DOI: 10.1046/j.1365-2958.2003.03799.x. Stop codon recognition and interactions with peptide release factor RF3 of truncated and chimeric RF1 and RF2 from <i>Escherichia coli</i>

Stop codon recognition and interactions with peptide release factor RF3 of truncated and chimeric RF1 and RF2 from Escherichia coli

10.1046/j.1365-2958.2003.03799.x

Crossref journal-article

Wiley

Molecular Microbiology (311)

Abstract

SummaryRelease factors RF1 and RF2 recognize stop codons present at the A‐site of the ribosome and activate hydrolysis of peptidyl‐tRNA to release the peptide chain. Interactions with RF3, a ribosome‐dependent GTPase, then initiate a series of reactions that accelerate the dissociation of RF1 or RF2 and their recycling between ribosomes. Two regions of Escherichia coli RF1 and RF2 were identified previously as involved in stop codon recognition and peptidyl‐tRNA hydrolysis. We show here that removing the N‐terminal domain of RF1 or RF2 or exchanging this domain between the two factors does not affect RF specificity but has different effects on the activity of RF1 and RF2: truncated RF1 remains highly active and able to support rapid cell growth, whereas cells with truncated RF2 grow only poorly. Transplanting a loop of 13 amino acid residues from RF2 to RF1 switches the stop codon specificity. The interaction of the truncated factors with RF3 on the ribosome is defective: they fail to stimulate guanine nucleotide exchange on RF3, recycling is not stimulated by RF3, and nucleotide‐free RF3 fails to stabilize the binding of RF1 or RF2 to the ribosome. However, the N‐terminal domain seems not to be required for the expulsion of RF1 or RF2 by RF3:GTP.

Bibliography

Mora, L., Zavialov, A., Ehrenberg, M., & Buckingham, R. H. (2003). Stop codon recognition and interactions with peptide release factor RF3 of truncated and chimeric RF1 and RF2 from Escherichia coli. Molecular Microbiology, 50(5), 1467â1476. Portico.

Authors 4

Liliana Mora (first)
Andrei Zavialov (additional)
Måns Ehrenberg (additional)
Richard H. Buckingham (additional)

References 36 Referenced 41

10.1016/S0300-9084(00)01162-7
{'key': 'e_1_2_6_3_1', 'first-page': '363', 'volume-title': 'Transfer RNA: Structure, Properties and Recognition', 'author': 'Cantor C.R.', 'year': '1979'} / Transfer RNA: Structure, Properties and Recognition by Cantor C.R. (1979)
10.1093/emboj/19.24.6900
{'key': 'e_1_2_6_5_1', 'first-page': '541', 'volume-title': 'The Ribosome, Structure, Function, Antibiotics and Cellular Interactions', 'author': 'Ehrenberg M.', 'year': '2000'} / The Ribosome, Structure, Function, Antibiotics and Cellular Interactions by Ehrenberg M. (2000)
10.1093/emboj/16.13.4126
10.1017/S135583829999043X
10.1017/S135583820099143X
10.1093/emboj/21.4.769
10.1038/35001115
10.1073/pnas.142690099
10.1073/pnas.76.7.3174
10.1093/embo-reports/kve156
10.1016/S0968-0004(00)01669-8
10.1093/emboj/cdg017
10.1038/nature01225
10.1016/S0960-9822(01)00028-8
10.1016/S0014-5793(98)01669-X
10.1046/j.1365-2958.2003.03301.x
10.1016/S0092-8674(00)81331-8
10.1016/S0092-8674(00)80845-4
10.1126/science.270.5241.1464
10.1016/S0167-4781(00)00162-7
10.1016/S0092-8674(02)00619-0
10.1038/nature01224
10.1007/BF00327411
{'key': 'e_1_2_6_27_1', 'first-page': '27', 'article-title': 'Mapping functionally important motifs SPF and GGQ of the decoding release factor RF2 to the Escherichia coli ribosome by hydroxyl radical footprinting. Implications for macromolecular mimicry and structural changes in RF2', 'volume': '27', 'author': 'Scarlett D.J.', 'year': '2003', 'journal-title': 'J Biol Chem'} / J Biol Chem / Mapping functionally important motifs SPF and GGQ of the decoding release factor RF2 to the Escherichia coli ribosome by hydroxyl radical footprinting. Implications for macromolecular mimicry and structural changes in RF2 by Scarlett D.J. (2003)
10.1093/nar/29.19.3982
10.1093/embo-reports/kvf178
10.1016/S0021-9258(17)44043-9
10.1016/S0022-2836(03)00537-0
10.1016/S0022-2836(02)00304-2
10.1016/S1097-2765(01)00415-4
10.1128/jb.184.4.1200-1203.2002
10.1073/pnas.100127597
10.1016/S0092-8674(01)00508-6
10.1016/S1097-2765(02)00691-3

