Deep genome annotation of the opportunistic human pathogen Streptococcus pneumoniae D39.

Details

Ressource 1Download: gky725-1.pdf (4154.05 [Ko])
State: Public
Version: Final published version
Serval ID
serval:BIB_151CD7F06A08
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Deep genome annotation of the opportunistic human pathogen Streptococcus pneumoniae D39.
Journal
Nucleic acids research
Author(s)
Slager J., Aprianto R., Veening J.W.
ISSN
1362-4962 (Electronic)
ISSN-L
0305-1048
Publication state
Published
Issued date
02/11/2018
Peer-reviewed
Oui
Volume
46
Number
19
Pages
9971-9989
Language
english
Notes
Publication types: Journal Article ; Research Support, Non-U.S. Gov't
Publication Status: ppublish
Abstract
A precise understanding of the genomic organization into transcriptional units and their regulation is essential for our comprehension of opportunistic human pathogens and how they cause disease. Using single-molecule real-time (PacBio) sequencing we unambiguously determined the genome sequence of Streptococcus pneumoniae strain D39 and revealed several inversions previously undetected by short-read sequencing. Significantly, a chromosomal inversion results in antigenic variation of PhtD, an important surface-exposed virulence factor. We generated a new genome annotation using automated tools, followed by manual curation, reflecting the current knowledge in the field. By combining sequence-driven terminator prediction, deep paired-end transcriptome sequencing and enrichment of primary transcripts by Cappable-Seq, we mapped 1015 transcriptional start sites and 748 termination sites. We show that the pneumococcal transcriptional landscape is complex and includes many secondary, antisense and internal promoters. Using this new genomic map, we identified several new small RNAs (sRNAs), RNA switches (including sixteen previously misidentified as sRNAs), and antisense RNAs. In total, we annotated 89 new protein-encoding genes, 34 sRNAs and 165 pseudogenes, bringing the S. pneumoniae D39 repertoire to 2146 genetic elements. We report operon structures and observed that 9% of operons are leaderless. The genome data are accessible in an online resource called PneumoBrowse (https://veeninglab.com/pneumobrowse) providing one of the most complete inventories of a bacterial genome to date. PneumoBrowse will accelerate pneumococcal research and the development of new prevention and treatment strategies.
Keywords
Base Sequence, Chromosome Inversion, Chromosome Mapping, Gene Expression Regulation, Bacterial, Gene Ontology, Genome, Bacterial, High-Throughput Nucleotide Sequencing, Humans, Molecular Sequence Annotation, Operon, Opportunistic Infections/microbiology, Pneumococcal Infections/microbiology, Promoter Regions, Genetic, RNA, Antisense/classification, RNA, Antisense/genetics, RNA, Antisense/metabolism, RNA, Bacterial/classification, RNA, Bacterial/genetics, RNA, Bacterial/metabolism, RNA, Small Untranslated/classification, RNA, Small Untranslated/genetics, RNA, Small Untranslated/metabolism, Sequence Inversion, Streptococcus pneumoniae/genetics, Streptococcus pneumoniae/isolation & purification, Streptococcus pneumoniae/metabolism, Streptococcus pneumoniae/pathogenicity, Transcriptome, Virulence Factors/genetics, Virulence Factors/metabolism
Pubmed
Web of science
Open Access
Yes
Create date
20/08/2018 13:29
Last modification date
20/08/2019 13:44
Usage data