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Strout RI, Graham CA, Dodd AN, Nagel DH. Investigating Circadian Gating of Temperature Responsive Genes. Methods Mol Biol 2024; 2795:213-225. [PMID: 38594541 DOI: 10.1007/978-1-0716-3814-9_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Understanding gene expression dynamics in the context of the time of day and temperature response is an important part of understanding plant thermotolerance in a changing climate. Performing "gating" experiments under constant conditions and light-dark cycles allows users to identify and dissect the contribution of the time of day and circadian clock to the dynamic nature of stress-responsive genes. Here, we describe the design of specific laboratory experiments in plants (Arabidopsis thaliana and bread wheat, Triticum aestivum) to investigate temporal responses to heat (1 h at 37 °C) or cold (3 h at 4 °C), and we include known marker genes that have circadian-gated responses to temperature changes.
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Affiliation(s)
- Rachel I Strout
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Calum A Graham
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Antony N Dodd
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, UK.
| | - Dawn H Nagel
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA.
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2
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Bonnot T, Somayanda I, Jagadish SVK, Nagel DH. Time of day and genotype sensitivity adjust molecular responses to temperature stress in sorghum. Plant J 2023; 116:1081-1096. [PMID: 37715988 DOI: 10.1111/tpj.16467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 08/30/2023] [Accepted: 09/05/2023] [Indexed: 09/18/2023]
Abstract
Sorghum is one of the four major C4 crops that are considered to be tolerant to environmental extremes. Sorghum shows distinct growth responses to temperature stress depending on the sensitivity of the genetic background. About half of the transcripts in sorghum exhibit diurnal rhythmic expressions emphasizing significant coordination with the environment. However, an understanding of how molecular dynamics contribute to genotype-specific stress responses in the context of the time of day is not known. We examined whether temperature stress and the time of day impact the gene expression dynamics in thermo-sensitive and thermo-tolerant sorghum genotypes. We found that time of day is highly influencing the temperature stress responses, which can be explained by the rhythmic expression of most thermo-responsive genes. This effect is more pronounced in thermo-tolerant genotypes, suggesting a stronger regulation of gene expression by the time of day and/or by the circadian clock. Genotypic differences were mostly observed on average gene expression levels, which may be responsible for contrasting sensitivities to temperature stress in tolerant versus susceptible sorghum varieties. We also identified groups of genes altered by temperature stress in a time-of-day and genotype-specific manner. These include transcriptional regulators and several members of the Ca2+ -binding EF-hand protein family. We hypothesize that expression variation of these genes between genotypes along with time-of-day independent regulation may contribute to genotype-specific fine-tuning of thermo-responsive pathways. These findings offer a new opportunity to selectively target specific genes in efforts to develop climate-resilient crops based on their time-of-day and genotype variation responses to temperature stress.
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Affiliation(s)
- Titouan Bonnot
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, California, 92507, USA
| | - Impa Somayanda
- Department of Plant and Soil Science, Texas Tech University, Lubbock, Texas, 79409-2122, USA
| | - S V Krishna Jagadish
- Department of Plant and Soil Science, Texas Tech University, Lubbock, Texas, 79409-2122, USA
| | - Dawn H Nagel
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, California, 92507, USA
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3
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Medina-Chávez L, Camacho C, Martínez-Rodríguez JA, Barrera-Figueroa BE, Nagel DH, Juntawong P, Peña-Castro JM. Submergence Stress Alters the Expression of Clock Genes and Configures New Zeniths and Expression of Outputs in Brachypodium distachyon. Int J Mol Sci 2023; 24:ijms24108555. [PMID: 37239900 DOI: 10.3390/ijms24108555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/04/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
Plant networks of oscillating genes coordinate internal processes with external cues, contributing to increased fitness. We hypothesized that the response to submergence stress may dynamically change during different times of the day. In this work, we determined the transcriptome (RNA sequencing) of the model monocotyledonous plant, Brachypodium distachyon, during a day of submergence stress, low light, and normal growth. Two ecotypes of differential tolerance, Bd21 (sensitive) and Bd21-3 (tolerant), were included. We submerged 15-day-old plants under a long-day diurnal cycle (16 h light/8 h dark) and collected samples after 8 h of submergence at ZT0 (dawn), ZT8 (midday), ZT16 (dusk), ZT20 (midnight), and ZT24 (dawn). Rhythmic processes were enriched both with up- and down-regulated genes, and clustering highlighted that the morning and daytime oscillator components (PRRs) show peak expression in the night, and a decrease in the amplitude of the clock genes (GI, LHY, RVE) was observed. Outputs included photosynthesis-related genes losing their known rhythmic expression. Up-regulated genes included oscillating suppressors of growth, hormone-related genes with new late zeniths (e.g., JAZ1, ZEP), and mitochondrial and carbohydrate signaling genes with shifted zeniths. The results highlighted genes up-regulated in the tolerant ecotype such as METALLOTHIONEIN3 and ATPase INHIBITOR FACTOR. Finally, we show by luciferase assays that Arabidopsis thaliana clock genes are also altered by submergence changing their amplitude and phase. This study can guide the research of chronocultural strategies and diurnal-associated tolerance mechanisms.
