DNA Sequencing Analysis of African Xanthomonas oryzae pv. oryzae Virulence Gene (AXaVrg) DNA Marker

Open access

Abstract

Global rice production is constrained by bacterial leaf blight (BLB) disease caused by Xanthomonas oryzae pv. oryzae (Xoo). BLB disease incidence in West Africa was between 70–85% and yield loss in farmers’ fields was in the range of 50–90% from 2005 to 2010. In the present study, African Xoo virulence gene OPP-172000 DNA marker was identified and purified using randomly amplified polymorphic DNA polymerase chain reaction (RAPD-PCR) products from 50 Xoo isolates. Genomic DNA of 50 Xoo isolates were analyzed using OPP-17 primer in RAPD-PCR during which African Xoo virulence gene OPP-172000 DNA marker was identified, purified, cloned, and sequenced. Cloning and DNA sequencing of African Xoo virulence gene OPP-172000 DNA generated a 1953 bp nucleotide sequence consequently tagged as AXaVrg-1953. BLAST homologous analysis of the AXaVrg-1953 sequence provides comprehensive identification of the type II secretion genes and secreted proteins, type III secretion genes and secreted proteins in African Xoo virulence gene. Phylogenetic unweighted pairgroup method arithmetic (UPGMA) analysis revealed the African AXaVrg-1953 sequence was distinct from the other Xoo virulence gene sequences from China, Japan, Korea, Germany, and the United States. This information is potentially useful for effective management of BLB disease in West Africa.

Adhikari TB, Vera Cruz CM, Zhang Q, Nelson RJ, Skinner DZ, Mew TW, Leach JE (1995): Genetic diversity of Xanthomonas oryzae pv. oryzae in Asia. Applied and Environmental Microbiology, 61, 966–971.

Adhikari TB, Basnyat RC, Mew TW (1999): Virulence of Xanthomonas oryzae pv. oryzae on rice lines containing single resistance genes and gene combinations. Plant Disease, 83, 46–50. doi: 10.1094/PDIS.1999.83.1.46.

Akanji BO, Ajele JO, Onasanya A, Oyelakin O (2011): Genetic fingerprinting of Pseudomonas aeruginosa involved in nosocomial infection as revealed by RAPD-PCR markers. Biotechnology, 10, 70–77. doi: 10.3923/biotech.2011.70.77.

Alfano JR, Collmer A (1996): Bacterial pathogens in plants: life up against the wall. Plant Cell, 8, 1683–1698. doi: 10.1105/tpc.8.10.1683.

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990): Basic local alignment search tool. Journal of Molecular Biology, 215, 403–410. doi: 10.1016/S0022-2836(05)80360-2.

Basso A, Onasanya A, Issaka S, Sido AY, Haougui A, Adam T, Sere Y, Saadou M (2011): Bacterial leaf blight of rice in Niger: Pathological diversity of isolates collected on irrigated lands. Journal of Applied Biosciences, 38, 2551–2563.

Buttner D, Lorenz C, Weber E, Bonas U (2006): Targeting of two effector protein classes to the type III secretion system by a HpaC- and HpaB-dependent protein complex from Xanthomonas campestris pv. vesicatoria. Molecular Microbiology, 59, 513–527. doi: 10.1111/j.1365-2958.2005.04924.x.

Chatterjee S, Sankaranarayanan R, Sonti RV (2003): PhyA, a secreted protein of Xanthomonas oryzae pv. oryzae, is required for optimum virulence and growth on phytic acid as a sole phosphate source. Molecular Plant–Microbe Interactions, 16, 973–982. doi: 10.1094/MPMI.2003.16.11.973.

Dewa KMK, Banito A, Onasanya A, Kpemoua KE, Sere Y (2011): Rice bacterial blight in Togo: importance of the disease and virulence of the pathogen. Current Research in Bacteriology, 4, 94–100. doi: 10.3923/crb.2011.94.100.

Furutani A, Tsuge S, Oku T, Tsuno K, Inoue Y, Ochiai H, Kaku H, Kubo Y (2003): Hpa1 secretion via type III secretion system in Xanthomonas oryzae pv. oryzae. Journal of General Plant Pathology, 69, 271–275. doi: 10.1007/s10327-003-0042-2.

Goel AK, Rajagopal L, Nagesh N, Sonti RV (2002): Genetic locus encoding functions involved in biosynthesis and outer membrane localization of xanthomonadin in Xanthomonas oryzae pv. oryzae. Journal of Bacteriology, 184, 3539–3548. doi: 10.1128/JB.184.13.3539-3548.2002.

Gonzalez C, Szurek B, Manceau C, Mathieu T, Sere Y, Verdier V (2007): Molecular and pathotypic characterization of new Xanthomonas oryzae strains from West Africa. Molecular Plant–Microbe Interactions, 20, 534–546. doi: 10.1094/MPMI-20-5-0534.

Gurlebeck D, Thieme F, Bonas U (2006): Type III effector proteins from the plant pathogen Xanthomonas and their role in the interaction with the host plant. Journal of Plant Physiology, 163, 233–255. doi: 10.1016/j.jplph.2005.11.011.

Jiang GH, Xia ZH, Zhou YL, Wan J, Li DY, Chen RS, Zhai WX, Zhu LH (2006): Testifying the rice bacterial blight resistance gene xa5 by genetic complementation and further analyzing xa5 (Xa5) in comparison with its homolog TFIIAγ1. Molecular Genetics and Genomics, 275, 354–366. doi: 10.1007/s00438-005-0091-7.