Dates

Type	When
Created	21 years, 9 months ago (Nov. 20, 2003, 4:43 p.m.)
Deposited	1 year, 10 months ago (Oct. 13, 2023, 5:59 a.m.)
Indexed	1 month, 3 weeks ago (July 11, 2025, 6:41 a.m.)
Issued	21 years, 9 months ago (Nov. 17, 2003)
Published	21 years, 9 months ago (Nov. 17, 2003)
Published Online	21 years, 9 months ago (Nov. 17, 2003)
Published Print	21 years, 9 months ago (Dec. 1, 2003)

Funders 0

None

BibTeX

@article{Mora_2003, title={Stop codon recognition and interactions with peptide release factor RF3 of truncated and chimeric RF1 and RF2 from Escherichia coli}, volume={50}, ISSN={1365-2958}, url={http://dx.doi.org/10.1046/j.1365-2958.2003.03799.x}, DOI={10.1046/j.1365-2958.2003.03799.x}, number={5}, journal={Molecular Microbiology}, publisher={Wiley}, author={Mora, Liliana and Zavialov, Andrei and Ehrenberg, Måns and Buckingham, Richard H.}, year={2003}, month=nov, pages={1467–1476} }

JSON

{
  "indexed": {
    "date-parts": [
      [
        2025,
        7,
        11
      ]
    ],
    "date-time": "2025-07-11T10:41:43Z",
    "timestamp": 1752230503724
  },
  "reference-count": 36,
  "publisher": "Wiley",
  "issue": "5",
  "license": [
    {
      "start": {
        "date-parts": [
          [
            2003,
            11,
            17
          ]
        ],
        "date-time": "2003-11-17T00:00:00Z",
        "timestamp": 1069027200000
      },
      "content-version": "vor",
      "delay-in-days": 0,
      "URL": "http://onlinelibrary.wiley.com/termsAndConditions#vor"
    }
  ],
  "content-domain": {
    "domain": [],
    "crossmark-restriction": false
  },
  "published-print": {
    "date-parts": [
      [
        2003,
        12
      ]
    ]
  },
  "abstract": "<jats:title>Summary</jats:title><jats:p>Release factors RF1 and RF2 recognize stop codons present at the A\u2010site of the ribosome and activate hydrolysis of peptidyl\u2010tRNA to release the peptide chain. Interactions with RF3, a ribosome\u2010dependent GTPase, then initiate a series of reactions that accelerate the dissociation of RF1 or RF2 and their recycling between ribosomes. Two regions of <jats:italic>Escherichia coli</jats:italic> RF1 and RF2 were identified previously as involved in stop codon recognition and peptidyl\u2010tRNA hydrolysis. We show here that removing the N\u2010terminal domain of RF1 or RF2 or exchanging this domain between the two factors does not affect RF specificity but has different effects on the activity of RF1 and RF2: truncated RF1 remains highly active and able to support rapid cell growth, whereas cells with truncated RF2 grow only poorly. Transplanting a loop of 13 amino acid residues from RF2 to RF1 switches the stop codon specificity. The interaction of the truncated factors with RF3 on the ribosome is defective: they fail to stimulate guanine nucleotide exchange on RF3, recycling is not stimulated by RF3, and nucleotide\u2010free RF3 fails to stabilize the binding of RF1 or RF2 to the ribosome. However, the N\u2010terminal domain seems not to be required for the expulsion of RF1 or RF2 by RF3:GTP.</jats:p>",
  "DOI": "10.1046/j.1365-2958.2003.03799.x",
  "type": "journal-article",
  "created": {
    "date-parts": [
      [
        2003,
        11,
        20
      ]
    ],
    "date-time": "2003-11-20T21:43:53Z",
    "timestamp": 1069364633000
  },
  "page": "1467-1476",
  "source": "Crossref",
  "is-referenced-by-count": 41,
  "title": "Stop codon recognition and interactions with peptide release factor RF3 of truncated and chimeric RF1 and RF2 from <i>Escherichia coli</i>",
  "prefix": "10.1111",
  "volume": "50",
  "author": [
    {
      "given": "Liliana",
      "family": "Mora",
      "sequence": "first",
      "affiliation": []
    },
    {
      "given": "Andrei",
      "family": "Zavialov",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "M\u00e5ns",
      "family": "Ehrenberg",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "Richard H.",
      "family": "Buckingham",
      "sequence": "additional",
      "affiliation": []
    }
  ],
  "member": "311",
  "published-online": {
    "date-parts": [
      [
        2003,
        11,
        17
      ]
    ]
  },
  "reference": [
    {
      "key": "e_1_2_6_2_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0300-9084(00)01162-7"
    },
    {
      "key": "e_1_2_6_3_1",
      "first-page": "363",
      "volume-title": "Transfer RNA: Structure, Properties and Recognition",
      "author": "Cantor C.R.",
      "year": "1979"
    },
    {
      "key": "e_1_2_6_4_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1093/emboj/19.24.6900"
    },
    {
      "key": "e_1_2_6_5_1",
      "first-page": "541",
      "volume-title": "The Ribosome, Structure, Function, Antibiotics and Cellular Interactions",
      "author": "Ehrenberg M.",
      "year": "2000"
    },
    {
      "key": "e_1_2_6_6_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1093/emboj/16.13.4126"
    },
    {
      "key": "e_1_2_6_7_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1017/S135583829999043X"
    },
    {
      "key": "e_1_2_6_8_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1017/S135583820099143X"