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Affiliation(s)
- Lucisabel Medina-Chávez
- Centro de Investigaciones Científicas, Instituto de Biotecnología, Universidad del Papaloapan, Tuxtepec 68301, Oaxaca, Mexico
- Programa de Doctorado en Biotecnología, División de Estudios de Posgrado, Universidad del Papaloapan, Tuxtepec 68301, Oaxaca, Mexico
| | - Christian Camacho
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Jorge Arturo Martínez-Rodríguez
- Laboratorio de Biotecnología Vegetal, Instituto de Biotecnología, Universidad del Papaloapan, Tuxtepec 68301, Oaxaca, Mexico
| | - Blanca Estela Barrera-Figueroa
- Centro de Investigaciones Científicas, Instituto de Biotecnología, Universidad del Papaloapan, Tuxtepec 68301, Oaxaca, Mexico
- Laboratorio de Biotecnología Vegetal, Instituto de Biotecnología, Universidad del Papaloapan, Tuxtepec 68301, Oaxaca, Mexico
| | - Dawn H Nagel
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Piyada Juntawong
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
| | - Julián Mario Peña-Castro
- Centro de Investigaciones Científicas, Instituto de Biotecnología, Universidad del Papaloapan, Tuxtepec 68301, Oaxaca, Mexico
- Laboratorio de Biotecnología Vegetal, Instituto de Biotecnología, Universidad del Papaloapan, Tuxtepec 68301, Oaxaca, Mexico
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Bonnot T, Gillard MB, Nagel DH. CAST-R: An application to visualize circadian and heat stress-responsive genes in plants. Plant Physiol 2022; 190:994-1004. [PMID: 35294034 PMCID: PMC9516734 DOI: 10.1093/plphys/kiac121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 02/21/2022] [Indexed: 05/08/2023]
Abstract
The circadian clock helps organisms to anticipate and coordinate gene regulatory responses to changes in environmental stimuli. Under stresses, both time of day and the circadian clock closely control the magnitude of plant responses. The identification of clock-regulated genes is, therefore, important when studying the influence of environmental factors. Here, we present CAST-R (Circadian And heat STress-Responsive), a "Shiny" application that allows users to identify and visualize circadian and heat stress-responsive genes in plants. More specifically, users can generate and export profiles and heatmaps representing transcript abundance of a single or of multiple Arabidopsis (Arabidopsis thaliana) genes over a 24-h time course, in response to heat stress and during recovery following the stress. The application also takes advantage of published Arabidopsis chromatin immunoprecipitation-sequencing datasets to visualize the connections between clock proteins and their targets in an interactive network. In addition, CAST-R offers the possibility to perform phase (i.e. timing of expression) enrichment analyses for rhythmic datasets from any species, within and beyond plants. This functionality combines statistical analyses and graphical representations to identify significantly over- and underrepresented phases within a subset of genes. Lastly, profiles of transcript abundance can be visualized from multiple circadian datasets generated in Arabidopsis, Brassica rapa, barley (Hordeum vulgare), and rice (Oryza sativa). In summary, CAST-R is a user-friendly interface that allows the rapid identification of circadian and stress-responsive genes through multiple modules of visualization. We anticipate that this tool will make it easier for users to obtain temporal and dynamic information on genes of interest that links plant responses to environmental signals.
