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Silva BM, Santos LH, de Almeida JPP, de Magalhães MTQ. Rad5 HIRAN domain: Structural insights into its interaction with ssDNA through molecular modeling approaches. J Biomol Struct Dyn 2022; 41:3062-3075. [PMID: 35249470 DOI: 10.1080/07391102.2022.2045222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The Rad5 protein is an SWI/SNF family ubiquitin ligase that contains an N-terminal HIRAN domain and a RING C3HC4 motif. The HIRAN domain is critical for recognition of the stalled replication fork during the replication process and acts as a sensor to initiate the damaged DNA checkpoint. It is a conserved domain widely distributed in eukaryotic organisms and is present in several DNA-binding proteins from all kingdoms. Here we showed that distant species have important differences in key residues that affect affinity for ssDNA. Based on these findings, we hypothesized that different HIRAN domains might affect fork reversal and translesion synthesis through different metabolic processes. To address this question, we predicted the tertiary structure of both yeast and human HIRAN domains using molecular modeling. Structural dynamics experiments showed that the yeast HIRAN domain exhibited higher structural denaturation than its human homolog, although both domains became stable in the presence of ssDNA. Analysis of atomic contacts revealed that a greater number of interactions between the ssDNA nucleotides and the Rad5 domain are electrostatic. Taken together, these results provide new insights into the molecular mechanism of the HIRAN domain of Rad5 and may guide us to further elucidate differences in the ancient eukaryotes HIRAN sequences and their DNA affinity. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bruno M Silva
- Inter-unit postgraduate studies program in Bioinformatics, Federal University of Minas Gerais, Instituto de Ciências Biológicas, Belo Horizonte, Brazil.,Macromolecular Biophysics Laboratory (LBM), Biological Sciences Institute (ICB), Federal University of Minas Gerais, Instituto de Ciências Biológicas, Belo Horizonte, Brazil
| | - Lucianna H Santos
- Inter-unit postgraduate studies program in Bioinformatics, Federal University of Minas Gerais, Instituto de Ciências Biológicas, Belo Horizonte, Brazil.,Molecular Modeling and Drug Planning Laboratory, Department of Biochemistry and Immunology, Biological Sciences Institute (ICB), Federal University of Minas Gerais, Instituto de Ciências Biológicas, Belo Horizonte, Brazil
| | - João Paulo P de Almeida
- Inter-unit postgraduate studies program in Bioinformatics, Federal University of Minas Gerais, Instituto de Ciências Biológicas, Belo Horizonte, Brazil
| | - Mariana T Q de Magalhães
- Inter-unit postgraduate studies program in Bioinformatics, Federal University of Minas Gerais, Instituto de Ciências Biológicas, Belo Horizonte, Brazil.,Macromolecular Biophysics Laboratory (LBM), Biological Sciences Institute (ICB), Federal University of Minas Gerais, Instituto de Ciências Biológicas, Belo Horizonte, Brazil
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Lefoulon E, Foster JM, Truchon A, Carlow CKS, Slatko BE. The Wolbachia Symbiont: Here, There and Everywhere. Results Probl Cell Differ 2021; 69:423-451. [PMID: 33263882 DOI: 10.1007/978-3-030-51849-3_16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Wolbachia symbionts, first observed in the 1920s, are now known to be present in about 30-70% of tested arthropod species, in about half of tested filarial nematodes (including the majority of human filarial nematodes), and some plant-parasitic nematodes. In arthropods, they are generally viewed as parasites while in nematodes they appear to be mutualists although this demarcation is not absolute. Their presence in arthropods generally leads to reproductive anomalies, while in nematodes, they are generally required for worm development and reproduction. In mosquitos, Wolbachia inhibit RNA viral infections, leading to populational reductions in human RNA virus pathogens, whereas in filarial nematodes, their requirement for worm fertility and survival has been channeled into their use as drug targets for filariasis control. While much more research on these ubiquitous symbionts is needed, they are viewed as playing significant roles in biological processes, ranging from arthropod speciation to human health.
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Affiliation(s)
- Emilie Lefoulon
- Molecular Parasitology Group, New England Biolabs, Inc., Ipswich, MA, USA
| | - Jeremy M Foster
- Molecular Parasitology Group, New England Biolabs, Inc., Ipswich, MA, USA
| | - Alex Truchon
- Molecular Parasitology Group, New England Biolabs, Inc., Ipswich, MA, USA
| | - C K S Carlow
- Molecular Parasitology Group, New England Biolabs, Inc., Ipswich, MA, USA
| | - Barton E Slatko
- Molecular Parasitology Group, New England Biolabs, Inc., Ipswich, MA, USA.
