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Nicoletti G, White K. The Anti-Fungal Activity of Nitropropenyl Benzodioxole (NPBD), a Redox-Thiol Oxidant and Tyrosine Phosphatase Inhibitor. Antibiotics (Basel) 2022; 11:antibiotics11091188. [PMID: 36139967 PMCID: PMC9495065 DOI: 10.3390/antibiotics11091188] [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: 08/05/2022] [Revised: 08/28/2022] [Accepted: 08/30/2022] [Indexed: 11/16/2022] Open
Abstract
Phylogenetically diverse fungal species are an increasing cause of severe disease and mortality. Identification of new targets and development of new fungicidal drugs are required to augment the effectiveness of current chemotherapy and counter increasing resistance in pathogens. Nitroalkenyl benzene derivatives are thiol oxidants and inhibitors of cysteine-based molecules, which show broad biological activity against microorganisms. Nitropropenyl benzodioxole (NPBD), one of the most active antimicrobial derivatives, shows high activity in MIC assays for phylogenetically diverse saprophytic, commensal and parasitic fungi. NPBD was fungicidal to all species except the dermatophytic fungi, with an activity profile comparable to that of Amphotericin B and Miconazole. NPBD showed differing patterns of dynamic kill rates under different growth conditions for Candida albicans and Aspergillus fumigatus and was rapidly fungicidal for non-replicating vegetative forms and microconidia. It did not induce resistant or drug tolerant strains in major pathogens on long term exposure. A literature review highlights the complexity and interactivity of fungal tyrosine phosphate and redox signaling pathways, their differing metabolic effects in fungal species and identifies some targets for inhibition. A comparison of the metabolic activities of Amphotericin B, Miconazole and NPBD highlights the multiple cellular functions of these agents and the complementarity of many mechanisms. The activity profile of NPBD illustrates the functional diversity of fungal tyrosine phosphatases and thiol-based redox active molecules and contributes to the validation of tyrosine phosphatases and redox thiol molecules as related and complementary selective targets for antimicrobial drug development. NPBD is a selective antifungal agent with low oral toxicity which would be suitable for local treatment of skin and mucosal infections.
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Cruz-Magalhães V, Nieto-Jacobo MF, Rostás M, Echaide-Aquino JF, Naranjo UE, Stewart A, Loguercio LL, Mendoza-Mendoza A. Histidine kinase two-component response regulators Ssk1, Skn7 and Rim15 differentially control growth, developmental and volatile organic compounds emissions as stress responses in Trichoderma atroviride. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100139. [PMID: 35909598 PMCID: PMC9325911 DOI: 10.1016/j.crmicr.2022.100139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 05/02/2022] [Accepted: 05/16/2022] [Indexed: 12/02/2022] Open
Abstract
Ssk1 may function as a hub-like RR in T. atroviride, as growth, and differentiation (conidiation). Skn7 has a significant role in the production of volatile organic compounds. Ssk1 and Rim15 have a role in mycoparasitism and both are negative regulators of volatile organic compounds. Rim15 seems to be a negative regulator of either the accumulation or biosynthesis of terpenes.
The Skn7, Ssk1 and Rim15 proteins are response regulators involved in osmotic, oxidative and nutritional stress in fungi. In order to verify the involvement of these genes in Trichoderma atroviride IMI206040’s growth, conidiation, direct antagonism against plant pathogens (Rhizoctonia solani and Sclerotinia sclerotiorum), production of volatile organic compounds (VOCs) with fungistatic effect, and interaction with plants (growth promotion), single mutants were generated, and the phenotypic patterns were analysed in comparison to the wild-type (wt) strain. The mutants were submitted to osmotic, oxidative, membrane and cell wall stress conditions in vitro. The Δskn7 and Δrim15 mutants did not show either significant differences at morphological level, or marked decreases in mycelial growth and conidiation in relation to wt, whereas Δssk1 had altered phenotypes in most conditions tested. The plant-growth promotion of Arabidopsis thaliana seedlings induced by VOCs was not quantitatively modified by any of the mutants in relation to the wt strain, although possible differences in secondary root hairs was noticed for Δrim15. The fungistatic activity was significantly altered for Δssk1 and Δrim15. Overall, the Δssk1 strain showed remarkable morphological differences, with decrease in mycelial growth and conidiation, being also affected in the antagonistic capacity against plant pathogens. The impacts demonstrated by the deletion of ssk1 suggest this gene has a relevant participation in the signalling response to different stresses in T. atroviride and in the interactive metabolism with phytopathogens and plants. On the other hand, unlike other fungal models, Skn7 did not appear to have a critical participation in the above-mentioned processes; Rim15 seemed to confirm its involvement in modulating cellular responses to nutritional status, although with a possible cross-talk with other cellular processes. Our results suggest that Ssk1 likely plays a key regulatory role, not only in basic metabolisms of T. atroviride, but also in biocontrol-related characteristics.
