Santosh Kumar Upadhyay

Santosh Kumar Upadhyay
Verified
Santosh verified their affiliation via an institutional email.
Verified
Santosh verified their affiliation via an institutional email.
Panjab University · Department of Botany

Ph.D.
Molecular characterization of defence-related proteins

About

178
Publications
164,840
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
4,853
Citations
Introduction
We are working on characterization of various defense and development related proteins in bread wheat. Featured in top 2% world scientists in the list of Stanford University and Elsevier, and top 2% in country by the AD Scientific Index in the Agriculture and Plant Science category since last several years.
Additional affiliations
September 2014 - present
Panjab University
Position
  • Professor (Assistant)
March 2013 - September 2014
National Agri-Food Biotechnology Institute
Position
  • DST-INSPIRE Faculty
January 2006 - February 2013
National Botanical Research Institute
Position
  • National Botanical Research Institute
Education
February 2007 - February 2013
National Botanical Research Institute - India; UPTU, Lucknow
Field of study
  • Biotechnology

Publications

Publications (178)
Article
Full-text available
Long non-coding RNAs (lncRNAs) are a family of regulatory RNAs that play essential role in the various developmental processes and stress responses. Recent advances in sequencing technology and computational methods enabled identification and characterization of lncRNAs in certain plant species, but they are less known in Triticum aestivum (bread w...
Article
Full-text available
The leucine rich repeat receptor like kinases (LRRK) constitute the largest subfamily of receptor like kinases (RLK), which play critical roles in plant development and stress responses. Herein, we identified 531 TaLRRK genes in Triticum aestivum (bread wheat), which were distributed throughout the A, B, and D sub-genomes and chromosomes. These wer...
Article
The sodium/calcium exchanger-like (NCL) transporters are members of Ca2+/Cation antiporters (CaCAs) family, localized at the tonoplast, and primarily involved in Ca2+ homeostasis and stress response. They transport Ca2+ to the cytosol and sequester cytosolic Na+ into the vacuole. Therefore, the atncl mutant of Arabidopsis thaliana is prone to salin...
Article
Full-text available
Vascular plant one-zinc-finger (VOZ) transcription factors play indispensable roles in orchestrating growth and stress responses in plants. These plant-specific regulators are integral to important biological processes such as flowering. Despite being a vital regulator of numerous biological processes, significant information about their role is no...
Article
Abiotic stress, including osmotic and salinity stress, significantly affects plant growth and productivity. Copper chaperone for superoxide dismutase (CCS) is essential for copper homeostasis and oxidative stress management. In this study, we investigated the role of the TaCCS1‐B gene of bread wheat in enhancing stress tolerance in yeast and transg...
Article
Full-text available
The ARABIDOPSIS FUS3 COMPLEMENT (AFC) proteins belong to the LAMMER protein kinase family and have dual-specificity for serine-arginine-rich (SR) protein phosphorylation. These proteins are involved in regulating the mRNA splicing. The bread wheat genome consists of a total of nine TaAFC genes that are evenly distributed on chromosome groups 3 and...
Article
Legumes represent a significant source of protein, roughage, minerals and carbohydrates in global diets. They are cultivated primarily for human consumption, forage and as a green manure. However, the growth and productivity of legumes are often hindered by a range of biological and environmental factors. The most prevalent diseases afflicting legu...
Book
Full-text available
Holistic approach to the herbal aspects of nutraceuticals and their implementation in the health and agriculture sectors Herbal Nutraceuticals: Products and Processes delivers comprehensive coverage of the herbal aspects of nutraceuticals along with their many applications in the health and agriculture sectors. The book begins with an overview of...
Article
Full-text available
Pre-mRNA processing factor 4 kinases (PRP4Ks) are crucial for eukaryotic organisms. These proteins are dual specificity kinases that phosphorylate the proteins involved in spliceosomal assembly during pre-mRNA processing. A repertoire of six TaPRP4K genes with conserved architecture is found in the allohexaploid genome of Triticum aestivum. These g...
