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Plant-Influenced Gene Expression in the Rice Endophyte Burkholderia kururiensis M130

January 2015 , Volume 28 , Number  1
Pages  10 - 21

Bruna G. Coutinho,1,2 Danilo Licastro,3 Lucia Mendonça-Previato,4 Miguel Cámara,5 and Vittorio Venturi1

1Bacteriology Group, International Centre for Genetic Engineering & Biotechnology, Padriciano 99, 34149 Trieste, Italy; 2The Capes Foundation, Ministry of Education of Brazil, Cx postal 250, Brasilia, DF 70.040-020, Brazil; 3CBM S.c.r.l., Area Science Park–Basovizza, Trieste, Italy; 4Universidade Federal do Rio de Janeiro, Centro de Ciências da Saúde, Instituto de Biofísica Carlos Chagas Filho-Ilha da Cidade Universitária, CEP 21.990-400 Rio de Janeiro, RJ, Brazil; 5School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham NG7 2RD, U.K.

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Accepted 25 September 2014.

Burkholderia kururiensis M130 is one of the few rice endophytic diazotrophic bacteria identified thus far which is able to enhance growth of rice. To date, very little is known of how strain M130 and other endophytes enter and colonize plants. Here, we identified genes of strain M130 that are differentially regulated in the presence of rice plant extract. A genetic screening of a promoter probe transposon mutant genome bank and RNAseq analysis were performed. The screening of 10,100 insertions of the genomic transposon reporter library resulted in the isolation of 61 insertions displaying differential expression in response to rice macerate. The RNAseq results validated this screen and indicated that this endophytic bacterium undergoes major changes in the presence of plant extract regulating 27.7% of its open reading frames. A large number of differentially expressed genes encode membrane transporters and secretion systems, indicating that the exchange of molecules is an important aspect of bacterial endophytic growth. Genes related to motility, chemotaxis, and adhesion were also overrepresented, further suggesting plant–bacteria interaction. This work highlights the potential close signaling taking place between plants and bacteria and helps us to begin to understand the adaptation of an endophyte in planta.

© 2015 The American Phytopathological Society