Dissecting the Acid Stress Response of Rhizobium tropici CIAT 899

Abstract

Rhizobium tropici CIAT899 is a nodule-forming α-proteobacterium displaying intrinsic resistance to several abiotic stress conditions such as low pH and high temperatures, which are common in tropical environments. It is a good competitor for Phaseolus vulgaris (common bean) nodule occupancy at low pH values, however little is known about the genetic and physiological basis of the tolerance to acidic conditions. To identify genes in R. tropici involved in pH stress response we combined two different approaches: (1) A Tn5 mutant library of R. tropici CIAT899 was screened and 26 acid-sensitive mutants were identified. For 17 of these mutants, the transposon insertion sites could be identified. (2) We also studied the transcriptomes of cells grown under different pH conditions using RNA-Seq. RNA was extracted from cells grown for several generations in minimal medium at 6.8 or 4.5 (adapted cells). In addition, we acid-shocked cells pre-grown at pH 6.8 for 45 min at pH 4.5. Of the 6,289 protein-coding genes annotated in the genome of R. tropici CIAT 899, 383 were differentially expressed under acidic conditions (pH 4.5) vs. control condition (pH 6.8). Three hundred and fifty one genes were induced and 32 genes were repressed; only 11 genes were induced upon acid shock. The acid stress response of R. tropici CIAT899 is versatile: we found genes encoding response regulators and membrane transporters, enzymes involved in amino acid and carbohydrate metabolism and proton extrusion, in addition to several hypothetical genes. Our findings enhance our understanding of the core genes that are important during the acid stress response in R. tropici.

Metatranscriptomic Analysis of the Bacterial Symbiont Dactylopiibacterium carminicum from the Carmine Cochineal Dactylopius coccus (Hemiptera: Coccoidea: Dactylopiidae)

“…A modified RNEeasy (Qiagen) procedure with lysozyme and DNAse I was used as reported by Guerrero-Castro et al [27]. RNA was quantified by Nanodrop and visualized in 1% electrophoresis gels.…”

The Rhizobium-Legume Symbiosis: Co-opting Successful Stress Management

“…Transcriptomic studies addressing the response of rhizobium to acidic pH and have revealed large networks regulating multiple genes in response to acidic pH ( Hellweg et al, 2009 ; Guerrero-Castro et al, 2018 ). The response of rhizobia to acidic pH is primarily regulated though two-component systems, actR/S and chvI / exoS / exoR ( Dilworth et al, 2000 ; Fenner et al, 2004 ).…”

Revealing potential functions of hypothetical proteins induced by genistein in the symbiosis island of Bradyrhizobium japonicum commercial strain SEMIA 5079 (= CPAC 15)

“…The BJS_07621 protein was predicted as a lyase, a glutathione-dependent formaldehyde-activating (GFA) enzyme (Gfa protein, EC 4.4.1.22), of the glutathione-dependent formaldehyde oxidation pathway, involved in C1 metabolism and methanol oxidation in B. diazoefficiens [ 76 ]. In B. diazoefficiens USDA 110, gfa was induced in cells grown with vanillin (aromatic compound) as sole source of carbon [ 77 ], in M. loti MAFF303099 in response to salt stress [ 78 ], in R. tropici CIAT 899 to acid stress [ 79 ], and in USDA 110 cells exposed to elevated atmospheric CO 2 [ 80 ]. Therefore, the enzyme has been associated with bacterial growth under different environmental stresses, and the several copies found in SEMIA 5079 might indicate advantages under stressful conditions.…”