Comprehensive Resources for Tomato Functional Genomics Based on the Miniature Model Tomato Micro-Tom

Matsukura, Chiaki; Aoki, Koh; Fukuda, Naoya; Mizoguchi, Tsuyoshi; Asamizu, Erika; Saito, Takeshi; Shibata, Daisuke; Ezura, Hiroshi

doi:10.2174/138920208786241225

Cited by 62 publications

(43 citation statements)

References 73 publications

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“…To date, genome-wide identification of plant ubiquitin E2 enzymes has been reported only for Arabidopsis and rice (Oryza sativa; Kraft et al, 2005;Bae and Kim, 2014). The tomato genome is one of the smallest diploid genomes in the family Solanaceae, and its genome sequence serves as a reference for other plant species in the family (Rensink et al, 2005;Matsukura et al, 2008). The identification of a complete set of tomato ubiquitin E2 enzymes thus provides the foundation for functional characterization of this class of enzyme in tomato and other crops in the Solanaceae.…”

Section: Discussionmentioning

confidence: 99%

A Subset of Ubiquitin-Conjugating Enzymes Is Essential for Plant Immunity

et al. 2016

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Of the three classes of enzymes involved in ubiquitination, ubiquitin-conjugating enzymes (E2) have been often incorrectly considered to play merely an auxiliary role in the process, and few E2 enzymes have been investigated in plants. To reveal the role of E2 in plant innate immunity, we identified and cloned 40 tomato genes encoding ubiquitin E2 proteins. Thioester assays indicated that the majority of the genes encode enzymatically active E2. Phylogenetic analysis classified the 40 tomato E2 enzymes into 13 groups, of which members of group III were found to interact and act specifically with AvrPtoB, a Pseudomonas syringae pv tomato effector that uses its ubiquitin ligase (E3) activity to suppress host immunity. Knocking down the expression of group III E2 genes in Nicotiana benthamiana diminished the AvrPtoB-promoted degradation of the Fen kinase and the AvrPtoB suppression of host immunity-associated programmed cell death. Importantly, silencing group III E2 genes also resulted in reduced pattern-triggered immunity (PTI). By contrast, programmed cell death induced by several effector-triggered immunity elicitors was not affected on group III-silenced plants. Functional characterization suggested redundancy among group III members for their role in the suppression of plant immunity by AvrPtoB and in PTI and identified UBIQUITIN-CONJUGATING11 (UBC11), UBC28, UBC29, UBC39, and UBC40 as playing a more significant role in PTI than other group III members. Our work builds a foundation for the further characterization of E2s in plant immunity and reveals that AvrPtoB has evolved a strategy for suppressing host immunity that is difficult for the plant to thwart.Ubiquitination as a major posttranslational modification of proteins in eukaryotes has emerged in recent years as an important regulatory mechanism underlying plant innate immunity Fu et al., 2012;Marino et al., 2012;Li et al., 2014). The ubiquitination process involves a consecutive, threestep enzymatic cascade that is catalyzed by three different classes of enzymes: ubiquitin-activating (E1), ubiquitin-conjugating (E2), and ubiquitin ligase (E3) enzymes. The first step of the process activates ubiquitin, a highly conserved 76-amino acid protein, in an ATP-dependent manner by attaching ubiquitin to an E1 enzyme. The activated ubiquitin is then transferred from the E1 to the Cys residue at the active site of an E2 conjugating enzyme. An E3 ligase then recruits the substrate protein to the E2 to transfer the ubiquitin molecule from E2 to the substrate. Through the action of E1, E2, and E3, ubiquitin is covalently attached usually to the Lys residue of a substrate through an isopeptide bond (Hershko and Ciechanover, 1998). Of the three enzymes involved in ubiquitination, E3 ubiquitin ligases have been the focus of many studies due to their key role in determining substrate specificity for the ubiquitination

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Section: Discussionmentioning

confidence: 99%

A Subset of Ubiquitin-Conjugating Enzymes Is Essential for Plant Immunity

et al. 2016

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“…Beginning in April 2007, we started sharing our EMSmutagenized resource with the French National Institute for Agricultural Research (INRA), which has already generated approximately 8000 EMS-mutagenized M 2 populations of 'Micro-Tom' (Matsukura et al, 2008). This international collaboration is expected to expand the scale of the mutagenized population to a level required for reverse genetics approach-based mutant analyses.…”

Section: Development Of Mutant Resources Based On 'Micro-tom'mentioning

confidence: 99%

Mutant Resources for the Miniature Tomato (<i>Solanum lycopersicum</i> L.) ‘Micro-Tom’

