RNA-Seq analysis of Citrus reticulata in the early stages of Xylella fastidiosa infection reveals auxin-related genes as a defense response

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Rodrigues, Carolina M ^a   de Souza, Alessandra A ^a   Takita, Marco A ^a   Kishi, Luciano T ^b   Machado, Marcos A ^a  

^a Centro APTA Citros Sylvio Moreira/IAC   (Brazil)

^b FEDERAL UNIVERSITY OF SÃO CARLOS   (Brazil)

Author keywords

CVC; Gene expression; Pera sweet orange; Plant pathogen interaction; Ponkan mandarin; Resistance

Indexed keywords

ABSCISIC ACID; AUXIN; JASMONIC ACID; PATTERN RECOGNITION RECEPTOR; PLANT RNA; INDOLEACETIC ACID DERIVATIVE; UBIQUITIN; VEGETABLE PROTEIN;

ARTICLE; BACTERIUM IDENTIFICATION; BIOSYNTHESIS; CONTROLLED STUDY; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; GENETIC TRANSCRIPTION; GENOME ANALYSIS; HORMONE SYNTHESIS; MANDARIN; MOLECULAR DYNAMICS; NONHUMAN; PLANT DISEASE; PLANT GENE; PLANT GENOME; PLANT METABOLISM; PROTEIN DETERMINATION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION; SPECIES COMPARISON; SWEET ORANGE; UPREGULATION; XYLELLA FASTIDIOSA; CELL WALL; CITRUS; DRUG EFFECTS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; IMMUNOLOGY; METABOLISM; MICROBIOLOGY; PHYSIOLOGICAL STRESS; PHYSIOLOGY; PLANT IMMUNITY; PROCEDURES; PROTEIN DEGRADATION; REPRODUCIBILITY; SECONDARY METABOLISM; XYLELLA;

CITRUS; CITRUS RETICULATA; CITRUS SINENSIS; PERA; XYLELLA FASTIDIOSA;

CELL WALL; CITRUS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; INDOLEACETIC ACIDS; PLANT DISEASES; PLANT IMMUNITY; PLANT PROTEINS; PROTEOLYSIS; REPRODUCIBILITY OF RESULTS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SECONDARY METABOLISM; SEQUENCE ANALYSIS, RNA; STRESS, PHYSIOLOGICAL; UBIQUITIN; UP-REGULATION; XYLELLA;

EID: 84884850228     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-676     Document Type: Article

References (57)

