GENOMIC FLUX: GENOME EVOLUTION BY GENE LOSS AND ACQIBSITION Jeffrey G. LAwrence and John R. Roth 15 Genome evolution is the process by which the introduction of mitochondria and chloro­ content and organization of a species' genetic plasts). In bacteria, however, both genetics and information changes over time. This process genome analysis provide extensive evidence involves four sorts of changes: (i) point mu­ for gene loss and horizontal genetic transfer. tations and gene conversion events gradually Analyses of these data suggest that gene loss alter internal information; (ii) rearrangements and acquisition are likely to be the primary (e.g., inversions, translocations, plasmid inte­ mechanisms by which bacteria adapt geneti­ gration, and transpositions) alter chromosome cally to novel environments and by which topology with little change in information bacterial populations diverge and form sepa­ content; (iii) deletions cause irreversible loss of rate, evolutionarily distinct species. We sug­ information; and (iv) insertions of foreign ma­ gest that bacterial adaptation and speciation are terial can add novel information to a genome. determined predominantly by acquisition of Although the first two processes can create selectively valuable genes (by horizontal trans­ new genes, they act very slowly. Gene loss and fer) and by loss of weakly contributing genes acquisition are genomic changes that can rad­ (by mutation, deletion, and drift from the ically and rapidly increase fitness or alter some population) during periods of relaxed selec­ aspect of lifestyle. tion. Most thought on genome evolution has fo­ We propose that a limitation of genome cused on how the slow sequence changes can expansion couples the rates of gene acquisition cause divergence of gene functions. This is and loss. Genome size may be limited in part understandable because available data suggest by population-based factors that limit the abil­ that horizontal genetic transfer has been a mi­ ity of cells to selectively maintain information; nor contributor to the evolution of eukaryotic some limitation may also be imposed by phys­ lineages (with notable exceptions, such as the iological considerations. The balance between selective gene acquisition and secondarily im­ posed gene loss implies that addition of a for­ eign gene increases the probability of loss of Jeffrey G. Lawrence, Department of Biological Sciences, Uni­ some resident function of lower selective versity of Pittsburgh, Pittsburgh, PA 15260. John R. Roth, Department of Biology, University of Utah, Salt Lake value. The interaction of these factors, we City, UT 84112. Organization of the Prokaryotic Gmomt, Edited by Robert L. Charlebois, © 1999 American Society for Microbiology, Washington, D.C. 263 264 • LA WRENCE AND ROTH suggest, drives the divergence of bacterial others may provide a benefit only under cer­ types. tain circumstances (e.g., TMAO reductase). In this way, one may sort bacterial genes into DYNAMICS OF GENE LOSS broad classes that reflect their average impor­ tance to the cell (Table 1). Mutations in genes Existence of a Gene Implies making essential or very important contribu­ a Function tions to the cell will be strongly counterse­ Traditional bacterial genetics allows identifi­ lected in bacterial populations, since these cation of gene function by correlating mutant mutants cannot compete effectively against growth phenotypes with biochemical defects. otherwise uncompromised conspecific indi­ One can demonstrate the functional impor­ viduals. However, mutations in genes that do tance of many DNA sequences by observing not contribute to cell fitness (e.g., selfish genes the consequences of their disruption. In con­ on transposons) will not be counterselected, trast, genomic analyses identify genes solely as since these neutral mutants do not put their open reading frames, with possible similarity bearers at a selective disadvantage. to genes of known function but without a di­ Between these extremes lies the gray area rect tie to either phenotype or biochemical of mutations that have subtle effects on fitness; defect. we include two extreme classes of genes. In identifying a gene by its sequence, rather Some genes may make a minimal contribution than by mutations and phenotypes, one as­ to fitness under all growth conditions; others sumes implicitly that the very presence of a may make a large contribution to fitness but gene implies that it must confer a selectable do so only in a rare subset of environments. function. That is, the gene could only have For either class of gene, the average selection remained in the population if the encoded coefficient is low. The fate of mutations in the function is important; that is, mutants lacking most weakly selected