The tmRNA website: reductive evolution of tmRNA in plastids and other endosymbionts

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D104-8. doi: 10.1093/nar/gkh102.

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.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Base Sequence
  • Computational Biology
  • Databases, Nucleic Acid*
  • Evolution, Molecular*
  • Internet*
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Plastids / genetics*
  • RNA, Bacterial / chemistry
  • RNA, Bacterial / genetics*
  • RNA, Plant / chemistry
  • RNA, Plant / genetics*
  • Symbiosis / genetics*

Substances

  • RNA, Bacterial
  • RNA, Plant
  • tmRNA

Associated data

  • GENBANK/AF169625
  • GENBANK/AF169626
  • GENBANK/AF550350
  • GENBANK/AF550351
  • GENBANK/AF550352
  • GENBANK/AF550353
  • GENBANK/AF550354
  • GENBANK/AF550355
  • GENBANK/AF550356
  • GENBANK/AF550357
  • GENBANK/AY313266
  • GENBANK/AY313267
  • GENBANK/AY313268
  • GENBANK/AY313269
  • GENBANK/AY313270