1. Bovè JM, Ayres AJ. Etiology of three recent diseases of citrus in São Paulo state: sudden death, Variegated Chlorosis and Huanglongbing. IUBMB Life 2007, 59(4-5):346-354.
2. Hopkins DL. Xylella fastidiosa xylem-limited bacterial pathogen of plants. Annu Rev Phytopathol 1989, 27:271-290.
3. De Souza AA, Takita MA, Coletta-Filho HD, Caldana C, Goldman GH, Yanai GM, Muto NH, Oliveira RC, Nunes LR, Machado MA. Analysis of gene expression in two growth states of Xylella fastidiosa and its relationship with pathogenicity. Mol Plant Microbe Interact 2003, 16:867-875. 10.1094/MPMI.2003.16.10.867, 14558688.
4. Pérez-Donoso AG, Sun Q, Roper MC, Greve LC, Kirkpatrick B, Labavitch JM. Cell wall-degrading enzymes enlarge the pore size of intervessel pit membranes in healthy and Xylella fastidiosa-infected grapevines. Plant physiol 2010, 152(3):1748-1759. 10.1104/pp.109.148791, 2832268, 20107028.
5. Coletta-Filho HD, Pereira EO, De Souza AA, Takita MA, Cristofani-Yaly M, Machado MA. Analysis of the resistance to Xylella fastidiosa within a hybrid population of Pera sweet orange and Murcott tangor. Plant Pathol 2007, 56:661-668.
6. De Souza AA, Takita MA, Coletta-Filho HD, Campos MA, Teixeira JEC, Targon MLPN, Carlos EF, Ravasi JR, Fischer CN, Machado MA. Comparative analysis of differentially expressed sequence tags of sweet orange and mandarin infected with Xylella fastidiosa. Genet Mol Biol 2007, 30(3):965-971.
7. De Souza AA, Takita MA, Amaral AM, Coletta-Filho HD, Machado MA. Citrus responses to Xylella fastidiosa infection, the causal agent de citrus variegated chlorosis. Tree For Sci Biotech 2009, 2(3):957-964.
8. Jones JDG, Dangl JL. The plant immune system. Nature 2006, 444:323-329. 10.1038/nature05286, 17108957.
9. Nicaise V, Roux M, Zipfel C. Recent advances in PAMP-triggered immunity against bacteria: pattern recognition receptors watch over and raise the alarm. Plant Physiol 2009, 150:1638-1647. 10.1104/pp.109.139709, 2719144, 19561123.
10. Lehti-Shiu MD, Zou C, Hanada K, Shiu S-H. Evolutionary history and stress regulation of plant receptor-like Kinase/Pelle genes. Plant Physiol 2009, 150:12-26. 10.1104/pp.108.134353, 2675737, 19321712.
11. Boller T, He SY. Innate immunity in plants: an arms race between pattern recognition receptors in plants and effectors in microbial pathogens. Science 2009, 324(5928):742-744. 10.1126/science.1171647, 2729760, 19423812.
12. Mizuno S, Osakabe Y, Maruyama K, Ito T, Osakabe K, Sato T, Shinozaki K, Yamaguchi-Shinozaki K. Receptor-like protein kinase 2 (RPK 2) is a novel factor controlling anther development in Arabidopsis thaliana. Plant J 2007, 50(5):751-766. 10.1111/j.1365-313X.2007.03083.x, 17419837.
13. Bleckmann A, Weidtkamp-Peters S, Seidel CAM, Simon RD. Stem cell signaling in Arabidopsis requires CRN to localize CLV2 to the plasma membrane. Plant Physiol 2010, 152:166-176. 10.1104/pp.109.149930, 2799354, 19933383.
14. Wang G, Long Y, Thomma BPHJ, De Wit PJGM, Angenent GC, Fiers M. Functional analyses of the CLAVATA2-like proteins and their domains that contribute to CLAVATA2 specificity. Plant Physiol 2010, 152:320-331. 10.1104/pp.109.148197, 2799366, 19897604.
15. Simpson AJG, Reinach FC, Arruda P, et al. The genome sequence of the plant pathogen Xylella fastidiosa. Nature 2000, 40:151-159.
16. Abramovitch RB, Anderson JC, Martin GB. Bacterial elicitation and evasion of plant innate immunity. Nat Rev Mol Cell Biol 2006, 7(8):601-611. 10.1038/nrm1984, 2842591, 16936700.
17. Lotze MT, Zeh HJ, Rubartelli A, Sparvero LJ, Amoscato AA, Washburn NR, DeVera ME, Liang X, Tör M, Billiar T. The grateful dead: damage associated molecular pattern molecules and reduction/oxidation regulate immunity. Immunol Rev 2007, 220:60-81. 10.1111/j.1600-065X.2007.00579.x, 17979840.
18. Boller T, Georg F. A renaissance of elicitors: perception of microbe-associated molecular patterns and danger signals by pattern-recognition receptors. Annu Rev Plant Biol 2009, 60:379-406. 10.1146/annurev.arplant.57.032905.105346, 19400727.
