A mutant Arabidopsis heterotrimeric G-protein beta subunit affects leaf, flower, and fruit development

G-Protein Phosphorylation: Aspects of Binding Specificity and Function in the Plant Kingdom

Plant survival depends on adaptive mechanisms that constantly rely on signal recognition and transduction. The predominant class of signal discriminators is receptor kinases, with a vast member composition in plants. The transduction of signals occurs in part by a simple repertoire of heterotrimeric G proteins, with a core composed of α-, β-, and γ-subunits, together with a 7-transmembrane Regulator G Signaling (RGS) protein. With a small repertoire of G proteins in plants, phosphorylation by receptor kinases is critical in regulating the active state of the G-protein complex. This review describes the in vivo detected phosphosites in plant G proteins and conservation scores, and their in vitro corresponding kinases. Furthermore, recently described outcomes, including novel arrestin-like internalization of RGS and a non-canonical phosphorylation switching mechanism that drives G-protein plasticity, are discussed.

Integration of Light and Brassinosteroid Signaling during Seedling Establishment

Light and brassinosteroid (BR) are external stimuli and internal cue respectively, that both play critical roles in a wide range of developmental and physiological process. Seedlings grown in the light exhibit photomorphogenesis, while BR promotes seedling etiolation. Light and BR oppositely control the development switch from shotomorphogenesis in the dark to photomorphogenesis in the light. Recent progress report that substantial components have been identified as hubs to integrate light and BR signals. Photomorphogenic repressors including COP1, PIFs, and AGB1 have been reported to elevate BR response, while photomorphogenesis-promoting factors such as HY5, BZS1, and NF-YCs have been proven to repress BR signal. In addition, BR components also modulate light signal. Here, we review the current research on signaling network associated with light and brassinosteroids, with a focus on the integration of light and BR signals enabling plants to thrive in the changeable environment.

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.

Arabidopsis G-Protein β Subunit AGB1 Negatively Regulates DNA Binding of MYB62, a Suppressor in the Gibberellin Pathway

Plant G proteins are versatile components of transmembrane signaling transduction pathways. The deficient mutant of heterotrimeric G protein leads to defects in plant growth and development, suggesting that it regulates the GA pathway in Arabidopsis. However, the molecular mechanism of G protein regulation of the GA pathway is not understood in plants. In this study, two G protein β subunit (AGB1) mutants, agb1-2 and N692967, were dwarfed after exogenous application of GA₃. AGB1 interacts with the DNA-binding domain MYB62, a GA pathway suppressor. Transgenic plants were obtained through overexpression of MYB62 in two backgrounds including the wild-type (MYB62/WT Col-0) and agb1 mutants (MYB62/agb1) in Arabidopsis. Genetic analysis showed that under GA₃ treatment, the height of the transgenic plants MYB62/WT and MYB62/agb1 was lower than that of WT. The height of MYB62/agb1 plants was closer to MYB62/WT plants and higher than that of mutants agb1-2 and N692967, suggesting that MYB62 is downstream of AGB1 in the GA pathway. qRT-PCR and competitive DNA binding assays indicated that MYB62 can bind MYB elements in the promoter of GA2ox7, a GA degradation gene, to activate GA2ox7 transcription. AGB1 affected binding of MYB62 on the promoter of GA2ox7, thereby negatively regulating th eactivity of MYB62.

Arabidopsis PEAPODs function with LIKE HETEROCHROMATIN PROTEIN1 to regulate lateral organ growth

In higher plants, lateral organs are usually of determinate growth. It remains largely elusive how the determinate growth is achieved and maintained. Previous reports have shown that Arabidopsis PEAPOD (PPD) proteins suppress proliferation of dispersed meristematic cells partly through a TOPLESS corepressor complex. Here, we identified a new PPD-interacting partner, LIKE HETEROCHROMATIN PROTEIN1 (LHP1), using the yeast two-hybrid system, and their interaction is mediated by the chromo shadow domain and the Jas domain in LHP1 and PPD2, respectively. Our genetic data demonstrate that the phenotype of ppd2 lhp1 is more similar to lhp1 than to ppd2, indicating epistasis of lhp1 to ppd2. Microarray analysis reveals that PPD2 and LHP1 can regulate expression of a common set of genes directly or indirectly. Consistently, chromatin immunoprecipitation results confirm that PPD2 and LHP1 are coenriched at the promoter region of their targets such as D3-TYPE CYCLINS and HIGH MOBILITY GROUP A, which are upregulated in ppd2, lhp1 and ppd2 lhp1 mutants, and that PPDs mediate repressive histone 3 lysine-27 trimethylation at these loci. Taken together, our data provide evidence that PPD and LHP1 form a corepressor complex that regulates lateral organ growth.

