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Galatolo D, Kuo ME, Mullen P, Meyer-Schuman R, Doccini S, Battini R, Lieto M, Tessa A, Filla A, Francklyn C, Antonellis A, Santorelli FM. Bi-allelic mutations in HARS1 severely impair histidyl-tRNA synthetase expression and enzymatic activity causing a novel multisystem ataxic syndrome. Hum Mutat 2020; 41:1232-1237. [PMID: 32333447 DOI: 10.1002/humu.24024] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/09/2020] [Accepted: 04/13/2020] [Indexed: 12/31/2022]
Abstract
Mutations in histidyl-tRNA synthetase (HARS1), an enzyme that charges transfer RNA with the amino acid histidine in the cytoplasm, have only been associated to date with autosomal recessive Usher syndrome type III and autosomal dominant Charcot-Marie-Tooth disease type 2W. Using massive parallel sequencing, we identified bi-allelic HARS1 variants in a child (c.616G>T, p.Asp206Tyr and c.730delG, p.Val244Cysfs*6) and in two sisters (c.1393A>C, p.Ile465Leu and c.910_912dupTTG, p.Leu305dup), all characterized by a multisystem ataxic syndrome. All mutations are rare, segregate with the disease, and are predicted to have a significant effect on protein function. Functional studies helped to substantiate their disease-related roles. Indeed, yeast complementation assays showing that one out of two mutations in each patient is loss-of-function, and the reduction of messenger RNA and protein levels and enzymatic activity in patient's skin-derived fibroblasts, together support the pathogenicity of the identified HARS1 variants in the patient phenotypes. Thus, our efforts expand the allelic and clinical spectrum of HARS1-related disease.
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Affiliation(s)
- Daniele Galatolo
- Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Stella Maris Foundation, Pisa, Italy
| | - Molly E Kuo
- Medical Scientist Training Program, University of Michigan Medical School, Ann Arbor, Michigan.,Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, Michigan
| | - Patrick Mullen
- Department of Biochemistry, College of Medicine, University of Vermont, Burlington, Vermont
| | - Rebecca Meyer-Schuman
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Stefano Doccini
- Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Stella Maris Foundation, Pisa, Italy
| | - Roberta Battini
- Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Stella Maris Foundation, Pisa, Italy
| | - Maria Lieto
- Department of Neurosciences and Reproductive and Odontostomatological Sciences, Federico II University, Naples, Italy
| | - Alessandra Tessa
- Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Stella Maris Foundation, Pisa, Italy
| | - Alessandro Filla
- Department of Neurosciences and Reproductive and Odontostomatological Sciences, Federico II University, Naples, Italy
| | - Christopher Francklyn
- Department of Biochemistry, College of Medicine, University of Vermont, Burlington, Vermont
| | - Anthony Antonellis
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, Michigan.,Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Filippo M Santorelli
- Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Stella Maris Foundation, Pisa, Italy
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2
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Royer‐Bertrand B, Tsouni P, Mullen P, Campos Xavier B, Mittaz Crettol L, Lobrinus AJ, Ghika J, Baumgartner MR, Rivolta C, Superti‐Furga A, Kuntzer T, Francklyn C, Tran C. Peripheral neuropathy and cognitive impairment associated with a novel monoallelic HARS variant. Ann Clin Transl Neurol 2019; 6:1072-1080. [PMID: 31211171 PMCID: PMC6562026 DOI: 10.1002/acn3.791] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 03/20/2019] [Accepted: 04/05/2019] [Indexed: 12/31/2022] Open
Abstract
Background A 49‐year‐old male presented with late‐onset demyelinating peripheral neuropathy, cerebellar atrophy, and cognitive deficit. Nerve biopsy revealed intra‐axonal inclusions suggestive of polyglucosan bodies, raising the suspicion of adult polyglucosan bodies disease (OMIM 263570). Methods and Results While known genes associated with polyglucosan bodies storage were negative, whole‐exome sequencing identified an unreported monoallelic variant, c.397G>T (p.Val133Phe), in the histidyl‐tRNA synthetase (HARS) gene. While we did not identify mutations in genes known to be associated with polygucosan body disease, whole‐exome sequencing revealed an unreported monoallelic variant, c.397G>T in the histidyl‐tRNA synthetase (HARS) gene, encoding a substitution (Val133Phe) in the catalytic domain. Expression of this variant in patient cells resulted in reduced aminoacylation activity in extracts obtained from dermal fibroblasts, without compromising overall protein synthesis. Interpretation Genetic variants in the genes coding for the different aminoacyl‐tRNA synthases are associated with various clinical conditions. To date, a number of HARS variant have been associated with peripheral neuropathy, but not cognitive deficits. Further studies are needed to explore why HARS mutations confer a neuronal‐specific phenotype.
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Affiliation(s)
- Béryl Royer‐Bertrand
- Division of Genetic MedicineLausanne University Hospital (CHUV)LausanneSwitzerland
- Department of Computational BiologyUnit of Medical GeneticsUniversity of LausanneLausanneSwitzerland
| | - Pinelopi Tsouni
- Nerve‐Muscle UnitDepartment of Clinical NeurosciencesLausanne University Hospital (CHUV)LausanneSwitzerland
- Leenaards Memory CentreDepartment of Clinical NeurosciencesLausanne University Hospital (CHUV)LausanneSwitzerland
| | - Patrick Mullen
- Department of BiochemistryLarner College of MedicineUniversity of VermontBurlingtonVermont
| | | | | | | | - Joseph Ghika
- Leenaards Memory CentreDepartment of Clinical NeurosciencesLausanne University Hospital (CHUV)LausanneSwitzerland
| | - Matthias R. Baumgartner
- Division of Metabolism and Children's Research Center (CRC)University Children's HospitalZurichSwitzerland
- radiz ‐ Rare Disease Initiative ZurichClinical Research Priority Program for Rare DiseasesUniversity of ZurichZurichSwitzerland
| | - Carlo Rivolta
- Department of Computational BiologyUnit of Medical GeneticsUniversity of LausanneLausanneSwitzerland
- Department of Genetics and Genome BiologyUniversity of LeicesterLeicesterUnited Kingdom
| | - Andrea Superti‐Furga
- Division of Genetic MedicineLausanne University Hospital (CHUV)LausanneSwitzerland
| | - Thierry Kuntzer
- Nerve‐Muscle UnitDepartment of Clinical NeurosciencesLausanne University Hospital (CHUV)LausanneSwitzerland
| | - Christopher Francklyn
- Department of BiochemistryLarner College of MedicineUniversity of VermontBurlingtonVermont
| | - Christel Tran
- Division of Genetic MedicineLausanne University Hospital (CHUV)LausanneSwitzerland
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3
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Waldron A, Wilcox C, Francklyn C, Ebert A. Knock-Down of Histidyl-tRNA Synthetase Causes Cell Cycle Arrest and Apoptosis of Neuronal Progenitor Cells in vivo. Front Cell Dev Biol 2019; 7:67. [PMID: 31134197 PMCID: PMC6524715 DOI: 10.3389/fcell.2019.00067] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 04/09/2019] [Indexed: 01/18/2023] Open
Abstract
Histidyl-tRNA Synthetase (HARS) is a member of the aminoacyl-tRNA synthetase family, which attach amino acids to their associated tRNA molecules. This reaction is a crucial step in protein synthesis that must be carried out in every cell of an organism. However, a number of tissue-specific, human genetic disorders have been associated with mutations in the genes for aminoacyl-tRNA synthetases, including HARS. These associations indicate that, while we know a great deal about the molecular and biochemical properties of this enzyme, we still do not fully understand how these proteins function in the context of an entire organism. To this end, we set out to knock-down HARS expression in the zebrafish and characterize the developmental consequences. Through our work we show that some tissues, particularly the nervous system, are more sensitive to HARS loss than others and we reveal a link between HARS and the proliferation and survival of neuronal progenitors during development.