19. Salomon D, Sessa G. Identification of growth inhibition phenotypes induced by expression of bacterial type III effectors in yeast. J Vis Exp 2012, 37:e1865.
20. Newman LJ, Campbell MM. MYB proteins and xylem differentiation. Cell and molecular biology of wood formation 1999, 437-444. Oxford, UK: Bios Academic Publishing, Savidge RA, Barnett JR, Napier R.
21. Hogetsu T. Mechanism for formation of the secondary wall thickening in tracheary elements-microtubules and microfibrils of tracheary elements of Pisum-Sativum L and Commelina-Communis L and the effects of Amiprophosmethyl. Planta 1991, 185:190-200.
22. Tamagnone L, Merida A, Parr A, Mackay S, Culianez-Macia FA, et al. The AmMYB308 and AmMYB330 transcription factors from antirrhinum regulate phenylpropanoid and lignin biosynthesis in transgenic tobacco. Plant Cell 1998, 10:135-154. 143979, 9490739.
23. Patzlaff A, McInnis S, Courtenay A, Surman C, Newman LJ, et al. Characterization of a pine MYB that regulates lignification. Plant J 2003, 36:743-754. 10.1046/j.1365-313X.2003.01916.x, 14675440.
24. Fornale S, Shi X, Chai C, Encina A, Irar S, et al. ZmMYB31 directly represses maize lignin genes and redirects the phenylpropanoid metabolic flux. Plant J 2010, 64:633-644. 10.1111/j.1365-313X.2010.04363.x, 21070416.
25. De Luca V, St Pierre B. The cell and developmental biology of alkaloid biosynthesis. Trends Plant Sci 2000, 5(4):168-173. 10.1016/S1360-1385(00)01575-2, 10740298.
26. Taylor NG, Howells RM, Huttly AK, Vickers K, Turner SR. Interactions among three distinct CesA proteins essential for cellulose synthesis. Proc Natl Acad Sci USA 2003, 100(3):1450-1455. 10.1073/pnas.0337628100, 298793, 12538856.
27. Nürnberger T, Scheel D. Signal transmission in the plant immune response. Trends Plant Sci 2001, 6(8):372-379. 10.1016/S1360-1385(01)02019-2, 11495791.
28. Lecourieux D, Ranjeva R, Pugin A. Calcium in plant defence-signalling pathways. New Phytol 2006, 171(2):249-269. 10.1111/j.1469-8137.2006.01777.x, 16866934.
29. Melotto M, Underwood W, Koczan J, Nomura K, He SY. Plant Stomata Function in Innate Immunity against Bacterial Invasion. Cell 2006, 126:969-980. 10.1016/j.cell.2006.06.054, 16959575.
30. Bari R, Jones JDG. Role of plant hormones in plant defence responses. Plant Mol Biol 2009, 69:473-488. 10.1007/s11103-008-9435-0, 19083153.
31. Delker C, Stenzel I, Hause B, Miersch O, Feussner I, Wasternack C. Jasmonate biosynthesis in Arabidopsis thaliana-enzymes, products, regulation. Plant Biol 2006, 8(3):297-306. 10.1055/s-2006-923935, 16807821.
32. Clarke SM, Cristescu SM, Miersch O, Harren FJ, Wasternack C, Mur LA. JAs act with salicylic acid to confer basal thermotolerance in Arabidopsis thaliana. New Phytol 2009, 182:175-187. 10.1111/j.1469-8137.2008.02735.x, 19140948.
33. Zhou J, Zhang H, Yang Y, Zhang Z, Zhang H, et al. Abscisic acid regulates TSRF1-mediated resistance to Ralstonia solanacearum by modifying the expression of GCC box-containing genes in tobacco. J Exp Bot 2008, 59(3):645-652. 10.1093/jxb/erm353, 18252700.
34. Zhang X, Garreton V, Chua N-H. The AIP2 E3 ligase acts as a novel negative regulator of ABA signaling by promoting ABI3 degradation. Gene Dev 2005, 19:1532-1543. 10.1101/gad.1318705, 1172060, 15998807.
35. Woodward AW, Bartel B. Auxin: regulation, action, and interaction. Ann Bot 2005, 95:707-735. 10.1093/aob/mci083, 15749753.
36. Paponov IA, Teale WD, Trebar M, Blilou K, Palme K. The PIN auxin efflux facilitators: evolutionary and functional perspectives. Trends Plant Sci 2005, 10:170-177. 10.1016/j.tplants.2005.02.009, 15817418.
37. Ding X, Cao Y, Huang L, Zhao J, Xu C, Li X, Wang S. Activation of the indole-3-acetic acid-amidosynthetase GH3-8 suppresses expansin expression and promotes salicylate- and jasmonate-independent basal immunity in rice. Plant Cell 2008, 20:228-240. 10.1105/tpc.107.055657, 2254934, 18192436.
38. Reineke G, Heinze B, Schirawski J, Buettner H, Kahmann R, Basse CW. Indole-3-acetic acid (IAA) biosynthesis in the smut fungus Ustilagomaydis and its relevance for increased IAA levels in infected tissue and host tumour formation. Mol Plant Pathol 2008, 9:339-355. 10.1111/j.1364-3703.2008.00470.x, 18705875.
