Can heterotrimeric G proteins help to feed the world?

When Size Matters: New Insights on How Seed Size Can Contribute to the Early Stages of Plant Development

The seed habit is the most complex and successful method of sexual reproduction in vascular plants. It represents a remarkable moment in the evolution of plants that afterward spread on land. In particular, seed size had a pivotal role in evolutionary success and agronomic traits, especially in the field of crop domestication. Given that crop seeds constitute one of the primary products for consumption, it follows that seed size represents a fundamental determinant of crop yield. This adaptative feature is strictly controlled by genetic traits from both maternal and zygotic tissues, although seed development and growth are also affected by environmental cues. Despite being a highly exploited topic for both basic and applied research, there are still many issues to be elucidated for developmental biology as well as for agronomic science. This review addresses a number of open questions related to cues that influence seed growth and size and how they influence seed germination. Moreover, new insights on the genetic-molecular control of this adaptive trait are presented.

Influence of expression and purification protocols on Gα biochemical activity: kinetics of plant and mammalian G protein cycles

Heterotrimeric G proteins are a class of signal transduction complexes with broad roles in human health and agriculturally important plant traits. In the classic paradigm, guanine nucleotide binding to the Gα subunit regulates the activation status of the complex. Using the Arabidopsis thaliana Gα subunit, GPA1, we developed a rapid StrepII-tag mediated purification method that facilitates isolation of protein with increased enzymatic activities as compared to conventional methods, and is demonstrably also applicable to mammalian Gα subunits. We subsequently utilized domain swaps of GPA1 and human GNAO1 to demonstrate the instability of recombinant GPA1 is a function of the interaction between the Ras and helical domains, and can be partially uncoupled from the rapid nucleotide binding kinetics displayed by GPA1.

Enhancing grain shape, thermotolerance, and alkaline tolerance via Gγ protein manipulation in rice

KEY MESSAGE

Our findings highlight a valuable breeding resource, demonstrating the potential to concurrently enhance grain shape, thermotolerance, and alkaline tolerance by manipulating Gγ protein in rice. Temperate Geng/Japonica (GJ) rice yields have improved significantly, bolstering global food security. However, GJ rice breeding faces challenges, including enhancing grain quality, ensuring stable yields at warmer temperatures, and utilizing alkaline land. In this study, we employed CRISPR/Cas9 gene-editing technology to knock out the GS3 locus in seven elite GJ varieties with superior yield performance. Yield component measurements revealed that GS3 knockout mutants consistently enhanced grain length and reduced plant height in diverse genetic backgrounds. The impact of GS3 on the grain number per panicle and setting rate depended on the genetic background. GS3 knockout did not affect milling quality and minimally altered protein and amylose content but notably influenced chalkiness-related traits. GS3 knockout indiscriminately improved heat and alkali stress tolerance in the GJ varieties studied. Transcriptome analysis indicated differential gene expression between the GS3 mutants and their wild-type counterparts, enriched in biological processes related to photosynthesis, photosystem II stabilization, and pathways associated with photosynthesis and cutin, suberine, and wax biosynthesis. Our findings highlight GS3 as a breeding resource for concurrently improving grain shape, thermotolerance, and alkaline tolerance through Gγ protein manipulation in rice.

Transgenic, high-protein sorghums display promise in poultry diets in an initial comparison

This study aimed to compare the inclusion of transgenic sorghums against commercially available sorghums on growth performance in broiler chickens. Isonitrogenous and isoenergetic diets were offered to a total 288 male Ross 308 broiler chickens from 14 to 35 d posthatch. Three dietary treatments were diets based on transgenic sorghums with a mean protein content of 154.7 g/kg and 5 treatments were based on commercially available sorghum hybrids with a mean protein content of 90.6 g/kg. Soybean meal inclusions in the commercial sorghum diets averaged 215 g/kg, which was reduced to 171 g/kg in the transgenic sorghum diets because of the higher protein contents. Overall growth performance was highly satisfactory, and commercial sorghums supported 2.55% (2,330 vs. 2,272 g/bird; P = 0.010) more weight gains and 2.74% (2,929 vs. 2,851 g/bird; P = 0.012) higher feed intakes; however, the transgenic sorghums supported a fractionally better FCR (1.255 vs 1.257; P = 0.826). There were no statistical differences in apparent jejunal and ileal starch and protein (N) digestibility coefficients between treatments. The transgenic sorghum diets generated slightly, but significantly, higher AME:GE ratios and AMEn, but the commercial sorghum diets generated 6.33% (235 vs. 221 g/kg; P < 0.001) greater breast meat yields. Apparent ileal digestibility coefficients of 16 amino acids averaged 0.839 and 0.832 for transgenic and commercial sorghum-based diets, respectively, without any significant differences in individual amino acids. This outcome suggests amino acid digestibilities of the transgenic sorghums may be inherently higher than commercial hybrid sorghums as the 25.7% higher average soybean meal inclusions would have advantaged amino acid digestibilities in commercial sorghum diets. The possibility that the digestibilities of amino acids in the kafirin component of transgenic sorghums was enhanced by modifications to the structure of kafirin protein bodies is discussed. In conclusion, transgenic sorghums with higher protein concentrations led to 20.5% reduction of soybean meal inclusions in broiler diets, and this change did not compromise feed conversion efficiency compared to standard commercial hybrid sorghums.

The DEP1 Mutation Improves Stem Lodging Resistance and Biomass Saccharification by Affecting Cell Wall Biosynthesis in Rice

BACKGROUND

Plant cell walls have evolved precise plasticity in response to environmental stimuli. The plant heterotrimeric G protein complexes could sense and transmit extracellular signals to intracellular signaling systems, and activate a series of downstream responses. dep1 (Dense and Erect Panicles 1), the gain-of-function mutation of DEP1 encoding a G protein γ subunit, confers rice multiple improved agronomic traits. However, the effects of DEP1 on cell wall biosynthesis and wall-related agronomic traits remain largely unknown.

RESULTS

In this study, we showed that the DEP1 mutation affects cell wall biosynthesis, leading to improved lodging resistance and biomass saccharification. The DEP1 is ubiquitously expressed with a relatively higher expression level in tissues rich in cell walls. The CRISPR/Cas9 editing mutants of DEP1 (dep1-cs) displayed a significant enhancement in stem mechanical properties relative to the wild-type, leading to a substantial improvement in lodging resistance. Cell wall analyses showed that the DEP1 mutation increased the contents of cellulose, hemicelluloses, and pectin, and reduced lignin content and cellulose crystallinity (CrI). Additionally, the dep1-cs seedlings exhibited higher sensitivity to cellulose biosynthesis inhibitors, 2,6-Dichlorobenzonitrile (DCB) and isoxaben, compared with the wild-type, confirming the role of DEP1 in cellulose deposition. Moreover, the DEP1 mutation-mediated alterations of cell walls lead to increased enzymatic saccharification of biomass after the alkali pretreatment. Furthermore, the comparative transcriptome analysis revealed that the DEP1 mutation substantially altered expression of genes involved in carbohydrate metabolism, and cell wall biosynthesis.

CONCLUSIONS

Our findings revealed the roles of DEP1 in cell wall biosynthesis, lodging resistance, and biomass saccharification in rice and suggested genetic modification of DEP1 as a potential strategy to develop energy rice varieties with high lodging resistance.

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.

