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Genomic organization, tissue distribution and functional characterization of the rat Pate gene cluster.

Rajesh A, Yenugu S - PLoS ONE (2012)

Bottom Line: PATE and PATE-F three dimensional protein structure was found to be similar to that of the toxin bucandin.Recombinant PATE protein exhibited potent antibacterial activity, whereas PATE-F did not exhibit any antibacterial activity.Based on our results, we conclude that rat PATE proteins may contribute to the reproductive and defense functions.

View Article: PubMed Central - PubMed

Affiliation: Department of Animal Sciences, University of Hyderabad, Hyderabad, India.

ABSTRACT
The cysteine rich prostate and testis expressed (Pate) proteins identified till date are thought to resemble the three fingered protein/urokinase-type plasminogen activator receptor proteins. In this study, for the first time, we report the identification, cloning and characterization of rat Pate gene cluster and also determine the expression pattern. The rat Pate genes are clustered on chromosome 8 and their predicted proteins retained the ten cysteine signature characteristic to TFP/Ly-6 protein family. PATE and PATE-F three dimensional protein structure was found to be similar to that of the toxin bucandin. Though Pate gene expression is thought to be prostate and testis specific, we observed that rat Pate genes are also expressed in seminal vesicle and epididymis and in tissues beyond the male reproductive tract. In the developing rats (20-60 day old), expression of Pate genes seem to be androgen dependent in the epididymis and testis. In the adult rat, androgen ablation resulted in down regulation of the majority of Pate genes in the epididymides. PATE and PATE-F proteins were found to be expressed abundantly in the male reproductive tract of rats and on the sperm. Recombinant PATE protein exhibited potent antibacterial activity, whereas PATE-F did not exhibit any antibacterial activity. Pate expression was induced in the epididymides when challenged with LPS. Based on our results, we conclude that rat PATE proteins may contribute to the reproductive and defense functions.

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Genomic localization of rat Pate genes.Arrows indicate direction of transcription. Positions were taken from the Mapview (RGSC v3.4) at the National Center for Biotechnology Information (NCBI) website. Distance between genes is not to scale. Rat Pate sequences were submitted to GenBank and were assigned the accession numbers: Pate-P – JQ031758; Pate-Q – JF412807; Pate-F – JF412806; Pate-A – JF412804; Pate-C – HQ687475; Pate-E – JF412805; Pate-N – HQ687476; Pate – JF412809; Pate-2 – HQ687477; Pate-Dj – HQ916281.
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pone-0032633-g001: Genomic localization of rat Pate genes.Arrows indicate direction of transcription. Positions were taken from the Mapview (RGSC v3.4) at the National Center for Biotechnology Information (NCBI) website. Distance between genes is not to scale. Rat Pate sequences were submitted to GenBank and were assigned the accession numbers: Pate-P – JQ031758; Pate-Q – JF412807; Pate-F – JF412806; Pate-A – JF412804; Pate-C – HQ687475; Pate-E – JF412805; Pate-N – HQ687476; Pate – JF412809; Pate-2 – HQ687477; Pate-Dj – HQ916281.

Mentions: Ten of the eleven (the exception being Pate-B, which is already reported in Gen Bank) rat Pate mRNA transcripts were amplified and sequenced. They are localized on chromosome 8q21 within a 2.5 kb segment present between the Acrv1 and Ddx25 genes, a characteristic feature observed in the humans and mice (Figure 1). PCR amplification using gene specific primers resulted in two amplicons each for Pate and Pate-2. Sequence analysis of the Pate amplicons revealed that the 378 bp amplicon corresponds to Pate, whereas the 400 bp amplicon seems to be its alternate transcript. Similarly, an alternate transcript for Pate-2 was also observed. The Pate sequences were submitted to GenBank and were assigned the accession numbers - Pate-P – JQ031758; Pate-Q – JF412807; Pate-F – JF412806; Pate-A – JF412804; Pate-C – HQ687475; Pate-E – JF412805; Pate-N – HQ687476; Pate – JF412809; Pate-2 – HQ687477; Pate-Dj – HQ916281. Majority of them contained three exons (Figure S1). However, Pate, its alternate transcript, Pate-2 and its alternate transcript contained more than three exons. The number of exons reported in this study for each Pate transcript is in agreement with the information available in the rat genome. In silico protein translation analyses revealed that all the Pate mRNA transcripts except for the alternate transcripts of Pate and Pate-2, encode for proteins that are cysteine rich and contain the characteristic TFP/Ly-6/uPAR domain with a highly conserved distribution of 10 cysteines in two motifs (Figure 2). This is in agreement with the predictions available in the rat genome. Based on the ClustalW2 score, the homology among the rat PATE proteins was found to be high (Table 1). The rat PATE proteins are highly homologous to their known mouse and human counterparts (Table 2). All the Pate proteins identified in this study contain a signal peptide and seem to be secretory in nature (Figure S1). The predicted physical characteristics of the rat PATE proteins are given in Table 2. The alternate transcripts of Pate and Pate-2 contained a premature stop codon, because of which they do not encode the full length proteins (Figure S1) and hence were not characterized further.


