Limits...
Comparative and genetic analysis of the four sequenced Paenibacillus polymyxa genomes reveals a diverse metabolism and conservation of genes relevant to plant-growth promotion and competitiveness.

Eastman AW, Heinrichs DE, Yuan ZC - BMC Genomics (2014)

Bottom Line: Although a variety of plant-growth promoting traits are encoded by all strains, only P. polymyxa CR1 encodes the unique nitrogen fixation cluster found in other Paenibacillus sp.This study provides an in-depth understanding of the genome architecture of this species, thus facilitating future genetic engineering and applications in agriculture, industry and medicine.Furthermore, this study highlights the current gap in our understanding of complex plant biomass metabolism in Gram-positive bacteria.

View Article: PubMed Central - PubMed

Affiliation: Southern Crop Protection & Food Research Centre, Agriculture & Agri-Food Canada, 1391 Sandford Street, London, Ontario N5V 4 T3, Canada. zyuan27@uwo.ca.

ABSTRACT

Background: Members of the genus Paenibacillus are important plant growth-promoting rhizobacteria that can serve as bio-reactors. Paenibacillus polymyxa promotes the growth of a variety of economically important crops. Our lab recently completed the genome sequence of Paenibacillus polymyxa CR1. As of January 2014, four P. polymyxa genomes have been completely sequenced but no comparative genomic analyses have been reported.

Results: Here we report the comparative and genetic analyses of four sequenced P. polymyxa genomes, which revealed a significantly conserved core genome. Complex metabolic pathways and regulatory networks were highly conserved and allow P. polymyxa to rapidly respond to dynamic environmental cues. Genes responsible for phytohormone synthesis, phosphate solubilization, iron acquisition, transcriptional regulation, σ-factors, stress responses, transporters and biomass degradation were well conserved, indicating an intimate association with plant hosts and the rhizosphere niche. In addition, genes responsible for antimicrobial resistance and non-ribosomal peptide/polyketide synthesis are present in both the core and accessory genome of each strain. Comparative analyses also reveal variations in the accessory genome, including large plasmids present in strains M1 and SC2. Furthermore, a considerable number of strain-specific genes and genomic islands are irregularly distributed throughout each genome. Although a variety of plant-growth promoting traits are encoded by all strains, only P. polymyxa CR1 encodes the unique nitrogen fixation cluster found in other Paenibacillus sp.

Conclusions: Our study revealed that genomic loci relevant to host interaction and ecological fitness are highly conserved within the P. polymyxa genomes analysed, despite variations in the accessory genome. This work suggets that plant-growth promotion by P. polymyxa is mediated largely through phytohormone production, increased nutrient availability and bio-control mechanisms. This study provides an in-depth understanding of the genome architecture of this species, thus facilitating future genetic engineering and applications in agriculture, industry and medicine. Furthermore, this study highlights the current gap in our understanding of complex plant biomass metabolism in Gram-positive bacteria.

Show MeSH

Related in: MedlinePlus

Circular Representation of thePaenibacillus polymyxachromosomes. The rings represent the following features labelled from outside to centre, where the outermost circle represents the scale in Mbps. 1st ring; plus-strand CDS (cyan), 2nd ring; minus-strand CDS (cyan), 3rd ring; plus-strand strain specific CDS (purple), 4th ring; minus-strand strain specific CDS (purple), 5th ring; putative horizontally transferred genes (dark green), 6th ring; phage-related genes (orange), tandem repeats (brick red), transposons (dark blue), 7th ring; ribosomal rRNA genes (bright blue), 8th ring; tRNA genes (red), 9th ring; GC-plot where black and grey correspond to above and below average GC content respectively, 10th ring; GC-skew where black and grey correspond to above and below average GC-skew respectively. Strain-specific genes were identified using mGenomeSubtractor with an H-value cut off of ≤0.41. Putative horizontally transferred genes were identified using IslandViewer 2.0. Annotation was obtained from the NCBI GeneBank database. Phage genes, tandem repeats and transposons were identified using PHAST and IS Finder, respectively. rRNA and tRNA genes were obtained from available annotations.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC4209062&req=5

