151
|
Chen HY, Huh JH, Yu YC, Ho LH, Chen LQ, Tholl D, Frommer WB, Guo WJ. The Arabidopsis vacuolar sugar transporter SWEET2 limits carbon sequestration from roots and restricts Pythium infection. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:1046-58. [PMID: 26234706 DOI: 10.1111/tpj.12948] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 07/17/2015] [Accepted: 07/20/2015] [Indexed: 05/04/2023]
Abstract
Plant roots secrete a significant portion of their assimilated carbon into the rhizosphere. The putative sugar transporter SWEET2 is highly expressed in Arabidopsis roots. Expression patterns of SWEET2-β-glucuronidase fusions confirmed that SWEET2 accumulates highly in root cells and thus may contribute to sugar secretion, specifically from epidermal cells of the root apex. SWEET2-green fluorescent protein fusions localized to the tonoplast, which engulfs the major sugar storage compartment. Functional analysis of SWEET2 activity in yeast showed low uptake activity for the glucose analog 2-deoxyglucose, consistent with a role in the transport of glucose across the tonoplast. Loss-of-function sweet2 mutants showed reduced tolerance to excess glucose, lower glucose accumulation in leaves, and 15-25% higher glucose-derived carbon efflux from roots, suggesting that SWEET2 has a role in preventing the loss of sugar from root tissue. SWEET2 root expression was induced more than 10-fold during Pythium infection. Importantly, sweet2 mutants were more susceptible to the oomycete, showing impaired growth after infection. We propose that root-expressed vacuolar SWEET2 modulates sugar secretion, possibly by reducing the availability of glucose sequestered in the vacuole, thereby limiting carbon loss to the rhizosphere. Moreover, the reduced availability of sugar in the rhizosphere due to SWEET2 activity contributes to resistance to Pythium.
Collapse
Affiliation(s)
- Hsin-Yi Chen
- Institute of Tropical Plant Science, National Cheng Kung University, Tainan City, 7013, Taiwan
| | - Jung-Hyun Huh
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Ya-Chi Yu
- Institute of Tropical Plant Science, National Cheng Kung University, Tainan City, 7013, Taiwan
| | - Li-Hsuan Ho
- Institute of Tropical Plant Science, National Cheng Kung University, Tainan City, 7013, Taiwan
| | - Li-Qing Chen
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Dorothea Tholl
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Wolf B Frommer
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Woei-Jiun Guo
- Institute of Tropical Plant Science, National Cheng Kung University, Tainan City, 7013, Taiwan
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| |
Collapse
|
152
|
Fettke J, Fernie AR. Intracellular and cell-to-apoplast compartmentation of carbohydrate metabolism. TRENDS IN PLANT SCIENCE 2015; 20:490-497. [PMID: 26008154 DOI: 10.1016/j.tplants.2015.04.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 04/20/2015] [Accepted: 04/28/2015] [Indexed: 06/04/2023]
Abstract
In most plants, carbohydrates represent the major energy store as well as providing the building blocks for essential structural polymers. Although the major pathways for carbohydrate biosynthesis, degradation, and transport are well characterized, several key steps have only recently been discovered. In addition, several novel minor metabolic routes have been uncovered in the past few years. Here we review current studies of plant carbohydrate metabolism detailing the expanding compendium of functionally characterized transport proteins as well as our deeper comprehension of more minor and conditionally activated metabolic pathways. We additionally explore the pertinent questions that will allow us to enhance our understanding of the response of both major and minor carbohydrate fluxes to changing cellular circumstances.
Collapse
Affiliation(s)
- Joerg Fettke
- Biopolymer Analytics, University of Potsdam, Potsdam-Golm, Germany.
