Comparative genomics and metabolic profiling of the genus Lysobacter

Irene de Bruijn, Xu Cheng, Victor de Jager, Ruth Gómez Expósito, Jeramie Watrous, Nrupali Patel, Joeke Postma, P.C. Dorrestein, Donald Kobayashi, Jos M. Raaijmakers

Research output: Contribution to journalArticleAcademicpeer-review

33 Citations (Scopus)

Abstract

Background: Lysobacter species are Gram-negative bacteria widely distributed in soil, plant and freshwater habitats. Lysobacter owes its name to the lytic effects on other microorganisms. To better understand their ecology and interactions with other (micro)organisms, five Lysobacter strains representing the four species L. enzymogenes, L. capsici, L. gummosus and L. antibioticus were subjected to genomics and metabolomics analyses. Results: Comparative genomics revealed a diverse genome content among the Lysobacter species with a core genome of 2,891 and a pangenome of 10,028 coding sequences. Genes encoding type I, II, III, IV, V secretion systems and type IV pili were highly conserved in all five genomes, whereas type VI secretion systems were only found in L. enzymogenes and L. gummosus. Genes encoding components of the flagellar apparatus were absent in the two sequenced L. antibioticus strains. The genomes contained a large number of genes encoding extracellular enzymes including chitinases, glucanases and peptidases. Various nonribosomal peptide synthase (NRPS) and polyketide synthase (PKS) gene clusters encoding putative bioactive metabolites were identified but only few of these clusters were shared between the different species. Metabolic profiling by imaging mass spectrometry complemented, in part, the in silico genome analyses and allowed visualisation of the spatial distribution patterns of several secondary metabolites produced by or induced in Lysobacter species during interactions with the soil-borne fungus Rhizoctonia solani. Conclusions: Our work shows that mining the genomes of Lysobacter species in combination with metabolic profiling provides novel insights into the genomic and metabolic potential of this widely distributed but understudied and versatile bacterial genus.

LanguageEnglish
Article number991
Number of pages16
JournalBMC Genomics
Volume16
Issue number1
DOIs
Publication statusPublished - 2015

Fingerprint

Lysobacter
Genomics
Genome
Soil
Polyketide Synthases
Rhizoctonia
Gene Components
Chitinases
Metabolomics
Multigene Family
Ecology
Fresh Water
Gram-Negative Bacteria
Computer Simulation
Genes
Names
Ecosystem
Mass Spectrometry
Peptide Hydrolases
Fungi

Keywords

  • Comparative genomics
  • Lysobacter
  • Mass spectrometry imaging
  • Microbial interactions
  • Nonribosomal peptide synthesis

Cite this

de Bruijn, I., Cheng, X., de Jager, V., Expósito, R. G., Watrous, J., Patel, N., ... Raaijmakers, J. M. (2015). Comparative genomics and metabolic profiling of the genus Lysobacter. BMC Genomics, 16(1), [991]. https://doi.org/10.1186/s12864-015-2191-z
de Bruijn, Irene ; Cheng, Xu ; de Jager, Victor ; Expósito, Ruth Gómez ; Watrous, Jeramie ; Patel, Nrupali ; Postma, Joeke ; Dorrestein, P.C. ; Kobayashi, Donald ; Raaijmakers, Jos M. / Comparative genomics and metabolic profiling of the genus Lysobacter. In: BMC Genomics. 2015 ; Vol. 16, No. 1.
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abstract = "Background: Lysobacter species are Gram-negative bacteria widely distributed in soil, plant and freshwater habitats. Lysobacter owes its name to the lytic effects on other microorganisms. To better understand their ecology and interactions with other (micro)organisms, five Lysobacter strains representing the four species L. enzymogenes, L. capsici, L. gummosus and L. antibioticus were subjected to genomics and metabolomics analyses. Results: Comparative genomics revealed a diverse genome content among the Lysobacter species with a core genome of 2,891 and a pangenome of 10,028 coding sequences. Genes encoding type I, II, III, IV, V secretion systems and type IV pili were highly conserved in all five genomes, whereas type VI secretion systems were only found in L. enzymogenes and L. gummosus. Genes encoding components of the flagellar apparatus were absent in the two sequenced L. antibioticus strains. The genomes contained a large number of genes encoding extracellular enzymes including chitinases, glucanases and peptidases. Various nonribosomal peptide synthase (NRPS) and polyketide synthase (PKS) gene clusters encoding putative bioactive metabolites were identified but only few of these clusters were shared between the different species. Metabolic profiling by imaging mass spectrometry complemented, in part, the in silico genome analyses and allowed visualisation of the spatial distribution patterns of several secondary metabolites produced by or induced in Lysobacter species during interactions with the soil-borne fungus Rhizoctonia solani. Conclusions: Our work shows that mining the genomes of Lysobacter species in combination with metabolic profiling provides novel insights into the genomic and metabolic potential of this widely distributed but understudied and versatile bacterial genus.",
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de Bruijn, I, Cheng, X, de Jager, V, Expósito, RG, Watrous, J, Patel, N, Postma, J, Dorrestein, PC, Kobayashi, D & Raaijmakers, JM 2015, 'Comparative genomics and metabolic profiling of the genus Lysobacter', BMC Genomics, vol. 16, no. 1, 991. https://doi.org/10.1186/s12864-015-2191-z

