IMP GPI Lipid Anchor Project IMP-Bioinformatics

Occurence of potentially GPI modified proteins in kingdoms of life

Contact:
Birgit Eisenhaber (MDC/IMP)
Peer Bork (MDC/EMBL)
Frank Eisenhaber (IMP)

Proprotein sequences to be posttranslationally GPI-modified are searched for in complete genomes with the recently developed big-PI predictor. The results indicate that GPI-anchoring is present among Eukaryota and possibly among a subgroup of the Archaea but it appears absent in other Archaea and all Eubacteria studied. The chromosomal distribution of GPI-modified proteins is uneven. Dozens of proteins annotated just as hypothetical could be characterized as GPI-anchored.

Previous work:

  1. Sequence analysis of GPI-anchored proteins on the proprotein level
    An analysis of physical properties of amino acid residues at given sequence positions in the vicinity of the GPI-modification site allowed the construction of a model of the active site of the putative transamidase complex (Eisenhaber et al., Prot.Eng., 11, 1155-1161,1998).

  2. The GPI-modification motif and its recognition in proprotein sequences
    For the first time, a new prediction technique locating potential GPI-modification sites in precursor sequences has been applied for large-scale protein sequence database searches.
    (Eisenhaber et al., JMB, 292 (3), 741-758, 1999)

    Data sheets: Prediction of potentially GPI modified proteins in complete genomes/chromosomes
    (Nov 2000)

    Summary Table

    Eukaryota:

  3. Arabidopsis thaliana (Chr02+Chr04)
  4. Caenorhabditis elegans (wormpep 17)
  5. Caenorhabditis elegans (wormpep 31)
  6. Leishmania major (Chr01)
  7. Plasmodium falciparum (Chr02+Chr03)
  8. Saccharomyces cerevisiae (Oct 1999)
  9. Saccharomyces cerevisiae (Nov 2000)

    Archaea:

  10. Aeropyrum pernix K1
  11. Archaeoglobus fulgidus
  12. Halobacterium sp. NRC-1
  13. Methanobacterium thermoautotrophicum
  14. Methanococcus jannaschii
  15. Pyrococcus abyssi
  16. Pyrococcus furiosus
  17. Pyrococcus horikoshii
  18. Thermoplasma acidophilum

    19. Eubacteria:

  19. Aquifex aeolicus
  20. Bacillus halodurans C-125
  21. Bacillus subtilis
  22. Borrelia burgdorferi
  23. Buchnera sp. APS
  24. Campylobacter jejuni
  25. Chlamydia muridarum
  26. Chlamydia pneumoniae
  27. Chlamydia pneumoniae AR39
  28. Chlamydia pneumoniae J138
  29. Chlamydia trachomatis
  30. Chlamydia trachomatis MoPn
  31. Deinococcus radiodurans R1
  32. Escherichia coli
  33. Haemophilus influenzae Rd
  34. Helicobacter pylori
  35. Helicobacter pylori J99
  36. Mycobacterium tuberculosis
  37. Mycoplasma genitalium
  38. Mycoplasma pneumoniae
  39. Neisseria meningitidis serogroup A strain Z2491
  40. Neisseria meningitidis serogroup B strain MC58
  41. Pseudomonas aeruginosa PA01
  42. Rickettsia prowazekii
  43. Synechocystis
  44. Thermotoga maritima
  45. Treponema pallidum
  46. Ureaplasma urealyticum
  47. Vibrio cholerae
  48. Xylella fastidiosa

Acknowledgement:

The protein sequences for the complete genomes/chromosomes were taken from the following web-pages:

A.thaliana:
ftp://ncbi.nlm.nih.gov/genbank/genomes/A_thaliana/
C.elegans:
ftp://ftp.sanger.ac.uk/pub/databases/wormpep/wormpep17
ftp://ftp.sanger.ac.uk/pub/databases/wormpep/wormpep31
L.major:
http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/altik?gi=13580&db=Genome&from=0&to=0
P.falciparum:
Chr.02: ftp://ftp.tigr.org/pub/data/p_falciparum/chr2/complete_sequence/
Chr.03: ftp://ncbi.nlm.nih.gov/genbank/genomes/P_falciparum/
S.cerevisiae:
ftp://ncbi.nlm.nih.gov/genbank/genomes/S_cerevisiae
All complete genomes for Archaea and Eubacteria:
ftp://ncbi.nlm.nih.gov/genbank/genomes/bacteria
with the exception of
Pyrococcus furiosus:
http://www.genome.utah.edu
Campylobacter jejuni:
ftp://ftp.sanger.ac.uk/pub/pathogens/cj
Chlamydia trachomatis MoPn:
ftp://ftp.tigr.org/pub/data/c_trachomatis/
Helicobacter pylori:
ftp://ftp.tigr.org/pub/data/h_pylori

Last modified: 13th June 2002