Genome-wide analysis of restriction-modification system in unicellular and filamentous cyanobacteria

2006 ◽  
Vol 24 (3) ◽  
pp. 181-190 ◽  
Author(s):  
Fangqing Zhao ◽  
Xiaowen Zhang ◽  
Chengwei Liang ◽  
Jinyu Wu ◽  
Qiyu Bao ◽  
...  
Keyword(s):  
Positive Selection ◽  
Draft Genome ◽  
Gene Clusters ◽  
Pcr Analysis ◽  
Type I ◽  
Type Ii ◽  
Filamentous Cyanobacteria ◽  
Modification System ◽  
Wide Range ◽  
Restriction Modification

Cyanobacteria are an ancient group of gram-negative bacteria with strong genome size variation ranging from 1.6 to 9.1 Mb. Here, we first retrieved all the putative restriction-modification (RM) genes in the draft genome of Spirulina and then performed a range of comparative and bioinformatic analyses on RM genes from unicellular and filamentous cyanobacterial genomes. We have identified 6 gene clusters containing putative Type I RMs and 11 putative Type II RMs or the solitary methyltransferases (MTases). RT-PCR analysis reveals that 6 of 18 MTases are not expressed in Spirulina, whereas one hsdM gene, with a mutated cognate hsdS, was detected to be expressed. Our results indicate that the number of RM genes in filamentous cyanobacteria is significantly higher than in unicellular species, and this expansion of RM systems in filamentous cyanobacteria may be related to their wide range of ecological tolerance. Furthermore, a coevolutionary pattern is found between hsdM and hsdR, with a large number of site pairs positively or negatively correlated, indicating the functional importance of these pairing interactions between their tertiary structures. No evidence for positive selection is found for the majority of RMs, e.g., hsdM, hsdS, hsdR, and Type II restriction endonuclease gene families, while a group of MTases exhibit a remarkable signature of adaptive evolution. Sites and genes identified here to have been under positive selection would provide targets for further research on their structural and functional evaluations.

scholarly journals Draft Genome Sequence of 11399, a Transformable Citrus-Pathogenic Strain of Xylella fastidiosa

2016 ◽  
Vol 4 (5) ◽  
Author(s):  
Bárbara Niza ◽  
Marcus V. Merfa ◽  
Valquíria C. Alencar ◽  
Fabiano B. Menegidio ◽  
Luiz R. Nunes ◽  
...  
Keyword(s):  
Genome Size ◽  
Genome Sequence ◽  
Xylella Fastidiosa ◽  
Draft Genome ◽  
Pathogenic Strain ◽  
Draft Genome Sequence ◽  
Type I ◽  
Modification System ◽  
Restriction Modification System ◽  
Restriction Modification

The draft genome of Xylella fastidiosa subsp. pauca strain 11399, a transformable citrus-pathogenic strain, is reported here. The 11399 genome size is 2,690,704 bp and has a G+C content of 52.7%. The draft genome of 11399 reveals the absence of four type I restriction-modification system genes.

scholarly journals Diversification of the restriction–modification system of Streptococcus pyogenes through its acquisition of mobile elements

2020 ◽  
Author(s):  
Atsushi Ota ◽  
Yukiko Nishiuchi ◽  
Noriko Nakanishi ◽  
Yoshio Iijima ◽  
Tomotada Iwamoto ◽  
...  
Keyword(s):  
Streptococcus Pyogenes ◽  
Complete Genome ◽  
Type I ◽  
Sequence Specificity ◽  
Type Ii ◽  
Genome Sequences ◽  
Modification System ◽  
Dna Sequence Specificity ◽  
Restriction Modification System ◽  
Restriction Modification

ABSTRACTRestriction–modification (RM) systems are typically regarded as “primitive immune systems” in bacteria. The roles of methylation in gene regulation, segregation, and mismatch repair are increasingly recognized. To analyze methyltransferase (MTase) diversity in Streptococcus pyogenes, we compared the RM system distribution in eight new complete genome sequences obtained here and in the database-deposited complete genome sequences of 51 strains. The MTase gene distribution showed that type I MTases often change DNA sequence specificity via switching target recognition domains between strains. The type II MTases in the included strains fell into two groups: a prophage-dominant one and a CRISPR-dominant one. Some highly variable type II MTases were found in the prophage region, suggesting that MTases acquired from phage DNA can generate methylome diversity. Additionally, to investigate the possible contribution of DNA methylation to phenotype, we compared the methylomes and transcriptomes from the four most closely related strains, the results of which suggest that phage-derived methylases possibly regulate the methylome, and, hence, regulate expression levels in S. pyogenes. Our findings will benefit further experimental work on the relationship between virulence genes and pathogenicity in S. pyogenes.

