Descriptive and functional characterization of variation in the Fundulus heteroclitus Ldh-B proximal promoter.

Variation in enzyme expression may be an important mechanism for physiological and evolutionary adaptation. The Ldh-B locus in the teleost fish Fundulus heteroclitus is one of a very few loci for which an evolutionary difference in transcription rate between populations has been demonstrated. To begin to understand the molecular modifications that are responsible for altering transcription, we have characterized the Ldh-B proximal promoter using a combination of sequence analysis, transient transfection, and in vivo footprinting. The Ldh-B gene has several transcription start sites and a TATA-less, Inr (initiator of transcription motif) containing promoter with multiple Sp1-like motifs. Transfection experiments reveal that Sp1 sites, TCC repeats, and Inrs are functional components of the proximal promoter. We find substantial sequence variation between populations within the proximal promoter (250 bp from the transcription start sites) and footprinting analysis indicates that some of this sequence variation is associated with differential protein binding to the apparent TFIID binding site and Sp1 sites. Together, these data suggest that variation in the Ldh-B proximal promoter may play a role in the observed difference in transcription rates between northern and southern populations of F. heteroclitus.

[1]  J. Darnell,et al.  Dependence of liver-specific transcription on tissue organization , 1985, Molecular and cellular biology.

[2]  L. Ercolani,et al.  Identification of a core motif that is recognized by three members of the HMG class of transcriptional regulators: IRE‐ABP, SRY, and TCF‐1α , 1992, Journal of cellular biochemistry.

[3]  D. Cooper,et al.  Regulatory mutations and human genetic disease. , 1992, Annals of medicine.

[4]  M. D. Brennan,et al.  Redundant cis-acting elements control expression of the Drosophila affinidisjuncta Adh gene in the larval fat body. , 1994, Nucleic acids research.

[5]  K. Jeang,et al.  In vitro and in vivo binding of human immunodeficiency virus type 1 Tat protein and Sp1 transcription factor , 1993, Journal of virology.

[6]  Knut Schmidt-Nielsen,et al.  Animal Physiology: Adaptation and Environment , 1985 .

[7]  J. Darnell,et al.  Hepatoma variants (C2) are defective for transcriptional and post‐transcriptional actions from both endogenous and viral genomes. , 1987, The EMBO journal.

[8]  M. Takiguchi,et al.  In vitro analysis of the rat liver-type arginase promoter. , 1991, The Journal of biological chemistry.

[9]  G. Crabtree,et al.  A transcriptional hierarchy involved in mammalian cell-type specification , 1992, Nature.

[10]  W. W. Jong,et al.  Duck Lactate Dehydrogenase B/ε-Crystallin Gene: Lens Recruitment of a GC-promoter , 1993 .

[11]  Z. Wang,et al.  A second transcriptionally active DNA-binding site for the Wilms tumor gene product, WT1. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[12]  M. Sporn,et al.  Regulation of the transforming growth factor-β1 and -β3 promoters by transcription factor Spl , 1993 .

[13]  J E Darnell,et al.  Multiple hepatocyte-enriched nuclear factors function in the regulation of transthyretin and alpha 1-antitrypsin genes , 1989, Molecular and cellular biology.

[14]  B. Wold,et al.  In vivo footprinting of a muscle specific enhancer by ligation mediated PCR. , 1990, Science.

[15]  D. Baltimore,et al.  The “initiator” as a transcription control element , 1989, Cell.

[16]  J. Darnell,et al.  Rapid in vivo footprinting technique identifies proteins bound to the TTR gene in the mouse liver. , 1991, Genes & development.

[17]  A. Kahn,et al.  Competition between transcription factors HNF1 and HNF3, and alternative cell-specific activation by DBP and C/EBP contribute to the regulation of the liver-specific aldolase B promoter. , 1993, Nucleic acids research.

[18]  J. Darnell,et al.  A cell-specific enhancer of the mouse alpha 1-antitrypsin gene has multiple functional regions and corresponding protein-binding sites , 1988, Molecular and cellular biology.

