, such as initiation factors and the ribosome constituent proteins ([41] and references therein). Furthermore, it has been suggested that a B excess provokes inhibition of RNA-dependent processes, such as transcription and translation, owing to the ability of B to form complexes with ribose molecules [42]. In this regard, Tanaka et al. [43] have suggested that B or boric acid acts on the translation machinery likely forming complexes with cis-diol groups of rRNA and tRNA. In addition, it has currently been proposed that high-B stress enhances ribosome frequency on stop codons leading to a global ribosome stalling [44]. Consequently, the high contents of leaf-soluble B in Pachía seedlings subjected to 10 mM B reported by Mamani-Huarcaya et al. [27] would generate an increased formation of B complexes with cis-diol groups of RNA that would damage ribosomes leading to a drop in protein synthesis likely through a global ribosome stalling. The strong overexpression of several ribosomal proteins would maintain the Pachía ribosome stability in B toxicity (Tables S2 and 3). These results are consistent with those reported for rice, where several ribosomal protein large subunit genes were upregulated under temperature stress, suggesting that their encoded proteins might be involved in stress amelioration, likely maintaining the proper functioning of ribosomes [41]. Interestingly, the eukaryotic translation initiation factor 3 subunit A (eIF3a) was exclusively detected in B toxicity in Pachía (Table 6). These factors are one of the most significant components involved in plant protein synthesis and, specifically, rice eIF3A has been proposed to play an important role in different stresses [45]. Therefore, eIF3a would also help to alleviate the drop in protein synthesis in Pachía. Thereby, Pachía would partly ameliorate injuries caused by B toxicity on protein synthesis and ribosome by overexpressing a high number of transcription- and translation-related proteins, abolishing a non-viable reduction of transcription and translation processes.

3.2. Proteins that would confer Sama more B toxicity tolerance

Polyamine oxidase 1 (PAO1) is an interesting protein that was clearly up-accumulated in Sama when compared to Pachía at 10 mM B and was also strongly induced in Sama by B toxicity (Table 4 and Table 5). This enzyme catalyzes the back conversion of spermine (Spm) to spermidine (Spd), and Spd to putrescine (Put) [46]. Maize polyamines play a crucial role in abiotic stress response [33]. In fact, it has been reported that Put protects the plant photosynthetic apparatus against several abiotic stresses [47]. Moreover, the conjugation of Put to PSII proteins may lead to the structural and functional stability of PSII [46,48]. Therefore, the over-accumulation of PAO1 in Sama plants subjected to B toxicity would generate an increase in Put levels that would protect their photosynthetic apparatus resulting in the higher PN observed in Sama under this stress, as described by Mamani-Huarcaya et al. [27]. This finding is consistent with results reported for Karoon, a drought-tolerant maize cultivar. Pakdel et al. [46] proposed that higher expression of PAO genes and enzymatic polyamine oxidation activity would protect the photosynthetic apparatus of Karoon under water stress.

3.2.1. Lower repression of photosynthesis-related proteins would enhance the B-toxicity tolerance of Sama

Photosynthesis is one of the essential physiological processes affected by B toxicity [2,22]. Photosynthetic efficiency could be achieved in Sama under B toxicity conditions increasing the synthesis of photosynthetic pigments, since chlorophyll content is a major limiting component of the photosynthetic efficiency [49]. Interestingly, Sama had a strong over-accumulation of magnesium-chelatase subunit H1 chloroplastic (ChlH1) at 10 mM B in comparison with those from Pachía (Table 5). ChlH binds to porphyrin and catalyzes the insertion of Mg2+ into protoporphyrin IX [50]. Accordingly, the over-accumulation of ChlH1 in Sama would explain its higher contents of chlorophyll a in B toxicity and the higher PN described by Mamani-Huarcaya et al. [27].
In this study, 25 proteins related to photosynthetic light reactions were differentially accumulated, most of them involved in electron transport, light harvesting, and oxygen evolving processes (Table S2). Pachía and Sama presented several photosynthesis-related proteins that were repressed by B toxicity when their expressions were compared with those of Pachía and Sama, respectively, in media with 0.05 mM B (Table S2). However, the number of these DAPs was lower in Sama than in Pachía (11 versus 16, respectively; Table S2) and, besides, those proteins commonly down-accumulated in both landraces had a weaker decrease in Sama (Table 2). In addition, only two photosynthetic proteins were strongly down-expressed 3-fold or more (corresponding to FC≤ 0.33) by B toxicity in Sama in contrast to ten proteins found in Pachía (Table 3 and Table 4). This decreased accumulation of photosynthesis related-proteins may cause lower photosynthetic performance in B-toxicity-treated Pachía plants than in Sama plants, as described by Mamani-Huarcaya et al. [27]. Therefore, Sama would retain sufficient levels of photosynthesis-related proteins in 10 mM B, which would allow it to maintain photosynthetic parameters at similar levels to those of the control conditions, as reported by Mamani-Huarcaya et al. [27]. Furthermore, three photosynthesis-related proteins were up-accumulated in Sama when their expressions were compared with those of Pachía in 10 mM B, namely, oxygen-evolving enhancer protein 2-1 chloroplastic (OEE2-1), post-illumination chlorophyll fluorescence increase (ZmPIFI), and NAD(P)H-quinone oxidoreductase subunit S chloroplastic (NDHS) (Tables 5 and S2). OEE2-1 is likely an extrinsic protein of the oxygen-evolving complex (OEC) (UniProt; https://www.uniprot.org/). The OEC is stabilized and protected by extrinsic polypeptides [51]. The strong OEE2-1 over-accumulation in 10 mM B in Sama could facilitate the stability and protection of the OEC leading to the higher photosynthetic electron transporter rate (ETR) observed in this landrace [27]. Regarding ZmPIFI, it is homologous to the PIFI protein of Arabidopsis thaliana (AtPIFI), an essential component of the NAD(P)H dehydrogenase (NDH) complex involved in chlororespiratory electron transport around PSI [52]. The Atpifi mutant had a lower nonphotochemical quenching (NPQ) than wild type under high light irradiances, suggesting that AtPIFI would protect plants from photooxidative stress triggered by excessive light [52]. Consequently, both ZmPIFI over-accumulation and the higher NPQ values that Sama showed in 10 mM B, unlike those from Pachía (Table 5; [27]), suggest that ZmPIFI would also be a component of the maize NDH complex playing a role in oxidative photoprotection of this landrace under B-toxicity conditions. Furthermore, unlike Sama, several subunits of the NDH complex were markedly repressed in Pachía by B toxicity (Tables S2, 3, and 4). The NDH complex mediates cyclic electron transport around PSI playing a crucial role in C4 photosynthesis [53,54]. NDH-mediated cycle electron transport (NDH-CET) performs two functions: 1) maintaining photosynthetic redox balance in the electron transfer avoiding stromal overreduction and functioning as a safety valve for excess electrons under stress, and 2) supplying ATP for efficient carbon assimilation, especially under stressful conditions [53,54,55,56]. The finding that none of the above components of the NDH complex was significantly repressed by B-toxicity in Sama suggests that its NDH-CET would prevent stromal overreduction and would protect against photooxidation. This fact would explain the high values of net photosynthetic CO2 assimilation (PN), maximum photochemical efficiency (Fv’/Fm’), and quantum yield efficiency of PSII electron transport (ΦPSII) reported in Sama at 10 mM B, which were similar to those of control conditions [27]. Consistent with our data, Zhu et al. [56] have suggested that an increased abundance of NDH subunits in salt-stressed wheat would enhance NDH-CET alleviating the accumulation of excess electrons and maintaining energy homeostasis. Moreover, the subunit S of the NDH complex was over-accumulated in Sama under B toxicity when compared to those from Pachía, leading to a likely higher amount of NDH-complex that would provide extra ATP to achieve better PN and growth at this landrace in media with 10 mM B as, in fact, was observed by Mamani-Huarcaya et al. [27]. In addition, a higher supply of ATP could be obtained in Sama in comparison to Pachía under B toxicity from a weaker decrease of the α- and β-chloroplastic subunits of ATP synthase in Sama (Table 2). Although B excess causes photosynthetic damage [2,22], plants have evolved mechanisms to repair these injuries that require a high amount of ATP from chloroplastic ATP synthase [57,58]. In Sama, B toxicity barely affected photosynthetic parameters [27]. This finding points out that this landrace would own mechanisms to repair its photosynthetic machinery. Likely, one of these mechanisms would be to provide greater ATP availability, which would be achieved by maintaining sufficient levels of NDH and ATP synthase complexes that would synthesize the amounts of ATP needed to repair its photosynthetic machinery and, therefore, to maintain its photosynthetic values at levels similar to those of control conditions.

4. Materials and Methods

4.1. Plant materials and growth conditions

Sama and Pachía, two Peruvian maize landraces from the Sama valley and the Pachía district (to the east of Tacna), were used in this study. Seeds were surface-sterilized as described by Mamani-Huarcaya et al. [27]. Afterwards, the seeds were placed in seedbeds filled with a perlite/vermiculite mixture (1/1, v/v) and watered with deionized H2O. After seven days, seedlings were transplanted to 30-L plastic containers with a nutrient solution (NS) that was identical to the one used by Mamani-Huarcaya et al. [27]. After two days of acclimation to hydroponic medium, the seedlings were divided into groups and transferred to fresh NS supplemented with 10 mM H3BO3 (B toxicity conditions) or 0.05 mM H3BO3 (control conditions). This medium was aerated by air pumps and renewed twice a week. The seedlings were germinated and grown hydroponically in a growth chamber under a 12 h light/12 h dark regime (215 µmol m–2 s–1 of photosynthetically active radiation at plant height), at 22ºC and 50% relative humidity. The plants were randomly harvested 10 days after the onset of the B treatments and their leaves were quickly separated with a scalpel, frozen in liquid nitrogen and stored at –80°C until further analysis.

4.2. Protein extraction and digestion

Maize leaves (200-250 mg fresh weight) from four separate seedlings per condition (B treatment and maize landrace) were ground to a fine powder in a mortar precooled with liquid nitrogen. Proteins were extracted with trichloroacetic acid (TCA)/acetone-phenol [59], solubilized in a solution containing 7 M urea, 2 M thiourea and 2% (w/v) CHAPS (3 [(3-cholamidopropyl) dimethylammonium]-1-propanesulfonate), and quantified by the Bradford method using bovine serum albumin (BSA) as a standard [60].
The cleaning of maize protein extract, protein digestion, and mass spectrometry determinations were carried out at the Proteomics Facility for Research Support Central Service (SCAI) of the University of Córdoba (Spain) as follows.
Biological quadruplicate samples were separated and cleaned as described. Leaf protein extracts (50 µg of BSA protein equivalents per sample) were electrophoretically pre-concentrated in a centimeter band of 10% (w/v) SDS-PAGE gel. Protein bands were excised from the gels and, afterwards, the gel pieces were distained in 200 mM ammonium bicarbonate/50% acetonitrile for 15 min, followed by 5 min in 100% acetonitrile. Proteins were reduced by addition of 20 mM dithiothreitol in 25 mM ammonium bicarbonate and incubated for 20 min at 55 °C. The mixture was cooled to room temperature and then free thiols were alkylated by adding 40 mM iodoacetamide in 25 mM ammonium bicarbonate for 20 min in the dark. Finally, the gel pieces were washed twice in 25 mM ammonium bicarbonate.
Proteolytic digestion was performed by addition of trypsin to a final concentration of 12.5 ng/µL in 25 mM ammonium bicarbonate at 37 ºC overnight. Protein digestion was stopped by adding trifluoroacetic acid at a final concentration of 1% (v/v). Finally, the digested samples were vacuum-dried and dissolved in a mixture of 2% (v/v) acetonitrile and 0.05% (v/v) trifluoroacetic acid.

