3.6: Proteins, Genes and Evolution- How Many Proteins are We?
- Page ID
- 88912
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\(\newcommand{\avec}{\mathbf a}\) \(\newcommand{\bvec}{\mathbf b}\) \(\newcommand{\cvec}{\mathbf c}\) \(\newcommand{\dvec}{\mathbf d}\) \(\newcommand{\dtil}{\widetilde{\mathbf d}}\) \(\newcommand{\evec}{\mathbf e}\) \(\newcommand{\fvec}{\mathbf f}\) \(\newcommand{\nvec}{\mathbf n}\) \(\newcommand{\pvec}{\mathbf p}\) \(\newcommand{\qvec}{\mathbf q}\) \(\newcommand{\svec}{\mathbf s}\) \(\newcommand{\tvec}{\mathbf t}\) \(\newcommand{\uvec}{\mathbf u}\) \(\newcommand{\vvec}{\mathbf v}\) \(\newcommand{\wvec}{\mathbf w}\) \(\newcommand{\xvec}{\mathbf x}\) \(\newcommand{\yvec}{\mathbf y}\) \(\newcommand{\zvec}{\mathbf z}\) \(\newcommand{\rvec}{\mathbf r}\) \(\newcommand{\mvec}{\mathbf m}\) \(\newcommand{\zerovec}{\mathbf 0}\) \(\newcommand{\onevec}{\mathbf 1}\) \(\newcommand{\real}{\mathbb R}\) \(\newcommand{\twovec}[2]{\left[\begin{array}{r}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\ctwovec}[2]{\left[\begin{array}{c}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\threevec}[3]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\cthreevec}[3]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\fourvec}[4]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\cfourvec}[4]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\fivevec}[5]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\cfivevec}[5]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\mattwo}[4]{\left[\begin{array}{rr}#1 \amp #2 \\ #3 \amp #4 \\ \end{array}\right]}\) \(\newcommand{\laspan}[1]{\text{Span}\{#1\}}\) \(\newcommand{\bcal}{\cal B}\) \(\newcommand{\ccal}{\cal C}\) \(\newcommand{\scal}{\cal S}\) \(\newcommand{\wcal}{\cal W}\) \(\newcommand{\ecal}{\cal E}\) \(\newcommand{\coords}[2]{\left\{#1\right\}_{#2}}\) \(\newcommand{\gray}[1]{\color{gray}{#1}}\) \(\newcommand{\lgray}[1]{\color{lightgray}{#1}}\) \(\newcommand{\rank}{\operatorname{rank}}\) \(\newcommand{\row}{\text{Row}}\) \(\newcommand{\col}{\text{Col}}\) \(\renewcommand{\row}{\text{Row}}\) \(\newcommand{\nul}{\text{Nul}}\) \(\newcommand{\var}{\text{Var}}\) \(\newcommand{\corr}{\text{corr}}\) \(\newcommand{\len}[1]{\left|#1\right|}\) \(\newcommand{\bbar}{\overline{\bvec}}\) \(\newcommand{\bhat}{\widehat{\bvec}}\) \(\newcommand{\bperp}{\bvec^\perp}\) \(\newcommand{\xhat}{\widehat{\xvec}}\) \(\newcommand{\vhat}{\widehat{\vvec}}\) \(\newcommand{\uhat}{\widehat{\uvec}}\) \(\newcommand{\what}{\widehat{\wvec}}\) \(\newcommand{\Sighat}{\widehat{\Sigma}}\) \(\newcommand{\lt}{<}\) \(\newcommand{\gt}{>}\) \(\newcommand{\amp}{&}\) \(\definecolor{fillinmathshade}{gray}{0.9}\)If evolution did not have to select totally new proteins for each new cellular function, then how many genes does it really take to make an organism? Estimates have suggested that it takes from nineteen thousand to twenty-five thousand coding genes to make and to operate a human and all its proteins (Check out Pertea and Salzberg at # of genes in a human genome and Abascal, F. et al. at ~20% of human genes are mysterious!). Nevertheless, our cells, and those of eukaryotes generally, may express as many as one hundred thousand different proteins. Our protein-coding genes may be far fewer than the number of proteins we make. How is this possible? It appears that there must be better, more efficient ways to evolve new and useful cellular tasks than evolving new genes!
As we already noted, the use of the same twenty amino acids to make proteins in all living things speaks to their early (even prebiotic) 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 such substructures as by an accumulation of base substitutions in otherwise redundant genes. Likewise, motifs and folds might also be shared in this way. The protein count also exceeds gene number in part because cells can produce different mRNA variants from the same genes by alternate splicing, a process that produces mRNAs that code for different combinations of substructures from the same gene! Alternate splicing is discussed in detail in a later chapter. These transcriptional and post-transcriptional phenomena explain eukaryotic protein numbers, but also the conservation of gene and amino-acid sequences across species (e.g., histones and globins), the key testimony to their common ancestry.
Along with the synthesis of alternate versions of a single 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.
After your readings here (and maybe some extra research), cite examples of additional proteins that share a domain or motif, and explain why shared domains or motifs might be selected in evolution.
Mycoplasma mycoides has a \(10^6\) bp-genome encoding only about a thousand genes. C. Venter (of human genome fame) engineered M. mycoides to survive with just 473 genes from the related M. capricolum species (the cause of leprosy and tuberculosis). This is the smallest genome known to support life (see Synthetic Mycobacterium Lives with Small Genome for more). What are some likely functions of the 473 M. capricolum genes, and what might proteins encoded by the “other” (nearly five hundred) genes in normal M. capricolum cells be doing?