Transcriptome analysis and identification of candidate genes involved in glyphosate resistance in the fungus Fusarium verticillioides

References

• Amrhein, N.; Deus, B.; Gehrke, P.; Steinrucken, H. C. The Site of the Inhibition of the Shikimate Pathway by Glyphosate: II. Interference of Glyphosate with Chorismate Formation in Vivo and in Vitro. Plant Physiol. 1980, 66, 830–834. DOI: 10.1104/pp.66.5.830.
   PubMed Web of Science ®Google Scholar
• Lanie, A. J.; Griffin, J. L.; Vidrine, P. R.; Reynolds, D. B. Herbicide Combinations for Soybean (Glycine max) Planted in Stale Seedbed. Weed Technol. 1994, 8, 17–22. DOI: 10.1017/S0890037X00039130.
   Web of Science ®Google Scholar
• Li, A. P.; Long, T. J. An Evaluation of the Genotoxic Potential of Glyphosate. Fundam. Appl. Toxicol. 1988, 10, 537–546. DOI: 10.1016/0272-0590(88)90300-4.
   PubMedGoogle Scholar
• Mesnage, R.; Antoniou, M. N. Facts and Fallacies in the Debate on Glyphosate Toxicity. Front Public Health 2017, 5, 316. DOI: 10.3389/fpubh.2017.00316.
   PubMed Web of Science ®Google Scholar
• Beckie, H. J.; Flower, K. C.; Ashworth, M. B. Farming without Glyphosate? Plants (Basel ) 2020, 9, 96. DOI: 10.3390/plants9010096.
   PubMedGoogle Scholar
• Cruvinel, G. T.; Neves, H. I.; Spira, B. Glyphosate Induces the Synthesis of ppGpp. Mol Genet Genom. 2019, 294, 191–198. DOI: 10.1007/s00438-018-1499-1.
   PubMed Web of Science ®Google Scholar
• Zhou, M.; Xu, H.; Wei, X.; Ye, Z.; Wei, L.; Gong, W.; Wang, Y.; Zhu, Z. Identification of a Glyphosate-Resistant Mutant of Rice 5-Enolpyruvylshikimate 3-Phosphate Synthase Using a Directed Evolution Strategy. Plant Physiol. 2006, 140, 184–195. DOI: 10.1104/pp.105.068577.
   PubMed Web of Science ®Google Scholar
• Moore, J. K.; Braymer, H. D.; Larson, A. D. Isolation of a Pseudomonas sp. which Utilizes the Phosphonate Herbicide Glyphosate. Appl. Environ. Microbiol. 1983, 46, 316–320. DOI: 10.1128/aem.46.2.316-320.1983.
   PubMed Web of Science ®Google Scholar
• Sh, J.; Jin, D.; Lu, W.; Zhang, X.; Zhang, C.; Li, L.; Ma, R.; Xiao, L.; Wang, Y.; Lin, M. Isolation and Characterization of a New Glyphosate-Resistant Strain from Extremely Polluted Environment. Weishengwu Xuebao 2008, 48, 824–828.
   Google Scholar
• Zhang, C.; Wu, D. D.; Feng, L.; Tian, X. S.; Guo, A. L. Cloning and Resistance Verification of a Target Gene of Glyphosate from Klebsiella pneumoniae S001. Sci. Agric. Sin. 2014, 475, 80–89.
   Google Scholar
• Manogaran, M.; Shukor, M. Y.; Yasid, N. A.; Johari, W. L. W.; Ahmad, S. A. Isolation and Characterisation of Glyphosate-Degrading Bacteria Isolated from Local Soils in Malaysia. Rend. Fis. Acc. Lincei 2017, 28, 471–479. DOI: 10.1007/s12210-017-0620-4.
   Google Scholar
• Sviridov, A. V.; Shushkova, T. V.; Ermakova, I. T.; Ivanova, E. V.; Epiktetov, D. O.; Leontievsky, A. A. Microbial Degradation of Glyphosate Herbicides (Review). Appl. Biochem. Microbiol. 2015, 51, 188–195. DOI: 10.1134/S0003683815020209.
