DOI: 10.1261/rna.2152306. Ubiquitin binding by a variant Jab1/MPN domain in the essential pre-mRNA splicing factor Prp8p

Ubiquitin binding by a variant Jab1/MPN domain in the essential pre-mRNA splicing factor Prp8p

10.1261/rna.2152306

Crossref journal-article

Cold Spring Harbor Laboratory

RNA (246)

Abstract

The U1, U2, U4/U6, and U5 small nuclear ribonucleoproteins (snRNPs) are components of the spliceosome, which catalyzes pre-mRNA splicing. One of the largest and the most highly conserved proteins in the spliceosome is Prp8p, a component of the U5 snRNP. Despite its size and conservation, very few motifs have been identified that suggest specific biochemical functions. A variant of the Jab1/MPN domain found in a class of deubiquitinating enzymes is present near the C terminus of Prp8p. Ubiquitination regulates a broad range of cellular pathways, and its functions generally require ubiquitin recognition by one or more ubiquitin-binding domains (UBDs). No precise role for ubiquitin has been defined in the pre-mRNA splicing pathway, and no known UBDs have been found within splicing proteins. Here we show that a Prp8p fragment containing the Jab1/MPN domain binds directly to ubiquitin with an affinity comparable to other known UBDs. Several mutations within this domain that compromise splicing also reduce interaction of the fragment with ubiquitin-Sepharose. Our results define a new UBD and suggest functional links between ubiquitin and the pre-mRNA splicing machinery.

Bibliography

BELLARE, P., KUTACH, A. K., RINES, A. K., GUTHRIE, C., & SONTHEIMER, E. J. (2006). Ubiquitin binding by a variant Jab1/MPN domain in the essential pre-mRNA splicing factor Prp8p. RNA, 12(2), 292â302.

Authors 5

PRIYA BELLARE (first)
ALAN K. KUTACH (additional)
AMY K. RINES (additional)
CHRISTINE GUTHRIE (additional)
ERIK J. SONTHEIMER (additional)

References 65 Referenced 67

10.1128/MCB.18.11.6756 / Mol. Cell. Biol. (1998)
10.1371/journal.pbio.0020002
10.1093/genetics/154.1.61 / Genetics (2000)
10.1016/0076-6879(89)80111-9
10.1534/genetics.105.042044
10.1146/annurev.genet.36.043002.091635
10.1002/j.1460-2075.1992.tb05457.x / EMBO J. (1992)
10.1101/gad.13.15.1970
10.1126/science.1075901
10.1017/S1355838201016077
10.1038/nature00935
10.1038/376745a0
{'key': '2021112105403391000_12.2.292.13', 'first-page': '1554', 'volume': '7', 'year': '2001', 'journal-title': 'RNA'} / RNA (2001)
10.1261/rna.2220705
{'key': '2021112105403391000_12.2.292.15', 'first-page': '1', 'volume': '194', 'year': '1991', 'journal-title': 'Methods Enzymol.'} / Methods Enzymol. (1991)
10.1016/S0021-9258(19)75933-X / J. Biol. Chem. (1987)
10.1074/jbc.M102755200
10.1038/nrm1701
10.1002/yea.320110406
10.1016/S1097-2765(03)00270-3
10.1016/S0006-291X(03)01009-X
10.18388/abp.1998_4346 / Acta Biochim. Pol. (1998)
{'key': '2021112105403391000_12.2.292.23', 'first-page': '260', 'volume': '1', 'year': '1995', 'journal-title': 'RNA'} / RNA (1995)
10.1093/genetics/155.4.1667 / Genetics (2000)
10.1016/S1097-2765(00)80175-6
10.1073/pnas.102304299
10.1021/bi971296x
10.1128/MCB.19.3.2008 / Mol. Cell. Biol. (1999)
10.1126/science.1077783
10.1093/emboj/20.10.2553
10.1038/sj.emboj.7600241
10.1186/1471-2091-3-28 / BMC Biochem. (2002)
10.1074/jbc.M212353200
10.1002/j.1460-2075.1996.tb00810.x / EMBO J. (1996)
10.1038/nsb906
10.1038/nbt849
10.1093/emboj/21.10.2397
10.1016/S1097-2765(04)00217-5
10.1038/nsmb962
10.1016/S0960-9822(07)00345-4
10.1101/gr.473902
{'key': '2021112105403391000_12.2.292.42', 'first-page': '213', 'volume': '2', 'year': '1996', 'journal-title': 'RNA'} / RNA (1996)
10.1017/S1355838299981785
10.1101/gad.13.15.1983
10.1073/pnas.93.24.13641
10.1074/jbc.M103248200
10.1016/S0092-8674(00)80925-3
10.1073/pnas.96.13.7226
{'key': '2021112105403391000_12.2.292.49', 'first-page': '1543', 'volume': '7', 'year': '2001', 'journal-title': 'RNA'} / RNA (2001)
10.1126/science.7770774
10.1016/S1097-2765(04)00129-7
10.1002/j.1460-2075.1995.tb07258.x / EMBO J. (1995)
10.1093/nar/23.3.320
10.1074/jbc.M400023200
10.1021/bi035033g
10.1101/gad.9.7.855
{'key': '2021112105403391000_12.2.292.57', 'first-page': '584', 'volume': '1', 'year': '1995', 'journal-title': 'RNA'} / RNA (1995)
10.1093/genetics/143.2.723 / Genetics (1996)
10.1093/genetics/157.4.1451 / Genetics (2001)
10.1016/S0092-8674(01)00387-7
10.1126/science.1075898
10.1073/pnas.87.6.2216
10.1016/S0022-2836(02)01145-2
10.1016/j.cub.2004.11.058
10.1038/nature01071

