Functional Genomics Approaches to Studying Symbioses between Legumes and Nitrogen-Fixing Rhizobia

Abstract

Biological nitrogen fixation gives legumes a pronounced growth advantage in nitrogen-deprived soils and is of considerable ecological and economic interest. In exchange for reduced atmospheric nitrogen, typically given to the plant in the form of amides or ureides, the legume provides nitrogen-fixing rhizobia with nutrients and highly specialised root structures called nodules. To elucidate the molecular basis underlying physiological adaptations on a genome-wide scale, functional genomics approaches, such as transcriptomics, proteomics, and metabolomics, have been used. This review presents an overview of the different functional genomics approaches that have been performed on rhizobial symbiosis, with a focus on studies investigating the molecular mechanisms used by the bacterial partner to interact with the legume. While rhizobia belonging to the alpha-proteobacterial group (alpha-rhizobia) have been well studied, few studies to date have investigated this process in beta-proteobacteria (beta-rhizobia).

Expanding the Regulon of the Bradyrhizobium diazoefficiens NnrR Transcription Factor: New Insights Into the Denitrification Pathway

“…A custom-designed B. diazoefficiens GeneChip BJAPETHa520090 (Affymetrix, Santa Clara, CA, United States; Hauser et al, 2007) was used to analyze the transcriptional profile of the nnrR mutant in comparison to the WT. This GeneChip has successfully been used in a wealth of global transcriptional studies performed with B. diazoefficiens (reviewed in Lardi and Pessi, 2018). Both the nnrR mutant and WT strains were cultivated under anoxic conditions in YEM medium supplemented with nitrate (hereafter named as anoxic denitrifying conditions) as described above.…”

An Integrated Systems Approach Unveils New Aspects of Microoxia-Mediated Regulation in Bradyrhizobium diazoefficiens

“…Many gene and protein expression profiling studies of B. diazoefficiens cells grown under free-living conditions or in symbiosis (Lardi and Pessi, 2018 and Discussion) have been performed with B. diazoefficiens 110 spc 4 (Regensburger and Hennecke, 1983). Given the split from the USDA 110 reference strain 36 years ago, strain 110 spc 4 might well harbor genomic differences compared to the 9,105,828 bp genome of the reference strain (NC_004463; Kaneko et al, 2002).…”

“…We used B. diazoefficiens strain 110 spc 4 as a model, as a wealth of functional genomics data have been compiled for this strain. These comprise microarray-based gene expression and RNA-Seq studies, including experiments carried out under microoxia, a number of shotgun proteomics studies and efforts to integrate transcriptomics, proteomics and metabolomics datasets (Hauser et al, 2007; Lindemann et al, 2007; Pessi et al, 2007; Hacker et al, 2008; Lang et al, 2008; Mesa et al, 2008, 2009; Delmotte et al, 2010; Koch et al, 2010, 2014; Reutimann et al, 2010; Masloboeva et al, 2012; Serventi et al, 2012; Torres et al, 2014; Čuklina et al, 2016; Lardi et al, 2016; reviewed in Lardi and Pessi, 2018). Motivated by previous observations that the genome of this important strain might differ from that of the NCBI USDA 110 reference strain (Kaneko et al, 2002), we sequenced and de novo assembled the complete genome of B. diazoefficiens 110 spc 4 using long reads from PacBio's third generation sequencing technology.…”

Biotechnological Perspectives of Omics and Genetic Engineering Methods in Alfalfa

“…Over the last two decades, several methods have been developed that allowed the examination of global transcriptional changes. The most used ones are the hybridization of cDNAs (DNA microarrays) and the deep sequencing of cDNA (RNA-Seq; Schena et al, 1995;Wang et al, 2009;Lardi and Pessi, 2018). RNA-Seq, a massive parallel sequencing method for transcriptome analysis, was developed 10 years ago (Wang et al, 2009).…”

“…In contrast to microarrays, ribosomal RNA (rRNA) does not hybridize to the chip, as homologous probes are not present. In RNA-Seq, the abundant rRNA is removed (Lardi and Pessi, 2018). Originally, transcriptomic studies were based on Sanger sequencing of expressed sequence tags (ESTs) or microarrays, which was used in alfalfa and barrel medic (Aziz et al, 2005;Cheung et al, 2006;Yang et al, 2010).…”