Quantitative Proteomics Analysis of Camelina sativa Seeds Overexpressing the AGG3 Gene to Identify the Proteomic Basis of Increased Yield and Stress Tolerance

Pivotal role of heterotrimeric G protein in the crosstalk between sugar signaling and abiotic stress response in plants

Heterotrimeric G-proteins are key modulators of multiple signaling and developmental pathways in plants, in which they act as molecular switches to engage in transmitting various stimuli signals from outside into the cells. Substantial studies have identified G proteins as essential components of the organismal response to abiotic stress, leading to adaptation and survival in plants. Meanwhile, sugars are also well acknowledged key players in stress perception, signaling, and gene expression regulation. Connections between the two significant signaling pathways in stress response are of interest to a general audience in plant biology. In this article, advances unraveling a pivotal role of G proteins in the process of sugar signals outside the cells being translated into the operation of autophagy in cells during stress are reviewed. In addition, we have presented recent findings on G proteins regulating the response to drought, salt, alkali, cold, heat and other abiotic stresses. Perspectives on G-protein research are also provided in the end. Since G protein signaling regulates many agronomic traits, elucidation of detailed mechanism of the related pathways would provide useful insights for the breeding of abiotic stress resistant and high-yield crops.

Agronomic potential of plant-specific Gγ proteins

The vascular plant-specific type III Gγ proteins have emerged as important targets for biotechnological applications. These proteins are exemplified by Arabidopsis AGG3, rice Grain Size 3 (GS3), Dense and Erect Panicle 1 (DEP1), and GGC2 and regulate plant stature, seed size, weight and quality, nitrogen use efficiency, and multiple stress responses. These Gγ proteins are an integral component of the plant heterotrimeric G-protein complex and differ from the canonical Gγ proteins due to the presence of a long, cysteine-rich C-terminal region. Most cereal genomes encode three or more of these proteins, which have similar N-terminal Gγ domains but varying lengths of the C-terminal domain. The C-terminal domain is hypothesized to give specificity to the protein function. Intriguingly, many accessions of cultivated cereals have natural deletion of this region in one or more proteins, but the mechanistic details of protein function remain perplexing. Distinct, sometimes contrasting, effects of deletion of the C-terminal region have been reported in different crops or under varying environmental conditions. This review summarizes the known roles of type III Gγ proteins, the possible action mechanisms, and a perspective on what is needed to comprehend their full agronomic potential.

Overexpression of a Plant-Specific Gγ Protein, AGG3, in the Model Monocot Setaria viridis Confers Tolerance to Heat Stress

The vascular plant-specific, cysteine-rich type III Gγ proteins, which are integral components of the heterotrimeric G-protein complex, play crucial roles in regulating a multitude of plant processes, including those related to crop yield and responses to abiotic stresses. The presence of multiple copies of type III Gγ proteins in most plants and a propensity of the presence of specific truncated alleles in many cultivated crops present an ambiguous picture of their roles in modulating specific responses. AGG3 is a canonical type III Gγ protein of Arabidopsis, and its overexpression in additional model crops offers the opportunity to directly evaluate the effects of protein expression levels on plant phenotypes. We have shown that AGG3 overexpression in the monocot model Setaria viridis leads to an increase in seed yield. In this study, we have investigated the response of the S. viridis plants overexpressing AGG3 to heat stress (HS), one of the most important abiotic stresses affecting crops worldwide. We show that a short span of HS at a crucial developmental time point has a significant effect on plant yield in the later stages. We also show that plants with higher levels of AGG3 are more tolerant to HS. This is attributed to an altered regulation of stress-responsive genes and improved modulation of the photosynthetic efficiency during the stress. Overall, our results confirm that AGG3 plays a crucial role in regulating plant responses to unfavorable environmental conditions and may contribute positively to avoiding crop yield losses.

