Abstract
BackgroundSmall RNAs regulate a number of developmental processes in plants and animals. However, the role of small RNAs in legume-rhizobial symbiosis is largely unexplored. Symbiosis between legumes (e.g. soybean) and rhizobia bacteria (e.g. Bradyrhizobium japonicum) results in root nodules where the majority of biological nitrogen fixation occurs. We sought to identify microRNAs (miRNAs) regulated during soybean-B. japonicum symbiosis.ResultsWe sequenced ~350000 small RNAs from soybean roots inoculated with B. japonicum and identified conserved miRNAs based on similarity to miRNAs known in other plant species and new miRNAs based on potential hairpin-forming precursors within soybean EST and shotgun genomic sequences. These bioinformatics analyses identified 55 families of miRNAs of which 35 were novel. A subset of these miRNAs were validated by Northern analysis and miRNAs differentially responding to B. japonicum inoculation were identified. We also identified putative target genes of the identified miRNAs and verified in vivo cleavage of a subset of these targets by 5'-RACE analysis. Using conserved miRNAs as internal control, we estimated that our analysis identified ~50% of miRNAs in soybean roots.ConclusionConstruction and analysis of a small RNA library led to the identification of 20 conserved and 35 novel miRNA families in soybean. The availability of complete and assembled genome sequence information will enable identification of many other miRNAs. The conserved miRNA loci and novel miRNAs identified in this study enable investigation of the role of miRNAs in rhizobial symbiosis.
Highlights
Small RNAs regulate a number of developmental processes in plants and animals
BMC Genomics 2008, 9:160 http://www.biomedcentral.com/1471-2164/9/160 rial signals which are in turn recognized by plants [1,2,3] resulting in the attachment of bacterial cells to plant root hairs
This approach identified the most number of novel miRNA sequences in our analysis (Table 1) and all 5 novel miRNAs tested were validated by Northern analysis (Figure 4)
Summary
Small RNAs regulate a number of developmental processes in plants and animals. Symbiosis between legumes (e.g. soybean) and rhizobia bacteria (e.g. Bradyrhizobium japonicum) results in root nodules where the majority of biological nitrogen fixation occurs. We sought to identify microRNAs (miRNAs) regulated during soybean-B. japonicum symbiosis. Symbiotic association between leguminous plants and rhizobia bacteria results in specialized nitrogen-fixing structures called root nodules. Signal transduction leading to the process of nodule development commences upon recognition of compatible bacterial LCOs on the root surface by the plants. MiRNAs are short ~21 nt molecules that regulate gene expression post-transcriptionally and have been identified in both animals and plants. MiRNAs have been clearly shown to regulate a number of developmental and physiological processes [10,11,12,13,14]
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