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Xiong YQ, Li Y, Goncheva MI, Elsayed AM, Zhu F, Li L, Abdelhady W, Flannagan RS, Yeaman MR, Bayer AS, Heinrichs DE. The Purine Biosynthesis Repressor, PurR, Contributes to Vancomycin Susceptibility of Methicillin-resistant Staphylococcus aureus in Experimental Endocarditis. J Infect Dis 2024; 229:1648-1657. [PMID: 38297970 PMCID: PMC11175694 DOI: 10.1093/infdis/jiad577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Indexed: 02/02/2024] Open
Abstract
BACKGROUND Staphylococcus aureus is the most common cause of life-threatening endovascular infections, including infective endocarditis (IE). These infections, especially when caused by methicillin-resistant strains (MRSA), feature limited therapeutic options and high morbidity and mortality rates. METHODS Herein, we investigated the role of the purine biosynthesis repressor, PurR, in virulence factor expression and vancomycin (VAN) treatment outcomes in experimental IE due to MRSA. RESULTS The PurR-mediated repression of purine biosynthesis was confirmed by enhanced purF expression and production of an intermediate purine metabolite in purR mutant strain. In addition, enhanced expression of the transcriptional regulators, sigB and sarA, and their key downstream virulence genes (eg, fnbA, and hla) was demonstrated in the purR mutant in vitro and within infected cardiac vegetations. Furthermore, purR deficiency enhanced fnbA/fnbB transcription, translating to increased fibronectin adhesion versus the wild type and purR-complemented strains. Notably, the purR mutant was refractory to significant reduction in target tissues MRSA burden following VAN treatment in the IE model. CONCLUSIONS These findings suggest that the purine biosynthetic pathway intersects the coordination of virulence factor expression and in vivo persistence during VAN treatment, and may represent an avenue for novel antimicrobial development targeting MRSA.
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Affiliation(s)
- Yan Q Xiong
- The Lundquist Institute for Biomedical Innovation, Harbor-University of California Los Angeles Medical Center, Torrance, California, USA
- Department of Medicine, Division of Infectious Diseases, Harbor-University of California Los Angeles Medical Center, Torrance, California, USA
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Yi Li
- The Lundquist Institute for Biomedical Innovation, Harbor-University of California Los Angeles Medical Center, Torrance, California, USA
| | - Mariya I Goncheva
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
| | - Ahmed M Elsayed
- The Lundquist Institute for Biomedical Innovation, Harbor-University of California Los Angeles Medical Center, Torrance, California, USA
| | - Fengli Zhu
- The Lundquist Institute for Biomedical Innovation, Harbor-University of California Los Angeles Medical Center, Torrance, California, USA
| | - Liang Li
- The Lundquist Institute for Biomedical Innovation, Harbor-University of California Los Angeles Medical Center, Torrance, California, USA
| | - Wessam Abdelhady
- The Lundquist Institute for Biomedical Innovation, Harbor-University of California Los Angeles Medical Center, Torrance, California, USA
| | - Ronald S Flannagan
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
| | - Michael R Yeaman
- The Lundquist Institute for Biomedical Innovation, Harbor-University of California Los Angeles Medical Center, Torrance, California, USA
- Department of Medicine, Division of Infectious Diseases, Harbor-University of California Los Angeles Medical Center, Torrance, California, USA
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
- Department of Medicine, Division of Molecular Medicine, Harbor-University of California Los Angeles Medical Center, Torrance, California, USA
| | - Arnold S Bayer
- The Lundquist Institute for Biomedical Innovation, Harbor-University of California Los Angeles Medical Center, Torrance, California, USA
- Department of Medicine, Division of Infectious Diseases, Harbor-University of California Los Angeles Medical Center, Torrance, California, USA
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - David E Heinrichs
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
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2
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Pugazhendhi AS, Neal CJ, Ta KM, Molinari M, Kumar U, Wei F, Kolanthai E, Ady A, Drake C, Hughes M, Yooseph S, Seal S, Coathup MJ. A neoteric antibacterial ceria-silver nanozyme for abiotic surfaces. Biomaterials 2024; 307:122527. [PMID: 38518591 DOI: 10.1016/j.biomaterials.2024.122527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/01/2024] [Accepted: 03/08/2024] [Indexed: 03/24/2024]
Abstract
Community-associated and hospital-acquired infections caused by bacteria continue to yield major global challenges to human health. Bacterial contamination on abiotic surfaces is largely spread via high-touch surfaces and contemporary standard disinfection practices show limited efficacy, resulting in unsatisfactory therapeutic outcomes. New strategies that offer non-specific and broad protection are urgently needed. Herein, we report our novel ceria-silver nanozyme engineered at a molar ratio of 5:1 and with a higher trivalent (Ce3+) surface fraction. Our results reveal potent levels of surface catalytic activity on both wet and dry surfaces, with rapid, and complete eradication of Pseudomonas aeruginosa, Staphylococcus aureus, and methicillin resistant S. aureus, in both planktonic and biofilm form. Preferential electrostatic adherence of anionic bacteria to the cationic nanozyme surface leads to a catastrophic loss in both aerobic and anaerobic respiration, DNA damage, osmodysregulation, and finally, programmed bacterial lysis. Our data reveal several unique mechanistic avenues of synergistic ceria-Ag efficacy. Ag potentially increases the presence of Ce3+ sites at the ceria-Ag interface, thereby facilitating the formation of harmful H2O2, followed by likely permeation across the cell wall. Further, a weakened Ag-induced Ce-O bond may drive electron transfer from the Ec band to O2, thereby further facilitating the selective reduction of O2 toward H2O2 formation. Ag destabilizes the surface adsorption of molecular H2O2, potentially leading to higher concentrations of free H2O2 adjacent to bacteria. To this end, our results show that H2O2 and/or NO/NO2-/NO3- are the key liberators of antibacterial activity, with a limited immediate role being offered by nanozyme-induced ROS including O2•- and OH•, and likely other light-activated radicals. A mini-pilot proof-of-concept study performed in a pediatric dental clinic setting confirms residual, and continual nanozyme antibacterial efficacy over a 28-day period. These findings open a new approach to alleviate infections caused by bacteria for use on high-touch hard surfaces.
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Affiliation(s)
- Abinaya Sindu Pugazhendhi
- Biionix Cluster, College of Medicine, University of Central Florida, Orlando, FL, 32827, United States
| | - Craig J Neal
- Advanced Materials Processing and Analysis Centre, Nanoscience Technology Center (NSTC), University of Central Florida, Orlando, FL, 32826, United States
| | - Khoa Minh Ta
- Department of Chemical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, HD1 3DH, United Kingdom
| | - Marco Molinari
- Department of Chemical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, HD1 3DH, United Kingdom.
| | - Udit Kumar
- Advanced Materials Processing and Analysis Centre, Nanoscience Technology Center (NSTC), University of Central Florida, Orlando, FL, 32826, United States
| | - Fei Wei
- Biionix Cluster, College of Medicine, University of Central Florida, Orlando, FL, 32827, United States
| | - Elayaraja Kolanthai
- Advanced Materials Processing and Analysis Centre, Nanoscience Technology Center (NSTC), University of Central Florida, Orlando, FL, 32826, United States
| | - Andrew Ady
- Biionix Cluster, College of Medicine, University of Central Florida, Orlando, FL, 32827, United States
| | - Christina Drake
- Kismet Technologies, 7101 TPC Drive, Suite 130, Orlando, FL, 32822, United States
| | - Megan Hughes
- University of Cardiff, Cardiff, CF10 3AT, Wales, United Kingdom
| | - Shibu Yooseph
- Kravis Department of Integrated Sciences, Claremont McKenna College, Claremont, CA 91711, United States
| | - Sudipta Seal
- Biionix Cluster, College of Medicine, University of Central Florida, Orlando, FL, 32827, United States; Advanced Materials Processing and Analysis Centre, Nanoscience Technology Center (NSTC), University of Central Florida, Orlando, FL, 32826, United States
| | - Melanie J Coathup
- Biionix Cluster, College of Medicine, University of Central Florida, Orlando, FL, 32827, United States.
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3
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Prax M, McDonald CP, Bekeredjian-Ding I, Cloutier M, Gravemann U, Grothaus A, Krut O, Mpumlwana X, O'Flaherty N, Satake M, Stafford B, Suessner S, Vollmer T, Ramirez-Arcos S. Characterization of transfusion-relevant bacteria reference strains in a lyophilized format. Vox Sang 2024. [PMID: 38754952 DOI: 10.1111/vox.13654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 04/29/2024] [Accepted: 04/29/2024] [Indexed: 05/18/2024]
Abstract
BACKGROUND AND OBJECTIVES Blood safety measures used by blood establishments to increase blood component safety can be validated using Transfusion-Relevant Bacterial Reference Strains (TRBRS). Ultra-cold storage conditions and manual preparation of the current TRBRS may restrict their practical use. To address this issue, the ISBT Transfusion-Transmitted Infectious Diseases Working Party's Bacterial Subgroup organized an international study to validate TRBRS in a user-friendly, lyophilised format. MATERIALS AND METHODS Two bacterial strains Klebsiella pneumoniae PEI-B-P-08 and Staphylococcus aureus PEI-B-P-63 were manufactured as lyophilised material. The lyophilised bacteria were distributed to 11 different labs worldwide to assess the robustness for enumeration, identification and determination of growth kinetics in platelet concentrates (PCs). RESULTS Production of lyophilised TRBRS had no impact on the growth properties compared with the traditional format. The new format allows a direct low-quantity spiking of approximately 30 bacteria in PCs for transfusion-relevant experiments. In addition, the lyophilised bacteria exhibit long-term stability across a broad temperature range and can even be directly rehydrated in PCs without losing viability. Interlaboratory comparative study demonstrated the robustness of the new format as 100% of spiked PC exhibited growth. CONCLUSION Lyophilised TRBRS provide a user-friendly material for transfusion-related studies. TRBRS in the new format have improved features that may lead to a more frequent use in the quality control of transfusion-related safety measures in the future.
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Affiliation(s)
| | | | | | | | - Ute Gravemann
- German Red Cross Blood Service NSTOB, Springe, Germany
| | | | - Oleg Krut
- Paul-Ehrlich-Institut, Langen, Germany
| | - Xoliswa Mpumlwana
- Constantia Kloof, South African National Blood Service, Johannesburg, South Africa
| | | | | | | | - Susanne Suessner
- Red Cross Transfusion Service of Upper Austria, Austrian Red Cross, Linz, Austria
| | - Tanja Vollmer
- Institut für Laboratoriums- und Transfusionsmedizin, Herz- und Diabeteszentrum NRW, Universitätsklinik der Ruhr-Universität Bochum, Bad Oeynhausen, Germany
| | - Sandra Ramirez-Arcos
- Innovation & Portfolio Management, Canadian Blood Services, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
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4
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Huang SW, Lim SK, Yu YA, Pan YC, Lien WJ, Mou CY, Hu CMJ, Mou KY. Overcoming the nutritional immunity by engineering iron-scavenging bacteria for cancer therapy. eLife 2024; 12:RP90798. [PMID: 38747577 PMCID: PMC11095936 DOI: 10.7554/elife.90798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024] Open
Abstract
Certain bacteria demonstrate the ability to target and colonize the tumor microenvironment, a characteristic that positions them as innovative carriers for delivering various therapeutic agents in cancer therapy. Nevertheless, our understanding of how bacteria adapt their physiological condition to the tumor microenvironment remains elusive. In this work, we employed liquid chromatography-tandem mass spectrometry to examine the proteome of E. coli colonized in murine tumors. Compared to E. coli cultivated in the rich medium, we found that E. coli colonized in tumors notably upregulated the processes related to ferric ions, including the enterobactin biosynthesis and iron homeostasis. This finding indicated that the tumor is an iron-deficient environment to E. coli. We also found that the colonization of E. coli in the tumor led to an increased expression of lipocalin 2 (LCN2), a host protein that can sequester the enterobactin. We therefore engineered E. coli in order to evade the nutritional immunity provided by LCN2. By introducing the IroA cluster, the E. coli synthesizes the glycosylated enterobactin, which creates steric hindrance to avoid the LCN2 sequestration. The IroA-E. coli showed enhanced resistance to LCN2 and significantly improved the anti-tumor activity in mice. Moreover, the mice cured by the IroA-E. coli treatment became resistant to the tumor re-challenge, indicating the establishment of immunological memory. Overall, our study underscores the crucial role of bacteria's ability to acquire ferric ions within the tumor microenvironment for effective cancer therapy.
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Affiliation(s)
- Sin-Wei Huang
- Institute of Biomedical Sciences, Academia SinicaTaipeiTaiwan
| | - See-Khai Lim
- Institute of Biomedical Sciences, Academia SinicaTaipeiTaiwan
| | - Yao-An Yu
- Institute of Biomedical Sciences, Academia SinicaTaipeiTaiwan
- Doctoral Degree Program of Translational Medicine, National Yang Ming Chiao Tung University and Academia SinicaTaipeiTaiwan
| | - Yi-Chung Pan
- Institute of Biomedical Sciences, Academia SinicaTaipeiTaiwan
| | - Wan-Ju Lien
- Institute of Biomedical Sciences, Academia SinicaTaipeiTaiwan
| | - Chung-Yuan Mou
- Department of Chemistry, National Taiwan UniversityTaipeiTaiwan
| | - Che-Ming Jack Hu
- Institute of Biomedical Sciences, Academia SinicaTaipeiTaiwan
- Doctoral Degree Program of Translational Medicine, National Yang Ming Chiao Tung University and Academia SinicaTaipeiTaiwan
| | - Kurt Yun Mou
- Institute of Biomedical Sciences, Academia SinicaTaipeiTaiwan
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5
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Yang L, Wu Z, Ma TY, Zeng H, Chen M, Zhang YA, Zhou Y. Identification of ClpB, a molecular chaperone involved in the stress tolerance and virulence of Streptococcus agalactiae. Vet Res 2024; 55:60. [PMID: 38750480 PMCID: PMC11094935 DOI: 10.1186/s13567-024-01318-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 03/06/2024] [Indexed: 05/19/2024] Open
Abstract
Bacterial ClpB is an ATP-dependent disaggregate that belongs to the Hsp100/Clp family and facilitates bacterial survival under hostile environmental conditions. Streptococcus agalactiae, which is regarded as the major bacterial pathogen of farmed Nile tilapia (Oreochromis niloticus), is known to cause high mortality and large economic losses. Here, we report a ClpB homologue of S. agalactiae and explore its functionality. S. agalactiae with a clpB deletion mutant (∆clpB) exhibited defective tolerance against heat and acidic stress, without affecting growth or morphology under optimal conditions. Moreover, the ΔclpB mutant exhibited reduced intracellular survival in RAW264.7 cells, diminished adherence to the brain cells of tilapia, increased sensitivity to leukocytes from the head kidney of tilapia and whole blood killing, and reduced mortality and bacterial loads in a tilapia infection assay. Furthermore, the reduced virulence of the ∆clpB mutant was investigated by transcriptome analysis, which revealed that deletion of clpB altered the expression levels of multiple genes that contribute to the stress response as well as certain metabolic pathways. Collectively, our findings demonstrated that ClpB, a molecular chaperone, plays critical roles in heat and acid stress resistance and virulence in S. agalactiae. This finding provides an enhanced understanding of the functionality of this ClpB homologue in gram-positive bacteria and the survival strategy of S. agalactiae against immune clearance during infection.