Heterotrimeric G Protein Signaling in Abiotic Stress

As sessile organisms, plants exhibit extraordinary plasticity and have evolved sophisticated mechanisms to adapt and mitigate the adverse effects of environmental fluctuations. Heterotrimeric G proteins (G proteins), composed of α, β, and γ subunits, are universal signaling molecules mediating the response to a myriad of internal and external signals. Numerous studies have identified G proteins as essential components of the organismal response to stress, leading to adaptation and ultimately survival in plants and animal systems. In plants, G proteins control multiple signaling pathways regulating the response to drought, salt, cold, and heat stresses. G proteins signal through two functional modules, the Gα subunit and the Gβγ dimer, each of which can start either independent or interdependent signaling pathways. Improving the understanding of the role of G proteins in stress reactions can lead to the development of more resilient crops through traditional breeding or biotechnological methods, ensuring global food security. In this review, we summarize and discuss the current knowledge on the roles of the different G protein subunits in response to abiotic stress and suggest future directions for research.

Genome-wide survey of Gγ subunit gene family in eight Rosaceae and expression analysis of PbrGGs in pear (Pyrus bretschneideri)

BACKGROUND

Heterotrimeric G-proteins, composed of Gα, Gβ and Gγ subunits, are important signal transmitters, mediating the cellular response to multiple stimuli in animals and plants. The Gγ subunit is an essential component of the G-protein, providing appropriate functional specificity to the heterotrimer complex and has been well studied in many species. However, the evolutionary history, expression pattern and functional characteristics of Gγ subunits has not been explored in the Rosaceae, representing many important fruit crops.

RESULTS

In this study, 35 Gγ subunit genes were identified from the eight species belonging to the Rosaceae family. Based on the structural gene characteristics, conserved protein motifs and phylogenetic analysis of the Gγ subunit genes, the genes were classified into three clades. Purifying selection was shown to play an important role in the evolution of Gγ subunit genes, while a recent whole-genome duplication event was the principal force determining the expansion of the Gγ subunit gene family in the subfamily Maloideae. Gγ subunit genes exhibited diverse spatiotemporal expression patterns in Chinese white pear, including fruit, root, ovary and bud, and under abiotic stress conditions, the relative expression of Gγ subunit genes were up-regulated or down-regulated. In addition, seven of the Gγ subunit proteins in pear were located on the plasma membrane, in the cytoplasm or nucleus.

CONCLUSION

Overall, this study of the Gγ subunit gene family in eight Rosaceae species provided useful information to better understand the evolution and expression of these genes and facilitated further exploration of their functions in these important crop plants.

Study of Terpenoid Synthesis and Prenyltransferase in Roots of Rehmannia glutinosa Based on iTRAQ Quantitative Proteomics

Rehmannia glutinosa has important medicinal value; terpenoid is one of the main active components in R. glutinosa. In this study, iTRAQ technique was used to analyze the relative abundance of proteins in roots of R. glutinosa, and 6,752 reliable proteins were quantified. GO enrichment results indicated that most proteins were involved in metabolic process or cellular process, 57.63% proteins had catalytic activity, and 65.80% proteins were enriched in membrane-bounded organelle. In roots of R. glutinosa, there were 38 KEGG enrichments with significance, more DEPs were found in some pathways, especially the proteasome pathway and TCA cycle with 15.0% DEPs between elongation stage and expansion stage of roots. Furthermore, five KEGG pathways of terpenoid synthesis were found. Most prenyltransferases belong to FPP/GGPP synthase family, involved in terpenoid backbone biosynthesis, and all interacted with biotin carboxylase CAC2. Compared with that at the elongation stage, many prenyltransferases exhibited higher expression at the expansion stage or maturation stage of roots. In addition, eight FPP/GGPP synthase encoding genes were cloned from R. glutinosa, namely FPPS, FPPS1, GGPS, GGPS3, GGPS4, GGPS5, GPPS and GPPS2, introns were also found in FPPS, FPPS1, GGPS5 and GGPS2, and FPP/GPP synthases were more conservative in organisms, especially in viridiplantae, in which the co-occurrence of GPPS or GPPS2 was significantly higher in plants. Further analysis found that FPP/GGPP synthases of R. glutinosa were divided into three kinds, GGPS, GPPS and FPPS, and their gene expression was significantly diverse in different varieties, growth periods, or tissues of R. glutinosa. Compared with that of GGPS, the expression of GPPS and FPPS was much higher in R. glutinosa, especially at the expansion stage and maturation stage. Thus, the synthesis of terpenoids in roots of R. glutinosa is intricately regulated and needs to be further studied.

