Cell Vm is defined as the per-generation increase in the math- Salmonella flagellar synthesis genes(Simon et al., 1980). ematical variance of a quantitative trait across a population The promoter is surrounded by inverted repeats, which due to random, unselected mutations. Mutational vari- are subject to frequent recombination events that result ance is typically measured by allowing a broad spectrum in promoter inversion. When the promoter inverts, the ex of unselected mutations to accumulate by passaging indi- pression of one flagellar gene is arrested, and a second tion sizes (eliminating any but the strongest effects of though the precise biological function of this phase varia- selection), followed by measurement of the phenotype tion remains emonstrated f two different flagellar antigens may help to evade the host im- Given a mutation rate and a target size, one may, in prin mune system and/or to infect different tissues(van der ple, predict the stability of a phenotype of interest. How- Woude and Baumler, 2004). Many other contingency loci ever, researchers have discovered several cellular mech- have been described, mostly in pathogenic microorgan- anisms that increase or decrease the rates of change a subset of phenotypes. It is useful here to distinguish be- pression of cell-surface antigens. A special case is that tween regulation of global variation, locus-specific varia- of the trypanosomes, which contain an arsenal of about tion, and temporal regulation of variation(local or global; 1000 silent"variant surface glycoproteins"(VSGs ). Only Jablonka and Lamb, 2005: Metzgar and Wills, 2000) the one gene localized in the active VSG expression site The broad idea that cells have evolved the ability to regu- is transcribed. By regularly replacing the VSG gene ate the global tempo of phenotypic change is irrefutable. the active expression site, the parasites constantly switch The existence of proofreading activities and sophisticated their outer surface coat(Barry and McCulloch, 2001) error-correction systems encoded in most genomes dem Another interesting case of contingency loci is found in onstrates that evolution has selected for systems that the common brewer's yeast Saccharomyces cerevisiae modulate the fidelity of information transfer between gen- Many S. cerevisiae cell-surface genes contain tandemly erations. Indeed, subpopulations of cells lacking proof repeated DNA sequences in their coding sequences reading activities known as "mutators, are found a (Verstrepen et aL., 2004, 2005). The repeats are subject high frequencies (often on the order of 1%)in microbes to frequent recombination events, which often result in gathered from the environment(LeClerc et al., 1996). repeats being gained or lost(Figure 2). One such gene, However, we aim specifically to discuss examples of FLO1, encodes a cell-surface protein that enables yeast localized variation in the fidelity of information transfer cells to adhere to various substrates. Cells carrying a (genotypic or, in some cases, exclusively phenotypic). greater number of repeats in FLo1 show a stronger adher- We will also discuss mechanisms that regulate the timing ence to plastic surfaces such as those used in medical de of variability, with cellular stress generally leading to in- vices. Repeat variation may therefore allow fungi to rapidly creased variation. Finally, we describe a few examples attune their cell surfaces to new environments. It is inter where cells are able to influence both the timing and loca- esting to note that in this case, the repeats do not ca tion of variability in response to environmental cues. switching of expression states in a repertoire of cell-sur- face genes. Instead, unstable intragenic repeats generate Localized variation limited changes in a small set of expressed proteins. Sim- Contingency Loci and Rapid Genotypic Variation ilar repeat variation in genes of pathogenic fungi may con- Analysis of mutation rates in the E. coli Lac operon tribute to the cell-surface variability needed to evade the showed that many mutation hot spots corresponded not host immune system (Verstrepen et al., 2005) to base substitutions but to insertions and deletions in Although they are usually not referred to as contingency short repeated sequences(Farabaugh et al., 1978). Since loci, similar hypervariable loci are also found in m then, numerous examples have been described of rapid zoans, including humans(where they are often associated sequence change associated with hypervariable DNa with diseases). Classic examples include neurodegenera- loci, termed"contingency loci"(for a review, see van der tive diseases, such as Huntington's chorea and fragile x Woude and Baumler, 2004). Through various mecha syndrome, where expansion of intragenic repeats leads nisms, these loci are unusually prone to specific types of to malfunction of the associated gene. The timescale of mutations that result in the altemating on- and off-switch these expansion/contraction events has been extensivel ing of specific genes. Switching between the two resulting studied in fragile X syndrome, where the rate of repeat ex- phenotypes(called"phase variation")enables organisms pansion varies depending on the sex of the carrier and the to quickly adapt to frequent and recurring changes in the initial(pre-existing) number of repeats: in females carrying environment. Switching frequencies as high as 10 alleles with 90-100 repeats, up to 87% of the offspring in- have been reported, although frequencies on the order herit a disease-causing full mutation (200 repeats). This of one switch in every 102-105 generations are more com- rate drops to m5% for the offspring of mothers carrying mon(van der Woude and Baumler, 2004) between 55 and 59 repeats, whereas mothers with fewer The best known examples of contingency loci are in than 55 repeats never pass on the full mutation to their bacteria. The term"contingency locus"was first coined children(Nolin et al., 2003). Interestingly, at many of these to describe the reversible promoter that controls the repeat-containing genes, repetition is highly conserved ce128,655668. February23,2007@2007 Elsevier Inc.657Vm is defined as the per-generation increase in the math￾ematical variance of a quantitative trait across a population due