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Matarredona L, Zafrilla B, Rubio-Portillo E, Bonete MJ, Esclapez J. Deepening the knowledge of universal stress proteins in Haloferax mediterranei. Appl Microbiol Biotechnol 2024; 108:124. [PMID: 38229402 DOI: 10.1007/s00253-023-12899-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 10/10/2023] [Accepted: 10/13/2023] [Indexed: 01/18/2024]
Abstract
Haloarchaea, like many other microorganisms, have developed defense mechanisms such as universal stress proteins (USPs) to cope with environmental stresses affecting microbial growth. Despite the wide distribution of these proteins in Archaea, their biochemical characteristics still need to be discovered, and there needs to be more knowledge about them focusing on halophilic Archaea. Therefore, elucidating the role of USPs would provide valuable information to improve future biotechnological applications. Accordingly, transcriptional expression of the 37 annotated USPs in the Haloferax mediterranei genome has been examined under different stress conditions. From a global perspective, finding a clear tendency between particular USPs and specific stress conditions was not possible. Contrary, data analysis indicates that there is a recruitment mechanism of proteins with a similar sequence able to modulate the H. mediterranei growth, accelerating or slowing it, depending on their number. In fact, only three of these USPs were expressed in all the tested conditions, pointing to the cell needing a set of USPs to cope with stress conditions. After analysis of the RNA-Seq data, three differentially expressed USPs were selected and homologously overexpressed. According to the growth data, the overexpression of USPs induces a gain of tolerance in response to stress, as a rule. Therefore, this is the only work that studies all the USPs in an archaeon. It represents a significant first base to continue advancing, not only in this important family of stress proteins but also in the field of biotechnology and, at an industrial level, to improve applications such as designing microorganisms resistant to stress situations. KEY POINTS: • Expression of Haloferax mediterranei USPs has been analyzed in stress conditions. • RNA-seq analysis reveals that most of the USPs in H. mediterranei are downregulated. • Homologous overexpression of USPs results in more stress-tolerant strains.
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Affiliation(s)
- Laura Matarredona
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, Ap 99, 03080, Alicante, Spain
| | - Basilio Zafrilla
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, Ap 99, 03080, Alicante, Spain
| | - Esther Rubio-Portillo
- Department of Physiology, Genetics and Microbiology, Faculty of Science, University of Alicante, Ap 99, 03080, Alicante, Spain
| | - María-José Bonete
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, Ap 99, 03080, Alicante, Spain
| | - Julia Esclapez
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, Ap 99, 03080, Alicante, Spain.
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2
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Nabi B, Kumawat M, Ahlawat N, Ahlawat S. Molecular, Structural, and Functional Diversity of Universal Stress Proteins (USPs) in Bacteria, Plants, and Their Biotechnological Applications. Protein J 2024; 43:437-446. [PMID: 38492187 DOI: 10.1007/s10930-024-10192-2] [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] [Accepted: 03/08/2024] [Indexed: 03/18/2024]
Abstract
Universal stress proteins (USPs) are widely distributed and play crucial roles in cellular responses to biotic and abiotic stresses. These roles include regulating cell growth and development, cell motility, hypoxia responses, and ion sequestration. With the increasing frequency and intensity of extreme weather events due to climate change, pathogens have developed different strategies to withstand environmental stresses, in which USPs play a significant role in their survival and virulence. In this study, we analyzed the importance of USPs in various organisms, such as archaea, plants, and fungi, as a parameter that influences their survival. We discussed the different types Of USPs and their role, aiming to carry out fundamental research in this field to identify significant constraints for better understanding of USP functions at molecular level. Additionally, we discussed concepts and research techniques that could help overcome these hurdles and facilitate new molecular approaches to better understand and target USPs as important stress adaptation and survival regulators. Although the precise characteristics of USPs are still unclear, numerous innovative uses have already been developed, tested, and implemented. Complementary approaches to basic research and applications, as well as new technology and analytical techniques, may offer insights into the cryptic but crucial activities of USPs in various living systems.
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Affiliation(s)
- Bilkees Nabi
- Department of Biochemistry & Biochemical Engineering, SHUATS, Allahabad, 211007, India
| | - Manoj Kumawat
- Department of Microbiology, ICMR- National Institute for Research in Environmental Health, Bhopal, 462030, India.
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, 462066, Madhya Pradesh, India.
| | - Neeraj Ahlawat
- Department of Animal Husbandry and Dairying, SHUATS, Allahabad, 211007, India
| | - Sushma Ahlawat
- Department of Biochemistry & Biochemical Engineering, SHUATS, Allahabad, 211007, India.
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Singh A, Singhal C, Sharma AK, Khurana P. An auxin regulated Universal stress protein (TaUSP_3B-1) interacts with TaGolS and provides tolerance under drought stress and ER stress. PHYSIOLOGIA PLANTARUM 2024; 176:e14390. [PMID: 38899466 DOI: 10.1111/ppl.14390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 05/10/2024] [Accepted: 05/23/2024] [Indexed: 06/21/2024]
Abstract
A previously identified wheat drought stress responsive Universal stress protein, TaUSP_3B-1 has been found to work in an auxin dependent manner in the plant root tissues in the differentiation zone. We also found a novel interacting partner, TaGolS, which physically interacts with TaUSP_3B-1 and colocalizes in the endoplasmic reticulum. TaGolS is a key enzyme in the RFO (Raffinose oligosaccharides) biosynthesis which is well reported to provide tolerance under water deficit conditions. TaUSP_3B-1 overexpression lines showed an early flowering phenotype under drought stress which might be attributed to the increased levels of AtTPPB and AtTPS transcripts under drought stress. Moreover, at the cellular levels ER stress induced TaUSP_3B-1 transcription and provides tolerance in both adaptive and acute ER stress via less ROS accumulation in the overexpression lines. TaUSP_3B-1 overexpression plants had increased silique numbers and a denser root architecture as compared to the WT plants under drought stress.
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Affiliation(s)
- Arunima Singh
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Chanchal Singhal
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Arun Kumar Sharma
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Paramjit Khurana
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
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Yan T, Li M, Wang Q, Wang M, Liu L, Ma C, Xiang X, Zhou Q, Liu Z, Gong Z. Structures, functions, and regulatory networks of universal stress proteins in clinically relevant pathogenic Bacteria. Cell Signal 2024; 116:111032. [PMID: 38185228 DOI: 10.1016/j.cellsig.2023.111032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/14/2023] [Accepted: 12/30/2023] [Indexed: 01/09/2024]
Abstract
Universal stress proteins are a class of proteins widely present in bacteria, archaea, plants, and invertebrates, playing essential roles in bacterial adaptation to various environmental stresses. The functions of bacterial universal stress proteins are versatile, including resistance to oxidative stress, maintenance of cell wall integrity, DNA damage repair, regulation of cell division and growth, among others. When facing stresses such as temperature changes, pH shifts, fluctuations in oxygen concentration, and exposure to toxins, these proteins can bind to specific DNA sequences and rapidly adjust bacterial metabolic pathways and gene expression patterns to adapt to the new environment. In summary, bacterial universal stress proteins play a crucial role in bacterial adaptability and survival. A comprehensive understanding of bacterial stress response mechanisms and the development of new antibacterial strategies are of great significance. This review summarizes the research progress on the structure, function, and regulatory factors of universal stress proteins in clinically relevant bacteria, aiming to facilitate deeper investigations by clinicians and researchers into universal stress proteins.
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Affiliation(s)
- Tao Yan
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Min Li
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Qiuyan Wang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Meng Wang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Lijuan Liu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Chengcheng Ma
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xiaohong Xiang
- School of Pharmacy, Chongqing Medical and Pharmaceutical College, Chongqing, China
| | - Qiang Zhou
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Zhou Liu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.
| | - Zhen Gong
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.
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Sharma D, Gautam S, Srivastava N, Khan AM, Bisht D. Comparative Proteomic Analysis of Capsule Proteins in Aminoglycoside-Resistant and Sensitive Mycobacterium tuberculosis Clinical Isolates: Unraveling Potential Drug Targets. Int J Mycobacteriol 2024; 13:197-205. [PMID: 38916392 DOI: 10.4103/ijmy.ijmy_47_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 05/22/2024] [Indexed: 06/26/2024] Open
Abstract
BACKGROUND Tuberculosis (TB), a global infectious threat, has seen a concerning rise in aminoglycoside-resistant Mycobacterium tuberculosis (M.tb) strains. The potential role of capsule proteins remains largely unexplored. This layer acts as the primary barrier for tubercle bacilli, attempting to infiltrate host cells and subsequent disease development. METHODS The study aims to bridge this gap by investigating the differentially expressed capsule proteins in aminoglycoside-resistant M.tb clinical isolates compared with drug-sensitive isolates employing two-dimensional gel electrophoresis, mass spectrometry, and bioinformatic approaches. RESULTS We identified eight proteins that exhibited significant upregulation in aminoglycoside-resistant isolates. Protein Rv3029c and Rv2110c were associated with intermediary metabolism and respiration; Rv2462c with cell wall and cell processes; Rv3804c with lipid metabolism; Rv2416c and Rv2623 with virulence and detoxification/adaptation; Rv0020c with regulatory functions; and Rv0639 with information pathways. Notably, the Group-based Prediction System for Prokaryotic Ubiquitin-like Protein (GPS-PUP) algorithm identified potential pupylation sites within all proteins except Rv3804c. Interactome analysis using the STRING 12.0 database revealed potential interactive partners for these proteins, suggesting their involvement in aminoglycoside resistance. Molecular docking studies revealed suitable binding between amikacin and kanamycin drugs with Rv2462c, Rv3804c, and Rv2623 proteins. CONCLUSION As a result, our findings illustrate the multifaceted nature of aminoglycoside resistance in M.tb and the importance of understanding how capsule proteins play a role in counteracting drug efficacy. Identifying the role of these proteins in drug resistance is crucial for developing more effective treatments and diagnostics for TB.
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Affiliation(s)
- Devesh Sharma
- Department of Biochemistry, ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, Uttar Pradesh, India
- School of Studies in Biochemistry, Jiwaji University, Gwalior, Madhya Pradesh, India
| | - Sakshi Gautam
- Department of Biochemistry, ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, Uttar Pradesh, India
| | - Nalini Srivastava
- School of Studies in Biochemistry, Jiwaji University, Gwalior, Madhya Pradesh, India
| | - Abdul Mabood Khan
- Division of Clinical Trails and Implementation Research, ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, Uttar Pradesh, India
| | - Deepa Bisht
- Department of Biochemistry, ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, Uttar Pradesh, India
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Ufimtseva EG, Eremeeva NI. Drug-Tolerant Mycobacterium tuberculosis Adopt Different Survival Strategies in Alveolar Macrophages of Patients with Pulmonary Tuberculosis. Int J Mol Sci 2023; 24:14942. [PMID: 37834390 PMCID: PMC10573496 DOI: 10.3390/ijms241914942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 08/31/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
The rapid spread of drug-resistant M. tuberculosis (Mtb) strains and the phenomenon of phenotypic tolerance to drugs present challenges toward achieving the goal of tuberculosis (TB) elimination worldwide. By using the ex vivo cultures of alveolar macrophages obtained from lung tissues of TB patients after intensive antimicrobial chemotherapy before surgery, different subpopulations of multidrug-tolerant Mtb with a spectrum of phenotypic and growth features were identified in the same TB lesions. Our results are indicative of not only passive mechanisms generating nonheritable resistance of Mtb to antibiotics, which are associated mainly with a lack of Mtb growth, but also some active mechanisms of Mtb persistence, such as cell wall and metabolic pathway remodeling. In one of the subpopulations, non-acid-fast Mtb have undergone significant reprogramming with the restoration of acid-fastness, lipoarabinomannan expression and replication in host cells of some patients after withdrawal of anti-TB drugs. Our data indicate the universal stress protein Rv2623 as a clinically relevant biomarker of Mtb that has lost acid-fastness in human lungs. The studies of Mtb survival, persistence, dormancy, and resumption and the identification of biomarkers characterizing these phenomena are very important concerning the development of vaccines and drug regimens with individualized management of patients for overcoming the resistance/tolerance crisis in anti-TB therapy.
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Affiliation(s)
- Elena G Ufimtseva
- Laboratory of Medical Biotechnology, Research Institute of Biochemistry, Federal Research Center of Fundamental and Translational Medicine, 2 Timakova Street, 630117 Novosibirsk, Russia
| | - Natalya I Eremeeva
- Institute of Disinfectology, F.F. Erisman Federal Scientific Center of Hygiene of the Federal Service on Surveillance for Consumer Rights Protection and Human Well-Being, 18a Nauchniy Proezd, 117246 Moscow, Russia
- Scientific Department, Ural Research Institute for Phthisiopulmonology, National Medical Research Center of Tuberculosis and Infectious Diseases of Ministry of Health of the Russian Federation, 50 XXII Partsyezda Street, 620039 Yekaterinburg, Russia
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Singh A, Singhal C, Sharma AK, Khurana P. Identification of universal stress proteins in wheat and functional characterization during abiotic stress. PLANT CELL REPORTS 2023; 42:1487-1501. [PMID: 37341826 DOI: 10.1007/s00299-023-03043-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 06/12/2023] [Indexed: 06/22/2023]
Abstract
KEY MESSAGE TaUSPs are localized in Endoplasmic reticulum and form homo and hetero dimers within themselves. They play significant role in multiple abiotic stress responses in yeast heterologous system and in plants. Universal Stress Proteins are stress responsive proteins present in a variety of life forms ranging from bacteria to multicellular plants and animals. In this study we have identified 85 TaUSP genes in the wheat genome and have characterised their abiotic stress responsive members in yeast under different stress conditions. Localization and Y2H studies suggest that wheat, USP proteins are localized in the ER complex, and extensively crosstalk amongst themselves through forming hetero and homodimers. Expression analysis of these TaUSP genes suggests their role in adaptation to multiple abiotic stresses. TaUSP_5D-1 was found to have some DNA binding activity in yeast. Certain abiotic stress responsive TaUSP genes are found to impart tolerance to temperature stress, oxidative stress, ER stress (DTT treatment) and LiCl2 stress in the yeast heterologous system. TaUSP_5D-1 overexpression in A. thaliana imparts drought tolerance via better lateral root network in transgenic lines. The TaUSP represents an important repertoire of genes for engineering abiotic stress responsiveness in crop plants.
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Affiliation(s)
- Arunima Singh
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Chanchal Singhal
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Arun Kumar Sharma
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Paramjit Khurana
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India.
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McDowell JR, Bai G, Lasek-Nesselquist E, Eisele LE, Wu Y, Hurteau G, Johnson R, Bai Y, Chen Y, Chan J, McDonough KA. Mycobacterial phosphodiesterase Rv0805 is a virulence determinant and its cyclic nucleotide hydrolytic activity is required for propionate detoxification. Mol Microbiol 2023; 119:401-422. [PMID: 36760076 PMCID: PMC10315211 DOI: 10.1111/mmi.15030] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 01/15/2023] [Accepted: 01/21/2023] [Indexed: 02/11/2023]
Abstract
Cyclic AMP (cAMP) signaling is essential to Mycobacterium tuberculosis (Mtb) pathogenesis. However, the roles of phosphodiesterases (PDEs) Rv0805, and the recently identified Rv1339, in cAMP homeostasis and Mtb biology are unclear. We found that Rv0805 modulates Mtb growth within mice, macrophages and on host-associated carbon sources. Mycobacterium bovis BCG grown on a combination of propionate and glycerol as carbon sources showed high levels of cAMP and had a strict requirement for Rv0805 cNMP hydrolytic activity. Supplementation with vitamin B12 or spontaneous genetic mutations in the pta-ackA operon restored the growth of BCGΔRv0805 and eliminated propionate-associated cAMP increases. Surprisingly, reduction of total cAMP levels by ectopic expression of Rv1339 restored only 20% of growth, while Rv0805 complementation fully restored growth despite a smaller effect on total cAMP levels. Deletion of an Rv0805 localization domain also reduced BCG growth in the presence of propionate and glycerol. We propose that localized Rv0805 cAMP hydrolysis modulates activity of a specialized pathway associated with propionate metabolism, while Rv1339 has a broader role in cAMP homeostasis. Future studies will address the biological roles of Rv0805 and Rv1339, including their impacts on metabolism, cAMP signaling and Mtb pathogenesis.
