scholarly journals Epigenetic Regulation of Nostoc punctiforme ATCC 29133 in Response to Nitrogen Availability

2021 ◽  
Vol 10 (3) ◽  
Author(s):  
Claire Shaw ◽  
Charles Brooke ◽  
Angel Avalos ◽  
Matthew Blow ◽  
Nicole Shapiro ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Epigenetic Regulation ◽  
Nitrate Reduction ◽  
Nitrogen Availability ◽  
Nostoc Punctiforme ◽  
Modification System ◽  
Restriction Modification System ◽  
Nitrate Availability ◽  
Assimilatory Nitrate Reduction ◽  
Restriction Modification

Here, we report the restriction modification system of Nostoc punctiforme ATCC 29133, along with its methylated genome sequence, under contrasting nitrate availability. Generated methylation profiles revealed increased methylation for key enzymes of assimilatory nitrate reduction, suggesting that Nostoc punctiforme employs DNA methylation to regulate its nitrogen metabolism.

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 Characterization of the Type I Restriction Modification System Broadly Conserved among Group A Streptococci

mSphere ◽  
2021 ◽  
Author(s):  
Sruti DebRoy ◽  
William C. Shropshire ◽  
Chau Nguyen Tran ◽  
Haiping Hao ◽  
Marc Gohel ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Epigenetic Modification ◽  
Type I ◽  
Whole Genome ◽  
Group A Streptococci ◽  
Modification System ◽  
Restriction Modification System ◽  
Group A ◽  
Restriction Modification

The advent of whole-genome approaches capable of detecting DNA methylation has markedly expanded appreciation of the diverse roles of epigenetic modification in prokaryotic physiology. For example, recent studies have suggested that DNA methylation impacts gene expression in some streptococci.

scholarly journals The Patchy Distribution of Restriction–Modification System Genes and the Conservation of Orphan Methyltransferases in Halobacteria

Genes ◽  
2019 ◽  
Vol 10 (3) ◽  
pp. 233 ◽  
Author(s):  
Matthew S. Fullmer ◽  
Matthew Ouellette ◽  
Artemis S. Louyakis ◽  
R. Thane Papke ◽  
Johann Peter Gogarten
Keyword(s):  
Dna Methylation ◽  
Gene Transfer ◽  
Dna Methyltransferase ◽  
Dna Uptake ◽  
Modification System ◽  
Selfish Genetic Element ◽  
Restriction Modification System ◽  
Repair Protein ◽  
Restriction Modification

Restriction–modification (RM) systems in bacteria are implicated in multiple biological roles ranging from defense against parasitic genetic elements, to selfish addiction cassettes, and barriers to gene transfer and lineage homogenization. In bacteria, DNA-methylation without cognate restriction also plays important roles in DNA replication, mismatch repair, protein expression, and in biasing DNA uptake. Little is known about archaeal RM systems and DNA methylation. To elucidate further understanding for the role of RM systems and DNA methylation in Archaea, we undertook a survey of the presence of RM system genes and related genes, including orphan DNA methylases, in the halophilic archaeal class Halobacteria. Our results reveal that some orphan DNA methyltransferase genes were highly conserved among lineages indicating an important functional constraint, whereas RM systems demonstrated patchy patterns of presence and absence. This irregular distribution is due to frequent horizontal gene transfer and gene loss, a finding suggesting that the evolution and life cycle of RM systems may be best described as that of a selfish genetic element. A putative target motif (CTAG) of one of the orphan methylases was underrepresented in all of the analyzed genomes, whereas another motif (GATC) was overrepresented in most of the haloarchaeal genomes, particularly in those that encoded the cognate orphan methylase.

scholarly journals The Patchy Distribution of Restriction-Modification System Genes and the Conservation of Orphan Methyltransferases in Halobacteria

2019 ◽  
Author(s):  
Matthew S. Fullmer ◽  
Matthew Ouellette ◽  
Artemis S. Louyakis ◽  
R. Thane Papke ◽  
J. Peter Gogarten
Keyword(s):  
Dna Methylation ◽  
Gene Transfer ◽  
Dna Methyltransferase ◽  
Dna Uptake ◽  
Modification System ◽  
Selfish Genetic Element ◽  
Restriction Modification System ◽  
Repair Protein ◽  
Restriction Modification

