Julia Frugoli | Clemson University (original) (raw)

Papers by Julia Frugoli

Current Issues in Molecular Biology, May 27, 2023

Analysis Reveals Disruption of the SUNN Pathway Causes Constitutive Expression Changes in Some Ge... more Analysis Reveals Disruption of the SUNN Pathway Causes Constitutive Expression Changes in Some Genes, but Overall Response to Rhizobia Resembles Wild-Type, Including Induction of TML1 and TML2. Curr.

Genome, Aug 1, 2003

The pooid subfamily of grasses includes some of the most important crop, forage and turf species,... more The pooid subfamily of grasses includes some of the most important crop, forage and turf species, such as wheat, barley and Lolium. Developing genomic resources, such as whole-genome physical maps, for analysing the large and complex genomes of these crops and for facilitating biological research in grasses is an important goal in plant biology. We describe a bacterial artificial chromosome (BAC)-based physical map of the wild pooid grass Brachypodium distachyon and integrate this with whole genome shotgun sequence (WGS) assemblies using BAC end sequences (BES). The resulting physical map contains 26 contigs spanning the 272 Mb genome. BES from the physical map were also used to integrate a genetic map. This provides an independent vaildation and confirmation of the published WGS assembly. Mapped BACs were used in Fluorescence In Situ Hybridisation (FISH) experiments to align the integrated physical map and sequence assemblies to chromosomes with high resolution. The physical, genetic and cytogenetic maps, integrated with whole genome shotgun sequence assemblies, enhance the accuracy and durability of this important genome sequence and will directly facilitate gene isolation.

Plant Methods, Mar 25, 2023

Frontiers in Plant Science, Apr 7, 2022

Frontiers in Plant Science, Oct 31, 2019

Root nodulation results from a symbiotic relationship between a plant host and Rhizobium bacteria... more Root nodulation results from a symbiotic relationship between a plant host and Rhizobium bacteria. Synchronized gene expression patterns over the course of rhizobial infection result in activation of pathways that are unique but overlapping with the highly conserved pathways that enable mycorrhizal symbiosis. We performed RNA sequencing of 30 Medicago truncatula root maturation zone samples at five distinct time points. These samples included plants inoculated with Sinorhizobium medicae and control plants that did not receive any Rhizobium. Following gene expression quantification, we identified 1,758 differentially expressed genes at various time points. We constructed a gene co-expression network (GCN) from the same data and identified link community modules (LCMs) that were comprised entirely of differentially expressed genes at specific time points post-inoculation. One LCM included genes that were up-regulated at 24 h following inoculation, suggesting an activation of allergen family genes and carbohydratebinding gene products in response to Rhizobium. We also identified two LCMs that were comprised entirely of genes that were down regulated at 24 and 48 h post-inoculation. The identity of the genes in these modules suggest that down-regulating specific genes at 24 h may result in decreased jasmonic acid production with an increase in cytokinin production. At 48 h, coordinated down-regulation of a specific set of genes involved in lipid biosynthesis may play a role in nodulation. We show that GCN-LCM analysis is an effective method to preliminarily identify polygenic candidate biomarkers of root nodulation and develop hypotheses for future discovery.

bioRxiv (Cold Spring Harbor Laboratory), Jan 20, 2023

Transcriptome analysis of Medicago truncatula Autoregulation of Nodulation mutants reveals that d... more 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.

