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Article ; Online: Genome-wide identification of 2-oxoglutarate and Fe (II)-dependent dioxygenase family genes and their expression profiling under drought and salt stress in potato.

Chauhan, Hanny / Aiana / Singh, Kashmir

2023 Volume 11, Page(s) e16449

Abstract: The 2-Oxoglutatrate-dependent dioxygenases (2OGDs) comprise the 2-Oxoglutatrate and Fe(II)-dependent dioxygenases (2ODD) enzyme families that facilitate the biosynthesis of various compounds like gibberellin, ethylene, ...

Abstract	The 2-Oxoglutatrate-dependent dioxygenases (2OGDs) comprise the 2-Oxoglutatrate and Fe(II)-dependent dioxygenases (2ODD) enzyme families that facilitate the biosynthesis of various compounds like gibberellin, ethylene,
MeSH term(s)	Solanum tuberosum/genetics ; Ketoglutaric Acids ; Gene Expression Profiling/methods ; Plant Proteins/genetics ; Droughts ; Gibberellins ; Dioxygenases/genetics ; Salt Stress
Chemical Substances	Ketoglutaric Acids ; Plant Proteins ; Gibberellins ; Dioxygenases (EC 1.13.11.-)
Language	English
Publishing date	2023-11-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	2703241-3
ISSN	2167-8359 ; 2167-8359
ISSN (online)	2167-8359
ISSN	2167-8359
DOI	10.7717/peerj.16449
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Article: Investigation of two-pore K

Kaur, Amandeep / Madhu / Sharma, Alok / Singh, Kashmir / Upadhyay, Santosh Kumar

Heliyon

2024 Volume 10, Issue 6, Page(s) e27814

Abstract: ... Two-pore ... ...

Abstract	Two-pore K
Language	English
Publishing date	2024-03-13
Publishing country	England
Document type	Journal Article
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2024.e27814
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Article ; Online: Genome-wide analysis of Catalase gene family reveal insights into abiotic stress response mechanism in Brassica juncea and B. rapa.

Verma, Deepika / Kaushal, Nishant / Balhara, Rinku / Singh, Kashmir

Plant science : an international journal of experimental plant biology

2023 Volume 330, Page(s) 111620

Abstract: Environmental stresses affect the yield and productivity of Brassica crops. Catalases are important antioxidant enzymes involved in reducing excess hydrogen peroxide produced by environmental stresses. In the present study, nine and seven CAT family ... ...

Abstract	Environmental stresses affect the yield and productivity of Brassica crops. Catalases are important antioxidant enzymes involved in reducing excess hydrogen peroxide produced by environmental stresses. In the present study, nine and seven CAT family members in two oilseed Brassica species (B. juncea and B. rapa) were identified with complete characterization based on gene and protein structure. Phylogenetic classification categorized CAT proteins into three classes and differentiated the monocot and dicot-specific CAT proteins. Further, the gene and protein characterizations revealed a high degree of conservation across the CAT family members. Differences were observed in the CAT-HEME binding affinity in CAT1, CAT2, and CAT3 isozymes, which could suggest their differential enzyme activities in different conditions. Furthermore, protein-protein interaction with other antioxidant proteins suggested their coordinated role in ROS scavenging mechanisms. Notably, the differential gene expression of BjuCATs and BraCATs and CAT enzyme activities suggested their crucial roles in major abiotic stresses faced by Brassica species. Promoter analysis in BjuCATs and BraCATs suggested the presence of abiotic-stress responsive cis-regulatory elements. Gene regulatory network analysis suggested miRNA and TF mediated stress response in BjuCATs and BraCATs. CAT family screening and characterization in Brassica sp. has established a basic ground for further functional validation in abiotic and heavy-metal stresses which can help in developing stress tolerant crops.
MeSH term(s)	Antioxidants/metabolism ; Catalase/genetics ; Catalase/metabolism ; Gene Expression Regulation, Plant ; Mustard Plant/genetics ; Mustard Plant/metabolism ; Phylogeny ; Plant Proteins/metabolism ; Stress, Physiological/genetics
Chemical Substances	Antioxidants ; Catalase (EC 1.11.1.6) ; Plant Proteins
Language	English
Publishing date	2023-02-02
Publishing country	Ireland
Document type	Journal Article
ZDB-ID	742010-9
ISSN	1873-2259 ; 0168-9452
ISSN (online)	1873-2259
ISSN	0168-9452
DOI	10.1016/j.plantsci.2023.111620
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Article: Understanding role of Glutathione Reductase gene family in drought and heat stresses in Brassica juncea and B. rapa

Verma, Deepika / Singh, Kashmir

Environmental and experimental botany. 2021 Oct., v. 190

2021

Abstract: In the era of global environmental changes, high curiosity in identifying and characterizing new antioxidant enzymes in plants has been witnessed. Previous studies reported the pivotal role played by Glutathione reductase (GR) in maintaining the reduced ... ...

