The Complete Genome of Bacillus amyloliquefaciens subsp.
            <i>plantarum</i>
            CAU B946 Contains a Gene Cluster for Nonribosomal Synthesis of Iturin A

Blom, Jochen; Rueckert, Christian; Niu, Ben; Wang, Qi; Borriss, Rainer

doi:10.1128/jb.06762-11

Cited by 35 publications

(21 citation statements)

References 18 publications

(18 reference statements)

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“…It is likely that orthologs of the respective signature enzymes act in a different secondary metabolism pathway. The NPS ortholog in B. amyloliquefaciens for example, is part of the iturin A biosynthetic cluster [90] and the PKS in A. tereus seems to be part of a cluster with a second neighboring PKS gene. Mutations and genome reorganizations might be the driving force behind the re-shuffling and deletion of pathway genes and the creation of putatively novel metabolic products.…”

Section: Discussionmentioning

confidence: 99%

The Fusarium graminearum Genome Reveals More Secondary Metabolite Gene Clusters and Hints of Horizontal Gene Transfer

et al. 2014

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Fungal secondary metabolite biosynthesis genes are of major interest due to the pharmacological properties of their products (like mycotoxins and antibiotics). The genome of the plant pathogenic fungus Fusarium graminearum codes for a large number of candidate enzymes involved in secondary metabolite biosynthesis. However, the chemical nature of most enzymatic products of proteins encoded by putative secondary metabolism biosynthetic genes is largely unknown. Based on our analysis we present 67 gene clusters with significant enrichment of predicted secondary metabolism related enzymatic functions. 20 gene clusters with unknown metabolites exhibit strong gene expression correlation in planta and presumably play a role in virulence. Furthermore, the identification of conserved and over-represented putative transcription factor binding sites serves as additional evidence for cluster co-regulation. Orthologous cluster search provided insight into the evolution of secondary metabolism clusters. Some clusters are characteristic for the Fusarium phylum while others show evidence of horizontal gene transfer as orthologs can be found in representatives of the Botrytis or Cochliobolus lineage. The presented candidate clusters provide valuable targets for experimental examination.

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Section: Discussionmentioning

confidence: 99%

The Fusarium graminearum Genome Reveals More Secondary Metabolite Gene Clusters and Hints of Horizontal Gene Transfer

et al. 2014

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“…For instance, B. amyloliquefaciens FZB42 T isolated from the rhizosphere of Beta vulgaris (sugar beet) is widely used as a commercial plant growth-promoting rhizobacteria (PGPR), based on its abilities for plant root-colonizing and antibiotics production (Borriss et al, 2011; Chowdhury et al, 2015); while B. amyloliquefaciens LL3, isolated from fermented vegetables (Korean bibimbap), has been applied as an industrial strain for poly-γ-glutamic acid production (Geng et al, 2011). Recently, whole-genome sequencing of numerous Bacillus strains has uncovered the molecular basis for their versatile performance under different environments (Kunst et al, 1997; Deng et al, 2011; Blom et al, 2012; He et al, 2012). Based on a comparative genomic analysis within Bacillus spp., Alcaraz et al indicated that the pathogen B. cereus possesses enriched genes involved in defense mechanisms, while the soil dweller B. subtilis harbors over-represented genes relevant to carbohydrates degradation (Alcaraz et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

Comparative Genomic Analysis of Bacillus amyloliquefaciens and Bacillus subtilis Reveals Evolutional Traits for Adaptation to Plant-Associated Habitats

et al. 2016

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Bacillus subtilis and its sister species B. amyloliquefaciens comprise an evolutionary compact but physiologically versatile group of bacteria that includes strains isolated from diverse habitats. Many of these strains are used as plant growth-promoting rhizobacteria (PGPR) in agriculture and a plant-specialized subspecies of B. amyloliquefaciens—B. amyloliquefaciens subsp. plantarum, has recently been recognized, here we used 31 whole genomes [including two newly sequenced PGPR strains: B. amyloliquefaciens NJN-6 isolated from Musa sp. (banana) and B. subtilis HJ5 from Gossypium sp. (cotton)] to perform comparative analysis and investigate the genomic characteristics and evolution traits of both species in different niches. Phylogenomic analysis indicated that strains isolated from plant-associated (PA) habitats could be distinguished from those from non-plant-associated (nPA) niches in both species. The core genomes of PA strains are more abundant in genes relevant to intermediary metabolism and secondary metabolites biosynthesis as compared with those of nPA strains, and they also possess additional specific genes involved in utilization of plant-derived substrates and synthesis of antibiotics. A further gene gain/loss analysis indicated that only a few of these specific genes (18/192 for B. amyloliquefaciens and 53/688 for B. subtilis) were acquired by PA strains at the initial divergence event, but most were obtained successively by different subgroups of PA stains during the evolutional process. This study demonstrated the genomic differences between PA and nPA B. amyloliquefaciens and B. subtilis from different niches and the involved evolutional traits, and has implications for screening of PGPR strains in agricultural production.