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Affiliation(s)
- James R. McDowell
- Wadsworth Center, New York State Department of Health, Albany, NY 12208
- Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany NY 12208
| | - Guangchun Bai
- Wadsworth Center, New York State Department of Health, Albany, NY 12208
- Department of Immunology and Microbial Disease, MC-151, Albany Medical College, Albany, NY 12208-3479
| | - Erica Lasek-Nesselquist
- Wadsworth Center, New York State Department of Health, Albany, NY 12208
- Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany NY 12208
| | - Leslie E. Eisele
- Wadsworth Center, New York State Department of Health, Albany, NY 12208
| | - Yan Wu
- Wadsworth Center, New York State Department of Health, Albany, NY 12208
| | - Gregory Hurteau
- Wadsworth Center, New York State Department of Health, Albany, NY 12208
| | - Richard Johnson
- Wadsworth Center, New York State Department of Health, Albany, NY 12208
- Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany NY 12208
| | - Yinlan Bai
- Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany NY 12208
| | - Yong Chen
- Albert Einstein College of Medicine, Bronx, NY
| | - John Chan
- Albert Einstein College of Medicine, Bronx, NY
| | - Kathleen A. McDonough
- Wadsworth Center, New York State Department of Health, Albany, NY 12208
- Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany NY 12208
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O'Connor A, Jurado‐Martín I, Mysior MM, Manzira AL, Drabinska J, Simpson JC, Lucey M, Schaffer K, Berisio R, McClean S. A universal stress protein upregulated by hypoxia has a role in Burkholderia cenocepacia intramacrophage survival: Implications for chronic infection in cystic fibrosis. Microbiologyopen 2023; 12:e1311. [PMID: 36825886 PMCID: PMC9733578 DOI: 10.1002/mbo3.1311] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 07/29/2022] [Accepted: 07/29/2022] [Indexed: 12/13/2022] Open
Abstract
Universal stress proteins (USPs) are ubiquitously expressed in bacteria, archaea, and eukaryotes and play a lead role in adaptation to environmental conditions. They enable adaptation of bacterial pathogens to the conditions encountered in the human niche, including hypoxia, oxidative stress, osmotic stress, nutrient deficiency, or acid stress, thereby facilitating colonization. We previously reported that all six USP proteins encoded within a low-oxygen activated (lxa) locus in Burkholderia cenocepacia showed increased abundance during chronic colonization of the cystic fibrosis (CF) lung. However, the role of USPs in chronic cystic fibrosis infection is not well understood. Structural modeling identified surface arginines on one lxa-encoded USP, USP76, which suggested it mediated interactions with heparan sulfate. Using mutants derived from the B. cenocepacia strain, K56-2, we show that USP76 is involved in host cell attachment. Pretreatment of lung epithelial cells with heparanase reduced the binding of the wild-type and complement strains but not the Δusp76 mutant strain, indicating that USP76 is directly or indirectly involved in receptor recognition on the surface of epithelial cells. We also show that USP76 is required for growth and survival in many conditions associated with the CF lung, including acidic conditions and oxidative stress. Moreover, USP76 also has a role in survival in macrophages isolated from people with CF. Overall, while further elucidation of the exact mechanism(s) is required, we can conclude that USP76, which is upregulated during chronic infection, is involved in bacterial survival within CF macrophages, a hallmark of Burkholderia infection.
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Affiliation(s)
- Andrew O'Connor
- School of Biomolecular and Biomedical SciencesUniversity College DublinBelfieldDublinIreland
| | - Irene Jurado‐Martín
- School of Biomolecular and Biomedical SciencesUniversity College DublinBelfieldDublinIreland
- UCD Conway Institute of Biomolecular and Biomedical ScienceBefieldDublinIreland
| | - Margaritha M. Mysior
- UCD Conway Institute of Biomolecular and Biomedical ScienceBefieldDublinIreland
- Cell Screening Laboratory, School of Biology and Environmental ScienceUniversity College DublinBelfieldDublinIreland
| | - Anotidaishe L. Manzira
- School of Biomolecular and Biomedical SciencesUniversity College DublinBelfieldDublinIreland
- UCD Conway Institute of Biomolecular and Biomedical ScienceBefieldDublinIreland
| | - Joanna Drabinska
- School of Biomolecular and Biomedical SciencesUniversity College DublinBelfieldDublinIreland
- UCD Conway Institute of Biomolecular and Biomedical ScienceBefieldDublinIreland
| | - Jeremy C. Simpson
- UCD Conway Institute of Biomolecular and Biomedical ScienceBefieldDublinIreland
- Cell Screening Laboratory, School of Biology and Environmental ScienceUniversity College DublinBelfieldDublinIreland
| | - Mary Lucey
- Department of MicrobiologySt. Vincent's University HospitalElm ParkDublinIreland
| | - Kirsten Schaffer
- Department of MicrobiologySt. Vincent's University HospitalElm ParkDublinIreland
| | - Rita Berisio
- Institute of Biostructures and BioimagingNational Research CouncilNaplesItaly
| | - Siobhán McClean
- School of Biomolecular and Biomedical SciencesUniversity College DublinBelfieldDublinIreland
- UCD Conway Institute of Biomolecular and Biomedical ScienceBefieldDublinIreland
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Allué-Guardia A, Garcia-Vilanova A, Olmo-Fontánez AM, Peters J, Maselli DJ, Wang Y, Turner J, Schlesinger LS, Torrelles JB. Host- and Age-Dependent Transcriptional Changes in Mycobacterium tuberculosis Cell Envelope Biosynthesis Genes after Exposure to Human Alveolar Lining Fluid. Int J Mol Sci 2022; 23:ijms23020983. [PMID: 35055170 PMCID: PMC8780516 DOI: 10.3390/ijms23020983] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/09/2022] [Accepted: 01/10/2022] [Indexed: 12/16/2022] Open
Abstract
Tuberculosis (TB) infection, caused by the airborne pathogen Mycobacterium tuberculosis (M.tb), resulted in almost 1.4 million deaths in 2019, and the number of deaths is predicted to increase by 20% over the next 5 years due to the COVID-19 pandemic. Upon reaching the alveolar space, M.tb comes into close contact with the lung mucosa before and after its encounter with host alveolar compartment cells. Our previous studies show that homeostatic, innate soluble components of the alveolar lining fluid (ALF) can quickly alter the cell envelope surface of M.tb upon contact, defining subsequent M.tb-host cell interactions and infection outcomes in vitro and in vivo. We also demonstrated that ALF from 60+ year old elders (E-ALF) vs. healthy 18- to 45-year-old adults (A-ALF) is dysfunctional, with loss of homeostatic capacity and impaired innate soluble responses linked to high local oxidative stress. In this study, a targeted transcriptional assay shows that M.tb exposure to human ALF alters the expression of its cell envelope genes. Specifically, our results indicate that A-ALF-exposed M.tb upregulates cell envelope genes associated with lipid, carbohydrate, and amino acid metabolism, as well as genes associated with redox homeostasis and transcriptional regulators. Conversely, M.tb exposure to E-ALF shows a lesser transcriptional response, with most of the M.tb genes unchanged or downregulated. Overall, this study indicates that M.tb responds and adapts to the lung alveolar environment upon contact, and that the host ALF status, determined by factors such as age, might play an important role in determining infection outcome.
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Affiliation(s)
- Anna Allué-Guardia
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (A.G.-V.); (A.M.O.-F.)
- Correspondence: (A.A.-G.); (J.B.T.)
| | - Andreu Garcia-Vilanova
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (A.G.-V.); (A.M.O.-F.)
| | - Angélica M. Olmo-Fontánez
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (A.G.-V.); (A.M.O.-F.)
- Integrated Biomedical Sciences Program, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Jay Peters
- Division of Pulmonary and Critical Care Medicine, School of Medicine, UT Health San Antonio, San Antonio, TX 78229, USA; (J.P.); (D.J.M.)
| | - Diego J. Maselli
- Division of Pulmonary and Critical Care Medicine, School of Medicine, UT Health San Antonio, San Antonio, TX 78229, USA; (J.P.); (D.J.M.)
| | - Yufeng Wang
- Department of Molecular Microbiology and Immunology, South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX 78249, USA;
| | - Joanne Turner
- Host-Pathogen Interactions Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (J.T.); (L.S.S.)
| | - Larry S. Schlesinger
- Host-Pathogen Interactions Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (J.T.); (L.S.S.)
| | - Jordi B. Torrelles
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (A.G.-V.); (A.M.O.-F.)
- Correspondence: (A.A.-G.); (J.B.T.)
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Joshi H, Kandari D, Bhatnagar R. Insights into the molecular determinants involved in Mycobacterium tuberculosis persistence and their therapeutic implications. Virulence 2021; 12:2721-2749. [PMID: 34637683 PMCID: PMC8565819 DOI: 10.1080/21505594.2021.1990660] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/17/2021] [Accepted: 10/05/2021] [Indexed: 01/08/2023] Open
Abstract
The establishment of persistent infections and the reactivation of persistent bacteria to active bacilli are the two hurdles in effective tuberculosis treatment. Mycobacterium tuberculosis, an etiologic tuberculosis agent, adapts to numerous antibiotics and resists the host immune system causing a disease of public health concern. Extensive research has been employed to combat this disease due to its sheer ability to persist in the host system, undetected, waiting for the opportunity to declare itself. Persisters are a bacterial subpopulation that possesses transient tolerance to high doses of antibiotics. There are certain inherent mechanisms that facilitate the persister cell formation in Mycobacterium tuberculosis, some of those had been characterized in the past namely, stringent response, transcriptional regulators, energy production pathways, lipid metabolism, cell wall remodeling enzymes, phosphate metabolism, and proteasome protein degradation. This article reviews the recent advancements made in various in vitro persistence models that assist to unravel the mechanisms involved in the persister cell formation and to hunt for the possible preventive or treatment measures. To tackle the persister population the immunodominant proteins that express specifically at the latent phase of infection can be used for diagnosis to distinguish between the active and latent tuberculosis, as well as to select potential drug or vaccine candidates. In addition, we discuss the genes engaged in the persistence to get more insights into resuscitation and persister cell formation. The in-depth understanding of persistent cells of mycobacteria can certainly unravel novel ways to target the pathogen and tackle its persistence.
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Affiliation(s)
- Hemant Joshi
- Molecular Biology and Genetic Engineering Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Divya Kandari
- Molecular Biology and Genetic Engineering Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Rakesh Bhatnagar
- Molecular Biology and Genetic Engineering Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
- Amity University of Rajasthan, Jaipur, Rajasthan, India
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12
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Hafeez MN, Khan MA, Sarwar B, Hassan S, Ali Q, Husnain T, Rashid B. Mutant Gossypium universal stress protein-2 (GUSP-2) gene confers resistance to various abiotic stresses in E. coli BL-21 and CIM-496-Gossypium hirsutum. Sci Rep 2021; 11:20466. [PMID: 34650178 PMCID: PMC8516947 DOI: 10.1038/s41598-021-99900-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 09/27/2021] [Indexed: 11/24/2022] Open
Abstract
Gossypium arboreum is considered a rich source of stress-responsive genes and the EST database revealed that most of its genes are uncharacterized. The full-length Gossypium universal stress protein-2 (GUSP-2) gene (510 bp) was cloned in E. coli and Gossypium hirsutum, characterized and point mutated at three positions, 352–354, Lysine to proline (M1-usp-2) & 214–216, aspartic acid to serine (M2-usp-2) & 145–147, Lysine to Threonine (M3-usp-2) to study its role in abiotic stress tolerance. It was found that heterologous expression of one mutant (M1-usp-2) provided enhanced tolerance against salt and osmotic stresses, recombinant cells have higher growth up to 10-5dilution in spot assay as compared to cells expressing W-usp-2 (wild type GUSP-2), M2-usp-2 and M3-usp-2 genes. M1-usp-2 gene transcript profiling exhibited significant expression (8.7 fold) in CIM-496-Gossypium hirsutum transgenic plants and enhance drought tolerance. However, little tolerance against heat and cold stresses in bacterial cells was observed. The results from our study concluded that the activity of GUSP-2 was enhanced in M1-usp-2 but wipe out in M2-usp-2 and M3-usp-2 response remained almost parallel to W-usp-2. Further, it was predicted through in silico analysis that M1-usp-2, W-usp-2 and M3-usp-2 may be directly involved in stress tolerance or function as a signaling molecule to activate the stress adaptive mechanism. However, further investigation will be required to ascertain its role in the adaptive mechanism of stress tolerance.
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Affiliation(s)
- Muhammad Nadeem Hafeez
- Centre of Excellence in Molecular Biology, University of the Punjab Lahore, Lahore, Pakistan. .,Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland. .,School of PhD Program in Cellular and Molecular Biotechnology, University of Teramo, Teramo, Italy. .,Department of Pharmacy, University of Chieti - Pescara "G. d'Annunzio", Chieti, Italy.
| | - Mohsin Ahmad Khan
- Centre of Excellence in Molecular Biology, University of the Punjab Lahore, Lahore, Pakistan
| | - Bilal Sarwar
- Centre of Excellence in Molecular Biology, University of the Punjab Lahore, Lahore, Pakistan
| | - Sameera Hassan
- Centre of Excellence in Molecular Biology, University of the Punjab Lahore, Lahore, Pakistan
| | - Qurban Ali
- Centre of Excellence in Molecular Biology, University of the Punjab Lahore, Lahore, Pakistan. .,Institute of Molecular Biology and Biotechnology, University of Lahore, Lahore, Pakistan.
| | - Tayyab Husnain
- Centre of Excellence in Molecular Biology, University of the Punjab Lahore, Lahore, Pakistan
| | - Bushra Rashid
- Centre of Excellence in Molecular Biology, University of the Punjab Lahore, Lahore, Pakistan
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13
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Masamba P, Kappo AP. Parasite Survival and Disease Persistence in Cystic Fibrosis, Schistosomiasis and Pathogenic Bacterial Diseases: A Role for Universal Stress Proteins? Int J Mol Sci 2021; 22:10878. [PMID: 34639223 PMCID: PMC8509486 DOI: 10.3390/ijms221910878] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/15/2021] [Accepted: 09/28/2021] [Indexed: 12/16/2022] Open
Abstract
Universal stress proteins (USPs) were originally discovered in Escherichia coli over two decades ago and since then their presence has been detected in various organisms that include plants, archaea, metazoans, and bacteria. As their name suggests, they function in a series of various cellular responses in both abiotic and biotic stressful conditions such as oxidative stress, exposure to DNA damaging agents, nutrient starvation, high temperature and acidic stress, among others. Although a highly conserved group of proteins, the molecular and biochemical aspects of their functions are largely evasive. This is concerning, as it was observed that USPs act as essential contributors to the survival/persistence of various infectious pathogens. Their ubiquitous nature in various organisms, as well as their augmentation during conditions of stress, is a clear indication of their direct or indirect importance in providing resilience against such conditions. This paper seeks to clarify what has already been reported in the literature on the proposed mechanism of action of USPs in pathogenic organisms.
