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A Leap Forward Towards Unraveling Newer Anti-infective Agents from an Unconventional Source: a Draft Genome Sequence Illuminating the Future Promise of Marine Heterotrophic Bacillus sp. Against Drug-Resistant Pathogens

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Abstract

During the previous decade, genome-built researches on marine heterotrophic microorganisms displayed the chemical heterogeneity of natural product resources coupled with the efficacies of harnessing the genetic divergence in various strains. Herein, we describe the whole genome data of heterotrophic Bacillus amyloliquefaciens MB6 (MTCC 12,716), isolated from a marine macroalga Hypnea valentiae, a 4,107,511-bp circular chromosome comprising 186 contigs, with 4154 protein-coding DNA sequences and a coding ratio of 86%. Simultaneously, bioactivity-guided purification of the bacterial extract resulted in six polyketide classes of compounds with promising antibacterial activity. Draft genome sequence of B. amyloliquefaciens MB6 unveiled biosynthetic gene clusters (BGCs) engaged in the biosynthesis of polyketide–originated macrolactones with prospective antagonistic activity (MIC ≤ 5 µg/mL) against nosocomial pathogens. Genome analysis manifested 34 putative BGCs necessitated to synthesize biologically active polyketide-originated frameworks or their derivatives. These results provide insights into the genetic basis of heterotrophic B. amyloliquefaciens MTCC 12,716 as a prospective lead for biotechnological and pharmaceutical applications.

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Availability of Data and Material

The whole-genome sequence of the candidate bacteria was submitted in GenBank with an accession number of QKQQ00000000.

Abbreviations

135DEPT :

Distortionless enhancement by polarization transfer

13C NMR:

Carbon-13 nuclear magnetic resonance

ACP:

Acyl carrier proteins

AT:

Acyl transferase

ATCC:

American Type Culture Collection

BGC:

Biosynthetic gene cluster

CHCI3 :

Chloroform

COSY:

Correlation spectroscopy

DH:

Dehydratase

ER:

Enoyl reductase

EtOAc:

Ethyl acetate

FTIR:

Fourier-transform infrared

GC-MS:

Gas chromatography-mass spectrometry

HMBC:

Heteronuclear multiple-bond correlation spectroscopy

HPLC:

High pressure liquid chromatography

HRESIMS:

High resolution electrospray ionization mass spectrometry

HSQC:

Heteronuclear single-quantum correlation spectroscopy

KS:

Ketosynthase

MALDI-TOF MS:

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

MeOH:

Methanol

MHA :

Mueller–Hinton agar

MIC:

Minimum inhibitory concentration

MRSA:

Methicillin-resistant Staphylococcus aureus

MTCC:

Microbial Type Culture Collection and Gene Bank

NCBI BlastP :

National Center for Biotechnology Information Basic Local Alignment Search for Protein

NMR:

Nuclear magnetic resonance

NOESY:

Nuclear overhauser effect spectroscopy

nrps :

Non-ribosomal peptide synthetase gene

PBP:

Penicillin-binding protein

PDF:

Peptide deformylase

pks :

Polyketide synthase gene

RCSB pdb:

Research Collaborator for Structural Bioinformatics Protein Databank

RP-C18 HPLC:

Reverse phase C18 high pressure liquid chromatography

rRNA:

Ribosomal RNA

TE:

Thioesterase

TLC:

Thin layer chromatography

VREfs:

Vancomycin-resistant Enterococcus faecalis

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Acknowledgements

The authors thank the Director, Central Marine Fisheries Research Institute and Dean, Faculty of Marine Sciences, Lakeside Campus, Cochin University of Science and Technology for support. Thanks are due to the Head, Marine Biotechnology Division, Central Marine Fisheries Research Institute for facilitating the research activity.

Funding

This work was funded by the Indian Council of Agricultural Research (ICAR) under the project titled as “Development of Bioactive Pharmacophores from Marine Organisms” (Grant No. MBT/HLT/SUB23) and Kerala State Council for Science, Technology and Environment (Grant No. 040/FSHP-LSS/2014/KSCSTE).

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Author notes

  1. Kajal Chakraborty and Vinaya Kizhakkepatt Kizhakkekalam have equally contributed to this work.

Authors and Affiliations

  1. Marine Bioprospecting Section of Marine Biotechnology Division, Central Marine Fisheries Research Institute, Ernakulam North P.O., P.B. No. 1603, Cochin, 682018, Kerala, India

    Kajal Chakraborty, Vinaya Kizhakkepatt Kizhakkekalam & Minju Joy

  2. Faculty of Marine Sciences, Lakeside Campus, Cochin University of Science and Technology, Kerala State, Cochin, India

    Vinaya Kizhakkepatt Kizhakkekalam

  3. Crustacean Fisheries Division, Central Marine Fisheries Research Institute, Ernakulam North, P.B. No. 1603, Cochin, India

    Rekha Devi Chakraborty

Authors
  1. Kajal Chakraborty
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  2. Vinaya Kizhakkepatt Kizhakkekalam
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  3. Minju Joy
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  4. Rekha Devi Chakraborty
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Contributions

KC conceived and designed the research, acquired funds, and conducted the experiments. VKK acquired funds and conducted the experiments. VKK and RDC analyzed the genome data. KC and MJ purified the compounds and analyzed the spectroscopic data. All the authors drafted and approved the manuscript.

Corresponding author

Correspondence to Kajal Chakraborty.

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Chakraborty, K., Kizhakkekalam, V.K., Joy, M. et al. A Leap Forward Towards Unraveling Newer Anti-infective Agents from an Unconventional Source: a Draft Genome Sequence Illuminating the Future Promise of Marine Heterotrophic Bacillus sp. Against Drug-Resistant Pathogens. Mar Biotechnol 23, 790–808 (2021). https://doi.org/10.1007/s10126-021-10064-1

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