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Sen H, Choudhury GB, Pawar G, Sharma Y, Bhalerao SE, Chaudhari VD, Datta S, Raychaudhuri S. Diversity in the ligand binding pocket of HapR attributes to its uniqueness towards several inhibitors with respect to other homologues - A structural and molecular perspective. Int J Biol Macromol 2023; 233:123495. [PMID: 36739058 DOI: 10.1016/j.ijbiomac.2023.123495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/06/2023] [Accepted: 01/28/2023] [Indexed: 02/05/2023]
Abstract
Vibrio cholerae is a prolific bacterium. Cumulative studies clearly demonstrate the key role of quorum sensing on the lifecycle of this bacterium. Of the sensory network components, HapR is known as high cell density master regulator. Until now, no information is available on native HapR ligand despite the protein having a ligand binding pocket. Interestingly, function of SmcR, a HapR homologue of Vibrio vulnificus is inhibited by a small molecule Qstatin. Structural analysis of SmcR with Qstatin identifies key interacting residues in SmcR ligand binding domain. Despite bearing significant homology with SmcR, HapR function remained unabated by Qstatin. Sequence alignment indicates divergence in the key residues of ligand binding pocket between these two regulators. A series of ligand binding domain mutants of HapR was constructed where only HapR quadruple mutant responded to Qstatin and newly synthesized IMT-VC-212. Crystal structure analysis revealed four key residues are responsible for changes in the volume of ligand binding pocket of HapR quadruple mutant compared to the wild type counterpart, thereby increasing the accessibility of Qstatin and its derivative in case of the former. The mechanistic insights exuberating from this study will remain instrumental in designing inhibitors against wild type HapR.
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Affiliation(s)
- Himanshu Sen
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Gourab Basu Choudhury
- CSIR-Indian Institute of Chemical Biology, Raja S C Mullick Road, Jadavpur, Kolkata 700032, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Ganesh Pawar
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Yogesh Sharma
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | | | - Vinod D Chaudhari
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India..
| | - Saumen Datta
- CSIR-Indian Institute of Chemical Biology, Raja S C Mullick Road, Jadavpur, Kolkata 700032, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India..
| | - Saumya Raychaudhuri
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India.
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Zhao J, Li Y, Huang Y, Jin L, Xu Y, Xu M, Quan C, Chen M. Heterologous expression of quorum sensing transcriptional regulator LitR and its function in virulence-related gene regulation in foodborne pathogen Aeromonas hydrophila. Mol Biol Rep 2023; 50:2049-2060. [PMID: 36542235 DOI: 10.1007/s11033-022-07866-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 08/11/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Aeromonas hydrophila is an important foodborne and zoonotic pathogen causing serious diseases. Hence, revealing the pathogenic mechanism of A. hydrophila will be of importance in the development of novel therapies. Aeromonas hydrophila litR was reported to be regulated by two quorum sensing (QS) pathways, indicating that it is involved in QS network regulation correlated with bacterial virulence. However, the function of LitR is currently not understood. Therefore, we aimed to reveal the potential regulatory mechanisms of LitR on virulence-related genes. METHODS AND RESULTS In this study, amino acid sequences analysis of LitR was conducted, providing bioinformatics evidence for its function as a potential transcriptional regulator. LitR protein was heterologous expressed, purified and its in-vitro multimeric forms were observed with gel filtration chromatography. The correlation between intracellular LitR expression level and cell density was analyzed with immunoblots. Regulation mechanisms of LitR on several important virulence-related factors were investigated with qRT-PCR, EMSA, DNase I footprinting and microscale thermophoresis binding assays, etc. Results showed that recombinant LitR protein aggregated mainly as dimer and hexamer in vitro. Intracellular expression level of LitR was positively correlated with cell density of A. hydrophila. Furthermore, LitR exhibited complicated regulation modes on virulence-related genes; it could directly bind to promoter regions of the hemolysin, serine protease and T6SS effector protein VgrG encoded genes. The promoter region of the hemolysin gene showed high binding affinity and mainly two binding sites for LitR. Different dissociation constants were obtained for LitR interaction with the hemolysin gene binding motifs I and II. Assays focusing on physiological characteristics of A. hydrophila prove that LitR positively regulated hemolytic and total extracellular protease activities. CONCLUSIONS This study investigated the function of LitR as a quorum sensing transcriptional regulator in regulation of virulence-related genes, which will help reveal the mechanisms of A. hydrophila pathogenicity. LitR could serve as a potential target for development of new antimicrobial agents from the perspective of QS regulation.
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Affiliation(s)
- Jing Zhao
- Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, Dalian, 116600, China
- College of Life Science, Dalian Minzu University, Dalian, 116600, China
| | - Yue Li
- College of Bioengineering, Dalian Polytechnic University, Dalian, 116034, China
| | - Yan Huang
- College of Bioengineering, Dalian Polytechnic University, Dalian, 116034, China
| | - Liming Jin
- Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, Dalian, 116600, China
- College of Life Science, Dalian Minzu University, Dalian, 116600, China
| | - Yongbin Xu
- Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, Dalian, 116600, China
- College of Life Science, Dalian Minzu University, Dalian, 116600, China
| | - Menghao Xu
- College of Life Science, Dalian Minzu University, Dalian, 116600, China
| | - Chunshan Quan
- Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, Dalian, 116600, China.
