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Chen B, Ding Z, Zhou X, Wang Y, Huang F, Sun J, Chen J, Han W. Integrated Full-Length Transcriptome and MicroRNA Sequencing Approaches Provide Insights Into Salt Tolerance in Mangrove ( Sonneratia apetala Buch.-Ham.). Front Genet 2022; 13:932832. [PMID: 35899202 PMCID: PMC9310009 DOI: 10.3389/fgene.2022.932832] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/08/2022] [Indexed: 11/13/2022] Open
Abstract
MicroRNAs (miRNAs) are small RNA molecules that serve as key players in plant stress responses. Although stress-regulated miRNAs have been explored in various plants, they are not well studied in mangroves. Herein, we combined PacBio isoform sequencing (Iso-Seq) with BGISEQ short-read RNA-seq to probe the role of miRNAs in the salt stress response of the mangrove plant, Sonneratia apetala Buch.-Ham. A total of 1,702,463 circular consensus sequencing reads were generated that produced 295,501 nonredundant full-length transcripts from the leaves of a 1-year-old S. apetala. After sequencing nine small RNA libraries constructed from control and 1- and 28-day 300 mM NaCl treatments, we identified 143 miRNAs (114 known and 29 novel) from a total of >261 million short reads. With the criteria of |log2FC| ≥ 1 and q-value < 0.05, 42 and 70 miRNAs were differentially accumulated after 1- and 28-day salt treatments, respectively. These differential accumulated miRNAs potentially targeted salt-responsive genes encoding transcription factors, ion homeostasis, osmotic protection, and detoxificant-related proteins, reminiscent of their responsibility for salinity adaptation in S. apetala. Particularly, 62 miRNAs were Sonneratia specific under salt stress, of which 34 were co-expressed with their 131 predicted targets, thus producing 140 miRNA-target interactions. Of these, 82 miRNA-target pairs exhibited negative correlations. Eighteen miRNA targets were categorized for the 'environmental information processing' during KEGG analysis and were related to plant hormone signal transduction (ko04075), MAPK signaling pathway-plant (ko04016), and ABC transporters (ko02010). These results underscored miRNAs as possible contributors to mangrove success in severe environments and offer insights into an miRNA-mediated regulatory mechanism of salt response in S. apetala.
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Affiliation(s)
- Beibei Chen
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, China
| | - Zeyi Ding
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, China
| | - Xiang Zhou
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, China
| | - Yue Wang
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
| | - Fei Huang
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, China
| | - Jiaxin Sun
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, China
| | - Jinhui Chen
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
| | - Weidong Han
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, China
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Dahibhate NL, Shukla SK, Kumar K. A Cyclic Disulfide Diastereomer From Bioactive Fraction of Bruguiera gymnorhiza Shows Anti- Pseudomonas aeruginosa Activity. Front Pharmacol 2022; 13:890790. [PMID: 35721160 PMCID: PMC9201687 DOI: 10.3389/fphar.2022.890790] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 04/14/2022] [Indexed: 01/08/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that commonly causes hospital-acquired infection and is of great concern in immunocompromised patients. The quorum sensing (QS) mechanism of P. aeruginosa is well studied and known to be responsible for pathogenicity and virulence. The QS inhibitor derived from the natural product can be an important therapeutic agent for pathogen control. The present study reports the role of Bruguiera gymnorhiza purified fraction (BG138) in inhibiting virulence factor production, biofilm formation, quorum sensing molecules, and expression of QS-related genes of P. aeruginosa. Structural characterization of BG138 by high resolution mass spectrometry, Fourier transform infrared spectroscopy, 1D (1H and 13C NMR) and 2D NMR reveals that the fraction is a mixture of already known cyclic disulfide diastereomer, namely, brugierol and isobrugierol. The minimum inhibitory concentration (MIC) of BG138 against P. aeruginosa was 32 μg/ml. Biofilm formation was significantly reduced at sub-MIC concentrations of BG138. Scanning electron microscopy analysis reports the concentration-dependent biofilm inhibition and morphological changes of P. aeruginosa. Flow cytometry–based cell viability assay showed that P. aeruginosa cells exhibit increased propidium iodide uptake on treatment with 32 and 64 μg/ml of BG138. At sub-MIC concentrations, BG138 exhibited significant inhibition of virulence factors and reduced swimming and swarming motility of P. aeruginosa. Furthermore, the effect of BG138 on the expression of QS-related genes was investigated by qRT-PCR. Taken together, our study reports the isolation and structural characterization of bioactive fraction BG138 from B. gymnorhiza and its anti-biofilm, anti-virulence, anti-quorum sensing, and cell-damaging activities against P. aeruginosa.
