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Data from the following species were assembled into presumptive orthology groups (hereafter, proteins) and aligned [ 36 ] : Aquifex aeolicus , Bacillus subtilis , Borrelia burgdorferi , Chlamydia trachomatis , Escherichia coli , Haemophilus influenzae , Helicobacter pylori, Mycobacterium tuberculosis, Mycoplasma genitalium, Mycoplasma pneumoniae , Rickettsia prowazekii, Synechocystis sp., and Treponema pallidum (Eubacteria), Archaeoglobus fulgidus, Methanobacterium thermoautotrophicum, Methanococcus jannaschii, Pyrococcus abyssi , and P. horikoshii (Archaebacteria: Euryarchaeota), and Arabidopsis thaliana, Caenorhabditis elegans, Dictyostelium discoideum, Drosophila melanogaster, Gallus gallus, Homo sapiens, Mus musculus, Oryza saticva, Plasmodium falciparum, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Trypanosoma sp. , and Xenopus laevis (Eukaryota).
The other solution involved a new candidate for the role of CysRS, the MJ1477 protein from M. jannaschii.
These analogous steps in different pathways were originally used in formulating the recruitment hypothesis for evolutionary acquisition of new function [ 37], and it is interesting that the citramalate synthase gene shown in M. jannaschii had previously been annotated as α-isopropylmalate synthase (which catalyzes the initial step of leucine biosynthesis).
In a screen for the TS in M. jannaschii, the ORF method picked the MJ0757 protein as the most likely homolog of the canonical TS family [ 27].
In particular, if the identification of the M. jannaschii cysteinyl-tRNA synthetase is indeed correct, this enzyme would have to be a derivative of a specific family of polysaccharide hydrolases containing a signal peptide but no recognizable ATP-binding or RNA-binding domains.
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