Clavibacter michiganensis subsp. phaseoli subsp. nov., pathogenic in bean

González, Ana J.; Trapiello, Estefanía

doi:10.1099/ijs.0.058099-0

Cited by 39 publications

(39 citation statements)

References 23 publications

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“…Actinobacteria can live in aquatic (65) or terrestrial (66) environments and can also be pathogenic to both animals (67) and plants (68). Moreover, the phylum includes rod-shaped as well as filamentous bacteria, and some of the organisms can also undergo differentiation into spores (69) or other dormant forms (70).…”

Section: Resultsmentioning

confidence: 99%

Environmental Sensing in Actinobacteria: a Comprehensive Survey on the Signaling Capacity of This Phylum

et al. 2015

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Signal transduction is an essential process that allows bacteria to sense their complex and ever-changing environment and adapt accordingly. Three distinct major types of signal-transducing proteins (STPs) can be distinguished: one-component systems (1CSs), two-component systems (2CSs), and extracytoplasmic-function factors (ECFs). Since Actinobacteria are particularly rich in STPs, we comprehensively investigated the abundance and diversity of STPs encoded in 119 actinobacterial genomes, based on the data stored in the Microbial Signal Transduction (MiST) database. Overall, we observed an approximately linear correlation between the genome size and the total number of encoded STPs. About half of all membrane-anchored 1CSs are protein kinases. For both 1CSs and 2CSs, a detailed analysis of the domain architectures identified novel proteins that are found only in actinobacterial genomes. Many actinobacterial genomes are particularly enriched for ECFs. As a result of this study, almost 500 previously unclassified ECFs could be classified into 18 new ECF groups. This comprehensive survey demonstrates that actinobacterial genomes encode previously unknown STPs, which may represent new mechanisms of signal transduction and regulation. This information not only expands our knowledge of the diversity of bacterial signal transduction but also provides clear and testable hypotheses about their mechanisms, which can serve as starting points for experimental studies. IMPORTANCEIn the wake of the genomic era, with its enormous increase in the amount of available sequence information, the challenge has now shifted toward making sense and use of this treasure chest. Such analyses are a prerequisite to provide meaningful information that can help guide subsequent experimental efforts, such as mechanistic studies on novel signaling strategies. This work provides a comprehensive analysis of signal transduction proteins from 119 actinobacterial genomes. We identify, classify, and describe numerous novel and conserved signaling devices. Hence, our work serves as an important resource for any researcher interested in signal transduction of this important bacterial phylum, which contains organisms of ecological, biotechnological, and medical relevance. Bacterial survival critically depends on the ability to swiftly respond to environmental changes. To efficiently monitor the surrounding environment, microbial genomes encode numerous and highly diverse proteins that can sense a given extracellular stimulus, transmit the signal to the cytoplasm, and elicit a proper response. These signal-transducing proteins (STPs) can be divided into three major groups: one-component systems (1CSs), two-component systems (2CSs), and extracytoplasmic-function factors (ECFs). The vast majority of STPs in bacteria are 1CSs. These systems are composed of a single protein that contains an input domain, which senses the stimulus, and an output domain, which elicits the response by binding nucleic acids, modifying proteins, or performing an enzymati...

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Section: Resultsmentioning

confidence: 99%

Environmental Sensing in Actinobacteria: a Comprehensive Survey on the Signaling Capacity of This Phylum

et al. 2015

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“…tessellarius causing leaf freckles and leaf spots in wheat ( Triticum aestivum ) (Carlson & Vidaver, 1982a, b). Recently, a new subspecies was described (González & Trapiello, 2012, 2014), Clavibacter michiganensis subsp. phaseoli , that infects bean ( Phaseolus vulgaris L.) and causes bacterial bean leaf yellowing.…”

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confidence: 99%

Seed-associated subspecies of the genus Clavibacter are clearly distinguishable from Clavibacter michiganensis subsp. michiganensis

