1
|
Kuanar SR, Sarkar RK, Panigrahi R, Mohapatra PK. Introgression of SUB1 aggravates the susceptibility of the popular rice cultivars Swarna and Savitri to stagnant flooding. Sci Rep 2023; 13:9032. [PMID: 37270542 DOI: 10.1038/s41598-023-35251-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 05/15/2023] [Indexed: 06/05/2023] Open
Abstract
Identification of the Sub1 gene for tolerance to flash flooding and its introgression into high-yielding rice cultivars are major targets in rice breeding for flood-prone rice agro-ecosystems for ensuring yield stability. However, knowledge is scant on the response of the modified genotypes under stagnant flooding (SF) to meet the challenge of finding a superior allele that may confer greater resilience to the plant under a stress-prone environment. In pursuance, we have tested the response of Sub1-introgression in two popular rice varieties, Swarna and Savitri to SF by comparing the biochemical factors in the control of flag leaf senescence and its primary production mechanisms of the parental lines' versus Sub1-introgressed lines. The activities of antioxidant enzymes like superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GR), and ascorbate peroxidase (APX) increased while various parameters of primary production like total chlorophyll content, stomatal conductance (gs), normalized difference vegetation index (NDVI) and photosynthetic activity (Pn) decreased progressively with passage of time in the flag leaf of the cultivars during the post-anthesis period and SF-treatment increased the enzyme activity while depressing primary production further. Introgression of Sub1 had no influence on these activities under control conditions but widened the margin of effects under SF. It was concluded that the functional ability of flag leaf in mega rice cultivars like Swarna and Savitri decreased significantly by SF because of an ethylene-mediated promotion of senescence of the flag leaf. The enhancement of antioxidant enzyme activity by SF could not sustain the stability of primary production in the flag leaf. The introgression of the Sub1 gene made the cultivars more vulnerable to SF because the gene induced overexpression of ethylene.
Collapse
Affiliation(s)
- Sandhya Rani Kuanar
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
- Anchal College, Padampur, 768036, India
| | | | - Rashmi Panigrahi
- School of Life Science, Sambalpur University, Jyoti Vihar, Sambalpur, 768019, India
| | | |
Collapse
|
2
|
Panigrahi R, Kailasam S. Mapping allosteric pathway in NIa-Pro using computational approach. Quant Biol 2023. [DOI: 10.15302/j-qb-022-0296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
|
3
|
Panigrahi R, Glover JNM, Nallusamy S. A look into DGAT1 through the EM lenses. Biochim Biophys Acta Biomembr 2023; 1865:184069. [PMID: 36216097 DOI: 10.1016/j.bbamem.2022.184069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 10/03/2022] [Indexed: 11/05/2022]
Abstract
With the advent of modern detectors and robust structure solution pipeline, cryogenic electron microscopy has recently proved to be game changer in structural biology. Membrane proteins are challenging targets for structural biologists. This minireview focuses a membrane embedded triglyceride synthesizing machine, DGAT1. Decades of research had built the foundational knowledge on this enzyme's activity. However, recently solved cryo-EM structures of this enzyme, in apo and bound form, has provided critical mechanistic insights. The flipping of the catalytic histidine is critical of enzyme catalysis. The structures explain why the enzyme has preference to long fatty acyl chains over the short forms.
Collapse
Affiliation(s)
- Rashmi Panigrahi
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.
| | - J N Mark Glover
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Saranya Nallusamy
- Department of Plant Molecular Biology and Bioinformatics, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India.
| |
Collapse
|
4
|
Sarker H, Panigrahi R, Hardy E, Glover JNM, Elahi S, Fernandez-Patron C. Glucocorticoids Bind to SARS-CoV-2 S1 at Multiple Sites Causing Cooperative Inhibition of SARS-CoV-2 S1 Interaction With ACE2. Front Immunol 2022; 13:906687. [PMID: 35784352 PMCID: PMC9242398 DOI: 10.3389/fimmu.2022.906687] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/12/2022] [Indexed: 12/15/2022] Open
Abstract
Dexamethasone may reduce mortality in COVID-19 patients. Whether dexamethasone or endogenous glucocorticoids, such as cortisol, biochemically interact with SARS-CoV-2 spike 1 protein (S1), or its cellular receptor ACE2, is unknown. Using molecular dynamics (MD) simulations and binding energy calculations, we identified 162 druggable pockets in various conformational states of S1 and all possible binding pockets for cortisol and dexamethasone. Through biochemical binding studies, we confirmed that cortisol and dexamethasone bind to S1. Limited proteolysis and mass spectrometry analyses validated several MD identified binding pockets for cortisol and dexamethasone on S1. Interaction assays indicated that cortisol and dexamethasone separately and cooperatively disrupt S1 interaction with ACE2, through direct binding to S1, without affecting ACE2 catalytic activity. Cortisol disrupted the binding of the mutant S1 Beta variant (E484K, K417N, N501Y) to ACE2. Delta and Omicron variants are mutated in or near identified cortisol-binding pockets in S1, which may affect cortisol binding to them. In the presence of cortisol, we find increased inhibition of S1 binding to ACE2 by an anti-SARS-CoV-2 S1 human chimeric monoclonal antibody against the receptor binding domain. Whether glucocorticoid/S1 direct interaction is an innate defence mechanism that may have contributed to mild or asymptomatic SARS-CoV-2 infection deserves further investigation.