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Affiliation(s)
- Priscilla Masamba
- Molecular Biophysics and Structural Biology (MBSB) Group, Department of Biochemistry, Kingsway Campus, University of Johannesburg, Auckland Park 2006, South Africa;
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14
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Allué-Guardia A, Garcia-Vilanova A, M Olmo-Fontánez A, Peters J, Maselli DJ, Wang Y, Turner J, Schlesinger LS, Torrelles JB. Host- and age-dependent transcriptional changes in Mycobacterium tuberculosis cell envelope biosynthesis genes after exposure to human alveolar lining fluid. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 34580670 DOI: 10.1101/2021.09.08.459334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Tuberculosis (TB) infection, caused by the airborne pathogen Mycobacterium tuberculosis ( M . tb ), resulted in almost 1.4 million deaths in 2019 and the number of deaths is predicted to increase by 20% over the next 5 years due to the COVID-19 pandemic. Upon reaching the alveolar space, M . tb comes in close contact with the lung mucosa before and after its encounter with host alveolar compartment cells. Our previous studies show that homeostatic innate soluble components of the alveolar lining fluid (ALF) can quickly alter the cell envelope surface of M . tb upon contact, defining subsequent M . tb -host cell interactions and infection outcomes in vitro and in vivo . We also demonstrated that ALF from 60+ year old elders (E-ALF) vs . healthy 18- to 45-year-old adults (A-ALF) is dysfunctional with loss of homeostatic capacity and impaired innate soluble responses linked to high local oxidative stress. In this study, a targeted transcriptional assay demonstrates that M . tb exposure to human ALF alters the expression of its cell envelope genes. Specifically, our results indicate that A-ALF-exposed M . tb upregulates cell envelope genes associated with lipid, carbohydrate, and amino acid metabolism, as well as genes associated with redox homeostasis and transcriptional regulators. Conversely, M . tb exposure to E-ALF shows lesser transcriptional response, with most of the M . tb genes unchanged or downregulated. Overall, this study indicates that M . tb responds and adapts to the lung alveolar environment upon contact, and that the host ALF status determined by factors such as age might play an important role in determining infection outcome.
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15
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Isokpehi RD, McInnis DS, Destefano AM, Johnson GS, Walker AD, Hall YA, Mapp BW, Johnson MO, Simmons SS. Bioinformatics Investigations of Universal Stress Proteins from Mercury-Methylating Desulfovibrionaceae. Microorganisms 2021; 9:microorganisms9081780. [PMID: 34442859 PMCID: PMC8401546 DOI: 10.3390/microorganisms9081780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/30/2021] [Accepted: 08/06/2021] [Indexed: 11/26/2022] Open
Abstract
The presence of methylmercury in aquatic environments and marine food sources is of global concern. The chemical reaction for the addition of a methyl group to inorganic mercury occurs in diverse bacterial taxonomic groups including the Gram-negative, sulfate-reducing Desulfovibrionaceae family that inhabit extreme aquatic environments. The availability of whole-genome sequence datasets for members of the Desulfovibrionaceae presents opportunities to understand the microbial mechanisms that contribute to methylmercury production in extreme aquatic environments. We have applied bioinformatics resources and developed visual analytics resources to categorize a collection of 719 putative universal stress protein (USP) sequences predicted from 93 genomes of Desulfovibrionaceae. We have focused our bioinformatics investigations on protein sequence analytics by developing interactive visualizations to categorize Desulfovibrionaceae universal stress proteins by protein domain composition and functionally important amino acids. We identified 651 Desulfovibrionaceae universal stress protein sequences, of which 488 sequences had only one USP domain and 163 had two USP domains. The 488 single USP domain sequences were further categorized into 340 sequences with ATP-binding motif and 148 sequences without ATP-binding motif. The 163 double USP domain sequences were categorized into (1) both USP domains with ATP-binding motif (3 sequences); (2) both USP domains without ATP-binding motif (138 sequences); and (3) one USP domain with ATP-binding motif (21 sequences). We developed visual analytics resources to facilitate the investigation of these categories of datasets in the presence or absence of the mercury-methylating gene pair (hgcAB). Future research could utilize these functional categories to investigate the participation of universal stress proteins in the bacterial cellular uptake of inorganic mercury and methylmercury production, especially in anaerobic aquatic environments.
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Affiliation(s)
- Raphael D. Isokpehi
- College of Science, Engineering and Mathematics, Bethune-Cookman University, Daytona Beach, FL 32114, USA; (D.S.M.); (A.M.D.); (G.S.J.); (A.D.W.); (Y.A.H.); (B.W.M.)
- Correspondence:
| | - Dominique S. McInnis
- College of Science, Engineering and Mathematics, Bethune-Cookman University, Daytona Beach, FL 32114, USA; (D.S.M.); (A.M.D.); (G.S.J.); (A.D.W.); (Y.A.H.); (B.W.M.)
| | - Antoinette M. Destefano
- College of Science, Engineering and Mathematics, Bethune-Cookman University, Daytona Beach, FL 32114, USA; (D.S.M.); (A.M.D.); (G.S.J.); (A.D.W.); (Y.A.H.); (B.W.M.)
| | - Gabrielle S. Johnson
- College of Science, Engineering and Mathematics, Bethune-Cookman University, Daytona Beach, FL 32114, USA; (D.S.M.); (A.M.D.); (G.S.J.); (A.D.W.); (Y.A.H.); (B.W.M.)
| | - Akimio D. Walker
- College of Science, Engineering and Mathematics, Bethune-Cookman University, Daytona Beach, FL 32114, USA; (D.S.M.); (A.M.D.); (G.S.J.); (A.D.W.); (Y.A.H.); (B.W.M.)
| | - Yessenia A. Hall
- College of Science, Engineering and Mathematics, Bethune-Cookman University, Daytona Beach, FL 32114, USA; (D.S.M.); (A.M.D.); (G.S.J.); (A.D.W.); (Y.A.H.); (B.W.M.)
| | - Baraka W. Mapp
- College of Science, Engineering and Mathematics, Bethune-Cookman University, Daytona Beach, FL 32114, USA; (D.S.M.); (A.M.D.); (G.S.J.); (A.D.W.); (Y.A.H.); (B.W.M.)
| | - Matilda O. Johnson
- College of Nursing and Health Sciences, Bethune-Cookman University, Daytona Beach, FL 32114, USA;
| | - Shaneka S. Simmons
- Department of Science and Mathematics, Jarvis Christian College, Hawkins, TX 75765, USA;
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16
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Vaccination with BCGΔBCG1419c protects against pulmonary and extrapulmonary TB and is safer than BCG. Sci Rep 2021; 11:12417. [PMID: 34127755 PMCID: PMC8203684 DOI: 10.1038/s41598-021-91993-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 06/03/2021] [Indexed: 02/07/2023] Open
Abstract
A single intradermal vaccination with an antibiotic-less version of BCGΔBCG1419c given to guinea pigs conferred a significant improvement in outcome following a low dose aerosol exposure to M. tuberculosis compared to that provided by a single dose of BCG Pasteur. BCGΔBCG1419c was more attenuated than BCG in murine macrophages, athymic, BALB/c, and C57BL/6 mice. In guinea pigs, BCGΔBCG1419c was at least as attenuated as BCG and induced similar dermal reactivity to that of BCG. Vaccination of guinea pigs with BCGΔBCG1419c resulted in increased anti-PPD IgG compared with those receiving BCG. Guinea pigs vaccinated with BCGΔBCG1419c showed a significant reduction of M. tuberculosis replication in lungs and spleens compared with BCG, as well as a significant reduction of pulmonary and extrapulmonary tuberculosis (TB) pathology measured using pathology scores recorded at necropsy. Evaluation of cytokines produced in lungs of infected guinea pigs showed that BCGΔBCG1419c significantly reduced TNF-α and IL-17 compared with BCG-vaccinated animals, with no changes in IL-10. This work demonstrates a significantly improved protection against pulmonary and extrapulmonary TB provided by BCGΔBCG1419c in susceptible guinea pigs together with an increased safety compared with BCG in several models. These results support the continued development of BCGΔBCG1419c as an effective vaccine for TB.
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17
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Dutta A, Batish M, Parashar V. Structural basis of KdpD histidine kinase binding to the second messenger c-di-AMP. J Biol Chem 2021; 296:100771. [PMID: 33989637 PMCID: PMC8214093 DOI: 10.1016/j.jbc.2021.100771] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 05/03/2021] [Accepted: 05/07/2021] [Indexed: 11/17/2022] Open
Abstract
The KdpDE two-component system regulates potassium homeostasis and virulence in various bacterial species. The KdpD histidine kinases (HK) of this system contain a universal stress protein (USP) domain which binds to the second messenger cyclic-di-adenosine monophosphate (c-di-AMP) for regulating transcriptional output from this two-component system in Firmicutes such as Staphylococcus aureus. However, the structural basis of c-di-AMP specificity within the KdpD-USP domain is not well understood. Here, we resolved a 2.3 Å crystal structure of the S. aureus KdpD-USP domain (USPSa) complexed with c-di-AMP. Binding affinity analyses of USPSa mutants targeting the observed USPSa:c-di-AMP structural interface enabled the identification of the sequence residues that are required for c-di-AMP specificity. Based on the conservation of these residues in other Firmicutes, we identified the binding motif, (A/G/C)XSXSX2N(Y/F), which allowed us to predict c-di-AMP binding in other KdpD HKs. Furthermore, we found that the USPSa domain contains structural features distinct from the canonical standalone USPs that bind ATP as a preferred ligand. These features include inward-facing conformations of its β1-α1 and β4-α4 loops, a short α2 helix, the absence of a triphosphate-binding Walker A motif, and a unique dual phospho-ligand binding mode. It is therefore likely that USPSa-like domains in KdpD HKs represent a novel subfamily of the USPs.
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Affiliation(s)
- Anirudha Dutta
- Department of Medical and Molecular Sciences, University of Delaware, Newark, Delaware, USA
| | - Mona Batish
- Department of Medical and Molecular Sciences, University of Delaware, Newark, Delaware, USA
| | - Vijay Parashar
- Department of Medical and Molecular Sciences, University of Delaware, Newark, Delaware, USA.
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18
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Jagadeb M, Pattanaik KP, Rath SN, Sonawane A. Identification and evaluation of immunogenic MHC-I and MHC-II binding peptides from Mycobacterium tuberculosis. Comput Biol Med 2020; 130:104203. [PMID: 33450502 DOI: 10.1016/j.compbiomed.2020.104203] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/22/2020] [Accepted: 12/23/2020] [Indexed: 11/18/2022]
Abstract
Due to several limitations of the only available BCG vaccine, to generate adequate protective immune responses, it is important to develop potent and cost-effective vaccines against tuberculosis (TB). In this study, we have used an immune-informatics approach to identify potential peptide based vaccine targets against TB. The proteome of Mycobacterium tuberculosis (Mtb), the causative agent of TB, was analyzed for secretory or surface localized antigenic proteins as potential vaccine candidates. The T- and B-cell epitopes as well as MHC molecule binding efficiency were identified and mapped in the modelled structures of the selected proteins. Based on antigenicity score and molecular dynamic simulation (MD) studies two peptides namely Pep-9 and Pep-15 were analyzed, modelled and docked with MHC-I and MHC-II structures. Both peptides exhibited no cytotoxicity and were able to induce proinflammatory cytokine secretion in stimulated macrophages. The molecular docking, MD and in-vitro studies of the predicted B and T-cell epitopes of Pep-9 and Pep-15 peptides with the modelled MHC structures exhibited strong binding affinity and antigenic properties, suggesting that the complex is stable, and that these peptides can be considered as a potential candidates for the development of vaccine against TB.
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Affiliation(s)
- Manaswini Jagadeb
- School of Biotechnology, KIIT University, Bhubaneswar, Odisha, India.
| | | | - Surya Narayan Rath
- Department of Bioinformatics, Odisha University of Agriculture and Technology, Bhubaneswar, Odisha, India.
| | - Avinash Sonawane
- School of Biotechnology, KIIT University, Bhubaneswar, Odisha, India; Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore (IIT Indore), Simrol, Madhya Pradesh, India.
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The ATP-Binding Cassette (ABC) Transport Systems in Mycobacterium tuberculosis: Structure, Function, and Possible Targets for Therapeutics. BIOLOGY 2020; 9:biology9120443. [PMID: 33291531 PMCID: PMC7761784 DOI: 10.3390/biology9120443] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 11/06/2020] [Accepted: 11/12/2020] [Indexed: 12/22/2022]
Abstract
Simple Summary Mycobacterium tuberculosis is a bacterium of great medical importance because it causes tuberculosis, a disease that affects millions of people worldwide. Two important features are related to this bacterium: its ability to infect and survive inside the host, minimizing the immune response, and the burden of clinical isolates that are highly resistant to antibiotics treatment. These two phenomena are directly affected by cell envelope proteins, such as proteins from the ATP-Binding Cassette (ABC transporters) superfamily. In this review, we have compiled information on all the M. tuberculosis ABC transporters described so far, both from a functional and structural point of view, and show their relevance for the bacillus and the potential targets for studies aiming to control the microorganism and structural features. Abstract Mycobacterium tuberculosis is the etiological agent of tuberculosis (TB), a disease that affects millions of people in the world and that is associated with several human diseases. The bacillus is highly adapted to infect and survive inside the host, mainly because of its cellular envelope plasticity, which can be modulated to adapt to an unfriendly host environment; to manipulate the host immune response; and to resist therapeutic treatment, increasing in this way the drug resistance of TB. The superfamily of ATP-Binding Cassette (ABC) transporters are integral membrane proteins that include both importers and exporters. Both types share a similar structural organization, yet only importers have a periplasmic substrate-binding domain, which is essential for substrate uptake and transport. ABC transporter-type importers play an important role in the bacillus physiology through the transport of several substrates that will interfere with nutrition, pathogenesis, and virulence. Equally relevant, exporters have been involved in cell detoxification, nutrient recycling, and antibiotics and drug efflux, largely affecting the survival and development of multiple drug-resistant strains. Here, we review known ABC transporters from M. tuberculosis, with particular focus on the diversity of their structural features and relevance in infection and drug resistance.
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20
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Ye X, van der Does C, Albers SV. SaUspA, the Universal Stress Protein of Sulfolobus acidocaldarius Stimulates the Activity of the PP2A Phosphatase and Is Involved in Growth at High Salinity. Front Microbiol 2020; 11:598821. [PMID: 33304342 PMCID: PMC7693658 DOI: 10.3389/fmicb.2020.598821] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 10/23/2020] [Indexed: 11/13/2022] Open
Abstract
In Sulfolobus acidocaldarius, the protein phosphatase PP2A plays important regulatory roles in many cellular processes, including cell growth, cell shape and synthesis of the archaellum. A conserved prokaryotic protein, designated as SaUspA, was identified as an interaction partner of the phosphatase PP2A. SaUspA belongs to the universal stress protein (USP) superfamily, members of which are found in bacteria, archaea, plants and invertebrates. Biochemical analysis showed that SaUspA is a homodimeric ATP-binding protein, which also in vitro binds to PP2A. SaUspA did not hydrolyze ATP, but stimulated the phosphatase activity of PP2A and might in this manner affect many other processes. Interestingly, binding of ATP further enhanced SaUspA's interaction with PP2A. In contrast to bacterial usp genes, environmental stress conditions including stationary phase, starvation stress, high salinity stress and UV stress did not stimulate expression of saUspA. Deletion of saUspA led to premature production of the archaellin FlaB in S. acidocaldarius although motility was not affected. The ΔsaUspA mutant showed a significant growth defect under high salinity stress and complementation of ATP-binding deficient mutant SaUspAG97A failed to restore this growth defect. Compared with the wild type strain, its growth or survival was not affected under heavy metal stress and UV stress. To date, this is the first study in which the physiological role of USP homologs in archaea have been reported.