Yasuhara-Bell

Alvarez

2015

International Journal of Systematic and Evolutionary Microbiology

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The genus Clavibacter contains one recognized species, Clavibacter michiganensis. Clavibacter michiganensis is subdivided into subspecies based on host specificity and bacteriological characteristics, with Clavibacter michiganensis subsp. michiganensis causing bacterial canker of tomato. Clavibacter michiganensis subsp. michiganensis is often spread through contaminated seed leading to outbreaks of bacterial canker in tomato production areas worldwide. The frequent occurrence of non-pathogenic Clavibacter michiganensis subsp. michiganensis-like bacteria (CMB) is a concern for seed producers because Clavibacter michiganensis subsp. michiganensis is a quarantine organism and detection of a nonpathogenic variant may result in destruction of an otherwise healthy seed lot. A thorough biological and genetic characterization of these seed-associated CMB strains was performed using standard biochemical tests, cell wall analyses, metabolic profiling using Biolog, and singlegene and multilocus sequence analyses. Combined, these tests revealed two distinct populations of seed-associated members of the genus Clavibacter that differed from each other, as well as from all other described subspecies of Clavibacter michiganensis. DNA-DNA hybridization values are 70 % or higher, justifying placement into the single recognized species, C. michiganensis, but other analyses justify separate subspecies designations. Additionally, strains belonging to the genus Clavibacter isolated from pepper also represent a distinct population and warrant separate subspecies designation. On the basis of these data we propose subspecies designations for separate non-pathogenic subpopulations of Clavibacter michiganensis: Clavibacter michiganensis subsp. californiensis subsp. nov. and Clavibacter michiganensis subsp. chilensis subsp. nov. for seed-associated strains represented by C55 T (5ATCC BAA-2691 T 5CFBP 8216 T) and ZUM3936 T (5ATCC BAA-2690 T 5CFBP 8217 T), respectively. Recognition of separate subspecies is essential for improved international seed testing operations.

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“…The pure DNA of the type strain of the newly described subspecies C. michiganensis subsp. phaseoli (LMG 27667; Gonzalez & Trapiello, 2014; Table 2) was also used in all molecular and phylogenetic analyses.…”

Section: Detection With Specific Pcrsmentioning

confidence: 99%

Pathogenicity and phylogenetic analysis of Clavibacter michiganensis strains associated with tomato plants in Iran

et al. 2017

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During 2013–2016, 277 tomato fields were surveyed across Iran to monitor the status of bacterial canker of tomato, caused by Clavibacter michiganensis subsp. michiganensis. Altogether, 450 plant samples were collected, both with and without symptoms, from which 35 bacterial strains were recovered. These were positive for the PCR test performed using the Clavibacter‐specific primer pair CMR16F1/CMR16R1. Based on the phylogeny of the gyrB gene sequences, 31, three and one of the 35 strains were identified as C. michiganensis, Microbacterium sp. and Agrococcus sp., respectively. The 31 strains of C. michiganensis were further identified as C. michiganensis subsp. michiganensis (23 strains), C. michiganensis subsp. tessellarius (six strains) and Clavibacter spp. (two strains). This was subsequently confirmed by multilocus sequence analysis (MLSA) of five housekeeping genes (atpD, gyrB, ppk, recA and rpoB). In pathogenicity tests, all 23 strains induced wilting symptoms on tomato plants in greenhouse conditions, while no symptoms were observed on eggplant, bell pepper and chili pepper plants. All evaluated pathogenicity determinant genes (celA, pat‐1, tomA, ppaA, chpC and chpG) were detected in 18 out of 31 C. michiganensis strains, using eight specific primer pairs. Estimation of the number of nucleotide differences, sequence similarity matrix and MLSA clustered two peach‐coloured strains (Tom495 and Tom532) separately from all nine previously described subspecies, thereby suggesting these two strains are a new subspecies of C. michiganensis. However, a detailed taxonomic study using multiphased molecular approaches is needed to delineate a formal taxonomic name for these atypical strains.

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Clavibacter michiganensis subsp. phaseoli subsp. nov., pathogenic in bean

Cited by 39 publications

References 23 publications

Environmental Sensing in Actinobacteria: a Comprehensive Survey on the Signaling Capacity of This Phylum

Environmental Sensing in Actinobacteria: a Comprehensive Survey on the Signaling Capacity of This Phylum

Seed-associated subspecies of the genus Clavibacter are clearly distinguishable from Clavibacter michiganensis subsp. michiganensis

Pathogenicity and phylogenetic analysis of Clavibacter michiganensis strains associated with tomato plants in Iran

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