Collapse
Affiliation(s)
- Hassan Sarker
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Rashmi Panigrahi
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | | | - J. N. Mark Glover
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Shokrollah Elahi
- Department of Dentistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Carlos Fernandez-Patron
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
- *Correspondence: Carlos Fernandez-Patron,
| |
Collapse
|
5
|
Panigrahi R, Glover JNM. Structural insights into DNA double-strand break signaling. Biochem J 2021; 478:135-156. [PMID: 33439989 DOI: 10.1042/bcj20200066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 12/10/2020] [Accepted: 12/15/2020] [Indexed: 12/14/2022]
Abstract
Genomic integrity is most threatened by double-strand breaks, which, if left unrepaired, lead to carcinogenesis or cell death. The cell generates a network of protein-protein signaling interactions that emanate from the DNA damage which are now recognized as a rich basis for anti-cancer therapy development. Deciphering the structures of signaling proteins has been an uphill task owing to their large size and complex domain organization. Recent advances in mammalian protein expression/purification and cryo-EM-based structure determination have led to significant progress in our understanding of these large multidomain proteins. This review is an overview of the structural principles that underlie some of the key signaling proteins that function at the double-strand break site. We also discuss some plausible ideas that could be considered for future structural approaches to visualize and build a more complete understanding of protein dynamics at the break site.
Collapse
Affiliation(s)
- Rashmi Panigrahi
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - J N Mark Glover
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| |
Collapse
|
6
|
Long W, Fatehi M, Soni S, Panigrahi R, Philippaert K, Yu Y, Kelly R, Boonen B, Barr A, Golec D, Campbell SA, Ondrusova K, Hubert M, Baldwin T, Lemieux MJ, Light PE. Vitamin D is an endogenous partial agonist of the transient receptor potential vanilloid 1 channel. J Physiol 2020; 598:4321-4338. [PMID: 32721035 PMCID: PMC7589233 DOI: 10.1113/jp279961] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 07/20/2020] [Indexed: 12/30/2022] Open
Abstract
KEY POINTS 25-Hydroxyvitamin D (25OHD) is a partial agonist of TRPV1 whereby 25OHD can weakly activate TRPV1 yet antagonize the stimulatory effects of the full TRPV1 agonists capsaicin and oleoyl dopamine. 25OHD binds to TRPV1 within the same vanilloid binding pocket as capsaicin. 25OHD inhibits the potentiating effects of PKC-mediated TRPV1 activity. 25OHD reduces T-cell activation and trigeminal neuron calcium signalling mediated by TRPV1 activity. These results provide evidence that TRPV1 is a novel receptor for the biological actions of vitamin D in addition to the well-documented effects of vitamin D upon the nuclear vitamin D receptor. The results may have important implications for our current understanding of certain diseases where TRPV1 and vitamin D deficiency have been implicated, such as chronic pain and autoimmune diseases, such as type 1 diabetes. ABSTRACT The capsaicin receptor TRPV1 plays an important role in nociception, inflammation and immunity and its activity is regulated by exogenous and endogenous lipophilic ligands. As vitamin D is lipophilic and involved in similar biological processes as TRPV1, we hypothesized that it directly regulates TRPV1 activity and function. Our calcium imaging and electrophysiological data demonstrate that vitamin D (25-hydroxyvitamin D (25OHD) and 1,25-hydroxyvitamin D (1,25OHD)) can weakly activate TRPV1 at physiologically relevant concentrations (100 nM). Furthermore, both 25OHD and 1,25OHD can inhibit capsaicin-induced TRPV1 activity (IC50 = 34.3 ± 0.2 and 11.5 ± 0.9 nM, respectively), but not pH-induced TRPV1 activity, suggesting that vitamin D interacts with TRPV1 in the same region as the TRPV1 agonist capsaicin. This hypothesis is supported by our in silico TRPV1 structural modelling studies, which place 25OHD in the same binding region as capsaicin. 25OHD also attenuates PKC-dependent TRPV1 potentiation via interactions with a known PKC phospho-acceptor residue in TRPV1. To provide evidence for a physiological role for the interaction of vitamin D with TRPV1, we employed two different cellular models known to express TRPV1: mouse CD4+ T-cells and trigeminal neurons. Our results indicate that 25OHD reduces TRPV1-induced cytokine release from T-cells and capsaicin-induced calcium activity in trigeminal neurons. In summary, we provide evidence that vitamin D is a novel endogenous regulator of TRPV1 channel activity that may play an important physiological role in addition to its known effects through the canonical nuclear vitamin D receptor pathway.
Collapse
Affiliation(s)
- Wentong Long
- Alberta Diabetes InstituteFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
- Departments of PharmacologyFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
| | - Mohammad Fatehi
- Alberta Diabetes InstituteFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
- Departments of PharmacologyFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
| | - Shubham Soni
- Alberta Diabetes InstituteFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
| | - Rashmi Panigrahi
- BiochemistryFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
| | - Koenraad Philippaert
- Alberta Diabetes InstituteFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
- Departments of PharmacologyFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
- Laboratory for Ion Channel ResearchDepartment of Cellular and Molecular MedicineVIB Center for Brain and Disease ResearchKU LeuvenLeuvenBelgium
| | - Yi Yu
- Alberta Diabetes InstituteFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
- Departments of PharmacologyFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
| | - Rees Kelly
- Medical Microbiology & ImmunologyFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
| | - Brett Boonen
- Laboratory for Ion Channel ResearchDepartment of Cellular and Molecular MedicineVIB Center for Brain and Disease ResearchKU LeuvenLeuvenBelgium
| | - Amy Barr
- Alberta Diabetes InstituteFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
- Departments of PharmacologyFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
| | - Dominic Golec
- Alberta Diabetes InstituteFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
- Departments of PharmacologyFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
| | - Scott A. Campbell
- Alberta Diabetes InstituteFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
- Departments of PharmacologyFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
| | - Katarina Ondrusova
- Alberta Diabetes InstituteFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
- Departments of PharmacologyFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
| | - Matt Hubert
- Alberta Diabetes InstituteFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
- Departments of PharmacologyFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
| | - Troy Baldwin
- Medical Microbiology & ImmunologyFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
| | - M. Joanne Lemieux
- BiochemistryFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
| | - Peter E. Light
- Alberta Diabetes InstituteFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
- Departments of PharmacologyFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
| |
Collapse
|
7
|
