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Liu D, Bhunia AK. Anchorless Bacterial Moonlighting Metabolic Enzymes Modulate the Immune System and Contribute to Pathogenesis. ACS Infect Dis 2024; 10:2551-2566. [PMID: 39066728 DOI: 10.1021/acsinfecdis.4c00323] [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] [Indexed: 07/30/2024]
Abstract
Moonlighting proteins (MPs), characterized by their ability to perform multiple physiologically unrelated functions without alterations to their primary structures, represent a fascinating class of biomolecules with significant implications for host-pathogen interactions. This Review highlights the emerging importance of metabolic moonlighting proteins (MetMPs) in bacterial pathogenesis, focusing on their non-canonical secretion and unconventional surface anchoring mechanisms. Despite lacking typical signal peptides and anchoring motifs, MetMPs such as acetaldehyde alcohol dehydrogenase (AdhE) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) are secreted and localized to the bacterial surface under stress conditions, facilitating host colonization and immune evasion. The secretion of MetMPs, often observed during conditions such as resource scarcity or infection, suggests a complex regulation akin to the overexpression of heat shock proteins in response to environmental stresses. This Review proposes two potential pathways for MetMP secretion: membrane damage-induced permeability and co-transportation with traditionally secreted proteins, highlighting a remarkable bacterial adaptability. Biophysically, surface anchoring of MetMPs is driven by electrostatic interactions, bypassing the need for conventional anchoring sequences. This mechanism is exemplified by the interaction between the bifunctional enzyme AdhE (known as Listeria adhesion protein, LAP) and the internalin B (InlB) in Listeria monocytogenes, which is mediated by charged residues facilitating adhesion to host tissues. Furthermore, MetMPs play critical roles in iron homeostasis, immune modulation, and evasion, underscoring their multifaceted roles in bacterial pathogenicity. The intricate dynamics of MetMP secretion and anchoring underline the need for further research to unravel the molecular mechanisms underpinning these processes, offering potential new targets for therapeutic intervention against bacterial infections.
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Affiliation(s)
- Dongqi Liu
- Molecular Food Microbiology Laboratory, Department of Food Science, Purdue University, West Lafayette, Indiana 47907, United States
- Purdue Institute of Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, Indiana 47907, United States
| | - Arun K Bhunia
- Molecular Food Microbiology Laboratory, Department of Food Science, Purdue University, West Lafayette, Indiana 47907, United States
- Purdue Institute of Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, Indiana 47907, United States
- Department of Comparative Pathobiology, Purdue University, West Lafayette, Indiana 47907, United States
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2
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King KA, Benton AH, Caudill MT, Stoyanof ST, Kang L, Michalak P, Lahmers KK, Dunman PM, DeHart TG, Ahmad SS, Jutras BL, Poncin K, De Bolle X, Caswell CC. Post-transcriptional control of the essential enzyme MurF by a small regulatory RNA in Brucella abortus. Mol Microbiol 2024; 121:129-141. [PMID: 38082493 DOI: 10.1111/mmi.15207] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/22/2023] [Accepted: 11/25/2023] [Indexed: 01/15/2024]
Abstract
Brucella abortus is a facultative, intracellular, zoonotic pathogen that resides inside macrophages during infection. This is a specialized niche where B. abortus encounters various stresses as it navigates through the macrophage. In order to survive this harsh environment, B. abortus utilizes post-transcriptional regulation of gene expression through the use of small regulatory RNAs (sRNAs). Here, we characterize a Brucella sRNAs called MavR (for MurF- and virulence-regulating sRNA), and we demonstrate that MavR is required for the full virulence of B. abortus in macrophages and in a mouse model of chronic infection. Transcriptomic and proteomic studies revealed that a major regulatory target of MavR is MurF. MurF is an essential protein that catalyzes the final cytoplasmic step in peptidoglycan (PG) synthesis; however, we did not detect any differences in the amount or chemical composition of PG in the ΔmavR mutant. A 6-nucleotide regulatory seed region within MavR was identified, and mutation of this seed region resulted in dysregulation of MurF production, as well as significant attenuation of infection in a mouse model. Overall, the present study underscores the importance of sRNA regulation in the physiology and virulence of Brucella.
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Affiliation(s)
- Kellie A King
- Department of Biomedical Sciences and Pathobiology, Center for One Health Research, VA-MD College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia, USA
| | - Angela H Benton
- Department of Biomedical Sciences and Pathobiology, Center for One Health Research, VA-MD College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia, USA
| | - Mitchell T Caudill
- Department of Biomedical Sciences and Pathobiology, Center for One Health Research, VA-MD College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia, USA
| | - S Tristan Stoyanof
- Department of Biomedical Sciences and Pathobiology, Center for One Health Research, VA-MD College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia, USA
| | - Lin Kang
- Department of Biomedical Sciences, Edward Via College of Osteopathic Medicine, Monroe, Louisiana, USA
- College of Pharmacy, University of Louisiana Monroe, Monroe, Louisiana, USA
- Center for One Health Research, Edward Via College of Osteopathic Medicine, Blacksburg, Virginia, USA
| | - Pawel Michalak
- Department of Biomedical Sciences, Edward Via College of Osteopathic Medicine, Monroe, Louisiana, USA
- Center for One Health Research, Edward Via College of Osteopathic Medicine, Blacksburg, Virginia, USA
- Institute for Evolution, University of Haifa, Haifa, Israel
| | - Kevin K Lahmers
- Department of Biomedical Sciences and Pathobiology, Center for One Health Research, VA-MD College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia, USA
| | - Paul M Dunman
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Tanner G DeHart
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, USA
| | - Saadman S Ahmad
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, USA
| | - Brandon L Jutras
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, USA
| | - Katy Poncin
- URBM, Narilis, University of Namur, Namur, Belgium
| | | | - Clayton C Caswell
- Department of Biomedical Sciences and Pathobiology, Center for One Health Research, VA-MD College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia, USA
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3
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Batour M, Laurent S, Moalic Y, Chamieh H, Taha S, Jebbar M. The secretome of Thermococcus barophilus in the presence of carbohydrates and the potential role of the TrmBL4 regulator. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:530-544. [PMID: 37496315 PMCID: PMC10667668 DOI: 10.1111/1758-2229.13186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 06/19/2023] [Indexed: 07/28/2023]
Abstract
Global transcriptional regulators are crucial for supporting rapid adaptive responses in changing environments. In Thermococcales, the TrmB sugar-sensing regulator family is well represented but knowledge of the functional role/s of each of its members is limited. In this study, we examined the link between TrmBL4 and the degree of protein secretion in different sugar environments in the hyperthermophilic Archaeon Thermococcus barophilus. Although the absence of TrmBL4 did not induce any growth defects, proteomics analysis revealed different secretomes depending on the sugar and/or genetic contexts. Notably, 33 secreted proteins present in the supernatant were differentially detected. Some of these proteins are involved in sugar assimilation and transport, such as the protein encoded by TERMP_01455 (cyclomaltodextrin glucanotransferase), whereas others have intracellular functions, such as the protein encoded by TERMP_01556 (pyruvate: ferredoxin oxidoreductase Δsubunit). Then, using reverse transcription quantitative polymerase chain reaction experiments, we observed effective transcription regulation by TrmBL4 of the genes encoding at least two ABC-type transporters according to sugar availability.
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Affiliation(s)
- Maria Batour
- Univ Brest, CNRS, Ifremer, Laboratoire de Biologie et d'Écologie des Écosystèmes marins profonds (BEEP), IUEMPlouzanéFrance
- Laboratory of Applied Biotechnology, Azm Center for Research in Biotechnology and Its ApplicationsLebanese UniversityTripoliLebanon
| | - Sébastien Laurent
- Univ Brest, CNRS, Ifremer, Laboratoire de Biologie et d'Écologie des Écosystèmes marins profonds (BEEP), IUEMPlouzanéFrance
| | - Yann Moalic
- Univ Brest, CNRS, Ifremer, Laboratoire de Biologie et d'Écologie des Écosystèmes marins profonds (BEEP), IUEMPlouzanéFrance
- LabISEN, Yncréa OuestBrestFrance
| | - Hala Chamieh
- Laboratory of Applied Biotechnology, Azm Center for Research in Biotechnology and Its ApplicationsLebanese UniversityTripoliLebanon
| | - Samir Taha
- Laboratory of Applied Biotechnology, Azm Center for Research in Biotechnology and Its ApplicationsLebanese UniversityTripoliLebanon
| | - Mohamed Jebbar
- Univ Brest, CNRS, Ifremer, Laboratoire de Biologie et d'Écologie des Écosystèmes marins profonds (BEEP), IUEMPlouzanéFrance
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4
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Yadav P, Singh R, Sur S, Bansal S, Chaudhry U, Tandon V. Moonlighting proteins: beacon of hope in era of drug resistance in bacteria. Crit Rev Microbiol 2023; 49:57-81. [PMID: 35220864 DOI: 10.1080/1040841x.2022.2036695] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Moonlighting proteins (MLPs) are ubiquitous and provide a unique advantage to bacteria performing multiple functions using the same genomic content. Targeting MLPs can be considered as a futuristic approach in fighting drug resistance problem. This review follows the MLP trail from its inception to the present-day state, describing a few bacterial MLPs, viz., glyceraldehyde 3'-phosphate dehydrogenase, phosphoglucose isomerase glutamate racemase (GR), and DNA gyrase. Here, we carve out that targeting MLPs are the beacon of hope in an era of increasing drug resistance in bacteria. Evolutionary stability, structure-functional relationships, protein diversity, possible drug targets, and identification of new drugs against bacterial MLP are given due consideration. Before the final curtain calls, we provide a comprehensive list of small molecules that inhibit the biochemical activity of MLPs, which can aid the development of novel molecules to target MLPs for therapeutic applications.