Book
Abiotic and biotic stresses significantly affect the productivity of various agricultural and horticultural crops. Abiotic stress largely includes heat, cold, drought, heavy metals, UV, various chemicals, etc., while biotic stress is generally caused by bacterial, viral and fungal pathogens, and insect pests. To cope up with these stress conditions...
Article
Full-text available
The BTB (broad-complex, tramtrack, and bric-a-brac) domain, also known as the POZ (POX virus and zinc finger) domain, is a conserved protein-protein interaction domain present in various organisms. In this study, we conducted a genome-wide search to identify and characterize BTB genes in Solanum tuberosum. A total of 57 StBTBs were identified and a...
Article
Full-text available
Iron is an essential plant nutrient, and a continuous supply of it is required as it is a key factor in various metabolic processes, including photosynthesis, chlorophyll synthesis, and respiration. Various transcription factors are known to regulate iron homeostasis in plants, and the bHLH transcription factor family is one of them. The StbHLH47 i...
Article
Full-text available
Two-pore K⁺ (TPK) channels are voltage-independent and involved in stress response in plants. Herein, we identified 12 TaTPK genes located on nine chromosomes in the Triticum aestivum genome. The majority of TaTPK genes comprised two exons. Each TaTPK channel comprised four transmembrane (TM) helices, N- and C-terminal ion-channel domains, two EF-h...
Article
Full-text available
Ca2+ and H2O2 interact with each other to regulate plant systemic responses. However, their precise mechanism is not fully understood. A recent study revealed that the Ca2+ regulates the glycolate oxidase-catalase (GC) switch-mediated photorespiratory H2O2 during wounding. Glutamate-receptor-like (GLR) Ca2+ channels (GLR 3.3 and GLR3.6) are respons...
Article
Serine/arginine protein kinases (SRPKs) are members of the serine-threonine kinase family that phosphorylate the Serine/arginine-rich (SR) proteins involved in alternate splicing. They are reported in various eukaryotes including mammals, and in a few plants, but seldom explored in important crop species. Herein, we identified a total of nine TaSRP...
Article
Full-text available
Respiratory burst oxidase homolog (RBOH) proteins in plants generate reactive oxygen species (ROS) in the apoplast to regulate developmental processes and stress responses. Herein, a total of 40 TaRBOH genes are identified in the genome of Triticum aestivum by a genome-wide search using the latest database. Phylogenetic analysis separated the RBOH...
Article
Drought stress has been extensively studied for its effect on the downstream signaling cascade and stress-responsive gene expression, but understanding the process has remained elusive. Recently, Zhao et al. identified DROOPY LEAF1 (DPY1) as an osmosensor and revealed a novel mechanism of DPY1-STRESS ACTIVATED PROTEIN KINASE6 (SAPK6)-mediated droug...
Article
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 peroxis...
Article
Full-text available
Ascorbate oxidases (AAOs) are apoplastic enzymes of the multi-copper oxidase family and have a significant role in redox homeostasis. Herein, we identified 14 TaAAO genes consisting of two to five exons in the bread wheat genome. These genes are present on the A, B, and D subgenomes of chromosomes 5 and 7. Analyses of gene regulatory networks revea...
Article
Full-text available
Hypoxia triggers reactive oxygen species (ROS)-induced elevation in cytoplasmic calcium (Ca²⁺) in the plant cells. Calcium-dependent protein kinase 12 (CPK12) acts as a sensor to recognize the Ca²⁺ signature and is activated by autophosphorylation. Then, the CPK12 moves into the nucleus with the help of phosphatidic acid (PA) and phosphorylates ERF...
Article
Glutathione peroxidases (GPXs) are known to play an essential role in guarding cells against oxidative stress by catalyzing the reduction of hydrogen peroxide and organic hydroperoxides. The current study aims functional characterization of the TaGPX1-D gene of bread wheat (Triticum aestivum) for salinity and osmotic stress tolerance. To achieve th...
