Biology subjects

Frugoli, J.

Publications and source records attributed to Frugoli, J..

3 recordsLinked to original sources

bioRxiv2023

The Single-Cell Transcriptome Program of Nodule Development Cellular Lineages in Medicago truncatula

Legumes can establish a symbiotic relationship with nitrogen-fixing rhizobia by developing nodules after root exposure to lipo-chito-oligosaccharides secreted by the bacteria. Nodule development initiates with anticlinal mitotic divisions in the pericycle and endodermal and inner cortical cells, establishing cell lineages that ultimately form each nodule compartment. We characterized these lineages by isolating and sequencing the transcriptome of Medicago truncatula single nuclei derived from uninoculated roots and roots undergoing early nodule development at 24, 48, and 96 hours after inoculation. To enrich samples for cells responding to the rhizobia, we complemented the analysis of the Medicago wild-type genotype A17 with a mutant for the autoregulation of nodulation, sunn-4. Analysis of cell lineage trajectories derived from the cortex indicates that their transcriptome is initially enriched for cytokinin perception and signaling while repressing auxin accumulation. As these cells differentiate to form nodules, expression of genes related to auxin biosynthesis, transport, and signaling was enhanced, while genes involved in cytokinin degradation were activated as lineages bifurcated to form the nodule meristem and infection zones. While the contribution of auxin and cytokinin in nodule development has been recognized, this single-cell resource quantifies the expression of each of their regulators, receptors and targets as cells divide and differentiate to form each nodule compartment.

plant biology↗

bioRxiv2023

A laser capture microdissection transcriptome of M. truncatula roots responding to rhizobia reveals spatiotemporal tissue expression patterns of genes involved in nodule signaling and organogenesis

We report a public resource for examining the spatiotemporal RNA expression of 54,893 M. truncatula genes during the first 72 hours of response to rhizobial inoculation. Using a methodology that allows synchronous inoculation and growth of over 100 plants in a single media container, we harvested the same segment of each root responding to rhizobia in the initial inoculation over a time course, collected individual tissues from these segments with laser capture microdissection, and created and sequenced RNA libraries generated from these tissues. We demonstrate the utility of the resource by examining the expression patterns of a set of genes induced very early in nodule signaling, as well as two gene families (CLE peptides and nodule specific PLAT-domain proteins) and show that despite similar whole root expression patterns, there are tissue differences in expression between the genes. Using a rhizobial response data set generated from transcriptomics on intact root segments, we also examined differential temporal expression patterns and determined that, after nodule tissue, the epidermis and cortical cells contained the most temporally patterned genes. We circumscribed gene lists for each time and tissue examined and developed an expression pattern visualization tool. Finally, we explored transcriptomic differences between the inner cortical cells that become nodules and those that do not, confirming that the expression of ACC synthases distinguishes inner cortical cells that become nodules and provide and describe potential downstream genes involved in early nodule cell division.

plant biology↗

bioRxiv2023

Transcriptome analysis of Medicago truncatula Autoregulation of Nodulation mutants reveals that disruption of the SUNN pathway causes constitutive expression changes in a small group of genes, but the overall response to rhizobia resembles wild type, including induction of TML1 and TML2.

Nodule number regulation in legumes is controlled by a feedback loop that integrates nutrient and rhizobia symbiont status signals to regulate nodule development. Signals from the roots are perceived by shoot receptors, including a CLV1-like receptor-like kinase known as SUNN in the annual medic Medicago truncatula. In the absence of functional SUNN, the autoregulation feedback loop is disrupted, resulting in hypernodulation. To elucidate early autoregulation mechanisms disrupted in SUNN mutants, we searched for genes with altered expression in the loss-of-function sunn-4 mutant and included the rdn1-2 autoregulation mutant for comparison. We identified constitutively altered expression of small groups of genes in sunn-4 roots, including higher levels of transcription factor NF-YA2, and in sunn-4 shoots. All genes with verified roles in nodulation that were induced in wild type roots during the establishment of nodules were also induced in sunn-4, including, surprisingly, autoregulation genes TML2 and TML1. Among all genes with a differential response to rhizobia in wild type roots, only an isoflavone-7-O-methyltransferase gene (Medtr7g014510) was found to be unresponsive in sunn-4. In shoot tissues of wild type, eight rhizobia-responsive genes were identified, including a MYB family transcription factor gene (Medtr3111880) which remained at a baseline level in sunn-4; three genes were found to be induced by rhizobia in shoots of sunn-4 but not wild type. We also cataloged the temporal induction profiles of many small secreted peptide (MtSSP) genes in nodulating root tissues, encompassing members of twenty-four peptide families, including the CLE and IRON MAN families. The discovery that expression of TML genes in roots, a key factor in inhibiting nodulation in response to autoregulation signals, is also triggered in sunn-4 in the section of roots analyzed suggests that the mechanism of TML regulation in M. truncatula may be more complex than published models.

plant biology↗