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Affiliation(s)
- Pramod Yadav
- Special Center for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India.,Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, New Delhi, India
| | - Raja Singh
- Special Center for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Souvik Sur
- Research and Development Center, Teerthanker Mahaveer University, Uttar Pradesh, India
| | - Sandhya Bansal
- Norton Thoracic Institute, St. Joseph's Hospital, and Medical Center, Phoenix, AZ, USA
| | - Uma Chaudhry
- Bhaskaracharya College of Applied Sciences, University of Delhi, New Delhi, India
| | - Vibha Tandon
- Special Center for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
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5
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Identification of Ensifer meliloti genes required for survival during peat-based bioinoculant maturation by STM-seq. J Biotechnol 2023; 362:12-23. [PMID: 36535417 DOI: 10.1016/j.jbiotec.2022.12.004] [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: 09/19/2022] [Revised: 12/11/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Rhizobial inoculants are sold either as rhizobia within a liquid matrix; or as rhizobia adhered to granules composed of peat prill or finely ground peat moss. During the production of peat-based inoculants, a series of physiological changes occur that result in an increased capability of the rhizobia to survive on the seeds. The number of viable rhizobia on preinoculated seeds at the point of sale, however, is often a limiting factor, as is the inefficiency of the inoculant bacteria to compete with the local rhizobia for the host colonization. In the present work, we used STM-seq for the genome-wide screening of Ensifer meliloti mutants affected in the survival during the maturation of peat-based inoculant formulations. Through this approach, we were able to identify a set of mutants whose behavior suggests that persistence in peat inoculants involves a complex phenotype that is connected to diverse cellular activities, mainly related to satisfying the requirements of bacterial nutrition (e.g., carbon sources, ions) and to coping with specific stresses (e.g., oxidative, mutational). These results also provide a base knowledge that could be used to more completely understand the survival mechanisms used by rhizobia during the maturation of peat-based inoculants, as well as for the design and implementation of practical strategies to improve inoculant formulations.
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Boni FG, Hamdi I, Moukendza Koundi L, Dai Y, Shrestra K, Abokadoum MA, Ekomi Moure UA, Suleiman IM, Xie J. The Gene and Regulatory Network Involved in Ethambutol Resistance in Mycobacterium tuberculosis. Microb Drug Resist 2022; 29:175-189. [PMID: 35939307 DOI: 10.1089/mdr.2021.0239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Ethambutol (EMB) is used in combination with isoniazid and rifampicin for the treatment of tuberculosis caused by Mycobacterium tuberculosis. However, the incidence of EMB resistance is alarming. The EMB targets the cell wall arabinan biosynthesis. It is important to comprehensively understand the molecular basis of EMB to slow down the drug resistance rate of EMB. This study summarized the genes implicated in EMB resistance, regulatory network and the pharmacoproteomic effect of EMB in M. tuberculosis. Many of the genes related to EMB are implicated in membrane components, drug efflux, lipid metabolism, ribosome, and detoxification. The differential response model may help to design a novel anti-tuberculosis antibiotic.
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Affiliation(s)
- Funmilayo Grâce Boni
- Institute of Modern Biopharmaceuticals State Key Laboratory, Breeding Base Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Insaf Hamdi
- Institute of Modern Biopharmaceuticals State Key Laboratory, Breeding Base Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Liadrine Moukendza Koundi
- Institute of Modern Biopharmaceuticals State Key Laboratory, Breeding Base Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Yongdong Dai
- Institute of Modern Biopharmaceuticals State Key Laboratory, Breeding Base Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Kanshan Shrestra
- Institute of Modern Biopharmaceuticals State Key Laboratory, Breeding Base Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Mohamed Abdellah Abokadoum
- Institute of Modern Biopharmaceuticals State Key Laboratory, Breeding Base Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China.,Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Assuit, Egypt
| | - Ulrich Aymard Ekomi Moure
- Institute of Modern Biopharmaceuticals State Key Laboratory, Breeding Base Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Ismail Mohamed Suleiman
- Institute of Modern Biopharmaceuticals State Key Laboratory, Breeding Base Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Jianping Xie
- Institute of Modern Biopharmaceuticals State Key Laboratory, Breeding Base Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
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7
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Arega AM, Mahapatra RK. Glycoconjugates, hypothetical proteins, and post-translational modification: Importance in host-pathogen interaction and antitubercular intervention development. Chem Biol Drug Des 2021; 98:30-48. [PMID: 33838076 DOI: 10.1111/cbdd.13845] [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: 11/20/2020] [Revised: 02/18/2021] [Accepted: 03/08/2021] [Indexed: 11/30/2022]
Abstract
With the emergence of multidrug-resistant bacteria, insufficiency of the established chemotherapy, and the existing vaccine BCG, tuberculosis (TB) subsists as the chief cause of death in different parts of the world. Thus, identification of novel target proteins is urgently required to develop more effective TB interventions. However, the novel vaccine and drug target knowledge based on the essentiality of the pathogen cell envelope components such as glycoconjugates, glycans, and the peptidoglycan layer of the lipid-rich capsule are limited. Furthermore, most of the genes encoding proteins are characterized as hypothetical and functionally unknown. Correspondingly, some researchers have shown that the lipid and sugar components of the envelope glycoconjugates are largely in charge of TB pathogenesis and encounter many drugs and vaccines. Therefore, in this review we provide an insight into a comprehensive study concerning the importance of cell envelope glycoconjugates and hypothetical proteins, the impact of post-translational modification, and the bioinformatics-based implications for better antitubercular intervention development.
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Affiliation(s)
- Aregitu Mekuriaw Arega
- School of Biotechnology, KIIT Deemed to be University, Bhubaneswar, India.,National Veterinary Institute, Debre Zeit, Ethiopia
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8
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Bacterial Metabolites of Human Gut Microbiota Correlating with Depression. Int J Mol Sci 2020; 21:ijms21239234. [PMID: 33287416 PMCID: PMC7730936 DOI: 10.3390/ijms21239234] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 11/23/2020] [Accepted: 12/02/2020] [Indexed: 02/06/2023] Open
Abstract
Depression is a global threat to mental health that affects around 264 million people worldwide. Despite the considerable evolution in our understanding of the pathophysiology of depression, no reliable biomarkers that have contributed to objective diagnoses and clinical therapy currently exist. The discovery of the microbiota-gut-brain axis induced scientists to study the role of gut microbiota (GM) in the pathogenesis of depression. Over the last decade, many of studies were conducted in this field. The productions of metabolites and compounds with neuroactive and immunomodulatory properties among mechanisms such as the mediating effects of the GM on the brain, have been identified. This comprehensive review was focused on low molecular weight compounds implicated in depression as potential products of the GM. The other possible mechanisms of GM involvement in depression were presented, as well as changes in the composition of the microbiota of patients with depression. In conclusion, the therapeutic potential of functional foods and psychobiotics in relieving depression were considered. The described biomarkers associated with GM could potentially enhance the diagnostic criteria for depressive disorders in clinical practice and represent a potential future diagnostic tool based on metagenomic technologies for assessing the development of depressive disorders.
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Dineshkumar K, Aparna V, Wu L, Wan J, Abdelaziz MH, Su Z, Wang S, Xu H. Bacterial bug-out bags: outer membrane vesicles and their proteins and functions. J Microbiol 2020; 58:531-542. [DOI: 10.1007/s12275-020-0026-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 05/06/2020] [Accepted: 05/12/2020] [Indexed: 01/08/2023]
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Espinosa-Cantú A, Cruz-Bonilla E, Noda-Garcia L, DeLuna A. Multiple Forms of Multifunctional Proteins in Health and Disease. Front Cell Dev Biol 2020; 8:451. [PMID: 32587857 PMCID: PMC7297953 DOI: 10.3389/fcell.2020.00451] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 05/14/2020] [Indexed: 12/23/2022] Open
Abstract
Protein science has moved from a focus on individual molecules to an integrated perspective in which proteins emerge as dynamic players with multiple functions, rather than monofunctional specialists. Annotation of the full functional repertoire of proteins has impacted the fields of biochemistry and genetics, and will continue to influence basic and applied science questions - from the genotype-to-phenotype problem, to our understanding of human pathologies and drug design. In this review, we address the phenomena of pleiotropy, multidomain proteins, promiscuity, and protein moonlighting, providing examples of multitasking biomolecules that underlie specific mechanisms of human disease. In doing so, we place in context different types of multifunctional proteins, highlighting useful attributes for their systematic definition and classification in future research directions.