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Blair EJ, Goralogia GS, Lincoln MJ, Imaizumi T, Nagel DH. Clock-Controlled and Cold-Induced CYCLING DOF FACTOR6 Alters Growth and Development in Arabidopsis. Front Plant Sci 2022; 13:919676. [PMID: 35958204 PMCID: PMC9361860 DOI: 10.3389/fpls.2022.919676] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
The circadian clock represents a critical regulatory network, which allows plants to anticipate environmental changes as inputs and promote plant survival by regulating various physiological outputs. Here, we examine the function of the clock-regulated transcription factor, CYCLING DOF FACTOR 6 (CDF6), during cold stress in Arabidopsis thaliana. We found that the clock gates CDF6 transcript accumulation in the vasculature during cold stress. CDF6 mis-expression results in an altered flowering phenotype during both ambient and cold stress. A genome-wide transcriptome analysis links CDF6 to genes associated with flowering and seed germination during cold and ambient temperatures, respectively. Analysis of key floral regulators indicates that CDF6 alters flowering during cold stress by repressing photoperiodic flowering components, FLOWERING LOCUS T (FT), CONSTANS (CO), and BROTHER OF FT (BFT). Gene ontology enrichment further suggests that CDF6 regulates circadian and developmental-associated genes. These results provide insights into how the clock-controlled CDF6 modulates plant development during moderate cold stress.
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Affiliation(s)
- Emily J. Blair
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Greg S. Goralogia
- Department of Biology, University of Washington, Seattle, WA, United States
| | - Matthew J. Lincoln
- Department of Biology, University of Washington, Seattle, WA, United States
| | - Takato Imaizumi
- Department of Biology, University of Washington, Seattle, WA, United States
| | - Dawn H. Nagel
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
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Bonnot T, Blair EJ, Cordingley SJ, Nagel DH. Circadian coordination of cellular processes and abiotic stress responses. Curr Opin Plant Biol 2021; 64:102133. [PMID: 34773857 DOI: 10.1016/j.pbi.2021.102133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 09/24/2021] [Accepted: 09/27/2021] [Indexed: 06/13/2023]
Abstract
Diel changes in the environment are perceived by the circadian clock which transmits temporal information throughout the plant cell to synchronize daily and seasonal environmental signals with internal biological processes. Dynamic modulations of diverse levels of clock gene regulation within the plant cell are impacted by stress. Recent insights into circadian control of cellular processes such as alternative splicing, polyadenylation, and noncoding RNAs are discussed. We highlight studies on the circadian regulation of reactive oxygen species, calcium signaling, and gating of temperature stress responses. Finally, we briefly summarize recent work on the translation-specific rhythmicity of cell cycle genes and the control of subcellular localization and relocalization of oscillator components. Together, this mini-review highlights these cellular events in the context of clock gene regulation and stress responses in Arabidopsis.
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Affiliation(s)
- Titouan Bonnot
- University of California, Riverside, Department of Botany and Plant Sciences, Riverside, CA 92507, USA
| | - Emily J Blair
- University of California, Riverside, Department of Botany and Plant Sciences, Riverside, CA 92507, USA
| | - Samantha J Cordingley
- University of California, Riverside, Department of Botany and Plant Sciences, Riverside, CA 92507, USA
| | - Dawn H Nagel
- University of California, Riverside, Department of Botany and Plant Sciences, Riverside, CA 92507, USA.
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7
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Bonnot T, Nagel DH. Time of the day prioritizes the pool of translating mRNAs in response to heat stress. Plant Cell 2021; 33:2164-2182. [PMID: 33871647 PMCID: PMC8364243 DOI: 10.1093/plcell/koab113] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/07/2021] [Indexed: 05/24/2023]
Abstract
The circadian clock helps organisms to anticipate and coordinate gene regulatory responses to changes in environmental stimuli. Under growth limiting temperatures, the time of the day modulates the accumulation of polyadenylated mRNAs. In response to heat stress, plants will conserve energy and selectively translate mRNAs. How the clock and/or the time of the day regulates polyadenylated mRNAs bound by ribosomes in response to heat stress is unknown. In-depth analysis of Arabidopsis thaliana translating mRNAs found that the time of the day gates the response of approximately one-third of the circadian-regulated heat-responsive translatome. Specifically, the time of the day and heat stress interact to prioritize the pool of mRNAs in cue to be translated. For a subset of mRNAs, we observed a stronger gated response during the day, and preferentially before the peak of expression. We propose previously overlooked transcription factors (TFs) as regulatory nodes and show that the clock plays a role in the temperature response for select TFs. When the stress was removed, the redefined priorities for translation recovered within 1 h, though slower recovery was observed for abiotic stress regulators. Through hierarchical network connections between clock genes and prioritized TFs, our work provides a framework to target key nodes underlying heat stress tolerance throughout the day.