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Affiliation(s)
- Ashley Waldron
- Department of Biology, The University of Vermont, Burlington, VT, United States
| | - Claire Wilcox
- Department of Biology, The University of Vermont, Burlington, VT, United States
| | - Christopher Francklyn
- Department of Biochemistry, The University of Vermont, Burlington, VT, United States
| | - Alicia Ebert
- Department of Biology, The University of Vermont, Burlington, VT, United States
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4
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Siekierska A, Stamberger H, Deconinck T, Oprescu SN, Partoens M, Zhang Y, Sourbron J, Adriaenssens E, Mullen P, Wiencek P, Hardies K, Lee JS, Giong HK, Distelmaier F, Elpeleg O, Helbig KL, Hersh J, Isikay S, Jordan E, Karaca E, Kecskes A, Lupski JR, Kovacs-Nagy R, May P, Narayanan V, Pendziwiat M, Ramsey K, Rangasamy S, Shinde DN, Spiegel R, Timmerman V, von Spiczak S, Helbig I, Weckhuysen S, Francklyn C, Antonellis A, de Witte P, De Jonghe P. Biallelic VARS variants cause developmental encephalopathy with microcephaly that is recapitulated in vars knockout zebrafish. Nat Commun 2019; 10:708. [PMID: 30755616 PMCID: PMC6372652 DOI: 10.1038/s41467-018-07953-w] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 10/03/2018] [Indexed: 11/09/2022] Open
Abstract
Aminoacyl tRNA synthetases (ARSs) link specific amino acids with their cognate transfer RNAs in a critical early step of protein translation. Mutations in ARSs have emerged as a cause of recessive, often complex neurological disease traits. Here we report an allelic series consisting of seven novel and two previously reported biallelic variants in valyl-tRNA synthetase (VARS) in ten patients with a developmental encephalopathy with microcephaly, often associated with early-onset epilepsy. In silico, in vitro, and yeast complementation assays demonstrate that the underlying pathomechanism of these mutations is most likely a loss of protein function. Zebrafish modeling accurately recapitulated some of the key neurological disease traits. These results provide both genetic and biological insights into neurodevelopmental disease and pave the way for further in-depth research on ARS related recessive disorders and precision therapies. tRNAs are linked with their cognate amino acid by aminoacyl tRNA synthetases (ARS). Here, the authors report a developmental encephalopathy associated with biallelic VARS variants (valyl-tRNA synthetase) that lead to loss of function, as determined by several in vitro assays and a vars knockout zebrafish model.
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Affiliation(s)
- Aleksandra Siekierska
- Laboratory for Molecular Biodiscovery, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, 3000, Belgium
| | - Hannah Stamberger
- Neurogenetics Group, Center for Molecular Neurology, VIB, University of Antwerp, Antwerp, 2610, Belgium.,Institute Born Bunge, University of Antwerp, Antwerp, 2610, Belgium.,Department of Neurology, Antwerp University Hospital, Antwerp, 2650, Belgium
| | - Tine Deconinck
- Neurogenetics Group, Center for Molecular Neurology, VIB, University of Antwerp, Antwerp, 2610, Belgium.,Institute Born Bunge, University of Antwerp, Antwerp, 2610, Belgium
| | - Stephanie N Oprescu
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Michèle Partoens
- Laboratory for Molecular Biodiscovery, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, 3000, Belgium
| | - Yifan Zhang
- Laboratory for Molecular Biodiscovery, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, 3000, Belgium
| | - Jo Sourbron
- Laboratory for Molecular Biodiscovery, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, 3000, Belgium
| | - Elias Adriaenssens
- Institute Born Bunge, University of Antwerp, Antwerp, 2610, Belgium.,Peripheral Neuropathy Research Group, Department of Biomedical Sciences, University of Antwerp, Antwerp, 2610, Belgium
| | - Patrick Mullen
- Department of Biochemistry, University of Vermont, Burlington, VT, 05405, USA
| | - Patrick Wiencek
- Department of Biochemistry, University of Vermont, Burlington, VT, 05405, USA
| | - Katia Hardies
- Neurogenetics Group, Center for Molecular Neurology, VIB, University of Antwerp, Antwerp, 2610, Belgium.,Institute Born Bunge, University of Antwerp, Antwerp, 2610, Belgium
| | - Jeong-Soo Lee
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea.,KRIBB School, University of Science and Technology, Daejeon, 34141, Republic of Korea.,Dementia DTC R&D Convergence Program, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea
| | - Hoi-Khoanh Giong
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea.,KRIBB School, University of Science and Technology, Daejeon, 34141, Republic of Korea.,Dementia DTC R&D Convergence Program, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea
| | - Felix Distelmaier
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, University Children's Hospital, Heinrich-Heine-University Düsseldorf, Düsseldorf, 40225, Germany
| | - Orly Elpeleg
- Monique and Jacques Roboh Department of Genetic Research, Hadassah-Hebrew University Medical Center, Jerusalem, 01120, Israel
| | - Katherine L Helbig
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Joseph Hersh
- Department of Pediatrics, Medicine, University of Louisville School of Medicine, 571S Floyd Street, Louisville, Kentucky, 40202, USA
| | - Sedat Isikay
- Department of Physiotherapy and Rehabilitation, Hasan Kalyoncu University, School of Health Sciences, Gaziantep, 27410, Turkey
| | - Elizabeth Jordan
- The Ohio State University Division of Human Genetics, Department of Internal Medicine, 460 W 12th Ave, Columbus, Ohio, 43210, USA
| | - Ender Karaca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Genetics, University of Alabama, Birmingham, AL, 35233, USA
| | - Angela Kecskes
- Laboratory for Molecular Biodiscovery, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, 3000, Belgium.,Department of Pharmacology and Pharmacotherapy, University of Pecs, Pecs, 7622, Hungary
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA.,Texas Children's Hospital, Houston, TX, 77030, USA
| | - Reka Kovacs-Nagy
- Institute of Human Genetics, Technische Universität München, München, 81675, Germany
| | - Patrick May
- Luxembourg Center for Systems Biomedicine, University Luxembourg, Esch-sur-Alzette, 4365, Luxembourg
| | - Vinodh Narayanan
- Center for Rare Childhood Disorders, The Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Manuela Pendziwiat
- Department of Neuropediatrics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein, Campus Kiel, 24105, Germany
| | - Keri Ramsey
- Center for Rare Childhood Disorders, The Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Sampathkumar Rangasamy
- Center for Rare Childhood Disorders, The Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Deepali N Shinde
- Division of Clinical Genomics, Ambry Genetics, Aliso Viejo, CA, 92656, USA
| | - Ronen Spiegel
- Pediatric Department B' Emek Medical Center, Afula, 1834111, Israel.,Rappaport School of Medicine, Technion, Haifa, 3200003, Israel
| | - Vincent Timmerman
- Institute Born Bunge, University of Antwerp, Antwerp, 2610, Belgium.,Peripheral Neuropathy Research Group, Department of Biomedical Sciences, University of Antwerp, Antwerp, 2610, Belgium
| | - Sarah von Spiczak
- Department of Neuropediatrics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein, Campus Kiel, 24105, Germany.,Northern German Epilepsy Center for Children and Adolescents, Schwentinental-Raisdorf, 24223, Germany
| | - Ingo Helbig
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.,Department of Neuropediatrics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein, Campus Kiel, 24105, Germany
| | | | | | - Sarah Weckhuysen
- Neurogenetics Group, Center for Molecular Neurology, VIB, University of Antwerp, Antwerp, 2610, Belgium.,Institute Born Bunge, University of Antwerp, Antwerp, 2610, Belgium.,Department of Neurology, Antwerp University Hospital, Antwerp, 2650, Belgium
| | | | - Anthony Antonellis
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Neurology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Peter de Witte
- Laboratory for Molecular Biodiscovery, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, 3000, Belgium.
