DOI: 10.1101/gad.14.3.339. Activation mutants in yeast RNA polymerase II subunit RPB3 provide evidence for a structurally conserved surface required for activation in eukaryotes and bacteria

Activation mutants in yeast RNA polymerase II subunit RPB3 provide evidence for a structurally conserved surface required for activation in eukaryotes and bacteria

10.1101/gad.14.3.339

Crossref journal-article

Cold Spring Harbor Laboratory

Genes & Development (246)

Abstract

We have identified a mutant in RPB3, the third-largest subunit of yeast RNA polymerase II, that is defective in activator-dependent transcription, but not defective in activator-independent, basal transcription. The mutant contains two amino-acid substitutions, C92R and A159G, that are both required for pronounced defects in activator-dependent transcription. Synthetic enhancement of phenotypes of C92R and A159G, and of several other pairs of substitutions, is consistent with a functional relationship between residues 92–95 and 159–161. Homology modeling of RPB3 on the basis of the crystallographic structure of αNTD indicates that residues 92–95 and 159–162 are likely to be adjacent within the structure of RPB3. In addition, homology modeling indicates that the location of residues 159–162 within RPB3 corresponds to the location of an activation target within αNTD (the target of activating region 2 of catabolite activator protein, an activation target involved in a protein–protein interaction that facilitates isomerization of the RNA polymerase promoter closed complex to the RNA polymerase promoter open complex). The apparent finding of a conserved surface required for activation in eukaryotes and bacteria raises the possibility of conserved mechanisms of activation in eukaryotes and bacteria.

Bibliography

Tan, Q., Linask, K. L., Ebright, R. H., & Woychik, N. A. (2000). Activation mutants in yeast RNA polymerase II subunit RPB3 provide evidence for a structurally conserved surface required for activation in eukaryotes and bacteria. Genes & Development, 14(3), 339â348.

Authors 4

Qian Tan (first)
K. Liisi Linask (additional)
Richard H. Ebright (additional)
Nancy A. Woychik (additional)

References 41 Referenced 41

10.1016/0076-6879(87)54076-9
10.1046/j.1365-2958.1997.2771641.x
10.1006/jmbi.1999.3161
10.1074/jbc.271.50.32359
10.1016/0959-437X(95)80008-5
10.1101/gad.13.16.2134
10.1016/S0014-5793(98)00431-1
10.1016/S0092-8674(00)81514-7
10.1016/0092-8674(90)90118-X
10.1016/S0955-0674(97)80002-6
10.1016/0168-9525(93)90042-G
10.1073/pnas.93.19.10162
10.1016/0378-1119(89)90358-2
10.1006/jmbi.1998.1823
Kaiser C. Michaelis S. Mitchell A. (1994) Methods in yeast genetics. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY).
10.1006/jmbi.1995.0621
10.1006/jmbi.1995.0258
10.1074/jbc.272.41.25851
{'key': '2021111419181290000_14.3.339.19', 'first-page': '5387', 'article-title': 'RNA polymerase II subunit RPB3 is an essential component of the mRNA transcription apparatus.', 'volume': '9', 'author': 'Kolodziej', 'year': '1989', 'journal-title': 'Mol. Cell. Biol.'} / Mol. Cell. Biol. / RNA polymerase II subunit RPB3 is an essential component of the mRNA transcription apparatus. by Kolodziej (1989)
{'key': '2021111419181290000_14.3.339.20', 'first-page': '4669', 'article-title': 'Mutations in the three largest subunits of yeast RNA polymerase II that affect enzyme assembly.', 'volume': '11', 'year': '1991', 'journal-title': 'Mol. Cell. Biol.'} / Mol. Cell. Biol. / Mutations in the three largest subunits of yeast RNA polymerase II that affect enzyme assembly. (1991)
10.1074/jbc.272.19.12824
10.1101/gad.5.12b.2431
10.1007/s004380051061
10.1002/yea.320080202
10.1073/pnas.94.5.1709
10.1074/jbc.273.43.27757
Niu W. (1998) “Identification and characterization of interactions between a transcription activator and the transcription machinery,” Ph.D. thesis. (Rutgers University, Piscataway, NJ).
10.1016/S0092-8674(00)81806-1
10.1093/nar/25.2.326
Sentenac A. Riva M. Thuriaux P. Buhler J.-M. Treich I. Carles C. Werner M. Ruet A. Huet J. Mann C. (1992) Yeast RNA polymerase subunits and genes. in Transcriptional Regulation, eds McKnight S.L. Yamamoto K.R. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY), pp 27–54.
10.1093/genetics/122.1.19 / Genetics / A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. by Sikorski (1989)
10.1074/jbc.273.18.10827
Treco D.A. Lundblad V. (1993) Preparation of yeast media. in Current protocols in molecular biology, ed Janssen K. (Greene Publishing Associates/John Wiley & Sons, New York, NY), pp 13.11.11–13.11.17.
10.1016/S0021-9258(18)54732-3 / J. Biol. Chem. / Zinc-binding subunits of yeast RNA polymerases. by Treich (1991)
10.1074/jbc.271.9.5085
10.1111/j.1365-2958.1991.tb02126.x
10.1093/genetics/107.2.179 / Genetics / Mutations affecting Ty-mediated expression of the HIS4 gene of Saccharomyces cerevisiae. by Winston (1984)
{'key': '2021111419181290000_14.3.339.38', 'first-page': '4555', 'article-title': 'Transcriptional activation in an improved whole-cell extract from Saccharomyces cerevisiae.', 'volume': '11', 'author': 'Wootner', 'year': '1991', 'journal-title': 'Mol. Cell. Biol.'} / Mol. Cell. Biol. / Transcriptional activation in an improved whole-cell extract from Saccharomyces cerevisiae. by Wootner (1991)
10.1146/annurev.bi.60.070191.003353
10.1126/science.281.5374.262
10.1016/S0092-8674(00)81515-9

