Regulation of Small RNAs and Corresponding Targets in Nod Factor-Induced Phaseolus vulgaris Root Hair Cells.
A genome-wide analysis identified the set of small RNAs (sRNAs) from the agronomical important legume Phaseolus vulgaris (common bean), including novel P. vulgaris-specific microRNAs (miRNAs) potentially important for the regulation of the rhizobia-symbiotic process. Generally, novel miRNAs are difficult to identify and study because they are very lowly expressed in a tissue- or cell-specific manner. In this work, we aimed to analyze sRNAs from common bean root hairs (RH), a single-cell model, induced with pure Rhizobium etli nodulation factors (NF), a unique type of signal molecule. The sequence analysis of samples from NF-induced and control libraries led to the identity of 132 mature miRNAs, including 63 novel miRNAs and 1984 phasiRNAs. From these, six miRNAs were significantly differentially expressed during NF induction, including one novel miRNA: miR-RH82. A parallel degradome analysis of the same samples revealed 29 targets potentially cleaved by novel miRNAs specifically in NF-induced RH samples; however, these novel miRNAs were not differentially accumulated in this tissue. This study reveals Phaseolus vulgaris-specific novel miRNA candidates and their corresponding targets that meet all criteria to be involved in the regulation of the early nodulation events, thus setting the basis for exploring miRNA-mediated improvement of the common bean-rhizobia symbiosis.
Centro de Ciencias Gen&#243;micas, Universidad Nacional Aut&#243;noma de M&#233;xico (UNAM), Avenida Universidad 1001, Cuernavaca 62210, Morelos, Mexico. formey@ccg.unam.mx.
Damien
D
Formey
Centro de Ciencias Gen&#243;micas, Universidad Nacional Aut&#243;noma de M&#233;xico (UNAM), Avenida Universidad 1001, Cuernavaca 62210, Morelos, Mexico. jamartin@ccg.unam.mx.
José Ángel
JÁ
Martín-Rodríguez
Centro de Ciencias Gen&#243;micas, Universidad Nacional Aut&#243;noma de M&#233;xico (UNAM), Avenida Universidad 1001, Cuernavaca 62210, Morelos, Mexico. leija@ccg.unam.mx.
Alfonso
A
Leija
Departamento de Biolog&#237;a Molecular de Plantas, Instituto de Biotecnolog&#237;a (UNAM), Avenida Universidad 2001, Cuernavaca 62210, Morelos, Mexico. olivia@ibt.unam.mx.
Olivia
O
Santana
Departamento de Biolog&#237;a Molecular de Plantas, Instituto de Biotecnolog&#237;a (UNAM), Avenida Universidad 2001, Cuernavaca 62210, Morelos, Mexico. quinto@ibt.unam.mx.
Carmen
C
Quinto
Departamento de Biolog&#237;a Molecular de Plantas, Instituto de Biotecnolog&#237;a (UNAM), Avenida Universidad 2001, Cuernavaca 62210, Morelos, Mexico. luisc@ibt.unam.mx.
Luis
L
Cárdenas
Centro de Ciencias Gen&#243;micas, Universidad Nacional Aut&#243;noma de M&#233;xico (UNAM), Avenida Universidad 1001, Cuernavaca 62210, Morelos, Mexico. gina@ccg.unam.mx.
Georgina
G
Hernández
D019295:Computational Biology / Q000379:methods; D018506:Gene Expression Regulation, Plant; D059014:High-Throughput Nucleotide Sequencing; D035683:MicroRNAs / Q000235:genetics*; D027805:Phaseolus / Q000235:genetics*; D055170:Plant Root Nodulation / Q000235:genetics*; D018517:Plant Roots / Q000235:genetics*; D034622:RNA Interference; D012333:RNA, Messenger / Q000235:genetics*; D017422:Sequence Analysis, DNA
D035683:MicroRNAs; D012333:RNA, Messenger
common bean; legume-rhizobia interaction; miRNAs; phasiRNAs