| | - Peter De Jonghe
- Neurogenetics Group, Center for Molecular Neurology, VIB, University of Antwerp, Antwerp, 2610, Belgium. .,Institute Born Bunge, University of Antwerp, Antwerp, 2610, Belgium. .,Department of Neurology, Antwerp University Hospital, Antwerp, 2650, Belgium.
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5
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Abbott JA, Meyer-Schuman R, Lupo V, Feely S, Mademan I, Oprescu SN, Griffin LB, Alberti MA, Casasnovas C, Aharoni S, Basel-Vanagaite L, Züchner S, De Jonghe P, Baets J, Shy ME, Espinós C, Demeler B, Antonellis A, Francklyn C. Cover Image, Volume 39, Issue 3. Hum Mutat 2018. [DOI: 10.1002/humu.23405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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6
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Abbott JA, Meyer-Schuman R, Lupo V, Feely S, Mademan I, Oprescu SN, Griffin LB, Alberti MA, Casasnovas C, Aharoni S, Basel-Vanagaite L, Züchner S, De Jonghe P, Baets J, Shy ME, Espinós C, Demeler B, Antonellis A, Francklyn C. Substrate interaction defects in histidyl-tRNA synthetase linked to dominant axonal peripheral neuropathy. Hum Mutat 2018; 39:415-432. [PMID: 29235198 PMCID: PMC5983030 DOI: 10.1002/humu.23380] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/01/2017] [Accepted: 12/07/2017] [Indexed: 11/09/2022]
Abstract
Histidyl-tRNA synthetase (HARS) ligates histidine to cognate tRNA molecules, which is required for protein translation. Mutations in HARS cause the dominant axonal peripheral neuropathy Charcot-Marie-Tooth disease type 2W (CMT2W); however, the precise molecular mechanism remains undefined. Here, we investigated three HARS missense mutations associated with CMT2W (p.Tyr330Cys, p.Ser356Asn, and p.Val155Gly). The three mutations localize to the HARS catalytic domain and failed to complement deletion of the yeast ortholog (HTS1). Enzyme kinetics, differential scanning fluorimetry (DSF), and analytical ultracentrifugation (AUC) were employed to assess the effect of these substitutions on primary aminoacylation function and overall dimeric structure. Notably, the p.Tyr330Cys, p.Ser356Asn, and p.Val155Gly HARS substitutions all led to reduced aminoacylation, providing a direct connection between CMT2W-linked HARS mutations and loss of canonical ARS function. While DSF assays revealed that only one of the variants (p.Val155Gly) was less thermally stable relative to wild-type, all three HARS mutants formed stable dimers, as measured by AUC. Our work represents the first biochemical analysis of CMT-associated HARS mutations and underscores how loss of the primary aminoacylation function can contribute to disease pathology.
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Affiliation(s)
- Jamie A. Abbott
- Department of Biochemistry, University of Vermont, College of Medicine, Burlington, Vermont
| | - Rebecca Meyer-Schuman
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Vincenzo Lupo
- Unit of Genetics and Genomics of Neuromuscular Disorders, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Shawna Feely
- Department of Neurology, University of Iowa Hospitals and Clinics, Iowa City, Iowa
| | - Inès Mademan
- Neurogenetics Group, Center for Molecular Neurology, VIB, Antwerp, Belgium
- Laboratory of Neuromuscular Pathology, Institute Born-Bunge, University of Antwerp, Antwerpen, Belgium
| | - Stephanie N. Oprescu
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Laurie B. Griffin
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, Michigan
- Medical Scientist Training Program, University of Michigan Medical School, Ann Arbor, Michigan
| | - M. Antonia Alberti
- Department of Neurology, Hospital Universitario de Bellvitge, Barcelona, Spain
| | - Carlos Casasnovas
- Department of Neurology, Hospital Universitario de Bellvitge, Barcelona, Spain
| | - Sharon Aharoni
- Institute of Child Neurology, Schneider Children’s Medical Center of Israel, Petah Tikva, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Lina Basel-Vanagaite
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Raphael Recanati Genetic Institute, Rabin Medical Center, Beilinson Campus, Petah Tikva, Israel
- Pediatric Genetics Unit, Schneider Children’s Medical Center, Petah Tikva, Israel
- Felsenstein Medical Research Center, Rabin Medical Center, Petah Tikva, Israel
| | - Stephan Züchner
- Dr John T McDonald Foundation Department of Human Genetics & John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida
| | - Peter De Jonghe
- Neurogenetics Group, Center for Molecular Neurology, VIB, Antwerp, Belgium
- Laboratory of Neuromuscular Pathology, Institute Born-Bunge, University of Antwerp, Antwerpen, Belgium
- Department of Neurology, Antwerp University Hospital, Antwerpen, Belgium
| | - Jonathan Baets
- Neurogenetics Group, Center for Molecular Neurology, VIB, Antwerp, Belgium
- Laboratory of Neuromuscular Pathology, Institute Born-Bunge, University of Antwerp, Antwerpen, Belgium
- Department of Neurology, Antwerp University Hospital, Antwerpen, Belgium
| | - Michael E. Shy
- Department of Neurology, University of Iowa Hospitals and Clinics, Iowa City, Iowa
| | - Carmen Espinós
- Unit of Genetics and Genomics of Neuromuscular Disorders, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Borries Demeler
- Department of Biochemistry, The University of Texas Health Sciences at San Antonio, San Antonio, Texas
| | - Anthony Antonellis
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, Michigan
| | - Christopher Francklyn
- Department of Biochemistry, University of Vermont, College of Medicine, Burlington, Vermont
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8
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Wo P, Wellman T, Howe A, Francklyn C, Lounsbury KM. Abstract 5224: Non-canonical activity of threonyl-tRNA synthetase promotes angiogenesis and invasion in a mouse model of ovarian cancer. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-5224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Despite clear connections between the tumor microenvironment and ovarian cancer invasion, the underlying molecular mechanisms remain elusive. We have recently shown that the protein synthesis regulator threonyl-tRNA synthetase (TARS) has a unique extracellular angiogenic activity separate from its canonical function. Secreted TARS promotes endothelial cell migration and tube formation, and a selective TARS inhibitor, BC194, disrupts normal vessel development in zebra fish and chick embryo models. TARS expression also correlates with tumor stage and angiogenesis in human ovarian cancer. The objective of this study was to validate the biological and clinical relationship between TARS and ovarian tumor progression using a syngenic mouse model of epithelial ovarian cancer. Tumors were initiated by intraperitoneal injection of ID8 mouse ovarian cancer cells, and tumors formed at 4-6 weeks were scored for invasiveness and analyzed by immunostaining for TARS expression and microvascular density. To test the hypothesis that overexpression of TARS promotes invasion, cells were stably transfected with a TARS expression plasmid prior to injection. To test the hypothesis that TARS inhibition reduces tumor invasion, animals harboring ID8 tumors were treated with the high-affinity TARS inhibitor BC194. We found that TARS levels were elevated in ovarian tumors as compared with normal ovarian tissue. Overexpression of TARS in ID8 cells also resulted in enhanced invasiveness and microvascular density of the resulting tumors (p = 0.026). Preliminary results also indicated that inhibition of TARS by BC194 treatment reduced tumor angiogenesis and growth (p = 0.005) without observed toxicities in the animals. Overall, these results show that modifying TARS expression or activity can affect in vivo ovarian tumor angiogenesis and progression. These results encourage further study of TARS as a regulator of the tumor microenvironment and as a possible target for diagnosis and treatment of ovarian cancer.