Oryza CLIMtools: A genome-environment association resource reveals adaptive roles for heterotrimeric G proteins in the regulation of rice agronomic traits

Modern crop varieties display a degree of mismatch between their current distributions and the suitability of the local climate for their productivity. To address this issue, we present Oryza CLIMtools (https://gramene.org/CLIMtools/oryza_v1.0/), the first resource for pan-genome prediction of climate-associated genetic variants in a crop species. Oryza CLIMtools consists of interactive web-based databases that enable the user to (1) explore the local environments of traditional rice varieties (landraces) in South-East Asia and (2) investigate the environment by genome associations for 658 Indica and 283 Japonica rice landrace accessions collected from georeferenced local environments and included in the 3K Rice Genomes Project. We demonstrate the value of these resources by identifying an interplay between flowering time and temperature in the local environment that is facilitated by adaptive natural variation in OsHD2 and disrupted by a natural variant in OsSOC1. Prior quantitative trait locus analysis has suggested the importance of heterotrimeric G proteins in the control of agronomic traits. Accordingly, we analyzed the climate associations of natural variants in the different heterotrimeric G protein subunits. We identified a coordinated role of G proteins in adaptation to the prevailing potential evapotranspiration gradient and revealed their regulation of key agronomic traits, including plant height and seed and panicle length. We conclude by highlighting the prospect of targeting heterotrimeric G proteins to produce climate-resilient crops.

Arabidopsis G-protein β subunit AGB1 represses abscisic acid signaling via attenuation of the MPK3-VIP1 phosphorylation cascade

Heterotrimeric G proteins play key roles in cellular processes. Although phenotypic analyses of Arabidopsis Gβ (AGB1) mutants have implicated G proteins in abscisic acid (ABA) signaling, the AGB1-mediated modules involved in ABA responses remain unclear. We found that a partial AGB1 protein was localized to the nucleus where it interacted with ABA-activated VirE2-interacting protein 1 (VIP1) and mitogen-activated protein kinase 3 (MPK3). AGB1 acts as an upstream negative regulator of VIP1 activity by initiating responses to ABA and drought stress, and VIP1 regulates the ABA signaling pathway in an MPK3-dependent manner in Arabidopsis. AGB1 outcompeted VIP1 for interaction with the C-terminus of MPK3, and prevented phosphorylation of VIP1 by MPK3. Importantly, ABA treatment reduced AGB1 expression in the wild type, but increased in vip1 and mpk3 mutants. VIP1 associates with ABA response elements present in the AGB1 promoter, forming a negative feedback regulatory loop. Thus, our study defines a new mechanism for fine-tuning ABA signaling through the interplay between AGB1 and MPK3-VIP1. Furthermore, it suggests a common G protein mechanism to receive and transduce signals from the external environment.

Breeding rice for yield improvement through CRISPR/Cas9 genome editing method: current technologies and examples

The impending climate change is threatening the rice productivity of the Asian subcontinent as instances of crop failures due to adverse abiotic and biotic stress factors are becoming common occurrences. CRISPR-Cas9 mediated genome editing offers a potential solution for improving rice yield as well as its stress adaptation. This technology allows modification of plant's genetic elements and is not dependent on foreign DNA/gene insertion for incorporating a particular trait. In this review, we have discussed various CRISPR-Cas9 mediated genome editing tools for gene knockout, gene knock-in, simultaneously disrupting multiple genes by multiplexing, base editing and prime editing the genes. The review here also presents how these genome editing technologies have been employed to improve rice productivity by directly targeting the yield related genes or by indirectly manipulating various abiotic and biotic stress responsive genes. Lately, many countries treat genome-edited crops as non-GMOs because of the absence of foreign DNA in the final product. Thus, genome edited rice plants with improved yield attributes and stress resilience are expected to be accepted by the public and solve food crisis of a major portion of the globe.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-024-01423-y.

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.

Oryza CLIMtools: A Genome-Environment Association Resource Reveals Adaptive Roles for Heterotrimeric G Proteins in the Regulation of Rice Agronomic Traits

Modern crop varieties display a degree of mismatch between their current distributions and the suitability of the local climate for their productivity. To this end, we present Oryza CLIMtools (https://gramene.org/CLIMtools/oryza_v1.0/), the first resource for pan-genome prediction of climate-associated genetic variants in a crop species. Oryza CLIMtools consists of interactive web-based databases that allow the user to: i) explore the local environments of traditional rice varieties (landraces) in South-Eastern Asia, and; ii) investigate the environment by genome associations for 658 Indica and 283 Japonica rice landrace accessions collected from georeferenced local environments and included in the 3K Rice Genomes Project. We exemplify the value of these resources, identifying an interplay between flowering time and temperature in the local environment that is facilitated by adaptive natural variation in OsHD2 and disrupted by a natural variant in OsSOC1. Prior QTL analysis has suggested the importance of heterotrimeric G proteins in the control of agronomic traits. Accordingly, we analyzed the climate associations of natural variants in the different heterotrimeric G protein subunits. We identified a coordinated role of G proteins in adaptation to the prevailing Potential Evapotranspiration gradient and their regulation of key agronomic traits including plant height and seed and panicle length. We conclude by highlighting the prospect of targeting heterotrimeric G proteins to produce crops that are climate resilient.

Moving beyond the arabidopsis-centric view of G-protein signaling in plants

Heterotrimeric G-protein-mediated signaling is a key mechanism to transduce a multitude of endogenous and environmental signals in diverse organisms. The scope and expectations of plant G-protein research were set by pioneering work in metazoans. Given the similarity of the core constituents, G-protein-signaling mechanisms were presumed to be universally conserved. However, because of the enormous diversity of survival strategies and endless forms among eukaryotes, the signal, its interpretation, and responses vary even among different plant groups. Earlier G-protein research in arabidopsis (Arabidopsis thaliana) has emphasized its divergence from Metazoa. Here, we compare recent evidence from diverse plant lineages with the available arabidopsis G-protein model and discuss the conserved and novel protein components, signaling mechanisms, and response regulation.

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.

Extra-large G proteins have extra-large effects on agronomic traits and stress tolerance in maize and rice

Heterotrimeric G proteins - comprising Gα, Gβ, and Gγ subunits - are ubiquitous elements in eukaryotic cell signaling. Plant genomes contain both canonical Gα subunit genes and a family of plant-specific extra-large G protein genes (XLGs) that encode proteins consisting of a domain with Gα-like features downstream of a long N-terminal domain. In this review we summarize phenotypes modulated by the canonical Gα and XLG proteins of arabidopsis and highlight recent studies in maize and rice that reveal dramatic phenotypic consequences of XLG clustered regularly interspaced short palindromic repeats (CRISPR) mutagenesis in these important crop species. XLGs have both redundant and specific roles in the control of agronomically relevant plant architecture and resistance to both abiotic and biotic stresses. We also point out areas of current controversy, suggest future research directions, and propose a revised, phylogenetically-based nomenclature for XLG protein genes.

RGA1 Negatively Regulates Thermo-tolerance by Affecting Carbohydrate Metabolism and the Energy Supply in Rice

BACKGROUND

Signal transduction mediated by heterotrimeric G proteins, which comprise the α, β, and γ subunits, is one of the most important signaling pathways in rice plants. RGA1, which encodes the Gα subunit of the G protein, plays an important role in the response to various types of abiotic stress, including salt, drought, and cold stress. However, the role of RGA1 in the response to heat stress remains unclear.

