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Article: Exitrons: offering new roles to retained introns-the novel regulators of protein diversity and utility.

Shamnas V, Muhammed / Singh, Akanksha / Kumar, Anuj / Mishra, Gyan Prakash / Sinha, Subodh Kumar

2024 Volume 16, Issue 2, Page(s) plae014

Abstract: Exitrons are exonic introns. This subclass of intron retention alternative splicing does not contain a Pre-Terminating stop Codon. Therefore, when retained, they are always a part of a protein. Intron retention is a frequent phenomenon predominantly ... ...

Abstract	Exitrons are exonic introns. This subclass of intron retention alternative splicing does not contain a Pre-Terminating stop Codon. Therefore, when retained, they are always a part of a protein. Intron retention is a frequent phenomenon predominantly found in plants, which results in either the degradation of the transcripts or can serve as a stable intermediate to be processed upon induction by specific signals or the cell status. Interestingly, exitrons have coding ability and may confer additional attributes to the proteins that retain them. Therefore, exitron-containing and exitron-spliced isoforms will be a driving force for creating protein diversity in the proteome of an organism. This review establishes a basic understanding of exitron, discussing its genesis, key features, identification methods and functions. We also try to depict its other potential roles. The present review also aims to provide a fundamental background to those who found such exitronic sequences in their gene(s) and to speculate the future course of studies.
Language	English
Publishing date	2024-03-20
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2555823-7
ISSN	2041-2851
ISSN	2041-2851
DOI	10.1093/aobpla/plae014
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Article: Molecular Characterization of GS2 and Fd-GOGAT Homeologues and Their Biased Response to Nitrogen Stress in Bread Wheat (Triticum aestivum L.)

Gayatri / Venkatesh, Karnam / Sinha, Subodh Kumar / Roy, Pranita / Mandal, Pranab Kumar

Journal of plant growth regulation. 2022 Aug., v. 41, no. 6

2022

Abstract: Nitrogen (N) is one of the major limiting elements affecting the growth and productivity of cereal crops including bread wheat. Identification and detailed characterization of the candidate genes involved in the assimilation of N from inorganic to ... ...

Abstract	Nitrogen (N) is one of the major limiting elements affecting the growth and productivity of cereal crops including bread wheat. Identification and detailed characterization of the candidate genes involved in the assimilation of N from inorganic to organic form is very important for better N utilization. Glutamine synthetase 2 (GS2) and Ferredoxin-dependent-glutamate synthase (Fd-GOGAT) are the two critical enzymes involved in GS/GOGAT cycle, which are necessary for primary N-assimilation. In the present study, GS2 and Fd-GOGAT genes were cloned from a popular bread wheat variety HD-2967 and their individual homeologues (A, B and D) were characterized under different levels of N-stress. Homeologous cDNAs of GS2 and Fd-GOGAT showed > 93% and > 98% sequence similarity, respectively, in the coding region but were distinguishable at UTRs. The expression patterns and contribution of each homeologue of both the genes in HD-2967 under different N treatments showed downregulation in the shoot and upregulation in the root tissues. However, the contribution of the individual homeologue varied with the tissue, time point and level of N-stress. Further, when the expression pattern and contribution of each homeologue were studied in a diverse set of wheat genotypes, a generalised contribution pattern of each homeologue of wheat was observed. While the transcript ratio of A and D homeologues of both the genes demonstrated to be compensating each other, Fd-GOGAT-B showed the least contribution in all the conditions and at all stages of growth. Substantial variation in cis-regulatory elements was observed among all three homeologues of both the genes. Overall, characterization and spatio-temporal contribution of GS2 and Fd-GOGAT homeologues would provide applied value for further detailed studies as well as their exploration in primary N-assimilation process in wheat.
Keywords	Triticum aestivum ; glutamate-ammonia ligase ; nitrogen ; plant growth ; sequence homology ; wheat
Language	English
Dates of publication	2022-08
Size	p. 2555-2569.
Publishing place	Springer US
Document type	Article
ZDB-ID	586787-3
ISSN	1435-8107 ; 0721-7595
ISSN (online)	1435-8107
ISSN	0721-7595
DOI	10.1007/s00344-021-10433-z
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Article ; Online: Physio-molecular traits of contrasting bread wheat genotypes associated with

Kumar, Amresh / Kumar, Sarvendra / Venkatesh, Karnam / Singh, Nagendra Kumar / Mandal, Pranab Kumar / Sinha, Subodh Kumar

Planta

2022 Volume 255, Issue 5, Page(s) 104

Abstract: Main conclusion: The high affinity nitrate transport system is a potential target for improving nitrogen use efficiency of bread wheat growing either under optimal or limiting nitrate concentration. Nitrate uptake is one of the most important traits to ... ...