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Affiliation(s)
- Adriana Espinosa-Cantú
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados, Guanajuato, Mexico
| | - Erika Cruz-Bonilla
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados, Guanajuato, Mexico
| | - Lianet Noda-Garcia
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Alexander DeLuna
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados, Guanajuato, Mexico
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11
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Abstract
The skin microbiome is rich in opportunities for novel therapeutics for skin diseases, and synthetic biology offers the advantage of providing novel functionality or therapeutic benefit to live biotherapeutic products. The development of novel bacterial strains whose growth can be controlled without the use of antibiotics or genetic elements conferring antibiotic resistance enables modulation of therapeutic exposure and improves safety. This study presents the design and in vitro evidence of a skin commensal whose growth can be controlled through d-alanine. The basis of this strain will support future clinical studies of this strain in humans. Using live microbes as therapeutic candidates is a strategy that has gained traction across multiple therapeutic areas. In the skin, commensal microorganisms play a crucial role in maintaining skin barrier function, homeostasis, and cutaneous immunity. Alterations of the homeostatic skin microbiome are associated with a number of skin diseases. Here, we present the design of an engineered commensal organism, Staphylococcus epidermidis, for use as a live biotherapeutic product (LBP) candidate for skin diseases. The development of novel bacterial strains whose growth can be controlled without the use of antibiotics or genetic elements conferring antibiotic resistance enables modulation of therapeutic exposure and improves safety. We therefore constructed an auxotrophic strain of S. epidermidis that requires exogenously supplied d-alanine. The S. epidermidis NRRL B-4268 Δalr1 Δalr2 Δdat strain (SEΔΔΔ) contains deletions of three biosynthetic genes: two alanine racemase genes, alr1 and alr2 (SE1674 and SE1079), and the d-alanine aminotransferase gene, dat (SE1423). These three deletions restricted growth in d-alanine-deficient medium, pooled human blood, and skin. In the presence of d-alanine, SEΔΔΔ colonized and increased expression of human β-defensin 2 in cultured human skin models in vitro. SEΔΔΔ showed a low propensity to revert to d-alanine prototrophy and did not form biofilms on plastic in vitro. These studies support the potential safety and utility of SEΔΔΔ as a live biotherapeutic strain whose growth can be controlled by d-alanine. IMPORTANCE The skin microbiome is rich in opportunities for novel therapeutics for skin diseases, and synthetic biology offers the advantage of providing novel functionality or therapeutic benefit to live biotherapeutic products. The development of novel bacterial strains whose growth can be controlled without the use of antibiotics or genetic elements conferring antibiotic resistance enables modulation of therapeutic exposure and improves safety. This study presents the design and in vitro evidence of a skin commensal whose growth can be controlled through d-alanine. The basis of this strain will support future clinical studies of this strain in humans.
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12
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Lin JC, Wang XZ, Shen T, Zhang JY. iTRAQ-based quantitative analysis reveals the mechanism underlying the changes in physiological activity in a glutamate racemase mutant strain of Streptococcus mutans UA159. Mol Biol Rep 2020; 47:3719-3733. [PMID: 32338332 DOI: 10.1007/s11033-020-05463-x] [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: 01/02/2020] [Accepted: 04/17/2020] [Indexed: 11/30/2022]
Abstract
Streptococcus mutans UA159 is responsible for human dental caries with robust cariogenic potential. Our previous study noted that a glutamate racemase (MurI) mutant strain (designated S. mutans FW1718), with the hereditary background of UA159, displayed alterations of morphogenesis, attenuated stress tolerance, and weakened biofilm-forming capabilities, accompanying with unclear mechanisms. In this study, we applied isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomics to characterize the proteome profiles of the murI mutant strain vs. the wild-type strain in chemically defined media to elucidate the mechanisms by which S. mutans copes with MurI deficiency. Whole-cell proteins of S. mutans FW1718 and UA159 were assessed by iTRAQ-coupled LC-ESI-MS/MS. Furthermore, differentially expressed proteins (DEPs) were identified by Mascot, Gene Ontology (GO) annotation, Cluster of Orthologous Groups of proteins (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Finally, a protein-protein interaction (PPI) network was established using the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING). Among 1173 total bacterial proteins identified, 112 DEPs exhibited altered expression patterns in S. mutans UA159 with or without the murI mutation. The ΔmurI cells displayed an increase in the relative expression of 93 proteins (fold change ≥ 1.2, p < 0.05) and a decrease in 29 proteins (fold change ≤ 0.833, p < 0.05) compared with the wild-type cells. PPI analysis revealed a complex network of DEPs containing 191 edges and 122 nodes. The DEPs significantly upregulated after murI knockout had roles in diverse functional processes spanning cell-wall biosynthesis, energy production, and DNA replication and repair. We identified distinct variations and diverse modulators caused by murI mutation in the proteome of S. mutans, indicating that the modification of cell membrane structure, redistribution of energy metabolism and enhanced nucleic acid machinery contributed to the S. mutans response to specific environmental contexts.
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Affiliation(s)
- Jia-Cheng Lin
- Department of Pediatric Dentistry, Guanghua School of Stomatology, Affiliated Stomatological Hospital, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiang-Zhu Wang
- Operative Dentistry and Endodontics, Xiangya School of Stomatology, Xiangya Stomatological Hospital, Central South University, Changsha, Hunan, China
| | - Ting Shen
- Operative Dentistry and Endodontics, Xiangya School of Stomatology, Xiangya Stomatological Hospital, Central South University, Changsha, Hunan, China
| | - Jian-Ying Zhang
- Operative Dentistry and Endodontics, Xiangya School of Stomatology, Xiangya Stomatological Hospital, Central South University, Changsha, Hunan, China.
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13
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Abstract
Moonlighting refers to a protein with at least two unrelated, mechanistically different functions. As a concept, moonlighting describes a large and diverse group of proteins which have been discovered in a multitude of organisms. As of today, a systematized view on these proteins is missing. Here, we propose a classification of moonlighting proteins by two classifiers. We use the function of the protein as a first classifier: activating - activating (Type I), activating - inhibiting (Type II), inhibiting - activating (Type III) and inhibiting - inhibiting (Type IV). To further specify the type of moonlighting protein, we used a second classifier based on the character of the factor that switches the function of the protein: external factor affecting the protein (Type A), change in the first pathway (Type B), change in the second pathway (Type C), equal competition between both pathways (Type D). Using a small two-pathway model we simulated these types of moonlighting proteins to elucidate possible behaviors of the types of moonlighting proteins. We find that, using the results of our simulations, we can classify the behavior of the moonlighting types into Blinker, Splitter andSwitch.
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Affiliation(s)
- Maria Krantz
- Theoretical Biophysics, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Edda Klipp
- Theoretical Biophysics, Humboldt-Universität zu Berlin, Berlin, Germany
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14
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Gupta MN, Pandey S, Ehtesham NZ, Hasnain SE. Medical implications of protein moonlighting. Indian J Med Res 2020; 149:322-325. [PMID: 31249195 PMCID: PMC6607823 DOI: 10.4103/ijmr.ijmr_2192_18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
- M N Gupta
- Former Professor, Department of Chemistry, Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi 110 016, India
| | - Saurabh Pandey
- Department of Biochemistry, JH Institute of Molecular Medicine, Jamia Hamdard, New Delhi 110 062, India
| | | | - Seyed E Hasnain
- Molecular Infection and Functional Biology Laboratory, Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi 110 016; JH Institute of Molecular Medicine, Jamia Hamdard, New Delhi 110 062; Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Hyderabad 500 007, Telangana, India
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15
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Rópolo AS, Feliziani C, Touz MC. Unusual proteins in Giardia duodenalis and their role in survival. ADVANCES IN PARASITOLOGY 2019; 106:1-50. [PMID: 31630755 DOI: 10.1016/bs.apar.2019.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The capacity of the parasite Giardia duodenalis to perform complex functions with minimal amounts of proteins and organelles has attracted increasing numbers of scientists worldwide, trying to explain how this parasite adapts to internal and external changes to survive. One explanation could be that G. duodenalis evolved from a structurally complex ancestor by reductive evolution, resulting in adaptation to its parasitic lifestyle. Reductive evolution involves the loss of genes, organelles, and functions that commonly occur in many parasites, by which the host renders some structures and functions redundant. However, there is increasing data that Giardia possesses proteins able to perform more than one function. During recent decades, the concept of moonlighting was described for multitasking proteins, which involves only proteins with an extra independent function(s). In this chapter, we provide an overview of unusual proteins in Giardia that present multifunctional properties depending on the location and/or parasite requirement. We also discuss experimental evidence that may allow some giardial proteins to be classified as moonlighting proteins by examining the properties of moonlighting proteins in general. Up to date, Giardia does not seem to require the numerous redundant proteins present in other organisms to accomplish its normal functions, and thus this parasite may be an appropriate model for understanding different aspects of moonlighting proteins, which may be helpful in the design of drug targets.
