Evidence for stabilizing selection in a eukaryotic enhancer element

Eukaryotic gene expression is mediated by compact cis-regulatory modules, or enhancers, which are bound by specific sets of transcription factors. The combinatorial interaction of these bound transcription factors determines time- and tissue-specific gene activation or repression. The even-skipped stripe 2 element controls the expression of the second transverse stripe of even-skipped messenger RNA in Drosophila melanogaster embryos, and is one of the best characterized eukaryotic enhancers. Although even-skipped stripe 2 expression is strongly conserved in Drosophila, the stripe 2 element itself has undergone considerable evolutionary change in its binding-site sequences and the spacing between them. We have investigated this apparent contradiction, and here we show that two chimaeric enhancers, constructed by swapping the 5′ and 3′ halves of the native stripe 2 elements of two species, no longer drive expression of a reporter gene in the wild-type pattern. Sequence differences between species have functional consequences, therefore, but they are masked by other co-evolved differences. On the basis of these results, we present a model for the evolution of eukaryotic regulatory sequences.

[1]  J. Sulston,et al.  Dopaminergic neurons in the nematode Caenorhabditis elegans , 1975, The Journal of comparative neurology.

[2]  M. Kimura,et al.  The neutral theory of molecular evolution. , 1983, Scientific American.

[3]  M. Kimura,et al.  Possibility of extensive neutral evolution under stabilizing selection with special reference to nonrandom usage of synonymous codons. , 1981, Proceedings of the National Academy of Sciences of the United States of America.

[4]  H. Horvitz,et al.  Serotonin and octopamine in the nematode Caenorhabditis elegans. , 1982, Science.

[5]  M. Kimura.  The Neutral Theory of Molecular Evolution: Introduction , 1983 .

[6]  A. Wilson,et al.  Molecular Evolution in Drosophila and the Higher Diptera II. A Time Scale for Fly Evolution , 1984 .

[7]  M. Frasch,et al.  Complementary patterns of even-skipped and fushi tarazu expression involve their differential regulation by a common set of segmentation genes in Drosophila. , 1987, Genes & development.

[8]  P. V. von Hippel,et al.  Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. , 1987, Journal of molecular biology.

[9]  Tom Maniatis,et al.  Early and late periodic patterns of even skipped expression are controlled by distinct regulatory elements that respond to different spatial cues , 1989, Cell.

[10]  M. Levine,et al.  Autoregulatory and gap gene response elements of the even‐skipped promoter of Drosophila. , 1989, The EMBO journal.

[11]  T. Ohta,et al.  Theoretical study of near neutrality. I. Heterozygosity and rate of mutant substitution. , 1990, Genetics.

[12]  H. Horvitz,et al.  Effects of starvation and neuroactive drugs on feeding in Caenorhabditis elegans. , 1990, The Journal of experimental zoology.

[13]  M. Levine,et al.  Regulation of a segmentation stripe by overlapping activators and repressors in the Drosophila embryo. , 1991, Science.

[14]  M. Levine,et al.  Regulation of even‐skipped stripe 2 in the Drosophila embryo. , 1992, The EMBO journal.

[15]  C. Kenyon,et al.  A C. elegans mutant that lives twice as long as wild type , 1993, Nature.

[16]  Jun S. Liu,et al.  Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. , 1993, Science.

[17]  M. Levine,et al.  Spacing ensures autonomous expression of different stripe enhancers in the even-skipped promoter. , 1993, Development.

[18]  L. Avery,et al.  The genetics of feeding in Caenorhabditis elegans. , 1993, Genetics.

[19]  M. Kreitman,et al.  Evolutionary dynamics of the enhancer region of even-skipped in Drosophila. , 1995, Molecular biology and evolution.

[20]  A. Astrup,et al.  Long-term effects of fluoxetine on glycemic control in obese patients with non-insulin-dependent diabetes mellitus or glucose intolerance: influence on muscle glycogen synthase and insulin receptor kinase activity. , 1995, Metabolism: clinical and experimental.

