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Article ; Online: Silencing suppressor protein PRT of rice tungro bacilliform virus interacts with the plant RNA silencing-related protein SGS3.

Naresh, Madhvi / Purkayastha, Arunima / Dasgupta, Indranil

2023 Volume 581, Page(s) 71–80

Abstract: Background: Rice tungro bacilliform virus (RTBV) is a double stranded DNA containing virus which causes the devastating tungro disease of rice in association with an RNA virus, rice tungro spherical virus. RNA silencing is an evolutionarily conserved ... ...

Abstract	Background: Rice tungro bacilliform virus (RTBV) is a double stranded DNA containing virus which causes the devastating tungro disease of rice in association with an RNA virus, rice tungro spherical virus. RNA silencing is an evolutionarily conserved antiviral defence pathway in plants as well as in several classes of higher organisms. Many viruses, in turn, encode proteins which are termed Viral Suppressor of RNA Silencing (VSR) because they downregulate or suppress RNA silencing. Results: Using an RNA silencing suppressor assay we show that RTBV protease (PRT) acts as a mild VSR. A truncated version of PRT gene abolished the silencing suppression activity. We also show in planta interaction of PRT with the SGS3 protein of Solanum tuberosum and Arabidopsis thaliana using bimolecular fluorescence complementation assay (BIFC). Transient expression of PRT in Nicotiana benthamiana caused an increased accumulation of the begomovirus Sri Lankan cassava mosaic virus (SLCMV) DNA-A, which indicated a virulence function imparted on an unrelated virus. Conclusion: The finding supports the idea that PRT acts as suppressor of RNA silencing and this action may be mediated by its interaction with SGS3.
MeSH term(s)	RNA Interference ; Plant Proteins/genetics ; Plant Proteins/metabolism ; Tungrovirus/genetics ; Peptide Hydrolases/metabolism ; Arabidopsis ; Endopeptidases/genetics ; Plant Diseases ; Oryza ; Arabidopsis Proteins/genetics
Chemical Substances	Plant Proteins ; Peptide Hydrolases (EC 3.4.-) ; Endopeptidases (EC 3.4.-) ; SGS3 protein, Arabidopsis ; Arabidopsis Proteins
Language	English
Publishing date	2023-03-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	200425-2
ISSN	1096-0341 ; 0042-6822
ISSN (online)	1096-0341
ISSN	0042-6822
DOI	10.1016/j.virol.2023.02.013
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Article ; Online: P4 protein of an Indian isolate of rice tungro bacilliform virus modulates gene silencing.

Naresh, Madhvi / Purkayastha, Arunima / Dasgupta, Indranil

Virus genes

2023 Volume 60, Issue 1, Page(s) 55–64

Abstract: Plant hosts and their viral pathogens are engaged in a constant cycle of defense and counter-defense as part of a molecular arms race, principal among them being the plant RNAi defense and the viral RNAi suppressor counter-defense. Rice tungro ... ...

Abstract	Plant hosts and their viral pathogens are engaged in a constant cycle of defense and counter-defense as part of a molecular arms race, principal among them being the plant RNAi defense and the viral RNAi suppressor counter-defense. Rice tungro bacilliform virus (RTBV), member of the family Caulimoviridae, genus Tungrovirus, species Tungrovirus oryzae, infects rice in South- and Southeast Asia and causes severe symptoms of stunting, yellow-orange discoloration and twisting of leaf tips. To better understand the possible counter-defensive roles of RTBV against the host RNAi defense system, we explored the ability of the P4 protein of an Indian isolate of RTBV to act as a possible modulator of RNAi. Using a transient silencing and silencing suppression assay in Nicotiana benthamiana, we show that P4 not only displays an RNAi suppressor function, but also potentially enhances RNAi. The results also suggests that the N-terminal 168 amino acid residues of P4 are sufficient to maintain RNAi suppressor activity. Taken together with the earlier reports this work strengthens the view that the P4 protein carries out RNAi suppressor and a potential RNAi enhancer function.
MeSH term(s)	Tungrovirus/genetics ; Gene Silencing ; RNA Interference ; Oryza/genetics ; Plant Diseases/genetics
Language	English
Publishing date	2023-12-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	639496-6
ISSN	1572-994X ; 0920-8569
ISSN (online)	1572-994X
ISSN	0920-8569
DOI	10.1007/s11262-023-02039-2
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Article ; Online: Silencing suppressor protein PRT of rice tungro bacilliform virus interacts with the plant RNA silencing-related protein SGS3

