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Article ; Online: Computational exploration of the genomic assignments, molecular structure, and dynamics of the

Chaudhary, Shobhi / Ali, Waseem / Yadav, Mohit / Singh, Garima / Gupta, Nomita / Grover, Sonam / Ghosh, Chaitali / Chandra, Subhash / Rathore, Jitendra Singh

Journal of biomolecular structure & dynamics

2024 , Page(s) 1–15

Abstract: Toxin-antitoxin (TA) modules, initially discovered on bacterial plasmids and subsequently identified within chromosomal contexts, hold a pivotal role in the realm of bacterial physiology. Among these, the pioneering TA system, ...

Abstract	Toxin-antitoxin (TA) modules, initially discovered on bacterial plasmids and subsequently identified within chromosomal contexts, hold a pivotal role in the realm of bacterial physiology. Among these, the pioneering TA system,
Language	English
Publishing date	2024-02-07
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2024.2311337
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Article ; Online: Functional and transcriptional analysis of chromosomal encoded hipBA

Yadav, Mohit / Rathore, Jitendra Singh

Microbial pathogenesis

2021 Volume 162, Page(s) 105309

Abstract: Xenorhabdus nematophila is an entomopathogenic bacterium that synthesizes numerous toxins and kills its larval insect host. Apart from such toxins, its genome also has a plethora of toxin-antitoxin (TA) systems. The role of TA systems in bacterial ... ...

Abstract	Xenorhabdus nematophila is an entomopathogenic bacterium that synthesizes numerous toxins and kills its larval insect host. Apart from such toxins, its genome also has a plethora of toxin-antitoxin (TA) systems. The role of TA systems in bacterial physiology is debatable; however, they are associated with maintaining bacterial genomic stability and their survival under adverse environmental conditions. Here, we explored the functionality and transcriptional regulation of the type II hipBA
MeSH term(s)	Antitoxins/genetics ; Bacterial Proteins/genetics ; DNA-Binding Proteins ; Escherichia coli/genetics ; Escherichia coli Proteins ; Toxin-Antitoxin Systems/genetics ; Xenorhabdus/genetics
Chemical Substances	Antitoxins ; Bacterial Proteins ; DNA-Binding Proteins ; Escherichia coli Proteins ; hipB protein, E coli (144515-91-3) ; hipA protein, E coli (144515-93-5)
Language	English
Publishing date	2021-11-25
Publishing country	England
Document type	Journal Article
ZDB-ID	632772-2
ISSN	1096-1208 ; 0882-4010
ISSN (online)	1096-1208
ISSN	0882-4010
DOI	10.1016/j.micpath.2021.105309
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Article: In-silico analysis of genomic distribution and functional association of hipBA toxin-antitoxin (TA) homologs in entomopathogen Xenorhabdus nematophila

Yadav, Mohit / Rathore, Jitendra Singh

Korean Society of Applied Entomology Journal of Asia-Pacific entomology. 2022 Sept., v. 25, no. 3

2022

Abstract: Bacteria have a particular strategy to invade the host immune system by forming an undetectable dormant state that may resuscitate and cause disease even after inhabiting for years in a host body. Several mechanisms are known to be responsible for ... ...

Abstract	Bacteria have a particular strategy to invade the host immune system by forming an undetectable dormant state that may resuscitate and cause disease even after inhabiting for years in a host body. Several mechanisms are known to be responsible for bacterial dormancy, among them the hipBA toxin-antitoxin (TA) system which was initially identified in Escherichia coli. Here we explore the genomic distribution and functional association of hipBA TA homologs from an entomopathogenic bacterium Xenorhabdus nematophila. This bacterium is a symbiotic model with the nematode Steinernema carpocapsae. We found that HipA toxin homologs are more closely related than HipB antitoxins and have satisfactory adenine (for HipA homologs) and nucleic acid (for HipB homologs) ligand partners with a typical TA interaction network that may promote the X. nematophila towards a stringent response to form the dormant state. Such homologs distribution is an inclusion in the current TA repertoire of X. nematophila.
Keywords	Escherichia coli ; Steinernema carpocapsae ; Xenorhabdus nematophila ; adenine ; computer simulation ; dormancy ; entomology ; entomopathogenic bacteria ; genomics ; immune system ; ligands ; models ; nucleic acids ; stress response ; toxins
Language	English
Dates of publication	2022-09
Publishing place	Elsevier B.V.
Document type	Article
ISSN	1226-8615
DOI	10.1016/j.aspen.2022.101949
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Article: Functional and transcriptional analysis of chromosomal encoded hipBAXn2 type II toxin-antitoxin (TA) module from Xenorhabdus nematophila