Dates

Type	When
Created	19 years, 7 months ago (Jan. 20, 2006, 4:28 p.m.)
Deposited	3 years, 9 months ago (Nov. 21, 2021, 8:45 a.m.)
Indexed	1 year ago (Sept. 2, 2024, 1:50 a.m.)
Issued	19 years, 7 months ago (Jan. 20, 2006)
Published	19 years, 7 months ago (Jan. 20, 2006)
Published Online	19 years, 7 months ago (Jan. 20, 2006)
Published Print	19 years, 7 months ago (Feb. 1, 2006)

Funders 0

None

BibTeX

@article{BELLARE_2006, title={Ubiquitin binding by a variant Jab1/MPN domain in the essential pre-mRNA splicing factor Prp8p}, volume={12}, ISSN={1469-9001}, url={http://dx.doi.org/10.1261/rna.2152306}, DOI={10.1261/rna.2152306}, number={2}, journal={RNA}, publisher={Cold Spring Harbor Laboratory}, author={BELLARE, PRIYA and KUTACH, ALAN K. and RINES, AMY K. and GUTHRIE, CHRISTINE and SONTHEIMER, ERIK J.}, year={2006}, month=jan, pages={292–302} }

JSON

{
  "indexed": {
    "date-parts": [
      [
        2024,
        9,
        2
      ]
    ],
    "date-time": "2024-09-02T05:50:40Z",
    "timestamp": 1725256240479
  },
  "reference-count": 65,
  "publisher": "Cold Spring Harbor Laboratory",
  "issue": "2",
  "content-domain": {
    "domain": [],
    "crossmark-restriction": false
  },
  "published-print": {
    "date-parts": [
      [
        2006,
        2
      ]
    ]
  },
  "abstract": "<jats:p>The U1, U2, U4/U6, and U5 small nuclear ribonucleoproteins (snRNPs) are components of the spliceosome, which catalyzes pre-mRNA splicing. One of the largest and the most highly conserved proteins in the spliceosome is Prp8p, a component of the U5 snRNP. Despite its size and conservation, very few motifs have been identified that suggest specific biochemical functions. A variant of the Jab1/MPN domain found in a class of deubiquitinating enzymes is present near the C terminus of Prp8p. Ubiquitination regulates a broad range of cellular pathways, and its functions generally require ubiquitin recognition by one or more ubiquitin-binding domains (UBDs). No precise role for ubiquitin has been defined in the pre-mRNA splicing pathway, and no known UBDs have been found within splicing proteins. Here we show that a Prp8p fragment containing the Jab1/MPN domain binds directly to ubiquitin with an affinity comparable to other known UBDs. Several mutations within this domain that compromise splicing also reduce interaction of the fragment with ubiquitin-Sepharose. Our results define a new UBD and suggest functional links between ubiquitin and the pre-mRNA splicing machinery.</jats:p>",
  "DOI": "10.1261/rna.2152306",
  "type": "journal-article",
  "created": {
    "date-parts": [
      [
        2006,
        1,
        20
      ]
    ],
    "date-time": "2006-01-20T21:28:38Z",
    "timestamp": 1137792518000
  },
  "page": "292-302",
  "source": "Crossref",
  "is-referenced-by-count": 67,
  "title": "Ubiquitin binding by a variant Jab1/MPN domain in the essential pre-mRNA splicing factor Prp8p",
  "prefix": "10.1261",
  "volume": "12",
  "author": [
    {
      "given": "PRIYA",
      "family": "BELLARE",
      "sequence": "first",
      "affiliation": []
    },
    {
      "given": "ALAN K.",
      "family": "KUTACH",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "AMY K.",
      "family": "RINES",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "CHRISTINE",
      "family": "GUTHRIE",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "ERIK J.",
      "family": "SONTHEIMER",
      "sequence": "additional",
      "affiliation": []
    }
  ],
  "member": "246",
  "published-online": {
    "date-parts": [
      [
        2006,
        1,
        20
      ]
    ]
  },
  "reference": [
    {
      "key": "2021112105403391000_12.2.292.1",
      "doi-asserted-by": "crossref",
      "first-page": "6756",
      "DOI": "10.1128/MCB.18.11.6756",
