Allison Gaudinier

University of California, Davis

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Siobhán M. Brady

Howard Hughes Medical Institute

Daniel J. Kliebenstein

University of California, Davis

Anne-Maarit Bågman

University of California, Davis

Michelle Tang

Pacific Northwest Diabetes Research Institute

Nicholas J. Provart

University of Toronto

Ted Toal

University of California, Davis

Doreen Ware

Cornell University

Baohua Li

Northwest A&F University

Mallorie Taylor‐Teeples

University of Washington

Wolfgang Busch

Salk Institute for Biological Studies

Cooperative Institutions

University of California, Davis

Duke University

University of California, Berkeley

Ghent University

University of Nottingham

University of Cambridge

Plant (United States)

University of Toronto

Howard Hughes Medical Institute

VIB-UGent Center for Plant Systems Biology

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RALFL34 regulates formative cell divisions in Arabidopsis pericycle during lateral root initiation

Journal of Experimental Botany (2016)

Evan Murphy Lam Dai Vu Lisa Van den Broeck Zhefeng Lin Priya Ramakrishna

In plants, many signalling molecules, such as phytohormones, miRNAs, transcription factors, and small signalling peptides, drive growth and development. However, very few small signalling peptides have been shown to be necessary for lateral root development. Here, we describe the role of the peptide RALFL34 during early events in lateral root development, and demonstrate its specific importance in orchestrating formative cell divisions in the pericycle. Our results further suggest that this small signalling peptide acts on the transcriptional cascade leading to a new lateral root upstream of GATA23, an important player in lateral root formation. In addition, we describe a role for ETHYLENE RESPONSE FACTORs (ERFs) in regulating RALFL34 expression. Taken together, we put forward RALFL34 as a new, important player in lateral root initiation.

Pericycle

Lateral root

Signalling

10.1093/jxb/erw281

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Citations (80)

Systems Analysis of Plant Functional, Transcriptional, Physical Interaction, and Metabolic Networks

The Plant Cell (2012)

George W. Bassel Allison Gaudinier Siobhán M. Brady Lars Hennig Seung Y. Rhee

Physiological responses, developmental programs, and cellular functions rely on complex networks of interactions at different levels and scales. Systems biology brings together high-throughput biochemical, genetic, and molecular approaches to generate omics data that can be analyzed and used in mathematical and computational models toward uncovering these networks on a global scale. Various approaches, including transcriptomics, proteomics, interactomics, and metabolomics, have been employed to obtain these data on the cellular, tissue, organ, and whole-plant level. We summarize progress on gene regulatory, cofunction, protein interaction, and metabolic networks. We also illustrate the main approaches that have been used to obtain these networks, with specific examples from Arabidopsis thaliana, and describe the pros and cons of each approach.

Gene regulatory network

10.1105/tpc.112.100776

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Citations (89)

Supplemental Material for Toal et al., 2018

Figshare (2018)

Ted Toal Mily Ron Donald Gibson Kaisa Kajala Bessie L. Splitt

Supplemental Files for Regulation of Root Angle and Gravitropism

10.6084/m9.figshare.7237562

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A Genome-Scale TF-DNA Interaction Network of Transcriptional Regulation of Arabidopsis Primary and Specialized Metabolism

bioRxiv (Cold Spring Harbor Laboratory) (2021)

Michelle Tang Baohua Li Xue Zhou Tayah Bolt Jia Jie Li

Summary In single-celled microbes, transcriptional regulation by single transcription factors is sufficient to shift primary metabolism. Corresponding genome-level transcriptional regulatory maps of metabolism reveal the underlying design principles responsible for these shifts as a model in which master regulators largely coordinate specific metabolic pathways. Relative to individual microbes, plant metabolism is more complex. Primary and specialized metabolism occur within innumerable cell types, and their reactions shift depending on internal and external cues. Given the importance of plants and their metabolites in providing humanity with food, fiber and medicine, we set out to develop a genome-scale transcriptional regulatory map of Arabidopsis metabolic genes. A comprehensive set of protein-DNA interactions between Arabidopsis thaliana transcription factors and promoters of primary metabolism and specialized metabolism were mapped. To demonstrate the utility of this resource, we identified and functionally validated regulators of the TCA cycle. The resulting network suggests that plant metabolic design principles are distinct from that of microbes. Instead, metabolism appears to be transcriptionally coordinated via developmental- and stress-conditional processes that can coordinate across primary and specialized metabolism. These data represent the most comprehensive resource of interactions between TFs and metabolic genes in plants.

Secondary metabolism

Cell metabolism

Transcription

10.1101/2021.05.13.443927

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Citations (5)

Evolutionary processes from the perspective of flowering time diversity

New Phytologist (2019)

Allison Gaudinier Benjamin K. Blackman

Although it is well appreciated that genetic studies of flowering time regulation have led to fundamental advances in the fields of molecular and developmental biology, the ways in which genetic studies of flowering time diversity have enriched the field of evolutionary biology have received less attention despite often being equally profound. Because flowering time is a complex, environmentally responsive trait that has critical impacts on plant fitness, crop yield, and reproductive isolation, research into the genetic architecture and molecular basis of its evolution continues to yield novel insights into our understanding of domestication, adaptation, and speciation. For instance, recent studies of flowering time variation have reconstructed how, when, and where polygenic evolution of phenotypic plasticity proceeded from standing variation and de novo mutations; shown how antagonistic pleiotropy and temporally varying selection maintain polymorphisms in natural populations; and provided important case studies of how assortative mating can evolve and facilitate speciation with gene flow. In addition, functional studies have built detailed regulatory networks for this trait in diverse taxa, leading to new knowledge about how and why developmental pathways are rewired and elaborated through evolutionary time.