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Affiliation(s)
- Andrea S Rópolo
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, INIMEC-CONICET-Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Constanza Feliziani
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, INIMEC-CONICET-Universidad Nacional de Córdoba, Córdoba, Argentina
| | - María C Touz
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, INIMEC-CONICET-Universidad Nacional de Córdoba, Córdoba, Argentina.
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16
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Singh H, Das S, Yadav J, Srivastava VK, Jyoti A, Kaushik S. In search of novel protein drug targets for treatment of Enterococcus faecalis infections. Chem Biol Drug Des 2019; 94:1721-1739. [PMID: 31260188 DOI: 10.1111/cbdd.13582] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 06/08/2019] [Accepted: 06/17/2019] [Indexed: 12/27/2022]
Abstract
Enterococcus faecalis (Ef) is one of the major pathogens involved in hospital-acquired infections. It can cause nosocomial bacteremia, surgical wound infection, and urinary tract infection. It is important to mention here that Ef is developing resistance against many commonly occurring antibiotics. The occurrence of multidrug resistance (MDR) and extensive-drug resistance (XDR) is now posing a major challenge to the medical community. In this regard, to combat the infections caused by Ef, we have to look for an alternative. Rational structure-based drug design exploits the three-dimensional structure of the target protein, which can be unraveled by various techniques such as X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. In this review, we have discussed the complete picture of Ef infections, the possible treatment available at present, and the alternative treatment options to be explored. This study will help in better understanding of novel biological targets against Ef and the compounds, which are likely to bind with these targets. Using these detailed structural informations, rational structure-based drug design is achievable and tight inhibitors against Ef can be prepared.
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Affiliation(s)
- Harpreet Singh
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Satyajeet Das
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Jyoti Yadav
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | | | - Anupam Jyoti
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Sanket Kaushik
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
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17
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Muthuramalingam M, White JC, Murphy T, Ames JR, Bourne CR. The toxin from a ParDE toxin-antitoxin system found in Pseudomonas aeruginosa offers protection to cells challenged with anti-gyrase antibiotics. Mol Microbiol 2019; 111:441-454. [PMID: 30427086 PMCID: PMC6368863 DOI: 10.1111/mmi.14165] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/25/2018] [Indexed: 12/13/2022]
Abstract
Toxin-antitoxin systems are mediators of diverse activities in bacterial physiology. For the ParE-type toxins, their reported role of gyrase inhibition utilized during plasmid-segregation killing indicates they are toxic. However, their location throughout chromosomes leads to questions about function, including potential non-toxic outcomes. The current study has characterized a ParDE system from the opportunistic human pathogen Pseudomonas aeruginosa (Pa). We identified a protective function for this ParE toxin, PaParE, against effects of quinolone and other antibiotics. However, higher concentrations of PaParE are themselves toxic to cells, indicating the phenotypic outcome can vary based on its concentration. Our assays confirmed PaParE inhibition of gyrase-mediated supercoiling of DNA with an IC50 value in the low micromolar range, a species-specificity that resulted in more efficacious inhibition of Escherichia coli derived gyrase versus Pa gyrase, and overexpression in the absence of antitoxin yielded an expected filamentous morphology with multi-foci nucleic acid material. Additional data revealed that the PaParE toxin is monomeric and interacts with dimeric PaParD antitoxin with a KD in the lower picomolar range, yielding a heterotetramer. This work provides novel insights into chromosome-encoded ParE function, whereby its expression can impart partial protection to cultures from selected antibiotics.
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Affiliation(s)
- Meenakumari Muthuramalingam
- The University of Oklahoma, Department of Chemistry and BiochemistryNorman73019OKUSA
- Present address:
Department of Pharmaceutical ChemistryUniversity of KansasLawrence66047 KSUSA
| | - John C. White
- The University of Oklahoma, Department of Chemistry and BiochemistryNorman73019OKUSA
| | - Tamiko Murphy
- The University of Oklahoma, Department of Chemistry and BiochemistryNorman73019OKUSA
| | - Jessica R. Ames
- The University of Oklahoma, Department of Chemistry and BiochemistryNorman73019OKUSA
| | - Christina R. Bourne
- The University of Oklahoma, Department of Chemistry and BiochemistryNorman73019OKUSA
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18
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Pawar A, Jha P, Konwar C, Chaudhry U, Chopra M, Saluja D. Ethambutol targets the glutamate racemase of Mycobacterium tuberculosis—an enzyme involved in peptidoglycan biosynthesis. Appl Microbiol Biotechnol 2018; 103:843-851. [DOI: 10.1007/s00253-018-9518-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/06/2018] [Accepted: 11/11/2018] [Indexed: 12/11/2022]
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19
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Shey RA, Ghogomu SM, Njume FN, Gainkam LOT, Poelvoorde P, Mutesa L, Robert A, Humblet P, Munyampundu JP, Kamgno J, Lelubre C, Vanhamme L, Souopgui J. Prediction and validation of the structural features of Ov58GPCR, an immunogenic determinant of Onchocerca volvulus. PLoS One 2018; 13:e0202915. [PMID: 30256790 PMCID: PMC6157839 DOI: 10.1371/journal.pone.0202915] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 08/11/2018] [Indexed: 11/18/2022] Open
Abstract
Onchocerciasis is a severely debilitating yet neglected tropical disease (NTD) that creates social stigma, generates and perpetuates poverty, and leads ultimately in some cases to irreversible unilateral or bilateral blindness if untreated. Consequently, the disease is a major impediment to socioeconomic development. Many control programs have been launched for the disease with moderate successes achieved. This mitigated hit is partially due to the lingering need for reliable, non-invasive and easily applicable tools for mapping endemic regions and post-elimination surveillance. In this work, bioinformatics analyses combined with immunological assays were applied in a bid to develop potential tools for diagnosis and assessing the success of drug treatment programs. We report that (i) the O. volvulus antigen, Ov58GPCR is a G-protein coupled receptor (GPCR) conserved in related nematodes, (ii) synthetic peptides predicted to be in the extracellular domain (ECD) of Ov58GPCR are indeed immunogenic epitopes in actively-infected individuals, (iii) synthetic peptide cocktails discriminate between actively-infected individuals, treated individuals and healthy African controls, (iv) polyclonal antibodies against one of the peptides or against the bacterially-expressed ECD reacted specifically with the native antigen of O. volvulus total and surface extracts, (v) Ov58GPCR is transcribed in both larvae and adult parasite stages, (vi) IgG and IgE responses to the recombinant ECD decline with ivermectin treatment. All these findings suggest that the extracellular domain and synthetic peptides of Ov58GPCR, as well as the specific immune response generated could be harnessed in the context of disease diagnosis and surveillance.
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Affiliation(s)
- Robert Adamu Shey
- Department of Molecular Biology, Institute of Biology and Molecular Medicine, IBMM Universite Libre de Bruxelles, Gosselies Campus, Gosselies, Hainaut, Belgium
- Molecular and Cell Biology Laboratory, Biotechnology Unit, Faculty of Science, University of Buea, Buea, Cameroon
| | - Stephen Mbigha Ghogomu
- Molecular and Cell Biology Laboratory, Biotechnology Unit, Faculty of Science, University of Buea, Buea, Cameroon
| | - Ferdinand Ngale Njume
- Department of Molecular Biology, Institute of Biology and Molecular Medicine, IBMM Universite Libre de Bruxelles, Gosselies Campus, Gosselies, Hainaut, Belgium
- Molecular and Cell Biology Laboratory, Biotechnology Unit, Faculty of Science, University of Buea, Buea, Cameroon
| | - Lea Olive Tchouate Gainkam
- Department of Molecular Biology, Institute of Biology and Molecular Medicine, IBMM Universite Libre de Bruxelles, Gosselies Campus, Gosselies, Hainaut, Belgium
| | - Philippe Poelvoorde
- Department of Molecular Biology, Institute of Biology and Molecular Medicine, IBMM Universite Libre de Bruxelles, Gosselies Campus, Gosselies, Hainaut, Belgium
| | - Leon Mutesa
- Center for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - Annie Robert
- Faculté de santé publique, Institut de recherche expérimentale et clinique, Pôle d'épidémiologie et biostatistique, Université Catholique de Louvain, Clos Chapelle-aux-champs, Woluwe-Saint-Lambert, Belgium
| | - Perrine Humblet
- École de santé publique, Université Libre de Bruxelles, Bruxelles, Belgium
| | - Jean-Pierre Munyampundu
- Center for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - Joseph Kamgno
- Department of Epidemiology, Centre for research on filariasis and other tropical diseases, (CRFilMT), Yaoundé, Cameroon
| | - Christophe Lelubre
- Laboratoire de Médecine Expérimentale, Université Libre de Bruxelles (ULB) - Unité 222, CHU Charleroi (Hôpital André Vésale), Montigny-Le-Tilleul, Belgium
| | - Luc Vanhamme
- Department of Molecular Biology, Institute of Biology and Molecular Medicine, IBMM Universite Libre de Bruxelles, Gosselies Campus, Gosselies, Hainaut, Belgium
| | - Jacob Souopgui
- Department of Molecular Biology, Institute of Biology and Molecular Medicine, IBMM Universite Libre de Bruxelles, Gosselies Campus, Gosselies, Hainaut, Belgium
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20
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Vajda S, Beglov D, Wakefield AE, Egbert M, Whitty A. Cryptic binding sites on proteins: definition, detection, and druggability. Curr Opin Chem Biol 2018; 44:1-8. [PMID: 29800865 PMCID: PMC6088748 DOI: 10.1016/j.cbpa.2018.05.003] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 05/03/2018] [Indexed: 12/30/2022]
Abstract
Many proteins in their unbound structures lack surface pockets appropriately sized for drug binding. Hence, a variety of experimental and computational tools have been developed for the identification of cryptic sites that are not evident in the unbound protein but form upon ligand binding, and can provide tractable drug target sites. The goal of this review is to discuss the definition, detection, and druggability of such sites, and their potential value for drug discovery. Novel methods based on molecular dynamics simulations are particularly promising and yield a large number of transient pockets, but it has been shown that only a minority of such sites are generally capable of binding ligands with substantial affinity. Based on recent studies, current methodology can be improved by combining molecular dynamics with fragment docking and machine learning approaches.