Article
Full-text available
Phtheirospermum japonicum shows induced expression of PjPME and PjPMEI genes during haustoria development in rice and Arabidopsis with increased PME activity, which leads to the modulated cell wall during parasitism. Moreover, how PME and PMEI proteins interact and balance during haustoria development remains elusive.
Article
Full-text available
A deficiency in inorganic phosphate (Pi) induces the expression of miRNA399 and the accumulation of its target Pi transporters (PHT1s) mRNA, which is contrary to the goal of miRNA-mediated gene regulation. Recently, a novel mechanism of RNA/RNA-duplex formation between the transcripts of a Pi deficiency-induced long non-coding RNA (PILNCR2) and PHT...
Book
Full-text available
Microorganisms constitute the invisible majority of all living creatures on Earth. They are found virtually everywhere on the planet, including in environments too extreme for any larger organisms to exist. They form a hugely significant resource whose potential value for human society cannot be overlooked. The creation of microorganism- based bior...
Chapter
Microbial resources have good potential to produce a broad range of high-value compounds. In recent years, microbial-originated nitrilase enzymes have been used to convert nitriles into beneficial chemical compounds and clean up nitrile-contaminated soil and water. Due to their ease of handling, manipulation, and culture under controlled conditions...
Article
Methanol is noxious to insect pests, but most plants do not make enough of it to shield themselves from encroaching insects. Methanol emission is known to increase in the instance of herbivory. In the current study, we showed that Aspergillus niger pectin methylesterase over-expression increases methanol emission and confers resistance to polyphago...
Article
Cadmium (Cd) is a heavy metal that occurs naturally in the environment and is toxic to both animals and plants. The impact of Cd toxicity is shown to be reduced by the exogenous application of calcium (Ca) in crop plants. The sodium/calcium exchanger-like (NCL) protein is involved in Ca enrichment in the cytoplasm by transporting it from the vacuol...
Article
Full-text available
Piezo channels belong to an important class of cell membrane-bound, Ca 2+-permeable, mechanosensitive channels consisting of a pore and multiple transmembrane helices. In plants, the functional aspects of Piezo channels have been less studied than other mechanosensitive channels. However, a few studies that have been carried out indicate the involv...
Book
Full-text available
In Plants as Bioreactors for Industrial Molecules, a team of distinguished researchers delivers an insightful and global perspective on the use of plants as bioreactors. In the book, you’ll find coverage of the basic, applied, biosynthetic, and translational approaches to the exploitation of plant technology in the production of high-value biomolec...
Article
Full-text available
Volatile organic compounds emanating from plant surfaces serve as a sustainable natural solution to combat biotic stresses in plants. Leaf methanol is the simplest and second major volatile organic compound after isoprene emitted through the leaf surface. Methanol has been neglected as a by-product of other secondary metabolites for a long time, bu...
Chapter
Full-text available
The use of plants as a bioreactor is an emerging area of research in plant biotechnology. The advancement in the field of biotechnology provides an opportunity to utilize plants for the production of sugars, proteins, lipids, and secondary metabolites. In plants, we can overproduce not only the nonplant products like proteins, carbohydrates, and li...
Article
Full-text available
Native/endogenous promoters have several fundamental limitations in terms of their size,Cis-elements distribution/patterning, and mode of induction, which is ultimately reflected in theirinsufficient transcriptional activity. Several customized synthetic promoters were designed andtested in plants during the past decade to circumvent such constrain...
Article
Full-text available
Stomatal immunity is regulated by pathogen-associated molecular patterns (PAMPs)- andabscisic acid (ABA)-triggered signalling in different ways. Cytoplasmic Ca2+ signature in the guardcells plays a vital function in stomatal immunity, but the mechanism of Ca2+ import is unknown.It has been very recently established that the hyperosmolality-gated ca...
Chapter
Thaumatin-like proteins (TLPs) are a large and composite family, which falls under the pathogenesis-related 5 (PR5) superfamily. These are multifunctional proteins, induces in response to various abiotic and biotic stresses. TLPs are also involved in plant growth and development. TLP family also has thaumatin-like protein kinases (TLPKs), which are...