Dates

Type	When
Created	3 years, 9 months ago (Nov. 14, 2021, 10:27 p.m.)
Deposited	3 years, 9 months ago (Nov. 14, 2021, 10:29 p.m.)
Indexed	2 months, 2 weeks ago (June 4, 2025, 9:58 p.m.)
Issued	25 years, 6 months ago (Feb. 1, 2000)
Published	25 years, 6 months ago (Feb. 1, 2000)
Published Online	25 years, 6 months ago (Feb. 1, 2000)
Published Print	25 years, 6 months ago (Feb. 1, 2000)

Funders 0

None

BibTeX

@article{Tan_2000, title={Activation mutants in yeast RNA polymerase II subunit RPB3 provide evidence for a structurally conserved surface required for activation in eukaryotes and bacteria}, volume={14}, ISSN={1549-5477}, url={http://dx.doi.org/10.1101/gad.14.3.339}, DOI={10.1101/gad.14.3.339}, number={3}, journal={Genes & Development}, publisher={Cold Spring Harbor Laboratory}, author={Tan, Qian and Linask, K. Liisi and Ebright, Richard H. and Woychik, Nancy A.}, year={2000}, month=feb, pages={339–348} }

JSON

{
  "indexed": {
    "date-parts": [
      [
        2025,
        6,
        5
      ]
    ],
    "date-time": "2025-06-05T01:58:31Z",
    "timestamp": 1749088711213
  },
  "reference-count": 41,
  "publisher": "Cold Spring Harbor Laboratory",
  "issue": "3",
  "content-domain": {
    "domain": [],
    "crossmark-restriction": false
  },
  "published-print": {
    "date-parts": [
      [
        2000,
        2,
        1
      ]
    ]
  },
  "abstract": "<jats:p>We have identified a mutant in RPB3, the third-largest subunit of yeast RNA polymerase II, that is defective in activator-dependent transcription, but not defective in activator-independent, basal transcription. The mutant contains two amino-acid substitutions, C92R and A159G, that are both required for pronounced defects in activator-dependent transcription. Synthetic enhancement of phenotypes of C92R and A159G, and of several other pairs of substitutions, is consistent with a functional relationship between residues 92\u201395 and 159\u2013161. Homology modeling of RPB3 on the basis of the crystallographic structure of \u03b1NTD indicates that residues 92\u201395 and 159\u2013162 are likely to be adjacent within the structure of RPB3. In addition, homology modeling indicates that the location of residues 159\u2013162 within RPB3 corresponds to the location of an activation target within \u03b1NTD (the target of activating region 2 of catabolite activator protein, an activation target involved in a protein\u2013protein interaction that facilitates isomerization of the RNA polymerase promoter closed complex to the RNA polymerase promoter open complex). The apparent finding of a conserved surface required for activation in eukaryotes and bacteria raises the possibility of conserved mechanisms of activation in eukaryotes and bacteria.</jats:p>",
  "DOI": "10.1101/gad.14.3.339",
  "type": "journal-article",
  "created": {
    "date-parts": [
      [
        2021,
        11,
        15
      ]
    ],
    "date-time": "2021-11-15T03:27:54Z",
    "timestamp": 1636946874000
  },
  "page": "339-348",
  "source": "Crossref",
  "is-referenced-by-count": 41,
  "title": "Activation mutants in yeast RNA polymerase II subunit RPB3 provide evidence for a structurally conserved surface required for activation in eukaryotes and bacteria",
  "prefix": "10.1101",
  "volume": "14",
  "author": [
    {
      "given": "Qian",
      "family": "Tan",
      "sequence": "first",
      "affiliation": []
    },
    {
      "given": "K. Liisi",
      "family": "Linask",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "Richard H.",
      "family": "Ebright",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "Nancy A.",
      "family": "Woychik",
      "sequence": "additional",
      "affiliation": []
    }
  ],
  "member": "246",
  "published-online": {
    "date-parts": [
      [
        2000,
        2,
        1
      ]
    ]
  },
  "reference": [
    {
      "key": "2021111419181290000_14.3.339.1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/0076-6879(87)54076-9"
    },
    {
      "key": "2021111419181290000_14.3.339.2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1046/j.1365-2958.1997.2771641.x"
    },
    {
      "key": "2021111419181290000_14.3.339.3",
