DOI: 10.1073/pnas.212628899. An mRNA structure that controls gene expression by binding FMN

An mRNA structure that controls gene expression by binding FMN

10.1073/pnas.212628899

Crossref journal-article

Proceedings of the National Academy of Sciences

Proceedings of the National Academy of Sciences (341)

Abstract

The RFN element is a highly conserved domain that is found frequently in the 5′-untranslated regions of prokaryotic mRNAs that encode for flavin mononucleotide (FMN) biosynthesis and transport proteins. We report that this domain serves as the receptor for a metabolite-dependent riboswitch that directly binds FMN in the absence of proteins. Our results also indicate that in Bacillus subtilis , the riboswitch most likely controls gene expression by causing premature transcription termination of the ribDEAHT operon and precluding access to the ribosome-binding site of ypaA mRNA. Sequence and structural analyses indicate that the RFN element is a natural FMN-binding aptamer, the allosteric character of which is harnessed to control gene expression.

Bibliography

Winkler, W. C., Cohen-Chalamish, S., & Breaker, R. R. (2002). An mRNA structure that controls gene expression by binding FMN. Proceedings of the National Academy of Sciences, 99(25), 15908â15913.

Authors 3

Wade C. Winkler (first)
Smadar Cohen-Chalamish (additional)
Ronald R. Breaker (additional)

References 31 Referenced 564

10.1073/pnas.88.4.1479
10.1016/S1074-5521(02)00224-7
10.1073/pnas.161168098
10.1038/nature01145
10.1016/S1369-5274(00)00067-9
10.1007/s00203-002-0407-5
10.1073/pnas.162366799
10.1016/S0168-9525(99)01856-9
10.1093/nar/gkf433
10.1128/JB.180.4.950-955.1998
10.1128/JB.183.24.7371-7380.2001
Gusarov I. I., Kreneva, R. A., Podcharniaev, D. A., Iomantas, I. V., Abalakina, E. G., Stoinova, N. V., Perumov, D. A. & Kozlov, I. I. (1997) Mol. Biol.31,446-453. / Mol. Biol. by Gusarov I. I. (1997)
10.1007/BF00265448
Kreneva R. A., Gelfand, M. S., Mironov, A. A., Yomantas, J. A., Kozlov, Y. I., Mironov, A. S. & Perumov, D. A. (2000) Russ. J. Genet. [Transl. of Genetika (Moscow)]36,972-974. / Russ. J. Genet. [Transl. of Genetika (Moscow)] by Kreneva R. A. (2000)
Perkins J. B. & Pero J. (2002) in Bacillus subtilis and Its Closest Relatives: From Genes to Cells eds. Sonenshein A. L. Hoch J. A. & Losick R. (Am. Soc. Microbiol. Washington DC) pp. 271–286.
10.1111/j.1365-2958.1993.tb02671.x
Mironov V. N., Perumov, D. A., Krayev, A. S., Stepanov, A. I. & Skryabin, K. G. (1990) Mol. Biol.24,256-260. / Mol. Biol. by Mironov V. N. (1990)
10.1038/86723
10.1017/S1355838299990891
10.1017/S1355838201002175
10.1073/pnas.94.9.4262
10.1016/S0076-6879(00)17012-0
10.1038/36786
10.1073/pnas.92.19.8793
10.1016/S1097-2765(00)80477-3
10.1002/bies.10125
Merino E. & Yanofsky C. (2002) in Bacillus subtilis and Its Closest Relatives: From Genes to Cells eds. Sonenshein A. L. Hoch J. A. & Losick R. (Am. Soc. Microbiol. Washington DC) pp. 323–336.
10.1073/pnas.94.1.59
10.1016/S0959-437X(97)80050-0
10.1073/pnas.130013897
10.1073/pnas.181334498

Dates

Type	When
Created	22 years, 8 months ago (Dec. 10, 2002, 12:42 p.m.)
Deposited	3 years, 4 months ago (April 13, 2022, 7:52 a.m.)
Indexed	3 minutes ago (Aug. 28, 2025, 5:35 p.m.)
Issued	22 years, 9 months ago (Nov. 27, 2002)
Published	22 years, 9 months ago (Nov. 27, 2002)
Published Online	22 years, 9 months ago (Nov. 27, 2002)
Published Print	22 years, 8 months ago (Dec. 10, 2002)

Funders 0

None

BibTeX

@article{Winkler_2002, title={An mRNA structure that controls gene expression by binding FMN}, volume={99}, ISSN={1091-6490}, url={http://dx.doi.org/10.1073/pnas.212628899}, DOI={10.1073/pnas.212628899}, number={25}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Winkler, Wade C. and Cohen-Chalamish, Smadar and Breaker, Ronald R.}, year={2002}, month=nov, pages={15908–15913} }