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Affiliation(s)
- Nilesh Lakshman Dahibhate
- Department of Biological Sciences, Birla Institute of Technology & Science Pilani, K. K. Birla Goa Campus, Goa, India
| | - Sanjeev K Shukla
- Sophisticated Analytical Instrument Facility, CSIR-Central Drug Research Institute, Lucknow, India
| | - Kundan Kumar
- Department of Biological Sciences, Birla Institute of Technology & Science Pilani, K. K. Birla Goa Campus, Goa, India
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Dahibhate NL, Kumar K. Metabolite profiling of Bruguiera cylindrica reveals presence of potential bioactive compounds. PEERJ ANALYTICAL CHEMISTRY 2022. [DOI: 10.7717/peerj-achem.16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bruguiera cylindrica parts are commonly used in Chinese and Indian traditional medicine to treat diarrhea, fever, and many ailments. The present study aims non targeted analysis of key secondary metabolites of B. cylindrica by gas chromatography mass spectrometry (GC-MS) and ultra-high performance liquid chromatography hybrid quadrupole-Exactive-Orbitrap high resolution mass spectrometry (UHPLC-Q-Exactive Orbitrap HRMS). GC-MS and UHPLC-Q-Exactive Orbitrap HRMS were utilized for metabolic profiling of ethyl acetate extract of B. cylindrica leaves. Key metabolites in the extract were identified and predicted based on chemical similarity using online databases such as ChemSpider and mzCloud. Thirty-six compounds belonging to different classes of secondary metabolites viz. flavonoids, fatty acids, fatty acid amides, carboxylic acids, and alkaloids were identified in the extract. Pentacyclic triterpenes like betulin, ursolic acid and a tropine, an alkaloid with potential pharmacological and therapeutic activities such as anticancer properties, neuromuscular blockers and antioxidants, were also identified. This study combined GC-MS and UHPLC-Q-Exactive Orbitrap HRMS with available online database for effective and rapid identification of bioactive metabolites in the ethyl acetate extract of mangrove without individual standard application. This is the first report on the HRMS based secondary metabolic profiling of B. cylindrica, with comprehensive map of its biologically important metabolites.
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Beulah G, Divya D, Kumar NSS, Sravya MVN, Rao KG, Chintagunta AD, Divya G, Chandana SH, Blessy BD, Simhachalam G. Purification and characterization of bioactive compounds extracted from Suaeda maritima leaf and its impact on pathogenicity of Pseudomonas aeruginosa in Catla catla fingerlings. AMB Express 2021; 11:135. [PMID: 34623537 PMCID: PMC8501176 DOI: 10.1186/s13568-021-01295-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 09/30/2021] [Indexed: 12/03/2022] Open
Abstract
Incidence of various dreadful microbial infections and the development of antibiotic resistance by infection causative microbes are the main reasons for reducing aquaculture productivity. Hence, there is an immense need for the discovery of alternative and efficient treatment for quick recovery of diseased fishes. In the present study, Suaeda maritima leaf extracts (hexane, diethyl ether, ethanol, and water) were screened for in vitro and in vivo antibacterial and antioxidant activities. Out of all the four extracts, ethanolic extract showed highest antibacterial activity against S. aureus (4.9 ± 1.3 mm), B. subtilis (1.6 ± 0.3 mm), K. pneumoniae (4.2 ± 1.8 mm), and P. aeruginosa (4.1 ± 1.2 mm). Similarly, antioxidant activity was also higher for ethanolic extract (500 µg/mL) based on DPPH radical scavenging ability (71.6 ± 1.4%) and reducing potential (149 μg/mL) assays. Further, ethanolic extract was purified consecutively via column chromatography and preparative TLC where an active fraction was selected based on highest antibacterial (10.1 ± 1.4 mm) and antioxidant properties (82.3 ± 2.8%). Active fraction was loaded onto mass spectroscopy and identified the presence of four active constituents such as 1,2,9,10-tetramethoxy-6-methyl-5,6,6a,7-tetrahydro-4H-dibenzo[de,g]quinolin-3-yl) methanol; 3',7-Dimethoxy-3-hydroxyflavone; Saponin and (19R)9acetyl19hydroxy10,14dimethyl20oxopentacyclo[11.8.0.0 < 2,10 > .0 < 4,9 > .0 < 14,19 >]henicos-17-yl-acetate. Besides, in vivo studies were conducted on Catla catla fingerlings infected with P. aeruginosa under laboratory conditions. The fingerlings were segregated into 5 groups, among which group 4 and 5 were treated with crude and purified extracts. Both the extracts were efficient in treating infected fingerlings and recorded 100% survival rate which is even better than group-3 treated with a synthetic antibiotic (77%). Hence, S. maritima leaf extract can be considered as a possible alternative medicine in aquaculture.
