Os11g0225300 - Revision history

Liming Pan at 14:54, 20 October 2016

2016-10-20T14:54:50Z

Rice2012: /* References */

2015-06-13T09:04:53Z

‎References

Lmw2015: /* Structured Information */

2015-06-12T04:23:55Z

‎Structured Information

Tangbo13: /* Evolution */

2014-06-03T04:52:02Z

‎Evolution

Tangbo13: /* Evolution */

2014-06-03T04:51:16Z

‎Evolution

Tangbo13: /* Evolution */

2014-06-03T04:48:35Z

‎Evolution

Tangbo13: /* Evolution */

2014-06-03T04:48:13Z

‎Evolution

Tangbo13: /* Expression */

2014-06-03T04:44:46Z

‎Expression

Tangbo13: /* Expression */

2014-06-03T04:43:31Z

‎Expression

Tangbo13: /* Expression */

2014-06-03T04:40:58Z

‎Expression

@@ Line 1: / Line 1: @@
-Please input one-sentence summary here.
+The rice '''''Os11g0225300''''' was reported as '''''RGA5''''' in 2013 <ref name="ref1" /> by researchers from France and Japan.
 ==Annotated Information==
 ===Function===
+* '''''RGA4''''' and '''''RGA5''''' encodes NB-LRR protein
-Plant resistance to microbial pathogens is a complex process relying on two major levels of resistance controlled by distinct types of plant receptors (Jones and Dangl, 2006; Dodds and Rathjen, 2010). The first line of plant defense is activated by plasma membrane proteins called pattern recognition receptors,which perceive conserved microbial molecules called pathogenassociated molecular patterns (PAMPs). Adapted plant pathogens are able to bypass this PAMP-triggered immunity by producing secreted effectors that act inside or outside the host cell and manipulate key components of plant defense (Jones and Dangl, 2006). The second layer of plant immunity relies on the specific recognition of certain pathogen-derived effectors called Avirulence (Avr) proteins by so-called plant resistance (R) proteins. This effector-triggered immunity (ETI) gives rise to stronger and faster defense responses than PAMP-triggered immunity and often involves a form of localized programmed cell death called the hypersensitive response (HR) (Dodds and Rathjen, 2010). The largest class of R proteins belongs to the conserved family of NB-LRR proteins (Tameling and Takken,2007). They contain a central nucleotide binding (NB) domain,also known as the NB-ARC (for NB adaptor shared by Apaf-1,certain R proteins, and CED-4) domain, and a C-terminal leucinerich repeat (LRR) domain. In monocot R proteins, the LRR repeatmotif is often not conserved (Bai et al., 2002) and in those cases,the domain is called leucine-rich domain (Monosi et al., 2004;Zhou et al., 2004). NB-LRR proteins are further subdivided according
+* '''''RGA4''''' and '''''RGA5''''' Confer Pia and Pi-CO39 Resistance
-to their N-terminal domain into two major subclasses(Meyers et al., 1999; Pan et al., 2000). Proteins of the TIR-NB-LRR class possess an N-terminal Toll Interleukin-1 (TIR) domain,whereas CC-NB-LRR class proteins harbor a structured coiledcoil(CC) domain. Both N-terminal domains seem to be involved in R protein homodimerization and in the activation of defensesignaling (Bernoux et al., 2011; Maekawa et al., 2011). In the absence of the Avr protein, R proteins are maintained in an inactive conformation to avoid inappropriate defense activationand cell death (Takken and Goverse, 2012).<ref name="ref1" /> <ref name="ref2" />
+* '''''RGA4''''' and '''''RGA5''''' were found to be required for the recognition of the Magnaporthe oryzae effector AVR1-CO39.
+* '''''RGA4''''' and '''''RGA5''''' also mediate recognition of the unrelated M. oryzae effector AVR-Pia, indicating that the corresponding R proteins possess dual recognition specificity.
-===Expression===
+* '''''RGA4''''' and '''''RGA5''''' interact Functionally to Recognize Two Sequence-Unrelated Effectors
 ==Labs working on this gene==
-*INRA, UMR 385 Biologie et Génétique des Interactions Plante-Parasite, F-34398 Montpellier, France