RESULTS

The heat-resistant mutant ett1 (enhanced thermo-tolerance 1) with a new allele of the RGA1 gene was derived from an ethane methyl sulfonate-induced Zhonghua11 mutant. After 45 °C heat stress treatment for 36 h and recovery for 7 d, the survival rate of the ett1 mutants was significantly higher than that of wild-type (WT) plants. The malondialdehyde content was lower, and the maximum fluorescence quantum yield of photosystem II, peroxidase activity, and hsp expression were higher in ett1 mutants than in WT plants after 12 h of exposure to 45 °C. The RNA-sequencing results revealed that the expression of genes involved in the metabolism of carbohydrate, nicotinamide adenine dinucleotide, and energy was up-regulated in ett1 under heat stress. The carbohydrate content and the relative expression of genes involved in sucrose metabolism indicated that carbohydrate metabolism was accelerated in ett1 under heat stress. Energy parameters, including the adenosine triphosphate (ATP) content and the energy charge, were significantly higher in the ett1 mutants than in WT plants under heat stress. Importantly, exogenous glucose can alleviate the damages on rice seedling plants caused by heat stress.

CONCLUSION

RGA1 negatively regulates the thermo-tolerance in rice seedling plants through affecting carbohydrate and energy metabolism.

OsmiR159 Modulate BPH Resistance Through Regulating G-Protein γ Subunit GS3 Gene in Rice

Brown planthopper (BPH) is the most destructive insect pest to rice that causes tremendous yield loss each year in rice planting Asia and South-East Asia areas. Compared with traditional chemical-based treatment, utilization of plant endogenous resistance is a more effective and environmental-friendly way for BPH control. Accordingly, quite a few quantitative trait loci (QTLs) for BPH resistance were cloned using forward genetics. However, BPH is apt to change quickly into new biotypes to overcome plant resistance, therefore, new resistance resources and genes are continuously needed. miRNAs are important regulators in both plant development and physiological regulation including immunity, and might be used as effective supplements for BPH resistance QTLs. miR159 is an ancient and conserved miRNA. In this study, we found that each OsMIR159 gene in rice responded to BPH feeding very obviously, and genetic function assay proved them to negatively regulate BPH resistance, with STTM159 showing resistance to BPH, and over expression of OsmiR159d susceptible to BPH. One target genes of OsmiR159, OsGAMYBL2, positively regulated BPH resistance. Further biochemical studies revealed that OsGAMYBL2 could directly bind to the promoter of G-protein γ subunit encoding GS3 gene and repress its expression. And genetically, GS3 responded to BPH feeding promptly and negatively regulated BPH resistance, GS3 over expression plants were susceptible to BPH, while GS3 knock-out plants were resistant to BPH. Thus, we identified new function of OsmiR159-OsGAMYBL2 in mediating BPH response, and revealed a new OsmiR159-G protein pathway that mediates BPH resistance in rice.

RGA1 alleviates low-light-repressed pollen tube elongation by improving the metabolism and allocation of sugars and energy

Low-light stress compromises photosynthetic and energy efficiency and leads to spikelet sterility; however, the effect of low-light stress on pollen tube elongation in the pistil remains poorly understood. The gene RGA1, which encodes a Gα-subunit of the heterotrimeric G-protein, enhanced low-light tolerance at anthesis by preventing the cessation of pollen tube elongation in the pistil of rice plants. In this process, marked increases in the activities of acid invertase (INV), sucrose synthase (SUS) and mitochondrial respiratory electron transport chain complexes, as well as the relative expression levels of SUTs (sucrose transporter), SWEETs (sugars will eventually be exported transporters), SUSs, INVs, CINs (cell-wall INV 1), SnRK1A (sucrose-nonfermenting 1-related kinase 1) and SnRK1B, were observed in OE-1 plants. Accordingly, notable increases in contents of ATP and ATPase were presented in OE-1 plants under low-light conditions, while they were decreased in d1 plants. Importantly, INV and ATPase activators (sucrose and Na₂ SO₃ , respectively) increased spikelet fertility by improving the energy status in the pistil under low-light conditions, and the ATPase inhibitor Na₂ VO₄ induced spikelet sterility and decreased ATPase activity. These results suggest that RGA1 could alleviate the low-light stress-induced impairment of pollen tube elongation to increase spikelet fertility by promoting sucrose unloading in the pistil and improving the metabolism and allocation of energy.

QTL Detection for Rice Grain Length and Fine Mapping of a Novel Locus qGL6.1

BACKGROUND

Grain length (GL) that is directly associated with appearance quality is a key target of selection in rice breeding. Although abundant quantitative trait locus (QTL) associated with GL have been identified, it was still relatively weak to identify QTL for GL from japonica genetic background, as the shortage of japonica germplasms with long grains. We performed QTLs analysis for GL using a recombinant inbred lines (RILs) population derived from the cross between japonica variety GY8 (short grains) and LX1 (long grains) in four environments.

RESULTS

A total of 197 RILs were genotyped with 285 polymorphic SNP markers. Three QTLs qGL5.3, qGL6.1 and qGL11 were detected to control GL by individual environmental analyses and multi-environment joint analysis. Of these, a major-effect and stable QTL qGL6.1 was identified to be a novel QTL, and its LX1 allele had a positive effect on GL. For fine-mapping qGL6.1, a BC₁F₂ population consisting of 2,487 individuals was developed from a backcross between GY8 and R176, one line with long grain. Eight key informative recombinants were identified by nine kompetitive allele specific PCR (KASP) markers. By analyzing key recombinants, the qGL6.1 locus was narrowed down to a 40.41 kb genomic interval on chromosome 6. One candidate gene LOC_Os06g43304.1 encoding cytochrome P450 (CYP71D55) was finally selected based on the difference in the transcriptional expression and variations in its upstream and downstream region.

CONCLUSIONS

Three QTLs qGL5.3, qGL6.1 and qGL11 were identified to control grain length in rice. One novel QTL qGL6.1 was fine mapped within 40.41 kb region, and LOC_Os06g43304.1 encoding cytochrome P450 (CYP71D55) may be its candidate gene. We propose that the further cloning of the qGL6.1 will facilitate improving appearance quality in japonica varieties.

Discovery and Validation of Grain Shape Loci in U.S. Rice Germplasm Through Haplotype Characterization

Rice grain shape is a major determinant of rice market value and the end-use. We mapped quantitative trait loci (QTL) for grain shape traits in a bi-parental recombinant inbred line population (Trenasse/Jupiter) and discovered two major grain length QTLs—qGL3.1 and qGL7.1. Previously, a major grain shape gene GS3 was reported in the qGL3.1 region and grain length gene GL7 was reported to be encompassing qGL7.1 locus. The re-sequencing SNP data on the International Rice Research Institute (IRRI) 3K Rice Genome Project (RGP) panel were obtained from the IRRI SNP-Seek database for both genes and haplotype diversity was characterized for each gene in this diverse panel. United States rice germplasm was not well represented in the IRRI 3K RGP database. Therefore, a minimum SNP set was identified for each gene that could differentiate all the characterized haplotypes. These haplotypes in the 3K RGP panel were screened across 323 elite U.S. genotypes using the minimum SNP set. The screening of haplotypes and phenotype association confirmed the role of GS3 under qGL3.1. However, screening of the GL7 haplotypes in the U.S. germplasm panel showed that GL7 did not play a role in qGL7.1, and in addition, GL7.1 did not segregate in the Trenasse/Jupiter RIL population. This concluded that qGL7.1 is a novel QTL discovered on chr7 for grain shape in the Trenasse/Jupiter RIL population. A high-throughput KASP-based SNP marker for each locus (GS3 and qGL7.1) was identified and validated in elite U.S. rice germplasm to be used in an applied rice breeding program.

