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Heckmann A, Perochon A, Doohan FM. Genome-wide analysis of salicylic acid and jasmonic acid signalling marker gene families in wheat. PLANT BIOLOGY (STUTTGART, GERMANY) 2024; 26:691-704. [PMID: 38864777 DOI: 10.1111/plb.13659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 03/25/2024] [Indexed: 06/13/2024]
Abstract
Jasmonic acid (JA) and salicylic acid (SA) phytohormone pathways are important regulators of stress tolerance. Knowledge regarding the diversity, phylogeny and functionality of wheat genes involved in JA and SA response is limited. Using Arabidopsis, rice and wheat genomic and wheat disease transcriptomic data, we deduced the size, phylogenetic diversity and pathogen-responsiveness of seven hormone-responsive gene families, and thus selected 14 candidates as potential hormone responsive gene markers. Gene-specific expression studies assessed the impact of exogenous JA and SA on their transcriptional activation in leaves of two distinct wheat cultivars. RNAseq data were interrogated to assess their disease responsiveness and tissue-specific expression. This study elucidated the number, phylogeny and pathogen-responsiveness of wheat genes from seven families, including 12 TaAOS, 6 TaJAMyb, 256 TaWRKY group III, 85 TaPR1, 205 TaPR2, 76 TaPR3 and 124 TaPR5. This included the first description of the wheat AOS, JAMyb, PR2, PR3 and PR5 gene families. Gene expression studies delineated TaAOS1-5B and TaJAMyb-4A as JA-responsive in leaves, but not significantly responsive to SA treatment, while TaWRKY45-B was a SA- but not a JA-responsive marker. Other candidate genes were either unresponsive or non-specific to SA or JA. Our findings highlight that all seven gene families are greatly expanded in wheat as compared to other plants (up to 7.6-fold expansion), and demonstrate disparity in the response to biotic stress between some homoeologous and paralogous sequences within these families. The SA- and JA-responsive marker genes identified herein will prove useful tools to monitor these signalling pathways in wheat.
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Affiliation(s)
- A Heckmann
- UCD School of Biology and Environmental Science and Earth Institute, College of Science, University College Dublin, Dublin, Ireland
| | - A Perochon
- UCD School of Biology and Environmental Science and Earth Institute, College of Science, University College Dublin, Dublin, Ireland
| | - F M Doohan
- UCD School of Biology and Environmental Science and Earth Institute, College of Science, University College Dublin, Dublin, Ireland
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Manasseh R, Sathuvalli V, Pappu HR. Transcriptional and functional predictors of potato virus Y-induced tuber necrosis in potato ( Solanum tuberosum). FRONTIERS IN PLANT SCIENCE 2024; 15:1369846. [PMID: 38638354 PMCID: PMC11024271 DOI: 10.3389/fpls.2024.1369846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 02/26/2024] [Indexed: 04/20/2024]
Abstract
Introduction Potato (Solanum tuberosum L.), the fourth most important food crop in the world, is affected by several viral pathogens with potato virus Y (PVY) having the greatest economic impact. At least nine biologically distinct variants of PVY are known to infect potato. These include the relatively new recombinant types named PVY-NTN and PVYN-Wi, which induce tuber necrosis in susceptible cultivars. To date, the molecular plant-virus interactions underlying this pathogenicity have not been fully characterized. We hypothesized that this necrotic behavior is supported by transcriptional and functional signatures that are unique to PVY-NTN and PVYN-Wi. Methods To test this hypothesis, transcriptional responses of cv. Russet Burbank, a PVY susceptible cultivar, to three PVY strains PVY-O, PVY-NTN, and PVYN-Wi were studied using mRNA-Seq. A haploid-resolved genome assembly for tetraploid potato was used for bioinformatics analysis. Results The study revealed 36 GO terms and nine KEGG 24 pathways that overlapped across the three PVY strains, making them generic features of PVY susceptibility in potato. Ten GO terms and three KEGG pathways enriched for PVY-NTN and PVYN-Wi only, which made them candidate functional signatures associated with PVY-induced tuber necrosis in potato. In addition, five other pathways were enriched for PVYNTN or PVYN-Wi. One carbon pool by folate was enriched exclusively in response to PVY-NTN infection; PVYN-Wi infection specifically impacted cutin, suberine and wax biosynthesis, phenylalanine metabolism, phenylalanine, tyrosine and tryptophan biosynthesis, and monoterpenoid biosynthesis. Discussion Results suggest that PVYN-Wi-induced necrosis may be mechanistically distinguishable from that of PVY-NTN. Our study provides a basis for understanding the mechanism underlying the development of PVY-induced tuber necrosis in potato.
