If evolution did not have to select totally new proteins for each new cellular function, then how many genes does it take to make an organism? The number of genes in an organism that encode proteins may be far fewer than the number of proteins they actually make. Current estimates suggest that it takes just 25,000 genes make and operate a human and all its proteins (check out Pertea and Salzberg at Estimating the number of genes in the human genome). However, our cells (and those of eukaryotes generally) may express as many as 100,000 different proteins. How is this possible? Are there more efficient ways to evolve new and useful cellular tasks than evolving a new genes?
As we already noted, the use of the same 20 amino acids to make proteins in all living things speaks to their early (even pre-biotic) selection and to the common ancestry of all living things. Complex conserved domain structures shared among otherwise different proteins imply that evolution of protein function has occurred as much by recombinatorial exchange of DNA segments encoding these substructures, as by an accumulation of base substitutions in otherwise redundant genes. Likewise, motifs and folds might also be shared in this way. Protein number can exceed gene number in eukaryotes, in part because cells can produce different RNA variants from the same genes by “alternative splicing”, which can create mRNAs that code different combinations of substructures from same gene! Alternate splicing is discussed in detail in a later chapter). The conservation of amino acid sequences across species (e.g., histones, globins, etc.) is testimony to the common ancestry of eukaryotes. Along with the synthesis of alternate versions of an RNA, an ongoing repurposing of useful regions of protein structure may prove a strategy for producing new proteins without adding new genes to a genome.