Chapter
Plants use a variety of systems to respond and adapt to the constantly changing environmental variables to survive and grow. The understanding of plant reaction to diverse stresses will aid in the improvement of plant tolerance to abiotic stress through genetic engineering, hence promoting the advent of new agriculture. In plants, receptor-like kin...
Chapter
Plants are exposed to a variety of environmental stresses during their lifespan and to counter these stresses they have evolved multiple strategies. Perception of various stresses is carried out through specialized proteins which recognize the stress signals through various mechanisms. Receptor-like protein kinases (RLKs) are the largest family of...
Chapter
Receptor-like kinases (RLKs) and receptor-like proteins have a vital role in plant disease resistance where they act as pathogen recognition receptors. Structurally, RLKs consist of three domains- an extracellular domain (ECD), a transmembrane domain, and an intracellular domain. RLKs bind and identify diverse ligands depending on variability in th...
Chapter
Somatic embryogenesis receptor-like kinase (SERK) belongs to the leucine-rich repeat receptor-like kinases (LRR-RLK) family of RLKs. The principal function of SERK has been studied in the regulation of somatic embryogenesis, where they are predominantly responsible for transforming somatic cells into embryogenic cells. They also play a role in the...
Chapter
Plants have evolved a series of specialized membrane receptor kinases which sense the diversity of extracellular stimuli and activate the downstream signaling pathways. These receptor kinases coordinate various growth and developmental processes and constitute the first line of the defense system in plants, as well. The leucine-rich repeat receptor...
Chapter
Full-text available
Transcription factors (TFs) regulate almost all the critical processes in plant biology. As major regulatory proteins, TFs perform their functions through the interaction with the cis-elements of their target gene promoters or through protein–protein interactions. The regulation of the expression levels of the key genes of major biosynthetic and de...
Article
Full-text available
Erigeron annuus L. is a flowering herb of North America, Europe, Asia and Russia. This plant is used as folk medicine in China for the cure of indigestion, enteritis, epidemic hepatitis, haematuria and diabetes. Phytochemical studies showed the presence of 170 bioactive compounds like coumarins, flavonoids, terpenoids, polyacetylenic compounds; γ-p...
Article
Full-text available
The rhizomes of ginger have been in use in many forms of traditional and alternative medicines. Besides being employed as condiment and flavoring agent, it is used in the treatment of nausea, osteoarthritis, muscle pain, menstrual pain, chronic indigestion, Alzheimer’s disease, and cancer. Ginger rhizome contains volatile oils, phenolic compounds a...
Article
Full-text available
Plant secondary metabolites are well-recognized medicinally important compounds. Gossypol is an important plant secondary metabolite with several medicinal properties. Carbon nanotubes (CNTs) are allotropes of carbon with diverse applicability in chemical, physical, and biological sciences due to their high surface area. The current study demonstra...
Article
Full-text available
The hyperosmolality-gated calcium-permeable channels (OSCA) are pore-forming transmembrane proteins that function as osmosensors during various plant developmental processes and stress responses. In our analysis, through in silico approaches, a total of 42 OSCA genes are identified in the Triticum aestivum genome. A phylogenetic analysis reveals th...
Article
Full-text available
Insect pests impose a serious threat to agricultural productivity. Initially, for pest management, several breeding approaches were applied which have now been gradually replaced by genome editing (GE) strategies as they are more efficient and less laborious. CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeat/CRISPR-associated sy...
Chapter
The proteins containing the lysin motif (LysM) are involved in the host-pathogen interaction, known as a kind of carbohydrate-binding protein. Plant LysM proteins largely act as pattern recognition receptors (PRRs) that recognize chitin to stimulate the immunity of the plant. Contrastingly, fungal LysM prevents chitin sensing or signaling to decrea...
Chapter
Lectin receptor-like kinase (LecRLK) is considered the second largest class of very influential cell surface receptor proteins referred to as receptor-like kinases (RLKs). The LecRLK consists of a lectin and serine/threonine kinase domain at its amino-terminus and carboxyl-terminus, respectively. In addition to these domains, LecRLK is endowed with...
