Identification of conserved and new miRNAs that affect nodulation and strain selectivity in the Phaseolus vulgaris–Rhizobium etli symbiosis through differential analysis of host small RNAs

Abstract

Phaseolus vulgaris plants from the Mesoamerican centre of genetic diversification establish a preferential and more efficient root nodule symbiosis with sympatric Rhizobium etli strains. This is mediated by changes in host gene expression, which might occur either at the transcriptional or at the post-transcriptional level. However, the implication of small RNA (sRNA)mediated control of gene expression in strain selectivity has remained elusive.sRNA sequencing was used to identify host microRNAs (miRNAs) differentially regulated in roots at an early stage of the symbiotic interaction, which were further characterized by applying a reverse genetic approach.In silico analysis identified known and new miRNAs that accumulated to a greater extent in the preferential and more efficient interaction. One of them, designated as Pvu-miR5924, participates in the mechanisms that determine the selection of R. etli strains that will colonize the nodules. In addition, the functional analysis of Pvu-miR390b verified that this miRNA is a negative modulator of nodule formation and bacterial infection.This study not only extended the list of miRNAs identified in P. vulgaris but also enabled the identification of miRNAs that play relevant functions in nodule formation, rhizobial infection and the selection of the rhizobial strains that will occupy the nodule.

Biochemical and Phylogenetic Analysis of Italian Phaseolus vulgaris Cultivars as Sources of α-Amylase and α-Glucosidase Inhibitors

“…Usually, plant miRNAs associate with Argonaute protein 1 to promote RNA posttranscriptional gene silencing by coupling target sequences and determining RNA slicing and/or translation inhibition [ 35 , 36 ]. In the last few years, many miRNAs have been identified in P. vulgaris [ 37 , 38 ]. Based on this second hypothesis, the α-glucosidase inhibitory activity observed in the cultivars without α-AI activity could be linked to the presence of flavonol glycosides and caffeic acid derivatives in the homogenates.…”

A lateral organ boundaries domain transcription factor acts downstream of the auxin response factor 2 to control nodulation and root architecture in Medicago truncatula

“…The miR390 guides ARGONAUTE 7 (AGO7)‐mediated endonucleolytic cleavage of the TAS3 transcript, triggering the production of secondary trans ‐acting small interference RNAs (tasiRNAs), which bound to AGO1 guide endonucleolytic cleavage of ARF2 , ARF3 and ARF4 mRNAs (Xia et al ., 2017). We have previously shown that the miR390/ TAS3 / ARF module mediates the control of lateral root formation and root nodule symbiosis (Hobecker et al ., 2017; Kirolinko et al ., 2021; Castaingts et al ., 2022). Activation of the miR390/ TAS3 / ARF module by overexpression of miR390 in M. truncatula roots altered root architecture and impaired nodule formation and infection by Sinorhizobium meliloti , whereas inactivation of this module by expression of a target mimicry of miR390 or mutations in AGO7 promotes nodule organogenesis and bacterial infection (Hobecker et al ., 2017).…”

Estudio funcional de genes involucrados en la simbiosis fijadora de nitrógeno

“…Estudios transcriptómicos nos han permitido identificar transcriptos que se acumulan diferencialmente en respuesta a cepas de rizobio que son seleccionados por la planta y que presentan una mayor eficiencia simbiótica. A partir de esta información se identificaron RNAs no codificantes pequeños (miRNAs y siRNAs) (Castaingts., 2022), RNAs no codificantes largos (lncRNAs) y mRNAs que codifican proteínas que participan del silenciamiento postranscripcional (Dalla Via et al, 2015;Clúa et al, 2022).…”

“…Teniendo en cuenta que la proteína IDN2 de A. thaliana participa en el proceso de metilación del DNA guiada por RNA y que plantas mutantes idn2 de Arabidopsis exhiben niveles de metilación de citosinas alterados en todos sus contextos (CG, CHG y CHH) (Ausin et al, 2009), nos propusimos identificar cambios en los niveles de metilación del DNA como consecuencia del silenciamiento de PvIDN2 en P. vulgaris en el contexto de la infección rizobiana. A partir de bibliotecas generadas en nuestro laboratorio de RNAs pequeños (sRNAs) de plantas de poroto de la variedad Mesoamericana NAG12 24 hpi con la bacteria más eficiente R. etli SC15, con la bacteria menos eficiente 55N1 o con medio YEM como control (Castaingts et al, 2022), se llevó a cabo un análisis bioinformático para identificar pequeños RNAs de interferencia (siRNAs) de 24 nucleótidos que actúan a nivel de la cromatina promoviendo su compactación (denominados hetsiRNAs, por siRNAs de heterocromatina) (resultados no publicados, Artunián, Reynoso, Blanco). Se identificaron 236 picos de hetsiRNAs diferencialmente acumulados, de los cuales 25 están próximos a genes regulados en respuesta a la cepa nodC-α (SC15) o nodC-δ (55N1).…”