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Characterization of Smoc-1 uncovers two transcript variants showing differential tissue and age specific expression in Bubalus bubalis.

Srivastava J, Premi S, Kumar S, Parwez I, Ali S - BMC Genomics (2007)

Bottom Line: Buffalo Smoc-1 was found to encode a secreted matricellular glycoprotein containing two EF-hand calcium binding motifs homologous to that of BM-40/SPARC family.Though this gene was found to be evolutionarily conserved, the buffalo Smoc-1 showed conspicuous nucleotide/amino acid changes altering its secondary structure compared to that in other mammals.The relative expression of variant-02 was markedly higher compared to that of variant-01 in all the tissues examined.

View Article: PubMed Central - HTML - PubMed

Affiliation: Molecular Genetics Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi-110 067, India. jayanshi@gmail.com

ABSTRACT

Background: Secreted modular calcium binding protein-1 (Smoc-1) belongs to the BM-40 family which has been implicated with tissue remodeling, angiogenesis and bone mineralization. Besides its anticipated role in embryogenesis, Smoc-1 has been characterized only in a few mammalian species. We made use of the consensus sequence (5' CACCTCTCCACCTGCC 3') of 33.15 repeat loci to explore the buffalo transcriptome and uncovered the Smoc-1 transcript tagged with this repeat. The main objective of this study was to gain an insight into its structural and functional organization, and expressional status of Smoc-1 in water buffalo, Bubalus bubalis.

Results: We cloned and characterized the buffalo Smoc-1, including its copy number status, in-vitro protein expression, tissue & age specific transcription/translation, chromosomal mapping and localization to the basement membrane zone. Buffalo Smoc-1 was found to encode a secreted matricellular glycoprotein containing two EF-hand calcium binding motifs homologous to that of BM-40/SPARC family. In buffalo, this single copy gene consisted of 12 exons and was mapped onto the acrocentric chromosome 11. Though this gene was found to be evolutionarily conserved, the buffalo Smoc-1 showed conspicuous nucleotide/amino acid changes altering its secondary structure compared to that in other mammals. In silico analysis of the Smoc-1 proposed its glycoprotein nature with a calcium dependent conformation. Further, we unveiled two transcript variants of this gene, varying in their 3'UTR lengths but both coding for identical protein(s). Smoc-1 evinced highest expression of both the variants in liver and modest to negligible in other tissues. The relative expression of variant-02 was markedly higher compared to that of variant-01 in all the tissues examined. Moreover, expression of Smoc-1, though modest during the early ages, was conspicuously enhanced after 1 year and remained consistently higher during the entire life span of buffalo with gradual increment in expression of variant-02. Immunohistochemically, Smoc-1 was localized in the basement membrane zones and extracellular matrices of various tissues.

Conclusion: These data added to our understandings about the tissue, age and species specific functions of the Smoc-1. It also enabled us to demonstrate varying expression of the two transcript variants of Smoc-1 amongst different somatic tissues/gonads and ages, in spite of their identical coding frames. Pursuance of these variants for their roles in various disease phenotypes such as hepatocellular carcinoma and angiogenesis is envisaged to establish broader biological significance of this gene.

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Two transcript variants of Smoc-1. Northern blot showing two transcript variants of Smoc-1 in different somatic and gonadal tissues of water buffalo. Note two distinct bands with varying intensity in each tissue along with highest expression in liver, and lowest in lung, kidney, and heart.
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Figure 2: Two transcript variants of Smoc-1. Northern blot showing two transcript variants of Smoc-1 in different somatic and gonadal tissues of water buffalo. Note two distinct bands with varying intensity in each tissue along with highest expression in liver, and lowest in lung, kidney, and heart.

Mentions: Northern blot detected two bands of 3.5 kb and 2.0 kb (Fig. 2) which were confirmed to be two transcript variants of Smoc-1 with RACE and sequencing (Fig. 1 and Additional file 1), variant-01 of 3474 bp [GenBank: DQ159955] and variant-02 of 1933 bp [GenBank: EF446167]. Both the variants encoded for identical proteins but showed differences in their 3'UTR length, polyadenylation signals and Poly(A) tails. In the 3' UTR of variant-01 & -02, five & two copies of mRNA instability motif (ATTTA), respectively, were observed. In addition, there were orthodox polyadenylation signals (AATAAA), 1787 and 334 bp downstream of the translation termination codon, in transcript variant-01 and -02, respectively (Additional file 1). Interestingly, two types of transcripts of Smoc-1 have been reported independently in the literature for human [GenBank: AJ249900 and BC011548] and cattle [GenBank: XM_612029 and NM_01079771]. Database search and multiple nucleotide sequence alignment of both the variants showed their conservation across various species (Additional file 2).


