1
|
Radwan AA, Al-Anazi FK, Al-Agamy M, Alghaith AF, Mahrous GM, Alhuzani MR, Alghamdi AS. Design, synthesis and molecular modeling of isatin-aminobenzoic acid hybrids as antibacterial and antibiofilm agents. Saudi Pharm J 2023; 31:101781. [PMID: 37860684 PMCID: PMC10582576 DOI: 10.1016/j.jsps.2023.101781] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 09/03/2023] [Indexed: 10/21/2023] Open
Abstract
Number of factors, including newly emerging infectious diseases and an increase in multi-drug resistant microbial pathogens with particular relevance for Gram-positive bacteria, make the treatment of infectious diseases in hospital-based healthcare a major challenge in the medical community. 4-Aminobenzoic acid (PABA), has demonstrated a variety of biological actions particularly, antimicrobial activity. In our study we coupled this vitamin-like molecule with different isatin derivatives. We investigated the antibacterial activity of the synthesized Schiff's bases. The compounds showed high selective activity against Gram-positive bacteria and showed weak or no activity against both Gram-negative bacteria and fungi. Compound 2a showed highest activity against S. aureus and B. subtilis (MIC 0.09 mmol/L). Additionally, these substances exhibit strong anti-B. Subtilis biofilm formation. We were able to shed insight on the binding mode of these new inhibitors using in silico docking of the compounds in the binding sites of a 3D structure of B. subtilis histidine kinase/Walk. The binding free energy of the compound 2a to the catalytic domain walk, of histidine kinase enzyme of B. subtilis bacteria, was calculated using molecular mechanics/generalized born surface area scoring. The key residues for macromolecule-ligand binding were postulated. The optimized 3D protein-ligand binding modes shed light on the B. subtilis HK/Walk-ligand interactions that afford a means to assess binding affinity to design new HK/Walk inhibitor as antibacterial agents.
Collapse
Affiliation(s)
- Awwad A. Radwan
- Kayyali Chair, College of Pharmacy, King Saud University, PO Box 2457, Riyadh 11451, Saudi Arabia
- Department of Pharmaceutics, College of Pharmacy, King Saud University, PO Box 2457, Riyadh 11451, Saudi Arabia
| | - Fares K. Al-Anazi
- Kayyali Chair, College of Pharmacy, King Saud University, PO Box 2457, Riyadh 11451, Saudi Arabia
- Department of Pharmaceutics, College of Pharmacy, King Saud University, PO Box 2457, Riyadh 11451, Saudi Arabia
| | - Mohammed Al-Agamy
- Department of Pharmaceutics, College of Pharmacy, King Saud University, PO Box 2457, Riyadh 11451, Saudi Arabia
| | - Adel F. Alghaith
- Department of Pharmaceutics, College of Pharmacy, King Saud University, PO Box 2457, Riyadh 11451, Saudi Arabia
| | - Gamal M. Mahrous
- Department of Pharmaceutics, College of Pharmacy, King Saud University, PO Box 2457, Riyadh 11451, Saudi Arabia
| | - Mohammad R. Alhuzani
- Department of Pharmaceutics, College of Pharmacy, King Saud University, PO Box 2457, Riyadh 11451, Saudi Arabia
| | - Abdulrhman S.A. Alghamdi
- Department of Pharmaceutics, College of Pharmacy, King Saud University, PO Box 2457, Riyadh 11451, Saudi Arabia
| |
Collapse
|
2
|
Arya R, Kim T, Youn JW, Bae T, Kim KK. Identification of an antivirulence agent targeting the master regulator of virulence genes in Staphylococcus aureus. Front Cell Infect Microbiol 2023; 13:1268044. [PMID: 38029271 PMCID: PMC10644738 DOI: 10.3389/fcimb.2023.1268044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/10/2023] [Indexed: 12/01/2023] Open
Abstract
The emergence of bactericidal antibiotic-resistant strains has increased the demand for alternative therapeutic agents, such as antivirulence agents targeting the virulence regulators of pathogens. Staphylococcus aureus exoprotein expression (sae) locus, the master regulator of virulence gene expression in multiple drug-resistant S. aureus, is a promising therapeutic target. In this study, we screened a small-molecule library using a SaeRS green fluorescent protein (GFP)-reporter that responded to transcription controlled by the sae locus. We identified the compound, N-(2-methylcyclohexyl)-11-oxo-10,11-dihydrodibenzo[b,f][1,4]thiazepine-8-carboxamide (SKKUCS), as an efficient repressor of sae-regulated GFP activity. SKKUCS inhibited hemolysin production and reduced α-hemolysin-mediated cell lysis. Moreover, SKKUCS substantially reduced the expression levels of various virulence genes controlled by the master regulators, sae, and the accessory gene regulator (agr), demonstrating its potential as an antivirulence reagent targeting the key virulence regulators. Furthermore, autokinase inhibition assay and molecular docking suggest that SKKUCS inhibits the kinase activity of SaeS and potentially targets the active site of SaeS kinase, possibly inhibiting ATP binding. Next, we evaluated the efficacy and toxicity of SKKUCS in vivo using murine models of staphylococcal intraperitoneal and skin infections. Treatment with SKKUCS markedly increased animal survival and significantly decreased the bacterial burden in organs and skin lesion sizes. These findings highlight SKKUCS as a potential antivirulence drug for drug-resistant staphylococcal infections.
