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Pinilla CMB, Stincone P, Brandelli A. Proteomic analysis reveals differential responses of Listeria monocytogenes to free and nanoencapsulated nisin. Int J Food Microbiol 2021; 346:109170. [PMID: 33770680 DOI: 10.1016/j.ijfoodmicro.2021.109170] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 03/04/2021] [Accepted: 03/08/2021] [Indexed: 12/18/2022]
Abstract
The ability of Listeria monocytogenes grow on ready-to-eat food is a major concern in food safety. Natural antimicrobials, such as nisin, can be used to control this pathogen, but the increasing reports of nisin tolerance and resistance make necessary novel approaches to increase its effectiveness, such as encapsulation. The goal of this study was to investigate how L. monocytogenes ATCC7644 regulates and shapes its proteome in response to sublethal doses of nisin and nisin-loaded phosphatidylcholine liposomes (lipo-nisin), compared to untreated cells growing under optimal conditions. Total proteins were extracted from L. monocytogenes cells treated for 1 h with free and lipo-nisin. As result, of 803 proteins that were initially identified, 64 and 53 proteins were differentially upregulated and downregulated respectively, in the treatments with nisin and lipo-nisin. Changes of Listeria proteome in response to treatments containing nisin were mainly related to ATP-binding cassette (ABC) transporter systems, transmembrane proteins, RNA-binding proteins and diverse stress response proteins. Some of the proteins uniquely detected in samples treated with free nisin were the membrane proteins SecD, Lmo1539 and the YfhO enzyme, which are related to translocation of L. monocytogenes virulence factors, activation of the LiaR-mediated stress defense and glycosylation of wall teichoic acid, respectively. The L. monocytogenes treated with liposome encapsulated nisin showed no expression of some stress response factors as compared with the free nisin, suggesting a reduction of stress mediated response and production of nisin-resistance factors by exposure to encapsulated nisin.
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Affiliation(s)
| | - Paolo Stincone
- Laboratório de Bioquímica e Microbiologia Aplicada, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Adriano Brandelli
- Laboratório de Bioquímica e Microbiologia Aplicada, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.
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52
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The Pup-Proteasome System Protects Mycobacteria from Antimicrobial Antifolates. Antimicrob Agents Chemother 2021; 65:AAC.01967-20. [PMID: 33468462 DOI: 10.1128/aac.01967-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 12/30/2020] [Indexed: 12/21/2022] Open
Abstract
Protein turnover via the Pup-proteasome system (PPS) is essential for nitric oxide resistance and virulence of Mycobacterium tuberculosis, the causative agent of tuberculosis. Our study revealed components of PPS as novel determinants of intrinsic antifolate resistance in both M. tuberculosis and nonpathogenic M. smegmatis The lack of expression of the prokaryotic ubiquitin-like protein (Pup) or the ligase, PafA, responsible for ligating Pup to its protein targets, enhanced antifolate susceptibility in M. smegmatis Cross-species expression of M. tuberculosis homologs restored wild-type resistance to M. smegmatis proteasomal mutants. Targeted deletion of prcA and prcB, encoding the structural components of the PPS proteolytic core, similarly resulted in reduced antifolate resistance. Furthermore, sulfonamides were synergistic with acidified nitrite, and the synergy against mycobacteria was enhanced in the absence of proteasomal activity. In M. tuberculosis, targeted mutagenesis followed by genetic complementation of mpa, encoding the regulatory subunit responsible for translocating pupylated proteins to the proteolytic core, demonstrated a similar function of PPS in antifolate resistance. The overexpression of dihydrofolate reductase, responsible for the reduction of dihydrofolate to tetrahydrofolate, or disruption of the Lonely Guy gene, responsible for PPS-controlled production of cytokinins, abolished PPS-mediated antifolate sensitivity. Together, our results show that PPS protects mycobacteria from antimicrobial antifolates via regulating both folate reduction and cytokinin production.
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Abstract
The evolution of coenzymes, or their impact on the origin of life, is fundamental for understanding our own existence. Having established reasonable hypotheses about the emergence of prebiotic chemical building blocks, which were probably created under palaeogeochemical conditions, and surmising that these smaller compounds must have become integrated to afford complex macromolecules such as RNA, the question of coenzyme origin and its relation to the evolution of functional biochemistry should gain new impetus. Many coenzymes have a simple chemical structure and are often nucleotide-derived, which suggests that they may have coexisted with the emergence of RNA and may have played a pivotal role in early metabolism. Based on current theories of prebiotic evolution, which attempt to explain the emergence of privileged organic building blocks, this Review discusses plausible hypotheses on the prebiotic formation of key elements within selected extant coenzymes. In combination with prebiotic RNA, coenzymes may have dramatically broadened early protometabolic networks and the catalytic scope of RNA during the evolution of life.
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Affiliation(s)
- Andreas Kirschning
- Institut für Organische Chemie und Biomolekulares Wirkstoffzentrum (BMWZ)Leibniz Universität HannoverSchneiderberg 1B30167HannoverGermany
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54
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Wilt HM, Yu P, Tan K, Wang YX, Stagno JR. Tying the knot in the tetrahydrofolate (THF) riboswitch: A molecular basis for gene regulation. J Struct Biol 2021; 213:107703. [PMID: 33571639 DOI: 10.1016/j.jsb.2021.107703] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/28/2021] [Accepted: 01/31/2021] [Indexed: 10/22/2022]
Abstract
Effective gene regulation by the tetrahydrofolate riboswitch depends not only on ligand affinity but also on the kinetics of ligand association, which involves two cooperative binding sites. We have determined a 1.9-Å resolution crystal structure of the ligand-free THF riboswitch aptamer. The pseudoknot binding site 'unwinds' in the absence of ligand, whereby the adjacent helical domains (P1, P2, and P3) become disjointed, resulting in rotation and misalignment of the gene-regulatory P1 helix with respect to P3. In contrast, the second binding site at the three-way junction, which is the first to fold, is structurally conserved between apo and holo forms. This suggests a kinetic role for this site, in which binding of the first ligand molecule to the stably folded three-way junction promotes formation of the regulatory pseudoknot site and subsequent binding of the second molecule. As such, these findings provide a molecular basis for both conformational switching and kinetic control.
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Affiliation(s)
- Haley M Wilt
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Ping Yu
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Kemin Tan
- Structural Biology Center, X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, 9700 S. Cass Ave. Lemont, IL 60439, USA
| | - Yun-Xing Wang
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Jason R Stagno
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
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55
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Schmitz RA, Peeters SH, Versantvoort W, Picone N, Pol A, Jetten MSM, Op den Camp HJM. Verrucomicrobial methanotrophs: ecophysiology of metabolically versatile acidophiles. FEMS Microbiol Rev 2021; 45:6125968. [PMID: 33524112 PMCID: PMC8498564 DOI: 10.1093/femsre/fuab007] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 01/15/2021] [Indexed: 12/26/2022] Open
Abstract
Methanotrophs are an important group of microorganisms that counteract methane emissions to the atmosphere. Methane-oxidising bacteria of the Alpha- and Gammaproteobacteria have been studied for over a century, while methanotrophs of the phylum Verrucomicrobia are a more recent discovery. Verrucomicrobial methanotrophs are extremophiles that live in very acidic geothermal ecosystems. Currently, more than a dozen strains have been isolated, belonging to the genera Methylacidiphilum and Methylacidimicrobium. Initially, these methanotrophs were thought to be metabolically confined. However, genomic analyses and physiological and biochemical experiments over the past years revealed that verrucomicrobial methanotrophs, as well as proteobacterial methanotrophs, are much more metabolically versatile than previously assumed. Several inorganic gases and other molecules present in acidic geothermal ecosystems can be utilised, such as methane, hydrogen gas, carbon dioxide, ammonium, nitrogen gas and perhaps also hydrogen sulfide. Verrucomicrobial methanotrophs could therefore represent key players in multiple volcanic nutrient cycles and in the mitigation of greenhouse gas emissions from geothermal ecosystems. Here, we summarise the current knowledge on verrucomicrobial methanotrophs with respect to their metabolic versatility and discuss the factors that determine their diversity in their natural environment. In addition, key metabolic, morphological and ecological characteristics of verrucomicrobial and proteobacterial methanotrophs are reviewed.
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Affiliation(s)
- Rob A Schmitz
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Stijn H Peeters
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Wouter Versantvoort
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Nunzia Picone
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Arjan Pol
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
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56
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Lu C, Liu Y, Li J, Liu L, Du G. Engineering of Biosynthesis Pathway and NADPH Supply for Improved L-5-Methyltetrahydrofolate Production by Lactococcus lactis. J Microbiol Biotechnol 2021; 31:154-162. [PMID: 31893598 PMCID: PMC9705839 DOI: 10.4014/jmb.1910.10069] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 12/17/2019] [Indexed: 12/15/2022]
Abstract
L-5-methyltetrahydrofolate (5-MTHF) is one of the biological active forms of folate, which is widely used as a nutraceutical. However, low yield and serious pollution associated with the chemical synthesis of 5-MTHF hampers its sustainable supply. In this study, 5-MTHF production was improved by engineering the 5-MTHF biosynthesis pathway and NADPH supply in Lactococcus lactis for developing a green and sustainable biosynthesis approach. Specifically, overexpressing the key rate-limiting enzyme methylenetetrahydrofolate reductase led to intracellular 5-MTHF accumulation, reaching 18 μg/l. Next, 5-MTHF synthesis was further enhanced by combinatorial overexpression of 5-MTHF synthesis pathway enzymes with methylenetetrahydrofolate reductase, resulting in 1.7-fold enhancement. The folate supply pathway was strengthened by expressing folE encoding GTP cyclohydrolase I, which increased 5-MTHF production 2.4-fold to 72 μg/l. Furthermore, glucose-6-phosphate dehydrogenase was overexpressed to improve the redox cofactor NADPH supply for 5-MTHF biosynthesis, which led to a 60% increase in intracellular NADPH and a 35% increase in 5-MTHF production (97 μg/l). To reduce formation of the by-product 5-formyltetrahydrofolate, overexpression of 5-formyltetrahydrofolate cyclo-ligase converted 5-formyltetrahydrofolate to 5,10-methyltetrahydrofolate, which enhanced the 5-MTHF titer to 132 μg/l. Finally, combinatorial addition of folate precursors to the fermentation medium boosted 5-MTHF production, reaching 300 μg/l. To the best of our knowledge, this titer is the highest achieved by L. lactis. This study lays the foundation for further engineering of L. lactis for efficient 5-MTHF biosynthesis.
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Affiliation(s)
- Chuanchuan Lu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 2422, P.R. China,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 141, P.R. China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 2422, P.R. China,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 141, P.R. China,Corresponding authors Y.Liu Phone: +86-510-85197117 Fax: +86-510-85918309 E-mail:
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 2422, P.R. China,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 141, P.R. China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 2422, P.R. China,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 141, P.R. China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 2422, P.R. China,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 141, P.R. China,G.Du Phone: +86-510-85918309 Fax: +86-510-85918309 E-mail:
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57
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Wang R, Li K, Yu J, Deng J, Chen Y. Mutations of folC cause increased susceptibility to sulfamethoxazole in Mycobacterium tuberculosis. Sci Rep 2021; 11:1352. [PMID: 33446754 PMCID: PMC7809127 DOI: 10.1038/s41598-020-80213-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 11/20/2020] [Indexed: 11/30/2022] Open
Abstract
Previous studies showed that mutation of folC caused decreased expression of the dihydropteroate synthase encoding gene folP2 in Mycobacterium tuberculosis (M. tuberculosis). We speculated that mutation of folC in M. tuberculosis might affect the susceptibility to sulfamethoxazole (SMX). To prove this, 53 clinical isolates with folC mutations were selected and two folC mutants (I43A, I43T) were constructed based on M. tuberculosis H37Ra. The results showed that 42 of the 53 clinical isolates (79.2%) and the two lab-constructed folC mutants were more sensitive to SMX. To probe the mechanism by which folC mutations make M. tuberculosis more sensitive to SMX, folP2 was deleted in H37Ra, and expression levels of folP2 were compared between H37Ra and the two folC mutants. Although deletion of folP2 resulted in increased susceptibility to SMX, no difference in folP2 expression was observed. Furthermore, production levels of para-aminobenzoic acid (pABA) were compared between the folC mutants and the wild-type strain, and results showed that folC mutation resulted in decreased production of pABA. Taken together, we show that folC mutation leads to decreased production of pABA in M. tuberculosis and thus affects its susceptibility to SMX, which broadens our understanding of mechanisms of susceptibilities to antifolates in this bacterium.
