Complete Genome Sequence of Serratia marcescens WW4

Chung, Wan-Chia; Chen, Lingling; Lo, Wen‐Sui; Kuo, Pei-An; Tu, Jenn; Kuo, Chih-Horng

doi:10.1128/genomea.00126-13

Cited by 33 publications

(30 citation statements)

References 15 publications

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“…strains. For serrawettins, serrawettin W1 was produced by pigmented S. marcescens ATCC 274 [70], S. marcescens CH-1 [71], S. marcescens NS-38 [72], S. marcescens WW4 [73] and so on, while serrawettin W2 and W3 were produced by nonpigmented Serratia strains [11, 73]. Moreover, Serratia strains that could produce more than one type of serrawettin have not been recognized.…”

Section: Discussionmentioning

confidence: 99%

Analysis of the genomic sequences and metabolites of Serratia surfactantfaciens sp. nov. YD25T that simultaneously produces prodigiosin and serrawettin W2

Xiang

Liu

et al. 2016

BMC Genomics

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BackgroundGram-negative bacteria of the genus Serratia are potential producers of many useful secondary metabolites, such as prodigiosin and serrawettins, which have potential applications in environmental bioremediation or in the pharmaceutical industry. Several Serratia strains produce prodigiosin and serrawettin W1 as the main bioactive compounds, and the biosynthetic pathways are co-regulated by quorum sensing (QS). In contrast, the Serratia strain, which can simultaneously produce prodigiosin and serrawettin W2, has not been reported. This study focused on analyzing the genomic sequence of Serratia sp. strain YD25T isolated from rhizosphere soil under continuously planted burley tobacco collected from Yongding, Fujian province, China, which is unique in producing both prodigiosin and serrawettin W2.ResultsA hybrid polyketide synthases (PKS)-non-ribosomal peptide synthetases (NRPS) gene cluster putatively involved in biosynthesis of antimicrobial serrawettin W2 was identified in the genome of YD25T, and its biosynthesis pathway was proposed. We found potent antimicrobial activity of serrawettin W2 purified from YD25T against various pathogenic bacteria and fungi as well as antitumor activity against Hela cells. Subsequently, comparative genomic analyses were performed among a total of 133 Serratia species. The prodigiosin biosynthesis gene cluster in YD25T belongs to the type I pig cluster, which is the main form of pig-encoding genes existing in most of the pigmented Serratia species. In addition, a complete autoinducer-2 (AI-2) system (including luxS, lsrBACDEF, lsrGK, and lsrR) as a conserved bacterial operator is found in the genome of Serratia sp. strain YD25T. Phylogenetic analysis based on concatenated Lsr and LuxS proteins revealed that YD25T formed an independent branch and was clearly distant from the strains that solely produce either prodigiosin or serrawettin W2. The Fe (III) ion reduction assay confirmed that strain YD25T could produce an AI-2 signal molecule. Phylogenetic analysis using the genomic sequence of YD25T combined with phylogenetic and phenotypic analyses support this strain as a member of a novel and previously uncharacterized Serratia species.ConclusionGenomic sequence and metabolite analysis of Serratia surfactantfaciens YD25T indicate that this strain can be further explored for the production of useful metabolites. Unveiling the genomic sequence of S. surfactantfaciens YD25T benefits the usage of this unique strain as a model system for studying the biosynthesis regulation of both prodigiosin and serrawettin W2 by the QS system.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3171-7) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Analysis of the genomic sequences and metabolites of Serratia surfactantfaciens sp. nov. YD25T that simultaneously produces prodigiosin and serrawettin W2

Xiang

Liu

et al. 2016

BMC Genomics

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“…These prokaryotic sequences possibly originate from endophytes and/or epiphytes associated with the plant even though we attempted to clean and sterilize the surface of the plant material by wiping with ethanol. We note that in the study by Davey and colleagues [12] there was also some bacterial sequence present in the M. balbisiana genomic re-sequencing data: 3.03% of Davey's data aligned to the prokaryotic genome sequences, with coverage of 94.3% of the Propionibacterium acnes 266 [17] chromosome, and 60.8% of the Serratia marcescens WW4 [18] chromosome. Therefore, it seems that bacterial contamination of plant genome sequence data is not unique to our study.…”