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Affiliation(s)
- Titouan Bonnot
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA
| | - Dawn H. Nagel
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA
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Pruneda-Paz JL, Breton G, Nagel DH, Kang SE, Bonaldi K, Doherty CJ, Ravelo S, Galli M, Ecker JR, Kay SA. A genome-scale resource for the functional characterization of Arabidopsis transcription factors. Cell Rep 2014; 8:622-32. [PMID: 25043187 DOI: 10.1016/j.celrep.2014.06.033] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 05/28/2014] [Accepted: 06/19/2014] [Indexed: 12/31/2022] Open
Abstract
Extensive transcriptional networks play major roles in cellular and organismal functions. Transcript levels are in part determined by the combinatorial and overlapping functions of multiple transcription factors (TFs) bound to gene promoters. Thus, TF-promoter interactions provide the basic molecular wiring of transcriptional regulatory networks. In plants, discovery of the functional roles of TFs is limited by an increased complexity of network circuitry due to a significant expansion of TF families. Here, we present the construction of a comprehensive collection of Arabidopsis TFs clones created to provide a versatile resource for uncovering TF biological functions. We leveraged this collection by implementing a high-throughput DNA binding assay and identified direct regulators of a key clock gene (CCA1) that provide molecular links between different signaling modules and the circadian clock. The resources introduced in this work will significantly contribute to a better understanding of the transcriptional regulatory landscape of plant genomes.
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Affiliation(s)
- Jose L Pruneda-Paz
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Center for Chronobiology, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Ghislain Breton
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Dawn H Nagel
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Center for Chronobiology, University of California, San Diego, La Jolla, CA 92093, USA
| | - S Earl Kang
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Center for Chronobiology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Katia Bonaldi
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Center for Chronobiology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Colleen J Doherty
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Center for Chronobiology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Stephanie Ravelo
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mary Galli
- Genomic Analysis Laboratory, Howard Hughes Medical Institute and The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Joseph R Ecker
- Genomic Analysis Laboratory, Howard Hughes Medical Institute and The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Steve A Kay
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Center for Chronobiology, University of California, San Diego, La Jolla, CA 92093, USA.
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Abstract
Endogenous circadian rhythms regulate many aspects of an organism's behavior, physiology and development. These daily oscillations synchronize with the environment to generate robust rhythms, resulting in enhanced fitness and growth vigor in plants. Collective studies over the years have focused on understanding the transcription-based oscillator in Arabidopsis. Recent advances combining mechanistic data with genome-wide approaches have contributed significantly to a more comprehensive understanding of the molecular interactions within the oscillator, and with clock-controlled pathways. This review focuses on the regulatory mechanisms within the oscillator, highlighting key connections between new and existing components, and direct mechanistic links to downstream pathways that control overt rhythms in the whole plant.
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Affiliation(s)
- Dawn H. Nagel
- Section of Cell and Developmental Biology, Division of Biological Sciences; University of California San Diego, La Jolla, CA 92093, USA
- Center for Chronobiology; University of California San Diego, La Jolla, CA 92093, USA
| | - Steve A. Kay
- Section of Cell and Developmental Biology, Division of Biological Sciences; University of California San Diego, La Jolla, CA 92093, USA
- Center for Chronobiology; University of California San Diego, La Jolla, CA 92093, USA
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Wei F, Stein JC, Liang C, Zhang J, Fulton RS, Baucom RS, De Paoli E, Zhou S, Yang L, Han Y, Pasternak S, Narechania A, Zhang L, Yeh CT, Ying K, Nagel DH, Collura K, Kudrna D, Currie J, Lin J, Kim H, Angelova A, Scara G, Wissotski M, Golser W, Courtney L, Kruchowski S, Graves TA, Rock SM, Adams S, Fulton LA, Fronick C, Courtney W, Kramer M, Spiegel L, Nascimento L, Kalyanaraman A, Chaparro C, Deragon JM, Miguel PS, Jiang N, Wessler SR, Green PJ, Yu Y, Schwartz DC, Meyers BC, Bennetzen JL, Martienssen RA, McCombie WR, Aluru S, Clifton SW, Schnable PS, Ware D, Wilson RK, Wing RA. Detailed analysis of a contiguous 22-Mb region of the maize genome. PLoS Genet 2009; 5:e1000728. [PMID: 19936048 PMCID: PMC2773423 DOI: 10.1371/journal.pgen.1000728] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2009] [Accepted: 10/16/2009] [Indexed: 12/20/2022] Open