to random, unselected mutations. Mutational vari￾ance is typically measured by allowing a broad spectrum of unselected mutations to accumulate by passaging indi￾viduals of a species independently at very small popula￾tion sizes (eliminating any but the strongest effects of selection), followed by measurement of the phenotype of interest. Given a mutation rate and a target size, one may, in prin￾ciple, predict the stability of a phenotype of interest. How￾ever, researchers have discovered several cellular mech￾anisms that increase or decrease the rates of change of a subset of phenotypes. It is useful here to distinguish be￾tween regulation of global variation, locus-specific varia￾tion, and temporal regulation of variation (local or global; Jablonka and Lamb, 2005; Metzgar and Wills, 2000). The broad idea that cells have evolved the ability to regu￾late the global tempo of phenotypic change is irrefutable. The existence of proofreading activities and sophisticated error-correction systems encoded in most genomes dem￾onstrates that evolution has selected for systems that modulate the fidelity of information transfer between gen￾erations. Indeed, subpopulations of cells lacking proof￾reading activities, known as ‘‘mutators,’’ are found at high frequencies (often on the order of 1%) in microbes gathered from the environment (LeClerc et al., 1996). However, we aim specifically to discuss examples of localized variation in the fidelity of information transfer (genotypic or, in some cases, exclusively phenotypic). We will also discuss mechanisms that regulate the timing of variability, with cellular stress generally leading to in￾creased variation. Finally, we describe a few examples where cells are able to influence both the timing and loca￾tion of variability in response to environmental cues. Localized Variation Contingency Loci and Rapid Genotypic Variation Analysis of mutation rates in the E. coli Lac operon showed that many mutation hot spots corresponded not to base substitutions but to insertions and deletions in short repeated sequences (Farabaugh et al., 1978). Since then, numerous examples have been described of rapid sequence change associated with hypervariable DNA loci, termed ‘‘contingency loci’’ (for a review, see van der Woude and Baumler, 2004). Through various mecha￾nisms, these loci are unusually prone to specific types of mutations that result in the alternating on- and off-switch￾ing of specific genes. Switching between the two resulting phenotypes (called ‘‘phase variation’’) enables organisms to quickly adapt to frequent and recurring changes in the environment. Switching frequencies as high as 101 have been reported, although frequencies on the order of one switch in every 103 –105 generations are more com￾mon (van der Woude and Baumler, 2004). The best known examples of contingency loci are in bacteria. The term ‘‘contingency locus’’ was first coined to describe the reversible promoter that controls the Salmonella flagellar synthesis genes (Simon et al., 1980). The promoter is surrounded by inverted repeats, which are subject to frequent recombination events that result in promoter inversion. When the promoter inverts, the ex￾pression of one flagellar gene is arrested, and a second gene on the other side of the promoter is activated. Al￾though the precise biological function of this phase varia￾tion remains to be demonstrated, the expression of two different flagellar antigens may help to evade the host im￾mune system and/or to infect different tissues (van der Woude and Baumler, 2004). Many other contingency loci have been described, mostly in pathogenic microorgan￾isms, where hypervariable loci commonly control the ex￾pression of cell-surface antigens. A special case is that of the trypanosomes, which contain an arsenal of about 1000 silent ‘‘variant surface glycoproteins’’ (VSGs). Only the one gene localized in the active VSG expression site is transcribed. By regularly replacing the VSG gene in the active expression site, the parasites constantly switch their outer surface coat (Barry and McCulloch, 2001). Another interesting case of contingency loci is found in the common brewer’s yeast Saccharomyces cerevisiae. Many S. cerevisiae cell-surface genes contain tandemly repeated DNA sequences in their coding sequences (Verstrepen et al., 2004, 2005). The repeats are subject to frequent recombination events, which often result in repeats being gained or lost (Figure 2). One such gene, FLO1, encodes a cell-surface protein that enables yeast cells to adhere to various substrates. Cells carrying a greater number of repeats in FLO1 show a stronger adher￾ence to plastic surfaces such as those used in medical de￾vices. Repeat variation may therefore allow fungi to rapidly attune their cell surfaces to new environments. It is inter￾esting to note that in this case, the repeats do not cause switching of expression states in a repertoire of cell-sur￾face genes. Instead, unstable intragenic repeats generate limited changes in a small set of expressed proteins. Sim￾ilar repeat variation in genes of pathogenic fungi may con￾tribute to the cell-surface variability needed to evade the host immune system (Verstrepen et al., 2005). Although they are usually not referred to as contingency loci, similar hypervariable loci are also found in meta￾zoans, including humans (where they are often associated with diseases). Classic examples include neurodegenera￾tive diseases, such as Huntington’s chorea and fragile X syndrome, where expansion of intragenic repeats leads to malfunction of the associated gene. The timescale of these expansion/contraction events has been extensively studied in fragile X syndrome, where the rate of repeat ex￾pansion varies depending on the sex of the carrier and the initial (pre-existing) number of repeats: in females carrying alleles with 90–100 repeats, up to 87% of the offspring in￾herit a disease-causing full mutation (>200 repeats). This rate drops to 5% for the offspring of mothers carrying between 55 and 59 repeats, whereas mothers with fewer than 55 repeats never pass on the full mutation to their children (Nolin et al., 2003). Interestingly, at many of these repeat-containing genes, repetition is highly conserved Cell 128, 655–668, February 23, 2007 ª2007 Elsevier Inc. 657