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Affiliation(s)
- Ruiqi Wang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Kun Li
- School of Life Sciences, Southwest University, Chongqing, People's Republic of China.,Central Laboratory, Chongqing Public Health Medical Center, Chongqing, 400036, People's Republic of China
| | - Jifang Yu
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Jiaoyu Deng
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China.
| | - Yaokai Chen
- Central Laboratory, Chongqing Public Health Medical Center, Chongqing, 400036, People's Republic of China.
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58
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Shi G, Shaw GX, Zhu F, Tarasov SG, Ji X. Bisubstrate inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: Transition state analogs for high affinity binding. Bioorg Med Chem 2021; 29:115847. [PMID: 33199204 PMCID: PMC7855645 DOI: 10.1016/j.bmc.2020.115847] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 10/20/2020] [Accepted: 11/02/2020] [Indexed: 11/22/2022]
Abstract
6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) is a key enzyme in the folate biosynthesis pathway. It catalyzes pyrophosphoryl transfer from ATP to 6-hydroxymethyl-7,8-dihydropterin (HP). HPPK is essential for microorganisms but absent in mammals; therefore, it is an attractive target for developing novel antimicrobial agents. Previously, based on our studies of the structure and mechanism of HPPK, we created first-generation bisubstrate inhibitors by linking 6-hydroxymethylpterin to adenosine through phosphate groups, and developed second-generation inhibitors by replacing the phosphate bridge with a linkage that contains a piperidine moiety. Here, we report third-generation inhibitors designed based on the piperidine-containing inhibitor, mimicking the transition state. We synthesized two such inhibitors, characterized their protein-binding and enzyme inhibition properties, and determined their crystal structures in complex with HPPK, advancing the development of such bisubstrate analog inhibitors.
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Affiliation(s)
- Genbin Shi
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Gary X Shaw
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Fengxia Zhu
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, USA; School of Chemistry and Chemical Engineering, Huaiyin Normal University, Huaiyin, Jiangsu Province, China(1)
| | - Sergey G Tarasov
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Xinhua Ji
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, USA.
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59
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Li EW, Katinas J, Jones MA, Hamaker CG. Structural characterization of naphthalene sulfonamides and a sulfonate ester and their in vitro efficacy against Leishmania tarentolae promastigotes. NEW J CHEM 2021. [DOI: 10.1039/d0nj06320g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Structural and biological activity analyses of two naphthalene sulfonamides and a naphthalene sulfonate ester.
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Affiliation(s)
- Edward W. Li
- Department of Chemistry
- Illinois State University Normal
- USA
- William Fremd High School
- Palatine
| | - Jade Katinas
- Department of Chemistry
- Illinois State University Normal
- USA
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60
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Hou X, Zhang W, Meng Y, Zhou W, Peng G, Lei J, Cong S, Song M, Li G, Li X. A New Anti‐Immune Evasion Strategy against Methicillin‐Resistant
Staphylococcus Aureus
(MRSA) Infections: Simulating Complement Immunotherapy Based on Complement‐Mimic Antibiotic Delivery System. ADVANCED THERAPEUTICS 2020. [DOI: 10.1002/adtp.202000167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Xucheng Hou
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug System, School of Pharmaceutical Sciences Peking University Health Science Center Beijing 100191 China
- Institute of Medicinal Biotechnology Chinese Academy of Medical Science and Peking Union Medical College Beijing 100050 China
| | - Wenxi Zhang
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug System, School of Pharmaceutical Sciences Peking University Health Science Center Beijing 100191 China
| | - Yansha Meng
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug System, School of Pharmaceutical Sciences Peking University Health Science Center Beijing 100191 China
| | - Wenkai Zhou
- Institute of Medicinal Biotechnology Chinese Academy of Medical Science and Peking Union Medical College Beijing 100050 China
| | - Guanghua Peng
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug System, School of Pharmaceutical Sciences Peking University Health Science Center Beijing 100191 China
| | - Jiongxi Lei
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug System, School of Pharmaceutical Sciences Peking University Health Science Center Beijing 100191 China
| | - Shuangchen Cong
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug System, School of Pharmaceutical Sciences Peking University Health Science Center Beijing 100191 China
| | - Maoyuan Song
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug System, School of Pharmaceutical Sciences Peking University Health Science Center Beijing 100191 China
| | - Guiling Li
- Institute of Medicinal Biotechnology Chinese Academy of Medical Science and Peking Union Medical College Beijing 100050 China
| | - Xinru Li
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug System, School of Pharmaceutical Sciences Peking University Health Science Center Beijing 100191 China
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61
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Albors-Vaquer A, Rizvi A, Matzapetakis M, Lamosa P, Coelho AV, Patel AB, Mande SC, Gaddam S, Pineda-Lucena A, Banerjee S, Puchades-Carrasco L. Active and prospective latent tuberculosis are associated with different metabolomic profiles: clinical potential for the identification of rapid and non-invasive biomarkers. Emerg Microbes Infect 2020; 9:1131-1139. [PMID: 32486916 PMCID: PMC7448900 DOI: 10.1080/22221751.2020.1760734] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 04/19/2020] [Indexed: 12/22/2022]
Abstract
Although 23% of world population is infected with Mycobacterium tuberculosis (M. tb), only 5-10% manifest the disease. Individuals surely exposed to M. tb that remain asymptomatic are considered potential latent TB (LTB) cases. Such asymptomatic M. tb.-exposed individuals represent a reservoir for active TB cases. Although accurate discrimination and early treatment of patients with active TB and asymptomatic M. tb.-exposed individuals are necessary to control TB, identifying those individuals at risk of developing active TB still remains a tremendous clinical challenge. This study aimed to characterize the differences in the serum metabolic profile specifically associated to active TB infected individuals or to asymptomatic M. tb.-exposed population. Interestingly, significant changes in a specific set of metabolites were shared when comparing either asymptomatic house-hold contacts of active TB patients (HHC-TB) or active TB patients (A-TB) to clinically healthy controls (HC). Furthermore, this analysis revealed statistically significant lower serum levels of aminoacids such as alanine, lysine, glutamate and glutamine, and citrate and choline in patients with A-TB, when compared to HHC-TB. The predictive ability of these metabolic changes was also evaluated. Although further validation in independent cohorts and comparison with other pulmonary infectious diseases will be necessary to assess the clinical potential, this analysis enabled the discrimination between HHC-TB and A-TB patients with an AUC value of 0.904 (confidence interval 0.81-1.00, p-value < 0.0001). Overall, the strategy described in this work could provide a sensitive, specific, and minimally invasive method that could eventually be translated into a clinical tool for TB control.
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Affiliation(s)
- A. Albors-Vaquer
- Drug Discovery Unit, Instituto de Investigación Sanitaria La Fe, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - A. Rizvi
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | | | | | | | | | - S. C. Mande
- National Centre For Cell Science, Pune, India
- Council of Scientific and Industrial Research, New Delhi, India
| | - S. Gaddam
- Department of Immunology, Bhagwan Mahavir Medical Research Center, Hyderabad, India
- Department of Genetics, Osmania University, Hyderabad, India
| | - A. Pineda-Lucena
- Drug Discovery Unit, Instituto de Investigación Sanitaria La Fe, Hospital Universitario y Politécnico La Fe, Valencia, Spain
- Molecular Therapeutics Program, Centro de Investigación Médica Aplicada, University of Navarra, Pamplona, Spain
| | - S. Banerjee
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - L. Puchades-Carrasco
- Drug Discovery Unit, Instituto de Investigación Sanitaria La Fe, Hospital Universitario y Politécnico La Fe, Valencia, Spain
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62
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Gupta A, Sharma P, Singh TP, Sharma S. Phosphopantetheine Adenylyltransferase: A promising drug target to combat antibiotic resistance. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140566. [PMID: 33271445 DOI: 10.1016/j.bbapap.2020.140566] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/12/2020] [Accepted: 11/16/2020] [Indexed: 01/11/2023]
Abstract
Phosphopantetheine Adenylyltransferase (PPAT) is an enzyme that catalyzes the penultimate step in the biosynthesis of Coenzyme A (CoA), which is the active and physiologically functional form of dietary Vitamin B5. CoA serves as a cofactor for numerous metabolic reactions which makes it essential for cellular survival. This enzyme is also subject to feedback inhibition by CoA to maintain its cellular concentration. The steps of the CoA biosynthesis pathway remain conserved from prokaryotes to eukaryotes, with humans and pathogenic micro-organisms showing significant diversity on a sequence, structure and mechanistic level. This suggests that the development of selective inhibitors of microbial CoA biosynthesis should be possible using these enzymes as targets for drug development. Bacterial PPAT shows significant mechanistic difference from its human counterpart CoA synthase, which is a dual protein carrying the activity of both PPAT and next step in the pathway catalyzed by the enzyme Dephospho CoA kinase (DPCK). This review covers the detailed description of the mechanistic, structural and functional aspects of this enzyme. Also, all the attempts to design high efficiency inhibitors of this enzyme using the approach of structure based drug design have been discussed in detail. This comprehensive structural and functional discussion of PPAT will help in further exploiting it as a drug target.
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Affiliation(s)
- Akshita Gupta
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Pradeep Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Tej P Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India.
| | - Sujata Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India.
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63
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Colilla M, Vallet-Regí M. Targeted Stimuli-Responsive Mesoporous Silica Nanoparticles for Bacterial Infection Treatment. Int J Mol Sci 2020; 21:E8605. [PMID: 33203098 PMCID: PMC7696808 DOI: 10.3390/ijms21228605] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 02/07/2023] Open
Abstract
The rise of antibiotic resistance and the growing number of biofilm-related infections make bacterial infections a serious threat for global human health. Nanomedicine has entered into this scenario by bringing new alternatives to design and develop effective antimicrobial nanoweapons to fight against bacterial infection. Among them, mesoporous silica nanoparticles (MSNs) exhibit unique characteristics that make them ideal nanocarriers to load, protect and transport antimicrobial cargoes to the target bacteria and/or biofilm, and release them in response to certain stimuli. The combination of infection-targeting and stimuli-responsive drug delivery capabilities aims to increase the specificity and efficacy of antimicrobial treatment and prevent undesirable side effects, becoming a ground-breaking alternative to conventional antibiotic treatments. This review focuses on the scientific advances developed to date in MSNs for infection-targeted stimuli-responsive antimicrobials delivery. The targeting strategies for specific recognition of bacteria are detailed. Moreover, the possibility of incorporating anti-biofilm agents with MSNs aimed at promoting biofilm penetrability is overviewed. Finally, a comprehensive description of the different scientific approaches for the design and development of smart MSNs able to release the antimicrobial payloads at the infection site in response to internal or external stimuli is provided.
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Affiliation(s)
- Montserrat Colilla
- Departamento de Química en Ciencias Farmacéuticas, Unidad de Química Inorgánica y Bioinorgánica, Universidad Complutense de Madrid, Instituto de Investigación Sanitaria Hospital 12 de Octubre i+12, Plaza Ramón y Cajal s/n, 28040 Madrid, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina, CIBER-BBN, 28040 Madrid, Spain
| | - María Vallet-Regí
- Departamento de Química en Ciencias Farmacéuticas, Unidad de Química Inorgánica y Bioinorgánica, Universidad Complutense de Madrid, Instituto de Investigación Sanitaria Hospital 12 de Octubre i+12, Plaza Ramón y Cajal s/n, 28040 Madrid, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina, CIBER-BBN, 28040 Madrid, Spain
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64
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Zhang A, Li W, Liu X, Wu M, Xuan G. Synthesis, Biological Evaluation and in Silico Studies of Several Substituted Benzene Sulfonamides as Potential Antibacterial Agents. ACTA ACUST UNITED AC 2020. [DOI: 10.1088/1742-6596/1624/2/022058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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65
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Affiliation(s)
- Andreas Kirschning
- Institut für Organische Chemie und Biomolekulares Wirkstoffzentrum (BMWZ) Leibniz Universität Hannover Schneiderberg 1B 30167 Hannover Deutschland
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66
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Jiang L, Luirink J, Kooijmans SAA, van Kessel KPM, Jong W, van Essen M, Seinen CW, de Maat S, de Jong OG, Gitz-François JFF, Hennink WE, Vader P, Schiffelers RM. A post-insertion strategy for surface functionalization of bacterial and mammalian cell-derived extracellular vesicles. Biochim Biophys Acta Gen Subj 2020; 1865:129763. [PMID: 33065252 DOI: 10.1016/j.bbagen.2020.129763] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 08/26/2020] [Accepted: 09/21/2020] [Indexed: 01/03/2023]
Abstract
Extracellular vesicles (EVs) are nanoparticles which are released by cells from all three domains of life: Archaea, Bacteria and Eukarya. They can mediate cell-cell communication by transferring cargoes such as proteins and nucleic acids between cells. EVs receive great interest in both academia and industry as they have the potential to be natural drug carriers or vaccine candidates. However, limitations to their clinical translation exist as efficient isolation, loading, labelling and surface-engineering methods are lacking. In this article, we investigate a 'post-insertion' approach, which is commonly used in the functionalization of liposomes in the pharmaceutical field, on two different EV types: mammalian cell-derived EVs and bacteria-derived EVs. We aimed to find an easy and flexible approach to functionalize EVs, thereby improving the labelling, isolation, and surface-engineering.