Section: Whole-genome Sequencingmentioning

confidence: 99%

A Draft Genome Sequence for Ensete ventricosum, the Drought-Tolerant “Tree Against Hunger”

et al. 2014

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We present a draft genome sequence for enset (Ensete ventricosum) available via the Sequence Read Archive (accession number SRX202265) and GenBank (accession number AMZH01. Enset feeds 15 million people in Ethiopia, but is arguably the least studied African crop. Our sequence data suggest a genome size of approximately 547 megabases, similar to the 523-megabase genome of the closely related banana (Musa acuminata). At least 1.8% of the annotated M. acuminata genes are not conserved in E. ventricosum. Furthermore, enset contains genes not present in banana, including reverse transcriptases and virus-like sequences as well as a homolog of the RPP8-like resistance gene. We hope that availability of genome-wide sequence data will stimulate and accelerate research on this important but neglected crop.

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“…Wholegenome sequence data for S. marcescens from the environment and clinical samples have only recently become available (Chung et al 2013;Liu et al 2013;Iguchi et al 2014;Wan et al 2015). Taken together, these indicate that the S. marcescens genome is highly dynamic, which reflects the diversity of environmental niches that the bacterium occupies and the opportunistic pathogenic nature of the organism.…”

mentioning

confidence: 99%

“…Taken together, these indicate that the S. marcescens genome is highly dynamic, which reflects the diversity of environmental niches that the bacterium occupies and the opportunistic pathogenic nature of the organism. In addition to bacteriocin and pigment genes, clinical isolates have been shown to harbor various beta-lactamases, including ampC beta-lactamase, metallo-beta-lactamase, and several putative multidrug efflux pumps (Chung et al 2013;Liu et al 2013;Iguchi et al 2014;Wan et al 2015). As with other Gram-negative nosocomial bacteria, antimicrobial resistance determinants are mainly located on the accessory elements of the S. marcescens genome (Chung et al 2013;Liu et al 2013;Iguchi et al 2014;Wan et al 2015).…”

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confidence: 99%

Recent independent emergence of multiple multidrug-resistantSerratia marcescensclones within the United Kingdom and Ireland

et al. 2016

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Serratia marcescens, a member of the Enterobacteriaceae family, is a Gram-negative bacterium responsible for a wide range of nosocomial infections. The emergence of multidrug-resistant strains is an increasing danger to public health. To design effective means to control the dissemination of S. marcescens, an in-depth analysis of the population structure and variation is required. Utilizing whole-genome sequencing, we characterized the population structure and variation, as well as the antimicrobial resistance determinants, of a systematic collection of antimicrobial-resistant S. marcescens associated with bloodstream infections in hospitals across the United Kingdom and Ireland between 2001 and 2011. Our results show that S. marcescens is a diverse species with a high level of genomic variation. However, the collection was largely composed of a limited number of clones that emerged from this diverse background within the past few decades. We identified potential recent transmissions of these clones, within and between hospitals, and showed that they have acquired antimicrobial resistance determinants for different beta-lactams, ciprofloxacin, and tetracyclines on multiple occasions. The expansion of these multidrug-resistant clones suggests that the treatment of S. marcescens infections will become increasingly difficult in the future.

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Complete Genome Sequence of Serratia marcescens WW4

Cited by 33 publications

References 15 publications

Analysis of the genomic sequences and metabolites of Serratia surfactantfaciens sp. nov. YD25T that simultaneously produces prodigiosin and serrawettin W2

Analysis of the genomic sequences and metabolites of Serratia surfactantfaciens sp. nov. YD25T that simultaneously produces prodigiosin and serrawettin W2

A Draft Genome Sequence for Ensete ventricosum, the Drought-Tolerant “Tree Against Hunger”

Recent independent emergence of multiple multidrug-resistantSerratia marcescensclones within the United Kingdom and Ireland

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