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Shibl AA, Ochsenkühn MA, Mohamed AR, Isaac A, Coe LSY, Yun Y, Skrzypek G, Raina JB, Seymour JR, Afzal AJ, Amin SA. Molecular mechanisms of microbiome modulation by the eukaryotic secondary metabolite azelaic acid. eLife 2024; 12:RP88525. [PMID: 38189382 PMCID: PMC10945470 DOI: 10.7554/elife.88525] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2024] Open
Abstract
Photosynthetic eukaryotes, such as microalgae and plants, foster fundamentally important relationships with their microbiome based on the reciprocal exchange of chemical currencies. Among these, the dicarboxylate metabolite azelaic acid (Aze) appears to play an important, but heterogeneous, role in modulating these microbiomes, as it is used as a carbon source for some heterotrophs but is toxic to others. However, the ability of Aze to promote or inhibit growth, as well as its uptake and assimilation mechanisms into bacterial cells are mostly unknown. Here, we use transcriptomics, transcriptional factor coexpression networks, uptake experiments, and metabolomics to unravel the uptake, catabolism, and toxicity of Aze on two microalgal-associated bacteria, Phycobacter and Alteromonas, whose growth is promoted or inhibited by Aze, respectively. We identify the first putative Aze transporter in bacteria, a 'C4-TRAP transporter', and show that Aze is assimilated through fatty acid degradation, with further catabolism occurring through the glyoxylate and butanoate metabolism pathways when used as a carbon source. Phycobacter took up Aze at an initial uptake rate of 3.8×10-9 nmol/cell/hr and utilized it as a carbon source in concentrations ranging from 10 μM to 1 mM, suggesting a broad range of acclimation to Aze availability. For growth-impeded bacteria, we infer that Aze inhibits the ribosome and/or protein synthesis and that a suite of efflux pumps is utilized to shuttle Aze outside the cytoplasm. We demonstrate that seawater amended with Aze becomes enriched in bacterial families that can catabolize Aze, which appears to be a different mechanism from that in soil, where modulation by the host plant is required. This study enhances our understanding of carbon cycling in the oceans and how microscale chemical interactions can structure marine microbial populations. In addition, our findings unravel the role of a key chemical currency in the modulation of eukaryote-microbiome interactions across diverse ecosystems.
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Affiliation(s)
- Ahmed A Shibl
- Biology Program, New York University Abu DhabiAbu DhabiUnited Arab Emirates
| | | | - Amin R Mohamed
- Biology Program, New York University Abu DhabiAbu DhabiUnited Arab Emirates
| | - Ashley Isaac
- Biology Program, New York University Abu DhabiAbu DhabiUnited Arab Emirates
- Max Planck Institute for Marine MicrobiologyBremenGermany
| | - Lisa SY Coe
- Biology Program, New York University Abu DhabiAbu DhabiUnited Arab Emirates
| | - Yejie Yun
- Biology Program, New York University Abu DhabiAbu DhabiUnited Arab Emirates
| | - Grzegorz Skrzypek
- West Australian Biogeochemistry Centre, School of Biological Sciences, The University of Western AustraliaPerthAustralia
| | - Jean-Baptiste Raina
- Climate Change Cluster, Faculty of Science, University of Technology SydneyUltimoAustralia
| | - Justin R Seymour
- Climate Change Cluster, Faculty of Science, University of Technology SydneyUltimoAustralia
| | - Ahmed J Afzal
- Biology Program, New York University Abu DhabiAbu DhabiUnited Arab Emirates
| | - Shady A Amin
- Biology Program, New York University Abu DhabiAbu DhabiUnited Arab Emirates
- Center for Genomics and Systems Biology (CGSB), New York University Abu DhabiAbu DhabiUnited Arab Emirates
- Arabian Center for Climate and Environmental Sciences (ACCESS), New York University Abu DhabiAbu DhabiUnited Arab Emirates
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Palanikumar L, Kalmouni M, Houhou T, Abdullah O, Ali L, Pasricha R, Thomas S, Afzal AJ, Barrera FN, Magzoub M. pH-responsive upconversion mesoporous silica nanospheres for combined multimodal diagnostic imaging and targeted photodynamic and photothermal cancer therapy. bioRxiv 2023:2023.05.22.541491. [PMID: 37292655 PMCID: PMC10245854 DOI: 10.1101/2023.05.22.541491] [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] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Photodynamic therapy (PDT) and photothermal therapy (PTT) have garnered considerable interest as non-invasive cancer treatment modalities. However, these approaches remain limited by low solubility, poor stability and inefficient targeting of many common photosensitizers (PSs) and photothermal agents (PTAs). To overcome these limitations, we have designed biocompatible and biodegradable tumor-targeted upconversion nanospheres with imaging capabilities. The multifunctional nanospheres consist of a sodium yttrium fluoride core doped with lanthanides (ytterbium, erbium and gadolinium) and bismuth selenide (NaYF 4 :Yb/Er/Gd,Bi 2 Se 3 ) within a mesoporous silica shell that encapsulates a PS, Chlorin e6 (Ce6), in its pores. NaYF 4 :Yb/Er converts deeply penetrating near-infrared (NIR) light to visible light, which excites the Ce6 to generate cytotoxic reactive oxygen species (ROS), while the PTA Bi 2 Se 3 efficiently converts absorbed NIR light to heat. Additionally, Gd enables magnetic resonance imaging (MRI) of the nanospheres. The mesoporous silica shell is coated with lipid/polyethylene glycol (DPPC/cholesterol/DSPE-PEG) to ensure retention of the encapsulated Ce6 and minimize interactions with serum proteins and macrophages that impede tumor targeting. Finally, the coat is functionalized with the acidity-triggered rational membrane (ATRAM) peptide, which promotes specific and efficient internalization into cancer cells within the mildly acidic tumor microenvironment. Following uptake by cancer cells in vitro , NIR laser irradiation of the nanospheres caused substantial cytotoxicity due to ROS production and hyperthermia. The nanospheres facilitated tumor MRI and thermal imaging, and exhibited potent NIR laser light-induced antitumor effects in vivo via combined PDT and PTT, with no observable toxicity to healthy tissue, thereby substantially prolonging survival. Our results demonstrate that the ATRAM-functionalized, lipid/PEG-coated upconversion mesoporous silica nanospheres (ALUMSNs) offer multimodal diagnostic imaging and targeted combinatorial cancer therapy.