[19]  R. Tjian,et al.  The promoter-specific transcription factor Sp1 binds to upstream sequences in the SV40 early promoter , 1983, Cell.

[20]  Lau Cc.  Genetic variation affecting the expression of enzyme-coding genes in Drosophila: an evolutionary perspective. , 1985 .

[21]  B. Spiegelman,et al.  Independent regulation of adipose tissue-specificity and obesity response of the adipsin promoter in transgenic mice. , 1994, The Journal of biological chemistry.

[22]  I. Pastan,et al.  Epidermal growth factor receptor gene promoter. Deletion analysis and identification of nuclear protein binding sites. , 1988, The Journal of biological chemistry.

[23]  R. Tjian,et al.  Transcriptional regulation in mammalian cells by sequence-specific DNA binding proteins. , 1989, Science.

[24]  D. Crawford,et al.  Molecular basis of evolutionary adaptation at the lactate dehydrogenase-B locus in the fish Fundulus heteroclitus. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[25]  M. Goodman,et al.  Phylogenetic footprinting reveals unexpected complexity in trans factor binding upstream from the epsilon-globin gene. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[26]  J. Darnell,et al.  Factors that interact with the rat albumin promoter are present both in hepatocytes and other cell types. , 1987, Genes & development.

[27]  R. Roeder,et al.  The complexities of eukaryotic transcription initiation: regulation of preinitiation complex assembly. , 1991, Trends in biochemical sciences.

[28]  M. D. Brennan,et al.  Multiple cis-acting sequences contribute to evolved regulatory variation for Drosophila Adh genes. , 1992, Genetics.

[29]  R. Hudson,et al.  Inferring the evolutionary histories of the Adh and Adh-dup loci in Drosophila melanogaster from patterns of polymorphism and divergence. , 1991, Genetics.

[30]  M. Schartl,et al.  Transient expression directed by homologous and heterologous promoter and enhancer sequences in fish cells. , 1990, Nucleic acids research.

[31]  W. Liao,et al.  Expression of rat serum amyloid A1 gene involves both C/EBP-like and NF kappa B-like transcription factors. , 1991, The Journal of biological chemistry.

[32]  G. Stamatoyannopoulos,et al.  Genomic footprinting and sequencing of human beta-globin locus. Tissue specificity and cell line artifact. , 1994, The Journal of biological chemistry.

[33]  P. Sharp,et al.  The interaction of GATA-binding proteins and basal transcription factors with GATA box-containing core promoters. A model of tissue-specific gene expression. , 1994, The Journal of biological chemistry.

[34]  J E Darnell,et al.  Evidence that interaction of hepatocytes with the collecting (hepatic) veins triggers position-specific transcription of the glutamine synthetase and ornithine aminotransferase genes in the mouse liver , 1991, Molecular and cellular biology.

[35]  G. Bernardi,et al.  Concordant mitochondrial and nuclear DNA phylogenies for populations of the teleost fish Fundulus heteroclitus. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[36]  S. J. Degen,et al.  The human prothrombin gene: transcriptional regulation in HepG2 cells. , 1992, Biochemistry.

[37]  D. Crawford,et al.  Evolutionary adaptation to different thermal environments via transcriptional regulation. , 1992, Molecular biology and evolution.

[38]  B. Roe,et al.  Characterization and sequence of the promoter region of the human epidermal growth factor receptor gene. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[39]  D. Accili,et al.  Structural and functional analysis of the insulin receptor promoter. , 1990, Molecular endocrinology.

[40]  D. Baltimore,et al.  Transcriptional activation by Sp1 as directed through TATA or initiator: specific requirement for mammalian transcription factor IID. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[41]  A. Wilson,et al.  Evolution and transcription of old world monkey globin genes. , 1989, Journal of molecular biology.

[42]  S. Smale,et al.  Mechanism of initiator-mediated transcription: evidence for a functional interaction between the TATA-binding protein and DNA in the absence of a specific recognition sequence. , 1993, Molecular and cellular biology.

[43]  A. Sentenac,et al.  RNA polymerase B (II) and general transcription factors. , 1990, Annual review of biochemistry.