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Affiliation(s)
- Lan Yang
- National Key Laboratory of Agricultural Microbiology; Hubei Hongshan Laboratory; Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education; Shenzhen Institute of Nutrition and Health, College of Fisheries, Huazhong Agricultural University, Wuhan, 430000, China
| | - Zhihao Wu
- National Key Laboratory of Agricultural Microbiology; Hubei Hongshan Laboratory; Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education; Shenzhen Institute of Nutrition and Health, College of Fisheries, Huazhong Agricultural University, Wuhan, 430000, China
| | - Tian-Yu Ma
- National Key Laboratory of Agricultural Microbiology; Hubei Hongshan Laboratory; Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education; Shenzhen Institute of Nutrition and Health, College of Fisheries, Huazhong Agricultural University, Wuhan, 430000, China
| | - Hui Zeng
- National Key Laboratory of Agricultural Microbiology; Hubei Hongshan Laboratory; Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education; Shenzhen Institute of Nutrition and Health, College of Fisheries, Huazhong Agricultural University, Wuhan, 430000, China
| | - Ming Chen
- National Key Laboratory of Agricultural Microbiology; Hubei Hongshan Laboratory; Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education; Shenzhen Institute of Nutrition and Health, College of Fisheries, Huazhong Agricultural University, Wuhan, 430000, China
| | - Yong-An Zhang
- National Key Laboratory of Agricultural Microbiology; Hubei Hongshan Laboratory; Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education; Shenzhen Institute of Nutrition and Health, College of Fisheries, Huazhong Agricultural University, Wuhan, 430000, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510000, China.
| | - Yang Zhou
- National Key Laboratory of Agricultural Microbiology; Hubei Hongshan Laboratory; Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education; Shenzhen Institute of Nutrition and Health, College of Fisheries, Huazhong Agricultural University, Wuhan, 430000, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510000, China.
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture,, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China.
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6
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Lê-Bury P, Echenique-Rivera H, Pizarro-Cerdá J, Dussurget O. Determinants of bacterial survival and proliferation in blood. FEMS Microbiol Rev 2024; 48:fuae013. [PMID: 38734892 PMCID: PMC11163986 DOI: 10.1093/femsre/fuae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 04/29/2024] [Accepted: 05/10/2024] [Indexed: 05/13/2024] Open
Abstract
Bloodstream infection is a major public health concern associated with high mortality and high healthcare costs worldwide. Bacteremia can trigger fatal sepsis whose prevention, diagnosis, and management have been recognized as a global health priority by the World Health Organization. Additionally, infection control is increasingly threatened by antimicrobial resistance, which is the focus of global action plans in the framework of a One Health response. In-depth knowledge of the infection process is needed to develop efficient preventive and therapeutic measures. The pathogenesis of bloodstream infection is a dynamic process resulting from the invasion of the vascular system by bacteria, which finely regulate their metabolic pathways and virulence factors to overcome the blood immune defenses and proliferate. In this review, we highlight our current understanding of determinants of bacterial survival and proliferation in the bloodstream and discuss their interactions with the molecular and cellular components of blood.
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Affiliation(s)
- Pierre Lê-Bury
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, 28 rue du Dr Roux, 75015 Paris, France
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Autoimmune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), 18 route du Panorama, 92260 Fontenay-aux-Roses, France
| | - Hebert Echenique-Rivera
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, 28 rue du Dr Roux, 75015 Paris, France
| | - Javier Pizarro-Cerdá
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, 28 rue du Dr Roux, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, Yersinia National Reference Laboratory, WHO Collaborating Research & Reference Centre for Plague FRA-146, 28 rue du Dr Roux, 75015 Paris, France
| | - Olivier Dussurget
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, 28 rue du Dr Roux, 75015 Paris, France
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7
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Hernandez DM, Marzouk M, Cole M, Fortoul MC, Kethireddy SR, Contractor R, Islam H, Moulder T, Kalifa AR, Meneses EM, Mendoza MB, Thomas R, Masud S, Pubien S, Milanes P, Diaz-Tang G, Lopatkin AJ, Smith RP. Purine and pyrimidine synthesis differently affect the strength of the inoculum effect for aminoglycoside and β-lactam antibiotics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.09.588696. [PMID: 38645041 PMCID: PMC11030397 DOI: 10.1101/2024.04.09.588696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
The inoculum effect has been observed for nearly all antibiotics and bacterial species. However, explanations accounting for its occurrence and strength are lacking. We previously found that growth productivity, which captures the relationship between [ATP] and growth, can account for the strength of the inoculum effect for bactericidal antibiotics. However, the molecular pathway(s) underlying this relationship, and therefore determining the inoculum effect, remain undiscovered. We show that nucleotide synthesis can determine the relationship between [ATP] and growth, and thus the strength of inoculum effect in an antibiotic class-dependent manner. Specifically, and separate from activity through the tricarboxylic acid cycle, we find that transcriptional activity of genes involved in purine and pyrimidine synthesis can predict the strength of the inoculum effect for β-lactam and aminoglycosides antibiotics, respectively. Our work highlights the antibiotic class-specific effect of purine and pyrimidine synthesis on the severity of the inoculum effect and paves the way for intervention strategies to reduce the inoculum effect in the clinic.
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Affiliation(s)
- Daniella M. Hernandez
- Cell Therapy Institute, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, 33314
| | - Melissa Marzouk
- Cell Therapy Institute, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, 33314
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL, 33314
| | - Madeline Cole
- Department of Medical Education, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, 33314
| | - Marla C. Fortoul
- Department of Medical Education, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, 33314
| | - Saipranavi Reddy Kethireddy
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL, 33314
| | - Rehan Contractor
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL, 33314
| | - Habibul Islam
- Department of Chemical Engineering, University of Rochester; Rochester, NY 14627; USA
| | - Trent Moulder
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL, 33314
| | - Ariane R. Kalifa
- Cell Therapy Institute, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, 33314
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL, 33314
| | - Estefania Marin Meneses
- Cell Therapy Institute, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, 33314
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL, 33314
| | - Maximiliano Barbosa Mendoza
- Cell Therapy Institute, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, 33314
| | - Ruth Thomas
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL, 33314
| | - Saad Masud
- Department of Medical Education, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, 33314
| | - Sheena Pubien
- Department of Medical Education, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, 33314
| | - Patricia Milanes
- Department of Medical Education, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, 33314
| | - Gabriela Diaz-Tang
- Cell Therapy Institute, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, 33314
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL, 33314
| | - Allison J. Lopatkin
- Department of Chemical Engineering, University of Rochester; Rochester, NY 14627; USA
- Department of Microbiology and Immunology, University of Rochester Medical Center; Rochester, NY 14627; USA
- Department of Biomedical Engineering, University of Rochester Medical Center; Rochester, NY 14627; USA
| | - Robert P. Smith
- Cell Therapy Institute, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, 33314
- Department of Medical Education, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, 33314
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8
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Ayoub N, Gedeon A, Munier-Lehmann H. A journey into the regulatory secrets of the de novo purine nucleotide biosynthesis. Front Pharmacol 2024; 15:1329011. [PMID: 38444943 PMCID: PMC10912719 DOI: 10.3389/fphar.2024.1329011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 02/01/2024] [Indexed: 03/07/2024] Open
Abstract
De novo purine nucleotide biosynthesis (DNPNB) consists of sequential reactions that are majorly conserved in living organisms. Several regulation events take place to maintain physiological concentrations of adenylate and guanylate nucleotides in cells and to fine-tune the production of purine nucleotides in response to changing cellular demands. Recent years have seen a renewed interest in the DNPNB enzymes, with some being highlighted as promising targets for therapeutic molecules. Herein, a review of two newly revealed modes of regulation of the DNPNB pathway has been carried out: i) the unprecedent allosteric regulation of one of the limiting enzymes of the pathway named inosine 5'-monophosphate dehydrogenase (IMPDH), and ii) the supramolecular assembly of DNPNB enzymes. Moreover, recent advances that revealed the therapeutic potential of DNPNB enzymes in bacteria could open the road for the pharmacological development of novel antibiotics.
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Affiliation(s)
- Nour Ayoub
- Institut Pasteur, Université Paris Cité, INSERM UMRS-1124, Paris, France
| | - Antoine Gedeon
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS UMR7203, Laboratoire des Biomolécules, LBM, Paris, France
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9
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Meiller TF, Fraser CM, Grant-Beurmann S, Humphrys M, Tallon L, Sadzewicz LD, Jabra-Rizk MA, Alfaifi A, Kensara A, Molitoris JK, Witek M, Mendes WS, Regine WF, Tran PT, Miller RC, Sultan AS. A Longitudinal Metagenomic Comparative Analysis of Oral Microbiome Shifts in Patients Receiving Proton Radiation versus Photon Radiation for Head and Neck Cancer. JOURNAL OF CANCER & ALLIED SPECIALTIES 2024; 10:579. [PMID: 38259673 PMCID: PMC10793722 DOI: 10.37029/jcas.v10i1.579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 12/01/2023] [Indexed: 01/24/2024]
Abstract
Introduction Due to the radiation-sparing effects on salivary gland acini, changes in the composition of the oral microbiome may be a driver for improved outcomes in patients receiving proton radiation, with potentially worse outcomes in patients exposed to photon radiation therapy. To date, a head-to-head comparison of oral microbiome changes at a metagenomic level with longitudinal sampling has yet to be performed in these patient cohorts. Methods and Materials To comparatively analyze oral microbiome shifts during head and neck radiation therapy, a prospective pilot cohort study was performed at the Maryland Proton Treatment Center and the University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center. A longitudinal metagenomic comparative analysis of oral microbiome shifts was performed at three time points (pre-radiation, during radiation, and immediately post-radiation). Head and neck cancer patients receiving proton radiation (n = 4) were compared to photon radiation (n = 4). Additional control groups included healthy age- and sex-matched controls (n = 5), head and neck cancer patients who never received radiation therapy (n = 8), and patients with oral inflammatory disease (n = 3). Results Photon therapy patients presented with lower microbial alpha diversity at all timepoints, and there was a trend towards reduced species richness as compared with proton therapy. Healthy controls and proton patients exhibited overall higher and similar diversity. A more dysbiotic state was observed in patients receiving photon therapy as compared to proton therapy, in which oral microbial homeostasis was maintained. Mucositis was observed in 3/4 photon patients and was not observed in any proton patients during radiation therapy. The bacterial de novo pyrimidine biosynthesis pathway and the nitrate reduction V pathway were comparatively higher following photon exposure. These functional changes in bacterial metabolism may suggest that photon exposure produces a more permissive environment for the proliferation of pathogenic bacteria. Conclusion Oral microbiome dysbiosis in patients receiving photon radiation may be associated with increased mucositis occurrence. Proton radiation therapy for head and neck cancer demonstrates a safer side effect profile in terms of oral complications, oral microbiome dysbiosis, and functional metabolic status.
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Affiliation(s)
- Timothy F. Meiller
- Department of Oncology and Diagnostic Sciences, School of Dentistry, University of Maryland, Baltimore, United States
- University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, United States
| | - Claire M. Fraser
- Department of Medicine, University of Maryland School of Medicine, Baltimore, United States
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, United States
| | - Silvia Grant-Beurmann
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, United States
| | - Mike Humphrys
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, United States
| | - Luke Tallon
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, United States
| | - Lisa D. Sadzewicz
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, United States
| | - Mary Ann Jabra-Rizk
- Department of Oncology and Diagnostic Sciences, School of Dentistry, University of Maryland, Baltimore, United States
- Department of Microbiology and Immunology, School of Medicine, University of Maryland, Baltimore, United States
| | - Areej Alfaifi
- Department of Oncology and Diagnostic Sciences, School of Dentistry, University of Maryland, Baltimore, United States
- Department of Restorative and Prosthetic Dental Sciences, College of Dentistry King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Anmar Kensara
- Department of Advanced Oral Sciences and Therapeutics, School of Dentistry, University of Maryland, Baltimore, United States
- Department of Restorative Dentistry, College of Dentistry, Umm Al Qura University, Makkah, Saudi Arabia
| | - Jason K. Molitoris
- University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, United States
- Department of Radiation Oncology, University of Maryland Medical Center, Baltimore, United States
- Maryland Proton Treatment Center, 850 W Baltimore St, Baltimore, United States
| | - Matthew Witek
- University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, United States
- Department of Radiation Oncology, University of Maryland Medical Center, Baltimore, United States
- Maryland Proton Treatment Center, 850 W Baltimore St, Baltimore, United States
| | - William S. Mendes
- Department of Radiation Oncology, University of Maryland Medical Center, Baltimore, United States
| | - William F. Regine
- University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, United States
- Department of Radiation Oncology, University of Maryland Medical Center, Baltimore, United States
- Maryland Proton Treatment Center, 850 W Baltimore St, Baltimore, United States
| | - Phuoc T. Tran
- Department of Radiation Oncology, University of Maryland Medical Center, Baltimore, United States
- Maryland Proton Treatment Center, 850 W Baltimore St, Baltimore, United States
| | - Robert C. Miller
- Department of Radiation Medicine, University of Kentucky College of Medicine, Lexington, United States
| | - Ahmed S. Sultan
- Department of Oncology and Diagnostic Sciences, School of Dentistry, University of Maryland, Baltimore, United States
- University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, United States
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10
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Tan CAZ, Chong KKL, Yeong DYX, Ng CHM, Ismail MH, Yap ZH, Khetrapal V, Tay VSY, Drautz-Moses DI, Ali Y, Chen SL, Kline KA. Purine and carbohydrate availability drive Enterococcus faecalis fitness during wound and urinary tract infections. mBio 2024; 15:e0238423. [PMID: 38078746 PMCID: PMC10790769 DOI: 10.1128/mbio.02384-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 10/24/2023] [Indexed: 01/17/2024] Open
Abstract
IMPORTANCE Although E. faecalis is a common wound pathogen, its pathogenic mechanisms during wound infection are unexplored. Here, combining a mouse wound infection model with in vivo transposon and RNA sequencing approaches, we identified the E. faecalis purine biosynthetic pathway and galactose/mannose MptABCD phosphotransferase system as essential for E. faecalis acute replication and persistence during wound infection, respectively. The essentiality of purine biosynthesis and the MptABCD PTS is driven by the consumption of purine metabolites by E. faecalis during acute replication and changing carbohydrate availability during the course of wound infection. Overall, our findings reveal the importance of the wound microenvironment in E. faecalis wound pathogenesis and how these metabolic pathways can be targeted to better control wound infections.
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Affiliation(s)
- Casandra Ai Zhu Tan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University Singapore, Singapore, Singapore
| | - Kelvin Kian Long Chong
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University Singapore, Singapore, Singapore
| | - Daryl Yu Xuan Yeong
- School of Biological Sciences, Nanyang Technological University Singapore, Singapore, Singapore
| | - Celine Hui Min Ng
- School of Biological Sciences, Nanyang Technological University Singapore, Singapore, Singapore
| | - Muhammad Hafiz Ismail
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University Singapore, Singapore, Singapore
| | - Zhei Hwee Yap
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University Singapore, Singapore, Singapore
| | - Varnica Khetrapal
- Infectious Diseases Translational Research Programme, Division of Infectious Diseases, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Vanessa Shi Yun Tay
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore, Singapore
| | - Daniela I. Drautz-Moses
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University Singapore, Singapore, Singapore
| | - Yusuf Ali
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore, Singapore
- Singapore Eye Research Institute (SERI), Singapore General Hospital, Singapore, Singapore
| | - Swaine L. Chen
- Infectious Diseases Translational Research Programme, Division of Infectious Diseases, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Laboratory of Bacterial Genomics, Genome Institute of Singapore, Singapore, Singapore
| | - Kimberly A. Kline
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University Singapore, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University Singapore, Singapore, Singapore
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
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11
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Kruszewska-Naczk B, Grinholc M, Waleron K, Bandow JE, Rapacka-Zdończyk A. Can antimicrobial blue light contribute to resistance development? Genome-wide analysis revealed aBL-protective genes in Escherichia coli. Microbiol Spectr 2024; 12:e0249023. [PMID: 38063383 PMCID: PMC10782963 DOI: 10.1128/spectrum.02490-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 10/24/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE Increasing antibiotic resistance and the lack of new antibiotic-like compounds to combat bacterial resistance are significant problems of modern medicine. The development of new alternative therapeutic strategies is extremely important. Antimicrobial blue light (aBL) is an innovative approach to combat multidrug-resistant microorganisms. aBL has a multitarget mode of action; however, the full mechanism of aBL antibacterial action requires further investigation. In addition, the potential risk of resistance development to this treatment should be considered.