+* INRA,UMR 385 Biologie et Génétique des Interactions Plante-Parasite, F-34398 Montpellier, France
-*CIRAD, UMR Biologie et Génétique des Interactions Plante-Parasite, F-34398 Montpellier, France
+* CIRAD UMR Biologie et Génétique des Interactions Plante-Parasite, F-34398 Montpellier, France
-*CNRS, Plateforme Imagerie-Microscopie, Fédération de Recherche FR3450, 31326 Castanet-Tolosan, France
+* CNRS, Plateforme Imagerie-Microscopie, Fédération de Recherche FR3450, 31326 Castanet-Tolosan, France
-*INRA, UMR 441 Laboratoire des Interactions Plantes-Microorganismes, F-31326 Castanet-Tolosan, France
+* INRA, UMR 441 Laboratoire des Interactions Plantes-Microorganismes, F-31326 Castanet-Tolosan, France
-*CNRS, UMR 2594 Laboratoire des Interactions Plantes-Microorganismes, F-31326 Castanet-Tolosan, France
+* CNRS, UMR 2594 Laboratoire des Interactions Plantes-Microorganismes, F-31326 Castanet-Tolosan, France
-*Iwate Biotechnology Research Center, Kitakami, Iwate 024-0003, Japan
+* Iwate Biotechnology Research Center, Kitakami, Iwate 024-0003, Japan
 ==References==
 <references>
-<ref name="ref1">Stella Cesari;Gaëtan Thilliez;Cécile Ribot, et al. (2013) The Rice Resistance Protein Pair RGA4/RGA5 Recognizes the Magnaporthe oryzae Effectors AVR-Pia and AVR1-CO39 by Direct Binding.The Plant Cell, 25(4): 1463-1481.</ref>
+* <ref name="ref1">
-<ref name="ref2">Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z.,Miller, W., and Lipman, D.J. (1997). Gapped BLAST and PSIBLAST:A new generation of protein database search programs.Nucleic Acids Res. 25: 3389–3402.</ref>
+Cesari S, Thilliez G, Ribot C, Chalvon V, Michel C, Jauneau A, Rivas S, Alaux
-<ref name="ref3">Ashikawa, I., Hayashi, N., Yamane, H., Kanamori, H., Wu, J.,Matsumoto, T., Ono, K., and Yano, M. (2008). Two adjacent nucleotide-binding site-leucine-rich repeat class genes are required toconfer Pikm-specific rice blast resistance. Genetics 180: 2267–2276.</ref>
+L, Kanzaki H, Okuyama Y, Morel JB, Fournier E, Tharreau D, Terauchi R, Kroj T.
-<ref name="ref4">Bai, J., Pennill, L.A., Ning, J., Lee, S.W., Ramalingam, J., Webb,C.A., Zhao, B., Sun, Q., Nelson, J.C., Leach, J.E., and Hulbert,S.H. (2002). Diversity in nucleotide binding site-leucine-rich repeatgenes in cereals. Genome Res. 12: 1871–1884.</ref>
+The rice resistance protein pair RGA4/RGA5 recognizes the Magnaporthe oryzae
-<ref name="ref5">Ballini, E., Morel, J.B., Droc, G., Price, A., Courtois, B., Notteghem,J.L., and Tharreau, D. (2008). A genome-wide meta-analysis of rice blast resistance genes and quantitative trait loci provides newinsights into partial and complete resistance. Mol. Plant Microbe Interact. 21: 859–868.</ref>
+effectors AVR-Pia and AVR1-CO39 by direct binding. Plant Cell. 2013
-<ref name="ref6">Bernoux,M., Ve, T., Williams, S.,Warren, C., Hatters, D., Valkov, E.,Zhang, X., Ellis, J.G., Kobe, B., and Dodds, P.N. (2011). Structural and functional analysis of a plant resistance protein TIR domainreveals interfaces for self-association, signaling, and autoregulation.Cell Host Microbe 9: 200–211.</ref>
+Apr;25(4):1463-81. doi: 10.1105/tpc.112.107201. Epub 2013 Apr 2. PubMed PMID:
-<ref name="ref7">Berruyer, R., Adreit, H., Milazzo, J., Gaillard, S., Berger, A., Dioh,W., Lebrun, M.-H., and Tharreau, D. (2003). Identification and finemapping of Pi33, the rice resistance gene corresponding to theMagnaporthe grisea avirulence gene ACE1. Theor. Appl. Genet.107: 1139–1147.</ref>
+23548743; PubMed Central PMCID: PMC3663280.
-<ref name="ref8">Birker, D., Heidrich, K., Takahara, H., Narusaka, M., Deslandes, L.,Narusaka, Y., Reymond, M., Parker, J.E., and O’Connell, R.J.(2009). A locus conferring resistance to Colletotrichum higginsianum isshared by four geographically distinct Arabidopsis accessions. Plant J.60: 602–613.</ref>
+</ref>
 </references>

