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Systematic identification and integrative analysis of novel genes expressed specifically or predominantly in mouse epididymis.

Oh J, Lee J, Woo JM, Choi E, Park I, Han C, Baek N, Lee H, Kim do H, Cho C - BMC Genomics (2006)

Bottom Line: We found that expression of the half of the genes is regulated by androgens.A number of the novel genes are putative epididymal protease inhibitors or beta-defensins.We identified and characterized 32 novel epididymis-specific or -predominant genes by an integrative approach.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Life Science, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea. tornado94@hanmail.net <tornado94@hanmail.net>

ABSTRACT

Background: Maturation of spermatozoa, including development of motility and the ability to fertilize the oocyte, occurs during transit through the microenvironment of the epididymis. Comprehensive understanding of sperm maturation requires identification and characterization of unique genes expressed in the epididymis.

Results: We systematically identified 32 novel genes with epididymis-specific or -predominant expression in the mouse epididymis UniGene library, containing 1505 gene-oriented transcript clusters, by in silico and in vitro analyses. The Northern blot analysis revealed various characteristics of the genes at the transcript level, such as expression level, size and the presence of isoform. We found that expression of the half of the genes is regulated by androgens. Further expression analyses demonstrated that the novel genes are region-specific and developmentally regulated. Computational analysis showed that 15 of the genes lack human orthologues, suggesting their implication in male reproduction unique to the mouse. A number of the novel genes are putative epididymal protease inhibitors or beta-defensins. We also found that six of the genes have secretory activity, indicating that they may interact with sperm and have functional roles in sperm maturation.

Conclusion: We identified and characterized 32 novel epididymis-specific or -predominant genes by an integrative approach. Our study is unique in the aspect of systematic identification of novel epididymal genes and should be a firm basis for future investigation into molecular mechanisms underlying sperm maturation in the epididymis.

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Putative domains and motifs in proteins encoded by the novel genes. The predicted amino acid sequences of the novel genes were analyzed using various bioinformatics tools (see Materials and Methods) and genes containing putative domains or motifs are listed. The proteins are indicated by boxes and, the putative domains or motifs are shaded. The size of the scale bar is shown as number of amino acids (aa) below each protein. Domain/motif abbreviations are as follows: WFDB, whey-acid-protein four-disulfide binding core domain; ACBP, acyl-CoA binding protein; Glyco_hydro_35, Glycosyl hydrolases family 35; SCP, sperm coating protein-like extracellular protein; FN2, type II fibronectin collagen-binding domain; ABC transport, ATP binding cassette transport; KU, BPTI (bovine pancreatic trypsin inhibitor)/Kunitz family of serine protease inhibitors; KAZAL_PSTI, Kazal-type pancreatic secretory trypsin inhibitors (PSTI) and related proteins; Tryp_SPc, trypsin-like serine protease; CUB, CUB domain.
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Figure 6: Putative domains and motifs in proteins encoded by the novel genes. The predicted amino acid sequences of the novel genes were analyzed using various bioinformatics tools (see Materials and Methods) and genes containing putative domains or motifs are listed. The proteins are indicated by boxes and, the putative domains or motifs are shaded. The size of the scale bar is shown as number of amino acids (aa) below each protein. Domain/motif abbreviations are as follows: WFDB, whey-acid-protein four-disulfide binding core domain; ACBP, acyl-CoA binding protein; Glyco_hydro_35, Glycosyl hydrolases family 35; SCP, sperm coating protein-like extracellular protein; FN2, type II fibronectin collagen-binding domain; ABC transport, ATP binding cassette transport; KU, BPTI (bovine pancreatic trypsin inhibitor)/Kunitz family of serine protease inhibitors; KAZAL_PSTI, Kazal-type pancreatic secretory trypsin inhibitors (PSTI) and related proteins; Tryp_SPc, trypsin-like serine protease; CUB, CUB domain.

Mentions: To gain an insight into the structures and functions of proteins expressed from the novel genes, a protein-coding region in each gene was defined by selecting the longest amino-acid-coding sequence, which terminates before a polyadenylation signal (if one is present), and these amino acid sequences were subjected to protein database searches. For most of the genes, the predicted coding regions are considered to be accurate. The exceptions are the eight genes whose transcripts are known to be significantly smaller in size than indicated by the Northern blots (Figures 2 and 3). Nevertheless, it should be noted that all of these genes contain complete coding sequences, suggesting that 5' or 3' UTR sequences are responsible for the size discrepancy between the Northern-blot results and the UniGene database. Analysis of the amino acid sequences defined from the cDNAs by BLAST search revealed that eight genes contained conserved domains characteristic of protease inhibitors such as the Kazal-type serine protease inhibitor domain (Mm.117440, Mm.99782, and Mm.190482) or the whey-acid-protein (WAP) four-disulfide core domain (Mm.235619, Mm.234248, Mm.293365, Mm.190489, and Mm.99690). Furthermore, an additional six genes were found to contain conserved cysteine residues typical of β-defensins (Mm.190454, Mm.99530, Mm.99387, Mm.99065, Mm.82875, and Mm.245908) (Figure 6) [14,15].


