Transcriptome analysis of Streptococcus mutans planktonic cells deficient in the DpnII restriction-modification system
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ABSTRACT:
PROVIDER: PRJNA1104234 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28793842_1.fastq.gz | Fastqsanger.gz | |||
| SRR28793842_2.fastq.gz | Fastqsanger.gz | |||
| SRR28793843_1.fastq.gz | Fastqsanger.gz | |||
| SRR28793843_2.fastq.gz | Fastqsanger.gz | |||
| SRR28793844_1.fastq.gz | Fastqsanger.gz |
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Project description:Human pathogens use cell-cell communication systems, quorum sensing, to regulate virulence factors. Our recent work aiming at deciphering the quorum sensing regulon of Streptococcus mutans, a caries pathogen, revealed a locus encoding an atypical type II restriction-modification (R-M) system, DpnII, comprising two adenine methyltransferases. A recent survey of bacterial genomes demonstrated the widespread occurrence of methylated DNA, and the importance of DNA methylation was highlighted by the diverse processes in which they function. The present study aimed at deciphering the role of DNA methylation during S. mutans planktonic growth. A mutant strain, deficient in the DpnII R-M locus composed of the SMU.504 and SMU.505 genes encoding the two adenine methyltransferases and the SMU.506 gene encoding the DpnII restriction enzyme, was constructed in S. mutans wild-type (WT) strain. Transcriptome analysis was then performed to evaluate the differential planktonic gene expression between the WT cells and the DpnII R-M deficient cells.
2025-03-19 | GSE265802 | GEO
Project description:In vitro comparative transcriptome analysis was carried to determine genes that are differentially expressed in S. mutans biofilm compared with free-living cells. DNA-microarray analyses indicated that about 12 % of genes showed significant differential expression: 139 were activated and 104 were repressed in biofilm vs. planktonic environment. Keywords: cell type comparison
2007-05-07 | GSE6744 | GEO
Project description:Genetically programmed deaths play important roles in the biology of unicellular prokaryotic cells. Some gene complexes force their maintenance on the host bacterial cells by killing cells that have lost them. This form of programmed death called post-segregational killing or genetic addiction is brought about by several Type II restriction-modification gene complexes, through restriction attack on the undermethylated chromosome, and underlie their behavior as selfish mobile elements. To learn the genetic steps to death, we examined how carriage and loss of PaeR7I restriction-modification gene complex affect host Escherichia coli cells through transcriptome and experimental analyses. The PaeR7I complex was on a temperature-sensitive plasmid so that the killing was induced by a temperature shift. We used microarrays to detail the global program of gene expression underlying cell death process mediated by PaeR7I restriction-modification system in E. coli. Keywords: time course
2009-06-23 | GSE7326 | GEO
Project description:Gene expression profiling of Streptococcus mutans in biofilm and planktonic conditions
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Project description:Genetically programmed deaths play important roles in the biology of unicellular prokaryotic cells. Some gene complexes force their maintenance on the host bacterial cells by killing cells that have lost them. This form of programmed death called post-segregational killing or genetic addiction is brought about by several Type II restriction-modification gene complexes, through restriction attack on the undermethylated chromosome, and underlie their behavior as selfish mobile elements. To learn the genetic steps to death, we examined how carriage and loss of PaeR7I restriction-modification gene complex affect host Escherichia coli cells through transcriptome and experimental analyses. The PaeR7I complex was on a temperature-sensitive plasmid so that the killing was induced by a temperature shift. We used microarrays to detail the global program of gene expression underlying cell death process mediated by PaeR7I restriction-modification system in E. coli. Experiment Overall Design: Post-segregational cell killing was induced by blocking replication of a temperature sensitive plasmid carrying PaeR7I RM gene complex by shifting up the cultivation temperature. At 30℃, the permissive temperature for the plasmid replication, growth as monitored by OD660, of MG1655/pTN9 (r+m+) was indistinguishable from those of MG1655/pTN11 (r-m+) and MG1655/pHSG415 (vector). Cell death was observed at least 4 h after the temperature shift only in MG1655/pTN9 (r+m+) as in the previous works; the increase in viable cell counts stopped and resulted in decrease of cell viability. To analyze global gene expression when cells went to death, we performed transcriptome analysis 0 h, 1h, 1 h 50 min, and 3h after the temperature shift. We used Affimetrix E. coli antisense genome array. Experiments were performed independently twice.
2009-07-04 | E-GEOD-7326 | biostudies-arrayexpress
Project description:Transcriptional profiling of N. gonorrhoeae comparing wild type cells to cells with inactivated by kanamycin cassette (km) gene involved in restriction modification NgoAXP or with chloramphenicol cassette (cm) gene involved in restriction-modification NgoAV. The Goal was to study the role of M.NgoAXP and NgoAV methyltransferases in overall expression profile.