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Bharudin I, Ab Wahab AFF, Abd Samad MA, Xin Yie N, Zairun MA, Abu Bakar FD, Abdul Murad AM. Review Update on the Life Cycle, Plant–Microbe Interaction, Genomics, Detection and Control Strategies of the Oil Palm Pathogen Ganoderma boninense. BIOLOGY 2022; 11:biology11020251. [PMID: 35205119 PMCID: PMC8869222 DOI: 10.3390/biology11020251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/25/2022] [Accepted: 02/03/2022] [Indexed: 11/16/2022]
Abstract
Plant pathogens are key threats to agriculture and global food security, causing various crop diseases that lead to massive economic losses. Palm oil is a commodity export of economic importance in Southeast Asia, especially in Malaysia and Indonesia. However, the sustainability of oil palm plantations and production is threatened by basal stem rot (BSR), a devastating disease predominantly caused by the fungus Ganoderma boninense Pat. In Malaysia, infected trees have been reported in nearly 60% of plantation areas, and economic losses are estimated to reach up to ~USD500 million a year. This review covers the current knowledge of the mechanisms utilized by G. boninense during infection and the methods used in the disease management to reduce BSR, including cultural practices, chemical treatments and antagonistic microorganism manipulations. Newer developments arising from multi-omics technologies such as whole-genome sequencing (WGS) and RNA sequencing (RNA-Seq) are also reviewed. Future directions are proposed to increase the understanding of G. boninense invasion mechanisms against oil palm. It is hoped that this review can contribute towards an improved disease management and a sustainable oil palm production in this region.
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Affiliation(s)
- Izwan Bharudin
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM, Bangi 43600, Malaysia; (A.F.F.A.W.); (M.A.A.S.); (N.X.Y.); (M.A.Z.); (F.D.A.B.); (A.M.A.M.)
- Fraser’s Hill Research Centre (PPBF), Faculty of Science & Technology, Universiti Kebangsaan Malaysia, UKM, Bangi 43600, Malaysia
- Correspondence:
| | - Anis Farhan Fatimi Ab Wahab
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM, Bangi 43600, Malaysia; (A.F.F.A.W.); (M.A.A.S.); (N.X.Y.); (M.A.Z.); (F.D.A.B.); (A.M.A.M.)
- FGV Innovation Centre (Biotechnology), Pt. 23417 Lengkuk Teknologi, Bandar Enstek 71760, Malaysia
| | - Muhammad Asyraff Abd Samad
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM, Bangi 43600, Malaysia; (A.F.F.A.W.); (M.A.A.S.); (N.X.Y.); (M.A.Z.); (F.D.A.B.); (A.M.A.M.)
| | - Ng Xin Yie
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM, Bangi 43600, Malaysia; (A.F.F.A.W.); (M.A.A.S.); (N.X.Y.); (M.A.Z.); (F.D.A.B.); (A.M.A.M.)
| | - Madihah Ahmad Zairun
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM, Bangi 43600, Malaysia; (A.F.F.A.W.); (M.A.A.S.); (N.X.Y.); (M.A.Z.); (F.D.A.B.); (A.M.A.M.)
- Plant Pathology & Biosecurity Unit, Biology & Sustainability Research Division, 6, Malaysian Palm Oil Board, Bandar Baru Bangi, Kajang 43000, Malaysia
| | - Farah Diba Abu Bakar
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM, Bangi 43600, Malaysia; (A.F.F.A.W.); (M.A.A.S.); (N.X.Y.); (M.A.Z.); (F.D.A.B.); (A.M.A.M.)
| | - Abdul Munir Abdul Murad
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM, Bangi 43600, Malaysia; (A.F.F.A.W.); (M.A.A.S.); (N.X.Y.); (M.A.Z.); (F.D.A.B.); (A.M.A.M.)