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Affiliation(s)
- Xing Ye
- Molecular Biology of Archaea, Faculty of Biology, Institute of Biology II, University of Freiburg, Freiburg, Germany
| | - Chris van der Does
- Molecular Biology of Archaea, Faculty of Biology, Institute of Biology II, University of Freiburg, Freiburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Faculty of Biology, Institute of Biology II, University of Freiburg, Freiburg, Germany
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21
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Lopez Quezada L, Smith R, Lupoli TJ, Edoo Z, Li X, Gold B, Roberts J, Ling Y, Park SW, Nguyen Q, Schoenen FJ, Li K, Hugonnet JE, Arthur M, Sacchettini JC, Nathan C, Aubé J. Activity-Based Protein Profiling Reveals That Cephalosporins Selectively Active on Non-replicating Mycobacterium tuberculosis Bind Multiple Protein Families and Spare Peptidoglycan Transpeptidases. Front Microbiol 2020; 11:1248. [PMID: 32655524 PMCID: PMC7324553 DOI: 10.3389/fmicb.2020.01248] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 05/15/2020] [Indexed: 11/13/2022] Open
Abstract
As β-lactams are reconsidered for the treatment of tuberculosis (TB), their targets are assumed to be peptidoglycan transpeptidases, as verified by adduct formation and kinetic inhibition of Mycobacterium tuberculosis (Mtb) transpeptidases by carbapenems active against replicating Mtb. Here, we investigated the targets of recently described cephalosporins that are selectively active against non-replicating (NR) Mtb. NR-active cephalosporins failed to inhibit recombinant Mtb transpeptidases. Accordingly, we used alkyne analogs of NR-active cephalosporins to pull down potential targets through unbiased activity-based protein profiling and identified over 30 protein binders. None was a transpeptidase. Several of the target candidates are plausibly related to Mtb's survival in an NR state. However, biochemical tests and studies of loss of function mutants did not identify a unique target that accounts for the bactericidal activity of these beta-lactams against NR Mtb. Instead, NR-active cephalosporins appear to kill Mtb by collective action on multiple targets. These results highlight the ability of these β-lactams to target diverse classes of proteins.
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Affiliation(s)
- Landys Lopez Quezada
- Department of Microbiology & Immunology, Weill Cornell Medical College, New York, NY, United States
| | - Robert Smith
- Chemical Methodologies & Library Development Center, The University of Kansas, Lawrence, KS, United States
| | - Tania J. Lupoli
- Department of Microbiology & Immunology, Weill Cornell Medical College, New York, NY, United States
| | - Zainab Edoo
- Sorbonne Université, Sorbonne Paris Cité, Université de Paris, INSERM, Centre de Recherche des Cordeliers, CRC, Paris, France
| | - Xiaojun Li
- Departments of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Ben Gold
- Department of Microbiology & Immunology, Weill Cornell Medical College, New York, NY, United States
| | - Julia Roberts
- Department of Microbiology & Immunology, Weill Cornell Medical College, New York, NY, United States
| | - Yan Ling
- Department of Microbiology & Immunology, Weill Cornell Medical College, New York, NY, United States
| | - Sae Woong Park
- Department of Microbiology & Immunology, Weill Cornell Medical College, New York, NY, United States
| | - Quyen Nguyen
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Frank J. Schoenen
- Chemical Methodologies & Library Development Center, The University of Kansas, Lawrence, KS, United States
| | - Kelin Li
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jean-Emmanuel Hugonnet
- Sorbonne Université, Sorbonne Paris Cité, Université de Paris, INSERM, Centre de Recherche des Cordeliers, CRC, Paris, France
| | - Michel Arthur
- Sorbonne Université, Sorbonne Paris Cité, Université de Paris, INSERM, Centre de Recherche des Cordeliers, CRC, Paris, France
| | - James C. Sacchettini
- Departments of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Carl Nathan
- Department of Microbiology & Immunology, Weill Cornell Medical College, New York, NY, United States
| | - Jeffrey Aubé
- Chemical Methodologies & Library Development Center, The University of Kansas, Lawrence, KS, United States
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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Gallant J, Mouton J, Ummels R, Ten Hagen-Jongman C, Kriel N, Pain A, Warren RM, Bitter W, Heunis T, Sampson SL. Identification of gene fusion events in Mycobacterium tuberculosis that encode chimeric proteins. NAR Genom Bioinform 2020; 2:lqaa033. [PMID: 33575588 PMCID: PMC7671302 DOI: 10.1093/nargab/lqaa033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 04/16/2020] [Accepted: 05/05/2020] [Indexed: 02/07/2023] Open
Abstract
Mycobacterium tuberculosis is a facultative intracellular pathogen responsible for causing tuberculosis. The harsh environment in which M. tuberculosis survives requires this pathogen to continuously adapt in order to maintain an evolutionary advantage. However, the apparent absence of horizontal gene transfer in M. tuberculosis imposes restrictions in the ways by which evolution can occur. Large-scale changes in the genome can be introduced through genome reduction, recombination events and structural variation. Here, we identify a functional chimeric protein in the ppe38-71 locus, the absence of which is known to have an impact on protein secretion and virulence. To examine whether this approach was used more often by this pathogen, we further develop software that detects potential gene fusion events from multigene deletions using whole genome sequencing data. With this software we could identify a number of other putative gene fusion events within the genomes of M. tuberculosis isolates. We were able to demonstrate the expression of one of these gene fusions at the protein level using mass spectrometry. Therefore, gene fusions may provide an additional means of evolution for M. tuberculosis in its natural environment whereby novel chimeric proteins and functions can arise.
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Affiliation(s)
- James Gallant
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Science, Faculty of Medicine and Health Science, Stellenbosch University, Tygerberg, Cape Town 7505, South Africa.,Section of Molecular Microbiology, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, 1081 HZ Amsterdam, The Netherlands
| | - Jomien Mouton
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Science, Faculty of Medicine and Health Science, Stellenbosch University, Tygerberg, Cape Town 7505, South Africa
| | - Roy Ummels
- Medical Microbiology and Infection Control, Vrije Universiteit Amsterdam, Amsterdam UMC, 1081 HZ Amsterdam, The Netherlands
| | - Corinne Ten Hagen-Jongman
- Section of Molecular Microbiology, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, 1081 HZ Amsterdam, The Netherlands
| | - Nastassja Kriel
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Science, Faculty of Medicine and Health Science, Stellenbosch University, Tygerberg, Cape Town 7505, South Africa
| | - Arnab Pain
- Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia.,Global Station for Zoonosis Control, GI-CoRE, Hokkaido University, 001-0020, N20 W10 Kita-ku, Sapporo, Japan
| | - Robin M Warren
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Science, Faculty of Medicine and Health Science, Stellenbosch University, Tygerberg, Cape Town 7505, South Africa
| | - Wilbert Bitter
- Section of Molecular Microbiology, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, 1081 HZ Amsterdam, The Netherlands.,Medical Microbiology and Infection Control, Vrije Universiteit Amsterdam, Amsterdam UMC, 1081 HZ Amsterdam, The Netherlands
| | - Tiaan Heunis
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Science, Faculty of Medicine and Health Science, Stellenbosch University, Tygerberg, Cape Town 7505, South Africa.,Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Samantha L Sampson
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Science, Faculty of Medicine and Health Science, Stellenbosch University, Tygerberg, Cape Town 7505, South Africa
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23
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Havis S, Rangel J, Mali S, Bodunrin A, Housammy Z, Zimmerer R, Murphy J, Widger WR, Bark SJ. A color-based competition assay for studying bacterial stress responses in Micrococcus luteus. FEMS Microbiol Lett 2019; 366:5379281. [PMID: 30865770 DOI: 10.1093/femsle/fnz054] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 03/12/2019] [Indexed: 12/30/2022] Open
Abstract
Competition assays measure differences between populations of bacteria after stress adaptation, populations of different bacteria and mutations in antibiotic resistance genes. We have developed a competition-based assay to evaluate if genes upregulated under starvation are important for bacterial survival. Stress responses are critical for survival in non-pathogenic and pathogenic bacteria alike including Mycobacterium tuberculosis, Enterococcus fecaelis, Escherichia coli and Staphylococcus aureus. Unfortunately, most stress-survival proteins are poorly understood because suitable model bacteria and techniques are limited. To address this problem, we have engineered Micrococcus luteus NCTC 2665 (M. luteus) for competition assays by inactivating the sarcinaxanthin biosynthesis gene crtE (ΔcrtE), changing M. luteus colonies from yellow to white. This change allows easy identification in mixed cultures. The crtE knockout is relatively neutral for growth in complex and minimal acetate media and shows a measured fitness of one in competition with yellow wild-type bacteria. The ΔcrtE M. luteus competition assay identified a competition defect in a M. luteus strain when a specific universal stress protein was inactivated, suggesting a negative survival phenotype for this protein. We anticipate this competition assay can identify defects in other gene knockouts and mutational studies in M. luteus and will enhance our understanding of bacterial survival mechanisms.
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Affiliation(s)
- Spencer Havis
- Department of Biology and Biochemistry, The University of Houston, Houston, TX, USA
| | - Jonathan Rangel
- Department of Biology and Biochemistry, The University of Houston, Houston, TX, USA
| | - Sujina Mali
- Department of Biology, Washington University, St. Louis, MO, USA
| | - Abiodun Bodunrin
- Department of Biology and Biochemistry, The University of Houston, Houston, TX, USA
| | - Zina Housammy
- University of North Texas Health Sciences Center, Fort Worth, TX, USA
| | - Rene Zimmerer
- Department of Biology and Biochemistry, The University of Houston, Houston, TX, USA
| | - Jesse Murphy
- Department of Biology and Biochemistry, The University of Houston, Houston, TX, USA
| | - William R Widger
- Department of Biology and Biochemistry, The University of Houston, Houston, TX, USA
| | - Steven J Bark
- Department of Biology and Biochemistry, The University of Houston, Houston, TX, USA
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24
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Fang QJ, Han YX, Shi YJ, Huang HQ, Fang ZG, Hu YH. Universal stress proteins contribute Edwardsiella piscicida adversity resistance and pathogenicity and promote blocking host immune response. FISH & SHELLFISH IMMUNOLOGY 2019; 95:248-258. [PMID: 31654767 DOI: 10.1016/j.fsi.2019.10.035] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 10/02/2019] [Accepted: 10/19/2019] [Indexed: 06/10/2023]
Abstract
Universal stress proteins (Usps) exist ubiquitously in bacteria and other organisms. Usps play an important role in adaptation of bacteria to a variety of environmental stresses. There is increasing evidence that Usps facilitate pathogens to adapt host environment and are involved in pathogenicity. Edwardsiella piscicida (formerly included in E. tarda) is a severe fish pathogen and infects various important economic fish including tilapia (Oreochromis niloticus). In E. piscicida, a number of systems and factors that are involved in stress resistance and pathogenesis were identified. However, the function of Usps in E. piscicida is totally unknown. In this study, we examined the expressions of 13 usp genes in E. piscicida and found that most of these usp genes were up-regulated expression under high temperature, oxidative stress, acid stress, and host serum stress. Particularly, among these usp genes, usp13, exhibited dramatically high expression level upon several stress conditions. To investigate the biological role of usp13, a markerless usp13 in-frame mutant strain, TX01Δusp13, was constructed. Compared to the wild type TX01, TX01Δusp13 exhibited markedly compromised tolerance to high temperature, hydrogen peroxide, and low pH. Deletion of usp13 significantly retarded bacterial biofilm growth and decreased resistance against serum killing. Pathogenicity analysis showed that the inactivation of usp13 significantly impaired the ability of E. piscicida to invade into host cell and infect host tissue. Introduction of a trans-expressed usp13 gene restored the lost virulence of TX01Δusp13. In support of these results, host immune response induced by TX01 and TX01Δusp13 was examined, and the results showed reactive oxygen species (ROS) levels in TX01Δusp13-infected macrophages were significantly higher than those in TX01-infected cells. The expression level of several cytokines (IL-6, IL-8, IL-10, TNF-α, and CC2) in TX01Δusp13-infected fish was significantly higher than that in TX01-infected fish. These results suggested that the deletion of usp13 attenuated the ability of bacteria to overcome the host immune response to pathogen infection. Taken together, our study indicated Usp13 of E. piscicida was not only important participant in adversity resistance, but also was essential for E. piscicida pathogenicity and contributed to block host immune response to pathogen infection.
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Affiliation(s)
- Qing-Jian Fang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, College of Marine Science, Hainan University, Haikou, 570228, China; Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Yue-Xin Han
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Yan-Jie Shi
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Hui-Qin Huang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China; Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bio-resources, Haikou, 571101, China
| | - Zai-Guang Fang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, College of Marine Science, Hainan University, Haikou, 570228, China.
| | - Yong-Hua Hu
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), China; Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bio-resources, Haikou, 571101, China.
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25
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A Universal Stress Protein That Controls Bacterial Stress Survival in Micrococcus luteus. J Bacteriol 2019; 201:JB.00497-19. [PMID: 31548273 DOI: 10.1128/jb.00497-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 09/05/2019] [Indexed: 12/14/2022] Open
Abstract
Bacteria have remarkable mechanisms to survive severe external stresses, and one of the most enigmatic is the nonreplicative persistent (NRP) state. Practically, NRP bacteria are difficult to treat, and so inhibiting the proteins underlying this survival state may render such bacteria more susceptible to external stresses, including antibiotics. Unfortunately, we know little about the proteins and mechanisms conferring survival through the NRP state. Here, we report that a universal stress protein (Usp) is a primary regulator of bacterial survival through the NRP state in Micrococcus luteus NCTC 2665, a biosafety level 1 (BSL1) mycobacterial relative. Usps are widely conserved, and bacteria, including Mycobacterium tuberculosis, Mycobacterium smegmatis, and Escherichia coli, have multiple paralogs with overlapping functions that have obscured their functional roles. A kanamycin resistance cassette inserted into the M. luteus universal stress protein A 616 gene (ΔuspA616::kan M. luteus) ablates the UspA616 protein and drastically impairs M. luteus survival under even short-term starvation (survival, 83% wild type versus 32% ΔuspA616::kan M. luteus) and hypoxia (survival, 96% wild type versus 48% ΔuspA616::kan M. luteus). We observed no detrimental UspA616 knockout phenotype in logarithmic growth. Proteomics demonstrated statistically significant log-phase upregulation of glyoxylate pathway enzymes isocitrate lyase and malate synthase in ΔuspA616::kan M. luteus We note that these enzymes and the M. tuberculosis UspA616 homolog (Rv2623) are important in M. tuberculosis virulence and chronic infection, suggesting that Usps are important stress proteins across diverse bacterial species. We propose that UspA616 is a metabolic switch that controls survival by regulating the glyoxylate shunt.IMPORTANCE Bacteria tolerate severe external stresses, including antibiotics, through a nonreplicative persistent (NRP) survival state, yet the proteins regulating this survival state are largely unknown. We show a specific universal stress protein (UspA616) controls the NRP state in Micrococcus luteus Usps are widely conserved across bacteria, but their biological function(s) has remained elusive. UspA616 inactivation renders M. luteus susceptible to stress: bacteria die instead of adapting through the NRP state. UspA616 regulates malate synthase and isocitrate lyase, glyoxylate pathway enzymes important for chronic Mycobacterium tuberculosis infection. These data show that UspA616 regulates NRP stress survival in M. luteus and suggest a function for homologous proteins in other bacteria. Importantly, inhibitors of UspA616 and homologs may render NRP bacteria more susceptible to stresses, including current antibiotics.