← Older revision		Revision as of 09:04, 13 June 2015
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	[[Category:Japonica Chromosome 11]]		[[Category:Japonica Chromosome 11]]
	[[Category:Chromosome 11]]		[[Category:Chromosome 11]]
		+	==Structured Information==

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 </references>
 [[Category:Genes]]
 [[Category:Japonica mRNA]]

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 ===Evolution===
 Phylogenetic Analysis:To identify homologous protein sequences in the Nipponbare rice reference genome, BLASTp searches (Altschul et al., 1997) against the OrygenesDB database were performed  (Droc et al., 2006). The protein alignment generated with ClustalX (Larkin et al., 2007) was manually edited and curated, and gaps were removed for further analyses. We used MEGA 5.05 (Tamura et al., 2011) to reconstruct maximum parsimony, maximum likelihood, and distance trees. For the maximum parsimony analysis, we used the heuristic search algorithm to explore the possible topologies. For the maximum likelihood analysis, we used the JTT + G amino acid substitution model. Accordingto the smallest Akaike information criterion (AIC), this model was determined
-to be the best-fit model using ProtTest 3 (Darriba et al., 2011),which estimates the likelihood and the parameter values of 112 different protein evolution models using a maximum likelihood framework. For the distance analysis, we used neighbor joining with the JTT + G amino acid substitution model. For the three analyses, we performed 1000 bootstrap replicates to assess the support for the nodes and displayed the bootstrap consensus tree.
+to be the best-fit model using ProtTest 3 (Darriba et al., 2011),which estimates the likelihood and the parameter values of 112 different protein evolution models using a maximum likelihood framework. For the distance analysis, we used neighbor joining with the JTT + G amino acid substitution model. For the three analyses, we performed 1000 bootstrap replicates to assess the support for the nodes and displayed the bootstrap consensus tree.<ref name="ref7" />
 Interestingly, RGA4 and RGA5 also confer resistance againstM. oryzae isolates expressing the avirulence gene AVR-Pia,which shows no sequence similarity to AVR1-CO39 (Yoshidaet al., 2009; Okuyama et al., 2011). Therefore, RGA4 and RGA5 together constitute the genetically defined Pia and Pi-CO39resistance genes. Accordingly, perfect association between Pia and Pi-CO39 resistance was observed when a collection of rice cultivars was analyzed for resistance to M. oryzae strains carrying
-either AVR-Pia or AVR1-CO39. Hence, our study demonstrates that the pair of CC-NB-LRR proteins RGA4 and RGA5 possesses a dual Avr recognition specificity. Such dual specificity for a pair of NB-LRR proteins had previously been demonstrated for RPS4 and RRS1, a TIR-NB-LRR pair that is required to recognize the P. syringae effector AvrRps4, the Ralstonia solanacearum effector PopP2, and a still uncharacterized factor produced by Colletotrichum higginsianum (Gassmann et al.,1999; Deslandes et al., 2002; Birker et al., 2009; Narusaka et al.,2009). The present work provides therefore an example of dualrecognition mediated by a pair of distinct CC-NB-LRR proteins.
+either AVR-Pia or AVR1-CO39. Hence, our study demonstrates that the pair of CC-NB-LRR proteins RGA4 and RGA5 possesses a dual Avr recognition specificity. Such dual specificity for a pair of NB-LRR proteins had previously been demonstrated for RPS4 and RRS1, a TIR-NB-LRR pair that is required to recognize the P. syringae effector AvrRps4, the Ralstonia solanacearum effector PopP2, and a still uncharacterized factor produced by Colletotrichum higginsianum (Gassmann et al.,1999; Deslandes et al., 2002; Birker et al., 2009; Narusaka et al.,2009). The present work provides therefore an example of dualrecognition mediated by a pair of distinct CC-NB-LRR proteins.<ref name="ref8" />
 ==Labs working on this gene==

