A versatile palindromic amphipathic repeat coding sequence horizontally distributed among diverse bacterial and eucaryotic microbes.

BMC Genomics
Kerstin RöskeKim S Wise

Abstract

Intragenic tandem repeats occur throughout all domains of life and impart functional and structural variability to diverse translation products. Repeat proteins confer distinctive surface phenotypes to many unicellular organisms, including those with minimal genomes such as the wall-less bacterial monoderms, Mollicutes. One such repeat pattern in this clade is distributed in a manner suggesting its exchange by horizontal gene transfer (HGT). Expanding genome sequence databases reveal the pattern in a widening range of bacteria, and recently among eucaryotic microbes. We examined the genomic flux and consequences of the motif by determining its distribution, predicted structural features and association with membrane-targeted proteins. Using a refined hidden Markov model, we document a 25-residue protein sequence motif tandemly arrayed in variable-number repeats in ORFs lacking assigned functions. It appears sporadically in unicellular microbes from disparate bacterial and eucaryotic clades, representing diverse lifestyles and ecological niches that include host parasitic, marine and extreme environments. Tracts of the repeats predict a malleable configuration of recurring domains, with conserved hydrophobic residues forming an ...Continue Reading

References

Jan 1, 1996·Nucleic Acids Research·B L MaidakC R Woese
Oct 1, 1996·Nature Structural Biology·W C Wimley, S H White
Aug 1, 1997·Cellular and Molecular Life Sciences : CMLS·I CallebautJ P Mornon
Jan 27, 1999·Bioinformatics·S R Eddy
Feb 10, 2000·Molecular Biology and Evolution·W J BrunoA L Halpern
Jul 7, 2000·Clinical and Diagnostic Laboratory Immunology·E M AbdoJ Frey
Oct 13, 2000·Science·H OgataJ M Claverie
Dec 20, 2000·Bioinformatics·K RutherfordB Barrell
Sep 12, 2001·Journal of Structural Biology·M A AndradeC P Ponting
Nov 24, 2001·Mechanisms of Ageing and Development·Trudy F C Mackay
Dec 26, 2001·Nucleic Acids Research·Alex BatemanErik L L Sonnhammer
Apr 25, 2002·Nucleic Acids Research·Eduardo P C Rocha, Alain Blanchard
May 9, 2002·Genome Research·Hiroyuki OgataJean-Michel Claverie
Jun 12, 2002·Journal of Bacteriology·Anja PerssonFrançois Poumarat
Feb 11, 2003·Trends in Biochemical Sciences·Jean-Michel Claverie, Hiroyuki Ogata
Mar 21, 2003·Biophysical Chemistry·Raphael ZidovetzkiIsrael Pecht
Aug 26, 2003·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Peter Tompa
Nov 25, 2003·Analytical Chemistry·Alexey I NesvizhskiiRuedi Aebersold
Dec 9, 2003·Trends in Biochemical Sciences·Luca D D'Andrea, Lynne Regan
Jan 23, 2004·BMC Bioinformatics·Benjamin Schuster-BöcklerSven Rahmann
Feb 21, 2004·Bioinformatics·Robertson Craig, Ronald C Beavis
Mar 23, 2004·Nucleic Acids Research·Robert C Edgar
May 21, 2004·Protein Science : a Publication of the Protein Society·Leila K MosaviZheng-Yu Peng
Jun 23, 2004·Research in Microbiology·Vincent Burrus, Matthew K Waldor
Jul 20, 2004·Proceedings of the National Academy of Sciences of the United States of America·Koichiro TamuraSudhir Kumar
Oct 2, 2004·Science·E Virginia ArmbrustDaniel S Rokhsar
Feb 8, 2005·Genome Biology·Alexis DufresneFrédéric Partensky
Mar 2, 2005·Nature Reviews. Molecular Cell Biology·H Jane Dyson, Peter E Wright
Jun 7, 2005·Trends in Microbiology·Hiroyuki OgataJean-Michel Claverie
Jun 21, 2005·Genome Research·Victor KuninChristos A Ouzounis
Jun 25, 2005·Bioinformatics·Tim J CarverJulian Parkhill
Aug 9, 2005·Nature Genetics·Kevin J VerstrepenGerald R Fink
Sep 21, 2005·Proceedings of the National Academy of Sciences of the United States of America·Hervé TettelinClaire M Fraser
Sep 24, 2005·Proceedings of the National Academy of Sciences of the United States of America·Robert G BeikoMark A Ragan
Oct 1, 2005·BMC Bioinformatics·Thomas J Magliery, Lynne Regan
Oct 8, 2005·Nature Biotechnology·H Kaspar BinzAndreas Plückthun
Nov 16, 2005·Annual Review of Genetics·Eugene V Koonin
Dec 7, 2005·Proceedings of the National Academy of Sciences of the United States of America·E F MongodinF Rodriguez-Valera
Dec 31, 2005·Nucleic Acids Research·Victor M MarkowitzNikos C Kyrpides
May 17, 2006·Trends in Ecology & Evolution·Patrick J KeelingMichael W Gray

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Datasets Mentioned

BETA
EEC50352.1

Methods Mentioned

BETA
ICE
sequence-based predictions

Software Mentioned

TMHMM2
rdp
InterPro
SEQUEST
Biology WorkBench
Tree Builder
MUSCLE
ProteinProphet
Artemis
PARCELs

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