Genetic and signalling pathways of dry fruit size: targets for genome editing-based crop improvement

Fruit is seed-bearing structures specific to angiosperm that form from the gynoecium after flowering. Fruit size is an important fitness character for plant evolution and an agronomical trait for crop domestication/improvement. Despite the functional and economic importance of fruit size, the underlying genes and mechanisms are poorly understood, especially for dry fruit types. Improving our understanding of the genomic basis for fruit size opens the potential to apply gene-editing technology such as CRISPR/Cas to modulate fruit size in a range of species. This review examines the genes involved in the regulation of fruit size and identifies their genetic/signalling pathways, including the phytohormones, transcription and elongation factors, ubiquitin-proteasome and microRNA pathways, G-protein and receptor kinases signalling, arabinogalactan and RNA-binding proteins. Interestingly, different plant taxa have conserved functions for various fruit size regulators, suggesting that common genome edits across species may have similar outcomes. Many fruit size regulators identified to date are pleiotropic and affect other organs such as seeds, flowers and leaves, indicating a coordinated regulation. The relationships between fruit size and fruit number/seed number per fruit/seed size, as well as future research questions, are also discussed.

Genome-Wide Association Study of Wood Anatomical and Morphological Traits in Populus trichocarpa

To understand the genetic mechanisms underlying wood anatomical and morphological traits in Populus trichocarpa, we used 869 unrelated genotypes from a common garden in Clatskanie, Oregon that were previously collected from across the distribution range in western North America. Using GEMMA mixed model analysis, we tested for the association of 25 phenotypic traits and nine multitrait combinations with 6.741 million SNPs covering the entire genome. Broad-sense trait heritabilities ranged from 0.117 to 0.477. Most traits were significantly correlated with geoclimatic variables suggesting a role of climate and geography in shaping the variation of this species. Fifty-seven SNPs from single trait GWAS and 11 SNPs from multitrait GWAS passed an FDR threshold of 0.05, leading to the identification of eight and seven nearby candidate genes, respectively. The percentage of phenotypic variance explained (PVE) by the significant SNPs for both single and multitrait GWAS ranged from 0.01% to 6.18%. To further evaluate the potential roles of candidate genes, we used a multi-omic network containing five additional data sets, including leaf and wood metabolite GWAS layers and coexpression and comethylation networks. We also performed a functional enrichment analysis on coexpression nearest neighbors for each gene model identified by the wood anatomical and morphological trait GWAS analyses. Genes affecting cell wall composition and transport related genes were enriched in wood anatomy and stomatal density trait networks. Signaling and metabolism related genes were also common in networks for stomatal density. For leaf morphology traits (leaf dry and wet weight) the networks were significantly enriched for GO terms related to photosynthetic processes as well as cellular homeostasis. The identified genes provide further insights into the genetic control of these traits, which are important determinants of the suitability and sustainability of improved genotypes for lignocellulosic biofuel production.

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.

The BIG protein distinguishes the process of CO2 -induced stomatal closure from the inhibition of stomatal opening by CO2

We conducted an infrared thermal imaging-based genetic screen to identify Arabidopsis mutants displaying aberrant stomatal behavior in response to elevated concentrations of CO₂ . This approach resulted in the isolation of a novel allele of the Arabidopsis BIG locus (At3g02260) that we have called CO₂ insensitive 1 (cis1). BIG mutants are compromised in elevated CO₂ -induced stomatal closure and bicarbonate activation of S-type anion channel currents. In contrast with the wild-type, they fail to exhibit reductions in stomatal density and index when grown in elevated CO₂ . However, like the wild-type, BIG mutants display inhibition of stomatal opening when exposed to elevated CO₂ . BIG mutants also display wild-type stomatal aperture responses to the closure-inducing stimulus abscisic acid (ABA). Our results indicate that BIG is a signaling component involved in the elevated CO₂ -mediated control of stomatal development. In the control of stomatal aperture by CO₂ , BIG is only required in elevated CO₂ -induced closure and not in the inhibition of stomatal opening by this environmental signal. These data show that, at the molecular level, the CO₂ -mediated inhibition of opening and promotion of stomatal closure signaling pathways are separable and BIG represents a distinguishing element in these two CO₂ -mediated responses.