Heterotrimeric G protein signalling in plant biotic and abiotic stress response

Heterotrimeric G proteins act as molecular switches to participate in transmitting various stimuli signals from outside of cells. G proteins have three subunits, Gα, Gβ and Gγ, which function mutually to modulate many biological processes in plants, including plant growth and development, as well as biotic and abiotic stress responses. In plants, the number of Gγ subunits is larger than that of the α and β subunits. Based on recent breakthroughs in studies of plant G protein signal perception, transduction and downstream effectors, this review summarizes and analyses the connections between different subunits and the interactions of G proteins with other signalling pathways, especially in plant biotic and abiotic stress responses. Based on current progress and unresolved questions in the field, we also suggest future research directions on G proteins in plants.

Joint expression of Zmpepc, Zmppdk, and Zmnadp-me is more efficient than expression of one or two of those genes in improving the photosynthesis of Arabidopsis

This study assessed the effects of seven combinations of maize (Zea mays) genes phosphoenolpyruvate carboxylase (pepc), pyruvate phosphate dikinase (ppdk), and NADP-malic enzyme (nadp-me), on the photosynthesis of Arabidopsis. The photosynthetic rate, carboxylation efficiency, and shoot-dry-weight of Zmpepc (PC), Zmpepc + Zmppdk (PCK), Zmpepc + Zmnadp-me (PCM), and Zmpepc + Zmppdk + Zmnadp-me (PCKM) were significantly higher than those of the control wild-type (WT), with a trends to be PCKM > PCK > PC and PCM > WT. This indicated that Zmpepc was a prerequisite for improved photosynthetic performance; Zmppdk had a positive effect on Zmpepc, and the triple gene combination had the most significant synergistic effects. PCKM significantly enhanced activity of photosystem (PS)II (K, J phase) and PSI, light energy absorption (ABS/CSm) and conversion (TRo/ABS), and electron transfer (ETo/TRo). PCKM up-regulated 18 photosynthesis-related proteins, among which, 11 were involved in light reaction resulting in improved light-energy absorption and conversion efficiency, electron transfer, activity and stability of PSII and PSI, and the ATP and NADPH production. The remaining seven proteins were involved in dark reaction. The up-regulation of these proteins in PCKM improved the coordinated operation of light and dark reaction, increasing the photosynthesis and dry weight ultimately. These results also provide a promising strategy for the genetic improvement of the photosynthetic performance of C₃ crops by inserting major C₄ photosynthetic genes.

Bringing New Methods to the Seed Proteomics Platform: Challenges and Perspectives

For centuries, crop plants have represented the basis of the daily human diet. Among them, cereals and legumes, accumulating oils, proteins, and carbohydrates in their seeds, distinctly dominate modern agriculture, thus play an essential role in food industry and fuel production. Therefore, seeds of crop plants are intensively studied by food chemists, biologists, biochemists, and nutritional physiologists. Accordingly, seed development and germination as well as age- and stress-related alterations in seed vigor, longevity, nutritional value, and safety can be addressed by a broad panel of analytical, biochemical, and physiological methods. Currently, functional genomics is one of the most powerful tools, giving direct access to characteristic metabolic changes accompanying plant development, senescence, and response to biotic or abiotic stress. Among individual post-genomic methodological platforms, proteomics represents one of the most effective ones, giving access to cellular metabolism at the level of proteins. During the recent decades, multiple methodological advances were introduced in different branches of life science, although only some of them were established in seed proteomics so far. Therefore, here we discuss main methodological approaches already employed in seed proteomics, as well as those still waiting for implementation in this field of plant research, with a special emphasis on sample preparation, data acquisition, processing, and post-processing. Thereby, the overall goal of this review is to bring new methodologies emerging in different areas of proteomics research (clinical, food, ecological, microbial, and plant proteomics) to the broad society of seed biologists.

