The Transportome of the Human Mucosal Pathogen Ureaplasma urealyticum
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Date
2007-06
Authors
Sudhakar, Padhmanad
Subramani, Prasanth
Journal Title
Journal ISSN
Volume Title
Publisher
Lethbridge Undergraduate Research Journal
Abstract
Ureaplasma urealyticum has been one of the most prominent mucosal
pathogens having many tropisms in humans. This pathogen is most
notable for its high gene density in its genome i.e. the genes, more than
600, encode almost 95% of the genome, which is suggestive of the fact
that it has dispensed with many regulatory and biosynthetic genes for
many metabolites and nutrients. By evolution, transporters have either
substituted other genes or have duplicated themselves into paralogous members in Ureaplasma. SwissProt analysis and Transporter classification
database were used to identify 67 open reading frames which represented
the transporter dataset proteins from the whole genome. By this method,
we identified a total of 20 transporters for haeme and/or iron (inclusive of
binding and membrane subunits), 7 for inorganic cations (3 for Co2+, and
one each for Mg2+, Cu2+, Ca2+ and K+), 11 for protons/ions, 5 for
oligopeptides, 2 for amino acids, 2 for ammonium generated by urea
hydrolysis, 4 for spermidine-putrescine, 4 for inorganic phosphate, 4 for
sugars, and 2 belonging to the MOP (Multidrug-Oligosaccharidyl-lipid-
Polysaccharide Flippase Superfamily) MATE (Mullti drug and Toxin
Extrusion) class of membrane proteins. In addition, there are 6 other
transporters, among which 5 belong to the ABC transporter family which
translocate unidentified substrates. Two groups of paralogous iron
transporters were identified by phylogenetic analysis using PHYLIP.
Conserved residues and domains in individual transporter families were
obtained by using Pro Dom and Pfam databases. In order to incorporate
the missing transporters of Ureaplasma urealyticum in our work, we have
also included the studies relating to the possibility of finding
transmembrane-signature bearing proteins from among the hypothetical
proteins. With this end in sight, we have utilized 5 different tools (TMHMM,
SOSUI, HMMTOP, TopPred, and waveTM) to estimate the probable
transporter proteins. Each of these tools follows completely different
algorithms. Since these tools are prone to errors mainly as a result of false
predictions of signal peptides as transmembrane segments, we have
utilized an additional tool: SignalP, which provides to exclude the signal
peptide-bearing proteins from the dataset. Transportome based studies of
mucosal pathogens can give rise to many new drug and vaccine targets for
prophylactic and therapeutic interventions.
Description
Keywords
Mucous membrane , Pathogenic microorganism
Citation
Sudhakar, P., Subramani, P. (2007). The Transportome of the Human Mucosal Pathogen Ureaplasma urealyticum. Lethbridge Undergraduate Research Journal, 2(1).