2017-02-13 | GSE71703 | GEO
Project description:Lysine malonylation is an evolutionarily conserved PTM from bacteria to mammals and involves malonyl-coenzyme (CoA) as a cofactor. Since the malonyl group has an acidic carboxylic group under physiological pH, malonylated lysine is negatively charged, which might impact on protein function and enzymatic activities. Like other short-chain acyl-CoAs, malonyl-CoA can be synthesized from its corresponding short-chain acyl salt, malonate, catalyzed by malonyl-CoA synthetase (Witkowski et al., 2011). In addition, malonyl-CoA can be produced during the carboxylation of acetyl-CoA by acetyl-CoA carboxylase (ACC), the carboxylation of acetyl-CoA by propionyl-CoA carboxylase, and the β-oxidation of old-chain-length dicarboxylic acids (Peng et al., 2011). Most studies on Kmal have been performed in mammalian systems and identified thousands of malonylated sites, revealing its role in the progress of diseases like type 2 diabetes, schizophrenia, and cardiac hypertrophy (Du et al., 2015; Smith et al., 2022; Wu et al., 2022). There has been increasing interest in dissecting the regulatory roles of Kmal in several bacterial species, such as Escherichia coli (Qian et al., 2016), Bacillus amyloliquefaciens (Fan et al., 2017), Mycobacterium tuberculosis (Bi et al., 2022), and Staphylococcus aureus (Shi et al., 2021), which demonstrates that Kmal exists in diverse prokaryotic organisms and participates in the regulation of various physiological processes. Even so, whether Kmal exists and affects protein functions in streptococci remains unknown. S. mutans is considered to be the most prevalent and cariogenic species in active carious lesions of humans, residing primarily in dental plaque, which is a biofilm that forms on the tooth surfaces. During the past decades, studies of S. mutans have focused on revealing the molecular mechanisms underlying the robust biofilm formation on tooth surfaces, the metabolism of a wide variety of carbohydrates obtained from the host diet, and the adaption of numerous environmental challenges (Lemos et al., 2019). Several studies have been performed to reveal the roles of PTMs in biofilm and cariogenic virulence. Wang et al. found that the phosphorylation of VicR could inhibit the expression of the glucosyltransferases gtfBC, thereby reducing the synthesis of extracellular polysaccharides (EPS), the major component of cariogenic biofilm (Wang et al., 2021). Acetylome study on the S. mutans depicted that acetylated substrates were globally altered in the biofilm state compared to the planktonic state, and the acetylated GtfBC showed decreased activities (Lei et al., 2021; Ma et al., 2021). Our previous study revealed that the S-glutathionylation of a thioredoxin-like protein is important for interspecies competition and cariogenicity of S. mutans(Li et al., 2020). These results suggest that various PTM types exist in S. mutans and participate in diverse physiological processes. The genome of S. mutans UA159 codes an acetyl coenzyme A carboxylase (ACC), which could synthesize malonyl-CoA through the carboxylation of acetyl-CoA (Ajdić et al., 2002), implying the existence of malonylation in this bacterium. Therefore, this study aimed to confirm the existence of Kmal in S. mutans and identify the malonylated sites globally. The present findings provide a systematic view of the functional roles of Kmal in various metabolic pathways of S. mutans.
2022-11-17 | PXD038045 | Pride
Project description:Despite the widespread use of antiseptics such as chlorhexidine digluconate (CHX) in dental practice and oral care, the risks of potential resistance toward antiseptics in oral bacteria have only been highlighted very recently. Since the molecular mechanisms behind antiseptic resistance or adaptation are not entirely clear yet and the bacterial stress response has not been investigated systematically so far, the aim of the present study was to investigate the transcriptomic stress response in Streptococcus mutans after treatment with CHX using RNA sequencing. Planktonic cultures of stationary phase S. mutans were treated with a sublethal dose of CHX (125 µg/mL) for 5 min. After treatment, RNA was extracted, and RNA sequencing was performed on the Illumina NextSeq 500. Differential expressed genes were analyzed and validated by qRT-PCR. The analysis of the differential gene expression following pathway analysis revealed a considerable number of genes and pathways significantly regulated in S. mutans after sublethal treatment with CHX. In summary, expression of 423 genes was up-regulated and 295 genes down-regulated after CHX treatment. Analysis of differentially expressed genes and significantly regulated pathways showed regulation of genes involved in purine nucleotide synthesis, biofilm formation, transport systems and stress responses. In conclusion, these results show an overview of the transcriptomic stress response in S. mutans upon exposure to CHX and give an insight in potential mechanisms that may result in development of resistances.
2022-03-30 | GSE197633 | GEO
Project description:Multiple S. mutans genes that are subject to SloR control are likely contributors to virulence. The regulation of these genes in response to metal ion limitation vs. availability in the oral cavity can significantly facilitate the caries-forming process and hence continued analysis of these data can reveal novel candidate genes for the purposes of therapeutic intervention and/or prevention. Keywords: Genetic modification, dose response, metalloregulation
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Project description:Mining the methylome reveals extensive diversity in Staphylococcus epidermidis restriction modification
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