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Affiliation(s)
- Linglei Jiang
- CDL Research, Division LAB, UMC Utrecht, Utrecht, the Netherlands Faculty of Medicine, Utrecht University, Utrecht, the Netherlands
| | - Joen Luirink
- Department of Molecular Microbiology, Amsterdam Institute for Molecules Medicines and Systems (AIMMS), Vrije Universiteit, Amsterdam, the Netherlands; Abera Bioscience AB, Solna, Sweden
| | - Sander A A Kooijmans
- CDL Research, Division LAB, UMC Utrecht, Utrecht, the Netherlands Faculty of Medicine, Utrecht University, Utrecht, the Netherlands
| | | | | | - Max van Essen
- CDL Research, Division LAB, UMC Utrecht, Utrecht, the Netherlands Faculty of Medicine, Utrecht University, Utrecht, the Netherlands
| | - Cor W Seinen
- CDL Research, Division LAB, UMC Utrecht, Utrecht, the Netherlands Faculty of Medicine, Utrecht University, Utrecht, the Netherlands
| | - Steven de Maat
- CDL Research, Division LAB, UMC Utrecht, Utrecht, the Netherlands Faculty of Medicine, Utrecht University, Utrecht, the Netherlands
| | - Olivier G de Jong
- CDL Research, Division LAB, UMC Utrecht, Utrecht, the Netherlands Faculty of Medicine, Utrecht University, Utrecht, the Netherlands
| | - Jerney F F Gitz-François
- CDL Research, Division LAB, UMC Utrecht, Utrecht, the Netherlands Faculty of Medicine, Utrecht University, Utrecht, the Netherlands
| | - Wim E Hennink
- Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Pieter Vader
- CDL Research, Division LAB, UMC Utrecht, Utrecht, the Netherlands Faculty of Medicine, Utrecht University, Utrecht, the Netherlands; Laboratory of Experimental Cardiology, UMC Utrecht, Utrecht, the Netherlands
| | - Raymond M Schiffelers
- CDL Research, Division LAB, UMC Utrecht, Utrecht, the Netherlands Faculty of Medicine, Utrecht University, Utrecht, the Netherlands.
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67
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Jonkers TJH, Steenhuis M, Schalkwijk L, Luirink J, Bald D, Houtman CJ, Kool J, Lamoree MH, Hamers T. Development of a high-throughput bioassay for screening of antibiotics in aquatic environmental samples. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 729:139028. [PMID: 32498177 DOI: 10.1016/j.scitotenv.2020.139028] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/24/2020] [Accepted: 04/25/2020] [Indexed: 05/26/2023]
Abstract
The goal of the present study was to select a Gram-positive (Gram+) and Gram-negative (Gram-) strain to measure antimicrobial activity in environmental samples, allowing high-throughput environmental screening. The sensitivity of eight pre-selected bacterial strains were tested to a training set of ten antibiotics, i.e. three Gram+ Bacillus subtilis strains with different read-outs, and five Gram- strains. The latter group consisted of a bioluminescent Allivibrio fischeri strain and four Escherichia coli strains, i.e. a wild type (WT) and three strains with a modified cell envelope to increase their sensitivity. The WT B. subtilis and an E. coli strain newly developed in this study, were most sensitive to the training set. This E. coli strain carries an open variant of an outer membrane protein combined with an inactivated multidrug efflux transport system. The assay conditions of these two strains were optimized and validated by exposure to a validation set of thirteen antibiotics with clinical and environmental relevance. The assay sensitivity ranged from the ng/mL to μg/mL range. The applicability of the assays for toxicological characterization of aquatic environmental samples was demonstrated for hospital effluent extract. A future application includes effect-directed analysis to identify yet unknown antibiotic contaminants or their transformation products.
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Affiliation(s)
- Tim J H Jonkers
- Department of Environment & Health, Faculty of Science, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, the Netherlands.
| | - Maurice Steenhuis
- Department of Molecular Microbiology, Faculty of Science, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, the Netherlands
| | - Louis Schalkwijk
- Department of Environment & Health, Faculty of Science, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, the Netherlands
| | - Joen Luirink
- Department of Molecular Microbiology, Faculty of Science, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, the Netherlands
| | - Dirk Bald
- Department of Molecular Cell Biology, Faculty of Science, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, the Netherlands
| | - Corine J Houtman
- The Water Laboratory, J.W. Lucasweg 2, 2031 BE Haarlem, the Netherlands
| | - Jeroen Kool
- Biomolecular Analysis Group, Faculty of Science, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, the Netherlands
| | - Marja H Lamoree
- Department of Environment & Health, Faculty of Science, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, the Netherlands; KWR Watercycle Research Institute, P.O. Box 1072, 3430 BB Nieuwegein, the Netherlands
| | - Timo Hamers
- Department of Environment & Health, Faculty of Science, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, the Netherlands
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68
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Kronenberger T, Ferreira GM, de Souza ADF, da Silva Santos S, Poso A, Ribeiro JA, Tavares MT, Pavan FR, Trossini GHG, Dias MVB, Parise-Filho R. Design, synthesis and biological activity of novel substituted 3-benzoic acid derivatives as MtDHFR inhibitors. Bioorg Med Chem 2020; 28:115600. [DOI: 10.1016/j.bmc.2020.115600] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 06/02/2020] [Accepted: 06/16/2020] [Indexed: 10/24/2022]
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69
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Cheong MS, Seo KH, Chohra H, Yoon YE, Choe H, Kantharaj V, Lee YB. Influence of Sulfonamide Contamination Derived from Veterinary Antibiotics on Plant Growth and Development. Antibiotics (Basel) 2020; 9:antibiotics9080456. [PMID: 32731577 PMCID: PMC7460019 DOI: 10.3390/antibiotics9080456] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/25/2020] [Accepted: 07/27/2020] [Indexed: 11/16/2022] Open
Abstract
Veterinary antibiotics such as sulfonamides are widely used to increase feed efficiency and to protect against disease in livestock production. The sulfonamide antimicrobial mechanism involves the blocking of folate biosynthesis by inhibiting bacterial dihydropteroate synthase (DHPS) activity competitively. Interestingly, most treatment antibiotics can be released into the environment via manure and result in significant diffuse pollution in the environment. However, the physiological effects of sulfonamide during plant growth and development remain elusive because the plant response is dependent on folate biosynthesis and the concentration of antibiotics. Here, we present a chemical interaction docking model between Napa cabbage (Brassica campestris) DHPS and sulfamethoxazole and sulfamethazine, which are the most abundant sulfonamides detected in the environment. Furthermore, seedling growth inhibition was observed in lentil bean (Lens culinaris), rice (Oryza sativa), and Napa cabbage plants upon sulfonamide exposure. The results revealed that sulfonamide antibiotics target plant DHPS in a module similar to bacterial DHPS and affect early growth and the development of crop seedlings. Taking these results together, we suggest that sulfonamides act as pollutants in crop fields.
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Affiliation(s)
- Mi Sun Cheong
- Division of Applied Life Science (BK 21 Plus Program), Gyeongsang National University, Jinju 52828, Korea; (M.S.C.); (H.C.); (Y.E.Y.); (H.C.); (V.K.)
- Institute of Agriculture and Life Science (IALS), Gyeongsang National University, Jinju 52828, Korea
| | - Kyung Hye Seo
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science, RDA, Eumsung 27709, Korea;
| | - Hadjer Chohra
- Division of Applied Life Science (BK 21 Plus Program), Gyeongsang National University, Jinju 52828, Korea; (M.S.C.); (H.C.); (Y.E.Y.); (H.C.); (V.K.)
| | - Young Eun Yoon
- Division of Applied Life Science (BK 21 Plus Program), Gyeongsang National University, Jinju 52828, Korea; (M.S.C.); (H.C.); (Y.E.Y.); (H.C.); (V.K.)
| | - Hyeonji Choe
- Division of Applied Life Science (BK 21 Plus Program), Gyeongsang National University, Jinju 52828, Korea; (M.S.C.); (H.C.); (Y.E.Y.); (H.C.); (V.K.)
| | - Vimalraj Kantharaj
- Division of Applied Life Science (BK 21 Plus Program), Gyeongsang National University, Jinju 52828, Korea; (M.S.C.); (H.C.); (Y.E.Y.); (H.C.); (V.K.)
| | - Yong Bok Lee
- Division of Applied Life Science (BK 21 Plus Program), Gyeongsang National University, Jinju 52828, Korea; (M.S.C.); (H.C.); (Y.E.Y.); (H.C.); (V.K.)
- Institute of Agriculture and Life Science (IALS), Gyeongsang National University, Jinju 52828, Korea
- Correspondence: ; Tel.: +82-557-721-967
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70
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MYCO WELL D-ONE detection of Ureaplasma spp. and Mycoplasma hominis in sexual health patients in Wales. Eur J Clin Microbiol Infect Dis 2020; 39:2427-2440. [PMID: 32725499 PMCID: PMC7669805 DOI: 10.1007/s10096-020-03993-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 07/20/2020] [Indexed: 10/26/2022]
Abstract
The genital mycoplasmas are a unique group of inherently antibiotic-resistant sexually transmitted bacteria, often associated with non-gonococcal urethritis and bacterial vaginosis. The MYCO WELL D-ONE is a culture-based assay that aims to detect these organisms whilst concurrently screening them for antibiotic resistance. Urine and/or swabs from 856 informed and consented participants attending Welsh sexual health clinics were subjected to MYCO WELL D-ONE analysis, alongside qPCR and culture titration methodologies to determine sensitivity, specificity, PPV, NPV and accuracy. Resistance was confirmed by CLSI-compliant susceptibility testing and genetic mechanisms determined. The MYCO WELL D-ONE displayed a sensitivity and specificity of 91.98% and 96.44% for the detection of Ureaplasma spp., with sensitivity and specificity values of 78.23% and 98.84% for Mycoplasma hominis, compared with qPCR. Swabs harboured significantly greater bacterial loads than urine samples for both Ureaplasma spp. and M. hominis. Levofloxacin resistance rates, mediated by Ser83Leu mutation in ParC, for Ureaplasma spp. were 0.54%. Tetracycline resistance rates, mediated by tet(M), were 0.54% and 2% for Ureaplasma spp. and M. hominis, respectively; sequence analysis of tet(M)-positive Ureaplasma spp. and M. hominis strains isolated from a single individual confirmed separate resistance gene origins. The MYCO WELL D-ONE is a sensitive and specific assay for the detection of Ureaplasma spp. and M. hominis in genitourinary medicine samples, facilitating the accurate detection of these organisms within low-technology environments. While good for antibiotic resistance screening, accurate confirmation by MIC determination or molecular methods are required, and more optimally performed on urine samples.