@@ Line 18: / Line 18: @@
 Phylogenetic Analysis:To identify homologous protein sequences in the Nipponbare rice reference genome, BLASTp searches (Altschul et al., 1997) against the OrygenesDB database were performed  (Droc et al., 2006). The protein alignment generated with ClustalX (Larkin et al., 2007) was manually edited and curated, and gaps were removed for further analyses. We used MEGA 5.05 (Tamura et al., 2011) to reconstruct maximum parsimony, maximum likelihood, and distance trees. For the maximum parsimony analysis, we used the heuristic search algorithm to explore the possible topologies. For the maximum likelihood analysis, we used the JTT + G amino acid substitution model. Accordingto the smallest Akaike information criterion (AIC), this model was determined
 to be the best-fit model using ProtTest 3 (Darriba et al., 2011),which estimates the likelihood and the parameter values of 112 different protein evolution models using a maximum likelihood framework. For the distance analysis, we used neighbor joining with the JTT + G amino acid substitution model. For the three analyses, we performed 1000 bootstrap replicates to assess the support for the nodes and displayed the bootstrap consensus tree.
 ==Labs working on this gene==

@@ Line 12: / Line 12: @@
 recognized by the product of the so far uncharacterized Pi-CO39R gene (Ribot et al., 2013).<ref name="ref3" />
 The molecular mechanism of M. oryzae Avr protein recognition has only been investigated in the case of AVR-Pita and AVR-Pik (Jia et al., 2000; Kanzaki et al., 2012). AVR-Pita is recognized through direct binding to the Pi-ta C-terminal LRD domain, whereas AVR-Pik specifically associates with an N-terminal domain of Pik-1, including the CC domain and additional unclassified sequences upstream of the NB domain.Hence, those examples illustrate two cases of direct recognitionthat seem to implicate different R protein domains and different mechanisms.<ref name="ref4" />
-Transient Protein Expression in N. benthamiana For Agrobacterium-mediated N. benthamiana leaf transformations,transformed GV3101 pMP90 strains were grown in Luria-Bertani liquid medium containing 50 mg mL21 rifampicin, 15 mg mL21 gentamycin, and 25 mg mL21 kanamycin at 28°C for 24 h before use. Bacteria were
+Transient Protein Expression in N. benthamiana For Agrobacterium-mediated N. benthamiana leaf transformations,transformed GV3101 pMP90 strains were grown in Luria-Bertani liquid medium containing 50 mg mL21 rifampicin, 15 mg mL21 gentamycin, and 25 mg mL21 kanamycin at 28°C for 24 h before use. Bacteria were.<ref name="ref5" />
-harvested by centrifugation, resuspended in infiltration medium (10 mM MES, pH 5.6, 10 mM MgCl2, and 150 mM acetosyringone) to an OD600 of1, and incubated for 2 h at room temperature before leaf infiltration. The infiltrated plants were incubated for 36 or 48 h in growth chambers under controlled conditions for FRET-FLIM or coimmunoprecipitation experiments,respectively.
+harvested by centrifugation, resuspended in infiltration medium (10 mM MES, pH 5.6, 10 mM MgCl2, and 150 mM acetosyringone) to an OD600 of1, and incubated for 2 h at room temperature before leaf infiltration. The infiltrated plants were incubated for 36 or 48 h in growth chambers under controlled conditions for FRET-FLIM or coimmunoprecipitation experiments,respectively.<ref name="ref6" />
 ===Evolution===

@@ Line 8: / Line 8: @@
 ===Expression===
-  Seven Avr genes from M. oryzae have been cloned. Except ACE1 and AVR-Pita, which encode an enzyme involved in the synthesis of a secondary metabolite (Böhnert et al., 2004) and a putative metalloprotease (Orbach et al., 2000), respectively,Avr genes from the rice blast fungus encode small secreted proteins of unknown function. Experimental evidence indicates that recognition of AVR-Pita, AVR-Pia, and AVR-Pik/km/kp occurs inside host cells by their corresponding cytoplasmic R
+Seven Avr genes from M. oryzae have been cloned. Except ACE1 and AVR-Pita, which encode an enzyme involved in the synthesis of a secondary metabolite (Böhnert et al., 2004) and a putative metalloprotease (Orbach et al., 2000), respectively,Avr genes from the rice blast fungus encode small secreted proteins of unknown function. Experimental evidence indicates that recognition of AVR-Pita, AVR-Pia, and AVR-Pik/km/kp occurs inside host cells by their corresponding cytoplasmic R
 proteins (Jia et al., 2000; Yoshida et al., 2009; Kanzaki et al.,2012). Recently, we characterized molecularly the AVR1-CO39gene and demonstrated that it encodes a small secreted protein,expressed specifically during infection (Ribot et al., 2013). AVR1-CO39 is translocated inside the cytoplasm of rice cells where it is
 recognized by the product of the so far uncharacterized Pi-CO39R gene (Ribot et al., 2013).<ref name="ref3" />