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The Genome of the Plant-Associated Lactic Acid Bacterium Lactococcus lactis KF147 Harbors a Hybrid NRPS-PKS System Conserved in Strains of the Dental Cariogenic Streptococcus mutans

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Abstract

Lactococcus lactis subsp. lactis KF147 as a non-dairy strain from lactic acid bacteria (LAB) can inhabit plant tissues. It can grow on complex carbohydrates derived from plant cell walls. Its genome size is one of the largest among the sequenced lactococcal strains, possessing many genes that do not have homologues in the published genome sequences of dairy-associated L. lactis strains. In silico analysis has identified a gene cluster encoding a hybrid NRPS-PKS system (composed of non-ribosomal peptide synthetases and polyketide synthases) in the L. lactis KF147 genome, as first example of a LAB possessing such hybrid mega-enzymes. Hybrid systems produce hybrid NRP-PK secondary metabolites (natural products) in a wide variety of bacteria, fungi, and plants. In the hybrid NRPS-PKS system of L. lactis KF147, a total of 21 NRPS and 8 PKS domains were identified that are arranged into 6 NRPS modules, 3 PKS modules, and two single functional domains (trans-acyl-transferase “transAT” and thioesterase). We found homologous hybrid systems having similar gene, module, and domain organization in six other L. lactis strains and 25 strains of the dental cariogenic Streptococcus mutans. This study mainly aimed to predict the structure and function of the hybrid NRP-PK product of L. lactis KF147 using comparative genomics techniques, and included a detailed analysis of the regulatory system. Various bioinformatical approaches were used to predict the substrate specificity of the six A domains and the iterative transAT domain. Functional conservation of the A domains within different-niche-associated strains supported the prediction of the primary core structure of the putative hybrid natural product to be Leu-DLeu-Asp-DAsn-Gly-MC-MC-MC-DAsp (MC = Malonyl-CoA). Oxidative stress resistance and biofilm formation are the most probable functions of this hybrid system. The need for such a system in two different niches is argued, as an adaptation of L. lactis and S. mutans to adhere to plant tissues and human teeth, respectively, in an oxidative environment.

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Acknowledgements

We would like to thank Professor Rene De Mot and Professor Rob Lavigne for their valuable suggestions and comments.

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Authors and Affiliations

  1. Center for Molecular and Biomolecular Informatics, Radboud UMC, Nijmegen, The Netherlands

    Barzan I. Khayatt & Roland J. Siezen

  2. Center of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium

    Barzan I. Khayatt & Vera van Noort

  3. Department of Natural Resources, College of Agricultural Engineering Sciences, University of Sulaimani, Sulaimani, Kurdistan, Iraq

    Barzan I. Khayatt

  4. Institute of Biology Leiden, Leiden University, Leiden, The Netherlands

    Vera van Noort

  5. Microbial Bioinformatics, Ede, The Netherlands

    Roland J. Siezen

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  1. Barzan I. Khayatt
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Correspondence to Roland J. Siezen.

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Electronic supplementary material

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Genes involved in the hybrid NRPS-PKS gene cluster of L. lactis KF147 (PDF 93 kb)

284_2019_1799_MOESM2_ESM.pdf

L. lactis and S. mutans strains coding for the hybrid NRPS-PKS systems homologous to the hybrid NRPS-PKS system of L. lactis KF147 (PDF 34 kb)

Genome-based phylogeny of L. lactis strains (PDF 113 kb)

Clustering according to specificity-conferring codes of A domains (PNG 491 kb)

antiSMASH 4.0 prediction of the primary structures of the putative hybrid NRPS-PKS products (PDF 142 kb)

284_2019_1799_MOESM6_ESM.pdf

Four parts of a bootstrap phylogenetic tree, showing clustering of the NRPS A domains (from A1 to A6) of L. lactis KF147 (PDF 373 kb)

Bootstrap phylogeny showing the clustering of the AT domain (BMP 39352 kb)

Phylogeny of PKSs and NRPSs of L. lactis KF147 (PDF 235 kb)

Bootstrap NJ tree of 270 two-component system histidine kinases (PDF 491 kb)

Bootstrap NJ tree of two-component system response regulators (PNG 606 kb)

PhyML tree of TC system response regulator DNA-binding domains (BMP 23492 kb)

284_2019_1799_MOESM12_ESM.pdf

Multiple sequence alignment of the output (DNA-binding) domain of the response regulators of the L. lactis and S. mutans strains. And multiple sequence alignment of the upstream regions of the highly conserved genes downstream of the TC systems of L. lactis and S. mutans strains (PDF 515 kb)

Bootstrap phylogenetic tree showing clustering of the NRPS A domains (BMP 112198 kb)

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Khayatt, B.I., van Noort, V. & Siezen, R.J. The Genome of the Plant-Associated Lactic Acid Bacterium Lactococcus lactis KF147 Harbors a Hybrid NRPS-PKS System Conserved in Strains of the Dental Cariogenic Streptococcus mutans. Curr Microbiol 77, 136–145 (2020). https://doi.org/10.1007/s00284-019-01799-1

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