YODA MAP3K kinase regulates plant immune responses conferring broad-spectrum disease resistance

Mitogen-activated protein kinases (MAPKs) cascades play essential roles in plants by transducing developmental cues and environmental signals into cellular responses. Among the latter are microbe-associated molecular patterns perceived by pattern recognition receptors (PRRs), which trigger immunity. We found that YODA (YDA) - a MAPK kinase kinase regulating several Arabidopsis developmental processes, like stomatal patterning - also modulates immune responses. Resistance to pathogens is compromised in yda alleles, whereas plants expressing the constitutively active YDA (CA-YDA) protein show broad-spectrum resistance to fungi, bacteria, and oomycetes with different colonization modes. YDA functions in the same pathway as ERECTA (ER) Receptor-Like Kinase, regulating both immunity and stomatal patterning. ER-YDA-mediated immune responses act in parallel to canonical disease resistance pathways regulated by phytohormones and PRRs. CA-YDA plants exhibit altered cell-wall integrity and constitutively express defense-associated genes, including some encoding putative small secreted peptides and PRRs whose impairment resulted in enhanced susceptibility phenotypes. CA-YDA plants show strong reprogramming of their phosphoproteome, which contains protein targets distinct from described MAPKs substrates. Our results suggest that, in addition to stomata development, the ER-YDA pathway regulates an immune surveillance system conferring broad-spectrum disease resistance that is distinct from the canonical pathways mediated by described PRRs and defense hormones.

Overview of OVATE FAMILY PROTEINS, A Novel Class of Plant-Specific Growth Regulators

OVATE FAMILY PROTEINS (OFPs) are a class of proteins with a conserved OVATE domain. OVATE protein was first identified in tomato as a key regulator of fruit shape. OFPs are plant-specific proteins that are widely distributed in the plant kingdom including mosses and lycophytes. Transcriptional activity analysis of Arabidopsis OFPs (AtOFPs) in protoplasts suggests that they act as transcription repressors. Functional characterization of OFPs from different plant species including Arabidopsis, rice, tomato, pepper, and banana suggests that OFPs regulate multiple aspects of plant growth and development, which is likely achieved by interacting with different types of transcription factors including the KNOX and BELL classes, and/or directly regulating the expression of target genes such as Gibberellin 20 oxidase (GA20ox). Here, we examine how OVATE was originally identified, summarize recent progress in elucidation of the roles of OFPs in regulating plant growth and development, and describe possible mechanisms underpinning this regulation. Finally, we review potential new research directions that could shed additional light on the functional biology of OFPs in plants.

The Multifunction of CLAVATA2 in Plant Development and Immunity

The CLAVATA2 (CLV2) gene encodes a leucine-rich repeat receptor-like protein, a class of cell surface receptors that lacks a cytoplasmic kinase domain. As such, CLV2 is capable of functioning in concert with additional receptor(s), possibly receptor-like kinase(s), to activate cellular responses upon ligand perception. Accumulating data indicate that CLV2 is implicated in distinct biological processes including plant growth and development as well as innate immunity to microbe and nematode infections. This article focuses on recent advances in our understanding of multiple signaling pathways mediated by multifunctional CLV2 that modulate various physiological processes. The challenges and future perspectives of elucidating the specificity of CLV2-mediated signaling pathways and identifying potential co-receptors and putative ligands for CLV2 are also discussed.

Heterotrimeric G protein-coupled signaling in plants

Investigators studying G protein-coupled signaling--often called the best-understood pathway in the world owing to intense research in medical fields--have adopted plants as a new model to explore the plasticity and evolution of G signaling. Much research on plant G signaling has not disappointed. Although plant cells have most of the core elements found in animal G signaling, differences in network architecture and intrinsic properties of plant G protein elements make G signaling in plant cells distinct from the animal paradigm. In contrast to animal G proteins, plant G proteins are self-activating, and therefore regulation of G activation in plants occurs at the deactivation step. The self-activating property also means that plant G proteins do not need and therefore do not have typical animal G protein-coupled receptors. Targets of activated plant G proteins, also known as effectors, are unlike effectors in animal cells. The simpler repertoire of G signal elements in Arabidopsis makes G signaling easier to manipulate in a multicellular context.

The plant-specific G protein γ subunit AGG3 influences organ size and shape in Arabidopsis thaliana

• Control of organ size and shape by cell proliferation and cell expansion is a fundamental developmental process, but the mechanisms that set the size and shape of determinate organs are largely unknown in plants. • Molecular, genetic, cytological and biochemical approaches were used to characterize the roles of the Arabidopsis thaliana G protein γ subunit (AGG3) gene in organ growth. • Here, we describe A. thaliana AGG3, which promotes petal growth by increasing the period of cell proliferation. Both the N-terminal region and the C-terminal domains of AGG3 are necessary for the function of AGG3. By contrast, analysis of a series of AGG3 derivatives with deletions in specific domains showed that the deletion of any of these domains cannot completely abolish the function of AGG3. The GFP-AGG3 fusion protein is localized to the plasma membrane. The predicted transmembrane domain plays an important role in the plasma membrane localization of AGG3. Genetic analyses revealed that AGG3 action requires a functional G protein α subunit (GPA1) and G protein β subunit (AGB1). • Our findings demonstrate that AGG3, GPA1 and AGB1 act in the same genetic pathway to influence organ size and shape in A. thaliana.