Article
In plants, Ca²⁺ is an integral element in several stresses related signallings. During environmental stresses, the cytosolic Ca²⁺ concentration tends to rise rapidly, which is further co-ordinate with EF-hand domain-containing proteins. In our study, a total of 586 EF-hand domain-containing proteins were identified in Triticum aestivum as calmoduli...
Article
Full-text available
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 TaPERK genes in the genome of T. aestivum, exploring their evolutionary and syntenic relationship and analyzing their gene and protein structures, various cis-regulatory elem...
Article
Full-text available
Boron (B) is an essential micronutrient of plants. Plants grapple with a narrow range of B between its toxicity and deficiency. B homeostasis mechanism is required to rescue plants from such a quagmire. B transporters are specialized proteins involved in the homeostasis of B. In the present study, a total of 29 BOR genes were identified in five maj...
Article
Full-text available
Key message A total of seven glutathione reductase (GR) genes were identified in Triticum aestivum, which were used for comparative structural characterization, phylogenetic analysis and expression profiling with the GR genes of other cereal plants. The modulated gene expression and enzyme activity revealed the role of GRs in abiotic stress respons...
Article
Full-text available
Key Message APX and APX-R gene families were identified and characterized in two important oilseed species of Brassica. Gene expression under abiotic stress conditions, recombinant protein expression, and analysis further divulged their drought, heat, and salt-responsive behavior. Abstract Ascorbate peroxidases (APX) are heme-dependent enzymes tha...
Chapter
For centuries, microbes have been used in different industries such as food, brewing, pharmaceutics, and agriculture. In agriculture, microbes are mainly used as an inoculant for providing nutrition and protection to plants. Several strains of bacteria can influence the growth, production, and protection of plants. Bacterial strains, which are used...
Article
Full-text available
The three amino acid loop extension (TALE) genes of the homeobox superfamily are responsible for numerous biological functions in plants. Herein, we identified a total of 72 TaTALE genes in the allohexaploid genome of bread wheat (Triticum aestivum L.) and performed a comprehensive investigation for gene and protein structural properties, phylogeny...
Article
Full-text available
Glutathione peroxidases (GPXs) are key reactive oxygen species (ROS) scavenging enzyme that catalyses the reduction of H2O2 to prevent the cellular machinery from H2O2 damage. Plant GPXs are similar to animal GPXs, but their active region contains cysteine instead of selenocysteine. Plant GPXs are monomeric proteins that are linked to thioredoxin (...
Chapter
Iron is an essential micronutrient required by plants for their growth and development. The iron in the soil is abundant but is not bioavailable to the plants. To combat this issue, plants have evolved different strategies for efficient iron uptake and enabling plants to adapt to low iron conditions. The strategies comprised iron acquisition from t...
Chapter
Full-text available
Cation transporters are involved in the movement of various ions in the plants. These are known to play pivotal roles in many physiological processes like cell signaling, cellular integrity, osmoregulation, nutrition uptake, stress tolerance, ion homeostasis, and photosynthesis. The plants require a well-developed system to maintain ion balance, as...
Chapter
Soil salinity is known to be a major problem for agricultural practices, worldwide. Furthermore, the situation is deteriorating with the increase in vagaries in the climate and increasing soil salinization. Scientists across the globe are in a race to find a suitable answer to the threat of soil salinity. One such effort includes the exploration of...
Chapter
Boron (B) is one of the essential micronutrients required by plants. B functions mainly in the cell wall biosynthesis along with other physiological processes including organic translocation, nitrogen metabolism, etc. Both deficiency and overdose of B pose a problem for major food crops worldwide, and thus its homeostasis is required in plants. It...
