Complete genome sequence of the rapeseed plant-growth promoting Serratia plymuthica strain AS9

Neupane, Saraswoti; Högberg, Nils; Alström, Sadhna; Lucas, Susan; Han, Jianxin; Lapidus, Alla; Cheng, Jan‐Fang; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Peters, Lin; Ovchinnikova, Galina; Lu, Megan; Han, Cliff; Detter, John C.; Tapia, Roxanne; Fiebig, Anne; Land, Miriam; Hauser, Loren; Kyrpides, Nikos C.; Ivanova, Natalia; Pagani, Ioanna; Klenk, Hans‐Peter; Woyke, Tanja; Finlay, Roger D.

doi:10.4056/sigs.2595762

Cited by 27 publications

(21 citation statements)

References 32 publications

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“…The GC-content of the predicted polyketide/nonribosomal peptide operon ranges from 55% to 70% with an average of 61% which is comparable yet slightly higher than in the genus Serratia (52% to 60%) [19]. Blast database searches revealed the presence of an almost identical, unannotated region (99% identities, 99% similarities) in Serratia plymuthica AS12 (GenBank accession number: CP002774 ) [20], Serratia plymuthica AS9 (CP002773) [21] and Serratia sp. AS13 (CP002775).…”

Section: Resultsmentioning

confidence: 98%

“…More specifically, they have been shown to inhibit rice seed root and shoot germination [18]. Now, with Serratia plymuthica strain RVH1 and the rapeseed plant-associated Serratia plymuthica AS12 [20], AS13 and AS9 [21], four additional phylogenetically closely related, rhizosphere associated bacterial strains have been identified that harbor the zeamine biosynthesis genes. Therefore, it is plausible that horizontal gene transfer contributed to the spread of the zeamine-producing potential among plant-associated soil bacteria.…”

Section: Discussionmentioning

confidence: 99%

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A PKS/NRPS/FAS Hybrid Gene Cluster from Serratia plymuthica RVH1 Encoding the Biosynthesis of Three Broad Spectrum, Zeamine-Related Antibiotics

et al. 2013

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Serratia plymuthica strain RVH1, initially isolated from an industrial food processing environment, displays potent antimicrobial activity towards a broad spectrum of Gram-positive and Gram-negative bacterial pathogens. Isolation and subsequent structure determination of bioactive molecules led to the identification of two polyamino antibiotics with the same molecular structure as zeamine and zeamine II as well as a third, closely related analogue, designated zeamine I. The gene cluster encoding the biosynthesis of the zeamine antibiotics was cloned and sequenced and shown to encode FAS, PKS as well as NRPS related enzymes in addition to putative tailoring and export enzymes. Interestingly, several genes show strong homology to the pfa cluster of genes involved in the biosynthesis of long chain polyunsaturated fatty acids in marine bacteria. We postulate that a mixed FAS/PKS and a hybrid NRPS/PKS assembly line each synthesize parts of the backbone that are linked together post-assembly in the case of zeamine and zeamine I. This interaction reflects a unique interplay between secondary lipid and secondary metabolite biosynthesis. Most likely, the zeamine antibiotics are produced as prodrugs that undergo activation in which a nonribosomal peptide sequence is cleaved off.

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Section: Resultsmentioning

confidence: 98%

Section: Discussionmentioning

confidence: 99%

A PKS/NRPS/FAS Hybrid Gene Cluster from Serratia plymuthica RVH1 Encoding the Biosynthesis of Three Broad Spectrum, Zeamine-Related Antibiotics

et al. 2013

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“…Signal peptide-containing proteins were identified using the SignalP 4.1 server ( http://www.cbs.dtu.dk/services/SignalP/ , last accessed August 6, 2014) ( Petersen et al 2011 ). For the interspecies comparison, following four genomes were used: S. proteamaculans strain 568 (GenBank accession number CP000826) and S. plymuthica strains AS9 (CP002773) ( Neupane et al 2012 ) and 4Rx13 (CP006250) ( Weise et al 2014 ), which were all isolated from plants, and S. odorifera strain DSM4582 (from human sputum) (ADBY00000000).…”

