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Schleif R. A Career's Work, the l-Arabinose Operon: How It Functions and How We Learned It. EcoSal Plus 2022; 10:eESP00122021. [PMID: 36519894 PMCID: PMC10729937 DOI: 10.1128/ecosalplus.esp-0012-2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 07/20/2021] [Indexed: 06/17/2023]
Abstract
Very few labs have had the good fortune to have been able to focus for more than 50 years on a relatively narrow research topic and to be in a field in which both basic knowledge and the research technology and methods have progressed as rapidly as they have in molecular biology. My research group, first at Brandeis University and then at Johns Hopkins University, has had this opportunity. In this review, therefore, I will describe largely the work from my laboratory that has spanned this period and which was carried out by 40 plus graduate students, several postdoctoral associates, my technician, and me. In addition to presenting the scientific findings or results, I will place many of the topics in scientific context and, because we needed to develop a good many of the experimental methods behind our findings, I will also describe some of these methods and their importance. Also included will be occasional comments on how the research community or my research group functioned. Because a wide variety of approaches were used throughout our work, no ideal organization of this review is apparent. Therefore, I have chosen to use a hybrid structure in which there are six sections. Within each of the sections, experiments and findings will be described roughly in chronological order. Frequent cross references between parts and sections will be made because some findings and experimental approaches could logically have been described in more than one place.
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Picard HR, Schwingen KS, Green LM, Shis DL, Egan SM, Bennett MR, Swint-Kruse L. Allosteric regulation within the highly interconnected structural scaffold of AraC/XylS homologs tolerates a wide range of amino acid changes. Proteins 2022; 90:186-199. [PMID: 34369028 PMCID: PMC8671227 DOI: 10.1002/prot.26206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/20/2021] [Accepted: 08/02/2021] [Indexed: 01/03/2023]
Abstract
To create bacterial transcription "circuits" for biotechnology, one approach is to recombine natural transcription factors, promoters, and operators. Additional novel functions can be engineered from existing transcription factors such as the E. coli AraC transcriptional activator, for which binding to DNA is modulated by binding L-arabinose. Here, we engineered chimeric AraC/XylS transcription activators that recognized ara DNA binding sites and responded to varied effector ligands. The first step, identifying domain boundaries in the natural homologs, was challenging because (i) no full-length, dimeric structures were available and (ii) extremely low sequence identities (≤10%) among homologs precluded traditional assemblies of sequence alignments. Thus, to identify domains, we built and aligned structural models of the natural proteins. The designed chimeric activators were assessed for function, which was then further improved by random mutagenesis. Several mutational variants were identified for an XylS•AraC chimera that responded to benzoate; two enhanced activation to near that of wild-type AraC. For an RhaR•AraC chimera, a variant with five additional substitutions enabled transcriptional activation in response to rhamnose. These five changes were dispersed across the protein structure, and combinatorial experiments testing subsets of substitutions showed significant non-additivity. Combined, the structure modeling and epistasis suggest that the common AraC/XylS structural scaffold is highly interconnected, with complex intra-protein and inter-domain communication pathways enabling allosteric regulation. At the same time, the observed epistasis and the low sequence identities of the natural homologs suggest that the structural scaffold and function of transcriptional regulation are nevertheless highly accommodating of amino acid changes.
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Affiliation(s)
- Hunter R. Picard
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS 66160
| | - Kristen S. Schwingen
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS 66160
| | - Lisa M. Green
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS 66160
| | - David L. Shis
- Department of Biosciences and Department of Bioengineering, Rice University, Houston, TX 77005
| | - Susan M. Egan
- Department of Molecular Biosciences, The University of Kansas, Lawrence, KS 66045
| | - Matthew R. Bennett
- Department of Biosciences and Department of Bioengineering, Rice University, Houston, TX 77005
| | - Liskin Swint-Kruse
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS 66160,To whom correspondence should be addressed: ; 913-588-0399
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Cortés-Avalos D, Martínez-Pérez N, Ortiz-Moncada MA, Juárez-González A, Baños-Vargas AA, Estrada-de Los Santos P, Pérez-Rueda E, Ibarra JA. An update of the unceasingly growing and diverse AraC/XylS family of transcriptional activators. FEMS Microbiol Rev 2021; 45:6219864. [PMID: 33837749 DOI: 10.1093/femsre/fuab020] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 03/31/2021] [Indexed: 01/09/2023] Open
Abstract
Transcriptional factors play an important role in gene regulation in all organisms, especially in Bacteria. Here special emphasis is placed in the AraC/XylS family of transcriptional regulators. This is one of the most abundant as many predicted members have been identified and more members are added because more bacterial genomes are sequenced. Given the way more experimental evidence has mounded in the past decades, we decided to update the information about this captivating family of proteins. Using bioinformatics tools on all the data available for experimentally characterized members of this family, we found that many members that display a similar functional classification can be clustered together and in some cases they have a similar regulatory scheme. A proposal for grouping these proteins is also discussed. Additionally, an analysis of surveyed proteins in bacterial genomes is presented. Altogether, the current review presents a panoramic view into this family and we hope it helps to stimulate future research in the field.