Pleiotropy

Trait

Genetic algorithm

Genetic architecture

Reproductive isolation

Assortative mating

10.1111/nph.16205

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Citations (98)

Mapping spatiotemporal gene regulatory networks in the Arabidopsis root stele

Developmental Biology (2011)

Mallorie Taylor‐Teeples Allison Gaudinier Lifang Zhang John Reece-Hoyes Sebastian E. Ahnert

Multicellular organism

Stele

Gene regulatory network

Lateral root

10.1016/j.ydbio.2011.05.035

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Citations (2)

An Arabidopsis gene regulatory network for secondary cell wall synthesis

Nature (2014)

Mallorie Taylor‐Teeples Li Lin Miguel de Lucas Gina Turco Ted Toal

Secondary cell wall

Gene regulatory network

10.1038/nature14099

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Citations (656)

A genome‐scale TF–DNA interaction network of transcriptional regulation ofArabidopsisprimary and specialized metabolism

Molecular Systems Biology (2021)

Michelle Tang Baohua Li Xue Zhou Tayah Bolt Jia Jie Li

Plant metabolism is more complex relative to individual microbes. In single-celled microbes, transcriptional regulation by single transcription factors (TFs) is sufficient to shift primary metabolism. Corresponding genome-level transcriptional regulatory maps of metabolism reveal the underlying design principles responsible for these shifts as a model in which master regulators largely coordinate specific metabolic pathways. Plant primary and specialized metabolism occur within innumerable cell types, and their reactions shift depending on internal and external cues. Given the importance of plants and their metabolites in providing humanity with food, fiber, and medicine, we set out to develop a genome-scale transcriptional regulatory map of Arabidopsis metabolic genes. A comprehensive set of protein-DNA interactions between Arabidopsis thaliana TFs and gene promoters in primary and specialized metabolic pathways were mapped. To demonstrate the utility of this resource, we identified and functionally validated regulators of the tricarboxylic acid (TCA) cycle. The resulting network suggests that plant metabolic design principles are distinct from those of microbes. Instead, metabolism appears to be transcriptionally coordinated via developmental- and stress-conditional processes that can coordinate across primary and specialized metabolism. These data represent the most comprehensive resource of interactions between TFs and metabolic genes in plants.

10.15252/msb.202110625

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Citations (24)

Proteome-wide, Structure-Based Prediction of Protein-Protein Interactions/New Molecular Interactions Viewer

PLANT PHYSIOLOGY (2019)

Shaowei Dong Vincent Lau Richard Song Matthew Ierullo Eddi Esteban

Determining the complete Arabidopsis (Arabidopsis thaliana) protein-protein interaction network is essential for understanding the functional organization of the proteome. Numerous small-scale studies and a couple of large-scale ones have elucidated a fraction of the estimated 300,000 binary protein-protein interactions in Arabidopsis. In this study, we provide evidence that a docking algorithm has the ability to identify real interactions using both experimentally determined and predicted protein structures. We ranked 0.91 million interactions generated by all possible pairwise combinations of 1,346 predicted structure models from an Arabidopsis predicted "structure-ome" and found a significant enrichment of real interactions for the top-ranking predicted interactions, as shown by cosubcellular enrichment analysis and yeast two-hybrid validation. Our success rate for computationally predicted, structure-based interactions was 63% of the success rate for published interactions naively tested using the yeast two-hybrid system and 2.7 times better than for randomly picked pairs of proteins. This study provides another perspective in interactome exploration and biological network reconstruction using protein structural information. We have made these interactions freely accessible through an improved Arabidopsis Interactions Viewer and have created community tools for accessing these and ∼2.8 million other protein-protein and protein-DNA interactions for hypothesis generation by researchers worldwide. The Arabidopsis Interactions Viewer is freely available at http://bar.utoronto.ca/interactions2/.

Proteome

10.1104/pp.18.01216

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Citations (43)

Mapping Transcriptional Networks in Plants: Data-Driven Discovery of Novel Biological Mechanisms

Annual Review of Plant Biology (2016)

Allison Gaudinier Siobhán M. Brady

In plants, systems biology approaches have led to the generation of a variety of large data sets. Many of these data are created to elucidate gene expression profiles and their corresponding transcriptional regulatory mechanisms across a range of tissue types, organs, and environmental conditions. In an effort to map the complexity of this transcriptional regulatory control, several types of experimental assays have been used to map transcriptional regulatory networks. In this review, we discuss how these methods can be best used to identify novel biological mechanisms by focusing on the appropriate biological context. Translating network biology back to gene function in the plant, however, remains a challenge. We emphasize the need for validation and insight into the underlying biological processes to successfully exploit systems approaches in an effort to determine the emergent properties revealed by network analyses.

Gene regulatory network

Biological data

Biological pathway

10.1146/annurev-arplant-043015-112205

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Citations (53)