JSON

{
  "indexed": {
    "date-parts": [
      [
        2025,
        8,
        28
      ]
    ],
    "date-time": "2025-08-28T21:35:06Z",
    "timestamp": 1756416906029
  },
  "reference-count": 31,
  "publisher": "Proceedings of the National Academy of Sciences",
  "issue": "25",
  "content-domain": {
    "domain": [
      "www.pnas.org"
    ],
    "crossmark-restriction": true
  },
  "published-print": {
    "date-parts": [
      [
        2002,
        12,
        10
      ]
    ]
  },
  "abstract": "<jats:p>\n            The\n            <jats:italic>RFN</jats:italic>\n            element is a highly conserved domain that is found frequently in the 5\u2032-untranslated regions of prokaryotic mRNAs that encode for flavin mononucleotide (FMN) biosynthesis and transport proteins. We report that this domain serves as the receptor for a metabolite-dependent riboswitch that directly binds FMN in the absence of proteins. Our results also indicate that in\n            <jats:italic>Bacillus subtilis</jats:italic>\n            , the riboswitch most likely controls gene expression by causing premature transcription termination of the\n            <jats:italic>ribDEAHT</jats:italic>\n            operon and precluding access to the ribosome-binding site of\n            <jats:italic>ypaA</jats:italic>\n            mRNA. Sequence and structural analyses indicate that the\n            <jats:italic>RFN</jats:italic>\n            element is a natural FMN-binding aptamer, the allosteric character of which is harnessed to control gene expression.\n          </jats:p>",
  "DOI": "10.1073/pnas.212628899",
  "type": "journal-article",
  "created": {
    "date-parts": [
      [
        2002,
        12,
        10
      ]
    ],
    "date-time": "2002-12-10T17:42:57Z",
    "timestamp": 1039542177000
  },
  "page": "15908-15913",
  "update-policy": "http://dx.doi.org/10.1073/pnas.cm10313",
  "source": "Crossref",
  "is-referenced-by-count": 564,
  "title": "An mRNA structure that controls gene expression by binding FMN",
  "prefix": "10.1073",
  "volume": "99",
  "author": [
    {
      "given": "Wade C.",
      "family": "Winkler",
      "sequence": "first",
      "affiliation": [
        {
          "name": "Department of Molecular, Cellular, and Developmental Biology, Yale University, P.O. Box 208103, New Haven, CT 06520-8103"
        }
      ]
    },
    {
      "given": "Smadar",
      "family": "Cohen-Chalamish",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "Department of Molecular, Cellular, and Developmental Biology, Yale University, P.O. Box 208103, New Haven, CT 06520-8103"
        }
      ]
    },
    {
      "given": "Ronald R.",
      "family": "Breaker",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "Department of Molecular, Cellular, and Developmental Biology, Yale University, P.O. Box 208103, New Haven, CT 06520-8103"
        }
      ]
    }
  ],
  "member": "341",
  "published-online": {
    "date-parts": [
      [
        2002,
        11,
        27
      ]
    ]
  },
  "reference": [
    {
      "key": "e_1_3_3_1_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.88.4.1479"
    },
    {
      "key": "e_1_3_3_2_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S1074-5521(02)00224-7"
    },
    {
      "key": "e_1_3_3_3_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.161168098"
    },
    {
      "key": "e_1_3_3_4_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/nature01145"
    },
    {
      "key": "e_1_3_3_5_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S1369-5274(00)00067-9"
    },
    {
      "key": "e_1_3_3_6_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1007/s00203-002-0407-5"
    },
    {
      "key": "e_1_3_3_7_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.162366799"
    },
    {
      "key": "e_1_3_3_8_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0168-9525(99)01856-9"
    },
    {
      "key": "e_1_3_3_9_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1093/nar/gkf433"
    },
    {
      "key": "e_1_3_3_10_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1128/JB.180.4.950-955.1998"
    },
    {
      "key": "e_1_3_3_11_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1128/JB.183.24.7371-7380.2001"
    },
    {
      "key": "e_1_3_3_12_2",
      "first-page": "446",
      "volume": "31",
      "author": "Gusarov I. I.",
      "year": "1997",
      "unstructured": "Gusarov I. I., Kreneva, R. A., Podcharniaev, D. A., Iomantas, I. V., Abalakina, E. G., Stoinova, N. V., Perumov, D. A. & Kozlov, I. I. (1997) Mol. Biol.31,446-453.",
      "journal-title": "Mol. Biol."
    },
    {
      "key": "e_1_3_3_13_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1007/BF00265448"
    },
    {