genes is governed by a the function show reduced fitness and are re­ complex interaction of natural selection, ran­ moved from the population by natural selec­ dom genetic drift, population size, population tion. This evolutionary argument implies that subdivision, and genetic exchange within the a mutant phenotype (perhaps difficult to dem­ species. onstrate) will result if the gene is disrupted. In For any one species, a different fraction of principle, a few genes might be encountered genes may make up each category in Table 1. which either have just been introduced or In small genomes (e.g., that of Mycoplasmagen­ have escaped selection, and the process of italium), a large fraction of genes are likely to elimination has not yet run its course; data be essential (42), while a smaller fraction of supporting such cases will be pres~nted below. genes are likely to be essential in prokaryotes An important question arises when one tries with larger genomes (e.g., Escherichia colt). Re­ to define the function of a gene (or determine gardless of the distribution, some genes in any whether it is one of the rare nonfunctional genome will fall at the bottom of the list and examples). That is, how important must a make a minimal contribution to cellular fitness function be to assure the maintenance of its (i.e., they are nearly neutral). These genes will gene? How large a fitness contribution must a be at greatest risk for functional loss by mu­ gene confer to remain in a genome? tation, deletion, and genetic drift. This class of genes may comprise a large portion of ge­ A Spectrum of Fitness Contributions nomic information. All bacterial genes are not equally important. In E. coli, few of the 4,286 protein-coding Functions performed by bacterial cells are di­ genes are essential. Isolation of temperature­ verse, and while some are essential for life un­ sensitive lethal mutations suggests that only der all conditions (e.g., RNA polymerase), ~200 genes are essential on rich medium (55). 15. GENOMIC FLUX • 265 TABLE 1 Fitness contributions of bacterial genes Fitness con- Class Physiological role Consequence of null mutation tribution Top Large Essential Lethality High Large Very important Strong impairment Middle Moderate Important Obvious impairment Low (I) Very low Minimally useful in all Subtle impairment; hard to detect experimen­ conditions tally Low (II) Very low Important in rare con- Strong impairment in some environments ditions Neutral None None None This estimate of the minimal number of es­ fitness contributions c2.n be maintained in a sential genes in the E. coli chromosome (even population. If mutation rates are high, a when adjusted for failure to detect some genes stronger selective coefficient would be re­ by this method) is congruent with theoretical quired to maintain a gene in a population of estimates of minimal gene number (256 genes) the same size. Therefore, s is proportional to based on comparisons of several bacterial ge­ the mutation rate, µ,(sex: µ,).As the mutation nomes (42). Moreover, a similar number of rate increases, null mutations in a gene under genes are detected by mutations that cause a weak selection are more likely to drift to fix­ nutritional requirement for growth. Together, ation, since defective alleles are created more these rather important gene classes constitute rapidly than they can be removed by selection. approximately 10% of the E. coli genome; the As population size decreases, loss by drift be­ remaining 90% of genes must make smaller comes more likely and more genes become contributions to fitness or be needed only un­ effectively neutral (49, 50). In these smaller der particular conditions. This conclusion is populations, a larger selective value is required supported by the analysis of E. coli mutants to maintain a gene in the population. That is, described above and by the observation that a gene must make a stronger contribution to the genomes of free-living bacteria vary fitness to be selectively maintained. Therefore, greatly in size. In additism, experimental ap­ s is inversely proportional to the effective pop­ proaches have revealed that lesions in a large ulation size, N, (s ex: µ,/ N,). The dynamics of proportion of genes in the yeast Saccharomyces how selection acts on mutant alleles is influ­ cerevisiae have only minimal effects on fitness enced by the rate of intraspecific recombina­ (65). tion. As the recombination rate increases, se­ lection can more effectively remove the steady A Minimal Fitness Contribution Is accumulation of detrimental alleles from a Required for Gene Maintenance . population, and the species can avoid to some While a complete description of the processes extent the fitness decline mandated by Mul­ governing the selective maintenance