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26
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Yang M, Che S, Zhang Y, Wang H, Wei T, Yan G, Song W, Yu W. Universal stress protein in Malus sieversii confers enhanced drought tolerance. JOURNAL OF PLANT RESEARCH 2019; 132:825-837. [PMID: 31482250 DOI: 10.1007/s10265-019-01133-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 08/16/2019] [Indexed: 06/10/2023]
Abstract
Drought is an important environmental factor that can severely affect plant growth and reproduction. Although many genes related to drought tolerance have been studied in economically important crops, very few genes have been functionally identified in Malus sieversii. In this study, we isolated a new gene based on throughput RNA sequencing analysis and constructed genetic expression vectors and transformed in Arabidopsis thaliana for functional verification. The results showed that MsUspA ectopic expression driven by constitutive (CaMV 35S) promoter gave rise to substantial improvements in ability of transgenic A. thaliana plants to survive under extreme drought conditions. Improved drought resistance mainly depends on more compact cellular structure, longer roots, strong resilience and low-level ROS. Molecular expression analysis showed that MsUspA may be involved in hormone and secondary metabolite synthesis regulation to improve drought resistance.
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Affiliation(s)
- Meiling Yang
- Institute of Surface-Earth System Science, Tianjin University, Tianjin, 300072, China
- College of Life Sciences, Nankai University, Tianjin, 300071, China
- College of Horticulture and Landscape, Tianjin Agricultural University, Tianjin, 300384, China
| | - Shiyou Che
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China
| | - Yunxiu Zhang
- College of Horticulture and Landscape, Tianjin Agricultural University, Tianjin, 300384, China
| | - Hongbin Wang
- College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Tao Wei
- College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Guorong Yan
- College of Horticulture and Landscape, Tianjin Agricultural University, Tianjin, 300384, China.
| | - Wenqin Song
- College of Life Sciences, Nankai University, Tianjin, 300071, China.
| | - Weiwei Yu
- College of Horticulture and Landscape, Tianjin Agricultural University, Tianjin, 300384, China.
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27
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Wang C, Zhang Q, Wang Y, Tang X, An Y, Li S, Xu H, Li Y, Luan W, Wang X, Liu M, Yu L. Comparative proteomics analysis between biofilm and planktonic cells of Mycobacterium tuberculosis. Electrophoresis 2019; 40:2736-2746. [PMID: 31141184 DOI: 10.1002/elps.201900030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 05/01/2019] [Accepted: 05/22/2019] [Indexed: 12/19/2022]
Abstract
Tuberculosis is highly persistent and displays phenotypic resistance to high concentrations of antimicrobials. Recent reports exhibited that Mycobacterium tuberculosis biofilm was implicated to its pathogenicity and drug resistance. In this study, there were 47 kinds of differential proteins in the biofilm of M. tuberculosis H37Rv cells compared with the planktonic bacteria, and 37 proteins were nonredundant and identified by proteomics approach, such as 2DE and LC-MS/MS. Moreover, six kinds of proteins were identified as HspX, which were conservative and highly expressed in biofilm. Note that 47 differential proteins were divided into seven categories, such as cell wall and cell processes, conserved hypotheticals, intermediary metabolism and respiration, and so on by TUBERCULIST. The Gene Ontology classification results showed that the largest protein group involved in metabolism, binding proteins, and catalytic function accounts for 30% and 57% of all identified proteins, respectively. Moreover, the protein interaction network analyzed by STRING showed that the minority proteins such as RpoA, SucC, Cbs, Tuf, DnaK, and GroeL in the interaction network have high network connectivity. These results implied that the proteins involved in metabolic process and catalytic function and the minority proteins mentioned above may play an important role in M. tuberculosis biofilm formation. To our knowledge, this is the first report about differential proteins between biofilm and planktonic M. tuberculosis, which provided the potential antigens for vaccines and target proteins for anti-mycobacterial drugs.
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Affiliation(s)
- Chao Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, Department of Infectious Diseases, First Hospital of Jilin University, College of Veterinary Medicine, Jilin University, Changchun, P. R. China
| | - Qiaoli Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, Department of Infectious Diseases, First Hospital of Jilin University, College of Veterinary Medicine, Jilin University, Changchun, P. R. China
| | - Yang Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, Department of Infectious Diseases, First Hospital of Jilin University, College of Veterinary Medicine, Jilin University, Changchun, P. R. China
| | - Xudong Tang
- Key Lab for New Drug Research of TCM, Research Institute of Tsinghua University in Shenzhen, Shenzhen, P. R. China
| | - Yanan An
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, Department of Infectious Diseases, First Hospital of Jilin University, College of Veterinary Medicine, Jilin University, Changchun, P. R. China
| | - Shulin Li
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, Department of Infectious Diseases, First Hospital of Jilin University, College of Veterinary Medicine, Jilin University, Changchun, P. R. China
| | - Hongyue Xu
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, Department of Infectious Diseases, First Hospital of Jilin University, College of Veterinary Medicine, Jilin University, Changchun, P. R. China
| | - Yan Li
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, Department of Infectious Diseases, First Hospital of Jilin University, College of Veterinary Medicine, Jilin University, Changchun, P. R. China
| | - Wenjing Luan
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, Department of Infectious Diseases, First Hospital of Jilin University, College of Veterinary Medicine, Jilin University, Changchun, P. R. China
| | - Xuefei Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, Department of Infectious Diseases, First Hospital of Jilin University, College of Veterinary Medicine, Jilin University, Changchun, P. R. China
| | - Mingyuan Liu
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, Department of Infectious Diseases, First Hospital of Jilin University, College of Veterinary Medicine, Jilin University, Changchun, P. R. China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, P. R. China
| | - Lu Yu
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, Department of Infectious Diseases, First Hospital of Jilin University, College of Veterinary Medicine, Jilin University, Changchun, P. R. China
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28
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Briffotaux J, Liu S, Gicquel B. Genome-Wide Transcriptional Responses of Mycobacterium to Antibiotics. Front Microbiol 2019; 10:249. [PMID: 30842759 PMCID: PMC6391361 DOI: 10.3389/fmicb.2019.00249] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 01/30/2019] [Indexed: 11/13/2022] Open
Abstract
Antibiotics can stimulate or depress gene expression in bacteria. The analysis of transcriptional responses of Mycobacterium to antimycobacterial compounds has improved our understanding of the mode of action of various drug classes and the efficacy and effect of such compounds on the global metabolism of Mycobacterium. This approach can provide new insights for known antibiotics, for example those currently used for tuberculosis treatment, as well as help to identify the mode of action and predict the targets of new compounds identified by whole-cell screening assays. In addition, changes in gene expression profiles after antimycobacterial treatment can provide information about the adaptive ability of bacteria to escape the effects of antibiotics and allow monitoring of the physiology of the bacteria during treatment. Genome-wide expression profiling also makes it possible to pinpoint genes differentially expressed between drug sensitive Mycobacterium and multidrug-resistant clinical isolates. Finally, genes involved in adaptive responses and drug tolerance could become new targets for improving the efficacy of existing antibiotics.
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Affiliation(s)
- Julien Briffotaux
- Department of Tuberculosis Control and Prevention, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, China.,Emerging Bacterial Pathogens Unit, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Shengyuan Liu
- Department of Tuberculosis Control and Prevention, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, China
| | - Brigitte Gicquel
- Department of Tuberculosis Control and Prevention, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, China.,Emerging Bacterial Pathogens Unit, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China.,Mycobacterial Genetics Unit, Institut Pasteur, Paris, France
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29
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Chi YH, Koo SS, Oh HT, Lee ES, Park JH, Phan KAT, Wi SD, Bae SB, Paeng SK, Chae HB, Kang CH, Kim MG, Kim WY, Yun DJ, Lee SY. The Physiological Functions of Universal Stress Proteins and Their Molecular Mechanism to Protect Plants From Environmental Stresses. FRONTIERS IN PLANT SCIENCE 2019; 10:750. [PMID: 31231414 PMCID: PMC6560075 DOI: 10.3389/fpls.2019.00750] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 05/22/2019] [Indexed: 05/13/2023]
Abstract
Since the original discovery of a Universal Stress Protein (USP) in Escherichia coli, a number of USPs have been identified from diverse sources including archaea, bacteria, plants, and metazoans. As their name implies, these proteins participate in a broad range of cellular responses to biotic and abiotic stresses. Their physiological functions are associated with ion scavenging, hypoxia responses, cellular mobility, and regulation of cell growth and development. Consistent with their roles in resistance to multiple stresses, USPs show a wide range of structural diversity that results from the diverse range of other functional motifs fused with the USP domain. As well as providing structural diversity, these catalytic motifs are responsible for the diverse biochemical properties of USPs and enable them to act in a number of cellular signaling transducers and metabolic regulators. Despite the importance of USP function in many organisms, the molecular mechanisms by which USPs protect cells and provide stress resistance remain largely unknown. This review addresses the diverse roles of USPs in plants and how the proteins enable plants to resist against multiple stresses in ever-changing environment. Bioinformatic tools used for the collection of a set of USPs from various plant species provide more than 2,100 USPs and their functional diversity in plant physiology. Data from previous studies are used to understand how the biochemical activity of plant USPs modulates biotic and abiotic stress signaling. As USPs interact with the redox protein, thioredoxin, in Arabidopsis and reactive oxygen species (ROS) regulates the activity of USPs, the involvement of USPs in redox-mediated defense signaling is also considered. Finally, this review discusses the biotechnological application of USPs in an agricultural context by considering the development of novel stress-resistant crops through manipulating the expression of USP genes.
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Affiliation(s)
- Yong Hun Chi
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Sung Sun Koo
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Hun Taek Oh
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Eun Seon Lee
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Joung Hun Park
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Kieu Anh Thi Phan
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Seong Dong Wi
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Su Bin Bae
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Seol Ki Paeng
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Ho Byoung Chae
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Chang Ho Kang
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Min Gab Kim
- College of Pharmacy and Research Institute of Pharmaceutical Science, Gyeongsang National University, Jinju, South Korea
| | - Woe-Yeon Kim
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
- Institute of Agricultural and Life Science (IALS), Gyeongsang National University, Jinju, South Korea
| | - Dae-Jin Yun
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, South Korea
| | - Sang Yeol Lee
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
- *Correspondence: Sang Yeol Lee,
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30
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Aceves-Sánchez MDJ, Flores-Valdez MA, Shanley C, Orme I, Bielefeldt-Ohmann H. Vaccination of guinea pigs with BCGΔBCG1419c transiently reduces hematogenous spread of M. tuberculosis to the spleen. Pathog Dis 2018; 76:5222634. [PMID: 30500936 DOI: 10.1093/femspd/fty088] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 11/28/2018] [Indexed: 01/08/2023] Open
Abstract
The guinea pig has proven to be a reliable model for testing vaccine candidates against tuberculosis (TB) because of its capacity to produce human-like disease associated to primary TB, thus providing a more stringent test of the ability of a vaccine to prevent disease and deaths. Here, the BCGΔBCG1419c vaccine candidate, which previously has been shown to provide protection in mice, was tested in a guinea pig model. We found that this vaccine candidate was as effective as parental BCG in reducing M. tuberculosis H37Rv replication in lungs, and significantly reducing hematogenous spread to spleen at 60 days post-infection in comparison with BCG. Moreover, lung histopathological examination revealed comparable protection between the parental and mutant BCG strains, with some differences in prevention of primary lesions or necrosis at a single time point post-infection in a strain-dependent manner. Our results show that the BCGΔBCG1419c vaccine candidate is as effective as BCG in reducing M. tuberculosis H37Rv replication in lungs and reducing lung pathology, as well as significantly improving control of its dissemination to spleens up to 60 days post-infection.
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Affiliation(s)
- Michel de Jesús Aceves-Sánchez
- Centro de Investigación y Asistencia en Tecnología y diseño del Estado de Jalisco, A.C. Biotecnología Médica y Farmacéutica. Av. Normalistas 800, Col. Colinas de la Normal, Guadalajara, Jalisco, 44270, México
| | - Mario Alberto Flores-Valdez
- Centro de Investigación y Asistencia en Tecnología y diseño del Estado de Jalisco, A.C. Biotecnología Médica y Farmacéutica. Av. Normalistas 800, Col. Colinas de la Normal, Guadalajara, Jalisco, 44270, México
| | - Crystal Shanley
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, 1682 Campus Delivery, Fort Collins, CO 80523-1682, USA
| | - Ian Orme
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, 1682 Campus Delivery, Fort Collins, CO 80523-1682, USA
| | - Helle Bielefeldt-Ohmann
- School of Veterinary Science, The University of Queensland Gatton Campus, Qld 4343, Australia
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Girardin RC, Bai G, He J, Sui H, McDonough KA. AbmR (Rv1265) is a novel transcription factor of Mycobacterium tuberculosis that regulates host cell association and expression of the non-coding small RNA Mcr11. Mol Microbiol 2018; 110:811-830. [PMID: 30207611 PMCID: PMC6282994 DOI: 10.1111/mmi.14126] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/07/2018] [Accepted: 09/09/2018] [Indexed: 12/11/2022]
Abstract
Gene regulatory networks used by Mycobacterium tuberculosis (Mtb) during infection include many genes of unknown function, confounding efforts to determine their roles in Mtb biology. Rv1265 encodes a conserved hypothetical protein that is expressed during infection and in response to elevated levels of cyclic AMP. Here, we report that Rv1265 is a novel auto‐inhibitory ATP‐binding transcription factor that upregulates expression of the small non‐coding RNA Mcr11, and propose that Rv1265 be named ATP‐binding mcr11regulator (AbmR). AbmR directly and specifically bound DNA, as determined by electrophoretic mobility shift assays, and this DNA‐binding activity was enhanced by AbmR’s interaction with ATP. Genetic knockout of abmR in Mtb increased abmR promoter activity and eliminated growth phase‐dependent increases in mcr11 expression during hypoxia. Mutagenesis identified arginine residues in the carboxy terminus that are critical for AbmR’s DNA‐binding activity and gene regulatory function. Limited similarity to other DNA‐ or ATP‐binding domains suggests that AbmR belongs to a novel class of DNA‐ and ATP‐binding proteins. AbmR was also found to form large organized structures in solution and facilitate the serum‐dependent association of Mtb with human lung epithelial cells. These results indicate a potentially complex role for AbmR in Mtb biology.
