1. An rpoB signature sequence provides unique resolution for the molecular typing of cyanobacteria
- Author
-
Simonetta Gribaldo, Virginie Gaget, Nicole Tandeau de Marsac, Collection des Cyanobactéries, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris], We wish to thank the CAE (Centre d'Analyses Environnementales) of Veolia Environment, the Institut Pasteur and CNRS URA-2172 for funding this work. We are grateful to the CAE of Veolia Environment for providing a thesis fellowship to V. G., and to K. Delabre and F. Enguehard for constant support during this study. We express our gratitude to T. Rose for his advice on three-dimensional predictions and thank J. P. Rasmussen for helpful comments and his revision of the English during the preparation of this paper., Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and Institut Pasteur [Paris] (IP)
- Subjects
DNA, Bacterial ,NJ ,[SDV]Life Sciences [q-bio] ,Biology ,Cyanobacteria ,Microbiology ,MESH: Bacterial Typing Techniques ,MESH: INDEL Mutation ,03 medical and health sciences ,chemistry.chemical_compound ,Bacterial Proteins ,INDEL Mutation ,maximum-parsimony ,RNA polymerase ,Indel ,Gene ,MESH: Bacterial Proteins ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,Genetics ,0303 health sciences ,MESH: Molecular Typing ,030306 microbiology ,MP ,DNA-Directed RNA Polymerases ,General Medicine ,MESH: Cyanobacteria ,rpoB ,16S ribosomal RNA ,ML ,neighbour-joining ,MESH: DNA, Bacterial ,Bacterial Typing Techniques ,MESH: DNA-Directed RNA Polymerases ,Molecular Typing ,[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology ,chemistry ,Evolutionary biology ,Metagenomics ,maximum-likelihood ,Subgenus ,DNA - Abstract
The use of morphological characters for the classification of cyanobacteria has often led to ambiguous strain assignment. In the past two decades, the availability of sequences, such as those of the 16S rRNA,nif,cpcandrpoC1genes, and the use of metagenomics, has steadily increased and has made the reconstruction of evolutionary relationships of some cyanobacterial groups possible in addition to improving strain assignment. Conserved indels (insertions/deletions) are present in all cyanobacterial RpoB (βsubunit of RNA polymerase) sequences presently available in public databases. These indels are located in the Rpb2_6 domain of RpoB, which is involved in DNA binding and DNA-directed RNA polymerase activity. They are variable in length (6–44 aa) and sequence, and form part of what appears to be a longer signature sequence (43–81 aa). Indeed, a number of these sequences turn out to be distinctive among several strains of a given genus and even among strains of a given species. These signature sequences can thus be used to identify cyanobacteria at a subgenus level and can be useful molecular markers to establish the taxonomic positions of cyanobacterial isolates in laboratory cultures, and/or to assess cyanobacterial biodiversity in space and time in natural ecosystems.
- Published
- 2011