Abstract
Most of our understanding of plant genome structure and evolution has come from the careful annotation of small (e.g., 100 kb) sequenced genomic regions or from automated annotation of complete genome sequences. Here, we sequenced and carefully annotated a contiguous 22 Mb region of maize chromosome 4 using an improved pseudomolecule for annotation. The sequence segment was comprehensively ordered, oriented, and confirmed using the maize optical map. Nearly 84% of the sequence is composed of transposable elements (TEs) that are mostly nested within each other, of which most families are low-copy. We identified 544 gene models using multiple levels of evidence, as well as five miRNA genes. Gene fragments, many captured by TEs, are prevalent within this region. Elimination of gene redundancy from a tetraploid maize ancestor that originated a few million years ago is responsible in this region for most disruptions of synteny with sorghum and rice. Consistent with other sub-genomic analyses in maize, small RNA mapping showed that many small RNAs match TEs and that most TEs match small RNAs. These results, performed on approximately 1% of the maize genome, demonstrate the feasibility of refining the B73 RefGen_v1 genome assembly by incorporating optical map, high-resolution genetic map, and comparative genomic data sets. Such improvements, along with those of gene and repeat annotation, will serve to promote future functional genomic and phylogenomic research in maize and other grasses.
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Affiliation(s)
- Fusheng Wei
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
| | - Joshua C. Stein
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Chengzhi Liang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Jianwei Zhang
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
| | - Robert S. Fulton
- The Genome Center and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Regina S. Baucom
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Emanuele De Paoli
- Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, United States of America
| | - Shiguo Zhou
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, University of Wisconsin Madison, Madison, Wisconsin, United States of America
| | - Lixing Yang
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Yujun Han
- Department of Plant Biology, University of Georgia, Athens, Georgia, United States of America
| | - Shiran Pasternak
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Apurva Narechania
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Lifang Zhang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Cheng-Ting Yeh
- Department of Agronomy and Center for Plant Genomics, Iowa State University, Ames, Iowa, United States of America
| | - Kai Ying
- Department of Agronomy and Center for Plant Genomics, Iowa State University, Ames, Iowa, United States of America
| | - Dawn H. Nagel
- Department of Plant Biology, University of Georgia, Athens, Georgia, United States of America
| | - Kristi Collura
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
| | - David Kudrna
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
| | - Jennifer Currie
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
| | - Jinke Lin
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
| | - HyeRan Kim
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
| | - Angelina Angelova
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
| | - Gabriel Scara
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
| | - Marina Wissotski
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
| | - Wolfgang Golser
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
| | - Laura Courtney
- The Genome Center and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Scott Kruchowski
- The Genome Center and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Tina A. Graves
- The Genome Center and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Susan M. Rock
- The Genome Center and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Stephanie Adams
- The Genome Center and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Lucinda A. Fulton
- The Genome Center and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Catrina Fronick
- The Genome Center and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - William Courtney
- The Genome Center and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Melissa Kramer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Lori Spiegel
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Lydia Nascimento
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Ananth Kalyanaraman
- School of Electrical Engineering and Computer Science, Washington State University, Pullman, Washington, United States of America
| | - Cristian Chaparro
- Université de Perpignan Via Domitia, CNRS UMR 5096, Perpignan, France
| | - Jean-Marc Deragon
- Université de Perpignan Via Domitia, CNRS UMR 5096, Perpignan, France
| | - Phillip San Miguel
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, United States of America
| | - Ning Jiang
- Department of Horticulture, Michigan State University, East Lansing, Michigan, United States of America
| | - Susan R. Wessler
- Department of Plant Biology, University of Georgia, Athens, Georgia, United States of America
| | - Pamela J. Green
- Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, United States of America
| | - Yeisoo Yu
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
| | - David C. Schwartz
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, University of Wisconsin Madison, Madison, Wisconsin, United States of America
| | - Blake C. Meyers
- Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, United States of America
| | - Jeffrey L. Bennetzen
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Robert A. Martienssen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - W. Richard McCombie
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Srinivas Aluru
- Department of Electrical and Computer Engineering, Iowa State University, Ames, Iowa, United States of America
| | - Sandra W. Clifton
- The Genome Center and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Patrick S. Schnable
- Department of Agronomy and Center for Plant Genomics, Iowa State University, Ames, Iowa, United States of America
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Richard K. Wilson
- The Genome Center and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Rod A. Wing
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
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Lu SE, Henn RA, Nagel DH. First Report of Ear Soft Rot of Corn (Zea mays) Caused by Burkholderia gladioli in the United States. Plant Dis 2007; 91:1514. [PMID: 30780771 DOI: 10.1094/pdis-91-11-1514c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
During the summer of 2005, an uncharacterized disease was observed on sweet corn 'Mirai 301BC' commercially grown in Sunflower County, Mississippi. Initial symptoms developing at the base of the ear on interior husk leaves were brown, water-soaked, irregular lesions. These gradually enlarged up to 10 cm in diameter. Market value was significantly affected when the corn ears had visible symptoms of this disease. Bacterial cell streaming was observed at a magnification of ×675 from the diseased husk. A bacterium was consistently isolated from lesions on nutrient broth yeast (NBY) agar. Colonies on NBY were yellowish white, slightly convex, shiny, and circular with entire margins. Isolates MS102 and MS103, which were chosen for further characterization, were gram negative, lacked arginine dihydrolase, did not produce fluorescent pigment on Pseudomonas F medium, accumulated poly-β-hydroxybutyrate, and grew aerobically. The isolates were able to utilize l-arabinose, d-mannitol, N-acetylglucosamine, capric acid, malic acid, adipic acid, and phenylacetic acid, but not d-maltose. These characteristics are the same as those described previously for Burkholderia gladioli (3). Analysis of fatty acid methyl ester profiles (Sherlock version TSBA 4.10; Microbial Identification System, Newark, DE) characterized the isolates as B. gladioli (similarity indices: 0.23 to 0.38) and revealed that they have C16:0 3OH, the most characteristic fatty acid for the genus Burkholderia. Confirmation was made by PCR amplification of the nearly complete16S rRNA gene (1,471 bp; GenBank Accession No. EU053154) using universal primers (forward: 5'-AGAGTTTGATCCTGGCTCAG and reverse: 5'-GGCTACCTTGTTACGACTTC). DNA sequence analysis demonstrated that the 16S rRNA gene of the bacterium shared highest identities (99.4 to 99.6%) with that of B. gladioli strains 321gr-6, 223gr-1, and S10 (4). A PCR product (approximately 300 bp) characteristic of B. gladioli also was obtained from both isolates using species-specific primers GLA-f and GLA-r (2). To confirm pathogenicity, cell suspensions (108 CFU/ml in phosphate buffer) of isolates MS102 and MS103 were injected into interior husk leaves of field-grown sweet corn with a 20-gauge needle and syringe (2 ml per ear). Control corn ear husks were injected with phosphate buffer. After 3 days, ear rot symptoms were observed on all plants inoculated with the isolates but not those injected with phosphate buffer. Cell suspension of isolates dropped on nonwounded husks also incited the same symptoms as those inoculated with the syringe. Koch's postulates were fulfilled with reisolation from the inoculated tissues. The identity of the reisolated pathogen was proved by sequencing the 16S rRNA gene. This disease was previously reported in Brazil (1). To our knowledge, this is the first report of B. gladioli causing a disease of corn in the United States. Although the impact of this disease was not observed from 2005 to 2006 because of dry weather and rotation to other crops in the affected field, there is a potential that the bacterium could become established in corn-producing areas as a member of the corn ear rot complex if environmental conditions are favorable. Reference: (1) I. M. G. Almeida et al. Arq. Inst. Biol. Sao Paulo 66:141, 1999. (2) N. Furuya et al. J. Gen. Plant Pathol. 68:220, 2002. (3) M. Gillis et al. Int. J. Syst. Bacteriol. 45:274, 1995. (4) R. Nandakumar et al. Phytopathology (Abstr.) 95(suppl.):S73, 2005.
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Affiliation(s)
- S-E Lu
- Department of Entomology and Plant Pathology, Mississippi State University, Mississippi State
| | - R A Henn
- Department of Entomology and Plant Pathology, Mississippi State University, Mississippi State
| | - D H Nagel
- Department of Plant and Soil Sciences, Mississippi State University, Mississippi State
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