4. How many genes are essential?

3.4 How many genes are essential?

Natural selection is the force that ensures that useful genes are retained in the genome. Mutations occur at random, and their most common effect in an open reading frame will be to damage the protein product. An organism with a damaging mutation will be at a disadvantage in evolution, and ultimately the mutation will be eliminated by the competitive failure of organisms carrying it. The frequency of a disadvantageous allele in the population is balanced between the generation of new mutations and the elimination of old mutations. Reversing this argument, whenever we see an intact open reading frame in the genome, we assume that its product plays a useful role in the organism. Natural selection must have prevented mutations from accumulating in the gene. The ultimate fate of a gene that ceases to be useful is to accumulate mutations until it is no longer recognizable.

The maintenance of a gene implies that it confers a selective advantage on the organism. But in the course of evolution, even a small relative advantage may be the subject of natural selection. However, we should like to know how many genes are actually essential. This means that their absence is lethal to the organism. In the case of diploid organisms, it means of course that the homozygous null mutation is lethal.

Figure 3.5 Genome sizes and gene numbers are known from complete sequences for several organisms (Arabidopsis, Drosophila, and man are estimated from partial data). Lethal loci are estimated from genetic data.

We might assume that the proportion of essential genes will decline with increase in genome size, given that larger genomes may have multiple, related copies of particular gene functions. So far this expectation has not been borne out by the data (see Figure 3.5).

One approach to the issue of gene number is to determine the number of essential genes by mutational analysis. If we saturate some specified region of the chromosome with mutations that are lethal, the mutations should map into a number of complementation groups that corresponds to the number of lethal loci in that region. By extrapolating to the genome as a whole, we may calculate the total essential gene number .

In the organism with the smallest known genome (Mycoplasma genitalium), random insertions inactivate only about two thirds of the genes (Hutchison et al., 1999).Similarly, fewer than half of the genes of E. coli appear to be essential (Goebl and Petes, 1986). An experiment to determine what proportion of genes are essential has produced an analogous result in the yeast S. cerevisiae. The genome is relatively small, and a large fraction (>50%) is transcribed, compared with higher eukaryotes. When insertions were introduced at random into the genome, only 12% were lethal, and another 14% impeded growth. The majority (70%) of the insertions had no effect. Analyses such as this suggest that only a minority of genes have lethal effects or directly impair growth (Goebl et al., 1982).

The most extensive analyses of essential gene number in a higher eukaryote have been made in Drosophila through attempts to correlate visible aspects of chromosome structure with the number of functional genetic units. The notion that this might be possible arose originally from the presence of bands in the polytene chromosomes of D. melanogaster. (These chromosomes are found at certain developmental stages and represent an unusually extended physical form, in which a series of bands [more formally called chromomeres] can be seen. We discuss their properties in 18 Chromosomes.) From the early concept that the bands might represent a linear order of genes, we have come to the attempt to correlate the organization of genes with the organization of bands. There are ~5000 bands in the D. melanogaster haploid set; they vary in size over an order of magnitude, but on average there is ~20 kb of DNA per band.

The basic approach is to saturate a chromosomal region with mutations. Usually the mutations are simply collected as lethals, without analyzing the cause of the lethality. Any mutation that is lethal is taken to identify a locus that is essential for the organism. Sometimes mutations cause visible deleterious effects short of lethality, in which case we also count them as identifying an essential locus. When the mutations are placed into complementation groups, the number can be compared with the number of bands in the region, or individual complementation groups may even be assigned to individual bands. The purpose of these experiments has been to determine whether there is a consistent relationship between bands and genes; for example, does every band contain a single gene?

Totaling the analyses that have been carried out over the past 30 years, the number of lethal complementation groups is ~70% of the number of bands. It is an open question whether there is any functional significance to this relationship. But irrespective of the cause, the equivalence gives us a reasonable estimate for the lethal gene number of ~3600. If we assume that the organization of the Drosophila and mammalian genomes is in principle similar, then by comparing the average sizes of their genes and genomes, we would predict >75,000 lethal genes for man. By any measure, the number of lethal loci in Drosophila is significantly less than the total number of genes, and presumably the same is true of man (Judd et al., 1972).

How do we explain the survival of genes whose deletion appears to have no effect? One possibility is that there is redundancy, that such genes are present in multiple copies. This is certainly true in some cases, in which multiple (related) genes must be knocked out in order to produce an effect. It is clear that there are cases in which a genome has more than one gene capable of providing a protein to fulfill a certain function, and all of them must be deleted to produce a lethal effect.

The idea that some genes are not essential (or at least cannot be shown to have serious effects upon the phenotype) raises some important questions. Does the genome contain genuinely dispensable genes, or do these genes actually have effects upon the phenotype that are significant at least during the long march of evolution? The theory of natural selection would suggest that the loss of individual genes in such circumstances produces a small disadvantage, which although not evident to us, is sufficient for the gene to be retained during the course of evolution.

Key questions that remain to be answered systematically are: What proportion of the total number of genes is essential, in how many do mutations produce at least detectable effects, and are there genes that are genuinely dispensable? Subsidiary questions about the genome as a whole are: What are the functions (if any) of DNA that does not reside in genes? What effect does a large change in total size have on the operation of the genome, as in the case of the related amphibians?

This section updated 1-11-2000

Research

Goebl, M. G. and Petes, T. D. (1986). Most of the yeast genomic sequences are not essential for cell growth and division. Cell 46, 983-992.

Goebl, M. G. et al. (1982). Most of the yeast genomic sequences are not essential for cell growth and division.. Cell 46, 983-992.

Hutchison, C. A. et al. (1999). Global transposon mutagenesis and a minimal myoplasma genome.. Science 286, 2165-2169.

Judd, N. H., Shen, M. W., and Kaufman, T. C. (1972). The anatomy and function of a segment of the X chromosome of D. melanogaster. Genetics 71, 139-156.