Systematic identification and integrative analysis of novel genes expressed specifically or predominantly in mouse epididymis.

Oh J, Lee J, Woo JM, Choi E, Park I, Han C, Baek N, Lee H, Kim do H, Cho C - BMC Genomics (2006)

Putative domains and motifs in proteins encoded by the novel genes. The predicted amino acid sequences of the novel genes were analyzed using various bioinformatics tools (see Materials and Methods) and genes containing putative domains or motifs are listed. The proteins are indicated by boxes and, the putative domains or motifs are shaded. The size of the scale bar is shown as number of amino acids (aa) below each protein. Domain/motif abbreviations are as follows: WFDB, whey-acid-protein four-disulfide binding core domain; ACBP, acyl-CoA binding protein; Glyco_hydro_35, Glycosyl hydrolases family 35; SCP, sperm coating protein-like extracellular protein; FN2, type II fibronectin collagen-binding domain; ABC transport, ATP binding cassette transport; KU, BPTI (bovine pancreatic trypsin inhibitor)/Kunitz family of serine protease inhibitors; KAZAL_PSTI, Kazal-type pancreatic secretory trypsin inhibitors (PSTI) and related proteins; Tryp_SPc, trypsin-like serine protease; CUB, CUB domain.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1764739&req=5

Figure 6: Putative domains and motifs in proteins encoded by the novel genes. The predicted amino acid sequences of the novel genes were analyzed using various bioinformatics tools (see Materials and Methods) and genes containing putative domains or motifs are listed. The proteins are indicated by boxes and, the putative domains or motifs are shaded. The size of the scale bar is shown as number of amino acids (aa) below each protein. Domain/motif abbreviations are as follows: WFDB, whey-acid-protein four-disulfide binding core domain; ACBP, acyl-CoA binding protein; Glyco_hydro_35, Glycosyl hydrolases family 35; SCP, sperm coating protein-like extracellular protein; FN2, type II fibronectin collagen-binding domain; ABC transport, ATP binding cassette transport; KU, BPTI (bovine pancreatic trypsin inhibitor)/Kunitz family of serine protease inhibitors; KAZAL_PSTI, Kazal-type pancreatic secretory trypsin inhibitors (PSTI) and related proteins; Tryp_SPc, trypsin-like serine protease; CUB, CUB domain.
Mentions: To gain an insight into the structures and functions of proteins expressed from the novel genes, a protein-coding region in each gene was defined by selecting the longest amino-acid-coding sequence, which terminates before a polyadenylation signal (if one is present), and these amino acid sequences were subjected to protein database searches. For most of the genes, the predicted coding regions are considered to be accurate. The exceptions are the eight genes whose transcripts are known to be significantly smaller in size than indicated by the Northern blots (Figures 2 and 3). Nevertheless, it should be noted that all of these genes contain complete coding sequences, suggesting that 5' or 3' UTR sequences are responsible for the size discrepancy between the Northern-blot results and the UniGene database. Analysis of the amino acid sequences defined from the cDNAs by BLAST search revealed that eight genes contained conserved domains characteristic of protease inhibitors such as the Kazal-type serine protease inhibitor domain (Mm.117440, Mm.99782, and Mm.190482) or the whey-acid-protein (WAP) four-disulfide core domain (Mm.235619, Mm.234248, Mm.293365, Mm.190489, and Mm.99690). Furthermore, an additional six genes were found to contain conserved cysteine residues typical of β-defensins (Mm.190454, Mm.99530, Mm.99387, Mm.99065, Mm.82875, and Mm.245908) (Figure 6) [14,15].

Bottom Line: We found that expression of the half of the genes is regulated by androgens.A number of the novel genes are putative epididymal protease inhibitors or beta-defensins.We identified and characterized 32 novel epididymis-specific or -predominant genes by an integrative approach.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Life Science, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea. tornado94@hanmail.net <tornado94@hanmail.net>

ABSTRACT

Background: Maturation of spermatozoa, including development of motility and the ability to fertilize the oocyte, occurs during transit through the microenvironment of the epididymis. Comprehensive understanding of sperm maturation requires identification and characterization of unique genes expressed in the epididymis.

Results: We systematically identified 32 novel genes with epididymis-specific or -predominant expression in the mouse epididymis UniGene library, containing 1505 gene-oriented transcript clusters, by in silico and in vitro analyses. The Northern blot analysis revealed various characteristics of the genes at the transcript level, such as expression level, size and the presence of isoform. We found that expression of the half of the genes is regulated by androgens. Further expression analyses demonstrated that the novel genes are region-specific and developmentally regulated. Computational analysis showed that 15 of the genes lack human orthologues, suggesting their implication in male reproduction unique to the mouse. A number of the novel genes are putative epididymal protease inhibitors or beta-defensins. We also found that six of the genes have secretory activity, indicating that they may interact with sperm and have functional roles in sperm maturation.

Conclusion: We identified and characterized 32 novel epididymis-specific or -predominant genes by an integrative approach. Our study is unique in the aspect of systematic identification of novel epididymal genes and should be a firm basis for future investigation into molecular mechanisms underlying sperm maturation in the epididymis.

Show MeSH