Comparative genomics and metabolic profiling of the genus Lysobacter. / de Bruijn, Irene; Cheng, Xu; de Jager, Victor; Expósito, Ruth Gómez; Watrous, Jeramie; Patel, Nrupali; Postma, Joeke; Dorrestein, P.C.; Kobayashi, Donald; Raaijmakers, Jos M.

In: BMC Genomics, Vol. 16, No. 1, 991, 2015.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - Comparative genomics and metabolic profiling of the genus Lysobacter

AU - de Bruijn, Irene

AU - Cheng, Xu

AU - de Jager, Victor

AU - Expósito, Ruth Gómez

AU - Watrous, Jeramie

AU - Patel, Nrupali

AU - Postma, Joeke

AU - Dorrestein, P.C.

AU - Kobayashi, Donald

AU - Raaijmakers, Jos M.

PY - 2015

Y1 - 2015

N2 - Background: Lysobacter species are Gram-negative bacteria widely distributed in soil, plant and freshwater habitats. Lysobacter owes its name to the lytic effects on other microorganisms. To better understand their ecology and interactions with other (micro)organisms, five Lysobacter strains representing the four species L. enzymogenes, L. capsici, L. gummosus and L. antibioticus were subjected to genomics and metabolomics analyses. Results: Comparative genomics revealed a diverse genome content among the Lysobacter species with a core genome of 2,891 and a pangenome of 10,028 coding sequences. Genes encoding type I, II, III, IV, V secretion systems and type IV pili were highly conserved in all five genomes, whereas type VI secretion systems were only found in L. enzymogenes and L. gummosus. Genes encoding components of the flagellar apparatus were absent in the two sequenced L. antibioticus strains. The genomes contained a large number of genes encoding extracellular enzymes including chitinases, glucanases and peptidases. Various nonribosomal peptide synthase (NRPS) and polyketide synthase (PKS) gene clusters encoding putative bioactive metabolites were identified but only few of these clusters were shared between the different species. Metabolic profiling by imaging mass spectrometry complemented, in part, the in silico genome analyses and allowed visualisation of the spatial distribution patterns of several secondary metabolites produced by or induced in Lysobacter species during interactions with the soil-borne fungus Rhizoctonia solani. Conclusions: Our work shows that mining the genomes of Lysobacter species in combination with metabolic profiling provides novel insights into the genomic and metabolic potential of this widely distributed but understudied and versatile bacterial genus.

AB - Background: Lysobacter species are Gram-negative bacteria widely distributed in soil, plant and freshwater habitats. Lysobacter owes its name to the lytic effects on other microorganisms. To better understand their ecology and interactions with other (micro)organisms, five Lysobacter strains representing the four species L. enzymogenes, L. capsici, L. gummosus and L. antibioticus were subjected to genomics and metabolomics analyses. Results: Comparative genomics revealed a diverse genome content among the Lysobacter species with a core genome of 2,891 and a pangenome of 10,028 coding sequences. Genes encoding type I, II, III, IV, V secretion systems and type IV pili were highly conserved in all five genomes, whereas type VI secretion systems were only found in L. enzymogenes and L. gummosus. Genes encoding components of the flagellar apparatus were absent in the two sequenced L. antibioticus strains. The genomes contained a large number of genes encoding extracellular enzymes including chitinases, glucanases and peptidases. Various nonribosomal peptide synthase (NRPS) and polyketide synthase (PKS) gene clusters encoding putative bioactive metabolites were identified but only few of these clusters were shared between the different species. Metabolic profiling by imaging mass spectrometry complemented, in part, the in silico genome analyses and allowed visualisation of the spatial distribution patterns of several secondary metabolites produced by or induced in Lysobacter species during interactions with the soil-borne fungus Rhizoctonia solani. Conclusions: Our work shows that mining the genomes of Lysobacter species in combination with metabolic profiling provides novel insights into the genomic and metabolic potential of this widely distributed but understudied and versatile bacterial genus.

KW - Comparative genomics

KW - Lysobacter

KW - Mass spectrometry imaging

KW - Microbial interactions

KW - Nonribosomal peptide synthesis

U2 - 10.1186/s12864-015-2191-z

DO - 10.1186/s12864-015-2191-z

M3 - Article

VL - 16

JO - BMC Genomics

T2 - BMC Genomics

JF - BMC Genomics

SN - 1471-2164

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ER -