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Affiliation(s)
- Roxie C Girardin
- Department of Biomedical Sciences, School of Public Health, University at Albany, PO Box 22002, Albany, NY, 12201-2002, USA
| | - Guangchun Bai
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY, USA
| | - Jie He
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Haixin Sui
- Department of Biomedical Sciences, School of Public Health, University at Albany, PO Box 22002, Albany, NY, 12201-2002, USA.,Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Kathleen A McDonough
- Department of Biomedical Sciences, School of Public Health, University at Albany, PO Box 22002, Albany, NY, 12201-2002, USA.,Wadsworth Center, New York State Department of Health, Albany, NY, USA
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Chatterjee N, Ojha R, Khatoon N, Prajapati VK. Scrutinizing Mycobacterium tuberculosis membrane and secretory proteins to formulate multiepitope subunit vaccine against pulmonary tuberculosis by utilizing immunoinformatic approaches. Int J Biol Macromol 2018; 118:180-188. [DOI: 10.1016/j.ijbiomac.2018.06.080] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 06/15/2018] [Accepted: 06/15/2018] [Indexed: 11/17/2022]
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Espinola SM, Cancela MP, Brisolara Corrêa L, Zaha A. Evolutionary fates of universal stress protein paralogs in Platyhelminthes. BMC Evol Biol 2018; 18:10. [PMID: 29390964 PMCID: PMC5793430 DOI: 10.1186/s12862-018-1129-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 01/23/2018] [Indexed: 11/16/2022] Open
Abstract
Background Universal stress proteins (USPs) are present in all domains of life. Their expression is upregulated in response to a large variety of stress conditions. The functional diversity found in this protein family, paired with the sequence degeneration of the characteristic ATP-binding motif, suggests a complex evolutionary pattern for the paralogous USP-encoding genes. In this work, we investigated the origin, genomic organization, expression patterns and evolutionary history of the USP gene family in species of the phylum Platyhelminthes. Results Our data showed a cluster organization, a lineage-specific distribution, and the presence of several pseudogenes among the USP gene copies identified. The absence of a well conserved -CCAATCA- motif in the promoter region was positively correlated with low or null levels of gene expression, and with amino acid changes within the ligand binding motifs. Despite evidence of the pseudogenization of various USP genes, we detected an important functional divergence at several residues, mostly located near sites that are critical for ligand interaction. Conclusions Our results provide a broad framework for the evolution of the USP gene family, based on the emergence of new paralogs that face very contrasting fates, including pseudogenization, subfunctionalization or neofunctionalization. This framework aims to explain the sequence and functional diversity of this gene family, providing a foundation for future studies in other taxa in which USPs occur. Electronic supplementary material The online version of this article (10.1186/s12862-018-1129-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sergio Martin Espinola
- Programa de Pós Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Martin Pablo Cancela
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Programa de Pós Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Lauís Brisolara Corrêa
- Programa de Pós Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Arnaldo Zaha
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil. .,Programa de Pós Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.
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Venkatesan A, Palaniyandi K, Sharma D, Bisht D, Narayanan S. Characterization of FtsY, its interaction with Ffh, and proteomic identification of their potential substrates in Mycobacterium tuberculosis. Can J Microbiol 2018; 64:243-251. [PMID: 29361248 DOI: 10.1139/cjm-2017-0385] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The universally conserved signal recognition particle (SRP) pathway that mediates co-translational targeting of membrane and secretory proteins is essential for eukaryotic and prokaryotic cells. The Mycobacterium tuberculosis SRP pathway consists of 2 proteins, Ffh and FtsY, and a 4.5S RNA molecule. Although the Escherichia coli SRP pathway is well studied, understanding of the M. tuberculosis SRP pathway components is very limited. In this study, we have overexpressed and characterized the M. tuberculosis SRP receptor (SR) FtsY as a GTP binding protein. Further, we established the direct protein-protein interaction between Ffh and FtsY. The Ffh-FtsY complex formation resulted in mutual stimulation of their GTP hydrolysis activity. We also attempted to biochemically characterize the SRP components by constructing the antisense gene knockdown strains of ffh and ftsY in M. tuberculosis. Loss of ffh and ftsY resulted in a decreased in vitro growth rate of the antisense ffh strain as compared with the antisense ftsY strain. Finally, 2-D gel electrophoresis of antisense depleted ffh and ftsY strains identified differential expression of 14 proteins.
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Affiliation(s)
- Arunkumar Venkatesan
- a Department of Immunology, National Institute for Research in Tuberculosis, Mayor Sathiyamoorthy Road, Chetpet, Chennai 600031, India
| | - Kannan Palaniyandi
- a Department of Immunology, National Institute for Research in Tuberculosis, Mayor Sathiyamoorthy Road, Chetpet, Chennai 600031, India
| | - Divakar Sharma
- b Department of Biochemistry, National JALMA Institute for Leprosy & other Mycobacterial Diseases, Dr. Matsuki Miyazaki Road, Tajganj, Agra 282004, India
| | - Deepa Bisht
- b Department of Biochemistry, National JALMA Institute for Leprosy & other Mycobacterial Diseases, Dr. Matsuki Miyazaki Road, Tajganj, Agra 282004, India
| | - Sujatha Narayanan
- a Department of Immunology, National Institute for Research in Tuberculosis, Mayor Sathiyamoorthy Road, Chetpet, Chennai 600031, India
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Melencion SMB, Chi YH, Pham TT, Paeng SK, Wi SD, Lee C, Ryu SW, Koo SS, Lee SY. RNA Chaperone Function of a Universal Stress Protein in Arabidopsis Confers Enhanced Cold Stress Tolerance in Plants. Int J Mol Sci 2017; 18:ijms18122546. [PMID: 29186920 PMCID: PMC5751149 DOI: 10.3390/ijms18122546] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 11/23/2017] [Accepted: 11/25/2017] [Indexed: 02/07/2023] Open
Abstract
The physiological function of Arabidopsis thaliana universal stress protein (AtUSP) in plant has remained unclear. Thus, we report here the functional role of the Arabidopsis universal stress protein, AtUSP (At3g53990). To determine how AtUSP affects physiological responses towards cold stress, AtUSP overexpression (AtUSP OE) and T-DNA insertion knock-out (atusp, SALK_146059) mutant lines were used. The results indicated that AtUSP OE enhanced plant tolerance to cold stress, whereas atusp did not. AtUSP is localized in the nucleus and cytoplasm, and cold stress significantly affects RNA metabolism such as by misfolding and secondary structure changes of RNA. Therefore, we investigated the relationship of AtUSP with RNA metabolism. We found that AtUSP can bind nucleic acids, including single- and double-stranded DNA and luciferase mRNA. AtUSP also displayed strong nucleic acid-melting activity. We expressed AtUSP in RL211 Escherichia coli, which contains a hairpin-loop RNA structure upstream of chloramphenicol acetyltransferase (CAT), and observed that AtUSP exhibited anti-termination activity that enabled CAT gene expression. AtUSP expression in the cold-sensitive Escherichia coli (E. coli) mutant BX04 complemented the cold sensitivity of the mutant cells. As these properties are typical characteristics of RNA chaperones, we conclude that AtUSP functions as a RNA chaperone under cold-shock conditions. Thus, the enhanced tolerance of AtUSP OE lines to cold stress is mediated by the RNA chaperone function of AtUSP.
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Affiliation(s)
- Sarah Mae Boyles Melencion
- Division of Applied Life Science (BK21+ Program), PMBBRC, Gyeongsang National University, Jinju 52828, Korea.
| | - Yong Hun Chi
- Division of Applied Life Science (BK21+ Program), PMBBRC, Gyeongsang National University, Jinju 52828, Korea.
| | - Thuy Thi Pham
- Division of Applied Life Science (BK21+ Program), PMBBRC, Gyeongsang National University, Jinju 52828, Korea.
| | - Seol Ki Paeng
- Division of Applied Life Science (BK21+ Program), PMBBRC, Gyeongsang National University, Jinju 52828, Korea.
| | - Seong Dong Wi
- Division of Applied Life Science (BK21+ Program), PMBBRC, Gyeongsang National University, Jinju 52828, Korea.
| | - Changyu Lee
- Division of Applied Life Science (BK21+ Program), PMBBRC, Gyeongsang National University, Jinju 52828, Korea.
| | - Seoung Woo Ryu
- Division of Applied Life Science (BK21+ Program), PMBBRC, Gyeongsang National University, Jinju 52828, Korea.
| | - Sung Sun Koo
- Division of Applied Life Science (BK21+ Program), PMBBRC, Gyeongsang National University, Jinju 52828, Korea.
| | - Sang Yeol Lee
- Division of Applied Life Science (BK21+ Program), PMBBRC, Gyeongsang National University, Jinju 52828, Korea.
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36
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Vollmer AC, Bark SJ. Twenty-Five Years of Investigating the Universal Stress Protein: Function, Structure, and Applications. ADVANCES IN APPLIED MICROBIOLOGY 2017; 102:1-36. [PMID: 29680123 DOI: 10.1016/bs.aambs.2017.10.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Since the initial discovery of universal stress protein A (UspA) 25 years ago, remarkable advances in molecular and biochemical technologies have revolutionized our understanding of biology. Many studies using these technologies have focused on characterization of the uspA gene and Usp-type proteins. These studies have identified the conservation of Usp-like proteins across bacteria, archaea, plants, and even some invertebrate animals. Regulation of these proteins under diverse stresses has been associated with different stress-response genes including spoT and relA in the stringent response and the dosR two-component signaling pathways. These and other foundational studies suggest Usps serve regulatory and protective roles to enable adaptation and survival under external stresses. Despite these foundational studies, many bacterial species have multiple paralogs of genes encoding these proteins and ablation of the genes does not provide a distinct phenotype. This outcome has limited our understanding of the biochemical functions of these proteins. Here, we summarize the current knowledge of Usps in general and UspA in particular across different genera as well as conclusions about their functions from seminal studies in diverse organisms. Our objective has been to organize the foundational studies in this field to identify the significant impediments to further understanding of Usp functions at the molecular level. We propose ideas and experimental approaches that may overcome these impediments and drive future development of molecular approaches to understand and target Usps as central regulators of stress adaptation and survival. Despite the fact that the full functions of Usps are still not known, creative many applications have already been proposed, tested, and used. The complementary approaches of basic research and applications, along with new technology and analytic tools, may yield the elusive yet critical functions of universal stress proteins in diverse systems.
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37
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Garcia-Morales L, Leon-Solis L, Monroy-Muñoz IE, Talavera-Paulin M, Serafin-López J, Estrada-Garcia I, Rivera-Gutierrez S, Cerna-Cortes JF, Helguera-Repetto AC, Gonzalez-Y-Merchand JA. Comparative proteomic profiles reveal characteristic Mycobacterium tuberculosis proteins induced by cholesterol during dormancy conditions. MICROBIOLOGY-SGM 2017; 163:1237-1247. [PMID: 28771131 DOI: 10.1099/mic.0.000512] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Cholesterol has been reported to play an important role during Mycobacterium tuberculosis infection and during its dormant state inside the host. We present the determination of proteomic profiles of M. tuberculosis H37Rv in the presence of cholesterol as the sole carbon source under exponential growth and in two in vitro dormancy phases (NRP1 and NRP2). Using 2D-PAGE, we detected that M. tuberculosis expressed a high diversity of proteins in both exponential and non-replicative phases. We also found that cholesterol was involved in the overexpression of some proteins related to sulfur metabolism (CysA2), electron transport (FixB), cell wall synthesis (Ald), iron storage (BfrB), protein synthesis (Tig and EF-Tu) and dormancy maintenance (HspX and TB 31.7). According to our results we propose that proteins Ald, BfrB, FadA5 and TB31.7 are likely to play a fundamental role during in vitro dormancy of M. tuberculosis in the presence of cholesterol, helping to counteract its intracellular hostile microenvironment.
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Affiliation(s)
- Lazaro Garcia-Morales
- Departamento de Microbiologia, Escuela Nacional de Ciencias Biologicas (ENCB), Instituto Politecnico Nacional (IPN), Prolongacion Carpio y Plan de Ayala s/n, Ciudad de Mexico, 11340, Mexico
| | - Lizbel Leon-Solis
- Laboratorios de Biologicos y Reactivos de México S.A. de C.V., Birmex. Instituto Nacional de Virologia. Prolongacion Manuel Carpio No. 492, Delegacion Miguel Hidalgo 11340, Ciudad de Mexico, Mexico
| | - Irma E Monroy-Muñoz
- Departamento de Genetica y Genomica Humana, Torre de Investigacion, Instituto Nacional de Perinatologia Isidro Espinosa de los Reyes, SSA. Montes Urales 800, Lomas de Chapultepec, Ciudad de Mexico, 11000, Mexico
| | - Moises Talavera-Paulin
- Departamento de Inmunologia, Escuela Nacional de Ciencias Biologicas (ENCB), Instituto Politecnico Nacional (IPN), Prolongacion Carpio y Plan de Ayala s/n, Ciudad de Mexico, 11340, Mexico
| | - Jeanet Serafin-López
- Departamento de Inmunologia, Escuela Nacional de Ciencias Biologicas (ENCB), Instituto Politecnico Nacional (IPN), Prolongacion Carpio y Plan de Ayala s/n, Ciudad de Mexico, 11340, Mexico
| | - Iris Estrada-Garcia
- Departamento de Inmunologia, Escuela Nacional de Ciencias Biologicas (ENCB), Instituto Politecnico Nacional (IPN), Prolongacion Carpio y Plan de Ayala s/n, Ciudad de Mexico, 11340, Mexico
| | - Sandra Rivera-Gutierrez
- Departamento de Microbiologia, Escuela Nacional de Ciencias Biologicas (ENCB), Instituto Politecnico Nacional (IPN), Prolongacion Carpio y Plan de Ayala s/n, Ciudad de Mexico, 11340, Mexico
| | - Jorge F Cerna-Cortes
- Departamento de Microbiologia, Escuela Nacional de Ciencias Biologicas (ENCB), Instituto Politecnico Nacional (IPN), Prolongacion Carpio y Plan de Ayala s/n, Ciudad de Mexico, 11340, Mexico
| | - Addy C Helguera-Repetto
- Departamento de Inmunobioquimica, Torre de Investigacion, Instituto Nacional de Perinatologia Isidro Espinosa de los Reyes, SSA. Montes Urales 800, Lomas de Chapultepec, Ciudad de Mexico, 11000, Mexico
| | - Jorge A Gonzalez-Y-Merchand
- Departamento de Microbiologia, Escuela Nacional de Ciencias Biologicas (ENCB), Instituto Politecnico Nacional (IPN), Prolongacion Carpio y Plan de Ayala s/n, Ciudad de Mexico, 11340, Mexico
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Troudt J, Creissen E, Izzo L, Bielefeldt-Ohmann H, Casonato S, Manganelli R, Izzo AA. Mycobacterium tuberculosis sigE mutant ST28 used as a vaccine induces protective immunity in the guinea pig model. Tuberculosis (Edinb) 2017; 106:99-105. [PMID: 28802412 DOI: 10.1016/j.tube.2017.07.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 07/17/2017] [Accepted: 07/20/2017] [Indexed: 11/29/2022]
Abstract
With more than 9 million new infections and 1.5 million deaths claimed every year, tuberculosis remains one of the major scourges of humankind. The only vaccine available against this disease, the attenuated strain Mycobacterium bovis, BCG is effective against severe forms of the disease in infants, but scarcely effective in protecting adults from the pulmonary form of the disease, thus not stopping transmission. Consequently, the development of an effective anti-tuberculosis vaccine is a major goal for improving global health. The most common concept is that a more effective vaccine should include a first immunization with a live vaccine followed by the administration of an acellular boosting vaccine. In this approach, the live vaccine might be either BCG or a different, more efficient attenuated strain. Recently, we showed that a Mycobacterium tuberculosis mutant missing the gene encoding for the extracellular function sigma factor SigE, is strongly attenuated and is able to induce a more effective protection from M. tuberculosis infection compared to BCG in mice. We now further characterize the protective potential of this novel strain in the guinea pig model of tuberculosis. In the guinea pig, it had limited growth but induced a Th1 immune response and was able to significantly reduce the number of colony forming units as well as prolong survival. Taken together these data provide evidence for the use of the M. tuberculosis sigE mutant as the basis for further development as a vaccine against infection.
