Elucidation of subfamily segregation and intramolecular coevolution of the olfactomedin-like proteins by comprehensive phylogenetic analysis and gene expression pattern assessment.

The categorization of genes by structural distinctions relevant to biological characteristics is very important for understanding of gene functions and predicting functional implications of uncharacterized genes. It was absolutely necessary to deploy an effective and efficient strategy to deal with the complexity of the large olfactomedin-like (OLF) gene family sharing sequence similarity but playing diversified roles in many important biological processes, as the simple highest-hit homology analysis gave incomprehensive results and led to inappropriate annotation for some uncharacterized OLF members. In light of evolutionary information that may facilitate the classification of the OLF family and proper association of novel OLF genes with characterized homologs, we performed phylogenetic analysis on all 116 OLF proteins currently available, including two novel members cloned by our group. The OLF family segregated into seven subfamilies and members with similar domain compositions or functional properties all fell into relevant subfamilies. Furthermore, our Northern blot analysis and previous studies revealed that the typical human OLF members in each subfamily exhibited tissue-specific expression patterns, which in turn supported the segregation of the OLF subfamilies with functional divergence. Interestingly, the phylogenetic tree topology for the OLF domains alone was almost identical with that of the full-length tree representing the unique phylogenetic feature of full-length OLF proteins and their particular domain compositions. Moreover, each of the major functional domains of OLF proteins kept the same phylogenetic feature in defining similar topology of the tree. It indicates that the OLF domain and the various domains in flanking non-OLF regions have coevolved and are likely to be functionally interdependent. Expanded by a plausible gene duplication and domain couplings scenario, the OLF family comprises seven evolutionarily and functionally distinct subfamilies, in which each member shares similar structural and functional characteristics including the composition of coevolved and interdependent domains. The phylogenetically classified and preliminarily assessed subfamily framework may greatly facilitate the studying on the OLF proteins. Furthermore, it also demonstrated a feasible and reliable strategy to categorize novel genes and predict the functional implications of uncharacterized proteins based on the comprehensive phylogenetic classification of the subfamilies and their relevance to preliminary functional characteristics.

[Molecular cloning and characterization of hMGRAP, a human secreted protein with multiple glutamine repeat].

To search for human novel secreted proteins and study their biological functions, using bioinformatical tools and experimental approaches, a novel secreted protein, human hMGRAP (Human Multiple Glutamine Repeat Acidic Protein) was obtained. hMGRAP consists of six coding exons spanning 1547bp of genomic DNA on the human chromosome 7q22.1, which encodes a protein with 248 amino acids. hMGRAP is rich of glutamic acid repeated sequence and the PI is 4.6. The coding sequence of hMGRAP was cloned by PCR method from the cDNA pool composed of nine human tissues. Western blot showed that hMGRAP protein was massively secreted out from the transiently transfected Cos-7 cells. RT-PCR result indicated hMGRAP mRNA was abundantly expressed in testis. In summary, a novel human gene encoding a secreted protein hMGRAP has been screened and cloned, and its biological function may specifically relate to its repeated glutamic acid sequence.

hOLF44, a secreted glycoprotein with distinct expression pattern, belongs to an uncharacterized olfactomedin-like subfamily newly identified by phylogenetic analysis.

Secreted proteins are indispensable for the development and differentiation of multicellular organisms. Cloning and characterization of novel or hypothetical genes encoding these proteins are therefore inviting great incentives. Using bioinformatics tools and experimental approaches, we isolated and characterized a human secreted glycoprotein, hOLF44, which contains a highly conserved olfactomedin-like (OLF) domain in the C-terminal. However, phylogenetic analysis revealed that hOLF44 is not clustered into any of the OLF subfamilies containing characterized members, and obviously falls into a newly identified uncharacterized OLF subfamily. Western blot analysis showed that hOLF44 protein is robustly secreted from the transfected COS-7 cells. Expression levels of hOLF44 mRNA are abundant in placenta, moderate in liver and heart, whereas fairly weak in other tissues examined. Immunohistochemical study on human term placenta demonstrated that hOLF44 is mainly localized extracellularly surrounding the syncytiotrophoblastic cells and very rarely expressed in the maternal decidua layer. These results suggest that hOLF44 may have matrix-related function involved in human placental and embryonic development, or play a similar role in other physiological processes. The further functional characterization of hOLF44 may provide insights into a better understanding of the newly identified OLF subfamily.

Isolation and characterization of a novel human thioredoxin-like gene hTLP19 encoding a secretory protein.

A novel human gene, named as hTLP19, was isolated and characterized as secretory protein by combining bioinformatics tools with experiments. The hTLP19 encodes 172 amino acid residues with signal peptide in its N-terminal and a thioredoxin (Trx) domain that is homologous with some genes in Mus musculus, Xenopus laevis, etc. Moreover, the result from insulin reduction assay indicated that the hTLP19 protein has Trx enzymatic activity. By comparing full-length cDNA with human genomic DNA, the hTLP19 gene might have seven coding exons spanning 35 kb of genomic DNA on the human chromosome 1p32.3. Northern blot analysis showed that human hTLP19 is expressed widely in many tissues with 1.6 kb band and extra 1.2 kb band in placenta. Subcellular localization and immunoblotting assays indicated that hTLP19 might be secreted out of cell through trans-Golgi network (TGN).

Evolutionary and biomedical implications of a Schistosoma japonicum complementary DNA resource.

Schistosoma japonicum causes schistosomiasis in humans and livestock in the Asia-Pacific region. Knowledge of the genome of this parasite should improve understanding of schistosome-host interactions, biomedical aspects of schistosomiasis and invertebrate evolution. We assigned 43,707 expressed sequence tags (ESTs) derived from adult S. japonicum and their eggs to 13,131 gene clusters. Of these, 35% shared no similarity with known genes and 75% had not been reported previously in schistosomes. Notably, S. japonicum encoded mammalian-like receptors for insulin, progesterone, cytokines and neuropeptides, suggesting that host hormones, or endogenous parasite homologs, could orchestrate schistosome development and maturation and that schistosomes modulate anti-parasite immune responses through inhibitors, molecular mimicry and other evasion strategies.

Cloning and characterization of a novel human secretory protein: secretogranin III.

We have cloned a new member of the granin family, termed human secretogranin III (SgIII), that encodes 468 amino acid residues. The human SgIII protein possesses an N-terminal signal peptide, seven dibasic sites, and the repeated DSTK sequences. These structure characteristics are similar to other members of secretogranin family. The human SgIII has homologous proteins in mouse, rat, and Xenopus laevis. Genomic organization shows the gene includes 12 coding exons spanning 39 kb of genomic DNA on the human chromosome 15. Human SgIII is expressed widely as showed in Northern blot and its cDNA hybridizes to 2.2 kb and 1.9 kb bands in many tissues, with two additional 4.5 kb and 3.3 kb bands in brain. Subcelluar localization and immunoblotting indicated SgIII was secreted out of cell through trans-Golgi network (TGN). SgIII may take effect in the biogenesis of secretory granules as a helper protein and be involved in the production or release of peptide hormones in the regulated secretory pathway.