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71
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Sulfamethoxazole drug stress upregulates antioxidant immunomodulatory metabolites in Escherichia coli. Nat Microbiol 2020; 5:1319-1329. [PMID: 32719505 PMCID: PMC7581551 DOI: 10.1038/s41564-020-0763-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 06/29/2020] [Indexed: 02/08/2023]
Abstract
Escherichia coli is an important model organism in microbiology and a prominent member of the human microbiota1. Environmental isolates readily colonize the gastrointestinal tract of humans and other animals, and they can serve diverse probiotic, commensal and pathogenic roles in the host2-4. Although certain strains have been associated with the severity of inflammatory bowel disease (IBD)2,5, the diverse immunomodulatory phenotypes remain largely unknown at the molecular level. Here, we decode a previously unknown E. coli metabolic pathway that produces a family of hybrid pterin-phenylpyruvate conjugates, which we named the colipterins. The metabolites are upregulated by subinhibitory levels of the antifolate sulfamethoxazole, which is used to treat infections including in patients with IBD6,7. The genes folX/M and aspC/tyrB involved in monapterin biosynthesis8-10 and aromatic amino acid transamination,11 respectively, were required to initiate the colipterin pathway. We show that the colipterins are antioxidants, harbour diverse immunological activities in primary human tissues, activate anti-inflammatory interleukin-10 and improve colitis symptoms in a colitis mouse model. Our study defines an antifolate stress response in E. coli and links its associated metabolites to a major immunological marker of IBD.
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72
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Nambiar D, Sharma O, Duff MR, Howell EE. Effects of Osmolytes on Ligand Binding to Dihydropteroate Synthase from Bacillus anthracis. J Phys Chem B 2020; 124:6212-6224. [PMID: 32580556 DOI: 10.1021/acs.jpcb.0c03311] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Osmolyte interactions with ligands can affect their affinity for proteins and are dependent upon the cosolute and the functional groups of the ligand. Here, we explored ligand binding to Bacillus anthracis dihydropteroate synthase (BaDHPS) under osmotic stress conditions. Osmolyte effects were specific to the cosolute and ligand, suggesting interaction of the osmolytes with the free ligands in solution. The association rates of pterin pyrophosphate were mostly unaffected by the osmolytes, except for a 2-fold decrease in the presence of 1 M trehalose, while the dissociation rates decreased in most osmolyte solutions. The viscosity and dielectric constant of the solution did not correlate with the effects of the osmolytes. Experimental results were compared with predicted preferential interaction coefficients (Δμ23/RT) between the osmolytes and ligands. The Δμ23/RT were able to predict the experimental data for most of the osmolytes. Trehalose and proline effects did not correlate with the predicted values, indicating that these two osmolytes may affect binding in more complex ways than simple preferential interactions. Additionally, osmolytes weakly interacted with the sulfa drug sulfathiazole, which altered its affinity for BaDHPS, suggesting that these types of weak interactions can also impact drug binding. As osmolytes affect ligands binding to two different folate cycle enzymes (DHFRs and DHPS), we predicted how ligand binding to other folate cycle enzymes will be altered by the presence of osmolytes.
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Affiliation(s)
- Deepika Nambiar
- Department of Biochemistry & Cellular and Molecular Biology Department, University of Tennessee-Knoxville, Knoxville, Tennessee 37996, United States
| | - Ojaswini Sharma
- Department of Biochemistry & Cellular and Molecular Biology Department, University of Tennessee-Knoxville, Knoxville, Tennessee 37996, United States
| | - Michael R Duff
- Department of Biochemistry & Cellular and Molecular Biology Department, University of Tennessee-Knoxville, Knoxville, Tennessee 37996, United States
| | - Elizabeth E Howell
- Department of Biochemistry & Cellular and Molecular Biology Department, University of Tennessee-Knoxville, Knoxville, Tennessee 37996, United States
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73
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Dihydrofolate Reductase Is a Valid Target for Antifungal Development in the Human Pathogen Candida albicans. mSphere 2020; 5:5/3/e00374-20. [PMID: 32581079 PMCID: PMC7316490 DOI: 10.1128/msphere.00374-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The folate biosynthetic pathway is a promising and understudied source for novel antifungals. Even dihydrofolate reductase (DHFR), a well-characterized and historically important drug target, has not been conclusively validated as an antifungal target. Here, we demonstrate that repression of DHFR inhibits growth of Candida albicans, a major human fungal pathogen. Methotrexate, an antifolate, also inhibits growth but through pH-dependent activity. In addition, we show that C. albicans has a limited ability to take up or utilize exogenous folates as only the addition of high concentrations of folinic acid restored growth in the presence of methotrexate. Finally, we show that repression of DHFR in a mouse model of infection was sufficient to eliminate host mortality. Our work conclusively establishes DHFR as a valid antifungal target in C. albicans. While the folate biosynthetic pathway has provided a rich source of antibacterial, antiprotozoal, and anticancer therapies, it has not yet been exploited to develop uniquely antifungal agents. Although there have been attempts to develop fungal-specific inhibitors of dihydrofolate reductase (DHFR), the protein itself has not been unequivocally validated as essential for fungal growth or virulence. The purpose of this study was to establish dihydrofolate reductase as a valid antifungal target. Using a strain with doxycycline-repressible transcription of DFR1 (PTETO-DFR1 strain), we were able to demonstrate that Dfr1p is essential for growth in vitro. Furthermore, nutritional supplements of most forms of folate are not sufficient to restore growth when Dfr1p expression is suppressed or when its activity is directly inhibited by methotrexate, indicating that Candida albicans has a limited capacity to acquire or utilize exogenous sources of folate. Finally, the PTETO-DFR1 strain was rendered avirulent in a mouse model of disseminated candidiasis upon doxycycline treatment. Collectively, these results confirm the validity of targeting dihydrofolate reductase and, by inference, other enzymes in the folate biosynthetic pathway as a strategy to devise new and efficacious therapies to combat life-threatening invasive fungal infections. IMPORTANCE The folate biosynthetic pathway is a promising and understudied source for novel antifungals. Even dihydrofolate reductase (DHFR), a well-characterized and historically important drug target, has not been conclusively validated as an antifungal target. Here, we demonstrate that repression of DHFR inhibits growth of Candida albicans, a major human fungal pathogen. Methotrexate, an antifolate, also inhibits growth but through pH-dependent activity. In addition, we show that C. albicans has a limited ability to take up or utilize exogenous folates as only the addition of high concentrations of folinic acid restored growth in the presence of methotrexate. Finally, we show that repression of DHFR in a mouse model of infection was sufficient to eliminate host mortality. Our work conclusively establishes DHFR as a valid antifungal target in C. albicans.
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74
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Mondal SI, Akter A, Koga R, Hosokawa T, Dayi M, Murase K, Tanaka R, Shigenobu S, Fukatsu T, Kikuchi T. Reduced Genome of the Gut Symbiotic Bacterium " Candidatus Benitsuchiphilus tojoi" Provides Insight Into Its Possible Roles in Ecology and Adaptation of the Host Insect. Front Microbiol 2020; 11:840. [PMID: 32435239 PMCID: PMC7218078 DOI: 10.3389/fmicb.2020.00840] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 04/07/2020] [Indexed: 12/27/2022] Open
Abstract
Diverse animals, including insects, harbor microbial symbionts within their gut, body cavity, or cells. The subsocial parastrachiid stinkbug Parastrachia japonensis is well-known for its peculiar ecological and behavioral traits, including its prolonged non-feeding diapause period and maternal care of eggs/nymphs in an underground nest. P. japonensis harbors a specific bacterial symbiont within the gut cavity extracellularly, which is vertically inherited through maternal excretion of symbiont-containing white mucus. Thus far, biological roles of the symbiont in the host lifecycle has been little understood. Here we sequenced the genome of the uncultivable gut symbiont “Candidatus Benitsuchiphilus tojoi.” The symbiont has an 804 kb circular chromosome encoding 606 proteins and a 14.5 kb plasmid encoding 13 proteins. Phylogenetic analysis indicated that the bacterium is closely related to other obligate insect symbionts belonging to the Gammaproteobacteria, including Buchnera of aphids and Blochmannia of ants, and the most closely related to Ishikawaella, an extracellular gut symbiont of plataspid stinkbugs. These data suggested that the symbiont genome has evolved like highly reduced gamma-proteobacterial symbiont genomes reported from a variety of insects. The presence of genes involved in biosynthesis pathways for amino acids, vitamins, and cofactors in the genome implicated the symbiont as a nutritional mutualist, supplementing essential nutrients to the host. Interestingly, the symbiont’s plasmid encoded genes for thiamine and carotenoid synthesis pathways, suggesting the possibility of additional functions of the symbiont for protecting the host against oxidative stress and DNA damage. Finally, possible involvement of the symbiont in uric acid metabolism during diapause is discussed.
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Affiliation(s)
- Shakhinur Islam Mondal
- Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan.,Genetic Engineering and Biotechnology Department, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Arzuba Akter
- Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan.,Biochemistry and Molecular Biology Department, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Ryuichi Koga
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Takahiro Hosokawa
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan.,Faculty of Science, Kyushu University, Fukuoka, Japan
| | - Mehmet Dayi
- Forestry Vocational School, Düzce University, Düzce, Turkey
| | - Kazunori Murase
- Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Ryusei Tanaka
- Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Shuji Shigenobu
- NIBB Core Research Facilities, National Institute for Basic Biology, Okazaki, Japan
| | - Takema Fukatsu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.,Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Taisei Kikuchi
- Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
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75
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Wallace MJ, Dharuman S, Fernando DM, Reeve SM, Gee CT, Yao J, Griffith EC, Phelps GA, Wright WC, Elmore JM, Lee RB, Chen T, Lee RE. Discovery and Characterization of the Antimetabolite Action of Thioacetamide-Linked 1,2,3-Triazoles as Disruptors of Cysteine Biosynthesis in Gram-Negative Bacteria. ACS Infect Dis 2020; 6:467-478. [PMID: 31887254 DOI: 10.1021/acsinfecdis.9b00406] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Increasing rates of drug-resistant Gram-negative (GN) infections, combined with a lack of new GN-effective antibiotic classes, are driving the need for the discovery of new agents. Bacterial metabolism represents an underutilized mechanism of action in current antimicrobial therapies. Therefore, we sought to identify novel antimetabolites that disrupt key metabolic pathways and explore the specific impacts of these agents on bacterial metabolism. This study describes the successful application of this approach to discover a new series of chemical probes, N-(phenyl)thioacetamide-linked 1,2,3-triazoles (TAT), that target cysteine synthase A (CysK), an enzyme unique to bacteria that is positioned at a key juncture between several fundamental pathways. The TAT class was identified using a high-throughput screen against Escherichia coli designed to identify modulators of pathways related to folate biosynthesis. TAT analog synthesis demonstrated a clear structure-activity relationship, and activity was confirmed against GN antifolate-resistant clinical isolates. Spontaneous TAT resistance mutations were tracked to CysK, and mode of action studies led to the identification of a false product formation mechanism between the CysK substrate O-acetyl-l-serine and the TATs. Global transcriptional responses to TAT treatment revealed that these antimetabolites impose substantial disruption of key metabolic networks beyond cysteine biosynthesis. This study highlights the potential of antimetabolite drug discovery as a promising approach to the discovery of novel GN antibiotics and the pharmacological promise of TAT CysK probes.
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Affiliation(s)
- Miranda J. Wallace
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
- Department of Microbiology, Immunology, and Biochemistry, The University of Tennessee Health Science Center, 858 Madison Avenue, Memphis, Tennessee 38163, United States
| | - Suresh Dharuman
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Dinesh M. Fernando
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Stephanie M. Reeve
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Clifford T. Gee
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Jiangwei Yao
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Elizabeth C. Griffith
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Gregory A. Phelps
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - William C. Wright
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - John M. Elmore
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Robin B. Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Richard E. Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
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76
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Satuluri SH, Katari SK, Pasala C, Amineni U. Novel and potent inhibitors for dihydropteroate synthase of Helicobacter pylori. J Recept Signal Transduct Res 2020; 40:246-256. [PMID: 32098568 DOI: 10.1080/10799893.2020.1731533] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
An endless drug-resistant strains of Helicobacter pylori and multitudinous drug reactions are obstacles in the treatment of H. pylori infections, thereby ambitious novel proof-of-concept for inhibitor design was practiced in advancement of medication. Dihydropteroate synthase (DHPS) is an alluring target that plays a great role in folate synthesis pathway essential for amino acids biosynthesis was selected for designing novel drugs to prevent infections caused by pathogenic H. pylori. In the present study, a reliable tertiary structure of DHPS in complex with inhibitor 6MB was constructed by Modeler 9v19. DrugBank compounds of DHPS, published inhibitors, and co-crystal ligand (6MB) were docked against DHPS. The best docked compounds were screened against 28.5 million compounds resulted 1186 structural analogs. Virtual screening workflow and quantum polarized ligand dockings of these compounds against DHPS resulted three leads that showed better XP Gscores, ADME properties, and binding-free energies compared to 6MB, DrugBank compounds, and published inhibitors. The proposed leads were also validated by receiver operative characteristic (ROC) curve metrics in the presence of thousand decoys and the best docked existing compounds against DHPS. Long-range molecular dynamics (MD) simulations for 100 ns were executed after post-docking evaluations. Trajectory analysis showed the lead-DHPS docking complex's inter-molecular interactions were stable throughout the entire runtime of MD simulations than 6MB-DHPS complex and Eliglustat-DHPS complex. The study outcomes showed good competitive binding propensity and active-tunneling of leads over the existing inhibitors, thereby these leads could be ideal inhibitors against DHPS to target H. pylori.
