Genome-Wide Metabolic And Evolutionary Analysis Of Paenibacillus Polymyxa Atcc 15970
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Date
2015-08
Authors
Sim, Kee Shin
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Abstract
Paenibacillus polymyxa ATCC 15970 is a Gram positive free-living nitrogen fixing bacterium known for its ability to promote plant growth, production of antimicrobial compounds and secretion of hydrolytic enzymes. Genome sequencing of this bacterium was performed using next generation sequencing technology: Roche 454 FLX, Hiseq2000 Illumina Solexa and Pacbio RS II CLR. The draft genome assembled into 3 contig with total bases of 6,202,583 bp with a mean GC content of 45.6%. Genome annotation predicted a total of 5342 protein-coding genes. The genome revealed a single nitrogen fixation operon arranged as nifBHDKENXV and hesA. A metabolic reconstruction analysis indicated that P. polymyxa ATCC 15970 has the genes for the biosynthesis of lanthionine (a secondary metabolite), plant growth hormones, butanol and glycogen metabolism. A comparative whole genome investigation demonstrated high similarity among the genomes of P. polymyxa (strains E681, SC2, M1, CR1, ATCC12321), P. durus, P. macerans and P. terrae HPL-003. The analysis was result a questionable phage out of 7 predicted regions. This species possess also 6 CRISPR loci with size ranging from 23 to 45 bp. It also possessed 18 GIs predicted by SIGI-HMM. The promoter analysis suggested the nitrogen fixing process could be regulated by the promoter found at upstream of nifB and nifH. The phylogenetic relationship analysis of concatenated nifHDK revealed Paenibacillus and Frankia were clustered into monophyletic group. In addition, phylogenomic analysis suggested nitrogen fixing had been present in P. durus ATCC 35767.
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