39. Kazan K, Manners JM. Linking development to defense: auxin in plant-pathogen interactions. Trends Plant Sci 2009, 14(7):373-382. 10.1016/j.tplants.2009.04.005, 19559643.
40. Liu Y, Wang F, Zhang H, He H, Ma L, Deng XW. Functional characterization of the Arabidopsis ubiquitin-specific protease gene family reveals specific role and redundancy of individual members in development. Plant J 2008, 55:844-856. 10.1111/j.1365-313X.2008.03557.x, 18485060.
41. Gil P, Dewey E, Friml J, Zhao Y, Snowden KC, et al. BIG: a calossin-like protein required for polar auxin transport in Arabidopsis. Gene Dev 2001, 15(15):1985-1997. 10.1101/gad.905201, 312751, 11485992.
42. Navarro L, Dunoyer P, Jay F, Arnold B, Dharmasiri N, et al. A plant miRNA contributes to antibacterial resistance by repressing auxin signaling. Science 2006, 312:436-439. 10.1126/science.1126088, 16627744.
43. Wang D, Pajerowska-Mukhtar K, Culler AH, Dong X. Salicylic acid inhibits pathogen growth in plants through repression of the auxin signaling pathway. Curr Biol 2007, 17:1784-1790. 10.1016/j.cub.2007.09.025, 17919906.
44. Llorente F, Muskett P, Sánchez-Vallet A, López G, Ramos B, et al. Repression of the auxin response pathway increases Arabidopsis susceptibility to necrotrophic fungi. Mol Plant 2008, 1:496-509. 10.1093/mp/ssn025, 19825556.
45. Cosgrove DJ. How do plant cell walls extend?. Plant Physiol 1993, 102(1):1-6. 158739, 11536544.
46. Catalá C, Rose JKC, Bennett AB. Auxin regulation and spatial localization of an endo-1,4-b-d-glucanase and a xyloglucan endotransglycosylase in expanding tomato hypocotyls. Plant J 1997, 12:417-426. 10.1046/j.1365-313X.1997.12020417.x, 9301092.
47. Fu J, Wand S. Insights into auxin signaling in plant-pathogen interactions. Plant Sci 2011, 2(74):1-7.
48. De Souza AA, Takita MA, Coletta-Filho HD, Caldana C, Yanai GM, Muto NH, Costa De Oliveira R, Nunes LR, Machado MA. Gene expression profile of the plant pathogen Xylella fastidiosa during biofilm formation in vitro. FEMS Microbiol Lett 2004, 237:41-353. 10.1111/j.1574-6968.2004.tb09676.x, 15268936.
49. De Souza AA, Takita MA, Pereira EO, Coletta-Filho HD, Machado MA. Expression of pathogenicity-related genes of Xylella fastidiosa in vitro and in plant. Curr Microbiol 2005, 50:223-228. 10.1007/s00284-004-4447-8, 15902471.
50. Murray MG, Thompson WF. Rapid isolation of high molecular weight plant DNA. Nuclec Acids Res 1980, 8:4321-4325.
51. Oliveira AC, Garcia AN, Cristofani M, Machado MA. Identification of citrus hybridis through the combination of leaf apex morphology and SSR markers. Euphytic 2002, 128:397-403.
52. Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009, 25(9):1105-1111. 10.1093/bioinformatics/btp120, 2672628, 19289445.
53. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, Van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNASeq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 2010, 28(5):511-518. 10.1038/nbt.1621, 3146043, 20436464.
54. Thimm O, Bläsing O, Gibon Y, Nagel A, Meyer S, Krüger P, Selbig J, Müller LA, Rhee SY, Stitt M. MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J 2004, 37(6):914-939. 10.1111/j.1365-313X.2004.02016.x, 14996223.
55. Artico S, Nardeli SM, Brilhante O, Grossi-De-Sa MF, Alves-Ferreira M. Identification and evaluation of new reference genes in Gossypium hirsutum for accurate normalization of real-time quantitative RT-PCR data. BMC Plant Biol 2010, 21:10-49.
56. Vandesompele J, De Pretter K, Pattyn F, Poppe B, Roy NV, De Paepe A, Speleman F. Accurate normalization of real-time RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 2002, 3(7):1-12.
57. Boava LP, Laia ML, Jacob TR, Dabbas KM, Gonçalves JF, Ferro JA, Ferro MIT, Furtado EL. Selection of endogenous genes for gene expression studies in Eucalyptus under biotic (Puccinia psidii) and abiotic (acibenzolar-S-methyl) stresses using RT-qPCR. BMC Res Notes 2010, 43(3):1-9.