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| |
Collapse
|
153
|
Chandran D. Co-option of developmentally regulated plant SWEET transporters for pathogen nutrition and abiotic stress tolerance. IUBMB Life 2015; 67:461-71. [PMID: 26179993 DOI: 10.1002/iub.1394] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 06/15/2015] [Indexed: 11/07/2022]
Abstract
Plant sugar will eventually be exported transporter (SWEET) sugar transporters have been implicated in various developmental processes where sugar efflux is essential, including sucrose loading of phloem for long-distance sugar transport, nectar secretion, embryo and pollen nutrition, and maintenance of sugar homeostasis in plant organs. Notably, these transporters are selectively targeted by pathogens to gain access to host sugars. In most cases, when SWEET function is blocked, the growth and virulence of the pathogen is also reduced. There is growing evidence to suggest that the lifestyle of the pathogen may dictate which SWEET or set of SWEET genes are recruited for pathogen growth and proliferation. Furthermore, SWEET transporters may also play a role in abiotic stress tolerance by enabling plant growth under unfavorable environmental conditions. This review provides an overview of the diverse functions of SWEET proteins in plant development, pathogen nutrition, and abiotic stress tolerance. In addition, utility of the model legume Medicago truncatula as a tool to elucidate SWEET function in diverse host-microbe interactions is discussed.
Collapse
Affiliation(s)
- Divya Chandran
- Regional Center for Biotechnology, NCR Biotech Science Cluster, Faridabad, Haryana, India
| |
Collapse
|
154
|
Feng L, Frommer WB. Structure and function of SemiSWEET and SWEET sugar transporters. Trends Biochem Sci 2015; 40:480-6. [PMID: 26071195 DOI: 10.1016/j.tibs.2015.05.005] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 05/12/2015] [Accepted: 05/18/2015] [Indexed: 11/20/2022]
Abstract
SemiSWEETs and SWEETs have emerged as unique sugar transporters. First discovered in plants with the help of fluorescent biosensors, homologs exist in all kingdoms of life. Bacterial and plant homologs transport hexoses and sucrose, whereas animal SWEETs transport glucose. Prokaryotic SemiSWEETs are small and comprise a parallel homodimer of an approximately 100 amino acid-long triple helix bundle (THB). Duplicated THBs are fused to create eukaryotic SWEETs in a parallel orientation via an inversion linker helix, producing a similar configuration to that of SemiSWEET dimers. Structures of four SemiSWEETs have been resolved in three states: open outside, occluded, and open inside, indicating alternating access. As we discuss here, these atomic structures provide a basis for exploring the evolution of structure-function relations in this new class of transporters.
Collapse
Affiliation(s)
- Liang Feng
- Department of Molecular and Cellular Physiology, 279 Campus Drive, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Wolf B Frommer
- Carnegie Institution for Science, Department of Plant Biology, 260 Panama St, Stanford, CA 94305, USA.
| |
Collapse
|
155
|
Eom JS, Chen LQ, Sosso D, Julius BT, Lin IW, Qu XQ, Braun DM, Frommer WB. SWEETs, transporters for intracellular and intercellular sugar translocation. CURRENT OPINION IN PLANT BIOLOGY 2015; 25:53-62. [PMID: 25988582 DOI: 10.1016/j.pbi.2015.04.005] [Citation(s) in RCA: 290] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Revised: 04/07/2015] [Accepted: 04/09/2015] [Indexed: 05/21/2023]
Abstract
Three families of transporters have been identified as key players in intercellular transport of sugars: MSTs (monosaccharide transporters), SUTs (sucrose transporters) and SWEETs (hexose and sucrose transporters). MSTs and SUTs fall into the major facilitator superfamily; SWEETs constitute a structurally different class of transporters with only seven transmembrane spanning domains. The predicted topology of SWEETs is supported by crystal structures of bacterial homologs (SemiSWEETs). On average, angiosperm genomes contain ∼20 paralogs, most of which serve distinct physiological roles. In Arabidopsis, AtSWEET8 and 13 feed the pollen; SWEET11 and 12 provide sucrose to the SUTs for phloem loading; AtSWEET11, 12 and 15 have distinct roles in seed filling; AtSWEET16 and 17 are vacuolar hexose transporters; and SWEET9 is essential for nectar secretion. The remaining family members await characterization, and could play roles in the gametophyte as well as other important roles in sugar transport in the plant. In rice and cassava, and possibly other systems, sucrose transporting SWEETs play central roles in pathogen resistance. Notably, the human genome also contains a glucose transporting isoform. Further analysis promises new insights into mechanism and regulation of assimilate allocation and a new potential for increasing crop yield.