4.3. Shotgun-DDA-LC-MS/MS analysis

Peptide separations were performed on a nano-LC using Dionex Ultimate 3000 nano UPLC (Thermo Scientific, San Jose, CA, USA), equipped with a C18 75 μm × 50 cm Acclaim Pepmap column (Thermo Scientific, San Jose, CA, USA), at 40 °C at a flow rate of 300 nL/min. Peptide mixtures were previously concentrated and cleaned up on a 300 µm x 5 mm Acclaim Pepmap precolumn (Thermo Scientific, San Jose, CA, USA) using 2% acetonitrile/0.05% trifluoroacetic acid at 5 µL/min for 5 min. Peptides were eluted with a gradient of 60 min ranging from 96% solvent A (0.1% formic acid) to 90% solvent B (80% acetonitrile and 0.1% formic acid), followed by an 8 min wash at 90% solvent B and a 12 min re-equilibration at 4% solvent B. Eluted peptides were converted to gas-phase ions by nanoelectrospray ionization and analyzed on a Thermo Orbitrap Fusion mass spectrometer (Thermo Scientific, San Jose, CA, USA) operated in the positive mode. Survey scans of peptide precursors were acquired over the m/z range 400−1500 at 120K resolution (at 200 m/z) with a 4 × 105 ion count target. Tandem MS was performed by isolation at 1.2 Da with the quadrupole. Monoisotopic precursor ions were fragmented by CID (Chemically Induced Dimerization) in the ion trap, which was set up as follows: automatic gain control, 2 × 103; maximum injection time, 50 ms; and normalized collision energy of 35%. Only those precursors with charge state 2–5 were sampled for MS2. A dynamic exclusion time of 15 s and a tolerance of 10 ppm around the selected precursor and its isotopes were used to avoid redundant fragmentations. The instrument was run in top 30 mode with 3-s cycles, meaning the instrument would continuously perform MS2 events until a maximum of top 30 non-excluded precursors or 3 s, whichever was shorter.

4.4. Protein quantification

Charge state deconvolution and deisotoping were not performed. MS2 spectra were searched using MaxQuant software v. 1.5.7.4 [61]. MS2 spectra were searched with Andromeda engines against a database of Uniprot Zea mays_Jun19. Peptides generated from tryptic digestion were searched employing the following parameters: up to one missed cleavage, carbamidomethylation of cysteines as fixed modifications, and oxidation of methionine as variable modifications. The precursor mass tolerance was 10 ppm and product ions were searched at 0.6 Da tolerances. A target-decoy search strategy was applied, which integrates multiple peptide parameters such as length, charge, number of modifications, and identification score into a single quality that acts as statistical evidence on the quality of each single peptide spectrum match. The identified peptides were grouped into proteins according to the law of parsimony and filtered to 1% false discovery rate (FDR). Peptide quantification was carried out using MaxQuant software, in a MaxLFQ label-free quantification method [62]. In the MaxLFQ label-free quantification method, a retention time alignment and identification transfer protocol (“match-between runs” feature inMaxQuant) was applied. Proteins identified from only one peptide were not taken into account in this analysis. Peak intensities across the whole set of quantitative data for all peptides in the samples were imported from the LFQ intensities of proteins from the MaxQuant analysis and normalized according to Cox et al. [62]. LFQ normalized intensity values were transformed to a logarithmic scale with base two. Protein quantification and calculation of statistical significance were carried out using Student-t test and error correction (P-value ≤ 0.05). The criteria used to consider a protein as differentially expressed were as follows: (a) the protein was consistently present in at least three biological replicates per condition; (b) it had statistically significant differences (Student-t test, P ≤ 0.05) between genotypes or B treatments; and (c) a fold change ≥ 1.5 or ≤ 0.66667. The differentially accumulated proteins were manually categorized by function using different databases (Uniprot, https://www.uniprot.org/; Maize Genetics and Genomics, https://www.maizegdb.org/; ExplorEnz, https://www.enzyme-database.org/; BRENDA, https://www.brenda-enzymes.org/; KEGG: Kyoto Encyclopedia of Genes and Genomes, https://www.genome.jp/kegg/; and PANTHER: Protein ANalysis THrough Evolutionary Relationships, http://pantherdb.org/).

5. Conclusions

Overexpression of several proteases and transcription- and translation-related proteins would allow Pachía to degrade and replace partially the proteins damaged by B toxicity achieving survival under this stress condition.
In Sama, PAO1 over-accumulation and weaker knockdown of several subunits of NDH and ATP synthase complexes under B excess would confer a greater B toxicity tolerance to this landrace by: 1) acting as an electron safety valve that would avoid stromal overreduction, and thus decrease photosynthetic damage and, 2) providing an additional supply of ATP that would contribute to repair the photosynthetic system of Sama.

Supplementary Materials

The following supporting information can be downloaded at the website of this paper posted on Preprints.org. Table S1a: Dataset of proteins identified by shotgun-DDA analysis; Table S1b: Dataset, statistical analysis and fold change of proteins identified by shotgun-DDA analysis; Table S2: Fold change ratios, P-values and statistical significances of all significantly accumulated proteins classified by functional categories.

Author Contributions

Plant growth and harvesting, and protein extraction and quantification, B.M.M.-H. with substantial contribution of M.T.N.-G. and J.R.; research planning and design, J.R. with the help of all authors; analysis and interpretation of data, J.R.; writing - first draft, J.R.; editing and review - second draft, J.R. and A.G.-F. All authors critically revised the manuscript and made significant contributions. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by Agencia Andaluza de Cooperación Internacional para el Desarrollo (Consejería de Igualdad y Políticas Sociales) from Junta de Andalucía (2016SEC014), and by the Consejería de Economía, Innovación, Ciencia y Empleo from Junta de Andalucía (BIO-266).

Data Availability Statement

The data presented in this study are available in the text and supplemental data.

Acknowledgments

The authors would like to thank SCAI of the University of Córdoba (Spain) for protein identification and, especially, to Carlos Fuentes Almagro his skillful technical assistance.

Conflicts of Interest

The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results.