Citation Format: Peibin Wo, Theresa Wellman, Alan Howe, Christopher Francklyn, Karen M. Lounsbury. Non-canonical activity of threonyl-tRNA synthetase promotes angiogenesis and invasion in a mouse model of ovarian cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 5224. doi:10.1158/1538-7445.AM2015-5224
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Affiliation(s)
- Peibin Wo
- University of Vermont, College of Medicine, Burlington, VT
| | | | - Alan Howe
- University of Vermont, College of Medicine, Burlington, VT
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9
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Abstract
We describe experimental evidence that ancestral peptide catalysts substantially accelerated development of genetic coding. Structurally invariant 120-130-residue Urzymes (Ur = primitive plus enzyme) derived from Class I and Class II aminoacyl-tRNA synthetases (aaRSs) acylate tRNA far faster than the uncatalyzed rate of nonribosomal peptide bond formation from activated amino acids. These new data allow us to demonstrate statistically indistinguishable catalytic profiles for Class I and II aaRSs in both amino acid activation and tRNA acylation, over a time period extending to well before the assembly of full-length enzymes and even further before the Last Universal Common Ancestor. Both Urzymes also exhibit ∼60% of the contemporary catalytic proficiencies. Moreover, they are linked by ancestral sense/antisense genetic coding, and their evident modularities suggest descent from even simpler ancestral pairs also coded by opposite strands of the same gene. Thus, aaRS Urzymes substantially pre-date modern aaRS but are, nevertheless, highly evolved. Their unexpectedly advanced catalytic repertoires, sense/antisense coding, and ancestral modularities imply considerable prior protein-tRNA co-evolution. Further, unlike ribozymes that motivated the RNA World hypothesis, Class I and II Urzyme·tRNA pairs represent consensus ancestral forms sufficient for codon-directed synthesis of nonrandom peptides. By tracing aaRS catalytic activities back to simpler ancestral peptides, we demonstrate key steps for a simpler and hence more probable peptide·RNA development of rapid coding systems matching amino acids with anticodon trinucleotides.
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Affiliation(s)
- Li Li
- From the Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599-7260 and
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10
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Puffenberger EG, Jinks RN, Sougnez C, Cibulskis K, Willert RA, Achilly NP, Cassidy RP, Fiorentini CJ, Heiken KF, Lawrence JJ, Mahoney MH, Miller CJ, Nair DT, Politi KA, Worcester KN, Setton RA, Dipiazza R, Sherman EA, Eastman JT, Francklyn C, Robey-Bond S, Rider NL, Gabriel S, Morton DH, Strauss KA. Genetic mapping and exome sequencing identify variants associated with five novel diseases. PLoS One 2012; 7:e28936. [PMID: 22279524 PMCID: PMC3260153 DOI: 10.1371/journal.pone.0028936] [Citation(s) in RCA: 214] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Accepted: 11/17/2011] [Indexed: 01/12/2023] Open
Abstract
The Clinic for Special Children (CSC) has integrated biochemical and molecular methods into a rural pediatric practice serving Old Order Amish and Mennonite (Plain) children. Among the Plain people, we have used single nucleotide polymorphism (SNP) microarrays to genetically map recessive disorders to large autozygous haplotype blocks (mean = 4.4 Mb) that contain many genes (mean = 79). For some, uninformative mapping or large gene lists preclude disease-gene identification by Sanger sequencing. Seven such conditions were selected for exome sequencing at the Broad Institute; all had been previously mapped at the CSC using low density SNP microarrays coupled with autozygosity and linkage analyses. Using between 1 and 5 patient samples per disorder, we identified sequence variants in the known disease-causing genes SLC6A3 and FLVCR1, and present evidence to strongly support the pathogenicity of variants identified in TUBGCP6, BRAT1, SNIP1, CRADD, and HARS. Our results reveal the power of coupling new genotyping technologies to population-specific genetic knowledge and robust clinical data.
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Affiliation(s)
- Erik G Puffenberger
- Clinic for Special Children, Strasburg, Pennsylvania, United States of America.
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11
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Farris M, Lague A, Manuelyan Z, Statnekov J, Francklyn C. Altered nuclear cofactor switching in retinoic-resistant variants of the PML-RARα oncoprotein of acute promyelocytic leukemia. Proteins 2012; 80:1095-109. [PMID: 22228505 DOI: 10.1002/prot.24010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Revised: 11/18/2011] [Accepted: 11/28/2011] [Indexed: 11/06/2022]
Abstract
Acute promyelocytic leukemia (APL) results from a reciprocal translocation that fuses the gene for the PML tumor suppressor to that encoding the retinoic acid receptor alpha (RARα). The resulting PML-RARα oncogene product interferes with multiple regulatory pathways associated with myeloid differentiation, including normal PML and RARα functions. The standard treatment for APL includes anthracycline-based chemotherapeutic agents plus the RARα agonist all-trans retinoic acid (ATRA). Relapse, which is often accompanied by ATRA resistance, occurs in an appreciable frequency of treated patients. One potential mechanism suggested by model experiments featuring the selection of ATRA-resistant APL cell lines involves ATRA-resistant versions of the PML-RARα oncogene, where the relevant mutations localize to the RARα ligand-binding domain (LBD). Such mutations may act by compromising agonist binding, but other mechanisms are possible. Here, we studied the molecular consequence of ATRA resistance by use of circular dichroism, protease resistance, and fluorescence anisotropy assays employing peptides derived from the NCOR nuclear corepressor and the ACTR nuclear coactivator. The consequences of the mutations on global structure and cofactor interaction functions were assessed quantitatively, providing insights into the basis of agonist resistance. Attenuated cofactor switching and increased protease resistance represent features of the LBDs of ATRA-resistant PML-RARα, and these properties may be recapitulated in the full-length oncoproteins.
