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de Paula Filho MFF, Lopes Chrisóstomo LL, Cansanção IF. HPV16 Genomes: In Silico Analysis of E6 and E7 Oncoproteins in 20 South American Variants. Curr Genomics 2024; 25:316-321. [PMID: 39156730 PMCID: PMC11327806 DOI: 10.2174/0113892029293113240427065916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 03/19/2024] [Accepted: 03/31/2024] [Indexed: 08/20/2024] Open
Abstract
Background Human papillomavirus (HPV) is the main risk factor for the development of squamous cell cervical cancer, and E6 oncoprotein and E7 oncoprotein are important components of the viral genome and its oncogenic potential. It is known that different viral variants of HPV16 have different pathology and impact on the development of neoplasia, although few studies have been performed on South American variants. Objective Therefore, the present study aimed to analyze in silico the genomic diversity of HPV16 in 20 complete genome variants of South America in the National Center for Biotechnology Information (NCBI) database. Methods We performed a descriptive study to characterize the polymorphic regions of the E6 and E7 genes in HPV16 variants, using software for genomic data and single nucleotide polymorphism (SNP) analysis and others for phylogenetic analysis. Results The variants analyzed included six SNPs linked to cancer (A131G, G145T, C335T, T350G, C712A, and T732C) and significant variation (798 nucleotide substitutions). Despite this, the variants showed low genetic diversity. Eighteen variants of unclear significance (VUS) were identified, 10 of which were in the coding E6 regions and 8 in the coding E7 regions. The prevalence of lineage D variants is of concern due to their pathology in cervical cancer and requires more research and epidemiological vigilance regarding their prevalence in the population. Conclusion The data obtained in this study may contribute to future research on South American variants of HPV16, their pathogenicity, and the development of treatments.
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Affiliation(s)
| | - Lara Luísa Lopes Chrisóstomo
- Medicine Collegiate, Campus Paulo Afonso, Universidade Federal do Vale do São Francisco (UNIVASF), Paulo Afonso, BA, 48605-780, Brazil
| | - Isaac Farias Cansanção
- Medicine Collegiate, Campus Paulo Afonso, Universidade Federal do Vale do São Francisco (UNIVASF), Paulo Afonso, BA, 48605-780, Brazil
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2
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Esposti MD. Eukaryotes inherited inositol lipids from bacteria: implications for the models of eukaryogenesis. FEBS Lett 2023; 597:2484-2496. [PMID: 37507225 DOI: 10.1002/1873-3468.14708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 07/11/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023]
Abstract
The merger of two very different microbes, an anaerobic archaeon and an aerobic bacterium, led to the birth of eukaryotic cells. Current models hypothesize that an archaeon engulfed bacteria through external protrusions that then fused together forming the membrane organelles of eukaryotic cells, including mitochondria. Images of cultivated Lokiarchaea sustain this concept, first proposed in the inside-out model which assumes that the membrane traffic system of archaea drove the merging with bacterial cells through membrane expansions containing inositol lipids, considered to have evolved first in archaea. This assumption has been evaluated here in detail. The data indicate that inositol lipids first emerged in bacteria, not in archaea. The implications of this finding for the models of eukaryogenesis are discussed.
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3
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Kudo F, Eguchi T. Biosynthesis of cyclitols. Nat Prod Rep 2022; 39:1622-1642. [PMID: 35726901 DOI: 10.1039/d2np00024e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Review covering up to 2021Cyclitols derived from carbohydrates are naturally stable hydrophilic substances under ordinary physiological conditions, increasing the water solubility of whole molecules in cells. The stability of cyclitols is derived from their carbocyclic structures bearing no acetal groups, in contrast to sugar molecules. Therefore, carbocycle-forming reactions are critical for the biosynthesis of cyclitols. Herein, we review naturally occurring cyclitols that have been identified to date and categorize them according to the type of carbocycle-forming enzymatic reaction. Furthermore, the cyclitol-forming enzymatic reaction mechanisms and modification pathways of the initially generated cyclitols are reviewed.
