Abstract
Simultaneous quantification of transcripts of the whole bacterial genome allows the analysis of the global transcriptional response under changing conditions. RNA-seq and microarrays are the most used techniques to measure these transcriptomic changes, and both complement each other in transcriptome profiling. In this review, we exhaustively compiled the symbiosis-related transcriptomic reports (microarrays and RNA sequencing) carried out hitherto in rhizobia. This review is specially focused on transcriptomic changes that takes place when five rhizobial species, Bradyrhizobium japonicum (=diazoefficiens) USDA 110, Rhizobium leguminosarum biovar viciae 3841, Rhizobium tropici CIAT 899, Sinorhizobium (=Ensifer) meliloti 1021 and S. fredii HH103, recognize inducing flavonoids, plant-exuded phenolic compounds that activate the biosynthesis and export of Nod factors (NF) in all analysed rhizobia. Interestingly, our global transcriptomic comparison also indicates that each rhizobial species possesses its own arsenal of molecular weapons accompanying the set of NF in order to establish a successful interaction with host legumes.
Highlights
Quantification of the global expression level of a bacterial genome in response to specific cues allows the analysis of the transcriptional responses to changing environmental conditions.Several transcriptome profiling methods have been developed in the last years
Despite the fact that most of these genes code for proteins with unknown functions (66%), the up-regulation of well-known genes indicates that several physiological processes are enhanced when this rhizobial species colonizes plant roots, such as acid organic metabolism (dctA and pckA genes, implied in C4-dicarboxylate transport and Phosphoenolyruvate (PEP)-carboxykinase production, respectively), molecular transport [54] and osmotic adaptation [55]
Many Rhizobium leguminosarum bv. viciae (Rlv)3841 genes are induced in the rhizosphere of legume plants, including the nodABCEFIJLMNO operon, but not in the sugar beet rhizosphere
Summary
Quantification of the global expression level of a bacterial genome in response to specific cues allows the analysis of the transcriptional responses to changing environmental conditions.Several transcriptome profiling methods have been developed in the last years. Quantification of the global expression level of a bacterial genome in response to specific cues allows the analysis of the transcriptional responses to changing environmental conditions. DNA microarrays and RNA sequencing (RNA-seq) are the two most used genome-wide gene expression quantification techniques [1,2,3,4]. Microarrays are based on the hybridization of oligonucleotide DNA sequences representing the entire set of genes of an organism arranged in a grid pattern with DNA molecules representing the transcriptome in a specific condition [5,6,7]. By mapping the resulting short-sequence reads onto the reference genome, both the relative and absolute expression levels of each gene can be quantified [3,8]. The efficiency of RNA-seq is marred with the problem of an
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