Section: Methodsmentioning

confidence: 99%

Genome Evolution and Plasticity of Serratia marcescens, an Important Multidrug-Resistant Nosocomial Pathogen

Iguchi

Nagaya

Pradel

et al. 2014

Genome Biology and Evolution

163

149

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Serratia marcescens is an important nosocomial pathogen that can cause an array of infections, most notably of the urinary tract and bloodstream. Naturally, it is found in many environmental niches, and is capable of infecting plants and animals. The emergence and spread of multidrug-resistant strains producing extended-spectrum or metallo beta-lactamases now pose a threat to public health worldwide. Here we report the complete genome sequences of two carefully selected S. marcescens strains, a multidrug-resistant clinical isolate (strain SM39) and an insect isolate (strain Db11). Our comparative analyses reveal the core genome of S. marcescens and define the potential metabolic capacity, virulence, and multidrug resistance of this species. We show a remarkable intraspecies genetic diversity, both at the sequence level and with regards genome flexibility, which may reflect the diversity of niches inhabited by members of this species. A broader analysis with other Serratia species identifies a set of approximately 3,000 genes that characterize the genus. Within this apparent genetic diversity, we identified many genes implicated in the high virulence potential and antibiotic resistance of SM39, including the metallo beta-lactamase and multiple other drug resistance determinants carried on plasmid pSMC1. We further show that pSMC1 is most closely related to plasmids circulating in Pseudomonas species. Our data will provide a valuable basis for future studies on S. marcescens and new insights into the genetic mechanisms that underlie the emergence of pathogens highly resistant to multiple antimicrobial agents.

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“…Recently, several genomes of Serratia spp. with biocontrol ability have been sequenced, and different genetic traits that might be involved in biocontrol mechanisms and their regulation have been reported (Taghavi et al ., ; Neupane et al ., 2012a,b,c; 2013). However, additional functional studies are required to understand regulatory mechanisms involved in biocontrol‐related traits.…”

Section: Introductionmentioning

confidence: 99%

Transcriptional responses of the bacterial antagonist Serratia plymuthica to the fungal phytopathogen Rhizoctonia solani

Neupane

Finlay

Alström

et al. 2014

Environ Microbiol Rep

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Rhizobacteria with biocontrol ability exploit a range of mechanisms to compete successfully with other microorganisms and to ensure their growth and survival in the rhizosphere, ultimately promoting plant growth. The rhizobacterium Serratia plymuthica AS13 is able to promote oilseed rape growth and improve seedling survival in the presence of the fungal pathogen, Rhizoctonia solani AG 2-1; however, our understanding of the mechanisms underlying the antagonism of Serratia is limited. To elucidate possible mechanisms, genome-wide gene expression profiling of S. plymuthica AS13 was carried out in the presence or absence of R. solani. We used RNA sequencing methodology to obtain a comprehensive overview of Serratia gene expression in response to R. solani. The differential gene expression profiles of S. plymuthica AS13 revealed significantly increased expression of genes related to the biosynthesis of the antibiotic pyrrolnitrin (prnABCD), protease production and transporters. The results presented here provide evidence that antibiosis is a major functional mechanism underlying the antagonistic behaviour of S. plymuthica AS13.

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Complete genome sequence of the rapeseed plant-growth promoting Serratia plymuthica strain AS9

Cited by 27 publications

References 32 publications

A PKS/NRPS/FAS Hybrid Gene Cluster from Serratia plymuthica RVH1 Encoding the Biosynthesis of Three Broad Spectrum, Zeamine-Related Antibiotics

A PKS/NRPS/FAS Hybrid Gene Cluster from Serratia plymuthica RVH1 Encoding the Biosynthesis of Three Broad Spectrum, Zeamine-Related Antibiotics

Genome Evolution and Plasticity of Serratia marcescens, an Important Multidrug-Resistant Nosocomial Pathogen

Transcriptional responses of the bacterial antagonist Serratia plymuthica to the fungal phytopathogen Rhizoctonia solani

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