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Affiliation(s)
- Sandor Vajda
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, United States; Department of Chemistry, Boston University, Boston, MA 02215, United States.
| | - Dmitri Beglov
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, United States
| | - Amanda E Wakefield
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, United States; Department of Chemistry, Boston University, Boston, MA 02215, United States
| | - Megan Egbert
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, United States
| | - Adrian Whitty
- Department of Chemistry, Boston University, Boston, MA 02215, United States.
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21
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Walworth NG, Hutchins DA, Dolzhenko E, Lee MD, Fu F, Smith AD, Webb EA. Biogeographic conservation of the cytosine epigenome in the globally important marine, nitrogen-fixing cyanobacterium Trichodesmium. Environ Microbiol 2017; 19:4700-4713. [PMID: 28925547 DOI: 10.1111/1462-2920.13934] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 08/07/2017] [Accepted: 08/30/2017] [Indexed: 01/31/2023]
Abstract
Cytosine methylation has been shown to regulate essential cellular processes and impact biological adaptation. Despite its evolutionary importance, only a handful of bacterial, genome-wide cytosine studies have been conducted, with none for marine bacteria. Here, we examine the genome-wide, C5 -Methyl-cytosine (m5C) methylome and its correlation to global transcription in the marine nitrogen-fixing cyanobacterium Trichodesmium. We characterize genome-wide methylation and highlight conserved motifs across three Trichodesmium isolates and two Trichodesmium metagenomes, thereby identifying highly conserved, novel genomic signatures of potential gene regulation in Trichodesmium. Certain gene bodies with the highest methylation levels correlate with lower expression levels. Several methylated motifs were highly conserved across spatiotemporally separated Trichodesmium isolates, thereby elucidating biogeographically conserved methylation potential. These motifs were also highly conserved in Trichodesmium metagenomic samples from natural populations suggesting them to be potential in situ markers of m5C methylation. Using these data, we highlight predicted roles of cytosine methylation in global cellular metabolism providing evidence for a 'core' m5C methylome spanning different ocean regions. These results provide important insights into the m5C methylation landscape and its biogeochemical implications in an important marine N2 -fixer, as well as advancing evolutionary theory examining methylation influences on adaptation.
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Affiliation(s)
- Nathan G Walworth
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - David A Hutchins
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Egor Dolzhenko
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Michael D Lee
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Feixue Fu
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Andrew D Smith
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Eric A Webb
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
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22
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Martínez-Núñez MA, Rodríguez-Escamilla Z, Rodríguez-Vázquez K, Pérez-Rueda E. Tracing the Repertoire of Promiscuous Enzymes along the Metabolic Pathways in Archaeal Organisms. Life (Basel) 2017; 7:life7030030. [PMID: 28703743 PMCID: PMC5617955 DOI: 10.3390/life7030030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 07/09/2017] [Accepted: 07/10/2017] [Indexed: 01/10/2023] Open
Abstract
The metabolic pathways that carry out the biochemical transformations sustaining life depend on the efficiency of their associated enzymes. In recent years, it has become clear that promiscuous enzymes have played an important role in the function and evolution of metabolism. In this work we analyze the repertoire of promiscuous enzymes in 89 non-redundant genomes of the Archaea cellular domain. Promiscuous enzymes are defined as those proteins with two or more different Enzyme Commission (E.C.) numbers, according the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. From this analysis, it was found that the fraction of promiscuous enzymes is lower in Archaea than in Bacteria. A greater diversity of superfamily domains is associated with promiscuous enzymes compared to specialized enzymes, both in Archaea and Bacteria, and there is an enrichment of substrate promiscuity rather than catalytic promiscuity in the archaeal enzymes. Finally, the presence of promiscuous enzymes in the metabolic pathways was found to be heterogeneously distributed at the domain level and in the phyla that make up the Archaea. These analyses increase our understanding of promiscuous enzymes and provide additional clues to the evolution of metabolism in Archaea.
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Affiliation(s)
- Mario Alberto Martínez-Núñez
- Laboratorio de Estudios Ecogenómicos, Facultad de Ciencias, Unidad Académica de Ciencias y Tecnología de la UNAM en Yucatán, Universidad Nacional Autónoma de México, Carretera Sierra Papacal-Chuburna Km. 5, C.P. 97302, Mérida, Yucatán, Mexico.
| | - Zuemy Rodríguez-Escamilla
- Departamento de Microbiología, Instituto de Biotecnología, Universidad Nacional, Autónoma de México, C.P. 62210, Cuernavaca, Morelos, Mexico.
| | - Katya Rodríguez-Vázquez
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Ciudad Universitaria, C.P. 04510, Ciudad de México, Mexico.
| | - Ernesto Pérez-Rueda
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, C.P. 62210, Cuernavaca, Morelos, Mexico.
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica Yucatán, Carretera Sierra Papacal-Chuburna Km. 5, C.P. 97302, Mérida, Yucatán, Mexico.
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23
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Fakhar Z, Naiker S, Alves CN, Govender T, Maguire GEM, Lameira J, Lamichhane G, Kruger HG, Honarparvar B. A comparative modeling and molecular docking study on Mycobacterium tuberculosis targets involved in peptidoglycan biosynthesis. J Biomol Struct Dyn 2016; 34:2399-417. [PMID: 26612108 DOI: 10.1080/07391102.2015.1117397] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
An alarming rise of multidrug-resistant Mycobacterium tuberculosis strains and the continuous high global morbidity of tuberculosis have reinvigorated the need to identify novel targets to combat the disease. The enzymes that catalyze the biosynthesis of peptidoglycan in M. tuberculosis are essential and noteworthy therapeutic targets. In this study, the biochemical function and homology modeling of MurI, MurG, MraY, DapE, DapA, Alr, and Ddl enzymes of the CDC1551 M. tuberculosis strain involved in the biosynthesis of peptidoglycan cell wall are reported. Generation of the 3D structures was achieved with Modeller 9.13. To assess the structural quality of the obtained homology modeled targets, the models were validated using PROCHECK, PDBsum, QMEAN, and ERRAT scores. Molecular dynamics simulations were performed to calculate root mean square deviation (RMSD) and radius of gyration (Rg) of MurI and MurG target proteins and their corresponding templates. For further model validation, RMSD and Rg for selected targets/templates were investigated to compare the close proximity of their dynamic behavior in terms of protein stability and average distances. To identify the potential binding mode required for molecular docking, binding site information of all modeled targets was obtained using two prediction algorithms. A docking study was performed for MurI to determine the potential mode of interaction between the inhibitor and the active site residues. This study presents the first accounts of the 3D structural information for the selected M. tuberculosis targets involved in peptidoglycan biosynthesis.