Fig5: Circular Representation of thePaenibacillus polymyxachromosomes. The rings represent the following features labelled from outside to centre, where the outermost circle represents the scale in Mbps. 1st ring; plus-strand CDS (cyan), 2nd ring; minus-strand CDS (cyan), 3rd ring; plus-strand strain specific CDS (purple), 4th ring; minus-strand strain specific CDS (purple), 5th ring; putative horizontally transferred genes (dark green), 6th ring; phage-related genes (orange), tandem repeats (brick red), transposons (dark blue), 7th ring; ribosomal rRNA genes (bright blue), 8th ring; tRNA genes (red), 9th ring; GC-plot where black and grey correspond to above and below average GC content respectively, 10th ring; GC-skew where black and grey correspond to above and below average GC-skew respectively. Strain-specific genes were identified using mGenomeSubtractor with an H-value cut off of ≤0.41. Putative horizontally transferred genes were identified using IslandViewer 2.0. Annotation was obtained from the NCBI GeneBank database. Phage genes, tandem repeats and transposons were identified using PHAST and IS Finder, respectively. rRNA and tRNA genes were obtained from available annotations.

Mentions: Foreign DNA acquired by horizontal gene transfer (HGT) is commonly associated with insertion sequence (IS) elements, tRNA genes, tmRNA genes and transposons and is identified by an anomalous GC content, codon bias, di/trinucleotide differences and GC skew [53]. To visualize the general structure of completely sequenced P. polymyxa genomes, plus and minus strand CDS, RNA genes, transposons, phage related genes, insertion elements, potential horizontally transferred loci and strain-specific genes were annotated in Artemis [54] and plotted using DNAPlotter [55] (Figure 5). Putative HGT events were identified using IslandViewer 2.0 [56], which scans the target genome for perturbations in the average GC content using a Hidden Markov Model [57]. Although robust, this method omits potential HGT between bacteria with a similar G + C content. Notably, the variation observed earlier among P. polymyxa strains (Figure 2) appears to be largely generated through HGT events, as most strain-specific genes correspond to putative HGT loci.Figure 5


Comparative and genetic analysis of the four sequenced Paenibacillus polymyxa genomes reveals a diverse metabolism and conservation of genes relevant to plant-growth promotion and competitiveness.

Eastman AW, Heinrichs DE, Yuan ZC - BMC Genomics (2014)

Circular Representation of thePaenibacillus polymyxachromosomes. The rings represent the following features labelled from outside to centre, where the outermost circle represents the scale in Mbps. 1st ring; plus-strand CDS (cyan), 2nd ring; minus-strand CDS (cyan), 3rd ring; plus-strand strain specific CDS (purple), 4th ring; minus-strand strain specific CDS (purple), 5th ring; putative horizontally transferred genes (dark green), 6th ring; phage-related genes (orange), tandem repeats (brick red), transposons (dark blue), 7th ring; ribosomal rRNA genes (bright blue), 8th ring; tRNA genes (red), 9th ring; GC-plot where black and grey correspond to above and below average GC content respectively, 10th ring; GC-skew where black and grey correspond to above and below average GC-skew respectively. Strain-specific genes were identified using mGenomeSubtractor with an H-value cut off of ≤0.41. Putative horizontally transferred genes were identified using IslandViewer 2.0. Annotation was obtained from the NCBI GeneBank database. Phage genes, tandem repeats and transposons were identified using PHAST and IS Finder, respectively. rRNA and tRNA genes were obtained from available annotations.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4209062&req=5