Panigrahi R, Kariali E, Panda BB, Lafarge T, Mohapatra PK. Corrigendum to: Controlling the trade-off between spikelet number and grain filling: the hierarchy of starch synthesis in spikelets of rice panicle in relation to hormone dynamics. Funct Plant Biol 2019; 46:595. [PMID: 32172735 DOI: 10.1071/fp18153_co] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The advent of dwarf statured rice varieties enabled a major breakthrough in yield and production, but raising the ceiling of genetically determined yield potential even further has been the breeding priority. Grain filling is asynchronous in the rice panicle; the inferior spikelets particularly on secondary branches of the basal part do not produce grains of a quality suitable for human consumption. Of the various strategies being considered, the control of ethylene production at anthesis has been a valuable route to potentially enhance genetic yield level of rice. The physiology underlying spikelet development has revealed spikelet position-specific ethylene levels determine the extent of grain filling, with higher levels resulting in ill-developed spikelet embodying poor endosperm starch content. To break the yield barrier, breeders have increased spikelet number per panicle in new large-panicle rice plants. However, the advantage of panicles with numerous spikelets has not resulted in enhanced yield because of poor filling of inferior spikelets. High spikelet number stimulates ethylene production and downgrading of starch synthesis, suggesting a trade-off between spikelet number and grain filling. High ethylene production in inferior spikelets suppresses expression of genes encoding endosperm starch synthesising enzymes. Hence, ethylene could be a retrograde signal that dictates the transcriptome dynamics for the cross talk between spikelet number and grain filling in the rice panicle, so attenuation of its activity may provide a solution to the problem of poor grain filling in large-panicle rice. This physiological linkage that reduces starch biosynthesis of inferior kernels is not genetically constitutive and amenable for modification through chemical, biotechnological, surgical and allelic manipulations. Studies on plant genotypes with different panicle architecture have opened up possibilities of selectively improving starch biosynthesis of inferior spikelets and thereby increasing grain yield through a physiological route.
Collapse
|
8
|
Panigrahi R, Kariali E, Panda BB, Lafarge T, Mohapatra PK. Controlling the trade-off between spikelet number and grain filling: the hierarchy of starch synthesis in spikelets of rice panicle in relation to hormone dynamics. Funct Plant Biol 2019; 46:507-523. [PMID: 30961785 DOI: 10.1071/fp18153] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 02/13/2019] [Indexed: 06/09/2023]
Abstract
The advent of dwarf statured rice varieties enabled a major breakthrough in yield and production, but raising the ceiling of genetically determined yield potential even further has been the breeding priority. Grain filling is asynchronous in the rice panicle; the inferior spikelets particularly on secondary branches of the basal part do not produce grains of a quality suitable for human consumption. Of the various strategies being considered, the control of ethylene production at anthesis has been a valuable route to potentially enhance genetic yield level of rice. The physiology underlying spikelet development has revealed spikelet position-specific ethylene levels determine the extent of grain filling, with higher levels resulting in ill-developed spikelet embodying poor endosperm starch content. To break the yield barrier, breeders have increased spikelet number per panicle in new large-panicle rice plants. However, the advantage of panicles with numerous spikelets has not resulted in enhanced yield because of poor filling of inferior spikelets. High spikelet number stimulates ethylene production and downgrading of starch synthesis, suggesting a trade-off between spikelet number and grain filling. High ethylene production in inferior spikelets suppresses expression of genes encoding endosperm starch synthesising enzymes. Hence, ethylene could be a retrograde signal that dictates the transcriptome dynamics for the cross talk between spikelet number and grain filling in the rice panicle, so attenuation of its activity may provide a solution to the problem of poor grain filling in large-panicle rice. This physiological linkage that reduces starch biosynthesis of inferior kernels is not genetically constitutive and amenable for modification through chemical, biotechnological, surgical and allelic manipulations. Studies on plant genotypes with different panicle architecture have opened up possibilities of selectively improving starch biosynthesis of inferior spikelets and thereby increasing grain yield through a physiological route.
Collapse
Affiliation(s)
- Rashmi Panigrahi
- School of Life Sciences, Sambalpur University, Jyoti vihar, Sambalpur, 768019, India
| | - Ekamber Kariali
- School of Life Sciences, Sambalpur University, Jyoti vihar, Sambalpur, 768019, India
| | - Binay Bhusan Panda
- Environmental Biotechnology Laboratory, Institute of Life Science, Bhubaneswar, 751023, India
| | - Tanguy Lafarge
- CIRAD, UMR AGAP, F-34398 Montpellier, France; and AGAP, University of Montpellier, CIRAD, INRA, INRIA, Montpellier SupAgro, Montpellier, France
| | - Pravat Kumar Mohapatra
- School of Life Sciences, Sambalpur University, Jyoti vihar, Sambalpur, 768019, India; and Corresponding author. Emails:
| |
Collapse
|
9
|
Lian J, Bahitham W, Panigrahi R, Nelson R, Li L, Watts R, Thiesen A, Lemieux MJ, Lehner R. Genetic variation in human carboxylesterase CES1 confers resistance to hepatic steatosis. Biochim Biophys Acta Mol Cell Biol Lipids 2018; 1863:688-699. [DOI: 10.1016/j.bbalip.2018.04.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Revised: 02/21/2018] [Accepted: 04/05/2018] [Indexed: 12/12/2022]
|
10
|
Caldo KMP, Acedo JZ, Panigrahi R, Vederas JC, Weselake RJ, Lemieux MJ. Diacylglycerol Acyltransferase 1 Is Regulated by Its N-Terminal Domain in Response to Allosteric Effectors. Plant Physiol 2017; 175:667-680. [PMID: 28827454 PMCID: PMC5619907 DOI: 10.1104/pp.17.00934] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 08/17/2017] [Indexed: 05/06/2023]
Abstract
Diacylglycerol acyltransferase 1 (DGAT1) is an integral membrane enzyme catalyzing the final and committed step in the acyl-coenzyme A (CoA)-dependent biosynthesis of triacylglycerol (TAG). The biochemical regulation of TAG assembly remains one of the least understood areas of primary metabolism to date. Here, we report that the hydrophilic N-terminal domain of Brassica napus DGAT1 (BnaDGAT11-113) regulates activity based on acyl-CoA/CoA levels. The N-terminal domain is not necessary for acyltransferase activity and is composed of an intrinsically disordered region and a folded segment. We show that the disordered region has an autoinhibitory function and a dimerization interface, which appears to mediate positive cooperativity, whereas the folded segment of the cytosolic region was found to have an allosteric site for acyl-CoA/CoA. Under increasing acyl-CoA levels, the binding of acyl-CoA with this noncatalytic site facilitates homotropic allosteric activation. Enzyme activation, on the other hand, is prevented under limiting acyl-CoA conditions (low acyl-CoA-to-CoA ratio), whereby CoA acts as a noncompetitive feedback inhibitor through interaction with the same folded segment. The three-dimensional NMR solution structure of the allosteric site revealed an α-helix with a loop connecting a coil fragment. The conserved amino acid residues in the loop interacting with CoA were identified, revealing details of this important regulatory element for allosteric regulation. Based on these results, a model is proposed illustrating the role of the N-terminal domain of BnaDGAT1 as a positive and negative modulator of TAG biosynthesis.