References

  1. Warington, K. The effect of boric acid and borax on the broad bean and certain other plants. Ann. Bot. 1923, 37, 629–672. [Google Scholar] [CrossRef]
  2. Princi, M.P.; Lupini, A.; Araniti, F.; Longo, C.; Mauceri, A.; Sunseri, F.; Abenavoli, M.R. Boron toxicity and tolerance in plants: recent advances and future perspectives. In Plant Metal Interaction: Emerging Remediation Techniques; Ahmad, P., Ed.; Elsevier Inc: Amsterdam, Netherlands, 2016; pp. 115–147. [Google Scholar]
  3. González-Fontes, A.; Fujiwara, T. Advances in plant boron. Int. J. Mol. Sci. 2020, 21, 4107. [Google Scholar] [CrossRef]
  4. González-Fontes, A. Why boron is an essential element for vascular plants. New Phytol. 2020, 226, 1228–1230. [Google Scholar] [CrossRef]
  5. Wimmer, M.A.; Abreu, I.; Bell, R.W.; Bienert, M.D.; Brown, P.H.; Dell, B.; Fujiwara, T.; Goldbach, H.E.; Lehto, T.; Mock, H.-P.; et al. Boron: an essential element for vascular plants. New Phytol. 2020, 226, 1232–1237. [Google Scholar] [CrossRef]
  6. Ishii, T.; Matsunaga, T. Isolation and characterization of a boron-rhamnogalacturonan-II complex from cell walls of sugar beet pulp. Carbohydr. Res. 1996, 284, 1–9. [Google Scholar] [CrossRef]
  7. Kobayashi, M.; Matoh, T.; Azuma, J. Two chains of rhamnogalacturonan II are cross-linked by borate-diol ester bonds in higher plant cell walls. Plant Physiol. 1996, 110, 1017–1020. [Google Scholar] [CrossRef]
  8. O’Neill, M.A.; Warrenfeltz, D.; Kates, K.; Pellerin, P.; Doco, T.; Darvill, A.G.; Albersheim, P. Rhamnogalacturonan-II, a pectic polysaccharide in the walls of growing plant cell, forms a dimer that is covalently cross-linked by a borate ester. J. Biol. Chem. 1996, 271, 22923–22930. [Google Scholar] [CrossRef]
  9. Cakmak, I.; Römheld, V. Boron deficiency-induced impairments of cellular functions in plants. Plant Soil 1997, 193, 71–83. [Google Scholar] [CrossRef]
  10. Goldbach, H.E.; Yu, Q.; Wingender, R.; Schulz, M.; Wimmer, M.; Findeklee, P.; Baluška, F. Rapid response reactions of roots to boron deprivation. J. Plant Nutr. Soil Sci. 2001, 164, 173–181. [Google Scholar] [CrossRef]
  11. Brown, P.H.; Bellaloui, N.; Wimmer, M.A.; Bassil, E.S.; Ruiz, J.; Hu, H.; Pfeffer, H.; Dannel, F.; Römheld, V. Boron in plant biology. Plant Biol. 2002, 4, 205–223. [Google Scholar] [CrossRef]
  12. Voxeur, A.; Fry, S.C. Glycosylinositol phosphorylceramides from Rosa cell cultures are boron-bridged in the plasma membrane and form complexes with rhamnogalacturonan II. Plant J. 2014, 79, 139–149. [Google Scholar] [CrossRef]
  13. Wang, N.; Yang, C.; Pan, Z.; Liu, Y.; Peng, S. Boron deficiency in woody plants: various responses and tolerance mechanisms. Front. Plant Sci. 2015, 6, 916. [Google Scholar] [CrossRef] [PubMed]
  14. Blevins, D.G.; Lukaszewski, K.M. Boron in plant structure and function. Annu. Rev. Plant Physiol. Plant Molec. Biol. 1998, 49, 481–500. [Google Scholar] [CrossRef] [PubMed]
  15. Camacho-Cristóbal, J.J.; Navarro-Gochicoa, M.T.; Rexach, J.; González-Fontes, A.; Herrera-Rodríguez, M.B. Plant response to boron deficiency and boron use efficiency in crop plants. In Plant Micronutrient Use Efficiency. Molecular and Genomic Perspectives in Crop Plants; Hossain, M.A., Kamiya, T., Burritt, D.J., Phan Tran, L.-S., Fujiwara., T., Eds.; Elsevier Inc., 2018; pp. 109–121. [Google Scholar]
  16. Shireen, F.; Nawaz, M.A.; Chen, C.; Zhang, Q.; Zheng, Z.; Sohail, H.; Sun, J.; Cao, H.; Huang, Y.; Bie, Z. Boron: functions and approaches to enhance its availability in plants for sustainable agriculture. Int. J. Mol. Sci. 2018, 19, 1856. [Google Scholar] [CrossRef] [PubMed]
  17. Reid, R.J.; Hayes, J.E.; Post, A.; Stangoulis, J.C.R.; Graham, R.D. A critical analysis of the causes of boron toxicity in plants. Plant Cell Environ. 2004, 27, 1405–1414. [Google Scholar] [CrossRef]
  18. Camacho-Cristóbal, J.J.; Rexach, J.; González-Fontes, A. Boron in plants: deficiency and toxicity. J. Integr. Plant Biol. 2008, 50, 1247–1255. [Google Scholar] [CrossRef]
  19. Beato, V.M.; Rexach, J.; Navarro-Gochicoa, M.T.; Camacho-Cristóbal, J.J.; Herrera-Rodríguez, M.B.; Maldonado, J.M.; González-Fontes, A. A tobacco asparagine synthetase gene responds to carbon and nitrogen status and its root expression is affected under boron stress. Plant Sci. 2010, 178, 289–298. [Google Scholar] [CrossRef]
  20. Beato, V.M.; Navarro-Gochicoa, M.T.; Rexach, J.; Herrera-Rodríguez, M.B.; Camacho-Cristóbal, J.J.; Kempa, S.; Weckwerth, W.; González-Fontes, A. Expression of root glutamate dehydrogenase genes in tobacco plants subjected to boron deprivation. Plant Physiol. Biochem. 2011, 49, 1350–1354. [Google Scholar] [CrossRef]
  21. Liu, X.; Zhang, J.-W.; Guo, L.-X.; Liu, Y.-Z.; Jin, L.-F.; Hussain, S.B.; Du, W.; Deng, Z.; Peng, S.-A. Transcriptome changes associated with boron deficiency in leaves of two citrus scion-rootstock combinations. Front. Plant Sci. 2017, 8, 317. [Google Scholar] [CrossRef]
  22. Landi, M.; Margaritopoulou, T.; Papadakis, I.E.; Araniti, F. Boron toxicity in higher plants: an update. Planta 2019, 250, 1011–1032. [Google Scholar] [CrossRef]
  23. Brdar-Jokanovi´c, M. Boron toxicity and deficiency in agricultural plants. Int. J. Mol. Sci. 2020, 21, 1424. [Google Scholar] [CrossRef]
  24. Kabay, N.; Güler, E.; Bryjak, M. Boron in seawater and methods for its separation—a review. Desalination 2010, 261, 212–217. [Google Scholar] [CrossRef]
  25. Chatzistathis, T.; Fanourakis, D.; Aliniaeifard, S.; Kotsiras, A.; Delis, C.; Tsaniklidis, G. Leaf age-dependent effects of boron toxicity in two Cucumis melo varieties. Agronomy. 2021, 11, 759. [Google Scholar] [CrossRef]
  26. Uluisik, I.; Karakaya, H.C.; Koc, A. The importance of boron in biological systems. J. Trace Elem. Med. Biol. 2018, 45, 156–162. [Google Scholar] [CrossRef]
  27. Mamani-Huarcaya, B.M.; González-Fontes, A.; Navarro-Gochicoa, M.T.; Camacho-Cristóbal, J.J.; Ceacero, C.J.; Herrera-Rodríguez, M.B.; Fernández Cutire, Ó.; Rexach, J. Characterization of two Peruvian maize landraces differing in boron toxicity tolerance. Plant Physiol. Biochem. 2022, 185, 167–177. [Google Scholar] [CrossRef] [PubMed]
  28. Behera, B.; Kancheti, M.; Raza, M.B.; Shiv, A.; Mangal, V.; Rathod, G.; Altaf, M.A.; Kumar, A.; Aftab, T.; Kumar, R.; et al. Mechanistic insight on boron-mediated toxicity in plant vis-a-vis its mitigation strategies: a review. Int. J. Phytoremediat. 2023, 25, 9–26. [Google Scholar] [CrossRef]
  29. Ralston, N.V.C.; Hunt, C.D. Diadenosine phosphates and S-adenosylmethionine: novel boron binding biomolecules detected by capillary electrophoresis. Biochim. Biophys. Acta 2001, 1527, 20–30. [Google Scholar] [CrossRef] [PubMed]
  30. Liang, Z.; Pandey, P.; Stoerger, V.; Xu, Y.; Qiu, Y.; Ge, Y.; Schnable, J.C. Conventional and hyperspectral timeseries imaging of maize lines widely used in field trials. GigaScience 2018, 72, 1–11. [Google Scholar]
  31. Andorf, C.; Beavis, W.D.; Hufford, M.; Smith, S.; Suza, W.P.; Wang, K.; Woodhouse, M.; Yu, J.; Lübberstedt, T. Technological advances in maize breeding: past, present, and future. Theor. Appl. Genet. 2019, 132, 817–849. [Google Scholar] [CrossRef]
  32. Kausch, A.P.; Wang, K.; Kaeppler, H.F.; Gordon-Kamm, W. Maize transformation: history, progress, and perspectives. Mol. Breed. 2021, 41, 38. [Google Scholar] [CrossRef]
  33. Xi, Y.; Hu, W.; Zhou, Y.; Liu, X.; Qian, Y. Genome-wide identification and functional analysis of polyamine oxidase genes in maize reveal essential roles in abiotic stress tolerance. Front. Plant Sci. 2022, 13, 950064. [Google Scholar] [CrossRef]
  34. Ogunwole, A.A.; Otusanya, O.O.; Oloyede, F.A.; Olabamiji, T.M. Comparative effects of boron toxicity and deficiency on the growth, chlorophyll, protein and some cations accumulation in Zea mays seedlings. Int. J. Sci. Res. Innov. 2015, 17, 316–335. [Google Scholar]
  35. Gotz, L.F.; Silvestrin, F.; Motta, A.C.V.; Pauletti, V. Response to application and tissue diagnosis of boron deficiency and toxicity in maize. Commun. Soil Sci. Plant Anal. 2021, 52, 2898–2911. [Google Scholar] [CrossRef]
  36. Sang, W.; Huang, Z.-R.; Yang, L.-T.; Guo, P.; Ye, X.; Chen, L.-S. Effects of high toxic boron concentration on protein profiles in roots of two citrus species differing in boron-tolerance revealed by a 2-DE based MS approach. Front. Plant Sci. 2017, 8, 180. [Google Scholar] [CrossRef]
  37. Fan, T.; Bykova, N.V.; Rampitsch, C.; Xing, T. Identification and characterization of a serine protease from wheat leaves. Eur. J. Plant Pathol. 2016, 146, 293–304. [Google Scholar] [CrossRef]
  38. Malefo, M.B.; Mathibela, E.O.; Crampton, B.G.; Makgopa, M.E. Investigating the role of Bowman-Birk serine protease inhibitor in Arabidopsis plants under drought stress. Plant Physiol. Biochem. 2020, 149, 286–293. [Google Scholar] [CrossRef]
  39. D’Ippolito, S.; Rey-Burusco, M.F.; Feingold, S.E.; Guevara, M.G. Role of proteases in the response of plants to drought. Plant Physiol. Biochem. 2021, 168, 1–9. [Google Scholar] [CrossRef]
  40. Sharma, P.; Gayen, D. Plant protease as regulator and signaling molecule for enhancing environmental stress-tolerance. Plant Cell Reports. 2021, 40, 2081–2095. [Google Scholar] [CrossRef]
  41. Moin, M.; Bakshi, A.; Saha, A.; Dutta, M.; Madhav, S.M.; Kirti, P.B. Rice ribosomal protein large subunit genes and their spatio-temporal and stress regulation. Front. Plant Sci. 2016, 7, 1284. [Google Scholar] [CrossRef]
  42. Nozawa, A.; Miwa, K.; Kobayashi, M.; Fujiwara, T. Isolation of Arabidopsis thaliana cDNAs that confer yeast boric acid tolerance. Biosci. Biotechnol. Biochem. 2006, 70, 1724–1730. [Google Scholar] [CrossRef]
