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 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 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.

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 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.

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 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 Genome sequence of Pseudomonas aeruginosa PAO1161, a PAO1 derivative with the ICEPae1161 integrative and conjugative element

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Adam Kawalek ◽  
Karolina Kotecka ◽  
Magdalena Modrzejewska ◽  
Jan Gawor ◽  
Grazyna Jagura-Burdzy ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Genome Sequence ◽  
Dna Methyltransferase ◽  
Laboratory Strain ◽  
Mercury Resistance ◽  
Nucleotide Polymorphisms ◽  
Modification System ◽  
Restriction Modification System ◽  
Integrative Conjugative Element ◽  
Restriction Modification

Abstract Background Pseudomonas aeruginosa is a cause of nosocomial infections, especially in patients with cystic fibrosis and burn wounds. PAO1 strain and its derivatives are widely used to study the biology of this bacterium, however recent studies demonstrated differences in the genomes and phenotypes of derivatives from different laboratories. Results Here we report the genome sequence of P. aeruginosa PAO1161 laboratory strain, a leu-, RifR, restriction-modification defective PAO1 derivative, described as the host of IncP-8 plasmid FP2, conferring the resistance to mercury. Comparison of PAO1161 genome with PAO1-UW sequence revealed lack of an inversion of a large genome segment between rRNA operons and 100 nucleotide polymorphisms, short insertions and deletions. These included a change in leuA, resulting in E108K substitution, which caused leucine auxotrophy and a mutation in rpoB, likely responsible for the rifampicin resistance. Nonsense mutations were detected in PA2735 and PA1939 encoding a DNA methyltransferase and a putative OLD family endonuclease, respectively. Analysis of revertants in these two genes showed that PA2735 is a component of a restriction-modification system, independent of PA1939. Moreover, a 12 kb RPG42 prophage and a novel 108 kb PAPI-1 like integrative conjugative element (ICE) encompassing a mercury resistance operon were identified. The ICEPae1161 was transferred to Pseudomonas putida cells, where it integrated in the genome and conferred the mercury resistance. Conclusions The high-quality P. aeruginosa PAO1161 genome sequence provides a reference for further research including e.g. investigation of horizontal gene transfer or comparative genomics. The strain was found to carry ICEPae1161, a functional PAPI-1 family integrative conjugative element, containing loci conferring mercury resistance, in the past attributed to the FP2 plasmid of IncP-8 incompatibility group. This indicates that the only known member of IncP-8 is in fact an ICE.

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