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Affiliation(s)
- Mindy Farris
- Department of Microbiology and Molecular Genetics, University of Vermont, Health Sciences Complex, Burlington, Vermont 05405, USA
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12
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Li L, Weinreb V, Francklyn C, Carter CW. Histidyl-tRNA synthetase urzymes: Class I and II aminoacyl tRNA synthetase urzymes have comparable catalytic activities for cognate amino acid activation. J Biol Chem 2011; 286:10387-95. [PMID: 21270472 PMCID: PMC3060492 DOI: 10.1074/jbc.m110.198929] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2010] [Revised: 01/13/2011] [Indexed: 11/06/2022] Open
Abstract
Four minimal (119-145 residue) active site fragments of Escherichia coli Class II histidyl-tRNA synthetase were constructed, expressed as maltose-binding protein fusions, and assayed for histidine activation as fusion proteins and after TEV cleavage, using the (32)PP(i) exchange assay. All contain conserved Motifs 1 and 2. Two contain an N-terminal extension of Motif 1 and two contain Motif 3. Five experimental results argue strongly for the authenticity of the observed catalytic activities: (i) active site titration experiments showing high (∼0.1-0.55) fractions of active molecules, (ii) release of cryptic activity by TEV cleavage of the fusion proteins, (iii) reduced activity associated with an active site mutation, (iv) quantitative attribution of increased catalytic activity to the intrinsic effects of Motif 3, the N-terminal extension and their synergistic effect, and (v) significantly altered K(m) values for both ATP and histidine substrates. It is therefore plausible that neither the insertion domain nor Motif 3 were essential for catalytic activity in the earliest Class II aminoacyl-tRNA synthetases. The mean rate enhancement of all four cleaved constructs is ∼10(9) times that of the estimated uncatalyzed rate. As observed for the tryptophanyl-tRNA synthetase (TrpRS) Urzyme, these fragments bind ATP tightly but have reduced affinity for cognate amino acids. These fragments thus likely represent Urzymes (Ur = primitive, original, earliest + enzyme) comparable in size and catalytic activity and coded by sequences proposed to be antisense to that coding the previously described Class I TrpRS Urzyme. Their catalytic activities provide metrics for experimental recapitulation of very early evolutionary events.
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Affiliation(s)
- Li Li
- From the Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599 -7260 and
| | - Violetta Weinreb
- From the Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599 -7260 and
| | | | - Charles W. Carter
- From the Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599 -7260 and
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13
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Zhang CM, Perona JJ, Ryu K, Francklyn C, Hou YM. Distinct kinetic mechanisms of the two classes of Aminoacyl-tRNA synthetases. J Mol Biol 2006; 361:300-11. [PMID: 16843487 DOI: 10.1016/j.jmb.2006.06.015] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2006] [Revised: 05/30/2006] [Accepted: 06/08/2006] [Indexed: 11/26/2022]
Abstract
Aminoacyl-tRNA synthetases are divided into two classes based on both functional and structural criteria. Distinctions between the classes have heretofore been based on general features, such as the position of aminoacylation on the 3'-terminal tRNA ribose, and the topology and tRNA-binding orientation of the active-site protein fold. Here we show instead that transient burst kinetics provides a distinct mechanistic signature dividing the two classes of tRNA synthetases, and that this distinction has significant downstream effects on protein synthesis. Steady-state and transient kinetic analyses of class I CysRS and ValRS, and class II AlaRS and ProRS, reveal that class I tRNA synthetases are rate-limited by release of aminoacyl-tRNA, while class II synthetases are limited by a step prior to aminoacyl transfer. The tight aminoacyl-tRNA product binding by class I enzymes correlates with the ability of EF-Tu to form a ternary complex with class I but not class II synthetases, and the further capacity of this protein to enhance the rate of aminoacylation by class I synthetases. These results emphasize that the distinct mechanistic signatures of class I versus class II tRNA synthetases ensure rapid turnover of aminoacyl-tRNAs during protein synthesis.
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Affiliation(s)
- Chun-Mei Zhang
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
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14
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Affiliation(s)
- Michael Ibba
- Department of Microbiology, Ohio State University, Columbus, OH 43210-1292, USA.
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15
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Francklyn C. tRNA synthetase paralogs: evolutionary links in the transition from tRNA-dependent amino acid biosynthesis to de novo biosynthesis. Proc Natl Acad Sci U S A 2003; 100:9650-2. [PMID: 12913115 PMCID: PMC187799 DOI: 10.1073/pnas.1934245100] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Christopher Francklyn
- Department of Biochemistry, University of Vermont Health Sciences Complex, Burlington, VT 05405, USA.
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16
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Abstract
Aminoacyl-tRNA synthetases attach amino acids to the 3' termini of cognate tRNAs to establish the specificity of protein synthesis. A recent Asilomar conference (California, January 13-18, 2002) discussed new research into the structure-function relationship of these crucial enzymes, as well as a multitude of novel functions, including participation in amino acid biosynthesis, cell cycle control, RNA splicing, and export of tRNAs from nucleus to cytoplasm in eukaryotic cells. Together with the discovery of their role in the cellular synthesis of proteins to incorporate selenocysteine and pyrrolysine, these diverse functions of aminoacyl-tRNA synthetases underscore the flexibility and adaptability of these ancient enzymes and stimulate the development of new concepts and methods for expanding the genetic code.
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17
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Sankaranarayanan R, Dock Bregeon AC, Rees B, Bovee M, Caillet J, Romby P, Francklyn C, Moras D. Zinc ion mediated amino acid recognition by threonyl-tRNA synthetase. Acta Crystallogr A 2000. [DOI: 10.1107/s0108767300022595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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18
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Abstract
In Lactococcus lactis there is a protein, HisZ, in the histidine-biosynthetic operon that exhibits significant sequence identity with histidyl-tRNA synthetase (HisRS) but does not aminoacylate tRNA. HisRS homologs that, like HisZ, cannot aminoacylate tRNA are represented in a highly divergent set of bacteria (including an aquificale, cyanobacteria, firmicutes, and proteobacteria), yet are missing from other bacteria, including mycrobacteria and certain proteobacteria. Phylogenetic analysis of the HisRS and HisRS-like family suggests that the HisZ proteins form a monophyletic group that attaches outside the predominant bacterial HisRS clade. These observations are consistent with a model in which the absences of HisZ from bacteria are due to its loss during evolution. It has recently been shown that HisZ from L. lactis binds to the ATP-PRPP transferase (HisG) and that both HisZ and HisG are required for catalyzing the first reaction in histidine biosynthesis. Phylogenetic analysis of HisG sequences shows conclusively that proteobacterial HisG and histidinol dehydrogenase (HisD) sequences are paraphyletic and that the partition of the Proteobacteria associated with the presence/absence of HisZ corresponds to that based on HisG and HisD paraphyly. Our results suggest that horizontal gene transfer played an important role in the evolution of the regulation of histidine biosynthesis.
