General comments


Function of the identified proteins

The detailed list of the identified proteins sorted according to the biological process in which they are involved is provided in Table 1.

A summary of the data is presented below:

Carbon metabolism, protein metabolism and biosynthesis of small molecules are the three major categories of biological processes to which belong the identified proteins. These categories correspond, respectively, to 15 %, 27 % and 27 % of the identified proteins.

Among the identified proteins of unknown function, four proteins were considered as hypothetical proteins: Tpa1p, Yer067wp, Yir035cp, and Yor021cp (SGD, release July 10 2006). Their identification provides the first evidence of their expression in yeast cells.

 


Cellular location of the identified proteins

The cellular location of the identified proteins is reported below:

   

All major categories of cellular components are represented. Comparison of the distribution of identified proteins and total yeast proteins (SGD, release July 10 2006) among these categories shows that cytoplasm proteins are over represented on 2-D gels and that membrane proteins are under represented.

 


CBI and protein identification

Codon bias index (CBI) is calculated from the gene sequence and reflects the propensity for a gene to utilize the same codon to encode an amino acid although other codons would encode the same amino acid. In S. cerevisiae, CBI is a good predictor of the level of expression of a gene, and consequently of the abundance of its protein: highly expressed genes have CBI close to 1 and poorly expressed genes, CBI close to 0.

The proteins which are expected to migrate on our gels on the basis of their calculated pI and Mr have been grouped according to their CBI, the number and percentage of proteins identified in each class have been considered.

 

 

  • Highly expressed proteins (CBI value >0.4)
    All proteins with a CBI value higher than 0.8 have been identified, with the exception of two proteins, Pma1p, a plasma membrane protein, and Hsp150p, a cell wall protein. Among the 243 proteins with a CBI value >0.4, only 73 are not identified. A large number of these proteins correspond to cell wall proteins (30) and membrane proteins (12) which, presumably, are not solubilized by our extraction procedure.

  • Proteins of middle abundance (0.4<CBI value >0.2)
    40% of these proteins have been identified.

  • Proteins of low abundance (0.2<CBI value)
    Only 67 proteins corresponding to low CBI values are identified. Among them 12 have a CBI lower than 0.1 (Hat2p, His3p, Mtf2p, Nnt1p, Rpn10p, Sec17p, Snf7p, Spe4p, Trp1p, Ura4p, Ure2p and Yar1p). In comparison, 2000 low abundance proteins are expected to migrate on our gels.


Protein abundance

 

We took advantage of the data from Ghaemmaghami et al (Nature 2003, 425, 737-741) to evaluate the abundance of the identified proteins of our reference map.

The levels of the identified proteins show a large dynamic range, varying from 500 to more than one million molecules per cell, with the highest frequency of proteins peaking between 8000 and 16,000 molecules per cell.

Considering that one yeast cell contains about 50 millions molecules of protein, it can be concluded that the faintest spots identified correspond to about 10 ppm of cellular proteins.

 

 

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