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Affiliation(s)
- Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-Okayama, Meguro-ku, Tokyo, Japan.
| | - Tadashi Eguchi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-Okayama, Meguro-ku, Tokyo, Japan.
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Das JK, Heryakusuma C, Susanti D, Choudhury PP, Mukhopadhyay B. Reduced Protein Sequence Patterns in Identifying Key Structural Elements of Dissimilatory Sulfite Reductase Homologs. Comput Biol Chem 2022; 98:107691. [DOI: 10.1016/j.compbiolchem.2022.107691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 04/26/2022] [Accepted: 04/26/2022] [Indexed: 11/03/2022]
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Ahmed S, Muhammod R, Khan ZH, Adilina S, Sharma A, Shatabda S, Dehzangi A. ACP-MHCNN: an accurate multi-headed deep-convolutional neural network to predict anticancer peptides. Sci Rep 2021; 11:23676. [PMID: 34880291 PMCID: PMC8654959 DOI: 10.1038/s41598-021-02703-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 11/17/2021] [Indexed: 01/10/2023] Open
Abstract
Although advancing the therapeutic alternatives for treating deadly cancers has gained much attention globally, still the primary methods such as chemotherapy have significant downsides and low specificity. Most recently, Anticancer peptides (ACPs) have emerged as a potential alternative to therapeutic alternatives with much fewer negative side-effects. However, the identification of ACPs through wet-lab experiments is expensive and time-consuming. Hence, computational methods have emerged as viable alternatives. During the past few years, several computational ACP identification techniques using hand-engineered features have been proposed to solve this problem. In this study, we propose a new multi headed deep convolutional neural network model called ACP-MHCNN, for extracting and combining discriminative features from different information sources in an interactive way. Our model extracts sequence, physicochemical, and evolutionary based features for ACP identification using different numerical peptide representations while restraining parameter overhead. It is evident through rigorous experiments using cross-validation and independent-dataset that ACP-MHCNN outperforms other models for anticancer peptide identification by a substantial margin on our employed benchmarks. ACP-MHCNN outperforms state-of-the-art model by 6.3%, 8.6%, 3.7%, 4.0%, and 0.20 in terms of accuracy, sensitivity, specificity, precision, and MCC respectively. ACP-MHCNN and its relevant codes and datasets are publicly available at: https://github.com/mrzResearchArena/Anticancer-Peptides-CNN . ACP-MHCNN is also publicly available as an online predictor at: https://anticancer.pythonanywhere.com/ .
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Affiliation(s)
- Sajid Ahmed
- Department of Computer Science and Engineering, United International University, Dhaka, Bangladesh
| | - Rafsanjani Muhammod
- Department of Computer Science and Engineering, United International University, Dhaka, Bangladesh
| | - Zahid Hossain Khan
- Department of Computer Science and Engineering, United International University, Dhaka, Bangladesh
| | - Sheikh Adilina
- Department of Computer Science and Engineering, United International University, Dhaka, Bangladesh
| | - Alok Sharma
- Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
- Institute for Integrated and Intelligent Systems, Griffith University, Brisbane, QLD, 4111, Australia
| | - Swakkhar Shatabda
- Department of Computer Science and Engineering, United International University, Dhaka, Bangladesh.
| | - Abdollah Dehzangi
- Department of Computer Science, Rutgers University, Camden, NJ, 08102, USA.
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, 08102, USA.
