New insights into the dimerization of small GTPase Rac/ROP guanine nucleotide exchange factors in rice

Akamatsu, Akira; Uno, Kazumi; Kato, Midori; Wong, Hann Ling; Shimamoto, Ko; Kawano, Yoji

doi:10.1080/15592324.2015.1044702

Cited by 18 publications

(10 citation statements)

References 32 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Another example constituted the guanine nucleotide exchange factors (GEFs), which are known as activators of Rho‐type GTPases of plants (ROPs; involved in various signal transductions) (Akamatsu et al ., 2015). RopGEF performs its function through a plant‐specific ROP nucleotide exchanger domain (PRONE); moreover, we reported recently that 12 genes have a PRONE domain in rice (Kim et al ., 2020).…”

Section: Resultsmentioning

confidence: 99%

CAFRI‐Rice: CRISPR applicable functional redundancy inspector to accelerate functional genomics in rice

Hong

Kim

et al. 2020

The Plant Journal

View full text Add to dashboard Cite

Rice (Oryza sativa L.) is a staple crop with agricultural traits that have been intensively investigated. However, despite the variety of mutant population and multi-omics data that have been generated, rice functional genomic research has been bottlenecked due to the functional redundancy in the genome. This phenomenon has masked the phenotypes of knockout mutants by functional compensation and redundancy. Here, we present an intuitive tool, CRISPR applicable functional redundancy inspector to accelerate functional genomics in rice (CAFRI-Rice; cafri-rice.khu.ac.kr). To create this tool, we generated a phylogenetic heatmap that can estimate the similarity between protein sequences and expression patterns, based on 2,617 phylogenetic trees and eight tissue RNA-sequencing datasets. In this study, 33,483 genes were sorted into 2,617 families, and about 24,980 genes were tested for functional redundancy using a phylogenetic heatmap approach. It was predicted that 7,075 genes would have functional redundancy, according to the threshold value validated by an analysis of 111 known genes functionally characterized using knockout mutants and 5,170 duplicated genes. In addition, our analysis demonstrated that an anther/pollen-preferred gene cluster has more functional redundancy than other clusters. Finally, we showed the usefulness of the CAFRI-Rice-based approach by overcoming the functional redundancy between two root-preferred genes via loss-of-function analyses as well as confirming the functional dominancy of three genes through a literature search. This CAFRI-Rice-based target selection for CRISPR/Cas9-mediated mutagenesis will not only accelerate functional genomic studies in rice but can also be straightforwardly expanded to other plant species.

show abstract

Section: Resultsmentioning

confidence: 99%

CAFRI‐Rice: CRISPR applicable functional redundancy inspector to accelerate functional genomics in rice

Hong

Kim

et al. 2020

The Plant Journal

View full text Add to dashboard Cite

show abstract

“…The X-ray structure analysis provided that the catalytic PRONE domain of AtRopGEF8 is found in a ternary complex with Rop4 and GDP (Thomas et al, 2007 ) and immunity studies have provided evidence that PRONE-type OsRacGEFs may be involved in disease responses through activation of OsRAC1 in rice (Kawasaki et al 2009 ; Kawano et al, 2010 ), and OsRopGEF10 regulates small papillae development through activating OsRAC1 (Yoo et al 2011 ). Additionally, yeast two-hybrid assays displayed that OsRAC1 interacts with OsRacGEF1 and OsRacGEF2 via their PRONE domain (Akamatsu et al 2013 , 2015 ), and the CEBiP/CERK1-OsRacGEF-OsRac1 module plays a major role for early signaling in rice chitin-triggered immunity (Akamatsu et al 2013 ). The above-mentioned evidence suggested that OsRopGEFs act at the upstream of OsRACs.…”

Section: Discussionmentioning

confidence: 99%

Guanine Nucleotide Exchange Factor 7B (RopGEF7B) is involved in floral organ development in Oryza sativa