Springer eBooks, 2013

Soil bacteria collectively called rhizobia establish a unique beneficial interaction with most le... more Soil bacteria collectively called rhizobia establish a unique beneficial interaction with most legumes and a few nonleguminous plants in the family of Ulmaceae (Parasponia sp.). This endosymbiosis between rhizobia and the host plant leads to the formation of N2-fixing nodules, in which bacteria are provided with a carefully regulated oxygen and carbon supply allowing the bacteria to reduce nitrogen efficiently for the plant. The early steps of this symbiosis begin with exchange of signals, a molecular dialogue between the symbiotic partners. The chemical signals involved determine a high degree of host specificity. The release of the plant-derived chemicals to the rhizosphere activates the expression of the bacterial nodulation genes, resulting in the production of lipochitooligosaccharide signaling molecules called Nod factors. Nod factors induce a cascade of events in the host plant that leads to the formation of nodule primordia. Since nodulation and the subsequent nitrogen fixation are energy-intensive processes, the host plant maintains a balance between cost and benefit by limiting the number of nodules that form through autoregulation of nodulation. Functional nodules are not maintained throughout the life cycle of plants and nodules senesce when they get old. This review examines the current state of knowledge of signals and mechanisms involved in the early establishment of rhizobium–legume symbioses, focusing on how the host plant induces Nod factor production, how these signals are perceived and transduced in the host plant, and the physiological and morphological changes associated with root nodule development.

We report a public resource for examining the spatiotemporal RNA expression of 54,893M. truncatul... more We report a public resource for examining the spatiotemporal RNA expression of 54,893M. truncatulagenes 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...

Science and Engineering Ethics, 2006

bioRxiv (Cold Spring Harbor Laboratory), Jun 14, 2023

Legumes can establish a symbiotic relationship with nitrogen-fixing rhizobia by developing nodule... more 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 (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 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.

Journal of Plant Growth Regulation

Plants

Plants have mechanisms to relocate chloroplasts based on light intensities in order to maximize p... more Plants have mechanisms to relocate chloroplasts based on light intensities in order to maximize photosynthesis and reduce photodamage. Under low light, chloroplasts move to the periclinal walls to increase photosynthesis (accumulation) and move to the anticlinal walls under high light to avoid photodamage, and even cell death (avoidance). Arabidopsis blue light receptors phot1 and phot2 (phototropins) have been reported to regulate chloroplast movement. This study discovered that another blue light receptor, FLAVIN-BINDING KELCH REPEAT F-BOX1 (FKF1), regulates chloroplast photorelocation by physically interacting with chloroplast unusual positioning protein 1 (CHUP1), a critical component of the chloroplast motility system. Leaf cross-sectioning and red-light transmittance results showed that overexpression of FKF1 compromised the avoidance response, while the absence of FKF1 enhanced chloroplast movements under high light. Western blot analysis showed that CHUP1 protein abundance i...

Plant Methods

Background Various growth systems are available for studying plant root growth and plant–microbe ... more Background Various growth systems are available for studying plant root growth and plant–microbe interactions including hydroponics and aeroponics. Although some of these systems work well with Arabidopsis thaliana and smaller cereal model plants, they may not scale up as well for use with hundreds of plants at a time from a larger plant species. The aim of this study is to present step-by-step instructions for fabricating an aeroponic system, also called a “caisson,” that has been in use in several legume research labs studying the development of symbiotic nitrogen fixing nodules, but for which detailed directions are not currently available. The aeroponic system is reusable and is adaptable for many other types of investigations besides root nodulation. Results An aeroponic system that is affordable and reusable was adapted from a design invented by French engineer René Odorico. It consists of two main components: a modified trash can with a lid of holes and a commercially availab...

BMC Research Notes, 2020

Objectives Earlier work in our lab identified a spontaneous mutant (likesunnsupernodulator-lss) i... more Objectives Earlier work in our lab identified a spontaneous mutant (likesunnsupernodulator-lss) in Medicago truncatula, resulting in increased nodulation. Molecular genetic evidence indicated the phenotype was due to an unknown lesion resulting in cis-silencing of the SUNN gene. Altered methylation of the promoter was suspected, but analysis of the SUNN promoter by bisulfite sequencing at the time of publication revealed no significant methylation differences between the SUNN promoter in wild type and lss plants. Using advances in methylome generation we compared the methylome of wild type and the lss mutant in the larger 810 kB area of the genome where lss maps. Data description The data show the distribution of types of methylation across the entire genome between A17 wild type and lss mutants, the number of differentially methylated cytosines between genotypes, and the overall pattern of gene methylation between genotypes. We expect the wild type data will be especially useful as...