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Affiliation(s)
- L. Palanikumar
- Biology Program, Division of Science, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Mona Kalmouni
- Biology Program, Division of Science, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Tatiana Houhou
- Biology Program, Division of Science, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Osama Abdullah
- Core Technology Platforms, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Liaqat Ali
- Core Technology Platforms, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Renu Pasricha
- Core Technology Platforms, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Sneha Thomas
- Core Technology Platforms, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Ahmed J. Afzal
- Biology Program, Division of Science, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Francisco N. Barrera
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee Knoxville, Knoxville, Tennessee, United States
| | - Mazin Magzoub
- Biology Program, Division of Science, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
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Loganathan P, Karpauskaite L, Al-Sayegh M, Chehade I, Ali M, Hassan S, Maity D, Ali L, Kalmouni M, Houhou T, Esposito G, Afzal AJ, Hamilton AD, Kumar S, Magzoub M. Oligopyridylamide-based protein mimetic inhibits cancer-associated mutant p53 amyloid-like aggregation and restores its tumor suppressor function. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.1253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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4
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Alam M, Tahir J, Siddiqui A, Magzoub M, Shahzad-Ul-Hussan S, Mackey D, Afzal AJ. RIN4 homologs from important crop species differentially regulate the Arabidopsis NB-LRR immune receptor, RPS2. Plant Cell Rep 2021; 40:2341-2356. [PMID: 34486076 DOI: 10.1007/s00299-021-02771-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 04/07/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
KEY MESSAGE RIN4 homologs from important crop species differ in their ability to prevent ectopic activity of the nucleotide binding-leucine rich repeat resistance protein, RPS2. Pathogens deploy virulence effectors to perturb host processes. Plants utilize intracellular resistance (R) proteins to recognize pathogen effectors either by direct interaction or indirectly via effector-mediated perturbations of host components. RPM1-INTERACTING PROTEIN4 (RIN4) is a plant immune regulator that mediates the indirect activation of multiple, independently evolved R-proteins by multiple, unrelated effector proteins. One of these, RPS2 (RESISTANT TO P. SYRINGAE2), is activated upon cleavage of Arabidopsis (At)RIN4 by the Pseudomonas syringae effector AvrRpt2. To gain insight into the AvrRpt2-RIN4-RPS2 defense-activation module, we compared the function of AtRIN4 with RIN4 homologs present in a diverse range of plant species. We selected seven homologs containing conserved features of AtRIN4, including two NOI (Nitrate induced) domains, each containing a predicted cleavage site for AvrRpt2, and a C-terminal palmitoylation site predicted to mediate membrane tethering of the proteins. Palmitoylation-mediated tethering of AtRIN4 to the plasma membrane and cleavage by AvrRpt2 are required for suppression and activation of RPS2, respectively. While all seven homologs are localized at the plasma membrane, only four suppress RPS2 when transiently expressed in Nicotiana benthamiana. All seven homologs are cleaved by AvrRpt2 and, for those homologs that are able to suppress RPS2, cleavage relieves suppression of RPS2. Further, we demonstrate that the membrane-tethered, C-terminal AvrRpt2-generated cleavage fragment is sufficient for the suppression of RPS2. Lastly, we show that the membrane localization of RPS2 is unaffected by its suppression or activation status.
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Affiliation(s)
- Maheen Alam
- Department of Biology, Lahore University of Management Sciences, Sector U, DHA, Lahore, Pakistan
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, 43210, USA
| | - Jibran Tahir
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92-169, Auckland, 1025, New Zealand
| | - Anam Siddiqui
- Department of Plant Sciences, Rothamsted Research, West Common, Harpenden, AL52JQ, UK
| | - Mazin Magzoub
- Biology Program, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Syed Shahzad-Ul-Hussan
- Department of Biology, Lahore University of Management Sciences, Sector U, DHA, Lahore, Pakistan
| | - David Mackey
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, 43210, USA
- Department of Molecular Genetics and Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, 43210, USA
| | - A J Afzal
- Biology Program, New York University Abu Dhabi, Abu Dhabi, UAE.
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5
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Palanikumar L, Karpauskaite L, Al-Sayegh M, Chehade I, Alam M, Hassan S, Maity D, Ali L, Kalmouni M, Hunashal Y, Ahmed J, Houhou T, Karapetyan S, Falls Z, Samudrala R, Pasricha R, Esposito G, Afzal AJ, Hamilton AD, Kumar S, Magzoub M. Protein mimetic amyloid inhibitor potently abrogates cancer-associated mutant p53 aggregation and restores tumor suppressor function. Nat Commun 2021; 12:3962. [PMID: 34172723 PMCID: PMC8233319 DOI: 10.1038/s41467-021-23985-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 05/26/2021] [Indexed: 02/05/2023] Open
Abstract
Missense mutations in p53 are severely deleterious and occur in over 50% of all human cancers. The majority of these mutations are located in the inherently unstable DNA-binding domain (DBD), many of which destabilize the domain further and expose its aggregation-prone hydrophobic core, prompting self-assembly of mutant p53 into inactive cytosolic amyloid-like aggregates. Screening an oligopyridylamide library, previously shown to inhibit amyloid formation associated with Alzheimer's disease and type II diabetes, identified a tripyridylamide, ADH-6, that abrogates self-assembly of the aggregation-nucleating subdomain of mutant p53 DBD. Moreover, ADH-6 targets and dissociates mutant p53 aggregates in human cancer cells, which restores p53's transcriptional activity, leading to cell cycle arrest and apoptosis. Notably, ADH-6 treatment effectively shrinks xenografts harboring mutant p53, while exhibiting no toxicity to healthy tissue, thereby substantially prolonging survival. This study demonstrates the successful application of a bona fide small-molecule amyloid inhibitor as a potent anticancer agent.
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Affiliation(s)
- L Palanikumar
- Biology Program, Division of Science, New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | - Laura Karpauskaite
- Biology Program, Division of Science, New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | - Mohamed Al-Sayegh
- Biology Program, Division of Science, New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | - Ibrahim Chehade
- Biology Program, Division of Science, New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | - Maheen Alam
- Department of Biology, SBA School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
| | - Sarah Hassan
- Biology Program, Division of Science, New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | - Debabrata Maity
- Department of Chemistry, New York University, New York, NY, USA
| | - Liaqat Ali
- Core Technology Platforms, New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | - Mona Kalmouni
- Biology Program, Division of Science, New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | - Yamanappa Hunashal
- Chemistry Program, Division of Science, New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates.,DAME, Università di Udine, Udine, Italy
| | - Jemil Ahmed
- Department of Chemistry and Biochemistry and Knoebel Institute for Healthy Aging, The University of Denver, Denver, CO, USA
| | - Tatiana Houhou
- Biology Program, Division of Science, New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | - Shake Karapetyan
- Physics Program, Division of Science, New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | - Zackary Falls
- Department of Biomedical Informatics, School of Medicine and Biomedical Sciences, State University of New York (SUNY), Buffalo, NY, USA
| | - Ram Samudrala
- Department of Biomedical Informatics, School of Medicine and Biomedical Sciences, State University of New York (SUNY), Buffalo, NY, USA
| | - Renu Pasricha
- Core Technology Platforms, New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | - Gennaro Esposito
- Chemistry Program, Division of Science, New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates.,INBB, Rome, Italy
| | - Ahmed J Afzal
- Biology Program, Division of Science, New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | | | - Sunil Kumar
- Department of Chemistry and Biochemistry and Knoebel Institute for Healthy Aging, The University of Denver, Denver, CO, USA.
| | - Mazin Magzoub
- Biology Program, Division of Science, New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates.