scholarly journals Draft Genome Sequence of an Anthracimycin Producer, Streptomyces sp. TP-A0875

2015 ◽  
Vol 3 (5) ◽  
Author(s):  
Hisayuki Komaki ◽  
Natsuko Ichikawa ◽  
Akira Hosoyama ◽  
Nobuyuki Fujita ◽  
Enjuro Harunari ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Genome Sequence ◽  
Polyketide Synthase ◽  
Draft Genome ◽  
Gene Clusters ◽  
Draft Genome Sequence ◽  
Type I ◽  
Type Ii ◽  
Streptomyces Sp ◽  
Peptide Synthetase

Here, we report the draft genome sequence of an anthracimycin producer, Streptomyces sp. TP-A0875. The genome contains at least two type I polyketide synthase (PKS) gene clusters, two type II PKS gene clusters, and three nonribosomal peptide synthetase gene clusters. The gene cluster for anthracimycin biosynthesis was identified based on the PKS domain organization.

scholarly journals Complete Genome Sequence of Brevibacterium linens SMQ-1335

2016 ◽  
Vol 4 (6) ◽  
Author(s):  
Alessandra G. de Melo ◽  
Simon J. Labrie ◽  
Jeannot Dumaresq ◽  
Richard J. Roberts ◽  
Denise M. Tremblay ◽  
...  
Keyword(s):  
Complete Genome Sequence ◽  
Open Reading Frames ◽  
Type I ◽  
Industrial Strain ◽  
Modification System ◽  
Brevibacterium Linens ◽  
Restriction Modification System ◽  
New Type ◽  
Restriction Modification ◽  
Reading Frames

Brevibacterium linens is one of the main bacteria found in the smear of surface-ripened cheeses. The genome of the industrial strain SMQ-1335 was sequenced using PacBio. It has 4,209,935 bp, a 62.6% G+C content, 3,848 open reading frames, and 61 structural RNAs. A new type I restriction-modification system was identified.

scholarly journals DNA methylation from a Type I restriction modification system influences gene expression and virulence in Streptococcus pyogenes

2019 ◽  
Vol 15 (6) ◽  
pp. e1007841 ◽  
Author(s):  
Taylor M. Nye ◽  
Kristin M. Jacob ◽  
Elena K. Holley ◽  
Juan M. Nevarez ◽  
Suzanne Dawid ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Streptococcus Pyogenes ◽  
Type I ◽  
Modification System ◽  
Restriction Modification System ◽  
Restriction Modification

scholarly journals Unstable chromosome rearrangements in Staphylococcus aureus cause phenotype switching associated with persistent infections

2019 ◽  
Vol 116 (40) ◽  
pp. 20135-20140 ◽  
Author(s):  
Romain Guérillot ◽  
Xenia Kostoulias ◽  
Liam Donovan ◽  
Lucy Li ◽  
Glen P. Carter ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Genetic Basis ◽  
Host Cells ◽  
Type I ◽  
Modification System ◽  
Persistent Infections ◽  
Restriction Modification System ◽  
Long Read ◽  
Small Colony ◽  
Restriction Modification

Staphylococcus aureus small-colony variants (SCVs) are associated with unusually chronic and persistent infections despite active antibiotic treatment. The molecular basis for this clinically important phenomenon is poorly understood, hampered by the instability of the SCV phenotype. Here we investigated the genetic basis for an unstable S. aureus SCV that arose spontaneously while studying rifampicin resistance. This SCV showed no nucleotide differences across its genome compared with a normal-colony variant (NCV) revertant, yet the SCV presented the hallmarks of S. aureus linked to persistent infection: down-regulation of virulence genes and reduced hemolysis and neutrophil chemotaxis, while exhibiting increased survival in blood and ability to invade host cells. Further genome analysis revealed chromosome structural variation uniquely associated with the SCV. These variations included an asymmetric inversion across half of the S. aureus chromosome via recombination between type I restriction modification system (T1RMS) genes, and the activation of a conserved prophage harboring the immune evasion cluster (IEC). Phenotypic reversion to the wild-type–like NCV state correlated with reversal of the chromosomal inversion (CI) and with prophage stabilization. Further analysis of 29 complete S. aureus genomes showed strong signatures of recombination between hsdMS genes, suggesting that analogous CI has repeatedly occurred during S. aureus evolution. Using qPCR and long-read amplicon deep sequencing, we detected subpopulations with T1RMS rearrangements causing CIs and prophage activation across major S. aureus lineages. Here, we have discovered a previously unrecognized and widespread mechanism of reversible genomic instability in S. aureus associated with SCV generation and persistent infections.