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Affiliation(s)
- Beata Kruszewska-Naczk
- Laboratory of Photobiology and Molecular Diagnostics, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland
| | - Mariusz Grinholc
- Laboratory of Photobiology and Molecular Diagnostics, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Krzysztof Waleron
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland
| | - Julia Elisabeth Bandow
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstraße, Bochum, Germany
| | - Aleksandra Rapacka-Zdończyk
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland
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12
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Kano T, Ishikawa K, Furuta K, Kaito C. Knockout of adenylosuccinate synthase purA increases susceptibility to colistin in Escherichia coli. FEMS Microbiol Lett 2024; 371:fnae007. [PMID: 38305138 PMCID: PMC10876104 DOI: 10.1093/femsle/fnae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/19/2024] [Accepted: 01/31/2024] [Indexed: 02/03/2024] Open
Abstract
Colistin is a cationic cyclic antimicrobial peptide used as a last resort against multidrug-resistant gram-negative bacteria. To understand the factors involved in colistin susceptibility, we screened colistin-sensitive mutants from an E. coli gene-knockout library (Keio collection). The knockout of purA, whose product catalyzes the synthesis of adenylosuccinate from IMP in the de novo purine synthesis pathway, resulted in increased sensitivity to colistin. Adenylosuccinate is subsequently converted to AMP, which is phosphorylated to produce ADP, a substrate for ATP synthesis. The amount of ATP was lower in the purA-knockout mutant than that in the wild-type strain. ATP synthesis is coupled with proton transfer, and it contributes to the membrane potential. Using the membrane potential probe, 3,3'-diethyloxacarbocyanine iodide [DiOC2(3)], we found that the membrane was hyperpolarized in the purA-knockout mutant compared to that in the wild-type strain. Treatment with the proton uncoupler, carbonyl cyanide m-chlorophenyl hydrazone (CCCP), abolished the hyperpolarization and colistin sensitivity in the mutant. The purA-knockout mutant exhibited increased sensitivity to aminoglycosides, kanamycin, and gentamicin; their uptake requires a membrane potential. Therefore, the knockout of purA, an adenylosuccinate synthase, decreases ATP synthesis concurrently with membrane hyperpolarization, resulting in increased sensitivity to colistin.
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Affiliation(s)
- Tomonori Kano
- Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama 700–8530, Japan
| | - Kazuya Ishikawa
- Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama 700–8530, Japan
| | - Kazuyuki Furuta
- Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama 700–8530, Japan
| | - Chikara Kaito
- Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama 700–8530, Japan
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13
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Feng Y, Chang SK, Portnoy DA. The major role of Listeria monocytogenes folic acid metabolism during infection is the generation of N-formylmethionine. mBio 2023; 14:e0107423. [PMID: 37695058 PMCID: PMC10653936 DOI: 10.1128/mbio.01074-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 05/04/2023] [Indexed: 09/12/2023] Open
Abstract
IMPORTANCE Folic acid is an essential vitamin for bacteria, plants, and animals. The lack of folic acid leads to various consequences such as a shortage of amino acids and nucleotides that are fundamental building blocks for life. Though antifolate drugs are widely used for antimicrobial treatments, the underlying mechanism of bacterial folate deficiency during infection is unclear. This study compares the requirements of different folic acid end-products during the infection of Listeria monocytogenes, a facultative intracellular pathogen of animals and humans. The results reveal the critical importance of N-formylmethionine, the amino acid used by bacteria to initiate protein synthesis. This work extends the current understanding of folic acid metabolism in pathogens and potentially provides new insights into antifolate drug development in the future.
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Affiliation(s)
- Ying Feng
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Shannon K. Chang
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Daniel A. Portnoy
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
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14
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Wirth NT, Rohr K, Danchin A, Nikel PI. Recursive genome engineering decodes the evolutionary origin of an essential thymidylate kinase activity in Pseudomonas putida KT2440. mBio 2023; 14:e0108123. [PMID: 37732760 PMCID: PMC10653934 DOI: 10.1128/mbio.01081-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 07/27/2023] [Indexed: 09/22/2023] Open
Abstract
IMPORTANCE Investigating fundamental aspects of metabolism is vital for advancing our understanding of the diverse biochemical capabilities and biotechnological applications of bacteria. The origin of the essential thymidylate kinase function in the model bacterium Pseudomonas putida KT2440, seemingly interrupted due to the presence of a large genomic island that disrupts the cognate gene, eluded a satisfactory explanation thus far. This is a first-case example of an essential metabolic function, likely acquired by horizontal gene transfer, which "landed" in a locus encoding the same activity. As such, foreign DNA encoding an essential dNMPK could immediately adjust to the recipient host-instead of long-term accommodation and adaptation. Understanding how these functions evolve is a major biological question, and the work presented here is a decisive step toward this direction. Furthermore, identifying essential and accessory genes facilitates removing those deemed irrelevant in industrial settings-yielding genome-reduced cell factories with enhanced properties and genetic stability.
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Affiliation(s)
- Nicolas T. Wirth
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens, Lyngby, Denmark
| | - Katja Rohr
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens, Lyngby, Denmark
| | - Antoine Danchin
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong
| | - Pablo I. Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens, Lyngby, Denmark
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15
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Xu W, Cerna-Vargas JP, Tajuelo A, Lozano-Montoya A, Kivoloka M, Krink N, Monteagudo-Cascales E, Matilla MA, Krell T, Sourjik V. Systematic mapping of chemoreceptor specificities for Pseudomonas aeruginosa. mBio 2023; 14:e0209923. [PMID: 37791891 PMCID: PMC10653921 DOI: 10.1128/mbio.02099-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 08/16/2023] [Indexed: 10/05/2023] Open
Abstract
IMPORTANCE Chemotaxis of motile bacteria has multiple physiological functions. It enables bacteria to locate optimal ecological niches, mediates collective behaviors, and can play an important role in infection. These multiple functions largely depend on ligand specificities of chemoreceptors, and the number and identities of chemoreceptors show high diversity between organisms. Similar diversity is observed for the spectra of chemoeffectors, which include not only chemicals of high metabolic value but also bacterial, plant, and animal signaling molecules. However, the systematic identification of chemoeffectors and their mapping to specific chemoreceptors remains a challenge. Here, we combined several in vivo and in vitro approaches to establish a systematic screening strategy for the identification of receptor ligands and we applied it to identify a number of new physiologically relevant chemoeffectors for the important opportunistic human pathogen P. aeruginosa. This strategy can be equally applicable to map specificities of sensory domains from a wide variety of receptor types and bacteria.
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Affiliation(s)
- Wenhao Xu
- Max Planck Institute for Terrestrial Microbiology & Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Jean Paul Cerna-Vargas
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
- Centro de Biotecnología y Genómica de Plantas CBGP, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria/CSIC, Parque Científico y Tecnológico de la UPM, Pozuelo de Alarcón, Madrid, Spain
| | - Ana Tajuelo
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Andrea Lozano-Montoya
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Melissa Kivoloka
- Max Planck Institute for Terrestrial Microbiology & Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Nicolas Krink
- Max Planck Institute for Terrestrial Microbiology & Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Elizabet Monteagudo-Cascales
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Miguel A. Matilla
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Tino Krell
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology & Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
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16
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Takishita Y, Subramanian S, Souleimanov A, Smith DL. Interactive effects of Pseudomonas entomophila strain 23S and Clavibacter michiganensis subsp. michiganensis on proteome and anti-Cmm compound production. J Proteomics 2023; 289:105006. [PMID: 37717723 DOI: 10.1016/j.jprot.2023.105006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 09/03/2023] [Accepted: 09/08/2023] [Indexed: 09/19/2023]
Abstract
Pseudomonas entomophila strain 23S is an effective biocontrol bacterium for tomato bacterial canker caused by Clavibacter michiganensis subsp. michiganensis (Cmm); it produces an inhibitory compound affecting the growth of Cmm. In this study, the interactions between pure cultures of P. entomophila 23S and Cmm were investigated. First, the population dynamics of each bacterium during the interaction was determined using the selective media. Second, the amount of anti-Cmm compound produced by P. entomophila 23S in the presence of Cmm was quantified using HPLC. Lastly, a label-free shotgun proteomics study of P. entomophila 23S, Cmm, and a co-culture was conducted to understand the effects of the interaction of each bacterium at the proteomic level. Compared with the pure culture grown, the total number of proteins decreased in the interaction for both bacteria. P. entomophila 23S secreted stress-related proteins, such as chaperonins, peptidases, ABC-transporters and elongation factors. The bacterium also produced more proteins related with purine, pyrimidine, carbon and nitrogen metabolisms in the presence of Cmm. The population enumeration study revealed that the Cmm population declined dramatically during the interaction, while the population of P. entomophila 23S maintained. The quantification of anti-Cmm compound indicated that P. entomophila 23S produced significantly higher amount of anti-Cmm compound when it was cultured with Cmm. Overall, the study suggested that P. entomophila 23S, although is cidal to Cmm, was also negatively affected by the presence of Cmm, while trying to adapt to the stress condition, and that such an environment favored increased production of the anti-Cmm compound by P. entomophila 23S. SIGNIFICANCE: Pseudomonas entomophila strain 23S is an effective biocontrol bacterium for tomato bacterial canker caused by Clavibacter michiganensis subsp. michiganensis (Cmm); it produces an inhibitory compound affecting the growth of Cmm. In this study, secreted proteome of pure cultures of P. entomophila 23S and Cmm, and also of a co-culture was first time identified. Furthermore, the study found that P. entomophila strain 23S produced significantly higher amount of anti-Cmm compound when the bacterium was grown together with Cmm. Co-culture enhancing anti-Cmm compound production by P. entomophila 23S is useful information, particularly from a commercial point of view of biocontrol application, and for scale-up of anti-Cmm compound production.
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Affiliation(s)
- Yoko Takishita
- Department of Plant Science, Macdonald Campus, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada
| | - Sowmyalakshmi Subramanian
- Department of Plant Science, Macdonald Campus, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada
| | - Alfred Souleimanov
- Department of Plant Science, Macdonald Campus, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada
| | - Donald L Smith
- Department of Plant Science, Macdonald Campus, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada.
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17
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Sharma MF, Sharma SK, Streeter CC, Firestine SM. A Fluorescence-Based Assay for N 5 -Carboxyaminoimidazole Ribonucleotide Mutase. Chembiochem 2023; 24:e202300347. [PMID: 37474455 PMCID: PMC10644341 DOI: 10.1002/cbic.202300347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/04/2023] [Accepted: 07/18/2023] [Indexed: 07/22/2023]
Abstract
The enzyme N5 -carboxylaminoinidazole ribonucleotide (N5 -CAIR) mutase is found in microbial de novo purine biosynthesis but is absent in humans making it an attractive antimicrobial target. N5 -CAIR mutase catalyzes the synthesis of carboxyaminoimidazole ribonucleotide (CAIR) from N5 -CAIR which is itself prepared from aminoimidazole ribonucleotide (AIR) by the enzyme N5 -CAIR synthetase. During our research on identifying inhibitors of N5 -CAIR mutase, we developed an innovative, fluorescence-based assay to measure the activity of this enzyme. This assay relies upon our recent serendipitous observation that AIR reversibly reacts with the compound isatin. Reaction of a fluorescently-tagged isatin with AIR resulted in a large increase in fluorescence intensity allowing a measurement of the concentration of AIR in solution. From this observation, we developed a reproducible, non-continuous assay that can replicate the known kinetic parameters of the enzyme and can readily detect a recognized inhibitor of the enzyme. This assay should find utility in screening for inhibitors targeting N5 -CAIR mutase.
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Affiliation(s)
- Marcella F. Sharma
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, Michigan, 48201, United States
| | - Shiv K. Sharma
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, Michigan, 48201, United States
| | - Cale C. Streeter
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, Michigan, 48201, United States
| | - Steven M. Firestine
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, Michigan, 48201, United States
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18
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Belfon KK, Sharma N, Zigweid R, Bolejack M, Davies D, Edwards TE, Myler PJ, French JB. Structure-Guided Discovery of N 5-CAIR Mutase Inhibitors. Biochemistry 2023; 62:2587-2596. [PMID: 37552766 PMCID: PMC10484210 DOI: 10.1021/acs.biochem.2c00705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 04/20/2023] [Indexed: 08/10/2023]
Abstract
Because purine nucleotides are essential for all life, differences between how microbes and humans metabolize purines can be exploited for the development of antimicrobial therapies. While humans biosynthesize purine nucleotides in a 10-step pathway, most microbes utilize an additional 11th enzymatic activity. The human enzyme, aminoimidazole ribonucleotide (AIR) carboxylase generates the product 4-carboxy-5-aminoimidazole ribonucleotide (CAIR) directly. Most microbes, however, require two separate enzymes, a synthetase (PurK) and a mutase (PurE), and proceed through the intermediate, N5-CAIR. Toward the development of therapeutics that target these differences, we have solved crystal structures of the N5-CAIR mutase of the human pathogens Legionella pneumophila (LpPurE) and Burkholderia cenocepacia (BcPurE) and used a structure-guided approach to identify inhibitors. Analysis of the structures reveals a highly conserved fold and active site architecture. Using this data, and three additional structures of PurE enzymes, we screened a library of FDA-approved compounds in silico and identified a set of 25 candidates for further analysis. Among these, we identified several new PurE inhibitors with micromolar IC50 values. Several of these compounds, including the α1-blocker Alfuzosin, inhibit the microbial PurE enzymes much more effectively than the human homologue. These structures and the newly described PurE inhibitors are valuable tools to aid in further studies of this enzyme and provide a foundation for the development of compounds that target differences between human and microbial purine metabolism.
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Affiliation(s)
- Kafi K.
J. Belfon
- Department
of Biochemistry and Cell Biology, Stony
Brook University, Stony
Brook, New York 11794, United States
| | - Nandini Sharma
- The
Hormel Institute, University of Minnesota, Austin, Minnesota 55912, United States
| | - Rachael Zigweid
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Hospital, 307 Westlake Ave N Ste 500, Seattle, Washington 98109, United States
| | - Madison Bolejack
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
| | - Doug Davies
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- UCB-Bainbridge, Bainbridge Island, Washington 98110, United States
| | - Thomas E. Edwards
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- UCB-Bainbridge, Bainbridge Island, Washington 98110, United States
| | - Peter J. Myler
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Hospital, 307 Westlake Ave N Ste 500, Seattle, Washington 98109, United States
- Department
of Global Health and Department of Biomedical Informatics and Medical
Education, University of Washington, Seattle, Washington 98195, United States
| | - Jarrod B. French
- The
Hormel Institute, University of Minnesota, Austin, Minnesota 55912, United States
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19
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Alberti M, Sainas S, Ronchi E, Lolli ML, Boschi D, Rizzi M, Ferraris DM, Miggiano R. Biochemical characterization of Mycobacterium tuberculosis dihydroorotate dehydrogenase and identification of a selective inhibitor. FEBS Lett 2023; 597:2119-2132. [PMID: 37278160 DOI: 10.1002/1873-3468.14680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/24/2023] [Accepted: 05/25/2023] [Indexed: 06/07/2023]
Abstract
Mycobacterium tuberculosis (MTB) is the etiologic agent of tuberculosis (TB), an ancient disease which causes 1.5 million deaths worldwide. Dihydroorotate dehydrogenase (DHODH) is a key enzyme of the MTB de novo pyrimidine biosynthesis pathway, and it is essential for MTB growth in vitro, hence representing a promising drug target. We present: (i) the biochemical characterization of the full-length MTB DHODH, including the analysis of the kinetic parameters, and (ii) the previously unreleased crystal structure of the protein that allowed us to rationally screen our in-house chemical library and identify the first selective inhibitor of mycobacterial DHODH. The inhibitor has fluorescence properties, potentially instrumental to in cellulo imaging studies, and exhibits an IC50 value of 43 μm, paving the way to hit-to-lead process.
