Promiscuous methylation of non-canonical DNA sites by HaeIII methyltransferase

Cohen, Helen M.; Tawfik, Dan S.; Griffiths, Andrew D.

doi:10.1093/nar/gkf507

Cited by 36 publications

(38 citation statements)

References 24 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Based on these results, we concluded that the sequence specificity of Orf27 was GANTC and that this MTase did not show visible substrate promiscuity, which has been previously demonstrated for some other DNA MTases (45)(46)(47)(48).…”

Section: Resultssupporting

confidence: 69%

Molecular Characterization of a Novel Temperate Sinorhizobium Bacteriophage, ФLM21, Encoding DNA Methyltransferase with CcrM-Like Specificity

Dziewit

Oscik

Bartosik

et al. 2014

J Virol

View full text Add to dashboard Cite

ABSTRACT⌽LM21 is a temperate phage isolated from Sinorhizobium sp. strain LM21 (Alphaproteobacteria). Genomic analysis and electron microscopy suggested that ⌽LM21 is a member of the family Siphoviridae. The phage has an isometric head and a long noncontractile tail. The genome of ⌽LM21 has 50,827 bp of linear double-stranded DNA encoding 72 putative proteins, including proteins responsible for the assembly of the phage particles, DNA packaging, transcription, replication, and lysis. Virion proteins were characterized using mass spectrometry, leading to the identification of the major capsid and tail components, tape measure, and a putative portal protein. We have confirmed the activity of two gene products, a lytic enzyme (a putative chitinase) and a DNA methyltransferase, sharing sequence specificity with the cell cycle-regulating methyltransferase (CcrM) of the bacterial host. Interestingly, the genome of Sinorhizobium phage ⌽LM21 shows very limited similarity to other known phage genome sequences and is thus considered unique. IMPORTANCEProphages are known to play an important role in the genomic diversification of bacteria via horizontal gene transfer. The influence of prophages on pathogenic bacteria is very well documented. However, our knowledge of the overall impact of prophages on the survival of their lysogenic, nonpathogenic bacterial hosts is still limited. In particular, information on prophages of the agronomically important Sinorhizobium species is scarce. In this study, we describe the isolation and molecular characterization of a novel temperate bacteriophage, ⌽LM21, of Sinorhizobium sp. LM21. Since we have not found any similar sequences, we propose that this bacteriophage is a novel species. We conducted a functional analysis of selected proteins. We have demonstrated that the phage DNA methyltransferase has the same sequence specificity as the cell cycle-regulating methyltransferase CcrM of its host. We point out that this phenomenon of mimicking the host regulatory mechanisms by viruses is quite common in bacteriophages.

show abstract

Section: Resultssupporting

confidence: 69%

Molecular Characterization of a Novel Temperate Sinorhizobium Bacteriophage, ФLM21, Encoding DNA Methyltransferase with CcrM-Like Specificity

Dziewit

Oscik

Bartosik

et al. 2014

J Virol

View full text Add to dashboard Cite

show abstract

“…This concept is known as enzyme promiscuity and has been demonstrated in other methyltransferases (28,29). To test our hypothesis, we performed protein structure and function prediction using the I-TASSER server (30), comparing our sponge proteins against a typical SMT from the yeast Saccharomyces cerevisiae (ERG6) and a promiscuous SMT2 from the plant A. thaliana.…”

Section: Resultsmentioning

confidence: 99%

“…To test our hypothesis, we performed protein structure and function prediction using the I-TASSER server (30), comparing our sponge proteins against a typical SMT from the yeast Saccharomyces cerevisiae (ERG6) and a promiscuous SMT2 from the plant A. thaliana. ERG6 strictly performs a single C-24 methylation in yeast, producing the C 28 ergosterol, but if ERG6 is transgenically replaced with SMT2, C-24 methyl and ethyl sterols are produced, meaning SMT2 is sufficient to perform both alkylation steps (31). Although there is no crystal structure of SMT to compare our models against, I-TASSER correctly predicts the presence of seven central parallel β-sheets surrounded by 10 α-helices (32) as well as ligand binding sites for S-adenosyl-modified amino acids and active enzyme sites for methyltransferase activity (Fig.…”