Yadav, Mohit / Rathore, Jitendra Singh

Microbial pathogenesis. 2022 Jan., v. 162

2022

Abstract	Xenorhabdus nematophila is an entomopathogenic bacterium that synthesizes numerous toxins and kills its larval insect host. Apart from such toxins, its genome also has a plethora of toxin-antitoxin (TA) systems. The role of TA systems in bacterial physiology is debatable; however, they are associated with maintaining bacterial genomic stability and their survival under adverse environmental conditions. Here, we explored the functionality and transcriptional regulation of the type II hipBAXⁿ² TA system. This TA system was identified in the genome of X. nematophila ATCC 19061, which consists of the hipAXⁿ² toxin gene encoding 278 amino acid residues and hipBXⁿ² encoding antitoxin of 135 amino acid residues. We showed that overexpression of HipAXⁿ² toxin reduced the growth of Escherichia coli cells in a bacteriostatic manner, and amino-acids G8, H164, N167, and S169 were key residues for this growth reduction. Promoter activity and expression profiling of the hipBAXⁿ² TA system was showed that transcription was induced in both E. coli as well as X. nematophila upon exposure to different stress conditions. Further, we have exhibited the binding features of HipAXⁿ² toxin and HipBXⁿ² antitoxin to their promoter. This study provides evidence for the presence of a functional and well-regulated hipBAXⁿ² TA system in X. nematophila.
Keywords	Escherichia coli ; Xenorhabdus nematophila ; amino acids ; antibacterial properties ; antitoxins ; entomopathogenic bacteria ; genes ; genomics ; growth retardation ; insects ; microbial physiology ; pathogenesis ; toxins ; transcription (genetics)
Language	English
Dates of publication	2022-01
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	632772-2
ISSN	1096-1208 ; 0882-4010
ISSN (online)	1096-1208
ISSN	0882-4010
DOI	10.1016/j.micpath.2021.105309
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: The hipBA

Yadav, Mohit / Rathore, Jitendra Singh

Applied microbiology and biotechnology

2020 Volume 104, Issue 7, Page(s) 3081–3095

Abstract: Here, for the first time, we have investigated the ... ...

Abstract	Here, for the first time, we have investigated the hipBA
MeSH term(s)	Bacterial Proteins/chemistry ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Bacterial Proteins/physiology ; Catalytic Domain ; DNA-Binding Proteins/chemistry ; DNA-Binding Proteins/genetics ; DNA-Binding Proteins/metabolism ; DNA-Binding Proteins/physiology ; Gene Expression Regulation, Bacterial ; Models, Molecular ; Mutagenesis, Site-Directed ; Mutation ; Operon ; Promoter Regions, Genetic ; Stress, Physiological ; Toxin-Antitoxin Systems/genetics ; Toxin-Antitoxin Systems/physiology ; Xenorhabdus/genetics ; Xenorhabdus/physiology
Chemical Substances	Bacterial Proteins ; DNA-Binding Proteins
Language	English
Publishing date	2020-02-11
Publishing country	Germany
Document type	Journal Article
ZDB-ID	392453-1
ISSN	1432-0614 ; 0171-1741 ; 0175-7598
ISSN (online)	1432-0614
ISSN	0171-1741 ; 0175-7598
DOI	10.1007/s00253-020-10441-1
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Zs.A 2229: Show issues

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Article ; Online: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a newly emerged pathogen: an overview.

Rathore, Jitendra Singh / Ghosh, Chaitali

Pathogens and disease

2020 Volume 78, Issue 6

Abstract: Coronavirus disease 2019 (COVID-19) is a viral pneumonia, responsible for the recent pandemic, and originated from Wuhan, China, in December 2019. The causative agent of the outbreak was identified as coronavirus and designated as severe acute ... ...