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Affiliation(s)
- Marta Alberti
- Department of Pharmaceutical Sciences, University of Eastern Piedmont, Novara, Italy
| | - Stefano Sainas
- Department of Sciences and Drug Technology, University of Turin, Torino, Italy
| | - Erika Ronchi
- Department of Pharmaceutical Sciences, University of Eastern Piedmont, Novara, Italy
| | - Marco L Lolli
- Department of Sciences and Drug Technology, University of Turin, Torino, Italy
| | - Donatella Boschi
- Department of Sciences and Drug Technology, University of Turin, Torino, Italy
| | - Menico Rizzi
- Department of Pharmaceutical Sciences, University of Eastern Piedmont, Novara, Italy
| | - Davide M Ferraris
- Department of Pharmaceutical Sciences, University of Eastern Piedmont, Novara, Italy
| | - Riccardo Miggiano
- Department of Pharmaceutical Sciences, University of Eastern Piedmont, Novara, Italy
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20
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Holmes CL, Wilcox AE, Forsyth V, Smith SN, Moricz BS, Unverdorben LV, Mason S, Wu W, Zhao L, Mobley HLT, Bachman MA. Klebsiella pneumoniae causes bacteremia using factors that mediate tissue-specific fitness and resistance to oxidative stress. PLoS Pathog 2023; 19:e1011233. [PMID: 37463183 PMCID: PMC10381055 DOI: 10.1371/journal.ppat.1011233] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 06/28/2023] [Indexed: 07/20/2023] Open
Abstract
Gram-negative bacteremia is a major cause of global morbidity involving three phases of pathogenesis: initial site infection, dissemination, and survival in the blood and filtering organs. Klebsiella pneumoniae is a leading cause of bacteremia and pneumonia is often the initial infection. In the lung, K. pneumoniae relies on many factors like capsular polysaccharide and branched chain amino acid biosynthesis for virulence and fitness. However, mechanisms directly enabling bloodstream fitness are unclear. Here, we performed transposon insertion sequencing (TnSeq) in a tail-vein injection model of bacteremia and identified 58 K. pneumoniae bloodstream fitness genes. These factors are diverse and represent a variety of cellular processes. In vivo validation revealed tissue-specific mechanisms by which distinct factors support bacteremia. ArnD, involved in Lipid A modification, was required across blood filtering organs and supported resistance to soluble splenic factors. The purine biosynthesis enzyme PurD supported liver fitness in vivo and was required for replication in serum. PdxA, a member of the endogenous vitamin B6 biosynthesis pathway, optimized replication in serum and lung fitness. The stringent response regulator SspA was required for splenic fitness yet was dispensable in the liver. In a bacteremic pneumonia model that incorporates initial site infection and dissemination, splenic fitness defects were enhanced. ArnD, PurD, DsbA, SspA, and PdxA increased fitness across bacteremia phases and each demonstrated unique fitness dynamics within compartments in this model. SspA and PdxA enhanced K. pnuemoniae resistance to oxidative stress. SspA, but not PdxA, specifically resists oxidative stress produced by NADPH oxidase Nox2 in the lung, spleen, and liver, as it was a fitness factor in wild-type but not Nox2-deficient (Cybb-/-) mice. These results identify site-specific fitness factors that act during the progression of Gram-negative bacteremia. Defining K. pneumoniae fitness strategies across bacteremia phases could illuminate therapeutic targets that prevent infection and sepsis.
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Affiliation(s)
- Caitlyn L Holmes
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Alexis E Wilcox
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Valerie Forsyth
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Sara N Smith
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Bridget S Moricz
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Lavinia V Unverdorben
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Sophia Mason
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Weisheng Wu
- Bioinformatics Core Facility, School of Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Lili Zhao
- Research Institute, Beaumont Hospital, Royal Oak, Michigan, United States of America
| | - Harry L T Mobley
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Michael A Bachman
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
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21
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Gomes MZR, de Lima EM, Martins Aires CA, Pereira PS, Yim J, Silva FH, Rodrigues CAS, Oliveira TRTE, da Silva PP, Eller CM, de Souza CMR, Rybak MJ, Albano RM, de Miranda AB, Machado E, Catanho M. Outbreak report of polymyxin-carbapenem-resistant Klebsiella pneumoniae causing untreatable infections evidenced by synergy tests and bacterial genomes. Sci Rep 2023; 13:6238. [PMID: 37069157 PMCID: PMC10110528 DOI: 10.1038/s41598-023-31901-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 03/20/2023] [Indexed: 04/19/2023] Open
Abstract
Polymyxin-carbapenem-resistant Klebsiella pneumoniae (PCR-Kp) with pan (PDR)- or extensively drug-resistant phenotypes has been increasingly described worldwide. Here, we report a PCR-Kp outbreak causing untreatable infections descriptively correlated with bacterial genomes. Hospital-wide surveillance of PCR-Kp was initiated in December-2014, after the first detection of a K. pneumoniae phenotype initially classified as PDR, recovered from close spatiotemporal cases of a sentinel hospital in Rio de Janeiro. Whole-genome sequencing of clinical PCR-Kp was performed to investigate similarities and dissimilarities in phylogeny, resistance and virulence genes, plasmid structures and genetic polymorphisms. A target phenotypic profile was detected in 10% (12/117) of the tested K. pneumoniae complex bacteria recovered from patients (8.5%, 8/94) who had epidemiological links and were involved in intractable infections and death, with combined therapeutic drugs failing to meet synergy. Two resistant bacterial clades belong to the same transmission cluster (ST437) or might have different sources (ST11). The severity of infection was likely related to patients' comorbidities, lack of antimicrobial therapy and predicted bacterial genes related to high resistance, survival, and proliferation. This report contributes to the actual knowledge about the natural history of PCR-Kp infection, while reporting from a time when there were no licensed drugs in the world to treat some of these infections. More studies comparing clinical findings with bacterial genetic markers during clonal spread are needed.
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Affiliation(s)
- Marisa Zenaide Ribeiro Gomes
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.
- Hospital Federal Servidores do Estado, Ministry of Health, Rio de Janeiro, Brazil.
- Laboratório de Pesquisa em Infecção Hospitalar, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil.
- Hospital Infection Control Committee, Hospital Universitário Pedro Ernesto, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil.
| | | | - Caio Augusto Martins Aires
- Laboratório de Pesquisa em Infecção Hospitalar, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
- Departamento de Ciência da Saúde, Universidade Federal Rural do Semi-Árido (UFERSA), Mossoró, Rio Grande do Norte, Brazil
| | - Polyana Silva Pereira
- Laboratório de Pesquisa em Infecção Hospitalar, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Juwon Yim
- Anti-Infective Research Laboratory, Eugene Applebaum College of Pharmacy and Health Sciences, Department of Medicine, Division of Infectious Diseases, School of Medicine, Wayne State University, Detroit, MI, USA
| | - Fernando Henrique Silva
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | | | | | - Priscila Pinho da Silva
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Cristiane Monteiro Eller
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Claudio Marcos Rocha de Souza
- Laboratório de Pesquisa em Infecção Hospitalar, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Michael J Rybak
- Anti-Infective Research Laboratory, Eugene Applebaum College of Pharmacy and Health Sciences, Department of Medicine, Division of Infectious Diseases, School of Medicine, Wayne State University, Detroit, MI, USA
| | - Rodolpho Mattos Albano
- Departamento de Bioquímica, IBRAG, Universidade do Estado do Rio de Janeiro,, Rio de Janeiro, Brazil
| | - Antonio Basílio de Miranda
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Edson Machado
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratório de Biologia Molecular Aplicada a Micobactérias, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Marcos Catanho
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.
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22
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Carfrae LA, Brown ED. Nutrient stress is a target for new antibiotics. Trends Microbiol 2023; 31:571-585. [PMID: 36709096 DOI: 10.1016/j.tim.2023.01.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/05/2023] [Accepted: 01/09/2023] [Indexed: 01/28/2023]
Abstract
Novel approaches are required to address the looming threat of pan-resistant Gram-negative pathogens and forestall the rise of untreatable infections. Unconventional targets that are uniquely important during infection and tractable to high-throughput drug discovery methods hold high potential for innovation in antibiotic discovery programs. In this context, inhibitors of bacterial nutrient stress are particularly exciting candidates for future antibiotic development. Amino acid, nucleotide, and vitamin biosynthesis pathways are critical for bacterial growth in nutrient-limiting conditions in the laboratory and the host. Although historically dismissed as dispensable for pathogens, a wealth of transposon mutagenesis and single-mutant studies have emerged which demonstrate that several such pathways are critical for infection. Indeed, high-throughput screens of diverse synthetic compounds and natural products have uncovered inhibitors of nutrient biosynthesis. Herein, we review bacterial nutrient biosynthesis and its role during host infection. Further, we explore screening platforms developed to search for inhibitors of these targets and highlight successes among these. Finally, we feature important and sometimes surprising connections between bacterial nutrient biosynthesis, antibiotic activity, and antibiotic resistance.
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Affiliation(s)
- Lindsey A Carfrae
- Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4L8, Canada; Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4L8, Canada
| | - Eric D Brown
- Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4L8, Canada; Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4L8, Canada; Present address: Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4L8, Canada.
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23
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Kabongo AT, Acharjee R, Sakura T, Bundutidi GM, Hartuti ED, Davies C, Gundogdu O, Kita K, Shiba T, Inaoka DK. Biochemical characterization and identification of ferulenol and embelin as potent inhibitors of malate:quinone oxidoreductase from Campylobacter jejuni. Front Mol Biosci 2023; 10:1095026. [PMID: 36776743 PMCID: PMC9908594 DOI: 10.3389/fmolb.2023.1095026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 01/18/2023] [Indexed: 01/27/2023] Open
Abstract
Campylobacter jejuni infection poses a serious global threat to public health. The increasing incidence and antibiotic resistance of this bacterial infection have necessitated the adoption of various strategies to curb this trend, primarily through developing new drugs with new mechanisms of action. The enzyme malate:quinone oxidoreductase (MQO) has been shown to be essential for the survival of several bacteria and parasites. MQO is a peripheral membrane protein that catalyses the oxidation of malate to oxaloacetate, a crucial step in the tricarboxylic acid cycle. In addition, MQO is involved in the reduction of the quinone pool in the electron transport chain and thus contributes to cellular bioenergetics. The enzyme is an attractive drug target as it is not conserved in mammals. As a preliminary step in assessing the potential application of MQO from C. jejuni (CjMQO) as a new drug target, we purified active recombinant CjMQO and conducted, for the first time, biochemical analyses of MQO from a pathogenic bacterium. Our study showed that ferulenol, a submicromolar mitochondrial MQO inhibitor, and embelin are nanomolar inhibitors of CjMQO. We showed that both inhibitors are mixed-type inhibitors versus malate and noncompetitive versus quinone, suggesting the existence of a third binding site to accommodate these inhibitors; indeed, such a trait appears to be conserved between mitochondrial and bacterial MQOs. Interestingly, ferulenol and embelin also inhibit the in vitro growth of C. jejuni, supporting the hypothesis that MQO is essential for C. jejuni survival and is therefore an important drug target.
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Affiliation(s)
- Augustin Tshibaka Kabongo
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan,Department of Molecular Infection Dynamics, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan,Department of Internal Medicine, Faculty of Medicine, Pharmacy and Public Health, University of Mbujimayi, Kinshasa, Congo
| | - Rajib Acharjee
- Department of Parasitology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan,Program for Nurturing Global Leaders in Tropical and Emerging Communicable Disease, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan,Department of Zoology, University of Chittagong, Chittagong, Bangladesh
| | - Takaya Sakura
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan,Department of Molecular Infection Dynamics, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Gloria Mavinga Bundutidi
- Department of Molecular Infection Dynamics, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan,Department of Parasitology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan,Program for Nurturing Global Leaders in Tropical and Emerging Communicable Disease, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan,Department of Pediatrics, Kinshasa University Hospital, University of Kinshasa, Kinshasa, Congo
| | - Endah Dwi Hartuti
- Department of Parasitology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan,Program for Nurturing Global Leaders in Tropical and Emerging Communicable Disease, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan,Research Center for Genetic Engineering, National Research and Innovation Agency, West Java, Indonesia
| | - Cadi Davies
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Ozan Gundogdu
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Kiyoshi Kita
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan,Department of Host-Defense Biochemistry, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan,Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tomoo Shiba
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto, Japan,*Correspondence: Tomoo Shiba, ; Daniel Ken Inaoka,
| | - Daniel Ken Inaoka
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan,Department of Molecular Infection Dynamics, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan,Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan,*Correspondence: Tomoo Shiba, ; Daniel Ken Inaoka,
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24
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Genome-wide screen in human plasma identifies multifaceted complement evasion of Pseudomonas aeruginosa. PLoS Pathog 2023; 19:e1011023. [PMID: 36696456 PMCID: PMC9901815 DOI: 10.1371/journal.ppat.1011023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 02/06/2023] [Accepted: 11/23/2022] [Indexed: 01/26/2023] Open
Abstract
Pseudomonas aeruginosa, an opportunistic Gram-negative pathogen, is a leading cause of bacteremia with a high mortality rate. We recently reported that P. aeruginosa forms a persister-like sub-population of evaders in human plasma. Here, using a gain-of-function transposon sequencing (Tn-seq) screen in plasma, we identified and validated previously unknown factors affecting bacterial persistence in plasma. Among them, we identified a small periplasmic protein, named SrgA, whose expression leads to up to a 100-fold increase in resistance to killing. Additionally, mutants in pur and bio genes displayed higher tolerance and persistence, respectively. Analysis of several steps of the complement cascade and exposure to an outer-membrane-impermeable drug, nisin, suggested that the mutants impede membrane attack complex (MAC) activity per se. Electron microscopy combined with energy-dispersive X-ray spectroscopy (EDX) revealed the formation of polyphosphate (polyP) granules upon incubation in plasma of different size in purD and wild-type strains, implying the bacterial response to a stress signal. Indeed, inactivation of ppk genes encoding polyP-generating enzymes lead to significant elimination of persisting bacteria from plasma. Through this study, we shed light on a complex P. aeruginosa response to the plasma conditions and discovered the multifactorial origin of bacterial resilience to MAC-induced killing.