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6
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Zhang ZC, He B, Sun S, Zhang X, Li T, Wang HH, Xu LR, Afzal AJ, Geng XQ. The phytotoxin COR induces transcriptional reprogramming of photosynthetic, hormonal and defence networks in tomato. Plant Biol (Stuttg) 2021; 23 Suppl 1:69-79. [PMID: 33512048 DOI: 10.1111/plb.13239] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 01/16/2021] [Indexed: 06/12/2023]
Abstract
Coronatine (COR) is a non-host specific phytotoxin secreted by Pseudomonas syringae pv. tomato that can induce leaf chlorosis and increase the virulence of pathogens during plant-pathogen interactions. Studies have shown that COR can regulate multiple physiological processes in plants, but its involvement in bacterial pathogenesis and plant growth regulation is not well understood. In this study, transcriptome sequencing was carried out on 4-week-old tomato leaves that were either mock-treated or treated with COR. Transcriptome sequencing led to the identification of 6144 differentially expressed genes (DEGs), of which 4361 genes were downregulated and 1783 genes were upregulated upon COR treatment. To obtain functional information on the DEGs, we annotated these genes using GO and KEGG databases. Functional classification analysis showed that the DEGs were primarily involved in photosynthesis, chlorophyll and carotenoid biosynthesis, jasmonic acid (JA) synthesis and phenylpropane metabolism. A total of 23 genes related to chlorophyll biosynthesis had significant changes, of which 22 genes were downregulated and one gene was upregulated, indicating that chlorophyll biosynthesis was inhibited upon COR treatment. A total of 17 photosystem I related genes and 22 photosystem II related genes involving 20 protein subunits were also downregulated. In the JA synthesis pathway, 25 genes were up regulated, and six genes were downregulated in COR treated samples. COR was also involved in the regulation of multiple secondary metabolites. The identified DEGs will help us better understand the virulence effects and physiological functions of COR and provide a theoretical basis for breeding resistance into economically important crops.
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Affiliation(s)
- Z C Zhang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - B He
- Institute of Quality and Safety Testing Center for Agro-products, Xining City, China
| | - S Sun
- Shanxi Agricultural University, Taigu, China
| | - X Zhang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - T Li
- Shanxi Agricultural University, Taigu, China
| | - H H Wang
- Edisto Research and Education Center, Clemson University, Blackville, SC, USA
| | - L R Xu
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - A J Afzal
- Division of Science, New York University, Abu Dhabi, UAE
| | - X Q Geng
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
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Rai MI, Alam M, Lightfoot DA, Gurha P, Afzal AJ. Classification and experimental identification of plant long non-coding RNAs. Genomics 2019; 111:997-1005. [DOI: 10.1016/j.ygeno.2018.04.014] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 04/13/2018] [Accepted: 04/17/2018] [Indexed: 02/07/2023]
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Iqbal MJ, Majeed M, Humayun M, Lightfoot DA, Afzal AJ. Proteomic Profiling and the Predicted Interactome of Host Proteins in Compatible and Incompatible Interactions Between Soybean and Fusarium virguliforme. Appl Biochem Biotechnol 2016; 180:1657-1674. [PMID: 27491306 DOI: 10.1007/s12010-016-2194-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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] [Received: 11/24/2015] [Accepted: 07/13/2016] [Indexed: 12/27/2022]
Abstract
Sudden death syndrome (SDS) is a complex of two diseases of soybean (Glycine max), caused by the soil borne pathogenic fungus Fusarium virguliforme. The root rot and leaf scorch diseases both result in significant yield losses worldwide. Partial SDS resistance has been demonstrated in multiple soybean cultivars. This study aimed to highlight proteomic changes in soybean roots by identifying proteins which are differentially expressed in near isogenic lines (NILs) contrasting at the Rhg1/Rfs2 locus for partial resistance or susceptibility to SDS. Two-dimensional gel electrophoresis resolved approximately 1000 spots on each gel; 12 spots with a significant (P < 0.05) difference in abundance of 1.5-fold or more were picked, trypsin-digested, and analyzed using quadruple time-of-flight tandem mass spectrometry. Several spots contained more than one protein, so that 18 distinct proteins were identified overall. A functional analysis performed to categorize the proteins depicted that the major pathways altered by fungal infection include disease resistance, stress tolerance, and metabolism. This is the first report which identifies proteins whose abundances are altered in response to fungal infection leading to SDS. The results provide valuable information about SDS resistance in soybean plants, and plant partial resistance responses in general. More importantly, several of the identified proteins could be good candidates for the development of SDS-resistant soybean plants.
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Affiliation(s)
- M Javed Iqbal
- Department of Plant Sciences, University of California, Davis, California, 95616, USA
| | - Maryam Majeed
- Department of Biology, SBA School of Science and Engineering, Lahore University of Management Sciences, Lahore, 54792, Pakistan
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Maheen Humayun
- Department of Biology, SBA School of Science and Engineering, Lahore University of Management Sciences, Lahore, 54792, Pakistan
| | - David A Lightfoot
- Department of Molecular Biology, Microbiology, and Biochemistry, Genomics Core Facility and Center for Excellence in Soybean Research, Teaching, and Outreach, and Department of Plant Biology, Southern Illinois University, Carbondale, Illinois, 62901, USA
| | - Ahmed J Afzal
- Department of Biology, SBA School of Science and Engineering, Lahore University of Management Sciences, Lahore, 54792, Pakistan.
- Department of Molecular Biology, Microbiology, and Biochemistry, Genomics Core Facility and Center for Excellence in Soybean Research, Teaching, and Outreach, and Department of Plant Biology, Southern Illinois University, Carbondale, Illinois, 62901, USA.
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9
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Abstract
Here we present an overview of our existing knowledge on the function of RIN4 as a regulator of plant defense and as a guardee of multiple plant R-proteins. Domain analysis of RIN4 reveals two NOI domains. The NOI domain was originally identified in a screen for nitrate induced genes. The domain is comprised of approximately 30 amino acids and contains 2 conserved motifs (PXFGXW and Y/FTXXF). The NOI gene family contains members exclusively from the plant lineage as far back as moss. In addition to the conserved NOI domain, members within the family also contain conserved C-terminal cysteine residue(s) which are sites for acylation and membrane tethering. Other than these two characteristic features, the sequence of the family of NOI-containing proteins is diverse and, with the exception of RIN4, their functions are not known. Recently published interactome data showing interactions between RIN4 and components of the exocyst complex prompt us to raise the hypothesis that RIN4 might be involved in defense associated vesicle trafficking.
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Affiliation(s)
- Ahmed J Afzal
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, USA.
