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The phagosomal nutrient transporter (Pht) family

¹ Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
² Scripps Genome Center, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093-0202, USA
³ Department of Biochemistry, University of California at Berkeley, Berkeley, CA, USA
⁴ Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA

Correspondence
Milton H. Saier, Jr
msaier{at}ucsd.edu

Phagosomal transporters (Phts), required for intracellular growth of Legionella pneumophila, comprise a novel family of multispanning -helical proteins within the major facilitator superfamily (MFS). The members of this family derive exclusively from bacteria. Multiple paralogues are present in a restricted group of Alpha- and Gammaproteobacteria, but single members were also found in Chlamydia and Cyanobacteria. Their protein sequences were aligned, yielding a phylogenetic tree showing the relations of the proteins to each other. Topological analyses revealed a probable 12 -helical transmembrane segment (TMS) topology. Motif identification and statistical analyses provided convincing evidence that these proteins arose from a six TMS precursor by intragenic duplication. The phylogenetic tree revealed some potential orthologous relationships, suggestive of common function. However, several probable examples of lateral transfer of the encoding genetic material between bacteria were identified and analysed. The Pht family most closely resembles a smaller MFS family (the UMF9 family) with no functionally characterized members. However, the UMF9 family occurs in a broader range of prokaryotic organism types, including Archaea. These two families differ in that organisms bearing members of the Pht family often have numerous paralogues, whereas organisms bearing members of the UMF9 family never have more than two. This work serves to characterize two novel families within the MFS and provides compelling evidence for horizontal transfer of some of the family members.

Supplementary figures showing multiple sequence alignments, and hydropathy, amphipathicity and similarity plots for members of the Pht and UMF9 families, supplementary tables listing the proteins of the Pht and UMF9 families, and a series of codon usage tables are available with the online version of this paper.