Genomic, transcriptomic, and proteomic approaches towards understanding the molecular mechanisms of salt tolerance in Frankia strains isolated from Casuarina trees

Abstract

BackgroundSoil salinization is a worldwide problem that is intensifying because of the effects of climate change. An effective method for the reclamation of salt-affected soils involves initiating plant succession using fast growing, nitrogen fixing actinorhizal trees such as the Casuarina. The salt tolerance of Casuarina is enhanced by the nitrogen-fixing symbiosis that they form with the actinobacterium Frankia. Identification and molecular characterization of salt-tolerant Casuarina species and associated Frankia is imperative for the successful utilization of Casuarina trees in saline soil reclamation efforts. In this study, salt-tolerant and salt-sensitive Casuarina associated Frankia strains were identified and comparative genomics, transcriptome profiling, and proteomics were employed to elucidate the molecular mechanisms of salt and osmotic stress tolerance.ResultsSalt-tolerant Frankia strains (CcI6 and Allo2) that could withstand up to 1000 mM NaCl and a salt-sensitive Frankia strain (CcI3) which could withstand only up to 475 mM NaCl were identified. The remaining isolates had intermediate levels of salt tolerance with MIC values ranging from 650 mM to 750 mM. Comparative genomic analysis showed that all of the Frankia isolates from Casuarina belonged to the same species (Frankia casuarinae). Pangenome analysis revealed a high abundance of singletons among all Casuarina isolates. The two salt-tolerant strains contained 153 shared single copy genes (most of which code for hypothetical proteins) that were not found in the salt-sensitive(CcI3) and moderately salt-tolerant (CeD) strains. RNA-seq analysis of one of the two salt-tolerant strains (Frankia sp. strain CcI6) revealed hundreds of genes differentially expressed under salt and/or osmotic stress. Among the 153 genes, 7 and 7 were responsive to salt and osmotic stress, respectively. Proteomic profiling confirmed the transcriptome results and identified 19 and 8 salt and/or osmotic stress-responsive proteins in the salt-tolerant (CcI6) and the salt-sensitive (CcI3) strains, respectively.ConclusionGenetic differences between salt-tolerant and salt-sensitive Frankia strains isolated from Casuarina were identified. Transcriptome and proteome profiling of a salt-tolerant strain was used to determine molecular differences correlated with differential salt-tolerance and several candidate genes were identified. Mechanisms involving transcriptional and translational regulation, cell envelop remodeling, and previously uncharacterized proteins appear to be important for salt tolerance. Physiological and mutational analyses will further shed light on the molecular mechanism of salt tolerance in Casuarina associated Frankia isolates.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-4056-0) contains supplementary material, which is available to authorized users.

Stable Transformation of the Actinobacteria Frankia spp

“…S3). With this technique, Frankia colonies could be screened after 5 to 6 weeks of growth instead of waiting 5 extra weeks of growth in liquid culture for DNA extraction (30). These data confirmed the presence of the constructs in the two F. casuarinae strain CcI3(pBBR1MCS-3-22605) transformants tested.…”

“…Proof of concept of this mating transformation method based on salt tolerance of Frankia casuarinae strain CcI3. Genetic, transcriptomic, and proteomics approaches identified seven candidate genes that are responsive to salt stress (30). These candidates are present in the salt-tolerant Frankia sp.…”

Identification of salt tolerance-related genes of Lactobacillus plantarum D31 and T9 strains by genomic analysis

“…Accumulation of certain compatible solutes (e.g., glycine and betaine) is a common metabolic adaptation found in diverse species (Oshone et al 2017). The osmotic function of a compatible solute depends on the degree of methylation and length of the hydrocarbon chain (Peddie et al 1994).…”

“…Moreover, the gene encoding a membrane protein (D7Y65_03505, D7Y66_02210) was also identified in L. plantarum D31 and T9 genomes, which had 50% sequence similarity with the gene (CCI6_RS12035) in Frankia sp. Ccl6, which was involved in cell wall/ membrane/envelop biosynthesis and upregulated under the salt stress (Oshone et al 2017). L. plantarum D31 and T9 also contain the genes encoding a 1-acylglycerol-3-phosphate O-acyltransferase (D7Y65_09990, D7Y66_ 08235) and a phosphatidylglycerophosphatase A (D7Y65_11075, D7Y66_07900), which are involved in cell wall modification to response to the salt stress in Frankia strains (Oshone et al 2017).…”

“…The expression of these genes was upregulated in Frankia sp. Ccl6 grown in 1000 mmol/l NaCl (Oshone et al 2017). In addition, many differentially expressed proteins responding to 6.0% NaCl stress were identified in L. plantarum ATCC14917 (Huang et al 2010).…”