Abstract	Main conclusion: The high affinity nitrate transport system is a potential target for improving nitrogen use efficiency of bread wheat growing either under optimal or limiting nitrate concentration. Nitrate uptake is one of the most important traits to take into account to improve nitrogen use efficiency in wheat (Triticum aestivum L.). In this study, we aimed to gain an insight into the regulation of NO
MeSH term(s)	Bread ; Genotype ; Nitrate Transporters ; Nitrates/metabolism ; Nitrogen/metabolism ; Plant Roots/genetics ; Plant Roots/metabolism ; Soil ; Triticum/genetics ; Triticum/metabolism
Chemical Substances	Nitrate Transporters ; Nitrates ; Soil ; Nitrogen (N762921K75)
Language	English
Publishing date	2022-04-13
Publishing country	Germany
Document type	Journal Article
ZDB-ID	208909-9
ISSN	1432-2048 ; 0032-0935 ; 1866-2749
ISSN (online)	1432-2048
ISSN	0032-0935 ; 1866-2749
DOI	10.1007/s00425-022-03890-7
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Book: Development of informal economy

Pandey, Bharti / Sinha, Subodh Kumar

problems and challenges

2016

Author's details	editors: Dr. Bharti Pandey, Dr. Subodh Kumar Sinha
Keywords	Informelle Wirtschaft ; Indien
Language	English
Size	xv, 220 Seiten, Illustrationen
Publisher	Regal Publications
Publishing place	New Delhi
Document type	Book
Note	Enthält 18 Beiträge
ISBN	9788184845754 ; 8184845758
Database	ECONomics Information System

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Article ; Online: Genome-wide association studies for earliness, MYMIV resistance, and other associated traits in mungbean (

Kohli, Manju / Bansal, Hina / Mishra, Gyan Prakash / Dikshit, Harsh Kumar / Reddappa, Shashidhar B / Roy, Anirban / Sinha, Subodh Kumar / Shivaprasad, K M / Kumari, Nikki / Kumar, Atul / Kumar, Ranjeet R / Nair, Ramakrishnan Madhavan / Aski, Muraleedhar

PeerJ

2024 Volume 12, Page(s) e16653

Abstract: Yellow mosaic disease (YMD) remains a major constraint in mungbean ( ...

Abstract	Yellow mosaic disease (YMD) remains a major constraint in mungbean (
MeSH term(s)	Vigna/genetics ; Genome-Wide Association Study ; Genotype ; Bayes Theorem ; Plant Breeding
Language	English
Publishing date	2024-01-26
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.16653
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Article ; Online: Identification of quantitative trait loci (QTLs) regulating leaf SPAD value and trichome density in mungbean (

Kumari, Nikki / Mishra, Gyan Prakash / Dikshit, Harsh Kumar / Gupta, Soma / Roy, Anirban / Sinha, Subodh Kumar / Mishra, Dwijesh C / Das, Shouvik / Kumar, Ranjeet R / Nair, Ramakrishnan Madhavan / Aski, Muraleedhar

PeerJ

2024 Volume 12, Page(s) e16722

Abstract: Quantitative trait loci (QTL) mapping is used for the precise localization of genomic regions regulating various traits in plants. Two major QTLs regulating Soil Plant Analysis Development (SPAD) value ( ...

Abstract	Quantitative trait loci (QTL) mapping is used for the precise localization of genomic regions regulating various traits in plants. Two major QTLs regulating Soil Plant Analysis Development (SPAD) value (
MeSH term(s)	Quantitative Trait Loci/genetics ; Vigna/genetics ; Chromosome Mapping ; Genotype ; Soil ; Trichomes/genetics ; Plant Leaves/genetics
Chemical Substances	Soil
Language	English
Publishing date	2024-02-21
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.16722
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Article: Differential response of rice genotypes to nitrogen availability is associated with the altered nitrogen metabolism and ionomic balance

Kumari, Priyanka / Devi, Loitongbam Lorinda / Kumar, Amresh / Pandey, Ashutosh / Sinha, Subodh Kumar / Singh, Amar Pal

Environmental and experimental botany. 2022 Mar. 13,

2022

Abstract: Nitrogen (N) uptake and its assimilation are crucial steps for plant growth and productivity. Plant's N balance largely depends on nitrate (NO₃⁻) and ammonium (NH₄⁺) forms present in the rhizosphere. Due to the fluctuating and heterogeneous availability ... ...

