1
|
Najeeb N, Murukan AB, Renjitha A, Jayaram M, Jabbar AA, Haridasan H, Prijikumar A, Baiju S, Nixon AA, Krishnan PA, Rodriguez S, Kumar S, Polipalli SK, Singh KK, Nair BG, Ghate SD, Rao RSP, Kishor PBK, Aloor A, Suravajhala R, Chaubey G, Suravajhala P. Inferring Recombination Events in SARS-CoV-2 Variants In Silico. Adv Exp Med Biol 2023; 1412:253-270. [PMID: 37378772 DOI: 10.1007/978-3-031-28012-2_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Over the last 34 months, at least 10 severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) distinct variants have evolved. Among these, some were more infectious while others were not. These variants may serve as candidates for identification of the signature sequences linked to infectivity and viral transgressions. Based on our previous hijacking and transgression hypothesis, we aimed to investigate whether SARS-CoV-2 sequences associated with infectivity and trespassing of long noncoding RNAs (lncRNAs) provide a possible recombination mechanism to drive the formation of new variants. This work involved a sequence and structure-based approach to screen SARS-CoV-2 variants in silico, taking into account effects of glycosylation and links to known lncRNAs. Taken together, the findings suggest that transgressions involving lncRNAs may be linked with changes in SARS-CoV-2-host interactions driven by glycosylation events.
Collapse
Affiliation(s)
- Nihal Najeeb
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Aparna B Murukan
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Anagha Renjitha
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Malavika Jayaram
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Ayisha A Jabbar
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Haripriya Haridasan
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Akshara Prijikumar
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Sneha Baiju
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Adrial Ann Nixon
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | | | - Sunu Rodriguez
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Somesh Kumar
- Genome Sequencing Lab, Lok Nayak Hospital, Delhi, India
| | | | - Keshav K Singh
- Department of Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Kaul Genetics Building, Birmingham, AL, USA
| | - Bipin G Nair
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Sudeep D Ghate
- Center for Bioinformatics, NITTE University, Mangaluru, India
| | | | | | - Arya Aloor
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Renuka Suravajhala
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India
| | - Gyaneshwer Chaubey
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Prashanth Suravajhala
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India.
| |
Collapse
|
2
|
Reddy PS, Dhaware MG, Sivasakthi K, Divya K, Nagaraju M, Sri Cindhuri K, Kavi Kishor PB, Bhatnagar-Mathur P, Vadez V, Sharma KK. Pearl Millet Aquaporin Gene PgPIP2;6 Improves Abiotic Stress Tolerance in Transgenic Tobacco. Front Plant Sci 2022; 13:820996. [PMID: 35356115 PMCID: PMC8959815 DOI: 10.3389/fpls.2022.820996] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/13/2022] [Indexed: 05/24/2023]
Abstract
Pearl millet [Pennisetum glaucum (L) R. Br.] is an important cereal crop of the semiarid tropics, which can withstand prolonged drought and heat stress. Considering an active involvement of the aquaporin (AQP) genes in water transport and desiccation tolerance besides several basic functions, their potential role in abiotic stress tolerance was systematically characterized and functionally validated. A total of 34 AQP genes from P. glaucum were identified and categorized into four subfamilies, viz., plasma membrane intrinsic proteins (PIPs), tonoplast intrinsic proteins (TIPs), nodulin-26-like intrinsic proteins (NIPs), and small basic intrinsic proteins (SIPs). Sequence analysis revealed that PgAQPs have conserved characters of AQP genes with a closer relationship to sorghum. The PgAQPs were expressed differentially under high vapor pressure deficit (VPD) and progressive drought stresses where the PgPIP2;6 gene showed significant expression under high VPD and drought stress. Transgenic tobacco plants were developed by heterologous expression of the PgPIP2;6 gene and functionally characterized under different abiotic stresses to further unravel their role. Transgenic tobacco plants in the T2 generations displayed restricted transpiration and low root exudation rates in low- and high-VPD conditions. Under progressive drought stress, wild-type (WT) plants showed a quick or faster decline of soil moisture than transgenics. While under heat stress, PgPIP2;6 transgenics showed better adaptation to heat (40°C) with high canopy temperature depression (CTD) and low transpiration; under low-temperature stress, they displayed lower transpiration than their non-transgenic counterparts. Cumulatively, lower transpiration rate (Tr), low root exudation rate, declined transpiration, elevated CTD, and lower transpiration indicate that PgPIP2;6 plays a role under abiotic stress tolerance. Since the PgPIP2;6 transgenic plants exhibited better adaptation against major abiotic stresses such as drought, high VPD, heat, and cold stresses by virtue of enhanced transpiration efficiency, it has the potential to engineer abiotic stress tolerance for sustained growth and productivity of crops.
