A family of gram-negative bacterial outer membrane factors that function in the export of proteins, carbohydrates, drugs and heavy metals from gram-negative bacteria.

Gram-negative bacteria have evolved transport complexes that export macromolecules and toxic substances across the two membranes of the cell envelope in a single energy coupled step. The process requires (1) a cytoplasmic membrane export system, (2) a membrane fusion protein (MFP), and (3) an outer membrane factor (OMF). Families comprising the former two constituents have been described previously. We here present an analysis of the phylogenetic and structural characteristics of the OMF family. Twenty-one members of this family have been identified, and based on available evidence, they function in conjunction with ABC, RND, MFS and/or other types of cytoplasmic transport systems. OMFs exhibit fairly uniform sizes (398-495 residues with two exceptions), and based on computational analyses, they may form beta-barrel structures consisting of up to 16 beta-strands. Phylogenetic analyses reveal that while the MFPs cluster in accordance with the type of cytoplasmic membrane transport systems with which they function, OMFs do not. We conclude that OMFs probably comprise a family of outer membrane porin-type proteins of uniform structure which did not coevolve with their cognate cytoplasmic membrane transport systems.

[1]  I. Paulsen,et al.  Proton-dependent multidrug efflux systems , 1996, Microbiological reviews.

[2]  S. Létoffé,et al.  Protein secretion in gram‐negative bacteria: assembly of the three components of ABC protein‐mediated exporters is ordered and promoted by substrate binding. , 1996, The EMBO journal.

[3]  H. Nikaido.  Multidrug efflux pumps of gram-negative bacteria , 1996, Journal of bacteriology.

[4]  M. Montagu,et al.  Role of nodl and nodj in lipo‐chitooligosaccharide secretion in Azorhizobium caulinodans and Escherichia coli , 1996, Molecular microbiology.

[5]  M. Saier.  Phylogenetic approaches to the identification and characterization of protein families and superfamilies. , 1996, Microbial & comparative genomics.

[6]  M. Saier,et al.  Phylogenetic, structural and functional analyses of the LacI‐GalR family of bacterial transcription factors , 1995, FEBS letters.

[7]  M. Mergeay,et al.  Czc/Cnr efflux: a three‐component chemiosmotlc antiport pathway with a 12‐transmembrane‐helix protein , 1994, Molecular microbiology.

[8]  M H Saier,et al.  A family of extracytoplasmic proteins that allow transport of large molecules across the outer membranes of gram-negative bacteria , 1994, Journal of bacteriology.

[9]  H. Nikaido,et al.  Prevention of drug access to bacterial targets: permeability barriers and active efflux. , 1994, Science.

[10]  M. Saier,et al.  Two novel families of bacterial membrane proteins concerned with nodulation, cell division and transport , 1994, Molecular microbiology.

[11]  K. Lewis,et al.  Multidrug resistance pumps in bacteria: variations on a theme. , 1994, Trends in biochemical sciences.

[12]  M. Saier,et al.  Computer-aided analyses of transport protein sequences: gleaning evidence concerning function, structure, biogenesis, and evolution , 1994, Microbiological reviews.

[13]  G. Schulz,et al.  Structure of the membrane channel porin from Rhodopseudomonas blastica at 2.0 Å resolution , 1994, Protein science : a publication of the Protein Society.

[14]  R. Kolter,et al.  ABC transporters: bacterial exporters , 1993, Microbiological reviews.

[15]  K. Poole,et al.  Multiple antibiotic resistance in Pseudomonas aeruginosa: evidence for involvement of an efflux operon , 1993, Journal of bacteriology.

[16]  G. Schulz.  Bacterial porins: structure and function. , 1993, Current opinion in cell biology.

[17]  G. Rummel,et al.  Crystal structures explain functional properties of two E. coli porins , 1992, Nature.

[18]  A. Bairoch.  PROSITE: a dictionary of sites and patterns in proteins. , 1991, Nucleic acids research.

[19]  G. Schulz,et al.  The structure of porin from Rhodobacter capsulatus at 1.8 Å resolution , 1991, FEBS letters.

[20]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[21]  P. Delepelaire,et al.  TolC, an Escherichia coli outer membrane protein required for hemolysin secretion. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[22]  R F Doolittle,et al.  Progressive alignment and phylogenetic tree construction of protein sequences. , 1990, Methods in enzymology.

[23]  D. Lipman,et al.  Improved tools for biological sequence comparison. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[24]  W. C. Barker.  Of URFs and ORFs: A primer on how to analyze derived amino acid sequences: Russell F. Doolittle, University Science Books, Mill Valley, CA. Paperback. Under $15 , 1987 .

[25]  R. Doolittle.  Of urfs and orfs : a primer on how to analyze devised amino acid sequences , 1986 .

[26]  J. Devereux,et al.  A comprehensive set of sequence analysis programs for the VAX , 1984, Nucleic Acids Res..

[27]  R. Doolittle,et al.  A simple method for displaying the hydropathic character of a protein. , 1982, Journal of molecular biology.

[28]  J. Garnier,et al.  Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. , 1978, Journal of molecular biology.

[29]  P. Y. Chou,et al.  Empirical predictions of protein conformation. , 1978, Annual review of biochemistry.