Collapse
Affiliation(s)
- Joon-Seob Eom
- Carnegie Science, Department of Plant Biology, 260 Panama St., Stanford, CA 94305, USA
| | - Li-Qing Chen
- Carnegie Science, Department of Plant Biology, 260 Panama St., Stanford, CA 94305, USA
| | - Davide Sosso
- Carnegie Science, Department of Plant Biology, 260 Panama St., Stanford, CA 94305, USA
| | - Benjamin T Julius
- Division of Biological Sciences, Interdisciplinary Plant Group, and the Missouri Maize Center, University of Missouri, 110 Tucker Hall, Columbia, MO 65211, USA
| | - I W Lin
- Carnegie Science, Department of Plant Biology, 260 Panama St., Stanford, CA 94305, USA; Biology Department, Stanford University, Stanford, CA 94305, USA
| | - Xiao-Qing Qu
- Carnegie Science, Department of Plant Biology, 260 Panama St., Stanford, CA 94305, USA
| | - David M Braun
- Division of Biological Sciences, Interdisciplinary Plant Group, and the Missouri Maize Center, University of Missouri, 110 Tucker Hall, Columbia, MO 65211, USA
| | - Wolf B Frommer
- Carnegie Science, Department of Plant Biology, 260 Panama St., Stanford, CA 94305, USA; Biology Department, Stanford University, Stanford, CA 94305, USA.
| |
Collapse
|
156
|
Hedrich R, Sauer N, Neuhaus HE. Sugar transport across the plant vacuolar membrane: nature and regulation of carrier proteins. CURRENT OPINION IN PLANT BIOLOGY 2015; 25:63-70. [PMID: 26000864 DOI: 10.1016/j.pbi.2015.04.008] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 04/16/2015] [Accepted: 04/30/2015] [Indexed: 05/06/2023]
Abstract
The ability of higher plants to store sugars is of crucial importance for plant development, adaption to endogenous or environmental cues and for the economic value of crop species. Sugar storage and accumulation, and its homeostasis in plant cells are managed by the vacuole. Although transport of sugars across the vacuolar membrane has been monitored for about four decades, the molecular entities of the transporters involved have been identified in the last 10 years only. Thus, it is just recently that our pictures of the transporters that channel the sugar load across the tonoplast have gained real shape. Here we describe the molecular nature and regulation of an important group of tonoplast sugar transporter (TST) allowing accumulation of sugars against large concentration gradients. In addition, we report on proton-driven tonoplast sugar exporters and on facilitators, which are also involved in balancing cytosolic and vacuolar sugar levels.
Collapse
Affiliation(s)
- Rainer Hedrich
- Molecular Plant Physiology and Biophysics, University of Würzburg, Germany
| | - Norbert Sauer
- Molecular Plant Physiology, University of Erlangen-Nuremberg, Germany
| | | |
Collapse
|
157
|
Abstract
Soluble sugars serve five main purposes in multicellular organisms: as sources of carbon skeletons, osmolytes, signals, and transient energy storage and as transport molecules. Most sugars are derived from photosynthetic organisms, particularly plants. In multicellular organisms, some cells specialize in providing sugars to other cells (e.g., intestinal and liver cells in animals, photosynthetic cells in plants), whereas others depend completely on an external supply (e.g., brain cells, roots and seeds). This cellular exchange of sugars requires transport proteins to mediate uptake or release from cells or subcellular compartments. Thus, not surprisingly, sugar transport is critical for plants, animals, and humans. At present, three classes of eukaryotic sugar transporters have been characterized, namely the glucose transporters (GLUTs), sodium-glucose symporters (SGLTs), and SWEETs. This review presents the history and state of the art of sugar transporter research, covering genetics, biochemistry, and physiology-from their identification and characterization to their structure, function, and physiology. In humans, understanding sugar transport has therapeutic importance (e.g., addressing diabetes or limiting access of cancer cells to sugars), and in plants, these transporters are critical for crop yield and pathogen susceptibility.