Book
Full-text available
https://www.elsevier.com/books/cation-transporters-in-plants/upadhyay/978-0-323-85790-1
Chapter
Calcium ion (Ca²⁺) is the most common signaling messenger which implicates in plant responses to a wide range of environmental and physiological stimuli. The stimulus-specific signals are responsible for raising the Ca²⁺ concentration in the cytosol, which further comes in contact with various Ca²⁺-binding proteins or Ca²⁺ sensors to initiate a sig...
Article
Full-text available
Long non-coding RNAs (lncRNAs) are transcripts without protein-coding potential that contain more than 200 nucleotides that play important roles in plant survival in response to different stresses. They interact with molecules such as DNA, RNA, and protein, and play roles in the regulation of chromatin remodeling, RNA metabolism, and protein modifi...
Article
Full-text available
Thaumatin-like proteins (TLPs) are related to pathogenesis-related-5 (PR-5) family and involved in stress response. Herein, a total of 93 TLP genes were identified in the genome of Triticum aestivum. Further, we identified 26, 27, 39, and 37 TLP genes in the Brachypodium distachyon, Oryza sativa, Sorghum bicolor, and Zea mays genomes for comparativ...
Book
Full-text available
In Bioprospecting of Microorganism-Based Industrial Molecules, distinguished researchers and authors Sudhir P. Singh and Santosh Kumar Upadhyay deliver global perspectives of bioprospecting of biodiversity. The book covers diverse aspects of bioprospecting of microorganisms demonstrating biomass value of nutraceutical, pharmaceutical, biomedical, a...
Article
Full-text available
CRISPR/Cas mediated genome editing is a revolutionary approach for manipulating the plant genome. However, the success of this technology is highly dependent on selection of a specific vector and the other components. A plant-specific CRISPR/Cas vector usually consists of a Cas gene, target-specific gRNA, leader sequence, selectable marker gene, pr...
Preprint
Full-text available
Thaumatin-like proteins (TLPs) are related to the pathogenesis-related-5 (PR-5) family and involved in stress response. Herein, a total of 93 TLP genes were identified in the genome of Triticum aestivum. Further, we identified 26, 27, 39 and 37 TLP genes in the Brachypodium distachyon, Oryza sativa, Sorghum bicolor and Zea mays genomes for comparat...
Chapter
Microorganisms dominate the terrestrial environment at the Earth. They can thrive the moderate to harsh niches in the biosphere. It is desirable to explore the microbial resource for bioprospection, i.e. search for the seeds of useful biomolecules, biochemical, and genetic information. Bioprospection for microbes covers application to commodity che...
Chapter
Carbohydrate biopolymers are distinguished macromolecules of functional characteristics. Some of the well‐known examples of carbohydrate polymers include cellulose, dextran, levan, chitin, chitosan, xanthan gum, etc. Their production through microbial and enzymatic route are more preferred due to the high yield and purity of the final product. The...
Article
Lysin-motif (LysM) and LysM receptor-like kinase (LYK) proteins play a major role in defence-response. The allohexaploid genome of Triticum aestivum consisted of 42 TaLysM and 20 TaLYK genes. The occurrence of tandem duplication with retention of function suggested functional conservation of TaLYK proteins, but neo-functionalization and pseudo-func...
Article
Full-text available
Background Long non-coding RNAs (lncRNAs) are regulatory transcripts of length > 200 nt. Owing to the rapidly progressing RNA-sequencing technologies, lncRNAs are emerging as considerable nodes in the plant antifungal defense networks. Therefore, we investigated their role in Vitis vinifera (grapevine) in response to obligate biotrophic fungal phyt...
Chapter
Nature is an invaluable source of numerous beneficial products present in diverse biological entities. Exploration of these natural products for commercial use through bioprospecting has been in practice since the dawn of humanity itself. Recent advances have led to a well‐organized and a systematic search for valuable products from these natural r...
Book
Full-text available
This book presents the global perspectives of bioprospecting of plant biodiversity. The main focus is on natural compounds of plants origins, and the biological systems of health attributes. The research performed on enzymes, amino acids, vitamins, minerals, shortchain carbohydrate, phytochemicals, and other bioactive molecules are presented, with...