Characterization of Smoc-1 uncovers two transcript variants showing differential tissue and age specific expression in Bubalus bubalis.

Srivastava J, Premi S, Kumar S, Parwez I, Ali S - BMC Genomics (2007)

Two transcript variants of Smoc-1. Northern blot showing two transcript variants of Smoc-1 in different somatic and gonadal tissues of water buffalo. Note two distinct bands with varying intensity in each tissue along with highest expression in liver, and lowest in lung, kidney, and heart.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2235864&req=5

Figure 2: Two transcript variants of Smoc-1. Northern blot showing two transcript variants of Smoc-1 in different somatic and gonadal tissues of water buffalo. Note two distinct bands with varying intensity in each tissue along with highest expression in liver, and lowest in lung, kidney, and heart.
Mentions: Northern blot detected two bands of 3.5 kb and 2.0 kb (Fig. 2) which were confirmed to be two transcript variants of Smoc-1 with RACE and sequencing (Fig. 1 and Additional file 1), variant-01 of 3474 bp [GenBank: DQ159955] and variant-02 of 1933 bp [GenBank: EF446167]. Both the variants encoded for identical proteins but showed differences in their 3'UTR length, polyadenylation signals and Poly(A) tails. In the 3' UTR of variant-01 & -02, five & two copies of mRNA instability motif (ATTTA), respectively, were observed. In addition, there were orthodox polyadenylation signals (AATAAA), 1787 and 334 bp downstream of the translation termination codon, in transcript variant-01 and -02, respectively (Additional file 1). Interestingly, two types of transcripts of Smoc-1 have been reported independently in the literature for human [GenBank: AJ249900 and BC011548] and cattle [GenBank: XM_612029 and NM_01079771]. Database search and multiple nucleotide sequence alignment of both the variants showed their conservation across various species (Additional file 2).

Bottom Line: Buffalo Smoc-1 was found to encode a secreted matricellular glycoprotein containing two EF-hand calcium binding motifs homologous to that of BM-40/SPARC family.Though this gene was found to be evolutionarily conserved, the buffalo Smoc-1 showed conspicuous nucleotide/amino acid changes altering its secondary structure compared to that in other mammals.The relative expression of variant-02 was markedly higher compared to that of variant-01 in all the tissues examined.

View Article: PubMed Central - HTML - PubMed

Affiliation: Molecular Genetics Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi-110 067, India. jayanshi@gmail.com

ABSTRACT

Background: Secreted modular calcium binding protein-1 (Smoc-1) belongs to the BM-40 family which has been implicated with tissue remodeling, angiogenesis and bone mineralization. Besides its anticipated role in embryogenesis, Smoc-1 has been characterized only in a few mammalian species. We made use of the consensus sequence (5' CACCTCTCCACCTGCC 3') of 33.15 repeat loci to explore the buffalo transcriptome and uncovered the Smoc-1 transcript tagged with this repeat. The main objective of this study was to gain an insight into its structural and functional organization, and expressional status of Smoc-1 in water buffalo, Bubalus bubalis.

Results: We cloned and characterized the buffalo Smoc-1, including its copy number status, in-vitro protein expression, tissue & age specific transcription/translation, chromosomal mapping and localization to the basement membrane zone. Buffalo Smoc-1 was found to encode a secreted matricellular glycoprotein containing two EF-hand calcium binding motifs homologous to that of BM-40/SPARC family. In buffalo, this single copy gene consisted of 12 exons and was mapped onto the acrocentric chromosome 11. Though this gene was found to be evolutionarily conserved, the buffalo Smoc-1 showed conspicuous nucleotide/amino acid changes altering its secondary structure compared to that in other mammals. In silico analysis of the Smoc-1 proposed its glycoprotein nature with a calcium dependent conformation. Further, we unveiled two transcript variants of this gene, varying in their 3'UTR lengths but both coding for identical protein(s). Smoc-1 evinced highest expression of both the variants in liver and modest to negligible in other tissues. The relative expression of variant-02 was markedly higher compared to that of variant-01 in all the tissues examined. Moreover, expression of Smoc-1, though modest during the early ages, was conspicuously enhanced after 1 year and remained consistently higher during the entire life span of buffalo with gradual increment in expression of variant-02. Immunohistochemically, Smoc-1 was localized in the basement membrane zones and extracellular matrices of various tissues.

Conclusion: These data added to our understandings about the tissue, age and species specific functions of the Smoc-1. It also enabled us to demonstrate varying expression of the two transcript variants of Smoc-1 amongst different somatic tissues/gonads and ages, in spite of their identical coding frames. Pursuance of these variants for their roles in various disease phenotypes such as hepatocellular carcinoma and angiogenesis is envisaged to establish broader biological significance of this gene.

Show MeSH
Related in: MedlinePlus