Abstract	In the era of global environmental changes, high curiosity in identifying and characterizing new antioxidant enzymes in plants has been witnessed. Previous studies reported the pivotal role played by Glutathione reductase (GR) in maintaining the reduced glutathione pool during stress. However, the knowledge of GR family members and their evolutionary and functional characteristics in oilseed species is limited. In this study, 6 and 4 GRs were identified from Brassica juncea and B. rapa genomes, respectively. Phylogenetic analysis of protein sequences showed diversification of this gene family into cytosolic and chloroplastic GR. Duplication of a single ancestral gene might have led to the diversification of cytosolic and chloroplastic GR before the divergence of monocot and dicot. The cytosolic GRs consisted of complex gene architecture compared to the chloroplastic ones, which can increase their expression level. Chloroplastic GRs showed the presence of N-terminal signal peptide. A high degree of conservation in gene and protein structures in the same sub-cellular compartment was observed. Notably, all cytosolic GRs were found to be differentially expressed under heat and drought stresses. Predicted cis-regulatory elements and miRNA targets were found to be associated with abiotic, biotic and developmental responses. Our study explained the structural and functional information of the GR family and the roles of different members in maintaining redox homeostasis under abiotic stresses. The study has laid the basic ground work for detailed functional characterization in future studies and developing improved oilseed varieties better adaptive to environmental stress conditions.
Keywords	Brassica juncea ; Liliopsida ; botany ; drought ; genes ; glutathione ; glutathione-disulfide reductase ; heat ; homeostasis ; microRNA ; oilseeds ; phylogeny ; signal peptide
Language	English
Dates of publication	2021-10
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	195968-2
ISSN	0098-8472
ISSN	0098-8472
DOI	10.1016/j.envexpbot.2021.104595
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Article ; Online: Modulation in gene expression and enzyme activity suggested the roles of monodehydroascorbate reductase in development and stress response in bread wheat.

Madhu / Sharma, Alok / Kaur, Amandeep / Singh, Kashmir / Upadhyay, Santosh Kumar

Plant science : an international journal of experimental plant biology

2023 Volume 338, Page(s) 111902

Abstract: Monodehydroascorbate reductase (MDHAR) is a crucial enzymatic antioxidant of the ascorbate-glutathione pathway involved in reactive oxygen species scavenging. Herein, we identified 15 TaMDHAR genes in bread wheat. Phylogenetic analysis revealed their ... ...

Abstract	Monodehydroascorbate reductase (MDHAR) is a crucial enzymatic antioxidant of the ascorbate-glutathione pathway involved in reactive oxygen species scavenging. Herein, we identified 15 TaMDHAR genes in bread wheat. Phylogenetic analysis revealed their clustering into three groups, which are also related to the subcellular localization in the peroxisome matrix, peroxisome membrane, and chloroplast. Each TaMDHAR protein consisted of two conserved domains; Pyr_redox and Pyr_redox_2 of the pyridine nucleotide disulfide oxidoreductase family. The occurrence of diverse groups of cis-regulatory elements in the promoter region and their interaction with numerous transcription factors suggest assorted functions of TaMDHARs in growth and development and in light, phytohormones, and stress responses. Expression analysis in various tissues further revealed their importance in vegetative and reproductive development. In addition, the differential gene expression and enhanced enzyme activity during drought, heat, and salt treatments exposed their role in abiotic stress response. Interaction of MDHARs with various antioxidant enzymes and biochemicals related to the ascorbate-glutathione cycle exposed their synchronized functioning. Interaction with auxin indicated the probability of cross-talk between antioxidants and auxin signaling. The miR168a, miR169, miR172 and others interaction with various TaMDHARs further directed their association with developmental processes and stress responses. The current study provides extensive information about the importance of TaMDHARs, moreover, the precise role of each gene needs to be established in future studies.
MeSH term(s)	Antioxidants/metabolism ; Triticum/metabolism ; Bread ; Phylogeny ; Oxidoreductases/genetics ; Glutathione/metabolism ; Gene Expression ; Indoleacetic Acids/metabolism ; Gene Expression Regulation, Plant
Chemical Substances	Antioxidants ; semidehydroascorbic acid (6730-29-6) ; Oxidoreductases (EC 1.-) ; Glutathione (GAN16C9B8O) ; Indoleacetic Acids
Language	English
Publishing date	2023-10-23
Publishing country	Ireland
Document type	Journal Article
ZDB-ID	742010-9
ISSN	1873-2259 ; 0168-9452
ISSN (online)	1873-2259
ISSN	0168-9452
DOI	10.1016/j.plantsci.2023.111902
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Article ; Online: MSMEG_5850, a stress-induced TetR protein, involved in global transcription regulation in

Singh, Parul / Kumar, Arbind / Chhabra, Ravindresh / Singh, Kashmir / Kaur, Jagdeep

Future microbiology

2023 Volume 18, Page(s) 563–580

Abstract: Aim: ...