  43. Tanaka, M.; Sotta, N.; Yamazumi, Y.; Yamashita, Y.; Miwa, K.; Murota, K.; Chiba, Y.; Hirai, M.Y.; Akiyama, T.; Onouchi, H.; et al. The minimum open reading frame, AUG-stop, induces boron-dependent ribosome stalling and mRNA degradation. Plant Cell 2016, 28, 2830–2849. [Google Scholar] [CrossRef] [PubMed]
  44. Sotta, N.; Chiba, Y.; Miwa, K.; Takamatsu, S.; Tanaka, M.; Yamashita, Y.; Naito, S.; Fujiwara, T. Global analysis of boron-induced ribosome stalling reveals its effects on translation termination and unique regulation by AUG-stops in Arabidopsis shoots. Plant J. 2021, 106, 1455–1467. [Google Scholar] [CrossRef]
  45. Saidi, A.; Hajibarat, Z. In-silico analysis of eukaryotic translation initiation factors (eIFs) in response to environmental stresses in rice (Oryza sativa). Biologia 2020, 75, 1731–1738. [Google Scholar] [CrossRef]
  46. Pakdel, H.; Hassani, S.B.; Ghotbi-Ravandi, A.A.; Bernard, F. Contrasting the expression pattern change of polyamine oxidase genes and photosynthetic efficiency of maize (Zea mays L.) genotypes under drought stress. J. Biosci. 2020, 45, 73. [Google Scholar] [CrossRef]
  47. Shu, S.; Guo, S.-R.; Sun, J.; Yuan, L.-Y. Effects of salt stress on the structure and function of the photosynthetic apparatus in Cucumis sativus and its protection by exogenous putrescine. Physiol. Plant. 2012, 146, 285–296. [Google Scholar] [CrossRef]
  48. Hamdani, S.; Yaakoubi, H.; Carpentier, R. Polyamines interaction with thylakoid proteins during stress. J. Photochem. Photobiol. B-Biol. 2011, 104, 314–331. [Google Scholar] [CrossRef]
  49. Chen, M.; Blankenship, R.E. Expanding the solar spectrum used by photosynthesis. Trends Plant Sci. 2011, 16, 427–431. [Google Scholar] [CrossRef]
  50. Zhang, D.; Chang, E.; Yu, X.; Chen, Y.; Yang, Q.; Cao, Y.; Li, X.; Wang, Y.; Fu, A.; Xu, M. Molecular characterization of magnesium chelatase in soybean [Glycine max (L.) Merr.]. Front. Plant Sci. 2018, 9, 720. [Google Scholar] [CrossRef]
  51. Sasi, S.; Venkatesh, J.; Daneshi, R.F.; Gururani, M.A. Photosystem II extrinsic proteins and their putative role in abiotic stress tolerance in higher plants. Plants, 2018, 7, 100. [Google Scholar] [CrossRef] [PubMed]
  52. Wang, D.; Portis, A.R. A novel nucleus-encoded chloroplast protein, PIFI, is involved in NAD(P)H dehydrogenase complex-mediated chlororespiratory electron transport in Arabidopsis. Plant Physiol. 2007, 144, 1742–1752. [Google Scholar] [CrossRef] [PubMed]
  53. Ishikawa, N.; Takabayashi, A.; Noguchi, K.; Tazoe, Y.; Yamamoto, H.; von Caemmerer, S.; Sato, F.; Endo, T. NDH-mediated cyclic electron flow around photosystem I is crucial for C4 photosynthesis. Plant Cell Physiol. 2016, 57, 2020–2028. [Google Scholar] [CrossRef] [PubMed]
  54. Ma, M.; Liu, Y.; Bai, C.; Yong, J.W.H. The significance of chloroplast NAD(P)H dehydrogenase complex and its dependent cyclic electron transport in photosynthesis. Front. Plant Sci. 2021, 12, 661863. [Google Scholar] [CrossRef]
  55. Yamori, W.; Shikanai, T. Physiological functions of cyclic electron transport around photosystem I in sustaining photosynthesis and plant growth. Annu. Rev. Plant Biol. 2016, 67, 81–106. [Google Scholar] [CrossRef]
  56. Zhu, D.; Luo, F.; Zou, R.; Liu, J.; Yan, Y. Integrated physiological and chloroplast proteome analysis of wheat seedling leaves under salt and osmotic stresses. J. Proteomics 2021, 234, 104097. [Google Scholar] [CrossRef] [PubMed]
  57. Murata, N.; Nishiyama, Y. ATP is a driving force in the repair of photosystem II during photoinhibition. Plant Cell Environ. 2018, 41, 285–299. [Google Scholar] [CrossRef]
  58. Araniti, F.; Miras-Moreno, B.; Lucini, L.; Landi, M.; Abenavoli, M.R. Metabolomic, proteomic and physiological insights into the potential mode of action of thymol, a phytotoxic natural monoterpenoid phenol. Plant Physiol. Biochem. 2020, 153, 141–153. [Google Scholar] [CrossRef]
  59. Wang, W.; Vignani, R.; Scali, M.; Cresti, M. A universal and rapid protocol for protein extraction from recalcitrant plant tissues for proteomic analysis. Electrophoresis 2006, 27, 2782–2786. [Google Scholar] [CrossRef]
  60. Bradford, M.M. A rapid and sensitive method for the quantitation of microgram quantities of proteins utilizing the principle of protein-dye binding. Anal. Biochem. 1976, 72, 248–254. [Google Scholar] [CrossRef]
  61. Cox, J.; Mann, M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 2008, 26, 1367–1372. [Google Scholar] [CrossRef]
  62. Cox, J.; Hein, M.Y.; Luber, C.A.; Paron, I.; Nagaraj, N.; Mann, M. Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ. Mol. Cell. Proteomics 2014, 13, 2513–2526. [Google Scholar] [CrossRef] [PubMed]
Preprints 72661 g001
Figure 1. Number of significantly (P ≤ 0.05) accumulated proteins up or down, represented as positive and negative, respectively, comparing maize landraces and B treatments. Seedlings were subjected to 0.05 and 10 mM B for 10 days. Results were obtained from 3-4 separate plants of each landrace and B treatments. For more details, see Materials and Methods. S: Sama landrace; P: Pachía landrace; 0.05: 0.05 mM B (B control treatment); 10: 10 mM B (B toxicity treatment). The numbers above the columns represent the numbers of proteins accumulated up (green) or down (red).
Figure 1. Number of significantly (P ≤ 0.05) accumulated proteins up or down, represented as positive and negative, respectively, comparing maize landraces and B treatments. Seedlings were subjected to 0.05 and 10 mM B for 10 days. Results were obtained from 3-4 separate plants of each landrace and B treatments. For more details, see Materials and Methods. S: Sama landrace; P: Pachía landrace; 0.05: 0.05 mM B (B control treatment); 10: 10 mM B (B toxicity treatment). The numbers above the columns represent the numbers of proteins accumulated up (green) or down (red).
Preprints 72661 g001
Preprints 72661 g002
Figure 2. Number of differentially accumulated proteins (DAPs) in the different functional categories obtained from the four comparisons shown in Figure 1 and Table S2. Seedlings of Sama and Pachía landraces were subjected to 0.05 and 10 mM B for 10 days. Results were obtained by addition of the DAPs in the four comparisons. For more details, see Materials and Methods. Aa: amino acid metabolism; CA: carbon assimilation and Calvin cycle; CM: carbohydrate metabolism; CDe: cell death; CDi: cell division; CW: cell wall; DNA: DNA and chromatin organization and DNA repair; LM: lipid metabolism; NM: nitrogen metabolism; NPM: nucleotide, purine, and pyrimidine metabolism; OT: others; ORP: oxidation and reduction processes; PLR: photosynthetic light reactions; PB: pigment biosynthesis; PD: protein degradation; PSF: protein stabilization and folding; ROS: reactive oxygen species scavenging pathways/response to oxidative stress; R: respiration metabolism (glycolysis, TCA cycle, and mitochondrial electron transfer); RB: ribosome biogenesis; RBP: RNA binding and processing; SM: secondary metabolism; SG: signaling; ST: stress; TT: transcription and translation processes; TP: transporters and transport processes; NWK: not well-known proteins.
Figure 2. Number of differentially accumulated proteins (DAPs) in the different functional categories obtained from the four comparisons shown in Figure 1 and Table S2. Seedlings of Sama and Pachía landraces were subjected to 0.05 and 10 mM B for 10 days. Results were obtained by addition of the DAPs in the four comparisons. For more details, see Materials and Methods. Aa: amino acid metabolism; CA: carbon assimilation and Calvin cycle; CM: carbohydrate metabolism; CDe: cell death; CDi: cell division; CW: cell wall; DNA: DNA and chromatin organization and DNA repair; LM: lipid metabolism; NM: nitrogen metabolism; NPM: nucleotide, purine, and pyrimidine metabolism; OT: others; ORP: oxidation and reduction processes; PLR: photosynthetic light reactions; PB: pigment biosynthesis; PD: protein degradation; PSF: protein stabilization and folding; ROS: reactive oxygen species scavenging pathways/response to oxidative stress; R: respiration metabolism (glycolysis, TCA cycle, and mitochondrial electron transfer); RB: ribosome biogenesis; RBP: RNA binding and processing; SM: secondary metabolism; SG: signaling; ST: stress; TT: transcription and translation processes; TP: transporters and transport processes; NWK: not well-known proteins.
Preprints 72661 g002
Preprints 72661 g003
Figure 3. Functional categories of 303 maize proteins given as the number of those significantly expressed, represented as positive (up-accumulated) and negative (down-accumulated). Seedlings of Sama (S) and Pachía (P) landraces were subjected to 0.05 and 10 mM B for 10 days. Results were obtained from 3-4 separate plants of each landrace and B treatments. For more details, see Materials and Methods. 0.05: 0.05 mM B (B control treatment); 10: 10 mM B (B toxicity treatment).
Figure 3. Functional categories of 303 maize proteins given as the number of those significantly expressed, represented as positive (up-accumulated) and negative (down-accumulated). Seedlings of Sama (S) and Pachía (P) landraces were subjected to 0.05 and 10 mM B for 10 days. Results were obtained from 3-4 separate plants of each landrace and B treatments. For more details, see Materials and Methods. 0.05: 0.05 mM B (B control treatment); 10: 10 mM B (B toxicity treatment).
Preprints 72661 g003
Preprints 72661 g004