G-protein couples MAPK cascade through maize heterotrimeric Gβ subunit

G protein couples MAPK cascade through maize heterotrimeric Gβ subunit MGB1. Heterotrimeric G protein Gβ interacts with Gγ subunit to generate Gβγ dimer in modulation of various biological processes. The modulatory events at transcriptome scale of plant Gβ subunit remain largely unknown. To reveal the regulatory basis of Gβ subunit at transcriptome level, we first identified a canonical maize Gβ subunit MGB1 that physically interacted with Type C Gγ protein MGG4. For transcriptome analysis, two independent CRISPR/Cas9-edited MGB1 lines were generated, which all exhibited growth arrest, suggestive of MGB1 essential for maize seedling establishment. Transcriptomic outcomes showed that MGB1 knockout resulted in elevated transcriptional abundance of plant immune response marker PR and immune receptor RPM1. Integrated GO, KEGG, and GSEA analyses pinpointed the enrichment of differentially expressed genes in defense response pathway. Functional association network construction revealed MAPK cascade components and PR protein as hub regulators of MGB1-mediated immune signaling. MGB1 and scaffold protein ZmRACK1 together with MAPK cascade components coordinately modulated maize immune responses. We built a modulatory hierarchy of Gβ subunit at transcriptome and interacting scales, which is informative for our understanding of the regulatory basis of G protein signaling.

The RNA binding protein OsLa influences grain and anther development in rice

La proteins are found widely in eukaryotes and play a variety of vital roles. AtLa1 has been identified as an La protein that is necessary for embryogenesis in Arabidopsis; however, the existence and biological functions of La proteins in rice (Oryza sativa L.) remain unclear. In this study, we identified and characterized two La proteins in rice that are homologous to AtLa1 and named them OsLa1 and OsLa2. Both the OsLa1 and OsLa2 genes encode RNA-binding proteins with an La domain and two RNA-binding domains. Mutant OsLa1 reduced grain length and pollen fertility, whereas OsLa1 overexpression caused the opposite phenotypes. Further experiments indicated that OsLa1 modulates grain size by influencing cell expansion. Interestingly, mutant OsLa2 resulted in thin grains with decreased weight and a low seed-setting rate. We also found that OsLa1 interacted with OsLa2 and that both OsLa1 and OsLa2 interacted with OseIF6.1, a eukaryotic translation initiation factor involved in ribosome biogenesis. In addition, OsLa1 was able to bind to OseIF6.1 mRNA to modulate its expression. Complete OseIF6.1 knockout caused lethality and OseIF6.1/oseif6.1 heterozygous plants displayed low fertility and low seed setting. Together, our results enrich our knowledge of the role of La proteins in rice growth and development, as well as the relationship between La and eIF6 in rice.

Effective Strategies for Heterologous Expression of Plant Heterotrimeric G-protein γ Subunits without Gβ Subunit Partners

Background:

In plants, heterotrimeric G-protein (Gγ) subunits are diverse, and they have structural plasticity to provide functional selectivity to the heterotrimer. Although the Gβ and Gγ subunits dimerize to function in the signaling pathway, the interaction mechanism of various Gγ subunits with the Gβ subunit partners is still elusive.

Objective:

To better understand the interaction mechanism, one approach is to separate the subunits for the re-assembly in vitro. Hence, developing a reliable method for achieving the efficient production and purification of these proteins has become necessary.

Method:

In this study, Gγ1 and Gγ2 proteins from Oryza sativa and Arabidopsis thaliana were successfully identified, cloned, expressed in bacteria, and purified as recombinant proteins with the fusion tags. Highly expressed recombinant Gγ subunits in E. coli were digested by proteases, which were also produced in the presented study.

Results:

Preliminary structural characterization studies without the Gβ partners showed that Gγ1 proteins have disordered structures with coiled-coil, α-helix extensions, and loops, whereas the Gγ2 protein has a more dominant β-sheet and turns structure. Finally, computational analyses performed on Gγ genes have laid the foundation of new targets for biotechnological purposes.

Conclusion:

The proposed optimized expression and purification protocol can contribute to investigations on the Gβγ binding mechanism in plant G-protein signaling. The investigations on selective binding are critical to shed light on the role(s) of different plant Gγ subunit types in biological processes.

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.

The phosphoproteomic and interactomic landscape of qGL3/OsPPKL1-mediated brassinosteroid signaling in rice

Oryza sativa L. (rice) is one of the most important crops in the world, and grain size is a major component determining rice yield. Recent studies have identified a number of grain size regulators, which are involved in phytohormone signaling, G protein signaling, the mitogen-activated protein kinase signaling pathway, the ubiquitin-proteasome pathway or transcriptional regulation. In a previous study, we cloned qGL3/OsPPKL1 encoding a rice protein phosphatase that negatively modulates brassinosteroid (BR) signaling and grain length. Here, to further explore the qGL3-mediated BR signaling network, we performed phosphoproteomic screenings using two pairs of rice materials: the indica rice cultivar 9311 and its near-isogenic line NIL^qgl3 and the japonica rice cultivar Dongjin and its qGL3 knockout mutant m-qgl3. Together with qGL3-interacting proteins, we constructed the qGL3-mediated network, which reveals the relationships between BR signaling and other critical signaling pathways. Transgenic plants of these network components showed BR-related alterations in plant architecture. From this network, we validated a qGL3-interacting protein, O. sativa VERNALIZATION INSENSITIVE 3-LIKE 1 (OsVIL1), and demonstrated that qGL3 dephosphorylates OsVIL1 to modulate BR signaling. The qGL3-dependent network uncovered in this study increases our understanding of BR signaling and provides a profound foundation for addressing how BR modulates plant architecture in rice.

OsGGC2, Gγ Subunit of Heterotrimeric G Protein, Regulates Plant Height by Functionally Overlapping with DEP1 in Rice

Plant heterotrimeric G proteins have been shown to regulate the size of various organs. There are three types of Gγ subunits in plants: type A, consisting of a canonical Gγ domain; type B, possessing a plant-specific domain at the N-terminus of the Gγ domain; and type C, possessing a plant-specific domain at the C-terminal of the Gγ domain. There is one type A, one type B, and three type C of the five γ-subunits in the rice genome. In type C Gγ subunits, GS3, which controls grain size; DEP1, which controls plant height and panicle branching; and their homolog OsGGC2, which affects grain size, have been reported; however, the function of each gene, their interactions, and molecular mechanisms for the control of plant height have not yet been clarified. In this study, we generated loss-of-function mutants of DEP1 and OsGGC2, which have high homology and similar expression, and investigated their phenotypes. Since both dep1 and osggc2 mutants were dwarfed and the double mutants showed a synergistic phenotype, we concluded that both DEP1 and OsGGC2 are positive regulators of plant height and that their functions are redundant.

Simultaneous Improvement of Grain Yield and Quality through Manipulating Two Type C G Protein Gamma Subunits in Rice

Heterotrimeric G protein signaling is an evolutionarily conserved mechanism in diverse organisms that mediates intracellular responses to external stimuli. In rice, the G proteins are involved in the regulation of multiple important agronomic traits. In this paper, we present our finding that two type C G protein gamma subunits, DEP1 and GS3, antagonistically regulated grain yield and grain quality. The DEP1 gene editing we conducted, significantly increased the grain number per panicle but had a negative impact on taste value, texture properties, and chalkiness-related traits. The GS3 gene editing decreased grain number per panicle but significantly increased grain length. In addition, the GS3 gene-edited plants showed improved taste value, appearance, texture properties, and Rapid Visco Analyser (RVA) profiles. To combine the advantages of both gs3 and dep1, we conducted a molecular design breeding at the GS3 locus of a “super rice” variety, SN265, which has a truncated dep1 allele with erect panicle architecture, high-yield performance, and which is of mediocre eating quality. The elongated grain size of the sn265/gs3 gene-edited plants further increased the grain yield. More importantly, the texture properties and RVA profiles were significantly improved, and the taste quality was enhanced. Beyond showcasing the combined function of dep1 and gs3, this paper presents a strategy for the simultaneous improvement of rice grain yield and quality through manipulating two type C G protein gamma subunits in rice.