Naresh, Madhvi / Purkayastha, Arunima / Dasgupta, Indranil

Virology. 2023 Mar. 06,

2023

Abstract: Rice tungro bacilliform virus (RTBV) is a double stranded DNA containing virus which causes the devastating tungro disease of rice in association with an RNA virus, rice tungro spherical virus. RNA silencing is an evolutionarily conserved antiviral ... ...

Abstract	Rice tungro bacilliform virus (RTBV) is a double stranded DNA containing virus which causes the devastating tungro disease of rice in association with an RNA virus, rice tungro spherical virus. RNA silencing is an evolutionarily conserved antiviral defence pathway in plants as well as in several classes of higher organisms. Many viruses, in turn, encode proteins which are termed Viral Suppressor of RNA Silencing (VSR) because they downregulate or suppress RNA silencing. Using an RNA silencing suppressor assay we show that RTBV protease (PRT) acts as a mild VSR. A truncated version of PRT gene abolished the silencing suppression activity. We also show in planta interaction of PRT with the SGS3 protein of Solanum tuberosum and Arabidopsis thaliana using bimolecular fluorescence complementation assay (BIFC). Transient expression of PRT in Nicotiana benthamiana caused an increased accumulation of the begomovirus Sri Lankan cassava mosaic virus (SLCMV) DNA-A, which indicated a virulence function imparted on an unrelated virus. The finding supports the idea that PRT acts as suppressor of RNA silencing and this action may be mediated by its interaction with SGS3.
Keywords	African cassava mosaic virus ; Arabidopsis thaliana ; DNA ; Nicotiana benthamiana ; RNA ; Rice tungro bacilliform virus ; Rice tungro spherical virus ; Solanum tuberosum ; assays ; genes ; proteinases ; rice ; virology ; virulence ; viruses ; RNA silencing ; Silencing suppression ; RTBV ; PRT ; SGS3 ; SLCMV
Language	English
Dates of publication	2023-0306
Publishing place	Elsevier Inc.
Document type	Article ; Online
Note	Pre-press version
ZDB-ID	200425-2
ISSN	1096-0341 ; 0042-6822
ISSN (online)	1096-0341
ISSN	0042-6822
DOI	10.1016/j.virol.2023.02.013
Database	NAL-Catalogue (AGRICOLA)

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Article: Mitoquinone mesylate targets SARS-CoV-2 infection in preclinical models.

Petcherski, Anton / Sharma, Madhav / Satta, Sandro / Daskou, Maria / Vasilopoulos, Hariclea / Hugo, Cristelle / Ritou, Eleni / Dillon, Barbara Jane / Fung, Eileen / Garcia, Gustavo / Scafoglio, Claudio / Purkayastha, Arunima / Gomperts, Brigitte N / Fishbein, Gregory A / Arumugaswami, Vaithilingaraja / Liesa, Marc / Shirihai, Orian S / Kelesidis, Theodoros

bioRxiv : the preprint server for biology

2022

Abstract: To date, there is no effective oral antiviral against SARS-CoV-2 that is also anti-inflammatory. Herein, we show that the mitochondrial antioxidant mitoquinone/mitoquinol mesylate (Mito-MES), a dietary supplement, has potent antiviral activity against ... ...

Abstract	To date, there is no effective oral antiviral against SARS-CoV-2 that is also anti-inflammatory. Herein, we show that the mitochondrial antioxidant mitoquinone/mitoquinol mesylate (Mito-MES), a dietary supplement, has potent antiviral activity against SARS-CoV-2 and its variants of concern One-sentence summary: Mitoquinone/mitoquinol mesylate has potent antiviral and anti-inflammatory activity in preclinical models of SARS-CoV-2 infection.
Language	English
Publishing date	2022-06-23
Publishing country	United States
Document type	Preprint
DOI	10.1101/2022.02.22.481100
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Article ; Online: Targeting PEA3 transcription factors to mitigate small cell lung cancer progression.