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6
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Steele E, Alebous HD, Vickers M, Harris ME, Johnson MD. Co-culturing experiments reveal the uptake of myo-inositol phosphate synthase (EC 5.5.1.4) in an inositol auxotroph of Saccharomyces cerevisiae. Microb Cell Fact 2021; 20:138. [PMID: 34281557 PMCID: PMC8287684 DOI: 10.1186/s12934-021-01610-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 06/08/2021] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Myo-Inositol Phosphate Synthase (MIP) catalyzes the conversion of glucose 6- phosphate into inositol phosphate, an essential nutrient and cell signaling molecule. Data obtained, first in bovine brain and later in plants, established MIP expression in organelles and in extracellular environments. A physiological role for secreted MIP has remained elusive since its first detection in intercellular space. To provide further insight into the role of MIP in intercellular milieus, we tested the hypothesis that MIP may function as a growth factor, synthesizing inositol phosphate in intercellular locations requiring, but lacking ability to produce or transport adequate quantities of the cell-cell communicator. This idea was experimentally challenged, utilizing a Saccharomyces cerevisiae inositol auxotroph with no MIP enzyme, permeable membranes with a 0.4 µm pore size, and cellular supernatants as external sources of inositol isolated from S. cerevisiae cells containing either wild-type enzyme (Wt-MIP), no MIP enzyme, auxotroph (Aux), or a green fluorescent protein (GFP) tagged reporter enzyme (MIP- GFP) in co- culturing experiments. RESULTS Resulting cell densities and microscopic studies with corroborating biochemical and molecular analyses, documented sustained growth of Aux cells in cellular supernatant, concomitant with the uptakeof MIP, detected as MIP-GFP reporter enzyme. These findings revealed previously unknown functions, suggesting that the enzyme can: (1) move into and out of intercellular space, (2) traverse cell walls, and (3) act as a growth factor to promote cellular proliferation of an inositol requiring cell. CONCLUSIONS Co-culturing experiments, designed to test a probable function for MIP secreted in extracellular vesicles, uncovered previously unknown functions for the enzyme and advanced current knowledge concerning spatial control of inositol phosphate biosynthesis. Most importantly, resulting data identified an extracellular vesicle (a non-viral vector) that is capable of synthesizing and transporting inositol phosphate, a biological activity that can be used to enhance specificity of current inositol phosphate therapeutics.
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Affiliation(s)
- Erika Steele
- The University of Alabama, The Institute of Social Science Research, PO Box 8702161, Tuscaloosa, AL 35487 USA
| | - Hana D. Alebous
- Department of Biological Sciences, School of Science, The University of Jordan, PO Box 11942, Amman-Jordan, Jordan
| | - Macy Vickers
- Department of Biological Sciences, The University of Alabama, PO Box 870344, Tuscaloosa, AL 35487 USA
| | - Mary E. Harris
- Department of Biological Sciences, The University of Alabama, PO Box 870344, Tuscaloosa, AL 35487 USA
| | - Margaret D. Johnson
- Department of Biological Sciences, The University of Alabama, PO Box 870344, Tuscaloosa, AL 35487 USA
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7
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Das JK, Roy S. A study on non-synonymous mutational patterns in structural proteins of SARS-CoV-2. Genome 2021; 64:665-678. [PMID: 33788636 DOI: 10.1139/gen-2020-0157] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
SARS-CoV-2 is mutating and creating divergent variants across the world. An in-depth investigation of the amino acid substitutions in the genomic signature of SARS-CoV-2 proteins is highly essential for understanding its host adaptation and infection biology. A total of 9587 SARS-CoV-2 structural protein sequences collected from 49 different countries are used to characterize protein-wise variants, substitution patterns (type and location), and major substitution changes. The majority of the substitutions are distinct, mostly in a particular location, and lead to a change in an amino acid's biochemical properties. In terms of mutational changes, envelope (E) and membrane (M) proteins are relatively more stable than nucleocapsid (N) and spike (S) proteins. Several co-occurrence substitutions are observed, particularly in S and N proteins. Substitution specific to active sub-domains reveals that heptapeptide repeat, fusion peptides, transmembrane in S protein, and N-terminal and C-terminal domains in the N protein are remarkably mutated. We also observe a few deleterious mutations in the above domains. The overall study on non-synonymous mutation in structural proteins of SARS-CoV-2 at the start of the pandemic indicates a diversity amongst virus sequences.
