R EVIEWS Reductive evolution of resident genomes Siv G.E. Andersson and Charles G. Kurland he genomes of obligate Small, asexual populations are expected to Despite the differences in parasites, endosymbionts accumulate deleterious substitutions and evolutionary dynamics, the Tand cellular organelles deletions in an irreversible manner, which transmission of both types of evolve under conditions that in the long-term will lead to mutational resident genomes from one are radically different from meltdown and genome decay. Here, we host to the next frequently those of free-living organisms. discuss the influence of such reductive involves bottlenecks and repli- One distinguishing factor is processes on the evolution of genomes that cation in small populations, that they are residents of an replicate within the domain of a host with little opportunity for re- environment that is conditioned genome. combination between variants. by a host genome. For exam- For this reason, the resident ple, it is possible to imagine an S.G.E. Andersson* and C.G. Kurland are in the Dept genomes accumulate deleteri- evolutionary sequence in which of Molecular Biology, Biomedical Center, Uppsala ous mutations at a rate that is University, S-751-24 Uppsala, Sweden. a bacterium begins as a facul- *tel: ϩ46 18 471 4379, fax: ϩ46 18 55 77 23, higher than that for free-living tative resident within a cellular e-mail: [email protected] organisms. Some of these de- domain. During the course of leterious mutations lead to the adaptation to the intracellular environment, the bac- loss of coding sequences, while others lead to a terium can take one of two alternative evolutionary marked variability of resident genome architectures. routes. On the one hand, the host cell can become de- This tendency of small asexual populations to accu- pendent on products provided by the activities of the mulate deleterious mutations is referred to as Muller’s bacterial genome. In this case, the fates of the cell and ratchet3,4 (Box 1). the resident are linked through a symbiotic dependence The validity of Muller’s ratchet has been investi- that is progressively strengthened by the tendency to gated in RNA viruses, which have extraordinarily lose gene functions from one or other genome as a high mutation rates and are subjected to recurrent consequence of the redundancy of their overlapping bottlenecks5–7. Co-infection provides opportunities genomic functions. In the extreme, the two genomes for genetic exchange through recombination or seg- can evolve a relationship as profound as that between mentation in some viral lineages, while others repro- the eukaryote nucleus and the mitochondria. Here, duce in a strictly asexual manner. When populations the symbiosis initiated between the primitive eukary- of asexual and sexual viruses are forced through a se- ote nucleus and an aerobic bacterium has enabled the ries of bottlenecks, deleterious mutations accumulate eukaryote to evolve an aerobic lifestyle. Gene content by genetic drift, resulting in a loss of fitness in both is markedly reduced in mtDNAs, compared with populations. However, while this loss can be reversed those of their eubacterial ancestors1, and some mito- in sexual viruses by recombination and/or segmenta- chondrial genomes have undergone so much reduc- tion during intervening periods of mass selection in tive evolution that they seem to be on the verge of dis- large populations, loss of fitness is effectively irre- appearing entirely from the eukaryotic cells2. versible in asexual viral populations if the rate of On the other hand, the bacterium may become an compensatory back-mutations is low7. obligate parasite that offers no benefits to the host. Because of their obligate intracellular lifestyles, Thus, the fates of the host cell and the parasite are not there are few or no opportunities for resident genomes reciprocally coupled. Instead, a more or less elaborate of bacteria and organelles to recover from the fitness pattern of pathogenesis and defensive strategies evolves. decline caused by genetic drift during transmission Here, too, losses of neutralized genes will strengthen from one host to the other. Indeed, mitochondrial the dependence of the parasite on the host genome. genomes with low recombination frequencies under- The dependence can proceed so far that the parasite is go higher fixation rates for new mutations than their unable to grow outside its host domain. However, sexually reproducing host genomes8,9. Thus, we may whereas obligate endosymbionts are locked inside their wonder if some lineages of resident genomes, such as hosts for ever, most pathogens must find new hosts those of obligate intracellular parasites, are driven to regularly and, hence, are intrinsically more exposed extinction because of the effects of Muller’s ratchet. to the external environment. Thus, the evolutionary forces driving obligate endosymbionts are probably Mitochondria and their codes dictated by selective factors acting on their hosts to a The most extreme examples of reductively evolved much larger extent than those driving obligate intra- resident genomes are those of the cellular organelles. cellular parasites. Phylogenetic reconstructions suggest that mitochondrial Copyright © 1998 Elsevier Science Ltd. All rights reserved. 