Comprehensive phylogenetic analysis of bacterial group II intron-encoded ORFs lacking the DNA endonuclease domain reveals new varieties

Group II introns are self-splicing RNAs that act as mobile retroelements in the organelles of plants, fungi and protists. They are also widely distributed in bacteria, and are generally assumed to be the ancestors of nuclear spliceosomal introns. Most bacterial group II introns have a multifunctiona...

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Bibliographic Details
Published in:PloS one 2013-01, Vol.8 (1), p.e55102-e55102
Main Authors: Toro, Nicolás, Martínez-Abarca, Francisco
Format: Article
Language:English
Subjects:
Amino acids
Analysis
Bacteria
Bacteria - enzymology
Bacteria - genetics
Binding
Biology
Catalytic RNA
Chloroplasts
Cladistic analysis
Coding
D region
Deoxyribonuclease I - genetics
Deoxyribonucleic acid
DNA
DNA polymerases
Endonuclease
Fungi
Introns
Introns - genetics
New varieties
Open reading frames
Open Reading Frames - genetics
Organelles
Phylogenetics
Phylogeny
Protein Structure, Tertiary
Proteins
Ribonucleic acid
RNA
RNA-directed DNA polymerase
Sequence Analysis, DNA - methods
Splicing
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Summary:Group II introns are self-splicing RNAs that act as mobile retroelements in the organelles of plants, fungi and protists. They are also widely distributed in bacteria, and are generally assumed to be the ancestors of nuclear spliceosomal introns. Most bacterial group II introns have a multifunctional intron-encoded protein (IEP) ORF within the ribozyme domain IV (DIV). This ORF encodes an N-terminal reverse transcriptase (RT) domain, followed by a putative RNA-binding domain with RNA splicing or maturase activity and, in some cases, a C-terminal DNA-binding (D) region followed by a DNA endonuclease (En) domain. In this study, we focused on bacterial group II intron ORF phylogenetic classes containing only reverse transcriptase/maturase open reading frames, with no recognizable D/En region (classes A, C, D, E, F and unclassified introns). On the basis of phylogenetic analyses of the maturase domain and its C-terminal extension, which appears to be a signature characteristic of ORF phylogenetic class, with support from the phylogeny inferred from the RT domain, we have revised the proposed new class F, defining new intron ORF varieties. Our results increase knowledge of the lineage of group II introns encoding proteins lacking the En-domain.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0055102