- College of Life Science, Dalian Minzu University, Dalian, 116600, China.
| | - Ming Chen
- College of Bioengineering, Dalian Polytechnic University, Dalian, 116034, China.
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Yadav M, Pundir S, Kumari R, Kumar A, Venugopal SJ, Panigrahy R, Tak V, Chunchanur SK, Gautam H, Kapil A, Das B, Sood S, Salve HR, Malhotra S, Kant S, Hari P, Chaudhuri S, Mohapatra S. Virulence gene mutations as a differentiator of clinical phenotypes: insights from community-acquired uropathogenic Escherichia coli. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35380532 DOI: 10.1099/mic.0.001161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Uropathogenic Escherichia coli (UPEC) remains an important cause of urinary tract infection during pregnancy. Multiple molecular virulence determinants and antibiotic resistant genes facilitate its pathogenesis and virulence phenotype. Hence it is hypothesized that there will be considerable variation in genes among the isolates from symptomatic as well as asymptomatic bacteriuria (ABU) during pregnancy. The aim of this study was to decipher the genetic variation among the two phenotypes. Six different UPEC isolates collected from urine specimens of consecutive pregnant females (five, symptomatic bacteriuria and one, ABU) were tested for their growth kinetics, and biofilm formation. A total of 87 virulence determinants and 56 antibiotic resistance genes were investigated using whole-genome sequencing, to identify putative drives of virulence phenotype. In this analysis, we identified eight different types of fully functional toxin antitoxin (TA) systems [HipAB, YefM-YoeB, YeeU-YeeV (CbtA), YhaV-PrlF, ChpBS, HigAB, YgiUT and HicAB] in the isolates from symptomatic bacteriuria; whereas partially functional TA system with mutations were observed in the asymptomatic one. Isolates of both the groups showed equivalent growth characteristics and biofilm-formation ability. Genes for an iron transport system (Efe UOB system, Fhu system except FhuA) were observed functional among all symptomatic and asymptomatic isolates, however functional mutations were observed in the latter group. Gene YidE was observed predominantly associated with the biofilm formation along with few other genes (BssR, BssS, YjgK, etc.). This study outlines putative critical relevance of specific variations in the genes for the TA system, biofilm formation, cell adhesion and colonization among UPEC isolates from symptomatic and asymptomatic bacteriuria among pregnant women. Further functional genomic study in the same cohort is warranted to establish the pathogenic role of these genes.
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Affiliation(s)
- Manisha Yadav
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Swati Pundir
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Rajesh Kumari
- Department of Obstetrics and Gynaecology, All India Institute of Medical Science, New Delhi, India
| | - Arvind Kumar
- Department of Medicine, All India Institute of Medical Science, New Delhi, India
| | - Shwetha J Venugopal
- Department of Microbiology, Bangalore Medical College and Research Institute, Bangalore, India
| | - Rajashree Panigrahy
- Department of Microbiology, Institute of Medical Sciences and SUM Hospital, Bhubaneswar, India
| | - Vibhor Tak
- Department of Microbiology, All India Institute of Medical Science, Jodhpur, India
| | - Sneha K Chunchanur
- Department of Microbiology, Bangalore Medical College and Research Institute, Bangalore, India
| | - Hitender Gautam
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Arti Kapil
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Bimal Das
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Seema Sood
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Harshal Ramesh Salve
- Centre for Community Medicine, All India Institute of Medical Science, New Delhi, India
| | - Sumit Malhotra
- Centre for Community Medicine, All India Institute of Medical Science, New Delhi, India
| | - Shashi Kant
- Centre for Community Medicine, All India Institute of Medical Science, New Delhi, India
| | - Pankaj Hari
- Department of Pediatrics, All India Institute of Medical Science, New Delhi, India
| | - Susmita Chaudhuri
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Sarita Mohapatra
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
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Soni N, Hegde N, Dhariwal A, Kushalappa AC. Role of laccase gene in wheat NILs differing at QTL-Fhb1 for resistance against Fusarium head blight. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 298:110574. [PMID: 32771175 DOI: 10.1016/j.plantsci.2020.110574] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 06/16/2020] [Accepted: 06/19/2020] [Indexed: 05/20/2023]
Abstract
Fusarium head blight (FHB), caused mainly by Fusarium graminearum (Fg), is one of the most severe diseases of wheat. It affects grain yield and quality due to mycotoxin contamination, which is harmful for both human and livestock consumption. Cell wall lignification, following pathogen invasion, is one of the innate defense responses. Plant laccases are known to lignify the secondary cell walls. A metabolo-genomics study identified laccase as one of the candidate genes in QTL-Fhb1 of wheat NILs derived from Sumai 3*5/Thatcher cross. Based on phylogenetics, it was named as TaLAC4. Real-time qPCR revealed a strongly induced expression of TaLAC4 in NIL-R. The VIGS based transient silencing of TaLAC4 in NIL-R resulted in an increased susceptibility leading to Fg spread within the entire spike in 15dpi, contrasting to non-silenced where the infection was limited to inoculated spikelets. Histopathology revealed thickened cell walls, mainly due to G-lignin, in non-silenced NIL-R, relative to silenced, in conjunction with higher total lignin content. Metabolic profiling of TaLAC4 silenced NILs identified the accumulation of several precursor metabolites higher in abundances upstream TaLAC4. These results confirm that the resistance function of TaLAC4 in NIL-R is due to pathogen-induced lignification of secondary cell walls in the rachis.