Saito

Asamizu

Mizoguchi

et al. 2009

J. Japan. Soc. Hort. Sci.

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Mutant-based studies have contributed to the elucidation of gene functions in plants including tomato. In this review, we introduce some outstanding research performed using spontaneous and artificially induced mutants. Tomato (Solanum lycopersicum L.) is a model species in the solanaceae family and research tools and information necessary to perform functional genomics study are being developed worldwide. Saturation mutagenesis is a powerful strategy that enables exploration of gene function on a genome-wide scale. We reviewed conventional mutant resources of tomato, including the ethyl methanesulfonate (EMS)-mutagenized population of the 'M82', which was developed in Israel (Menda et al., 2004). Recently, a miniature cultivar, 'Micro-Tom', has attracted the attention of tomato researchers due to its small size and rapid life cycle, which make it an ideal experimental organism for handling in the laboratory. We are developing a unique mutant resource, 10,000 EMS-mutagenized and gamma-ray-irradiated lines derived from 'Micro-Tom'. Distinct mutant phenotypes, including plant size, leaf shape, and fruit morphology, are described. The status of newly developed tools for using this mutant resource, such as an efficient transformation method and the Targeting Induced Local Lesions In Genomes (TILLING) system, are also summarized.

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“…Because it is well-known genetically, it has a relatively moderate size of diploid genome (950 megabases, Mb, n = 12) (The Tomato Genome Consortium 2012), having hundreds of mapped traits, developed DNA markers, abundant collections of germplasm and mutants, an increasing number of expressed sequence tags (ESTs), completed sequencing and assembly of tomato genome in 2012 (The Tomato Genome Consortium 2012) and it is transformable (Matsukura et al 2008). Despite the crucial roles of Dof proteins in transcriptional regulation of plant growth and development, little is known about this family in tomato.…”

Section: Introductionmentioning

confidence: 99%

Genome‐wide Analysis of Plant‐specific Dof Transcription Factor Family in Tomato

Cai

Zhang

et al. 2013

JIPB

146

144

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The Dof (DNA binding with One Finger) family encoding single zinc finger proteins has been known as a family of plant-specific transcription factors. These transcription factors are involved in a variety of functions of importance for different biological processes in plants. In the current study, we identified 34 Dof family genes in tomato (Solanum lycopersicum L.), distributed on 11 chromosomes. A complete overview of SlDof genes in tomato is presented, including the gene structures, chromosome locations, phylogeny, protein motifs and evolution pattern. Phylogenetic analysis of 34 SlDof proteins resulted in four classes constituting six clusters. In addition, a comparative analysis between these genes in tomato, Arabidopsis (Arabidopsis thaliana L.) and rice (Oryza sativa L.) was also performed. The tomato Dof family expansion has been dated to recent duplication events, and segmental duplication is predominant for the SlDof genes. Furthermore, the SlDof genes displayed differential expression either in their transcript abundance or in their expression patterns under normal growth conditions. This is the first step towards genome-wide analyses of the Dof genes in tomato. Our study provides a very useful reference for cloning and functional analysis of the members of this gene family in tomato and other species. Keywords: Dof; tomato; duplication; gene expression; motif; phylogenetic analysis.Cai X, Zhang Y, Zhang C, Zhang T, Hu T, Ye J, Zhang J, Wang T, Li H, Ye Z (2013) Genome-wide analysis of plant-specific dof transcription factor family in tomato.

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Comprehensive Resources for Tomato Functional Genomics Based on the Miniature Model Tomato Micro-Tom

Cited by 62 publications

References 73 publications

A Subset of Ubiquitin-Conjugating Enzymes Is Essential for Plant Immunity

A Subset of Ubiquitin-Conjugating Enzymes Is Essential for Plant Immunity

Mutant Resources for the Miniature Tomato (<i>Solanum lycopersicum</i> L.) ‘Micro-Tom’

Genome‐wide Analysis of Plant‐specific Dof Transcription Factor Family in Tomato

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Comprehensive Resources for Tomato Functional Genomics Based on the Miniature Model Tomato Micro-Tom

Cited by 62 publications

References 73 publications

A Subset of Ubiquitin-Conjugating Enzymes Is Essential for Plant Immunity

A Subset of Ubiquitin-Conjugating Enzymes Is Essential for Plant Immunity

Mutant Resources for the Miniature Tomato (<i>Solanum lycopersicum</i> L.) &lsquo;Micro-Tom&rsquo;

Genome‐wide Analysis of Plant‐specific Dof Transcription Factor Family in Tomato

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Mutant Resources for the Miniature Tomato (<i>Solanum lycopersicum</i> L.) ‘Micro-Tom’