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Carrasco-Navarro U, Aguirre J. H 2O 2 Induces Major Phosphorylation Changes in Critical Regulators of Signal Transduction, Gene Expression, Metabolism and Developmental Networks in Aspergillus nidulans. J Fungi (Basel) 2021; 7:624. [PMID: 34436163 PMCID: PMC8399174 DOI: 10.3390/jof7080624] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 12/13/2022] Open
Abstract
Reactive oxygen species (ROS) regulate several aspects of cell physiology in filamentous fungi including the antioxidant response and development. However, little is known about the signaling pathways involved in these processes. Here, we report Aspergillus nidulans global phosphoproteome during mycelial growth and show that under these conditions, H2O2 induces major changes in protein phosphorylation. Among the 1964 phosphoproteins we identified, H2O2 induced the phosphorylation of 131 proteins at one or more sites as well as the dephosphorylation of a larger set of proteins. A detailed analysis of these phosphoproteins shows that H2O2 affected the phosphorylation of critical regulatory nodes of phosphoinositide, MAPK, and TOR signaling as well as the phosphorylation of multiple proteins involved in the regulation of gene expression, primary and secondary metabolism, and development. Our results provide a novel and extensive protein phosphorylation landscape in A. nidulans, indicating that H2O2 induces a shift in general metabolism from anabolic to catabolic, and the activation of multiple stress survival pathways. Our results expand the significance of H2O2 in eukaryotic cell signaling.
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Affiliation(s)
| | - Jesús Aguirre
- Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Apartado Postal 70-242, Ciudad de México 04510, Mexico;
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Novel Structural Variation and Evolutionary Characteristics of Chloroplast tRNA in Gossypium Plants. Genes (Basel) 2021; 12:genes12060822. [PMID: 34071968 PMCID: PMC8228828 DOI: 10.3390/genes12060822] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/16/2021] [Accepted: 05/24/2021] [Indexed: 11/16/2022] Open
Abstract
Cotton is one of the most important fiber and oil crops in the world. Chloroplast genomes harbor their own genetic materials and are considered to be highly conserved. Transfer RNAs (tRNAs) act as "bridges" in protein synthesis by carrying amino acids. Currently, the variation and evolutionary characteristics of tRNAs in the cotton chloroplast genome are poorly understood. Here, we analyzed the structural variation and evolution of chloroplast tRNA (cp tRNA) based on eight diploid and two allotetraploid cotton species. We also investigated the nucleotide evolution of chloroplast genomes in cotton species. We found that cp tRNAs in cotton encoded 36 or 37 tRNAs, and 28 or 29 anti-codon types with lengths ranging from 60 to 93 nucleotides. Cotton chloroplast tRNA sequences possessed specific conservation and, in particular, the Ψ-loop contained the conserved U-U-C-X3-U. The cp tRNAs of Gossypium L. contained introns, and cp tRNAIle contained the anti-codon (C-A-U), which was generally the anti-codon of tRNAMet. The transition and transversion analyses showed that cp tRNAs in cotton species were iso-acceptor specific and had undergone unequal rates of evolution. The intergenic region was more variable than coding regions, and non-synonymous mutations have been fixed in cotton cp genomes. On the other hand, phylogeny analyses indicated that cp tRNAs of cotton were derived from several inferred ancestors with greater gene duplications. This study provides new insights into the structural variation and evolution of chloroplast tRNAs in cotton plants. Our findings could contribute to understanding the detailed characteristics and evolutionary variation of the tRNA family.
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Mohanta TK, Mishra AK, Hashem A, Qari SH, Abd Allah EF, Khan AL, Al-Harrasi A. Genome-wide analysis revealed novel molecular features and evolution of Anti-codons in cyanobacterial tRNAs. Saudi J Biol Sci 2019; 27:1195-1200. [PMID: 32346324 PMCID: PMC7182786 DOI: 10.1016/j.sjbs.2019.12.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 12/01/2019] [Accepted: 12/11/2019] [Indexed: 11/30/2022] Open
Abstract
Transfer RNAs (tRNAs) play important roles to decode the genetic information contained in mRNA in the process of translation. The tRNA molecules possess conserved nucleotides at specific position to regulate the unique function. However, several nucleotides at different position of the tRNA undergo modification to maintain proper stability and function. The major modifications include the presence of pseudouridine (Ψ) residue instead of uridine and the presence of m5-methylation sites. We found that, Ψ13 is conserved in D-stem, whereas Ψ38 & Ψ39 were conserved in the anti-codon loop (AL) and anti-codon arm (ACA), respectively. Furthermore, Ψ55 found to be conserved in the Ψ loop. Although, fourteen possible methylation sites can be found in the tRNA, cyanobacterial tRNAs were found to possess conserved G9, m3C32, C36, A37, m5C38 and U54 methylation sites. The presence of multiple conserved methylation sites might be responsible for providing necessary stability to the tRNA. The evolutionary study revealed, tRNAMet and tRNAIle were evolved earlier than other tRNA isotypes and their evolution is date back to at least 4000 million years ago. The presence of novel pseudouridination and m5-methylation sites in the cyanobacterial tRNAs are of particular interest for basic biology. Further experimental study can delineate their functional significance in protein translation.