Abstract	Coronavirus disease 2019 (COVID-19) is a viral pneumonia, responsible for the recent pandemic, and originated from Wuhan, China, in December 2019. The causative agent of the outbreak was identified as coronavirus and designated as severe acute respiratory syndrome coronavirus 2 (SARS- CoV-2). Few years back, the severe acute respiratory syndrome coronavirus (SARS- CoV) and the Middle East respiratory syndrome coronavirus (MERS-CoV) were reported to be highly pathogenic and caused severe infections in humans. In the current situation SARS-CoV-2 has become the third highly pathogenic coronavirus that is responsible for the present outbreak in human population. At the time of this review, there were more than 14 007 791 confirmed COVID-19 patients which associated with over 597 105 deaths in more then 216 countries across the globe (as reported by World Health Organization). In this review we have discussed about SARS-CoV, MERS-CoV and SARC-CoV-2, their reservoirs, role of spike proteins and immunogenicity. We have also covered the diagnosis, therapeutics and vaccine status of SARS-CoV-2.
MeSH term(s)	Angiotensin-Converting Enzyme 2 ; Animals ; Antiviral Agents/therapeutic use ; Betacoronavirus/drug effects ; Betacoronavirus/genetics ; Betacoronavirus/immunology ; COVID-19 ; Coronavirus Infections/drug therapy ; Coronavirus Infections/epidemiology ; Coronavirus Infections/pathology ; Disease Reservoirs/veterinary ; Disease Reservoirs/virology ; Humans ; Middle East Respiratory Syndrome Coronavirus/drug effects ; Middle East Respiratory Syndrome Coronavirus/genetics ; Middle East Respiratory Syndrome Coronavirus/immunology ; Pandemics ; Peptidyl-Dipeptidase A/metabolism ; Pneumonia, Viral/drug therapy ; Pneumonia, Viral/epidemiology ; Pneumonia, Viral/pathology ; SARS-CoV-2 ; Severe Acute Respiratory Syndrome/drug therapy ; Severe Acute Respiratory Syndrome/epidemiology ; Severe Acute Respiratory Syndrome/pathology ; Spike Glycoprotein, Coronavirus/immunology ; Spike Glycoprotein, Coronavirus/metabolism ; Zoonoses/virology
Chemical Substances	Antiviral Agents ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; Peptidyl-Dipeptidase A (EC 3.4.15.1) ; ACE2 protein, human (EC 3.4.17.23) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
Keywords	covid19
Language	English
Publishing date	2020-08-25
Publishing country	United States
Document type	Journal Article ; Review
ISSN	2049-632X
ISSN (online)	2049-632X
DOI	10.1093/femspd/ftaa042
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Article ; Online: Bacterial toxin-antitoxin modules: classification, functions, and association with persistence.

Singh, Garima / Yadav, Mohit / Ghosh, Chaitali / Rathore, Jitendra Singh

Current research in microbial sciences

2021 Volume 2, Page(s) 100047

Abstract: Toxin-antitoxin (TA) modules are ubiquitous gene loci among bacteria and are comprised of a toxin part and its cognate antitoxin part. Under normal physiological conditions, antitoxin counteracts the toxicity of the toxin whereas, during stress ... ...

Abstract	Toxin-antitoxin (TA) modules are ubiquitous gene loci among bacteria and are comprised of a toxin part and its cognate antitoxin part. Under normal physiological conditions, antitoxin counteracts the toxicity of the toxin whereas, during stress conditions, TA modules play a crucial role in bacterial physiology through involvement in the post-segregational killing, abortive infection, biofilms, and persister cell formation. Most of the toxins are proteinaceous that affect translation or DNA replication, although some other intracellular molecular targets have also been described. While antitoxins may be a protein or RNA, that generally neutralizes its cognate toxin by direct interaction or with the help of other signaling elements and thus helps in the TA module regulation. In this review, we have discussed the current state of the multifaceted TA (type I-VIII) modules by highlighting their classification and specific targets. We have also discussed the presence of TA modules in the various pathogens and their role in antibiotic persistence development as well as biofilm formation, by influencing the different cellular processes. In the end, assembling knowledge about ubiquitous TA systems from pathogenic bacteria facilitated us to propose multiple novel antibacterial strategies involving artificial activation of TA modules.
Language	English
Publishing date	2021-07-07
Publishing country	Netherlands
Document type	Journal Article ; Review
ISSN	2666-5174
ISSN (online)	2666-5174
DOI	10.1016/j.crmicr.2021.100047
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Article ; Online: Assessment of epidemiological profile of hip fractures and their risk factors in a Tertiary Care Centre

Surendra Singh Rathore / Jitendra Singh Rathore / Lokpal Singh Bhati / Devendra Singh Rathore

Advances in Human Biology, Vol 11, Iss 4, Pp 95-

A case–control study

2021 Volume 98

Abstract: Introduction: Hip fractures are common injuries contributing to both morbidity and mortality in the elderly. The present case–control study was conducted to assess the epidemiological profile of hip fractures and their risk factors in a tertiary care ... ...