Cadmium Immobilization in the Rhizosphere and Plant Cellular Detoxification: Role of Plant-Growth-Promoting Rhizobacteria as a Sustainable Solution

Food is the major cadmium (Cd)-exposure pathway from agricultural soils to humans and other living entities and must be reduced in an effective way. A plant can select beneficial microbes, like plant-growth-promoting rhizobacteria (PGPR), depending upon the nature of root exudates in the rhizosphere, for its own benefits, such as plant growth promotion as well as protection from metal toxicity. This review intends to seek out information on the rhizo-immobilization of Cd in polluted soils using the PGPR along with plant nutrient fertilizers. This review suggests that the rhizo-immobilization of Cd by a combination of PGPR and nanohybrid-based plant nutrient fertilizers would be a potential and sustainable technology for phytoavailable Cd immobilization in the rhizosphere and plant cellular detoxification, by keeping the plant nutrition flow and green dynamics of plant nutrition and boosting the plant growth and development under Cd stress.

Greenbug (Schizaphis graminum) herbivory significantly impacts protein and phosphorylation abundance in switchgrass (Panicum virgatum)

Switchgrass (Panicum virgatum L.) is an important crop for biofuel production but it also serves as host for greenbugs (Schizaphis graminum Rondani; GB). Although transcriptomic studies have been done to infer the molecular mechanisms of plant defense against GB, little is known about the effect of GB infestation on the switchgrass protein expression and phosphorylation regulation. The global response of the switchgrass cultivar Summer proteome and phosphoproteome was monitored by label-free proteomics shotgun in GB-infested and uninfested control plants at 10 days post infestation. Peptides matching a total of 3,594 proteins were identified and 429 were differentially expressed proteins in GB-infested plants relative to uninfested control plants. Among these, 291 and 138 were up and downregulated by GB infestation, respectively. Phosphoproteome analysis identified 310 differentially phosphorylated proteins (DP) from 350 phosphopeptides with a total of 399 phosphorylated sites. These phosphopeptides had more serine phosphorylated residues (79%), compared to threonine phosphorylated sites (21%). Overall, KEGG pathway analysis revealed that GB feeding led to the enriched accumulation of proteins important for biosynthesis of plant defense secondary metabolites and repressed the accumulation of proteins involved in photosynthesis. Interestingly, defense modulators such as terpene synthase, papain-like cysteine protease, serine carboxypeptidase, and lipoxygenase2 were upregulated at the proteome level, corroborating previously published transcriptomic data.

Spaceflight induces novel regulatory responses in Arabidopsis seedling as revealed by combined proteomic and transcriptomic analyses

BACKGROUND

Understanding of gravity sensing and response is critical to long-term human habitation in space and can provide new advantages for terrestrial agriculture. To this end, the altered gene expression profile induced by microgravity has been repeatedly queried by microarray and RNA-seq experiments to understand gravitropism. However, the quantification of altered protein abundance in space has been minimally investigated.