Collapse
Affiliation(s)
- Kristian Mark P. Caldo
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5, Canada
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Jeella Z. Acedo
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Rashmi Panigrahi
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - John C. Vederas
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Randall J. Weselake
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5, Canada
- Address correspondence to or
| | - M. Joanne Lemieux
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Address correspondence to or
| |
Collapse
|
11
|
Soueidan OM, Scully TW, Kaur J, Panigrahi R, Belovodskiy A, Do V, Matier CD, Lemieux MJ, Wuest F, Cheeseman C, West FG. Fluorescent Hexose Conjugates Establish Stringent Stereochemical Requirement by GLUT5 for Recognition and Transport of Monosaccharides. ACS Chem Biol 2017; 12:1087-1094. [PMID: 28205432 DOI: 10.1021/acschembio.6b01101] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The specificity characteristics of transporters can be exploited for the development of novel diagnostic therapeutic probes. The facilitated hexose transporter family (GLUTs) has a distinct set of preferences for monosaccharide substrates, and while some are expressed ubiquitously (e.g., GLUT1), others are quite tissue specific (e.g., GLUT5, which is overexpressed in some breast cancer tissues). While these differences have enabled the development of new molecular probes based upon hexose- and tissue-selective uptake, substrate design for compounds targeting these GLUT transporters has been encumbered by a limited understanding of the molecular interactions at play in hexose binding and transport. Four new fluorescently labeled hexose derivatives have been prepared, and their transport characteristics were examined in two breast cancer cell lines expressing mainly GLUTs 1, 2, and 5. Our results demonstrate, for the first time, a stringent stereochemical requirement for recognition and transport by GLUT5. 6-NBDF, in which all substituents are in the d-fructose configuration, is taken up rapidly into both cell lines via GLUT5. On the other hand, inversion of a single stereocenter at C-3 (6-NBDP), C-4 (6-NBDT), or C-5 (6-NDBS) results in selective transport via GLUT1. An in silico docking study employing the recently published GLUT5 crystal structure confirms this stereochemical dependence. This work provides insight into hexose-GLUT interactions at the molecular level and will facilitate structure-based design of novel substrates targeting individual members of the GLUT family and forms the basis of new cancer imaging or therapeutic agents.
Collapse
Affiliation(s)
- Olivier-Mohamad Soueidan
- Department
of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, Alberta, Canada T6G 2G2
- Department
of Physiology, University of Alberta, 7-55 Medical Sciences Building, Edmonton, Alberta, Canada T6G 2H7
| | - Thomas W. Scully
- Department
of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, Alberta, Canada T6G 2G2
| | - Jatinder Kaur
- Department
of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, Alberta, Canada T6G 1Z2
| | - Rashmi Panigrahi
- Department
of Biochemistry, University of Alberta, 451 Medical Sciences Building, Edmonton, Alberta, Canada T6G 2H7
| | - Alexandr Belovodskiy
- Department
of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, Alberta, Canada T6G 2G2
| | - Victor Do
- Department
of Physiology, University of Alberta, 7-55 Medical Sciences Building, Edmonton, Alberta, Canada T6G 2H7
| | - Carson D. Matier
- Department
of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, Alberta, Canada T6G 2G2
| | - M. Joanne Lemieux
- Department
of Biochemistry, University of Alberta, 451 Medical Sciences Building, Edmonton, Alberta, Canada T6G 2H7
| | - Frank Wuest
- Department
of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, Alberta, Canada T6G 1Z2
| | - Chris Cheeseman
- Department
of Physiology, University of Alberta, 7-55 Medical Sciences Building, Edmonton, Alberta, Canada T6G 2H7
| | - F. G. West
- Department
of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, Alberta, Canada T6G 2G2
| |
Collapse
|
12
|
Long W, Panigrahi R, Panwar P, Wong K, O′Neill D, Chen XZ, Lemieux MJ, Cheeseman CI. Identification of Key Residues for Urate Specific Transport in Human Glucose Transporter 9 (hSLC2A9). Sci Rep 2017; 7:41167. [PMID: 28117388 PMCID: PMC5259734 DOI: 10.1038/srep41167] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 12/14/2016] [Indexed: 11/08/2022] Open
Abstract
Human glucose transporter 9 (hSLC2A9) is critical in human urate homeostasis, for which very small deviations can lead to chronic or acute metabolic disorders. Human SLC2A9 is unique in that it transports hexoses as well as the organic anion, urate. This ability is in contrast to other homologous sugar transporters such as glucose transporters 1 and 5 (SLC2A1 &SLC2A5) and the xylose transporter (XylE), despite the fact that these transporters have similar protein structures. Our in silico substrate docking study has revealed that urate and fructose bind within the same binding pocket in hSLC2A9, yet with distinct orientations, and allowed us to identify novel residues for urate binding. Our functional studies confirmed that N429 is a key residue for both urate binding and transport. We have shown that cysteine residues, C181, C301 and C459 in hSLC2A9 are also essential elements for mediating urate transport. Additional data from chimæric protein analysis illustrated that transmembrane helix 7 of hSLC2A9 is necessary for urate transport but not sufficient to allow urate transport to be induced in glucose transporter 5 (hSLC2A5). These data indicate that urate transport in hSLC2A9 involves several structural elements rather than just a unique substrate binding pocket.