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Tomilov YV, Menchikov LG, Novikov RA, Ivanova OA, Trushkov IV. Methods for the synthesis of donor-acceptor cyclopropanes. RUSSIAN CHEMICAL REVIEWS 2018. [DOI: 10.1070/rcr4787] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Jha R, Gangwar M, Chahar D, Setty Balakrishnan A, Negi MPS, Misra-Bhattacharya S. Humans from Wuchereria bancrofti endemic area elicit substantial immune response to proteins of the filarial parasite Brugia malayi and its endosymbiont Wolbachia. Parasit Vectors 2017; 10:40. [PMID: 28118850 PMCID: PMC5259955 DOI: 10.1186/s13071-016-1963-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 12/30/2016] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND In the past, immune responses to several Brugia malayi immunodominant antigens have been characterized in filaria-infected populations; however, little is known regarding Wolbachia proteins. We earlier cloned and characterized few B. malayi (trehalose-6-phosphate phosphatase, Bm-TPP and heavy chain myosin, BmAF-Myo) and Wolbachia (translation initiation factor-1, Wol Tl IF-1 and NAD+-dependent DNA ligase, wBm-LigA) proteins and investigated the immune responses, which they triggered in animal models. The current study emphasizes on immunological characteristics of these proteins in three major categories of filarial endemic zones: endemic normal (EN, asymptomatic, amicrofilaraemic; putatively immune), microfilariae carriers (MF, asymptomatic but microfilaraemic), and chronic filarial patients (CP, symptomatic and mostly amicrofilaraemic). METHODS Immunoblotting and ELISA were carried out to measure IgG and isotype antibodies against these recombinant proteins in various clinical categories. Involvement of serum antibodies in infective larvae killing was assessed by antibody-dependent cellular adhesion and cytotoxicity assay. Cellular immune response was investigated by in vitro proliferation of peripheral blood mononuclear cells (PBMCs) and reactive oxygen species (ROS) generation in these cells after stimulation. RESULTS Immune responses of EN and CP displayed almost similar level of IgG to Wol Tl IF-1 while other three proteins had higher serum IgG in EN individuals only. Specific IgA, IgG1, IgG3 and IgM to Bm-TPP were high in EN subjects, while BmAF-Myo additionally showed elevated IgG2. Enhanced IgA and IgG3 were detected in both EN and CP individuals in response to Wol Tl IF-1 antigen, but IgG1 and IgM were high only in EN individuals. wBm-LigA and BmAF-Myo exhibited almost similar pattern of antibody responses. PBMC isolated from EN subjects exhibited higher proliferation and ROS generation when stimulated with all three proteins except for Wol Tl IF-1. CONCLUSIONS Overall, these findings display high immunogenicity of all four proteins in human subjects and revealed that the EN population was exposed to both B. malayi and Wolbachia proteins simultaneously. In addition, immune responses to Wol Tl IF-1 suggest possible role of this factor in Wolbachia-induced pathological responses while immune responses to other three proteins suggest that these can be explored further as vaccine candidates.
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Affiliation(s)
- Ruchi Jha
- Division of Parasitology, CSIR-Central Drug Research Institute, BS 10/1, Sector 10 Jankipuram Extension, Sitapur Road, Lucknow, UP, 226031, India
| | - Mamta Gangwar
- Division of Parasitology, CSIR-Central Drug Research Institute, BS 10/1, Sector 10 Jankipuram Extension, Sitapur Road, Lucknow, UP, 226031, India
| | - Dhanvantri Chahar
- Division of Parasitology, CSIR-Central Drug Research Institute, BS 10/1, Sector 10 Jankipuram Extension, Sitapur Road, Lucknow, UP, 226031, India.,Academy of Scientific and Innovative Research, New Delhi, India
| | - Anand Setty Balakrishnan
- Department of Genetic Engineering, School of Biotechnology, Madurai Kamraj University, Palkalai Nagar, Madurai, TN, 625021, India
| | - Mahendra Pal Singh Negi
- Biometry and Statistics Division, CSIR-Central Drug Research Institute, BS 10/1, Sector 10 Jankipuram Extension, Sitapur Road, Lucknow, UP, 226031, India
| | - Shailja Misra-Bhattacharya
- Division of Parasitology, CSIR-Central Drug Research Institute, BS 10/1, Sector 10 Jankipuram Extension, Sitapur Road, Lucknow, UP, 226031, India. .,Academy of Scientific and Innovative Research, New Delhi, India.
