Changes in the Common Bean Transcriptome in Response to Secreted and Surface Signal Molecules of Rhizobium etli

Abstract

Establishment of nitrogen-fixing symbiosis requires the recognition of rhizobial molecules to initiate the development of nodules. Using transcriptional profiling of roots inoculated with mutant strains defective in the synthesis of Nod Factor (NF), exopolysaccharide (EPS), or lipopolysaccharide (LPS), we identified 2,606 genes from common bean (Phaseolus vulgaris) that are differentially regulated at early stages of its interaction with Rhizobium etli. Many transcription factors from different families are modulated by NF, EPS, and LPS in different combinations, suggesting that the plant response depends on the integration of multiple signals. Some receptors identified as differentially expressed constitute excellent candidates to participate in signal perception of molecules derived from the bacteria. Several components of the ethylene signal response, a hormone that plays a negative role during early stages of the process, were down-regulated by NF and LPS. In addition, genes encoding proteins involved in small RNA-mediated gene regulation were regulated by these signal molecules, such as Argonaute7, a specific component of the trans-acting short interfering RNA3 pathway, an RNA-dependent RNA polymerase, and an XH/XP domaincontaining protein, which is part of the RNA-directed DNA methylation. Interestingly, a number of genes encoding components of the circadian central oscillator were down-regulated by NF and LPS, suggesting that a root circadian clock is adjusted at early stages of symbiosis. Our results reveal a complex interaction of the responses triggered by NF, LPS, and EPS that integrates information of the signals present in the surface or secreted by rhizobia.

Comparative phylogenetic and expression analysis of small GTPases families in legume and non-legume plants

“…NAG12 plants inoculated with different Rhizobium etli strains at 24 hours. 53 Two biological replicates were used for RNAseq and differentially expressed genes were identified using Cuffdiff. RT-qPCR analysis of differentially expressed genes confirmed expression data obtained by RNAseq for nine out of 11 genes.…”

Phosphate Deficiency Negatively Affects Early Steps of the Symbiosis between Common Bean and Rhizobia

“…At 1, 24 and 48 hours post-inoculation, the zone of the roots susceptible to rhizobium infection (hereafter referred as susceptible zone) was isolated, flash frozen in liquid nitrogen, and stored at -80 0 C until used for total RNA extraction. The susceptible zone encompassed a region of  1cm and is analogous to the distal region of the elongation zone and the entire differentiated zone of the root [54]. Four biological replicates, each one containing susceptible zones from four different seedlings, were independently generated.…”

How legumes recognize rhizobia

“…EPS and LPS negatively regulate two receptors with serine/threonine (Ser/Thr) kinase domains highly similar to the ethylene receptor ETR2 by an unknown process. 31 These receptors are regulated by abiotic stresses and hormones. Abbreviations: LRR: leucine rich repeats; NFR: Nod factor receptor; NFP: Nod factor perception; LYK3: LysM receptor kinase 3; DMI2: Does not Make Infection; SYMRK: Symbiosis receptor-like kinase; EPR3: EPS receptor 3; LysM: Lysin motif.…”

“…More recently, we have studied the transcriptional changes of common bean in response to LPS and EPS mutant strains of R. etli. 31 In this system, the LPS mutant did not form nodules, whereas the EPS strain showed a phenotype similar to the wild type. At 24 hours post inoculation, defense responses were still active in roots inoculated with the wild type strain, but no significant effects of LPS and EPS were detected at this early time point of the interaction.…”

“…Of particular interest are studies that used mutant strains of rhizobia to dissect the transcriptional changes associated to recognition of signal molecules from bacteria. 28,[30][31][32][33] (Table 1). Jones and collaborators 32 showed the differences in the M. truncatula transcriptional response when it was inoculated with the wild type strain or a succinoglycan-deficient strain of S. meliloti unable to establish a successful infection.…”