   Web of Science ®Google Scholar
• Singh, B. K.; Walker, A. Microbial Degradation of Organophosphorus Compounds. FEMS Microbiol. Rev. 2006, 30, 428–471. DOI: 10.1111/j.1574-6976.2006.00018.x.
   PubMed Web of Science ®Google Scholar
• Kryuchkova, Y. V.; Burygin, G. L.; Gogoleva, N. E.; Gogolev, Y. V.; Chernyshova, M. P.; Makarov, O. E.; Fedorov, E. E.; Turkovskaya, O. V. Isolation and Characterization of a Glyphosate-Degrading Rhizosphere Strain, Enterobacter cloacae K7. Microbiol. Res. 2014, 169, 99–105. DOI: 10.1016/j.micres.2013.03.002.
   PubMed Web of Science ®Google Scholar
• Zhao, T.; Lin, C. Y.; Shen, Z. C. Development of Transgenic Glyphosate-Resistant Rice with g6 Gene Encoding 5-Enolpyruvylshikimate-3-Phosphate Synthase. Agric. Sci. China 2011, 10, 1307–1312. DOI: 10.1016/S1671-2927(11)60123-5.
   Google Scholar
• Howe, A. R.; Gasser, C. S.; Brown, S. M.; Padgette, S. R.; Hart, J.; Parker, G. B.; Fromm, M. E.; Armstrong, C. L. Glyphosate as a Selective Agent for the Production of Fertile Transgenic Maize (Zea Mays L.) Plants. Mol. Breed 2002, 10, 153–164. DOI: 10.1023/A:1020396708088.
   Web of Science ®Google Scholar
• Zhao, F.; Xie, L. X.; Tian, Y. C.; Xu, P. Glyphosate-Resistant and Bollworm-Resistant Transgenic Cotton Plants with the aroAM12 and Bts1m Genes. Acta Agron. Sin. 2005, 31, 108–113.
   Google Scholar
• Guttikonda, S. K.; Valliyodan, B.; Neelakandan, A. K.; Tran, L. S.; Kumar, R.; Quach, T. N.; Voothuluru, P.; Gutierrez-Gonzalez, J. J.; Aldrich, D. L.; Pallardy, S. G.; et al. Overexpression of AtDREB1D Transcription Factor Improves Drought Tolerance in Soybean. Mol. Biol. Rep. 2014, 41, 7995–8008. DOI: 10.1007/s11033-014-3695-3.
   PubMed Web of Science ®Google Scholar
• Tao, B.; Shao, B. H.; Qiao, Y. X.; Wang, X. Q.; Chang, S. J.; Qiu, L. J. Identification and Functional Analysis of a New Glyphosate Resistance Gene from a Fungus cDNA Library. Pestic. Biochem. Physiol. 2017, 140, 65–68. DOI: 10.1016/j.pestbp.2017.05.013.
   PubMed Web of Science ®Google Scholar
• Liu, F.; Wang, W.; Chen, B. Z.; Xie, B. G. Homocitrate Synthase Expression and Lysine Content in Fruiting Body of Different Developmental Stages in Flammulina Velutipes. Curr. Microbiol. 2015, 70, 821–828. DOI: 10.1007/s00284-015-0791-0.
   PubMed Web of Science ®Google Scholar
• Hellin, P.; King, R.; Urban, M.; Hammond-Kosack, K. E.; Legreve, A. The Adaptation of Fusarium Culmorum to DMI Fungicides is Mediated by Major Transcriptome Modifications in Response to Azole Fungicide, Including the Overexpression of a PDR Transporter (FcABC1). Front. Microbiol. 2018, 9, 1385. DOI: 10.3389/fmicb.2018.01385.
   PubMed Web of Science ®Google Scholar
• Lai, P. J.; Ng, E. V.; Yang, S. K.; Moo, C. L.; Low, W. Y.; Yap, P. S. X.; Lim, S. H. E.; Lai, K. S. Transcriptomic Analysis of Multi-Drug Resistant Escherichia coli K-12 Strain in Response to Lavandula Angustifolia Essential Oil. 3 Biotech 2020, 10, 313. DOI: 10.1007/s13205-020-02304-3.
