Reclassification of the Specialized Metabolite Producer Pseudomonas mesoacidophila ATCC 31433 as a Member of the Burkholderia cepacia Complex

E Joel Loveridge, Cerith Jones, Matthew J Bull, Suzy C Moody, Małgorzata W Kahl, Zainab Khan, Louis Neilson, Marina Tomeva, Sarah E Adams, Andrew C Wood, Daniel Rodriguez-Martin, Ingrid Pinel, Julian Parkhill, Eshwar Mahenthiralingam, John Crosby

Research output: Contribution to journalArticle

Abstract

Pseudomonas mesoacidophila ATCC 31433 is a Gram-negative bacterium, first isolated from Japanese soil samples, that produces the monobactam isosulfazecin and the β-lactam-potentiating bulgecins. To characterize the biosynthetic potential of P. mesoacidophila ATCC 31433, its complete genome was determined using single-molecule real-time DNA sequence analysis. The 7.8-Mb genome comprised four replicons, three chromosomal (each encoding rRNA) and one plasmid. Phylogenetic analysis demonstrated that P. mesoacidophila ATCC 31433 was misclassified at the time of its deposition and is a member of the Burkholderia cepacia complex, most closely related to Burkholderia ubonensis The sequenced genome shows considerable additional biosynthetic potential; known gene clusters for malleilactone, ornibactin, isosulfazecin, alkylhydroxyquinoline, and pyrrolnitrin biosynthesis and several uncharacterized biosynthetic gene clusters for polyketides, nonribosomal peptides, and other metabolites were identified. Furthermore, P. mesoacidophila ATCC 31433 harbors many genes associated with environmental resilience and antibiotic resistance and was resistant to a range of antibiotics and metal ions. In summary, this bioactive strain should be designated B. cepacia complex strain ATCC 31433, pending further detailed taxonomic characterization.IMPORTANCE This work reports the complete genome sequence of Pseudomonas mesoacidophila ATCC 31433, a known producer of bioactive compounds. Large numbers of both known and novel biosynthetic gene clusters were identified, indicating that P. mesoacidophila ATCC 31433 is an untapped resource for discovery of novel bioactive compounds. Phylogenetic analysis demonstrated that P. mesoacidophila ATCC 31433 is in fact a member of the Burkholderia cepacia complex, most closely related to the species Burkholderia ubonensis Further investigation of the classification and biosynthetic potential of P. mesoacidophila ATCC 31433 is warranted.

Original languageEnglish
JournalJournal of Bacteriology
Volume199
Issue number13
DOIs
Publication statusPublished - 1 Jul 2017

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Burkholderia cepacia complex
Pseudomonas
Multigene Family
Genome
Burkholderia
Pyrrolnitrin
Monobactams
Polyketides
Lactams
Replicon
Microbial Drug Resistance
Gram-Negative Bacteria
DNA Sequence Analysis
Plasmids
Soil
Metals
Ions
Anti-Bacterial Agents
Peptides
Genes

