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. 1985 Nov;5(11):3168–3182. doi: 10.1128/mcb.5.11.3168

Myosin light-chain 1 and 3 gene has two structurally distinct and differentially regulated promoters evolving at different rates.

E E Strehler, M Periasamy, M A Strehler-Page, B Nadal-Ginard
PMCID: PMC369132  PMID: 3018505

Abstract

DNA fragments located 10 kilobases apart in the genome and containing, respectively, the first myosin light chain 1 (MLC1f) and the first myosin light chain 3 (MLC3f) specific exon of the rat myosin light chain 1 and 3 gene, together with several hundred base pairs of upstream flanking sequences, have been shown in runoff in vitro transcription assays to direct initiation of transcription at the cap sites of MLC1f and MLC3f mRNAs used in vivo. These results establish the presence of two separate, functional promoters within that gene. A comparison of the nucleotide sequence of the rat MLC1f/3f gene with the corresponding sequences from mouse and chicken shows that: the MLC1f promoter regions have been highly conserved up to position -150 from the cap site while the MLC3f promoter regions display a very poor degree of homology and even the absence or poor conservation of typical eucaryotic promoter elements such as TATA and CAT boxes; the exon/intron structure of this gene has been completely conserved in the three species; and corresponding exons, except for the regions encoding most of the 5' and 3' untranslated sequences, show greater than 75% homology while corresponding introns are similar in size but considerably divergent in sequence. The above findings indicate that the overall structure of the MLC1f/3f genes has been maintained between avian and mammalian species and that these genes contain two functional and widely spaced promoters. The fact that the structures of the alkali light chain gene from Drosophila melanogaster and of other related genes of the troponin C supergene family resemble a MLC3f gene without an upstream promoter and first exon strongly suggests that the present-day MLC1f/3f genes of higher vertebrates arose from a primordial alkali light chain gene through the addition of a far-upstream MLC1f-specific promoter and first exon. The two promoters have evolved at different rates, with the MLC1f promoter being more conserved than the MLC3f promoter. This discrepant evolutionary rate might reflect different mechanisms of promoter activation for the transcription of MLC1f and MLC3f RNA.

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Selected References

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  1. Baba M. L., Goodman M., Berger-Cohn J., Demaille J. G., Matsuda G. The early adaptive evolution of calmodulin. Mol Biol Evol. 1984 Nov;1(6):442–455. doi: 10.1093/oxfordjournals.molbev.a040330. [DOI] [PubMed] [Google Scholar]
  2. Benoff S., Nadal-Ginard B. Most myosin heavy chain mRNA in L6E9 rat myotubes has a short poly(A) tail. Proc Natl Acad Sci U S A. 1979 Apr;76(4):1853–1857. doi: 10.1073/pnas.76.4.1853. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Benoist C., Chambon P. In vivo sequence requirements of the SV40 early promotor region. Nature. 1981 Mar 26;290(5804):304–310. doi: 10.1038/290304a0. [DOI] [PubMed] [Google Scholar]
  4. Benoist C., O'Hare K., Breathnach R., Chambon P. The ovalbumin gene-sequence of putative control regions. Nucleic Acids Res. 1980 Jan 11;8(1):127–142. doi: 10.1093/nar/8.1.127. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Benyajati C., Spoerel N., Haymerle H., Ashburner M. The messenger RNA for alcohol dehydrogenase in Drosophila melanogaster differs in its 5' end in different developmental stages. Cell. 1983 May;33(1):125–133. doi: 10.1016/0092-8674(83)90341-0. [DOI] [PubMed] [Google Scholar]