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Affiliation(s)
- JoLynn Troudt
- Colorado State University, Department of Microbiology, Immunology & Pathology, 1682 Campus Delivery, Fort Collins, CO, 80523, USA
| | - Elizabeth Creissen
- Colorado State University, Department of Microbiology, Immunology & Pathology, 1682 Campus Delivery, Fort Collins, CO, 80523, USA
| | - Linda Izzo
- Colorado State University, Department of Microbiology, Immunology & Pathology, 1682 Campus Delivery, Fort Collins, CO, 80523, USA
| | - Helle Bielefeldt-Ohmann
- University of Queensland, Australian Infectious Diseases Research Centre, St. Lucia, Qld, 4072 & School of Veterinary Science, Gatton Campus, Qld, 4343, Australia
| | - Stefano Casonato
- University of Padova, Department Molecular Medicine, Via Gabelli 63, 35121, Padova, Italy
| | - Riccardo Manganelli
- University of Padova, Department Molecular Medicine, Via Gabelli 63, 35121, Padova, Italy
| | - Angelo A Izzo
- Colorado State University, Department of Microbiology, Immunology & Pathology, 1682 Campus Delivery, Fort Collins, CO, 80523, USA.
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Campanerut-Sá PAZ, Ghiraldi-Lopes LD, Meneguello JE, Teixeira JJV, Scodro RBDL, Siqueira VLD, Svidzinski TIE, Pavan FR, Cardoso RF. Systematic review on the proteomic profile of Mycobacterium tuberculosis
exposed to drugs. Proteomics Clin Appl 2017. [DOI: 10.1002/prca.201600077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | - Jean Eduardo Meneguello
- Department of Clinical Analyses and Biomedicine; State University of Maringá; Maringá Brazil
| | | | | | | | | | - Fernando Rogério Pavan
- Department of Biological Sciences; State University Paulista Júlio de Mesquita Filho; Faculty of Pharmaceutical Sciences of Araraquara; São Paulo Brazil
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40
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Glass LN, Swapna G, Chavadi SS, Tufariello JM, Mi K, Drumm JE, Lam TT, Zhu G, Zhan C, Vilchéze C, Arcos J, Chen Y, Bi L, Mehta S, Porcelli SA, Almo SC, Yeh SR, Jacobs WR, Torrelles JB, Chan J. Mycobacterium tuberculosis universal stress protein Rv2623 interacts with the putative ATP binding cassette (ABC) transporter Rv1747 to regulate mycobacterial growth. PLoS Pathog 2017; 13:e1006515. [PMID: 28753640 PMCID: PMC5549992 DOI: 10.1371/journal.ppat.1006515] [Citation(s) in RCA: 37] [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: 03/20/2017] [Revised: 08/09/2017] [Accepted: 07/06/2017] [Indexed: 12/25/2022] Open
Abstract
We have previously shown that the Mycobacterium tuberculosis universal stress protein Rv2623 regulates mycobacterial growth and may be required for the establishment of tuberculous persistence. Here, yeast two-hybrid and affinity chromatography experiments have demonstrated that Rv2623 interacts with one of the two forkhead-associated domains (FHA I) of Rv1747, a putative ATP-binding cassette transporter annotated to export lipooligosaccharides. FHA domains are signaling protein modules that mediate protein-protein interactions to modulate a wide variety of biological processes via binding to conserved phosphorylated threonine (pT)-containing oligopeptides of the interactors. Biochemical, immunochemical and mass spectrometric studies have shown that Rv2623 harbors pT and specifically identified threonine 237 as a phosphorylated residue. Relative to wild-type Rv2623 (Rv2623WT), a mutant protein in which T237 has been replaced with a non-phosphorylatable alanine (Rv2623T237A) exhibits decreased interaction with the Rv1747 FHA I domain and diminished growth-regulatory capacity. Interestingly, compared to WT bacilli, an M. tuberculosis Rv2623 null mutant (ΔRv2623) displays enhanced expression of phosphatidyl-myo-inositol mannosides (PIMs), while the ΔRv1747 mutant expresses decreased levels of PIMs. Animal studies have previously shown that ΔRv2623 is hypervirulent, while ΔRv1747 is growth-attenuated. Collectively, these data have provided evidence that Rv2623 interacts with Rv1747 to regulate mycobacterial growth; and this interaction is mediated via the recognition of the conserved Rv2623 pT237-containing FHA-binding motif by the Rv1747 FHA I domain. The divergent aberrant PIM profiles and the opposing in vivo growth phenotypes of ΔRv2623 and ΔRv1747, together with the annotated lipooligosaccharide exporter function of Rv1747, suggest that Rv2623 interacts with Rv1747 to modulate mycobacterial growth by negatively regulating the activity of Rv1747; and that Rv1747 might function as a transporter of PIMs. Because these glycolipids are major mycobacterial cell envelope components that can impact on the immune response, our findings raise the possibility that Rv2623 may regulate bacterial growth, virulence, and entry into persistence, at least in part, by modulating the levels of bacillary PIM expression, perhaps through negatively regulating the Rv1747-dependent export of the immunomodulatory PIMs to alter host-pathogen interaction, thereby influencing the fate of M. tuberculosis in vivo.
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Affiliation(s)
- Lisa N. Glass
- Department of Medicine, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
- Department of Microbiology and Immunology, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
| | - Ganduri Swapna
- Department of Medicine, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
- Department of Microbiology and Immunology, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
| | - Sivagami Sundaram Chavadi
- Department of Medicine, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
- Department of Microbiology and Immunology, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
| | - JoAnn M. Tufariello
- Department of Medicine, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
- Department of Microbiology and Immunology, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
| | - Kaixia Mi
- Department of Medicine, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
- Department of Microbiology and Immunology, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
| | - Joshua E. Drumm
- Department of Medicine, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
- Department of Microbiology and Immunology, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
| | - TuKiet T. Lam
- MS & Proteomics Resource of the W.M. Keck Biotechnology Resource Laboratory, Yale University School Medicine, New Haven, Connecticut, United States of America
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Guofeng Zhu
- Department of Medicine, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
- Department of Microbiology and Immunology, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
| | - Chenyang Zhan
- Department of Biochemistry, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
| | - Catherine Vilchéze
- Department of Microbiology and Immunology, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
- Howard Hughes Medical Institute, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
| | - Jesus Arcos
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Yong Chen
- Department of Medicine, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
- Department of Microbiology and Immunology, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
| | - Lijun Bi
- Department of Medicine, School of Stomatology and Medicine, Foshan University, Foshan, China
| | - Simren Mehta
- Department of Medicine, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
- Department of Microbiology and Immunology, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
| | - Steven A. Porcelli
- Department of Medicine, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
- Department of Microbiology and Immunology, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
| | - Steve C. Almo
- Department of Biochemistry, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
| | - Syun-Ru Yeh
- Departments of Physiology & Biophysics, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
| | - William R. Jacobs
- Department of Microbiology and Immunology, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
- Howard Hughes Medical Institute, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
| | - Jordi B. Torrelles
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - John Chan
- Department of Medicine, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
- Department of Microbiology and Immunology, Albert Einstein College of Medicine & Montefiore Medical Center, Bronx, New York, United States of America
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A Proteomic Signature of Dormancy in the Actinobacterium Micrococcus luteus. J Bacteriol 2017; 199:JB.00206-17. [PMID: 28484042 DOI: 10.1128/jb.00206-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 04/24/2017] [Indexed: 12/13/2022] Open
Abstract
Dormancy is a protective state in which diverse bacteria, including Mycobacterium tuberculosis, Staphylococcus aureus, Treponema pallidum (syphilis), and Borrelia burgdorferi (Lyme disease), curtail metabolic activity to survive external stresses, including antibiotics. Evidence suggests dormancy consists of a continuum of interrelated states, including viable but nonculturable (VBNC) and persistence states. VBNC and persistence contribute to antibiotic tolerance, reemergence from latent infections, and even quorum sensing and biofilm formation. Previous studies indicate that the protein mechanisms regulating persistence and VBNC states are not well understood. We have queried the VBNC state of Micrococcus luteus NCTC 2665 (MI-2665) by quantitative proteomics combining gel electrophoresis, high-performance liquid chromatography, and tandem mass spectrometry to elucidate some of these mechanisms. MI-2665 is a nonpathogenic actinobacterium containing a small (2.5-Mb), high-GC-content genome which exhibits a well-defined VBNC state induced by nutrient deprivation. The MI-2665 VBNC state demonstrated a loss of protein diversity accompanied by increased levels of 18 proteins that are conserved across actinobacteria, 14 of which have not been previously identified in VNBC. These proteins implicate an anaplerotic strategy in the transition to VBNC, including changes in the glyoxylate shunt, redox and amino acid metabolism, and ribosomal regulatory processes. Our data suggest that MI-2665 is a viable model for dissecting the protein mechanisms underlying the VBNC stress response and provide the first protein-level signature of this state. We expect that this protein signature will enable future studies deciphering the protein mechanisms of dormancy and identify novel therapeutic strategies effective against antibiotic-tolerant bacterial infections.IMPORTANCE Dormancy is a protective state enabling bacteria to survive antibiotics, starvation, and the immune system. Dormancy is comprised of different states, including persistent and viable but nonculturable (VBNC) states that contribute to the spread of bacterial infections. Therefore, it is imperative to identify how bacteria utilize these different dormancy states to survive antibiotic treatment. The objective of our research is to eliminate dormancy as a route to antibiotic tolerance by understanding the proteins that control dormancy in Micrococcus luteus NCTC 2665. This bacterium has unique advantages for studying dormancy, including a small genome and a well-defined and reproducible VBNC state. Our experiments implicate four previously identified and 14 novel proteins upregulated in VBNC that may regulate this critical survival mechanism.
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Duncan C, Jamieson FB, Troudt J, Izzo L, Bielefeldt-Ohmann H, Izzo A, Mehaffy C. Whole transcriptomic and proteomic analyses of an isogenic M. tuberculosis clinical strain with a naturally occurring 15 Kb genomic deletion. PLoS One 2017; 12:e0179996. [PMID: 28650996 PMCID: PMC5484546 DOI: 10.1371/journal.pone.0179996] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 06/07/2017] [Indexed: 11/19/2022] Open
Abstract
Tuberculosis remains one of the most difficult to control infectious diseases in the world. Many different factors contribute to the complexity of this disease. These include the ability of the host to control the infection which may directly relate to nutritional status, presence of co-morbidities and genetic predisposition. Pathogen factors, in particular the ability of different Mycobacterium tuberculosis strains to respond to the harsh environment of the host granuloma, which includes low oxygen and nutrient availability and the presence of damaging radical oxygen and nitrogen species, also play an important role in the success of different strains to cause disease. In this study we evaluated the impact of a naturally occurring 12 gene 15 Kb genomic deletion on the physiology and virulence of M. tuberculosis. The strains denominated ON-A WT (wild type) and ON-A NM (natural mutant) were isolated from a previously reported TB outbreak in an inner city under-housed population in Toronto, Canada. Here we subjected these isogenic strains to transcriptomic (via RNA-seq) and proteomic analyses and identified several gene clusters with differential expression in the natural mutant, including the DosR regulon and the molybdenum cofactor biosynthesis genes, both of which were found in lower abundance in the natural mutant. We also demonstrated lesser virulence of the natural mutant in the guinea pig animal model. Overall, our findings suggest that the ON-A natural mutant is less fit to cause disease, but nevertheless has the potential to cause extended transmission in at-risk populations.
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Affiliation(s)
| | - Frances B. Jamieson
- Public Health Ontario, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - JoLynn Troudt
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States of America
| | - Linda Izzo
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States of America
| | - Helle Bielefeldt-Ohmann
- School of Veterinary Science, University of Queensland, Gatton, QLD, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
- Australian Infectious Diseases Research Centre, University of Queensland, St Lucia, QLD, Australia
| | - Angelo Izzo
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States of America
| | - Carolina Mehaffy
- Public Health Ontario, Toronto, ON, Canada
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States of America
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Peddireddy V, Doddam SN, Ahmed N. Mycobacterial Dormancy Systems and Host Responses in Tuberculosis. Front Immunol 2017; 8:84. [PMID: 28261197 PMCID: PMC5309233 DOI: 10.3389/fimmu.2017.00084] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 01/18/2017] [Indexed: 12/15/2022] Open
Abstract
Tuberculosis (TB) caused by the intracellular pathogen, Mycobacterium tuberculosis (Mtb), claims more than 1.5 million lives worldwide annually. Despite promulgation of multipronged strategies to prevent and control TB, there is no significant downfall occurring in the number of new cases, and adding to this is the relapse of the disease due to the emergence of antibiotic resistance and the ability of Mtb to remain dormant after primary infection. The pathology of Mtb is complex and largely attributed to immune-evading strategies that this pathogen adopts to establish primary infection, its persistence in the host, and reactivation of pathogenicity under favorable conditions. In this review, we present various biochemical, immunological, and genetic strategies unleashed by Mtb inside the host for its survival. The bacterium enables itself to establish a niche by evading immune recognition via resorting to masking, establishment of dormancy by manipulating immune receptor responses, altering innate immune cell fate, enhancing granuloma formation, and developing antibiotic tolerance. Besides these, the regulatory entities, such as DosR and its regulon, encompassing various putative effector proteins play a vital role in maintaining the dormant nature of this pathogen. Further, reactivation of Mtb allows relapse of the disease and is favored by the genes of the Rtf family and the conditions that suppress the immune system of the host. Identification of target genes and characterizing the function of their respective antigens involved in primary infection, dormancy, and reactivation would likely provide vital clues to design novel drugs and/or vaccines for the control of dormant TB.
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Affiliation(s)
- Vidyullatha Peddireddy
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad , Hyderabad , India
| | - Sankara Narayana Doddam
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad , Hyderabad , India
| | - Niyaz Ahmed
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, India; Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh
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Gutiérrez-Beltrán E, Personat JM, de la Torre F, Del Pozo O. A Universal Stress Protein Involved in Oxidative Stress Is a Phosphorylation Target for Protein Kinase CIPK6. PLANT PHYSIOLOGY 2017; 173:836-852. [PMID: 27899535 PMCID: PMC5210712 DOI: 10.1104/pp.16.00949] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 11/26/2016] [Indexed: 05/27/2023]
Abstract
Calcineurin B-like interacting protein kinases (CIPKs) decode calcium signals upon interaction with the calcium sensors calcineurin B like proteins into phosphorylation events that result into adaptation to environmental stresses. Few phosphorylation targets of CIPKs are known and therefore the molecular mechanisms underlying their downstream output responses are not fully understood. Tomato (Solanum lycopersicum) Cipk6 regulates immune and susceptible Programmed cell death in immunity transforming Ca2+ signals into reactive oxygen species (ROS) signaling. To investigate SlCipk6-induced molecular mechanisms and identify putative substrates, a yeast two-hybrid approach was carried on and a protein was identified that contained a Universal stress protein (Usp) domain present in bacteria, protozoa and plants, which we named "SlRd2". SlRd2 was an ATP-binding protein that formed homodimers in planta. SlCipk6 and SlRd2 interacted using coimmunoprecipitation and bimolecular fluorescence complementation (BiFC) assays in Nicotiana benthamiana leaves and the complex localized in the cytosol. SlCipk6 phosphorylated SlRd2 in vitro, thus defining, to our knowledge, a novel target for CIPKs. Heterologous SlRd2 overexpression in yeast conferred resistance to highly toxic LiCl, whereas SlRd2 expression in Escherichia coli UspA mutant restored bacterial viability in response to H2O2 treatment. Finally, transient expression of SlCipk6 in transgenic N benthamiana SlRd2 overexpressors resulted in reduced ROS accumulation as compared to wild-type plants. Taken together, our results establish that SlRd2, a tomato UspA, is, to our knowledge, a novel interactor and phosphorylation target of a member of the CIPK family, SlCipk6, and functionally regulates SlCipk6-mediated ROS generation.