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Affiliation(s)
- Zeynab Fakhar
- a Catalysis and Peptide Research Unit, School of Health Sciences , University of KwaZulu-Natal , Durban 4001 , South Africa
| | - Suhashni Naiker
- a Catalysis and Peptide Research Unit, School of Health Sciences , University of KwaZulu-Natal , Durban 4001 , South Africa
| | - Claudio N Alves
- b Laboratório de Planejamento de Fármacos, Instituto de Ciências Exatas e Naturais , Instituto de Ciências Biológicas, Universidade Federal do Pará , CEP 66075-110, Belém , Pará , Brazil
| | - Thavendran Govender
- a Catalysis and Peptide Research Unit, School of Health Sciences , University of KwaZulu-Natal , Durban 4001 , South Africa
| | - Glenn E M Maguire
- a Catalysis and Peptide Research Unit, School of Health Sciences , University of KwaZulu-Natal , Durban 4001 , South Africa.,c School of Chemistry and Physics , University of KwaZulu-Natal , 4001 Durban , South Africa
| | - Jeronimo Lameira
- b Laboratório de Planejamento de Fármacos, Instituto de Ciências Exatas e Naturais , Instituto de Ciências Biológicas, Universidade Federal do Pará , CEP 66075-110, Belém , Pará , Brazil
| | - Gyanu Lamichhane
- d Division of Infectious Diseases, Center for Tuberculosis Research , Johns Hopkins University School of Medicine , Baltimore , MD 21205 , USA
| | - Hendrik G Kruger
- a Catalysis and Peptide Research Unit, School of Health Sciences , University of KwaZulu-Natal , Durban 4001 , South Africa
| | - Bahareh Honarparvar
- a Catalysis and Peptide Research Unit, School of Health Sciences , University of KwaZulu-Natal , Durban 4001 , South Africa
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24
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Exploring the structure of glutamate racemase from Mycobacterium tuberculosis as a template for anti-mycobacterial drug discovery. Biochem J 2016; 473:1267-80. [PMID: 26964898 DOI: 10.1042/bcj20160186] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 03/09/2016] [Indexed: 11/17/2022]
Abstract
Glutamate racemase (MurI) is responsible for providing D-glutamate for peptidoglycan biosynthesis in bacteria and has been a favoured target in pharmaceutical drug design efforts. It has recently been proven to be essential in Mycobacterium tuberculosis, the causative organism of tuberculosis, a disease for which new medications are urgently needed. In the present study, we have determined the protein crystal structures of MurI from both M. tuberculosis and Mycobacterium smegmatis in complex with D-glutamate to 2.3 Å and 1.8 Å resolution respectively. These structures are conserved, but reveal differences in their active site architecture compared with that of other MurI structures. Furthermore, compounds designed to target other glutamate racemases have been screened but do not inhibit mycobacterial MurI, suggesting that a new drug design effort will be needed to develop inhibitors. A new type of MurI dimer arrangement has been observed in both structures, and this arrangement becomes the third biological dimer geometry for MurI found to date. The mycobacterial MurI dimer is tightly associated, with a KD in the nanomolar range. The enzyme binds D- and L-glutamate specifically, but is inactive in solution unless the dimer interface is mutated. We created triple mutants of this interface in the M. smegmatis glutamate racemase (D26R/R105A/G194R or E) that have appreciable activity (kcat=0.056-0.160 min(-1) and KM=0.26-0.51 mM) and can be utilized to screen proposed antimicrobial candidates for inhibition.
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25
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Abstract
The complex cell envelope is a hallmark of mycobacteria and is anchored by the peptidoglycan layer, which is similar to that of Escherichia coli and a number of other bacteria but with modifications to the monomeric units and other structural complexities that are likely related to a role for the peptidoglycan in stabilizing the mycolyl-arabinogalactan-peptidoglycan complex (MAPc). In this article, we will review the genetics of several aspects of peptidoglycan biosynthesis in mycobacteria, including the production of monomeric precursors in the cytoplasm, assembly of the monomers into the mature wall, cell wall turnover, and cell division. Finally, we will touch upon the resistance of mycobacteria to β-lactam antibiotics, an important class of drugs that, until recently, have not been extensively exploited as potential antimycobacterial agents. We will also note areas of research where there are still unanswered questions.
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26
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Martínez-Núñez MA, Pérez-Rueda E. Do lifestyles influence the presence of promiscuous enzymes in bacteria and Archaea metabolism? ACTA ACUST UNITED AC 2016. [DOI: 10.1186/s40508-016-0047-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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27
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Martínez-Núñez MA, Rodríguez-Vázquez K, Pérez-Rueda E. The lifestyle of prokaryotic organisms influences the repertoire of promiscuous enzymes. Proteins 2015; 83:1625-31. [PMID: 26109005 DOI: 10.1002/prot.24847] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 06/01/2015] [Accepted: 06/21/2015] [Indexed: 01/12/2023]
Abstract
The metabolism of microbial organisms and its diversity are partly the result of an adaptation process to the characteristics of the environments that they inhabit. In this work, we analyze the influence of lifestyle on the content of promiscuous enzymes in 761 nonredundant bacterial and archaeal genomes. Promiscuous enzymes were defined as those proteins whose catalytic activities are defined by two or more different Enzyme Commission (E.C.) numbers. The genomes analyzed were categorized into four lifestyles for their exhaustive comparisons: free-living, extremophiles, pathogens, and intracellular. From these analyses we found that free-living organisms have larger genomes and an enrichment of promiscuous enzymes. In contrast, intracellular organisms showed smaller genomes and the lesser proportion of promiscuous enzymes. On the basis of our data, we show that the proportion of promiscuous enzymes in an organism is mainly influenced by the lifestyle, where fluctuating environments promote its emergence. Finally, we evidenced that duplication processes occur preferentially in metabolism of free-living and extremophiles species.
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Affiliation(s)
- Mario Alberto Martínez-Núñez
- Departamento de Ingeniería de Sistemas Computacionales y Automatización, Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de Mexico, Ciudad Universitaria, México, D.F., México.,Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Katya Rodríguez-Vázquez
- Departamento de Ingeniería de Sistemas Computacionales y Automatización, Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de Mexico, Ciudad Universitaria, México, D.F., México
| | - Ernesto Pérez-Rueda
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.,Unidad Multidisciplinaria de Docencia e Investigación, Sisal Facultad de Ciencias, Sisal, Yucatán, UNAM, México
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Watanabe Y, Kawata K, Watanabe S. Monitoring Technology for Gamma-Aminobutyric acid Production in Polished Mochi Barley Grains using a Carbon Dioxide Sensor. J Food Sci 2015; 80:H1418-24. [PMID: 25916326 DOI: 10.1111/1750-3841.12867] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 03/10/2015] [Indexed: 11/30/2022]
Abstract
Gamma-aminobutyric acid (GABA) has many biological functions, including the inhibition of blood pressure increases and acceleration of growth hormone secretion. In this study, we discovered the utility of measuring the concentration of carbon dioxide (CO2 ) dissolved in the reaction solution, for development of a real-time and convenient technique to estimate GABA production. In addition to mochi barley bran, we examined the polished grains of three species: mochi barley (a variant of hulless barley), barley, and Japanese millet, all soaked in l-glutamic acid (l-Glu) solution at pH 4.5. We found a positive correlation between GABA and CO2 concentrations, and the production of CO2 was suppressed in the absence of l-Glu at pH 4.5. These results suggest that GABA content can be easily predicted by measuring the aqueous CO2 content using a CO2 sensor, during the process of GABA production in polished mochi barley grains and bran.
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Affiliation(s)
- Yasuo Watanabe
- Faculty of Agriculture, Ehime Univ, Tarumi 3-5-7, Matsuyama, Ehime, 790-8566, Japan
| | - Kohki Kawata
- Faculty of Agriculture, Ehime Univ, Tarumi 3-5-7, Matsuyama, Ehime, 790-8566, Japan
| | - Seiya Watanabe
- Faculty of Agriculture, Ehime Univ, Tarumi 3-5-7, Matsuyama, Ehime, 790-8566, Japan
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Abstract
Moonlighting proteins perform multiple independent cellular functions within one polypeptide chain. Moonlighting proteins switch functions depending on various factors including the cell-type in which they are expressed, cellular location, oligomerization status and the binding of different ligands at different sites. Although an increasing number of moonlighting proteins have been experimentally identified in recent years, the quantity of known moonlighting proteins is insufficient to elucidate their overall landscape. Moreover, most moonlighting proteins have been identified as a serendipitous discovery. Hence, characterization of moonlighting proteins using bioinformatics approaches can have a significant impact on the overall understanding of protein function. In this work, we provide a short review of existing computational approaches for illuminating the functional diversity of moonlighting proteins.