Abstract	Nitrogen (N) uptake and its assimilation are crucial steps for plant growth and productivity. Plant's N balance largely depends on nitrate (NO₃⁻) and ammonium (NH₄⁺) forms present in the rhizosphere. Due to the fluctuating and heterogeneous availability of these N forms in the soils, plants encounter low to N deficiency. In contrast to low nitrogen, high N in the form of ammonium (NH₄⁺) severely hampers plant development and causes NH₄⁺ toxicity. In this study, we assessed eleven rice genotypes under sufficient (SN) and low N (LN) conditions. From the analysis, we identified a rice genotype, PB1, which is hypersensitive to SN and showed reduced root and shoot growth. In contrast to the SN condition, PB1 showed improved growth performance under the LN condition. Our data show that compromised growth of PB1 under SN condition is associated with increased activity of N responsive genes such as OsAMT1.1, OsAMT2.3, OsAMT3.1 and OsAMT3.2, OsNRT1.1A and OsNRT1.1B. Strikingly, LN treatment improved the root and shoot biomass with a concomitant increase in levels of NO₃⁻ and NH₄⁺ transporter genes along with an increase in shoot: root NO₃⁻ ratio. Additionally, we show that increased levels of N in PB1 under SN condition are associated with the enhanced activity of the GS-GOGAT pathway. Further, our ionomic analysis highlighted the role of N-defined Fe accumulation which is partially associated with the N toxicity. Taken together, our study led to identifying a rice genotype (Oryza sativa L.) which is associated with enhanced N levels and assimilation and could be used for raising N use efficient rice varieties using breeding approaches.
Keywords	Oryza sativa ; ammonium ; biomass ; genotype ; growth performance ; ionomics ; nitrates ; nitrogen ; nitrogen metabolism ; plant development ; plant growth ; rhizosphere ; rice ; toxicity
Language	English
Dates of publication	2022-0313
Publishing place	Elsevier B.V.
Document type	Article
Note	Pre-press version
ZDB-ID	195968-2
ISSN	0098-8472
ISSN	0098-8472
DOI	10.1016/j.envexpbot.2022.104847
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Article: Comparative Analysis of GS2 and Fd-GOGAT Genes in Cultivated Wheat and Their Progenitors Under N Stress

Gayatri / Jayaraman, Karikalan / Sinha, Subodh Kumar / Roy, Pranita / Mandal, Pranab Kumar

Plant molecular biology reporter. 2021 Sept., v. 39, no. 3

2021

Abstract: Polyploidization plays an important role in the genesis of cultivated wheat (hexaploid and tetraploid) from its diploid progenitors. Thus, evolution during polyploidization resulted in present-day hexaploid bread wheat. GS2 and Fd-GOGAT enzymes are core ... ...

Abstract	Polyploidization plays an important role in the genesis of cultivated wheat (hexaploid and tetraploid) from its diploid progenitors. Thus, evolution during polyploidization resulted in present-day hexaploid bread wheat. GS2 and Fd-GOGAT enzymes are core components involved in the assimilation of primary nitrogen (N) in plants. In the present study, we aimed to analyze these two important genes at their molecular level to find the extent of variation that occurred during evolution from the ancient diploid progenitors to the modern-day hexaploid bread wheat. Furthermore, we studied their gene expression pattern and assayed both the enzymes under N stress. We also investigated the degree of resilience among these species in terms of certain important morphophysiological and biochemical parameters under N stress. Comparison of the genomic sequences along with their promoter region revealed that both GS2 and Fd-GOGAT genes were located on chromosome 2 and were comprised of 13 and 33 exons respectively. A limited sequence divergence at cDNA and amino acid levels was observed among the genome species, but the divergence was significantly higher in the promoter region. Both these genes were present in three copies in the bread wheat, two copies in the durum wheat, and a single copy in their diploid progenitors. Differential gene expression among the five genome species under N stress suggested major differences in gene regulation due to the difference in cis-elements. Enzyme activity did not correlate with the gene expression level probably due to post-transcriptional and post-translational modification of the enzymes. There was neither correlation between the GS2 and Fd-GOGAT activity in any species. All growth parameters, except root length, decreased or remain unchanged with different degrees of plasticity in the genotypes under N stress and correlated with reduced Fd-GOGAT activity, which supply the primary assimilate glutamate. GS2/Fd-GOGAT enzyme activity along with total N accumulation, protein, chlorophyll, and carotenoid content in shoot were found responsive to the N stress through combined PCA analysis. Our study confirmed the conserved nature of GS2 and Fd-GOGAT enzymes at the CDS and protein level; however, their expression and subsequent effects were different in cultivated wheat and their progenitors.
Keywords	carotenoids ; chlorophyll ; chromosomes ; diploidy ; durum wheat ; enzyme activity ; evolution ; exons ; gene expression ; gene expression regulation ; genomics ; glutamic acid ; hexaploidy ; molecular biology ; nitrogen ; plasticity ; post-translational modification ; promoter regions ; protein content ; tetraploidy ; total nitrogen
Language	English
Dates of publication	2021-09
Size	p. 520-545.
Publishing place	Springer US
Document type	Article
ZDB-ID	2018592-3
ISSN	1572-9818 ; 0735-9640
ISSN (online)	1572-9818
ISSN	0735-9640
DOI	10.1007/s11105-020-01267-2
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Article: External Nitrogen and Carbon Source-Mediated Response on Modulation of Root System Architecture and Nitrate Uptake in Wheat Seedlings