Figure 4. Number of induced or repressed proteins in Sama and Pachía landraces in the different functional categories obtained from the comparisons between B toxicity and B control conditions shown in Table S2. Seedlings of Sama and Pachía landraces were subjected to 0.05 (control) and 10 mM (toxicity) B for 10 days. Results were obtained by addition of the induced or repressed proteins in Sama and Pachía. For more details, see Materials and Methods. Aa: amino acid metabolism; CA: carbon assimilation and Calvin cycle; CM: carbohydrate metabolism; CDe: cell death; CDi: cell division; CW: cell wall; DNA: DNA and chromatin organization and DNA repair; LM: lipid metabolism; NM: nitrogen metabolism; NPM: nucleotide, purine, and pyrimidine metabolism; OT: others; ORP: oxidation and reduction processes; PLR: photosynthetic light reactions; PB: pigment biosynthesis; PD: protein degradation; PSF: protein stabilization and folding; ROS: reactive oxygen species scavenging pathways/response to oxidative stress; R: respiration metabolism (glycolysis, TCA cycle, and mitochondrial electron transfer); RB: ribosome biogenesis; RBP: RNA binding and processing; SM: secondary metabolism; SG: signaling; ST: stress; TT: transcription and translation processes; TP: transporters and transport processes; NWK: not well-known proteins.
Figure 4. Number of induced or repressed proteins in Sama and Pachía landraces in the different functional categories obtained from the comparisons between B toxicity and B control conditions shown in Table S2. Seedlings of Sama and Pachía landraces were subjected to 0.05 (control) and 10 mM (toxicity) B for 10 days. Results were obtained by addition of the induced or repressed proteins in Sama and Pachía. For more details, see Materials and Methods. Aa: amino acid metabolism; CA: carbon assimilation and Calvin cycle; CM: carbohydrate metabolism; CDe: cell death; CDi: cell division; CW: cell wall; DNA: DNA and chromatin organization and DNA repair; LM: lipid metabolism; NM: nitrogen metabolism; NPM: nucleotide, purine, and pyrimidine metabolism; OT: others; ORP: oxidation and reduction processes; PLR: photosynthetic light reactions; PB: pigment biosynthesis; PD: protein degradation; PSF: protein stabilization and folding; ROS: reactive oxygen species scavenging pathways/response to oxidative stress; R: respiration metabolism (glycolysis, TCA cycle, and mitochondrial electron transfer); RB: ribosome biogenesis; RBP: RNA binding and processing; SM: secondary metabolism; SG: signaling; ST: stress; TT: transcription and translation processes; TP: transporters and transport processes; NWK: not well-known proteins.
Preprints 72661 g004
Table 1. Number of proteins detected in leaves of Pachía (P) and Sama (S) landraces under different boron (B) treatments and number of significant differentially accumulated proteins (DAPs) in Pachía and Sama landraces under different B treatments.
Table 1. Number of proteins detected in leaves of Pachía (P) and Sama (S) landraces under different boron (B) treatments and number of significant differentially accumulated proteins (DAPs) in Pachía and Sama landraces under different B treatments.
P0.05 mM (Control) P10 mM B (B toxicity) S0.05 mM (control) S10 mM (B toxicity)
Number of detected proteins1 1100 1040 1111 1145
S0.05 versus P0.05
(Control conditions) 		S10 versus P10
(B toxicity conditions)
Number of significant DAPs between Sama and Pachía 99 60
Sama
S10 versus S0.05 		Pachía
P10 versus P0.05
Number of significant DAPs by B toxicity 66 149
1 Numbers of proteins that were detected in at least one landrace (Sama or Pachía) and one B treatment analyzed.
Table 2. Commonly expressed proteins in both Pachía and Sama landraces in response to boron (B) toxicity.
Table 2. Commonly expressed proteins in both Pachía and Sama landraces in response to boron (B) toxicity.
Pachía Sama
Protein ID1 Gene Name/ID2 Protein name
/ Annotation		 FC3 P-value4 FC3 P-
value4 		FCSA/
FCPA5 		Function/Biological process6
Amino acid metabolism
B6SKB7 Zm00001d031013 Methylcrotonoyl-CoA carboxylase subunit α 4.44 0.0022 3.56 0.0049 0.80 Leucine degradation
A0A1D6K836 Zm00001d029848 Branched-chain-amino-acid aminotransferase 2.35 0.0272 1.65 0.0241 0.70 Branched-chain amino acid biosynthesis
B4G011 Zm00001d046923 D-3-phosphoglycerate dehydrogenase chloroplastic 2.31 0.0154 1.52 0.0202 0.66 Serine biosynthesis
A0A1D6DW07 Zm00001d002051 D-3-phosphoglycerate dehydrogenase 1.78 0.0494 1.69 0.0175 0.95 Serine biosynthesis
Carbon assimilation / Calvin cycle
O24574 Zm00001d004894 Ribulose bisphosphate carboxylase small chain 0.38 0.0113 0.33 0.0466 0.87 Carbon dioxide fixation
Carbohydrate metabolism
Q9FQ11 Zm00001d010523 Sucrose-phosphatase 1 1.50 0.0154 1.58 0.0420 1.05 Sucrose biosynthesis
A0A1D6IJ76 Zm00001d022107 Glyceraldehyde-3-phosphate dehydrogenase A 0.34 0.0319 0.51 0.0019 1.52 Carbon metabolism
Cell division
A0A1D6FRI4 Zm00001d010500 ERBB-3 binding protein 1 1.89 0.0387 1.58 0.0266 0.84 Cell division and cell growth regulation
Photosynthetic light reactions
A0A1D6HS38 Zm00001d018779 Oxygen-evolving enhancer protein 2-1 chloroplastic (OEE2-1) 0.27 0.0110 0.48 0.0354 1.78 Photosynthesis. Photosystem II oxygen evolving complex
B4FWG2 Zm00001d048422 Photosynthetic NDH subunit of subcomplex B 2 chloroplastic 0.25 0.0047 0.41 0.0200 1.62 Photosynthetic electron transport flow around photosystem I to produce ATP
A0A1X7YHG9 AtpA ATP synthase subunit α chloroplastic (ATPα) 0.20 0.0166 0.61 0.0163 2.99 Chloroplast ATP synthesis coupled proton transport
P46617 PetA Cytochrome f 0.18 0.0193 0.29 0.0161 1.59 Photosynthetic electron transport activity
P00827 Zm00001d006403 ATP synthase subunit β chloroplastic (ATPβ) 0.15 0.0076 0.52 0.0274 3.45 Chloroplast ATP synthesis coupled proton transport
Reactive Oxygen Species (ROS) Scavenging Pathways / Response to oxidative stress
A0A1D6MSE3 Zm00001d040721 Dihydrolipoyl dehydrogenase 2.30 0.0273 1.80 0.0205 0.78 Cell redox homeostasis
A0A1D6JPH3 Zm00001d027769 Glutathione reductase 2.21 0.0053 1.71 0.0436 0.77 Cell redox homeostasis. Glutathione metabolic process. Cellular oxidant detoxification
Ribosome biogenesis
K7UTH7 Zm00001d009596 GTPase ERA1 chloroplastic 2.61 0.0108 1.81 0.0126 0.69 Ribosome biogenesis. Ribosomal small subunit assembly. rRNA processing
Transcription and translation processes
A0A1D6LIV5 Zm00001d035802 Phenylalanine--tRNA ligase beta subunit cytoplasmic 2.56 0.0314 2.23 0.0093 0.87 Translation. Phenylalanyl-tRNA aminoacylation
Transporters and transport processes
B6SP43 Zm00001d007597 ABC family1 4.54 0.0103 2.69 0.0125 0.59 ATPase-coupled transmembrane transporter activity
1Proteins ID, Protein identification (ID) number in the UniProt database; 2Gene Name, name or ID number of the corresponding gene of the differentially expressed protein as searched in the Maize Genetics and Genomics Database (MaizeGDB; https://www.maizegdb.org/; 3Fold Change, is expressed as the ratio of LFQ intensities (on a logarithmic scale) of proteins between 10 and 0.05 mM B treatments; 4P-value, statistical level (using Student’s t-test) ≤ 0.05, at which differential protein expression was accepted as significant; 5FCSA/FCPA, is the ratio between fold change of Sama and Pachía. 6Function/Biological process, annotated biological functions or biological process based on different databases. Induced proteins are highlighted with light green rows and repressed proteins with light red rows. For more details, see Materials and Methods. Results were obtained from 3-4 separate plants of each landrace.
Table 3. Proteins with higher differential expression in Pachía leaves in response to boron (B) toxicity. This table shows the proteins strongly induced or repressed by B toxicity in Pachía by comparing their expressions with those of Pachía in medium with 0.05 mM B.
Table 3. Proteins with higher differential expression in Pachía leaves in response to boron (B) toxicity. This table shows the proteins strongly induced or repressed by B toxicity in Pachía by comparing their expressions with those of Pachía in medium with 0.05 mM B.
Protein ID1 Gene Name/ID2 Protein name/Annotation FC3 P-Value4 Function/Biological process5
AMINO ACID AND PEPTIDE METABOLISMS
Strongly induced proteins by B toxicity in Pachía
B6SKB7 Zm00001d031013 Methylcrotonoyl-CoA carboxylase subunit α 4.44 0.0022 Leucine degradation
B6SWZ4 Zm00001d050336 Methylcrotonoyl-CoA carboxylase β chain mitochondrial 2.85 0.0154 Leucine degradation
A0A1D6K836 Zm00001d029848 Branched-chain-amino-acid amino-transferase 2.35 0.0272 Branched-chain amino acid biosynthesis
B4G011 Zm00001d046923 D-3-phosphoglycerate dehydroge-nase chloroplastic 2.31 0.0154 Serine biosynthesis
C4J411 Zm00001d028464 Imidazole glycerol phosphate synthase hisHF 2.17 0.0017 Histidine biosynthesis
C4JBG7 Zm00001d015088 3-isopropylmalate dehydratase large subunit 2.14 0.0320 Leucine biosynthesis
Strongly repressed proteins by B toxicity in Pachía
B4FUH2 Zm00001d043382 Aspartate aminotransferase 0.48 0.0195 Amino acid metabolic process
B4FU01 Zm00001d045153 Cystathionine β-lyase chloroplas-tic 0.44 0.0235 Methionine biosynthetic. Cysteine biosynthetic process via cystathionine
A0A1D6ICL3 Zm00001d021596 Adenosine 5-phosphosulfate reductase-like1 0.29 0.0140 Cysteine biosynthetic process. Sulfate reduction
B6TZD1 Zm00001eb168430 Methylthioribose-1-phosphate isomerase 0.24 0.0461 Methionine biosynthesis
CARBON ASSIMILATION AND CALVIN CYCLE
Strongly induced proteins by B toxicity in Pachía
A0A1D6FQE4 Zm00001d010321 Pyruvate phosphate dikinase 2.31 0.0449 C4 photosynthetic carbon assimilation cycle
Strongly repressed proteins by B toxicity in Pachía
O24574 Zm00001d004894 Ribulose bisphosphate carboxylase small chain 0.38 0.0113 Carbon dioxide fixation
B4FQ59 Zm00001d017711 Phosphoribulokinase 0.33 0.0004 Calvin- Benson cycle
Q9ZT00 Zm00001eb164390 Ribulose bisphosphate carboxylase/oxygenase activase chloroplastic 0.26 0.0090 Carbon dioxide fixation. Rubisco activator activity
CARBOHYDRATE METABOLISM
Strongly induced proteins by B toxicity in Pachía