Collapse
Affiliation(s)
- Li-Qing Chen
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305;
| | | | | | | | | |
Collapse
|
158
|
Lee Y, Nishizawa T, Yamashita K, Ishitani R, Nureki O. Structural basis for the facilitative diffusion mechanism by SemiSWEET transporter. Nat Commun 2015; 6:6112. [PMID: 25598322 PMCID: PMC4309421 DOI: 10.1038/ncomms7112] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 12/15/2014] [Indexed: 02/07/2023] Open
Abstract
SWEET family proteins mediate sugar transport across biological membranes and play crucial roles in plants and animals. The SWEETs and their bacterial homologues, the SemiSWEETs, are related to the PQ-loop family, which is characterized by highly conserved proline and glutamine residues (PQ-loop motif). Although the structures of the bacterial SemiSWEETs were recently reported, the conformational transition and the significance of the conserved motif in the transport cycle have remained elusive. Here we report crystal structures of SemiSWEET from Escherichia coli, in the both inward-open and outward-open states. A structural comparison revealed that SemiSWEET undergoes an intramolecular conformational change in each protomer. The conserved PQ-loop motif serves as a molecular hinge that enables the 'binder clip-like' motion of SemiSWEET. The present work provides the framework for understanding the overall transport cycles of SWEET and PQ-loop family proteins.
Collapse
Affiliation(s)
- Yongchan Lee
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Tomohiro Nishizawa
- 1] Department of Biological Sciences, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan [2] Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | | | - Ryuichiro Ishitani
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| |
Collapse
|
159
|
Tarkowski ŁP, Van den Ende W. Cold tolerance triggered by soluble sugars: a multifaceted countermeasure. FRONTIERS IN PLANT SCIENCE 2015; 6:203. [PMID: 25926837 PMCID: PMC4396355 DOI: 10.3389/fpls.2015.00203] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 03/14/2015] [Indexed: 05/20/2023]
|
160
|
Wang J, Yan C, Li Y, Hirata K, Yamamoto M, Yan N, Hu Q. Crystal structure of a bacterial homologue of SWEET transporters. Cell Res 2014; 24:1486-9. [PMID: 25378180 PMCID: PMC4260346 DOI: 10.1038/cr.2014.144] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Jing Wang
- State Key Laboratory of Bio-membrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China
- Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Chuangye Yan
- State Key Laboratory of Bio-membrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China
- Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yini Li
- State Key Laboratory of Bio-membrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China
- Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Kunio Hirata
- Advanced Photon Technology Division, Research Infrastructure Group, SR Life Science Instrumentation Unit, 1-1-1 Kouto Sayo-cho Sayo-gun, Hyogo 679-5148, Japan
| | - Masaki Yamamoto
- Advanced Photon Technology Division, Research Infrastructure Group, SR Life Science Instrumentation Unit, 1-1-1 Kouto Sayo-cho Sayo-gun, Hyogo 679-5148, Japan
| | - Nieng Yan
- State Key Laboratory of Bio-membrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China
- Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Qi Hu
- State Key Laboratory of Bio-membrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China
- Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
| |
Collapse
|
161
|
Chong J, Piron MC, Meyer S, Merdinoglu D, Bertsch C, Mestre P. The SWEET family of sugar transporters in grapevine: VvSWEET4 is involved in the interaction with Botrytis cinerea. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:6589-601. [PMID: 25246444 DOI: 10.1093/jxb/eru375] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
During plant development, sugar export is determinant in multiple processes such as nectar production, pollen development and long-distance sucrose transport. The plant SWEET family of sugar transporters is a recently identified protein family of sugar uniporters. In rice, SWEET transporters are the target of extracellular bacteria, which have evolved sophisticated mechanisms to modify their expression and acquire sugars to sustain their growth. Here we report the characterization of the SWEET family of sugar transporters in Vitis vinifera. We identified 17 SWEET genes in the V. vinifera 40024 genome and show that they are differentially expressed in vegetative and reproductive organs. Inoculation with the biotrophic pathogens Erysiphe necator and Plasmopara viticola did not result in significant induction of VvSWEET gene expression. However, infection with the necrotroph Botrytis cinerea triggered a strong up-regulation of VvSWEET4 expression. Further characterization of VvSWEET4 revealed that it is a glucose transporter localized in the plasma membrane that is up-regulated by inducers of reactive oxygen species and virulence factors from necrotizing pathogens. Finally, Arabidopsis knockout mutants in the orthologous AtSWEET4 were found to be less susceptible to B. cinerea. We propose that stimulation of expression of a developmentally regulated glucose uniporter by reactive oxygen species production and extensive cell death after necrotrophic fungal infection could facilitate sugar acquisition from plant cells by the pathogen.