Section: Resultsmentioning

confidence: 99%

Sterol and genomic analyses validate the sponge biomarker hypothesis

Gold

Grabenstatter

Mendoza

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

119

121

View full text Add to dashboard Cite

Molecular fossils (or biomarkers) are key to unraveling the deep history of eukaryotes, especially in the absence of traditional fossils. In this regard, the sterane 24-isopropylcholestane has been proposed as a molecular fossil for sponges, and could represent the oldest evidence for animal life. The sterane is found in rocks ∼650-540 million y old, and its sterol precursor (24-isopropylcholesterol, or 24-ipc) is synthesized today by certain sea sponges. However, 24-ipc is also produced in trace amounts by distantly related pelagophyte algae, whereas only a few close relatives of sponges have been assayed for sterols. In this study, we analyzed the sterol and gene repertoires of four taxa (Salpingoeca rosetta, Capsaspora owczarzaki, Sphaeroforma arctica, and Creolimax fragrantissima), which collectively represent the major living animal outgroups. We discovered that all four taxa lack C 30 sterols, including 24-ipc. By building phylogenetic trees for key enzymes in 24-ipc biosynthesis, we identified a candidate gene (carbon-24/28 sterol methyltransferase, or SMT) responsible for 24-ipc production. Our results suggest that pelagophytes and sponges independently evolved C 30 sterol biosynthesis through clade-specific SMT duplications. Using a molecular clock approach, we demonstrate that the relevant sponge SMT duplication event overlapped with the appearance of 24-isopropylcholestanes in the Neoproterozoic, but that the algal SMT duplication event occurred later in the Phanerozoic. Subsequently, pelagophyte algae and their relatives are an unlikely alternative to sponges as a source of Neoproterozoic 24-isopropylcholestanes, consistent with growing evidence that sponges evolved long before the Cambrian explosion ∼542 million y ago.sponges | Porifera | sterols | steranes | Amorphea

show abstract

“…In contrast, a specific MTase could evolve to possess broad specificity without altering the modification of the cognate recognition site. Indeed, it was observed that many MTase clones exhibit promiscuous activity, viz., M.HaeIII, M.EcoRI, M.EcoRV, and M.FokI (160,(215)(216)(217).…”

Section: Future Perspectivesmentioning

confidence: 99%

Diverse Functions of Restriction-Modification Systems in Addition to Cellular Defense

Vasu

Nagaraja

2013

Microbiol Mol Biol Rev

522

462

View full text Add to dashboard Cite

SUMMARY Restriction-modification (R-M) systems are ubiquitous and are often considered primitive immune systems in bacteria. Their diversity and prevalence across the prokaryotic kingdom are an indication of their success as a defense mechanism against invading genomes. However, their cellular defense function does not adequately explain the basis for their immaculate specificity in sequence recognition and nonuniform distribution, ranging from none to too many, in diverse species. The present review deals with new developments which provide insights into the roles of these enzymes in other aspects of cellular function. In this review, emphasis is placed on novel hypotheses and various findings that have not yet been dealt with in a critical review. Emerging studies indicate their role in various cellular processes other than host defense, virulence, and even controlling the rate of evolution of the organism. We also discuss how R-M systems could have successfully evolved and be involved in additional cellular portfolios, thereby increasing the relative fitness of their hosts in the population.

show abstract

Promiscuous methylation of non-canonical DNA sites by HaeIII methyltransferase

Cited by 36 publications

References 24 publications

Molecular Characterization of a Novel Temperate Sinorhizobium Bacteriophage, ФLM21, Encoding DNA Methyltransferase with CcrM-Like Specificity

Molecular Characterization of a Novel Temperate Sinorhizobium Bacteriophage, ФLM21, Encoding DNA Methyltransferase with CcrM-Like Specificity

Sterol and genomic analyses validate the sponge biomarker hypothesis

Diverse Functions of Restriction-Modification Systems in Addition to Cellular Defense

Contact Info

Product

Resources

About