Abstract
Members of the genus Burkholderia occupy remarkably diverse niches, with genome sizes ranging from ~3.75 to 11.29 Mbp. The genome of Burkholderia glumae ranges in size from ~5.81 to 7.89 Mbp. Unlike other plant pathogenic bacteria, B. glumae can infect a wide range of monocot and dicot plants. Comparative genome analysis of B. glumae strains can provide insight into genome variation as well as differential features of whole metabolism or pathways between multiple strains of B. glumae infecting the same host. Comparative analysis of complete genomes among B. glumae BGR1, B. glumae LMG 2196, and B. glumae PG1 revealed the largest departmentalization of genes onto separate replicons in B. glumae BGR1 and considerable downsizing of the genome in B. glumae LMG 2196. In addition, the presence of large-scale evolutionary events such as rearrangement and inversion and the development of highly specialized systems were found to be related to virulence-associated features in the three B. glumae strains. This connection may explain why this bacterium broadens its host range and reinforces its interaction with hosts.
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References
Barash I (1990) Iron, siderophores and plant–pathogen interactions. Phytoparasitica 18:183–188
Chen Y, Wong J, Sun GW et al (2011) Regulation of type VI secretion system during Burkholderia pseudomallei infection. Infect Immun 79:3064–3073. doi:10.1128/IAI.05148-11
Coenye T, Vandamme P (2003) Diversity and significance of Burkholderia species occupying diverse ecological niches. Environ Microbiol 5:719–729. doi:10.1046/j.1462-2920.2003.00471.x
Coenye T, Vandamme P (2007) Burkholderia: molecular microbiology and genomics. Horizon Bioscience, Wymondham
Cohen SS (1997) A guide to the polyamines. Oxford University Press, New York
Devescovi G, Bigirimana J, Degrassi G et al (2007) Involvement of a quorum-sensing-regulated lipase secreted by a clinical isolate of Burkholderia glumae in severe disease symptoms in rice. Appl Environ Microbiol 73:4950–4958. doi:10.1128/AEM.00105-07
Fory P, Triplett L, Ballen C (2014) Comparative analysis of two emerging rice seed bacterial pathogens. Phytopathology 104:436–444
Ghosh S, Gupta SK, Gopaljee J (2014) Identification and functional analysis of AG1-IA specific genes of Rhizoctonia solani. Curr Genet 60:327–341. doi:10.1007/s00294-014-0438-x
Jaeger K, Reetz M (1998) Microbial lipases form versatile tools for biotechnology. Trends Biotechnol 16:396–403
Jeong Y, Kim J, Kim S, Kang Y (2003) Toxoflavin produced by Burkholderia glumae causing rice grain rot is responsible for inducing bacterial wilt in many field crops. Plant Dis 87:890–895
Jha G, Rajeshwari R, Sonti RV (2007) Functional interplay between two Xanthomonas oryzae pv. oryzae secretion systems in modulating virulence on rice. Mol Plant Microbe Interact 20:31–40
Ju K-S, Parales RE (2011) Evolution of a new bacterial pathway for 4-nitrotoluene degradation. Mol Microbiol 82:355–364. doi:10.1111/j.1365-2958.2011.07817.x
Kusaba M, Mochida T, Naridomi T et al (2014) Loss of a 1.6 Mb chromosome in Pyricularia oryzae harboring two alleles of AvrPik leads to acquisition of virulence to rice cultivars containing resistance alleles at the Pik locus. Curr Genet 60:315–325. doi:10.1007/s00294-014-0437-y
Lee YH, Chen Y, Ouyang X, Gan Y-H (2010) Identification of tomato plant as a novel host model for Burkholderia pseudomallei. BMC Microbiol 10:28. doi:10.1186/1471-2180-10-28
Meng F (2013) The virulence factors of the bacterial wilt pathogen Ralstonia solanacearum. J Plant Pathol Microbiol 04:3–5. doi:10.4172/2157-7471.1000168
Nandakumar R, Rush MC, Correa F (2007) Association of Burkholderia glumae and B. gladioli with panicle blight symptoms on rice in Panama. Plant Dis 91:767