Collapse
Affiliation(s)
- Wentong Long
- Department of Physiology, Faculty of Medicine and Dentistry, University of Alberta, Alberta, Canada
| | - Rashmi Panigrahi
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Alberta, Canada
| | - Pankaj Panwar
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Alberta, Canada
| | - Kenneth Wong
- Department of Physiology, Faculty of Medicine and Dentistry, University of Alberta, Alberta, Canada
| | - Debbie O′Neill
- Department of Physiology, Faculty of Medicine and Dentistry, University of Alberta, Alberta, Canada
| | - Xing-Zhen Chen
- Department of Physiology, Faculty of Medicine and Dentistry, University of Alberta, Alberta, Canada
| | - M. Joanne Lemieux
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Alberta, Canada
| | - Chris I. Cheeseman
- Department of Physiology, Faculty of Medicine and Dentistry, University of Alberta, Alberta, Canada
| |
Collapse
|
13
|
Panigrahi R, Arutyunova E, Panwar P, Gimpl K, Keller S, Lemieux MJ. Reversible Unfolding of Rhomboid Intramembrane Proteases. Biophys J 2016; 110:1379-90. [PMID: 27028647 DOI: 10.1016/j.bpj.2016.01.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 01/18/2016] [Accepted: 01/22/2016] [Indexed: 12/20/2022] Open
Abstract
Denaturant-induced unfolding of helical membrane proteins provides insights into their mechanism of folding and domain organization, which take place in the chemically heterogeneous, anisotropic environment of a lipid membrane. Rhomboid proteases are intramembrane proteases that play key roles in various diseases. Crystal structures have revealed a compact helical bundle with a buried active site, which requires conformational changes for the cleavage of transmembrane substrates. A dimeric form of the rhomboid protease has been shown to be important for activity. In this study, we examine the mechanism of refolding for two distinct rhomboids to gain insight into their secondary structure-activity relationships. Although helicity is largely abolished in the unfolded states of both proteins, unfolding is completely reversible for HiGlpG but only partially reversible for PsAarA. Refolding of both proteins results in reassociation of the dimer, with a 90% regain of catalytic activity for HiGlpG but only a 70% regain for PsAarA. For both proteins, a broad, gradual transition from the native, folded state to the denatured, partly unfolded state was revealed with the aid of circular dichroism spectroscopy as a function of denaturant concentration, thus arguing against a classical two-state model as found for many globular soluble proteins. Thermal denaturation has irreversible destabilizing effects on both proteins, yet reveals important functional details regarding substrate accessibility to the buried active site. This concerted biophysical and functional analysis demonstrates that HiGlpG, with a simple six-transmembrane-segment organization, is more robust than PsAarA, which has seven predicted transmembrane segments, thus rendering HiGlpG amenable to in vitro studies of membrane-protein folding.
Collapse
Affiliation(s)
- Rashmi Panigrahi
- Department of Biochemistry, Membrane Protein Disease Research Group, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Elena Arutyunova
- Department of Biochemistry, Membrane Protein Disease Research Group, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Pankaj Panwar
- Department of Biochemistry, Membrane Protein Disease Research Group, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Katharina Gimpl
- Molecular Biophysics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Sandro Keller
- Molecular Biophysics, University of Kaiserslautern, Kaiserslautern, Germany
| | - M Joanne Lemieux
- Department of Biochemistry, Membrane Protein Disease Research Group, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada.
| |
Collapse
|
14
|
Agarwal P, Panigrahi R. Sinonasal Mass-a Recent Study of Its Clinicopathological Profile. Indian J Surg Oncol 2016; 8:123-127. [PMID: 28546705 DOI: 10.1007/s13193-016-0570-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 10/18/2016] [Indexed: 10/20/2022] Open
Abstract
A variety of non-neoplastic and neoplastic conditions involving the nasal cavity, paranasal sinuses (PNS), and nasopharynx are commonly encountered in clinical practice. The objectives of the study were to identify various pathological conditions that present with sinus or nasal mass, to understand their varied clinical behavior, to know the distribution of various lesions among the different age and sex groups, and to study the management of sinonasal masses and its outcome on follow-up. A prospective study was carried out from September 2013 to August 2015, in the Otorhinolaryngology Department of Hi-Tech Medical College & Hospital, Bhubaneswar, Odisha. The study included patients of any age and sex presenting with nasal symptoms (suspected of a sinonasal mass). This study included all cases seen during the above duration. Complete history was taken and full clinical examination was carried out. Majority of the patients with sinonasal masses were in the age group 41-50 years. Male:female ratio was about 1.2:1. Nasal obstruction was the most common presentation. Most common non-neoplastic lesion was rhinosporidosis and most common benign lesion was hemangioma. Most common malignant lesion was maxillary carcinoma. The presenting features of all sinonasal lesions may be indistinguishable and pose diagnostic dilemma. Correlation of clinical, radiologic, and most importantly pathologic modalities is of utmost importance for accurate diagnosis.