  6. Berk A. J., Sharp P. A. Sizing and mapping of early adenovirus mRNAs by gel electrophoresis of S1 endonuclease-digested hybrids. Cell. 1977 Nov;12(3):721–732. doi: 10.1016/0092-8674(77)90272-0. [DOI] [PubMed] [Google Scholar]
  7. Birnboim H. C., Doly J. A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res. 1979 Nov 24;7(6):1513–1523. doi: 10.1093/nar/7.6.1513. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Blau H. M., Chiu C. P., Webster C. Cytoplasmic activation of human nuclear genes in stable heterocaryons. Cell. 1983 Apr;32(4):1171–1180. doi: 10.1016/0092-8674(83)90300-8. [DOI] [PubMed] [Google Scholar]
  9. Brady J., Radonovich M., Thoren M., Das G., Salzman N. P. Simian virus 40 major late promoter: an upstream DNA sequence required for efficient in vitro transcription. Mol Cell Biol. 1984 Jan;4(1):133–141. doi: 10.1128/mcb.4.1.133. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Breathnach R., Chambon P. Organization and expression of eucaryotic split genes coding for proteins. Annu Rev Biochem. 1981;50:349–383. doi: 10.1146/annurev.bi.50.070181.002025. [DOI] [PubMed] [Google Scholar]
  11. Cantor C. R., Efstratiadis A. Possible structures of homopurine-homopyrimidine S1-hypersensitive sites. Nucleic Acids Res. 1984 Nov 12;12(21):8059–8072. doi: 10.1093/nar/12.21.8059. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Chiu C. P., Blau H. M. Reprogramming cell differentiation in the absence of DNA synthesis. Cell. 1984 Jul;37(3):879–887. doi: 10.1016/0092-8674(84)90423-9. [DOI] [PubMed] [Google Scholar]
  13. Corden J., Wasylyk B., Buchwalder A., Sassone-Corsi P., Kedinger C., Chambon P. Promoter sequences of eukaryotic protein-coding genes. Science. 1980 Sep 19;209(4463):1406–1414. doi: 10.1126/science.6251548. [DOI] [PubMed] [Google Scholar]
  14. Cullen B. R., Lomedico P. T., Ju G. Transcriptional interference in avian retroviruses--implications for the promoter insertion model of leukaemogenesis. Nature. 1984 Jan 19;307(5948):241–245. doi: 10.1038/307241a0. [DOI] [PubMed] [Google Scholar]
  15. Efstratiadis A., Posakony J. W., Maniatis T., Lawn R. M., O'Connell C., Spritz R. A., DeRiel J. K., Forget B. G., Weissman S. M., Slightom J. L. The structure and evolution of the human beta-globin gene family. Cell. 1980 Oct;21(3):653–668. doi: 10.1016/0092-8674(80)90429-8. [DOI] [PubMed] [Google Scholar]
  16. Emerman M., Temin H. M. Genes with promoters in retrovirus vectors can be independently suppressed by an epigenetic mechanism. Cell. 1984 Dec;39(3 Pt 2):449–467. [PubMed] [Google Scholar]
  17. Evans T., Schon E., Gora-Maslak G., Patterson J., Efstratiadis A. S1-hypersensitive sites in eukaryotic promoter regions. Nucleic Acids Res. 1984 Nov 12;12(21):8043–8058. doi: 10.1093/nar/12.21.8043. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Falkenthal S., Parker V. P., Davidson N. Developmental variations in the splicing pattern of transcripts from the Drosophila gene encoding myosin alkali light chain result in different carboxyl-terminal amino acid sequences. Proc Natl Acad Sci U S A. 1985 Jan;82(2):449–453. doi: 10.1073/pnas.82.2.449. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Fire A., Samuels M., Sharp P. A. Interactions between RNA polymerase II, factors, and template leading to accurate transcription. J Biol Chem. 1984 Feb 25;259(4):2509–2516. [PubMed] [Google Scholar]
  20. Fornwald J. A., Kuncio G., Peng I., Ordahl C. P. The complete nucleotide sequence of the chick a-actin gene and its evolutionary relationship to the actin gene family. Nucleic Acids Res. 1982 Jul 10;10(13):3861–3876. doi: 10.1093/nar/10.13.3861. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Frank G., Weeds A. G. The amino-acid sequence of the alkali light chains of rabbit skeletal-muscle myosin. Eur J Biochem. 1974 May 15;44(2):317–334. doi: 10.1111/j.1432-1033.1974.tb03489.x. [DOI] [PubMed] [Google Scholar]
