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Genome mining of Pseudomonas spp. hints towards the production of under-pitched secondary metabolites

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Abstract

The recent advances in omics and computational analysis have enabled the capacity to identify the exclusive strain-specific metabolites and novel biosynthetic gene clusters. This study analyzed eight strains of P. aurantiaca including GS1, GS3, GS4, GS6, GS7, FS2, ARS38, PBSt2, one strain of P. chlororaphis RP4, one strain of P. aeruginosa (At1RP4), and one strain of P. fluorescens (RS1) for the production of rhamnolipids, quorum-sensing signals, and osmolytes. Seven rhamnolipid derivatives were variably detected in fluorescent pseudomonads. These rhamnolipids included Rha-C10-C8, Rha-Rha-C10-C10, Rha-C10-C12db, Rha-C10-C10, Rha-Rha-C10-C12, Rha-C10-C12, and Rha-Rha-C10-C12db. Pseudomonas spp. also showed the variable production of osmoprotectants including N-acetyl glutaminyl glutamine amide (NAGGN), betaine, ectoine, and trehalose. Betaine and ectoine were produced by all pseudomonads, however, NAGGN and trehalose were observed by five and three strains, respectively. Four strains including P. chlororaphis (RP4), P. aeruginosa (At1RP4), P. fluorescens (RS1), and P. aurantiaca (PBSt2) were exposed to 1– 4% NaCl concentrations and evaluated for the changes in phenazine production profile which were negligible. AntiSMASH 5.0 platform showed 50 biosynthetic gene clusters in PB-St2, of which 23 (45%) were classified as putative gene clusters with ClusterFinder algorithm, five (10%) were classified as non-ribosomal peptides synthetases (NRPS), five (10%) as saccharides, and four (8%) were classified as putative fatty acids. The genomic attributes and comprehensive insights into the metabolomic profile of these Pseudomonas spp. strains showcase their phytostimulatory, phyto-protective, and osmoprotective effects of diverse crops grown in normal and saline soils.

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Acknowledgements

Authors are grateful to Muhmmad Adeel (English Language Expert) for editing the manuscript.

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Authors and Affiliations

  1. Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan

    Izzah Shahid

  2. University of Victoria-Genome BC Proteomics Center, University of Victoria, Victoria, BC, V8Z 7X8, Canada

    Jun Han & Christoph H. Borchers

  3. Department of Statistics, Forman Christian College (A Chartered University), Lahore, 54600, Pakistan

    Sharoon Hanook

  4. Institute of Bioproduct Development (IBD), Universiti Teknologi Malaysia (UTM), 81310, Skudai, Malaysia

    Hesham Ali El Enshasy

  5. Faculty of Chemical and Energy Engineering, Universiti Teknologi Malaysia, 81310, Skudai, Malaysia

    Hesham Ali El Enshasy

  6. City of Scientific Research and Technology Applications (SRTA), New Burg Al Arab, Alexandria, 21934, Egypt

    Hesham Ali El Enshasy

  7. School of Life Sciences, Forman Christian College (A Chartered University), Lahore, 54600, Pakistan

    Samina Mehnaz

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  1. Izzah Shahid
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  2. Jun Han
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Contributions

IS wrote the manuscript and performed practical work. CHB and JH helped in LCMS data analysis. Heatmap and statistical analysis was performed by SH. SM conceived the study, edited the manuscript and HAE proofread the manuscript.

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Correspondence to Samina Mehnaz.

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Shahid, I., Han, J., Hanook, S. et al. Genome mining of Pseudomonas spp. hints towards the production of under-pitched secondary metabolites. 3 Biotech 13, 182 (2023). https://doi.org/10.1007/s13205-023-03607-x

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