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Affiliation(s)
- Jayanta Kumar Das
- Department of Pediatrics, Johns Hopkins University School of Medicine, Maryland, USA
| | - Swarup Roy
- Network Reconstruction & Analysis (NetRA) Lab, Department of Computer Applications, Sikkim University, Gangtok, India
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8
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Characterizing genomic variants and mutations in SARS-CoV-2 proteins from Indian isolates. GENE REPORTS 2021; 25:101044. [PMID: 33623833 PMCID: PMC7893251 DOI: 10.1016/j.genrep.2021.101044] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/25/2020] [Accepted: 01/29/2021] [Indexed: 12/17/2022]
Abstract
SARS-CoV-2 is mutating and creating divergent variants by altering the composition of essential constituent proteins. Pharmacologically, it is crucial to understand the diverse mechanism of mutations for stable vaccine or anti-viral drug design. Our current study concentrates on all the constituent proteins of 469 SARS-CoV-2 genome samples, derived from Indian patients. However, the study may easily be extended to the samples across the globe. We perform clustering analysis towards identifying unique variants in each of the SARS-CoV-2 proteins. A total of 536 mutated positions within the coding regions of SARS-CoV-2 proteins are detected among the identified variants from Indian isolates. We quantify mutations by focusing on the unique variants of each SARS-CoV-2 protein. We report the average number of mutation per variant, percentage of mutated positions, synonymous and non-synonymous mutations, mutations occurring in three codon positions and so on. Our study reveals the most susceptible six (06) proteins, which are ORF1ab, Spike (S), Nucleocapsid (N), ORF3a, ORF7a, and ORF8. Several non-synonymous substitutions are observed to be unique in different SARS-CoV-2 proteins. A total of 57 possible deleterious amino acid substitutions are predicted, which may impact on the protein functions. Several mutations show a large decrease in protein stability and are observed in putative functional domains of the proteins that might have some role in disease pathogenesis. We observe a good number of physicochemical property change during above deleterious substitutions.
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9
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Hu L, Zhou K, Ren G, Yang S, Liu Y, Zhang Z, Li Y, Gong X, Ma F. Myo-inositol mediates reactive oxygen species-induced programmed cell death via salicylic acid-dependent and ethylene-dependent pathways in apple. HORTICULTURE RESEARCH 2020; 7:138. [PMID: 32922810 PMCID: PMC7459343 DOI: 10.1038/s41438-020-00357-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 06/08/2020] [Accepted: 06/16/2020] [Indexed: 05/08/2023]
Abstract
As a versatile compound, myo-inositol plays vital roles in plant biochemistry and physiology. We previously showed that exogenous application of myo-inositol had a positive role in salinity tolerance in Malus hupehensis Rehd. In this study, we used MdMIPS (the rate-limiting gene of myo-inositol biosynthesis) transgenic apple lines to gain new insights into the physiological role of myo-inositol in apple. Decreasing myo-inositol biosynthesis in apple lines by RNA silencing of MdMIPS1/2 led to extensive programmed cell death, which manifested as necrosis of both the leaves and roots and, ultimately, plant death. Necrosis was directly caused by the excessive accumulation of reactive oxygen species, which may be closely associated with the cell wall polysaccharide-mediated increase in salicylic acid and a compromised antioxidant system, and this process was enhanced by an increase in ethylene production. In addition, a high accumulation of sorbitol promoted necrosis. This synergetic interplay between salicylic acid and ethylene was further supported by the fact that increased myo-inositol accumulation significantly delayed leaf senescence in MdMIPS1-overexpressing apple lines. Taken together, our results indicated that apple myo-inositol regulates reactive oxygen species-induced programmed cell death through salicylic acid-dependent and ethylene-dependent pathways.