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Affiliation(s)
- Nancy Soni
- Plant Science Department, McGill University, Ste.-Anne-de-Bellevue, QC, Canada
| | - Niranjan Hegde
- Plant Science Department, McGill University, Ste.-Anne-de-Bellevue, QC, Canada
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Ekka M, Mondal A, Singh R, Sen H, Datta S, Raychaudhuri S. Arginine 37 of Glycine Linker Dictates Regulatory Function of HapR. Front Microbiol 2020; 11:1949. [PMID: 32973706 PMCID: PMC7472637 DOI: 10.3389/fmicb.2020.01949] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 07/24/2020] [Indexed: 12/14/2022] Open
Abstract
HapR is designated as a high cell density quorum sensing master regulatory protein of Vibrio cholerae. It is a member of the TetR family protein and functions both as an activator and a repressor by directly communicating with cognate promoters, thus controlling the expression of a plethora of genes in a density-dependent manner. Molecular insights reveal the domain architecture and further unveil the significance of a cross talk between the DNA binding domain and the dimerization domain for the functionality of the wild-type protein. The DNA binding domain is made up of three α-helices, where a helix-turn-helix motif spans between the helices α2 and α3. The essentiality of the glycine-rich linker linking helices α1 and α2 came into prominence while unraveling the molecular basis of a natural non-functional variant of HapR. Subsequently, the importance of linker length was demonstrated. The present study, involving a series of biochemical analyses coupled with molecular dynamics simulation, has illustrated the indispensability of a critical arginine within the linker at position 37 contributing to HapR–DNA binding activity.
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Affiliation(s)
- Manjula Ekka
- Council of Scientific and Industrial Research (CSIR), Institute of Microbial Technology, Chandigarh, India
| | - Abhisek Mondal
- Council of Scientific and Industrial Research (CSIR), Indian Institute of Chemical Biology, Kolkata, India
| | - Richa Singh
- Council of Scientific and Industrial Research (CSIR), Institute of Microbial Technology, Chandigarh, India
| | - Himanshu Sen
- Council of Scientific and Industrial Research (CSIR), Institute of Microbial Technology, Chandigarh, India
| | - Saumen Datta
- Council of Scientific and Industrial Research (CSIR), Indian Institute of Chemical Biology, Kolkata, India
| | - Saumya Raychaudhuri
- Council of Scientific and Industrial Research (CSIR), Institute of Microbial Technology, Chandigarh, India
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Singh NS, Kachhap S, Singh R, Mishra RC, Singh B, Raychaudhuri S. The length of glycine-rich linker in DNA-binding domain is critical for optimal functioning of quorum-sensing master regulatory protein HapR. Mol Genet Genomics 2014; 289:1171-82. [PMID: 24997084 DOI: 10.1007/s00438-014-0878-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 06/06/2014] [Indexed: 01/03/2023]
Abstract
HapR is a quorum-sensing master regulatory protein in Vibrio cholerae. Though many facts are known regarding its structural and functional aspects, much still can be learnt from natural variants of this wild-type protein. While unraveling the underlying cause of functional inertness of a natural variant (HapRV2), the significance of a conserved glycine residue at position 39 in a glycine-rich linker in DNA-binding domain comes into light. This work aims at investigating how the length of glycine-rich linker (R(33)GIGRGG(39)) bridging helices α1 and α2 modulates the functionality of HapR. In pursuit of our interest, glycine residues were inserted after terminal glycine (G39) of the linker in a sequential manner. To evaluate functionality, all the glycine linker variants were subjected to a battery of performance tests under various conditions. Combined in vitro and in vivo results clearly demonstrated a gradual functional impairment of HapR linker variants coupled with increasing length of glycine-rich linker and finally, linker variant harboring four glycine residues resulted in a functionally compromised protein with significant loss of communication with cognate DNAs. Molecular dynamics studies of modeled HapR linker variants in complex with cognate promoter region show that residues namely Ser50, Thr53 and Asn56 are involved in varying degree of interactions with different nucleotides of HapR-DNA complex. The diminished functionality between variants and DNA appears to result from reduced or no interactions between Phe55 and nucleotides of cognate DNA as observed during simulations.
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Affiliation(s)
- Naorem Santa Singh
- Molecular Biology and Microbial Physiology Division, Institute of Microbial Technology (Council of Scientific and Industrial Research), Sector 39A, Chandigarh, 160036, India
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