1
|
Kaur A, Chopra M, Bhushan M, Gupta S, Kumari P H, Sivagurunathan N, Shukla N, Rajagopal S, Bhalothia P, Sharma P, Naravula J, Suravajhala R, Gupta A, Abbasi BA, Goswami P, Singh H, Narang R, Polavarapu R, Medicherla KM, Valadi J, Kumar S A, Chaubey G, Singh KK, Bandapalli OR, Kavi Kishor PB, Suravajhala P. The Omic Insights on Unfolding Saga of COVID-19. Front Immunol 2021; 12:724914. [PMID: 34745097 PMCID: PMC8564481 DOI: 10.3389/fimmu.2021.724914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 09/27/2021] [Indexed: 12/15/2022] Open
Abstract
The year 2019 has seen an emergence of the novel coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing coronavirus disease of 2019 (COVID-19). Since the onset of the pandemic, biological and interdisciplinary research is being carried out across the world at a rapid pace to beat the pandemic. There is an increased need to comprehensively understand various aspects of the virus from detection to treatment options including drugs and vaccines for effective global management of the disease. In this review, we summarize the salient findings pertaining to SARS-CoV-2 biology, including symptoms, hosts, epidemiology, SARS-CoV-2 genome, and its emerging variants, viral diagnostics, host-pathogen interactions, alternative antiviral strategies and application of machine learning heuristics and artificial intelligence for effective management of COVID-19 and future pandemics.
Collapse
Affiliation(s)
- Arvinpreet Kaur
- Department of Bioinformatics, Hans Raj Mahila Maha Vidyalaya, Punjab, India
- Bioclues.org, Hyderabad, India
| | - Mehak Chopra
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Mahak Bhushan
- Department of Biological Sciences, Indian Institute of Science Education and Research, Kolkata, India
| | - Sonal Gupta
- Bioclues.org, Hyderabad, India
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India
| | | | - Narmadhaa Sivagurunathan
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India
| | - Nidhi Shukla
- Bioclues.org, Hyderabad, India
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India
| | - Shalini Rajagopal
- Vignan’s Foundation for Science, Technology & Research (Deemed to be University), Guntur, India
| | - Purva Bhalothia
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India
| | - Purnima Sharma
- Department of Bioinformatics, Hans Raj Mahila Maha Vidyalaya, Punjab, India
| | - Jalaja Naravula
- Vignan’s Foundation for Science, Technology & Research (Deemed to be University), Guntur, India
| | - Renuka Suravajhala
- Bioclues.org, Hyderabad, India
- Department of Chemistry, School of Basic Sciences, Manipal University Jaipur, Jaipur, India
| | - Ayam Gupta
- Vignan’s Foundation for Science, Technology & Research (Deemed to be University), Guntur, India
| | - Bilal Ahmed Abbasi
- Functional Genomics Unit, Council of Scientific and Industrial Research- Institute of Genomics & Integrative Biology (CSIR-IGIB), Delhi, India
| | - Prittam Goswami
- Department of Biotechnology, Haldia Institute of Technology, West Bengal, India
| | - Harpreet Singh
- Department of Bioinformatics, Hans Raj Mahila Maha Vidyalaya, Punjab, India
- Bioclues.org, Hyderabad, India
| | - Rahul Narang
- Department of Microbiology, All India Institute of Medical Sciences, Bibinagar, Hyderabad, India
| | | | - Krishna Mohan Medicherla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India
| | - Jayaraman Valadi
- Bioclues.org, Hyderabad, India
- Department of Computer Science, Flame University, Pune, India
| | - Anil Kumar S
- Vignan’s Foundation for Science, Technology & Research (Deemed to be University), Guntur, India
| | - Gyaneshwer Chaubey
- Cytogenetics Laboratory, Department of Zoology, Benaras Hindu University, Varanasi, India
| | - Keshav K. Singh
- Department of Genetics, University of Alabama, Birmingham, AL, United States
| | - Obul Reddy Bandapalli
- Bioclues.org, Hyderabad, India
- German Cancer Research Centre (DKFZ), Heidelberg, Germany
- Department of Applied Biology, Council of Scientific and Industrial Research-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad, India
| | - Polavarapu Bilhan Kavi Kishor
- Bioclues.org, Hyderabad, India
- Vignan’s Foundation for Science, Technology & Research (Deemed to be University), Guntur, India
| | - Prashanth Suravajhala
- Bioclues.org, Hyderabad, India
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kerala, India
| |
Collapse
|
2
|
Kumar B, Bhalothia P. Evolutionary analysis of GRAS gene family for functional and structural insights into hexaploid bread wheat (Triticum aestivum). J Biosci 2021. [DOI: 10.1007/s12038-021-00163-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
3
|
Kumar B, Bhalothia P. Evolutionary analysis of GRAS gene family for functional and structural insights into hexaploid bread wheat ( Triticum aestivum). J Biosci 2021; 46:45. [PMID: 34047288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