Shia, David W / Choi, WooSuk / Vijayaraj, Preethi / Vuong, Valarie / Sandlin, Jenna M / Lu, Michelle M / Aziz, Adam / Marin, Caliope / Aros, Cody J / Sen, Chandani / Durra, Abdo / Lund, Andrew J / Purkayastha, Arunima / Rickabaugh, Tammy M / Graeber, Thomas G / Gomperts, Brigitte N

Oncogene

2022 Volume 42, Issue 6, Page(s) 434–448

Abstract: Small cell lung cancer (SCLC) remains a lethal disease with a dismal overall survival rate of 6% despite promising responses to upfront combination chemotherapy. The key drivers of such rapid mortality include early metastatic dissemination in the ... ...

Abstract	Small cell lung cancer (SCLC) remains a lethal disease with a dismal overall survival rate of 6% despite promising responses to upfront combination chemotherapy. The key drivers of such rapid mortality include early metastatic dissemination in the natural course of the disease and the near guaranteed emergence of chemoresistant disease. Here, we found that we could model the regression and relapse seen in clinical SCLC in vitro. We utilized time-course resolved RNA-sequencing to globally profile transcriptome changes as SCLC cells responded to a combination of cisplatin and etoposide-the standard-of-care in SCLC. Comparisons across time points demonstrated a distinct transient transcriptional state resembling embryonic diapause. Differential gene expression analysis revealed that expression of the PEA3 transcription factors ETV4 and ETV5 were transiently upregulated in the surviving fraction of cells which we determined to be necessary for efficient clonogenic expansion following chemotherapy. The FGFR-PEA3 signaling axis guided the identification of a pan-FGFR inhibitor demonstrating in vitro and in vivo efficacy in delaying progression following combination chemotherapy, observed inhibition of phosphorylation of the FGFR adaptor FRS2 and corresponding downstream MAPK and PI3K-Akt signaling pathways. Taken together, these data nominate PEA3 transcription factors as key mediators of relapse progression in SCLC and identify a clinically actionable small molecule candidate for delaying relapse of SCLC.
MeSH term(s)	Humans ; Small Cell Lung Carcinoma/drug therapy ; Small Cell Lung Carcinoma/genetics ; Small Cell Lung Carcinoma/pathology ; Phosphatidylinositol 3-Kinases/genetics ; Neoplasm Recurrence, Local ; Transcription Factors/genetics ; Transcription Factors/metabolism ; Lung Neoplasms/drug therapy ; Lung Neoplasms/genetics ; Lung Neoplasms/metabolism ; Cell Line, Tumor
Chemical Substances	Phosphatidylinositol 3-Kinases (EC 2.7.1.-) ; Transcription Factors
Language	English
Publishing date	2022-12-13
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	639046-8
ISSN	1476-5594 ; 0950-9232
ISSN (online)	1476-5594
ISSN	0950-9232
DOI	10.1038/s41388-022-02558-6
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Article ; Online: Virus-induced gene silencing for rice using agroinoculation.

Purkayastha, Arunima / Sharma, Shweta / Dasgupta, Indranil

Methods in molecular biology (Clifton, N.J.)

2013 Volume 975, Page(s) 33–45

Abstract: Virus-induced gene silencing (VIGS) is a reverse genetics technique that is based on the RNA-mediated defense against viruses in plants. VIGS is a method of gene knockdown triggered by a replicating viral nucleic acid engineered to carry a host gene to ... ...

Abstract	Virus-induced gene silencing (VIGS) is a reverse genetics technique that is based on the RNA-mediated defense against viruses in plants. VIGS is a method of gene knockdown triggered by a replicating viral nucleic acid engineered to carry a host gene to be silenced. While there are a number of excellent VIGS vectors available for dicots, only a few are available for monocots. Here, we describe the detailed method of the use of a newly developed VIGS vector for rice, based on the rice-infecting Rice tungro bacilliform virus, a pararetrovirus with dsDNA genome. Using a method based on Agrobacterium-mediated injection of the VIGS construct at the meristematic region of young rice plants, silencing of target genes can be achieved and the silenced phenotype can be visualized in 3 weeks.
MeSH term(s)	Agrobacterium tumefaciens/virology ; Cloning, Molecular ; Gene Knockdown Techniques/methods ; Genetic Vectors ; Oryza/genetics ; Oryza/virology ; RNA Interference ; Transformation, Bacterial ; Tungrovirus/genetics
Language	English
Publishing date	2013
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-62703-278-0_3
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Virus-induced gene silencing: a versatile tool for discovery of gene functions in plants.