[21]  D. Weinshenker,et al.  Genetic and pharmacological analysis of neurotransmitters controlling egg laying in C. elegans , 1995, The Journal of neuroscience : the official journal of the Society for Neuroscience.

[22]  M. Levine,et al.  The eve stripe 2 enhancer employs multiple modes of transcriptional synergy. , 1996, Development.

[23]  D. Riddle,et al.  Control of C. elegans Larval Development by Neuronal Expression of a TGF-β Homolog , 1996, Science.

[24]  Wendy S. Schackwitz,et al.  Chemosensory Neurons Function in Parallel to Mediate a Pheromone Response in C. elegans , 1996, Neuron.

[25]  D. Kuhn,et al.  Expression and Deletion Mutagenesis of Tryptophan Hydroxylase Fusion Proteins: Delineation of the Enzyme Catalytic Core , 1996, Journal of Neurochemistry.

[26]  D. Hogness,et al.  Effect of Polymorphism in the Drosophila Regulatory Gene Ultrabithorax on Homeotic Stability , 1996, Science.

[27]  Koutarou D. Kimura,et al.  daf-2, an insulin receptor-like gene that regulates longevity and diapause in Caenorhabditis elegans. , 1997, Science.

[28]  G. Ruvkun,et al.  The DAF-3 Smad protein antagonizes TGF-beta-related receptor signaling in the Caenorhabditis elegans dauer pathway. , 1997, Genes & development.

[29]  G. Ruvkun,et al.  The Fork head transcription factor DAF-16 transduces insulin-like metabolic and longevity signals in C. elegans , 1997, Nature.

[30]  R. Plasterk,et al.  Reverse genetics by chemical mutagenesis in Caenorhabditis elegans , 1997, Nature Genetics.

[31]  V. Csernus,et al.  Influence of melatonin and serotonin on glucose‐stimulated insulin release from perifused rat pancreatic islets in vitro , 1997, Journal of pineal research.

[32]  E. Davidson,et al.  The hardwiring of development: organization and function of genomic regulatory systems. , 1997, Development.

[33]  P. Sternberg,et al.  Two neuronal G proteins are involved in chemosensation of the Caenorhabditis elegans Dauer-inducing pheromone. , 1997, Genetics.

[34]  William R. Schafer,et al.  Control of Alternative Behavioral States by Serotonin in Caenorhabditis elegans , 1998, Neuron.

[35]  D. Riddle,et al.  Two pleiotropic classes of daf-2 mutation affect larval arrest, adult behavior, reproduction and longevity in Caenorhabditis elegans. , 1998, Genetics.

[36]  N. Patel,et al.  Functional analysis of eve stripe 2 enhancer evolution in Drosophila: rules governing conservation and change. , 1998, Development.

[37]  L. Tecott,et al.  Leptin-independent hyperphagia and type 2 diabetes in mice with a mutated serotonin 5-HT2C receptor gene , 1998, Nature Medicine.

[38]  H. Horvitz,et al.  The C. elegans Protein EGL-1 Is Required for Programmed Cell Death and Interacts with the Bcl-2–like Protein CED-9 , 1998, Cell.

[39]  B. Lakowski,et al.  The genetics of caloric restriction in Caenorhabditis elegans. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[40]  A. Long,et al.  Two sites in the Delta gene region contribute to naturally occurring variation in bristle number in Drosophila melanogaster. , 1998, Genetics.

[41]  A Bairoch,et al.  New insulin-like proteins with atypical disulfide bond pattern characterized in Caenorhabditis elegans by comparative sequence analysis and homology modeling. , 1998, Genome research.

[42]  J. Reinitz,et al.  Transcriptional repression by the Drosophila giant protein: cis element positioning provides an alternative means of interpreting an effector gradient. , 1999, Development.

[43]  Janet S. Duerr,et al.  The cat-1 Gene of Caenorhabditis elegansEncodes a Vesicular Monoamine Transporter Required for Specific Monoamine-Dependent Behaviors , 1999, The Journal of Neuroscience.