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Mueller AU, Chen J, Wu M, Chiu C, Nixon BT, Campbell EA, Darst SA. A general mechanism for transcription bubble nucleation in bacteria. Proc Natl Acad Sci U S A 2023; 120:e2220874120. [PMID: 36972428 PMCID: PMC10083551 DOI: 10.1073/pnas.2220874120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 03/01/2023] [Indexed: 03/29/2023] Open
Abstract
Bacterial transcription initiation requires σ factors for nucleation of the transcription bubble. The canonical housekeeping σ factor, σ70, nucleates DNA melting via recognition of conserved bases of the promoter -10 motif, which are unstacked and captured in pockets of σ70. By contrast, the mechanism of transcription bubble nucleation and formation during the unrelated σN-mediated transcription initiation is poorly understood. Herein, we combine structural and biochemical approaches to establish that σN, like σ70, captures a flipped, unstacked base in a pocket formed between its N-terminal region I (RI) and extra-long helix features. Strikingly, RI inserts into the nascent bubble to stabilize the nucleated bubble prior to engagement of the obligate ATPase activator. Our data suggest a general paradigm of transcription initiation that requires σ factors to nucleate an early melted intermediate prior to productive RNA synthesis.
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Affiliation(s)
- Andreas U. Mueller
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY10065
| | - James Chen
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY10065
| | - Mengyu Wu
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY10065
| | - Courtney Chiu
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY10065
| | - B. Tracy Nixon
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA16802
| | | | - Seth A. Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY10065
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Bolten M, Vahlensieck C, Lipp C, Leibundgut M, Ban N, Weber-Ban E. Depupylase Dop Requires Inorganic Phosphate in the Active Site for Catalysis. J Biol Chem 2017; 292:4044-4053. [PMID: 28119453 DOI: 10.1074/jbc.m116.755645] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Revised: 01/23/2017] [Indexed: 11/06/2022] Open
Abstract
Analogous to eukaryotic ubiquitination, proteins in actinobacteria can be post-translationally modified in a process referred to as pupylation, the covalent attachment of prokaryotic ubiquitin-like protein Pup to lysine side chains of the target protein via an isopeptide bond. As in eukaryotes, an opposing activity counteracts the modification by specific cleavage of the isopeptide bond formed with Pup. However, the enzymes involved in pupylation and depupylation have evolved independently of ubiquitination and are related to the family of ATP-binding and hydrolyzing carboxylate-amine ligases of the glutamine synthetase type. Furthermore, the Pup ligase PafA and the depupylase Dop share close structural and sequence homology and have a common evolutionary history despite catalyzing opposing reactions. Here, we investigate the role played by the nucleotide in the active site of the depupylase Dop using a combination of biochemical experiments and X-ray crystallographic studies. We show that, although Dop does not turn over ATP stoichiometrically with substrate, the active site nucleotide species in Dop is ADP and inorganic phosphate rather than ATP, and that non-hydrolyzable analogs of ATP cannot support the enzymatic reaction. This finding suggests that the catalytic mechanism is more similar to the mechanism of the ligase PafA than previously thought and likely involves the transient formation of a phosphorylated Pup-intermediate. Evidence is presented for a mechanism where the inorganic phosphate acts as the nucleophilic species in amide bond cleavage and implications for Dop function are discussed.
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Affiliation(s)
- Marcel Bolten
- From the ETH Zurich, Institute of Molecular Biology & Biophysics, 8093 Zurich, Switzerland
| | - Christian Vahlensieck
- From the ETH Zurich, Institute of Molecular Biology & Biophysics, 8093 Zurich, Switzerland
| | - Colette Lipp
- From the ETH Zurich, Institute of Molecular Biology & Biophysics, 8093 Zurich, Switzerland
| | - Marc Leibundgut
- From the ETH Zurich, Institute of Molecular Biology & Biophysics, 8093 Zurich, Switzerland
| | - Nenad Ban
- From the ETH Zurich, Institute of Molecular Biology & Biophysics, 8093 Zurich, Switzerland
| | - Eilika Weber-Ban
- From the ETH Zurich, Institute of Molecular Biology & Biophysics, 8093 Zurich, Switzerland
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Buck M, Engl C, Joly N, Jovanovic G, Jovanovic M, Lawton E, McDonald C, Schumacher J, Waite C, Zhang N. In vitro and in vivo methodologies for studying the Sigma 54-dependent transcription. Methods Mol Biol 2015; 1276:53-79. [PMID: 25665558 DOI: 10.1007/978-1-4939-2392-2_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Here we describe approaches and methods to assaying in vitro the major variant bacterial sigma factor, Sigma 54 (σ(54)), in a purified system. We include the complete transcription system, binding interactions between σ54 and its activators, as well as the self-assembly and the critical ATPase activity of the cognate activators which serve to remodel the closed promoter complexes. We also present in vivo methodologies that are used to study the impact of physiological processes, metabolic states, global signalling networks, and cellular architecture on the control of σ(54)-dependent gene expression.