GRAS proteins are multi-functional, regulating various aspects of plant growth and development. Besides, they are also involved in the stress tolerance of plants. Wheat is one of the major cereal crops of the world and efforts are being made to boost its productivity and stress tolerance to feed the increasing world population. Being a physiologically important transcription factor, GRAS genes can open up new avenues for improvement in wheat. The recent availability of the hexaploid genome sequence of bread wheat (Triticum aestivum) provides us an excellent opportunity to analyse the GRAS gene family and gain functional insights. In this study, we identified 183 GRAS genes coding for 194 GRAS proteins. Chromosomal location was identified for all the genes to give some idea about gene duplications. Sequence alignment, followed by phylogenetic analysis helped to classify the TaGRAS genes in 12 subfamilies. Gene and protein structure analysis revealed conservation among the different sub-families. Transcriptome analysis was done using available databases, to reveal the expression pattern under developmental conditions as well as different stress conditions. Altogether, these datasets give important insights into the functional role of different GRAS family members of bread wheat. Besides, it provides an important resource for future investigations into the physiological role of GRAS genes in bread wheat. Finally, this study identified potentially important TaGRAS genes which may help to boost yields and stress tolerance of wheat via control of various physiological aspects.
Collapse
Affiliation(s)
- Brijesh Kumar
- Plant Stress Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110 067, India
| | | |
Collapse
|
4
|
Kumar B, Bhalothia P. Orphan crops for future food security. J Biosci 2020; 45:131. [PMID: 33184247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Climate change, along with current agricultural practices, is going to pose a significant challenge for future food security, especially in developing countries. Orphan crops can help mitigate this threat due to their inherent properties of stress tolerance and nutrition content. Industrialization of agriculture has left these minor crops behind in terms of domestication. As a result, the potential of these crops is underutilized. These crops can be a game-changer in the long term if necessary steps are taken to improve the quality as well as quantity of yield. Concerted efforts by many groups around the world have been taken for research and development of these crops. Besides, the unique properties of these crops have caught the media attention, which hails these crops as superfoods. Favourable government policies to promote these crops can help in the large-scale adoption of these crops by the farming community. Besides, the stress-resilience of these crops can help boost the sustainability of agriculture and ensure food security for future generations.
Collapse
Affiliation(s)
- Brijesh Kumar
- Plant Stress Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | | |
Collapse
|
5
|
Bhalothia P, Sangwan C, Alok A, Mehrotra S, Mehrotra R. PP2C-like Promoter and Its Deletion Variants Are Induced by ABA but Not by MeJA and SA in Arabidopsis thaliana. Front Plant Sci 2016; 7:547. [PMID: 27200023 PMCID: PMC4853407 DOI: 10.3389/fpls.2016.00547] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 04/08/2016] [Indexed: 05/07/2023]
Abstract
Gene expression is mediated through interaction between cis regulatory elements and its cognate transcription factors. Cis regulatory elements are defined as non-coding DNA sequences that provide the binding sites for transcription factors and are clustered in the upstream region of genes. ACGT cis regulatory element is one of the important cis regulatory elements found to be involved in diverse biological processes like auxin response, salicylic acid (SA) response, UV light response, ABA response and jasmonic acid (JA) response. We identified through in silico analysis that the upstream region of protein phosphatase 2C (PP2C) gene has a distinct genetic architecture of ACGT elements. In the present study, the activation of the full length promoter and its deletion constructs like 900 base pair, 500 base pair, 400 base pair and NRM (Nathji Rajesh Mehrotra) were examined by stable transformation in Arabidopsis thaliana using β-glucuronidase as the reporter gene. Evaluation of deletion constructs of PP2C-like promoter was carried out in the presence of phytohormones like abscisic acid (ABA), SA and JA. Our result indicated that the full length and 900 base pair promoter-reporter constructs of PP2C-like promoter was induced in response to ABA but not to methyl jasmonate and SA.