A0A1D6NE29 Zm00001d043662 α-amylase 3 chloroplastic 2.05 0.0460 Starch degradation
Strongly repressed proteins by B toxicity in Pachía
A0A1D6M7C2 Zm00001d038579 Phosphoglycerate kinase cytosolic 0.49 0.0136 Glycolysis and gluconeogenesis
B4FRC9 Zm00001d011965 Transaldolase 0.41 0.0407 Pentose-phosphate shunt
A0A1D6IJ76 Zm00001d022107 Glyceraldehyde-3-phosphate dehydrogenase A 0.34 0.0319 Carbon metabolism
CELL DEATH
Strongly induced proteins by B toxicity in Pachía
B4F8B9 Zm00001d018468 S-(hydroxymethyl)glutathione dehydrogenase 2.81 0.0027 Cell death. Formaldehyde oxidation (glutathione-dependent)
CELL WALL
Strongly induced proteins by B toxicity in Pachía
B4F9J1 Zm00001d046357 β-galactosidase 3.17 0.0092 Xyloglucan degradation
DNA AND CHROMATIN ORGANIZATION AND DNA REPAIR
Strongly induced proteins by B toxicity in Pachía
B6TGH8 Zm00001d034479 Histone H1 3.60 0.0349 Chromosome condensation. Nucleosome assembly. Nucleosome positioning
C0P6Q6 Zm00001d040416 DNA gyrase subunit B 3.48 0.0007 DNA topological change
Strongly repressed proteins by B toxicity in Pachía
B6SK03 Zm00001d053295 Ubiquitin-conjugating enzyme E2 variant 1C 0.39 0.0409 DNA postreplication repair. Protein polyubiquitination
LIPID METABOLISM
Strongly induced proteins by B toxicity in Pachía
K7VQG5 Zm00001d008727 Phospholipase D 2.30 0.0244 Phospholipid degradation
A0A1D6NE81 Zm00001d043680 Phospholipase A1-IIδ 2.02 0.0390 Lipid degradation
Strongly repressed proteins by B toxicity
B4FLS8 Zm00001d003584 12-oxo-phytodienoic acid reductase 5 0.33 0.0436 Fatty acid and oxylipin biosynthesis
NITROGEN METABOLISM
Strongly induced proteins by B toxicity in Pachía
A0A1D6PZA5 Zm00001d049995 Nitrate reductase 2.19 0.0077 Nitrate reductase (NADH) activity. Nitrate assimilation
OTHERS
Strongly induced proteins by B toxicity in Pachía
A0A1D6JGY3 Zm00001d026515 Molybdopterin molybdenum-transferase 2.92 0.0023 Molybdenum cofactor biosynthesis
A0A1D6HUN3 Zm00001d019040 D-2-hydroxyglutarate dehydrogenase mitochondrial 2.09 0.0380 Lysine degradation
Strongly repressed proteins by B toxicity in Pachía
C0PDB6 Zm00001d039535 HXXXD-type acyl-transferase family protein 0.40 0.0112 N-acyltransferase activity
C0PE12 Zm00001d009877 Protein plastid transcriptionally active 16 chloroplastic 0.24 0.0121 Circadian rhythm
OXIDATION AND REDUCTION PROCESSES
Strongly induced proteins by B toxicity in Pachía
A0A1D6M498 Zm00001d038189 FAD/NAD(P)-binding oxidoreductase family protein 2.04 0.0101 Oxidoreductase activity
PHOTOSYNTHETIC LIGHT REACTIONS
Strongly repressed proteins by B toxicity in Pachía
B6SSB9 Zm00001d035859 Plastocyanin 0.50 0.0300 Photosynthetic electron transport
A0A1D6GU53 Zm00001d014564 Oxygen-evolving enhancer protein 1-1 chloroplastic 0.47 0.0268 Photosynthesis. Oxygen evolving activity. Photosystem II assembly and stabilization
B6SUC4 Zm00001d046786 Chlorophyll a-b binding protein, chloroplastic 0.41 0.0086 Photosynthesis. Light harvesting in photosystem I
B6T927 Zm00001d014349 NAD(P)H-quinone oxidoreductase subunit S chloroplastic (NDHS) 0.39 0.0095 Photosynthetic electron transport chain
P25709 NdhH NAD(P)H-quinone oxidoreductase subunit H, chloroplastic 0.37 0.0022 Photosynthesis, light reaction. Photosynthetic electron transport chain. Couples the photosynthetic redox reaction to proton translocation
B6SP99 Zm00001d024148 Photosynthetic NDH subunit of subcomplex B 1 chloroplastic 0.33 0.0137 Photosynthetic electron transport in photosystem I
B4FJP7 Zm00001d027729 Photosynthetic NDH subunit of subcomplex B 2 chloroplastic 0.32 0.0169 Photosynthetic electron transport in photosystem I
B4FR80 Zm00001d033098 Post-illumination chlorophyll fluorescence increase (ZmPIFI) 0.28 0.0270 Chlororespiration
A0A1D6HS38 Zm00001d018779 Oxygen-evolving enhancer protein 2-1 chloroplastic (OEE2-1) 0.27 0.0110 Photosynthesis. Photosystem II oxygen evolving complex
B4FWG2 Zm00001d048422 Photosynthetic NDH subunit of subcomplex B 2 chloroplastic 0.25 0.0047 Photosynthetic electron transport flow around photosystem I to produce ATP
P19124 NdhJ NAD(P)H-quinone oxidoreductase subunit J, chloroplastic 0.22 0.0147 Photosynthesis, light reaction, photosynthetic electron transport chain. Couples the photosynthetic redox reaction to proton translocation
A0A1X7YHG9 AtpA ATP synthase subunit α (ATPα) 0.20 0.0166 Chloroplast ATP synthesis coupled proton transport
P46617 PetA Cytochrome f 0.18 0.0193 Photosynthetic electron transport chain
P00827 Zm00001d009488 ATP synthase subunit β, chloroplastic (ATPβ) 0.15 0.0076 Chloroplast ATP synthesis coupled proton transport
A0A1D6JYG6 Zm00001d028670 Photosynthetic NDH subunit of lumenal location 1 chloroplastic 0.13 0.0134 Part of photosystem II oxygen evolving complex
PIGMENT BIOSYNTHESIS
Strongly repressed proteins by B toxicity in Pachía
A0A1D6FAV8 Zm00001d008203 Protoporphyrinogen oxidase 0.38 0.0173 3,8-divinyl-chlorophyllide a and protoporphyrinogen IX biosynthesis
PROTEIN DEGRADATION
Strongly induced proteins by B toxicity in Pachía
B4FS65 Zm00001d005391 Cysteine protease 14 4.38 0.0146 Proteolysis. Proteolysis involved in protein catabolic process
A0A1D6HM49 Zm00001d018282 Subtilisin-like protease SBT1.4 3.70 0.0399 Serine protease. Serine-type endopeptidase activity. Proteolysis
A0A1D6H4R4 Zm00001d015962 Prolyl oligopeptidase family protein 3.58 0.0080 Proteolysis. Serine protease. Serine-type peptidase activity
Q84TL7 Zm00001d011036 Legumin-like protein 2.86 0.0453 Protein ubiquitination. Nutrient reservoir activity. Storage protein
A0A1D6KWW2 Zm00001d033194 Subtilisin-like protease 2.85 0.0403 Proteolysis. Serine protease. Serine-type endopeptidase activity
A0A1D6KV27 Zm00001d032956 Acylamino-acid-releasing enzyme 2.54 0.0086 Proteolysis. Serine protease. Serine-type endopeptidase activity
C0HI51 Zm00001d044102 Zn-dependent exopeptidase superfamily protein 2.53 0.0131 Proteolysis. Aminopeptidase. Metalloaminopeptidase activity
Q84TL6 Zm00001d035597 Legumin-like protein 2.36 0.0386 Protein ubiquitination. Storage protein. Nutrient reservoir activity
A0A1D6HL34 Zm00001d018145 Presequence protease 2 chloroplastic/mitochondrial 2.22 0.0180 Proteolysis. Metalloendopeptidase activity. Protein processing
K7VGG8 Zm00001d010522 ATP-dependent zinc metalloprotease FTSH 10 mitochondrial 2.07 0.0359 Proteolysis. Metalloprotease mitochondrial
C4JC43 Zm00001d049100 Target of Myb protein 1 2.04 0.0450 Proteolysis. Protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway
Strongly repressed proteins by B toxicity in Pachía
A0A1D6H558 Zm00001d016036 Chloroplast processing peptidase 0.47 0.0438 Protease. Serine-type endopeptidase activity
B4FQJ6 Zm00001d018309 26S protease regulatory subunit 7 homolog A 0.46 0.0249 Proteolysis. Protein catabolic process. Peptidase activity
A0A1D6FKP2 Zm00001d009613 Protease Do-like 1 chloroplastic 0.45 0.0496 Proteolysis. Serine-type endopeptidase activity
K7TTX0 Zm00001d025628 Plant UBX domain-containing protein 4 0.44 0.0107 Proteasome-mediated ubiquitin-dependent protein catabolic process
PROTEIN STABILIZATION AND FOLDING
Strongly induced proteins by B toxicity in Pachía
A0A1D6FN98 Zm00001d009948 Heat shock 70 kDa protein 14 2.28 0.0487 Protein folding. Stress response
B6SZ69 Zm00001d028630 Heat shock cognate 70 kDa protein 2 2.02 0.0398 Protein refolding. Stress response
Strongly repressed proteins by B toxicity in Pachía
A0A1D6KC46 Zm00001d030346 Hsp20/alpha crystallin family protein 0.49 0.0499 Chaperone. Response to heat
C0PKD9 Zm00001d052101 Chaperonin10 0.42 0.0428 Chaperone cofactor-dependent protein refolding
Protein folding. Chaperone
G2XK63 Zm00001d040257 T-complex protein 1 subunit beta 0.27 0.0065 Protein folding. Chaperone
B4FR04 Zm00001d019052 Peptidylprolyl isomerase 0.23 0.0205 Protein folding. Rotamase
REACTIVE OXYGEN SPECIES (ROS) SCAVENGING PATHWAYS / RESPONSE TO OXIDATIVE STRESS
Strongly induced proteins by B toxicity in Pachía
A0A1D6K5D2 Zm00001d029457 Nucleoredoxin1 2.91 0.0117 Protection against oxidative stress. Cellular oxidant detoxification
A0A1D6MSE3 Zm00001d040721 Dihydrolipoyl dehydrogenase 2.30 0.0273 Cell redox homeostasis
A0A1D6JPH3 Zm00001d027769 Glutathione reductase 2.21 0.0053 Cell redox homeostasis. Cellular oxidant detoxification. Glutathione metabolic process.
K7US39 Zm00001d009163 Dihydrolipoyl dehydrogenase 2.19 0.0088 Cell redox homeostasis
RIBOSOME BIOGENESIS
Strongly induced proteins by B toxicity in Pachía
B4FPB7 Zm00001d006100 60S ribosomal protein L7a 2.63 0.0051 Ribosome biogenesis. Maturation of LSU-rRNA
K7UTH7 Zm00001d009596 GTPase ERA1 chloroplastic 2.61 0.0108 Ribosome biogenesis. Ribosomal small subunit assembly. rRNA processing
B4F7Y1 Zm00001d031640 60S ribosomal protein L7a-1 2.39 0.0448 Ribosomal protein. Maturation of LSU-rRNA
RNA BINDING AND PROCESSING
Strongly induced proteins by B toxicity in Pachía
A0A1D6HT50 Zm00001d018891 Chloroplast RNA processing 4 2.60 0.0142 mRNA catabolic process
SIGNALING
Strongly repressed proteins by B toxicity in Pachía
P49235 Zm00001eb411380 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1, chloroplastic 0.19 0.0090 Cytokinin signaling pathway
STRESS
Strongly induced proteins by B toxicity in Pachía
B4F9K2 Zm00001d005315 Calcium-dependent lipid-binding (CaLB domain) family protein 2.11 0.0402 Defense response. Response to stress
TRANSCRIPTION AND TRANSLATION PROCESSES
Strongly induced proteins by B toxicity in Pachía
A0A1D6LEN8 Zm00001d035139 MA3 domain-containing protein 4.95 0.0073 Negative regulation of transcription, DNA-templated. Regulation of translation
Q6R9D1 GRMZM5G806488 Ribosomal protein S7 3.89 0.0202 Translation. Ribosomal small subunit assembly. Structural constituent of ribosome