    },
    {
      "key": "e_1_2_6_9_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1093/emboj/21.4.769"
    },
    {
      "key": "e_1_2_6_10_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/35001115"
    },
    {
      "key": "e_1_2_6_11_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.142690099"
    },
    {
      "key": "e_1_2_6_12_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.76.7.3174"
    },
    {
      "key": "e_1_2_6_13_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1093/embo-reports/kve156"
    },
    {
      "key": "e_1_2_6_14_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0968-0004(00)01669-8"
    },
    {
      "key": "e_1_2_6_15_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1093/emboj/cdg017"
    },
    {
      "key": "e_1_2_6_16_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/nature01225"
    },
    {
      "key": "e_1_2_6_17_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0960-9822(01)00028-8"
    },
    {
      "key": "e_1_2_6_18_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0014-5793(98)01669-X"
    },
    {
      "key": "e_1_2_6_19_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1046/j.1365-2958.2003.03301.x"
    },
    {
      "key": "e_1_2_6_20_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0092-8674(00)81331-8"
    },
    {
      "key": "e_1_2_6_21_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0092-8674(00)80845-4"
    },
    {
      "key": "e_1_2_6_22_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1126/science.270.5241.1464"
    },
    {
      "key": "e_1_2_6_23_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0167-4781(00)00162-7"
    },
    {
      "key": "e_1_2_6_24_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0092-8674(02)00619-0"
    },
    {
      "key": "e_1_2_6_25_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/nature01224"
    },
    {
      "key": "e_1_2_6_26_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1007/BF00327411"
    },
    {
      "key": "e_1_2_6_27_1",
      "first-page": "27",
      "article-title": "Mapping functionally important motifs SPF and GGQ of the decoding release factor RF2 to the Escherichia coli ribosome by hydroxyl radical footprinting. Implications for macromolecular mimicry and structural changes in RF2",
      "volume": "27",
      "author": "Scarlett D.J.",
      "year": "2003",
      "journal-title": "J Biol Chem"
    },
    {
      "key": "e_1_2_6_28_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1093/nar/29.19.3982"
    },
    {
      "key": "e_1_2_6_29_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1093/embo-reports/kvf178"
    },
    {
      "key": "e_1_2_6_30_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0021-9258(17)44043-9"
    },
    {
      "key": "e_1_2_6_31_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0022-2836(03)00537-0"
    },
    {
      "key": "e_1_2_6_32_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0022-2836(02)00304-2"
    },
    {
      "key": "e_1_2_6_33_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S1097-2765(01)00415-4"
    },
    {
      "key": "e_1_2_6_34_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1128/jb.184.4.1200-1203.2002"
    },
    {
      "key": "e_1_2_6_35_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.100127597"
    },
    {
      "key": "e_1_2_6_36_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0092-8674(01)00508-6"
    },
    {
      "key": "e_1_2_6_37_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S1097-2765(02)00691-3"
    }
  ],
  "container-title": "Molecular Microbiology",
  "original-title": [],
  "language": "en",
  "link": [
    {
      "URL": "https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1046%2Fj.1365-2958.2003.03799.x",
      "content-type": "unspecified",
      "content-version": "vor",
      "intended-application": "text-mining"
    },
    {
      "URL": "https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-2958.2003.03799.x",
      "content-type": "unspecified",
      "content-version": "vor",
      "intended-application": "similarity-checking"
    }
  ],
  "deposited": {
    "date-parts": [
      [
        2023,
        10,
        13
      ]
    ],
    "date-time": "2023-10-13T09:59:21Z",
    "timestamp": 1697191161000
  },
  "score": 1,
  "resource": {
    "primary": {
      "URL": "https://onlinelibrary.wiley.com/doi/10.1046/j.1365-2958.2003.03799.x"
    }
  },
  "subtitle": [],
  "short-title": [],
  "issued": {
    "date-parts": [
      [
        2003,
        11,
        17
      ]
    ]
  },
  "references-count": 36,
  "journal-issue": {
    "issue": "5",
    "published-print": {
      "date-parts": [
        [
          2003,
          12
        ]
      ]
    }
  },
  "alternative-id": [
    "10.1046/j.1365-2958.2003.03799.x"
  ],
  "URL": "http://dx.doi.org/10.1046/j.1365-2958.2003.03799.x",
  "relation": {},
  "ISSN": [
    "0950-382X",
    "1365-2958"
  ],
  "subject": [],
  "container-title-short": "Molecular Microbiology",
  "published": {
    "date-parts": [
      [
        2003,
        11,
        17
      ]
    ]
  }
}