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25
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Shumyatsky G, Burrell A, Chaney H, Sami I, Koumbourlis AC, Freishtat RJ, Crandall KA, Zemanick ET, Hahn A. Using metabolic potential within the airway microbiome as predictors of clinical state in persons with cystic fibrosis. Front Med (Lausanne) 2023; 9:1082125. [PMID: 36698799 PMCID: PMC9868313 DOI: 10.3389/fmed.2022.1082125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/19/2022] [Indexed: 01/11/2023] Open
Abstract
Introduction Pulmonary exacerbations (PEx) in persons with cystic fibrosis (CF) are primarily related to acute or chronic inflammation associated with bacterial lung infections, which may be caused by several bacteria that activate similar bacterial genes and produce similar by-products. The goal of our study was to perform a stratified functional analysis of bacterial genes at three distinct time points in the treatment of a PEx in order to determine the role that specific airway microbiome community members may play within each clinical state (i.e., PEx, end of antibiotic treatment, and follow-up). Our secondary goal was to compare the change between clinical states with the metabolic activity of specific airway microbiome community members. Methods This was a prospective observational study of persons with CF treated with intravenous antibiotics for PEx between 2016 and 2020 at Children's National Hospital. Demographic and clinical information as well as respiratory samples were collected at hospital admission for PEx, end of antibiotic treatment, and follow-up. Metagenomic sequencing was performed; MetaPhlAn3 and HUMANn3 were used to assign sequences to bacterial species and bacterial metabolic genes, respectively. Results Twenty-two persons with CF, with a mean age of 14.5 (range 7-23) years, experienced 45 PEx during the study period. Two-hundred twenty-one bacterial species were identified in the respiratory samples from the study cohort. Ten bacterial species had differential gene abundance across changes in the clinical state including Staphylococcus aureus, Streptococcus salivarius, and Veillonella atypica (all padj < 0.01 and log2FoldChange > |2|). These corresponded to a differential abundance of bacterial genes, with S. aureus accounting for 81% of the genes more abundant in PEx and S. salivarius accounting for 83% of the genes more abundant in follow-up, all compared to the end of treatment. Lastly, 8,653 metabolic pathways were identified across samples, with again S. aureus and S. salivarius contributing to the differential abundance of pathways (106 in PEx vs. 66 in follow-up, respectively). V. atypica was associated with a single metabolic pathway (UDP-N-acetyl-D-glucosamine biosynthesis) increased in follow-up compared to PEx. Discussion Taken together, these data suggest that the metabolic potential of bacterial species can provide more insight into changes across clinical states than the relative abundance of the bacteria alone.
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Affiliation(s)
- Gabriella Shumyatsky
- Jefferson Biotechnology Program, Thomas Jefferson University, Philadelphia, PA, United States
| | - Aszia Burrell
- Center for Genetic Medicine Research, Children's National Research Institute, Washington, DC, United States
| | - Hollis Chaney
- Department of Pediatrics, George Washington University (GWU), Washington, DC, United States.,Division of Pulmonary Medicine, Children's National Hospital (CNH), Washington, DC, United States
| | - Iman Sami
- Department of Pediatrics, George Washington University (GWU), Washington, DC, United States.,Division of Pulmonary Medicine, Children's National Hospital (CNH), Washington, DC, United States
| | - Anastassios C Koumbourlis
- Department of Pediatrics, George Washington University (GWU), Washington, DC, United States.,Division of Pulmonary Medicine, Children's National Hospital (CNH), Washington, DC, United States
| | - Robert J Freishtat
- Center for Genetic Medicine Research, Children's National Research Institute, Washington, DC, United States.,Department of Pediatrics, George Washington University (GWU), Washington, DC, United States.,Division of Emergency Medicine, CNH, Washington, DC, United States
| | - Keith A Crandall
- Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, GWU, Washington, DC, United States
| | - Edith T Zemanick
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Andrea Hahn
- Center for Genetic Medicine Research, Children's National Research Institute, Washington, DC, United States.,Department of Pediatrics, George Washington University (GWU), Washington, DC, United States.,Division of Infectious Diseases, CNH, Washington, DC, United States
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26
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Skariyachan S, Praveen PKU, Uttarkar A, Niranjan V. Computational design of prospective molecular targets for Burkholderia cepacia complex by molecular docking and dynamic simulation studies. Proteins 2023; 91:724-738. [PMID: 36601892 DOI: 10.1002/prot.26462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/27/2022] [Accepted: 01/02/2023] [Indexed: 01/06/2023]
Abstract
The study aimed to screen prospective molecular targets of BCC and potential natural lead candidates as effective binders by computational modeling, molecular docking, and dynamic (MD) simulation studies. Based on the virulent functions, tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein (mnmC) and pyrimidine/purine nucleoside phosphorylase (ppnP) were selected as the prospective molecular targets. In the absence of experimental data, the three-dimensional (3D) structures of these targets were computationally predicted. After a thorough literature survey and database search, the drug-likeness, and pharmacokinetic properties of 70 natural molecules were computationally predicted and the effectual binding of the best lead molecules against both the targets was predicted by molecular docking. The stabilities of the best-docked complexes were validated by MD simulation and the binding energy calculations were carried out by MM-GBSA approaches. The present study revealed that the hypothetical models of mnmC and ppnP showed stereochemical accuracy. The study also showed that among 70 natural compounds subjected to computational screening, Honokiol (3',5-Di(prop-2-en-1-yl) [1,1'-biphenyl]-2,4'-diol) present in Magnolia showed ideal drug-likeness, pharmacokinetic features and showed effectual binding with mnmC and ppnP (binding energies -7.3 kcal/mol and -6.6 kcal/mol, respectively). The MD simulation and GBSA calculation studies showed that the ligand-protein complexes stabilized throughout tMD simulation. The present study suggests that Honokiol can be used as a potential lead molecule against mnmC and ppnP targets of BCC and this study provides insight into further experimental validation for alternative lead development against drug resistant BCC.
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Affiliation(s)
- Sinosh Skariyachan
- Department of Microbiology, St. Pius X College Rajapuram, Kasaragod, Kerala, India
| | | | - Akshay Uttarkar
- Department of Biotechnology, RV College of Engineering, Bengaluru, Karnataka, India
| | - Vidya Niranjan
- Department of Biotechnology, RV College of Engineering, Bengaluru, Karnataka, India
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27
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Lozano-Terol G, Gallego-Jara J, Sola-Martínez RA, Ortega Á, Martínez Vivancos A, Cánovas Díaz M, de Diego Puente T. Regulation of the pyrimidine biosynthetic pathway by lysine acetylation of E. coli OPRTase. FEBS J 2023; 290:442-464. [PMID: 35989594 PMCID: PMC10087573 DOI: 10.1111/febs.16598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 07/01/2022] [Accepted: 08/19/2022] [Indexed: 02/05/2023]
Abstract
The de novo pyrimidine biosynthesis pathway is an important route due to the relevance of its products, its implications in health and its conservation among organisms. Here, we investigated the regulation by lysine acetylation of this pathway. To this aim, intracellular and extracellular metabolites of the route were quantified, revealing a possible blockage of the pathway by acetylation of the OPRTase enzyme (orotate phosphoribosyltransferase). Chemical acetylation of OPRTase by acetyl-P involved a decrease in enzymatic activity. To test the effect of acetylation in this enzyme, K26 and K103 residues were selected to generate site-specific acetylated proteins. Several differences were observed in kinetic parameters, emphasizing that the kcat of these mutants showed a strong decrease of 300 and 150-fold for OPRTase-103AcK and 19 and 6.3-fold for OPRTase-26AcK, for forward and reverse reactions. In vivo studies suggested acetylation of this enzyme by a nonenzymatic acetyl-P-dependent mechanism and a reversion of this process by the CobB deacetylase. A complementation assay of a deficient strain in the pyrE gene with OPRTase-26AcK and OPRTase-103AcK was performed, and curli formation, stoichiometric parameters and orotate excretion were measured. Complementation with acetylated enzymes entailed a profile very similar to that of the ∆pyrE strain, especially in the case of complementation with OPRTase-103AcK. These results suggest regulation of the de novo pyrimidine biosynthesis pathway by lysine acetylation of OPRTase in Escherichia coli. This finding is of great relevance due to the essential role of this route and the OPRTase enzyme as a target for antimicrobial, antiviral and cancer treatments.
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Affiliation(s)
- Gema Lozano-Terol
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Spain
| | - Julia Gallego-Jara
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Spain
| | - Rosa Alba Sola-Martínez
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Spain
| | - Álvaro Ortega
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Spain
| | - Adrián Martínez Vivancos
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Spain
| | - Manuel Cánovas Díaz
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Spain
| | - Teresa de Diego Puente
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Spain
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Kaur H, Singh V, Kalia M, Mohan B, Taneja N. Identification and functional annotation of hypothetical proteins of uropathogenic Escherichia coli strain CFT073 towards designing antimicrobial drug targets. J Biomol Struct Dyn 2022; 40:14084-14095. [PMID: 34751095 DOI: 10.1080/07391102.2021.2000499] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Urinary tract infections are a serious health concern worldwide, especially in developing countries. Escherichia coli strain CFT073 is a highly virulent pathogenic bacterial strain. CFT073 proteome contains 4897 proteins, out of which 992 have been classified as hypothetical proteins. Identification and characterization of hypothetical proteins can aid in the selection of targets for drug design. In this study, we studied the hypothetical proteins from the UPEC strain CFT073 using various computational tools. By NCBI-CDD, 376 protein sequences showed conserved domains. Based on the functional motifs in their primary sequences, we classified these 376 hypothetical proteins into 7 functional categories. Further KEGG database was used to find the roles of these hypothetical proteins in several pathways. Protein interaction network analysis of hypothetical proteins identified 53 proteins as highly interacting metabolic proteins. Virulence factor analysis of the proteins identified 8 proteins as virulent. We conducted a non-homology search for the identified proteins of UPEC in the available human proteome. We observed that 35 proteins are non-homologous to humans and hence could be selected for drug designing targets. Qualitative characterization of the selected 35 non-homologous hypothetical proteins including essentiality analysis and evaluation of druggability by similarity search against drug bank database was performed. Out of these 35 proteins, three-dimensional structures of six proteins (NP_752562.1, NP_756345.1, NP_754893.1, NP_756600.2, NP_755264.1 and NP_752994.1) could be successfully modelled. These new annotations can help to better understand disease mechanisms at the molecular level, as well as provide new targets for drug development against the UPEC strain CFT073.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Harpreet Kaur
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Vikram Singh
- Center of Computational Biology and Bioinformatics, Central University of Himachal Pradesh, Dharamshala, India
| | - Manmohit Kalia
- Department of Biology, State University of New York, Binghamton, NY, USA
| | - Balvinder Mohan
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Neelam Taneja
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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Wong YC, Naeem R, Abd El Ghany M, Hoh CC, Pain A, Nathan S. Genome-wide transposon mutagenesis analysis of Burkholderia pseudomallei reveals essential genes for in vitro and in vivo survival. Front Cell Infect Microbiol 2022; 12:1062682. [PMID: 36619746 PMCID: PMC9816413 DOI: 10.3389/fcimb.2022.1062682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Introduction Burkholderia pseudomallei, a soil-dwelling microbe that infects humans and animals is the cause of the fatal disease melioidosis. The molecular mechanisms that underlie B. pseudomallei's versatility to survive within a broad range of environments are still not well defined. Methods We used the genome-wide screening tool TraDIS (Transposon Directed Insertion-site Sequencing) to identify B. pseudomallei essential genes. Transposon-flanking regions were sequenced and gene essentiality was assessed based on the frequency of transposon insertions within each gene. Transposon mutants were grown in LB and M9 minimal medium to determine conditionally essential genes required for growth under laboratory conditions. The Caenorhabditis elegans infection model was used to assess genes associated with in vivo B. pseudomallei survival. Transposon mutants were fed to the worms, recovered from worm intestines, and sequenced. Two selected mutants were constructed and evaluated for the bacteria's ability to survive and proliferate in the nematode intestinal lumen. Results Approximately 500,000 transposon-insertion mutants of B. pseudomallei strain R15 were generated. A total of 848,811 unique transposon insertion sites were identified in the B. pseudomallei R15 genome and 492 genes carrying low insertion frequencies were predicted to be essential. A total of 96 genes specifically required to support growth under nutrient-depleted conditions were identified. Genes most likely to be involved in B. pseudomallei survival and adaptation in the C. elegans intestinal lumen, were identified. When compared to wild type B. pseudomallei, a Tn5 mutant of bpsl2988 exhibited reduced survival in the worm intestine, was attenuated in C. elegans killing and showed decreased colonization in the organs of infected mice. Discussion The B. pseudomallei conditional essential proteins should provide further insights into the bacteria's niche adaptation, pathogenesis, and virulence.
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Affiliation(s)
- Yee-Chin Wong
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Malaysia
| | - Raeece Naeem
- Bioscience program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Jeddah, Saudi Arabia
| | - Moataz Abd El Ghany
- Bioscience program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Jeddah, Saudi Arabia,School of Public Health, The University of Sydney, Sydney, NSW, Australia,Centre for Infectious Disease and Microbiology, The Westmead Institute for Medical Research, Sydney, NSW, Australia,Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia
| | | | - Arnab Pain
- Bioscience program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Jeddah, Saudi Arabia
| | - Sheila Nathan
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Malaysia,*Correspondence: Sheila Nathan,
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Pettersen JS, Høg FF, Nielsen FD, Møller-Jensen J, Jørgensen MG. Global transcriptional responses of pneumococcus to human blood components and cerebrospinal fluid. Front Microbiol 2022; 13:1060583. [PMID: 36620004 PMCID: PMC9812572 DOI: 10.3389/fmicb.2022.1060583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 11/22/2022] [Indexed: 12/24/2022] Open
Abstract
Streptococcus pneumoniae (pneumococcus) is a leading cause of severe invasive infectious diseases such as sepsis and meningitis. Understanding how pneumococcus adapts and survive in the human bloodstream environment and cerebrospinal fluid (CSF) is important for development of future treatment strategies. This study investigates the global transcriptional response of pneumococcus to human blood components and CSF acquired from discarded and anonymized patient samples. Extensive transcriptional changes to human blood components were observed during early stages of interaction. Plasma-specific responses were primarily related to metabolic components and include strong downregulation of fatty acid biosynthesis genes, and upregulation of nucleotide biosynthesis genes. No transcriptional responses specific to the active plasma proteins (e.g., complement proteins) were observed during early stages of interaction as demonstrated by a differential expression analysis between plasma and heat-inactivated plasma. The red blood cell (RBC)-specific response was far more complex, and included activation of the competence system, differential expression of several two-component systems, phosphotransferase systems and transition metal transporter genes. Interestingly, most of the changes observed for CSF were also observed for plasma. One of the few CSF-specific responses, not observed for plasma, was a strong downregulation of the iron acquisition system piuBCDA. Intriguingly, this transcriptomic analysis also uncovers significant differential expression of more than 20 small non-coding RNAs, most of them in response to RBCs, including small RNAs from uncharacterized type I toxin-antitoxin systems. In summary, this transcriptomic study identifies key pneumococcal metabolic pathways and regulatory genes involved with adaptation to human blood and CSF. Future studies should uncover the potential involvement of these factors with virulence in-vivo.
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Tiwari D, Narang R, Sudhakar K, Singh V, Lal S, Devgun M. 1,3,4-oxadiazole derivatives as potential antimicrobial agents. Chem Biol Drug Des 2022; 100:1086-1121. [PMID: 35676800 DOI: 10.1111/cbdd.14100] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 05/12/2022] [Accepted: 06/05/2022] [Indexed: 01/25/2023]
Abstract
Due to the emergence of drug-resistant microbial strains, different research groups are continuously developing novel drug molecules against already exploited and unexploited targets. 1,3,4-Oxadiazole derivatives exhibited noteworthy antimicrobial activities. The presence of 1,3,4-oxadiazole moiety in antimicrobial agents can modify their polarity and flexibility, which significantly improves biological activities due to various bonded and non-bonded interactions viz. hydrogen bond, steric, electrostatic, and hydrophobic with target sites. The present review elaborates the therapeutic targets and mode of interaction of 1,3,4-oxadiazoles as antimicrobial agents. 1,3,4-oxadiazole derivatives target enoyl reductase (InhA), 14α-demethylase in the mycobacterial cell; GlcN-6-P synthase, thymidylate synthase, peptide deformylase, RNA polymerase, dehydrosqualene synthase in bacterial strains; ergosterol biosynthesis pathway, P450-14α demethylase, protein-N-myristoyltransferase in fungal strains; FtsZ protein, interfere with purine and functional protein synthesis in plant bacteria. The present review also summarizes the effect of different moieties and functional groups on the antimicrobial activity of 1,3,4-oxadiazole derivatives.