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Loveridge, E Joel ; Jones, Cerith ; Bull, Matthew J ; Moody, Suzy C ; Kahl, Małgorzata W ; Khan, Zainab ; Neilson, Louis ; Tomeva, Marina ; Adams, Sarah E ; Wood, Andrew C ; Rodriguez-Martin, Daniel ; Pinel, Ingrid ; Parkhill, Julian ; Mahenthiralingam, Eshwar ; Crosby, John. / Reclassification of the Specialized Metabolite Producer Pseudomonas mesoacidophila ATCC 31433 as a Member of the Burkholderia cepacia Complex. In: Journal of Bacteriology. 2017 ; Vol. 199, No. 13.
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title = "Reclassification of the Specialized Metabolite Producer Pseudomonas mesoacidophila ATCC 31433 as a Member of the Burkholderia cepacia Complex",
abstract = "Pseudomonas mesoacidophila ATCC 31433 is a Gram-negative bacterium, first isolated from Japanese soil samples, that produces the monobactam isosulfazecin and the β-lactam-potentiating bulgecins. To characterize the biosynthetic potential of P. mesoacidophila ATCC 31433, its complete genome was determined using single-molecule real-time DNA sequence analysis. The 7.8-Mb genome comprised four replicons, three chromosomal (each encoding rRNA) and one plasmid. Phylogenetic analysis demonstrated that P. mesoacidophila ATCC 31433 was misclassified at the time of its deposition and is a member of the Burkholderia cepacia complex, most closely related to Burkholderia ubonensis The sequenced genome shows considerable additional biosynthetic potential; known gene clusters for malleilactone, ornibactin, isosulfazecin, alkylhydroxyquinoline, and pyrrolnitrin biosynthesis and several uncharacterized biosynthetic gene clusters for polyketides, nonribosomal peptides, and other metabolites were identified. Furthermore, P. mesoacidophila ATCC 31433 harbors many genes associated with environmental resilience and antibiotic resistance and was resistant to a range of antibiotics and metal ions. In summary, this bioactive strain should be designated B. cepacia complex strain ATCC 31433, pending further detailed taxonomic characterization.IMPORTANCE This work reports the complete genome sequence of Pseudomonas mesoacidophila ATCC 31433, a known producer of bioactive compounds. Large numbers of both known and novel biosynthetic gene clusters were identified, indicating that P. mesoacidophila ATCC 31433 is an untapped resource for discovery of novel bioactive compounds. Phylogenetic analysis demonstrated that P. mesoacidophila ATCC 31433 is in fact a member of the Burkholderia cepacia complex, most closely related to the species Burkholderia ubonensis Further investigation of the classification and biosynthetic potential of P. mesoacidophila ATCC 31433 is warranted.",
author = "Loveridge, {E Joel} and Cerith Jones and Bull, {Matthew J} and Moody, {Suzy C} and Kahl, {Małgorzata W} and Zainab Khan and Louis Neilson and Marina Tomeva and Adams, {Sarah E} and Wood, {Andrew C} and Daniel Rodriguez-Martin and Ingrid Pinel and Julian Parkhill and Eshwar Mahenthiralingam and John Crosby",
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Loveridge, EJ, Jones, C, Bull, MJ, Moody, SC, Kahl, MW, Khan, Z, Neilson, L, Tomeva, M, Adams, SE, Wood, AC, Rodriguez-Martin, D, Pinel, I, Parkhill, J, Mahenthiralingam, E & Crosby, J 2017, 'Reclassification of the Specialized Metabolite Producer Pseudomonas mesoacidophila ATCC 31433 as a Member of the Burkholderia cepacia Complex' Journal of Bacteriology, vol. 199, no. 13. https://doi.org/10.1128/JB.00125-17

Reclassification of the Specialized Metabolite Producer Pseudomonas mesoacidophila ATCC 31433 as a Member of the Burkholderia cepacia Complex. / Loveridge, E Joel; Jones, Cerith; Bull, Matthew J; Moody, Suzy C; Kahl, Małgorzata W; Khan, Zainab; Neilson, Louis; Tomeva, Marina; Adams, Sarah E; Wood, Andrew C; Rodriguez-Martin, Daniel; Pinel, Ingrid; Parkhill, Julian; Mahenthiralingam, Eshwar; Crosby, John.

In: Journal of Bacteriology, Vol. 199, No. 13, 01.07.2017.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Reclassification of the Specialized Metabolite Producer Pseudomonas mesoacidophila ATCC 31433 as a Member of the Burkholderia cepacia Complex

AU - Loveridge, E Joel

AU - Jones, Cerith

AU - Bull, Matthew J

AU - Moody, Suzy C

AU - Kahl, Małgorzata W

AU - Khan, Zainab

AU - Neilson, Louis

AU - Tomeva, Marina

AU - Adams, Sarah E

AU - Wood, Andrew C

AU - Rodriguez-Martin, Daniel

AU - Pinel, Ingrid

AU - Parkhill, Julian

AU - Mahenthiralingam, Eshwar

AU - Crosby, John

N1 - Copyright © 2017 Loveridge et al.