Collapse
Affiliation(s)
- P Agarwal
- Department of Otorhinolaryngology, Hi-Tech Medical College & Hospital, Bhubaneswar, Odisha India
| | - R Panigrahi
- Department of Otorhinolaryngology and Head and neck surgery, Hi-Tech Medical College & Hospital, Bhubaneswar, India
| |
Collapse
|
15
|
Panigrahi R, Arutyunova E, Panwar P, Gimpl K, Keller S, Lemieux J. Understanding Structural and Functional Stability of two Rhomboid Proteases: HiGlpG and PsAarA. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.1268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
|
16
|
Sarkar N, Panigrahi R, Pal A, Biswas A, Singh SP, Kar SK, Bandopadhyay M, Das D, Saha D, Kanda T, Sugiyama M, Chakrabarti S, Banerjee A, Chakravarty R. Expression of microRNA-155 correlates positively with the expression of Toll-like receptor 7 and modulates hepatitis B virus via C/EBP-β in hepatocytes. J Viral Hepat 2015; 22:817-27. [PMID: 25720442 DOI: 10.1111/jvh.12390] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Accepted: 11/15/2014] [Indexed: 12/11/2022]
Abstract
Effective recognition of viral infection and successive activation of antiviral innate immune responses are vital for host antiviral defence, which largely depends on multiple regulators, including Toll-like receptors (TLRs) and microRNAs. Several early reports suggest that specific TLR-mediated immune responses can control hepatitis B virus (HBV) replication and express differentially with disease outcome. Considering the versatile function of miR-155 in the TLR-mediated innate immune response, we aimed to study the association between miR-155 and TLRs and their subsequent impact on HBV replication using both a HBV-replicating stable cell line (HepG2.2.15) and HBV-infected liver biopsy and serum samples. Our results showed that miR-155 was suppressed during HBV infection and a subsequent positive correlation of miR-155 with TLR7 activation was noted. Further, ectopic expression of miR-155 in vitro reduced HBV load as evidenced from reduced viral DNA, mRNA and subsequently reduced level of secreted viral antigens (HBsAg and HBeAg). Our results further suggested that CCAAT/enhancer-binding protein-β (C/EBP-β), a positive regulator of HBV transcription, was inhibited by miR-155. Taken together, our study established a correlation between miR-155 and TLR7 during HBV infection and also demonstrated in vitro that increased miR-155 level could help to reduce HBV viral load by targeting C/EBP-β.
Collapse
Affiliation(s)
- N Sarkar
- ICMR Virus Unit, Kolkata, ID & BG Hospital Campus, Kolkata, India
| | - R Panigrahi
- ICMR Virus Unit, Kolkata, ID & BG Hospital Campus, Kolkata, India
| | - A Pal
- ICMR Virus Unit, Kolkata, ID & BG Hospital Campus, Kolkata, India
| | - A Biswas
- ICMR Virus Unit, Kolkata, ID & BG Hospital Campus, Kolkata, India
| | - S P Singh
- Department of Gastroenterology, SCB Medical College, Cuttack, India.,Kalinga Gastroenterology Foundation, Beam Diagnostics Premises, Cuttack, India
| | - S K Kar
- Department of Gastroenterology, SCB Medical College, Cuttack, India
| | - M Bandopadhyay
- ICMR Virus Unit, Kolkata, ID & BG Hospital Campus, Kolkata, India
| | - D Das
- ICMR Virus Unit, Kolkata, ID & BG Hospital Campus, Kolkata, India
| | - D Saha
- ICMR Virus Unit, Kolkata, ID & BG Hospital Campus, Kolkata, India
| | - T Kanda
- Department of Medicine and Clinical Oncology, Chiba University, Graduate School of Medicine, Chiba, Japan
| | - M Sugiyama
- National Center for Global Health and Medicine (NCGM), Ichikawa, Japan
| | - S Chakrabarti
- ICMR Virus Unit, Kolkata, ID & BG Hospital Campus, Kolkata, India.,National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - A Banerjee
- ICMR Virus Unit, Kolkata, ID & BG Hospital Campus, Kolkata, India
| | - R Chakravarty
- ICMR Virus Unit, Kolkata, ID & BG Hospital Campus, Kolkata, India
| |
Collapse
|
17
|
Panda BB, Badoghar AK, Das K, Panigrahi R, Kariali E, Das SR, Dash SK, Shaw BP, Mohapatra PK. Compact panicle architecture is detrimental for growth as well as sucrose synthase activity of developing rice kernels. Funct Plant Biol 2015; 42:875-887. [PMID: 32480730 DOI: 10.1071/fp14363] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 05/29/2015] [Indexed: 06/11/2023]
Abstract
The increase of spikelet number in the panicles of modern super rice has made the architecture compact, as the extra spikelets are accommodated mostly on secondary branches than on primary branches. However, the grain yield did not improve because of poor grain filling, which was more visible in the basal spikelets than apical spikelets. The objective of this study was to examine the effect of the compactness and positional difference of spikelets in the panicle on grain filling by comparing the activity and genetic expression of starch synthesising enzymes in the developing kernels of lax-(Upahar and CR3856-45-11-2-7-2-5 (CR-45)) and compact-(Mahalaxmi and CR3856-29-14-2-1-1-1 (CR-29)) panicle cultivars. Upahar and Mahalaxmi are genetically related, whereas CR-45 and CR-29 are recombinant inbred lines. The grain carbohydrate concentration and activity of sucrose synthase (SUS) enzyme were estimated during the active period of grain filling. Further, expression of isoforms of SUS, ADP glucose pyrophosphorylase (APL and APS for large and small units respectively) and starch synthase (SS and GBSS for soluble and granule bound starch synthases respectively) were also assayed through PCR studies. The genotype approach used revealed grain SUS activity and starch concentration high and sugar concentration low in the lax- compared with compact-panicle cultivars and in the apical spikelets compared with basal ones. The margin of variation between apical and basal spikelets was higher in the compact- than the lax-panicle cultivars. Genetic expression of most of the isoforms of the enzymes was higher in the lax- than the compact-panicle cultivars as seen in RT-PCR studies. A quantitative appraisal of transcript levels of isoforms in the qRT-PCR identified greater expression of SUS3 in the basal spikelets of Upahar than that in Mahalaxmi and in CR-45 over CR-29, most prominently during the active period of grain filling. We conclude that proximal location as well as increased density of spikelets on panicles affected SUS3 expression in the basal spikelets. The metabolic dominance of a spikelet in rice panicle is dependent on the expression of the genes for different isoforms of starch synthesising enzymes, but the expression of SUS3 could be more specific than the others. SUS3 expression is most active during grain filling of the lax-panicle cultivars, but its dominance is reduced significantly in the kernels of the compact-panicle cultivars.