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10
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Afzal AJ, Srour A, Goil A, Vasudaven S, Liu T, Samudrala R, Dogra N, Kohli P, Malakar A, Lightfoot DA. Homo-dimerization and ligand binding by the leucine-rich repeat domain at RHG1/RFS2 underlying resistance to two soybean pathogens. BMC Plant Biol 2013; 13:43. [PMID: 23497186 PMCID: PMC3626623 DOI: 10.1186/1471-2229-13-43] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 02/05/2013] [Indexed: 05/26/2023]
Abstract
BACKGROUND The protein encoded by GmRLK18-1 (Glyma_18_02680 on chromosome 18) was a receptor like kinase (RLK) encoded within the soybean (Glycine max L. Merr.) Rhg1/Rfs2 locus. The locus underlies resistance to the soybean cyst nematode (SCN) Heterodera glycines (I.) and causal agent of sudden death syndrome (SDS) Fusarium virguliforme (Aoki). Previously the leucine rich repeat (LRR) domain was expressed in Escherichia coli. RESULTS The aims here were to evaluate the LRRs ability to; homo-dimerize; bind larger proteins; and bind to small peptides. Western analysis suggested homo-dimers could form after protein extraction from roots. The purified LRR domain, from residue 131-485, was seen to form a mixture of monomers and homo-dimers in vitro. Cross-linking experiments in vitro showed the H274N region was close (<11.1 A) to the highly conserved cysteine residue C196 on the second homo-dimer subunit. Binding constants of 20-142 nM for peptides found in plant and nematode secretions were found. Effects on plant phenotypes including wilting, stem bending and resistance to infection by SCN were observed when roots were treated with 50 pM of the peptides. Far-Western analyses followed by MS showed methionine synthase and cyclophilin bound strongly to the LRR domain. A second LRR from GmRLK08-1 (Glyma_08_g11350) did not show these strong interactions. CONCLUSIONS The LRR domain of the GmRLK18-1 protein formed both a monomer and a homo-dimer. The LRR domain bound avidly to 4 different CLE peptides, a cyclophilin and a methionine synthase. The CLE peptides GmTGIF, GmCLE34, GmCLE3 and HgCLE were previously reported to be involved in root growth inhibition but here GmTGIF and HgCLE were shown to alter stem morphology and resistance to SCN. One of several models from homology and ab-initio modeling was partially validated by cross-linking. The effect of the 3 amino acid replacements present among RLK allotypes, A87V, Q115K and H274N were predicted to alter domain stability and function. Therefore, the LRR domain of GmRLK18-1 might underlie both root development and disease resistance in soybean and provide an avenue to develop new variants and ligands that might promote reduced losses to SCN.
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Affiliation(s)
- Ahmed J Afzal
- Department of Molecular Biology, Microbiology and Biochemistry and Center for Excellence the Illinois Soybean Center, Southern Illinois University at Carbondale, IL 62901, USA.
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11
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Park CH, Chen S, Shirsekar G, Zhou B, Khang CH, Songkumarn P, Afzal AJ, Ning Y, Wang R, Bellizzi M, Valent B, Wang GL. The Magnaporthe oryzae effector AvrPiz-t targets the RING E3 ubiquitin ligase APIP6 to suppress pathogen-associated molecular pattern-triggered immunity in rice. Plant Cell 2012; 24:4748-62. [PMID: 23204406 PMCID: PMC3531864 DOI: 10.1105/tpc.112.105429] [Citation(s) in RCA: 352] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Revised: 10/24/2012] [Accepted: 11/08/2012] [Indexed: 05/17/2023]
Abstract
Although the functions of a few effector proteins produced by bacterial and oomycete plant pathogens have been elucidated in recent years, information for the vast majority of pathogen effectors is still lacking, particularly for those of plant-pathogenic fungi. Here, we show that the avirulence effector AvrPiz-t from the rice blast fungus Magnaporthe oryzae preferentially accumulates in the specialized structure called the biotrophic interfacial complex and is then translocated into rice (Oryza sativa) cells. Ectopic expression of AvrPiz-t in transgenic rice suppresses the flg22- and chitin-induced generation of reactive oxygen species (ROS) and enhances susceptibility to M. oryzae, indicating that AvrPiz-t functions to suppress pathogen-associated molecular pattern (PAMP)-triggered immunity in rice. Interaction assays show that AvrPiz-t suppresses the ubiquitin ligase activity of the rice RING E3 ubiquitin ligase APIP6 and that, in return, APIP6 ubiquitinates AvrPiz-t in vitro. Interestingly, agroinfection assays reveal that AvrPiz-t and AvrPiz-t Interacting Protein 6 (APIP6) are both degraded when coexpressed in Nicotiana benthamiana. Silencing of APIP6 in transgenic rice leads to a significant reduction of flg22-induced ROS generation, suppression of defense-related gene expression, and enhanced susceptibility of rice plants to M. oryzae. Taken together, our results reveal a mechanism in which a fungal effector targets the host ubiquitin proteasome system for the suppression of PAMP-triggered immunity in plants.
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Affiliation(s)
- Chan-Ho Park
- Department of Plant Pathology, Ohio State University, Columbus, OH 43210
| | - Songbiao Chen
- Department of Plant Pathology, Ohio State University, Columbus, OH 43210
- State Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, China
| | - Gautam Shirsekar
- Department of Plant Pathology, Ohio State University, Columbus, OH 43210
| | - Bo Zhou
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, 310021 China
| | - Chang Hyun Khang
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506
| | | | - Ahmed J. Afzal
- Department of Horticulture and Crop Science, Ohio State University, Columbus, OH 43210
| | - Yuese Ning
- State Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ruyi Wang
- State Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Maria Bellizzi
- Department of Plant Pathology, Ohio State University, Columbus, OH 43210
| | - Barbara Valent
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506
| | - Guo-Liang Wang
- Department of Plant Pathology, Ohio State University, Columbus, OH 43210
- State Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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12
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Srour A, Afzal AJ, Blahut-Beatty L, Hemmati N, Simmonds DH, Li W, Liu M, Town CD, Sharma H, Arelli P, Lightfoot DA. The receptor like kinase at Rhg1-a/Rfs2 caused pleiotropic resistance to sudden death syndrome and soybean cyst nematode as a transgene by altering signaling responses. BMC Genomics 2012; 13:368. [PMID: 22857610 PMCID: PMC3439264 DOI: 10.1186/1471-2164-13-368] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Accepted: 06/12/2012] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Soybean (Glycine max (L. Merr.)) resistance to any population of Heterodera glycines (I.), or Fusarium virguliforme (Akoi, O'Donnell, Homma & Lattanzi) required a functional allele at Rhg1/Rfs2. H. glycines, the soybean cyst nematode (SCN) was an ancient, endemic, pest of soybean whereas F. virguliforme causal agent of sudden death syndrome (SDS), was a recent, regional, pest. This study examined the role of a receptor like kinase (RLK) GmRLK18-1 (gene model Glyma_18_02680 at 1,071 kbp on chromosome 18 of the genome sequence) within the Rhg1/Rfs2 locus in causing resistance to SCN and SDS. RESULTS A BAC (B73p06) encompassing the Rhg1/Rfs2 locus was sequenced from a resistant cultivar and compared to the sequences of two susceptible cultivars from which 800 SNPs were found. Sequence alignments inferred that the resistance allele was an introgressed region of about 59 kbp at the center of which the GmRLK18-1 was the most polymorphic gene and encoded protein. Analyses were made of plants that were either heterozygous at, or transgenic (and so hemizygous at a new location) with, the resistance allele of GmRLK18-1. Those plants infested with either H. glycines or F. virguliforme showed that the allele for resistance was dominant. In the absence of Rhg4 the GmRLK18-1 was sufficient to confer nearly complete resistance to both root and leaf symptoms of SDS caused by F. virguliforme and provided partial resistance to three different populations of nematodes (mature female cysts were reduced by 30-50%). In the presence of Rhg4 the plants with the transgene were nearly classed as fully resistant to SCN (females reduced to 11% of the susceptible control) as well as SDS. A reduction in the rate of early seedling root development was also shown to be caused by the resistance allele of the GmRLK18-1. Field trials of transgenic plants showed an increase in foliar susceptibility to insect herbivory. CONCLUSIONS The inference that soybean has adapted part of an existing pathogen recognition and defense cascade (H.glycines; SCN and insect herbivory) to a new pathogen (F. virguliforme; SDS) has broad implications for crop improvement. Stable resistance to many pathogens might be achieved by manipulation the genes encoding a small number of pathogen recognition proteins.