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Affiliation(s)
- Daniel Cortés-Avalos
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Noemy Martínez-Pérez
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica Yucatán, Mérida, Yucatán, México
| | - Mario A Ortiz-Moncada
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Aylin Juárez-González
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Arturo A Baños-Vargas
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Paulina Estrada-de Los Santos
- Laboratorio de Biotecnología Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Ernesto Pérez-Rueda
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica Yucatán, Mérida, Yucatán, México.,Facultad de Ciencias, Centro de Genómica y Bioinformática, Universidad Mayor, Santiago, Chile
| | - J Antonio Ibarra
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
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Tischer A, Brown MJ, Schleif RF, Auton M. Arabinose Alters Both Local and Distal H-D Exchange Rates in the Escherichia coli AraC Transcriptional Regulator. Biochemistry 2019; 58:2875-2882. [PMID: 31199144 DOI: 10.1021/acs.biochem.9b00389] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In the absence of arabinose, the dimeric Escherichia coli regulatory protein of the l-arabinose operon, AraC, represses expression by looping the DNA between distant half-sites. Binding of arabinose to the dimerization domains forces AraC to preferentially bind two adjacent DNA half-sites, which stimulates RNA polymerase transcription of the araBAD catabolism genes. Prior genetic and biochemical studies hypothesized that arabinose allosterically induces a helix-coil transition of a linker between the dimerization and DNA binding domains that switches the AraC conformation to an inducing state [Brown, M. J., and Schleif, R. F. (2019) Biochemistry, preceding paper in this issue (DOI: 10.1021/acs.biochem.9b00234)]. To test this hypothesis, hydrogen-deuterium exchange mass spectrometry was utilized to identify structural regions involved in the conformational activation of AraC by arabinose. Comparison of the hydrogen-deuterium exchange kinetics of individual dimeric dimerization domains and the full-length dimeric AraC protein in the presence and absence of arabinose reveals a prominent arabinose-induced destabilization of the amide hydrogen-bonded structure of linker residues (I167 and N168). This destabilization is demonstrated to result from an increased probability to form a helix capping motif at the C-terminal end of the dimerizing α-helix of the dimerization domain that preceeds the interdomain linker. These conformational changes could allow for quaternary repositioning of the DNA binding domains required for induction of the araBAD promoter through rotation of peptide backbone dihedral angles of just a couple of residues. Subtle changes in exchange rates are also visible around the arabinose binding pocket and in the DNA binding domain.
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Affiliation(s)
- Alexander Tischer
- Division of Hematology, Departments of Internal Medicine and Biochemistry and Molecular Biology , Mayo Clinic , Rochester , Minnesota 55905 , United States
| | - Matthew J Brown
- Department of Biology , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Robert F Schleif
- Department of Biology , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Matthew Auton
- Division of Hematology, Departments of Internal Medicine and Biochemistry and Molecular Biology , Mayo Clinic , Rochester , Minnesota 55905 , United States
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Malaga F, Mayberry O, Park DJ, Rodgers ME, Toptygin D, Schleif RF. A genetic and physical study of the interdomain linker of E. Coli
AraC protein-a trans
-subunit communication pathway. Proteins 2016; 84:448-60. [DOI: 10.1002/prot.24990] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 12/23/2015] [Accepted: 01/12/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Fabiana Malaga
- Biology Department; UPCH; Lima San Martín De Porres Peru
| | - Ory Mayberry
- Department of Biology; Johns Hopkins University; Baltimore Maryland 21218
| | - David J. Park
- Tufts University Medical School; Boston Massachusetts
| | - Michael E. Rodgers
- Department of Biology; Johns Hopkins University; Baltimore Maryland 21218
| | - Dmitri Toptygin
- Department of Biology; Johns Hopkins University; Baltimore Maryland 21218
| | - Robert F. Schleif
- Department of Biology; Johns Hopkins University; Baltimore Maryland 21218
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