Abstract	Aim:
MeSH term(s)	Mycobacterium smegmatis/metabolism ; Bacterial Proteins/metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Bacterial
Chemical Substances	Bacterial Proteins
Language	English
Publishing date	2023-06-07
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2254620-0
ISSN	1746-0921 ; 1746-0913
ISSN (online)	1746-0921
ISSN	1746-0913
DOI	10.2217/fmb-2022-0238
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Article ; Online: Heterologous expression of Chlorophytum borivilianum Squalene epoxidase in tobacco modulates stigmasterol production and alters vegetative and reproductive growth.

Kaushal, Nishant / Verma, Deepika / Alok, Anshu / Pandey, Ashutosh / Singh, Kashmir

Plant cell reports

2023 Volume 42, Issue 5, Page(s) 909–919

Abstract: Keymessage: CbSE overexpression increased stigmasterol levels and altered plant morphology. The genes upstream and downstream of CbSE were found to be upregulated, which confirms its regulatory role in the saponin biosynthetic pathway. Chlorophytum ... ...

Abstract	Keymessage: CbSE overexpression increased stigmasterol levels and altered plant morphology. The genes upstream and downstream of CbSE were found to be upregulated, which confirms its regulatory role in the saponin biosynthetic pathway. Chlorophytum borivilianum is a high-value medicinal plant with many promising preclinical applications that include saponins as a major active ingredient. Squalene epoxidase (SE) is one of the major rate-limiting enzymes of the saponin biosynthetic pathway. Here, we functionally characterized C. borivilianum SE (CbSE) by over-expressing heterologously in Nicotiana tabacum. The heterologous expression of CbSE resulted in stunted pant growth with altered leaf and flower morphology. Next, RT-qPCR analysis of transgenic plants overexpressing CbSE revealed increased expression levels of Cycloartenol synthase (CAS), Beta amyrin synthase (βAS), and cytochrome P450 monooxygenase 51 (CYP51) (Cytochrome P450), which encode key enzymes for triterpenoid and phytosterol biosynthesis in C. borivilianum. Further, Methyl Jasmonate (MeJa) treatment upregulated Squalene synthase (SQS), SE, and Oxidosqualene cyclases (OSCs) to a significant level. GC-MS analysis of the leaf and hairy roots of the transformants showed an increased stigmasterol content (0.5-1.0 fold) compared to wild type (WT) plants. These results indicate that CbSE is a rate-limiting gene, which encodes an efficient enzyme responsible for phytosterol and triterpenoid production in C. borivilianum.
MeSH term(s)	Nicotiana/genetics ; Nicotiana/metabolism ; Stigmasterol ; Squalene Monooxygenase/genetics ; Squalene Monooxygenase/metabolism ; Saponins ; Phytosterols ; Triterpenes/metabolism ; Cytochrome P-450 Enzyme System/genetics ; Cytochrome P-450 Enzyme System/metabolism ; Gene Expression Regulation, Plant
Chemical Substances	Stigmasterol (99WUK5D0Y8) ; Squalene Monooxygenase (EC 1.14.14.17) ; Saponins ; Phytosterols ; Triterpenes ; Cytochrome P-450 Enzyme System (9035-51-2)
Language	English
Publishing date	2023-03-09
Publishing country	Germany
Document type	Journal Article
ZDB-ID	8397-5
ISSN	1432-203X ; 0721-085X ; 0721-7714
ISSN (online)	1432-203X
ISSN	0721-085X ; 0721-7714
DOI	10.1007/s00299-023-03000-1
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Article: Insight into the Roles of Proline-Rich Extensin-like Receptor Protein Kinases of Bread Wheat (

Shumayla / Mendu, Venugopal / Singh, Kashmir / Upadhyay, Santosh Kumar

Life (Basel, Switzerland)

2022 Volume 12, Issue 7

Abstract: Proline-rich extensin-like receptor protein kinases (PERKs) are known for their roles in the developmental processes and stress responses of many plants. We have identified ... ...