Collapse
Affiliation(s)
- Rekha Arya
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Institute of Antibacterial Resistance Research and Therapeutics, Suwon, Republic of Korea
- Department of Orthopedic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Truc Kim
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Institute of Antibacterial Resistance Research and Therapeutics, Suwon, Republic of Korea
| | - Joo Won Youn
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Institute of Antibacterial Resistance Research and Therapeutics, Suwon, Republic of Korea
| | - Taeok Bae
- Department of Microbiology and Immunology, Indiana University School of Medicine-Northwest, Gary, IN, United States
| | - Kyeong Kyu Kim
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Institute of Antibacterial Resistance Research and Therapeutics, Suwon, Republic of Korea
| |
Collapse
|
3
|
Crystal structure of the Escherichia coli CusS kinase core. J Struct Biol 2022; 214:107883. [PMID: 35907487 DOI: 10.1016/j.jsb.2022.107883] [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: 05/06/2022] [Revised: 07/07/2022] [Accepted: 07/23/2022] [Indexed: 10/16/2022]
Abstract
The CusS histidine kinase is a member of Escherichia coli two-component signal transduction system, engaged in a response to copper ions excess in the cell periplasm. The periplasmic sensor domain of CusS binds the free copper ions and the CusS kinase core phosphorylates the cognate CusR which regulates transcription of the efflux pomp CusCBA. A small amount of copper ions is indispensable for the aerobic cell metabolism. Nonetheless, its excess in the cytoplasm generates damaging and reactive hydroxyl radicals. For that reason, understanding the bacterial copper sensing mechanisms can contribute to reducing bacterial copper-resistance and developing bactericidal copper-based materials. The crystal structure of the CusS kinase core was solved at the resolution of 1.4 Å. The cytoplasmic catalytic core domains formed a homodimer. Based on the obtained structure, the intramolecular and intermolecular interactions crucial for the mechanism of CusS autophosphorylation were described.
Collapse
|
4
|
Chen H, Yu C, Wu H, Li G, Li C, Hong W, Yang X, Wang H, You X. Recent Advances in Histidine Kinase-Targeted Antimicrobial Agents. Front Chem 2022; 10:866392. [PMID: 35860627 PMCID: PMC9289397 DOI: 10.3389/fchem.2022.866392] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/16/2022] [Indexed: 11/15/2022] Open
Abstract
The prevalence of antimicrobial-resistant pathogens significantly limited the number of effective antibiotics available clinically, which urgently requires new drug targets to screen, design, and develop novel antibacterial drugs. Two-component system (TCS), which is comprised of a histidine kinase (HK) and a response regulator (RR), is a common mechanism whereby bacteria can sense a range of stimuli and make an appropriate adaptive response. HKs as the sensor part of the bacterial TCS can regulate various processes such as growth, vitality, antibiotic resistance, and virulence, and have been considered as a promising target for antibacterial drugs. In the current review, we highlighted the structural basis and functional importance of bacterial TCS especially HKs as a target in the discovery of new antimicrobials, and summarize the latest research progress of small-molecule HK-inhibitors as potential novel antimicrobial drugs reported in the past decade.