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Affiliation(s)
- J P Bond
- Department of Microbiology and Molecular Genetics, Markey Center for Molecular Genetics, University of Vermont College of Medicine, Burlington 05405, USA.
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19
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Sissler M, Delorme C, Bond J, Ehrlich SD, Renault P, Francklyn C. An aminoacyl-tRNA synthetase paralog with a catalytic role in histidine biosynthesis. Proc Natl Acad Sci U S A 1999; 96:8985-90. [PMID: 10430882 PMCID: PMC17719 DOI: 10.1073/pnas.96.16.8985] [Citation(s) in RCA: 106] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In addition to their essential catalytic role in protein biosynthesis, aminoacyl-tRNA synthetases participate in numerous other functions, including regulation of gene expression and amino acid biosynthesis via transamidation pathways. Herein, we describe a class of aminoacyl-tRNA synthetase-like (HisZ) proteins based on the catalytic core of the contemporary class II histidyl-tRNA synthetase whose members lack aminoacylation activity but are instead essential components of the first enzyme in histidine biosynthesis ATP phosphoribosyltransferase (HisG). Prediction of the function of HisZ in Lactococcus lactis was assisted by comparative genomics, a technique that revealed a link between the presence or the absence of HisZ and a systematic variation in the length of the HisG polypeptide. HisZ is required for histidine prototrophy, and three other lines of evidence support the direct involvement of HisZ in the transferase function. (i) Genetic experiments demonstrate that complementation of an in-frame deletion of HisG from Escherichia coli (which does not possess HisZ) requires both HisG and HisZ from L. lactis. (ii) Coelution of HisG and HisZ during affinity chromatography provides evidence of direct physical interaction. (iii) Both HisG and HisZ are required for catalysis of the ATP phosphoribosyltransferase reaction. This observation of a common protein domain linking amino acid biosynthesis and protein synthesis implies an early connection between the biosynthesis of amino acids and proteins.
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Affiliation(s)
- M Sissler
- Department of Biochemistry, College of Medicine, Given Building, University of Vermont, Burlington, VT 05405, USA
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20
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Abstract
The homeodomain (HD) is a ubiquitous protein fold that confers DNA binding function on a superfamily of eukaryotic gene regulatory proteins. Here, the DNA binding of recognition helix variants of the HD from the engrailed gene of Drosophila melanogaster was investigated by phage display. Nineteen different combinations of pairwise mutations at positions 50 and 54 were screened against a panel of four DNA sequences consisting of the engrailed consensus, a non-specific DNA control based on the lambda repressor operator OR1 and two model sequence targets con-taining imperfect versions of the 5'-TAAT-3' consensus. The resulting mutant proteins could be divided into four groups that varied with respect to their affinity for DNA and specificity for the engrailed consensus. The altered specificity phenotypes of several mutant proteins were confirmed by DNA mobility shift analysis. Lys50/Ala54 was the only mutant protein that exhibited preferential binding to a sequence other than the engrailed consensus. Arginine was also demonstrated to be a functional replacement for Ala54. The functional combinations at 50 and 54 identified by these experiments recapitulate the distribution of naturally occurring HD sequences and illustrate how the engrailed HD can be used as a framework to explore covariation among DNA binding residues.
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Affiliation(s)
- J P Connolly
- Department of Biochemistry, University of Vermont College of Medicine Health Sciences Complex, Burlington, VT 05405, USA
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21
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Francklyn C, Adams J, Augustine J. Catalytic defects in mutants of class II histidyl-tRNA synthetase from Salmonella typhimurium previously linked to decreased control of histidine biosynthesis regulation. J Mol Biol 1998; 280:847-58. [PMID: 9671554 DOI: 10.1006/jmbi.1998.1902] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The expression of histidine biosynthetic genes in enteric bacteria is regulated by an attenuation mechanism in which the level of histidyl-tRNA serves as a key sensor of the intracellular histidine pool. Among the early observations that led to the formation of this model for Salmonella typhimurium were the identification of mutants in the gene (hisS) encoding histidyl-tRNA synthetase. We report here the detailed biochemical characterization of five of these S. typhimurium bradytrophic mutants isolated by selection for resistance to histidine analogs, including identification of the deduced amino acid substitutions and determination of the resulting effects on the kinetics of adenylation and aminoacylation. Using the crystal structure of the closely related Escherichia coli histidyl-tRNA synthetase (HisRS) as a guide, two mutants were mapped to a highly conserved proline residue in motif 2 (P117S, P117Q), and were correlated with a fivefold decrease in the kcat for the pyrophosphate exchange reaction, as well as a tenfold increase in the Km for tRNA in the aminoacylation reaction. Another mutant substitution (A302T) mapped to a residue adjacent to the histidine binding pocket, leading to a tenfold increase in Km for histidine in the pyrophosphate exchange reaction. The remaining two mutants (S167F, N254T) substitute residues in or directly adjacent to the hinge region, which joins the insertion domain between motif 2 and motif 3 to the catalytic core, and cause the Km for tRNA to increase four- to tenfold. The kinetic analysis of these mutants establishes a direct link between critical interactions within the active site of HisRS and regulation of histidine biosynthesis, and provides further evidence for the importance of local conformational changes during the catalytic cycle.
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Affiliation(s)
- C Francklyn
- Department of Biochemistry, University of Vermont College of Medicine, Health Sciences Complex, Burlington, VT, 05405, USA. franck@emba/uvm.edu
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22
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Francklyn C, Musier-Forsyth K, Martinis SA. Aminoacyl-tRNA synthetases in biology and disease: new evidence for structural and functional diversity in an ancient family of enzymes. RNA 1997; 3:954-960. [PMID: 9292495 PMCID: PMC1369542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Affiliation(s)
- C Francklyn
- Department of Biochemistry, University of Vermont College of Medicine, Health Sciences Complex, Burlington 05405, USA
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23
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Abstract
Primordial aminoacyl-tRNA synthetases (aaRSs) based on the Rossman nucleotide binding fold of class I enzymes or the seven-stranded antiparallel beta-sheet fold of class II enzymes have been proposed to predate the contemporary aaRS. As part of an inquiry into class II aaRS evolution, the individual domains of the homodimeric Escherichia coli histidyl-tRNA synthetase (HisRS) were separately expressed and purified to determine their individual contributions to catalysis. A 320-residue fragment (Ncat HisRS) truncated immediately following motif 3 catalyzes both the specific aminoacylation of tRNA and pyrophosphate exchange, albeit less efficiently than the full-length enzyme. Ncat HisRS showed no mischarging of noncognate tRNAs but exhibited reduced selectivity for the C73 discriminator base, a principal aminoacylation determinant for histidine tRNAs. Size exclusion chromatography showed that Ncat HisRS is monomeric, indicating that the C-terminal domain is essential for maintaining the dimeric structure of the enzyme. The stably folded C-terminal domain (Cter HisRS) was inactive for both reactions and did not enhance the activity of Ncat HisRS when added in trans. The fusion of one or more accessory domains to a primordial catalytic domain may therefore have been a critical evolutionary step by which aminoacyl-tRNA synthetases acquired increased catalytic efficiency and substrate specificity.
