title: Intragenomic heterogeneity of the 16S rRNA gene in strain UFO1 caused by a 100-bp insertion in helix 6.
abstract: Two different versions of the 16S rRNA gene, one of which contained an unusual 100-bp insertion in helix 6, were detected in isolate UFO1 acquired from the Oak Ridge Integrated Field-Research Challenge (ORIFRC) site in Tennessee. rRNA was extracted from UFO1 and analyzed by reverse transcriptase-quantitative PCR with insert- and non-insert-specific primers; only the noninsert 16S rRNA gene sequence was detected. Similarly, PCR-based screening of a cDNA library (190 clones) constructed from reverse-transcribed rRNA from UFO1 did not detect any clones containing the 100-bp insert. Examination of cDNA with primers specific to the insert-bearing 16S rRNA gene, but downstream of the insert, suggests that the insert was excised from rRNA. Inspection of other 16S rRNA genes in the GenBank database revealed that a homologous insert sequence, also found in helix 6, has been reported in other environmental clones, including those acquired from ORIFRC enrichments. These findings demonstrate the existence of widely divergent copies of the 16S rRNA gene within the same organism, which may confound 16S rRNA gene-based methods of estimating microbial diversity in environmental samples.
authors.affiliation: Department of Biological Sciences, Idaho State University, Pocatello, ID, USA. alikona.ray@gmail.com
authors.forename: Allison E
authors.initials: AE
authors.lastname: Ray
authors.forename: Stephanie A
authors.initials: SA
authors.lastname: Connon
authors.forename: Peter P
authors.initials: PP
authors.lastname: Sheridan
authors.forename: Jeremy
authors.initials: J
authors.lastname: Gilbreath
authors.forename: Malcolm
authors.initials: M
authors.lastname: Shields
authors.forename: Deborah T
authors.initials: DT
authors.lastname: Newby
authors.forename: Yoshiko
authors.initials: Y
authors.lastname: Fujita
authors.forename: Timothy S
authors.initials: TS
authors.lastname: Magnuson
mesh_terms: D001419:Bacteria / Q000235:genetics*; D001483:Base Sequence; D004269:DNA, Bacterial / Q000235:genetics; D015723:Gene Library; D020459:Genes, rRNA; D008969:Molecular Sequence Data; D016254:Mutagenesis, Insertional; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S