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Sarfraz A, Qurrat-Ul-Ain Fatima S, Shehroz M, Ahmad I, Zaman A, Nishan U, Tayyab M, Sheheryar, Moura AA, Ullah R, Ali EA, Shah M. Decrypting the multi-genome data for chimeric vaccine designing against the antibiotic resistant Yersinia pestis. Int Immunopharmacol 2024; 132:111952. [PMID: 38555818 DOI: 10.1016/j.intimp.2024.111952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/14/2024] [Accepted: 03/26/2024] [Indexed: 04/02/2024]
Abstract
Yersinia pestis, the causative agent of plague, is a gram-negative bacterium that can be fatal if not treated properly. Three types of plague are currently known: bubonic, septicemic, and pneumonic plague, among which the fatality rate of septicemic and pneumonic plague is very high. Bubonic plague can be treated, but only if antibiotics are used at the initial stage of the infection. But unfortunately, Y. pestis has also shown resistance to certain antibiotics such as kanamycin, minocycline, tetracycline, streptomycin, sulfonamides, spectinomycin, and chloramphenicol. Despite tremendous progress in vaccine development against Y. pestis, there is no proper FDA-approved vaccine available to protect people from its infections. Therefore, effective broad-spectrum vaccine development against Y. pestis is indispensable. In this study, vaccinomics-assisted immunoinformatics techniques were used to find possible vaccine candidates by utilizing the core proteome prepared from 58 complete genomes of Y. pestis. Human non-homologous, pathogen-essential, virulent, and extracellular and membrane proteins are potential vaccine targets. Two antigenic proteins were prioritized for the prediction of lead epitopes by utilizing reverse vaccinology approaches. Four vaccine designs were formulated using the selected B- and T-cell epitopes coupled with appropriate linkers and adjuvant sequences capable of inducing potent immune responses. The HLA allele population coverage of the T-cell epitopes selected for vaccine construction was also analyzed. The V2 constructs were top-ranked and selected for further analysis on the basis of immunological, physicochemical, and immune-receptor docking interactions and scores. Docking and molecular dynamic simulations confirmed the stability of construct V2 interactions with the host immune receptors. Immune simulation analysis anticipated the strong immune profile of the prioritized construct. In silico restriction cloning ensured the feasible cloning ability of the V2 construct in the expression system of E. coli strain K12. It is anticipated that the designed vaccine construct may be safe, effective, and able to elicit strong immune responses against Y. pestis infections and may, therefore, merit investigation using in vitro and in vivo assays.
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Affiliation(s)
- Asifa Sarfraz
- Department of Biochemistry, Bahauddin Zakariya University, Multan 66000, Pakistan
| | | | - Muhammad Shehroz
- Department of Bioinformatics, Kohsar University Murree, Murree 47150, Pakistan
| | - Iqra Ahmad
- Department of Biochemistry, Bahauddin Zakariya University, Multan 66000, Pakistan
| | - Aqal Zaman
- Department of Microbiology & Molecular Genetics, Bahauddin Zakariya University, Multan 66000, Pakistan
| | - Umar Nishan
- Department of Chemistry, Kohat University of Science & Technology, Kohat, Pakistan
| | - Muhammad Tayyab
- Institute of Biotechnology & Genetic Engineering, The University of Agriculture Peshawar, Pakistan
| | - Sheheryar
- Department of Animal Science, Federal University of Ceara, Fortaleza, Brazil
| | | | - Riaz Ullah
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Essam A Ali
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohibullah Shah
- Department of Biochemistry, Bahauddin Zakariya University, Multan 66000, Pakistan.
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Bennasar-Figueras A. The Natural and Clinical History of Plague: From the Ancient Pandemics to Modern Insights. Microorganisms 2024; 12:146. [PMID: 38257973 PMCID: PMC10818976 DOI: 10.3390/microorganisms12010146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/02/2024] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
The human pathogen Yersinia pestis is responsible for bubonic, septicemic, and pneumonic plague. A deeply comprehensive overview of its historical context, bacteriological characteristics, genomic analysis based on ancient DNA (aDNA) and modern strains, and its impact on historical and actual human populations, is explored. The results from multiple studies have been synthesized to investigate the origins of plague, its transmission, and effects on different populations. Additionally, molecular interactions of Y. pestis, from its evolutionary origins to its adaptation to flea-born transmission, and its impact on human and wild populations are considered. The characteristic combinations of aDNA patterns, which plays a decisive role in the reconstruction and analysis of ancient genomes, are reviewed. Bioinformatics is fundamental in identifying specific Y. pestis lineages, and automated pipelines are among the valuable tools in implementing such studies. Plague, which remains among human history's most lethal infectious diseases, but also other zoonotic diseases, requires the continuous investigation of plague topics. This can be achieved by improving molecular and genetic screening of animal populations, identifying ecological and social determinants of outbreaks, increasing interdisciplinary collaborations among scientists and public healthcare providers, and continued research into the characterization, diagnosis, and treatment of these diseases.
