TMC and EVER genes belong to a larger novel family, the TMC gene family encoding transmembrane proteins

Abstract

Background: Mutations in the transmembrane cochlear expressed gene 1 (TMC1) cause deafness in human and mouse. Mutations in two homologous genes, EVER1 and EVER2 increase the susceptibility to infection with certain human papillomaviruses resulting in high risk of skin carcinoma. Here we report that TMC1, EVER1 and EVER2 (now TMC6 and TMC8) belong to a larger novel gene family, which is named TMC for trans membrane channel-like gene family.

Results: Using a combination of iterative database searches and reverse transcriptase-polymerase chain reaction (RT-PCR) experiments we assembled contigs for cDNA encoding human, murine, puffer fish, and invertebrate TMC proteins. TMC proteins of individual species can be grouped into three subfamilies A, B, and C. Vertebrates have eight TMC genes. The majority of murine TMC transcripts are expressed in most organs; some transcripts, however, in particular the three subfamily A members are rare and more restrictively expressed.

Conclusion: The eight vertebrate TMC genes are evolutionary conserved and encode proteins that form three subfamilies. Invertebrate TMC proteins can also be categorized into these three subfamilies. All TMC genes encode transmembrane proteins with intracellular amino- and carboxyl-termini and at least eight membrane-spanning domains. We speculate that the TMC proteins constitute a novel group of ion channels, transporters, or modifiers of such.

Figure 1

The murine TMC protein family Murine (Mm) TMC amino acid sequences were aligned using the MultAlin sequence comparison algorithm. Positions that are conserved (identical or similar) in all three subfamilies are marked orange (present in at least 4 of the 8 sequences) and red (conserved in at least 6 of the 8 sequences). Conserved positions within individual TMC protein subfamilies are depicted in blue. Amino acids that were considered similar based on the physicochemical features of their side chains: L, I, V and M; F and Y; E, D, N and Q; T and S; K and R. The TMC motif is denoted with a green bar. Presumptive transmembrane regions are underlined. Indicated with bold letters is experimentally verified TMC sequence.

Figure 2

Proposed structure of TMC proteins Schematic illustration of the presumptive TMC protein topology. Each circle represents an amino acid. Amino acid positions conserved in at least 50% and 75% of murine TMC proteins are shaded orange and red, respectively. Black lines represent regions of variable length within the TMC family. The position of the TMC signature sequence motif is indicated.

Figure 3

Comparison of murine and pufferfish TMC gene structures Comparison of murine (Mm)(A) and pufferfish (Fr)(B) TMC gene structures. To compare and visualize the gene structures of TMC genes, the predicted coding sequences (depicted here with white boxes) were aligned. Gaps were introduced when required for appropriate comparison (illustrated as black boxes). Triangles mark positions where the coding sequence is interrupted by introns in the genome (intron locations). The triangles are colour-coded to reflect the degree of conservation of the intron locations among TMC subfamilies A, B, and C. Positions of introns conserved in all members of the TMC family are denoted by black triangles; blue, red and yellow triangles label positions of introns conserved within individual TMC subfamilies; orange, magenta and green triangles denote intron positions shared by members of two subfamilies; intron positions unique to a single family member are indicated by open black triangles. (C) Phylogenetic tree drawn based on the similarity of the gene structures of murine TMC genes restricted to the conserved region of the TMC proteins. The corresponding matrix of distances is shown in additional file 1.

Figure 4

Evolutionary relationship of vertebrate and invertebrate TMC proteins Phylogenetic tree, based on comparison of TMC protein sequences, illustrating the evolutionary relationship of TMC proteins of Homo sapiens (Hs), Mus musculus (Mm), Fugu rubripes (Fr), Drosophila melanogaster (Dm), Anopheles gambiae (Ag), and Caenorhabditis elegans (Ce).

Figure 5

TMC expression analysis RT-PCR analysis of expression of TMC family members in mouse organs as judged by 32 and 42 cycles of amplification. Expression analysis of the ubiquitously expressed glyceraldehyde 3-phosphate dehydrogenase (GAPDH) is shown for reference. Dots indicate that one or two (small dot) or three and more (large dots) ESTs representing the respective organ are present in public databases.