Molecular coevolution within a Drosophila clock gene

Sunyaev

2002

284

358

We study fitness landscape in the space of protein sequences by relating sets of human pathogenic missense mutations in 32 proteins to amino acid substitutions that occurred in the course of evolution of these proteins. On average, Ϸ10% of deviations of a nonhuman protein from its human ortholog are compensated pathogenic deviations (CPDs), i.e., are caused by an amino acid substitution that, at this site, would be pathogenic to humans. Normal functioning of a CPD-containing protein must be caused by other, compensatory deviations of the nonhuman species from humans. Together, a CPD and the corresponding compensatory deviation form a Dobzhansky-Muller incompatibility that can be visualized as the corner on a fitness ridge. Thus, proteins evolve along fitness ridges which contain only Ϸ10 steps between successive corners. The fraction of CPDs among all deviations of a protein from its human ortholog does not increase with the evolutionary distance between the proteins, indicating that substitutions that carry evolving proteins around these corners occur in rapid succession, driven by positive selection. Data on fitness of interspecies hybrids suggest that the compensatory change that makes a CPD fit usually occurs within the same protein. Data on protein structures and on cooccurrence of amino acids at different sites of multiple orthologous proteins often make it possible to provisionally identify the substitution that compensates a particular CPD.E volution unfolds on a fitness landscape, a map that relates fitness to the genotype (1). Obviously, most of possible genotypes are always unfit, and some of rare fit genotypes must be arranged in continuous ridges (networks). This general paradigm can be applied, inter alia, to the evolution of proteins. ''If evolution . . . is to occur, functional proteins must form a continuous network which can be traversed by unit mutational steps without passing through non-functional intermediates'' (2). However, data on fitness landscapes are limited, because only a tiny fraction of all possible genotypes is actually available, and inferring fitness of currently nonexisting genotypes is difficult (3-6). Relating data on human pathogenic missense mutations, which represent unfit genotypes, to interspecies differences between homologous proteins, all of which must be fit, offers a novel opportunity to probe the fitness landscape in the space of proteins.Human pathogenic amino acid substitutions tend to occur at less variable sites of proteins (7). Thus, an amino acid that in a nonhuman protein is different from the amino acid at the homologous site of the human ortholog would probably be benign for humans if placed into this site. Still, exceptions to this rule have been described (8, 9).For example, the 53rd site of human ␣-synuclein is normally occupied by Ala, and Ala 3 Thr substitution at this site predisposes to Parkinson's disease. Nevertheless, healthy mice (and rats) carry Thr at the homologous site of their ␣-synucleins (8). We call such a situation a compensated pathog...

Section: Preponderance Of Intramolecular Compensationmentioning

confidence: 90%

Section: Preponderance Of Intramolecular Compensationmentioning

confidence: 99%

Dobzhansky–Muller incompatibilities in protein evolution

Sunyaev

2002

284

358

“…Transformation experiments in which the per gene from other species was introduced into D. melanogaster per 01 flies have revealed a DNA sequence that encodes the species-specific features of locomotor-activity rhythm or male courtship-song rhythm in Drosophila (34)(35)(36). Several clock genes including per and tim also may have DNA sequences for the species-specific circadian rhythms of Drosophila female mating activities.…”

Section: Resultsmentioning

confidence: 99%

Circadian rhythms of female mating activity governed by clock genes in Drosophila