   PubMedGoogle Scholar
• Riordan, J. T.; Dupre, J. M.; Cantore-Matyi, S. A.; Kumar-Singh, A.; Song, Y.; Zaman, S.; Horan, S.; Helal, N. S.; Nagarajan, V.; Elasri, M. O.; et al. Alterations in the Transcriptome and Antibiotic Susceptibility of Staphylococcus aureus Grown in the Presence of Diclofenac. Ann. Clin. Microbiol. Antimicrob. 2011, 10, 30. DOI: 10.1186/1476-0711-10-30.
   PubMed Web of Science ®Google Scholar
• Beseli, A.; da Silva, M. G.; Daub, M. E. The Role of Cercospora Zeae-Maydis Homologs of Rhodobacter sphaeroides 1O2-Resistance Genes in Resistance to the Photoactivated Toxin Cercosporin. FEMS Microbiol. Lett. 2015, 362, 1–7. DOI: 10.1093/femsle/fnu036.
   PubMed Web of Science ®Google Scholar
• Versluis, D.; D'Andrea, M. M.; Garcia, J. R.; Leimena, M. M.; Hugenholtz, F.; Zhang, J.; Ozturk, B.; Nylund, L.; Sipkema, D.; van Schaik, W.; et al. Mining Microbial Metatranscriptomes for Expression of Antibiotic Resistance Genes under Natural Conditions. Sci. Rep. 2015, 5, 11981. DOI: 10.1038/srep11981.
   PubMed Web of Science ®Google Scholar
• Khaledi, A.; Schniederjans, M.; Pohl, S.; Rainer, R.; Bodenhofer, U.; Xia, B.; Klawonn, F.; Bruchmann, S.; Preusse, M.; Eckweiler, D.; et al. Transcriptome Profiling of Antimicrobial Resistance in Pseudomonas aeruginosa. Antimicrob Agents Chemother. 2016, 60, 4722–4733. DOI: 10.1128/AAC.00075-16.
   PubMed Web of Science ®Google Scholar
• Alkasir, R.; Ma, Y.; Liu, F.; Li, J.; Lv, N.; Xue, Y.; Hu, Y.; Zhu, B. Characterization and Transcriptome Analysis of Acinetobacter baumannii Persister Cells. Microb. Drug Resist. 2018, 24, 1466–1474. DOI: 10.1089/mdr.2017.0341.
   PubMed Web of Science ®Google Scholar
• Bleriot, I.; Blasco, L.; Delgado-Valverde, M.; Gual-de-Torrella, A.; Ambroa, A.; Fernandez-Garcia, L.; Lopez, M.; Oteo-Iglesias, J.; Wood, T. K.; Pascual, A.; et al. Mechanisms of Tolerance and Resistance to Chlorhexidine in Clinical Strains of Klebsiella pneumoniae Producers of Carbapenemase: role of New Type II Toxin-Antitoxin System, PemIK. Toxins (Basel) 2020, 12, 566. DOI: 10.3390/toxins12090566.
   PubMed Web of Science ®Google Scholar
• Cools, H. J.; Hammond-Kosack, K. E. Exploitation of Genomics in Fungicide Research: current Status and Future Perspectives. Mol. Plant Pathol. 2013, 14, 197–210. DOI: 10.1111/mpp.12001.
   PubMed Web of Science ®Google Scholar
• Kim, D.; Langmead, B.; Salzberg, S. L. HISAT: A Fast Spliced Aligner with Low Memory Requirements. Nat. Methods. 2015, 12, 357–360. DOI: 10.1038/nmeth.3317.
   PubMed Web of Science ®Google Scholar
• DeLuca, D. S.; Levin, J. Z.; Sivachenko, A.; Fennell, T.; Nazaire, M. D.; Williams, C.; Reich, M.; Winckler, W.; Getz, G. RNA-SeQC: RNA-Seq Metrics for Quality Control and Process Optimization. Bioinformatics 2012, 28, 1530–1532. DOI: 10.1093/bioinformatics/bts196.