Collapse
Affiliation(s)
- Hongtong Chen
- Laboratory of Pharmacology/Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chengqi Yu
- School of Basic Medical Science, Capital Medical University, Beijing, China
| | - Han Wu
- School of Pharmacy, Minzu University of China, Beijing, China
- Key Laboratory of Ethnomedicine (Minzu University of China), Ministry of Education, Beijing, China
| | - Guoqing Li
- Laboratory of Pharmacology/Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Congran Li
- Laboratory of Pharmacology/Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wei Hong
- Beijing Institute of Collaborative Innovation, Beijing, China
| | - Xinyi Yang
- Laboratory of Pharmacology/Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- *Correspondence: Xinyi Yang, ; Hao Wang, ; Xuefu You,
| | - Hao Wang
- School of Pharmacy, Minzu University of China, Beijing, China
- Key Laboratory of Ethnomedicine (Minzu University of China), Ministry of Education, Beijing, China
- Institute of National Security, Minzu University of China, Beijing, China
- *Correspondence: Xinyi Yang, ; Hao Wang, ; Xuefu You,
| | - Xuefu You
- Laboratory of Pharmacology/Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- *Correspondence: Xinyi Yang, ; Hao Wang, ; Xuefu You,
| |
Collapse
|
5
|
Gushchin I, Aleksenko VA, Orekhov P, Goncharov IM, Nazarenko VV, Semenov O, Remeeva A, Gordeliy V. Nitrate- and Nitrite-Sensing Histidine Kinases: Function, Structure, and Natural Diversity. Int J Mol Sci 2021; 22:5933. [PMID: 34072989 PMCID: PMC8199190 DOI: 10.3390/ijms22115933] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/18/2022] Open
Abstract
Under anaerobic conditions, bacteria may utilize nitrates and nitrites as electron acceptors. Sensitivity to nitrous compounds is achieved via several mechanisms, some of which rely on sensor histidine kinases (HKs). The best studied nitrate- and nitrite-sensing HKs (NSHKs) are NarQ and NarX from Escherichia coli. Here, we review the function of NSHKs, analyze their natural diversity, and describe the available structural information. In particular, we show that around 6000 different NSHK sequences forming several distinct clusters may now be found in genomic databases, comprising mostly the genes from Beta- and Gammaproteobacteria as well as from Bacteroidetes and Chloroflexi, including those from anaerobic ammonia oxidation (annamox) communities. We show that the architecture of NSHKs is mostly conserved, although proteins from Bacteroidetes lack the HAMP and GAF-like domains yet sometimes have PAS. We reconcile the variation of NSHK sequences with atomistic models and pinpoint the structural elements important for signal transduction from the sensor domain to the catalytic module over the transmembrane and cytoplasmic regions spanning more than 200 Å.
Collapse
Affiliation(s)
- Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Vladimir A. Aleksenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Philipp Orekhov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ivan M. Goncharov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Vera V. Nazarenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Oleg Semenov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Valentin Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, 38000 Grenoble, France
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428 Jülich, Germany
| |
Collapse
|
6
|
Rahuman MH, Muthu S, Raajaraman BR, Raja M. Quantum computational, spectroscopic and molecular docking studies on 2-acetylthiophene and its bromination derivative. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128129] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
|
7
|
Goswami M, Wilke KE, Carlson EE. Rational Design of Selective Adenine-Based Scaffolds for Inactivation of Bacterial Histidine Kinases. J Med Chem 2017; 60:8170-8182. [PMID: 28933546 DOI: 10.1021/acs.jmedchem.7b01066] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Bacterial histidine kinases (HKs) are quintessential regulatory enzymes found ubiquitously in bacteria. Apart from their regulatory roles, they are also involved in the production of virulence factors and conferring resistance to various antibiotics in pathogenic microbes. We have previously reported compounds that inhibit multiple HKs by targeting the conserved catalytic and ATP-binding (CA) domain. Herein, we conduct a detailed structure-activity relationship assessment of adenine-based inhibitors using biochemical and docking methods. These studies have resulted in several observations. First, interaction of an inhibitor's amine group with the conserved active-site Asp is essential for activity and likely dictates its orientation in the binding pocket. Second, a N-NH-N triad in the inhibitor scaffold is highly preferred for binding to conserved Gly:Asp:Asn residues. Lastly, hydrophobic electron-withdrawing groups at several positions in the adenine core enhance potency. The selectivity of these inhibitors was tested against heat shock protein 90 (HSP90), which possesses a similar ATP-binding fold. We found that groups that target the ATP-lid portion of the catalytic domain, such as a six-membered ring, confer selectivity for HKs.