Gγ1+Gγ2+Gγ3=Gβ: the search for heterotrimeric G-protein γ subunits in Arabidopsis is over

In Arabidopsis, heterotrimeric G-proteins consist of one Gα (GPA1), one Gβ (AGB1) and three Gγ (AGG1, AGG2 and AGG3) subunits. Gβ and Gγ subunits function as obligate heterodimers, therefore any phenotypes observed in Gβ-deficient mutants should be apparent in Gγ-deficient mutants. Nevertheless, the first two Gγ subunits discovered failed to explain many of the phenotypes shown by the agb1 mutants in Arabidopsis, prompting the search for additional Gγ subunits. The recent discovery of an additional, although quite atypical, Gγ subunit in Arabidopsis (AGG3) has helped to complete the picture and explains almost all of the missing agb1 'orphan' phenotypes. There is nevertheless still one unexplained phenotype, the reduction in rosette size reported for agb1, that has not been observed in any of the individual agg mutants or the double agg1agg2 mutant. We have now created a triple gamma mutant (agg1agg2agg3) in Arabidopsis and show that it recapitulates the remaining 'orphan'agb1 phenotypes. Triple agg1agg2agg3 mutants show the reduction in rosette size previously observed in agb1 mutants. In addition we show that small differences in flower and silique size observed between agb1 and agg3 mutants are also accounted for by the triple agg1agg2agg3 mutant. Our results strongly suggest that there are no additional members of the G-protein family remaining to be discovered in Arabidopsis.

Site-directed mutagenesis of the Arabidopsis heterotrimeric G protein β subunit suggests divergent mechanisms of effector activation between plant and animal G proteins

Heterotrimeric G proteins are integral components of signal transduction in humans and other mammals and have been therefore extensively studied. However, while they are known to mediate many processes, much less is currently known about the effector pathways and molecular mechanisms used by these proteins to regulate effectors in plants. We designed a complementation strategy to study G protein signaling in Arabidopsis thaliana, particularly the mechanism of action of AGB1, the sole identified β subunit. We used biochemical and effector regulation data from human G protein studies to identify four potentially important residues for site-directed mutagenesis (T65, M111, D250 and W361 of AGB1). Each residue was individually mutated and the resulting mutated protein introduced in the agb1-2 mutant background under the control of the native AGB1 promoter. Interestingly, even though these mutations have been shown to have profound effects on effector signaling in humans, all the mutated subunits were able to restore thirteen of the fifteen Gβ-deficient phenotypes characterized in this study. Only one mutated protein, T65A was unable to complement the hypersensitivity to mannitol during germination observed in agb1 mutants; while only D250A failed to restore lateral root numbers in the agb1 mutant to wild-type levels. Our results suggest that the mechanisms used in mammalian G protein signaling are not well conserved in plant G protein signaling, and that either the effectors used by plant G proteins, or the mechanisms used to activate them, are at least partially divergent from the well-studied mammalian G proteins.

AtIRE1A/AtIRE1B and AGB1 independently control two essential unfolded protein response pathways in Arabidopsis

The endoplasmic reticulum (ER) has the ability to maintain the balance between demand for and synthesis of secretory proteins. To ensure protein-folding homeostasis in the ER, cells invoke signaling pathways known as the unfolded protein response (UPR). To initiate UPR, yeasts largely rely on a conserved sensor, IRE1. In metazoans, there are at least three independent UPR signalling pathways. Some UPR transducers have been identified in plants, but no genetic interaction among them has yet been examined. The Arabidopsis genome encodes two IRE1 sequence homologs, AtIRE1A and AtIRE1B. Here we provide evidence that AtIRE1A and AtIRE1B have overlapping functions that are essential for the plant UPR. A double mutant of AtIRE1A and AtIRE1B, atire1a atire1b, showed reduced ER stress tolerance and a compromised UPR activation phenotype. We have also established that Arabidopsis AGB1, a subunit of the ubiquitous heterotrimeric GTP-binding protein family, and AtIRE1A/AtIRE1B independently control two essential plant UPR pathways. By demonstrating that atire1a atire1b has a short root phenotype that is enhanced by an agb1 loss-of-function mutation, we have identified a role for UPR transducers in organ growth regulation.