  22. Garfinkel L. I., Periasamy M., Nadal-Ginard B. Cloning and characterization of cDNA sequences corresponding to myosin light chains 1, 2, and 3, troponin-C, troponin-T, alpha-tropomyosin, and alpha-actin. J Biol Chem. 1982 Sep 25;257(18):11078–11086. [PubMed] [Google Scholar]
  23. Gauthier G. F., Lowey S., Benfield P. A., Hobbs A. W. Distribution and properties of myosin isozymes in developing avian and mammalian skeletal muscle fibers. J Cell Biol. 1982 Feb;92(2):471–484. doi: 10.1083/jcb.92.2.471. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Gauthier G. F., Lowey S. Distribution of myosin isoenzymes among skeletal muscle fiber types. J Cell Biol. 1979 Apr;81(1):10–25. doi: 10.1083/jcb.81.1.10. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Gauthier G. F., Lowey S., Hobbs A. W. Fast and slow myosin in developing muscle fibres. Nature. 1978 Jul 6;274(5666):25–29. doi: 10.1038/274025a0. [DOI] [PubMed] [Google Scholar]
  26. Grabowski P. J., Padgett R. A., Sharp P. A. Messenger RNA splicing in vitro: an excised intervening sequence and a potential intermediate. Cell. 1984 Jun;37(2):415–427. doi: 10.1016/0092-8674(84)90372-6. [DOI] [PubMed] [Google Scholar]
  27. Grosschedl R., Birnstiel M. L. Delimitation of far upstream sequences required for maximal in vitro transcription of an H2A histone gene. Proc Natl Acad Sci U S A. 1982 Jan;79(2):297–301. doi: 10.1073/pnas.79.2.297. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Grosschedl R., Birnstiel M. L. Spacer DNA sequences upstream of the T-A-T-A-A-A-T-A sequence are essential for promotion of H2A histone gene transcription in vivo. Proc Natl Acad Sci U S A. 1980 Dec;77(12):7102–7106. doi: 10.1073/pnas.77.12.7102. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Grosveld G. C., de Boer E., Shewmaker C. K., Flavell R. A. DNA sequences necessary for transcription of the rabbit beta-globin gene in vivo. Nature. 1982 Jan 14;295(5845):120–126. doi: 10.1038/295120a0. [DOI] [PubMed] [Google Scholar]
  30. Hansen U., Sharp P. A. Sequences controlling in vitro transcription of SV40 promoters. EMBO J. 1983;2(12):2293–2303. doi: 10.1002/j.1460-2075.1983.tb01737.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Hansen U., Tenen D. G., Livingston D. M., Sharp P. A. T antigen repression of SV40 early transcription from two promoters. Cell. 1981 Dec;27(3 Pt 2):603–613. doi: 10.1016/0092-8674(81)90402-5. [DOI] [PubMed] [Google Scholar]
  32. Mahdavi V., Chambers A. P., Nadal-Ginard B. Cardiac alpha- and beta-myosin heavy chain genes are organized in tandem. Proc Natl Acad Sci U S A. 1984 May;81(9):2626–2630. doi: 10.1073/pnas.81.9.2626. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Manley J. L., Fire A., Cano A., Sharp P. A., Gefter M. L. DNA-dependent transcription of adenovirus genes in a soluble whole-cell extract. Proc Natl Acad Sci U S A. 1980 Jul;77(7):3855–3859. doi: 10.1073/pnas.77.7.3855. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Manley J. L., Fire A., Samuels M., Sharp P. A. In vitro transcription: whole-cell extract. Methods Enzymol. 1983;101:568–582. doi: 10.1016/0076-6879(83)01038-1. [DOI] [PubMed] [Google Scholar]
  35. Mathis D. J., Chambon P. The SV40 early region TATA box is required for accurate in vitro initiation of transcription. Nature. 1981 Mar 26;290(5804):310–315. doi: 10.1038/290310a0. [DOI] [PubMed] [Google Scholar]
  36. Matsuda G., Maita T., Umegane T. The primary structure of L-1 light chain of chicken fast skeletal muscle myosin and its genetic implication. FEBS Lett. 1981 Apr 6;126(1):111–113. doi: 10.1016/0014-5793(81)81045-9. [DOI] [PubMed] [Google Scholar]
  37. Maxam A. M., Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci U S A. 1977 Feb;74(2):560–564. doi: 10.1073/pnas.74.2.560. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Maxam A. M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. doi: 10.1016/s0076-6879(80)65059-9. [DOI] [PubMed] [Google Scholar]
