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Article ; Online: From swamp to field: how genes from mangroves and its associates can enhance crop salinity tolerance.

Govindan, Ganesan / Harini, Prakash / Alphonse, Vinoth / Parani, Madasamy

2024 Volume 51, Issue 1, Page(s) 598

Abstract: Salinity stress is a critical challenge in crop production and requires innovative strategies to enhance the salt tolerance of plants. Insights from mangrove species, which are renowned for their adaptability to high-salinity environments, provides ... ...

Abstract	Salinity stress is a critical challenge in crop production and requires innovative strategies to enhance the salt tolerance of plants. Insights from mangrove species, which are renowned for their adaptability to high-salinity environments, provides valuable genetic targets and resources for improving crops. A significant hurdle in salinity stress is the excessive uptake of sodium ions (Na
MeSH term(s)	Salt Tolerance/genetics ; Avicennia/genetics ; Avicennia/metabolism ; Gene Expression Regulation, Plant/genetics ; Plants, Genetically Modified/genetics ; Crops, Agricultural/genetics ; Crops, Agricultural/metabolism ; Plant Roots/genetics ; Plant Roots/metabolism ; Salinity ; Plant Proteins/genetics ; Plant Proteins/metabolism ; Sodium/metabolism ; Arabidopsis/genetics ; Arabidopsis/metabolism ; Salt-Tolerant Plants/genetics ; Salt-Tolerant Plants/metabolism
Chemical Substances	Plant Proteins ; Sodium (9NEZ333N27)
Language	English
Publishing date	2024-04-29
Publishing country	Netherlands
Document type	Journal Article ; Review
ZDB-ID	186544-4
ISSN	1573-4978 ; 0301-4851
ISSN (online)	1573-4978
ISSN	0301-4851
DOI	10.1007/s11033-024-09539-w
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Article ; Online: RNA N

Sharma, Bishwas / Govindan, Ganesan / Li, Yongfang / Sunkar, Ramanjulu / Gregory, Brian D

Non-coding RNA

2024 Volume 10, Issue 1

Abstract: Recently, post-transcriptional regulation of mRNA mediated by ... ...

Abstract	Recently, post-transcriptional regulation of mRNA mediated by N
Language	English
Publishing date	2024-01-19
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2813993-8
ISSN	2311-553X ; 2311-553X
ISSN (online)	2311-553X
ISSN	2311-553X
DOI	10.3390/ncrna10010008
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Article ; Online: The versatility of green synthesized zinc oxide nanoparticles in sustainable agriculture: A review on metal-microbe interaction that rewards agriculture

Gauba, Ankita / Hari, Sharath Kumar / Ramamoorthy, Vellaisamy / Vellasamy, Shanmugaiah / Govindan, Ganesan / Valan Arasu, M.

Physiological and Molecular Plant Pathology. 2023 Apr. 13, p.102023-

2023 , Page(s) 102023–

Abstract: The integration of nanotechnology in the realm of agriculture, specifically through the utilization of nanofertilizers and nanopesticides, has been a topic of increasing interest in recent years. The application of fertilizers in the form of ... ...