      "doi-asserted-by": "publisher",
      "DOI": "10.1006/jmbi.1999.3161"
    },
    {
      "key": "2021111419181290000_14.3.339.4",
      "doi-asserted-by": "publisher",
      "DOI": "10.1074/jbc.271.50.32359"
    },
    {
      "key": "2021111419181290000_14.3.339.5",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/0959-437X(95)80008-5"
    },
    {
      "key": "2021111419181290000_14.3.339.6",
      "doi-asserted-by": "publisher",
      "DOI": "10.1101/gad.13.16.2134"
    },
    {
      "key": "2021111419181290000_14.3.339.7",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0014-5793(98)00431-1"
    },
    {
      "key": "2021111419181290000_14.3.339.8",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0092-8674(00)81514-7"
    },
    {
      "key": "2021111419181290000_14.3.339.9",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/0092-8674(90)90118-X"
    },
    {
      "key": "2021111419181290000_14.3.339.10",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0955-0674(97)80002-6"
    },
    {
      "key": "2021111419181290000_14.3.339.11",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/0168-9525(93)90042-G"
    },
    {
      "key": "2021111419181290000_14.3.339.12",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.93.19.10162"
    },
    {
      "key": "2021111419181290000_14.3.339.13",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/0378-1119(89)90358-2"
    },
    {
      "key": "2021111419181290000_14.3.339.14",
      "doi-asserted-by": "publisher",
      "DOI": "10.1006/jmbi.1998.1823"
    },
    {
      "key": "2021111419181290000_14.3.339.15",
      "unstructured": "Kaiser C. Michaelis S. Mitchell A. (1994) Methods in yeast genetics. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY)."
    },
    {
      "key": "2021111419181290000_14.3.339.16",
      "doi-asserted-by": "publisher",
      "DOI": "10.1006/jmbi.1995.0621"
    },
    {
      "key": "2021111419181290000_14.3.339.17",
      "doi-asserted-by": "publisher",
      "DOI": "10.1006/jmbi.1995.0258"
    },
    {
      "key": "2021111419181290000_14.3.339.18",
      "doi-asserted-by": "publisher",
      "DOI": "10.1074/jbc.272.41.25851"
    },
    {
      "key": "2021111419181290000_14.3.339.19",
      "first-page": "5387",
      "article-title": "RNA polymerase II subunit RPB3 is an essential component of the mRNA transcription apparatus.",
      "volume": "9",
      "author": "Kolodziej",
      "year": "1989",
      "journal-title": "Mol. Cell. Biol."
    },
    {
      "key": "2021111419181290000_14.3.339.20",
      "first-page": "4669",
      "article-title": "Mutations in the three largest subunits of yeast RNA polymerase II that affect enzyme assembly.",
      "volume": "11",
      "year": "1991",
      "journal-title": "Mol. Cell. Biol."
    },
    {
      "key": "2021111419181290000_14.3.339.21",
      "doi-asserted-by": "publisher",
      "DOI": "10.1074/jbc.272.19.12824"
    },
    {
      "key": "2021111419181290000_14.3.339.22",
      "doi-asserted-by": "publisher",
      "DOI": "10.1101/gad.5.12b.2431"
    },
    {
      "key": "2021111419181290000_14.3.339.23",
      "doi-asserted-by": "publisher",
      "DOI": "10.1007/s004380051061"
    },
    {
      "key": "2021111419181290000_14.3.339.24",
      "doi-asserted-by": "publisher",
      "DOI": "10.1002/yea.320080202"
    },
    {
      "key": "2021111419181290000_14.3.339.25",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.94.5.1709"
    },
    {
      "key": "2021111419181290000_14.3.339.26",
      "doi-asserted-by": "publisher",
      "DOI": "10.1074/jbc.273.43.27757"
    },
    {
      "key": "2021111419181290000_14.3.339.27",
      "unstructured": "Niu W. (1998) \u201cIdentification and characterization of interactions between a transcription activator and the transcription machinery,\u201d Ph.D. thesis. (Rutgers University, Piscataway, NJ)."
    },
    {
      "key": "2021111419181290000_14.3.339.28",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0092-8674(00)81806-1"
    },
    {
      "key": "2021111419181290000_14.3.339.29",
      "doi-asserted-by": "publisher",
      "DOI": "10.1093/nar/25.2.326"
    },
    {