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Affiliation(s)
- Sri Harsha Satuluri
- Bioinformatics Centre, Department of Bioinformatics, SVIMS University, Tirupati, India
| | - Sudheer Kumar Katari
- Bioinformatics Centre, Department of Bioinformatics, SVIMS University, Tirupati, India
| | - Chiranjeevi Pasala
- Bioinformatics Centre, Department of Bioinformatics, SVIMS University, Tirupati, India
| | - Umamaheswari Amineni
- Bioinformatics Centre, Department of Bioinformatics, SVIMS University, Tirupati, India
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77
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Sun H, Pan Y, Chen X, Jiang W, Lin Z, Yin C. Regular time-dependent cross-phenomena induced by hormesis: A case study of binary antibacterial mixtures to Aliivibrio fischeri. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 187:109823. [PMID: 31639641 DOI: 10.1016/j.ecoenv.2019.109823] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 09/29/2019] [Accepted: 10/14/2019] [Indexed: 06/10/2023]
Abstract
Time-dependent cross-phenomenon in which the cross between the actual concentration-response curve (CRC) for mixture crosses the CRCs for reference model varies with time has been frequently reported in previous studies, expressed as a heterogeneous pattern of joint toxic action. However, the variation tendency of time-dependent cross-phenomenon is rarely addressed. In this study, the joint toxic actions of binary antibacterial mixtures (i.e., two quorum sensing inhibitors, tetracycline hydrochloride, erythromycin, and chloramphenicol with sulfonamides) were judged using independent action (IA) model to find the variation tendency of time-dependent cross-phenomenon. The results show that the time-dependent cross-phenomena of the test binary antibacterial mixtures follow a unified variation tendency and the corresponding joint toxic actions change regularly with an increase of both concentration and time. Through investigating the relationship between the stimulatory and inhibitory modes of action for the single agents and the time-dependent cross-phenomena of binary mixtures, the regular time-dependent cross-phenomena is speculated to be derived from the hormetic effects of the components in the mixtures. This study offers an advance for the variation tendency and mechanistic explanation of time-dependent cross-phenomenon, which will provide a support for the future development in the exploration of time-dependent cross-phenomenon and environmental risk assessment of pollutant mixtures.
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Affiliation(s)
- Haoyu Sun
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, China; Post-doctoral Research Station, College of Civil Engineering, Tongji University, Shanghai, 200092, China; Shanghai Key Lab of Chemical Assessment and Sustainability, Shanghai, China
| | - Yongzheng Pan
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, 201306, China
| | - Xiang Chen
- Shanghai Customs Inspection Center of Industrial Products & Raw Material, Shanghai, 200135, China
| | - Wei Jiang
- Shanghai Customs Inspection Center of Industrial Products & Raw Material, Shanghai, 200135, China
| | - Zhifen Lin
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, China; Shanghai Key Lab of Chemical Assessment and Sustainability, Shanghai, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, China.
| | - Chunsheng Yin
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, 201306, China.
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78
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Rambo IM, Dombrowski N, Constant L, Erdner D, Baker BJ. Metabolic relationships of uncultured bacteria associated with the microalgae Gambierdiscus. Environ Microbiol 2019; 22:1764-1783. [PMID: 31775181 DOI: 10.1111/1462-2920.14878] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 11/13/2019] [Accepted: 11/25/2019] [Indexed: 12/14/2022]
Abstract
Microbial communities inhabit algae cell surfaces and produce a variety of compounds that can impact the fitness of the host. These interactions have been studied via culturing, single-gene diversity and metagenomic read survey methods that are limited by culturing biases and fragmented genetic characterizations. Higher-resolution frameworks are needed to resolve the physiological interactions within these algal-bacterial communities. Here, we infer the encoded metabolic capabilities of four uncultured bacterial genomes (reconstructed using metagenomic assembly and binning) associated with the marine dinoflagellates Gambierdiscus carolinianus and G. caribaeus. Phylogenetic analyses revealed that two of the genomes belong to the commonly algae-associated families Rhodobacteraceae and Flavobacteriaceae. The other two genomes belong to the Phycisphaeraceae and include the first algae-associated representative within the uncultured SM1A02 group. Analyses of all four genomes suggest these bacteria are facultative aerobes, with some capable of metabolizing phytoplanktonic organosulfur compounds including dimethylsulfoniopropionate and sulfated polysaccharides. These communities may biosynthesize compounds beneficial to both the algal host and other bacteria, including iron chelators, B vitamins, methionine, lycopene, squalene and polyketides. These findings have implications for marine carbon and nutrient cycling and provide a greater depth of understanding regarding the genetic potential for complex physiological interactions between microalgae and their associated bacteria.
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Affiliation(s)
- Ian M Rambo
- Department of Marine Science, University of Texas at Austin, 750 Channel View Drive, Port Aransas, TX, 78373, USA
| | - Nina Dombrowski
- Department of Marine Science, University of Texas at Austin, 750 Channel View Drive, Port Aransas, TX, 78373, USA.,NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, Den Burg, The Netherlands
| | - Lauren Constant
- Department of Marine Science, University of Texas at Austin, 750 Channel View Drive, Port Aransas, TX, 78373, USA
| | - Deana Erdner
- Department of Marine Science, University of Texas at Austin, 750 Channel View Drive, Port Aransas, TX, 78373, USA
| | - Brett J Baker
- Department of Marine Science, University of Texas at Austin, 750 Channel View Drive, Port Aransas, TX, 78373, USA
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79
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Cai N, He L, Wang K, Feng Z, Cui Z, Ji M, Qi Z, Qin P, Li X. Novel sulfonamides against Botrytis cinerea with no positive cross-resistance to commercial fungicides: Design, synthesis and SAR study. Bioorg Med Chem Lett 2019; 30:126859. [PMID: 31889667 DOI: 10.1016/j.bmcl.2019.126859] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 10/30/2019] [Accepted: 11/25/2019] [Indexed: 12/16/2022]
Abstract
Thirty-four novel compounds were synthesized using chesulfamide (N-(2-trifluoromethyl-4-chlorophenyl)-2-oxocyclohexyl sulfonamide), a high-profile fungicide, as the lead compound, and their structures were characterized by 1H NMR, 13C NMR, MS and elemental analysis. Additionally, the structure of (1S,2R)-2-((3-bromophenethyl)amino)-N-(4-chloro-2-trifluoromethylphenyl)cyclohexane-1-sulfonamide (IV-9) was confirmed by X-ray single crystal diffraction. The mycelium inhibition tests, spore germination inhibition tests, tomato pot tests and field trials were performed against strains of B. cinerea. Bioassay results showed that most of target compounds had good fungicidal activity against B. cinerea, in particular, IV-9 exhibited similar or superior effects to procymidone, boscalid and pyrisoxazole in all in vitro and in vivo tests. Moreover, there was no positive cross-resistance found between the compound IV-9 and eight commercial fungicides (azoxystrobin, boscalid, chlorothalonil, diethofencarb, fludioxonil, procymidone, pyrimethanil and pyrisoxazole) in the cross-resistance validation test performed by an innovative method.
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Affiliation(s)
- Nan Cai
- Department of Pesticide Science, Plant Protection College, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
| | - Lu He
- Department of Pesticide Science, Plant Protection College, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
| | - Kai Wang
- Department of Pesticide Science, Plant Protection College, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
| | - Zhihui Feng
- Department of Pesticide Science, Plant Protection College, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
| | - Zining Cui
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Integrative Microbiology Research Centre, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Mingshan Ji
- Department of Pesticide Science, Plant Protection College, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
| | - Zhiqiu Qi
- Department of Pesticide Science, Plant Protection College, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
| | - Peiwen Qin
- Department of Pesticide Science, Plant Protection College, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
| | - Xinghai Li
- Department of Pesticide Science, Plant Protection College, Shenyang Agricultural University, Shenyang 110866, Liaoning, China.
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80
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Northrup JD, Mach RH, Sellmyer MA. Radiochemical Approaches to Imaging Bacterial Infections: Intracellular versus Extracellular Targets. Int J Mol Sci 2019; 20:E5808. [PMID: 31752318 PMCID: PMC6888724 DOI: 10.3390/ijms20225808] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 11/04/2019] [Accepted: 11/12/2019] [Indexed: 02/03/2023] Open
Abstract
The discovery of penicillin began the age of antibiotics, which was a turning point in human healthcare. However, to this day, microbial infections are still a concern throughout the world, and the rise of multidrug-resistant organisms is an increasing challenge. To combat this threat, diagnostic imaging tools could be used to verify the causative organism and curb inappropriate use of antimicrobial drugs. Nuclear imaging offers the sensitivity needed to detect small numbers of bacteria in situ. Among nuclear imaging tools, radiolabeled antibiotics traditionally have lacked the sensitivity or specificity necessary to diagnose bacterial infections accurately. One reason for the lack of success is that the antibiotics were often chelated to a radiometal. This was done without addressing the ramifications of how the radiolabeling would impact probe entry to the bacterial cell, or the mechanism of binding to an intracellular target. In this review, we approach bacterial infection imaging through the lens of bacterial specific molecular targets, their intracellular or extracellular location, and discuss radiochemistry strategies to guide future probe development.
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Affiliation(s)
- Justin D. Northrup
- Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104, USA; (J.D.N.); (R.H.M.)
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Robert H. Mach
- Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104, USA; (J.D.N.); (R.H.M.)
| | - Mark A. Sellmyer
- Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104, USA; (J.D.N.); (R.H.M.)
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
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81
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Nimbalkar P, Khedkar MA, Chavan PV, Bankar SB. Enhanced Biobutanol Production in Folic Acid-Induced Medium by Using Clostridium acetobutylicum NRRL B-527. ACS OMEGA 2019; 4:12978-12982. [PMID: 31460424 PMCID: PMC6690572 DOI: 10.1021/acsomega.9b00583] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 07/18/2019] [Indexed: 05/05/2023]
Abstract
The conventional acetone-butanol-ethanol fermentation process suffers from several key hurdles viz. low solvent titer, insufficient yield and productivity, and solvent intolerance which largely affect butanol commercialization. To counteract these issues, the effect of stimulator, namely, folic acid was investigated in the present study to improve butanol titer. Folic acid is involved in biosynthesis of a diverse range of cellular components, which subsequently alter the amino acid balance. Therefore, different concentrations of folic acid were screened, and 10 mg/L supplementation resulted in a maximum butanol production of 10.78 ± 0.09 g/L with total solvents of 18.91 ± 0.21 g/L. Folic acid addition at different time intervals was also optimized to get additional improvements in final butanol concentration. Overall, folic acid supplementation resulted in two-fold increase in butanol concentration and thus could be considered as a promising strategy to enhance solvent titers.
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Affiliation(s)
- Pranhita
R. Nimbalkar
- Department
of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O.
Box 16100, Aalto FI-00076, Finland
- Department
of Chemical Engineering, Bharati Vidyapeeth
Deemed University College of Engineering, Pune 411043, India
| | - Manisha A. Khedkar
- Department
of Chemical Engineering, Bharati Vidyapeeth
Deemed University College of Engineering, Pune 411043, India
| | - Prakash V. Chavan
- Department
of Chemical Engineering, Bharati Vidyapeeth
Deemed University College of Engineering, Pune 411043, India
- E-mail: . Phone: +91-020-24107390. Fax: +91-020-24372998 (P.V.C.)
| | - Sandip B. Bankar
- Department
of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O.
Box 16100, Aalto FI-00076, Finland
- E-mail: , . Phone: +358 505777898. Fax: +358 9462373 (S.B.B.)
