Genômica funcional da bactéria Nitrospirillum amazonense em interação com o fluido do apoplasto de cana-de-açúcar: abordagens transcriptômica e proteômica

Abstract

Nitrospirillum amazonense is a nitrogen-fixing bacterium isolated from several plants, such as rice, corn, sorghum and sugar cane. The CBAmC strain of N. amazonense was isolated from sugarcane stalks CB45-3 variety and it has been reported that this bacterium promotes the growth of the sugarcane variety RB867515 when inoculated under field conditions in consortium with four other bacteria nitrogen. The sugarcane apoplast represents a probable niche for the establishment of several bacteria, among them N. amazonense. The present work had the objective of accessing the influence of the sugarcane apoplastic fluid on the global transcriptomic and proteomic profiles. The bacterium was cultured in standard LGI culture medium in the presence or absence of apoplast fluid. Samples were collected in the middle of the exponential growth phase for extraction of RNA and proteins. Total RNA was extracted with trizol treatment at a temperature of 65ºC and a high-throughput sequencing method (RNA-Seq) was used. The protein extract was obtained by sonication and tandem mass spectrometry was used by liquid chromatography (LC-MS / MS). The comparative analysis between the transcriptome and proteome profiles showed strong consistency between the results of the two approaches. Data analysis revealed that expression levels of transcripts related to chemotaxis, bacterial flagella biosynthesis and TonB transporters were strongly repressed in the presence of apoplast fluid. In contrast, in energy-generating metabolism, the expression levels of the genes involved in the Krebs cycle were induced. In addition, genes involved in response to osmotic and oxidative stress, RND multidrug efflux transporters were strongly overexpressed, as detected in the transcriptome and proteome in the presence of the fluid. In conclusion, the results showed that the metabolic state of N. amazonense during apoplast culture is directed to proteins capable of supporting adaptation in a new complex environment such as sugarcane apoplast. The investigation of comparative analysis between the transcriptome and proteome in the interaction with the apoplast fluid will expand a better understanding of the interaction between the plant and the bacterium guiding future studies with the CBAmC strain as well as the potential development of an inoculant for the cane- sugar.