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Affiliation(s)
- Tapan Kumar Mohanta
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Oman
| | | | - Abeer Hashem
- Botany and Microbiology Department, College of Science, King Saud University, 11451 Riyadh, Saudi Arabia.,Mycology and Plant Disease Survey Department, Plant Pathology Research Institute, Agriculture Research Center, Giza, Egypt
| | - Sameer H Qari
- Biology Department, Aljumum University College, Umm Al-Qura University, Holy Makkah, Saudi Arabia
| | - Elsayed Fathi Abd Allah
- Plant Production Department, College of Food and Agriculture Science, King Saud University, 11451 Riyadh, Saudi Arabia
| | - Abdul Latif Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Oman
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Oman
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Yu XJ, Chen H, Huang CY, Zhu XY, Wang ZP, Wang DS, Liu XY, Sun J, Zheng JY, Li HJ, Wang Z. Transcriptomic Mechanism of the Phytohormone 6-Benzylaminopurine (6-BAP) Stimulating Lipid and DHA Synthesis in Aurantiochytrium sp. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:5560-5570. [PMID: 30901205 DOI: 10.1021/acs.jafc.8b07117] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The phytohormone 6-benzylaminopurine (6-BAP) significantly improves lipid synthesis of oleaginous microorganisms with the great potential applied in lipid production. In the current study, the lipid and DHA productions in oleaginous Aurantiochytrium sp. were found to be improved by 48.7% and 55.3%, respectively, induced by 6-BAP treatments. Then, using high-throughput RNA-seq technology, the overall de novo assembly of the cDNA sequence data generated 53871 unigenes, and 15902 of these were annotated in at least one database. The comparative transcriptomic profiles of cells with and without 6-BAP treatments revealed that a total of 717 were differently expressed genes (DE), with 472 upregulated and 245 downregulated. Further annotation and categorization indicated that some DE genes were involved in pathways crucial to lipid and DHA productions, such as fatty acid synthesis, central carbon metabolism, transcriptional factor, signal transduction, and mevalonate pathway. A regulation mode of 6-BAP, in turn, perception and transduction of 6-BAP signal, transcription factor, expression regulations of the downstream genes, and metabolic changes, respectively, was put forward for the first time in the present study. This research illuminates the transcriptomic mechanism of phytohormone stimulation of lipid and DHA production in an oleaginous microorganism and provides the potential targets modified using genetic engineering for improving lipid and DHA productivity.