Collapse
Affiliation(s)
- Manibarsha Goswami
- Department of Chemistry, University of Minnesota , 207 Pleasant Street SE, Minneapolis, Minnesota 55454, United States
| | - Kaelyn E Wilke
- Department of Chemistry, Indiana University , 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Erin E Carlson
- Department of Chemistry, University of Minnesota , 207 Pleasant Street SE, Minneapolis, Minnesota 55454, United States.,Department of Chemistry, Indiana University , 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States.,Department of Medicinal Chemistry, University of Minnesota , 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States.,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota , 321 Church Street SE, Minneapolis, Minnesota 55455, United States
| |
Collapse
|
8
|
Cai Y, Su M, Ahmad A, Hu X, Sang J, Kong L, Chen X, Wang C, Shuai J, Han A. Conformational dynamics of the essential sensor histidine kinase WalK. Acta Crystallogr D Struct Biol 2017; 73:793-803. [PMID: 28994408 PMCID: PMC5633905 DOI: 10.1107/s2059798317013043] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 09/12/2017] [Indexed: 12/26/2022] Open
Abstract
Two-component systems (TCSs) are key elements in bacterial signal transduction in response to environmental stresses. TCSs generally consist of sensor histidine kinases (SKs) and their cognate response regulators (RRs). Many SKs exhibit autokinase, phosphoryltransferase and phosphatase activities, which regulate RR activity through a phosphorylation and dephosphorylation cycle. However, how SKs perform different enzymatic activities is poorly understood. Here, several crystal structures of the minimal catalytic region of WalK, an essential SK from Lactobacillus plantarum that shares 60% sequence identity with its homologue VicK from Streptococcus mutans, are presented. WalK adopts an asymmetrical closed structure in the presence of ATP or ADP, in which one of the CA domains is positioned close to the DHp domain, thus leading both the β- and γ-phosphates of ATP/ADP to form hydrogen bonds to the ℇ- but not the δ-nitrogen of the phosphorylatable histidine in the DHp domain. In addition, the DHp domain in the ATP/ADP-bound state has a 25.7° asymmetrical helical bending coordinated with the repositioning of the CA domain; these processes are mutually exclusive and alternate in response to helicity changes that are possibly regulated by upstream signals. In the absence of ATP or ADP, however, WalK adopts a completely symmetric open structure with its DHp domain centred between two outward-reaching CA domains. In summary, these structures of WalK reveal the intrinsic dynamic properties of an SK structure as a molecular basis for multifunctionality.
Collapse
Affiliation(s)
- Yongfei Cai
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiang’an, Xiamen 361102, People’s Republic of China
| | - Mingyang Su
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiang’an, Xiamen 361102, People’s Republic of China
| | - Ashfaq Ahmad
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiang’an, Xiamen 361102, People’s Republic of China
| | - Xiaojie Hu
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiang’an, Xiamen 361102, People’s Republic of China
| | - Jiayan Sang
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiang’an, Xiamen 361102, People’s Republic of China
| | - Lingyuan Kong
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiang’an, Xiamen 361102, People’s Republic of China
| | - Xingqiang Chen
- Department of Physics, Xiamen University, Xiang’an, Xiamen 361102, People’s Republic of China
| | - Chen Wang
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiang’an, Xiamen 361102, People’s Republic of China
| | - Jianwei Shuai
- Department of Physics, Xiamen University, Xiang’an, Xiamen 361102, People’s Republic of China
| | - Aidong Han
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiang’an, Xiamen 361102, People’s Republic of China
| |
Collapse
|
9
|
Boibessot T, Zschiedrich CP, Lebeau A, Bénimèlis D, Dunyach-Rémy C, Lavigne JP, Szurmant H, Benfodda Z, Meffre P. The Rational Design, Synthesis, and Antimicrobial Properties of Thiophene Derivatives That Inhibit Bacterial Histidine Kinases. J Med Chem 2016; 59:8830-8847. [PMID: 27575438 DOI: 10.1021/acs.jmedchem.6b00580] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The emergence of multidrug-resistant bacteria emphasizes the urgent need for novel antibacterial compounds targeting unique cellular processes. Two-component signal transduction systems (TCSs) are commonly used by bacteria to couple environmental stimuli to adaptive responses, are absent in mammals, and are embedded in various pathogenic pathways. To attenuate these signaling pathways, we aimed to target the TCS signal transducer histidine kinase (HK) by focusing on their highly conserved adenosine triphosphate-binding domain. We used a structure-based drug design strategy that begins from an inhibitor-bound crystal structure and includes a significant number of structurally simplifiying "intuitive" modifications to arrive at the simple achiral, biaryl target structures. Thus, ligands were designed, leading to a series of thiophene derivatives. These compounds were synthesized and evaluated in vitro against bacterial HKs. We identified eight compounds with significant inhibitory activities against these proteins, two of which exhibited broad-spectrum antimicrobial activity. The compounds were also evaluated as adjuvants for the treatment of resistant bacteria. One compound was found to restore the sensivity of these bacteria to the respective antibiotics.
