A putative nuclear growth factor-like globular nematode specific protein

Eric Hamilton Karunanayake,Ranil Samantha Dassanayake,Naduviladath Vishvanath Chandrasekharan,Ovitigala Weerasena,Witharanage Rodrigo

doi:10.6026/97320630003370

Abstract

Expressed sequence tags (ESTs) are an effective approach for discovery of novel genes. In the current study, approximately 250 ESTs of the cattle parasitic nematode Setaria digitata were examined and a cDNA clone identified whose coding sequence could not be functionally annotated by searching over publicly available genome, protein, EST and STS databases. Here, we report the extensive characterization of this ORF (UP) and its homologues using a bioinformatic approach. Uncharacterized protein (SDUP) of S. digitata consists of 204 amino acids with a predicted molecular weight and isoelectric point of 22.8KDa and 9.94, respectively. A search carried out using SDUP over nucleotide, EST and protein databases at NCBI, NEMBASE3 and Parasite Genome Database (PGD) identified homologous counterparts from the human parasitic nematodes Wuchereria bancrofti (WB), Brugia malayi (BM), Onchocerca volvulus (OV), the mouse filarial worm Litomosoides sigmodontis (LS), swine parasitic nematodes Ascaris suum (AS) and diverged counterparts from the plant parasitic nematode Meloidogyne hapla (MH) and free living nematodes Caenorhabditis elegans (CE) and Caenorhabditis briggsae (CB). Phylogenetic analyses revealed the UPs to be undergoing divergent evolution. A search of the ESTs at PGD showed that UP is expressed in all the stages of BM. Secondary structure analyses of multiply-aligned sequences of homologues using Jpred server indicated UPs to be rich in beta-pleated structures. TMMHH server and beta barrel finder programme indicated, UPs to be neither transmembrane or beta barrels proteins but are likely to be globular proteins. Further, the Motif discovery tool of MEME identified three novel potential motifs for UPS, of which only two are present in CE, CB & MH. Analyses of UPs using Signal IP, TargetP, Psort servers predicted this group of proteins to be devoid of signal peptide cleavage sites, are not mitochondrial targeting peptides but appear to be localized to the nucleus, respectively. Further analyses of the UPs using ScanProsite server for phosphorylation revealed potential sites for cAMP- and cGMP-dependent protein kinase, Protein kinase C and Casein kinase II. Putative functional analysis using ProtFun 2.1 Server indicated UPs to be nonenzymatic, growth factor like protein. Finally, collating all the information derived from bioinformatic analyses, we conclude that the UPs of nematodes are most likely to be expressed at all stages in the life cycle, localized to the nucleus, regulated by phosphorylation, rich in beta-pleated strands and are growth factor like nematode specific proteins.

Highlights

Nematodes are the most numerous multicellular animals on earth and nearly 80,000 species have been described under the phylum Nematoda, of which over 15,000 are parasitic and infect humans, domestic animals and food crops [1]
Evolutionary relationships and the selective pressures can be ascertained using the information in genomes of these organisms. We have used the latter tools to systematically characterize a group of nematode specific proteins using an ORF we characterized from a parasitic nematode Setaria digitata
Both the structure and function of the nematodes specific proteins described in the current study are truly unknown

Summary

Background

Nematodes are the most numerous multicellular animals on earth and nearly 80,000 species have been described under the phylum Nematoda, of which over 15,000 are parasitic and infect humans, domestic animals and food crops [1]. Plant parasitic nematodes can cause even greater economic losses as they could infect crops that are important for both animals and humans. More recent estimates on global crop losses are not available, it may be very much higher with the increase in agricultural productivity Despite these facts, the biology of the vast majority of parasitic and free living nematode species is poorly understood. We have used the latter tools to systematically characterize a group of nematode specific proteins using an ORF we characterized from a parasitic nematode Setaria digitata This nematode is found in the peritoneal cavity of many ungulates including cattle and buffaloes and causes nematodiasis, a neuropathological disorder. A cDNA library of S. digitata was constructed in the the Parasite Genome Database [7] and nucleotide-protein vector λ Zap according to manufacturer’s instructions.

Bioiformatic analysis annotation of these cDNAs was attempted by performing a

Conclusion