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82
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Ribeiro JA, Chavez-Pacheco SM, de Oliveira GS, Silva CDS, Giudice JHP, Libreros-Zúñiga GA, Dias MVB. Crystal structures of the closed form of Mycobacterium tuberculosis dihydrofolate reductase in complex with dihydrofolate and antifolates. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2019; 75:682-693. [PMID: 31282477 DOI: 10.1107/s205979831900901x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Accepted: 06/24/2019] [Indexed: 12/19/2022]
Abstract
Tuberculosis is a disease caused by Mycobacterium tuberculosis and is the leading cause of death from a single infectious pathogen, with a high prevalence in developing countries in Africa and Asia. There still is a need for the development or repurposing of novel therapies to combat this disease owing to the long-term nature of current therapies and because of the number of reported resistant strains. Here, structures of dihydrofolate reductase from M. tuberculosis (MtDHFR), which is a key target of the folate pathway, are reported in complex with four antifolates, pyrimethamine, cycloguanil, diaverdine and pemetrexed, and its substrate dihydrofolate in order to understand their binding modes. The structures of all of these complexes were obtained in the closed-conformation state of the enzyme and a fine structural analysis indicated motion in key regions of the substrate-binding site and different binding modes of the ligands. In addition, the affinities, through Kd measurement, of diaverdine and methotrexate have been determined; MtDHFR has a lower affinity (highest Kd) for diaverdine than pyrimethamine and trimethoprim, and a very high affinity for methotrexate, as expected. The structural comparisons and analysis described in this work provide new information about the plasticity of MtDHFR and the binding effects of different antifolates.
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Affiliation(s)
- João Augusto Ribeiro
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Avenida Professor Lineu Prestes 1374, São Paulo 05508-000, Brazil
| | - Sair Maximo Chavez-Pacheco
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Avenida Professor Lineu Prestes 1374, São Paulo 05508-000, Brazil
| | - Gabriel Stephani de Oliveira
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Avenida Professor Lineu Prestes 1374, São Paulo 05508-000, Brazil
| | - Catharina Dos Santos Silva
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Avenida Professor Lineu Prestes 1374, São Paulo 05508-000, Brazil
| | - João Henrique Pimenta Giudice
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Avenida Professor Lineu Prestes 1374, São Paulo 05508-000, Brazil
| | - Gerardo Andres Libreros-Zúñiga
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Avenida Professor Lineu Prestes 1374, São Paulo 05508-000, Brazil
| | - Marcio Vinicius Bertacine Dias
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Avenida Professor Lineu Prestes 1374, São Paulo 05508-000, Brazil
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83
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Li Z, Xu M, Wei H, Wang L, Deng M. RNA‑seq analyses of antibiotic resistance mechanisms in Serratia marcescens. Mol Med Rep 2019; 20:745-754. [PMID: 31180518 PMCID: PMC6580034 DOI: 10.3892/mmr.2019.10281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 02/28/2019] [Indexed: 01/14/2023] Open
Abstract
The present study aimed to further clarify the genetic mechanisms responsible for the antimicrobial resistance of Serratia marcescens (S. marcescens) using RNA sequencing. Three drug-susceptible S. marcescens strains (named MYQT1, MYQT2, and MYQT3) and three multidrug-resistant S. marcescens strains (named MYQT4, MYQT5, and MYQT6) were isolated from six different patients and subjected to RNA sequencing. Differentially expressed genes (DEGs) between the multidrug-resistant S. marcescens strains and drug-susceptible strains were screened and compared, followed by functional enrichment analysis. In addition, a protein-protein interaction (PPI) network was constructed, and significant modules were extracted from it. Genes enriched in the significant modules were subjected to further enrichment analysis. MYQT3 had very a different expression pattern from MYQT1 and MYQT2, and thus, MYQT3 was excluded from the following analysis. A total of 225 DEGs were identified, of which SMDB11_RS09300 (GTP cyclohydrolase FolE2) was the most significantly upregulated with a log2 FC of 6.4; these DEGs were enriched in different GO terms, including hydrogen sulfide biosynthetic process, sulfur compound transmembrane transporter activity, and ABC transporter complex. Additionally, several genes were identified to be important genes in the PPI network, including SMDB11_RS17755 (upregulated; glutamate synthase large subunit), SMDB11_RS00590 (upregulated; sulfite reductase subunit α), and SMDB11_RS04505 (upregulated; cystathionine β-synthase). Thus, SMDB11_RS09300, SMDB11_RS17755, SMDB11_RS00590, and SMDB11_RS04505 may play significant roles in the antimicrobial resistance of S. marcescens by participating in folate metabolism or the integrity of cell membranes. However, further experiments are required to clarify these findings.
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Affiliation(s)
- Zhaodong Li
- Clinical Laboratory, Hangzhou Red Cross Hospital, Hangzhou, Zhejiang 310004, P.R. China
| | - Meihua Xu
- Clinical Laboratory, Hangzhou Red Cross Hospital, Hangzhou, Zhejiang 310004, P.R. China
| | - Hui Wei
- Clinical Laboratory, Hangzhou Red Cross Hospital, Hangzhou, Zhejiang 310004, P.R. China
| | - Lili Wang
- Clinical Laboratory, Hangzhou Red Cross Hospital, Hangzhou, Zhejiang 310004, P.R. China
| | - Min Deng
- Emergency Department, Hangzhou Red Cross Hospital, Hangzhou, Zhejiang 310004, P.R. China
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84
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Moradali MF, Ghods S, Angelini TE, Davey ME. Amino acids as wetting agents: surface translocation by Porphyromonas gingivalis. THE ISME JOURNAL 2019; 13:1560-1574. [PMID: 30783212 PMCID: PMC6775972 DOI: 10.1038/s41396-019-0360-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 01/11/2019] [Accepted: 01/17/2019] [Indexed: 02/06/2023]
Abstract
Our understanding of how oral microbiota adapt in response to changes in their surroundings remains limited. This is particularly true of the slow-growing anaerobes that persist below the gum line. Here, we report that the oral anaerobe Porphyromonas gingivalis strain 381 can surface translocate when sandwiched between two surfaces. We show that during movement, this bacterium alters its metabolism, specifically side products of arginine utilization including citrulline and ornithine accumulated in the translocating cells; while arginine, N-acetyl-arginine, and the polyamine putrescine, which is produced from arginine were consumed. In addition, our results indicate that movement requires modification of the surrounding environment via proteolysis, cell dispersion, cell-on-cell rolling, and sub-diffusive cell-driven motility. We also show that production of fimbriae and fimbriae-associated proteins; as well as the regulation of contact-dependent growth inhibition genes, which are known to be involved in self-nonself discrimination, and the type IX secretion system are central to surface translocation. These studies provide a first glimpse into P. gingivalis motility and its relationship to ecological variables.
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Affiliation(s)
- M Fata Moradali
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, 32610, USA
| | - Shirin Ghods
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, 32610, USA
| | - Thomas E Angelini
- Department of Mechanical & Aerospace Engineering, University of Florida, Gainesville, FL, 32610, USA
| | - Mary Ellen Davey
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, 32610, USA.
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85
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Kravanja G, Primožič M, Knez Ž, Leitgeb M. Chitosan-based (Nano)materials for Novel Biomedical Applications. Molecules 2019; 24:E1960. [PMID: 31117310 PMCID: PMC6572373 DOI: 10.3390/molecules24101960] [Citation(s) in RCA: 144] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 05/15/2019] [Accepted: 05/18/2019] [Indexed: 02/03/2023] Open
Abstract
Chitosan-based nanomaterials have attracted significant attention in the biomedical field because of their unique biodegradable, biocompatible, non-toxic, and antimicrobial nature. Multiple perspectives of the proposed antibacterial effect and mode of action of chitosan-based nanomaterials are reviewed. Chitosan is presented as an ideal biomaterial for antimicrobial wound dressings that can either be fabricated alone in its native form or upgraded and incorporated with antibiotics, metallic antimicrobial particles, natural compounds and extracts in order to increase the antimicrobial effect. Since chitosan and its derivatives can enhance drug permeability across the blood-brain barrier, they can be also used as effective brain drug delivery carriers. Some of the recent chitosan formulations for brain uptake of various drugs are presented. The use of chitosan and its derivatives in other biomedical applications is also briefly discussed.
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Affiliation(s)
- Gregor Kravanja
- University of Maribor; Faculty of Chemistry and Chemical Engineering; Laboratory for Separation Processes and Product Design; Smetanova ul. 17, 2000 Maribor, Slovenia.
| | - Mateja Primožič
- University of Maribor; Faculty of Chemistry and Chemical Engineering; Laboratory for Separation Processes and Product Design; Smetanova ul. 17, 2000 Maribor, Slovenia.
| | - Željko Knez
- University of Maribor; Faculty of Chemistry and Chemical Engineering; Laboratory for Separation Processes and Product Design; Smetanova ul. 17, 2000 Maribor, Slovenia.
- University of Maribor, Faculty of Medicine, Taborska ulica 8, 2000 Maribor, Slovenia.
| | - Maja Leitgeb
- University of Maribor; Faculty of Chemistry and Chemical Engineering; Laboratory for Separation Processes and Product Design; Smetanova ul. 17, 2000 Maribor, Slovenia.
- University of Maribor, Faculty of Medicine, Taborska ulica 8, 2000 Maribor, Slovenia.
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86
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Bueno R, Dawson A, Hunter WN. An assessment of three human methylenetetrahydrofolate dehydrogenase/cyclohydrolase-ligand complexes following further refinement. Acta Crystallogr F Struct Biol Commun 2019; 75:148-152. [PMID: 30839287 PMCID: PMC6404858 DOI: 10.1107/s2053230x18018083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 12/20/2018] [Indexed: 11/10/2022] Open
Abstract
The enzymes involved in folate metabolism are key drug targets for cell-growth modulation, and accurate crystallographic structures provide templates to be exploited for structure-based ligand design. In this context, three ternary complex structures of human methylenetetrahydrofolate dehydrogenase/cyclohydrolase have been published [Schmidt et al. (2000), Biochemistry, 39, 6325-6335] and potentially represent starting points for the development of new antifolate inhibitors. However, an inspection of the models and the deposited data revealed deficiencies and raised questions about the validity of the structures. A number of inconsistencies relating to the publication were also identified. Additional refinement was carried out with the deposited data, seeking to improve the models and to then validate the complex structures or correct the record. In one case, the inclusion of the inhibitor in the structure was supported and alterations to the model allowed details of enzyme-ligand interactions to be described that had not previously been discussed. For one weak inhibitor, the data suggested that the ligand may adopt two poses in the binding site, both with few interactions with the enzyme. In the third case, that of a potent inhibitor, inconsistencies were noted in the assignment of the chemical structure and there was no evidence to support the inclusion of the ligand in the active site.
