Phylogenetic characterization of novel transport protein families revealed by genome analyses

Milton H. Saier*, Brian H. Eng, Sharouz Fard, Joy Garg, David A. Haggerty, William J. Hutchinson, Donald L. Jack, Eric C. Lai, Howard J. Liu, David P. Nusinew, Asad M. Omar, Stephanie S. Pao, Ian T. Paulsen, John A. Quan, Marek Sliwinski, Tsai Tien Tseng, Shinichiro Wachi, Gregory B. Young

*Corresponding author for this work

Research output: Contribution to journalReview article

183 Citations (Scopus)

Abstract

As a result of recent genome sequencing projects as well as detailed biochemical, molecular genetic and physiological experimentation on representative transport proteins, we have come to realize that all organisms possess an extensive but limited array of transport protein types that allow the uptake of nutrients and excretion of toxic substances. These proteins fall into phylogenetic families that presumably reflect their evolutionary histories. Some of these families are restricted to a single phylogenetic group of organisms and may have arisen recently in evolutionary time while others are found ubiquitously and may be ancient. In this study we conduct systematic phylogenetic analyses of 26 families of transport systems that either had not been characterized previously or were in need of updating. Among the families analyzed are some that are bacterial-specific, others that are eukaryotic-specific, and others that are ubiquitous. They can function by either a channel-type or a carrier-type mechanism, and in the latter case, they are frequently energized by coupling solute transport to the flux of an ion down its electrochemical gradient. We tabulate the currently sequenced members of the 26 families analyzed, describe the properties of these families, and present partial multiple alignments, signature sequences and phylogenetic trees for them all. Copyright (C) 1999 Elsevier Science B.V.

Original languageEnglish
Pages (from-to)1-56
Number of pages56
JournalBiochimica et Biophysica Acta - Reviews on Biomembranes
Volume1422
Issue number1
DOIs
Publication statusPublished - 25 Feb 1999
Externally publishedYes

Keywords

  • Evolution
  • Membrane
  • Multiple alignment
  • Permease
  • Phylogenetic tree
  • Protein sequence
  • Signature sequence
  • Transport

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