Collapse
Affiliation(s)
- Thibaut Boibessot
- EA7352 CHROME, Rue du Dr G. Salan, University of Nîmes , 30021 Nîmes cedex 1, France
| | - Christopher P Zschiedrich
- Basic Medical Sciences, College of Osteopathic Medicine of the Pacific, Western University of Health Sciences , Pomona, California 91766, United States.,Department of Molecular and Experimental Medicine, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Alexandre Lebeau
- EA7352 CHROME, Rue du Dr G. Salan, University of Nîmes , 30021 Nîmes cedex 1, France
| | - David Bénimèlis
- EA7352 CHROME, Rue du Dr G. Salan, University of Nîmes , 30021 Nîmes cedex 1, France
| | - Catherine Dunyach-Rémy
- Institut National de la Santé et de la Recherche Médicale, U1047, Montpellier University , CHU de Nîmes, Place du Pr R. Debré, 30029 Nîmes, France
| | - Jean-Philippe Lavigne
- Institut National de la Santé et de la Recherche Médicale, U1047, Montpellier University , CHU de Nîmes, Place du Pr R. Debré, 30029 Nîmes, France
| | - Hendrik Szurmant
- Basic Medical Sciences, College of Osteopathic Medicine of the Pacific, Western University of Health Sciences , Pomona, California 91766, United States.,Department of Molecular and Experimental Medicine, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Zohra Benfodda
- EA7352 CHROME, Rue du Dr G. Salan, University of Nîmes , 30021 Nîmes cedex 1, France.,IBMM, UMR-CNRS5247, Université de Montpellier , Place Eugène Bataillon, 34095 Montpellier, France
| | - Patrick Meffre
- EA7352 CHROME, Rue du Dr G. Salan, University of Nîmes , 30021 Nîmes cedex 1, France.,IBMM, UMR-CNRS5247, Université de Montpellier , Place Eugène Bataillon, 34095 Montpellier, France
| |
Collapse
|
10
|
Ramundo MS, Beltrame CO, Botelho AMN, Coelho LR, Silva-Carvalho MC, Ferreira-Carvalho BT, Nicolás MF, Guedes IA, Dardenne LE, O'Gara J, Figueiredo AMS. A unique SaeS allele overrides cell-density dependent expression of saeR and lukSF-PV in the ST30-SCCmecIV lineage of CA-MRSA. Int J Med Microbiol 2016; 306:367-80. [PMID: 27265234 DOI: 10.1016/j.ijmm.2016.05.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 05/06/2016] [Accepted: 05/08/2016] [Indexed: 12/11/2022] Open
Abstract
ST30 (CC30)-SCCmec IV (USA1100) is one of the most common community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) lineages. ST30 isolates typically carry lukSF-PV genes encoding the Panton-Valentine leukocidin (PVL) and are responsible for outbreaks of invasive infections worldwide. In this study, twenty CC30 isolates were analyzed. All were very susceptible to non-β-lactam antimicrobials, 18/20 harbored the lukSF-PV genes, only 1/20 exhibited agr-rnaIII dysfunction, and the majority was not able to form biofilm on inert surfaces. Analysis of lukSF-PV temporal regulation revealed that opposite to other CA-MRSA isolates, these genes were more highly expressed in early log phase than in stationary phase. This inverted lukSF-PV temporal expression was associated with a similar pattern of saeRS expression in the ST30 isolates, namely high level expression in log phase and reduced expression in stationary phase. Reduced saeRS expression in stationary phase was associated with low expression levels of the sae regulators, agr and agr-upregulator sarA, which activate the stationary phase sae-P1 promoter and overexpression of agr-RNAIII restored the levels of saeR and lukSF-PV trancripts in stationary phase. Altered SaeRS activity in the ST30 isolates was attributed to amino acid substitutions (N227S, E268K and S351T) in the HTPase_c domain of SaeS (termed SaeS(SKT)). Complementation of a USA300 saeS mutant with the saeS(SKT) and saeS alleles under the direction of the log phase sae-P3 promoter revealed that saeR and lukSF-PV transcription levels were more significantly activated by saeS(SKT) than saeS. In summary our data identify a unique saeS allele (saeS(SKT)) which appears to override cell-density dependent SaeR and PVL expression in ST30 CA-MRSA isolates. Further studies to determine the contribution of saeS(SKT) allele to the pathogenesis of infections caused by ST30 isolates are merited.
