Supplementary material for Lange et al., Proc. Natl. Acad. Sci. USA, 10.1073/pnas.240454797
Table 1.
Occurence of putative genes of isopentenyl diphosphate (IPP) biosynthesis in completely sequenced genomes*Organism | DXP pathway | MVA pathway | |||||||||
DXPS† | DXR | MCT | CMK‡ | MECPS | AACT§ | HMGS¶ | HMGR | MK‡ | PMK‡ | MPDC | |
Archaebacteria | |||||||||||
Aeropyrum pernix | – | – | – | – | – | + | + | + | + | – | – |
Archaeoglobus fulgidus | – | – | – | – | – | + | + | + | + | – | – |
Methanobact. thermoautotr. | – | – | – | – | – | + | + | + | + | – | – |
Methanococcus jannashii | – | – | – | – | – | + | + | + | + | – | – |
Pyrococcus abyssi | – | – | – | – | – | + | + | + | + | – | – |
Pyrococcus horikoshii | – | – | + | – | – | + | + | + | + | – | – |
Eubacteria | |||||||||||
Aquifex aeolicus | + | + | + | + | + | – | – | – | – | – | – |
Bacillus subtilis | + | + | + | + | + | + | + | – | – | – | – |
Campylobacter jejuni | + | + | + | + | + | – | – | – | – | – | – |
Chlamydia muridarum | + | + | + | + | + | – | – | – | – | – | – |
Chlamydia trachomatis | + | + | + | + | + | – | – | – | – | – | – |
Chlamydophila pneumoniae | + | + | + | + | + | – | – | – | – | – | – |
Deinicoccus radiodurans | + | + | + | + | + | + | – | – | – | – | – |
Escherichia coli | + | + | + | + | + | + | – | – | – | – | – |
Haemophilus influenzae | + | + | + | + | + | + | – | – | – | – | – |
Helicobacter pylori | + | + | + | + | + | + | – | – | – | – | – |
Mycobacterium leprae | + | + | + | + | + | + | – | – | – | – | – |
Mycobacterium tuberculosis | + | + | + | + | + | + | – | – | – | – | – |
Neisseria meningitidis | + | + | + | + | + | – | – | – | – | – | |
Synechocystis | + | + | + | + | + | – | – | – | – | – | – |
Treponema pallidum | + | + | + | + | + | – | – | – | – | – | – |
Xylella fastidiosa | + | + | + | + | + | + | – | – | – | – | – |
Obligate parasitic eubacteria | |||||||||||
Borrelia burgdorferi | – | – | – | – | – | + | + | + | + | + | + |
Mycoplasma genitalium | – | – | – | – | – | – | – | – | – | – | – |
Rickettsia prowazeckii | – | – | – | – | – | + | – | – | – | – | – |
Yeasts | |||||||||||
Saccharomyces cerevisiae | – | – | – | – | – | + | + | + | + | + | + |
Schizosacch. pombe | – | – | – | – | – | + | + | + | + | + | + |
Metazoa | |||||||||||
Caenorhabditis elegans | – | – | – | – | – | + | + | + | – | – | – |
Drosophila melanogaster | – | – | – | – | – | + | + | + | + | + | + |
Homo sapiens || | – | – | – | – | – | + | + | + | + | + | + |
Plants | |||||||||||
Arabidopsis thaliana || | + | + | + | + | + | + | + | + | + | + | + |
Glycine max || | + | + | + | + | + | + | + | + | + | – | + |
Lycopersicon esculentum || | + | + | + | + | + | + | + | + | – | – | + |
Oryza sativa || | + | + | + | + | + | + | + | + | – | – | + |
Zea mays || | + | + | + | + | + | + | + | + | + | – | – |
*The "+" indicates that a hit was detected using the methods listed in refs. 1 and 2. The "–" indicates that no hit was detected at an E-value of < 10–4 using BLAST 2.0; for details see text.
†
DXPS has homology to other thiamin diphosphate-dependent enzymes such as transketolase and pyruvate:ferredoxin oxidoreductase.‡
MK, PMK, and CMK are members of the GHMP family of metabolite kinases. Their sequence displays significant homology to that of homoserine kinase.§
AACT is part of a larger family of proteins that also encompasses b -ketoacyl-CoA thiolase and metazoan sterol carrier proteins. Some archaebacterial sequences are distant homologues annotated as "hypothetical nonspecific lipid transfer proteins (acetyl-CoA synthetases)," and share roughly 40 % identity to the sterol carrier protein family of metazoa.¶
HMGS is part of a larger family of acetyl-CoA- and malonyl-CoA-condensing enzymes that also encompasses acyl carrier protein synthase and chalcone synthase.||
Genomes not entirely sequenced; partial cDNA clones, if available, were considered.References
1. Altschul, S. F., Gis, W., Miller, W., Myers, E. W. & Lipman, D. J. (1990) J. Mol. Biol. 215, 403–410.
2. Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. (1997) Nucleic Acids Res. 25, 3389–3402.