Proteomics

Proteomics

INTRODUCTION

Today we have the genome sequences for humans as well as many other animals, plants, fungi, and bacteria. All these data have given scientists a global view of the various genes in humans and others. However, genes are only the first step to understanding how an organism works. Genes are transcribed into mRNA and then translated into protein. So in order to truly understand gene function, the gene product or protein must be characterized also—hence the advent of proteomics. Proteomics refers to the global analysis of proteins, and the proteome refers to the entire protein complement of an organism. The translatome, or the complement of proteins under specific circumstances, also falls into this field of study. Note that the translatome is dynamic and changes when environmental conditions change.

The relationships among the genome, proteome, and translatome are not linear. The genome of a species is the most stable, but differences do exist between one person and the next, and between one generation and the next. The proteome correlates highly with the genome because proteins are the products of the majority of genes. However, some genes encode nontranslated RNA, and so do not contribute to the proteome. In addition, some genes, especially in higher eukaryotes, may give rise to multiple proteins because of alternative splicing. In contrast, the translatome is highly dynamic, changing from minute to minute depending on many different stimuli.

The genome ultimately dictates the changes in the translatome and proteome, but genomic changes do not always affect the translatome or proteome. Sometimes, for example, mRNA transcripts are made, but never translated into protein. MicroRNAs and siRNAs control the expression of many different proteins at the translational level. The rate of mRNA degradation and translation will have a huge impact on how much protein is actually made. Thus, although some genes give rise to a lot of mRNA, very little protein is made, because the transcripts are very unstable.

The translatome and proteome are also affected by modifications that occur after translation. For example, the function of many proteins is altered by addition or removal of various groups, such as phosphate, acetyl, AMP, or ADP-ribose. Also, many proteins, especially in eukaryotes, are altered by chemical modification of amino acid residues. Proteins also undergo proteolytic cleavage. Hence, the composition of the translatome is affected by the rate of protein degradation, and protein stability has a major influence. Finally, some proteins themselves may affect the expression of other proteins via assorted regulatory effects. All of these factors affect the protein makeup of the cell.