Abstract	Proline-rich extensin-like receptor protein kinases (PERKs) are known for their roles in the developmental processes and stress responses of many plants. We have identified 30
Language	English
Publishing date	2022-06-23
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662250-6
ISSN	2075-1729
ISSN	2075-1729
DOI	10.3390/life12070941
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Article ; Online: Identification of Pseudo-R genes in Vitis vinifera and characterization of their role as immunomodulators in host-pathogen interactions.

Garewal, Naina / Pathania, Shivalika / Bhatia, Garima / Singh, Kashmir

Journal of advanced research

2022

Abstract: Introduction: Duplication events are fundamental to co-evolution in host-pathogen interactions. Pseudogenes (Ψs) are dysfunctional paralogs of functional genes and resistance genes (Rs) in plants are the key to disarming pathogenic invasions. Thus, ... ...

Abstract	Introduction: Duplication events are fundamental to co-evolution in host-pathogen interactions. Pseudogenes (Ψs) are dysfunctional paralogs of functional genes and resistance genes (Rs) in plants are the key to disarming pathogenic invasions. Thus, deciphering the roles of pseudo-R genes in plant defense is momentous. Objectives: This study aimed to functionally characterize diverse roles of the resistance Ψs as novel gene footprints and as significant gene regulators in the grapevine genome. Methods: PlantPseudo pipeline and HMM-profiling identified whole-genome duplication-derived (WGD) Ψs associated with resistance genes (Ψ-Rs). Further, novel antifungal and antimicrobial peptides were characterized for fungal associations using protein-protein docking with Erysiphe necator proteins. miRNA and tasiRNA target sites and transcription factor (TF) binding sites were predicted in Ψ-Rs. Finally, differential co-expression patterns in Ψ-Rs-lncRNAs-coding genes were identified using the UPGMA method. Results: 2,746 Ψ-Rs were identified from 31,032 WGD Ψs in the genome of grapevine. 69-antimicrobial and 81-antifungal novel peptides were generated from Ψ-Rs. The putative genic potential was predicted for five novel antifungal peptides which were further characterized by docking against E. necator proteins. 395 out of 527 resistance loci-specific Ψ-Rs were acting as parental gene mimics. Further, to explore the diverse roles of Ψ-Rs in plant-defense, we identified 37,026 TF-binding sites, 208 miRNA, and 99 tasiRNA targeting sites on these Ψ-Rs. 194 Ψ-Rs were exhibiting tissue-specific expression patterns. The co-expression network analysis between Ψs-lncRNA-genes revealed six out of 79 pathogen-responsive Ψ-Rs as significant during pathogen invasion. Conclusions: Our study provides pathogen responsive Ψ-Rs integral for pathogen invasion, which will offer a useful resource for future experimental validations. In addition, our findings on novel peptide generations from Ψ-Rs offer valuable insights which can serve as a useful resource for predicting novel genes with the futuristic potential of being investigated for their bioactivities in the plant system.
Language	English
Publishing date	2022-08-03
Publishing country	Egypt
Document type	Journal Article
ZDB-ID	2541849-X
ISSN	2090-1224 ; 2090-1224
ISSN (online)	2090-1224
ISSN	2090-1224
DOI	10.1016/j.jare.2022.07.014
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Article: Microplastics in soil: Impacts and microbial diversity and degradation

KAUR, Paramdeep / SINGH, Kashmir / SINGH, Baljinder

Soil Science Society of China Pedosphere. 2022 Feb., v. 32, no. 1

2022

Abstract: Microplastics (MPs) are plastic particles less than 5 mm in size that have become a major environmental pollutant due to their ubiquitous and persistent nature. Microplastic contamination of the aquatic environment has received the most attention so far, ...

Abstract	Microplastics (MPs) are plastic particles less than 5 mm in size that have become a major environmental pollutant due to their ubiquitous and persistent nature. Microplastic contamination of the aquatic environment has received the most attention so far, whereas the current understanding of MP prevalence and its impacts in the terrestrial environment is largely limited. The MP contamination of soil can cause bioaccumulation and toxicity in terrestrial animals and plants, which can consequently affect human health. This review is aimed towards combining the available information on the occurrence, sources, and effects of MPs on the different aspects of the terrestrial environment and to highlight the limitations in our knowledge regarding the nature and impacts of MPs in soil. The review also highlights microbial degradation of MPs as an advancing research area, with numerous microorganisms being identified as capable of efficiently degrading this persistent contaminant.
Keywords	aquatic environment ; bioaccumulation ; biodegradation ; human health ; microplastics ; pollutants ; soil ; soil pollution ; toxicity
Language	English
Dates of publication	2022-02
Size	p. 49-60.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	1090441-4
ISSN	1002-0160
ISSN	1002-0160
DOI	10.1016/S1002-0160(21)60060-7
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