scholarly journals Effects of mutations in phage restriction sites during escape from restriction–modification

2017 ◽  
Vol 13 (12) ◽  
pp. 20170646 ◽  
Author(s):  
Maroš Pleška ◽  
Călin C. Guet
Keyword(s):  
Restriction Site ◽  
Response To Selection ◽  
Modification System ◽  
Restriction Modification System ◽  
Restriction Sites ◽  
Restriction Modification ◽  
Insight Into ◽  
Restriction Modification Systems ◽  
Site Avoidance

Restriction–modification systems are widespread genetic elements that protect bacteria from bacteriophage infections by recognizing and cleaving heterologous DNA at short, well-defined sequences called restriction sites. Bioinformatic evidence shows that restriction sites are significantly underrepresented in bacteriophage genomes, presumably because bacteriophages with fewer restriction sites are more likely to escape cleavage by restriction–modification systems. However, how mutations in restriction sites affect the likelihood of bacteriophage escape is unknown. Using the bacteriophage λ and the restriction–modification system EcoRI, we show that while mutation effects at different restriction sites are unequal, they are independent. As a result, the probability of bacteriophage escape increases with each mutated restriction site. Our results experimentally support the role of restriction site avoidance as a response to selection imposed by restriction–modification systems and offer an insight into the events underlying the process of bacteriophage escape.

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 Restriction-modification systems and DNA methylation profile of Pectobacterium carotovorum 2A

2021 ◽  
pp. 71-77
Author(s):  
Yulia V. Diubo ◽  
Artur E. Akhremchuk ◽  
Leonid N. Valentovich ◽  
Yevgeny A. Nikolaichik
Keyword(s):  
Methylation Profile ◽  
Type I ◽  
Pectobacterium Carotovorum ◽  
Modification System ◽  
Restriction Modification System ◽  
Type Iv ◽  
Oxford Nanopore ◽  
Dna Methylation Profile ◽  
Restriction Modification ◽  
Restriction Modification Systems

The methylation profile of Pectobacterium carotovorum 2A genome was studied using the Oxford Nanopore sequencing technology. The specificity of the methylase subunits of the three restriction-modification systems of this strain was determined. Analysis of homologous systems showed the uniqueness of the type I restriction-modification system and the type IV restriction system specific to methylated DNA of this strain. The work confirms the applicability of Oxford Nanopore technology to the analysis of bacterial DNA modifications and is also the first example of such an analysis for Pectobacterium spp.

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 Evolutionary Role of Restriction/Modification Systems as Revealed by Comparative Genome Analysis

2001 ◽  
Vol 11 (6) ◽  
pp. 946-958
Author(s):  
Eduardo P.C. Rocha ◽  
Antoine Danchin ◽  
Alain Viari
Keyword(s):  
Restriction Site ◽  
Bacterial Species ◽  
Genetic Material ◽  
Type Ii ◽  
Parasite Relationship ◽  
Host Parasite ◽  
Restriction Modification ◽  
Evolutionary Role ◽  
Restriction Modification Systems ◽  
Site Avoidance

Type II restriction modification systems (RMSs) have been regarded either as defense tools or as molecular parasites of bacteria. We extensively analyzed their evolutionary role from the study of their impact in the complete genomes of 26 bacteria and 35 phages in terms of palindrome avoidance. This analysis reveals that palindrome avoidance is not universally spread among bacterial species and that it does not correlate with taxonomic proximity. Palindrome avoidance is also not universal among bacteriophage, even when their hosts code for RMSs, and depends strongly on the genetic material of the phage. Interestingly, palindrome avoidance is intimately correlated with the infective behavior of the phage. We observe that the degree of palindrome and restriction site avoidance is significantly and consistently less important in phages than in their bacterial hosts. This result brings to the fore a larger selective load for palindrome and restriction site avoidance on the bacterial hosts than on their infecting phages. It is then consistent with a view where type II RMSs are considered as parasites possibly at the verge of mutualism. As a consequence, RMSs constitute a nontrivial third player in the host–parasite relationship between bacteria and phages.

Restriction-modification systems in Streptomyces antibioticus

1985 ◽  
Vol 31 (10) ◽  
pp. 942-946 ◽  
Author(s):  
Jesùs Sànchez ◽  
Covadonga Barbès ◽  
Angeles Hernandez ◽  
Clara-Rosa G. de los Reyes Gavilàn ◽  
Carlos Hardisson
Keyword(s):  
Biological Indicators ◽  
Modification System ◽  
Streptomyces Antibioticus ◽  
Restriction Modification System ◽  
Different Strains ◽  
Restriction Modification ◽  
Restriction Modification Systems

Several restriction systems were detected in different strains of Streptomyces antibioticus by using actinophages as biological indicators. Adsorption of phages to the bacteria, together with the study of the efficiency of plating gave an initial indication of restriction in three strains. The alternation of efficiency of plating values obtained from restricting and nonrestricting hosts, gave evidence for the presence of a restriction-modification system in another strain. No common modification systems were detected among the different strains tested. Two specific endonucleases with a possible role in restriction were detected in strains ATCC 11891 and ETH 7451, respectively.

scholarly journals Mobility of a Restriction-Modification System Revealed by Its Genetic Contexts in Three Hosts

2002 ◽  
Vol 184 (9) ◽  
pp. 2411-2419 ◽  
Author(s):  
Marc Naderer ◽  
Jessica R. Brust ◽  
Dieter Knowle ◽  
Robert M. Blumenthal
Keyword(s):  
Open Reading Frames ◽  
Modification System ◽  
Integrase Gene ◽  
Sequence Characterization ◽  
Restriction Modification System ◽  
Subunit Interface ◽  
Bacteriophage P4 ◽  
Flanking Sequences ◽  
Restriction Modification ◽  
Restriction Modification Systems

ABSTRACT The flow of genes among prokaryotes plays a fundamental role in shaping bacterial evolution, and restriction-modification systems can modulate this flow. However, relatively little is known about the distribution and movement of restriction-modification systems themselves. We have isolated and characterized the genes for restriction-modification systems from two species of Salmonella, S. enterica serovar Paratyphi A and S. enterica serovar Bareilly. Both systems are closely related to the PvuII restriction-modification system and share its target specificity. In the case of S. enterica serovar Paratyphi A, the restriction endonuclease is inactive, apparently due to a mutation in the subunit interface region. Unlike the chromosomally located Salmonella systems, the PvuII system is plasmid borne. We have completed the sequence characterization of the PvuII plasmid pPvu1, originally from Proteus vulgaris, making this the first completely sequenced plasmid from the genus Proteus. Despite the pronounced similarity of the three restriction-modification systems, the flanking sequences in Proteus and Salmonella are completely different. The SptAI and SbaI genes lie between an equivalent pair of bacteriophage P4-related open reading frames, one of which is a putative integrase gene, while the PvuII genes are adjacent to a mob operon and a XerCD recombination (cer) site.

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
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