Abstract	The integration of nanotechnology in the realm of agriculture, specifically through the utilization of nanofertilizers and nanopesticides, has been a topic of increasing interest in recent years. The application of fertilizers in the form of nanoparticles is one of the most promising solutions for the significant enhancement of agricultural production worldwide. This review highlights the versatility of green synthesized zinc oxide nanoparticles (ZnONPs) in sustainable agriculture and their interactions with plant-microbe systems. ZnONPs have been classified as a biosafe substance for biological species. Previous research has revealed the efficacy of ZnONPs in the induction of seed germination and plant growth, as well as its potential for biological control through its antimicrobial activities. However, it is important to note that the effects of ZnONPs on plant growth and metabolism can vary depending on the developmental phase of the plant. Furthermore, the uptake, transport and aggregation of ZnONPs by plants are dependent on the characteristics of the NPs and the morphology of the host plant. However, the use of ZnONPs in agriculture also poses some potential adverse effects, including toxicity to non-target organisms, accumulation in the food chain, and environmental pollution. These effects are influenced by various factors such as particle size, concentration, and exposure time. Thus, the review discusses the current knowledge on the toxicity and environmental impact of ZnONPs in agriculture and their potential mitigation strategies. Furthermore, this review aims to comprehensively highlight the potential applications of ZnONPs as a nanofertilizer in crop production, as well as to explore and understand the possible mechanisms of its antimicrobial activity. Additionally, the biological production of ZnONPs, its absorption, transport mechanisms, phytoremediation of heavy metals in plants and toxicity studies are also investigated.
Keywords	absorption ; antimicrobial properties ; biological control ; biological production ; crop production ; environmental impact ; exposure duration ; food chain ; host plants ; metabolism ; nanoparticles ; particle size ; phytoremediation ; plant growth ; plant pathology ; pollution ; seed germination ; sustainable agriculture ; toxicity ; zinc oxide ; Zinc-oxide nanoparticles ; Nanotechnology ; Nanofertilizers ; Metal microbe interaction ; Antimicrobial mechanism ; Green synthesis of nanoparticles ; Plant pathogen
Language	English
Dates of publication	2023-0413
Publishing place	Elsevier Ltd
Document type	Article ; Online
Note	Pre-press version
ZDB-ID	742470-x
ISSN	0885-5765
ISSN	0885-5765
DOI	10.1016/j.pmpp.2023.102023
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Article ; Online: High Daytime Temperature Responsive MicroRNA Profiles in Developing Grains of Rice Varieties with Contrasting Chalkiness.

Payne, David / Li, Yongfang / Govindan, Ganesan / Kumar, Anuj / Thomas, Julie / Addo-Quaye, Charles A / Pereira, Andy / Sunkar, Ramanjulu

International journal of molecular sciences

2023 Volume 24, Issue 14

Abstract: High temperature impairs starch biosynthesis in developing rice grains and thereby increases chalkiness, affecting the grain quality. Genome encoded microRNAs (miRNAs) fine-tune target transcript abundances in a spatio-temporal specific manner, and this ... ...

Abstract	High temperature impairs starch biosynthesis in developing rice grains and thereby increases chalkiness, affecting the grain quality. Genome encoded microRNAs (miRNAs) fine-tune target transcript abundances in a spatio-temporal specific manner, and this mode of gene regulation is critical for a myriad of developmental processes as well as stress responses. However, the role of miRNAs in maintaining rice grain quality/chalkiness during high daytime temperature (HDT) stress is relatively unknown. To uncover the role of miRNAs in this process, we used five contrasting rice genotypes (low chalky lines Cyp, Ben, and KB and high chalky lines LaGrue and NB) and compared the miRNA profiles in the R6 stage caryopsis samples from plants subjected to prolonged HDT (from the onset of fertilization through R6 stage of caryopsis development). Our small RNA analysis has identified approximately 744 miRNAs that can be grouped into 291 families. Of these, 186 miRNAs belonging to 103 families are differentially regulated under HDT. Only two miRNAs, Osa-miR444f and Osa-miR1866-5p, were upregulated in all genotypes, implying that the regulations greatly varied between the genotypes. Furthermore, not even a single miRNA was commonly up/down regulated specifically in the three tolerant genotypes. However, three miRNAs (Osa-miR1866-3p, Osa-miR5150-3p and canH-miR9774a,b-3p) were commonly upregulated and onemiRNA (Osa-miR393b-5p) was commonly downregulated specifically in the sensitive genotypes (LaGrue and NB). These observations suggest that few similarities exist within the low chalky or high chalky genotypes, possibly due to high genetic variation. Among the five genotypes used, Cypress and LaGrue are genetically closely related, but exhibit contrasting chalkiness under HDT, and thus, a comparison between them is most relevant. This comparison revealed a general tendency for Cypress to display miRNA regulations that could decrease chalkiness under HDT compared with LaGrue. This study suggests that miRNAs could play an important role in maintaining grain quality in HDT-stressed rice.
MeSH term(s)	Humans ; Temperature ; Oryza/genetics ; Hot Temperature ; Edible Grain/genetics ; MicroRNAs/genetics
Chemical Substances	MicroRNAs
Language	English
Publishing date	2023-07-19
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms241411631
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Article: Splice variants of superoxide dismutases in rice and their expression profiles under abiotic stresses

Saini, Ajay / Rohila, Jai Singh / Govindan, Ganesan / Li, Yong / Sunkar, Ramanjulu

International journal of molecular sciences. 2021 Apr. 13, v. 22, no. 8

2021

Abstract: The superoxide dismutases (SODs) play vital roles in controlling cellular reactive oxygen species (ROS) that are generated both under optimal as well as stress conditions in plants. Rice genome harbors seven SOD genes (CSD1, CSD2, CSD3, CSD4, FSD1, FSD2 ... ...