Sakai

Ishida

2001

240

204

The physiological and behavioral activities of many animals are restricted to specific times of the day. The daily fluctuation in the mating activity of some insects is controlled by an endogenous clock, but the genetic mechanism that controls it remains unknown. Here we demonstrate that wild-type Drosophila melanogaster display a robust circadian rhythm in the mating activity, and that these rhythms are abolished in period-or timeless-null mutant flies (per 01 and tim 01 ). Circadian rhythms were lost when rhythm mutant females were paired with wild-type males, demonstrating that female mating activity is governed by clock genes. Furthermore, we detected an antiphasic relationship in the circadian rhythms of mating activity between D. melanogaster and its sibling species Drosophila simulans. Female-and species-specific circadian rhythms in the mating activity of Drosophila seem to cause reproductive isolation.M ost organisms show circadian 24-h rhythmicity in their behavior and physiology. Various behavioral phenomena in insects are controlled by an endogenous clock (1). A core oscillator mechanism of circadian rhythm and feedback loops, involving several clock genes including period (per) and timeless (tim), control locomotor activity and eclosion of the fruit fly, Drosophila melanogaster (2-6). Mutants of D. melanogaster with defective feedback loops (7-10) provide the means of studying the relationship between behavioral rhythms and circadian clock genes.Mating by animals is the most important and fundamental process to select the best partner and to produce progeny. Insects in particular show daily rhythms in mating activity (11)(12)(13)(14)(15)(16)(17), and these are controlled in some by an endogenous clock (14,15). Mating activity of the fruit fly Drosophila mercatorum shows the daily rhythms of the mating activity under 12-h͞12-h light͞dark (LD) cycles (16), and several Drosophila species show the daily rhythms of male courtship under LD cycles (17). However, the genetic mechanism(s) that modulates mating rhythm in these insects remains unknown.The present study shows that wild-type D. melanogaster display a robust circadian rhythm in mating activity that is governed by clock genes and that females are responsible for generating the mating rhythms. Furthermore, we found that the mating activities of disconnected (disco) mutants, which have a severe defect in the optic lobe and are missing lateral neurons, are arrhythmic. We also identified an antiphasic relationship in the circadian rhythms of the mating activity between D. melanogaster and its sibling species, Drosophila simulans. Materials and MethodsFly Strains. D. melanogaster wild-type strains (Canton-S and OGS-4, Ogasawara, Japan), rhythm mutants [period 01 (per 01 ), timeless 01 (tim 01 ), and disconnected 3 forked (disco 3 f )], transgenic flies (hsp-per s13) carrying heat shock (HS)-inducible per coding sequences (18), forked ( f ) mutant, and D. simulans wild-type strains (Og, Ogasawara, Japan; and Ots, Otsuki, Japan) were grown on glucose͞yea...

“…Locomotor activity in LD 12:12 was recorded as described with data transformed to reduce contributions from unusually active͞inactive flies (8,10). For light pulse and T cycle experiments, 1-day-old flies were placed into the locomotor activity apparatus.…”

Section: Methodsmentioning

confidence: 99%

Disruption of Cryptochrome partially restores circadian rhythmicity to the arrhythmic period mutant of Drosophila

Collins

Dissel

Gaten

et al. 2005

Self Cite

The Drosophila melanogaster circadian clock is generated by interlocked feedback loops, and null mutations in core genes such as period and timeless generate behavioral arrhythmicity in constant darkness. In light-dark cycles, the elevation in locomotor activity that usually anticipates the light on or off signals is severely compromised in these mutants. Light transduction pathways mediated by the rhodopsins and the dedicated circadian blue light photoreceptor cryptochrome are also critical in providing the circadian clock with entraining light signals from the environment. The cry b mutation reduces the light sensitivity of the fly's clock, yet locomotor activity rhythms in constant darkness or light-dark cycles are relatively normal, because the rhodopsins compensate for the lack of cryptochrome function. Remarkably, when we combined a period-null mutation with cry b , circadian rhythmicity in locomotor behavior in light-dark cycles, as measured by a number of different criteria, was restored. This effect was significantly reduced in timeless-null mutant backgrounds. Circadian rhythmicity in constant darkness was not restored, and TIM protein did not exhibit oscillations in level or localize to the nuclei of brain neurons known to be essential for circadian locomotor activity. Therefore, we have uncovered residual rhythmicity in the absence of period gene function that may be mediated by a previously undescribed period-independent role for timeless in the Drosophila circadian pacemaker. Although we do not yet have a molecular correlate for these apparently iconoclastic observations, we provide a systems explanation for these results based on differential sensitivities of subsets of circadian pacemaker neurons to light.anticipation ͉ phase shift ͉ oscillator ͉ hourglass ͉ timeless T he PERIOD (PER) and TIMELESS (TIM) proteins are core components of the negative feedback loop that drives circadian oscillations in Drosophila. TIM stabilizes PER, and the PER and TIM proteins cooperate in nuclear entry and retention in key pacemaker cells at night (1). TIM degrades rapidly in response to light, releasing PER to repress per and tim transcription (1). D. melanogaster individuals carrying the null mutation per 01 display arrhythmic locomotor activity under constant darkness (DD), whereas in light-dark (LD) cycles, their locomotor activity is elevated under illumination and reduced in darkness, reflecting the ''masking'' effect of light (2, 3). Another mutation in the gene encoding the blue-light photoreceptor cryptochrome, cry b , gives attenuated light responses in a circadian context (4-7), but normal circadian locomotor behavior in 24-h LD cycles. As part of another study of seasonal behavioral responses to temperature and light effected via changes in per 3Ј splicing, we generated a per 01 ; cry b double mutant (8). We noted that a modest cycle in wild-type per 3Ј splicing in LD cycles at 29°C was exaggerated in per 01 and cry b mutants, yet in the double mutant, the amplitude of the splicing reverted back to ap...