Collapse
Affiliation(s)
- Purva Bhalothia
- Department of Biological Sciences, Birla Institute of Technology and SciencesPilani, India
| | - Chetna Sangwan
- Department of Biological Sciences, Birla Institute of Technology and SciencesPilani, India
| | - Anshu Alok
- Department of Biotechnology, National Agri-Food Biotechnology InstitutePunjab, India
| | - Sandhya Mehrotra
- Department of Biological Sciences, Birla Institute of Technology and SciencesPilani, India
| | - Rajesh Mehrotra
- Department of Biological Sciences, Birla Institute of Technology and SciencesPilani, India
- *Correspondence: Rajesh Mehrotra, ;
| |
Collapse
|
6
|
Mehrotra R, Bhalothia P, Bansal P, Basantani MK, Bharti V, Mehrotra S. Abscisic acid and abiotic stress tolerance - different tiers of regulation. J Plant Physiol 2014; 171:486-96. [PMID: 24655384 DOI: 10.1016/j.jplph.2013.12.007] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Revised: 12/12/2013] [Accepted: 12/13/2013] [Indexed: 05/21/2023]
Abstract
Abiotic stresses affect plant growth, metabolism and sustainability in a significant way and hinder plant productivity. Plants combat these stresses in myriad ways. The analysis of the mechanisms underlying abiotic stress tolerance has led to the identification of a highly complex, yet tightly regulated signal transduction pathway consisting of phosphatases, kinases, transcription factors and other regulatory elements. It is becoming increasingly clear that also epigenetic processes cooperate in a concerted manner with ABA-mediated gene expression in combating stress conditions. Dynamic stress-induced mechanisms, involving changes in the apoplastic pool of ABA, are transmitted by a chain of phosphatases and kinases, resulting in the expression of stress inducible genes. Processes involving DNA methylation and chromatin modification as well as post transcriptional, post translational and epigenetic control mechanisms, forming multiple tiers of regulation, regulate this gene expression. With recent advances in transgenic technology, it has now become possible to engineer plants expressing stress-inducible genes under the control of an inducible promoter, enhancing their ability to withstand adverse conditions. This review briefly discusses the synthesis of ABA, components of the ABA signal transduction pathway and the plants' responses at the genetic and epigenetic levels. It further focuses on the role of RNAs in regulating stress responses and various approaches to develop stress-tolerant transgenic plants.
Collapse
Affiliation(s)
- Rajesh Mehrotra
- Department of Biological Sciences, Birla Institute of Technology & Sciences, Pilani, Rajasthan 333031, India; G(o) Unit, Okinawa Institute of Science and Technology, 1919-1, Onnason, Okinawa, Japan
| | - Purva Bhalothia
- Department of Biological Sciences, Birla Institute of Technology & Sciences, Pilani, Rajasthan 333031, India
| | - Prashali Bansal
- Department of Biological Sciences, Birla Institute of Technology & Sciences, Pilani, Rajasthan 333031, India; Cancer Science Institute, National University of Singapore, Singapore, Singapore
| | - Mahesh Kumar Basantani
- Division of Endocrinology, University of Pittsburgh, 200 Lothrop Street, BST E1140, Pittsburgh, PA 15261, USA
| | - Vandana Bharti
- Department of Biotechnology, St. Columba's College, Vinoba Bhave University, Hazaribagh, India
| | - Sandhya Mehrotra
- Department of Biological Sciences, Birla Institute of Technology & Sciences, Pilani, Rajasthan 333031, India.
| |
Collapse
|
7
|
Mehrotra R, Sethi S, Zutshi I, Bhalothia P, Mehrotra S. Patterns and evolution of ACGT repeat cis-element landscape across four plant genomes. BMC Genomics 2013; 14:203. [PMID: 23530833 PMCID: PMC3622567 DOI: 10.1186/1471-2164-14-203] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 03/18/2013] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND Transcription factor binding is regulated by several interactions, primarily involving cis-element binding. These binding sites maintain specificity by means of their sequence, and other additional factors such as inter-motif distance and spacer specificity. The ACGT core sequence has been established as a functionally important cis-element which frequently regulates gene expression in synergy with other cis-elements. In this study, we used two monocotyledonous - Oryza sativa and Sorghum bicolor, and two dicotyledonous species - Arabidopsis thaliana and Glycine max to analyze the conservation of co-occurring ACGT core elements in plant promoters with respect to spacer distance between them. Using data generated from Arabidopsis thaliana and Oryza sativa, we also identified conserved regions across all spacers and possible conditions regulating gene promoters with multiple ACGT cis-elements. RESULTS Our data indicated specific predominant spacer lengths between co-occurring ACGT elements, but these lengths were not universally conserved across all species under analysis. However, the frequency distribution indicated local regions of high correlation among monocots and dicots. Sequence specificity data clearly revealed a preference for G at the first and C at the terminal position of a spacer sequence, suggesting that the G-box motif is the most prevalent for the ACGT class of promoters. Using gene expression databases, we also observed trends suggesting that co-occurring ACGT elements are responsible for gene regulation in response to exogenous stress. Conservation in patterns of ACGT (N) ACGT among orthologous genes also indicated the possibility that emergence of functional significance across species was a result of parallel evolution of these cis-elements. CONCLUSIONS Although the importance of ACGT elements has been acknowledged for several plant species, ours is the first study that attempts to compare their occurrence across four species and analyze conservation among them. The apparent preference for particular spacer distances suggest that these motifs might be implicated in important physiological functions which are yet to be identified. Variations in correlation patterns among monocots and dicots might arise out of differences in transcriptional regulation in the two classes. In accordance with literature, we established the involvement of co-occurring ACGT elements in stress responses and showed how this regulation differs with variation in the ACGT (N) ACGT motif. We believe that our study will be an essential resource in determining optimum spacer length and spacer sequence between ACGT elements for promoter design in future.