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Affiliation(s)
- Xin-Jun Yu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering , Zhejiang University of Technology , No. 18, Chaowang Road , Hangzhou 310014 , People's Republic of China
| | - Hong Chen
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering , Zhejiang University of Technology , No. 18, Chaowang Road , Hangzhou 310014 , People's Republic of China
| | - Chang-Yi Huang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering , Zhejiang University of Technology , No. 18, Chaowang Road , Hangzhou 310014 , People's Republic of China
| | - Xiao-Yu Zhu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering , Zhejiang University of Technology , No. 18, Chaowang Road , Hangzhou 310014 , People's Republic of China
| | - Zhi-Peng Wang
- Key Laboratory of Sustainable Development of Polar Fishery, Ministry of Agriculture and Rural Affairs , Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Qingdao 266071 , Shandong , People's Republic of China
| | - Dong-Sheng Wang
- Institute of Biological Resources , Jiangxi Academy of Sciences , Nanchang 330096 , Jiangxi , People's Republic of China
| | - Xiao-Yan Liu
- Jiangsu Key Laboratory for Biomass-based Energy and Enzyme Technology , Huaiyin Normal University , Huaian 223300 , People's Republic of China
| | - Jie Sun
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering , Zhejiang University of Technology , No. 18, Chaowang Road , Hangzhou 310014 , People's Republic of China
| | - Jian-Yong Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering , Zhejiang University of Technology , No. 18, Chaowang Road , Hangzhou 310014 , People's Republic of China
| | - Hui-Juan Li
- Department of Bioengineering, College of Chemical and Environmental Engineering , Shandong University of Science and Technology , Qingdao 266590 , People's Republic of China
| | - Zhao Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering , Zhejiang University of Technology , No. 18, Chaowang Road , Hangzhou 310014 , People's Republic of China
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Komis G, Šamajová O, Ovečka M, Šamaj J. Cell and Developmental Biology of Plant Mitogen-Activated Protein Kinases. ANNUAL REVIEW OF PLANT BIOLOGY 2018; 69:237-265. [PMID: 29489398 DOI: 10.1146/annurev-arplant-042817-040314] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Plant mitogen-activated protein kinases (MAPKs) constitute a network of signaling cascades responsible for transducing extracellular stimuli and decoding them to dedicated cellular and developmental responses that shape the plant body. Over the last decade, we have accumulated information about how MAPK modules control the development of reproductive tissues and gametes and the embryogenic and postembryonic development of vegetative organs such as roots, root nodules, shoots, and leaves. Of key importance to understanding how MAPKs participate in developmental and environmental signaling is the characterization of their subcellular localization, their interactions with upstream signal perception mechanisms, and the means by which they target their substrates. In this review, we summarize the roles of MAPK signaling in the regulation of key plant developmental processes, and we survey what is known about the mechanisms guiding the subcellular compartmentalization of MAPK modules.
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Affiliation(s)
- George Komis
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, 783 71 Olomouc, Czech Republic;
| | - Olga Šamajová
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, 783 71 Olomouc, Czech Republic;
| | - Miroslav Ovečka
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, 783 71 Olomouc, Czech Republic;
| | - Jozef Šamaj
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, 783 71 Olomouc, Czech Republic;
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Mohanta TK, Syed AS, Ameen F, Bae H. Novel Genomic and Evolutionary Perspective of Cyanobacterial tRNAs. Front Genet 2017; 8:200. [PMID: 29321793 PMCID: PMC5733544 DOI: 10.3389/fgene.2017.00200] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 11/21/2017] [Indexed: 11/30/2022] Open
Abstract
Transfer RNA (tRNA) plays a central role in protein synthesis and acts as an adaptor molecule between an mRNA and an amino acid. A tRNA has an L-shaped clover leaf-like structure and contains an acceptor arm, D-arm, D-loop, anti-codon arm, anti-codon loop, variable loop, Ψ-arm and Ψ-loop. All of these arms and loops are important in protein translation. Here, we aimed to delineate the genomic architecture of these arms and loops in cyanobacterial tRNA. Studies from tRNA sequences from 61 cyanobacterial species showed that, except for few tRNAs (tRNAAsn, tRNALeu, tRNAGln, and tRNAMet), all contained a G nucleotide at the 1st position in the acceptor arm. tRNALeu and tRNAMet did not contain any conserved nucleotides at the 1st position whereas tRNAAsn and tRNAGln contained a conserved U1 nucleotide. In several tRNA families, the variable region also contained conserved nucleotides. Except for tRNAMet and tRNAGlu, all other tRNAs contained a conserved A nucleotide at the 1st position in the D-loop. The Ψ-loop contained a conserved U1-U2-C3-x-A5-x-U7 sequence, except for tRNAGly, tRNAAla, tRNAVal, tRNAPhe, tRNAThr, and tRNAGln in which the U7 nucleotide was not conserved. However, in tRNAAsp, the U7 nucleotide was substituted with a C7 nucleotide. Additionally, tRNAArg, tRNAGly, and tRNALys of cyanobacteria contained a group I intron within the anti-codon loop region. Maximum composite likelihood study on the transition/transversion of cyanobacterial tRNA revealed that the rate of transition was higher than the rate of transversion. An evolutionary tree was constructed to understand the evolution of cyanobacterial tRNA and analyses revealed that cyanobacterial tRNA may have evolved polyphyletically with high rate of gene loss.
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Affiliation(s)
- Tapan K Mohanta
- School of Biotechnology, Yeungnam University, Gyeongsan, South Korea
| | - Asad S Syed
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Fuad Ameen
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Hanhong Bae
- School of Biotechnology, Yeungnam University, Gyeongsan, South Korea
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