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Affiliation(s)
- Deeksha Tiwari
- Institute of Pharmaceutical Sciences, Kurukshetra University, Kurukshetra, India
| | - Rakesh Narang
- Institute of Pharmaceutical Sciences, Kurukshetra University, Kurukshetra, India
| | - Kalvatala Sudhakar
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, India
| | - Vikramjeet Singh
- Department of Pharmaceutical Sciences, Guru Jambheshwar University of Science and Technology, Hisar, India
| | - Sukhbir Lal
- Institute of Pharmaceutical Sciences, Kurukshetra University, Kurukshetra, India
| | - Manish Devgun
- Institute of Pharmaceutical Sciences, Kurukshetra University, Kurukshetra, India
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Belanger CR, Dostert M, Blimkie TM, Lee AHY, Dhillon BK, Wu BC, Akhoundsadegh N, Rahanjam N, Castillo-Arnemann J, Falsafi R, Pletzer D, Haney CH, Hancock REW. Surviving the host: Microbial metabolic genes required for growth of Pseudomonas aeruginosa in physiologically-relevant conditions. Front Microbiol 2022; 13:1055512. [PMID: 36504765 PMCID: PMC9732424 DOI: 10.3389/fmicb.2022.1055512] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 10/31/2022] [Indexed: 11/27/2022] Open
Abstract
Pseudomonas aeruginosa, like other pathogens, adapts to the limiting nutritional environment of the host by altering patterns of gene expression and utilizing alternative pathways required for survival. Understanding the genes essential for survival in the host gives insight into pathways that this organism requires during infection and has the potential to identify better ways to treat infections. Here, we used a saturated transposon insertion mutant pool of P. aeruginosa strain PAO1 and transposon insertion sequencing (Tn-Seq), to identify genes conditionally important for survival under conditions mimicking the environment of a nosocomial infection. Conditions tested included tissue culture medium with and without human serum, a murine abscess model, and a human skin organoid model. Genes known to be upregulated during infections, as well as those involved in nucleotide metabolism, and cobalamin (vitamin B12) biosynthesis, etc., were required for survival in vivo- and in host mimicking conditions, but not in nutrient rich lab medium, Mueller Hinton broth (MHB). Correspondingly, mutants in genes encoding proteins of nucleotide and cobalamin metabolism pathways were shown to have growth defects under physiologically-relevant media conditions, in vivo, and in vivo-like models, and were downregulated in expression under these conditions, when compared to MHB. This study provides evidence for the relevance of studying P. aeruginosa fitness in physiologically-relevant host mimicking conditions and identified metabolic pathways that represent potential novel targets for alternative therapies.
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Affiliation(s)
- Corrie R. Belanger
- Centre for Microbial Diseases and Immunity Research, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Melanie Dostert
- Centre for Microbial Diseases and Immunity Research, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Travis M. Blimkie
- Centre for Microbial Diseases and Immunity Research, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Amy Huei-Yi Lee
- Centre for Microbial Diseases and Immunity Research, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Bhavjinder Kaur Dhillon
- Centre for Microbial Diseases and Immunity Research, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Bing Catherine Wu
- Centre for Microbial Diseases and Immunity Research, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Noushin Akhoundsadegh
- Centre for Microbial Diseases and Immunity Research, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Negin Rahanjam
- Centre for Microbial Diseases and Immunity Research, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Javier Castillo-Arnemann
- Centre for Microbial Diseases and Immunity Research, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Reza Falsafi
- Centre for Microbial Diseases and Immunity Research, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Daniel Pletzer
- Centre for Microbial Diseases and Immunity Research, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada,Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Cara H. Haney
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Robert E. W. Hancock
- Centre for Microbial Diseases and Immunity Research, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada,*Correspondence: Robert E. W. Hancock,
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Gonçalves LG, Santos S, Gomes LP, Armengaud J, Miragaia M, Coelho AV. Skin-to-blood pH shift triggers metabolome and proteome global remodelling in Staphylococcus epidermidis. Front Microbiol 2022; 13:1000737. [PMID: 36246270 PMCID: PMC9554481 DOI: 10.3389/fmicb.2022.1000737] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 08/29/2022] [Indexed: 11/13/2022] Open
Abstract
Staphylococcus epidermidis is one of the most common bacteria of the human skin microbiota. Despite its role as a commensal, S. epidermidis has emerged as an opportunistic pathogen, associated with 80% of medical devices related infections. Moreover, these bacteria are extremely difficult to treat due to their ability to form biofilms and accumulate resistance to almost all classes of antimicrobials. Thus new preventive and therapeutic strategies are urgently needed. However, the molecular mechanisms associated with S. epidermidis colonisation and disease are still poorly understood. A deeper understanding of the metabolic and cellular processes associated with response to environmental factors characteristic of SE ecological niches in health and disease might provide new clues on colonisation and disease processes. Here we studied the impact of pH conditions, mimicking the skin pH (5.5) and blood pH (7.4), in a S. epidermidis commensal strain by means of next-generation proteomics and 1H NMR-based metabolomics. Moreover, we evaluated the metabolic changes occurring during a sudden pH change, simulating the skin barrier break produced by a catheter. We found that exposure of S. epidermidis to skin pH induced oxidative phosphorylation and biosynthesis of peptidoglycan, lipoteichoic acids and betaine. In contrast, at blood pH, the bacterial assimilation of monosaccharides and its oxidation by glycolysis and fermentation was promoted. Additionally, several proteins related to virulence and immune evasion, namely extracellular proteases and membrane iron transporters were more abundant at blood pH. In the situation of an abrupt skin-to-blood pH shift we observed the decrease in the osmolyte betaine and changes in the levels of several metabolites and proteins involved in cellular redoxl homeostasis. Our results suggest that at the skin pH S. epidermidis cells are metabolically more active and adhesion is promoted, while at blood pH, metabolism is tuned down and cells have a more virulent profile. pH increase during commensal-to-pathogen conversion appears to be a critical environmental signal to the remodelling of the S. epidermidis metabolism toward a more pathogenic state. Targeting S. epidermidis proteins induced by pH 7.4 and promoting the acidification of the medical device surface or surrounding environment might be new strategies to treat and prevent S. epidermidis infections.
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Affiliation(s)
- Luis Gafeira Gonçalves
- Laboratory of Proteomics of Non-Model Organisms, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Susana Santos
- Laboratory of Proteomics of Non-Model Organisms, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Laidson Paes Gomes
- Laboratory of Proteomics of Non-Model Organisms, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé, SPI, Université Paris-Saclay, CEA, INRAE, Bagnols-sur-Cèze, France
| | - Maria Miragaia
- Laboratory of Bacterial Evolution and Molecular Epidemiology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- *Correspondence: Maria Miragaia,
| | - Ana Varela Coelho
- Laboratory of Proteomics of Non-Model Organisms, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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Shi X, Gao B, Srivastava A, Izzi Z, Abdalla Y, Shen W, Raj D. Alterations of gut microbial pathways and virulence factors in hemodialysis patients. Front Cell Infect Microbiol 2022; 12:904284. [PMID: 36093194 PMCID: PMC9461950 DOI: 10.3389/fcimb.2022.904284] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
Alterations in gut microbiota might contribute to uremic toxicity and immune dysregulation in patients with end-stage renal disease. Hemodialysis patients are prone to infection and higher mortality following sepsis. The virulence factors in the gut metagenome have not been well studied in hemodialysis patients, which could be employed by microorganisms to successfully thrive and flourish in their hosts. In this study, we performed shotgun metagenomics sequencing on fecal DNA collected from 16 control subjects and 24 hemodialysis patients. Our analysis shows that a number of microbial species, metabolic pathways, antibiotic resistance, and virulence factors were significantly altered in hemodialysis patients compared with controls. In particular, erythromycin resistance methylase, pyridoxamine 5-phosphate oxidase, and streptothricin-acetyl-transferase were significantly increased in hemodialysis patients. The findings in our study laid a valuable foundation to further elucidate the causative role of virulence factors in predisposing HD patients to infection and to develop treatment strategies to reduce the genetic capacities of antibiotic resistance and virulence factors in HD patients.
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Affiliation(s)
- Xiaochun Shi
- Department of Environmental Ecological Engineering, School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, Nanjing, China
| | - Bei Gao
- School of Marine Sciences, Nanjing University of Information Science and Technology, Nanjing, China
| | - Anvesha Srivastava
- Division of Kidney Diseases and Hypertension, George Washington University School of Medicine, Washington, DC, United States
| | - Zahra Izzi
- Langley High School, McLean, VA, United States
| | - Yoosif Abdalla
- Division of Kidney Diseases and Hypertension, George Washington University School of Medicine, Washington, DC, United States
| | - Weishou Shen
- Department of Environmental Ecological Engineering, School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, Nanjing, China
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Collaborative In-novation Center of Atmospheric Environment and Equipment Technology, Nanjing, China
- *Correspondence: Weishou Shen,
| | - Dominic Raj
- Division of Kidney Diseases and Hypertension, George Washington University School of Medicine, Washington, DC, United States
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Jiang Q, Lin L, Xie F, Jin W, Zhu W, Wang M, Qiu Q, Li Z, Liu J, Mao S. Metagenomic insights into the microbe-mediated B and K 2 vitamin biosynthesis in the gastrointestinal microbiome of ruminants. MICROBIOME 2022; 10:109. [PMID: 35864536 PMCID: PMC9306216 DOI: 10.1186/s40168-022-01298-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 06/02/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND B and K2 vitamins, essential nutrients in host metabolism, can be synthesized by the rumen microbiome in ruminants and subsequently absorbed by the host. However, the B and K2 vitamin biosynthesis by the whole gastrointestinal microbiome and their abundances in different dietary strategies are largely unknown. Here, we reanalyzed our previous large-scale metagenomic data on the gastrointestinal microbiome of seven ruminant species and recruited 17,425 nonredundant microbial genomes from published datasets to gain a comprehensive understanding of the microbe-mediated B and K2 vitamin biosynthesis in ruminants. RESULTS We identified 1,135,807 genes and 167 enzymes involved in B and K2 vitamin biosynthesis. Our results indicated that the total abundances of B and K2 vitamin biosynthesis were dominant in the stomach microbiome, while the biosynthesis of thiamine, niacin, and pyridoxine was more abundant in the large intestine. By examining 17,425 nonredundant genomes, we identified 2366 high-quality genomes that were predicted to de novo biosynthesize at least one vitamin. Genomic analysis suggested that only 2.7% of these genomes can synthesize five or more vitamins, and nearly half of genomes can synthesize only one vitamin. Moreover, we found that most genomes possessed cobalamin transporters or cobalamin-dependent enzymes to consume cobalamin directly, and only a few microbial genomes possessed a complete cobalamin biosynthesis pathway. Based on these genomic data, we examined the effect of the high-grain (HG) diet on the vitamin biosynthesis of the rumen microbiome of dairy cattle. We revealed that most vitamin biosynthesis was enhanced in the HG group, while only cobalamin synthesis was inhibited in the HG group, indicating that dietary fiber is vital for cobalamin biosynthesis. CONCLUSIONS We primarily provided a gene catalog and 2366 microbial genomes involved in B and K2 vitamin biosynthesis in ruminants. Our findings demonstrated the regional heterogeneity and dietary effect of vitamin biosynthetic potential in the ruminant gastrointestinal microbiome and interpreted the biosynthesis mechanisms of these microbes and their physiological adaptability. This study expands our understanding of microbe-mediated vitamin biosynthesis in ruminants and may provide novel targets for manipulation to improve the production of these essential vitamins. Video abstract.
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Affiliation(s)
- Qian Jiang
- Centre for Ruminant Nutrition and Feed Technology Research, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
| | - Limei Lin
- Centre for Ruminant Nutrition and Feed Technology Research, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
| | - Fei Xie
- Centre for Ruminant Nutrition and Feed Technology Research, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
| | - Wei Jin
- Centre for Ruminant Nutrition and Feed Technology Research, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
| | - Weiyun Zhu
- Centre for Ruminant Nutrition and Feed Technology Research, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
| | - Min Wang
- CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Qiang Qiu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Zhipeng Li
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Junhua Liu
- Centre for Ruminant Nutrition and Feed Technology Research, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China.
| | - Shengyong Mao
- Centre for Ruminant Nutrition and Feed Technology Research, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China.
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Abatedaga I, Perez Mora B, Tuttobene M, Müller G, Biancotti D, Borsarelli CD, Valle L, Mussi MA. Characterization of BLUF-photoreceptors present in Acinetobacter nosocomialis. PLoS One 2022; 17:e0254291. [PMID: 35442978 PMCID: PMC9020721 DOI: 10.1371/journal.pone.0254291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 03/01/2022] [Indexed: 11/18/2022] Open
Abstract
Acinetobacter nosocomialis is a Gram-negative opportunistic pathogen, whose ability to cause disease in humans is well recognized. Blue light has been shown to modulate important physiological traits related to persistence and virulence in this microorganism. In this work, we characterized the three Blue Light sensing Using FAD (BLUF) domain-containing proteins encoded in the A. nosocomialis genome, which account for the only canonical light sensors present in this microorganism. By focusing on a light-modulated bacterial process such as motility, the temperature dependence of light regulation was studied, as well as the expression pattern and spectroscopic characteristics of the different A. nosocomialis BLUFs. Our results show that the BLUF-containing proteins AnBLUF65 and AnBLUF46 encode active photoreceptors in the light-regulatory temperature range when expressed recombinantly. In fact, AnBLUF65 is an active photoreceptor in the temperature range from 15°C to 37°C, while AnBLUF46 between 15°C to 32°C, in vitro. In vivo, only the Acinetobacter baumannii BlsA’s ortholog AnBLUF65 was expressed in A. nosocomialis cells recovered from motility plates. Moreover, complementation assays showed that AnBLUF65 is able to mediate light regulation of motility in A. baumannii ΔblsA strain at 30°C, confirming its role as photoreceptor and in modulation of motility by light. Intra-protein interactions analyzed using 3D models built based on A. baumannii´s BlsA photoreceptor, show that hydrophobic/aromatic intra-protein interactions may contribute to the stability of dark/light- adapted states of the studied proteins, reinforcing the previous notion on the importance of these interactions in BLUF photoreceptors. Overall, the results presented here reveal the presence of BLUF photoreceptors in A. nosocomialis with idiosyncratic characteristics respect to the previously characterized A. baumannii’s BlsA, both regarding the photoactivity temperature-dependency as well as expression patterns, contributing thus to broaden our knowledge on the BLUF family.