Collapse
Affiliation(s)
- B B Panda
- Institute of Life Science, Nalco Square, Bhubaneswar 751023, India
| | - A K Badoghar
- Institute of Life Science, Nalco Square, Bhubaneswar 751023, India
| | - K Das
- Institute of Life Science, Nalco Square, Bhubaneswar 751023, India
| | - R Panigrahi
- School of Life Science, Sambalpur University, Jyoti vihar, Sambalpur 768019, India
| | - E Kariali
- School of Life Science, Sambalpur University, Jyoti vihar, Sambalpur 768019, India
| | - S R Das
- Department of Plant Breeding and Genetics, Orissa University of Agriculture and Technology, Bhubaneswar 751003, India
| | - S K Dash
- Crop Improvement Division, Central Rice Research Institute, Cuttack 753006, India
| | - B P Shaw
- Institute of Life Science, Nalco Square, Bhubaneswar 751023, India
| | - P K Mohapatra
- School of Life Science, Sambalpur University, Jyoti vihar, Sambalpur 768019, India
| |
Collapse
|
18
|
Bangera M, Panigrahi R, Sagurthi SR, Savithri HS, Murthy MRN. Structural and functional analysis of two universal stress proteins YdaA and YnaF from Salmonella typhimurium: possible roles in microbial stress tolerance. J Struct Biol 2015; 189:238-50. [PMID: 25600413 DOI: 10.1016/j.jsb.2015.01.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 01/09/2015] [Accepted: 01/09/2015] [Indexed: 11/29/2022]
Abstract
In many organisms "Universal Stress Proteins" (USPs) are induced in response to a variety of environmental stresses. Here we report the structures of two USPs, YnaF and YdaA from Salmonella typhimurium determined at 1.8Å and 2.4Å resolutions, respectively. YnaF consists of a single USP domain and forms a tetrameric organization stabilized by interactions mediated through chloride ions. YdaA is a larger protein consisting of two tandem USP domains. Two protomers of YdaA associate to form a structure similar to the YnaF tetramer. YdaA showed ATPase activity and an ATP binding motif G-2X-G-9X-G(S/T/N) was found in its C-terminal domain. The residues corresponding to this motif were not conserved in YnaF although YnaF could bind ATP. However, unlike YdaA, YnaF did not hydrolyse ATP in vitro. Disruption of interactions mediated through chloride ions by selected mutations converted YnaF into an ATPase. Residues that might be important for ATP hydrolysis could be identified by comparing the active sites of native and mutant structures. Only the C-terminal domain of YdaA appears to be involved in ATP hydrolysis. The structurally similar N-terminal domain was found to bind a zinc ion near the segment equivalent to the phosphate binding loop of the C-terminal domain. Mass spectrometric analysis showed that YdaA might bind a ligand of approximate molecular weight 800daltons. Structural comparisons suggest that the ligand, probably related to an intermediate in lipid A biosynthesis, might bind at a site close to the zinc ion. Therefore, the N-terminal domain of YdaA binds zinc and might play a role in lipid metabolism. Thus, USPs appear to perform several distinct functions such as ATP hydrolysis, altering membrane properties and chloride sensing.
Collapse
Affiliation(s)
- M Bangera
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - R Panigrahi
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - S R Sagurthi
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - H S Savithri
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - M R N Murthy
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.
| |
Collapse
|
19
|
Panigrahi R, Whelan J, Vrielink A. Exploring ligand recognition, selectivity and dynamics of TPR domains of chloroplast Toc64 and mitochondria Om64 fromArabidopsis thaliana. J Mol Recognit 2014; 27:402-14. [DOI: 10.1002/jmr.2360] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2013] [Revised: 01/14/2014] [Accepted: 01/15/2014] [Indexed: 01/31/2023]
Affiliation(s)
- Rashmi Panigrahi
- School of Chemistry and Biochemistry; University of Western Australia; 35 Stirling Highway Crawley WA 6009 Australia
| | - James Whelan
- ARC Centre of Excellence in Plant Energy Biology; University of Western Australia; 35 Stirling Highway Crawley WA 6009 Australia
- Department of Botany, School of Life Science; La Trobe University; Bundoora Victoria 3086 Australia
| | - Alice Vrielink
- School of Chemistry and Biochemistry; University of Western Australia; 35 Stirling Highway Crawley WA 6009 Australia
| |
Collapse
|
20
|
Panigrahi R, Adina-Zada A, Whelan J, Vrielink A. Ligand recognition by the TPR domain of the import factor Toc64 from Arabidopsis thaliana. PLoS One 2013; 8:e83461. [PMID: 24391770 PMCID: PMC3877065 DOI: 10.1371/journal.pone.0083461] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 11/04/2013] [Indexed: 01/21/2023] Open
Abstract
The specific targeting of protein to organelles is achieved by targeting signals being recognised by their cognate receptors. Cytosolic chaperones, bound to precursor proteins, are recognized by specific receptors of the import machinery enabling transport into the specific organelle. The aim of this study was to gain greater insight into the mode of recognition of the C-termini of Hsp70 and Hsp90 chaperones by the Tetratricopeptide Repeat (TPR) domain of the chloroplast import receptor Toc64 from Arabidopsis thaliana (At). The monomeric TPR domain binds with 1∶1 stoichiometry in similar micromolar affinity to both Hsp70 and Hsp90 as determined by isothermal titration calorimetry (ITC). Mutations of the terminal EEVD motif caused a profound decrease in affinity. Additionally, this study considered the contributions of residues upstream as alanine scanning experiments of these residues showed reduced binding affinity. Molecular dynamics simulations of the TPR domain helices upon peptide binding predicted that two helices within the TPR domain move backwards, exposing the cradle surface for interaction with the peptide. Our findings from ITC and molecular dynamics studies suggest that AtToc64_TPR does not discriminate between C-termini peptides of Hsp70 and Hsp90.