Genomic organization, tissue distribution and functional characterization of the rat Pate gene cluster.

Rajesh A, Yenugu S - PLoS ONE (2012)

Genomic localization of rat Pate genes.Arrows indicate direction of transcription. Positions were taken from the Mapview (RGSC v3.4) at the National Center for Biotechnology Information (NCBI) website. Distance between genes is not to scale. Rat Pate sequences were submitted to GenBank and were assigned the accession numbers: Pate-P – JQ031758; Pate-Q – JF412807; Pate-F – JF412806; Pate-A – JF412804; Pate-C – HQ687475; Pate-E – JF412805; Pate-N – HQ687476; Pate – JF412809; Pate-2 – HQ687477; Pate-Dj – HQ916281.
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Related In: Results  -  Collection

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pone-0032633-g001: Genomic localization of rat Pate genes.Arrows indicate direction of transcription. Positions were taken from the Mapview (RGSC v3.4) at the National Center for Biotechnology Information (NCBI) website. Distance between genes is not to scale. Rat Pate sequences were submitted to GenBank and were assigned the accession numbers: Pate-P – JQ031758; Pate-Q – JF412807; Pate-F – JF412806; Pate-A – JF412804; Pate-C – HQ687475; Pate-E – JF412805; Pate-N – HQ687476; Pate – JF412809; Pate-2 – HQ687477; Pate-Dj – HQ916281.
Mentions: Ten of the eleven (the exception being Pate-B, which is already reported in Gen Bank) rat Pate mRNA transcripts were amplified and sequenced. They are localized on chromosome 8q21 within a 2.5 kb segment present between the Acrv1 and Ddx25 genes, a characteristic feature observed in the humans and mice (Figure 1). PCR amplification using gene specific primers resulted in two amplicons each for Pate and Pate-2. Sequence analysis of the Pate amplicons revealed that the 378 bp amplicon corresponds to Pate, whereas the 400 bp amplicon seems to be its alternate transcript. Similarly, an alternate transcript for Pate-2 was also observed. The Pate sequences were submitted to GenBank and were assigned the accession numbers - Pate-P – JQ031758; Pate-Q – JF412807; Pate-F – JF412806; Pate-A – JF412804; Pate-C – HQ687475; Pate-E – JF412805; Pate-N – HQ687476; Pate – JF412809; Pate-2 – HQ687477; Pate-Dj – HQ916281. Majority of them contained three exons (Figure S1). However, Pate, its alternate transcript, Pate-2 and its alternate transcript contained more than three exons. The number of exons reported in this study for each Pate transcript is in agreement with the information available in the rat genome. In silico protein translation analyses revealed that all the Pate mRNA transcripts except for the alternate transcripts of Pate and Pate-2, encode for proteins that are cysteine rich and contain the characteristic TFP/Ly-6/uPAR domain with a highly conserved distribution of 10 cysteines in two motifs (Figure 2). This is in agreement with the predictions available in the rat genome. Based on the ClustalW2 score, the homology among the rat PATE proteins was found to be high (Table 1). The rat PATE proteins are highly homologous to their known mouse and human counterparts (Table 2). All the Pate proteins identified in this study contain a signal peptide and seem to be secretory in nature (Figure S1). The predicted physical characteristics of the rat PATE proteins are given in Table 2. The alternate transcripts of Pate and Pate-2 contained a premature stop codon, because of which they do not encode the full length proteins (Figure S1) and hence were not characterized further.

Bottom Line: PATE and PATE-F three dimensional protein structure was found to be similar to that of the toxin bucandin.Recombinant PATE protein exhibited potent antibacterial activity, whereas PATE-F did not exhibit any antibacterial activity.Based on our results, we conclude that rat PATE proteins may contribute to the reproductive and defense functions.

View Article: PubMed Central - PubMed

Affiliation: Department of Animal Sciences, University of Hyderabad, Hyderabad, India.

ABSTRACT
The cysteine rich prostate and testis expressed (Pate) proteins identified till date are thought to resemble the three fingered protein/urokinase-type plasminogen activator receptor proteins. In this study, for the first time, we report the identification, cloning and characterization of rat Pate gene cluster and also determine the expression pattern. The rat Pate genes are clustered on chromosome 8 and their predicted proteins retained the ten cysteine signature characteristic to TFP/Ly-6 protein family. PATE and PATE-F three dimensional protein structure was found to be similar to that of the toxin bucandin. Though Pate gene expression is thought to be prostate and testis specific, we observed that rat Pate genes are also expressed in seminal vesicle and epididymis and in tissues beyond the male reproductive tract. In the developing rats (20-60 day old), expression of Pate genes seem to be androgen dependent in the epididymis and testis. In the adult rat, androgen ablation resulted in down regulation of the majority of Pate genes in the epididymides. PATE and PATE-F proteins were found to be expressed abundantly in the male reproductive tract of rats and on the sperm. Recombinant PATE protein exhibited potent antibacterial activity, whereas PATE-F did not exhibit any antibacterial activity. Pate expression was induced in the epididymides when challenged with LPS. Based on our results, we conclude that rat PATE proteins may contribute to the reproductive and defense functions.

Show MeSH
Related in: MedlinePlus