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

Abstract

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...

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

“…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].…”

“…Biosynthesis of fusaricidins is encoded by the fus gene cluster, which is located in the P. polymyxa-M1 genome [21] between base positions 80.646 and 111.506 in close vicinity to the origin of replication. Similar to P. polymyxa PKB1 [32], the cluster consists of eight genes and covers around 32 kb (Figure 1a).…”

“…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.…”

“…The complete genome of Paenibacillus-M1 was sequenced and nine giant gene clusters involved in nonribosomal synthesis of lipopeptides and polyketides were detected [21], which have to be explored now by genome mining in combination with efficient, advanced methodology for structure elucidation, such as mass spectrometry and NMR-spectroscopy. The prominent products of this strain are two lipopeptide families, the polymyxins and the fusaricidins, which both are of industrial and medical interest.…”

Impact of the omic technologies for understanding the modes of action of biological control agents against plant pathogens

“…Such genes can for example be identified by comparison with plant-pathogen interaction pathways described in the KEGG database (Kanehisa et al 2002) or by comparative genomics with other bacteria isolated from the rhizosphere or endosphere of plants. These bacteria are, for example, plant growth promoting rhizobacteria (Mathimaran et al 2012;Niu et al 2011) or plant pathogens or commensal bacteria (Brown et al 2012). The genome sequence also enables identification of high level of redundancy for functions that are important in terms of the biocontrol properties, as chitinase genes in genomes of the Trichoderma species .…”