      "key": "e_1_3_3_14_2",
      "first-page": "972",
      "volume": "36",
      "author": "Kreneva R. A.",
      "year": "2000",
      "unstructured": "Kreneva R. A., Gelfand, M. S., Mironov, A. A., Yomantas, J. A., Kozlov, Y. I., Mironov, A. S. & Perumov, D. A. (2000) Russ. J. Genet. [Transl. of Genetika (Moscow)]36,972-974.",
      "journal-title": "Russ. J. Genet. [Transl. of Genetika (Moscow)]"
    },
    {
      "key": "e_1_3_3_15_2",
      "unstructured": "Perkins J. B. & Pero J. (2002) in Bacillus subtilis and Its Closest Relatives: From Genes to Cells eds. Sonenshein A. L. Hoch J. A. & Losick R. (Am. Soc. Microbiol. Washington DC) pp. 271\u2013286."
    },
    {
      "key": "e_1_3_3_16_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1111/j.1365-2958.1993.tb02671.x"
    },
    {
      "key": "e_1_3_3_17_2",
      "first-page": "256",
      "volume": "24",
      "author": "Mironov V. N.",
      "year": "1990",
      "unstructured": "Mironov V. N., Perumov, D. A., Krayev, A. S., Stepanov, A. I. & Skryabin, K. G. (1990) Mol. Biol.24,256-260.",
      "journal-title": "Mol. Biol."
    },
    {
      "key": "e_1_3_3_18_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/86723"
    },
    {
      "key": "e_1_3_3_19_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1017/S1355838299990891"
    },
    {
      "key": "e_1_3_3_20_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1017/S1355838201002175"
    },
    {
      "key": "e_1_3_3_21_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.94.9.4262"
    },
    {
      "key": "e_1_3_3_22_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0076-6879(00)17012-0"
    },
    {
      "key": "e_1_3_3_23_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/36786"
    },
    {
      "key": "e_1_3_3_24_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.92.19.8793"
    },
    {
      "key": "e_1_3_3_25_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S1097-2765(00)80477-3"
    },
    {
      "key": "e_1_3_3_26_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1002/bies.10125"
    },
    {
      "key": "e_1_3_3_27_2",
      "unstructured": "Merino E. & Yanofsky C. (2002) in Bacillus subtilis and Its Closest Relatives: From Genes to Cells eds. Sonenshein A. L. Hoch J. A. & Losick R. (Am. Soc. Microbiol. Washington DC) pp. 323\u2013336."
    },
    {
      "key": "e_1_3_3_28_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.94.1.59"
    },
    {
      "key": "e_1_3_3_29_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0959-437X(97)80050-0"
    },
    {
      "key": "e_1_3_3_30_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.130013897"
    },
    {
      "key": "e_1_3_3_31_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.181334498"
    }
  ],
  "container-title": "Proceedings of the National Academy of Sciences",
  "original-title": [],
  "language": "en",
  "link": [
    {
      "URL": "https://pnas.org/doi/pdf/10.1073/pnas.212628899",
      "content-type": "unspecified",
      "content-version": "vor",
      "intended-application": "similarity-checking"
    }
  ],
  "deposited": {
    "date-parts": [
      [
        2022,
        4,
        13
      ]
    ],
    "date-time": "2022-04-13T11:52:48Z",
    "timestamp": 1649850768000
  },
  "score": 1,
  "resource": {
    "primary": {
      "URL": "https://pnas.org/doi/full/10.1073/pnas.212628899"
    }
  },
  "subtitle": [],
  "short-title": [],
  "issued": {
    "date-parts": [
      [
        2002,
        11,
        27
      ]
    ]
  },
  "references-count": 31,
  "journal-issue": {
    "issue": "25",
    "published-print": {
      "date-parts": [
        [
          2002,
          12,
          10
        ]
      ]
    }
  },
  "alternative-id": [
    "10.1073/pnas.212628899"
  ],
  "URL": "http://dx.doi.org/10.1073/pnas.212628899",
  "relation": {},
  "ISSN": [
    "0027-8424",
    "1091-6490"
  ],
  "subject": [],
  "container-title-short": "Proc. Natl. Acad. Sci. U.S.A.",
  "published": {
    "date-parts": [
      [
        2002,
        11,
        27
      ]
    ]
  },
  "assertion": [
    {
      "value": "2002-09-27",
      "order": 0,
      "name": "received",
      "label": "Received",
      "group": {
        "name": "publication_history",
        "label": "Publication History"
      }
    },
    {
      "value": "2002-10-16",
      "order": 1,
      "name": "accepted",
      "label": "Accepted",
      "group": {
        "name": "publication_history",
        "label": "Publication History"
      }
    },
    {
      "value": "2002-11-27",
      "order": 2,
      "name": "published",
      "label": "Published",
      "group": {
        "name": "publication_history",
        "label": "Publication History"
      }
    }
  ]
}