   PubMed Web of Science ®Google Scholar
• Trapnell, C.; Roberts, A.; Goff, L.; Pertea, G.; Kim, D.; Kelley, D. R.; Pimentel, H.; Salzberg, S. L.; Rinn, J. L.; Pachter, L. Differential Gene and Transcript Expression Analysis of RNA-Seq Experiments with TopHat and Cufflinks. Nat. Protoc. 2012, 7, 562–578. DOI: 10.1038/nprot.2012.016.
   PubMed Web of Science ®Google Scholar
• Wang, R.; Lin, Y.; Jin, Q.; Yao, C.; Zhong, Y.; Wu, T. RNA-Seq Analysis of Gynoecious and Weak Female Cucumber Revealing the Cell Cycle Pathway May Regulate Sex Determination in Cucumber. Gene 2019, 687, 289–297. DOI: 10.1016/j.gene.2018.11.071.
   PubMed Web of Science ®Google Scholar
• Glass, N. L.; Donaldson, G. C. Development of Primer Sets Designed for Use with the PCR to Amplify Conserved Genes from Filamentous Ascomycetes. Appl. Environ. Microbiol. 1995, 61, 1323–1330. DOI: 10.1128/aem.61.4.1323-1330.1995.
   PubMed Web of Science ®Google Scholar
• Iqbal, Z.; Seleem, M. N.; Hussain, H. I.; Huang, L.; Hao, H.; Yuan, Z. Comparative Virulence Studies and Transcriptome Analysis of Staphylococcus aureus Strains Isolated from Animals. Sci. Rep. 2016, 6, 35442. DOI: 10.1038/srep35442.
   PubMed Web of Science ®Google Scholar
• Schmittgen, T. D.; Livak, K. J. Analyzing Real-Time PCR Data by the Comparative CT Method. Nat. Protoc. 2008, 3, 1101–1108. DOI: 10.1038/nprot.2008.73.
   PubMed Web of Science ®Google Scholar
• Schwartz, T.; Armant, O.; Bretschneider, N.; Hahn, A.; Kirchen, S.; Seifert, M.; Dötsch, A. Whole Genome and Transcriptome Analyses of Environmental Antibiotic Sensitive and Multi-Resistant Pseudomonas aeruginosa Isolates Exposed to Waste Water and Tap Water. Microb. Biotechnol. 2015, 8, 116–130. DOI: 10.1111/1751-7915.12156.
   PubMed Web of Science ®Google Scholar
• Liu, J.; Wang, S.; Qin, T.; Li, N.; Niu, Y.; Li, D.; Yuan, Y.; Geng, H.; Xiong, L.; Liu, D. Whole Transcriptome Analysis of Penicillium Digitatum Strains Treatmented with Prochloraz Reveals Their Drug-Resistant Mechanisms. BMC Genom. 2015, 16, 855. DOI: 10.1186/s12864-015-2043-x.
   PubMed Web of Science ®Google Scholar
• de Welzen, L.; Eldholm, V.; Maharaj, K.; Manson, A. L.; Earl, A. M.; Pym, A. S. Whole-Transcriptome and -Genome Analysis of Extensively Drug-Resistant mycobacterium tuberculosis Clinical Isolates Identifies Downregulation of ethA as a Mechanism of Ethionamide Resistance. Antimicrob. Agents Chemother. 2017, 61, e01461–e01417.
   PubMed Web of Science ®Google Scholar
• Yuan, M.; Chen, M.; Zhang, W.; Lu, W.; Wang, J.; Yang, M.; Zhao, P.; Tang, R.; Li, X.; Hao, Y.; et al. Genome Sequence and Transcriptome Analysis of the Radioresistant Bacterium Deinococcus gobiensis: insights into the Extreme Environmental Adaptations. PLoS One. 2012, 7, e34458. DOI: 10.1371/journal.pone.0034458.