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Affiliation(s)
- Lingyu Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, 712100 Yangling, Shaanxi China
| | - Kun Zhou
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, 712100 Yangling, Shaanxi China
| | - Guijin Ren
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, 712100 Yangling, Shaanxi China
| | - Shulin Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, 712100 Yangling, Shaanxi China
| | - Yuan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, 712100 Yangling, Shaanxi China
| | - Zhijun Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, 712100 Yangling, Shaanxi China
| | - Yangtiansu Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, 712100 Yangling, Shaanxi China
| | - Xiaoqing Gong
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, 712100 Yangling, Shaanxi China
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, 712100 Yangling, Shaanxi China
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Michon C, Kang CM, Karpenko S, Tanaka K, Ishikawa S, Yoshida KI. A bacterial cell factory converting glucose into scyllo-inositol, a therapeutic agent for Alzheimer's disease. Commun Biol 2020; 3:93. [PMID: 32123276 PMCID: PMC7052218 DOI: 10.1038/s42003-020-0814-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 02/11/2020] [Indexed: 12/28/2022] Open
Abstract
A rare stereoisomer of inositol, scyllo-inositol, is a therapeutic agent that has shown potential efficacy in preventing Alzheimer’s disease. Mycobacterium tuberculosis ino1 encoding myo-inositol-1-phosphate (MI1P) synthase (MI1PS) was introduced into Bacillus subtilis to convert glucose-6-phosphate (G6P) into MI1P. We found that inactivation of pbuE elevated intracellular concentrations of NAD+·NADH as an essential cofactor of MI1PS and was required to activate MI1PS. MI1P thus produced was dephosphorylated into myo-inositol by an intrinsic inositol monophosphatase, YktC, which was subsequently isomerized into scyllo-inositol via a previously established artificial pathway involving two inositol dehydrogenases, IolG and IolW. In addition, both glcP and glcK were overexpressed to feed more G6P and accelerate scyllo-inositol production. Consequently, a B. subtilis cell factory was demonstrated to produce 2 g L−1scyllo-inositol from 20 g L−1 glucose. This cell factory provides an inexpensive way to produce scyllo-inositol, which will help us to challenge the growing problem of Alzheimer’s disease in our aging society. Michon et al. describe the use of a recombinant Bacillus subtilis as a cell factory capable of producing scyllo-inositol, a therapeutic compound for Alzheimer’s disease, from inexpensive glucose. They demonstrate that it could produce 2 g L−1 of scyllo-inositol from 20 g L−1 glucose.
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Affiliation(s)
- Christophe Michon
- Department of Science, Technology and Innovation, Kobe University, Kobe, 657 8501, Japan.,CHROMagar, 4 Place du 18 Juin 1940, 75006, Paris, France
| | - Choong-Min Kang
- Department of Biological Sciences, California State University, Stanislaus, Turlock, CA, 95382, USA
| | - Sophia Karpenko
- Department of Science, Technology and Innovation, Kobe University, Kobe, 657 8501, Japan.,Sorbonne Universités, UPMC Univ. Paris 06, UMR 8237, Laboratoire Jean Perrin, F-75005, Paris, France.,CNRS UMR 8237, Laboratoire Jean Perrin, F-75005, Paris, France.,Paris Sciences & Lettres, 60 rue Mazarine, F-75006, Paris, France
| | - Kosei Tanaka
- Department of Science, Technology and Innovation, Kobe University, Kobe, 657 8501, Japan
| | - Shu Ishikawa
- Department of Science, Technology and Innovation, Kobe University, Kobe, 657 8501, Japan
| | - Ken-Ichi Yoshida
- Department of Science, Technology and Innovation, Kobe University, Kobe, 657 8501, Japan.