AbstractRestriction-modification (RM) systems in Bacteria are implicated in multiple biological roles ranging from defense against parasitic genetic elements, to selfish addiction cassettes, and barriers to gene transfer and lineage homogenization. In Bacteria, DNA-methylation without cognate restriction also plays important roles in DNA replication, mismatch repair, protein expression, and in in biasing DNA uptake. Little is known about archaeal RM systems and DNA methylation. To elucidate further understanding for the role of RM systems and DNA methylation in Archaea, we undertook a survey of the presence of RM system genes and related genes, including orphan DNA methylases, in the halophilic archaeal class Halobacteria. Our results reveal that some orphan DNA methyltransferase genes were highly conserved among lineages indicating an important functional constraint, whereas RM systems demonstrated patchy patterns of presence and absence. This irregular distribution is due to frequent horizontal gene transfer and gene loss, a finding suggesting that the evolution and life cycle of RM systems may be best described as that of a selfish genetic element. A putative target motif (CTAG) of one of the orphan methylases was underrepresented in all of the analyzed genomes, whereas another motif (GATC) was overrepresented in most of the haloarchaeal genomes, particularly in those that encoded the cognate orphan methylase.

scholarly journals A Type I Restriction Modification System Influences Genomic Evolution Driven by Horizontal Gene Transfer in Paenibacillus polymyxa

2021 ◽  
Vol 12 ◽  
Author(s):  
Ziyan Chen ◽  
Minjia Shen ◽  
Chengyao Mao ◽  
Chenyu Wang ◽  
Panhong Yuan ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Animal Husbandry ◽  
Paenibacillus Polymyxa ◽  
Genomic Islands ◽  
Type I ◽  
Genomic Evolution ◽  
Modification System ◽  
Restriction Modification System ◽  
Restriction Modification

Considered a “Generally Recognized As Safe” (GRAS) bacterium, the plant growth–promoting rhizobacterium Paenibacillus polymyxa has been widely applied in agriculture and animal husbandry. It also produces valuable compounds that are used in medicine and industry. Our previous work showed the presence of restriction modification (RM) system in P. polymyxa ATCC 842. Here, we further analyzed its genome and methylome by using SMRT sequencing, which revealed the presence of a larger number of genes, as well as a plasmid documented as a genomic region in a previous report. A number of mobile genetic elements (MGEs), including 78 insertion sequences, six genomic islands, and six prophages, were identified in the genome. A putative lysozyme-encoding gene from prophage P6 was shown to express lysin which caused cell lysis. Analysis of the methylome and genome uncovered a pair of reverse-complementary DNA methylation motifs which were widespread in the genome, as well as genes potentially encoding their cognate type I restriction-modification system PpoAI. Further genetic analysis confirmed the function of PpoAI as a RM system in modifying and restricting DNA. The average frequency of the DNA methylation motifs in MGEs was lower than that in the genome, implicating a role of PpoAI in restricting MGEs during genomic evolution of P. polymyxa. Finally, comparative analysis of R, M, and S subunits of PpoAI showed that homologs of the PpoAI system were widely distributed in species belonging to other classes of Firmicute, implicating a role of the ancestor of PpoAI in the genomic evolution of species beyond Paenibacillus.

Cloning the KpnI restriction-modification system in Escherichia coli

Gene ◽  
1991 ◽  
Vol 97 (1) ◽  
pp. 97-102 ◽  
Author(s):  
Alan W. Hammond ◽  
Gary F. Gerard ◽  
Deb K. Chatterjee
Keyword(s):  
Escherichia Coli ◽  
Modification System ◽  
Restriction Modification System ◽  
Restriction Modification

scholarly journals A putative mobile genetic element carrying a novel type IIF restriction-modification system (PluTI)

2010 ◽  
Vol 38 (9) ◽  
pp. 3019-3030 ◽  
Author(s):  
Feroz Khan ◽  
Yoshikazu Furuta ◽  
Mikihiko Kawai ◽  
Katarzyna H. Kaminska ◽  
Ken Ishikawa ◽  
...  
Keyword(s):  
Mobile Genetic Element ◽  
Genetic Element ◽  
Modification System ◽  
Restriction Modification System ◽  
Restriction Modification

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.

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