  39. McKnight S. L., Kingsbury R. Transcriptional control signals of a eukaryotic protein-coding gene. Science. 1982 Jul 23;217(4557):316–324. doi: 10.1126/science.6283634. [DOI] [PubMed] [Google Scholar]
  40. Messing J., Crea R., Seeburg P. H. A system for shotgun DNA sequencing. Nucleic Acids Res. 1981 Jan 24;9(2):309–321. doi: 10.1093/nar/9.2.309. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Nabeshima Y., Fujii-Kuriyama Y., Muramatsu M., Ogata K. Alternative transcription and two modes of splicing results in two myosin light chains from one gene. Nature. 1984 Mar 22;308(5957):333–338. doi: 10.1038/308333a0. [DOI] [PubMed] [Google Scholar]
  42. Nabeshima Y., Fujii-Kuriyama Y., Muramatsu M., Ogata K. Molecular cloning and nucleotide sequences of the complementary DNAs to chicken skeletal muscle myosin two alkali light chain mRNAs. Nucleic Acids Res. 1982 Oct 11;10(19):6099–6110. doi: 10.1093/nar/10.19.6099. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Nadal-Ginard B. Commitment, fusion and biochemical differentiation of a myogenic cell line in the absence of DNA synthesis. Cell. 1978 Nov;15(3):855–864. doi: 10.1016/0092-8674(78)90270-2. [DOI] [PubMed] [Google Scholar]
  44. Naora H., Deacon N. J. Clustered genes require extragenic territorial DNA sequences. Differentiation. 1982;21(1):1–6. doi: 10.1111/j.1432-0436.1982.tb01186.x. [DOI] [PubMed] [Google Scholar]
  45. Nudel U., Calvo J. M., Shani M., Levy Z. The nucleotide sequence of a rat myosin light chain 2 gene. Nucleic Acids Res. 1984 Sep 25;12(18):7175–7186. doi: 10.1093/nar/12.18.7175. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Obinata T., Maruyama K., Sugita H., Kohama K., Ebashi S. Dynamic aspects of structural proteins in vertebrate skeletal muscle. Muscle Nerve. 1981 Nov-Dec;4(6):456–488. doi: 10.1002/mus.880040604. [DOI] [PubMed] [Google Scholar]
  47. Padgett R. A., Konarska M. M., Grabowski P. J., Hardy S. F., Sharp P. A. Lariat RNA's as intermediates and products in the splicing of messenger RNA precursors. Science. 1984 Aug 31;225(4665):898–903. doi: 10.1126/science.6206566. [DOI] [PubMed] [Google Scholar]
  48. Patient R. K., Elkington J. A., Kay R. M., Williams J. G. Internal organization of the major adult alpha- and beta-globin genes of X. laevis. Cell. 1980 Sep;21(2):565–573. doi: 10.1016/0092-8674(80)90494-8. [DOI] [PubMed] [Google Scholar]
  49. Periasamy M., Strehler E. E., Garfinkel L. I., Gubits R. M., Ruiz-Opazo N., Nadal-Ginard B. Fast skeletal muscle myosin light chains 1 and 3 are produced from a single gene by a combined process of differential RNA transcription and splicing. J Biol Chem. 1984 Nov 10;259(21):13595–13604. [PubMed] [Google Scholar]
  50. Perler F., Efstratiadis A., Lomedico P., Gilbert W., Kolodner R., Dodgson J. The evolution of genes: the chicken preproinsulin gene. Cell. 1980 Jun;20(2):555–566. doi: 10.1016/0092-8674(80)90641-8. [DOI] [PubMed] [Google Scholar]
  51. Reudelhuber T. Upstream and downstream control of eukaryotic genes. Nature. 1984 Dec 20;312(5996):700–701. doi: 10.1038/312700a0. [DOI] [PubMed] [Google Scholar]
  52. Robert B., Daubas P., Akimenko M. A., Cohen A., Garner I., Guenet J. L., Buckingham M. A single locus in the mouse encodes both myosin light chains 1 and 3, a second locus corresponds to a related pseudogene. Cell. 1984 Nov;39(1):129–140. doi: 10.1016/0092-8674(84)90198-3. [DOI] [PubMed] [Google Scholar]
  53. Ruskin B., Krainer A. R., Maniatis T., Green M. R. Excision of an intact intron as a novel lariat structure during pre-mRNA splicing in vitro. Cell. 1984 Aug;38(1):317–331. doi: 10.1016/0092-8674(84)90553-1. [DOI] [PubMed] [Google Scholar]
  54. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  55. Schibler U., Hagenbüchle O., Wellauer P. K., Pittet A. C. Two promoters of different strengths control the transcription of the mouse alpha-amylase gene Amy-1a in the parotid gland and the liver. Cell. 1983 Jun;33(2):501–508. doi: 10.1016/0092-8674(83)90431-2. [DOI] [PubMed] [Google Scholar]