An atypical heterotrimeric G-protein γ-subunit is involved in guard cell K⁺-channel regulation and morphological development in Arabidopsis thaliana

Currently, there are strong inconsistencies in our knowledge of plant heterotrimeric G-proteins that suggest the existence of additional members of the family. We have identified a new Arabidopsis G-protein γ-subunit (AGG3) that modulates morphological development and ABA-regulation of stomatal aperture. AGG3 strongly interacts with the Arabidopsis G-protein β-subunit in vivo and in vitro. Most importantly, AGG3-deficient mutants account for all but one of the 'orphan' phenotypes previously unexplained by the two known γ-subunits in Arabidopsis. AGG3 has unique characteristics never before observed in plant or animal systems, such as its size (more than twice that of canonical γ-subunits) and the presence of a C-terminal Cys-rich domain. AGG3 thus represent a novel class of G-protein γ-subunits, widely spread throughout the plant kingdom but not present in animals. Homologues of AGG3 in rice have been identified as important quantitative trait loci for grain size and yield, but due to the atypical nature of the proteins their identity as G-protein subunits was thus far unknown. Our work demonstrates a similar trend in seeds of Arabidopsis agg3 mutants, and implicates G-proteins in such a crucial agronomic trait. The discovery of this highly atypical subunit reinforces the emerging notion that plant and animal G-proteins have distinct as well as shared evolutionary pathways.

Suppression of the rice heterotrimeric G protein β-subunit gene, RGB1, causes dwarfism and browning of internodes and lamina joint regions

In the present study, we investigated the function of the heterotrimeric G protein β-subunit (Gβ) gene (RGB1) in rice. RGB1 knock-down lines were generated in the wild type and d1-5, a mutant deficient for the heterotrimeric G protein α-subunit (Gα) gene (RGA1). Both transgenic lines showed browning of the lamina joint regions and nodes that could be attributed to a reduction of RGB1 function, as the abnormality was not observed in d1-5. The RGB1 knock-down lines generated in d1-5 were shorter, suggesting RGB1 to be a positive regulator of cellular proliferation, in addition to RGA1. The number of sterile seeds also increased in both RGB1 knock-down lines. These results suggest that Gβγ and Gα cooperatively function in cellular proliferation and seed fertility. We discuss the potential predominant role of RGB1 in G protein signaling in rice.

Boolean modeling of transcriptome data reveals novel modes of heterotrimeric G-protein action

Classical mechanisms of heterotrimeric G-protein signaling are observed to function in regulation of the transcriptome. Conversely, many theoretical regulatory modes of the G-protein are not manifested in the transcriptomes we investigate.

A new mechanism of G-protein signaling is revealed, in which the β subunit regulates gene expression identically in the presence or absence of the α subunit.

We find evidence of cross-talk between G-protein-mediated and hormone-mediated transcriptional regulation.

We find evidence of system specificity in G-protein signaling.

Heterotrimeric G-proteins, composed of α, β, and γ subunits, participate in a wide range of signaling pathways in eukaryotes (Morris and Malbon, 1999). According to the typical, mammalian paradigm, in its inactive state, the G-protein exists as an associated heterotrimer. G-protein signaling begins with ligand binding that results in a conformational change in a G-protein-coupled receptor (GPCR). Once activated by the GPCR, the Gα separates from the associated Gβγ dimer and the freed Gα and Gβγ proteins can then interact with downstream effector molecules, alone or in combination, to transduce the signal. Subsequent to signal propagation, Gα re-associates with the Gβγ dimer to reform the G-protein complex.

There are several classical routes for signal propagation through heterotrimeric G-proteins that have been categorized in mammalian systems (Marrari et al, 2007; Dupre et al, 2009). One route, which we designate classical I, requires the presence of both subunits, and can invoke one of two distinct mechanisms. In one mechanism, on GPCR activation, freed Gα and Gβγ each interact with downstream effectors to elicit the downstream response. In a related mechanism, Gα but not Gβγ interacts with downstream effectors, but the Gβγ dimer is nevertheless required to facilitate coupling of Gα with the relevant GPCR (Marrari et al, 2007). In a second route, which we designate classical II, it is solely the Gβγ dimer that interacts with downstream effectors; in this case, sequestration of Gβγ within the heterotrimer prevents signal propagation. In addition, a few non-classical G-protein regulatory modes have also been implicated in some systems, for example signaling by the intact heterotrimer in yeast (Klein et al, 2000; Frank et al, 2005). Observations such as these lead to a fundamental question, namely, which of all the theoretical regulatory modes of G-protein signaling are realized biologically. Our study answers this question in the context of the model plant Arabidopsis thaliana, and in addition analyzes the manner in which G-protein signaling couples with signaling by the plant hormone abscisic acid. The Arabidopsis genome encodes only one canonical Gα subunit, GPA1, and one canonical Gβ subunit, AGB1, and knockout mutants are available for each of these, allowing clear dissection of Gα- and Gβ-related phenotypes.

