Analysis of plasma protein encoded byX- Chromosome

Balamurugan.m

Introduction

• 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.

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:

Blood is taken in a test tube

Plasma fluid:Anti coagulate is added to the blood and allow it to settle for some time.

Plasma fluid:

Blood cell such as RBC, WBC will settle at the bottom

Where as the yellow colored fluid remain at the top is called plasma fluid

Plasma fluid:

Plasma fluid:

Plasma Fluid contains90% of water7% of blood protein ( fibrinogen, albumin, globulin etc)2% of nutrients (sugar, amino acid, lipids etc)Hormones (erythropoietin, insulin etc)Electrolyte (Na+, k+, Ca+ etc)

Plasma protein have diverse function such as • Auxiliary Transport• Activation• Cell adhesion activity• DNA binding• DNA Repair• Guanyl activity• RNA binding• Transcription factor Activity• Ubiquitin Specific protease activity

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 databasewww.ppd.org

Plasma protein coded By X-chromosome gene

Is filtered

Gene expression Analysis

SNP Analysis PTM AnalysisEctoplic

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 proteinNucleosome assembly protein 1 like 3Immunoglobulin binding protein 1Melanoma associated antigen B4Sushi repeat containing protein SRPXPlexin B3G-antigen family D2MAGEA iiPraline rice gamma carboxy glutamic acid protein 1AdlicanDKFZP564B147 proteinDOCk iiHypothetical protein FLJ11362FLJ12525Hypothetical protein FLJ12969FLJ22965

FLJ33516JM II proteinJM5 proteinHypothetical protein KIAA1318Leucine rich protein & calponin homology CH domain containing 2WD repeat domain 40BMelanoma antigen family C37CEAL8 proteinNF Kappa B activating proteinParaneoplastic antigen MA3Paraneoplastic antigen like5UTP u3 small nucleolar ribonucleoprotein Homology AHypothetical protein FLJ32867Plexin-A3Dysotropin related protein2

0

5

10

15

20

25

Isoforms

Isoforms

No of protein

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 isoformAbout 20-22% of protein have 1-2 isoform

SNP Analysis

SNP

No SNP

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 Analysis

PTM

NO PTM

PTM Analysis: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

Nucleus and cytoplasm

Plasma membrane andcytoplasm

plasma membrane

plasma membrane andextra cellular

Not available

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%).