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Manuka R, Saddhe AA, Srivastava AK, Kumar K, Penna S. Overexpression of rice OsWNK9 promotes arsenite tolerance in transgenic Arabidopsis plants. J Biotechnol 2021; 332:114-125. [PMID: 33864842 DOI: 10.1016/j.jbiotec.2021.04.001] [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] [Received: 07/20/2020] [Revised: 03/03/2021] [Accepted: 04/11/2021] [Indexed: 12/25/2022]
Abstract
Protein kinases are involved in the transfer of phosphate group to serine, threonine, and tyrosine residues of a target protein. With No Lysine (WNK) kinase is a member of the serine/threonine protein kinase family, which has conserved catalytic lysine (K) residue in subdomain I instead of being in subdomain II.The WNKs family members in plants are stress inducible and have been validated for their role in abiotic stress tolerance. In the present study, we have characterized Arabidopsis overexpressed lines of OsWNK9 regulated by the constitutive promoter under arsenite stress. Moreover, we have performed In silico expression analysis of OsWNK9 under nutrient deficiency and heavy metal stress. Three independent transgenic Arabidopsis (OsWNK9-OX T11, T12,andT13) lines showed tolerance to arsenite stress compared to wild-type (WT) plants. Under arsenite stress, transgenic lines T11, T12 and T13 showed 56.46, 57.8 and 51.66 % increased biomass respectively, as compared to WT plants. All three ArabidopsisOsWNK9-OX lines exhibited higher proline content, increased antioxidant enzyme activities and lower hydrogen peroxide levels under arsenite stress. Besides, the total antioxidant capacity in terms of DPPH (2, 2-diphenyl-1-picrylhydrazyl) free radical scavenging percentage was increased by 8-15 % in three independent OsWNK9-OX lines compared with those of WT plants. Protein-protein interaction analysis of OsWNK9 predicted interaction partners with protein kinase and oxidative stress-responsive protein. Co-expression analysis of OsWNK9 in phosphate deficiency and arsenate stress condition predicted various proteins including membrane transporter and transcription factors. Taken together, our results, for the first time, provide evidence that OsWNK9 could positively mediate arsenite stress tolerance in plants.
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Affiliation(s)
- Rakesh Manuka
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400084, India; Department of Biological Sciences, Birla Institute of Technology & Science Pilani, K. K. Birla Goa Campus, Goa, 403726, India; Department of Biological Sciences and Biotechnology, Institute of Advanced Research (IAR), Gandhinagar, Gujarat, 382426, India
| | - Ankush Ashok Saddhe
- Department of Biological Sciences, Birla Institute of Technology & Science Pilani, K. K. Birla Goa Campus, Goa, 403726, India; Institute of Experimental Botany of the Czech Academy of Sciences, 16502 Prague 6, Czech Republic
| | - Ashish Kumar Srivastava
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400084, India
| | - Kundan Kumar
- Department of Biological Sciences, Birla Institute of Technology & Science Pilani, K. K. Birla Goa Campus, Goa, 403726, India.
| | - Suprasanna Penna
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400084, India.
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Mathew S, Victório CP, Sidhi M S J, B.H BT. Biosynthesis of silver nanoparticle using flowers of Calotropis gigantea (L.) W.T. Aiton and activity against pathogenic bacteria. ARAB J CHEM 2020. [DOI: 10.1016/j.arabjc.2020.10.038] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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Dahibhate NL, Kumar D, Kumar K. Determination of Bioactive Polyphenols in Mangrove Species and Their in-Vitro anti-Candida Activities by Ultra-High-Performance Liquid Chromatography – Electrospray Ionization – Tandem Mass Spectrometry (UPLC-ESI-MS/MS). ANAL LETT 2020. [DOI: 10.1080/00032719.2020.1774600] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Nilesh Lakshman Dahibhate
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, K. K. Birla Goa Campus, Sancoale, Goa, India
| | - Devendra Kumar
- Central Sophisticated Instrumentation Facility, Birla Institute of Technology & Science Pilani, K. K. Birla Goa Campus, Sancoale, Goa, India
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Kundan Kumar
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, K. K. Birla Goa Campus, Sancoale, Goa, India
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