Collapse
Affiliation(s)
| | - Mahamaya G. Dhaware
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Kaliamoorthy Sivasakthi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Kummari Divya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Marka Nagaraju
- Department of Biochemistry, ICMR – National Institute of Nutrition, Hyderabad, India
| | - Katamreddy Sri Cindhuri
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Polavarapu Bilhan Kavi Kishor
- Department of Biotechnology, Vignan’s Foundation for Science, Technology & Research (Deemed to be University), Vadlamudi, India
| | - Pooja Bhatnagar-Mathur
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Vincent Vadez
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Kiran K. Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| |
Collapse
|
3
|
Guddimalli R, Somanaboina AK, Palle SR, Edupuganti S, Kummari D, Palakolanu SR, Naravula J, Gandra J, Qureshi IA, Marka N, Polavarapu R, Kavi Kishor PB. Overexpression of RNA-binding bacterial chaperones in rice leads to stay-green phenotype, improved yield and tolerance to salt and drought stresses. Physiol Plant 2021; 173:1351-1368. [PMID: 33583030 DOI: 10.1111/ppl.13369] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 01/18/2021] [Accepted: 02/10/2021] [Indexed: 06/12/2023]
Abstract
Genes encoding bacterial cold shock proteins A (CspA, 213 bp) and B (CspB, 216 bp) were isolated from Escherichia coli strain K12, which showed 100% homology with gene sequences isolated from other bacterial species. In silico domain, analysis showed eukaryotic conserved cold shock domain (CSD) and ribonuclease-binding domain (RBD) indicating that they bind to RNA and are involved in temperature stress tolerance. Overexpression of these two genes in E. coli resulted in higher growth in presence of 200 mM NaCl and 300 mM mannitol. Western blot confirmed the translational products of the two genes. Seedlings of indica rice were transformed with Agrobacterium tumefaciens containing pCAMBIA1301 CspA and CspB genes. Transgene integration was confirmed by β-glucuronidase (GUS) histochemical assay, polymerase chain reaction (PCR) amplification, and gene copy number by Southern blotting. Chlorophyll, proline, Na+ , and K+ contents were higher in transgenics exposed to 150 mM NaCl and drought (imposed by withholding water) stresses during floral initiation stage. Catalase (CAT), superoxide dismutase (SOD), and guaiacol peroxidase (GPX) activities increased, while malondialdehyde (MDA) content was low in transgenics. Transgenics displayed increased root, shoot, and panicle lengths, root dry mass, and a distinct stay-green (SGR) phenotype. Higher transcript levels of CspA, CspB, SGR, chlorophyllase, isopentenyl adenine transferase 1 (IPT1), 9-cis-epoxycarotenoid dioxygenase (NCED), SOD, and sirtuin 1 (SIRT1) genes were observed in transgenics compared to wild type plants (WT) under multiple stresses. Present work indicates that bacterial chaperone proteins are capable of imparting SGR phenotype, salt and drought stress tolerance alongside grain improvement.
Collapse
Affiliation(s)
| | - Anil Kumar Somanaboina
- Department of Biotechnology, Vignan's Foundation for Science, Technology and Research, Guntur, India
| | | | | | - Divya Kummari
- Cell, Molecular & Genetic Engineering Lab, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Sudhakar Reddy Palakolanu
- Cell, Molecular & Genetic Engineering Lab, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Jalaja Naravula
- Department of Biotechnology, Vignan's Foundation for Science, Technology and Research, Guntur, India
| | - Jawahar Gandra
- Department of Life Sciences, School of Sciences B-II, Jain University, Bengaluru, India
| | - Insaf A Qureshi
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Nagaraju Marka
- Biochemistry Division, ICMR-National Institute of Nutrition, Hyderabad, India
| | | | | |
Collapse
|
4
|
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
|
5
|
Srilaxmi P, Sareddy GR, Kavi Kishor PB, Setty OH, Babu PP. Protective efficacy of natansnin, a dibenzoyl glycoside from Salvinia natans against CCl4 induced oxidative stress and cellular degeneration in rat liver. BMC Pharmacol 2010; 10:13. [PMID: 20939865 PMCID: PMC2967507 DOI: 10.1186/1471-2210-10-13] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2009] [Accepted: 10/12/2010] [Indexed: 11/21/2022] Open
Abstract
Background Carbon tetra chloride (CCl4), an industrial solvent, is a hepatotoxic agent and it is the well established animal model for free radical-induced liver injury. The present investigation was carried out to establish the protective effect of natansnin, a novel dibenzoyl glycoside from Salvinia natans against CCl4 induced oxidative stress and cellular degeneration in rat liver. Results CCl4 significantly increased the levels of lipid peroxides, oxidized glutathione and decreased the levels of reduced glutathione, SOD and CAT. CCl4 induce marked histopathological changes and increase in the levels of apoptotic proteins. CCl4 treatment significantly increased the levels of apoptotic proteins such as caspases-3, PARP, Bax, Bid and cytochrome C and also increased the levels of inflammatory mediators iNos and Cox-2. Natansnin treatment significantly decreased the levels of CCl4 induced apoptotic proteins and inflammatory mediators. Further natansinin treatment significantly inhibited the CCl4 induced apoptosis which was evident form the reduced TUNEL positive cells. Conclusions In conclusion, our study demonstrated the protective effect of natansnin against CCl4 induced oxidative stress and cellular degeneration in rat liver tissue. This protective effect of natansnin can be correlated to its direct antioxidant effect.
Collapse
|