[Identification of new conserved and variable regions in the 16S rRNA gene of acetic acid bacteria and acetobacteraceae family].
The Acetobacteraceae family of the class Alpha Proteobacteria is comprised of high sugar and acid tolerant bacteria. The Acetic Acid Bacteria are the economically most significant group of this family because of its association with food products like vinegar, wine etc. Acetobacteraceae are often hard to culture in laboratory conditions and they also maintain very low abundances in their natural habitats. Thus identification of the organisms in such environments is greatly dependent on modern tools of molecular biology which require a thorough knowledge of specific conserved gene sequences that may act as primers and or probes. Moreover unconserved domains in genes also become markers for differentiating closely related genera. In bacteria, the 16S rRNA gene is an ideal candidate for such conserved and variable domains. In order to study the conserved and variable domains of the 16S rRNA gene of Acetic Acid Bacteria and the Acetobacteraceae family, sequences from publicly available databases were aligned and compared. Near complete sequences of the gene were also obtained from Kombucha tea biofilm, a known Acetobacteraceae family habitat, in order to corroborate the domains obtained from the alignment studies. The study indicated that the degree of conservation in the gene is significantly higher among the Acetic Acid Bacteria than the whole Acetobacteraceae family. Moreover it was also observed that the previously described hypervariable regions V1, V3, V5, V6 and V7 were more or less conserved in the family and the spans of the variable regions are quite distinct as well.
Department of Life Science and Biotechnology, Jadavpur University, Kolkata-700032, West Bengal, India.
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Chakravorty
Department of Life Science and Biotechnology, Jadavpur University, Kolkata-700032, West Bengal, India.
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Sarkar
Department of Life Science and Biotechnology, Jadavpur University, Kolkata-700032, West Bengal, India.|ratangachhui@yahoo.com.
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R
Gachhui
D019342:Acetic Acid / Q000378:metabolism; D016947:Acetobacteraceae / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D001483:Base Sequence; D002874:Chromosome Mapping; D017124:Conserved Sequence; D005798:Genes, Bacterial; D014644:Genetic Variation; D008969:Molecular Sequence Data; D010802:Phylogeny; D012329:RNA, Bacterial / Q000235:genetics*; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D016415:Sequence Alignment
D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S; D019342:Acetic Acid
16S rRNA; Acetic Acid Bacteria; Acetobacteraceae; Vienna RNA package; conserved domain prediction; hypervariable region