Genome‐wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms

We have carried out detailed statistical analyses of integral membrane proteins of the helix‐bundle class from eubacterial, archaean, and eukaryotic organisms for which genome‐wide sequence data are available. Twenty to 30% of all ORFs are predicted to encode membrane proteins, with the larger genomes containing a higher fraction than the smaller ones. Although there is a general tendency that proteins with a smaller number of transmembrane segments are more prevalent than those with many, uni‐cellular organisms appear to prefer proteins with 6 and 12 transmembrane segments, whereas Caenorhabditis elegansandHomo sapienshave a slight preference for proteins with seven transmembrane segments. In all organisms, there is a tendency that membrane proteins either have manytransmembrane segments with short connecting loops or few transmembrane segments with large extra‐membraneous domains. Membrane proteins from all organisms studied, except possibly the archaeon Methanococcus jannaschii, follow the so‐called “positive‐inside” rule; i.e., they tend to have a higher frequency of positively charged residues in cytoplasmic than in extra‐cytoplasmic segments.

[1]  T. Steitz,et al.  Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins. , 1986, Annual review of biophysics and biophysical chemistry.

[2]  G. Heijne.  The distribution of positively charged residues in bacterial inner membrane proteins correlates with the trans‐membrane topology , 1986, The EMBO journal.

[3]  K. Ito,et al.  Topology analysis of the SecY protein, an integral membrane protein involved in protein export in Escherichia coli. , 1987, The EMBO journal.

[4]  G. von Heijne,et al.  Topogenic signals in integral membrane proteins. , 1988, European journal of biochemistry.

[5]  T A Rapoport,et al.  Predicting the orientation of eukaryotic membrane-spanning proteins. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[6]  Gunnar von Heijne,et al.  Fine-tuning the topology of a polytopic membrane protein: Role of positively and negatively charged amino acids , 1990, Cell.

[7]  G von Heijne,et al.  The ‘positive‐inside rule’ applies to thylakoid membrane proteins , 1991, FEBS letters.

[8]  G. Heijne.  Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule. , 1992, Journal of molecular biology.

[9]  U. Hobohm,et al.  Selection of representative protein data sets , 1992, Protein science : a publication of the Protein Society.

[10]  G von Heijne,et al.  The distribution of charged amino acids in mitochondrial inner-membrane proteins suggests different modes of membrane integration for nuclearly and mitochondrially encoded proteins. , 1992, European journal of biochemistry.

[11]  G. von Heijne,et al.  Predicting the topology of eukaryotic membrane proteins. , 1993, European journal of biochemistry.

[12]  Manuel G. Claros,et al.  TopPred II: an improved software for membrane protein structure predictions , 1994, Comput. Appl. Biosci..

[13]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[14]  W R Taylor,et al.  A model recognition approach to the prediction of all-helical membrane protein structure and topology. , 1994, Biochemistry.

[15]  J. Rosenbusch,et al.  Folding pattern diversity of integral membrane proteins. , 1994, Science.

[16]  Hartmut Michel,et al.  Structure at 2.8 Å resolution of cytochrome c oxidase from Paracoccus denitrificans , 1995, Nature.

[17]  G. von Heijne,et al.  Properties of N-terminal tails in G-protein coupled receptors: a statistical study. , 1995, Protein engineering.

[18]  R. Fleischmann,et al.  The Minimal Gene Complement of Mycoplasma genitalium , 1995, Science.

[19]  T A Rapoport,et al.  Transport route for synaptobrevin via a novel pathway of insertion into the endoplasmic reticulum membrane. , 1995, The EMBO journal.

[20]  R. Fleischmann,et al.  Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. , 1995, Science.

[21]  M. Spiess,et al.  Transmembrane orientation of signal‐anchor proteins is affected by the folding state but not the size of the N‐terminal domain. , 1995, The EMBO journal.

[22]  M. Spiess,et al.  Heads or tails — what determines the orientation of proteins in the membrane , 1995, FEBS letters.

[23]  T A Rapoport,et al.  Protein transport across the eukaryotic endoplasmic reticulum and bacterial inner membranes. , 1996, Annual review of biochemistry.

[24]  T. Tomizaki,et al.  The Whole Structure of the 13-Subunit Oxidized Cytochrome c Oxidase at 2.8 Å , 1996, Science.

[25]  Patrick Argos,et al.  Topology prediction of membrane proteins , 1996, Protein science : a publication of the Protein Society.

[26]  B. Rost,et al.  Topology prediction for helical transmembrane proteins at 86% accuracy–Topology prediction at 86% accuracy , 1996, Protein science : a publication of the Protein Society.

[27]  Y. Nakamura,et al.  Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions (supplement). , 1996, DNA research : an international journal for rapid publication of reports on genes and genomes.

[28]  H. Hilbert,et al.  Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae. , 1996, Nucleic acids research.

[29]  B. Wilkinson,et al.  Determination of the Transmembrane Topology of Yeast Sec61p, an Essential Component of the Endoplasmic Reticulum Translocation Complex* , 1996, The Journal of Biological Chemistry.

[30]  Gunnar von Heijne,et al.  Principles of membrane protein assembly and structure. , 1996 .

[31]  André Goffeau,et al.  The yeast genome directory. , 1997, Nature.

[32]  S. Brunak,et al.  SHORT COMMUNICATION Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites , 1997 .

[33]  N. W. Davis,et al.  The complete genome sequence of Escherichia coli K-12. , 1997, Science.

[34]  Martin Spiess,et al.  Multiple Determinants Direct the Orientation of Signal–Anchor Proteins: The Topogenic Role of the Hydrophobic Signal Domain , 1997, The Journal of cell biology.

[35]  M Gerstein,et al.  A structural census of genomes: comparing bacterial, eukaryotic, and archaeal genomes in terms of protein structure. , 1997, Journal of molecular biology.

[36]  J Frank,et al.  Alignment of conduits for the nascent polypeptide chain in the ribosome-Sec61 complex. , 1997, Science.

[37]  A T Brünger,et al.  Are there dominant membrane protein families with a given number of helices? , 1997, Proteins.

[38]  Patrick Argos,et al.  Prediction of Membrane Protein Topology Utilizing Multiple Sequence Alignments , 1997, Journal of protein chemistry.

[39]  A Elofsson,et al.  Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: the dense alignment surface method. , 1997, Protein engineering.

[40]  G. von Heijne,et al.  The E. coli SRP: preferences of a targeting factor , 1997, FEBS letters.

[41]  A. Goffeau,et al.  The complete genome sequence of the Gram-positive bacterium Bacillus subtilis , 1997, Nature.

[42]  A. Kuhn,et al.  Negatively charged amino acid residues play an active role in orienting the Sec‐independent Pf3 coat protein in the Escherichia coli inner membrane , 1997, The EMBO journal.

[43]  R. Fleischmann,et al.  The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus , 1997, Nature.

[44]  G von Heijne,et al.  Topological Rules for Membrane Protein Assembly in Eukaryotic Cells* , 1997, The Journal of Biological Chemistry.

[45]  Mark Borodovsky,et al.  The complete genome sequence of the gastric pathogen Helicobacter pylori , 1997, Nature.