title: The tmRNA website: reductive evolution of tmRNA in plastids and other endosymbionts.
abstract: tmRNA combines tRNA- and mRNA-like properties and ameliorates problems arising from stalled ribosomes. Research on the mechanism, structure and biology of tmRNA is served by the tmRNA website (http://www.indiana.edu/~ tmrna), a collection of sequences, alignments, secondary structures and other information. Because many of these sequences are not in GenBank, a BLAST server has been added; another new feature is an abbreviated alignment for the tRNA-like domain only. Many tmRNA sequences from plastids have been added, five found in public sequence data and another 10 generated by direct sequencing; detection in early-branching members of the green plastid lineage brings coverage to all three primary plastid lineages. The new sequences include the shortest known tmRNA sequence. While bacterial tmRNAs usually have a lone pseudoknot upstream of the mRNA segment and a string of three or four pseudoknots downstream, plastid tmRNAs collectively show loss of pseudoknots at both postions. The pseudoknot-string region is also too short to contain the usual pseudoknot number in another new entry, the tmRNA sequence from a bacterial endosymbiont of insect cells, Tremblaya princeps. Pseudoknots may optimize tmRNA function in free-living bacteria, yet become dispensible when the endosymbiotic lifestyle relaxes selective pressure for fast growth.
authors.affiliation: Centro de Biofisica y Bioquimica, Instituto Venezolano de Investigaciones Cientificas, Altos de Pipe, MI, Venezuela.
authors.forename: Pulcherie
authors.initials: P
authors.lastname: Gueneau de Novoa
authors.forename: Kelly P
authors.initials: KP
authors.lastname: Williams
mesh_terms: D001483:Base Sequence; D019295:Computational Biology; D030561:Databases, Nucleic Acid; D019143:Evolution, Molecular; D020407:Internet; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D018087:Plastids / Q000235:genetics*; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics*; D018749:RNA, Plant / Q000737:chemistry / Q000235:genetics*; D013559:Symbiosis / Q000235:genetics*
chemical_list: D012329:RNA, Bacterial; D018749:RNA, Plant; C096222:tmRNA