Genome Sequence of the Polymyxin-Producing Plant-Probiotic Rhizobacterium
            <i>Paenibacillus polymyxa</i>
            E681

Kim, Jihyun F.; Jeong, Haeyoung; Park, Soo Young; Kim, Seong Bin; Park, Yon Kyoung; Choi, Soo Keun; Ryu, Choong‐Min; Hur, Cheol Goo; Ghim, Sa‐Youl; Oh, Tae Kwang; Kim, Jae Jong; Park, Chang Seuk; Park, Seung-Hwan

doi:10.1128/jb.00983-10

Cited by 78 publications

(65 citation statements)

References 22 publications

(18 reference statements)

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“…The cyclization reaction between D-Ala 6 and L-Thr 1 is most likely accomplished by the thioesterase (TE) domain located at the carboxy terminus of FusA (Figure 1b). This structure is identical to that found in other P. polymyxa strains producing fusaricidins [21][22][23][24][25][26][27][28]32].…”

Section: The Fus Gene Cluster and The Modular Organization Of Fusa Sysupporting

confidence: 62%

“…In recent times the genomes of numerous Paenibacillus strains have been sequenced, revealing the wealth of attractive secondary metabolites produced by these organisms [21][22][23][24][25][26][27][28][29]. In this work, also gene clusters for the biosynthesis of polyketide products were annotated, which have not yet been identified [21,22,25,27,28]. This report is part of exploring the biosynthetic capacity of Paenibacillus polymyxa-M1, a strain found among 202 bacterial isolates from surface sterilized wheat plants collected from Beijing and Henan Province, China.…”

Section: Introductionmentioning

confidence: 99%

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Characterization of Novel Fusaricidins Produced by Paenibacillus polymyxa-M1 Using MALDI-TOF Mass Spectrometry

Vater

Niu

Dietel³

et al. 2015

J. Am. Soc. Mass Spectrom.

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Abstract. Paenibacillus polymyxa-M1 is a potent producer of bioactive compounds, such as lipopeptides, polyketides, and lantibiotics of biotechnological and medical interest. Genome sequencing revealed nine gene clusters for nonribosomal biosynthesis of such agents. Here we report on the investigation of the fusaricidins, a complex of cyclic lipopeptides containing 15-guanidino-3-hydroxypentadecanoic acid (GHPD) as fatty acid component by matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). More than 20 variants of these compounds were detected and characterized in detail. Mass spectrometric sequence analysis was performed by MALDI-LIFT-TOF/TOF fragment analysis. The obtained product ion spectra show a specific processing in the fatty acid part. GHPD is cleaved between the α-and ß-position yielding two fragments a and b, one bearing the end-standing guanidine group and another one comprising the residual two C-atoms of GHPD with the attached peptide moiety. The complete sequence of all fusaricidins was derived from sets of b n -and y n -ions. The fusaricidin complex can be divided into four lipopeptide families, three of them showing variations of the amino acid in position 3, Val or Ile for the first and Tyr or Phe for families 2 and 3, respectively. A collection of novel fusaricidins was detected differing from those of families 1-3 by an additional residue of 71 Da (family 4). LIFT-TOF/TOF fragment spectra of these species imply that in their peptide moiety, an Ala-residue is attached by an ester bond to the free hydroxyl group of Thr 4 . More than 10 novel fusaricidins were characterized mass spectrometrically.

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Section: The Fus Gene Cluster and The Modular Organization Of Fusa Sysupporting

confidence: 62%

Section: Introductionmentioning

confidence: 99%

Characterization of Novel Fusaricidins Produced by Paenibacillus polymyxa-M1 Using MALDI-TOF Mass Spectrometry

Vater

Niu

Dietel³

et al. 2015

J. Am. Soc. Mass Spectrom.

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“…No polymyxin synthetase gene was found, but several unknown giant gene clusters were found in the B69 genome, including the genes for one polyketide synthetase (PKS), two nonribosomal peptide synthetases (NRPS), three hybrid NRPS-PKS synthetases, and a lantibiotic-synthetic gene cluster. Surprisingly, the genome size of P. elgii is larger than that of other Paenibacillus species with genome sequences available (3,6), such as P. polymyxa (ϳ5.7 Mb), suggesting that the size difference could have arisen through acquisition of more genes by gene duplication or horizontal transfer during evolution. Comparative genome analysis of Paenibacillus strains will help us identify diverse antibiotic biosynthetic genes and elucidate the evolution of biosynthetic pathways among the members of this genus.…”

mentioning

confidence: 91%

“…Recently, interest in the Paenibacillus genus has been rapidly growing, for many Paenibacillus species have been shown to produce various enzymes and antimicrobial substances, such as xylanase and polymyxins (3,7). There are more than 110 species that have been discovered in this genus (8).…”

mentioning

confidence: 99%

Draft Genome Sequence of Paenibacillus elgiiB69, a Strain with Broad Antimicrobial Activity

Ding

Qian

et al. 2011

J Bacteriol

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Here, we report the draft genome sequence of Paenibacillus elgii B69, which was isolated from soil and has broad-spectrum antimicrobial activity. As far as we know, the P. elgii genome is the largest of the Paenibacillus genus for which genome sequences are available. Multiple sets of genes related to antibiotic biosynthetic pathways have been found in the genome.