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“…plantarum strains as biological control agents and plant growth promoters (Ongena & Jacques, 2008; Pérez-García et al ., 2011; Shan et al ., 2013; Sharma & Satyanarayana, 2013; Shi et al ., 2014). In recent years, interest in understanding the mode of action of these strains has led to many genomes being published for these strains (Blom et al ., 2012; Cai et al ., 2014; Dunlap et al ., 2013; Geng et al ., 2011; Hao et al ., 2012; Lefort et al ., 2014; Manzoor et al ., 2013; Nelson et al ., 2014; Niazi et al ., 2014a, b; Yang et al ., 2011; Zhang et al ., 2011, 2014). At the time of writing, 28 genome assemblies had been reported for B. amyloliquefaciens and two had been reported for B. methylotrophicus.…”

Section: Introductionmentioning

confidence: 99%

Phylogenomic analysis shows that Bacillus amyloliquefaciens subsp. plantarum is a later heterotypic synonym of Bacillus methylotrophicus

Dunlap

Kim

Kwon

et al. 2015

International Journal of Systematic and Evolutionary Microbiology

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) does not cluster with other members of the B. amyloliquefaciens taxon. Instead, it clusters well within a clade of strains that are assigned to B. methylotrophicus, including the type strain of that species. Therefore, we propose that the subspecies B. amyloliquefaciens subsp. plantarum should be reclassified as a later heterotypic synonym of B. methylotrophicus. INTRODUCTIONBacillus methylotrophicus, isolated from rice rhizosphere soil (Korea), was recently described by Madhaiyan et al. (2010). The type strain, KACC 13105 T (5CBMB205 T ), was found to be closely related to members of the Bacillus subtilis species complex (see Rooney et al., 2009, for a recent review of this species complex), and showed 16S rRNA gene sequence similarity values ranging from 98.2 to 99.2 %. The strain was also shown to be a methylotrophic organism capable of utilizing methanol, triethylamine and ethanol as a sole carbon source.Bacillus amyloliquefaciens was recognized as a distinct species in 1987 and was originally described as a producer of extracellular enzymes (Priest et al., 1987). The species was recently divided into two subspecies, Bacillus amyloliquefaciens subsp. amyloliquefaciens and Bacillus amyloliquefaciens subsp. plantarum, based on complete genome comparisons . Strains of the B. amyloliquefaciens subsp. plantarum clade are plant-associated isolates and typically isolated from the soil or rhizosphere of plants Madhaiyan et al., 2010;Palazzini et al., 2007; Rückert et al., 2011;Schisler et al., 2002). These strains were typically isolated as biological control agents or plant growth promoters.Over the past decade, considerable interest has been shown in developing B. methylotrophicus and B. amyloliquefaciens subsp. plantarum strains as biological control agents and plant growth promoters (Ongena & Jacques, 2008; Pérez-García et al., 2011;Shan et al., 2013;Sharma & Satyanarayana, 2013;Shi et al., 2014). In recent years, interest in understanding the mode of action of these strains has led to many genomes being published for these strains (Blom et al., 2012;Cai et al., 2014;Dunlap et al., 2013;Geng et al., 2011; Hao et al., 2012; Lefort et al., 2014; Manzoor et al., 2013;Nelson et al., 2014;Niazi et al., 2014a T was cultured in tryptone-glucose-yeast extract media to early stationary phase (*24 h) and harvested by centrifugation. DNA extraction was performed on the pelleted bacterial biomass using a QIAcube instrument with a QIAmp DNA mini QIAcube kit (QIAGEN). The total genomic DNA extraction was subsequently fragmented to 400 bp using a bioruptor (Diagenode) and size-selected using an E-gel apparatus (Life Technologies). Sequencing adapters were ligated using an Ion Express Plus Fragment Library kit (Life Technologies). Emulsion PCR to incorporate the DNA fragment library to the sequencing beads was performed using the Ion OneTouch instrument with an Ion OneTouch System Template kit (Life Technologies). The library sample was finally sequenced on an Ion Torrent Personal Genome Machine using an Ion 318 chip and t...

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The Complete Genome of Bacillus amyloliquefaciens subsp. plantarum CAU B946 Contains a Gene Cluster for Nonribosomal Synthesis of Iturin A

Cited by 35 publications

References 18 publications

The Fusarium graminearum Genome Reveals More Secondary Metabolite Gene Clusters and Hints of Horizontal Gene Transfer

The Fusarium graminearum Genome Reveals More Secondary Metabolite Gene Clusters and Hints of Horizontal Gene Transfer

Comparative Genomic Analysis of Bacillus amyloliquefaciens and Bacillus subtilis Reveals Evolutional Traits for Adaptation to Plant-Associated Habitats

Phylogenomic analysis shows that Bacillus amyloliquefaciens subsp. plantarum is a later heterotypic synonym of Bacillus methylotrophicus

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