Fig5: Circular Representation of thePaenibacillus polymyxachromosomes. The rings represent the following features labelled from outside to centre, where the outermost circle represents the scale in Mbps. 1st ring; plus-strand CDS (cyan), 2nd ring; minus-strand CDS (cyan), 3rd ring; plus-strand strain specific CDS (purple), 4th ring; minus-strand strain specific CDS (purple), 5th ring; putative horizontally transferred genes (dark green), 6th ring; phage-related genes (orange), tandem repeats (brick red), transposons (dark blue), 7th ring; ribosomal rRNA genes (bright blue), 8th ring; tRNA genes (red), 9th ring; GC-plot where black and grey correspond to above and below average GC content respectively, 10th ring; GC-skew where black and grey correspond to above and below average GC-skew respectively. Strain-specific genes were identified using mGenomeSubtractor with an H-value cut off of ≤0.41. Putative horizontally transferred genes were identified using IslandViewer 2.0. Annotation was obtained from the NCBI GeneBank database. Phage genes, tandem repeats and transposons were identified using PHAST and IS Finder, respectively. rRNA and tRNA genes were obtained from available annotations.
Mentions: Foreign DNA acquired by horizontal gene transfer (HGT) is commonly associated with insertion sequence (IS) elements, tRNA genes, tmRNA genes and transposons and is identified by an anomalous GC content, codon bias, di/trinucleotide differences and GC skew [53]. To visualize the general structure of completely sequenced P. polymyxa genomes, plus and minus strand CDS, RNA genes, transposons, phage related genes, insertion elements, potential horizontally transferred loci and strain-specific genes were annotated in Artemis [54] and plotted using DNAPlotter [55] (Figure 5). Putative HGT events were identified using IslandViewer 2.0 [56], which scans the target genome for perturbations in the average GC content using a Hidden Markov Model [57]. Although robust, this method omits potential HGT between bacteria with a similar G + C content. Notably, the variation observed earlier among P. polymyxa strains (Figure 2) appears to be largely generated through HGT events, as most strain-specific genes correspond to putative HGT loci.Figure 5

Bottom Line: Although a variety of plant-growth promoting traits are encoded by all strains, only P. polymyxa CR1 encodes the unique nitrogen fixation cluster found in other Paenibacillus sp.This study provides an in-depth understanding of the genome architecture of this species, thus facilitating future genetic engineering and applications in agriculture, industry and medicine.Furthermore, this study highlights the current gap in our understanding of complex plant biomass metabolism in Gram-positive bacteria.

View Article: PubMed Central - PubMed

Affiliation: Southern Crop Protection & Food Research Centre, Agriculture & Agri-Food Canada, 1391 Sandford Street, London, Ontario N5V 4 T3, Canada. zyuan27@uwo.ca.

ABSTRACT

Background: Members of the genus Paenibacillus are important plant growth-promoting rhizobacteria that can serve as bio-reactors. Paenibacillus polymyxa promotes the growth of a variety of economically important crops. Our lab recently completed the genome sequence of Paenibacillus polymyxa CR1. As of January 2014, four P. polymyxa genomes have been completely sequenced but no comparative genomic analyses have been reported.

Results: Here we report the comparative and genetic analyses of four sequenced P. polymyxa genomes, which revealed a significantly conserved core genome. Complex metabolic pathways and regulatory networks were highly conserved and allow P. polymyxa to rapidly respond to dynamic environmental cues. Genes responsible for phytohormone synthesis, phosphate solubilization, iron acquisition, transcriptional regulation, σ-factors, stress responses, transporters and biomass degradation were well conserved, indicating an intimate association with plant hosts and the rhizosphere niche. In addition, genes responsible for antimicrobial resistance and non-ribosomal peptide/polyketide synthesis are present in both the core and accessory genome of each strain. Comparative analyses also reveal variations in the accessory genome, including large plasmids present in strains M1 and SC2. Furthermore, a considerable number of strain-specific genes and genomic islands are irregularly distributed throughout each genome. Although a variety of plant-growth promoting traits are encoded by all strains, only P. polymyxa CR1 encodes the unique nitrogen fixation cluster found in other Paenibacillus sp.

Conclusions: Our study revealed that genomic loci relevant to host interaction and ecological fitness are highly conserved within the P. polymyxa genomes analysed, despite variations in the accessory genome. This work suggets that plant-growth promotion by P. polymyxa is mediated largely through phytohormone production, increased nutrient availability and bio-control mechanisms. This study provides an in-depth understanding of the genome architecture of this species, thus facilitating future genetic engineering and applications in agriculture, industry and medicine. Furthermore, this study highlights the current gap in our understanding of complex plant biomass metabolism in Gram-positive bacteria.

Show MeSH
Related in: MedlinePlus