Collapse
Affiliation(s)
- Julie Chong
- Laboratoire Vigne, Biotechnologies et Environnement (LVBE, EA3991), Université de Haute Alsace, 33 rue de Herrlisheim, 68000 Colmar, France
| | - Marie-Christine Piron
- INRA, UMR 1131 Santé de la Vigne et Qualité du Vin, F-68000 Colmar, France Université de Strasbourg, UMR 1131 Santé de la Vigne et Qualité du Vin, F-68000 Colmar, France
| | - Sophie Meyer
- INRA, UMR 1131 Santé de la Vigne et Qualité du Vin, F-68000 Colmar, France Université de Strasbourg, UMR 1131 Santé de la Vigne et Qualité du Vin, F-68000 Colmar, France
| | - Didier Merdinoglu
- INRA, UMR 1131 Santé de la Vigne et Qualité du Vin, F-68000 Colmar, France Université de Strasbourg, UMR 1131 Santé de la Vigne et Qualité du Vin, F-68000 Colmar, France
| | - Christophe Bertsch
- Laboratoire Vigne, Biotechnologies et Environnement (LVBE, EA3991), Université de Haute Alsace, 33 rue de Herrlisheim, 68000 Colmar, France
| | - Pere Mestre
- INRA, UMR 1131 Santé de la Vigne et Qualité du Vin, F-68000 Colmar, France Université de Strasbourg, UMR 1131 Santé de la Vigne et Qualité du Vin, F-68000 Colmar, France
| |
Collapse
|
162
|
Tully JP, Hill AE, Ahmed HMR, Whitley R, Skjellum A, Mukhtar MS. Expression-based network biology identifies immune-related functional modules involved in plant defense. BMC Genomics 2014; 15:421. [PMID: 24888606 PMCID: PMC4070563 DOI: 10.1186/1471-2164-15-421] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 05/27/2014] [Indexed: 01/12/2023] Open
Abstract
Background Plants respond to diverse environmental cues including microbial perturbations by coordinated regulation of thousands of genes. These intricate transcriptional regulatory interactions depend on the recognition of specific promoter sequences by regulatory transcription factors. The combinatorial and cooperative action of multiple transcription factors defines a regulatory network that enables plant cells to respond to distinct biological signals. The identification of immune-related modules in large-scale transcriptional regulatory networks can reveal the mechanisms by which exposure to a pathogen elicits a precise phenotypic immune response. Results We have generated a large-scale immune co-expression network using a comprehensive set of Arabidopsis thaliana (hereafter Arabidopsis) transcriptomic data, which consists of a wide spectrum of immune responses to pathogens or pathogen-mimicking stimuli treatments. We employed both linear and non-linear models to generate Arabidopsis immune co-expression regulatory (AICR) network. We computed network topological properties and ascertained that this newly constructed immune network is densely connected, possesses hubs, exhibits high modularity, and displays hallmarks of a “real” biological network. We partitioned the network and identified 156 novel modules related to immune functions. Gene Ontology (GO) enrichment analyses provided insight into the key biological processes involved in determining finely tuned immune responses. We also developed novel software called OCCEAN (One Click Cis-regulatory Elements ANalysis) to discover statistically enriched promoter elements in the upstream regulatory regions of Arabidopsis at a whole genome level. We demonstrated that OCCEAN exhibits higher precision than the existing promoter element discovery tools. In light of known and newly discovered cis-regulatory elements, we evaluated biological significance of two key immune-related functional modules and proposed mechanism(s) to explain how large sets of diverse GO genes coherently function to mount effective immune responses. Conclusions We used a network-based, top-down approach to discover immune-related modules from transcriptomic data in Arabidopsis. Detailed analyses of these functional modules reveal new insight into the topological properties of immune co-expression networks and a comprehensive understanding of multifaceted plant defense responses. We present evidence that our newly developed software, OCCEAN, could become a popular tool for the Arabidopsis research community as well as potentially expand to analyze other eukaryotic genomes. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-421) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | | | | | | | | | - M Shahid Mukhtar
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, 35294-1170, USA.
| |
Collapse
|