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Affiliation(s)
- Renata Bueno
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
| | - Alice Dawson
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
| | - William N. Hunter
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
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Bousis S, Setyawati I, Diamanti E, Slotboom DJ, Hirsch AKH. Energy-Coupling Factor Transporters as Novel Antimicrobial Targets. ADVANCED THERAPEUTICS 2019. [DOI: 10.1002/adtp.201800066] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Spyridon Bousis
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI); Department of Drug Design and Optimization; Campus Building E8.1 66123 Saarbrücken Germany
- Stratingh Institute for Chemistry; University of Groningen; Nijenborgh 7 9747AG Groningen The Netherlands
- Department of Pharmacy; Saarland University; Saarbrücken, Campus Building E8.1 66123 Saarbrücken Germany
| | - Inda Setyawati
- Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; Nijenborgh 4 9747AG Groningen The Netherlands
- Department of Biochemistry; Bogor Agricultural University; Dramaga 16680 Bogor Indonesia
| | - Eleonora Diamanti
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI); Department of Drug Design and Optimization; Campus Building E8.1 66123 Saarbrücken Germany
- Stratingh Institute for Chemistry; University of Groningen; Nijenborgh 7 9747AG Groningen The Netherlands
| | - Dirk J. Slotboom
- Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; Nijenborgh 4 9747AG Groningen The Netherlands
- Department of Biochemistry; Bogor Agricultural University; Dramaga 16680 Bogor Indonesia
| | - Anna K. H. Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI); Department of Drug Design and Optimization; Campus Building E8.1 66123 Saarbrücken Germany
- Stratingh Institute for Chemistry; University of Groningen; Nijenborgh 7 9747AG Groningen The Netherlands
- Department of Pharmacy; Saarland University; Saarbrücken, Campus Building E8.1 66123 Saarbrücken Germany
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88
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Using a Chemical Genetic Screen to Enhance Our Understanding of the Antimicrobial Properties of Gallium against Escherichia coli. Genes (Basel) 2019; 10:genes10010034. [PMID: 30634525 PMCID: PMC6356860 DOI: 10.3390/genes10010034] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 12/17/2018] [Accepted: 01/04/2019] [Indexed: 12/13/2022] Open
Abstract
The diagnostic and therapeutic agent gallium offers multiple clinical and commercial uses including the treatment of cancer and the localization of tumors, among others. Further, this metal has been proven to be an effective antimicrobial agent against a number of microbes. Despite the latter, the fundamental mechanisms of gallium action have yet to be fully identified and understood. To further the development of this antimicrobial, it is imperative that we understand the mechanisms by which gallium interacts with cells. As a result, we screened the Escherichia coli Keio mutant collection as a means of identifying the genes that are implicated in prolonged gallium toxicity or resistance and mapped their biological processes to their respective cellular system. We discovered that the deletion of genes functioning in response to oxidative stress, DNA or iron–sulfur cluster repair, and nucleotide biosynthesis were sensitive to gallium, while Ga resistance comprised of genes involved in iron/siderophore import, amino acid biosynthesis and cell envelope maintenance. Altogether, our explanations of these findings offer further insight into the mechanisms of gallium toxicity and resistance in E. coli.
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89
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Zuo F, Yu R, Xiao M, Khaskheli GB, Sun X, Ma H, Ren F, Zhang B, Chen S. Transcriptomic analysis of Bifidobacterium longum subsp. longum BBMN68 in response to oxidative shock. Sci Rep 2018; 8:17085. [PMID: 30459453 PMCID: PMC6244367 DOI: 10.1038/s41598-018-35286-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 10/18/2018] [Indexed: 02/08/2023] Open
Abstract
Bifidobacterium longum strain BBMN68 is sensitive to low concentrations of oxygen. A transcriptomic study was performed to identify candidate genes for B. longum BBMN68's response to oxygen treatment (3%, v/v). Expression of genes and pathways of B. longum BBMN68 involved in nucleotide metabolism, amino acid transport, protein turnover and chaperones increased, and that of carbohydrate metabolism, translation and biogenesis decreased to adapt to the oxidative stress. Notably, expression of two classes of ribonucleotide reductase (RNR), which are important for deoxyribonucleotide biosynthesis, was rapidly and persistently induced. First, the class Ib RNR NrdHIEF was immediately upregulated after 5 min oxygen exposure, followed by the class III RNR NrdDG, which was upregulated after 20 min of exposure. The upregulated expression of branched-chain amino acids and tetrahydrofolate biosynthesis-related genes occurred in bifidobacteria in response to oxidative stress. These change toward to compensate for DNA and protein damaged by reactive oxygen species (ROS). In addition, oxidative stress resulted in improved B. longum BBMN68 cell hydrophobicity and autoaggregation. These results provide a rich resource for our understanding of the response mechanisms to oxidative stress in bifidobacteria.
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Affiliation(s)
- Fanglei Zuo
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China.,Key Laboratory of Functional Dairy, Department of Food Science and Engineering, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China.,Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-10691, Stockholm, Sweden
| | - Rui Yu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China.,Key Laboratory of Functional Dairy, Department of Food Science and Engineering, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
| | - Man Xiao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China.,Key Laboratory of Functional Dairy, Department of Food Science and Engineering, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
| | - Gul Bahar Khaskheli
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China.,Key Laboratory of Functional Dairy, Department of Food Science and Engineering, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
| | - Xiaofei Sun
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
| | - Huiqin Ma
- Department of Fruit Tree Sciences, College of Horticulture, China Agricultural University, Beijing, 100193, P. R. China
| | - Fazheng Ren
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
| | - Bing Zhang
- Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, P. R. China
| | - Shangwu Chen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China. .,Key Laboratory of Functional Dairy, Department of Food Science and Engineering, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China.
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90
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Das BK, Pv P, Chakraborty D. Computational insights into factor affecting the potency of diaryl sulfone analogs as Escherichia coli dihydropteroate synthase inhibitors. Comput Biol Chem 2018; 78:37-52. [PMID: 30497019 DOI: 10.1016/j.compbiolchem.2018.11.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 10/08/2018] [Accepted: 11/13/2018] [Indexed: 12/16/2022]
Abstract
Dihydropteroate synthase (DHPS) is an alluring target for designing novel drug candidates to prevent infections caused by pathogenic Escherichia coli strains. Diaryl Sulfone (SO) compounds are found to inhibit DHPS competitively with respect to the substrate pABA (p-aminobenzoate). The extra aromatic ring of diaryl sulfone compounds found to stabilize them in highly flexible pABA binding loops. In this present study, a statistically significant 3D-QSAR model was developed using a data set of diaryl sulfone compounds. The favourable and unfavourable contributions of substitutions in sulfone compounds were illustrated by contour plot obtained from the developed 3D-QSAR model. Molecular docking calculations were performed to investigate the putative binding mode of diaryl sulfone compounds at the catalytic pocket. DFT calculations were carried out using SCF approach, B3LYP- 6-31 G (d) basis set to compute the HOMO, LUMO energies and their respective location at pABA binding pocket. Further, the developed model was validated by FEP (Free Energy Perturbation) calculations. The calculated relative free energy of binding between the highly potent and less potent sulfone compound was found to be -3.78 kcal/ mol which is comparable to the experimental value of -5.85 kcal/mol. A 10 ns molecular dynamics simulation of inhibitor and DHPS confirmed its stability at pABA catalytic site. Outcomes of the present work provide deeper insight in designing novel drug candidates for pathogenic Escherichia coli strains.
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Affiliation(s)
- Bratin Kumar Das
- Department of Chemistry, National Institute of Technology Karnataka, Surathkal, Mangalore, 575025, India
| | - Pushyaraga Pv
- Department of Chemistry, National Institute of Technology Karnataka, Surathkal, Mangalore, 575025, India
| | - Debashree Chakraborty
- Department of Chemistry, National Institute of Technology Karnataka, Surathkal, Mangalore, 575025, India.
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91
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Metabolic models and gene essentiality data reveal essential and conserved metabolism in prokaryotes. PLoS Comput Biol 2018; 14:e1006556. [PMID: 30444863 PMCID: PMC6283598 DOI: 10.1371/journal.pcbi.1006556] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 12/06/2018] [Accepted: 10/09/2018] [Indexed: 01/13/2023] Open
Abstract
Essential metabolic reactions are shaping constituents of metabolic networks, enabling viable and distinct phenotypes across diverse life forms. Here we analyse and compare modelling predictions of essential metabolic functions with experimental data and thereby identify core metabolic pathways in prokaryotes. Simulations of 15 manually curated genome-scale metabolic models were integrated with 36 large-scale gene essentiality datasets encompassing a wide variety of species of bacteria and archaea. Conservation of metabolic genes was estimated by analysing 79 representative genomes from all the branches of the prokaryotic tree of life. We find that essentiality patterns reflect phylogenetic relations both for modelling and experimental data, which correlate highly at the pathway level. Genes that are essential for several species tend to be highly conserved as opposed to non-essential genes which may be conserved or not. The tRNA-charging module is highlighted as ancestral and with high centrality in the networks, followed closely by cofactor metabolism, pointing to an early information processing system supplied by organic cofactors. The results, which point to model improvements and also indicate faults in the experimental data, should be relevant to the study of centrality in metabolic networks and ancient metabolism but also to metabolic engineering with prokaryotes. If we tried to list every known chemical reaction within an organism–human, plant or even bacteria–we would get quite a long and confusing read. But when this information is represented in so-called genome-scale metabolic networks, we have the means to access computationally each of those reactions and their interconnections. Some parts of the network have alternatives, while others are unique and therefore can be essential for growth. Here, we simulate growth and compare essential reactions and genes for the simplest type of unicellular species–prokaryotes–to understand which parts of their metabolism are universally essential and potentially ancestral. We show that similar patterns of essential reactions echo phylogenetic relationships (this makes sense, as the genome provides the building plan for the enzymes that perform those reactions). Our computational predictions correlate strongly with experimental essentiality data. Finally, we show that a crucial step of protein synthesis (tRNA charging) and the synthesis and transformation of small molecules that enzymes require (cofactors) are the most essential and conserved parts of metabolism in prokaryotes. Our results are a step further in understanding the biology and evolution of prokaryotes but can also be relevant in applied studies including metabolic engineering and antibiotic design.
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92
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Coenzyme F 420-Dependent Glucose-6-Phosphate Dehydrogenase-Coupled Polyglutamylation of Coenzyme F 420 in Mycobacteria. J Bacteriol 2018; 200:JB.00375-18. [PMID: 30249701 DOI: 10.1128/jb.00375-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 09/07/2018] [Indexed: 12/15/2022] Open
Abstract
Coenzyme F420 plays a key role in the redox metabolisms of various archaea and bacteria, including Mycobacterium tuberculosis In M. tuberculosis, F420-dependent reactions have been linked to several virulence factors. F420 carries multiple glutamate residues in the side chain, forming F420-n species (n, number of glutamate residues), and the length of this side chain impacts cellular physiology. M. tuberculosis strains with F420 species carrying shorter side chains exhibit resistance to delamanid and pretomanid, two new tuberculosis (TB) drugs. Thus, the process of polyglutamylation of F420 is of great interest. It has been known from genetic analysis that in mycobacteria an F420-0 γ-glutamyl ligase (FbiB) introduces up to seven glutamate residues into F420 However, purified FbiB of M. tuberculosis (MtbFbiB) is either inefficient or incapable of incorporating more than two glutamates. We found that, in vitro, MtbFbiB synthesized side chains containing up to seven glutamate residues if F420 was presented to the enzyme in a two-electron reduced state (F420H2). Our genetic analysis in Mycobacterium bovis BCG and Mycobacterium smegmatis and an analysis of literature data on M. tuberculosis revealed that in these mycobacteria the polyglutamylation process requires the assistance of F420-dependent glucose-6-phosphate dehydrogenase (Fgd) which reduces F420 to F420H2 We hypothesize that, starting with F420-0H2, the amino-terminal domain of FbiB builds F420-2H2, which is then transferred to the carboxy-terminal domain for further glutamylation; F420-2H2 modifies the carboxy-terminal domain structurally to accommodate longer glutamyl chains. This system is analogous to folylpolyglutamate synthase, which introduces more than one glutamate residue into folate only after this vitamin is reduced to tetrahydrofolate.IMPORTANCE Coenzyme F420-dependent reactions of Mycobacterium tuberculosis, which causes tuberculosis, potentially contributes to the virulence of this bacterium. The coenzyme carries a glutamic acid-derived tail, the length of which influences the metabolism of M. tuberculosis Mutations that eliminate the production of F420 with longer tails make M. tuberculosis resistant to two new tuberculosis drugs. This report describes that the synthesis of longer glutamyl tails of F420 requires concerted actions of two enzymes, one of which reduces the coenzyme prior to the action of the other, which catalyzes polyglutamylation. This knowledge will help to develop more effective tuberculosis (TB) drugs. Remarkably, the introduction of multiple glutamate residues into the sidechain of folate (vitamin B9) requires similar concerted actions, where one enzyme reduces the vitamin to tetrahydrofolate and the other catalyzes polyglutamylation; folate is required for DNA and amino acid synthesis. Thus, the reported research has also revealed a key similarity between two important cellular systems.