scholarly journals Cancer Biology and Prevention in Diabetes

Cells ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. 1380 ◽  
Author(s):  
Swayam Prakash Srivastava ◽  
Julie E. Goodwin
Keyword(s):  
Type Ii Diabetes ◽  
Cancer Biology ◽  
Cancer Metastasis ◽  
Type I Diabetes ◽  
Type I ◽  
Type Ii ◽  
Mesenchymal Transition ◽  
Wide Range ◽  
Risk Of Cancer

The available evidence suggests a complex relationship between diabetes and cancer. Epidemiological data suggest a positive correlation, however, in certain types of cancer, a more complex picture emerges, such as in some site-specific cancers being specific to type I diabetes but not to type II diabetes. Reports share common and differential mechanisms which affect the relationship between diabetes and cancer. We discuss the use of antidiabetic drugs in a wide range of cancer therapy and cancer therapeutics in the development of hyperglycemia, especially antineoplastic drugs which often induce hyperglycemia by targeting insulin/IGF-1 signaling. Similarly, dipeptidyl peptidase 4 (DPP-4), a well-known target in type II diabetes mellitus, has differential effects on cancer types. Past studies suggest a protective role of DPP-4 inhibitors, but recent studies show that DPP-4 inhibition induces cancer metastasis. Moreover, molecular pathological mechanisms of cancer in diabetes are currently largely unclear. The cancer-causing mechanisms in diabetes have been shown to be complex, including excessive ROS-formation, destruction of essential biomolecules, chronic inflammation, and impaired healing phenomena, collectively leading to carcinogenesis in diabetic conditions. Diabetes-associated epithelial-to-mesenchymal transition (EMT) and endothelial-to-mesenchymal transition (EndMT) contribute to cancer-associated fibroblast (CAF) formation in tumors, allowing the epithelium and endothelium to enable tumor cell extravasation. In this review, we discuss the risk of cancer associated with anti-diabetic therapies, including DPP-4 inhibitors and SGLT2 inhibitors, and the role of catechol-o-methyltransferase (COMT), AMPK, and cell-specific glucocorticoid receptors in cancer biology. We explore possible mechanistic links between diabetes and cancer biology and discuss new therapeutic approaches.

scholarly journals Low-level expression of the Type II restriction–modification system confers potent bacteriophage resistance in Escherichia coli

DNA Research ◽  
2020 ◽  
Vol 27 (1) ◽  
Author(s):  
Karolina Wilkowska ◽  
Iwona Mruk ◽  
Beata Furmanek-Blaszk ◽  
Marian Sektas
Keyword(s):  
Dna Methyltransferase ◽  
Host Bacterium ◽  
Type Ii ◽  
Potential Conflict ◽  
Modification System ◽  
Biological Assays ◽  
Restriction Modification System ◽  
Highly Sensitive ◽  
System Maintenance ◽  
Restriction Modification

Abstract Restriction–modification systems (R–M) are one of the antiviral defense tools used by bacteria, and those of the Type II family are composed of a restriction endonuclease (REase) and a DNA methyltransferase (MTase). Most entering DNA molecules are usually cleaved by the REase before they can be methylated by MTase, although the observed level of fragmented DNA may vary significantly. Using a model EcoRI R–M system, we report that the balance between DNA methylation and cleavage may be severely affected by transcriptional signals coming from outside the R–M operon. By modulating the activity of the promoter, we obtained a broad range of restriction phenotypes for the EcoRI R–M system that differed by up to 4 orders of magnitude in our biological assays. Surprisingly, we found that high expression levels of the R–M proteins were associated with reduced restriction of invading bacteriophage DNA. Our results suggested that the regulatory balance of cleavage and methylation was highly sensitive to fluctuations in transcriptional signals both up- and downstream of the R–M operon. Our data provided further insights into Type II R–M system maintenance and the potential conflict within the host bacterium.

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