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Affiliation(s)
- Emilio Gutiérrez-Beltrán
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla/Consejo Superior de Investigaciones Científicas, 41092 Sevilla, Spain
| | - José María Personat
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla/Consejo Superior de Investigaciones Científicas, 41092 Sevilla, Spain
| | - Fernando de la Torre
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla/Consejo Superior de Investigaciones Científicas, 41092 Sevilla, Spain
| | - Olga Del Pozo
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla/Consejo Superior de Investigaciones Científicas, 41092 Sevilla, Spain
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45
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Tremonte P, Succi M, Coppola R, Sorrentino E, Tipaldi L, Picariello G, Pannella G, Fraternali F. Homology-Based Modeling of Universal Stress Protein from Listeria innocua Up-Regulated under Acid Stress Conditions. Front Microbiol 2016; 7:1998. [PMID: 28066336 PMCID: PMC5168468 DOI: 10.3389/fmicb.2016.01998] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 11/29/2016] [Indexed: 01/31/2023] Open
Abstract
An Universal Stress Protein (USP) expressed under acid stress condition by Listeria innocua ATCC 33090 was investigated. The USP was up-regulated not only in the stationary phase but also during the exponential growth phase. The three dimensional (3D) structure of USP was predicted using a combined proteomic and bioinformatics approach. Phylogenetic analysis showed that the USP from Listeria detected in our study was distant from the USPs of other bacteria (such as Pseudomonas spp., Escherichia coli, Salmonella spp.) and clustered in a separate and heterogeneous class including several USPs from Listeria spp. and Lactobacillus spp. An important information on the studied USP was obtained from the 3D-structure established through the homology modeling procedure. In detail, the Model_USP-691 suggested that the investigated USP had a homo-tetrameric quaternary structure. Each monomer presented an architecture analogous to the Rossmann-like α/β-fold with five parallel β-strands, and four α-helices. The analysis of monomer-monomer interfaces and quality of the structure alignments confirmed the model reliability. In fact, the structurally and sequentially conserved hydrophobic residues of the β-strand 5 (in particular the residues V146 and V148) were involved in the inter-chains contact. Moreover, the highly conserved residues I139 and H141 in the region α4 were involved in the dimer association and functioned as hot spots into monomer–monomer interface assembly. The hypothetical assembly of dimers was also supported by the large interface area and by the negative value of solvation free energy gain upon interface interaction. Finally, the structurally conserved ATP-binding motif G-2X-G-9X-G(S/T-N) suggested for a putative role of ATP in stabilizing the tetrameric assembly of the USP. Therefore, the results obtained from a multiple approach, consisting in the application of kinetic, proteomic, phylogenetic and modeling analyses, suggest that Listeria USP could be considered a new type of ATP-binding USP involved in the response to acid stress condition during the exponential growth phase.
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Affiliation(s)
- Patrizio Tremonte
- Department of Agricultural, Environmental and Food Sciences (DiAAA), University of Molise Campobasso, Italy
| | - Mariantonietta Succi
- Department of Agricultural, Environmental and Food Sciences (DiAAA), University of Molise Campobasso, Italy
| | - Raffaele Coppola
- Department of Agricultural, Environmental and Food Sciences (DiAAA), University of Molise Campobasso, Italy
| | - Elena Sorrentino
- Department of Agricultural, Environmental and Food Sciences (DiAAA), University of Molise Campobasso, Italy
| | - Luca Tipaldi
- Department of Agricultural, Environmental and Food Sciences (DiAAA), University of Molise Campobasso, Italy
| | - Gianluca Picariello
- Institute of Food Science, National Research Council (ISA-CNR) Avellino, Italy
| | - Gianfranco Pannella
- Department of Agricultural, Environmental and Food Sciences (DiAAA), University of Molise Campobasso, Italy
| | - Franca Fraternali
- Randall Division of Cellular and Molecular Biophysics, New Hunt's House King's College London, UK
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46
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Venkatesan A, Palaniyandi K, Sharma D, Bisht D, Narayanan S. Functional Characterization of PknI-Rv2159c Interaction in Redox Homeostasis of Mycobacterium tuberculosis. Front Microbiol 2016; 7:1654. [PMID: 27818650 PMCID: PMC5073100 DOI: 10.3389/fmicb.2016.01654] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 10/04/2016] [Indexed: 01/02/2023] Open
Abstract
Mycobacterium tuberculosis adapts to stress conditions by responding to the signals from its external environment. M. tuberculosis genome encodes 11 eukaryotic like serine/threonine protein kinases (STPK) and their importance in regulating the physiology and virulence of the bacteria are being explored. Previous study from our lab identified the M. tuberculosis STPK, PknI interacts with two peroxidase proteins such as Rv2159c and Rv0148. In this study, we have characterized the biological function behind the PknI-Rv2159c interaction in M. tuberculosis. Point mutation of Ala-Gly-Trp motif identified that only Ala49 and Gly50 amino acids of Rv2159c are responsible for interaction and there is no phosphorylation involved in the PknI-Rv2159c interaction. Rv2159c is a member from the carboxymuconolactone decarboxylase family with peroxidase activity. Enzymatic assays with catalytic site point mutants showed that Cys84 of Rv2159c was responsible for its alkylhydroperoxidase activity. Interestingly, interaction with PknI increased its peroxidase activity by several folds. Gene knockdown of Rv2159c in M. tuberculosis showed increased sensitivity to peroxides such as cumene hydroperoxide and hydrogen peroxide. Proteomic analysis of differentially expressing Rv2159c strains by 2D gel electrophoresis and mass spectrometry revealed the differential abundance of 21 proteins. The total absence of oxidoreductase, GuaB1 suggests the essential role of Rv2159c in redox maintenance. Our findings provide new insights on signaling mechanisms of PknI in maintaining the redox homeostasis during oxidative stresses.
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Affiliation(s)
- Arunkumar Venkatesan
- Department of Immunology, National Institute for Research in Tuberculosis Chennai, India
| | - Kannan Palaniyandi
- Department of Immunology, National Institute for Research in Tuberculosis Chennai, India
| | - Divakar Sharma
- Department of Biochemistry, National JALMA Institute for Leprosy and other Mycobacterial Diseases Agra, India
| | - Deepa Bisht
- Department of Biochemistry, National JALMA Institute for Leprosy and other Mycobacterial Diseases Agra, India
| | - Sujatha Narayanan
- Department of Immunology, National Institute for Research in Tuberculosis Chennai, India
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47
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Jia Q, Hu X, Shi D, Zhang Y, Sun M, Wang J, Mi K, Zhu G. Universal stress protein Rv2624c alters abundance of arginine and enhances intracellular survival by ATP binding in mycobacteria. Sci Rep 2016; 6:35462. [PMID: 27762279 PMCID: PMC5071874 DOI: 10.1038/srep35462] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 09/30/2016] [Indexed: 01/05/2023] Open
Abstract
The universal stress protein family is a family of stress-induced proteins. Universal stress proteins affect latency and antibiotic resistance in mycobacteria. Here, we showed that Mycobacterium smegmatis overexpressing M. tuberculosis universal stress protein Rv2624c exhibits increased survival in human monocyte THP-1 cells. Transcriptome analysis suggested that Rv2624c affects histidine metabolism, and arginine and proline metabolism. LC-MS/MS analysis showed that Rv2624c affects the abundance of arginine, a modulator of both mycobacteria and infected THP-1 cells. Biochemical analysis showed that Rv2624c is a nucleotide-binding universal stress protein, and an Rv2624c mutant incapable of binding ATP abrogated the growth advantage in THP-1 cells. Rv2624c may therefore modulate metabolic pathways in an ATP-dependent manner, changing the abundance of arginine and thus increasing survival in THP-1 cells.
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Affiliation(s)
- Qiong Jia
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Xinling Hu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, CAS, Beijing 100101, China.,The Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Dawei Shi
- Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, Beijing 100050, China
| | - Yan Zhang
- Zhangjiakou Center for Adverse Drug Reaction and Drug Abuse, Hebei 075000, China
| | - Meihao Sun
- College of Chemistry and Life Sciences, Zhejiang Normal University, Zhejiang 321004, China
| | - Jianwei Wang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Kaixia Mi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, CAS, Beijing 100101, China
| | - Guofeng Zhu
- Shanghai Municipal Center for Disease Control &Prevention, Shanghai 200336, China
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48
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Masamba P, Adenowo AF, Oyinloye BE, Kappo AP. Universal Stress Proteins as New Targets for Environmental and Therapeutic Interventions of Schistosomiasis. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2016; 13:E972. [PMID: 27706050 PMCID: PMC5086711 DOI: 10.3390/ijerph13100972] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 09/24/2016] [Accepted: 09/27/2016] [Indexed: 12/22/2022]
Abstract
In spite of various control measures and eradication methods that have been in progress, schistosomiasis still prevails as one of the most prevalent debilitating parasitic diseases, typically affecting the poor and the underprivileged that are predominantly concentrated in sub-Saharan Africa. The parasitic schistosome blood fluke responsible for causing the disease completes its complex developmental cycle in two hosts: humans and freshwater snails, where they physically undergo gross modifications to endure the different conditions associated with each host. Just like any other organism, the worm possesses mechanisms that help them respond to environmental insults. It has been hypothesized that a special class of proteins known as Universal Stress Proteins (USPs) are up-regulated during sudden environmental changes, thus assisting the worm to tolerate the unfavourable conditions associated with its developmental cycle. The position of praziquantel as the drug of choice against all schistosome infections has been deemed vulnerable due to mounting concerns over drug pressure and so the need for alternative treatment is now a matter of urgency. Therefore, this review seeks to explore the associations and possible roles of USPs in schistosomiasis as well as the functioning of these proteins in the schistosomulae stage in order to develop new therapeutic interventions against this disease.
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Affiliation(s)
- Priscilla Masamba
- Biotechnology and Structural Biochemistry (BSB) Group, Department of Biochemistry and Microbiology, University of Zululand, KwaDlangezwa 3886, South Africa.
| | - Abiola Fatimah Adenowo
- Biotechnology and Structural Biochemistry (BSB) Group, Department of Biochemistry and Microbiology, University of Zululand, KwaDlangezwa 3886, South Africa.
| | - Babatunji Emmanuel Oyinloye
- Biotechnology and Structural Biochemistry (BSB) Group, Department of Biochemistry and Microbiology, University of Zululand, KwaDlangezwa 3886, South Africa.
- Department of Biochemistry, Afe Babalola University, PMB 5454, Ado-Ekiti 360001, Nigeria.
| | - Abidemi Paul Kappo
- Biotechnology and Structural Biochemistry (BSB) Group, Department of Biochemistry and Microbiology, University of Zululand, KwaDlangezwa 3886, South Africa.
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49
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In silico and experimental validation of protein-protein interactions between PknI and Rv2159c from Mycobacterium tuberculosis. J Mol Graph Model 2015; 62:283-293. [PMID: 26546727 DOI: 10.1016/j.jmgm.2015.10.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 10/16/2015] [Accepted: 10/21/2015] [Indexed: 11/24/2022]
Abstract
Protein-protein interactions control the diverse and essential molecular processes inside the cell. To maintain the cellular physiology, protein kinases not only signal their substrates through reversible phosphorylation, but they also physically interact with them. PknI, a serine/threonine protein kinase of Mycobacterium tuberculosis is known to be important for cellular homoeostasis. In this study, we have identified the interacting proteins for PknI. We screened for proteins interacting with PknI using an in vitro assay, Far-western blot. This protein kinase specifically interacts with two peroxidase proteins of M. tuberculosis, Rv2159c and Rv0148. The PknI-Rv2159c interaction pair was further studied for the critical amino acid residues in Rv2159c that are responsible for the interaction. Rv2159c, a hypothetical protein is predicted to be an antioxidant with peroxidase activity. We performed homology modelling of Rv2159c protein and molecular docking using multiple docking servers such as Z-Dock and ClusPro. Further, the most favorable conformation of PknI-Rv2159c interaction was obtained using molecular dynamics simulation. The critical amino acid residues of the Rv2159c involved in interaction with PknI were identified. Mutation and docking analysis showed that the Ala1-Gly2-Trp3 residues in Rv2159c structure are responsible for the interaction. The free binding energy between the wild type and mutant complexes using MM-GBSA has provided insight about the stability of PknI-Rv2159c interaction. We propose that, PknI physically interacts with Rv2159c both in vitro and in silico studies.
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50
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Ranganathan S, Bai G, Lyubetskaya A, Knapp GS, Peterson MW, Gazdik M, C Gomes AL, Galagan JE, McDonough KA. Characterization of a cAMP responsive transcription factor, Cmr (Rv1675c), in TB complex mycobacteria reveals overlap with the DosR (DevR) dormancy regulon. Nucleic Acids Res 2015; 44:134-51. [PMID: 26358810 PMCID: PMC4705688 DOI: 10.1093/nar/gkv889] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 08/26/2015] [Indexed: 12/17/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) Cmr (Rv1675c) is a CRP/FNR family transcription factor known to be responsive to cAMP levels and during macrophage infections. However, Cmr's DNA binding properties, cellular targets and overall role in tuberculosis (TB) complex bacteria have not been characterized. In this study, we used experimental and computational approaches to characterize Cmr's DNA binding properties and identify a putative regulon. Cmr binds a 16-bp palindromic site that includes four highly conserved nucleotides that are required for DNA binding. A total of 368 binding sites, distributed in clusters among ∼200 binding regions throughout the Mycobacterium bovis BCG genome, were identified using ChIP-seq. One of the most enriched Cmr binding sites was located upstream of the cmr promoter, and we demonstrated that expression of cmr is autoregulated. cAMP affected Cmr binding at a subset of DNA loci in vivo and in vitro, including multiple sites adjacent to members of the DosR (DevR) dormancy regulon. Our findings of cooperative binding of Cmr to these DNA regions and the regulation by Cmr of the DosR-regulated virulence gene Rv2623 demonstrate the complexity of Cmr-mediated gene regulation and suggest a role for Cmr in the biology of persistent TB infection.
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Affiliation(s)
- Sridevi Ranganathan
- Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany, NY 12201, USA
| | - Guangchun Bai
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, PO Box 22002, Albany, NY 12201-2002, USA
| | - Anna Lyubetskaya
- Bioinformatics Program, Boston University, Boston, MA 02215, USA
| | - Gwendowlyn S Knapp
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, PO Box 22002, Albany, NY 12201-2002, USA
| | | | - Michaela Gazdik
- Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany, NY 12201, USA
| | | | - James E Galagan
- Bioinformatics Program, Boston University, Boston, MA 02215, USA Department of Microbiology, Boston University, Boston, MA 02215, USA Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA
| | - Kathleen A McDonough
- Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany, NY 12201, USA Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, PO Box 22002, Albany, NY 12201-2002, USA
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