Abstract	The superoxide dismutases (SODs) play vital roles in controlling cellular reactive oxygen species (ROS) that are generated both under optimal as well as stress conditions in plants. Rice genome harbors seven SOD genes (CSD1, CSD2, CSD3, CSD4, FSD1, FSD2 and MSD) that encode seven constitutive transcripts. Of these, five SOD genes (CSD2, CSD3, CSD4, FSD1 and MSD) utilizes alternative splicing (AS) strategy and generate seven additional splice varinats (SVs), i.e., three for CSD3, and one each for CSD2, CSD4, FSD1 and MSD. The exon-intron organization of these SVs revealed variations in number and length of the exons and/or UTRs. We determined the expression patterns of SVs along with their consititutive forms of SODs in rice seedlings exposed to salt, osmotic, cold and oxidative stresses as well as copper deprivation. The results revealed that all of the seven SVs were transcriptionally active both in roots and shoots. When compared to their corresponding constitutive transcripts, the profiles of five SVs were almost similar while opposite profiles for two specific SVs (CSD3-SV4 and MSD-SV2) were consistently observed under stress conditions. Taken together, the present study provide a comprehensive analysis of the SVs of SODs and their responses to stress conditions in shoots and roots of rice seedlings.
Keywords	cold ; exons ; reactive oxygen species ; rice ; superoxide dismutase ; transcription (genetics)
Language	English
Dates of publication	2021-0413
Document type	Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1661-6596
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms22083997
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Article ; Online: Programmable Site-Specific Nucleases for Targeted Genome Engineering in Higher Eukaryotes.

Govindan, Ganesan / Ramalingam, Sivaprakash

Journal of cellular physiology

2016 Volume 231, Issue 11, Page(s) 2380–2392

Abstract: Recent advances in the targeted genome engineering enable molecular biologists to generate sequence specific modifications with greater efficiency and higher specificity in complex eukaryotic genomes. Programmable site-specific DNA cleavage reagents and ... ...

Abstract	Recent advances in the targeted genome engineering enable molecular biologists to generate sequence specific modifications with greater efficiency and higher specificity in complex eukaryotic genomes. Programmable site-specific DNA cleavage reagents and cellular DNA repair mechanisms have made this possible. These reagents have become powerful tools for delivering a site-specific genomic double-strand break (DSB) at the desired chromosomal locus, which produces sequence alterations through error-prone non-homologous end joining (NHEJ) resulting in gene inactivations/knockouts. Alternatively, the DSB can be repaired through homology-directed repair (HDR) using a donor DNA template, which leads to the introduction of desired sequence modifications at the predetermined site. Here, we summarize the role of three classes of nucleases; zinc finger nucleases (ZFNs), transcription activator like effector nucleases (TALENs), and clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR associated protein 9 (Cas9) system in achieving targeted genome modifications. Further, we discuss the progress towards the applications of programmable site-specific nucleases (SSNs) in treating human diseases and other biological applications in economically important higher eukaryotic organisms such as plants and livestock. J. Cell. Physiol. 231: 2380-2392, 2016. © 2016 Wiley Periodicals, Inc.
MeSH term(s)	Animals ; Base Sequence ; Endonucleases/metabolism ; Eukaryota/genetics ; Gene Targeting ; Genetic Engineering/methods ; Genome ; Humans
Chemical Substances	Endonucleases (EC 3.1.-)
Language	English
Publishing date	2016-11
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	3116-1
ISSN	1097-4652 ; 0021-9541
ISSN (online)	1097-4652
ISSN	0021-9541
DOI	10.1002/jcp.25367
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Article ; Online: Splice Variants of Superoxide Dismutases in Rice and Their Expression Profiles under Abiotic Stresses.