Nandakumar R, Shahjahan AKM, Yuan XL et al (2009) Burkholderia glumae and B. gladioli cause bacterial panicle blight in rice in the Southern United States. Plant Dis 93:896–905
Prasertsincharoen N, Constantinoiu C, Gardiner C et al (2015) Effects of root colonization of the domestic Rice (Oryza sativa L. cv. Amaroo) by Burkholderia pseudomallei. Appl Environ Microbiol 81:4368–4375. doi:10.1128/AEM.00317-15
Ralebitso T, Senior E, Van Verseveld H (2002) Microbial aspects of atrazine degradation in natural environments. Biodegradation 13:11–19
Riera-Ruiz C, Vargas J, Cedeño C et al (2014) First report of Burkholderia glumae causing bacterial panicle blight on rice in Ecuador. Plant Dis 98:988
Sandkvist M (2001) Type II secretion and pathogenesis. Infect Immun 69:3523–3535. doi:10.1128/IAI.69.6.3523
Seo Y-S, Lim JY, Park J et al (2015) Comparative genome analysis of rice-pathogenic Burkholderia provides insight into capacity to adapt to different environments and hosts. BMC Genom 16:349. doi:10.1186/s12864-015-1558-5
Shah P, Swiatlo E (2008) A multifaceted role for polyamines in bacterial pathogens. Mol Microbiol 68:4–16. doi:10.1111/j.1365-2958.2008.06126.x
Siguier P, Gourbeyre E, Chandler M (2014) Bacterial insertion sequences: their genomic impact and diversity. FEMS Microbiol Rev 38:865–891. doi:10.1111/1574-6976.12067
Sotokawa N, Takikawa Y (2004) Occurrence of bacterial rot of onion bulbs caused by Burkholderia cepacia in Japan. J Gen Plant Pathol 70:348–352. doi:10.1007/s10327-004-0159-y
Stoyanova M, Pavlina I, Moncheva P, Bogatzevska N (2007) Biodiversity and incidence of Burkholderia species. Biotechnol Biotechnol Equip 21:306–310. doi:10.1080/13102818.2007.10817465
Sun J, Deng Z, Yan A (2014) Bacterial multidrug efflux pumps: mechanisms, physiology and pharmacological exploitations. Biochem Biophys Res Commun 453:254–267. doi:10.1016/j.bbrc.2014.05.090
Tamir-Ariel D, Rosenberg T, Navon N, Burdman S (2012) A secreted lipolytic enzyme from Xanthomonas campestris pv. vesicatoria is expressed in planta and contributes to its virulence. Mol Plant Pathol 13:556–567. doi:10.1111/j.1364-3703.2011.00771.x
Tatusov R, Koonin E, Lipman D (1997) A genomic perspective on protein families. Science (80) 278:631–638
Ura H, Furuya N, Iiyama K et al (2006) Burkholderia gladioli associated with symptoms of bacterial grain rot and leaf-sheath browning of rice plants. J Gen Plant Pathol 72:98–103. doi:10.1007/s10327-005-0256-6
Urakami T, Ito-Yoshida C, Araki H et al (1994) Transfer of Pseudomonas plantarii and Pseudomonas glumae to Burkholderia as Burkholderia spp. and description of Burkholderia vandii sp. nov. Int J Syst Evol Microbiol 44:235–245
Veasey EA, Karasawa MG, Santos PP et al (2004) Variation in the loss of seed dormancy during after-ripening of wild and cultivated rice species. Ann Bot 94:875–882. doi:10.1093/aob/mch215
Voget S, Knapp A, Poehlein A et al (2015) Complete genome sequence of the lipase producing strain Burkholderia glumae PG1. J Biotechnol 204:3–4. doi:10.1016/j.jbiotec.2015.03.022
Voigt CA, Schäfer W, Salomon S (2005) A secreted lipase of Fusarium graminearum is a virulence factor required for infection of cereals. Plant J 42:364–375. doi:10.1111/j.1365-313X.2005.02377.x
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This research was supported by a National Research Foundation of Korea (NRF) Grant funded by the Korean government (MEST) (No. 2013R1A1A2006716).
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Communicated by M. Kupiec.
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Lee, HH., Park, J., Kim, J. et al. Understanding the direction of evolution in Burkholderia glumae through comparative genomics. Curr Genet 62, 115–123 (2016). https://doi.org/10.1007/s00294-015-0523-9
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DOI: https://doi.org/10.1007/s00294-015-0523-9