Abstract	Introduction: Hip fractures are common injuries contributing to both morbidity and mortality in the elderly. The present case–control study was conducted to assess the epidemiological profile of hip fractures and their risk factors in a tertiary care centre. Materials and Methods: The present study was a retrospective case–control study carried out in a tertiary care hospital over a period of 1 year. Fifty patients aged 40 years and above who were admitted with radiologically detected fractures of the femur were included as cases. Controls were selected in an equal number of cases. All the physiological parameters were recorded. Other variables were also noted. Data were collected and analyzed using the SPSS software version 21.0. P < 0.05 was considered to be statistically significant. Results: The study population consisted of 50 cases and 50 controls with an equal male-female ratio. Out of 25 cases in males, 68% were extracapsular and 32% were intracapsular fractures. Out of 25 cases in females, 60% were extracapsular and 40% were intracapsular fractures. The extracapsular (24%) and intracapsular (16%) fractures were maximum in the age group of 40–50 years in males. The extracapsular fractures (28%) and intracapsular (16%) were maximum in the age group of 60–70 years in females. Fractures taking place indoors due to loss of balance were higher (38%). Fractures occurring outdoors due to slip higher (22%). The history of weight loss in the past year was more in cases (44%). Cases were more inactive (46%) in the past than controls. Cases were more inactive (34%) in the past than controls. History of chronic diseases such as diabetes was more in cases (14%), and hypertension was more in controls than cases. History of drug uses as some sought of medication was more in cases (52%) than controls, and usage of drugs for hypertension and calcium tablets was more in controls than cases. Addiction to smoking was more in cases, and alcohol was more in controls. Conclusion: Our study concluded that in males, ...
Keywords	extracapsular and intracapsular ; femur ; hip fractures ; Biology (General) ; QH301-705.5
Subject code	590
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Wolters Kluwer Medknow Publications
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Genomic assortment and interactive insights of the chromosomal encoded control of cell death (

Chaudhary, Shobhi / Yadav, Mohit / Mathpal, Shalini / Chandra, Subhash / Rathore, Jitendra Singh

Journal of biomolecular structure & dynamics

2022 Volume 41, Issue 15, Page(s) 7032–7044

Abstract: In the present circumstances, toxin-antitoxin (TA) modules have a great consideration due to their elusive role in bacterial physiology. TA modules consist of a toxic part and a counteracting antitoxin part and these are abundant genetic loci harbored on ...

Abstract	In the present circumstances, toxin-antitoxin (TA) modules have a great consideration due to their elusive role in bacterial physiology. TA modules consist of a toxic part and a counteracting antitoxin part and these are abundant genetic loci harbored on bacterial plasmids and chromosomes. The control of cell death (
Language	English
Publishing date	2022-08-24
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2022.2114940
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Article: The hipBAXn operon from Xenorhabdus nematophila functions as a bonafide toxin-antitoxin module

Yadav, Mohit / Rathore, Jitendra Singh

Applied microbiology and biotechnology. 2020 Apr., v. 104, no. 7

2020

Abstract: Here, for the first time, we have investigated the hipBAXn toxin-antitoxin (TA) module from entomopathogenic bacterium Xenorhabdus nematophila. It is a type II TA module that consists of HipAXn toxin and HipBXn antitoxin protein and located in the ... ...

Abstract	Here, for the first time, we have investigated the hipBAXn toxin-antitoxin (TA) module from entomopathogenic bacterium Xenorhabdus nematophila. It is a type II TA module that consists of HipAXn toxin and HipBXn antitoxin protein and located in the complementary strand of chromosome under XNC1_operon 0810 locus tag. For functional analysis, hipAXn toxin, hipBXn antitoxin, and an operon having both genes were cloned in pBAD/His C vector and transformed in Escherichia coli cells. The expression profiles and endogenous toxicity assay were performed in these cells. To determine the active amino acid residues responsible for the toxicity of HipAXn toxin, site-directed mutagenesis (SDM) was performed. SDM results showed that amino acid residues S149, D306, and D329 in HipAXn toxin protein were significantly essential for its toxicity. For transcriptional analysis, the 157 bp upstream region of the hipBAXn TA module was identified as a promoter with bioinformatics tools. Further, the LacZ reporter construct with promoter region was prepared and LacZ assays as well as reverse transcriptase-polymerase chain reaction (RT-PCR) analysis was performed under different stress conditions. Electrophoretic mobility shift assay (EMSA) was also performed with recombinant HipAXn toxin, HipBXn antitoxin protein, and 157 bp promoter region. Results showed that the hipBAXn TA module is a well-regulated system in which the upregulation of gene expression was also found compulsive in different SOS conditions. KEY POINTS: •Functional characterization of hipBA Xn TA module from Xenorhabdus nematophila. •hipBA Xn TA module is a functional type II TA module. •Transcriptional characterization of hipBA Xn TA module. •hipBA Xn TA module is a well regulated TA module. Graphical abstract
Keywords	Escherichia coli ; Xenorhabdus nematophila ; amino acids ; antitoxins ; bioinformatics ; entomopathogenic bacteria ; gel electrophoresis ; gene expression ; gene expression regulation ; loci ; operon ; promoter regions ; reverse transcriptase polymerase chain reaction ; site-directed mutagenesis ; toxicity ; transcription (genetics)
Language	English
Dates of publication	2020-04
Size	p. 3081-3095.
Publishing place	Springer Berlin Heidelberg
Document type	Article
ZDB-ID	392453-1
ISSN	1432-0614 ; 0171-1741 ; 0175-7598
ISSN (online)	1432-0614
ISSN	0171-1741 ; 0175-7598
DOI	10.1007/s00253-020-10441-1
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