Saini, Ajay / Rohila, Jai S / Govindan, Ganesan / Li, Yong-Fang / Sunkar, Ramanjulu

International journal of molecular sciences

2021 Volume 22, Issue 8

Abstract	The superoxide dismutases (SODs) play vital roles in controlling cellular reactive oxygen species (ROS) that are generated both under optimal as well as stress conditions in plants. The rice genome harbors seven SOD genes (
MeSH term(s)	Alternative Splicing/genetics ; Base Sequence ; Cold Temperature ; Copper/toxicity ; Exons/genetics ; Gene Expression Profiling ; Gene Expression Regulation, Enzymologic ; Gene Expression Regulation, Plant ; Introns/genetics ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Oryza/genetics ; Osmotic Pressure ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Stress, Physiological/genetics ; Superoxide Dismutase/genetics
Chemical Substances	MicroRNAs ; RNA, Messenger ; Copper (789U1901C5) ; Superoxide Dismutase (EC 1.15.1.1)
Language	English
Publishing date	2021-04-13
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms22083997
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Article: Ectopic expression of AmNAC1 from Avicennia marina (Forsk.) Vierh. confers multiple abiotic stress tolerance in yeast and tobacco

Murugesan, Ashok Kumar / Somasundaram, Suji / Mohan, Harikrishnan / Parida, Ajay K / Alphonse, Vinoth / Govindan, Ganesan

Plant cell, tissue, and organ culture. 2020 July, v. 142, no. 1

2020

Abstract: Abiotic factors like salinity, drought and cold affect agricultural productivity substantially worldwide. NAC (NAM, ATAF1/2 and CUC2) family transcription factors have been shown to play important roles in biotic and abiotic stress responses in many ... ...

Abstract	Abiotic factors like salinity, drought and cold affect agricultural productivity substantially worldwide. NAC (NAM, ATAF1/2 and CUC2) family transcription factors have been shown to play important roles in biotic and abiotic stress responses in many plant species. Our previous studies have shown that AmNAC1, a gene from mangrove Avicennia marina, is differentially regulated in response to salt, drought and cold stresses and salicylic acid treatment. To gain more insights into the function of AmNAC1 in abiotic stress, AmNAC1 was heterologously expressed in yeast and tobacco. Heterologous expression of AmNAC1 in yeast (Saccharomyces cerevisiae) resulted in improved tolerance to salinity (NaCl and LiCl), alkalinity (NaHCO₃) stresses. In addition, transgenic yeast exhibited enhanced tolerance compared to control when subjected to high (50 °C) and freezing (− 20 °C) temperature. Similarly, overexpression of AmNAC1 in tobacco using the constitutive promoter (2xCaMV) demonstrated increased tolerance to abiotic stresses such as salinity, drought and cold. Specifically, compared to wild type (WT) and vector control (VC), AmNAC1 transgenic lines exhibited higher germination, increased root length and better survival rates at the whole plant level. Collectively, these results indicate a role for AmNAC1 in multiple abiotic stress tolerance.
Keywords	Avicennia marina ; Saccharomyces cerevisiae ; acid treatment ; agricultural productivity ; alkalinity ; biotic stress ; cold stress ; drought ; environmental factors ; freezing ; genes ; genetically modified organisms ; germination ; heterologous gene expression ; lithium chloride ; promoter regions ; salicylic acid ; salinity ; salt tolerance ; sodium bicarbonate ; sodium chloride ; stress response ; stress tolerance ; survival rate ; temperature ; tobacco ; transcription factors ; vector control ; yeasts
Language	English
Dates of publication	2020-07
Size	p. 51-68.
Publishing place	Springer Netherlands
Document type	Article
ZDB-ID	406394-6
ISSN	1573-5044 ; 0167-6857
ISSN (online)	1573-5044
ISSN	0167-6857
DOI	10.1007/s11240-020-01830-5
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Article ; Online: mRNA N

Govindan, Ganesan / Sharma, Bishwas / Li, Yong-Fang / Armstrong, Christopher D / Merum, Pandrangaiah / Rohila, Jai S / Gregory, Brian D / Sunkar, Ramanjulu

The Plant journal : for cell and molecular biology

2022 Volume 111, Issue 4, Page(s) 1052–1068

Abstract: Plants respond to low temperatures by altering the mRNA abundance of thousands of genes contributing to numerous physiological and metabolic processes that allow them to adapt. At the post-transcriptional level, these cold stress-responsive transcripts ... ...