A0A1D6IAN8 Zm00001d021400 Octicosapeptide/Phox/Bem1p (PB1) domain-containing protein / tetratricopeptide repeat (TPR)-containing protein 3.47 0.0323 RNA processing
C0P456 Zm00001d002789 Pentatricopeptide repeat-containing protein 3.26 0.0259 Likely involved in posttranscriptional control of gene expression in organelles
A0A1D6NR59 Zm00001d044745 Probable alanine--tRNA ligase, chloroplastic 2.74 0.0097 Translation. Alanyl-tRNA aminoacylation
A0A1D6LIV5 Zm00001d035802 Phenylalanine--tRNA ligase beta subunit cytoplasmic 2.56 0.0314 Translation. Phenylalanyl-tRNA aminoacylation
B6T5F2 Zm00001d011992 60S ribosomal protein L13 2.48 0.0387 Translation. Structural constituent of ribosome
A0A1D6HM03 Zm00001d018274 Isoleucine--tRNA ligase chloroplastic/mitochondrial 2.29 0.0087 Translation. Isoleucyl-tRNA aminoacylation
A0A1D6QAN9 Zm00001d051885 ATG8-interacting protein 1 2.28 0.0047 Box C/D RNA 3'-end processing. rRNA processing
A0A1D6FRP3 Zm00001d010530 Cysteine--tRNA ligase 1 cytoplasmic 2.26 0.0470 Translation. Cysteinyl-tRNA aminoacylation
B4FMD3 Zm00001d012978 40S ribosomal protein S23-2 2.13 0.0451 Translation. Structural constituent of ribosome
K7UTZ2 Zm00001d009761 Spliceosome RNA helicase BAT1 isoform 1 2.10 0.0455 RNA splicing. RNA helicase activity
K7TY03 Zm00001d023741 Alanine--tRNA ligase 2.07 0.0144 Translation. Alanyl-tRNA aminoacylation
B4FYR2 Zm00001d038865 60S ribosomal protein L28 2.05 0.0275 Translation. Structural constituent of ribosome
B6U151 Zm00001d002104 Glutamyl-tRNA(Gln) amidotransferase subunit A, chloroplastic/mitochondrial 2.02 0.0464 Mitochondrial translation
Strongly repressed proteins by B toxicity in Pachía
C0P7X7 Zm00001d034808 30S ribosomal protein S6 alpha chloroplastic 0.50 0.0059 Translation. Structural constituent of ribosome
B4FUZ5 Zm00001d047581 30S ribosomal protein S1 0.46 0.0055 Translation. Ribosomal protein
O50018 Zm00001d046449 Elongation factor 1-α 0.29 0.0269 Translation. Translation elongation factor activity
TRANSPORTERS AND TRANSPORT PROCESSES
Strongly induced proteins by B toxicity in Pachía
B6SP43 Zm00001d007597 ABC family1 4.54 0.0103 ATPase-coupled transmembrane transporter activity
A0A1D6H2R4 Zm00001d015569 H+-exporting diphosphatase 4.34 0.0050 Ion transport. Pyrophosphate hydrolysis-driven proton transmembrane transporter activity
A0A1D6MS70 Zm00001d040686 Protein translocase subunit SECA1 chloroplastic 4.12 0.0173 Protein transport
A0A1D6DSW6 Zm00001d001788 K+ efflux antiporter 2 chloroplastic 3.79 0.0414 Chloroplast potassium ion trans-port
B6T5R1 Zm00001d010504 Ran-binding protein 1 3.16 0.0492 Intracellular transport. Protein and mRNA transport. Nucleocytoplasmic transport
A0A1D6KSB0 Zm00001d032615 Protein TIC110 chloroplastic 2.35 0.0118 Protein import into chloroplast stroma
NOT WELL-KNOWN PROTEINS
Strongly induced proteins by B toxicity in Pachía
A0A1D6KKK1 Zm00001d031677 MtN19-like protein 2.62 0.0464 Not well determined
A0A1D6JI62 Zm00001d026632 Stem-specific protein TSJT1 2.43 0.0283 Not well determined
Only proteins considered differentially expressed, namely those with fold-changes ≥2.0 or ≤ 0.5 and P-values ≤ 0.05, are shown in this table. Induced proteins are highlighted with light green rows and repressed proteins with light red rows. 1Proteins ID, Protein identification number in the UniProt database. 2Gene Name, name or ID number of the corresponding gene of the differentially expressed protein as searched in the Maize Genetics and Genomics Database (MaizeGDB; https://www.maizegdb.org/). 3Fold Change, is expressed as the ratio of LFQ intensities (on a logarithmic scale) of proteins between 10 and 0.05 mM B treatments in Pachía. Results were obtained from 3-4 separate plants. 4P-value, statistical level (using Student’s t-test) below ≤0.05, at which differential protein expression was accepted as significant. 5Function/Biological process, annotated biological functions or biological process based on different databases. For more details, see Materials and Methods.
Table 4. Proteins with higher differential expression in Sama leaves in response to boron (B) toxicity. This table shows the proteins strongly induced or repressed by B toxicity in Sama by comparing their expressions with those of Sama in medium with 0.05 mM B.
Table 4. Proteins with higher differential expression in Sama leaves in response to boron (B) toxicity. This table shows the proteins strongly induced or repressed by B toxicity in Sama by comparing their expressions with those of Sama in medium with 0.05 mM B.
Protein ID1 Gene Name/ID2 Protein name/Annotation FC3 P-value4 Function/Biological process5
AMINO ACID AND PEPTIDE METABOLISMS
Strongly induced proteins by B toxicity in Sama
B6SKB7 Zm00001d031013 Methylcrotonoyl-CoA carboxylase subunit alpha 3.56 0.0049 Leucine degradation
C4J3S6 Zm00001d004960 2-isopropylmalate synthase 1 chloroplastic 2.17 0.0025 Leucine biosynthesis
CARBON ASSIMILATION AND CALVIN CYCLE
Strongly repressed proteins by B toxicity in Sama
O24574 Zm00001d004894 Ribulose bisphosphate carboxylase small chain 0.33 0.0466 Carbon dioxide fixation
P05348 Rbcs Ribulose bisphosphate carboxylase small chain, chloroplastic 0.13 0.0096 Carbon dioxide fixation
CELL DIVISION
Strongly induced proteins by B toxicity in Sama
C0P4T2 Zm00001d042664 Patellin-1 3.05 0.0149 Cell division and cell cycle
NUCLEOTIDE, PURINE AND PYRIMIDINE METABOLISM
Strongly repressed proteins by B toxicity in Sama
A0A1D6P7V2 Zm00001d047217 5-hydroxyisourate hydrolase 0.50 0.0136 Purine metabolism
PHOTOSYNTHETIC LIGHT REACTIONS
Strongly repressed proteins by B toxicity in Sama
A0A1D6HS38 Zm00001d018779 Oxygen-evolving enhancer protein 2-1 chloroplastic (OEE2-1) 0.48 0.0354 Photosynthesis. Photosystem II oxygen evolving complex
B6SSN3 Zm00001d015385 Chlorophyll a-b binding protein, chloroplastic 0.43 0.0435 Light harvesting in photosystem I
B4FWG2 Zm00001d048422 Photosynthetic NDH subunit of subcomplex B 2 chloroplastic 0.41 0.0200 Photosynthetic electron transport flow around photosystem I to produce ATP
P06670 NdhK NAD(P)H-quinone oxidoreductase subunit K, chloroplastic 0.38 0.0149 Photosynthetic electron transport coupled photosynthetic proton transport
A0A1X7YHF7 PsbD Photosystem II D2 protein 0.35 0.0347 Photosynthetic electron transport in photosystem II
P46617 PetA Cytochrome f 0.29 0.0161 Photosynthetic electron transport chain
B6SQV5 Zm00001d049387 Photosystem II 10 kDa polypeptide 0.14 0.0438 Photosynthesis. Photosystem II oxygen evolving complex
PROTEIN STABILIZATION AND FOLDING
Strongly repressed proteins by B toxicity in Sama
A0A1D6GJM6 Zm00001d013455 Peptidylprolyl isomerase 0.40 0.0275 Protein folding. Rotamase
C4J6Y2 Zm00001d018077 Peptidylprolyl isomerase 0.18 0.0422 Protein folding. Rotamase
REACTIVE OXYGEN SPECIES (ROS) SCAVENGING PATHWAYS / RESPONSE TO OXIDATIVE STRESS
Strongly induced proteins by B toxicity in Sama
B4FSM5 Zm00001d040341 Peroxiredoxin 2.68 0.0112 Cellular response to oxidative stress. Hydrogen peroxide catabolic process. Cell redox homeostasis
Strongly repressed proteins by B toxicity in Sama
B6U038 Zm00001d005482 Thiol-disulfide isomerase and thioredoxins 0.44 0.0223 Antioxidant activity. Cellular oxidant detoxification. Thioredoxin-dependent peroxiredoxin activity
B4FZ35 Zm00001d002240 CHL-Zea mays chloroplastic li-pocalin 0.31 0.0272 Response to oxidative stress. Violaxanthin, antheraxanthin and zeaxanthin interconversion
SECONDARY METABOLISM
Strongly induced proteins by B toxicity in Sama
O64411 Zm00001d024281 Polyamine oxidase 1 (PAO1) 3.34 0.0108 Spermine degradation. Amine and polyamine degradation
Strongly repressed proteins by B toxicity in Sama
B6TAE7 Zm00001d028575 Tropinone reductase 0.44 0.0313 Tropane alkaloid biosynthesis
STRESS
Strongly induced proteins by B toxicity in Sama
A0A1D6NJS4 Zm00001d044222 Tetratricopeptide repeat (TPR)-containing protein 2.12 0.0428 N-terminal peptidyl-methionine acetylation. Protein maturation
TRANSCRIPTION AND TRANSLATION PROCESSES
Strongly induced proteins by B toxicity in Sama
A0A1D6IBP5 Zm00001d021507 Asparagine--tRNA ligase chloroplastic/mitochondrial 2.66 0.0491 Translation. Asparaginyl-tRNA aminoacylation
B4FSE0 Zm00001d033913 Alba DNA/RNA-binding protein 2.48 0.0244 Translational initiation. RNA binding
B6T872 Zm00001d021020 60S ribosomal protein L32 2.28 0.0415 Translation. Structural constituent of ribosome
A0A1D6LIV5 Zm00001d035802 Phenylalanine--tRNA ligase beta subunit cytoplasmic 2.23 0.0093 Translation. Phenylalanyl-tRNA aminoacylation
B4FJ27 Zm00001d011741 40S ribosomal protein S24 2.13 0.0363 Translation. Structural constituent of ribosome
TRANSPORTERS AND TRANSPORT PROCESSES
Strongly induced proteins by B toxicity in Sama
B6SP43 Zm00001d007597 ABC family1 2.69 0.0125 ATPase-coupled transmembrane transporter activity
Only proteins considered differentially expressed namely those with fold-changes ≥2.0 or ≤ 0.5 and P-values ≤ 0.05, are shown in this table. Induced proteins are highlighted with light green rows and repressed proteins with light red rows. 1Proteins ID, Protein identification number in the UniProt database. 2Gene Name, name or ID number of the corresponding gene of the differentially expressed protein as searched in the Maize Genetics and Genomics Database (MaizeGDB; https://www.maizegdb.org/). 3Fold Change, is expressed as the ratio of LFQ intensities (on a logarithmic scale) of proteins between 10 and 0.05 mM B treatments in Sama. Results were obtained from 3-4 separate plants. 4P-value, statistical level (using Student’s t-test), at which differential protein expression was accepted as significant (≤0.05). 5Function/Biological process, annotated biological functions or biological process based on different databases. For more details, see Materials and Methods.
