Analysis of plasma protein encoded by X- Chromosome Balamurugan.m
Introduction <ul><li>About 55% of our blood contains plasma fluid. Plasma Fluid is a Pale yellow colored fluid of which 90-92% is water. They play a very important role in our body. </li></ul>
Importance of plasma proteins 1. From ancient days we are using Blood as a diagnostic sample. Where we really examine the protein present in the plasma fluid. The act as a important diagnostic sample. 2. The protein present in the blood can also be called as Serum Protein. Animal cell are grown in GMEM media which contain 20% of serum content. It took 9 years to develop a serum free media for animal cell culture. Still the growth of cells in serum free media is not comparable with Serum containing media. They to need 5% of serum for the proper growth of cells. Serum free media should also need 5% of serum. Hence we cannot call it as a defined media. This indirectly means that complete composition of serum is not known yet. many hypothetical protein is also found in serum whose function is not known. Hence its very important to study the plasma protein function and understanding of its genetic function.
Plasma fluid : Plasma Fluid contains 90% of water 7% of blood protein ( fibrinogen, albumin, globulin etc) 2% of nutrients (sugar, amino acid, lipids etc) Hormones (erythropoietin, insulin etc) Electrolyte (Na+, k+, Ca+ etc)
<ul><li>Plasma protein have diverse function such as </li></ul><ul><li>Auxiliary Transport </li></ul><ul><li>Activation </li></ul><ul><li>Cell adhesion activity </li></ul><ul><li>DNA binding </li></ul><ul><li>DNA Repair </li></ul><ul><li>Guanyl activity </li></ul><ul><li>RNA binding </li></ul><ul><li>Transcription factor Activity </li></ul><ul><li>Ubiquitin Specific protease activity </li></ul>General function of plasma proteins:
Auxiliary Transport Cell adhesion activity DNA binding DNA Repair RNA binding Transcription factor Activity Visualizing of Plasma protein functioning
Genomic analysis of plasma protein : Plasma protein genome is taken from plasmaproteomdatabase.org, which is of course created and maintain by IOB and PANDAY Lab. Best part of this website is we can download the entire databank as a XML format. Plasma protein which are express in X-chromosome is filtered with the help of Microsoft EXCEL. These genes where further analyzed as mention in the flow chart
Plasma protein database www.ppd.org Plasma protein coded By X-chromosome gene Is filtered Gene expression Analysis SNP Analysis PTM Analysis Ectoplic Localization Work flow chart
Plasma proteins encoded in X-Chromosome: The plasma protein as declared by Human Protein organization (HuPO) which Are being encoded by X-Chromosome APXL protein Nucleosome assembly protein 1 like 3 Immunoglobulin binding protein 1 Melanoma associated antigen B4 Sushi repeat containing protein SRPX Plexin B3 G-antigen family D2 MAGEA ii Praline rice gamma carboxy glutamic acid protein 1 Adlican DKFZP564B147 protein DOCk ii Hypothetical protein FLJ11362 FLJ12525 Hypothetical protein FLJ12969 FLJ22965 FLJ33516 JM II protein JM5 protein Hypothetical protein KIAA1318 Leucine rich protein & calponin homology CH domain containing 2 WD repeat domain 40B Melanoma antigen family C3 7CEAL8 protein NF Kappa B activating protein Paraneoplastic antigen MA3 Paraneoplastic antigen like5 UTP u3 small nucleolar ribonucleoprotein Homology A Hypothetical protein FLJ32867 Plexin-A3 Dysotropin related protein2
Isoform analysis : Complete isoform studies shows that there is not much isoform found in plasma protein encoded by X-chromosome Only few protein 4-5% has 4-5 isoform About 20-22% of protein have 1-2 isoform
SNP analysis: 42% of protein shows SNP where as remaining 58% doesn’t show any SNPs. This highlights the possibility of occurrence of mutation in this region of X-chromosome. Mutation may let to the serious disorder. Hence this is consider as highly disease susceptible region.
PTM Analysi s : Only 6% of protein undergoes post-translation modification. The only type of post translation modification found in these protein was phosphorylation. They were no indication of any proteolytic cleavage.
Ectopic Localization : The ectopic localization of about 62% protein were still not known. 10% of protein were found in plasma membrane. The most significant part of this analysis is about 17% were found to be located at nucleus and cytoplasm which is quite unusual hence there is a deviation from their normal localization.
Conclusion: Plasma protein encoded by x-chromosome shows very less number of isoform which is very common in other proteins. They show very less post translation modification rate. And the only post translation modification they have shown is phosporylation. Where as glycosylation is very common in other protein. Non of the protein is cleaved with protolytic enzyme. This indirectly means no two protein fragment is coded by the single gene sequence. Plasma protein which are generally known to be present in blood is also present in nucleolus and cytoplasm at considerable amount (17%).