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Hazra A, Dasgupta N, Sengupta C, Das S. MIPS: Functional dynamics in evolutionary pathways of plant kingdom. Genomics 2019; 111:1929-1945. [DOI: 10.1016/j.ygeno.2019.01.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 11/22/2018] [Accepted: 01/02/2019] [Indexed: 10/27/2022]
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12
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Das JK, Choudhury PP, Chaturvedi N, Tayyab M, Hassan SS. Ranking and clustering of Drosophila olfactory receptors using mathematical morphology. Genomics 2019; 111:549-559. [DOI: 10.1016/j.ygeno.2018.03.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 02/12/2018] [Accepted: 03/07/2018] [Indexed: 11/26/2022]
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13
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Mukherjee R, Mukherjee A, Bandyopadhyay S, Mukherjee S, Sengupta S, Ray S, Majumder AL. Selective manipulation of the inositol metabolic pathway for induction of salt-tolerance in indica rice variety. Sci Rep 2019; 9:5358. [PMID: 30926863 PMCID: PMC6441109 DOI: 10.1038/s41598-019-41809-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 03/07/2019] [Indexed: 11/16/2022] Open
Abstract
Halophytes are rich sources of salt stress tolerance genes which have often been utilized for introduction of salt-tolerance character in salt-sensitive plants. In the present study, we overexpressed PcINO1 and PcIMT1 gene(s), earlier characterized in this laboratory from wild halophytic rice Porteresia coarctata, into IR64 indica rice either singly or in combination and assessed their role in conferring salt-tolerance. Homozygous T3/T4 transgenic plants revealed that PcINO1 transformed transgenic rice lines exhibit significantly higher tolerance upto 200 mM or higher salt concentration with negligible compromise in their growth or other physiological parameters compared to the untransformed system grown without stress. The PcIMT1-lines or the double transgenic lines (DC1) having PcINO1 and PcIMT1 introgressed together, were less efficient in such respect. Comparison of inositol and/or pinitol pool in three types of transgenic plants suggests that plants whose inositol production remains uninterrupted under stress by the functional PcINO1 protein, showed normal growth as in the wild-type plants without stress. It is conceivable that inositol itself acts as a stress-ameliorator and/or as a switch for a number of other pathways important for imparting salt-tolerance. Such selective manipulation of the inositol metabolic pathway may be one of the ways to combat salt stress in plants.
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Affiliation(s)
| | | | | | - Sritama Mukherjee
- Division of Plant Biology, Bose Institute, Kolkata, India.,Department of Botany, Bethune College, Kolkata, India
| | - Sonali Sengupta
- Division of Plant Biology, Bose Institute, Kolkata, India.,School of Plant Environment and Soil Sciences, Lousiana State University Agricultural Center, Lousiana, USA
| | - Sudipta Ray
- Division of Plant Biology, Bose Institute, Kolkata, India.,Department of Botany, Centre of Advanced Studies, University of Calcutta, Kolkata, India
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A Cotton ( Gossypium hirsutum) Myo-Inositol-1-Phosphate Synthase ( GhMIPS1D) Gene Promotes Root Cell Elongation in Arabidopsis. Int J Mol Sci 2019; 20:ijms20051224. [PMID: 30862084 PMCID: PMC6429088 DOI: 10.3390/ijms20051224] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 02/22/2019] [Accepted: 02/26/2019] [Indexed: 01/24/2023] Open
Abstract
Myo-inositol-1-phosphate synthase (MIPS, EC 5.5.1.4) plays important roles in plant growth and development, stress responses, and cellular signal transduction. MIPS genes were found preferably expressed during fiber cell initiation and early fast elongation in upland cotton (Gossypium hirsutum), however, current understanding of the function and regulatory mechanism of MIPS genes to involve in cotton fiber cell growth is limited. Here, by genome-wide analysis, we identified four GhMIPS genes anchoring onto four chromosomes in G. hirsutum and analyzed their phylogenetic relationship, evolutionary dynamics, gene structure and motif distribution, which indicates that MIPS genes are highly conserved from prokaryotes to green plants, with further exon-intron structure analysis showing more diverse in Brassicales plants. Of the four GhMIPS members, based on the significant accumulated expression of GhMIPS1D at the early stage of fiber fast elongating development, thereby, the GhMIPS1D was selected to investigate the function of participating in plant development and cell growth, with ectopic expression in the loss-of-function Arabidopsis mips1 mutants. The results showed that GhMIPS1D is a functional gene to fully compensate the abnormal phenotypes of the deformed cotyledon, dwarfed plants, increased inflorescence branches, and reduced primary root lengths in Arabidopsis mips1 mutants. Furthermore, shortened root cells were recovered and normal root cells were significantly promoted by ectopic expression of GhMIPS1D in Arabidopsis mips1 mutant and wild-type plants respectively. These results serve as a foundation for understanding the MIPS family genes in cotton, and suggest that GhMIPS1D may function as a positive regulator for plant cell elongation.