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93
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Chen X, Liu Y, Lin A, Huang N, Long L, Gang Y, Liu J. Folic acid-modified mesoporous silica nanoparticles with pH-responsiveness loaded with Amp for an enhanced effect against anti-drug-resistant bacteria by overcoming efflux pump systems. Biomater Sci 2018; 6:1923-1935. [PMID: 29850668 DOI: 10.1039/c8bm00262b] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Efflux pump system-mediated bacterial multidrug resistance is one of the main causes of antibiotic failure. Therefore, it is necessary to develop a novel nanocarrier that could effectively inhibit drug-resistant bacteria by increasing the intake and retention time of antibiotics. Herein, we constructed a pH-responsive nanocarrier (MSN@FA@CaP@FA) with double folic acid (FA) and calcium phosphate (CaP) covered on the surface of mesoporous silica (MSN) by electrostatic attraction and biomineralization, respectively. Afterward, loading the nanocomposites with ampicillin (Amp) effectively increased the uptake and reduced the efflux effect in Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) by the specific targeting of FA. Moreover, Amp-MSN@FA@CaP@FA could specifically transport Amp to the bacterial infection site. Similarly, antibacterial experiments revealed that the Amp-MSN@FA@CaP@FA could significantly enhance the activity of Amp for inhibiting drug-resistant bacteria, without producing drug resistance. Additionally, the Amp-MSN@FA@CaP@FA could reduce the content of protein and inhibit the protein activity in drug-resistant bacteria, so that it destroyed the bacterial membrane and led to the bacteria death. In vivo antibacterial experiments showed that the Amp-MSN@FA@CaP@FA could effectively reduce the mortality of drug-resistant E. coli infection and promote wound healing of drug-resistant S. aureus infection. In summary, Amp-MSN@FA@CaP@FA has a potential for application in sustained-release nanostructures and to inhibit drug-resistant bacteria.
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Affiliation(s)
- Xu Chen
- Department of Chemistry, Jinan University, Guangzhou 510632, China
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94
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Drug targets exploited in Mycobacterium tuberculosis: Pitfalls and promises on the horizon. Biomed Pharmacother 2018; 103:1733-1747. [PMID: 29864964 DOI: 10.1016/j.biopha.2018.04.176] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 04/24/2018] [Accepted: 04/24/2018] [Indexed: 01/10/2023] Open
Abstract
Tuberculosis is an ever evolving infectious disease that still claims about 1.8 million human lives each year around the globe. Although modern chemotherapy has played a pivotal role in combating TB, the increasing emergence of drug-resistant TB aligned with HIV pandemic threaten its control. This highlights both the need to understand how our current drugs work and the need to develop new and more effective drugs. TB drug discovery is revisiting the clinically validated drug targets in Mycobacterium tuberculosis using whole-cell phenotypic assays in search of better therapeutic scaffolds. Herein, we review the promises of current TB drug regimens, major pitfalls faced, key drug targets exploited so far in M. tuberculosis along with the status of newly discovered drugs against drug resistant forms of TB. New antituberculosis regimens that use lesser number of drugs, require shorter duration of treatment, are equally effective against susceptible and resistant forms of disease, have acceptable toxicity profiles and behave friendly with anti-HIV regimens remains top most priority in TB drug discovery.
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95
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Griffith EC, Wallace MJ, Wu Y, Kumar G, Gajewski S, Jackson P, Phelps GA, Zheng Z, Rock CO, Lee RE, White SW. The Structural and Functional Basis for Recurring Sulfa Drug Resistance Mutations in Staphylococcus aureus Dihydropteroate Synthase. Front Microbiol 2018; 9:1369. [PMID: 30065703 PMCID: PMC6057106 DOI: 10.3389/fmicb.2018.01369] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 06/06/2018] [Indexed: 11/13/2022] Open
Abstract
Staphylococcal species are a leading cause of bacterial drug-resistant infections and associated mortality. One strategy to combat bacterial drug resistance is to revisit compromised targets, and to circumvent resistance mechanisms using structure-assisted drug discovery. The folate pathway is an ideal candidate for this approach. Antifolates target an essential metabolic pathway, and the necessary detailed structural information is now available for most enzymes in this pathway. Dihydropteroate synthase (DHPS) is the target of the sulfonamide class of drugs, and its well characterized mechanism facilitates detailed analyses of how drug resistance has evolved. Here, we surveyed clinical genetic sequencing data in S. aureus to distinguish natural amino acid variations in DHPS from those that are associated with sulfonamide resistance. Five mutations were identified, F17L, S18L, T51M, E208K, and KE257_dup. Their contribution to resistance and their cost to the catalytic properties of DHPS were evaluated using a combination of biochemical, biophysical and microbiological susceptibility studies. These studies show that F17L, S18L, and T51M directly lead to sulfonamide resistance while unexpectedly increasing susceptibility to trimethoprim, which targets the downstream enzyme dihydrofolate reductase. The secondary mutations E208K and KE257_dup restore trimethoprim susceptibility closer to wild-type levels while further increasing sulfonamide resistance. Structural studies reveal that these mutations appear to selectively disfavor the binding of the sulfonamides by sterically blocking an outer ring moiety that is not present in the substrate. This emphasizes that new inhibitors must be designed that strictly stay within the substrate volume in the context of the transition state.
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Affiliation(s)
- Elizabeth C. Griffith
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Miranda J. Wallace
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, United States
- Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Yinan Wu
- Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Gyanendra Kumar
- Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Stefan Gajewski
- Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Pamela Jackson
- Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Gregory A. Phelps
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, United States
- Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Zhong Zheng
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Charles O. Rock
- Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Richard E. Lee
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Stephen W. White
- Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, United States
- Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, United States
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96
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Review on Abyssomicins: Inhibitors of the Chorismate Pathway and Folate Biosynthesis. Molecules 2018; 23:molecules23061371. [PMID: 29882815 PMCID: PMC6100094 DOI: 10.3390/molecules23061371] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 05/30/2018] [Accepted: 06/04/2018] [Indexed: 11/16/2022] Open
Abstract
Antifolates targeting folate biosynthesis within the shikimate-chorismate-folate metabolic pathway are ideal and selective antimicrobials, since higher eukaryotes lack this pathway and rely on an exogenous source of folate. Resistance to the available antifolates, inhibiting the folate pathway, underlines the need for novel antibiotic scaffolds and molecular targets. While para-aminobenzoic acid synthesis within the chorismate pathway constitutes a novel molecular target for antifolates, abyssomicins are its first known natural inhibitors. This review describes the abyssomicin family, a novel spirotetronate polyketide Class I antimicrobial. It summarizes synthetic and biological studies, structural, biosynthetic, and biological properties of the abyssomicin family members. This paper aims to explain their molecular target, mechanism of action, structure⁻activity relationship, and to explore their biological and pharmacological potential. Thirty-two natural abyssomicins and numerous synthetic analogues have been reported. The biological activity of abyssomicins includes their antimicrobial activity against Gram-positive bacteria and mycobacteria, antitumor properties, latent human immunodeficiency virus (HIV) reactivator, anti-HIV and HIV replication inducer properties. Their antimalarial properties have not been explored yet. Future analoging programs using the structure⁻activity relationship data and synthetic approaches may provide a novel abyssomicin structure that is active and devoid of cytotoxicity. Abyssomicin J and atrop-o-benzyl-desmethylabyssomicin C constitute promising candidates for such programs.
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97
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da Silva RN, Cunha Â, Tomé AC. Phthalocyanine–sulfonamide conjugates: Synthesis and photodynamic inactivation of Gram-negative and Gram-positive bacteria. Eur J Med Chem 2018; 154:60-67. [DOI: 10.1016/j.ejmech.2018.05.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 04/11/2018] [Accepted: 05/07/2018] [Indexed: 12/17/2022]
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98
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Simões D, Miguel SP, Ribeiro MP, Coutinho P, Mendonça AG, Correia IJ. Recent advances on antimicrobial wound dressing: A review. Eur J Pharm Biopharm 2018; 127:130-141. [DOI: 10.1016/j.ejpb.2018.02.022] [Citation(s) in RCA: 502] [Impact Index Per Article: 83.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 02/07/2018] [Accepted: 02/16/2018] [Indexed: 12/15/2022]
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99
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Passi A, Rajput NK, Wild DJ, Bhardwaj A. RepTB: a gene ontology based drug repurposing approach for tuberculosis. J Cheminform 2018; 10:24. [PMID: 29785561 PMCID: PMC5962481 DOI: 10.1186/s13321-018-0276-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 04/23/2018] [Indexed: 11/12/2022] Open
Abstract
Tuberculosis (TB) is the world’s leading infectious killer with 1.8 million deaths in 2015 as reported by WHO. It is therefore imperative that alternate routes of identification of novel anti-TB compounds are explored given the time and costs involved in new drug discovery process. Towards this, we have developed RepTB. This is a unique drug repurposing approach for TB that uses molecular function correlations among known drug-target pairs to predict novel drug-target interactions. In this study, we have created a Gene Ontology based network containing 26,404 edges, 6630 drug and 4083 target nodes. The network, enriched with molecular function ontology, was analyzed using Network Based Inference (NBI). The association scores computed from NBI are used to identify novel drug-target interactions. These interactions are further evaluated based on a combined evidence approach for identification of potential drug repurposing candidates. In this approach, targets which have no known variation in clinical isolates, no human homologs, and are essential for Mtb’s survival and or virulence are prioritized. We analyzed predicted DTIs to identify target pairs whose predicted drugs may have synergistic bactericidal effect. From the list of predicted DTIs from RepTB, four TB targets, namely, FolP1 (Dihydropteroate synthase), Tmk (Thymidylate kinase), Dut (Deoxyuridine 5′-triphosphate nucleotidohydrolase) and MenB (1,4-dihydroxy-2-naphthoyl-CoA synthase) may be selected for further validation. In addition, we observed that in some cases there is significant chemical structure similarity between predicted and reported drugs of prioritized targets, lending credence to our approach. We also report new chemical space for prioritized targets that may be tested further. We believe that with increasing drug-target interaction dataset RepTB will be able to offer better predictive value and is amenable for identification of drug-repurposing candidates for other disease indications too.
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Affiliation(s)
- Anurag Passi
- Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, 160036, India.,Academy of Scientific and Innovative Research, Council of Scientific and Industrial Research, Training and Development Complex, CSIR Campus, CSIR Road, Taramani, Chennai, Tamil Nadu, 600113, India
| | - Neeraj Kumar Rajput
- Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, 160036, India
| | - David J Wild
- School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, 47405, USA.
| | - Anshu Bhardwaj
- Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, 160036, India. .,Academy of Scientific and Innovative Research, Council of Scientific and Industrial Research, Training and Development Complex, CSIR Campus, CSIR Road, Taramani, Chennai, Tamil Nadu, 600113, India.
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100
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Thongkongkaew T, Ding W, Bratovanov E, Oueis E, Garcı́a-Altares M, Zaburannyi N, Harmrolfs K, Zhang Y, Scherlach K, Müller R, Hertweck C. Two Types of Threonine-Tagged Lipopeptides Synergize in Host Colonization by Pathogenic Burkholderia Species. ACS Chem Biol 2018; 13:1370-1379. [PMID: 29669203 DOI: 10.1021/acschembio.8b00221] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Bacterial infections of agriculturally important mushrooms and plants pose a major threat to human food sources worldwide. However, structures of chemical mediators required by the pathogen for host colonization and infection remain elusive in most cases. Here, we report two types of threonine-tagged lipopeptides conserved among mushroom and rice pathogenic Burkholderia species that facilitate bacterial infection of hosts. Genome mining, metabolic profiling of infected mushrooms, and heterologous expression of orphan gene clusters allowed the discovery of these unprecedented metabolites in the mushroom pathogen Burkholderia gladioli (haereogladin, burriogladin) and the plant pathogen Burkholderia glumae (haereoglumin and burrioglumin). Through targeted gene deletions, the molecular basis of lipopeptide biosynthesis by nonribosomal peptide synthetases was revealed. Surprisingly, both types of lipopeptides feature unusual threonine tags, which yield longer peptide backbones than one would expect based on the canonical colinearity of the NRPS assembly lines. Both peptides play an indirect role in host infection as biosurfactants that enable host colonization by mediating swarming and biofilm formation abilities. Moreover, MALDI imaging mass spectrometry was applied to investigate the biological role of the lipopeptides. Our results shed light on conserved mechanisms that mushroom and plant pathogenic bacteria utilize for host infection and expand current knowledge on bacterial virulence factors that may represent a new starting point for the targeted development of crop protection measures in the future.
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Affiliation(s)
- Tawatchai Thongkongkaew
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Wei Ding
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Evgeni Bratovanov
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Emilia Oueis
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Marı́a Garcı́a-Altares
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Nestor Zaburannyi
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Kirsten Harmrolfs
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Youming Zhang
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, 250100 Jinan, People’s Republic of China
| | - Kirstin Scherlach
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
- Chair for Natural Product Chemistry, Friedrich Schiller University, 07743 Jena, Germany
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