Collapse
Affiliation(s)
- Mariana Severo Ramundo
- Universidade Federal do Rio de Janeiro, Instituto de Microbiologia Paulo de Góes, Rio de Janeiro, RJ, Brazil.
| | - Cristiana Ossaille Beltrame
- Universidade Federal do Rio de Janeiro, Instituto de Microbiologia Paulo de Góes, Rio de Janeiro, RJ, Brazil.
| | - Ana Maria Nunes Botelho
- Universidade Federal do Rio de Janeiro, Instituto de Microbiologia Paulo de Góes, Rio de Janeiro, RJ, Brazil.
| | - Leonardo Rocchetto Coelho
- Universidade Federal do Rio de Janeiro, Instituto de Microbiologia Paulo de Góes, Rio de Janeiro, RJ, Brazil.
| | - Maria Cicera Silva-Carvalho
- Universidade Federal do Rio de Janeiro, Instituto de Microbiologia Paulo de Góes, Rio de Janeiro, RJ, Brazil.
| | | | | | | | | | - James O'Gara
- School of Natural Sciences, Microbiology Department, NUI Galway, Galway, Ireland.
| | - Agnes Marie Sá Figueiredo
- Universidade Federal do Rio de Janeiro, Instituto de Microbiologia Paulo de Góes, Rio de Janeiro, RJ, Brazil.
| |
Collapse
|
11
|
Ferris HU, Coles M, Lupas AN, Hartmann MD. Crystallographic snapshot of the Escherichia coli EnvZ histidine kinase in an active conformation. J Struct Biol 2014; 186:376-9. [PMID: 24681325 DOI: 10.1016/j.jsb.2014.03.014] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Revised: 03/14/2014] [Accepted: 03/17/2014] [Indexed: 11/17/2022]
Abstract
Sensor histidine kinases are important sensors of the extracellular environment and relay signals via conformational changes that trigger autophosphorylation of the kinase and subsequent phosphorylation of a response regulator. The exact mechanism and the regulation of this protein family are a matter of ongoing investigation. Here we present a crystal structure of a functional chimeric protein encompassing the entire catalytic part of the Escherichia coli EnvZ histidine kinase, fused to the HAMP domain of the Archaeoglobus fulgidus Af1503 receptor. The construct is thus equivalent to the full cytosolic part of EnvZ. The structure shows a putatively active conformation of the catalytic domain and gives insight into how this conformation could be brought about in response to sensory input. Our analysis suggests a sequential flip-flop autokinase mechanism.