Collapse
Affiliation(s)
- Rajesh Mehrotra
- Biological Sciences Department, Birla Institute of Technology and Science, Pilani, RJ, India
| | - Sachin Sethi
- Biological Sciences Department, Birla Institute of Technology and Science, Pilani, RJ, India
| | - Ipshita Zutshi
- Biological Sciences Department, Birla Institute of Technology and Science, Pilani, RJ, India
| | - Purva Bhalothia
- Biological Sciences Department, Birla Institute of Technology and Science, Pilani, RJ, India
| | - Sandhya Mehrotra
- Biological Sciences Department, Birla Institute of Technology and Science, Pilani, RJ, India
| |
Collapse
|
8
|
Mehrotra R, Yadav A, Bhalothia P, Karan R, Mehrotra S. Evidence for directed evolution of larger size motif in Arabidopsis thaliana genome. ScientificWorldJournal 2012; 2012:983528. [PMID: 22645502 PMCID: PMC3354754 DOI: 10.1100/2012/983528] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Accepted: 12/15/2011] [Indexed: 11/17/2022] Open
Abstract
Transcription control of gene expression depends on a variety of interactions mediated by the core promoter region, sequence specific DNA-binding proteins, and their cognate promoter elements. The prominent group of cis acting elements in plants contains an ACGT core. The cis element with this core has been shown to be involved in abscisic acid, salicylic acid, and light response. In this study, genome-wide comparison of the frequency of occurrence of two ACGT elements without any spacers as well as those separated by spacers of different length was carried out. In the first step, the frequency of occurrence of the cis element sequences across the whole genome was determined by using BLAST tool. In another approach the spacer sequence was randomized before making the query. As expected, the sequence ACGTACGT had maximum occurrence in Arabidopsis thaliana genome. As we increased the spacer length, one nucleotide at a time, the probability of its occurrence in genome decreased. This trend continued until an unexpectedly sharp rise in frequency of (ACGT)N25(ACGT). The observation of higher probability of bigger size motif suggests its directed evolution in Arabidopsis thaliana genome.
Collapse
Affiliation(s)
- Rajesh Mehrotra
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Rajasthan 333031, India.
| | | | | | | | | |
Collapse
|
9
|
Mehrotra R, Gupta G, Sethi R, Bhalothia P, Kumar N, Mehrotra S. Designer promoter: an artwork of cis engineering. Plant Mol Biol 2011; 75:527-36. [PMID: 21327513 DOI: 10.1007/s11103-011-9755-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2011] [Accepted: 02/02/2011] [Indexed: 05/20/2023]
Abstract
Advances in systematic computational biology and rapid elucidation of synergistic interplay between cis and trans factors governing transcriptional control have facilitated functional annotation of gene networks. The generation of data through deconstructive, reconstructive and database assisted promoter studies, and its integration to principles of synthetic engineering has started an era of designer promoters. Exploration of natural promoter architecture and the concept of cis engineering have not only enabled fine tuning of single or multiple transgene expression in response to perturbations in the chemical, physiological and environmental stimuli but also provided researchers with a unique answer to various problems in crop improvement in the form of bidirectional promoters.
Collapse
Affiliation(s)
- Rajesh Mehrotra
- Department of Biological Sciences, BITS, Pilani, Rajasthan, India.
| | | | | | | | | | | |
Collapse
|