Table 5. Proteins with higher differential expression between Sama and Pachía leaves under boron (B) toxicity condition. This table shows the strongly up- or down-accumulated proteins in Sama in media with 10 mM B compared to those of Pachía in 10 mM B.
Table 5. Proteins with higher differential expression between Sama and Pachía leaves under boron (B) toxicity condition. This table shows the strongly up- or down-accumulated proteins in Sama in media with 10 mM B compared to those of Pachía in 10 mM B.
Protein ID1 Gene Name/ID2 Protein name/Annotation FC3 P-value4 Function/Biological process5
AMINO ACID AND PEPTIDE METABOLISMS
Strongly up-accumulated proteins in Sama in media with 10 mM B
A0A1D6ICL3 Zm00001d021596 Adenosine 5-phosphosulfate reductase-like1 2.33 0.0417 Cysteine biosynthetic process. Sulfate reduction
CARBON ASSIMILATION AND CALVIN CYCLE
Strongly up-accumulated proteins in Sama in media with 10 mM B
A0A1D6EXF1 Zm00001d006520 PDK regulatory protein1 2.16 0.0167 Regulation of C4 photosynthetic carbon assimilation cycle
CARBOHYDRATE METABOLISM
Strongly up-accumulated proteins in Sama in media with 10 mM B
Q9SYS1 Zm00001d021702 β-amylase 2.63 0.0499 β-amylase activity. Starch degradation
Strongly down-accumulated proteins in Sama in media with 10 mM B
A0A1D6K5L6 Zm00001d029502 Glucose-6-phosphate 1-dehydrogenase 0.36 0.0411 Pentose phosphate pathway
A0A1D6LY56 Zm00001d037480 Alkaline α galactosidase 2 0.33 0.0438 Carbohydrate metabolic process
CELL DEATH
Strongly down-accumulated proteins in Sama in media with 10 mM B
A0A1D6JNJ8 Zm00001d027656 Lethal leaf-spot 1 0.32 0.0016 Cell death. Chlorophyll catabolic process
CELL DIVISION
Strongly down-accumulated proteins in Sama in media with 10 mM B
A0A1D6JH24 Zm00001d026532 Protein RCC2 0.42 0.0214 Cell division
CELL WALL
Strongly up-accumulated proteins in Sama in media with 10 mM B
A0A1D6MWZ7 Zm00001d041578 Glossy6 3.27 0.0403 Epicuticular wax accumulation. Intracellular trafficking of cuticular waxes
DNA AND CHROMATIN ORGANIZATION AND DNA REPAIR
Strongly down-accumulated proteins in Sama in media with 10 mM B
B4FQA5 Zm00001d018981 Histone1a 0.35 0.0318 Chromosome condensation. Nucleosome assembly
B6TGH8 Zm00001d034479 Histone H1 0.31 0.0138 Chromosome condensation. Nucleosome assembly. Nucleosome positioning
LIPID METABOLISM
Strongly up-accumulated proteins in Sama in media with 10 mM B
Q8W0V2 Zm00001d033623 Lipoxygenase 3 5.06 0.0455 Fatty acid and oxylipin biosynthesis
Q06XS3 Zm00001d053675 Lipoxygenase 10 3.44 0.0247 Fatty acid and oxylipin biosynthesis
OTHERS
Strongly down-accumulated proteins in Sama in media with 10 mM B
B6TY16 Zm00001d040331 SUN domain protein2 0.41 0.0262 Nuclear envelope organization
B4F7V3 Zm00001d021582 Protein phosphatase 2C isoform ε 0.39 0.0214 Protein dephosphorylation
A0A1D6HUN3 Zm00001d019040 D-2-hydroxyglutarate dehydrogenase mitochondrial 0.33 0.0024 Photorespiration
OXIDATION AND REDUCTION PROCESSES
Strongly down-accumulated proteins in Sama in media with 10 mM B
B4F987 Zm00001d020984 Putative sarcosine oxidase 0.23 0.0321 Sarcosine oxidase activity
PHOTOSYNTHETIC LIGHT REACTIONS
Strongly up-accumulated proteins in Sama in media with 10 mM B
B4FR80 Zm00001d033098 Post-illumination chlorophyll fluorescence increase (ZmPIFI) 2.52 0.0097 Chlororespiration
A0A1D6HS38 Zm00001d018779 Oxygen-evolving enhancer protein 2-1 chloroplastic (OEE2-1) 2.31 0.0325 Photosynthesis. Photosystem II oxygen evolving complex
PIGMENT BIOSYNTHESIS
Strongly up-accumulated proteins in Sama in media with 10 mM B
A0A1D6JHX0 Zm00001d026603 Magnesium-chelatase subunit ChlH1 chloroplastic (ChlH1) 2.90 0.0484 Chlorophyll biosynthetic process
PROTEIN STABILIZATION AND FOLDING
Strongly down-accumulated proteins in Sama in media with 10 mM B
A0A1D6KE29 Zm00001d030725 Heat shock protein 70 0.43 0.0406 Protein refolding. Protein folding chaperone. Cellular response to unfolded protein
RESPIRATION (GLYCOLISIS, TCA CYCLE AND MITOCHONDRIAL ELECTRON TRANSFER)
Strongly up-accumulated proteins in Sama in media with 10 mM B
B4G1C9 Zm00001d023606 Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex 2.04 0.0332 Acetyl-CoA biosynthetic process from pyruvate
Strongly down-accumulated proteins in Sama in media with 10 mM B
A0A1D6MAK9 Zm00001d038792 Phosphotransferase 0.49 0.0331 Glycolysis
SECONDARY METABOLISM
Strongly up-accumulated proteins in Sama in media with 10 mM B
O64411 Zm00001d024281 Polyamine oxidase 1 (PAO1) 5.15 0.0007 Spermine degradation. Amine and polyamine degradation
TRANSCRIPTION AND TRANSLATION
Strongly up-accumulated proteins in Sama in media with 10 mM B
B4FP25 Zm00001d047296 40S ribosomal protein S19 6.38 0.0289 Translation. Structural constituent of ribosome. Ribosomal small subunit assembly
B6TDF7 Zm00001d019898 Plastid-specific 30S ribosomal protein 2 2.31 0.0243 Ribosomal protein. Ribonucleoprotein complex. RNA-binding
C0PEC4 Zm00001d032420 30S ribosomal protein S5 chloroplastic 2.12 0.0487 Translation. Structural constituent of ribosome
Strongly down-accumulated proteins in Sama in media with 10 mM B
B6SX73 Zm00001d016549 60S ribosomal protein L35 0.42 0.0284 Translation. Structural constituent of ribosome
Q6R9D1 GRMZM5G806488 Ribosomal protein S7 0.35 0.0426 Translation. Structural constituent of ribosome. Ribosomal small subunit assembly
Transporter and transport processes
Strongly down-accumulated proteins in Sama in media with 10 mM B
A0A1D6H2R4 Zm00001d015569 H+-exporting diphosphatase 0.33 0.0169 Ion transport. Pyrophosphate hydrolysis-driven proton transmembrane transporter activity
A0A1D6K7N5 Zm00001d029762 Hexose transporter 0.20 0.0439 Hexose transporter
Unknown or not well determined
Strongly down-accumulated proteins in Sama in media with 10 mM B
A0A1D6KKK1 Zm00001d031677 MtN19-like protein 0.23 0.0121 Not well determined
Only proteins considered differentially expressed namely those with fold-changes ≥2.0 or ≤ 0.5 and P-values ≤ 0.05, are shown in this table. Induced proteins are highlighted with light green rows and repressed proteins with light red rows. 1Proteins ID, Protein identifying number in the UniProt database. 2Gene Name, name or ID number of the corresponding gene of the differentially expressed protein as searched in the Maize Genetics and Genomics Database (MaizeGDB; https://www.maizegdb.org/). 3Fold Change, is expressed as the ratio of LFQ intensities (on a logarithmic scale) of proteins between Sama and Pachía in media with 10 mM B. Results were obtained from 3-4 separate plants. 4P-value, statistical level (using Student’s t-test) below ≤0.05, at which protein differential expression was accepted as significant. 5Function/Biological process, annotated biological functions or biological process based on different databases. For more details, see Materials and Methods. .
Table 6. Proteins exclusively detected in Pachía or Sama leaves in at least one B treatment.
Table 6. Proteins exclusively detected in Pachía or Sama leaves in at least one B treatment.
Protein ID1 Gene Name/ID2 Protein name/Annotation Function/Biological process3
DNA AND CHROMATIN ORGANIZATION AND DNA REPAIR
Protein exclusively detected in Pachía in 10 mM B
A0A1D6KX75 Zm00001d033247 Nfc103a - nucleosome/chromatin assembly factor C Nucleosome/chromatin assembly. DNA repair. Chromatin remodeling, regulation of DNA-templated transcription
OTHERS
Protein exclusively detected in Sama in both B treatments
K7VAT7 Zm00001d046569 Protein kinase superfamily protein with octicosapeptide/Phox/Bem1p domain Protein serine/threonine kinase activity. Protein phosphorylation
REACTIVE OXYGEN SPECIES (ROS) SCAVENGING PATHWAYS / RESPONSE TO OXIDATIVE STRESS
Protein exclusively detected in Pachía in both B treatments
B4FKV6 Zm00001d014341 Peroxidase 54 Response to oxidative stress. Peroxidase activity
TRANSCRIPTION AND TRANSLATION
Protein exclusively detected in Pachía in 10 mM B
A0A096RFR6 Zm00001d039518 Eukaryotic translation initiation factor 3 subunit A (eIF3a) Translation initiation factor activity. Protein synthesis. Formation of cytoplasmic translation initiation complex
Transporter and transport processes
Proteins exclusively detected in Pachía in both B treatments
A0A1D6EU13 Zm00001d006238 Calcium lipid binding protein-like Lipid transport
A0A1D6JN64 Zm00001d027580 Outer mitochondrial membrane porin1 (ommp1) Voltage-gated anion channel activity. Inorganic anion transport, transmembrane transport, anion transmembrane transport
Protein exclusively detected proteins in Sama in both B treatments
Q7Y1W6 Zm00001d018693 Pentatricopeptide repeat 2 (PPR2) Chloroplast translation
Unknown or not well determined
Protein exclusively detected proteins in Sama in both B treatments
A0A1D6DWG9 Zm00001d002089 Tetratricopeptide repeat (TPR)-like superfamily protein Unknown
1Proteins ID, Protein identification number in the UniProt database. 2Gene Name, name or ID number of the corresponding gene of the identified protein as searched in the Maize Genetics and Genomics Database (MaizeGDB; https://www.maizegdb.org/). 3Function/Biological process, annotated biological functions or biological process based on different databases. For more details, see Materials and Methods. .
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content.
Copyright: This open access article is published under a Creative Commons CC BY 4.0 license, which permit the free download, distribution, and reuse, provided that the author and preprint are cited in any reuse.
Prerpints.org logo

Preprints.org is a free preprint server supported by MDPI in Basel, Switzerland.

facebook logotwitter logolinkedin logo
MDPI Initiatives
Important Links
Subscribe

Disclaimer

Terms of Use

Privacy Policy

© 2024 MDPI (Basel, Switzerland) unless otherwise stated