Abstract	Plants respond to low temperatures by altering the mRNA abundance of thousands of genes contributing to numerous physiological and metabolic processes that allow them to adapt. At the post-transcriptional level, these cold stress-responsive transcripts undergo alternative splicing, microRNA-mediated regulation and alternative polyadenylation, amongst others. Recently, m
MeSH term(s)	Arabidopsis/metabolism ; Arabidopsis Proteins/genetics ; Arabidopsis Proteins/metabolism ; Cold Temperature ; Freezing ; Gene Expression Regulation, Plant/genetics ; Pemetrexed/metabolism ; RNA, Messenger/genetics
Chemical Substances	Arabidopsis Proteins ; RNA, Messenger ; Pemetrexed (04Q9AIZ7NO)
Language	English
Publishing date	2022-07-13
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1088037-9
ISSN	1365-313X ; 0960-7412
ISSN (online)	1365-313X
ISSN	0960-7412
DOI	10.1111/tpj.15872
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Article: mRNA N6‐methyladenosine is critical for cold tolerance in Arabidopsis

Govindan, Ganesan / Sharma, Bishwas / Li, Yong‐Fang / Armstrong, Christopher D. / Merum, Pandrangaiah / Rohila, Jai S. / Gregory, Brian D. / Sunkar, Ramanjulu

plant journal. 2022 Aug., v. 111, no. 4

2022

Abstract: Plants respond to low temperatures by altering the mRNA abundance of thousands of genes contributing to numerous physiological and metabolic processes that allow them to adapt. At the post‐transcriptional level, these cold stress‐responsive transcripts ... ...

Abstract	Plants respond to low temperatures by altering the mRNA abundance of thousands of genes contributing to numerous physiological and metabolic processes that allow them to adapt. At the post‐transcriptional level, these cold stress‐responsive transcripts undergo alternative splicing, microRNA‐mediated regulation and alternative polyadenylation, amongst others. Recently, m⁶A, m⁵C and other mRNA modifications that can affect the regulation and stability of RNA were discovered, thus revealing another layer of post‐transcriptional regulation that plays an important role in modulating gene expression. The importance of m⁶A in plant growth and development has been appreciated, although its significance under stress conditions is still underexplored. To assess the role of m⁶A modifications during cold stress responses, methylated RNA immunoprecipitation sequencing was performed in Arabidopsis seedlings esposed to low temperature stress (4°C) for 24 h. This transcriptome‐wide m⁶A analysis revealed large‐scale shifts in this modification in response to low temperature stress. Because m⁶A is known to affect transcript stability/degradation and translation, we investigated these possibilities. Interestingly, we found that cold‐enriched m⁶A‐containing transcripts demonstrated the largest increases in transcript abundance coupled with increased ribosome occupancy under cold stress. The significance of the m⁶A epitranscriptome on plant cold tolerance was further assessed using the mta mutant in which the major m⁶A methyltransferase gene was mutated. Compared to the wild‐type, along with the differences in CBFs and COR gene expression levels, the mta mutant exhibited hypersensitivity to cold treatment as determined by primary root growth, biomass, and reactive oxygen species accumulation. Furthermore, and most importantly, both non‐acclimated and cold‐acclimated mta mutant demonstrated hypersensitivity to freezing tolerance. Taken together, these findings suggest a critical role for the epitranscriptome in cold tolerance of Arabidopsis.
Keywords	Arabidopsis ; biomass ; cold ; cold stress ; cold tolerance ; cold treatment ; gene expression ; genes ; hypersensitivity ; methylation ; methyltransferases ; mutants ; precipitin tests ; reactive oxygen species ; ribosomes ; root growth
Language	English
Dates of publication	2022-08
Size	p. 1052-1068.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	1088037-9
ISSN	1365-313X ; 0960-7412
ISSN (online)	1365-313X
ISSN	0960-7412
DOI	10.1111/tpj.15872
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