   PubMed Web of Science ®Google Scholar
• Bilz, N. C.; Jahn, K.; Lorenz, M.; Ludtke, A.; Hubschen, J. M.; Geyer, H.; Mankertz, A.; Hubner, D.; Liebert, U. G.; Claus, C. Rubella Viruses Shift Cellular Bioenergetics to a More Oxidative and Glycolytic Phenotype with a Strain-Specific Requirement for Glutamine. J. Virol. 2018, 92, e00934–18.
   PubMed Web of Science ®Google Scholar
• Lu, W.; Li, L.; Chen, M.; Zhou, Z.; Zhang, W.; Ping, S.; Yan, Y.; Wang, J.; Lin, M. Genome-Wide Transcriptional Responses of Escherichia coli to Glyphosate, a Potent Inhibitor of the Shikimate Pathway Enzyme 5-Enolpyruvylshikimate-3-Phosphate Synthase. Mol. Biosyst. 2013, 9, 522–530. DOI: 10.1039/c2mb25374g.
   PubMedGoogle Scholar
• Newman, M. M.; Lorenz, N.; Hoilett, N.; Lee, N. R.; Dick, R. P.; Liles, M. R.; Ramsier, C.; Kloepper, J. W. Changes in Rhizosphere Bacterial Gene Expression following Glyphosate Treatment. Sci. Total Environ. 2016, 553, 32–41. DOI: 10.1016/j.scitotenv.2016.02.078.
   PubMed Web of Science ®Google Scholar
• Fei, Y. Y.; Gai, J. Y.; Zhao, T. J. Identification of Regulated Genes Conferring Resistance to High Concentrations of Glyphosate in a New Strain of Enterobacter. FEMS Microbiol. Lett. 2013, 349, 135–143. DOI: 10.1111/1574-6968.12306.
   PubMed Web of Science ®Google Scholar
• Fateh, R.; Zaini, F.; Kordbacheh, P.; Falahati, M.; Rezaie, S.; Ghazvini, R. D.; Borhani, N.; Safara, M.; Fattahi, A.; Kanani, A.; et al. Identification and Sequencing of candida krusei Aconitate Hydratase Gene Using Rapid Amplification of cDNA Ends Method and Phylogenetic Analysis. Jundishapur J. Microbiol. 2015, 8, e25218. DOI: 10.5812/jjm.25218.
   PubMed Web of Science ®Google Scholar
• Terol, J.; Soler, G.; Talon, M.; Cercos, M. The Aconitate Hydratase Family from Citrus. BMC Plant Biol. 2010, 10, 222. DOI: 10.1186/1471-2229-10-222.
   PubMed Web of Science ®Google Scholar
• Pan, T. F.; Li, Y. Y.; Qiu, D. L. A Review of Molecular Mechanism during the Formation of Fruit Quality. Subtrop. Plant Sci. 2006, 35, 81–84.
   Google Scholar
• Lee, E. H.; Cho, Y. W.; Hwang, K. Y. Crystal Structure of LeuD from Methanococcus jannaschii. Biochem. Biophys. Res. Commun. 2012, 419, 160–164. DOI: 10.1016/j.bbrc.2012.01.125.
   PubMed Web of Science ®Google Scholar
• Jiang, Z. X.; 1 Department of Biology, Texas A&M University, College Station, TX 77840, USA,1 Department of Biology, Texas A & M University, College Station, TX 77840, USA; Wang, P.; Ma, X. Y.; Tian, J.; Zhang, J.; Jiang, H.; Shi, J.; Wang, Z. A. Discussion on the Biochemical Similarity in Metabolic Principles Based on Leucine Biosynthesis Pathway. Univ. Chem. 2019, 34, 80–87. DOI: 10.3866/PKU.DXHX201808004.
   Google Scholar
• Morohoshi, T.; Kamimura, Y.; Sato, N.; Iizumi, T. Distribution and Characterization of N-Acylhomoserine Lactone (AHL)-Degrading Activity and AHL Lactonase Gene (qsdS) in Sphingopyxis. J. Biosci. Bioeng. 2019, 127, 411–417. DOI: 10.1016/j.jbiosc.2018.10.005.
   PubMed Web of Science ®Google Scholar