Abscisic acid (ABA) is a major plant hormone, which inhibits growth and promotes tolerance of abiotic stresses such as drought, salinity, and cold. ABA signaling is known to interact with heterotrimeric G-protein signaling in both developmental and stress responses in a complex manner, causing, for example, ABA hyposensitivity of guard cell stomatal opening in gpa1 and agb1 single mutants as well as agb1 gpa1 double mutants (Fan et al, 2008), but ABA hypersensitivity of the inhibition of seed germination and post-germination seedling development in the same mutants (Pandey et al, 2006). These experimental observations implicate G-proteins as one of the components of ABA signaling, but to date no systematic study has been conducted in either plant or metazoan systems to define the co-regulatory modes of a G-protein and a hormone.

In this study, we conduct genome-wide gene expression profiling in G-protein subunit mutants of A. thaliana guard cells and leaves, with or without treatment with ABA. By introducing one or more mediators acting downstream of the G-protein and ABA to control transcript levels, we propose nine G-protein/ABA signaling pathways including ABA-independent G-protein signaling pathways, G-protein-independent ABA signaling pathways, and seven distinct ABA–G-protein-coupled signaling pathways (Figure 1). We develop a Boolean modeling framework to systematically enumerate 14 possible theoretical regulatory modes of the G-protein and 142 co-regulatory modes of the G-protein and ABA, and then use a pattern matching approach to associate target genes with theoretical regulatory modes.

Our analysis shows that the G-protein regulatory mode that requires the presence of both Gα and Gβγ subunits (consistent with classical I mechanisms), is well represented in both guard cells and leaves. The G-protein regulatory mode that requires a freed Gβγ subunit (classical II G-protein regulatory mechanism) is well supported in guard cells and somewhat less so in leaves. In addition, a G-protein regulatory mode representing a non-classical regulatory mechanism is prevalent in guard cells but less so in leaves (Figure 5). In this regulatory mode, signaling by Gβ(γ) occurs, and this signaling is not regulated in any way by Gα.

By relating the target genes with the nine proposed G-protein/ABA signaling pathways, we are able to gauge the plausibility of regulatory modes of the G-protein and ABA at the pathway level. We find that G-protein-independent ABA signaling pathways are prevalent in both guard cells and leaves. The existence of an ABA-independent regulatory activity of the G-protein is well supported in guard cells, but not supported in leaves. Additive regulation by G-protein signaling plus G-protein-independent ABA signaling is rare in both guard cells and leaves. In addition, combinatorial cross-talk between G-protein signaling and ABA signaling and additive cross-talk between ABA–G-protein signaling and G-protein-independent ABA signaling are observed in both guard cells and leaves. Our transcriptome analysis indicates that in some cases, ABA definitely does not influence G-protein signaling, though it may do so in some other cases.

To investigate whether previously observed hypersensitivity or hyposensitivity of developmental and dynamic transient responses to ABA in G-protein mutants is recapitulated at the level of transcriptional regulation, we compare gene regulation by ABA in guard cells and leaves of the G-protein mutants versus wild type. We find that in guard cells, equal ABA hyposensitivity of all mutants combined is significant, although hyposensitivity in individual mutants is not. There is also a separate group of genes in guard cells that show ABA hypersensitivity in the gpa1 mutant, suggesting complex interactions between ABA and G-protein signaling in gene regulation in this cell type. In leaves, ABA hyposensitivity of gene expression in the three individual mutants and equal hyposensitivity in all mutants are strongly supported. In addition, several of the functional categories identified by our analysis of G-protein regulatory modes have been implicated in previous physiological analyses of G-protein mutants, providing validation to the biological interpretation of our results.

In summary, by conducting a genome-wide gene expression profiling study in G-protein subunit mutants of A. thaliana guard cells and leaves and developing a Boolean modeling framework, we systematically evaluate the biological utilization of mechanisms of G-protein regulatory action and reveal novel regulatory modes of the G-protein. The results generate empirical evidence and insights regarding molecular events of G-protein signaling and response at the physiological level in both plants and mammals.

Heterotrimeric G-proteins mediate crucial and diverse signaling pathways in eukaryotes. Here, we generate and analyze microarray data from guard cells and leaves of G-protein subunit mutants of the model plant Arabidopsis thaliana, with or without treatment with the stress hormone, abscisic acid. Although G-protein control of the transcriptome has received little attention to date in any system, transcriptome analysis allows us to search for potentially uncommon yet significant signaling mechanisms. We describe the theoretical Boolean mechanisms of G-protein × hormone regulation, and then apply a pattern matching approach to associate gene expression profiles with Boolean models. We find that (1) classical mechanisms of G-protein signaling are well represented. Conversely, some theoretical regulatory modes of the G-protein are not supported; (2) a new mechanism of G-protein signaling is revealed, in which Gβ regulates gene expression identically in the presence or absence of Gα; (3) guard cells and leaves favor different G-protein modes in transcriptome regulation, supporting system specificity of G-protein signaling. Our method holds significant promise for analyzing analogous ‘switch-like' signal transduction events in any organism.

