title: The unusually long small subunit ribosomal RNA of Phreatamoeba balamuthi.
abstract: The small subunit ribosomal RNA (rRNA) of the anaerobic amoeba Phreatamoeba balamuthi is the longest 16S-like rRNA sequenced to date. Secondary structure analysis suggests that the additional sequence is incorporated in canonical eukaryotic expansion regions and is not due to the presence of introns. Reverse transcriptase sequencing of total RNA extracts confirmed that two uncommonly long expansion regions are present in native P. balamuthi 16S-like rRNA. Primary sequence comparison and similar secondary structure indicate a 61 base stem and loop repeat within an expansion region; a mechanism whereby the repeat may have been incorporated is presented. P. balamuthi provides further evidence that 16S-like rRNA length does not correlate with phylogenetic position.
authors.affiliation: Center for Molecular Evolution, Marine Biological Laboratory, Woods Hole, MA 02543.
authors.forename: G
authors.initials: G
authors.lastname: Hinkle
authors.forename: D D
authors.initials: DD
authors.lastname: Leipe
authors.forename: T A
authors.initials: TA
authors.lastname: Nerad
authors.forename: M L
authors.initials: ML
authors.lastname: Sogin
mesh_terms: D000656:Amoeba / Q000235:genetics*; D000818:Animals; D001483:Base Sequence; D006860:Hydrogen Bonding; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D012335:RNA, Ribosomal / Q000235:genetics*; D012091:Repetitive Sequences, Nucleic Acid; D012689:Sequence Homology, Nucleic Acid
chemical_list: D012335:RNA, Ribosomal