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Affiliation(s)
- Ali Srour
- Department of Molecular Biology, Microbiology and Biochemistry, Southern Illinois University at Carbondale, Carbondale, IL 62901, USA
- Department of Plant Soil and Agricultural Systems, Southern Illinois University at Carbondale, Carbondale, IL 62901-4415, USA
| | - Ahmed J Afzal
- Department of Molecular Biology, Microbiology and Biochemistry, Southern Illinois University at Carbondale, Carbondale, IL 62901, USA
- Department of Plant Soil and Agricultural Systems, Southern Illinois University at Carbondale, Carbondale, IL 62901-4415, USA
- Department of Horticulture and Crop Science, Ohio State University, 2021 Coffey Rd, Columbus, OH 43210, USA
| | - Laureen Blahut-Beatty
- Agriculture and Agri-Food Canada, Building 21, 960 Carling Ave, Ottawa, ON K1A 0C6, USA
| | - Naghmeh Hemmati
- Department of Molecular Biology, Microbiology and Biochemistry, Southern Illinois University at Carbondale, Carbondale, IL 62901, USA
| | - Daina H Simmonds
- Agriculture and Agri-Food Canada, Building 21, 960 Carling Ave, Ottawa, ON K1A 0C6, USA
| | - Wenbin Li
- Key Laboratory of Soybean Biology in the Chinese Ministry of Education, Harbin University, Harbin, China
| | - Miao Liu
- Key Laboratory of Soybean Biology in the Chinese Ministry of Education, Harbin University, Harbin, China
| | | | - Hemlata Sharma
- Department of Molecular Biology, Microbiology and Biochemistry, Southern Illinois University at Carbondale, Carbondale, IL 62901, USA
- Department of Plant Breeding & Genetics, Rajasthan College of Agriculture, MPUAT, Udaipur, India
| | | | - David A Lightfoot
- Department of Molecular Biology, Microbiology and Biochemistry, Southern Illinois University at Carbondale, Carbondale, IL 62901, USA
- Department of Plant Soil and Agricultural Systems, Southern Illinois University at Carbondale, Carbondale, IL 62901-4415, USA
- Key Laboratory of Soybean Biology in the Chinese Ministry of Education, Harbin University, Harbin, China
- Genomics Core Facility; Center for Excellence the Illinois Soybean Center, Southern Illinois University at Carbondale, Carbondale, IL 62901-4415, USA
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13
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Afzal AJ, Srour A, Saini N, Hemmati N, El Shemy HA, Lightfoot DA. Recombination suppression at the dominant Rhg1/Rfs2 locus underlying soybean resistance to the cyst nematode. Theor Appl Genet 2012; 124:1027-39. [PMID: 22200919 DOI: 10.1007/s00122-011-1766-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Accepted: 12/04/2011] [Indexed: 05/08/2023]
Abstract
Host resistance to "yellow dwarf" or "moonlight" disease cause by any population (Hg type) of Heterodera glycines I., the soybean cyst nematode (SCN), requires a functional allele at rhg1. The host resistance encoded appears to mimic an apoptotic response in the giant cells formed at the nematode feeding site about 24-48 h after nematode feeding commences. Little is known about how the host response to infection is mediated but a linked set of 3 genes has been identified within the rhg1 locus. This study aimed to identify the role of the genes within the locus that includes a receptor-like kinase (RLK), a laccase and an ion antiporter. Used were near isogeneic lines (NILs) that contrasted at their rhg1 alleles, gene-based markers, and a new Hg type 0 and new recombination events. A syntenic gene cluster on Lg B1 was found. The effectiveness of SNP probes from the RLK for distinguishing homolog sequence variants on LgB1 from alleles at the rhg1 locus on LgG was shown. The resistant allele of the rhg1 locus was shown to be dominant in NILs. None of the recombination events were within the cluster of the three candidate genes. Finally, rhg1 was shown to reduce the plant root development. A model for rhg1 as a dominant multi-gene resistance locus based on the developmental control was inferred.
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Affiliation(s)
- Ahmed J Afzal
- Department of Molecular Biology, Microbiology and Biochemistry, Southern Illinois University at Carbondale, Carbondale, IL 62901, USA
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14
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Afzal AJ, da Cunha L, Mackey D. Separable fragments and membrane tethering of Arabidopsis RIN4 regulate its suppression of PAMP-triggered immunity. Plant Cell 2011; 23:3798-811. [PMID: 21984695 PMCID: PMC3229150 DOI: 10.1105/tpc.111.088708] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
RPM1-interacting protein 4 (RIN4) is a multifunctional Arabidopsis thaliana protein that regulates plant immune responses to pathogen-associated molecular patterns (PAMPs) and bacterial type III effector proteins (T3Es). RIN4, which is targeted by multiple defense-suppressing T3Es, provides a mechanistic link between PAMP-triggered immunity (PTI) and effector-triggered immunity and effector suppression of plant defense. Here we report on a structure-function analysis of RIN4-mediated suppression of PTI. Separable fragments of RIN4, including those produced when the T3E AvrRpt2 cleaves RIN4 and each containing a plant-specific nitrate-induced (NOI) domain, suppress PTI. The N-terminal and C-terminal NOIs each contribute to PTI suppression and are evolutionarily conserved. Native RIN4 is anchored to the plasma membrane by C-terminal acylation. Nonmembrane-tethered derivatives of RIN4 activate a cell death response in wild-type Arabidopsis and are hyperactive PTI suppressors in a mutant background that lacks the cell death response. Our results indicate that RIN4 is a multifunctional suppressor of PTI and that a virulence function of AvrRpt2 may include cleaving RIN4 into active defense-suppressing fragments.
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Affiliation(s)
- Ahmed J. Afzal
- Department of Horticulture and Crop Science, Ohio State University, Columbus, Ohio 43210
| | - Luis da Cunha
- Department of Horticulture and Crop Science, Ohio State University, Columbus, Ohio 43210
| | - David Mackey
- Department of Horticulture and Crop Science, Ohio State University, Columbus, Ohio 43210
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210
- Address correspondence to
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15
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Chung EH, da Cunha L, Wu AJ, Gao Z, Cherkis K, Afzal AJ, Mackey D, Dangl JL. Specific threonine phosphorylation of a host target by two unrelated type III effectors activates a host innate immune receptor in plants. Cell Host Microbe 2011; 9:125-36. [PMID: 21320695 DOI: 10.1016/j.chom.2011.01.009] [Citation(s) in RCA: 148] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Revised: 12/13/2010] [Accepted: 01/13/2011] [Indexed: 11/26/2022]
Abstract
The Arabidopsis NB-LRR immune receptor RPM1 recognizes the Pseudomonas syringae type III effectors AvrB or AvrRpm1 to mount an immune response. Although neither effector is itself a kinase, AvrRpm1 and AvrB are known to target Arabidopsis RIN4, a negative regulator of basal plant defense, for phosphorylation. We show that RIN4 phosphorylation activates RPM1. RIN4(142-176) is necessary and, with appropriate localization sequences, sufficient to support effector-triggered RPM1 activation, with the threonine residue at position 166 being critical. Phosphomimic substitutions at T166 cause effector-independent RPM1 activation. RIN4 T166 is phosphorylated in vivo in the presence of AvrB or AvrRpm1. RIN4 mutants that lose interaction with AvrB cannot be coimmunoprecipitated with RPM1. This defines a common interaction platform required for RPM1 activation by phosphorylated RIN4 in response to pathogenic effectors. Conservation of an analogous threonine across all RIN4-like proteins suggests a key function for this residue beyond the regulation of RPM1.