Intersections between immune responses and morphological regulation in plants

Successful plant pathogens have developed strategies to interfere with the defence mechanisms of their host plants through evolution. Conversely, host plants have evolved systems to counteract pathogen attack. Some pathogens induce pathogenic symptoms on plants that include morphological changes in addition to interference with plant growth. Recent studies, based on molecular biology and genetics using Arabidopsis thaliana, have revealed that factors derived from pathogens can modulate host systems and/or host factors that play important roles in the morphological regulation of host plants. Other reports, meanwhile, have shown that factors known to have roles in plant morphology also function in plant immune responses. Evolutionary conservation of these factors and systems implies that host-pathogen interactions and the evolution they drive have yielded tight links between morphological processes and immune responses. In this review, recent findings about these topics are introduced and discussed.

Function and expression pattern of the alpha subunit of the heterotrimeric G protein in rice

The d1 mutant, which is deficient for the heterotrimeric G-protein alpha subunit (Galpha) gene of rice, shows dwarfism and sets small round seeds. To determine whether dwarfism in d1 is due to a reduction in cell number or to shortened cell length, the cell number of the leaf sheath, the internode, the root and the lemma was compared between Nipponbare, a wild-type rice and d1-5, a d1 allele derived from Nipponbare. Our results indicate that the cell number was reduced in all organs analyzed in d1-5. In addition, cell enlargement was found in roots and lemma of d1-5, although the organ length in d1-5 was shorter than that of wild-type rice. These results suggest that rice Galpha participates in cell proliferation in rice. Western blot analyses using anti-Galpha antibody and RT-PCR analyses indicate that Galpha is mostly expressed in the developing organs. Galpha promoter activity studies using the GUS reporter gene confirmed that the expression of Galpha was highest in developing organs. We conclude that rice Galpha participates in the regulation of cell number in a developmental stage-dependent manner.

Heterotrimeric G proteins regulate reproductive trait plasticity in response to water availability

Phenotypic plasticity is the ability of one genotype to display different phenotypes under different environmental conditions. Although variation for phenotypic plasticity has been documented in numerous species, little is known about the genetic mechanisms underlying phenotypic plasticity. Given their widespread roles in hormonal and environmental signaling, we examined whether genes which encode heterotrimeric G proteins are plasticity genes. We grew multiple alleles of heterotrimeric G-protein mutants, together with wild-type Arabidopsis thaliana, under different watering regimes to determine the contributions of G-protein genes to phenotypic plasticity for a number of developmental and reproduction-related traits. G-protein mutations did not affect significantly the amount of phenotypic variation within an environment for any trait, but did affect significantly the amount of phenotypic plasticity for certain traits. AGB1, which encodes the beta subunit of the heterotrimeric G protein in Arabidopsis, is a plasticity gene and regulates reproductive trait plasticity in response to water availability, resulting in increased fitness (defined as seed production) under drought stress.

AGB1 and PMR5 contribute to PEN2-mediated preinvasion resistance to Magnaporthe oryzae in Arabidopsis thaliana

Rice blast, caused by Magnaporthe oryzae, is a devastating disease of rice (Oryza sativa). The mechanisms involved in resistance of rice to blast have been studied extensively and the rice-M. oryzae pathosystem has become a model for plant-microbe interaction studies. However, the mechanisms involved in nonhost resistance (NHR) of other plants to rice blast are still poorly understood. Here, we investigated interactions between Arabidopsis thaliana and M. oryzae to identify the genetic basis of NHR. In A. thaliana accessions, preinvasion resistance to M. oryzae in Col-0 was stronger than that of Ler. To examine the genetic basis underlying the natural variation in the responses, we used a well-established set of recombinant inbred lines (RIL) derived from a Col x Ler cross and identified three quantitative trait loci that govern the expression of NHR in A. thaliana against M. oryzae. Among the penetration (pen) mutants, only the pen2 mutant allowed increased penetration into epidermal cells by M. oryzae. Double mutant analysis indicated that AGB1 and PMR5 contribute to PEN2-mediated preinvasion resistance to M. oryzae in A. thaliana, suggesting a complex genetic network regulating the resistance. Our results demonstrate that A. thaliana can be used to study mechanisms of NHR to M. oryzae.