  56. Schmidt A., Yamada Y., de Crombrugghe B. DNA sequence comparison of the regulatory signals at the 5' end of the mouse and chick alpha 2 type I collagen genes. J Biol Chem. 1984 Jun 25;259(12):7411–7415. [PubMed] [Google Scholar]
  57. Silberstein L., Lowey S. Isolated and distribution of myosin isoenzymes in chicken pectoralis muscle. J Mol Biol. 1981 May 15;148(2):153–189. doi: 10.1016/0022-2836(81)90510-6. [DOI] [PubMed] [Google Scholar]
  58. Simmen R. C., Tanaka T., Ts'ui K. F., Putkey J. A., Scott M. J., Lai E. C., Means A. R. The structural organization of the chicken calmodulin gene. J Biol Chem. 1985 Jan 25;260(2):907–912. [PubMed] [Google Scholar]
  59. Soeiro R., Birnboim H. C., Darnell J. E. Rapidly labeled HeLa cell nuclear RNA. II. Base composition and cellular localization of a heterogeneous RNA fraction. J Mol Biol. 1966 Aug;19(2):362–372. doi: 10.1016/s0022-2836(66)80010-4. [DOI] [PubMed] [Google Scholar]
  60. Strehler E. E., Mahdavi V., Periasamy M., Nadal-Ginard B. Intron positions are conserved in the 5' end region of myosin heavy-chain genes. J Biol Chem. 1985 Jan 10;260(1):468–471. [PubMed] [Google Scholar]
  61. Wasylyk B., Derbyshire R., Guy A., Molko D., Roget A., Téoule R., Chambon P. Specific in vitro transcription of conalbumin gene is drastically decreased by single-point mutation in T-A-T-A box homology sequence. Proc Natl Acad Sci U S A. 1980 Dec;77(12):7024–7028. doi: 10.1073/pnas.77.12.7024. [DOI] [PMC free article] [PubMed] [Google Scholar]
  62. Wasylyk B., Wasylyk C., Chambon P. A novel eukaryotic promoter element: the simian virus 40 72 base pair repeat. Fed Proc. 1984 Feb;43(2):226–234. [PubMed] [Google Scholar]
  63. Weeds A. G., Lowey S. Substructure of the myosin molecule. II. The light chains of myosin. J Mol Biol. 1971 Nov 14;61(3):701–725. doi: 10.1016/0022-2836(71)90074-x. [DOI] [PubMed] [Google Scholar]
  64. Weil P. A., Luse D. S., Segall J., Roeder R. G. Selective and accurate initiation of transcription at the Ad2 major late promotor in a soluble system dependent on purified RNA polymerase II and DNA. Cell. 1979 Oct;18(2):469–484. doi: 10.1016/0092-8674(79)90065-5. [DOI] [PubMed] [Google Scholar]
  65. Weissmann C. Molecular biology. Excision of introns in lariat form. Nature. 1984 Sep 13;311(5982):103–104. doi: 10.1038/311103a0. [DOI] [PubMed] [Google Scholar]
  66. Whalen R. G., Butler-Browne G. S., Gros F. Identification of a novel form of myosin light chain present in embryonic muscle tissue and cultured muscle cells. J Mol Biol. 1978 Dec 15;126(3):415–431. doi: 10.1016/0022-2836(78)90049-9. [DOI] [PubMed] [Google Scholar]
  67. Whalen R. G., Sell S. M., Butler-Browne G. S., Schwartz K., Bouveret P., Pinset-Härstöm I. Three myosin heavy-chain isozymes appear sequentially in rat muscle development. Nature. 1981 Aug 27;292(5826):805–809. doi: 10.1038/292805a0. [DOI] [PubMed] [Google Scholar]
  68. Wildeman A. G., Sassone-Corsi P., Grundström T., Zenke M., Chambon P. Stimulation of in vitro transcription from the SV40 early promoter by the enhancer involves a specific trans-acting factor. EMBO J. 1984 Dec 20;3(13):3129–3133. doi: 10.1002/j.1460-2075.1984.tb02269.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  69. Young R. A., Hagenbüchle O., Schibler U. A single mouse alpha-amylase gene specifies two different tissue-specific mRNAs. Cell. 1981 Feb;23(2):451–458. doi: 10.1016/0092-8674(81)90140-9. [DOI] [PubMed] [Google Scholar]
  70. Zakut R., Shani M., Givol D., Neuman S., Yaffe D., Nudel U. Nucleotide sequence of the rat skeletal muscle actin gene. Nature. 1982 Aug 26;298(5877):857–859. doi: 10.1038/298857a0. [DOI] [PubMed] [Google Scholar]

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