Purkayastha, Arunima / Dasgupta, Indranil

Plant physiology and biochemistry : PPB

2009 Volume 47, Issue 11-12, Page(s) 967–976

Abstract: Virus-induced gene silencing (VIGS) is a technology that exploits an antiviral defense mechanism in plants as a tool for plant reverse genetics. VIGS circumvents the need for plant transformation, is methodologically simple and yields rapid results. ... ...

Abstract	Virus-induced gene silencing (VIGS) is a technology that exploits an antiviral defense mechanism in plants as a tool for plant reverse genetics. VIGS circumvents the need for plant transformation, is methodologically simple and yields rapid results. Various VIGS vectors have been developed and have helped to unravel the functions of genes involved in processes such as disease resistance, abiotic stress, cellular signaling and secondary metabolite biosynthesis.
MeSH term(s)	Gene Silencing ; Genes, Plant ; Genetic Vectors ; Plant Viruses/physiology ; Plants/genetics ; Plants/metabolism ; Plants/virology
Language	English
Publishing date	2009-09-10
Publishing country	France
Document type	Journal Article ; Review
ZDB-ID	742978-2
ISSN	1873-2690 ; 0981-9428
ISSN (online)	1873-2690
ISSN	0981-9428
DOI	10.1016/j.plaphy.2009.09.001
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Article ; Online: SARS-CoV-2 infection rewires host cell metabolism and is potentially susceptible to mTORC1 inhibition

Peter J. Mullen / Gustavo Garcia / Arunima Purkayastha / Nedas Matulionis / Ernst W. Schmid / Milica Momcilovic / Chandani Sen / Justin Langerman / Arunachalam Ramaiah / David B. Shackelford / Robert Damoiseaux / Samuel W. French / Kathrin Plath / Brigitte N. Gomperts / Vaithilingaraja Arumugaswami / Heather R. Christofk

Nature Communications, Vol 12, Iss 1, Pp 1-

2021 Volume 10

Abstract: The pandemic of COVID-19, caused by SARS-CoV-2 infection, warrants immediate investigation for therapy options. Here the authors show, using epithelial and air-liquid interface cultures, that SARS-CoV-2 hijacks host cell metabolism to facilitate viral ... ...

Abstract	The pandemic of COVID-19, caused by SARS-CoV-2 infection, warrants immediate investigation for therapy options. Here the authors show, using epithelial and air-liquid interface cultures, that SARS-CoV-2 hijacks host cell metabolism to facilitate viral replication, and that inhibition of mTORC1, a master metabolic regulator, suppresses viral replication.
Keywords	Science ; Q
Language	English
Publishing date	2021-03-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: SARS-CoV-2 infection rewires host cell metabolism and is potentially susceptible to mTORC1 inhibition.

Mullen, Peter J / Garcia, Gustavo / Purkayastha, Arunima / Matulionis, Nedas / Schmid, Ernst W / Momcilovic, Milica / Sen, Chandani / Langerman, Justin / Ramaiah, Arunachalam / Shackelford, David B / Damoiseaux, Robert / French, Samuel W / Plath, Kathrin / Gomperts, Brigitte N / Arumugaswami, Vaithilingaraja / Christofk, Heather R

Nature communications

2021 Volume 12, Issue 1, Page(s) 1876

Abstract: Viruses hijack host cell metabolism to acquire the building blocks required for replication. Understanding how SARS-CoV-2 alters host cell metabolism may lead to potential treatments for COVID-19. Here we profile metabolic changes conferred by SARS-CoV-2 ...