RESULTS

Proteomic (iTRAQ-labelled LC-MS/MS) and transcriptomic (RNA-seq) analyses simultaneously quantified protein and transcript differential expression of three-day old, etiolated Arabidopsis thaliana seedlings grown aboard the International Space Station along with their ground control counterparts. Protein extracts were fractionated to isolate soluble and membrane proteins and analyzed to detect differentially phosphorylated peptides. In total, 968 RNAs, 107 soluble proteins, and 103 membrane proteins were identified as differentially expressed. In addition, the proteomic analyses identified 16 differential phosphorylation events. Proteomic data delivered novel insights and simultaneously provided new context to previously made observations of gene expression in microgravity. There is a sweeping shift in post-transcriptional mechanisms of gene regulation including RNA-decapping protein DCP5, the splicing factors GRP7 and GRP8, and AGO4,. These data also indicate AHA2 and FERONIA as well as CESA1 and SHOU4 as central to the cell wall adaptations seen in spaceflight. Patterns of tubulin-α 1, 3,4 and 6 phosphorylation further reveal an interaction of microtubule and redox homeostasis that mirrors osmotic response signaling elements. The absence of gravity also results in a seemingly wasteful dysregulation of plastid gene transcription.

CONCLUSIONS

The datasets gathered from Arabidopsis seedlings exposed to microgravity revealed marked impacts on post-transcriptional regulation, cell wall synthesis, redox/microtubule dynamics, and plastid gene transcription. The impact of post-transcriptional regulatory alterations represents an unstudied element of the plant microgravity response with the potential to significantly impact plant growth efficiency and beyond. What's more, addressing the effects of microgravity on AHA2, CESA1, and alpha tubulins has the potential to enhance cytoskeletal organization and cell wall composition, thereby enhancing biomass production and growth in microgravity. Finally, understanding and manipulating the dysregulation of plastid gene transcription has further potential to address the goal of enhancing plant growth in the stressful conditions of microgravity.

Genetic and Systematic Approaches Toward G Protein-Coupled Abiotic Stress Signaling in Plants

Heterotrimeric G protein, composed of Gα, Gβ, and Gγ subunits, modulates plant adaptations to environmental stresses such as high salinity, drought, extreme temperatures and high light intensity. Most of these evidence were however derived solely from conventional genetics methods with which stress-associated phenotypes were compared between wild type and various G protein mutant plants. Recent advances in systematic approaches, mainly transcriptome and proteome, have contributed to in-depth understanding of molecular linkages between G proteins and environmental changes. Here, we update our knowledge on the roles of G proteins in abiotic stress responses. Furthermore, we highlight the current whole genome studies and integrated omics approach to better understand the fundamental G protein functions involved in abiotic stress responses. It is our purpose here to bridge the gap between molecular mechanisms in G protein science and stress biology and pave the way toward crop improvement researches in the future.

Emerging themes in heterotrimeric G-protein signaling in plants

Heterotrimeric G-proteins are key signaling components involved during the regulation of a multitude of growth and developmental pathways in all eukaryotes. Although the core proteins (Gα, Gβ, Gγ subunits) and their basic biochemistries are conserved between plants and non-plant systems, seemingly different inherent properties of specific components, altered wirings of G-protein network architectures, and the presence of novel receptors and effector proteins make plant G-protein signaling mechanisms somewhat distinct from the well-established animal paradigm. G-protein research in plants is getting a lot of attention recently due to the emerging roles of these proteins in controlling many agronomically important traits. New findings on both canonical and novel G-protein components and their conserved and unique signaling mechanisms are expected to improve our understanding of this important module in affecting critical plant growth and development pathways and eventually their utilization to produce plants for the future needs. In this review, we briefly summarize what is currently known in plant G-protein research, describe new findings and how they are changing our perceptions of the field, and discuss important issues that still need to be addressed.