Huang

Liu

Berberich

et al. 2018

Rice

View full text Add to dashboard Cite

BackgroundRAC/ROP GTPase are versatile signaling molecules controlling diverse biological processes including cell polarity establishment, cell growth, morphogenesis, hormone responses and many other cellular processes in plants. The activities of ROPs are positively regulated by guanine nucleotide exchange factors (GEFs). Evidence suggests that RopGEFs regulate polar auxin transport and polar growth in pollen tube in Arabidopsis thaliana. However, the biological functions of rice RopGEFs during plant development remain largely unknown.ResultsWe investigated a member of the OsRopGEF family, namely OsRopGEF7B. OsRopGEF7Bpro:GUS analysis indicates that OsRopGEF7B is expressed in various tissues, especially in the floral meristem and floral organ primordia. Knock-out and -down of OsRopGEF7B by T-DNA insertion and RNA interference, respectively, predominantly caused an increase in the number of floral organs in the inner whorls (stamen and ovary), as well as abnormal paleae/lemmas and ectopic growth of lodicules, resulting in decline of rice seed setting. Bimolecular fluorescence complement (BiFC) assays as well as yeast two-hybrid assays indicate that OsRopGEF7B interacts with OsRACs.ConclusionsOsRopGEF7B plays roles in floral organ development in rice, affecting rice seed setting rate. Manipulation of OsRopGEF7B has potential for application in genetically modified crops.Electronic supplementary materialThe online version of this article (10.1186/s12284-018-0235-0) contains supplementary material, which is available to authorized users.

show abstract

“…OsRacGEF1 is chitin-dependently activated by the PRR receptor-like kinase module OsCEBiP/OsCERK1 via phosphorylation of a specific serine residue [ 23 , 27 , 28 ]. It has recently been reported that OsRacGEF1 can form homodimers and heterodimers with OsRacGEF2 at the plasma membrane (PM) and the endoplasmic reticulum (ER), but only OsRacGEF1 binds directly to OsCERK1 at the ER [ 29 ]. This RLK-GEF complex is then transported to the PM via a Sar1-dependent vesicular pathway to associate with OsRAC1, eventually forming a stable immune complex [ 30 ].…”

Section: Rice Osrac1 Acts In Plant Immunitymentioning

confidence: 99%

Regulation and Functions of ROP GTPases in Plant–Microbe Interactions

Engelhardt

Trutzenberg

Hückelhoven

2020

Cells

View full text Add to dashboard Cite

Rho proteins of plants (ROPs) form a specific clade of Rho GTPases, which are involved in either plant immunity or susceptibility to diseases. They are intensively studied in grass host plants, in which ROPs are signaling hubs downstream of both cell surface immune receptor kinases and intracellular nucleotide-binding leucine-rich repeat receptors, which activate major branches of plant immune signaling. Additionally, invasive fungal pathogens may co-opt the function of ROPs for manipulation of the cytoskeleton, cell invasion and host cell developmental reprogramming, which promote pathogenic colonization. Strikingly, mammalian bacterial pathogens also initiate both effector-triggered susceptibility for cell invasion and effector-triggered immunity via Rho GTPases. In this review, we summarize central concepts of Rho signaling in disease and immunity of plants and briefly compare them to important findings in the mammalian research field. We focus on Rho activation, downstream signaling and cellular reorganization under control of Rho proteins involved in disease progression and pathogen resistance.

show abstract

New insights into the dimerization of small GTPase Rac/ROP guanine nucleotide exchange factors in rice

Cited by 18 publications

References 32 publications

CAFRI‐Rice: CRISPR applicable functional redundancy inspector to accelerate functional genomics in rice

CAFRI‐Rice: CRISPR applicable functional redundancy inspector to accelerate functional genomics in rice

Guanine Nucleotide Exchange Factor 7B (RopGEF7B) is involved in floral organ development in Oryza sativa

Regulation and Functions of ROP GTPases in Plant–Microbe Interactions

Contact Info

Product

Resources

About