Collapse
Affiliation(s)
- Hedda U Ferris
- Department of Protein Evolution, Max-Planck-Institute for Developmental Biology, D-72076 Tübingen, Germany
| | - Murray Coles
- Department of Protein Evolution, Max-Planck-Institute for Developmental Biology, D-72076 Tübingen, Germany
| | - Andrei N Lupas
- Department of Protein Evolution, Max-Planck-Institute for Developmental Biology, D-72076 Tübingen, Germany.
| | - Marcus D Hartmann
- Department of Protein Evolution, Max-Planck-Institute for Developmental Biology, D-72076 Tübingen, Germany.
| |
Collapse
|
12
|
Wang C, Sang J, Wang J, Su M, Downey JS, Wu Q, Wang S, Cai Y, Xu X, Wu J, Senadheera DB, Cvitkovitch DG, Chen L, Goodman SD, Han A. Mechanistic insights revealed by the crystal structure of a histidine kinase with signal transducer and sensor domains. PLoS Biol 2013; 11:e1001493. [PMID: 23468592 PMCID: PMC3582566 DOI: 10.1371/journal.pbio.1001493] [Citation(s) in RCA: 123] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 01/14/2013] [Indexed: 02/02/2023] Open
Abstract
A crystal structure reveals an elegant mechanistic switch whereby helical bending and catalytic domain rotation allow self-activation of a histidine kinase during a bacterial stress response. Two-component systems (TCSs) are important for the adaptation and survival of bacteria and fungi under stress conditions. A TCS is often composed of a membrane-bound sensor histidine kinase (SK) and a response regulator (RR), which are relayed through sequential phosphorylation steps. However, the mechanism for how an SK is switched on in response to environmental stimuli remains obscure. Here, we report the crystal structure of a complete cytoplasmic portion of an SK, VicK from Streptococcus mutans. The overall structure of VicK is a long-rod dimer that anchors four connected domains: HAMP, Per-ARNT-SIM (PAS), DHp, and catalytic and ATP binding domain (CA). The HAMP, a signal transducer, and the PAS domain, major sensor, adopt canonical folds with dyad symmetry. In contrast, the dimer of the DHp and CA domains is asymmetric because of different helical bends in the DHp domain and spatial positions of the CA domains. Moreover, a conserved proline, which is adjacent to the phosphoryl acceptor histidine, contributes to helical bending, which is essential for the autokinase and phosphatase activities. Together, the elegant architecture of VicK with a signal transducer and sensor domain suggests a model where DHp helical bending and a CA swing movement are likely coordinated for autokinase activation. Two-component signal transduction systems (TCSs) are promising targets for new antimicrobial research because they help bacteria and fungi adapt and survive. One of the main components of TCSs is a sensor histidine kinase (SK), which relays extracellular signals to intracellular pathways. Despite intensive research, a full-length structure of an SK has yet to be solved. In this study, we report the first crystal structure of the complete cytoplasmic region of VicK, an important SK in the tooth decay pathogen S. mutans. VicK is composed of several domains (HAMP, PAS, DHp, and catalytic and ATP binding domain [CA]) in addition to a short transmembrane domain. We find that the dimeric VicK protein has an elegant rod-shaped structure with the domains linearly connected like beads on a string. The structure suggests that VicK kinase activates itself by helical bending of the DHp domain and coordinated swinging around of the catalytic CA domain to engage with the target histidine. Structure-based mutagenesis experiments also helped us to identify key residues that are required for VicK's opposing phosphatase activity. Our studies of the multi-modular VicK protein suggest a sequential kinase activation model that may involve helical bending of the DHp domain and repositioning of the CA domains.
Collapse
Affiliation(s)
- Chen Wang
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiangan, Xiamen, China
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Jiayan Sang
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiangan, Xiamen, China
| | - Jiawei Wang
- Department of Biology and Technology, Tsinghua University, Beijing, China
| | - Mingyan Su
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiangan, Xiamen, China
| | - Jennifer S. Downey
- Division of Biomedical Science, Herman Ostrow School of Dentistry of University of Southern California, Los Angeles, California, United States of America
| | - Qinggan Wu
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiangan, Xiamen, China
| | - Shida Wang
- Dental Research Institute, Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada
| | - Yongfei Cai
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiangan, Xiamen, China
| | - Xiaozheng Xu
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiangan, Xiamen, China
| | - Jun Wu
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiangan, Xiamen, China
| | - Dilani B. Senadheera
- Dental Research Institute, Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada
| | - Dennis G. Cvitkovitch
- Dental Research Institute, Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada
| | - Lin Chen
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Steven D. Goodman
- Division of Biomedical Science, Herman Ostrow School of Dentistry of University of Southern California, Los Angeles, California, United States of America
| | - Aidong Han
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiangan, Xiamen, China
- * E-mail:
| |
Collapse
|