Arabidopsis Type III Gγ Protein AGG3 Is a Positive Regulator of Yield and Stress Responses in the Model Monocot Setaria viridis

Heterotrimeric G-proteins are key regulators of a multitude of growth and development pathways in eukaryotes. Along with the conserved G-protein components found in all organisms, plants have certain novel variants with unique architecture, which may be involved in the regulation of plant-specific traits. The higher plant-specific type III (or Class C) Gγ protein, which possesses a large C terminal extension, represented by AGG3 in Arabidopsis, is one such variant of canonical Gγ proteins. The type III Gγ proteins are involved in regulation of many agronomically important traits in plants, including seed yield, organ size regulation, abscisic acid (ABA)-dependent signaling and stress responses, and nitrogen use efficiency. However, the extant data, especially in the monocots, present a relatively complex and sometimes contradictory picture of the regulatory role of these proteins. It remains unclear if the positive traits observed in certain naturally occurring populations are due to the presence of specific allelic variants of the proteins or due to the altered expression of the gene itself. To address these possibilities, we have overexpressed the Arabidopsis AGG3 gene in the model monocot Setaria viridis and systematically evaluated its role in conferring agriculturally relevant phenotypes. Our data show that AtAGG3 is indeed functional in Setaria and suggest that a subset of the traits affected by the type III Gγ proteins are indeed positively correlated with the gene expression level, while others might have more complex, allele specific regulation.

Function of heterotrimeric G-protein γ subunit RGG1 in providing salinity stress tolerance in rice by elevating detoxification of ROS

The present study provides evidence of a unique function of RGG1 in providing salinity stress tolerance in transgenic rice without affecting yield. It also provides a good example for signal transduction from the external environment to inside for enhanced agricultural production that withstands the extreme climatic conditions and ensures food security. The role of heterotrimeric G-proteins functioning as signalling molecules has not been studied as extensively in plants as in animals. Recently, their importance in plant stress signalling has been emerging. In this study, the function of rice G-protein γ subunit (RGG1) in the promotion of salinity tolerance in rice (Oryza sativa L. cv. IR64) was investigated. The overexpression of RGG1 driven by the CaMV35S promoter in transgenic rice conferred high salinity tolerance even in the presence of 200 mM NaCl. Transcript levels of antioxidative genes, i.e., CAT, APX, and GR, and their enzyme activities increased in salinity-stressed transgenic rice plants suggesting a better antioxidant system to cope the oxidative-damages caused by salinity stress. The RGG1-induced signalling events that conferred tolerance to salinity was mediated by increased gene expression of the enzymes that scavenged reactive oxygen species. In salinity-stressed RGG1 transgenic lines, the transcript levels of RGG2, RGB, RGA, DEP1, and GS3 also increased in addition to RGG1. These observations suggest that most likely the stoichiometry of the G-protein complex was not disturbed under stress. Agronomic parameters, endogenous sugar content (glucose and fructose) and hormones (GA3, zeatin and IAA) were also higher in the transgenic plants compared with the wild-type plants. A BiFC assay confirmed the interaction of RGG1 with different stress-responsive proteins which play active roles in signalling and prevention of aggregation of proteins under stress-induced perturbation. The present study will help in understanding the G-protein-mediated stress tolerance in plants.

Polyploidy and the proteome

Although major advances have been made during the past 20 years in our understanding of the genetic and genomic consequences of polyploidy, our knowledge of polyploidy and the proteome is in its infancy. One of our goals is to stimulate additional study, particularly broad-scale proteomic analyses of polyploids and their progenitors. Although it may be too early to generalize regarding the extent to which transcriptomic data are predictive of the proteome of polyploids, it is clear that the proteome does not always reflect the transcriptome. Despite limited data, important observations on the proteomes of polyploids are emerging. In some cases, proteomic profiles show qualitatively and/or quantitatively non-additive patterns, and proteomic novelty has been observed. Allopolyploids generally combine the parental contributions, but there is evidence of parental dominance of one contributing genome in some allopolyploids. Autopolyploids are typically qualitatively identical to but quantitatively different from their parents. There is also evidence of parental legacy at the proteomic level. Proteomes clearly provide insights into the consequences of genomic merger and doubling beyond what is obtained from genomic and/or transcriptomic data. Translating proteomic changes in polyploids to differences in morphology and physiology remains the holy grail of polyploidy--this daunting task of linking genotype to proteome to phenotype should emerge as a focus of polyploidy research in the next decade. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.