Sinha, Subodh Kumar / Mandal, Pranab Kumar / Tyagi, Akanksha

Journal of plant growth regulation. 2019 Mar., v. 38, no. 1

2019

Abstract: Nitrogen uptake efficiency is an important component trait that could be targeted for improving nitrogen use efficiency of crop plants. To understand the responses of different nitrate transport systems and the influence of root system architecture on ... ...

Abstract	Nitrogen uptake efficiency is an important component trait that could be targeted for improving nitrogen use efficiency of crop plants. To understand the responses of different nitrate transport systems and the influence of root system architecture on nitrate uptake under limited nitrate conditions in wheat (Triticum aestivum L.) at the seedling stage, we studied nitrate uptake, root system architecture, and expression of different nitrate transporter genes in induced and non-induced wheat seedlings. Further, effects of inclusion of sucrose and two amino acids (glutamine and asparagine) in induction medium on these parameters were also studied. We observed that the induced wheat root system took up more nitrate as compared to non-induced root system in a dose-dependent manner. Gene expression of both high- and low-affinity nitrate transporter gene showed differential expression in the induced root tissues, as compared to non-induced tissues, depending on the concentration of nitrate present in induction medium. External nutrient media containing sucrose, glutamine, and asparagine reduce nitrate concentration in both root and shoot tissues and also influence the gene expression of these transporters. Our observations indicate that upon induction with milder external nitrate concentrations, the root architecture is modulated by changing overall lateral root size and 1st order lateral root numbers along with activation of nitrate transporters which acquire and transport nitrate in roots and shoots, respectively, depending on the carbon and nitrogen source available to seedlings.
Keywords	asparagine ; carbon ; crops ; dose response ; gene expression regulation ; genes ; glutamine ; nitrates ; nitrogen ; nutrient use efficiency ; root systems ; roots ; seedlings ; shoots ; sucrose ; tissues ; transporters ; Triticum aestivum ; wheat
Language	English
Dates of publication	2019-03
Size	p. 283-297.
Publishing place	Springer US
Document type	Article
ZDB-ID	586787-3
ISSN	1435-8107 ; 0721-7595
ISSN (online)	1435-8107
ISSN	0721-7595
DOI	10.1007/s00344-018-9840-9
Database	NAL-Catalogue (AGRICOLA)

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Article: RNAi induced gene silencing in crop improvement.

Sinha, Subodh Kumar

Physiology and molecular biology of plants : an international journal of functional plant biology

2010 Volume 16, Issue 4, Page(s) 321–332

Abstract: The RNA silencing is one of the innovative and efficient molecular biology tools to harness the down-regulation of expression of gene(s) specifically. To accomplish such selective modification of gene expression of a particular trait, homology dependent ... ...

Abstract	The RNA silencing is one of the innovative and efficient molecular biology tools to harness the down-regulation of expression of gene(s) specifically. To accomplish such selective modification of gene expression of a particular trait, homology dependent gene silencing uses a stunning variety of gene silencing viz. co-suppression, post-transcriptional gene silencing, virus-induced gene silencing etc. This family of diverse molecular phenomena has a common exciting feature of gene silencing which is collectively called RNA interference abbreviated to as RNAi. This molecular phenomenon has become a focal point of plant biology and medical research throughout the world. As a result, this technology has turned out to be a powerful tool in understanding the function of individual gene and has ultimately led to the tremendous use in crop improvement. This review article illustrates the application of RNAi in a broad area of crop improvement where this technology has been successfully used. It also provides historical perspective of RNAi discovery and its contemporary phenomena, mechanism of RNAi pathway.
Language	English
Publishing date	2010-12-07
Publishing country	India
Document type	Journal Article
ZDB-ID	2487126-6
ISSN	0974-0430 ; 0971-5894
ISSN (online)	0974-0430
ISSN	0971-5894
DOI	10.1007/s12298-010-0036-4
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