0966 842X/98/$19.00 PII: S0966-842X(98)01312-2 TRENDS IN MICROBIOLOGY 263 VOL. 6 NO. 7 JULY 1998 R EVIEWS genomes derive from much larger genomes. In particu- Box 1. Muller’s ratchet lar, they appear to be most closely related to the Identifying the evolutionary forces that drive the fixation rates for ␣-proteobacteria and more specifically to an ancestor mutations is an important task of evolutionary biology. Nucleotide of the Rickettsiaceae10–13. Some mitochondrial substitutions consist of synonymous substitutions that do not genomes have retained Ͻ1% of the gene repertoire of alter the protein sequence and nonsynonymous substitutions that modern bacteria. This marked reduction in genome cause amino acid replacements. It is anticipated that some non- size can be partly explained by a massive transfer of synonymous substitutions will have a deleterious or slightly del- genes from the mitochondrial genome to the nuclear eterious effect on fitness. A gradual accumulation of deleterious genome14, a transfer that may have occurred as long mutations can induce an irreversible loss of the most-fit class of as 1–2 billion years ago when the ancestral bacterium organisms from the population5–7,56. This loss can be triggered by began to establish its symbiotic relationship with the high mutation rates, lack of recombination and/or small popu- eukaryotes15. Nevertheless, examples of transfer events lation sizes. Under these conditions, genetic drift can result in the from mitochondria to nuclear genomes as recently as successive loss of the most-fit class, in a ratchet-like manner. within the past 200 million years have been detected16,17, Such a gradual decline in the fitness of a population is referred to suggesting that the process might be continuing. as Muller’s ratchet3,4. A eukaryotic cell can contain hundreds of mito- However, most nonsynonymous mutations are unlikely to be chondria and thousands of mitochondrial genomes. fixed in the population. Indeed, Muller’s ratchet can be opposed These genomes are maternally inherited through the by high rates of compensatory mutations, sexual reproduction cytoplasm of the egg with little or no paternal contri- and/or by large population sizes driven by purifying selection. Be- bution. This mode of transmission effectively restricts cause resident genomes are effectively asexual and often sub- the exchange of genetic material between mitochondr- jected to bottlenecks during each transmission from one host to ial genomes; in effect, the egg is a bottleneck for mito- the other, the loss of fitness induced by genetic drift will not be chondrial genomes. Consequently, mitochondria from slowed down to the same extent as in large, free-living bacterial multicellular organisms display characteristics that are populations. Thus, abnormally higher fixation rates for nonsyn- generally associated with small, asexual populations of onymous substitutions, as observed for intracellularly replicating resident genomes8,9,18,19. They are the victims of drift bacteria, are an indicator that Muller’s ratchet is operative in and Muller’s ratchet, as well as the neutralizing effect these lineages. of the host genome on redundant genes. Animal mitochondria have diverged so far from their free-living bacterial ancestors that they have evolved new codes and a correspondingly specialized U C AG transfer RNA (tRNA) ensemble. If the universal gen- etic code were to be translated unambiguously into the canonical 20 amino acids, an absolute minimal set U C of 24 tRNA species would be required to translate the Phe Ser Tyr Cys A code. One tRNA species is required for each amino U Phe Ser Tyr Cys G acid that is coded by a single codon or by a two- or Leu Ser Term Term four-codon box (16 in total). Two tRNA species are Leu Ser Term Trp U C required for each amino acid encoded by the three- Leu Pro His Arg A codon box for isoleucine and by the six-codon boxes G C Leu Pro His Arg for leucine, serine and arginine. In this minimal set, Leu Pro Gln Arg U the tRNA species would have a greater redundancy Leu Pro Gln Arg C A than is normally seen; for example, each of the four Ile Thr Asn Ser G codon readers would be indifferent to the nucleotide A Ile Thr Asn Ser Ile Thr Lys Arg in codon position three. In some animal mitochon- Met Lys Arg U dria, the number of tRNA genes has decreased below Thr C A the canonical minimum of 24. Thus, there may be as Val Ala Asp Gly G 20 G Val Ala Asp Gly few as 22 tRNA species . The two missing tRNAs in Val Ala Glu Gly these systems correspond to an isoleucine–tRNA nor- Val Ala Glu Gly mally cognate to the codon AUA, and an arginine– Fig.