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Pergolizzi G, Wagner GK, Bowater RP. Biochemical and Structural Characterisation of DNA Ligases from Bacteria and Archaea. Biosci Rep 2016; 36:00391. [PMID: 27582505 PMCID: PMC5052709 DOI: 10.1042/bsr20160003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 08/28/2016] [Accepted: 08/30/2016] [Indexed: 12/13/2022] Open
Abstract
DNA ligases are enzymes that seal breaks in the backbones of DNA, leading to them being essential for the survival of all organisms. DNA ligases have been studied from many different types of cells and organisms and shown to have diverse sizes and sequences, with well conserved specific sequences that are required for enzymatic activity. A significant number of DNA ligases have been isolated or prepared in recombinant forms and, here, we review their biochemical and structural characterisation. All DNA ligases contain an essential lysine that transfers an adenylate group from a co-factor to the 5'-phosphate of the DNA end that will ultimately be joined to the 3'-hydroxyl of the neighbouring DNA strand. The essential DNA ligases in bacteria use nicotinamide adenine dinucleotide ( β -NAD+) as their co-factor whereas those that are essential in other cells use adenosine-5'-triphosphate (ATP) as their co-factor. This observation suggests that the essential bacterial enzyme could be targeted by novel antibiotics and the complex molecular structure of β -NAD+ affords multiple opportunities for chemical modification. Several recent studies have synthesised novel derivatives and their biological activity against a range of DNA ligases has been evaluated as inhibitors for drug discovery and/or non-natural substrates for biochemical applications. Here, we review the recent advances that herald new opportunities to alter the biochemical activities of these important enzymes. The recent development of modified derivatives of nucleotides highlights that the continued combination of structural, biochemical and biophysical techniques will be useful in targeting these essential cellular enzymes.
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Affiliation(s)
- Giulia Pergolizzi
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, N/A, United Kingdom
| | - Gerd K Wagner
- Department of Chemistry, King's College London, Faculty of Natural & Mathematical Sciences, Britannia House, 7 Trinity Street, London, N/A, United Kingdom
| | - Richard Peter Bowater
- School of Biological Sciences, University of East Anglia, Norwich, N/A, NR4 7TJ, United Kingdom
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Nag JK, Chahar D, Shrivastava N, Gupta CL, Bajpai P, Chandra D, Misra-Bhattacharya S. Functional attributes of evolutionary conserved Arg45 of Wolbachia (Brugia malayi) translation initiation factor-1. Future Microbiol 2016; 11:195-214. [PMID: 26855259 DOI: 10.2217/fmb.15.135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM Wolbachia is a promising antifilarial chemotherapeutic target. Translation initiation factor-1 (Tl IF-1) is an essential factor in prokaryotes. Functional characterization of Wolbachia's novel proteins/enzymes is necessary for the development of adulticidal drugs. MATERIALS & METHODS Mutant, Wol Tl IF-1 R45D was constructed by site directed mutagenesis. Fluorimetry and size exclusion chromatography were used to determine the biophysical characteristics. Mobility shift assay and fluorescence resonance energy transfer were used to investigate the functional aspect of Wol Tl IF-1 with its mutant. RESULTS Both wild and mutant were in monomeric native conformations. Wild exhibits nonspecific binding with ssRNA/ssDNA fragments under electrostatic conditions and showed annealing and displacement of RNA strands in comparison to mutant. CONCLUSION Point mutation impaired RNA chaperone activity of the mutant and its interaction with nucleotides.
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Affiliation(s)
- Jeetendra Kumar Nag
- Division of Parasitology, CSIR-Central Drug Research Institute, BS 10/1, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow (UP) 226031, India.,Department of Biochemistry, Lucknow University, Lucknow (UP) 226007, India
| | - Dhanvantri Chahar
- Division of Parasitology, CSIR-Central Drug Research Institute, BS 10/1, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow (UP) 226031, India.,Academy of Scientific & Innovative Research, Coordination Office, Mathura Road, CRRI, Jasola, New Delhi 110020, India
| | - Nidhi Shrivastava
- Division of Parasitology, CSIR-Central Drug Research Institute, BS 10/1, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow (UP) 226031, India
| | - Chhedi Lal Gupta
- Department of Biosciences, Integral University, Lucknow (UP) 226026, India
| | - Preeti Bajpai
- Department of Biosciences, Integral University, Lucknow (UP) 226026, India
| | - Deepak Chandra
- Department of Biochemistry, Lucknow University, Lucknow (UP) 226007, India
| | - Shailja Misra-Bhattacharya
- Division of Parasitology, CSIR-Central Drug Research Institute, BS 10/1, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow (UP) 226031, India.,Academy of Scientific & Innovative Research, Coordination Office, Mathura Road, CRRI, Jasola, New Delhi 110020, India
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