Abstract	Viruses hijack host cell metabolism to acquire the building blocks required for replication. Understanding how SARS-CoV-2 alters host cell metabolism may lead to potential treatments for COVID-19. Here we profile metabolic changes conferred by SARS-CoV-2 infection in kidney epithelial cells and lung air-liquid interface (ALI) cultures, and show that SARS-CoV-2 infection increases glucose carbon entry into the TCA cycle via increased pyruvate carboxylase expression. SARS-CoV-2 also reduces oxidative glutamine metabolism while maintaining reductive carboxylation. Consistent with these changes, SARS-CoV-2 infection increases the activity of mTORC1 in cell lines and lung ALI cultures. Lastly, we show evidence of mTORC1 activation in COVID-19 patient lung tissue, and that mTORC1 inhibitors reduce viral replication in kidney epithelial cells and lung ALI cultures. Our results suggest that targeting mTORC1 may be a feasible treatment strategy for COVID-19 patients, although further studies are required to determine the mechanism of inhibition and potential efficacy in patients.
MeSH term(s)	Animals ; Benzamides/pharmacology ; COVID-19/pathology ; Cell Line ; Chlorocebus aethiops ; Citric Acid Cycle/physiology ; Glucose/metabolism ; Glutamine/metabolism ; HEK293 Cells ; Humans ; Lung/metabolism ; Lung/virology ; Mechanistic Target of Rapamycin Complex 1/antagonists & inhibitors ; Mechanistic Target of Rapamycin Complex 1/metabolism ; Morpholines/pharmacology ; Naphthyridines/pharmacology ; Protein Kinase Inhibitors/pharmacology ; Pyrimidines/pharmacology ; Pyruvate Carboxylase/biosynthesis ; SARS-CoV-2/metabolism ; Vero Cells ; Virus Replication/drug effects
Chemical Substances	9-(6-aminopyridin-3-yl)-1-(3-(trifluoromethyl)phenyl)benzo(h)(1,6)naphthyridin-2(1H)-one ; Benzamides ; Morpholines ; Naphthyridines ; Protein Kinase Inhibitors ; Pyrimidines ; vistusertib (0BSC3P4H5X) ; Glutamine (0RH81L854J) ; Mechanistic Target of Rapamycin Complex 1 (EC 2.7.11.1) ; Pyruvate Carboxylase (EC 6.4.1.1) ; Glucose (IY9XDZ35W2)
Language	English
Publishing date	2021-03-25
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-021-22166-4
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Article ; Online: In vivo genetic dissection of tumor growth and the Warburg effect.

Wang, Cheng-Wei / Purkayastha, Arunima / Jones, Kevin T / Thaker, Shivani K / Banerjee, Utpal

eLife

2016 Volume 5

Abstract: A well-characterized metabolic landmark for aggressive cancers is the reprogramming from oxidative phosphorylation to aerobic glycolysis, referred to as the Warburg effect. Models mimicking this process are often incomplete due to genetic complexities of ...

Abstract	A well-characterized metabolic landmark for aggressive cancers is the reprogramming from oxidative phosphorylation to aerobic glycolysis, referred to as the Warburg effect. Models mimicking this process are often incomplete due to genetic complexities of tumors and cell lines containing unmapped collaborating mutations. In order to establish a system where individual components of oncogenic signals and metabolic pathways can be readily elucidated, we induced a glycolytic tumor in the Drosophila wing imaginal disc by activating the oncogene PDGF/VEGF-receptor (Pvr). This causes activation of multiple oncogenic pathways including Ras, PI3K/Akt, Raf/ERK, Src and JNK. Together this network of genes stabilizes Hifα (Sima) that in turn, transcriptionally up-regulates many genes encoding glycolytic enzymes. Collectively, this network of genes also causes inhibition of pyruvate dehydrogenase (PDH) activity resulting in diminished ox-phos levels. The high ROS produced during this process functions as a feedback signal to consolidate this metabolic reprogramming.
MeSH term(s)	Animals ; DNA-Binding Proteins/biosynthesis ; Disease Models, Animal ; Drosophila ; Drosophila Proteins/biosynthesis ; Gene Expression Regulation, Neoplastic ; Gene Regulatory Networks ; Glycolysis ; Neoplasms/metabolism ; Neoplasms/physiopathology ; Oxidative Phosphorylation ; Pyruvate Dehydrogenase Complex/biosynthesis
Chemical Substances	DNA-Binding Proteins ; Drosophila Proteins ; Pyruvate Dehydrogenase Complex ; Sima protein, Drosophila
Language	English
Publishing date	2016-09-01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.18126
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