The α subunit of the heterotrimeric G protein regulates mesophyll CO2 conductance and drought tolerance in rice

Mesophyll conductance g_m determines CO₂ diffusion rates from mesophyll intercellular air spaces to the chloroplasts and is an important factor limiting photosynthesis. Increasing g_m in cultivated plants is a potential strategy to increase photosynthesis and intrinsic water use efficiency (WUE_i ). The anatomy of the leaf and metabolic factors such as aquaporins and carbonic anhydrases have been identified as important determinants of g_m . However, genes involved in the regulation and modulation of g_m remain largely unknown. In this work, we investigated the role of heterotrimeric G proteins in g_m and drought tolerance in rice d1 mutants, which harbor a null mutation in the Gα subunit gene, RGA1. d1 mutants in both cv Nipponbare and cv Taichung 65 exhibited increased g_m , fostering improvement in photosynthesis, WUE_i , and drought tolerance compared with wild-type. The increased surface area of mesophyll cells and chloroplasts exposed to intercellular airspaces and the reduced cell wall and chloroplast thickness in the d1 mutant are evident contributors to the increase in g_m . Our results indicate that manipulation of heterotrimeric G protein signaling has the potential to improve crop WUE_i and productivity under drought.

Tomato and cotton G protein beta subunit mutants display constitutive autoimmune responses

Heterotrimeric G protein Gβ-deficient mutants in rice and maize display constitutive immune responses, whereas Arabidopsis Gβ mutants show impaired defense, suggesting the existence of functional differences between monocots and dicots. Using CRISPR/Cas9, we produced one hemizygous tomato line with a mutated SlGB1 Gβ gene. Homozygous slgb1 knockout mutants exhibit all the hallmarks of autoimmune mutants, including development of necrotic lesions, constitutive expression of defense-related genes, and high endogenous levels of salicylic acid (SA) and reactive oxygen species, resulting in early seedling lethality. Virus-induced silencing of Gβ in cotton reproduced the symptoms observed in tomato mutants, confirming that the autoimmune phenotype is not limited to monocot species but is also shared by dicots. Even though multiple genes involved in SA and ethylene signaling are highly induced by Gβ silencing in tomato and cotton, co-silencing of SA or ethylene signaling components in cotton failed to suppress the lethal phenotype, whereas co-silencing of the oxidative burst oxidase RbohD can repress lethality. Despite the autoimmune response observed in slgb1 mutants, we show that SlGB1 is a positive regulator of the pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) response in tomato. We speculate that the phenotypic differences observed between Arabidopsis and tomato/cotton/rice/maize Gβ knockouts do not necessarily reflect divergences in G protein-mediated defense mechanisms.

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.

The RING E3 ligase CLG1 targets GS3 for degradation via the endosome pathway to determine grain size in rice

G-protein signaling and ubiquitin-dependent degradation are both involved in grain development in rice, but how these pathways are coordinated in regulating this process is unknown. Here, we show that Chang Li Geng 1 (CLG1), which encodes an E3 ligase, regulates grain size by targeting the Gγ protein GS3, a negative regulator of grain length, for degradation. Overexpression of CLG1 led to increased grain length, while overexpression of mutated CLG1 with changes in three conserved amino acids decreased grain length. We found that CLG1 physically interacts with and ubiquitinats GS3which is subsequently degraded through the endosome degradation pathway, leading to increased grain size. Furthermore, we identified a critical SNP in the exon 3 of CLG1 that is significantly associated with grain size variation in a core collection of cultivated rice. This SNP results in an amino acid substitution from Arg to Ser at position 163 of CLG1 that enhances the E3 ligase activity of CLG1 and thus increases rice grain size. Both the expression level of CLG1 and the SNP CLG1^163S may be useful variations for manipulating grain size in rice.

Rice G protein γ subunit qPE9-1 modulates root elongation for phosphorus uptake by involving 14-3-3 protein OsGF14b and plasma membrane H+ -ATPase

Heterotrimeric G protein is involved in plant growth and development, while the role of rice (Oryza sativa) G protein γ subunit qPE9-1 in response to low-phosphorus (LP) conditions remains unclear. The gene expression of qPE9-1 was significantly induced in rice roots under LP conditions. Rice varieties carrying the qPE9-1 allele showed a stronger primary root response to LP than the varieties carrying the qpe9-1 allele (mutant of the qPE9-1 allele). Transgenic rice plants with the qPE9-1 allele had longer primary roots and higher P concentrations than those with the qpe9-1 allele under LP conditions. The plasma membrane (PM) H⁺ -ATPase was important for the qPE9-1-mediated response to LP. Furthermore, OsGF14b, a 14-3-3 protein that acts as a key component in activating PM H⁺ -ATPase for root elongation, is also involved in the qPE9-1 mediation. Moreover, the overexpression of OsGF14b in WYJ8 (carrying the qpe9-1 allele) partially increased primary root length under LP conditions. Experiments using R18 peptide (a 14-3-3 protein inhibitor) showed that qPE9-1 is important for primary root elongation and H⁺ efflux under LP conditions by involving the 14-3-3 protein. In addition, rhizosheath weight, total P content, and the rhizosheath soil Olsen-P concentration of qPE9-1 lines were higher than those of qpe9-1 lines under soil drying and LP conditions. These results suggest that the G protein γ subunit qPE9-1 in rice plants modulates root elongation for phosphorus uptake by involving the 14-3-3 protein OsGF14b and PM H⁺ -ATPase, which is required for rice P use.

GTP binding by Arabidopsis extra-large G protein 2 is not essential for its functions

The extra-large guanosine-5'-triphosphate (GTP)-binding protein 2, XLG2, is an unconventional Gα subunit of the Arabidopsis (Arabidopsis thaliana) heterotrimeric GTP-binding protein complex with a major role in plant defense. In vitro biochemical analyses and molecular dynamic simulations show that affinity of XLG2 for GTP is two orders of magnitude lower than that of the conventional Gα, AtGPA1. Here we tested the physiological relevance of GTP binding by XLG2. We generated an XLG2(T476N) variant with abolished GTP binding, as confirmed by in vitro GTPγS binding assay. Yeast three-hybrid, bimolecular fluorescence complementation, and split firefly-luciferase complementation assays revealed that the nucleotide-depleted XLG2(T476N) retained wild-type XLG2-like interactions with the Gβγ dimer and defense-related receptor-like kinases. Both wild-type and nucleotide-depleted XLG2(T476N) restored the defense responses against Fusarium oxysporum and Pseudomonas syringae compromised in the xlg2 xlg3 double mutant. Additionally, XLG2(T476N) was fully functional restoring stomatal density, root growth, and sensitivity to NaCl, but failed to complement impaired germination and vernalization-induced flowering. We conclude that XLG2 is able to function in a GTP-independent manner and discuss its possible mechanisms of action.