      "volume": "18",
      "year": "1998",
      "journal-title": "Mol. Cell. Biol."
    },
    {
      "key": "2021112105403391000_12.2.292.2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1371/journal.pbio.0020002"
    },
    {
      "key": "2021112105403391000_12.2.292.3",
      "doi-asserted-by": "crossref",
      "first-page": "61",
      "DOI": "10.1093/genetics/154.1.61",
      "volume": "154",
      "year": "2000",
      "journal-title": "Genetics"
    },
    {
      "key": "2021112105403391000_12.2.292.4",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/0076-6879(89)80111-9"
    },
    {
      "key": "2021112105403391000_12.2.292.5",
      "doi-asserted-by": "publisher",
      "DOI": "10.1534/genetics.105.042044"
    },
    {
      "key": "2021112105403391000_12.2.292.6",
      "doi-asserted-by": "publisher",
      "DOI": "10.1146/annurev.genet.36.043002.091635"
    },
    {
      "key": "2021112105403391000_12.2.292.7",
      "doi-asserted-by": "crossref",
      "first-page": "3721",
      "DOI": "10.1002/j.1460-2075.1992.tb05457.x",
      "volume": "11",
      "year": "1992",
      "journal-title": "EMBO J."
    },
    {
      "key": "2021112105403391000_12.2.292.8",
      "doi-asserted-by": "publisher",
      "DOI": "10.1101/gad.13.15.1970"
    },
    {
      "key": "2021112105403391000_12.2.292.9",
      "doi-asserted-by": "publisher",
      "DOI": "10.1126/science.1075901"
    },
    {
      "key": "2021112105403391000_12.2.292.10",
      "doi-asserted-by": "publisher",
      "DOI": "10.1017/S1355838201016077"
    },
    {
      "key": "2021112105403391000_12.2.292.11",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/nature00935"
    },
    {
      "key": "2021112105403391000_12.2.292.12",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/376745a0"
    },
    {
      "key": "2021112105403391000_12.2.292.13",
      "first-page": "1554",
      "volume": "7",
      "year": "2001",
      "journal-title": "RNA"
    },
    {
      "key": "2021112105403391000_12.2.292.14",
      "doi-asserted-by": "publisher",
      "DOI": "10.1261/rna.2220705"
    },
    {
      "key": "2021112105403391000_12.2.292.15",
      "first-page": "1",
      "volume": "194",
      "year": "1991",
      "journal-title": "Methods Enzymol."
    },
    {
      "key": "2021112105403391000_12.2.292.16",
      "doi-asserted-by": "crossref",
      "first-page": "345",
      "DOI": "10.1016/S0021-9258(19)75933-X",
      "volume": "262",
      "year": "1987",
      "journal-title": "J. Biol. Chem."
    },
    {
      "key": "2021112105403391000_12.2.292.17",
      "doi-asserted-by": "publisher",
      "DOI": "10.1074/jbc.M102755200"
    },
    {
      "key": "2021112105403391000_12.2.292.18",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/nrm1701"
    },
    {
      "key": "2021112105403391000_12.2.292.19",
      "doi-asserted-by": "publisher",
      "DOI": "10.1002/yea.320110406"
    },
    {
      "key": "2021112105403391000_12.2.292.20",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S1097-2765(03)00270-3"
    },
    {
      "key": "2021112105403391000_12.2.292.21",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0006-291X(03)01009-X"
    },
    {
      "key": "2021112105403391000_12.2.292.22",
      "doi-asserted-by": "crossref",
      "first-page": "869",
      "DOI": "10.18388/abp.1998_4346",
      "volume": "45",
      "year": "1998",
      "journal-title": "Acta Biochim. Pol."
    },
    {
      "key": "2021112105403391000_12.2.292.23",
      "first-page": "260",
      "volume": "1",
      "year": "1995",
      "journal-title": "RNA"
    },
    {
      "key": "2021112105403391000_12.2.292.24",
      "doi-asserted-by": "crossref",
      "first-page": "1667",
      "DOI": "10.1093/genetics/155.4.1667",
