Draft Genome Sequence of Bradyrhizobium japonicum Is-34, Which Is Incompatible with
            <i>Rj4</i>
            Genotype Soybeans

Tsurumaru, Hirohito; Kanesaki, Yu; Hashimoto, Syougo; Okizaki, Kouhei; Yoshikawa, Hideki; Yamakawa, Takeo

doi:10.1128/genomea.01316-14

Cited by 2 publications

(3 citation statements)

References 3 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…These treatments were performed using ATGC software, version 6.0.5 (Genetyx Corporation, Tokyo, Japan). The Tn5-flanking sequences were analyzed by a BLASTN search (21) against the draft genome of B. japonicum Is-34, which consisted of 248 contigs and was annotated by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP, version 2.8) (22). Based on the results of the BLASTN search, Tn5 insertion sites were identified.…”

Section: Plantsmentioning

confidence: 99%

See 1 more Smart Citation

A Putative Type III Secretion System Effector Encoded by the MA20_12780 Gene in Bradyrhizobium japonicum Is-34 Causes Incompatibility with Rj ₄ Genotype Soybeans

Tsurumaru

Hashimoto

Okizaki

et al. 2015

Appl Environ Microbiol

Self Cite

View full text Add to dashboard Cite

eThe nodulation of Bradyrhizobium japonicum Is-34 is restricted by Rj 4 genotype soybeans (Glycine max). To identify the genes responsible for this incompatibility, Tn5 mutants of B. japonicum Is-34 that were able to overcome this nodulation restriction were obtained. Analysis of the Tn5 mutants revealed that Tn5 was inserted into a region containing the MA20_12780 gene. In addition, direct disruption of this gene using marker exchange overcame the nodulation restriction by Rj 4 genotype soybeans. The MA20_12780 gene has a tts box motif in its upstream region, indicating a possibility that this gene encodes a type III secretion system (T3SS) effector protein. Bioinformatic characterization revealed that the MA20_12780 protein contains the small ubiquitin-like modifier (SUMO) protease domain of the C48 peptidase (ubiquitin-like protease 1 [Ulp1]) family. The results of the present study indicate that a putative T3SS effector encoded by the MA20_12780 gene causes the incompatibility with Rj 4 genotype soybeans, and they suggest the possibility that the nodulation restriction of B. japonicum Is-34 may be due to Rj 4 genotype soybeans recognizing the putative T3SS effector (MA20_12780 protein) as a virulence factor. S oybeans (Glycine max) are an important agricultural crop and are well known for establishing a symbiosis with nitrogenfixing bacteria (rhizobia), such as Bradyrhizobium and Ensifer species (1). The symbionts form nodules in the roots of the soybean plant and provide fixed nitrogen to the soybean. In return, the soybean provides carbohydrates to the symbionts (2). The nodulation of the symbionts is controlled by soybean genes that are referred to as Rj or rj genes. To date, eight Rj or rj genes (rj 1 , Rj 2 , Rfg1, Rj 3 , Rj 4 , rj 5 , rj 6 , and rj 7 ) have been identified (3). For example, the dominant Rj 4 gene in soybeans restricts the nodulation of specific strains of Bradyrhizobium bacteria (e.g., Bradyrhizobium japonicum Is-34 and Bradyrhizobium elkanii USDA 61) almost completely (3-5). The Rj 4 genotype may be an important trait of soybeans in the agricultural fields of Japan, because Glycine max cv. Fukuyutaka, harboring the Rj 4 gene, is the most cultivated cultivar in Japan, according to the 2012 statistics of the Ministry of Agriculture, Forestry, and Fisheries (MAFF) of Japan (http://www .maff.go.jp/j/seisan/ryutu/daizu/d_data/pdf/010.pdf [in Japanese; accessed January 2015]), and 24% of soybeans introduced into the United States from Japan exhibited the Rj 4 genotype (6). In addition, Ͼ60% of soybean cultivars introduced from Southeast Asia had the Rj 4 gene (6, 7). One possible explanation for the high abundance of the Rj 4 genotype in soybeans is its ability to restrict the nodulation of B. elkanii strains. B. elkanii strains are considered to be poor symbiotic partners of soybeans (7), because rhizobitoxine, produced by B. elkanii, induces chlorosis in soybeans (6). Recently, a product of the Rj 4 gene was identified as a thaumatin-like protein (TLP) (4, 7). Products of all the Rj (or r...

show abstract

Section: Plantsmentioning

confidence: 99%

“…Previously, a draft genome of B. japonicum Is-34 was deposited at DDBJ/EMBL/GenBank under accession no. JRPN00000000 (22). Based on the results of the current study, only contig 13 in this draft genome was reannotated.…”