RGB1 Regulates Grain Development and Starch Accumulation Through Its Effect on OsYUC11-Mediated Auxin Biosynthesis in Rice Endosperm Cells

RGB1, a subunit of heterotrimeric G protein, plays important roles in regulating grain size and weight of rice. However, the molecular mechanisms underlying controlling grain filling process by G protein are still largely unclear. In the present study, we show that RGB1 controls not only the grain size but also the grain filling process. Knock-down of RGB1 significantly delayed grain development and reduced starch accumulation and grain weight, which was closely related to the delayed and the lower expression of genes encoding sucrose metabolism and starch biosynthesis related enzymes during grain filling stage. Suppression of RGB1 expression also resulted in the lower auxin content in grains, which was correlated with the lower expression of OsNF-YB1 and OsYUC11 during grain filling stage. Further biochemical evidence showed that OsYUC11 expression was under control of OsNF-YB1 by its interaction with promoter of OsYUC11. Taken together, we propose that RGB1 controls rice grain development and grain filling process by changing auxin homeostasis in endosperm cells. OsNF-YB1, which acts as a key downstream effector of RGB1, interacts directly with the promoter of OsYUC11 and stimulates the OsYUC11 expression, thereby regulating auxin biosynthesis and starch accumulation and grain size.

Novel Mutant Alleles Reveal a Role of the Extra-Large G Protein in Rice Grain Filling, Panicle Architecture, Plant Growth, and Disease Resistance

Plant growth and grain filling are the key agronomical traits for grain weight and yield of rice. The continuous improvement in rice yield is required for a future sustainable global economy and food security. The heterotrimeric G protein complex containing a canonical α subunit (RGA1) couples extracellular signals perceived by receptors to modulate cell function including plant development and grain weight. We hypothesized that, besides RGA1, three atypical, extra-large GTP-binding protein (XLG) subunits also regulate panicle architecture, plant growth, development, grain weight, and disease resistance. Here, we identified a role of XLGs in agronomic traits and stress tolerance by genetically ablating all three rice XLGs individually and in combination using the CRISPR/Cas9 genome editing in rice. For this study, eight (three single, two double, and three triple) null mutants were selected. Three XLG proteins combinatorically regulate seed filling, because loss confers a decrease in grain weight from 14% with loss of one XLG and loss of three to 32% decrease in grain weight. Null mutations in XLG2 and XLG4 increase grain size. The mutants showed significantly reduced panicle length and number per plant including lesser number of grains per panicle compared to the controls. Loss-of-function of all individual XLGs contributed to 9% more aerial biomass compared to wild type (WT). The double mutant showed improved salinity tolerance. Moreover, loss of the XLG gene family confers hypersensitivity to pathogens. Our findings suggest that the non-canonical XLGs play important roles in regulating rice plant growth, grain filling, panicle phenotype, stress tolerance, and disease resistance. Genetic manipulation of XLGs has the potential to improve agronomic properties in rice.

Comparative population genomic analysis provides insights into breeding of modern indica rice in China

Comparative genomic analysis within Asian cultivated rice (Oryza sativa L.) populations has greatly enriched our knowledge regarding rice domestication and the divergence of the indica and japonica subspecies, while study on genomic regions associated with improvement within the indica subspecies is still limited. Here, through combined investigation of 2,429 indica cultivar genomes from public sequencing projects, we depict the improvement of modern indica rice in China. We identify three subgroups within indica populations: two geographically distinct, historical subgroups indica I (Ind_I) and indica III (Ind_III) and a modern subgroup indica II (Ind_II). The modern indica subgroup Ind_II shows admixture of the other two subgroups and enrichment of alleles that had been low-frequency in the other two subgroups. The Chinese indica cultivars exhibit a strong subgroup component change from Ind_I to Ind_II in the 1980s. Through haplotype-based comparative analysis, we detect 187 regions associated with separation of Ind_II compared to Ind_I or Ind_III. Within those regions we find strong representation of beneficial agricultural production-related alleles in Ind_II and a positive correlation between grain yield and number of differentiated haplotypes. Phenotypic features of long and slender grain, small tiller angle and decreased flowering time were detected for Ind_II. Through haplotype-based comparative analysis between rice subpopulations and subspecies, we find differentiated haplotypes not only from indica itself but also from japonica and aus, suggesting that introgression from other rice sub-populations has substantially contributed to modern indica rice breeds. These results help clarify the evolutionary landscape of modern indica rice in China and provide useful targets for future improvement.

Heterotrimeric Gα subunit regulates plant architecture, organ size and seed weight in the oilseed Brassica juncea

Two BjuGα proteins exhibit conserved GTP-binding and GTP-hydrolysis activities, and function in maintaining overall plant architecture and controlling multiple yield-related traits in the oilseed Brassica juncea. Heterotrimeric G-protein (Gα, Gβ and Gγ) are key signal transducers, well characterized in model plants Arabidopsis and rice. However, our knowledge about the roles played by G-proteins in regulating various growth and developmental traits in polyploid crops, having a complex G-protein signalling network, is quite sparse. In the present study, two Gα encoding genes (BjuA.Gα1 and BjuB.Gα1) were isolated from the allotetraploid Brassica juncea, a globally cultivated oilseed crop of the Brassicaceae family. BjuGα1 genes share a close evolutionary relationship, and the encoded proteins exhibit highly conserved G-protein activities while showing expression differentiation, wherein BjuA.Gα1 was the highly abundant transcript during plant growth and developmental stages. RNAi based suppression of BjuGα1 displayed compromised effects on most of the tested vegetative and reproductive parameters, particularly plant height (32-58%), flower and siliques dimensions, and seed weight (11-13%). Further, over-expression of a constitutively active Gα, lacking the GTPase activity, produced plants with increased height, organ size and seed weight (7-25%), without altering seed quality traits like fatty acid composition, glucosinolates, oil and protein contents. Our study demonstrates that BjuGα1 proteins control overall plant architecture and multiple yield-related traits in the oilseed B. juncea, suggesting that BjuGα1 could be a promising target for crop improvement.

Discovery of genomic regions and candidate genes for grain weight employing next generation sequencing based QTL-seq approach in rice (Oryza sativa L.)

Rice (Oryza sativa L.) yield enhancement is one of the prime objectives of plant breeders. Elucidation of the inheritance of grain weight, a key yield component trait, is of paramount importance for raising the yield thresholds in rice. In the present investigation, we employed Next-Generation Sequencing based QTL-seq approach to identify major genomic regions associated with grain weight using mapping populations derived from a cross between BPT5204 and MTU3626. QTL-seq analysis identified three grain weight quantitative trait loci (QTL) viz., qGW1 (35-40 Mb), qGW7 (10-18 Mb), and qGW8 (2-5 Mb) on chromosomes 1, 7 and 8, respectively and all are found to be novel. Further, qGW8 was confirmed through conventional QTL mapping in F₂, F₃ and BC₁F₂ populations and found to explain the phenotypic variance of 17.88%, 16.70% and 15.00%, respectively, indicating a major QTL for grain weight. Based on previous reports, two candidate genes in the qGW8 QTL were predicted i.e., LOC_Os08g01490 (Cytochrome P450), and LOC_Os08g01680 (WD domain, G-beta repeat domain containing protein) and through in silico analysis they were found to be highly expressed in reproductive organs during different stages of grain development. Here, we have demonstrated that QTL-seq is one of the rapid approaches to uncover novel QTLs controlling complex traits. The candidate genes identified in the present study undoubtedly enhance our understanding of the mechanism and inheritance of the grain weight. These candidate genes can be exploited for yield enhancement after confirmation through complementary studies.