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Affiliation(s)
- J Augustine
- Department of Biochemistry, University of Vermont College of Medicine, Burlington 05405, USA
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24
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Yan W, Augustine J, Francklyn C. A tRNA identity switch mediated by the binding interaction between a tRNA anticodon and the accessory domain of a class II aminoacyl-tRNA synthetase. Biochemistry 1996; 35:6559-68. [PMID: 8639604 DOI: 10.1021/bi952889f] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Identity elements in tRNAs and the intracellular balance of tRNAs allow accurate selection of tRNAs by aminoacyl-tRNA synthetases. The histidyl-tRNA from Escherichia coli is distinguished by a unique G-1.C73 base pair that upon exchange with other nucleotides leads to a marked decrease in the rate of aminoacylation in vitro. G-1.C73 is also a major identity element for histidine acceptance, such that the substitution of C73 brings about mischarging by glycyl-, glutaminyl-, and leucyl-tRNA synthetases. These identity conversions mediated by the G-1.C73 base pair were exploited to isolate secondary site revertants in the histidyl-tRNA synthetase from E. coli which restore histidine identity to a histidyl-tRNA suppressor carrying U73. The revertant substitutions confer a 3-4 fold reduction in the Michaelis constant for tRNAs carrying the amber-suppressing anticodon and map to the C-terminal domain of HisRS and its interface with the catalytic core. These findings demonstrate that the histidine tRNA anticodon plays a significant role in tRNA selection in vivo and that the C-terminal domain of HisRS is in large part responsible for recognizing this trinucleotide. The kinetic parameters determined also show a small degree of anticooperativity (delta delta G = -1.24 kcal/mol) between recognition of the discriminator base and the anticodon, suggesting that the two helical domains of the tRNA are not recognized independently. We propose that these effects substantially account for the ability of small changes in tRNA binding far removed from the site of a major determinant to bring about a complete conversion of tRNA identity.
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MESH Headings
- Anticodon/metabolism
- Base Composition
- Base Sequence
- Binding Sites
- Cloning, Molecular
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Histidine-tRNA Ligase/chemistry
- Histidine-tRNA Ligase/isolation & purification
- Histidine-tRNA Ligase/metabolism
- Membrane Potentials
- Models, Molecular
- Molecular Sequence Data
- Mutagenesis, Insertional
- Mutagenesis, Site-Directed
- Oligodeoxyribonucleotides
- Plasmids
- Point Mutation
- RNA, Transfer, Asp/chemistry
- RNA, Transfer, His/biosynthesis
- RNA, Transfer, His/chemistry
- Recombinant Proteins/chemistry
- Recombinant Proteins/isolation & purification
- Recombinant Proteins/metabolism
- Suppression, Genetic
- Transcription, Genetic
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Affiliation(s)
- W Yan
- Department of Biochemistry, University of Vermont College of Medicine, Burlington 05405, USA
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25
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Abstract
Histidyl-tRNA synthetase from Escherichia coli was over-expressed and purified by Q Sepharose and hydroxyapatite chromatography. Crystals of the complex containing histidyl-tRNA synthetase, ATP and histidine have been grown by vapor diffusion against reservoirs containing 0.1 M Tris (pH 7.4), 0.5 M NaCl and 10% polyethylene glycol 6000. Under these conditions, two crystal forms are obtained. The triclinic form has unit cell dimensions a = 61.3 A, b = 108.5 A, c = 110.2 A, alpha = 115.1 degrees, beta = 90.2 degrees and gamma = 97.2 degrees. The monoclinic form, space group P2(1), has cell dimensions a = 61.2 A, b = 109.7 A, c = 196.7 A and beta = 98.1 degrees. Both crystal forms diffract up to 2.7 A and are stable in the synchrotron beam. Assuming a dimeric mass of 96,000 daltons and Vm value of 3.4 A3/dalton, the asymmetric unit in both forms contains two dimers with a solvent content of approximately 60%. A 3.7 A resolution native dataset with an Rmerge on intensities of 7.9% has been collected from the monoclinic crystal form.
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Affiliation(s)
- C Francklyn
- Department of Biochemistry, University of Vermont College of Medicine, Burlington 05405
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26
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27
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Yan W, Francklyn C. Cytosine 73 is a discriminator nucleotide in vivo for histidyl-tRNA in Escherichia coli. J Biol Chem 1994; 269:10022-7. [PMID: 8144499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The acceptor helix of histidine tRNAs in Escherichia coli is capped by a unique base pair in which the cytosine at the discriminator position is paired with an extra guanosine at -1. In previous in vitro studies, the presence of the G-1:C73 base pair was found to be required to obtain both optimal histidylation by histidyl-tRNA synthetase and accurate 5' processing by RNase P. We investigated the role of G-1:C73 in histidine tRNA identity and found that nucleotide substitutions conferred mischarging by other amino acids in a pattern that correlated with the discriminator base and not with the extra nucleotide at -1. As shown by primer extension experiments, the relatively minor role of the -1 nucleotide in vivo could be attributed to altered RNase P processing. These studies show that interactions of tRNAs in vivo both with RNase P during tRNA biosynthesis and with the pool of aminoacyl-tRNA synthetases can modulate the effects of substitutions at recognition nucleotides, eliciting changes in transfer RNA identity.
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Affiliation(s)
- W Yan
- Department of Biochemistry, University of Vermont College of Medicine, Burlington 05405
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28
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Francklyn C, Musier-Forsyth K, Schimmel P. Small RNA helices as substrates for aminoacylation and their relationship to charging of transfer RNAs. Eur J Biochem 1992; 206:315-21. [PMID: 1375910 DOI: 10.1111/j.1432-1033.1992.tb16929.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
RNA microhelices that reconstruct the acceptor stems of transfer RNAs can be aminoacylated. The anticodon-independent aminoacylation is sequence-specific and suggests a relationship between amino acids and nucleotide sequences which is different from that of the classical genetic code. The specific aminoacylation of RNA microhelices also suggests a highly differentiated adaptation of the structures of aminoacyl-tRNA synthetases to sequences in the acceptor stems of transfer RNAs.