Collapse
Affiliation(s)
- Rashmi Panigrahi
- School of Chemistry and Biochemistry, University of Western Australia, Crawley, Western Australia, Australia
| | - Abdussalam Adina-Zada
- School of Chemistry and Biochemistry, University of Western Australia, Crawley, Western Australia, Australia
| | - James Whelan
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia, Australia
- Department of Botany, School of Life Science, La Trobe University, Bundoora, Victoria, Australia
| | - Alice Vrielink
- School of Chemistry and Biochemistry, University of Western Australia, Crawley, Western Australia, Australia
| |
Collapse
|
21
|
Panigrahi R, Majumder S, Gooptu M, Biswas A, Datta S, Chandra PK, Banerjee A, Chakrabarti S, Bandopadhyay D, De BK, Chakravarty R. Occult HBV infection among anti-HBc positive HIV-infected patients in apex referral centre, Eastern India. Ann Hepatol 2013; 11:870-5. [PMID: 23109450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND The prevalence of occult HBV, defined by the presence of HBV DNA in individuals with antibodies to HBV core antigen and with absence of HBV surface antigen, but its clinical significance and virological features in HIV-infected patients is still unclear. AIM To investigate the prevalence, clinical significance and molecular characterization of occult hepatitis B virus infection in ART-Naive HIV-positive individuals. MATERIAL AND METHODS Among the 1077 HIV-infected patients with different risk factors for HIV infection, 297 were HBsAg-ve ART-naive, of them 112 was randomly selected for the study. HBV DNA was tested by in-house PCR and quantified by qPCR. Molecular characterization was performed by sequencing the envelope and overlapping polymerase genes. RESULTS We found the prevalence of occult HBV to be 10.7% among a randomly selected group of HBsAg-ve/antiHBc+ve HIV-infected patients. Overall 33.9% (38 of 112) of the patients were antiHBc positive indicating exposure to HBV infection. HBV DNA was detected in 12/38 (31.5%) antiHBc positive samples and 50% of them had CD4 T cell count < 200 cells/mm(3). HCV coinfection was low (2.7%). No surrogate marker for OBI could be identified. Presence of antiHBs antibodies did not rule out OBI. Liver biopsy in six cases showed varying stages of chronic hepatitis. Several mutations were detected but not the common immune escape mutant G145R. CONCLUSION In conclusion the prevalence of OBI was significantly high among HIV coinfected patients, which highlights the importance of HBV DNA testing in these patients and indicates need for further prospective studies in larger cohorts to assess its clinical significance.
Collapse
Affiliation(s)
- R Panigrahi
- ICMR Virus Unit, Kolkata, West Bengal, India
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Kariali E, Sarangi S, Panigrahi R, Panda BB, Mohapatra PK. Variation in Senescence Pattern of Different Classes of Rice Tillers and Its Effect on Panicle Biomass Growth and Grain Yield. ACTA ACUST UNITED AC 2012. [DOI: 10.4236/ajps.2012.38125] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
23
|
Kanai S, Moghaieb RE, El-Shemy HA, Panigrahi R, Mohapatra PK, Ito J, Nguyen NT, Saneoka H, Fujita K. Potassium deficiency affects water status and photosynthetic rate of the vegetative sink in green house tomato prior to its effects on source activity. Plant Science 2011; 180:368-74. [PMID: 21421382 DOI: 10.1016/j.plantsci.2010.10.011] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Revised: 10/12/2010] [Accepted: 10/19/2010] [Indexed: 05/08/2023]
|
24
|
Chandra PK, Biswas A, Datta S, Banerjee A, Panigrahi R, Chakrabarti S, De BK, Chakravarty R. Subgenotypes of hepatitis B virus genotype D (D1, D2, D3 and D5) in India: differential pattern of mutations, liver injury and occult HBV infection. J Viral Hepat 2009; 16:749-56. [PMID: 19457142 DOI: 10.1111/j.1365-2893.2009.01129.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Hepatitis B genotype D (HBV/D) is the most widespread genotype and exists as at least five subgenotypes (HBV/D1-D5). However, little is known about the association of virological characteristics with clinical differences among HBV/D subgenotypes. To investigate the virological characteristics of these subgenotypes and their clinical implications, we selected a cohort of 109 genotype D infected individuals from the state of West Bengal, India, including 68 HBsAg positive patients and 41 with occult HBV infection. Among the HBsAg positive subjects 28 had chronic hepatitis B virus infection, 40 were asymptomatic carriers based on clinical examination, liver function test and ultrasonograph results. Overall, HBV/D1 was found in 17%, HBV/D2 in 29%, HBV/D3 in 34% and HBV/D5 in 20% of the cases. HBV/D1 was significantly associated with chronic liver disease (P = 0.01), and in this subgenotype A1896 (PreC mutations) were most common. Although BCP mutations (A/C1753 and T1762/A1764) were found to be frequently associated with HBV/D2 (33% and 33%) and D5 (47% and 59%), no apparent clinical correlation was observed. On the other hand, occult HBV infection was significantly associated with HBV/D3 infection, along with low level of BCP and PreC mutations and several non-synonymous substitutions in the catalytic reverse transcriptase (RT) domain of polymerase gene. Similar nucleotide substitutions in the surface (S) gene region were observed from both northern and eastern Indian HBV/D3 isolates. In conclusion, HBV/D subgenotypes differ in their mutational patterns in the S, polymerase and the BCP/PreC regions that may influence their clinical outcomes.
Collapse
|
25
|
Nanda U, Panigrahi R. A study on serum sperm agglutination in cases of infertility. J Obstet Gynaecol India 1978; 28:1062-5. [PMID: 751820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
|