Genome scale metabolic model combined with single molecule real-time sequencing to analyze Actinomycete chromosomal heterogeneity

Bin, Han; Li, Zonglin; Li, Zhimin

doi:10.1016/j.gene.2022.146959

Cited by 2 publications

(2 citation statements)

References 44 publications

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“…Furthermore, transcriptomic data on the mutant strain of S. roseosporus for m4C methyltransferase ( SroLm3 ) revealed an upregulation of genes encoding an ABC transporter and ribosomal proteins. Recently, a potential connection between DNA methyl modification and the synthesis of erythromycin A in Saccharopolyspora erythraea was discussed 36 . We cannot rule out that other modifications to S. coelicolor genomic DNA can occur, given the specificity of BS-sequencing for detecting m5C 17 .…”

Section: Discussionmentioning

confidence: 99%

The DNA cytosine methylome revealed two methylation motifs in the upstream regions of genes related to morphological and physiological differentiation in Streptomyces coelicolor A(3)2 M145

Pisciotta

Sampino

Presentato

et al. 2023

Sci Rep

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DNA methylation is an epigenetic modification detected in both prokaryotic and eukaryotic genomic DNAs. In bacteria, the importance of 5-methylcytosine (m5C) in gene expression has been less investigated than in eukaryotic systems. Through dot-blot analysis employing m5C antibodies against chromosomal DNA, we have previously demonstrated that m5C influences the differentiation of Streptomyces coelicolor A(3)2 M145 in solid sporulating and liquid non-sporulating complex media. Here, we mapped the methylated cytosines of the M145 strain growing in the defined Maltose Glutamate (MG) liquid medium. Sequencing of the M145 genome after bisulfite treatment (BS-sequencing) evidenced 3360 methylated cytosines and the two methylation motifs, GGCmCGG and GCCmCG, in the upstream regions of 321 genes. Besides, the role of cytosine methylation was investigated using the hypo-methylating agent 5′-aza-2′-deoxycytidine (5-aza-dC) in S. coelicolor cultures, demonstrating that m5C affects both growth and antibiotic biosynthesis. Finally, quantitative reverse-transcription polymerase-chain-reaction (RT-qPCR) analysis of genes containing the methylation motifs in the upstream regions showed that 5-aza-dC treatment influenced their transcriptional levels and those of the regulatory genes for two antibiotics. To the best of our knowledge, this is the first study that reports the cytosine methylome of S. coelicolor M145, supporting the crucial role ascribed to cytosine methylation in controlling bacterial gene expression.

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Section: Discussionmentioning

confidence: 99%

The DNA cytosine methylome revealed two methylation motifs in the upstream regions of genes related to morphological and physiological differentiation in Streptomyces coelicolor A(3)2 M145

Pisciotta

Sampino

Presentato

et al. 2023

Sci Rep

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“…According to the automatic error correction function of SMRT LINK v5.0.1 software ( https://www.pacb.com/support/software-downloads/ ) [ 9 , 10 ], long reads longer than 6,000 bp were selected as the seed sequence, and the remaining shorter reads were aligned to the seed sequence by Blasr (v1.3.1). In addition, the preliminary assembly results were polished using an arrow algorithm ( https://github.com/PacificBiosciences/GenomicConsensus ), followed by correction with Illumina data by bwa [ 11 ]. Furthermore, the result was filtered with a base minimum mass value of 20, a minimum read depth of 4 and a maximum read depth of 1,000.…”

Section: Methodsmentioning

confidence: 99%

Characterization and the first complete genome sequence of a novel strain of Bergeyella porcorum isolated from pigs in China

Liu,

Chen,

Jiang

et al. 2024

BMC Microbiol

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Background Bergeyella porcorum is a newly identified bacterium that has an ambiguous relationship with pneumonia in pigs. However, few studies have adequately characterized this species. Results In this study, we analyzed the morphological, physiological, and genomic characteristics of the newly identified B. porcorum sp. nov. strain QD2021 isolated from pigs. The complete genome sequence of the B. porcorum QD2021 strain consists of a single circular chromosome (2,271,736 bp, 38.51% G + C content), which encodes 2,578 genes. One plasmid with a size of 70,040 bp was detected. A total of 121 scattered repeat sequences, 319 tandem repeat sequences, 4 genomic islands, 5 prophages, 3 CRISPR sequences, and 51 ncRNAs were predicted. The coding genes of the B. porcorum genome were successfully annotated across eight databases (NR, GO, KEGG, COG, TCDB, Pfam, Swiss-Prot and CAZy) and four pathogenicity-related databases (PHI, CARD, VFDB and ARDB). In addition, a comparative genome analysis was performed to explore the evolutionary relationships of B. porcorum QD2021. Conclusions To our knowledge, this is the first study to provide fundamental phenotypic and whole-genome sequences for B. porcorum. Our results extensively expand the current knowledge and could serve as a valuable genomic resource for future research on B. porcorum.

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Genome scale metabolic model combined with single molecule real-time sequencing to analyze Actinomycete chromosomal heterogeneity

Cited by 2 publications

References 44 publications

The DNA cytosine methylome revealed two methylation motifs in the upstream regions of genes related to morphological and physiological differentiation in Streptomyces coelicolor A(3)2 M145

The DNA cytosine methylome revealed two methylation motifs in the upstream regions of genes related to morphological and physiological differentiation in Streptomyces coelicolor A(3)2 M145

Characterization and the first complete genome sequence of a novel strain of Bergeyella porcorum isolated from pigs in China

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