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Affiliation(s)
- Ishita K Khan
- Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA
| | - Daisuke Kihara
- Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA
- Department of Biological Science, Purdue University, West Lafayette, IN, 47907, USA
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30
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Morayya S, Awasthy D, Yadav R, Ambady A, Sharma U. Revisiting the essentiality of glutamate racemase in Mycobacterium tuberculosis. Gene 2014; 555:269-76. [PMID: 25447907 DOI: 10.1016/j.gene.2014.11.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 11/04/2014] [Accepted: 11/10/2014] [Indexed: 01/25/2023]
Abstract
Glutamate racemase (MurI) converts l-glutamate into d-glutamate which is an essential component of peptidoglycan in bacteria. The gene encoding glutamate racemase, murI has been shown to be essential for the growth of a number of bacterial species including Escherichia coli. However, in some Gram-positive species d-amino acid transaminase (Dat) can also convert l-glutamate into d-glutamate thus rendering MurI non-essential for growth. In a recent study the murI gene of Mycobacterium tuberculosis was shown to be non-essential. As d-glutamate is an essential component of peptidoglycan of M. tuberculosis, either Dat or MurI has to be essential for its survival. Since, a Dat encoding gene has not been reported in M. tuberculosis genome sequence, the reported non-essentiality of murI was unexplainable. In order to resolve this dilemma we tried to knockout murI in the presence of single and two copies of murI, in wild type and merodiploid strains respectively. It was found that murI could not be inactivated in the wild type background indicating that it could be an essential gene. Also, inactivation of murI could not be achieved in the presence of externally supplied d-glutamate in 7H9 medium suggesting that M. tuberculosis is unable to take up d-glutamate under the conditions tested. However we could generate murI knockout strains at high frequency when two copies of the gene were present indicating that at least one murI gene is required for cellular viability. The essential nature of MurI in M. tuberculosis H37Rv suggests that it could be a potential drug target.
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Affiliation(s)
- Sapna Morayya
- Present address: Biocon Bristol Myer squib R&D Centre, Biocon Park, Jigani Link Road, Bommasandra, Bangalore, India
| | - Disha Awasthy
- Present address: Strand Center for Genomics & Personalized Medicine, Strand Life Sciences Pvt. Ltd., Veterinary College Campus, Bellary Road, Bangalore, India
| | - Reena Yadav
- AstraZeneca India Pvt. Ltd., "Avishkar", Bellary Road, Hebbal, Bangalore, India
| | - Anisha Ambady
- Present address: Biocon Bristol Myer squib R&D Centre, Biocon Park, Jigani Link Road, Bommasandra, Bangalore, India
| | - Umender Sharma
- Present address: GangaGen Biotechnologies Pvt. Ltd, No 12, 5th Cross, Raghavendra Layout, Tumkur Road, Yeshwantpur, Bangalore, India.
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31
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Investigation of the essentiality of glutamate racemase in Mycobacterium smegmatis. J Bacteriol 2014; 196:4239-44. [PMID: 25246478 DOI: 10.1128/jb.02090-14] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The mycobacterial cell wall frequently has been used as a target for drug development, and d-glutamate, synthesized by glutamate racemase (MurI), is an important component of peptidoglycan. While the essentiality of the murI gene has been shown in several bacterial species, including Escherichia coli, Bacillus anthracis, and Streptococcus pneumoniae, studies in mycobacteria have not yet provided definitive results. This study aimed to determine whether murI is indeed essential and can serve as a possible target for structure-aided drug design. We have achieved this goal by creating a ΔmurI strain of Mycobacterium smegmatis, a close relative of Mycobacterium tuberculosis. The deletion of the murI gene in M. smegmatis could be achieved only in minimal medium supplemented with D-glutamate, demonstrating that MurI is essential for growth and that glutamate racemase is the only source of D-glutamate for peptidoglycan synthesis in M. smegmatis.
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32
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Munshi T, Gupta A, Evangelopoulos D, Guzman JD, Gibbons S, Keep NH, Bhakta S. Characterisation of ATP-dependent Mur ligases involved in the biogenesis of cell wall peptidoglycan in Mycobacterium tuberculosis. PLoS One 2013; 8:e60143. [PMID: 23555903 PMCID: PMC3605390 DOI: 10.1371/journal.pone.0060143] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Accepted: 02/21/2013] [Indexed: 11/30/2022] Open
Abstract
ATP-dependent Mur ligases (Mur synthetases) play essential roles in the biosynthesis of cell wall peptidoglycan (PG) as they catalyze the ligation of key amino acid residues to the stem peptide at the expense of ATP hydrolysis, thus representing potential targets for antibacterial drug discovery. In this study we characterized the division/cell wall (dcw) operon and identified a promoter driving the co-transcription of mur synthetases along with key cell division genes such as ftsQ and ftsW. Furthermore, we have extended our previous investigations of MurE to MurC, MurD and MurF synthetases from Mycobacterium tuberculosis. Functional analyses of the pure recombinant enzymes revealed that the presence of divalent cations is an absolute requirement for their activities. We also observed that higher concentrations of ATP and UDP-sugar substrates were inhibitory for the activities of all Mur synthetases suggesting stringent control of the cytoplasmic steps of the peptidoglycan biosynthetic pathway. In line with the previous findings on the regulation of mycobacterial MurD and corynebacterial MurC synthetases via phosphorylation, we found that all of the Mur synthetases interacted with the Ser/Thr protein kinases, PknA and PknB. In addition, we critically analyzed the interaction network of all of the Mur synthetases with proteins involved in cell division and cell wall PG biosynthesis to re-evaluate the importance of these key enzymes as novel therapeutic targets in anti-tubercular drug discovery.
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Affiliation(s)
- Tulika Munshi
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, University of London, London, United Kingdom
| | - Antima Gupta
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, University of London, London, United Kingdom
| | - Dimitrios Evangelopoulos
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, University of London, London, United Kingdom
| | - Juan David Guzman
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, University of London, London, United Kingdom
- Department of Pharmaceutical and Biological Chemistry, UCL School of Pharmacy, London, United Kingdom
| | - Simon Gibbons
- Department of Pharmaceutical and Biological Chemistry, UCL School of Pharmacy, London, United Kingdom
| | - Nicholas H. Keep
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, University of London, London, United Kingdom
| | - Sanjib Bhakta
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, University of London, London, United Kingdom
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33
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Michta E, Schad K, Blin K, Ort-Winklbauer R, Röttig M, Kohlbacher O, Wohlleben W, Schinko E, Mast Y. The bifunctional role of aconitase in Streptomyces viridochromogenes Tü494. Environ Microbiol 2012; 14:3203-19. [PMID: 23116164 DOI: 10.1111/1462-2920.12006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 09/24/2012] [Indexed: 12/01/2022]
Abstract
In many organisms, aconitases have dual functions; they serve as enzymes in the tricarboxylic acid cycle and as regulators of iron metabolism. In this study we defined the role of the aconitase AcnA in Streptomyces viridochromogenes Tü494, the producer of the herbicide phosphinothricyl-alanyl-alanine, also known as phosphinothricin tripeptide or bialaphos. A mutant in which the aconitase gene acnA was disrupted showed severe defects in morphology and physiology, as it was unable to form any aerial mycelium, spores nor phosphinothricin tripeptide. AcnA belongs to the iron regulatory proteins (IRPs). In addition to its catalytic function, AcnA plays a regulatory role by binding to iron responsive elements (IREs) located on the untranslated region of certain mRNAs. A mutation preventing the formation of the [4Fe-4S] cluster of AcnA eliminated its catalytic activity, but did not inhibit RNA-binding ability. In silico analysis of the S. viridochromogenes genome revealed several IRE-like structures. One structure is located upstream of recA, which is involved in the bacterial SOS response, and another one was identified upstream of ftsZ, which is required for the onset of sporulation in streptomycetes. The functionality of different IRE structures was proven with gel shift assays and specific IRE consensus sequences were defined. Furthermore, RecA was shown to be upregulated on post-transcriptional level under oxidative stress conditions in the wild-type strain but not in the acnA mutant, suggesting a regulatory role of AcnA in oxidative stress response.
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Affiliation(s)
- Ewelina Michta
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin (IMIT), Mikrobiologie/Biotechnologie, Fakultät für Biologie, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
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Selwood T, Jaffe EK. Dynamic dissociating homo-oligomers and the control of protein function. Arch Biochem Biophys 2012; 519:131-43. [PMID: 22182754 PMCID: PMC3298769 DOI: 10.1016/j.abb.2011.11.020] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Revised: 11/16/2011] [Accepted: 11/28/2011] [Indexed: 11/20/2022]
Abstract
Homo-oligomeric protein assemblies are known to participate in dynamic association/disassociation equilibria under native conditions, thus creating an equilibrium of assembly states. Such quaternary structure equilibria may be influenced in a physiologically significant manner either by covalent modification or by the non-covalent binding of ligands. This review follows the evolution of ideas about homo-oligomeric equilibria through the 20th and into the 21st centuries and the relationship of these equilibria to allosteric regulation by the non-covalent binding of ligands. A dynamic quaternary structure equilibria is described where the dissociated state can have alternate conformations that cannot reassociate to the original multimer; the alternate conformations dictate assembly to functionally distinct alternate multimers of finite stoichiometry. The functional distinction between different assemblies provides a mechanism for allostery. The requirement for dissociation distinguishes this morpheein model of allosteric regulation from the classical MWC concerted and KNF sequential models. These models are described alongside earlier dissociating allosteric models. The identification of proteins that exist as an equilibrium of diverse native quaternary structure assemblies has the potential to define new targets for allosteric modulation with significant consequences for further understanding and/or controlling protein structure and function. Thus, a rationale for identifying proteins that may use the morpheein model of allostery is presented and a selection of proteins for which published data suggests this mechanism may be operative are listed.