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Affiliation(s)
- Eui-Hwan Chung
- Department of Biology, University of North Carolina, Chapel Hill, 27599, USA
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16
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Afzal AJ, Natarajan A, Saini N, Iqbal MJ, Geisler M, El Shemy HA, Mungur R, Willmitzer L, Lightfoot DA. The nematode resistance allele at the rhg1 locus alters the proteome and primary metabolism of soybean roots. Plant Physiol 2009; 151:1264-80. [PMID: 19429603 PMCID: PMC2773059 DOI: 10.1104/pp.109.138149] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2009] [Accepted: 05/03/2009] [Indexed: 05/19/2023]
Abstract
Heterodera glycines, the soybean cyst nematode (SCN), causes the most damaging chronic disease of soybean (Glycine max). Host resistance requires the resistance allele at rhg1. Resistance destroys the giant cells created in the plant's roots by the nematodes about 24 to 48 h after commencement of feeding. In addition, 4 to 8 d later, a systemic acquired resistance develops that discourages later infestations. The molecular mechanisms that control the rhg1-mediated resistance response appear to be multigenic and complex, as judged by transcript abundance changes, even in near isogenic lines (NILs). This study aimed to focus on key posttranscriptional changes by identifying proteins and metabolites that were increased in abundance in both resistant and susceptible NILs. Comparisons were made among NILs 10 d after SCN infestation and without SCN infestation. Two-dimensional gel electrophoresis resolved more than 1,000 protein spots on each gel. Only 30 protein spots with a significant (P < 0.05) difference in abundance of 1.5-fold or more were found among the four treatments. The proteins in these spots were picked, trypsin digested, and analyzed using quadrupole time-of-flight tandem mass spectrometry. Protein identifications could be made for 24 of the 30 spots. Four spots contained two proteins, so that 28 distinct proteins were identified. The proteins were grouped into six functional categories. Metabolite analysis by gas chromatography-mass spectrometry identified 131 metabolites, among which 58 were altered by one or more treatment; 28 were involved in primary metabolism. Taken together, the data showed that 17 pathways were altered by the rhg1 alleles. Pathways altered were associated with systemic acquired resistance-like responses, including xenobiotic, phytoalexin, ascorbate, and inositol metabolism, as well as primary metabolisms like amino acid synthesis and glycolysis. The pathways impacted by the rhg1 allelic state and SCN infestation agreed with transcript abundance analyses but identified a smaller set of key proteins. Six of the proteins lay within the same small region of the interactome identifying a key set of 159 interacting proteins involved in transcriptional control, nuclear localization, and protein degradation. Finally, two proteins (glucose-6-phosphate isomerase [EC 5.3.1.9] and isoflavone reductase [EC 1.3.1.45]) and two metabolites (maltose and an unknown) differed in resistant and susceptible NILs without SCN infestation and may form the basis of a new assay for the selection of resistance to SCN in soybean.
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Affiliation(s)
| | | | | | | | | | | | | | | | - David A. Lightfoot
- Department of Molecular Biology, Microbiology, and Biochemistry (A.J.A., A.N., H.A.E.S., R.M., D.A.L.), Genomics Core Facility and Center for Excellence in Soybean Research, Teaching, and Outreach, Department of Plant Soil and Agricultural Systems (A.J.A., N.S., H.A.E.S., D.A.L.), and Department of Plant Biology (M.G., D.A.L.), Southern Illinois University, Carbondale, Illinois 62901; Institute for Advanced Learning and Research, Institute for Sustainable and Renewable Resources, Danville, Virginia 24540 (M.J.I.); and Max Planck Institute for Molecular Plant Physiology, Potsdam 14476, Germany (R.M., L.W.)
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17
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Iqbal MJ, Ahsan R, Afzal AJ, Jamai A, Meksem K, El-Shemy HA, Lightfoot DA. Multigeneic QTL: the laccase encoded within the soybean Rfs2/rhg1 locus inferred to underlie part of the dual resistance to cyst nematode and sudden death syndrome. Curr Issues Mol Biol 2009; 11 Suppl 1:i11-19. [PMID: 19193960] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2008] [Revised: 10/05/2008] [Accepted: 10/12/2008] [Indexed: 05/27/2023] Open
Abstract
Multigeneic QTL present significant problems to analysis. Resistance to soybean (Glycine max (L) Merr.) sudden death syndrome (SDS) caused by Fusarium virguliforme was partly underlain by QRfs2 that was clustered with, or pleiotropic to, the multigeneic rhg1 locus providing resistance to soybean cyst nematode (SCN; Heterodera glycines). A group of five genes were found between the two markers that delimited the Rfs2/rhg1 locus. One of the five genes was predicted to encode an unusual diphenol oxidase (laccase; EC 1.10.3.2). The aim of this study was to characterize this member of the soybean laccase gene-family and explore its involvement in SDS resistance. A genomic clone and a full length cDNA was isolated from resistant cultivar 'Forrest' that were different among susceptible cultivars 'Asgrow 3244' and 'Williams 82' at four residues R/H168, I/M271, R/H330, E/K470. Additional differences were found in six of the seven introns and the promoter region. Transcript abundance (TA) among genotypes that varied for resistance to SDS or SCN did not differ significantly. Therefore the protein activity was inferred to underlie resistance. Protein expressed in yeast pYES2/NTB had weak enzyme activity with common substrates but good activity with root phenolics. The Forrest isoform may underlie both QRfs2 and rhg1.
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Affiliation(s)
- M J Iqbal
- Institute for Sustainable and Renewable Resources (ISRR), Institute for Advanced Learning and Research (IALR), Danville, VA 24540, USA
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18
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Abstract
Plants are hosts to a wide array of pathogens from all kingdoms of life. In the absence of an active immune system or combinatorial diversifications that lead to recombination-driven somatic gene flexibility, plants have evolved different strategies to combat both individual pathogen strains and changing pathogen populations. The receptor-like kinase (RLK) gene-family expansion in plants was hypothesized to have allowed accelerated evolution among domains implicated in signal reception, typically a leucine-rich repeat (LRR). Under that model, the gene-family expansion represents a plant-specific adaptation that leads to the production of numerous and variable cell surface and cytoplasmic receptors. More recently, it has emerged that the LRR domains of RLK interact with a diverse group of proteins leading to combinatorial variations in signal response specificity. Therefore, the RLK appear to play a central role in signaling during pathogen recognition, the subsequent activation of plant defense mechanisms, and developmental control. The future challenges will include determinations of RLK modes of action, the basis of recognition and specificity, which cellular responses each receptor mediates, and how both receptor and kinase domain interactions fit into the defense signaling cascades. These challenges will be complicated by the limited information that may be derived from the primary sequence of the LRR domain. The review focuses upon implications derived from recent studies of the secondary and tertiary structures of several plant RLK that change understanding of plant receptor function and signaling. In addition, the biological functions of plant and animal RLK-containing receptors were reviewed and commonalities among their signaling mechanisms identified. Further elucidated were the genomic and structural organizations of RLK gene families, with special emphasis on RLK implicated in resistance to disease and development.
