ArticleNucleic acids research2018
Deep genome annotation of the opportunistic human pathogen Streptococcus pneumoniae D39.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 99 papers.
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99 citing papers in PubMed.
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- Pneumococcal S protein coordinates cell wall modification and repair to resist host antimicrobials.Nature microbiology · 2026Article
- Multi-omics profiling reveals atypical sugar utilization and a key membrane composition regulator in Streptococcus pneumoniae.Nature communications · 2025Article
- tRNA Modification Landscapes in Streptococci: Shared Losses and Clade-Specific Adaptations.bioRxiv : the preprint server for biology · 2025Article
- Label-free microscopy enables high-throughput identification of genes controlling biofilm development.bioRxiv : the preprint server for biology · 2025Article
- Commensal to pathogen switch in Streptococcus pneumoniae is influenced by a thermosensing master regulator.PLoS pathogens · 2025Article
- Genome-wide antibiotic-CRISPRi profiling identifies LiaR activation as a strategy to resensitize fluoroquinolone-resistant Streptococcus pneumoniae.Nature communications · 2025Article
- The ClpXP protease and the ClpX unfoldase control virulence, cell division, and autolysis inMicrobiology spectrum · 2025Article
- NrdR in Streptococcus and Listeria spp.: DNA Helix Phase Dependence of the Bacterial Ribonucleotide Reductase Repressor.Molecular microbiology · 2025Article
- Glycosylation of serine/threonine-rich intrinsically disordered regions of membrane-associated proteins in streptococci.Nature communications · 2025Article
- Make-or-break prime editing for genome engineering in Streptococcus pneumoniae.Nature communications · 2025Article
- Inhibition of pneumococcal growth and biofilm formation by human isolates ofApplied and environmental microbiology · 2025Article
- BacTermFinder: a comprehensive and general bacterial terminator finder using a CNN ensemble.NAR genomics and bioinformatics · 2025Article
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- Point mutations in functionally diverse genes are associated with increased natural DNA transformation in multidrug resistant Streptococcus pneumoniae.Nucleic acids research · 2025Article
39 more citing papers are in PubMed but not listed here.
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3 authors.
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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.
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