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Affiliation(s)
- Antoni Bennasar-Figueras
- Microbiologia—Departament de Biologia, Universitat de les Illes Balears (UIB), Campus UIB, Carretera de Valldemossa, Km 7.5, 07122 Palma de Mallorca, Spain; ; Tel.: +34-971172778
- Facultat de Medicina, Hospital Universitari Son Espases (HUSE), Universitat de les Illes Balears (UIB), Carretera de Valldemossa, 79, 07122 Palma de Mallorca, Spain
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Jin J, Xiao L, Wu Y, Sun Z, Xiong Z, Li Y, Zhao Y, Yao W, Shen L, Cui Y, Tan Y, Han Y, Du Z, Cui Y, Yang R, Song K, Song Y. Characterization of an aspartate aminotransferase encoded by YPO0623 with frequent nonsense mutations in Yersinia pestis. Front Cell Infect Microbiol 2023; 13:1288371. [PMID: 38089818 PMCID: PMC10713766 DOI: 10.3389/fcimb.2023.1288371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023] Open
Abstract
Yersinia pestis, the causative agent of plague, is a genetically monomorphic bacterial pathogen that evolved from Yersinia pseudotuberculosis approximately 7,400 years ago. We observed unusually frequent mutations in Y. pestis YPO0623, mostly resulting in protein translation termination, which implies a strong natural selection. These mutations were found in all phylogenetic lineages of Y. pestis, and there was no apparent pattern in the spatial distribution of the mutant strains. Based on these findings, we aimed to investigate the biological function of YPO0623 and the reasons for its frequent mutation in Y. pestis. Our in vitro and in vivo assays revealed that the deletion of YPO0623 enhanced the growth of Y. pestis in nutrient-rich environments and led to increased tolerance to heat and cold shocks. With RNA-seq analysis, we also discovered that the deletion of YPO0623 resulted in the upregulation of genes associated with the type VI secretion system (T6SS) at 26°C, which probably plays a crucial role in the response of Y. pestis to environment fluctuations. Furthermore, bioinformatic analysis showed that YPO0623 has high homology with a PLP-dependent aspartate aminotransferase in Salmonella enterica, and the enzyme activity assays confirmed its aspartate aminotransferase activity. However, the enzyme activity of YPO0623 was significantly lower than that in other bacteria. These observations provide some insights into the underlying reasons for the high-frequency nonsense mutations in YPO0623, and further investigations are needed to determine the exact mechanism.
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Affiliation(s)
- Junyan Jin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Liting Xiao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Yarong Wu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zhulin Sun
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Ziyao Xiong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanbing Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- Department of Laboratory Medicine, Xiangya Hospital of Central South University, Changsha, China
| | - Yanting Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Wenwu Yao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- Department of Microbiology and Department of Infectious Diseases, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Leiming Shen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yiming Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yafang Tan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yanping Han
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zongmin Du
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Kai Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yajun Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
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Xiao L, Jin J, Song K, Qian X, Wu Y, Sun Z, Xiong Z, Li Y, Zhao Y, Shen L, Cui Y, Yao W, Cui Y, Song Y. Regulatory Functions of PurR in Yersinia pestis: Orchestrating Diverse Biological Activities. Microorganisms 2023; 11:2801. [PMID: 38004812 PMCID: PMC10673613 DOI: 10.3390/microorganisms11112801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 11/11/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
The bacterium Yersinia pestis has developed various strategies to sense and respond to the complex stresses encountered during its transmission and pathogenic processes. PurR is a common transcriptional regulator of purine biosynthesis among microorganisms, and it modulates the transcription level of the pur operon to suppress the production of hypoxanthine nucleotide (IMP). This study aims to understand the functions and regulatory mechanisms of purR in Y. pestis. Firstly, we constructed a purR knockout mutant of Y. pestis strain 201 and compared certain phenotypes of the null mutant (201-ΔpurR) and the wild-type strain (201-WT). The results show that deleting purR has no significant impact on the biofilm formation, growth rate, or viability of Y. pestis under different stress conditions (heat and cold shock, high salinity, and hyperosmotic pressure). Although the cytotoxicity of the purR knockout mutant on HeLa and 293 cells is reduced, the animal-challenging test found no difference of the virulence in mice between 201-ΔpurR and 201-WT. Furthermore, RNA-seq and EMSA analyses demonstrate that PurR binds to the promoter regions of at least 15 genes in Y. pestis strain 201, primarily involved in purine biosynthesis, along with others not previously observed in other bacteria. Additionally, RNA-seq results suggest the presence of 11 potential operons, including a newly identified co-transcriptional T6SS cluster. Thus, aside from its role as a regulator of purine biosynthesis, purR in Y. pestis may have additional regulatory functions.
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Affiliation(s)
- Liting Xiao
- School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China; (L.X.); (X.Q.)