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“…The PGPR strains belonging to Paenibacillus polymyxa (1) promote plant growth by producing indole-3-acetic acid (IAA) (9) and volatile compounds (14). They are also known to suppress fungal phytopathogens (2, 5-7, 13, 31, 34) and plant-parasitic nematodes (12,29).…”

mentioning

confidence: 99%

The Genome of the Plant Growth-Promoting Rhizobacterium Paenibacillus polymyxa M-1 Contains Nine Sites Dedicated to Nonribosomal Synthesis of Lipopeptides and Polyketides

Niu

Rueckert

Blom

et al. 2011

Journal of Bacteriology

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The genome of Paenibacillus polymyxa M-1 consisted of a 5.8-Mb chromosome and a 360-kb plasmid. Nine sites were dedicated to nonribosomal synthesis of lipopeptides and polyketides. Eight of them were located at the chromosome, while one gene cluster predicted to encode an unknown secondary metabolite was present on the plasmid.Plant growth-promoting rhizobacteria (PGPR) have been applied as environmentally friendly alternatives to agrochemicals to improve crop yield and quality (16). The PGPR strains belonging to Paenibacillus polymyxa (1) promote plant growth by producing indole-3-acetic acid (IAA) (9) and volatile compounds (14). They are also known to suppress fungal phytopathogens (2, 5-7, 13, 31, 34) and plant-parasitic nematodes (12,29). Due to its action as a biocontrol agent, P. polymyxa produces several peptide antibiotics (3, 8, 10, 11, 15, 18, 20, 22-24, 26-28, 32) which might be important in control of plant pathogens (25).Strain M-1, isolated from surface-sterilized wheat root tissues, was identified by 16S rRNA gene sequencing and by physiological and biochemical analysis as being P. polymyxa (33). It is capable of colonizing root surfaces of wheat, promoting wheat growth, and suppressing wheat sharp eyespot disease. In addition, it acts antagonistically against several phytopathogens in vitro by producing antibiotics, including fusaricidin and polymyxin, and by secreting hydrolytic enzymes, for example, endo-␤-1,3-glucanase.Genomic DNA prepared from M-1 was used for construction of a 3-kb-long paired-end library with a GS FLX library preparation kit in combination with GS FLX paired-end adaptors (both from Roche, Mannheim, Germany) according to the manufacturer's protocol. The reads were assembled using the GS De Novo Assembler software program, and the resulting scaffolds were oriented based on the occurrence of unique single nucleotide polymorphisms (SNPs) in the repetitive rRNA (RRN) contigs. In total, 869,907 reads, including 312,451 paired reads, were assembled with a total of 185,008,620 bp. Utilization of the paired-end information allowed scaffolding of the 55 contigs larger than 500 bp into 16 scaffolds containing 45 contigs. Gap closure was done by long-range PCR (using Phusion polymerase; New England BioLabs, Frankfurt [Main], Germany) and subsequent Sanger sequencing (IIT Biotech, Bielefeld, Germany). Prediction of protein-encoding sequences was initially accomplished with the REGANOR server (17). Manual and automatic annotation was done using the annotation software program GenDB 2.4 (19).The complete genome sequence of M-1 consisted of a circular 5,864,546-bp chromosome and a 366,576-bp plasmid, with GϩC values of 54.58% and 37.61%, respectively. Five thousand sixty-one genes (CDS), 14 rRNA operons, and 110 tRNAs resided in the chromosome, while 345 genes were located on the plasmid. Many important genes were found to be plasmid linked, such as those encoding ribosomal proteins and genes involved in replication, repair and methylation, transcription, translation initiation, metabol...

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Genome Sequence of the Polymyxin-Producing Plant-Probiotic Rhizobacterium Paenibacillus polymyxa E681

Cited by 78 publications

References 22 publications

Characterization of Novel Fusaricidins Produced by Paenibacillus polymyxa-M1 Using MALDI-TOF Mass Spectrometry

Characterization of Novel Fusaricidins Produced by Paenibacillus polymyxa-M1 Using MALDI-TOF Mass Spectrometry

Draft Genome Sequence of Paenibacillus elgiiB69, a Strain with Broad Antimicrobial Activity

The Genome of the Plant Growth-Promoting Rhizobacterium Paenibacillus polymyxa M-1 Contains Nine Sites Dedicated to Nonribosomal Synthesis of Lipopeptides and Polyketides

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