High-resolution analysis of the pneumococcal transcriptome under a wide range of infection-relevant conditions

Aprianto, Rieza; Slager, Jelle; Holsappel, Siger; Veening, Jan‐Willem

doi:10.1101/283739

Cited by 18 publications

(35 citation statements)

References 75 publications

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“…The successful mapping of a significant number of reads indicated the presence of the plasmid in strains used in several studies (( 41 ), SRX2613845; ( 42 ), SRX1725406; ( 28 ), SRX472966). In contrast, RNA-seq data of D39V ( 9 , 10 , 25 ) contained zero reads that mapped to the plasmid, providing conclusive evidence that strain D39V lost the plasmid at some stage ( Supplementary Figure S1 ). Similarly, based on Illumina DNA-seq data, we determined that of the three clinical isolates shown in Figure 2A , only SP61 contained a similar plasmid ( 33 ).…”

Section: Resultsmentioning

confidence: 92%

“…After the sequence- and database-driven annotation process, we proceeded to study the transcriptome of S. pneumoniae . To maximize the number of expressed genes, we pooled RNA from cells grown at four different conditions (mimicking (i) lung, (ii) cerebral spinal fluid (CSF), or (iii) fever in CSF-like medium, and (iv) late competence (20 min after CSP addition) in C+Y medium; see ( 9 )). Strand-specific, paired-end RNA-seq data of the control library was used to extract start and end points and fragment sizes of the sequenced fragments.…”

Section: Resultsmentioning

confidence: 99%

“…Composition of media, a detailed description of conditions and the total RNA isolation protocol are described in the accompanying paper by Aprianto et al. ( 9 ). Isolated RNA was sent to vertis Biotechnologie AG for sequencing.…”

Section: Methodsmentioning

confidence: 99%

“…Defining an operon as a set of one or more genes controlled by a single promoter, putative operons were predicted for each primary TSS. Two consecutive features on the same strand were predicted to be in the same operon if (i) their expression across 22 infection-relevant conditions was strongly correlated (correlation value > 0.75, ( 9 )) and (ii) no strong terminator (>80% efficient) was found between the features. In a total of 70 leaderless transcripts, the TSS was found to overlap with the translation initiation site of the first encoded feature in the operon.…”

Section: Methodsmentioning

confidence: 99%

“…Finally, we created PneumoBrowse, an intuitive and accessible genome browser ( https://veeninglab.com/pneumobrowse ), based on JBrowse ( 8 ). PneumoBrowse provides a graphical and user-friendly interface to explore the genomic and transcriptomic landscape of S. pneumoniae D39V and allows direct linking to gene expression and co-expression data in PneumoExpress ( 9 ). The reported annotation pipeline and accompanying genome browser provide one of the best curated bacterial genomes currently available and may facilitate rapid and accurate annotation of other bacterial genomes.…”

Section: Introductionmentioning

confidence: 99%

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Deep genome annotation of the opportunistic human pathogen Streptococcus pneumoniae D39

Slager

Aprianto

Veening

2018

Nucleic Acids Research

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117

218

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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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Section: Resultsmentioning

confidence: 92%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Deep genome annotation of the opportunistic human pathogen Streptococcus pneumoniae D39

Slager

Aprianto

Veening

2018

Nucleic Acids Research

Self Cite

117

218

View full text Add to dashboard Cite

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Role of membrane proteins in bacterial resistance to antimicrobial peptides

Vimberg

Buriánková

Mazumdar

et al. 2021

Medicinal Research Reviews

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Several natural antimicrobial peptides (AMPs), including the novel semisynthetic lipoglycopeptide antibiotics telavancin, dalbavancin, and oritavancin, have been approved for clinical use to address the growing problem of multiple antibioticresistant Gram-positive bacterial infections. Nevertheless, the efficacy of these antibiotics has already been compromised. The SARS-CoV-2 pandemic led to the increased clinical use of all antibiotics, further promoting the development of bacterial resistance. Therefore, it is critical to gain a deeper understanding of the role of resistance mechanisms to minimize the consequential risks of long-term antibiotic use and misuse.Here, we summarize for the first time the current knowledge of resistance mechanisms that have been shown to cause resistance to clinically used AMPs, with particular focus on membrane proteins that have been reported to interfere with the activity of AMPs by affecting the binding of AMPs to bacteria.

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Construction of Fluorescent Pneumococci for In Vivo Imaging and Labeling of the Chromosome

Kjos

2019

Methods in Molecular Biology

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Advances in fluorescence imaging techniques and development and optimization of fluorescent proteins recent years have made major impacts on different fields of pneumococcal research. This chapter provides methodology for construction of fluorescent pneumococcal strains using fusions to DNA-binding proteins. By expressing fluorescent proteins fused to HlpA, a pneumococcal nucleoid binding protein, brightly fluorescent pneumococci are generated. HlpA fusions may be used both for in vivo imaging of pneumococci as well as for marking the nucleoid in cell biology studies. Furthermore, it will also be explained how to construct strains for imaging of specific chromosomal loci in pneumococci, using a heterologous ParBS system.

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High-resolution analysis of the pneumococcal transcriptome under a wide range of infection-relevant conditions

Abstract: Streptococcus

Cited by 18 publications

References 75 publications

Deep genome annotation of the opportunistic human pathogen Streptococcus pneumoniae D39

Deep genome annotation of the opportunistic human pathogen Streptococcus pneumoniae D39

Role of membrane proteins in bacterial resistance to antimicrobial peptides

Construction of Fluorescent Pneumococci for In Vivo Imaging and Labeling of the Chromosome

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