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Horizontal Gene Transfer of the Non-ribosomal Peptide Synthetase Gene Among Endophytic and Epiphytic Bacteria Associated with Ethnomedicinal Plants

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Abstract

This study genetically screened endophytic and epiphytic bacteria associated with ethnomedicinal plants for the presence of the non-ribosomal peptide synthetase (NRPS) gene and identified horizontal gene transfer (HGT) of the NRPS gene between the bacterial species. NRPSs are large multimodular enzymes that synthesize a wide range of biologically active natural compounds that are pharmacologically important. Twenty-nine plant-associated culturable bacteria were screened for the presence of the NRPS gene, of which seven bacterial NRPS gene fragments were successfully detected. According to our findings the presence of NRPS gene among the isolates does not always equate to their antagonistic ability. Phylogenetic analysis of the NRPS and 16S rRNA-encoding genes was used to predict HGT that may have occurred during gene evolution. The occurrence of HGT was demonstrated in the isolates (one inter-phylum and four intra-phyla) and was supported by phylogenetic analysis, mol% G+C content, and tetranucleotide usage pattern and codon usage frequency. Among the four intra-phyla HGT, one isolate showed inter-class HGT and three other isolates showed intra-class HGT.

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Acknowledgments

Authors acknowledge UGC, Govt of India for financial assistance in the form of fellowship, no. F. 17-113/08 (SA-I) dated 18th May 2012 and Department of Biotechnology, Govt. of India for the research project. Authors acknowledge the assistance received from Dr. Macmillan Nongkhlaw, Ms. Baphilinia J Mylliemngap, and Dr. Pynskhembok Swer in phylogenetic analysis.

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  1. Microbiology Laboratory, Department of Biotechnology and Bioinformatics, North-Eastern Hill University, Shillong, 793022, India

    Fenella Mary War Nongkhlaw & S. R. Joshi

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  1. Fenella Mary War Nongkhlaw
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Correspondence to S. R. Joshi.

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284_2015_910_MOESM1_ESM.tif

Fig. S1: The region where the NRPS gene is located in Bacillus cereus (A) and Bacillus weihenstephanensis (B) used for the analysis of HGT (mol% G+C content, tetranucleotide usage pattern and codon usage frequency) (TIFF 540 kb)

284_2015_910_MOESM2_ESM.tif

Fig. S2: Rooted Neighbour-Joining Tree for endophytic (EN) and epiphytic (EP) bacteria based on the 16S rRNA gene sequences with GenBank accession number and their nearest homologues of NCBI (the numbers at the nodes are bootstrap values based on 1000 replications). (TIFF 441 kb)

284_2015_910_MOESM3_ESM.tif

Fig. S3: The region where the NRPS gene is located in Bacillus subtilis (A) and Comamonas testosteroni (B) used for the analysis of HGT (mol% G+C content, tetranucleotide usage pattern and codon usage frequency) (TIFF 616 kb)

284_2015_910_MOESM4_ESM.tif

Fig. S4: The region where the NRPS gene is located in Pseudomonas sp. (A) and Raoultella ornithinolytica (B) used for the analysis of HGT (mol% G+C content, tetranucleotide usage pattern and codon usage frequency) (TIFF 635 kb)

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Nongkhlaw, F.M.W., Joshi, S.R. Horizontal Gene Transfer of the Non-ribosomal Peptide Synthetase Gene Among Endophytic and Epiphytic Bacteria Associated with Ethnomedicinal Plants. Curr Microbiol 72, 1–11 (2016). https://doi.org/10.1007/s00284-015-0910-y

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