Change search
ReferencesLink to record
Permanent link

Direct link
A bioinformatic analysis of ribonucleotide reductase genes in phage genomes and metagenomes
University of South Florida, USA.
University of South Florida, USA.
KTH Royal Institute of Technology. (Jarone Pinhassi)ORCID iD: 0000-0002-8779-6464
San Diego State University, USA.
Show others and affiliations
2013 (English)In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 13, no 1, 1-17 p., 33Article in journal (Refereed) Published
Abstract [en]

BackgroundRibonucleotide reductase (RNR), the enzyme responsible for the formation of deoxyribonucleotides from ribonucleotides, is found in all domains of life and many viral genomes. RNRs are also amongst the most abundant genes identified in environmental metagenomes. This study focused on understanding the distribution, diversity, and evolution of RNRs in phages (viruses that infect bacteria). Hidden Markov Model profiles were used to analyze the proteins encoded by 685 completely sequenced double-stranded DNA phages and 22 environmental viral metagenomes to identify RNR homologs in cultured phages and uncultured viral communities, respectively.

ResultsRNRs were identified in 128 phage genomes, nearly tripling the number of phages known to encode RNRs. Class I RNR was the most common RNR class observed in phages (70%), followed by class II (29%) and class III (28%). Twenty-eight percent of the phages contained genes belonging to multiple RNR classes. RNR class distribution varied according to phage type, isolation environment, and the host’s ability to utilize oxygen. The majority of the phages containing RNRs are Myoviridae (65%), followed by Siphoviridae (30%) and Podoviridae (3%). The phylogeny and genomic organization of phage and host RNRs reveal several distinct evolutionary scenarios involving horizontal gene transfer, co-evolution, and differential selection pressure. Several putative split RNR genes interrupted by self-splicing introns or inteins were identified, providing further evidence for the role of frequent genetic exchange. Finally, viral metagenomic data indicate that RNRs are prevalent and highly dynamic in uncultured viral communities, necessitating future research to determine the environmental conditions under which RNRs provide a selective advantage.

ConclusionsThis comprehensive study describes the distribution, diversity, and evolution of RNRs in phage genomes and environmental viral metagenomes. The distinct distributions of specific RNR classes amongst phages, combined with the various evolutionary scenarios predicted from RNR phylogenies suggest multiple inheritance sources and different selective forces for RNRs in phages. This study significantly improves our understanding of phage RNRs, providing insight into the diversity and evolution of this important auxiliary metabolic gene as well as the evolution of phages in response to their bacterial hosts and environments.

Place, publisher, year, edition, pages
2013. Vol. 13, no 1, 1-17 p., 33
Keyword [en]
Animal Systematics, Taxonomy, Biogeography, Entomology, Evolution, Evolutionary Biology, Genetics and Population Dynamics, Life Sciences, general, Metagenome, Phage, Phage metadata, Phylogenetics, Ribonucleotide Reductase, Split gene
National Category
Evolutionary Biology
Research subject
Ecology, Evolutionary Biology
URN: urn:nbn:se:lnu:diva-50955DOI: 10.1186/1471-2148-13-33OAI: diva2:912984
Available from: 2016-03-18 Created: 2016-03-17 Last updated: 2016-04-08Bibliographically approved

Open Access in DiVA

fulltext(2656 kB)11 downloads
File information
File name FULLTEXT01.pdfFile size 2656 kBChecksum SHA-512
Type fulltextMimetype application/pdf

Other links

Publisher's full text

Search in DiVA

By author/editor
Lundin, Daniel
In the same journal
BMC Evolutionary Biology
Evolutionary Biology

Search outside of DiVA

GoogleGoogle Scholar
Total: 11 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

Altmetric score

Total: 11 hits
ReferencesLink to record
Permanent link

Direct link