      "volume": "155",
      "year": "2000",
      "journal-title": "Genetics"
    },
    {
      "key": "2021112105403391000_12.2.292.25",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S1097-2765(00)80175-6"
    },
    {
      "key": "2021112105403391000_12.2.292.26",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.102304299"
    },
    {
      "key": "2021112105403391000_12.2.292.27",
      "doi-asserted-by": "publisher",
      "DOI": "10.1021/bi971296x"
    },
    {
      "key": "2021112105403391000_12.2.292.28",
      "doi-asserted-by": "crossref",
      "first-page": "2008",
      "DOI": "10.1128/MCB.19.3.2008",
      "volume": "19",
      "year": "1999",
      "journal-title": "Mol. Cell. Biol."
    },
    {
      "key": "2021112105403391000_12.2.292.29",
      "doi-asserted-by": "publisher",
      "DOI": "10.1126/science.1077783"
    },
    {
      "key": "2021112105403391000_12.2.292.30",
      "doi-asserted-by": "publisher",
      "DOI": "10.1093/emboj/20.10.2553"
    },
    {
      "key": "2021112105403391000_12.2.292.31",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/sj.emboj.7600241"
    },
    {
      "key": "2021112105403391000_12.2.292.32",
      "doi-asserted-by": "crossref",
      "first-page": "28",
      "DOI": "10.1186/1471-2091-3-28",
      "volume": "3",
      "year": "2002",
      "journal-title": "BMC Biochem."
    },
    {
      "key": "2021112105403391000_12.2.292.33",
      "doi-asserted-by": "publisher",
      "DOI": "10.1074/jbc.M212353200"
    },
    {
      "key": "2021112105403391000_12.2.292.34",
      "doi-asserted-by": "crossref",
      "first-page": "4368",
      "DOI": "10.1002/j.1460-2075.1996.tb00810.x",
      "volume": "15",
      "year": "1996",
      "journal-title": "EMBO J."
    },
    {
      "key": "2021112105403391000_12.2.292.35",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/nsb906"
    },
    {
      "key": "2021112105403391000_12.2.292.36",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/nbt849"
    },
    {
      "key": "2021112105403391000_12.2.292.37",
      "doi-asserted-by": "publisher",
      "DOI": "10.1093/emboj/21.10.2397"
    },
    {
      "key": "2021112105403391000_12.2.292.38",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S1097-2765(04)00217-5"
    },
    {
      "key": "2021112105403391000_12.2.292.39",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/nsmb962"
    },
    {
      "key": "2021112105403391000_12.2.292.40",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0960-9822(07)00345-4"
    },
    {
      "key": "2021112105403391000_12.2.292.41",
      "doi-asserted-by": "publisher",
      "DOI": "10.1101/gr.473902"
    },
    {
      "key": "2021112105403391000_12.2.292.42",
      "first-page": "213",
      "volume": "2",
      "year": "1996",
      "journal-title": "RNA"
    },
    {
      "key": "2021112105403391000_12.2.292.43",
      "doi-asserted-by": "publisher",
      "DOI": "10.1017/S1355838299981785"
    },
    {
      "key": "2021112105403391000_12.2.292.44",
      "doi-asserted-by": "publisher",
      "DOI": "10.1101/gad.13.15.1983"
    },
    {
      "key": "2021112105403391000_12.2.292.45",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.93.24.13641"
    },
    {
      "key": "2021112105403391000_12.2.292.46",
      "doi-asserted-by": "publisher",
      "DOI": "10.1074/jbc.M103248200"
    },
    {
      "key": "2021112105403391000_12.2.292.47",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0092-8674(00)80925-3"
    },
    {
      "key": "2021112105403391000_12.2.292.48",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.96.13.7226"
    },
    {
      "key": "2021112105403391000_12.2.292.49",
      "first-page": "1543",
      "volume": "7",
      "year": "2001",