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Affiliation(s)
- Ahmed J Afzal
- Department of Molecular Biology, Microbiology and Biochemistry, Southern Illinois University, Carbondale, IL 62901, USA
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19
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Afzal AJ, Lightfoot DA. Soybean disease resistance protein RHG1-LRR domain expressed, purified and refolded from Escherichia coli inclusion bodies: preparation for a functional analysis. Protein Expr Purif 2007; 53:346-55. [PMID: 17287130 DOI: 10.1016/j.pep.2006.12.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2006] [Revised: 12/19/2006] [Accepted: 12/20/2006] [Indexed: 10/23/2022]
Abstract
Introduction and expression of foreign genes in bacteria often results accumulation of the foreign protein(s) in inclusion bodies (IBs). The subsequent processes of refolding are slow, difficult and often fail to yield significant amounts of folded protein. RHG1 encoded by rhg1 was a soybean (Glycine max L. Merr.) transmembrane receptor-like kinase (EC 2.7.11.1) with an extracellular leucine-rich repeat domain. The LRR of RHG1 was believed to be involved in elicitor recognition and interaction with other plant proteins. The aim, here, was to express the LRR domain in Escherichia coli (RHG1-LRR) and produce refolded protein. Urea titration experiments showed that the IBs formed in E. coli by the extracellular domain of the RHG1 protein could be solubilized at different urea concentrations. The RHG1 proteins were eluted with 1.0-7.0M urea in 0.5M increments. Purified RHG1 protein obtained from the 1.5 and 7.0M elutions was analyzed for secondary structure through circular dichroism (CD) spectroscopy. Considerable secondary structure could be seen in the former, whereas the latter yielded CD curves characteristic of denatured proteins. Both elutions were subjected to refolding by slowly removing urea in the presence of arginine and reduced/oxidized glutathione. Detectable amounts of refolded protein could not be recovered from the 7.0M urea sample, whereas refolding from the 1.5M urea sample yielded 0.2mg/ml protein. The 7.0M treatment resulted in the formation of a homogenous denatured state with no apparent secondary structure. Refolding from this fully denatured state may confer kinetic and/or thermodynamic constraints on the refolding process, whereas the kinetic and/or thermodynamic barriers to attain the folded conformation appeared to be lesser, when refolding from a partially folded state.
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Affiliation(s)
- Ahmed J Afzal
- Department of Molecular Biology, Microbiology and Biochemistry and Center for Excellence in Soybean Research, Teaching and Outreach, Southern Illinois University at Carbondale, IL 62901, USA
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20
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Shultz JL, Yesudas C, Yaegashi S, Afzal AJ, Kazi S, Lightfoot DA. Three minimum tile paths from bacterial artificial chromosome libraries of the soybean (Glycine max cv. 'Forrest'): tools for structural and functional genomics. Plant Methods 2006; 2:9. [PMID: 16725032 PMCID: PMC1524761 DOI: 10.1186/1746-4811-2-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2006] [Accepted: 05/25/2006] [Indexed: 05/04/2023]
Abstract
BACKGROUND The creation of minimally redundant tile paths (hereafter MTP) from contiguous sets of overlapping clones (hereafter contigs) in physical maps is a critical step for structural and functional genomics. Build 4 of the physical map of soybean (Glycine max L. Merr. cv. 'Forrest') showed the 1 Gbp haploid genome was composed of 0.7 Gbp diploid, 0.1 Gbp tetraploid and 0.2 Gbp octoploid regions. Therefore, the size of the unique genome was about 0.8 Gbp. The aim here was to create MTP sub-libraries from the soybean cv. Forrest physical map builds 2 to 4. RESULTS The first MTP, named MTP2, was 14,208 clones (of mean insert size 140 kbp) picked from the 5,597 contigs of build 2. MTP2 was constructed from three BAC libraries (BamHI (B), HindIII (H) and EcoRI (E) inserts). MTP2 encompassed the contigs of build 3 that derived from build 2 by a series of contig merges. MTP2 encompassed 2 Gbp compared to the soybean haploid genome of 1 Gbp and does not distinguish regions by ploidy. The second and third MTPs, called MTP4BH and MTP4E, were each based on build 4. Each was semi-automatically selected from 2,854 contigs. MTP4BH was 4,608 B and H insert clones of mean size 173 kbp in the large (27.6 kbp) T-DNA vector pCLD04541. MTP4BH was suitable for plant transformation and functional genomics. MTP4E was 4,608 BAC clones with large inserts (mean 175 kbp) in the small (7.5 kbp) pECBAC1 vector. MTP4E was suitable for DNA sequencing. MTP4BH and MTP4E clones each encompassed about 0.8 Gbp, the 0.7 Gbp diploid regions and 0.05 Gbp each from the tetraploid and octoploid regions. MTP2 and MTP4BH were used for BAC-end sequencing, EST integration, micro-satellite integration into the physical map and high information content fingerprinting. MTP4E will be used for genome sequence by pooled genomic clone index. CONCLUSION Each MTP and associated BES will be useful to deconvolute and ultimately finish the whole genome shotgun sequence of soybean.