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Affiliation(s)
- C Francklyn
- Department of Biochemistry, University of Vermont College of Medicine, Burlington
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29
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Abstract
A seven-base pair microhelix that recapitulates a glycine transfer RNA (tRNA) acceptor helix can be specifically aminoacylated with glycine. A single base pair and the single-stranded discriminator base near the attachment site are essential for aminoacylation. These nucleotide sequence elements, and those in microhelices that can be charged with histidine and alanine, occur in the same positions and therefore overlap. Studies on a systematic set of sequence variants showed that no microhelix could be charged with more than one amino acid. Also, none of the three cognate aminoacyl-tRNA synthetases (aaRSs) gave a detectable amount of aminoacylation of the CCA trinucleotide that is common to the 3' ends of all tRNAs, showing that the specific acceptor stem nucleotide bases confer aminoacylation. An analysis of the relative contributions of these microhelices to overall tRNA recognition indicated that their interaction with aaRSs constitutes a substantial part of the recognition of the whole tRNAs.
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Affiliation(s)
- C Francklyn
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
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30
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Abstract
The major determinant for the identity of alanine tRNAs is a single base pair in the acceptor helix that is proximal to the site of amino acid attachment. A 7-base-pair microhelix that recreates the acceptor helix can be charged with alanine. No other examples of charging of small helices with specific amino acids have been reported, to our knowledge. We show here that a 13-base-pair and an 8-base-pair hairpin helix that reconstruct a domain and subdomain, respectively, of histidine tRNAs can be charged with histidine. We also show that transplantation of a base pair that is unique to histidine tRNAs is sufficient to consider histidine acceptance on a domain and subdomain of alanine tRNA. Both alanine and histidine aminoacyl-tRNA synthetases retain specificity for their cognate synthetic substrates. Alanine- and histidine-specific microhelices may resemble a system that arose early in the evolution of charging and coding.
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Affiliation(s)
- C Francklyn
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
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31
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Scaringe SA, Francklyn C, Usman N. Chemical synthesis of biologically active oligoribonucleotides using beta-cyanoethyl protected ribonucleoside phosphoramidites. Nucleic Acids Res 1990; 18:5433-41. [PMID: 2216717 PMCID: PMC332221 DOI: 10.1093/nar/18.18.5433] [Citation(s) in RCA: 231] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The preparation of fully protected diisopropylamino-beta-cyanoethyl ribonucleoside phosphoramidites with regioisomeric purity greater than 99.95% is described. It is demonstrated that the combination of standard DNA protecting groups, 5'-O-DMT, N-Bz (Ade and Cyt), N-iBu (Gua), beta-cyanoethyl for phosphate, in conjunction with TBDMS for 2'-hydroxyl protection, constitutes a reliable method for the preparation of fully active RNA. Average stepwise coupling yields in excess of 99% were achieved with these synthons on standard DNA synthesizers. Two steps completely deprotect the oligoribonucleotide and workup is reduced to a fifteen minute procedure. Further, it is shown that the deprotected oligoribonucleotides are free from 5'-2' linkages. This methodology was applied to the chemical synthesis of a 24-mer microhelix, a 35-mer minihelix and two halves of a catalytic 'Hammerhead Ribozyme'. These oligoribonucleotides were directly compared in two distinct biochemical assays with enzymatically (T7 RNA polymerase) prepared oligoribonucleotides and shown to possess equal or better activity.
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Affiliation(s)
- S A Scaringe
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
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32
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Abstract
We showed earlier that a single G3.U70 base pair within the amino acid acceptor helix is a major determinant of the identity of tRNA(Ala). In addition, we demonstrated that an RNA hairpin minihelix that recreates the 12 base pair acceptor-T psi C stem of tRNA(Ala) is also aminoacylated in a G3.U70-dependent manner. Determinants for efficient aminoacylation at pH 7.5 have been further investigated with minihelix substrates that have sequence variations at 3.70 and other locations. Although a U,U mismatch and other 3.70 nucleotide alternatives to G.U were recently proposed by others as also important for alanine acceptance, neither that mismatch nor any of four other 3.70 nucleotide combinations confer aminoacylation in vitro with alanine, even with substrate levels of enzyme. In contrast, permutations of the so-called discriminator nucleotide N73 (at position 73) strongly modulate, but do not block, aminoacylation of those substrates that encode G3.U70. In particular, the efficiency of G3.U70-dependent aminoacylation with alanine is strongly enhanced by having the wild-type A73. The effect of N73 alone can explain most of the difference in aminoacylation efficiency of a G3.U70-containing tRNA and a minihelix substrate whose sequences vary significantly from their tRNA(Ala) counterparts. Comparison with earlier work suggests that the substantial modulating effect of N73 is partly or completely obscured when N73 tRNA variants are expressed as amber suppressors in vivo.
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Affiliation(s)
- J P Shi
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
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33
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Abstract
The recognition of transfer RNAs (tRNAs) by aminoacyl tRNA synthetases establishes the connection between amino acids and trinucleotides. However, for E. coli alanine tRNA the trinucleotide sequence which specifies alanine is not important for recognition. Instead a single base pair is a major determinant for the identity of this tRNA. Even a synthetic RNA microhelix with seven base pairs can be aminoacylated if it includes the major determinant.
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34
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Abstract
The genetic code is determined by both the specificity of the triplet anticodon of tRNAs for codons in mRNAs and the specificity with which tRNAs are charged with amino acids. The latter depends on interactions between tRNAs and their charging enzymes, and an advance in understanding such interactions was provided recently by the demonstration that a major determinant of the identity of alanine tRNA is located in the amino-acid acceptor helix. Multiple substitutions in many distinct parts of the molecule do not prevent aminoacylation with alanine. Substitution of the G3.U70 base pair with G3.C70 or A3.U70 in the acceptor helix prevents aminoacylation in vivo and in vitro, however, and the introduction of this base pair into tRNA(Cys) (ref. 1) or tRNA(Phe) (refs 1, 2) enables both to accept alanine. The importance of a single base pair in the acceptor helix and the results of recent footprinting experiments promoted us to investigate the possibility that a minihelix, composed only of the amino-acid acceptor-T psi C helix, could be a substrate for alanine tRNA synthetase. We show here that a synthetic hairpin minihelix can be enzymatically aminoacylated with alanine. Alanine incorporation requires a single G.U base pair, and occurs in helices that otherwise differ significantly in sequence. Aminoacylation can be achieved with only seven base pairs in the helix.
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Affiliation(s)
- C Francklyn
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
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35
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Abstract
The state of Escherichia coli araI DNA occupancy by AraC protein has been found to change from a two-turn to a four-turn occupancy upon the addition of the inducer arabinose. The araI site is separable into two contiguous regions, araI1 and araI2. araI1 binds both ligand-bound and ligand-free AraC protein, whereas araI2 binds AraC protein in the presence of arabinose only. A mutation in araI and a known mutation in araC led to the loss of araI2 binding, while binding to araI1 was unaffected. Both mutants failed to activate the promoter of the araBAD operon. We propose that araI2 occupancy by AraC protein leads to RNA polymerase recognition of the araBAD promoter and that araI1 acts as a switch mechanism allowing both the repressor and the activator forms of AraC protein to regulate the araBAD promoter.
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Affiliation(s)
- N Lee
- Department of Biological Sciences, University of California, Santa Barbara 93106
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