      "journal-title": "RNA"
    },
    {
      "key": "2021112105403391000_12.2.292.50",
      "doi-asserted-by": "publisher",
      "DOI": "10.1126/science.7770774"
    },
    {
      "key": "2021112105403391000_12.2.292.51",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S1097-2765(04)00129-7"
    },
    {
      "key": "2021112105403391000_12.2.292.52",
      "doi-asserted-by": "crossref",
      "first-page": "2602",
      "DOI": "10.1002/j.1460-2075.1995.tb07258.x",
      "volume": "14",
      "year": "1995",
      "journal-title": "EMBO J."
    },
    {
      "key": "2021112105403391000_12.2.292.53",
      "doi-asserted-by": "publisher",
      "DOI": "10.1093/nar/23.3.320"
    },
    {
      "key": "2021112105403391000_12.2.292.54",
      "doi-asserted-by": "publisher",
      "DOI": "10.1074/jbc.M400023200"
    },
    {
      "key": "2021112105403391000_12.2.292.55",
      "doi-asserted-by": "publisher",
      "DOI": "10.1021/bi035033g"
    },
    {
      "key": "2021112105403391000_12.2.292.56",
      "doi-asserted-by": "publisher",
      "DOI": "10.1101/gad.9.7.855"
    },
    {
      "key": "2021112105403391000_12.2.292.57",
      "first-page": "584",
      "volume": "1",
      "year": "1995",
      "journal-title": "RNA"
    },
    {
      "key": "2021112105403391000_12.2.292.58",
      "doi-asserted-by": "crossref",
      "first-page": "723",
      "DOI": "10.1093/genetics/143.2.723",
      "volume": "143",
      "year": "1996",
      "journal-title": "Genetics"
    },
    {
      "key": "2021112105403391000_12.2.292.59",
      "doi-asserted-by": "crossref",
      "first-page": "1451",
      "DOI": "10.1093/genetics/157.4.1451",
      "volume": "157",
      "year": "2001",
      "journal-title": "Genetics"
    },
    {
      "key": "2021112105403391000_12.2.292.60",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0092-8674(01)00387-7"
    },
    {
      "key": "2021112105403391000_12.2.292.61",
      "doi-asserted-by": "publisher",
      "DOI": "10.1126/science.1075898"
    },
    {
      "key": "2021112105403391000_12.2.292.62",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.87.6.2216"
    },
    {
      "key": "2021112105403391000_12.2.292.63",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0022-2836(02)01145-2"
    },
    {
      "key": "2021112105403391000_12.2.292.64",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/j.cub.2004.11.058"
    },
    {
      "key": "2021112105403391000_12.2.292.65",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/nature01071"
    }
  ],
  "container-title": "RNA",
  "original-title": [],
  "language": "en",
  "link": [
    {
      "URL": "https://syndication.highwire.org/content/doi/10.1261/rna.2152306",
      "content-type": "unspecified",
      "content-version": "vor",
      "intended-application": "similarity-checking"
    }
  ],
  "deposited": {
    "date-parts": [
      [
        2021,
        11,
        21
      ]
    ],
    "date-time": "2021-11-21T13:45:01Z",
    "timestamp": 1637502301000
  },
  "score": 1,
  "resource": {
    "primary": {
      "URL": "http://rnajournal.cshlp.org/lookup/doi/10.1261/rna.2152306"
    }
  },
  "subtitle": [],
  "short-title": [],
  "issued": {
    "date-parts": [
      [
        2006,
        1,
        20
      ]
    ]
  },
  "references-count": 65,
  "journal-issue": {
    "issue": "2",
    "published-print": {
      "date-parts": [
        [
          2006,
          2
        ]
      ]
    }
  },
  "alternative-id": [
    "10.1261/rna.2152306"
  ],
  "URL": "http://dx.doi.org/10.1261/rna.2152306",
  "relation": {},
  "ISSN": [
    "1355-8382",
    "1469-9001"
  ],
  "subject": [],
  "container-title-short": "RNA",
  "published": {
    "date-parts": [
      [
        2006,
        1,
        20
      ]
    ]
  }
}