Jung G, Skroch PW, Nienhuis J, Coyne DP, Arnaud-Santana E, Ariyarathne HM, Marita JM (1999): Confirmation of QTL associated with bacterial blight resistance in four different genetic backgrounds in common bean. Crop Science, 39, 1448–1455. doi: 10.2135/cropsci1999.3951448x.

Makino S, Sugio A, White F, Bogdanove AJ (2006): Inhibition of resistance gene mediated defense in rice by Xanthomonas oryzae pv. oryzicola. Molecular Plant–Microbe Interactions, 19, 240–249. doi: 10.1094/MPMI-19-0240.

Narayanan NN, Baisakh N, Vera-Cruz CM, Gnanamanickam SS, Datta K, Datta SK (2002): Molecular breeding for the development of blast and bacterial blight resistance in rice cv. IR50. Crop Science, 42, 2072–2079. doi: 10.2135/cropsci2002.2072.

Nelson RJ, Baraoidan MR, Vera Cruz CM, Yap IV, Leach JE, Mew TW, Leung H (1994): Relationship between phylogeny and pathotype for the bacterial blight pathogen of rice. Applied and Environmental Microbiology, 60, 3275–3283.

Noel L, Thieme F, Nennstiel D, Bonas U (2002): Two novel type III-secreted proteins of Xanthomonas campestris pv. vesicatoria are encoded within the hrp pathogenicity island. Journal of Bacteriology, 184, 1340–1348. doi: 10.1128/JB.184.5.1340-1348.2002.

Oku T, Tanaka K, Iwamoto M, Inoue Y, Ochiai H, Kaku H, Tsuge S, Tsuno K (2004): Structural conservation of the hrp gene cluster in Xanthomons oryzae pv. oryzae. Journal of General Plant Pathology, 70, 159–167. doi: 10.1007/s10327-004-0106-y.

Onasanya A, Ekperigin MM, Nwilene FE, Sere Y, Onasanya RO (2009): Two pathotypes of Xanthomonas oryzae pv. oryzae virulence identified in West Africa. Current Research in Bacteriology, 2, 22–35. doi: 10.3923/crb.2009.22.35.

Onasanya A, Ekperigin MM, Afolabi A, Onasanya RO, Ojo AA, Ingelbrecht I (2013): Two genotypes of Xanthomonas oryzae pv. oryzae virulence identified in West Africa. International Journal of Genetics and Molecular Biology, 5, 28–36. doi: 10.5897/IJGMB2013.0070.

Qiagen (2001): QIAquick® Spin Handbook for QIAquick PCR Purification Kit, QIAquick Nucleotide Removal Kit, and QIAquick Gel Extraction Kit. https://www.calpoly.edu/~bio/ubl/protocols_files/pcrclean.pdf. Accessed 03, 2001.

Ray SK, Rajeshwari R, Sonti RV (2000): Mutants of Xanthomonas oryzae pv. oryzae deficient in general secretory pathway are virulence deficient and unable to secrete xylanase. Molecular Plant–Microbe Interactions, 13, 394–401. doi: 10.1094/MPMI.2000.13.4.394.

Roden JA, Belt B, Ross JB, Tachibana T, Vargas J, Mudgett MB (2004): A genetic screen to isolate type III effectors translocated into pepper cells during Xanthomonas infection. Proceedings of the National Academy of Sciences of the United States of America, 101, 16624–16629. doi: 10.1073/pnas.0407383101.

Sere Y, Onasanya A, Verdier V, Akator K, Ouedraogo LS, Segda Z, Coulibaly MM, Sido AY, Basso A (2005): Rice bacterial leaf blight in West Africa: preliminary studies on disease in farmers' fields and screening released varieties for resistance to the bacteria. Asian Journal of Plant Sciences, 4, 577–579. doi: 10.3923/ajps.2005.577.579.

Sun QH, Hu J, Huang GX, Ge C, Fang RX, He CZ (2005): Type-II secretion pathway structural gene xpsE, xylanase- and cellulase secretion and virulence in Xanthomonas oryzae pv. oryzae. Plant Pathology, 54, 15–21. doi: 10.1111/j.1365-3059.2004.01101.x.

Tsuge S, Terashima S, Furutani A, Ochiai H, Oku T, Tsuno K, Kaku H, Kubo Y (2005): Effects on promoter activity of base substitutions in the cis-acting regulatory element of HrpXo regulons in Xanthomonas oryzae pv. oryzae. Journal of Bacteriology, 187, 2308–2314. doi: 10.1128/JB.187.7.2308-2314.2005.

Vera Cruz CM, Ardales EY, Skinner DZ, Talag J, Nelson RJ, Louws FJ, Leung H, Mew TW, Leach JE (1996): Measurement of haplotypic variation in Xanthomonas oryzae pv. oryzae within a single field by rep-PCR and RFLP analyses. Phytopathology, 86, 1352–1359.

Yang B, White FF (2004): Diverse members of the AvrBs3/PthA family of type III effectors are major virulence determinants in bacterial blight disease of rice. Molecular Plant–Microbe Interactions, 17, 1192–1200. doi: 10.1094/MPMI.2004.17.11.1192.

Zhu W, Magbanua MM, White FF (2000): Identification of two novel hrp-associated genes in the hrp gene cluster of Xanthomonas oryzae pv. oryzae. Journal of Bacteriology, 182, 1844–1853. doi: 10.1128/JB.182.7.1844-1853.2000.

Scientia Agriculturae Bohemica

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