Section: Plantsmentioning

confidence: 99%

A Putative Type III Secretion System Effector Encoded by the MA20_12780 Gene in Bradyrhizobium japonicum Is-34 Causes Incompatibility with Rj ₄ Genotype Soybeans

Tsurumaru

Hashimoto

Okizaki

et al. 2015

Appl Environ Microbiol

Self Cite

View full text Add to dashboard Cite

show abstract

“…Hill, suggesting the presence of an asymbiotic T3 effector in the wild-type strain. Identification of a candidate gene encoding such a T3 effector was recently announced for strain B. japonicum Is-34, which is also incompatible with Rj4 soya beans [104]. A detailed characterization of this NopD/NopBG-related gene has not yet been published.…”

Section: Effector-triggered Plant Responses: Nops Are Double-edged Swmentioning

confidence: 99%

Nodulation outer proteins: double-edged swords of symbiotic rhizobia

Staehelin

Krishnan

2015

Biochemical Journal

115

View full text Add to dashboard Cite

Rhizobia are nitrogen-fixing bacteria that establish a nodule symbiosis with legumes. Nodule formation depends on signals and surface determinants produced by both symbiotic partners. Among them, rhizobial Nops (nodulation outer proteins) play a crucial symbiotic role in many strain-host combinations. Nops are defined as proteins secreted via a rhizobial T3SS (type III secretion system). Functional T3SSs have been characterized in many rhizobial strains. Nops have been identified using various genetic, biochemical, proteomic, genomic and experimental approaches. Certain Nops represent extracellular components of the T3SS, which are visible in electron micrographs as bacterial surface appendages called T3 (type III) pili. Other Nops are T3 effector proteins that can be translocated into plant cells. Rhizobial T3 effectors manipulate cellular processes in host cells to suppress plant defence responses against rhizobia and to promote symbiosis-related processes. Accordingly, mutant strains deficient in synthesis or secretion of T3 effectors show reduced symbiotic properties on certain host plants. On the other hand, direct or indirect recognition of T3 effectors by plant cells expressing specific R (resistance) proteins can result in effector triggered defence responses that negatively affect rhizobial infection. Hence Nops are double-edged swords that may promote establishment of symbiosis with one legume (symbiotic factors) and impair symbiotic processes when bacteria are inoculated on another legume species (asymbiotic factors). In the present review, we provide an overview of our current understanding of Nops. We summarize their symbiotic effects, their biochemical properties and their possible modes of action. Finally, we discuss future perspectives in the field of T3 effector research.

show abstract

Draft Genome Sequence of Bradyrhizobium japonicum Is-34, Which Is Incompatible with Rj4 Genotype Soybeans

Abstract: We report here the draft genome sequence of Bradyrhizobium japonicum Is-34, which is incompatible with Rj4 genotype soybeans. A candidate gene involved in this incompatibility was found to be present in this genome.

Cited by 2 publications

References 3 publications

A Putative Type III Secretion System Effector Encoded by the MA20_12780 Gene in Bradyrhizobium japonicum Is-34 Causes Incompatibility with Rj ₄ Genotype Soybeans

A Putative Type III Secretion System Effector Encoded by the MA20_12780 Gene in Bradyrhizobium japonicum Is-34 Causes Incompatibility with Rj ₄ Genotype Soybeans

Nodulation outer proteins: double-edged swords of symbiotic rhizobia

Contact Info

Product

Resources

About

Draft Genome Sequence of Bradyrhizobium japonicum Is-34, Which Is Incompatible with Rj4 Genotype Soybeans

Abstract: We report here the draft genome sequence of Bradyrhizobium japonicum Is-34, which is incompatible with Rj4 genotype soybeans. A candidate gene involved in this incompatibility was found to be present in this genome.

Cited by 2 publications

References 3 publications

A Putative Type III Secretion System Effector Encoded by the MA20_12780 Gene in Bradyrhizobium japonicum Is-34 Causes Incompatibility with Rj 4 Genotype Soybeans

A Putative Type III Secretion System Effector Encoded by the MA20_12780 Gene in Bradyrhizobium japonicum Is-34 Causes Incompatibility with Rj 4 Genotype Soybeans

Nodulation outer proteins: double-edged swords of symbiotic rhizobia

Contact Info

Product

Resources

About

A Putative Type III Secretion System Effector Encoded by the MA20_12780 Gene in Bradyrhizobium japonicum Is-34 Causes Incompatibility with Rj ₄ Genotype Soybeans

A Putative Type III Secretion System Effector Encoded by the MA20_12780 Gene in Bradyrhizobium japonicum Is-34 Causes Incompatibility with Rj ₄ Genotype Soybeans