Unique Features of a Japanese ‘Candidatus Liberibacter asiaticus’ Strain Revealed by Whole Genome Sequencing

Katoh, Hiroshi; Miyata, Sumiko; Inoue, Hirokazu; Iwanami, Toru

doi:10.1371/journal.pone.0106109

Cited by 60 publications

(65 citation statements)

References 45 publications

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“…CP004005; Lin et al, 2013); Las strain ishi-1 (taxid: 931202, GenBank accession no. NZ_AP014595; Katoh et al, 2014); Lam strain São Paulo (taxid: 1261131, GenBank accession no. CP006604; Wulff et al, 2014); Laf strain PTSAPSY (taxid: 1277257, GenBank accession no.…”

Section: Methodsmentioning

confidence: 99%

SEC-Translocon Dependent Extracytoplasmic Proteins of Candidatus Liberibacter asiaticus

Prasad

Zhang

et al. 2016

Front. Microbiol.

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Citrus Huanglongbing (HLB) is the most destructive citrus disease worldwide. HLB is associated with three species of the phloem-limited, gram-negative, fastidious α-proteobacteria: Candidatus Liberibacter asiaticus (Las), Ca. L. americanus (Lam), and Ca. L. africanus (Laf) with Las being the most widespread species. Las has not been cultured in artificial media, which has greatly hampered our efforts to understand its virulence mechanisms. Las contains a complete Sec-translocon, which has been suggested to transport Las proteins including virulence factors into the extracytoplasmic milieu. In this study, we characterized the Sec-translocon dependent, signal peptide containing extracytoplasmic proteins of Las. A total of 166 proteins of Las-psy62 strain were predicted to contain signal peptides targeting them out of the cell cytoplasm via the Sec-translocon using LipoP, SigalP 3.0, SignalP 4.1, and Phobius. We also predicated SP containing extracytoplasmic proteins for Las-gxpsy and Las-Ishi-1, Lam, Laf, Ca. L. solanacearum (Lso), and L. crescens (Lcr). For experimental validation of the predicted extracytoplasmic proteins, Escherichia coli based alkaline phosphatase (PhoA) gene fusion assays were conducted. A total of 86 out of the 166 predicted Las proteins were experimentally validated to contain signal peptides. Additionally, Las-psy62 lepB (CLIBASIA_04190), the gene encodes signal peptidase I, was able to partially complement the amber mutant of lepB of E. coli. This work will contribute to the identification of Sec-translocon dependent effector proteins of Las, which might be involved in virulence of Las.

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Section: Methodsmentioning

confidence: 99%

SEC-Translocon Dependent Extracytoplasmic Proteins of Candidatus Liberibacter asiaticus

Prasad

Zhang

et al. 2016

Front. Microbiol.

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“…The interest in Clas prophage stems from observations that a prophage-encoded peroxidase is an effector that suppresses plant defenses [3]. However, strains reported to lack prophages still induce HLB symptoms [16,8]. Hence, it has been hypothesized that prophages might contribute to bacterial virulence but are not required for CLas pathogenicity [6].…”

Section: Introductionmentioning

confidence: 99%

“…Prophage regions in CLas genomes are highly variable relative to the rest of the genome [16,8]. Comparative analyses of prophage sequences suggest endemism in CLas strains [17,14].…”

Section: Introductionmentioning

confidence: 99%

Functional and comparative genomic analysis of integrated prophage-like sequences inCandidatus Liberibacter asiaticus

Dominguez-Mirazo

Jin

Weitz

2019

Preprint

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Huanglongbing (HLB; yellow shoot disease) is a severe worldwide infectious disease for citrus family plants. The pathogen Candidatus Liberibacter asiaticus (CLas) is an alphaproteobacterium of the Rhizobiaceae family that has been identified as the cause. The virulence of CLas has been attributed, in part, to prophage encoded genes. Prophage and prophage like elements have been identified in 12 of the 15 CLas available genomes, and are classified into three prophage types. Here, we re-examined all 15 CLas genomes using a de novo prediction approach and expanded the number of prophage like elements from 16 to 33. Further, we find that all CLas contain at least one prophage-like sequence. Comparative analysis reveals a prevalent, albeit previously unknown, prophage-like sequence type that is a remnant of an integrated prophage. Notably, this remnant prophage is found in the Ishi-1 CLas strain that had previously been reported as lacking prophages. Our findings provide both a resource and new insights into the evolutionary relationship between phage and CLas pathogenicity.

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“…L. asiaticus" (Las), associated with huanglongbing (HLB) disease in citrus crops, were first described by Jagoueix, Bové and Garnier [9]. While the genome of Laf has not yet been sequenced, the Las genome sequence has been obtained from five different sources [12][13][14][15][16]. Comparison of a large number of Las 16S rDNA sequences indicates that there is a single haplotype in this species [17,18] in spite of the very wide geographic spread it has now reached [19].…”

Section: Introductionmentioning

confidence: 99%

Intragenomic homogeneity on Liberibacter 16S rDNA confirms phylogeny and explains ecological strategy

Nelson

Wulff

Bové³

2015

Preprint

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Three of the five currently recognized "Candidatus Liberibacter" spp., "Ca. L. asiaticus" (Las), "Ca. L. americanus" (Lam) and "Ca. L. solanacearum", and the newly erected genus Liberibacter species, L. crescens (Lcr), have had their genomes sequenced. In all four cases there are three homogeneous copies of the 16S rRNA gene, one present as the reverse complement of the other two. 16S intragenic homogeneity is common within the α-Proteobacteria. The presence of three 16S rRNA copies indicates an advantage for a rapid response of population increase to favourable growth conditions. The metabolic cost of carrying multiple copies is avoided during periods of low cellular activity as this situation occurs at low temperatures, for example overwintering in deciduous plants or in a dormant insect host. A large insertion in the 16S rDNA sequence of three species compared to the other three species indicates a dichotomy in the Liberibacter genus and provides a phylogenetic signal of closeness to the proximal node within the Rhizobiaceae. In spite of similar symptoms in Citrus crops associated with Lam and Las infections, these species belong on either side of this dichotomy, thus confirming Lam as phylogenetically closer to the proximal node than Las.

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Unique Features of a Japanese ‘Candidatus Liberibacter asiaticus’ Strain Revealed by Whole Genome Sequencing

Cited by 60 publications

References 45 publications

SEC-Translocon Dependent Extracytoplasmic Proteins of Candidatus Liberibacter asiaticus

SEC-Translocon Dependent Extracytoplasmic Proteins of Candidatus Liberibacter asiaticus

Functional and comparative genomic analysis of integrated prophage-like sequences inCandidatus Liberibacter asiaticus

Intragenomic homogeneity on Liberibacter 16S rDNA confirms phylogeny and explains ecological strategy

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