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Affiliation(s)
- Inés Abatedaga
- Instituto de Bionanotecnología del NOA (INBIONATEC-CONICET), Universidad Nacional de Santiago del Estero (UNSE), Santiago del Estero, Argentina
| | - Bárbara Perez Mora
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario (UNR), Rosario, Argentina
| | - Marisel Tuttobene
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario (UNR), Rosario, Argentina
| | - Gabriela Müller
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario (UNR), Rosario, Argentina
| | - Daiana Biancotti
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario (UNR), Rosario, Argentina
| | - Claudio D. Borsarelli
- Instituto de Bionanotecnología del NOA (INBIONATEC-CONICET), Universidad Nacional de Santiago del Estero (UNSE), Santiago del Estero, Argentina
- Instituto de Ciencias Químicas (ICQ), Facultad de Agronomía y Agroindustrias (FAyA), UNSE, Santiago del Estero, Argentina
| | - Lorena Valle
- Instituto de Bionanotecnología del NOA (INBIONATEC-CONICET), Universidad Nacional de Santiago del Estero (UNSE), Santiago del Estero, Argentina
- Instituto de Ciencias Químicas (ICQ), Facultad de Agronomía y Agroindustrias (FAyA), UNSE, Santiago del Estero, Argentina
- * E-mail: (MAM); (LV)
| | - Maria A. Mussi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario (UNR), Rosario, Argentina
- * E-mail: (MAM); (LV)
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Charoensutthivarakul S, Thomas SE, Curran A, Brown KP, Belardinelli JM, Whitehouse AJ, Acebrón-García-de-Eulate M, Sangan J, Gramani SG, Jackson M, Mendes V, Floto RA, Blundell TL, Coyne AG, Abell C. Development of Inhibitors of SAICAR Synthetase (PurC) from Mycobacterium abscessus Using a Fragment-Based Approach. ACS Infect Dis 2022; 8:296-309. [PMID: 35037462 PMCID: PMC7614835 DOI: 10.1021/acsinfecdis.1c00432] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Mycobacterium abscessus (Mab) has emerged as a challenging threat to individuals with cystic fibrosis. Infections caused by this pathogen are often impossible to treat due to the intrinsic antibiotic resistance leading to lung malfunction and eventually death. Therefore, there is an urgent need to develop new drugs against novel targets in Mab to overcome drug resistance and subsequent treatment failure. In this study, SAICAR synthetase (PurC) from Mab was identified as a promising target for novel antibiotics. An in-house fragment library screen and a high-throughput X-ray crystallographic screen of diverse fragment libraries were explored to provide crucial starting points for fragment elaboration. A series of compounds developed from fragment growing and merging strategies, guided by crystallographic information and careful hit-to-lead optimization, have achieved potent nanomolar binding affinity against the enzyme. Some compounds also show a promising inhibitory effect against Mab and Mtb. This work utilizes a fragment-based design and demonstrates for the first time the potential to develop inhibitors against PurC from Mab.
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Affiliation(s)
- Sitthivut Charoensutthivarakul
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom.,School of Bioinnovation and Bio-based Product Intelligence, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Sherine E Thomas
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Amy Curran
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Karen P Brown
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular Biology, University of Cambridge, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom.,Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge CB23 3RE, United Kingdom
| | - Juan M Belardinelli
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523-1682, United States
| | - Andrew J Whitehouse
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | | | - Jaspar Sangan
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular Biology, University of Cambridge, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom.,Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge CB23 3RE, United Kingdom
| | - Subramanian G Gramani
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523-1682, United States
| | - Vitor Mendes
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - R Andres Floto
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular Biology, University of Cambridge, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom.,Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge CB23 3RE, United Kingdom
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Anthony G Coyne
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Chris Abell
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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38
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Goncheva MI, Chin D, Heinrichs DE. Nucleotide biosynthesis: the base of bacterial pathogenesis. Trends Microbiol 2022; 30:793-804. [PMID: 35074276 DOI: 10.1016/j.tim.2021.12.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 01/08/2023]
Abstract
Most free-living organisms require the synthesis and/or acquisition of purines and pyrimidines, which form the basis of nucleotides, to survive. In most bacteria, the nucleotides are synthesized de novo and the products are used in many cell functions, including DNA replication, energy storage, and as signaling molecules. Due to their central role in the metabolism of bacteria, both nucleotide biosynthesis pathways have strong links with the virulence of opportunistic and bona fide bacterial pathogens. Recent findings have established a new, shared link in the control of nucleotide biosynthesis and the production of virulence factors. Furthermore, targeting of these pathways forms the basis of interspecies competition and can provide an open source for new antimicrobial compounds. Here, we highlight the contribution of nucleotide biosynthesis to bacterial pathogenesis in a plethora of different diseases and speculate on how they can be targeted by intervention strategies.
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Affiliation(s)
- Mariya I Goncheva
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada N6A 5C1
| | - Denny Chin
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada N6A 5C1
| | - David E Heinrichs
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada N6A 5C1.
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39
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Gao B, Wu TC, Lang S, Jiang L, Duan Y, Fouts DE, Zhang X, Tu XM, Schnabl B. Machine Learning Applied to Omics Datasets Predicts Mortality in Patients with Alcoholic Hepatitis. Metabolites 2022; 12:41. [PMID: 35050163 PMCID: PMC8781791 DOI: 10.3390/metabo12010041] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/31/2021] [Accepted: 01/01/2022] [Indexed: 12/14/2022] Open
Abstract
Alcoholic hepatitis is a major health care burden in the United States due to significant morbidity and mortality. Early identification of patients with alcoholic hepatitis at greatest risk of death is extremely important for proper treatments and interventions to be instituted. In this study, we used gradient boosting, random forest, support vector machine and logistic regression analysis of laboratory parameters, fecal bacterial microbiota, fecal mycobiota, fecal virome, serum metabolome and serum lipidome to predict mortality in patients with alcoholic hepatitis. Gradient boosting achieved the highest AUC of 0.87 for both 30-day mortality prediction using the bacteria and metabolic pathways dataset and 90-day mortality prediction using the fungi dataset, which showed better performance than the currently used model for end-stage liver disease (MELD) score.
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Affiliation(s)
- Bei Gao
- School of Marine Sciences, Nanjing University of Information Science and Technology, Nanjing 210044, China;
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA; (S.L.); (L.J.); (Y.D.)
| | - Tsung-Chin Wu
- Department of Mathematics, University of California San Diego, San Diego, CA 92093, USA;
- Division of Biostatistics and Bioinformatics, Herbert Wertheim School of Public Health, University of California San Diego, San Diego, CA 92093, USA; (X.Z.); (X.-M.T.)
| | - Sonja Lang
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA; (S.L.); (L.J.); (Y.D.)
| | - Lu Jiang
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA; (S.L.); (L.J.); (Y.D.)
- Department of Medicine, VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Yi Duan
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA; (S.L.); (L.J.); (Y.D.)
| | | | - Xinlian Zhang
- Division of Biostatistics and Bioinformatics, Herbert Wertheim School of Public Health, University of California San Diego, San Diego, CA 92093, USA; (X.Z.); (X.-M.T.)
| | - Xin-Ming Tu
- Division of Biostatistics and Bioinformatics, Herbert Wertheim School of Public Health, University of California San Diego, San Diego, CA 92093, USA; (X.Z.); (X.-M.T.)
| | - Bernd Schnabl
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA; (S.L.); (L.J.); (Y.D.)
- Department of Medicine, VA San Diego Healthcare System, San Diego, CA 92161, USA
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40
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Whole-genome sequencing reveals high genetic diversity of Streptococcus uberis isolated from cows with mastitis. BMC Vet Res 2021; 17:321. [PMID: 34620161 PMCID: PMC8496047 DOI: 10.1186/s12917-021-03031-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 09/17/2021] [Indexed: 11/18/2022] Open
Abstract
Background Bovine mastitis is an important cause of economic loss in dairy farms. Streptococcus uberis is among the most frequently isolated bacterial species isolated from cows with mastitis. The aim of this study was to perform an in-depth genetic assessment of S. uberis strains isolated from bovine clinical mastitis (CM) and to perform a phylogenetic analysis to represent the evolutionary relationship among S. uberis sequences. Results A total of 159 isolates was genetically characterized using whole genome sequencing. According to the virulence determinants, all strains harbored the hasC, leuS, perR, purH, and purN virulence genes. Thirty-four resistance genes were identified in at least one strain. In terms of acquired genes, we observed that 152 (95.6 %) strains had a resistance gene to lincosamine (lnuD), 48 (30.2 %) to tetracycline (tetM), 4 (2.51 %) to tobramicine (ant6), and 1 to lincosamide (lsa(E)). MLST detected the Sequence Type (ST)797 (n = 23), while 85.5 % of the strains did not match to known STs. Conclusions Then, eleven distinct ST were identified after we submitted the new alleles to assign new STs. The other prevalent STs observed were ST1215 (n = 58), ST1219 (n = 35), and ST1213 (n = 15). And it was not possible to identify the MLST of four strains. Phylogenetic lineages indicated a high genomic diversity of S. uberis in our collection, confirming that most strains isolated from bovine mastitis have different reservoirs, typical of environmental pathogens.
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41
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Complexed Crystal Structure of Saccharomyces cerevisiae Dihydroorotase with Inhibitor 5-Fluoroorotate Reveals a New Binding Mode. Bioinorg Chem Appl 2021; 2021:2572844. [PMID: 34630544 PMCID: PMC8497156 DOI: 10.1155/2021/2572844] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 07/30/2021] [Accepted: 09/14/2021] [Indexed: 02/08/2023] Open
Abstract
Dihydroorotase (DHOase) possesses a binuclear metal center in which two Zn ions are bridged by a posttranslationally carbamylated lysine. DHOase catalyzes the reversible cyclization of N-carbamoyl aspartate (CA-asp) to dihydroorotate (DHO) in the third step of the pathway for the biosynthesis of pyrimidine nucleotides and is an attractive target for potential anticancer and antimalarial chemotherapy. Crystal structures of ligand-bound DHOase show that the flexible loop extends toward the active site when CA-asp is bound (loop-in mode) or moves away from the active site, facilitating the product DHO release (loop-out mode). DHOase binds the product-like inhibitor 5-fluoroorotate (5-FOA) in a similar mode to DHO. In the present study, we report the crystal structure of DHOase from Saccharomyces cerevisiae (ScDHOase) complexed with 5-FOA at 2.5 Å resolution (PDB entry 7CA0). ScDHOase shares structural similarity with Escherichia coli DHOase (EcDHOase). However, our complexed structure revealed that ScDHOase bound 5-FOA differently from EcDHOase. 5-FOA ligated the Zn atoms in the active site of ScDHOase. In addition, 5-FOA bound to ScDHOase through the loop-in mode. We also characterized the binding of 5-FOA to ScDHOase by using the site-directed mutagenesis and fluorescence quenching method. Based on these lines of molecular evidence, we discussed whether these different binding modes are species- or crystallography-dependent.
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42
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Hyun H, Lee MS, Park I, Ko HS, Yun S, Jang DH, Kim S, Kim H, Kang JH, Lee JH, Kwon T. Analysis of Porcine Model of Fecal-Induced Peritonitis Reveals the Tropism of Blood Microbiome. Front Cell Infect Microbiol 2021; 11:676650. [PMID: 34527598 PMCID: PMC8435847 DOI: 10.3389/fcimb.2021.676650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 08/12/2021] [Indexed: 11/22/2022] Open
Abstract
Recent studies have suggested the existence of a blood microbiome in the healthy host. However, changes in the blood microbiome upon bloodstream infection are not known. Here, we analyzed the dynamics of the blood microbiome in a porcine model of polymicrobial bacteremia induced by fecal peritonitis. Surprisingly, we detected bacterial populations in the bloodstream even before the infection, and these populations were maintained over time. The native blood microbiome was notably taxonomically different from the fecal microbiome that was used to induce peritonitis, reflecting microbial tropism for the blood. Although the population composition after the infection was similar to that of the native blood microbiome, new bacterial strains entered the bloodstream upon peritonitis induction as clinical symptoms relevant to sepsis developed. This indicates that the bacteria detected in the blood before peritonitis induction were derived from the blood rather than a contamination. Comparison of the functional pathways enriched in the blood and fecal microbiomes revealed that communication and stress management pathways are essential for the survival of the blood microbiome.
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Affiliation(s)
- Hwi Hyun
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Min Seok Lee
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Inwon Park
- Department of Emergency Medicine, Seoul National University Bundang Hospital, Seongnam-si, South Korea
| | - Hwa Soo Ko
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Seongmin Yun
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Dong-Hyun Jang
- Department of Emergency Medicine, Seoul National University Bundang Hospital, Seongnam-si, South Korea
| | - Seonghye Kim
- Department of Emergency Medicine, Seoul National University Bundang Hospital, Seongnam-si, South Korea
| | - Hajin Kim
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Joo H Kang
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Jae Hyuk Lee
- Department of Emergency Medicine, Seoul National University Bundang Hospital, Seongnam-si, South Korea
| | - Taejoon Kwon
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea.,Center for Genomic Integrity, Institute for Basic Science, Ulsan, South Korea
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Guan HH, Huang YH, Lin ES, Chen CJ, Huang CY. Plumbagin, a Natural Product with Potent Anticancer Activities, Binds to and Inhibits Dihydroorotase, a Key Enzyme in Pyrimidine Biosynthesis. Int J Mol Sci 2021; 22:6861. [PMID: 34202294 PMCID: PMC8267945 DOI: 10.3390/ijms22136861] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/16/2021] [Accepted: 06/22/2021] [Indexed: 12/11/2022] Open
Abstract
Dihydroorotase (DHOase) is the third enzyme in the de novo biosynthesis pathway for pyrimidine nucleotides, and an attractive target for potential anticancer chemotherapy. By screening plant extracts and performing GC-MS analysis, we identified and characterized that the potent anticancer drug plumbagin (PLU), isolated from the carnivorous plant Nepenthes miranda, was a competitive inhibitor of DHOase. We also solved the complexed crystal structure of yeast DHOase with PLU (PDB entry 7CA1), to determine the binding interactions and investigate the binding modes. Mutational and structural analyses indicated the binding of PLU to DHOase through loop-in mode, and this dynamic loop may serve as a drug target. PLU exhibited cytotoxicity on the survival, migration, and proliferation of 4T1 cells and induced apoptosis. These results provide structural insights that may facilitate the development of new inhibitors targeting DHOase, for further clinical anticancer chemotherapies.
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Affiliation(s)
- Hong-Hsiang Guan
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan;
| | - Yen-Hua Huang
- School of Biomedical Sciences, Chung Shan Medical University, No. 110, Sec.1, Chien-Kuo N. Rd., Taichung City 402, Taiwan;
| | - En-Shyh Lin
- Department of Beauty Science, National Taichung University of Science and Technology, No. 193, Sec.1, San-Min Rd., Taichung City 403, Taiwan;
| | - Chun-Jung Chen
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan;
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan City 701, Taiwan
- Department of Physics, National Tsing Hua University, Hsinchu 30043, Taiwan
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 300193, Taiwan
| | - Cheng-Yang Huang
- School of Biomedical Sciences, Chung Shan Medical University, No. 110, Sec.1, Chien-Kuo N. Rd., Taichung City 402, Taiwan;
- Department of Medical Research, Chung Shan Medical University Hospital, No. 110, Sec.1, Chien-Kuo N. Rd., Taichung City 402, Taiwan
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Rosado D, Xavier R, Cable J, Severino R, Tarroso P, Pérez-Losada M. Longitudinal sampling of external mucosae in farmed European seabass reveals the impact of water temperature on bacterial dynamics. ISME COMMUNICATIONS 2021; 1:28. [PMID: 36739461 PMCID: PMC9723769 DOI: 10.1038/s43705-021-00019-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/13/2021] [Indexed: 02/06/2023]
Abstract
Fish microbiota are intrinsically linked to health and fitness, but they are highly variable and influenced by both biotic and abiotic factors. Water temperature particularly limits bacterial adhesion and growth, impacting microbial diversity and bacterial infections on the skin and gills. Aquaculture is heavily affected by infectious diseases, especially in warmer months, and industry practices often promote stress and microbial dysbiosis, leading to an increased abundance of potentially pathogenic bacteria. In this regard, fish mucosa health is extremely important because it provides a primary barrier against pathogens. We used 16 rRNA V4 metataxonomics to characterize the skin and gill microbiota of the European seabass, Dicentrarchus labrax, and the surrounding water over 12 months, assessing the impact of water temperature on microbial diversity and function. We show that the microbiota of external mucosae are highly dynamic with consistent longitudinal trends in taxon diversity. Several potentially pathogenic genera (Aliivibrio, Photobacterium, Pseudomonas, and Vibrio) were highly abundant, showing complex interactions with other bacterial genera, some of which with recognized probiotic activity, and were also significantly impacted by changes in temperature. The surrounding water temperature influenced fish microbial composition, structure and function over time (days and months). Additionally, dysbiosis was more frequent in warmer months and during transitions between cold/warm months. We also detected a strong seasonal effect in the fish microbiota, which is likely to result from the compound action of several unmeasured environmental factors (e.g., pH, nutrient availability) beyond temperature. Our results highlight the importance of performing longitudinal studies to assess the impact of environmental factors on fish microbiotas.