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Affiliation(s)
- Martin Buck
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK,
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Sysoeva TA, Yennawar N, Allaire M, Nixon BT. Crystallization and preliminary X-ray analysis of the ATPase domain of the σ(54)-dependent transcription activator NtrC1 from Aquifex aeolicus bound to the ATP analog ADP-BeFx. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1384-8. [PMID: 24316836 PMCID: PMC3855726 DOI: 10.1107/s174430911302976x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2013] [Accepted: 10/30/2013] [Indexed: 11/10/2022]
Abstract
One way that bacteria regulate the transcription of specific genes to adapt to environmental challenges is to use different σ factors that direct the RNA polymerase holoenzyme to distinct promoters. Unlike σ(70) RNA polymerase (RNAP), σ(54) RNAP is unable to initiate transcription without an activator: enhancer-binding protein (EBP). All EBPs contain one ATPase domain that belongs to the family of ATPases associated with various cellular activities (AAA+ ATPases). AAA+ ATPases use the energy of ATP hydrolysis to remodel different target macromolecules to perform distinct functions. These mechanochemical enzymes are known to form ring-shaped oligomers whose conformations strongly depend upon nucleotide status. Here, the crystallization of the AAA+ ATPase domain of an EBP from Aquifex aeolicus, NtrC1, in the presence of the non-hydrolyzable ATP analog ADP-BeFx is reported. X-ray diffraction data were collected from two crystals from two different protein fractions of the NtrC1 ATPase domain. Previously, this domain was co-crystallized with ADP and ATP, but the latter crystals were grown from the Walker B substitution variant E239A. Therefore, the new data sets are the first for a wild-type EBP ATPase domain co-crystallized with an ATP analog and they reveal a new crystal form. The resulting structure(s) will shed light on the mechanism of EBP-type transcription activators.
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Affiliation(s)
- Tatyana A. Sysoeva
- Biochemistry and Molecular Biology, Penn State University, University Park, PA 16802, USA
| | - Neela Yennawar
- Biochemistry and Molecular Biology, Penn State University, University Park, PA 16802, USA
| | - Marc Allaire
- NLSL, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - B. Tracy Nixon
- Biochemistry and Molecular Biology, Penn State University, University Park, PA 16802, USA
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Kim JH, Lee KK, Sun Y, Seo GJ, Cho SS, Kwon SH, Kwon ST. Broad nucleotide cofactor specificity of DNA ligase from the hyperthermophilic crenarchaeon Hyperthermus butylicus and its evolutionary significance. Extremophiles 2013; 17:515-22. [PMID: 23546841 DOI: 10.1007/s00792-013-0536-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 03/14/2013] [Indexed: 12/30/2022]
Abstract
The nucleotide cofactor specificity of the DNA ligase from the hyperthermophilic crenarchaeon Hyperthermus butylicus (Hbu) was studied to investigate the evolutionary relationship of DNA ligases. The Hbu DNA ligase gene was expressed under control of the T7lac promoter of pTARG in Escherichia coli BL21-CodonPlus(DE3)-RIL. The expressed enzyme was purified using the IMPACT™-CN system (intein-mediated purification with an affinity chitin-binding tag) and cation-ion (Arg-tag) chromatography. The optimal temperature for Hbu DNA ligase activity was 75 °C, and the optimal pH was 8.0 in Tris-HCl. The activity was highly dependent on MgCl2 or MnCl2 with maximal activity above 5 mM MgCl2 and 2 mM MnCl2. Notably, Hbu DNA ligase can use ADP and GTP in addition to ATP. The broad nucleotide cofactor specificity of Hbu DNA ligase might exemplify an undifferentiated ancestral stage in the evolution of DNA ligases. This study provides new evidence for possible evolutionary relationships among DNA ligases.
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Affiliation(s)
- Jun-Hwan Kim
- Department of Genetic Engineering, Sungkyunkwan University, 300 Cheoncheon-dong, Jangan-gu, Suwon 440-746, Korea
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Engagement of arginine finger to ATP triggers large conformational changes in NtrC1 AAA+ ATPase for remodeling bacterial RNA polymerase. Structure 2011; 18:1420-30. [PMID: 21070941 DOI: 10.1016/j.str.2010.08.018] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Revised: 08/28/2010] [Accepted: 08/30/2010] [Indexed: 11/23/2022]
Abstract
The NtrC-like AAA+ ATPases control virulence and other important bacterial activities through delivering mechanical work to σ54-RNA polymerase to activate transcription from σ54-dependent genes. We report the first crystal structure for such an ATPase, NtrC1 of Aquifex aeolicus, in which the catalytic arginine engages the γ-phosphate of ATP. Comparing the new structure with those previously known for apo and ADP-bound states supports a rigid-body displacement model that is consistent with large-scale conformational changes observed by low-resolution methods. First, the arginine finger induces rigid-body roll, extending surface loops above the plane of the ATPase ring to bind σ54. Second, ATP hydrolysis permits Pi release and retraction of the arginine with a reversed roll, remodeling σ54-RNAP. This model provides a fresh perspective on how ATPase subunits interact within the ring-ensemble to promote transcription, directing attention to structural changes on the arginine-finger side of an ATP-bound interface.
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Abstract
DNA ligases seal 5'-PO4 and 3'-OH polynucleotide ends via three nucleotidyl transfer steps involving ligase-adenylate and DNA-adenylate intermediates. DNA ligases are essential guardians of genomic integrity, and ligase dysfunction underlies human genetic disease syndromes. Crystal structures of DNA ligases bound to nucleotide and nucleic acid substrates have illuminated how ligase reaction chemistry is catalyzed, how ligases recognize damaged DNA ends, and how protein domain movements and active-site remodeling are used to choreograph the end-joining pathway. Although a shared feature of DNA ligases is their envelopment of the nicked duplex as a C-shaped protein clamp, they accomplish this feat by using remarkably different accessory structural modules and domain topologies. As structural, biochemical, and phylogenetic insights coalesce, we can expect advances on several fronts, including (i) pharmacological targeting of ligases for antibacterial and anticancer therapies and (ii) the discovery and design of new strand-sealing enzymes with unique substrate specificities.
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Affiliation(s)
- Stewart Shuman
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10065, USA.
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