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (J.J.); (Y.W.); (Z.S.); (Z.X.); (Y.L.); (Y.Z.); (L.S.); (Y.C.); (W.Y.)
| | - Junyan Jin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (J.J.); (Y.W.); (Z.S.); (Z.X.); (Y.L.); (Y.Z.); (L.S.); (Y.C.); (W.Y.)
| | - Kai Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (J.J.); (Y.W.); (Z.S.); (Z.X.); (Y.L.); (Y.Z.); (L.S.); (Y.C.); (W.Y.)
| | - Xiuwei Qian
- School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China; (L.X.); (X.Q.)
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (J.J.); (Y.W.); (Z.S.); (Z.X.); (Y.L.); (Y.Z.); (L.S.); (Y.C.); (W.Y.)
| | - Yarong Wu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (J.J.); (Y.W.); (Z.S.); (Z.X.); (Y.L.); (Y.Z.); (L.S.); (Y.C.); (W.Y.)
| | - Zhulin Sun
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (J.J.); (Y.W.); (Z.S.); (Z.X.); (Y.L.); (Y.Z.); (L.S.); (Y.C.); (W.Y.)
| | - Ziyao Xiong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (J.J.); (Y.W.); (Z.S.); (Z.X.); (Y.L.); (Y.Z.); (L.S.); (Y.C.); (W.Y.)
| | - Yanbing Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (J.J.); (Y.W.); (Z.S.); (Z.X.); (Y.L.); (Y.Z.); (L.S.); (Y.C.); (W.Y.)
| | - Yanting Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (J.J.); (Y.W.); (Z.S.); (Z.X.); (Y.L.); (Y.Z.); (L.S.); (Y.C.); (W.Y.)
| | - Leiming Shen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (J.J.); (Y.W.); (Z.S.); (Z.X.); (Y.L.); (Y.Z.); (L.S.); (Y.C.); (W.Y.)
| | - Yiming Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (J.J.); (Y.W.); (Z.S.); (Z.X.); (Y.L.); (Y.Z.); (L.S.); (Y.C.); (W.Y.)
| | - Wenwu Yao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (J.J.); (Y.W.); (Z.S.); (Z.X.); (Y.L.); (Y.Z.); (L.S.); (Y.C.); (W.Y.)
| | - Yujun Cui
- School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China; (L.X.); (X.Q.)
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (J.J.); (Y.W.); (Z.S.); (Z.X.); (Y.L.); (Y.Z.); (L.S.); (Y.C.); (W.Y.)
| | - Yajun Song
- School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China; (L.X.); (X.Q.)
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (J.J.); (Y.W.); (Z.S.); (Z.X.); (Y.L.); (Y.Z.); (L.S.); (Y.C.); (W.Y.)
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Chaaban T, Mohsen Y, Ezzeddine Z, Ghssein G. Overview of Yersinia pestis Metallophores: Yersiniabactin and Yersinopine. BIOLOGY 2023; 12:biology12040598. [PMID: 37106798 PMCID: PMC10136090 DOI: 10.3390/biology12040598] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/05/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023]
Abstract
The pathogenic anaerobic bacteria Yersinia pestis (Y. pestis), which is well known as the plague causative agent, has the ability to escape or inhibit innate immune system responses, which can result in host death even before the activation of adaptive responses. Bites from infected fleas in nature transmit Y. pestis between mammalian hosts causing bubonic plague. It was recognized that a host's ability to retain iron is essential in fighting invading pathogens. To proliferate during infection, Y. pestis, like most bacteria, has various iron transporters that enable it to acquire iron from its hosts. The siderophore-dependent iron transport system was found to be crucial for the pathogenesis of this bacterium. Siderophores are low-molecular-weight metabolites with a high affinity for Fe3+. These compounds are produced in the surrounding environment to chelate iron. The siderophore secreted by Y. pestis is yersiniabactin (Ybt). Another metallophore produced by this bacterium, yersinopine, is of the opine type and shows similarities with both staphylopine and pseudopaline produced by Staphylococcus aureus and Pseudomonas aeruginosa, respectively. This paper sheds light on the most important aspects of the two Y. pestis metallophores as well as aerobactin a siderophore no longer secreted by this bacterium due to frameshift mutation in its genome.
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Affiliation(s)
- Taghrid Chaaban
- Nursing Sciences Department, Faculty of Public Health, Islamic University of Lebanon, Khalde P.O. Box 30014, Lebanon
- Nursing Sciences Research Chair, Laboratory Educations and Health Practices (LEPS), (EA 3412), UFR SMBH, University Paris 13, Sorbonne Paris Cite, F-93017 Bobigny, France
| | - Yehya Mohsen
- Department of Medical Laboratory Technology, College of Health and Medical Technologies, Al-Ayen University, Nasiriyah 64001, Iraq
| | - Zeinab Ezzeddine
- Laboratory Sciences Department, Faculty of Public Health, Islamic University of Lebanon (IUL), Khalde P.O. Box 30014, Lebanon
- Faculty of Sciences V, Lebanese University, Nabatieh 1700, Lebanon
| | - Ghassan Ghssein
- Laboratory Sciences Department, Faculty of Public Health, Islamic University of Lebanon (IUL), Khalde P.O. Box 30014, Lebanon
- Faculty of Sciences V, Lebanese University, Nabatieh 1700, Lebanon
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