Proteomics Analysis of Plasma Membrane Fractions of the Root, Leaf, and Flower of Rice

The plasma membrane regulates biological processes such as ion transport, signal transduction, endocytosis, and cell differentiation/proliferation. To understand the functional characteristics and organ specificity of plasma membranes, plasma membrane protein fractions from rice root, etiolated leaf, green leaf, developing leaf sheath, and flower were analyzed by proteomics. Among the proteins identified, 511 were commonly accumulated in the five organs, whereas 270, 132, 359, 146, and 149 proteins were specifically accumulated in the root, etiolated leaf, green leaf, developing leaf sheath, and developing flower, respectively. The principle component analysis revealed that the functions of the plasma membrane in the root was different from those of green and etiolated leaves and that the plasma membrane protein composition of the leaf sheath was similar to that of the flower, but not that of the green leaf. Functional classification revealed that the root plasma membrane has more transport-related proteins than the leaf plasma membrane. Furthermore, the leaf sheath and flower plasma membranes were found to be richer in proteins involved in signaling and cell function than the green leaf plasma membrane. To validate the proteomics data, immunoblot analysis was carried out, focusing on four heterotrimeric G protein subunits, Gα, Gβ, Gγ1, and Gγ2. All subunits could be detected by both methods and, in particular, Gγ1 and Gγ2 required concentration by immunoprecipitation for mass spectrometry detection.

Oligomerization of A. thaliana Heterotrimeric G Protein Subunits AGB1 and AGG2 In Vitro

Plant heterotrimeric G proteins are a major group of signaling molecules involved in regulation of critical processes including stress adaptation, seed size, grain quality and immune responses. Despite an abundance of in situ functional studies; purification of the individual subunits of the plant heterotrimer for biophysical and structural characterization and for studies on their interactions are lacking. In this study cloning of the genes encoding the β subunit AGB1 of A. thaliana and its γ-subunits AGG1 and AGG2 using different E. coli expression vectors and screening of expression in several strains are reported. AGB1 could be expressed albeit at very low levels and in all cases it was accompanied by overexpression of E. coli chaperone proteins. AGG1 could only be detected in inclusion body fractions, whereas AGG2 was obtained in soluble fractions and was purified. Purified AGB1 and AGG2 subunits were shown to dimerize in vitro. Further characterization of AGG2 by small angle X-ray scattering measurements and by dynamic light scattering revealed that AGG2 formed homodimers with extended shape in solution. These results are also consistent with those from circular dichroism spectroscopy which yielded 39.4% helical and 50% random coil content for AGG2. This is the first study showing heterologous expression of a plant heterotrimeric G protein β subunit individually and presenting its interaction with a plant γ-subunit in vitro. Results also show that the AGG2 subunit has a disordered structure, which would account for its role in diverse interactions for establishing selectivity in signal propagation.

Plant receptor-like kinase signaling through heterotrimeric G-proteins

Heterotrimeric G-proteins regulate multiple aspects of plant growth, development, and response to biotic and abiotic stresses. While the core components of heterotrimeric G-proteins and their basic biochemistry are similar in plants and metazoans, key differences exist in their regulatory mechanisms. In particular, the activation mechanisms of plant G-proteins appear diverse and may include both canonical and novel modes. Classical G-protein-coupled receptor-like proteins exist in plants and interact with Gα proteins, but their ability to activate Gα by facilitating GDP to GTP exchange has not been demonstrated. Conversely, there is genetic and functional evidence that plant G-proteins interact with the highly prevalent receptor-like kinases (RLKs) and are phosphorylated by them. This suggests the exciting scenario that in plants the G-proteins integrate RLK-dependent signal perception at the plasma membrane with downstream effectors. Because RLKs are active kinases, it is also likely that the activity of plant G-proteins is regulated via phosphorylation/dephosphorylation rather than GTP-GDP exchange as in metazoans. This review discusses our current knowledge of the possible RLK-dependent regulatory mechanisms of plant G-protein signaling in the context of several biological systems and outlines the diversity that might exist in such regulation.

Heterotrimeric G protein are involved in the regulation of multiple agronomic traits and stress tolerance in rice

BACKGROUND

The heterotrimeric G protein complex, consisting of Gα, Gβ, and Gγ subunits, are conserved signal transduction mechanism in eukaryotes. Recent molecular researches had demonstrated that G protein signaling participates in the regulation of yield related traits. However, the effects of G protein genes on yield components and stress tolerance are not well characterized.

RESULTS

In this study, we generated heterotrimeric G protein mutants in rice using CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats) gene-editing technology. The effects of heterotrimeric G proteins on the regulation of yield components and stress tolerance were investigated. The mutants of gs3 and dep1 generated preferable agronomic traits compared to the wild-type, whereas the mutants of rga1 showed an extreme dwarf phenotype, which led to a dramatic decrease in grain production. The mutants showed improved stress tolerance, especially under salinity treatment. We found four putative extra-large G proteins (PXLG)1-4 that also participate in the regulation of yield components and stress tolerance. A yeast two hybrid showed that the RGB1 might interact with PXLG2 but not with PXLG1, PXLG3 or PXLG4.

CONCLUSION

These findings will not only improve our understanding of the repertoire of heterotrimeric G proteins in rice but also contribute to the application of heterotrimeric G proteins in rice breeding.

Identification of Multiple Grain Shape-Related Loci in Rice Using Bulked Segregant Analysis With High-Throughput Sequencing

Grain shape (GS) is an important agronomic trait that can improve rice breeding for optimal appearance quality, and it varies highly between indica and japonica subspecies. In this study, we conducted a genome sequencing of a series of recombination inbred lines (RILs) derived from a cross between japonica variety Shennong265 (SN265) and indica variety R99, and we successfully detected seven loci associated with GS. Subsequent analysis showed that a major quantitative trait locus (QTL) corresponded to the qSW5/GW5. To identify a main-effect locus, we conducted bulked segregant analysis (BSA) in two F₂ populations. A 0.8-Mb region on chromosome 9 was identified as the candidate region of GS. There are 101 predicted genes in this region, and eight single nucleotide polymorphisms/insertions and deletions (SNPs/INDELs) caused frameshift. We found that a 637-bp stretch in exon 5 of the DENSE AND ERECT PANICLE 1 (DEP1) locus in SN265 was replaced by a 12-bp sequence. The two types of CRISPR/Cas9 gene-edited plants confirmed that DEP1 affected GS, and both Gγ and Cys-rich domains participated in this regulatory mechanism. These findings improve our understanding of the underlying mechanism of GS in rice and provide an effective and rapid strategy for the identification of main-effect loci of target traits.

G-protein-coupled Receptors in Fungi

G-protein-coupled receptors (GPCRs) are the largest family of transmembrane receptors in fungi. These receptors have an important role in the transduction of extracellular signals into intracellular sites in response to diverse stimuli. They enable fungi to coordinate cell function and metabolism, thereby promoting their survival and propagation, and sense certain fundamentally conserved elements, such as nutrients, pheromones, and stress, for adaptation to their niches, environmental stresses, and host environment, causing disease and pathogen virulence. This chapter highlights the role of GPCRs in fungi in coordinating cell function and metabolism. Fungal cells sense the molecular interactions between extracellular signals. Their respective sensory systems are described here in detail.