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Affiliation(s)
- Trevor Selwood
- Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111
| | - Eileen K. Jaffe
- Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111
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35
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Collin F, Karkare S, Maxwell A. Exploiting bacterial DNA gyrase as a drug target: current state and perspectives. Appl Microbiol Biotechnol 2011; 92:479-97. [PMID: 21904817 PMCID: PMC3189412 DOI: 10.1007/s00253-011-3557-z] [Citation(s) in RCA: 394] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 08/08/2011] [Accepted: 08/18/2011] [Indexed: 12/17/2022]
Abstract
DNA gyrase is a type II topoisomerase that can introduce negative supercoils into DNA at the expense of ATP hydrolysis. It is essential in all bacteria but absent from higher eukaryotes, making it an attractive target for antibacterials. The fluoroquinolones are examples of very successful gyrase-targeted drugs, but the rise in bacterial resistance to these agents means that we not only need to seek new compounds, but also new modes of inhibition of this enzyme. We review known gyrase-specific drugs and toxins and assess the prospects for developing new antibacterials targeted to this enzyme.
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Affiliation(s)
- Frédéric Collin
- Department Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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36
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Henderson B, Martin A. Bacterial virulence in the moonlight: multitasking bacterial moonlighting proteins are virulence determinants in infectious disease. Infect Immun 2011; 79:3476-91. [PMID: 21646455 PMCID: PMC3165470 DOI: 10.1128/iai.00179-11] [Citation(s) in RCA: 359] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Men may not be able to multitask, but it is emerging that proteins can. This capacity of proteins to exhibit more than one function is termed protein moonlighting, and, surprisingly, many highly conserved proteins involved in metabolic regulation or the cell stress response have a range of additional biological actions which are involved in bacterial virulence. This review highlights the multiple roles exhibited by a range of bacterial proteins, such as glycolytic and other metabolic enzymes and molecular chaperones, and the role that such moonlighting activity plays in the virulence characteristics of a number of important human pathogens, including Staphylococcus aureus, Streptococcus pyogenes, Streptococcus pneumoniae, Helicobacter pylori, and Mycobacterium tuberculosis.
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Affiliation(s)
- Brian Henderson
- Department of Microbial Diseases, UCL-Eastman Dental Institute, University College London, 256 Gray's Inn Road, London WC1X 8LD, United Kingdom.
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37
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Moonlighting role of a poly-gamma-glutamate synthetase component from Bacillus subtilis: insight into novel extrachromosomal DNA maintenance. Appl Environ Microbiol 2011; 77:2796-8. [PMID: 21357437 DOI: 10.1128/aem.02649-10] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Bacillus subtilis structural gene pgsE was investigated as a tool for extrachromosomal DNA maintenance (EDM). It ameliorated the stability of high-copy-number vectors, regardless of whether they were derived from rolling-cycle or theta-mode replicons, without any selective pressure. This unique EDM phenomenon may occur via a trans-acting mechanism.
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38
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Henderson B, Martin A. Bacterial Moonlighting Proteins and Bacterial Virulence. Curr Top Microbiol Immunol 2011; 358:155-213. [DOI: 10.1007/82_2011_188] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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39
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Kateete DP, Okee M, Katabazi FA, Okeng A, Asiimwe J, Boom HW, Eisenach KD, Joloba ML. Rhomboid homologs in mycobacteria: insights from phylogeny and genomic analysis. BMC Microbiol 2010; 10:272. [PMID: 21029479 PMCID: PMC2989971 DOI: 10.1186/1471-2180-10-272] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Accepted: 10/29/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rhomboids are ubiquitous proteins with diverse functions in all life kingdoms, and are emerging as important factors in the biology of some pathogenic apicomplexa and Providencia stuartii. Although prokaryotic genomes contain one rhomboid, actinobacteria can have two or more copies whose sequences have not been analyzed for the presence putative rhomboid catalytic signatures. We report detailed phylogenetic and genomic analyses devoted to prokaryotic rhomboids of an important genus, Mycobacterium. RESULTS Many mycobacterial genomes contained two phylogenetically distinct active rhomboids orthologous to Rv0110 (rhomboid protease 1) and Rv1337 (rhomboid protease 2) of Mycobacterium tuberculosis H37Rv, which were acquired independently. There was a genome-wide conservation and organization of the orthologs of Rv1337 arranged in proximity with glutamate racemase (mur1), while the orthologs of Rv0110 appeared evolutionary unstable and were lost in Mycobacterium leprae and the Mycobacterium avium complex. The orthologs of Rv0110 clustered with eukaryotic rhomboids and contained eukaryotic motifs, suggesting a possible common lineage. A novel nonsense mutation at the Trp73 codon split the rhomboid of Mycobacterium avium subsp. Paratuberculosis into two hypothetical proteins (MAP2425c and MAP2426c) that are identical to MAV_1554 of Mycobacterium avium. Mycobacterial rhomboids contain putative rhomboid catalytic signatures, with the protease active site stabilized by Phenylalanine. The topology and transmembrane helices of the Rv0110 orthologs were similar to those of eukaryotic secretase rhomboids, while those of Rv1337 orthologs were unique. Transcription assays indicated that both mycobacterial rhomboids are possibly expressed. CONCLUSIONS Mycobacterial rhomboids are active rhomboid proteases with different evolutionary history. The Rv0110 (rhomboid protease 1) orthologs represent prokaryotic rhomboids whose progenitor may be the ancestors of eukaryotic rhomboids. The Rv1337 (rhomboid protease 2) orthologs appear more stable and are conserved nearly in all mycobacteria, possibly alluding to their importance in mycobacteria. MAP2425c and MAP2426c provide the first evidence for a split homologous rhomboid, contrasting whole orthologs of genetically related species. Although valuable insights to the roles of rhomboids are provided, the data herein only lays a foundation for future investigations for the roles of rhomboids in mycobacteria.
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Affiliation(s)
- David P Kateete
- Department of Medical Microbiology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Moses Okee
- Department of Medical Microbiology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Fred A Katabazi
- Department of Medical Microbiology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Alfred Okeng
- Department of Medical Microbiology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Jeniffer Asiimwe
- Department of Veterinary Parasitology & Microbiology, Faculty of Veterinary Medicine, Makerere University, Kampala, Uganda
| | - Henry W Boom
- Case Western Reserve University, Cleveland, OH, USA
| | - Kathleen D Eisenach
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Moses L Joloba
- Department of Medical Microbiology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
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40
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Henderson B, Lund PA, Coates ARM. Multiple moonlighting functions of mycobacterial molecular chaperones. Tuberculosis (Edinb) 2010; 90:119-24. [PMID: 20338810 DOI: 10.1016/j.tube.2010.01.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2009] [Revised: 01/14/2010] [Accepted: 01/26/2010] [Indexed: 10/19/2022]
Abstract
Molecular chaperones and protein folding catalysts are normally thought of as intracellular proteins involved in protein folding quality control. However, in the mycobacteria there is increasing evidence to support the hypothesis that molecular chaperones are also secreted intercellular signalling molecules or can control actions at the cell wall or indeed control the composition of the cell wall. The most recent evidence for protein moonlighting in the mycobacteria is the report that chaperonin 60.2 of Mycobacterium tuberculosis is important in the key event in tuberculosis - the entry of the bacterium into the macrophage. This brief overview highlights the potential importance of the moonlighting functions of molecular chaperones in the biology and pathobiology of the mycobacteria.
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Affiliation(s)
- Brian Henderson
- Department of Microbial Diseases, UCL-Eastman Dental Institute, University College London, 256 Gray's Inn Road, London WC1X 8LD, United Kingdom. <>
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41
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Huberts DHEW, van der Klei IJ. Moonlighting proteins: an intriguing mode of multitasking. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2010; 1803:520-5. [PMID: 20144902 DOI: 10.1016/j.bbamcr.2010.01.022] [Citation(s) in RCA: 328] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2009] [Revised: 01/28/2010] [Accepted: 01/29/2010] [Indexed: 11/29/2022]
Abstract
Proteins are macromolecules, which perform a large variety of functions. Most of them have only a single function, but an increasing number of proteins are being identified as multifunctional. Moonlighting proteins form a special class of multifunctional proteins. They perform multiple autonomous and often unrelated functions without partitioning these functions into different domains of the protein. Striking examples are enzymes, which in addition to their catalytic function are involved in fully unrelated processes such as autophagy, protein transport or DNA maintenance. In this contribution we present an overview of our current knowledge of moonlighting proteins and discuss the significant implications for biomedical and fundamental research.
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Affiliation(s)
- Daphne H E W Huberts
- Molecular Cell Biology, GBB, University of Groningen, Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 14, 9750 AA Haren, The Netherlands
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Occurrence and Biosynthetic Mechanism of Poly-Gamma-Glutamic Acid. AMINO-ACID HOMOPOLYMERS OCCURRING IN NATURE 2010. [DOI: 10.1007/978-3-642-12453-2_5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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