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Affiliation(s)
- Daniela Rosado
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal.
| | - Raquel Xavier
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal.
| | - Jo Cable
- School of Biosciences, Cardiff University, Cardiff, UK
| | - Ricardo Severino
- Piscicultura Vale da Lama, Sapal do Vale da Lama, Odiáxere, Lagos, Portugal
| | - Pedro Tarroso
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
| | - Marcos Pérez-Losada
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC, USA
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Brucella ovis Cysteine Biosynthesis Contributes to Peroxide Stress Survival and Fitness in the Intracellular Niche. Infect Immun 2021; 89:IAI.00808-20. [PMID: 33753413 DOI: 10.1128/iai.00808-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/15/2021] [Indexed: 11/20/2022] Open
Abstract
Brucella ovis is an ovine intracellular pathogen with tropism for the male genital tract. To establish and maintain infection, B. ovis must survive stressful conditions inside host cells, including low pH, nutrient limitation, and reactive oxygen species. The same conditions are often encountered in axenic cultures during stationary phase. Studies of stationary phase may thus inform our understanding of Brucella infection biology, yet the genes and pathways that are important in Brucella stationary-phase physiology remain poorly defined. We measured fitness of a barcoded pool of B. ovis Tn-himar mutants as a function of growth phase and identified cysE as a determinant of fitness in stationary phase. CysE catalyzes the first step in cysteine biosynthesis from serine, and we provide genetic evidence that two related enzymes, CysK1 and CysK2, function redundantly to catalyze cysteine synthesis at steps downstream of CysE. Deleting cysE (ΔcysE) or both cysK1 and cysK2 (ΔcysK1 ΔcysK2) results in premature entry into stationary phase, reduced culture yield, and sensitivity to exogenous hydrogen peroxide. These phenotypes can be chemically complemented by cysteine or glutathione. ΔcysE and ΔcysK1 ΔcysK2 strains have no defect in host cell entry in vitro but have significantly diminished intracellular fitness between 2 and 24 h postinfection. Our study has uncovered unexpected redundancy at the CysK step of cysteine biosynthesis in B. ovis and demonstrates that cysteine anabolism is a determinant of peroxide stress survival and fitness in the intracellular niche.
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46
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Abstract
Animals live in symbiosis with numerous microbe species. While some can protect hosts from infection and benefit host health, components of the microbiota or changes to the microbial landscape have the potential to facilitate infections and worsen disease severity. Pathogens and pathobionts can exploit microbiota metabolites, or can take advantage of a depletion in host defences and changing conditions within a host, to cause opportunistic infection. The microbiota might also favour a more virulent evolutionary trajectory for invading pathogens. In this review, we consider the ways in which a host microbiota contributes to infectious disease throughout the host's life and potentially across evolutionary time. We further discuss the implications of these negative outcomes for microbiota manipulation and engineering in disease management.
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Affiliation(s)
- Emily J. Stevens
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Kieran A. Bates
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Kayla C. King
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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Zhu B, Green SP, Ge X, Puccio T, Nadhem H, Ge H, Bao L, Kitten T, Xu P. Genome-wide identification of Streptococcus sanguinis fitness genes in human serum and discovery of potential selective drug targets. Mol Microbiol 2021; 115:658-671. [PMID: 33084151 PMCID: PMC8055731 DOI: 10.1111/mmi.14629] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/20/2020] [Accepted: 10/16/2020] [Indexed: 12/17/2022]
Abstract
Streptococcus sanguinis is a primary colonizer of teeth and is associated with oral health. When it enters the bloodstream, however, this bacterium may cause the serious illness infective endocarditis. The genes required for survival and proliferation in blood have not been identified. The products of these genes could provide a rich source of targets for endocarditis-specific antibiotics possessing greater efficacy for endocarditis, and also little or no activity against those bacteria that remain in the mouth. We previously created a comprehensive library of S. sanguinis mutants lacking every nonessential gene. We have now screened each member of this library for growth in human serum and discovered 178 mutants with significant abundance changes. The main biological functions disrupted in these mutants, including purine metabolism, were highlighted via network analysis. The components of an ECF-family transporter were required for growth in serum and were shown for the first time in any bacterium to be essential for endocarditis virulence. We also identified two mutants whose growth was reduced in serum but not in saliva. This strategy promises to enable selective targeting of bacteria based on their location in the body, in this instance, treating or preventing endocarditis while leaving the oral microbiome intact.
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Affiliation(s)
- Bin Zhu
- Philips Institute for Oral Health ResearchVirginia Commonwealth UniversityRichmondVAUSA
| | - Shannon P. Green
- Philips Institute for Oral Health ResearchVirginia Commonwealth UniversityRichmondVAUSA
- Department of Microbiology and ImmunologyVirginia Commonwealth UniversityRichmondVAUSA
| | - Xiuchun Ge
- Philips Institute for Oral Health ResearchVirginia Commonwealth UniversityRichmondVAUSA
| | - Tanya Puccio
- Philips Institute for Oral Health ResearchVirginia Commonwealth UniversityRichmondVAUSA
| | - Haider Nadhem
- Philips Institute for Oral Health ResearchVirginia Commonwealth UniversityRichmondVAUSA
| | - Henry Ge
- Philips Institute for Oral Health ResearchVirginia Commonwealth UniversityRichmondVAUSA
| | - Liang Bao
- Philips Institute for Oral Health ResearchVirginia Commonwealth UniversityRichmondVAUSA
| | - Todd Kitten
- Philips Institute for Oral Health ResearchVirginia Commonwealth UniversityRichmondVAUSA
- Department of Microbiology and ImmunologyVirginia Commonwealth UniversityRichmondVAUSA
| | - Ping Xu
- Philips Institute for Oral Health ResearchVirginia Commonwealth UniversityRichmondVAUSA
- Department of Microbiology and ImmunologyVirginia Commonwealth UniversityRichmondVAUSA
- Center for Biological Data ScienceVirginia Commonwealth UniversityRichmondVAUSA
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Kim S, Chung HY, Kwon JG, Choi SH, Lee JH. Fresh Crab Plays an Important Role as a Nutrient Reservoir for the Rapid Propagation of Vibrio vulnificus. Front Microbiol 2021; 12:645860. [PMID: 33767684 PMCID: PMC7985530 DOI: 10.3389/fmicb.2021.645860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 02/12/2021] [Indexed: 12/19/2022] Open
Abstract
Vibrio vulnificus is a well-known opportunistic pathogen causing food-borne illnesses by ingestion of contaminated seafood. A new strain of V. vulnificus FORC_016 was isolated from a patient's blood sample in South Korea. The genome consists of two circular DNA chromosomes: chromosome I (3,234,424 bp with a G + C contents of 46.60% containing 2,889 ORFs, 106 tRNA genes, and 31 rRNA genes) and chromosome II (1,837,945 bp with a GC content of 47.00% containing 1,572 ORFs, 13 tRNA genes, and 3 rRNA genes). In addition, chromosome I has a super integron (SI) containing 209 ORFs, which is probably associated with various additional functions including antibiotic resistance and pathogenicity. Pan-genome analysis with other V. vulnificus genomes revealed that core genome regions contain most of the important virulence factors. However, accessory genome regions are located in the SI region and contain unique genes regarding cell wall biosynthesis and generation of host cell protecting capsule, suggesting possible resistance ability against environmental stresses. Comparative RNA-Seq analysis of samples between contact and no contact to the crab conditions showed that expressions of amino acid/peptide and carbohydrate transport and utilization genes were down-regulated, but expressions of cell division and growth-related genes were up-regulated, suggesting that the crab may be a nutrition reservoir for rapid propagation of V. vulnificus. Therefore, consumption of the contaminated fresh crab would provide a large number of V. vulnificus to humans, which may be more dangerous. Consequently, biocontrol of V. vulnificus may be critical to ensure the safety in seafood consumption.
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Affiliation(s)
- Suyeon Kim
- National Research Laboratory of Molecular Microbiology and Toxicology, Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Seoul National University, Seoul, South Korea
| | - Han Young Chung
- National Research Laboratory of Molecular Microbiology and Toxicology, Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Seoul National University, Seoul, South Korea
| | - Joon-Gi Kwon
- Food Microbiome Laboratory, Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Seoul National University, Seoul, South Korea
| | - Sang Ho Choi
- National Research Laboratory of Molecular Microbiology and Toxicology, Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Seoul National University, Seoul, South Korea
| | - Ju-Hoon Lee
- Food Microbiome Laboratory, Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Seoul National University, Seoul, South Korea
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Dammann AN, Chamby AB, Catomeris AJ, Davidson KM, Tettelin H, van Pijkeren JP, Gopalakrishna KP, Keith MF, Elder JL, Ratner AJ, Hooven TA. Genome-Wide fitness analysis of group B Streptococcus in human amniotic fluid reveals a transcription factor that controls multiple virulence traits. PLoS Pathog 2021; 17:e1009116. [PMID: 33684178 PMCID: PMC7971860 DOI: 10.1371/journal.ppat.1009116] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 03/18/2021] [Accepted: 02/18/2021] [Indexed: 02/06/2023] Open
Abstract
Streptococcus agalactiae (group B Streptococcus; GBS) remains a dominant cause of serious neonatal infections. One aspect of GBS that renders it particularly virulent during the perinatal period is its ability to invade the chorioamniotic membranes and persist in amniotic fluid, which is nutritionally deplete and rich in fetal immunologic factors such as antimicrobial peptides. We used next-generation sequencing of transposon-genome junctions (Tn-seq) to identify five GBS genes that promote survival in the presence of human amniotic fluid. We confirmed our Tn-seq findings using a novel CRISPR inhibition (CRISPRi) gene expression knockdown system. This analysis showed that one gene, which encodes a GntR-class transcription factor that we named MrvR, conferred a significant fitness benefit to GBS in amniotic fluid. We generated an isogenic targeted deletion of the mrvR gene, which had a growth defect in amniotic fluid relative to the wild type parent strain. The mrvR deletion strain also showed a significant biofilm defect in vitro. Subsequent in vivo studies showed that while the mutant was able to cause persistent murine vaginal colonization, pregnant mice colonized with the mrvR deletion strain did not develop preterm labor despite consistent GBS invasion of the uterus and the fetoplacental units. In contrast, pregnant mice colonized with wild type GBS consistently deliver prematurely. In a sepsis model the mrvR deletion strain showed significantly decreased lethality. In order to better understand the mechanism by which this newly identified transcription factor controls GBS virulence, we performed RNA-seq on wild type and mrvR deletion GBS strains, which revealed that the transcription factor affects expression of a wide range of genes across the GBS chromosome. Nucleotide biosynthesis and salvage pathways were highly represented among the set of differentially expressed genes, suggesting that MrvR may be involved in regulating nucleotide availability. Group B Streptococcus (GBS) is a species of Gram-positive bacteria that often colonizes the healthy adult intestinal and reproductive tracts without causing serious symptoms. During pregnancy, however, GBS can invade the pregnant uterus, where it can cause infection of the placenta, fetal membranes, and fetus—a condition known as chorioamnionitis. Chorioamnionitis is associated with serious adverse pregnancy outcomes, including stillbirth, preterm labor, and severe infection of the newborn. GBS can survive in human amniotic fluid, which is low in bacterial nutrients and contains immune molecules that limit microbial persistence, and this ability likely contributes to GBS chorioamnionitis. This study is focused on a single GBS gene that encodes a genetic regulator we called MrvR, which we show is important for GBS resistance to human amniotic fluid. Using a series of genetic techniques combined with animal models of GBS colonization and infection, we show that MrvR also plays a key role in allowing GBS to invade the bloodstream and trigger the inflammatory responses that lead to preterm labor and stillbirth. The study concludes with a survey of other GBS genes whose activity is regulated by MrvR, which seems to be an important contributor to GBS virulence.
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Affiliation(s)
- Allison N. Dammann
- Department of Pediatrics, New York University School of Medicine, New York, New York, United States of America
| | - Anna B. Chamby
- University of Vermont Larner College of Medicine, Burlington, Vermont, United States of America
| | - Andrew J. Catomeris
- Georgetown University School of Medicine, Washington, District of Columbia, United States of America
| | - Kyle M. Davidson
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Hervé Tettelin
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Jan-Peter van Pijkeren
- Department of Food Science, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Kathyayini P. Gopalakrishna
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Mary F. Keith
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Jordan L. Elder
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Adam J. Ratner
- Department of Pediatrics, New York University School of Medicine, New York, New York, United States of America
- Department of Microbiology, New York University, New York, New York, United States of America
| | - Thomas A. Hooven
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Richard King Mellon Institute for Pediatric Research, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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Blaschke U, Skiebe E, Wilharm G. Novel Genes Required for Surface-Associated Motility in Acinetobacter baumannii. Curr Microbiol 2021; 78:1509-1528. [PMID: 33666749 PMCID: PMC7997844 DOI: 10.1007/s00284-021-02407-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 02/10/2021] [Indexed: 01/28/2023]
Abstract
Acinetobacter baumannii is an opportunistic and increasingly multi-drug resistant human pathogen rated as a critical priority one pathogen for the development of new antibiotics by the WHO in 2017. Despite the lack of flagella, A. baumannii can move along wet surfaces in two different ways: via twitching motility and surface-associated motility. While twitching motility is known to depend on type IV pili, the mechanism of surface-associated motility is poorly understood. In this study, we established a library of 30 A. baumannii ATCC® 17978™ mutants that displayed deficiency in surface-associated motility. By making use of natural competence, we also introduced these mutations into strain 29D2 to differentiate strain-specific versus species-specific effects of mutations. Mutated genes were associated with purine/pyrimidine/folate biosynthesis (e.g. purH, purF, purM, purE), alarmone/stress metabolism (e.g. Ap4A hydrolase), RNA modification/regulation (e.g. methionyl-tRNA synthetase), outer membrane proteins (e.g. ompA), and genes involved in natural competence (comEC). All tested mutants originally identified as motility-deficient in strain ATCC® 17978™ also displayed a motility-deficient phenotype in 29D2. By contrast, further comparative characterization of the mutant sets of both strains regarding pellicle biofilm formation, antibiotic resistance, and virulence in the Galleria mellonella infection model revealed numerous strain-specific mutant phenotypes. Our studies highlight the need for comparative analyses to characterize gene functions in A. baumannii and for further studies on the mechanisms underlying surface-associated motility.
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Affiliation(s)
- Ulrike Blaschke
- Robert Koch Institute, Project group P2, Burgstr. 37, 38855, Wernigerode, Germany.
| | - Evelyn Skiebe
- Robert Koch Institute, Project group P2, Burgstr. 37, 38855, Wernigerode, Germany
| | - Gottfried Wilharm
- Robert Koch Institute, Project group P2, Burgstr. 37, 38855, Wernigerode, Germany.
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