Complete Transcriptome of the Soybean Root Hair Cell, a Single-Cell Model, and Its Alteration in Response to Bradyrhizobium japonicum Infection

Division of Plant Sciences, National Center for Soybean Biotechnology, CS Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, USA.
Plant physiology (Impact Factor: 6.84). 11/2009; 152(2):541-52. DOI: 10.1104/pp.109.148379
Source: PubMed


Nodulation is the result of a mutualistic interaction between legumes and symbiotic soil bacteria (e.g. soybean [Glycine max] and Bradyrhizobium japonicum) initiated by the infection of plant root hair cells by the symbiont. Fewer than 20 plant genes involved in the nodulation process have been functionally characterized. Considering the complexity of the symbiosis, significantly more genes are likely involved. To identify genes involved in root hair cell infection, we performed a large-scale transcriptome analysis of B. japonicum-inoculated and mock-inoculated soybean root hairs using three different technologies: microarray hybridization, Illumina sequencing, and quantitative real-time reverse transcription-polymerase chain reaction. Together, a total of 1,973 soybean genes were differentially expressed with high significance during root hair infection, including orthologs of previously characterized root hair infection-related genes such as NFR5 and NIN. The regulation of 60 genes was confirmed by quantitative real-time reverse transcription-polymerase chain reaction. Our analysis also highlighted changes in the expression pattern of some homeologous and tandemly duplicated soybean genes, supporting their rapid specialization.

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    • "The process of infection thread formation is then repeated in the underlying cell layers allowing the rhizobia access to the inner root layers which have divided to form the NP. Root hair infection involves the upregulation of 100s of genes that regulate several different processes including host-symbiont signaling and diverse developmental processes including cell growth and engagement of the cell cycle (Libault et al., 2010; Breakspear et al., 2014). While maturing the nodule forms several developmental zones: an apical meristem (Zone I), an infection zone containing cells that form infection threads (ZII), a nitrogen fixing zone comprised of giant cells filled with endocytosed nitrogen-fixing rhizobia (ZIII), an interzone (IZ), and a senescent zone, where no nitrogen fixation takes place (ZIV). "
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    ABSTRACT: Genome-wide expression studies on nodulation have varied in their scale from entire root systems to dissected nodules or root sections containing nodule primordia (NP). More recently efforts have focused on developing methods for isolation of root hairs from infected plants and the application of laser-capture microdissection technology to nodules. Here we analyze two published data sets to identify a core set of infection genes that are expressed in the nodule and in root hairs during infection. Among the genes identified were those encoding phenylpropanoid biosynthesis enzymes including Chalcone-O-Methyltransferase which is required for the production of the potent Nod gene inducer 4',4-dihydroxy-2-methoxychalcone. A promoter-GUS analysis in transgenic hairy roots for two genes encoding Chalcone-O-Methyltransferase isoforms revealed their expression in rhizobially infected root hairs and the nodule infection zone but not in the nitrogen fixation zone. We also describe a group of Rhizobially Induced Peroxidases whose expression overlaps with the production of superoxide in rhizobially infected root hairs and in nodules and roots. Finally, we identify a cohort of co-regulated transcription factors as candidate regulators of these processes.
    Frontiers in Plant Science 08/2015; 6:575. DOI:10.3389/fpls.2015.00575 · 3.95 Impact Factor
    • " The tissue-specific expression patterns of these genes were then extracted from the soybean gene expression transcriptomics atlas (Libault et al. 2010). These publicly available transcriptomics data Planta (soyKB database, "
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    ABSTRACT: Main conclusion: Chemical analyses and glycome profiling demonstrate differences in the structures of the xyloglucan, galactomannan, glucuronoxylan, and rhamnogalacturonan I isolated from soybean ( Glycine max ) roots and root hair cell walls. The root hair is a plant cell that extends only at its tip. All other root cells have the ability to grow in different directions (diffuse growth). Although both growth modes require controlled expansion of the cell wall, the types and structures of polysaccharides in the walls of diffuse and tip-growing cells from the same plant have not been determined. Soybean (Glycine max) is one of the few plants whose root hairs can be isolated in amounts sufficient for cell wall chemical characterization. Here, we describe the structural features of rhamnogalacturonan I, rhamnogalacturonan II, xyloglucan, glucomannan, and 4-O-methyl glucuronoxylan present in the cell walls of soybean root hairs and roots stripped of root hairs. Irrespective of cell type, rhamnogalacturonan II exists as a dimer that is cross-linked by a borate ester. Root hair rhamnogalacturonan I contains more neutral oligosaccharide side chains than its root counterpart. At least 90 % of the glucuronic acid is 4-O-methylated in root glucuronoxylan. Only 50 % of this glycose is 4-O-methylated in the root hair counterpart. Mono O-acetylated fucose-containing subunits account for at least 60 % of the neutral xyloglucan from root and root hair walls. By contrast, a galacturonic acid-containing xyloglucan was detected only in root hair cell walls. Soybean homologs of the Arabidopsis xyloglucan-specific galacturonosyltransferase are highly expressed only in root hairs. A mannose-rich polysaccharide was also detected only in root hair cell walls. Our data demonstrate that the walls of tip-growing root hairs cells have structural features that distinguish them from the walls of other roots cells.
    Planta 06/2015; 242(5). DOI:10.1007/s00425-015-2344-y · 3.26 Impact Factor
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    • "To allow for gene duplication in the M. truncatula lineage post-divergence, the two highest scoring hits for each gene model were retained. Genes that we determined as having significantly changed expression (data for all wild-type rhizobial time-points as well as the skl mutant and Nod factor treatment were used) that have homologs with changed expression as determined by Libault et al. (2010) are listed in Supplemental Data Set 3 (Conserved Gm). Syntenic genes were identified using previously identified synteny blocks (Legume Information Portal web server, LegumeIP; Li et al. 2012). "
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    ABSTRACT: Nitrogen-fixing rhizobia colonize legume roots via plant-made intracellular infection threads. Genetics has identified some genes involved but has not provided sufficient detail to understand requirements for infection thread development. Therefore, we transcriptionally profiled Medicago truncatula root hairs prior to and during the initial stages of infection. This revealed changes in the responses to plant hormones, most notably auxin, strigolactone, gibberellic acid, and brassinosteroids. Several auxin responsive genes, including the ortholog of Arabidopsis thaliana Auxin Response Factor 16, were induced at infection sites and in nodule primordia, and mutation of ARF16a reduced rhizobial infection. Associated with the induction of auxin signaling genes, there was increased expression of cell cycle genes including an A-type cyclin and a subunit of the anaphase promoting complex. There was also induction of several chalcone O-methyltransferases involved in the synthesis of an inducer of Sinorhizobium meliloti nod genes, as well as a gene associated with Nod factor degradation, suggesting both positive and negative feedback loops that control Nod factor levels during rhizobial infection. We conclude that the onset of infection is associated with reactivation of the cell cycle as well as increased expression of genes required for hormone and flavonoid biosynthesis and that the regulation of auxin signaling is necessary for initiation of rhizobial infection threads.
    The Plant Cell 12/2014; 26:4680-4701. DOI:10.1105/tpc.114.133496 · 9.34 Impact Factor
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