The fukutin protein family – predicted enzymes modifying cell-surface molecules

Fukuyama type congenital muscular dystrophy (FCMD) is an autosomal recessive disorder that is observed predominantly in Japanese populations [1]. Recently, the cause of this syndrome was discovered to be lesions in the gene encoding the protein fukutin; these lesions involve retroposon insertion and point mutations, which result in a truncated protein [2]. Consistent with the phenotypic patterns of the disease, the fukutin mRNA has been found in skeletal muscles, heart, brain and pancreas [2]. Fukutin contains a signal peptide and is localized to the Golgi and secretory granules [2]. Here, we report on a detailed computer analysis of the fukutin protein sequence, resulting in the prediction that it is an enzyme that modifies cell-surface glycoproteins or glycolipids. A gapped BLASTP [3] search of the non-redundant (NR) database at the National Center for Biotechnology Information using the fukutin sequence as the query revealed significant hits (with evalues < 10–9) not only to Caenorhabditis elegans proteins, such as T07D3.4 and T07A5.1, but also to the uncharacterized protein RP688 from the intracellular parasitic bacterium Rickettsia prowazekii (e < 10–4). The RP688 sequence was used for further analysis of this protein family by iteratively searching the NR database using the PSI-BLAST program, which was run with the cut-off of e = 0.001 [3]. At convergence, not only fukutin and its C. elegans homologs, but also bacterial proteins involved in polysaccharide/phosphorylcholine modification and a yeast protein involved in mannosyl phosphorylation of oligosaccharides were retrieved from the database. Reverse searches with these sequences retrieved the original members of the fukutin family without any false positives. Fukutin, therefore, belongs to a family of proteins associated with the modification of the cell surface. A multiple alignment of the fukutin protein family was constructed using Gibbs sampling, as implemented in PROBE [4], in conjunction with the –m4 option of PSI-BLAST (Figure 1). The alignment shows prominent conservation in an amino-terminal block, followed by a weakly conserved carboxy-terminal region. The most notable feature of the amino-terminal region is the presence of the strictly conserved signature G[TS]hhGhhx4hhxaxxDxD (in single-letter amino acid code and in which ‘h’ is a hydrophobic amino acid, ‘a’ is an aromatic amino acid and ‘x’ denotes any amino acid). A pattern search with this motif recovers from the NR database the fukutin family in its entirety without any false positives. The carboxy-terminal region contains a motif with a conserved aspartate residue flanked by hydrophobic residues (Figure 1). Secondary structure prediction using the PHD program [5] suggests a compact α/β fold for the fukutin domain (Figure 1). LicD2 from Streptococcus pneumoniae is involved in the addition R836 Current Biology Vol 9 No 22