PY - 2017/7/1

Y1 - 2017/7/1

N2 - Pseudomonas mesoacidophila ATCC 31433 is a Gram-negative bacterium, first isolated from Japanese soil samples, that produces the monobactam isosulfazecin and the β-lactam-potentiating bulgecins. To characterize the biosynthetic potential of P. mesoacidophila ATCC 31433, its complete genome was determined using single-molecule real-time DNA sequence analysis. The 7.8-Mb genome comprised four replicons, three chromosomal (each encoding rRNA) and one plasmid. Phylogenetic analysis demonstrated that P. mesoacidophila ATCC 31433 was misclassified at the time of its deposition and is a member of the Burkholderia cepacia complex, most closely related to Burkholderia ubonensis The sequenced genome shows considerable additional biosynthetic potential; known gene clusters for malleilactone, ornibactin, isosulfazecin, alkylhydroxyquinoline, and pyrrolnitrin biosynthesis and several uncharacterized biosynthetic gene clusters for polyketides, nonribosomal peptides, and other metabolites were identified. Furthermore, P. mesoacidophila ATCC 31433 harbors many genes associated with environmental resilience and antibiotic resistance and was resistant to a range of antibiotics and metal ions. In summary, this bioactive strain should be designated B. cepacia complex strain ATCC 31433, pending further detailed taxonomic characterization.IMPORTANCE This work reports the complete genome sequence of Pseudomonas mesoacidophila ATCC 31433, a known producer of bioactive compounds. Large numbers of both known and novel biosynthetic gene clusters were identified, indicating that P. mesoacidophila ATCC 31433 is an untapped resource for discovery of novel bioactive compounds. Phylogenetic analysis demonstrated that P. mesoacidophila ATCC 31433 is in fact a member of the Burkholderia cepacia complex, most closely related to the species Burkholderia ubonensis Further investigation of the classification and biosynthetic potential of P. mesoacidophila ATCC 31433 is warranted.

AB - Pseudomonas mesoacidophila ATCC 31433 is a Gram-negative bacterium, first isolated from Japanese soil samples, that produces the monobactam isosulfazecin and the β-lactam-potentiating bulgecins. To characterize the biosynthetic potential of P. mesoacidophila ATCC 31433, its complete genome was determined using single-molecule real-time DNA sequence analysis. The 7.8-Mb genome comprised four replicons, three chromosomal (each encoding rRNA) and one plasmid. Phylogenetic analysis demonstrated that P. mesoacidophila ATCC 31433 was misclassified at the time of its deposition and is a member of the Burkholderia cepacia complex, most closely related to Burkholderia ubonensis The sequenced genome shows considerable additional biosynthetic potential; known gene clusters for malleilactone, ornibactin, isosulfazecin, alkylhydroxyquinoline, and pyrrolnitrin biosynthesis and several uncharacterized biosynthetic gene clusters for polyketides, nonribosomal peptides, and other metabolites were identified. Furthermore, P. mesoacidophila ATCC 31433 harbors many genes associated with environmental resilience and antibiotic resistance and was resistant to a range of antibiotics and metal ions. In summary, this bioactive strain should be designated B. cepacia complex strain ATCC 31433, pending further detailed taxonomic characterization.IMPORTANCE This work reports the complete genome sequence of Pseudomonas mesoacidophila ATCC 31433, a known producer of bioactive compounds. Large numbers of both known and novel biosynthetic gene clusters were identified, indicating that P. mesoacidophila ATCC 31433 is an untapped resource for discovery of novel bioactive compounds. Phylogenetic analysis demonstrated that P. mesoacidophila ATCC 31433 is in fact a member of the Burkholderia cepacia complex, most closely related to the species Burkholderia ubonensis Further investigation of the classification and biosynthetic potential of P. mesoacidophila ATCC 31433 is warranted.

U2 - 10.1128/JB.00125-17

DO - 10.1128/JB.00125-17

M3 - Article

VL - 199

JO - Journal of Bacteriology

JF - Journal of Bacteriology

SN - 0021-9193

IS - 13

ER -