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Affiliation(s)
- JL Shultz
- Dept of Soybean Genetics, United States Department of Agriculture, Stoneville, MS 38776, USA
- Dept. of Plant Soil and Agricultural Systems, Genomics and Biotechnology Facility, Center for Excellence in Soybean Research, Southern Illinois University, Carbondale, IL 62901, USA
| | - C Yesudas
- Dept. of Plant Soil and Agricultural Systems, Genomics and Biotechnology Facility, Center for Excellence in Soybean Research, Southern Illinois University, Carbondale, IL 62901, USA
| | - S Yaegashi
- Dept of Soybean Genetics, United States Department of Agriculture, Stoneville, MS 38776, USA
- Dept of Bioinformatics, University of Tokyo, Tokyo, Japan
| | - AJ Afzal
- Dept. of Plant Soil and Agricultural Systems, Genomics and Biotechnology Facility, Center for Excellence in Soybean Research, Southern Illinois University, Carbondale, IL 62901, USA
| | | | - DA Lightfoot
- Dept. of Plant Soil and Agricultural Systems, Genomics and Biotechnology Facility, Center for Excellence in Soybean Research, Southern Illinois University, Carbondale, IL 62901, USA
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Shultz JL, Kurunam D, Shopinski K, Iqbal MJ, Kazi S, Zobrist K, Bashir R, Yaegashi S, Lavu N, Afzal AJ, Yesudas CR, Kassem MA, Wu C, Zhang HB, Town CD, Meksem K, Lightfoot DA. The Soybean Genome Database (SoyGD): a browser for display of duplicated, polyploid, regions and sequence tagged sites on the integrated physical and genetic maps of Glycine max. Nucleic Acids Res 2006; 34:D758-65. [PMID: 16381975 PMCID: PMC1347413 DOI: 10.1093/nar/gkj050] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [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: 07/28/2005] [Revised: 10/04/2005] [Accepted: 10/04/2005] [Indexed: 11/19/2022] Open
Abstract
Genomes that have been highly conserved following increases in ploidy (by duplication or hybridization) like Glycine max (soybean) present challenges during genome analysis. At http://soybeangenome.siu.edu the Soybean Genome Database (SoyGD) genome browser has, since 2002, integrated and served the publicly available soybean physical map, bacterial artificial chromosome (BAC) fingerprint database and genetic map associated genomic data. The browser shows both build 3 and build 4 contiguous sets of clones (contigs) of the soybean physical map. Build 4 consisted of 2854 contigs that encompassed 1.05 Gb and 404 high-quality DNA markers that anchored 742 contigs. Many DNA markers anchored sets of 2-8 different contigs. Each contig in the set represented a homologous region of related sequences. GBrowse was adapted to show sets of homologous contigs at all potential anchor points, spread laterally and prevented from overlapping. About 8064 minimum tiling path (MTP2) clones provided 13,473 BAC end sequences (BES) to decorate the physical map. Analyses of BES placed 2111 gene models, 40 marker anchors and 1053 new microsatellite markers on the map. Estimated sequence tag probes from 201 low-copy gene families located 613 paralogs. The genome browser portal showed each data type as a separate track. Tetraploid, octoploid, diploid and homologous regions are shown clearly in relation to an integrated genetic and physical map.
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Affiliation(s)
- Jeffry L. Shultz
- Genomics Core-Facility, Southern Illinois University at CarbondaleCarbondale, IL 62901-4415, USA
- Department of Soil and Crop Sciences and Institute for Plant Genomics and Biotechnology, 2123 TAMU, Texas A&M UniversityCollege Station, TX 77843-2123, USA
- The Institute for Genomic ResearchMD, USA
| | - Deepak Kurunam
- Genomics Core-Facility, Southern Illinois University at CarbondaleCarbondale, IL 62901-4415, USA
- Department of Soil and Crop Sciences and Institute for Plant Genomics and Biotechnology, 2123 TAMU, Texas A&M UniversityCollege Station, TX 77843-2123, USA
- The Institute for Genomic ResearchMD, USA
| | - Kay Shopinski
- Genomics Core-Facility, Southern Illinois University at CarbondaleCarbondale, IL 62901-4415, USA
- Department of Soil and Crop Sciences and Institute for Plant Genomics and Biotechnology, 2123 TAMU, Texas A&M UniversityCollege Station, TX 77843-2123, USA
- The Institute for Genomic ResearchMD, USA
| | - M. Javed Iqbal
- Genomics Core-Facility, Southern Illinois University at CarbondaleCarbondale, IL 62901-4415, USA
- Department of Soil and Crop Sciences and Institute for Plant Genomics and Biotechnology, 2123 TAMU, Texas A&M UniversityCollege Station, TX 77843-2123, USA
- The Institute for Genomic ResearchMD, USA
| | - Samreen Kazi
- Genomics Core-Facility, Southern Illinois University at CarbondaleCarbondale, IL 62901-4415, USA
- Department of Soil and Crop Sciences and Institute for Plant Genomics and Biotechnology, 2123 TAMU, Texas A&M UniversityCollege Station, TX 77843-2123, USA
- The Institute for Genomic ResearchMD, USA
| | - Kimberley Zobrist
- Genomics Core-Facility, Southern Illinois University at CarbondaleCarbondale, IL 62901-4415, USA
- Department of Soil and Crop Sciences and Institute for Plant Genomics and Biotechnology, 2123 TAMU, Texas A&M UniversityCollege Station, TX 77843-2123, USA
- The Institute for Genomic ResearchMD, USA
| | - Rabia Bashir
- Genomics Core-Facility, Southern Illinois University at CarbondaleCarbondale, IL 62901-4415, USA
- Department of Soil and Crop Sciences and Institute for Plant Genomics and Biotechnology, 2123 TAMU, Texas A&M UniversityCollege Station, TX 77843-2123, USA
- The Institute for Genomic ResearchMD, USA
| | - Satsuki Yaegashi
- Genomics Core-Facility, Southern Illinois University at CarbondaleCarbondale, IL 62901-4415, USA
- Department of Soil and Crop Sciences and Institute for Plant Genomics and Biotechnology, 2123 TAMU, Texas A&M UniversityCollege Station, TX 77843-2123, USA
- The Institute for Genomic ResearchMD, USA
| | - Nagajyothi Lavu
- Genomics Core-Facility, Southern Illinois University at CarbondaleCarbondale, IL 62901-4415, USA
- Department of Soil and Crop Sciences and Institute for Plant Genomics and Biotechnology, 2123 TAMU, Texas A&M UniversityCollege Station, TX 77843-2123, USA
- The Institute for Genomic ResearchMD, USA
| | - Ahmed J. Afzal
- Genomics Core-Facility, Southern Illinois University at CarbondaleCarbondale, IL 62901-4415, USA
- Department of Soil and Crop Sciences and Institute for Plant Genomics and Biotechnology, 2123 TAMU, Texas A&M UniversityCollege Station, TX 77843-2123, USA
- The Institute for Genomic ResearchMD, USA
| | - Charles R. Yesudas
- Genomics Core-Facility, Southern Illinois University at CarbondaleCarbondale, IL 62901-4415, USA
- Department of Soil and Crop Sciences and Institute for Plant Genomics and Biotechnology, 2123 TAMU, Texas A&M UniversityCollege Station, TX 77843-2123, USA
- The Institute for Genomic ResearchMD, USA
| | - M. Abdelmajid Kassem
- Genomics Core-Facility, Southern Illinois University at CarbondaleCarbondale, IL 62901-4415, USA
- Department of Soil and Crop Sciences and Institute for Plant Genomics and Biotechnology, 2123 TAMU, Texas A&M UniversityCollege Station, TX 77843-2123, USA
- The Institute for Genomic ResearchMD, USA
| | - Chengcang Wu
- Department of Soil and Crop Sciences and Institute for Plant Genomics and Biotechnology, 2123 TAMU, Texas A&M UniversityCollege Station, TX 77843-2123, USA
| | - Hong Bin Zhang
- Department of Soil and Crop Sciences and Institute for Plant Genomics and Biotechnology, 2123 TAMU, Texas A&M UniversityCollege Station, TX 77843-2123, USA
| | | | - Khalid Meksem
- Genomics Core-Facility, Southern Illinois University at CarbondaleCarbondale, IL 62901-4415, USA
- Department of Soil and Crop Sciences and Institute for Plant Genomics and Biotechnology, 2123 TAMU, Texas A&M UniversityCollege Station, TX 77843-2123, USA
- The Institute for Genomic ResearchMD, USA
| | - David A. Lightfoot
- To whom correspondence should be addressed. Tel: +1 618 453 1797; Fax: +1 618 453 7457;
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