The Rice G Protein γ Subunit DEP1/qPE9-1 Positively Regulates Grain-Filling Process by Increasing Auxin and Cytokinin Content in Rice Grains

Heterotrimeric G protein-mediated signal transduction is one of the most important and highly conserved signaling pathways in eukaryotes, which involves in the regulation of many important biological processes. As compared with those in mammals and Arabidopsis thaliana, the functions of rice heterotrimeric G protein and their molecular mechanisms are largely unknown. The rice genome contains a single G_α (RGA1) and G_β (RGB1), and five G_γ (RGG1, RGG2, GS3, DEP1/qPE9-1, and GGC2) subunits. Recent genetic studies have shown that DEP1/qPE9-1, an atypical putative G_γ protein, is responsible for the grain size as well as the dense and erect panicles, but the biochemical and molecular mechanisms underlying the control of grain size are not well understood. Here, we report that rice plants carrying DEP1/qPE9-1 have more endosperm cells per grain than plants contain the dep1/qpe9-1 allele. The DEP1/qPE9-1 line has a higher rate and more prolonged period of starch accumulation than the dep1/qpe9-1 line. Additionally, the expression of several essential genes encoding enzymes catalyzing sucrose metabolism and starch biosynthesis is higher in the DEP1/qPE9-1 line than in the dep1/qpe9-1 line, especially from the mid to late grain-filling stage. Grains of the DEP1/qPE9-1 line also have higher contents of three phytohormones, ABA, auxin and cytokinin. Exogenous application of auxin or cytokinin enhanced the starch accumulation and the expression of genes encoding grain-filling-related enzymes in the grains of dep1/qpe9-1, whereas ABA produced no effects. Based on these results, we conclude that DEP1/qPE9-1 positively regulates starch accumulation primarily through auxin and cytokinin, which enhance the expression of genes encoding starch biosynthesis during the mid to late grain-filling stage, resulting in increased duration of the grain-filling process.

Genome-wide association study (GWAS) for morphological and yield-related traits in an oil palm hybrid (Elaeis oleifera x Elaeis guineensis) population

BACKGROUND

The genus Elaeis has two species of economic importance for the oil palm agroindustry: Elaeis oleifera (O), native to the Americas, and Elaeis guineensis (G), native to Africa. This work provides to our knowledge, the first association mapping study in an interspecific OxG oil palm population, which shows tolerance to pests and diseases, high oil quality, and acceptable fruit bunch production.

RESULTS

Using genotyping-by-sequencing (GBS), we identified a total of 3776 single nucleotide polymorphisms (SNPs) that were used to perform a genome-wide association analysis (GWAS) in 378 OxG hybrid population for 10 agronomic traits. Twelve genomic regions (SNPs) were located near candidate genes implicated in multiple functional categories, such as tissue growth, cellular trafficking, and physiological processes.

CONCLUSIONS

We provide new insights on genomic regions that mapped on candidate genes involved in plant architecture and yield. These potential candidate genes need to be confirmed for future targeted functional analyses. Associated markers to the traits of interest may be valuable resources for the development of marker-assisted selection in oil palm breeding.

Nucleotide exchange-dependent and nucleotide exchange-independent functions of plant heterotrimeric GTP-binding proteins

Heterotrimeric guanine nucleotide-binding proteins (G proteins), which are composed of α, β, and γ subunits, are versatile, guanine nucleotide-dependent, molecular on-off switches. In animals and fungi, the exchange of GDP for GTP on Gα controls G protein activation and is crucial for normal cellular responses to diverse extracellular signals. The model plant Arabidopsis thaliana has a single canonical Gα subunit, AtGPA1. We found that, in planta, the constitutively active, GTP-bound AtGPA1(Q222L) mutant and the nucleotide-free AtGPA1(S52C) mutant interacted with Gβγ1 and Gβγ2 dimers with similar affinities, suggesting that G protein heterotrimer formation occurred independently of nucleotide exchange. In contrast, AtGPA1(Q222L) had a greater affinity than that of AtGPA1(S52C) for Gβγ3, suggesting that the GTP-bound conformation of AtGPA1(Q222L) is distinct and tightly associated with Gβγ3. Functional analysis of transgenic lines expressing either AtGPA1(S52C) or AtGPA1(Q222L) in the gpa1-null mutant background revealed various mutant phenotypes that were complemented by either AtGPA1(S52C) or AtGPA1(Q222L). We conclude that, in addition to the canonical GDP-GTP exchange-dependent mechanism, plant G proteins can function independently of nucleotide exchange.

The heterotrimeric G protein β subunit RGB1 is required for seedling formation in rice

BACKGROUND

The heterotrimeric G protein β subunit RGB1 plays an important role in plant growth and development. However, the molecular mechanisms underlying the regulation of rice growth by RGB1 remain elusive.

RESULTS

Here, the rgb1 mutants rgb1-1 (+ 1 bp), rgb1-2 (- 1 bp), and rgb1-3 (- 11 bp) were isolated using the CRISPR/Cas9 system, and they were arrested at 1 day after germination and ultimately exhibited seedling lethality. The dynamic anatomical characteristics of the embryos of the rgb1 seedlings and WT during early postgermination and according to TUNEL assays showed that the suppressed growth of the rgb1 mutants was caused by cell death. In addition to the limited shoot and root development, the development of the embryo shoot-root axis was suppressed in the rgb1 mutants. RGB1 was expressed mainly in the root epidermal and vascular tissues of the embryo. Moreover, transcript profiling analysis revealed that the expression of a large number of auxin-, cytokinin-, and brassinosteroid-inducible genes was upregulated or downregulated in the rgb1 mutant compared to the wild type during seedling development.

CONCLUSIONS

Overall, the rgb1 mutants provide an ideal material for exploring the molecular mechanism underlying rice seedling formation during early postgermination development by G proteins.

SIGNIFICANCE STATEMENT

The heterotrimeric G protein β subunit RGB1 acts as a crucial factor in promoting early postgermination seedling development in rice.

Multifaceted plant G protein: interaction network, agronomic potential, and beyond

Heterotrimeric G protein and interacting effectors are relevant for agronomic significance. We can manipulate G protein and effectors, individually or in combination, to develop plant ideotypes by intelligent design breeding. Heterotrimeric guanine nucleotide-binding protein (G protein) is involved in a wide range of biological events, many of which with agronomic significance. In this review, we summarize recent advances of plant G protein research. We first retrieve maize G protein core subunits Gα, Gβ, and Gγ based on information of Arabidopsis and rice G proteins using integrated BLAST and domain confirmation. Then, we briefly introduce the distribution and function of G protein. We also describe the interaction between G protein and CLAVATA receptor, brassinosteroid signaling kinase complex, and MADS-domain transcription factor. Finally, we discuss the application of G protein knowledge in intelligent plant breeding with focus on the improvement of agronomically important traits.

Control of grain size by G protein signaling in rice

Heterotrimeric G proteins are involved in multiple cellular processes in eukaryotes by sensing and transducing various signals. G protein signaling in plants is quite different from that in animals, and the mechanisms of plant G protein signaling are still largely unknown. Several recent studies have provided new insights into the mechanisms of G protein signaling in rice grain size and yield control. In this review, we summarize recent advances on the function of G proteins in rice grain size control and discuss the potential genetic and molecular mechanisms of plant G protein signaling.

Heterotrimeric G-Protein Signaling in Plants: Conserved and Novel Mechanisms

Heterotrimeric GTP-binding proteins are key regulators of a multitude of signaling pathways in all eukaryotes. Although the core G-protein components and their basic biochemistries are broadly conserved throughout evolution, the regulatory mechanisms of G proteins seem to have been rewired in plants to meet specific needs. These proteins are currently the focus of intense research in plants due to their involvement in many agronomically important traits, such as seed yield, organ size regulation, biotic and abiotic stress responses, symbiosis, and nitrogen use efficiency. The availability of massive sequence information from a variety of plant species, extensive biochemical data generated over decades, and impressive genetic resources for plant G proteins have made it possible to examine their role, unique properties, and novel regulation. This review focuses on some recent advances in our understanding of the mechanistic details of this critical signaling pathway to enable the precise manipulation and generation of plants to meet future needs.