      "key": "2021111419181290000_14.3.339.30",
      "unstructured": "Sentenac A. Riva M. Thuriaux P. Buhler J.-M. Treich I. Carles C. Werner M. Ruet A. Huet J. Mann C. (1992) Yeast RNA polymerase subunits and genes. in Transcriptional Regulation, eds McKnight S.L. Yamamoto K.R. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY), pp 27\u201354."
    },
    {
      "key": "2021111419181290000_14.3.339.31",
      "doi-asserted-by": "crossref",
      "first-page": "19",
      "DOI": "10.1093/genetics/122.1.19",
      "article-title": "A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae.",
      "volume": "122",
      "author": "Sikorski",
      "year": "1989",
      "journal-title": "Genetics"
    },
    {
      "key": "2021111419181290000_14.3.339.32",
      "doi-asserted-by": "publisher",
      "DOI": "10.1074/jbc.273.18.10827"
    },
    {
      "key": "2021111419181290000_14.3.339.33",
      "unstructured": "Treco D.A. Lundblad V. (1993) Preparation of yeast media. in Current protocols in molecular biology, ed Janssen K. (Greene Publishing Associates/John Wiley & Sons, New York, NY), pp 13.11.11\u201313.11.17."
    },
    {
      "key": "2021111419181290000_14.3.339.34",
      "doi-asserted-by": "crossref",
      "first-page": "21971",
      "DOI": "10.1016/S0021-9258(18)54732-3",
      "article-title": "Zinc-binding subunits of yeast RNA polymerases.",
      "volume": "266",
      "author": "Treich",
      "year": "1991",
      "journal-title": "J. Biol. Chem."
    },
    {
      "key": "2021111419181290000_14.3.339.35",
      "doi-asserted-by": "publisher",
      "DOI": "10.1074/jbc.271.9.5085"
    },
    {
      "key": "2021111419181290000_14.3.339.36",
      "doi-asserted-by": "publisher",
      "DOI": "10.1111/j.1365-2958.1991.tb02126.x"
    },
    {
      "key": "2021111419181290000_14.3.339.37",
      "doi-asserted-by": "crossref",
      "first-page": "179",
      "DOI": "10.1093/genetics/107.2.179",
      "article-title": "Mutations affecting Ty-mediated expression of the HIS4 gene of Saccharomyces cerevisiae.",
      "volume": "107",
      "author": "Winston",
      "year": "1984",
      "journal-title": "Genetics"
    },
    {
      "key": "2021111419181290000_14.3.339.38",
      "first-page": "4555",
      "article-title": "Transcriptional activation in an improved whole-cell extract from Saccharomyces cerevisiae.",
      "volume": "11",
      "author": "Wootner",
      "year": "1991",
      "journal-title": "Mol. Cell. Biol."
    },
    {
      "key": "2021111419181290000_14.3.339.39",
      "doi-asserted-by": "publisher",
      "DOI": "10.1146/annurev.bi.60.070191.003353"
    },
    {
      "key": "2021111419181290000_14.3.339.40",
      "doi-asserted-by": "publisher",
      "DOI": "10.1126/science.281.5374.262"
    },
    {
      "key": "2021111419181290000_14.3.339.41",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0092-8674(00)81515-9"
    }
  ],
  "container-title": "Genes &amp; Development",
  "original-title": [],
  "language": "en",
  "link": [
    {
      "URL": "https://syndication.highwire.org/content/doi/10.1101/gad.14.3.339",
      "content-type": "unspecified",
      "content-version": "vor",
      "intended-application": "similarity-checking"
    }
  ],
  "deposited": {
    "date-parts": [
      [
        2021,
        11,
        15
      ]
    ],
    "date-time": "2021-11-15T03:29:39Z",
    "timestamp": 1636946979000
  },
  "score": 1,
  "resource": {
    "primary": {
      "URL": "http://genesdev.cshlp.org/lookup/doi/10.1101/gad.14.3.339"
    }
  },
  "subtitle": [],
  "short-title": [],
  "issued": {
    "date-parts": [
      [
        2000,
        2,
        1
      ]
    ]
  },
  "references-count": 41,
  "journal-issue": {
    "issue": "3",
    "published-print": {
      "date-parts": [
        [
          2000,
          2,
          1
        ]
      ]
    }
  },
  "alternative-id": [
    "10.1101/gad.14.3.339"
  ],
  "URL": "http://dx.doi.org/10.1101/gad.14.3.339",
  "relation": {},
  "ISSN": [
    "0890-9369",
    "1549-5477"
  ],
  "subject": [],
  "container-title-short": "Genes Dev.",
  "published": {
    "date-parts": [
      [
        2000,
        2,
        1
      ]
    ]
  }
}