The genome sequence of Streptomyces lividans 66 reveals a novel tRNA-dependent peptide biosynthetic system within a metal-related genomic island
The genome sequence of Streptomyces lividans 66 reveals a novel tRNA-dependent peptide biosynthetic system within a metal-related genomic island
The complete genome sequence of the original isolate of the model actinomycete Streptomyces lividans 66, also referred to as 1326, was deciphered after a combination of next-generation sequencing platforms and a hybrid assembly pipeline. Comparative analysis of the genomes of S. lividans 66 and closely related strains, including S. coelicolor M145 and S. lividans TK24, was used to identify strain-specific genes. The genetic diversity identified included a large genomic island with a mosaic structure, present in S. lividans 66 but not in the strain TK24. Sequence analyses showed that this genomic island has an anomalous (G +C) content, suggesting recent acquisition and that it is rich in metal-related genes. Sequences previously linked to a mobile conjugative element, termed plasmid SLP3 and defined here as a 94 kb region, could also be identified within this locus. Transcriptional analysis of the response of S. lividans 66 to copper was used to corroborate a role of this large genomic island, including two SLP3-borne "cryptic" peptide biosynthetic gene clusters, in metal homeostasis. Notably, one of these predicted biosynthetic systems includes an unprecedented nonribosomal peptide synthetase-tRNA-dependent transferase biosynthetic hybrid organization. This observation implies the recruitment of members of the leucyl/phenylalanyl-tRNA-protein transferase family to catalyze peptide bond formation within the biosynthesis of natural products. Thus, the genome sequence of S. lividans 66 not only explains long-standing genetic and phenotypic differences but also opens the door for further in-depth comparative genomic analyses of model Streptomyces strains, as well as for the discovery of novel natural products following genome-mining approaches.
Bacterial next-generation genome sequencing, Copper homeostasis, L/F trna transferase, Peptide biosynthesis, Streptomyces comparative genomics
1165-1175
Cruz-Morales, Pablo
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Vijgenboom, Erik
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Iruegas-Bocardo, Fernanda
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Girard, Geneviève
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Yáñez-Guerra, Luis Alfonso
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Ramos-Aboites, Hilda E.
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Pernodet, Jean Luc
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Anné, Jozef
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Van Wezel, Gilles P.
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Barona-Gómez, Francisco
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June 2013
Cruz-Morales, Pablo
75d96b74-68e4-4550-9020-286a0d9dd2f3
Vijgenboom, Erik
46d04660-9dc1-40e1-8a4a-71986a7bae0d
Iruegas-Bocardo, Fernanda
cd173072-ca61-498d-908c-8bc70fdda4ac
Girard, Geneviève
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Yáñez-Guerra, Luis Alfonso
cbca947b-bbf0-4b91-96b0-4a126e3b94b6
Ramos-Aboites, Hilda E.
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Pernodet, Jean Luc
5b208e7a-f82e-492e-9196-4e6afee94ce7
Anné, Jozef
e0ed0709-8dc4-4075-8a97-03fa552767e2
Van Wezel, Gilles P.
83cccd0e-dcfb-42c9-bbc7-3478b863cd05
Barona-Gómez, Francisco
baeecaf6-fb6d-4a03-9c90-2584b5b9dad0
Cruz-Morales, Pablo, Vijgenboom, Erik, Iruegas-Bocardo, Fernanda, Girard, Geneviève, Yáñez-Guerra, Luis Alfonso, Ramos-Aboites, Hilda E., Pernodet, Jean Luc, Anné, Jozef, Van Wezel, Gilles P. and Barona-Gómez, Francisco
(2013)
The genome sequence of Streptomyces lividans 66 reveals a novel tRNA-dependent peptide biosynthetic system within a metal-related genomic island.
Genome Biology and Evolution, 5 (6), .
(doi:10.1093/gbe/evt082).
Abstract
The complete genome sequence of the original isolate of the model actinomycete Streptomyces lividans 66, also referred to as 1326, was deciphered after a combination of next-generation sequencing platforms and a hybrid assembly pipeline. Comparative analysis of the genomes of S. lividans 66 and closely related strains, including S. coelicolor M145 and S. lividans TK24, was used to identify strain-specific genes. The genetic diversity identified included a large genomic island with a mosaic structure, present in S. lividans 66 but not in the strain TK24. Sequence analyses showed that this genomic island has an anomalous (G +C) content, suggesting recent acquisition and that it is rich in metal-related genes. Sequences previously linked to a mobile conjugative element, termed plasmid SLP3 and defined here as a 94 kb region, could also be identified within this locus. Transcriptional analysis of the response of S. lividans 66 to copper was used to corroborate a role of this large genomic island, including two SLP3-borne "cryptic" peptide biosynthetic gene clusters, in metal homeostasis. Notably, one of these predicted biosynthetic systems includes an unprecedented nonribosomal peptide synthetase-tRNA-dependent transferase biosynthetic hybrid organization. This observation implies the recruitment of members of the leucyl/phenylalanyl-tRNA-protein transferase family to catalyze peptide bond formation within the biosynthesis of natural products. Thus, the genome sequence of S. lividans 66 not only explains long-standing genetic and phenotypic differences but also opens the door for further in-depth comparative genomic analyses of model Streptomyces strains, as well as for the discovery of novel natural products following genome-mining approaches.
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Published date: June 2013
Keywords:
Bacterial next-generation genome sequencing, Copper homeostasis, L/F trna transferase, Peptide biosynthesis, Streptomyces comparative genomics
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Local EPrints ID: 483500
URI: http://eprints.soton.ac.uk/id/eprint/483500
ISSN: 1759-6653
PURE UUID: 6885ce28-9346-4c1f-9408-961c3fe6d96c
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Date deposited: 31 Oct 2023 18:24
Last modified: 18 Mar 2024 04:15
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Author:
Pablo Cruz-Morales
Author:
Erik Vijgenboom
Author:
Fernanda Iruegas-Bocardo
Author:
Geneviève Girard
Author:
Luis Alfonso Yáñez-Guerra
Author:
Hilda E. Ramos-Aboites
Author:
Jean Luc Pernodet
Author:
Jozef Anné
Author:
Gilles P. Van Wezel
Author:
Francisco Barona-Gómez
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