Over-expression of a truncated Arabidopsis thaliana heterotrimeric G protein gamma subunit results in a phenotype similar to alpha and beta subunit knockouts

Heterotrimeric G proteins (G-proteins) are a diverse class of signal transducing proteins which have been implicated in a variety of important roles in plants. When G-proteins are activated, they dissociate into two functional subunits (alpha and the betagamma dimer) that effectively relay the signal to a multitude of effectors. In animal systems, the betagamma dimer is anchored to the plasma membrane by a prenyl group present in the gamma subunit and membrane localization has proven vital for heterotrimer function. A semi-dominant negative strategy was designed aiming to disrupt heterotrimer function in Arabidopsis thaliana (ecotype Columbia) plants by over-expressing a truncated gamma subunit lacking the isoprenylation motif (gamma()). Northern analysis shows that the levels of expression of the mutant gamma subunit in several transgenic lines (35S-gamma()) are orders of magnitude higher than that of the native subunits. In-depth characterization of the 35S-gamma() lines has been carried out, specifically focusing on a number of developmental characteristics and responses to several stimuli previously shown to be affected in alpha- and beta-deficient mutants. In all cases, the transgenic lines expressing the mutant gamma subunit behave in the same way as the alpha- and/or the beta-deficient mutants, albeit with reduced severity of the phenotype. Our data indicates that signaling from both functional subunits, alpha and the beta/gamma dimer, is disrupted in the transgenic plants. Even though physical association of the subunits has been previously reported, our research provides evidence of the functional association of alpha and beta with the gamma subunits in Arabidopsis, while also suggesting that plasma membrane localization may be critical for function of plant heterotrimeric G proteins.

Plants: the latest model system for G-protein research

In humans, heterotrimeric G proteins couple stimulus perception by G-protein-coupled receptors (GPCRs) with numerous downstream effectors. By contrast, despite great complexity in their signal-transduction attributes, plants have a simpler repertoire of G-signalling components. Nonetheless, recent studies on Arabidopsis thaliana have shown the importance of plant G-protein signalling in such fundamental processes as cell proliferation, hormone perception and ion-channel regulation.

The WD-repeat protein superfamily in Arabidopsis: conservation and divergence in structure and function

BACKGROUND

The WD motif (also known as the Trp-Asp or WD40 motif) is found in a multitude of eukaryotic proteins involved in a variety of cellular processes. Where studied, repeated WD motifs act as a site for protein-protein interaction, and proteins containing WD repeats (WDRs) are known to serve as platforms for the assembly of protein complexes or mediators of transient interplay among other proteins. In the model plant Arabidopsis thaliana, members of this superfamily are increasingly being recognized as key regulators of plant-specific developmental events.

RESULTS

We analyzed the predicted complement of WDR proteins from Arabidopsis, and compared this to those from budding yeast, fruit fly and human to illustrate both conservation and divergence in structure and function. This analysis identified 237 potential Arabidopsis proteins containing four or more recognizable copies of the motif. These were classified into 143 distinct families, 49 of which contained more than one Arabidopsis member. Approximately 113 of these families or individual proteins showed clear homology with WDR proteins from the other eukaryotes analyzed. Where conservation was found, it often extended across all of these organisms, suggesting that many of these proteins are linked to basic cellular mechanisms. The functional characterization of conserved WDR proteins in Arabidopsis reveals that these proteins help adapt basic mechanisms for plant-specific processes.

CONCLUSIONS

Our results show that most Arabidopsis WDR proteins are strongly conserved across eukaryotes, including those that have been found to play key roles in plant-specific processes, with diversity in function conferred at least in part by divergence in upstream signaling pathways, downstream regulatory targets and /or structure outside of the WDR regions.

Receptor kinase signaling in plant development

The Arabidopsis genome sequence has revealed that plants contain a much larger complement of receptor kinase genes than other organisms. Early analysis of these genes revealed involvement in a diverse array of developmental and defense functions that included gametophyte development, pollen-pistil interactions, shoot apical meristem equilibrium, hormone perception, and cell morphogenesis. Amino acid sequence motifs and binding studies indicate that the ectodomains are capable of binding, either directly or indirectly, various classes of molecules including proteins, carbohydrates, and steroids. Genetic and biochemical approaches have begun to identify other components of several signal transduction pathways. Some receptor-like kinases (RLKs) appear to function with coreceptors lacking kinase domains, and genome analysis suggests this might be true for many RLKs. The KAPP protein phosphatase functions as a negative regulator of at least two RLK systems, and in vitro studies suggest it could be a common component of more. Whether plant signaling systems display a modularity similar to animal systems remains to be determined. Future efforts will reveal unknown functions of other RLKs and elucidate the relationships among their signaling networks.