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15
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Basak P, Sangma S, Mukherjee A, Agarwal T, Sengupta S, Ray S, Majumder AL. Functional characterization of two myo-inositol-1-phosphate synthase (MIPS) gene promoters from the halophytic wild rice (Porteresia coarctata). PLANTA 2018; 248:1121-1141. [PMID: 30066217 DOI: 10.1007/s00425-018-2957-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 07/19/2018] [Indexed: 06/08/2023]
Abstract
MAIN CONCLUSION The promoter deletion mutants from second isoform of INO1 (gene-encoding MIPS) from Porteresia coarctata of 932 bp (pPcINO1.2.932) and 793 bp (pPcINO1.2.793) prove to be very efficient as salt/drought stress-inducible promoters, while pPcINO1.2.932 is found to be responsive to cold stress as well. The promoters of the two identified myo-inositol-1-phosphate synthase (INO1) isoforms from salt-tolerant wild rice, Porteresia coarctata (PcINO1.1 and PcINO1.2) have been compared bioinformatically with their counterparts present in the salt-sensitive rice, Oryza sativa. PcINO1.2 promoter was found to be enriched with many abiotic stress-responsive elements, like abscisic acid-responsive elements, MYC-responsive elements, MYB-binding sites, low-temperature stress-responsive elements, and heat-shock elements similar to the ones found in the conserved motifs of the promoters of salt/drought stress-inducible INO1 promoters across Kingdom Planta. To have detailed analysis on the arrangement of cis-acting regulatory elements present in PcINO1 promoters, 5' deletion mutational studies were performed in dicot model plants. Both transient as well as stable transformation methods were used to check the influence of PcINO1 promoter deletion mutants under salt and physiologically drought conditions using β-glucuronidase as the reporter gene. The deletion mutant from the promoter of PcINO1.2 of length 932 bp (pPcINO1.2.932) was found to be significantly upregulated under drought stress and also in cold stress, while another deletion mutant, pPcINO1.2.793 (of 793 bp), was significantly upregulated under salt stress. P. coarctata being a halophytic species, the high inducibility of pPcINO1.2.932 upon exposure to low-temperature stress was an unexpected result.
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Affiliation(s)
- Papri Basak
- Division of Plant Biology, Bose Institute, Centenary Campus, Kolkata, West Bengal, India
| | - Shiny Sangma
- Division of Plant Biology, Bose Institute, Centenary Campus, Kolkata, West Bengal, India
- HSSLC Branch, Meghalaya Board of School Education, Tura, West Garo Hills, Shillong, Meghalaya, India
| | - Abhishek Mukherjee
- Division of Plant Biology, Bose Institute, Centenary Campus, Kolkata, West Bengal, India
| | - Tanushree Agarwal
- Department of Botany, University of Calcutta, Ballygunge Campus, Kolkata, West Bengal, India
| | - Sonali Sengupta
- Division of Plant Biology, Bose Institute, Centenary Campus, Kolkata, West Bengal, India
- School of Plant, Environment and Soil Sciences, Louisiana State University Agricultural Centre, Baton Rouge, LA, 70803, USA
| | - Sudipta Ray
- Department of Botany, University of Calcutta, Ballygunge Campus, Kolkata, West Bengal, India
| | - Arun Lahiri Majumder
- Division of Plant Biology, Bose Institute, Centenary Campus, Kolkata, West Bengal, India.
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