At the 1999 Medicago truncatula meeting in Amsterdam, it became obvious to participants that with... more At the 1999 Medicago truncatula meeting in Amsterdam, it became obvious to participants that with multiple laboratories generating mutants, the establishment of a policy for gene nomenclature for the species would prevent confusion in the literature. Many people shared experiences from other organisms they hoped rules would solve. Guided by nomenclature policies established for Arabidopsis, a policy was drafted by Julia Frugoli and Kate VandenBosch and circulated to key investigators in the field. After incorporation of comments by these investigators, the policy was published in Molecular Plant-Microbe Interactions. The Medicago steering committee at the time appointed Julia Frugoli to be the curator of gene names and the accompanying website. The publication of the nomenclature rules in 2001 noted that amendments to the rules could be considered at Medicago meetings and selection of the curator would be left to the steering committee, but no amendments have been proposed and the original curator remains.

Plant …, 2011

... Elise L. Schnabela,1, Tessema K. Kassawa,1, Lucinda S. Smithb, John F. Marshc, Giles E. Oldro... more ... Elise L. Schnabela,1, Tessema K. Kassawa,1, Lucinda S. Smithb, John F. Marshc, Giles E. Oldroydc, Sharon R. Longb, and Julia A. Frugolia ... have also been implicated in nodule number regulation (Nakagawa and Kawaguchi, 2006; Terakado et al., 2006). ...

Biochemistry and Molecular Biology Education, 2007

Teaching ethics across the curriculum is a strategy adopted by many universities. One of the fund... more Teaching ethics across the curriculum is a strategy adopted by many universities. One of the fundamental aims of teaching ethics across the curriculum is to get students to see ethics as truly relevant to the subjects they are studying. Ideally, students will come to see that ethics is a thread woven deeply in the fabric of all knowledge and practice. The standard approach, in which students are required to take a separate ethics course, is not especially well suited to this task, but incorporating ethics into science courses presents significant challenges and is likely to meet with resistance, if only because professors in the sciences are often untrained in the teaching of ethics. In an effort to raise the standard of science education as well as comply with a university-wide curricular mandate, we as a team developed the concept of an ''ethics lab.'' We discuss the design of the exercises done during laboratory sections, the training of the graduate students who run the exercises, and the iterations of the exercises over time. We report unanticipated rapid positive outcomes of an attempt to integrate ethics education into a sophomore/junior level science course, Introduction to Genetics.

The Plant Journal, 2016

Autoregulation of nodulation (AON), a systemic signaling pathway in legumes, limits the number of... more Autoregulation of nodulation (AON), a systemic signaling pathway in legumes, limits the number of nodules formed by the legume in its symbiosis with rhizobia. Recent research suggests a model for the systemic regulation in Medicago truncatula in which root signaling peptides are translocated to the shoot where they bind to a shoot receptor complex containing the leucine-rich repeat receptor-like kinase SUNN, triggering signal transduction which terminates nodule formation in roots. Here we show that a tagged SUNN protein capable of rescuing the sunn-4 phenotype is localized to the plasma membrane and is associated with the plasmodesmata. Using bimolecular fluorescence complementation analysis we show that, like its sequence ortholog Arabidopsis CLV1, SUNN interacts with homologous CLV1-interacting proteins MtCLAVATA2 and MtCORYNE. All three proteins were also able to form homomers and MtCRN and MtCLV2 also interact with each other. A crn Tnt1 insertion mutant of M. truncatula displayed a shoot controlled increased nodulation phenotype, similar to the clv2 mutants of pea and Lotus japonicus. Together these data suggest that legume AON signaling could occur through a multi-protein complex and that both MtCRN and MtCLV2 may play roles in AON together with SUNN.