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Affiliation(s)
- Richard Manasseh
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
| | - Vidyasagar Sathuvalli
- Hermiston Agricultural Research and Extension Center, Oregon State University, Hermiston, OR, United States
| | - Hanu R. Pappu
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
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Shah SMA, Khojasteh M, Wang Q, Haq F, Xu X, Li Y, Zou L, Osdaghi E, Chen G. Comparative Transcriptomic Analysis of Wheat Cultivars in Response to Xanthomonas translucens pv. cerealis and Its T2SS, T3SS, and TALEs Deficient Strains. PHYTOPATHOLOGY 2023; 113:2073-2082. [PMID: 37414408 DOI: 10.1094/phyto-02-23-0049-sa] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
Xanthomonas translucens pv. cerealis causes bacterial leaf streak disease on small grain cereals. Type II and III secretion systems (T2SS and T3SS) play a pivotal role in the pathogenicity of the bacterium, while no data are available on the transcriptomic profile of wheat cultivars infected with either wild type (WT) or mutants of the pathogen. In this study, WT, TAL-effector mutants, and T2SS/T3SS mutants of X. translucens pv. cerealis strain NXtc01 were evaluated for their effect on the transcriptomic profile of two wheat cultivars, 'Chinese Spring' and 'Yangmai-158', using Illumina RNA-sequencing technology. RNA-Seq data showed that the number of differentially expressed genes (DEGs) was higher in Yangmai-158 than in Chinese Spring, suggesting higher susceptibility of Yangmai-158 to the pathogen. In T2SS, most suppressed DEGs were related to transferase, synthase, oxidase, WRKY, and bHLH transcription factors. The gspD mutants showed significantly decreased disease development in wheat, suggesting an active contribution of T2SS in virulence. Moreover, the gspD mutant restored full virulence and its multiplication in planta by addition of gspD in trans. In the T3SS-deficient strain, downregulated DEGs were associated with cytochrome, peroxidases, kinases, phosphatases, WRKY, and ethylene-responsive transcription factors. In contrast, upregulated DEGs were trypsin inhibitors, cell number regulators, and calcium transporter. Transcriptomic analyses coupled with quantitative real-time-PCR indicated that some genes are upregulated in Δtal1/Δtal2 compared with the tal-free strain, but no direct interaction was observed. These results provide novel insight into wheat transcriptomes in response to X. translucens infection and pave the way for understanding host-pathogen interactions.
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Affiliation(s)
- Syed Mashab Ali Shah
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
- School of Agriculture and Biology/Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Moein Khojasteh
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
- School of Agriculture and Biology/Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qi Wang
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
- School of Agriculture and Biology/Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fazal Haq
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
- School of Agriculture and Biology/Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Xiameng Xu
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
- School of Agriculture and Biology/Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ying Li
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
- School of Agriculture and Biology/Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lifang Zou
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
- School of Agriculture and Biology/Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ebrahim Osdaghi
- Department of Plant Protection, University of Tehran, Karaj, Iran
| | - Gongyou Chen
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
- School of Agriculture and Biology/Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, Shanghai Jiao Tong University, Shanghai 200240, China
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Ahn E, Prom LK, Magill C. Multi-Trait Genome-Wide Association Studies of Sorghum bicolor Regarding Resistance to Anthracnose, Downy Mildew, Grain Mold and Head Smut. Pathogens 2023; 12:779. [PMID: 37375469 DOI: 10.3390/pathogens12060779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/18/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Multivariate linear mixed models (mvLMMs) are widely applied for genome-wide association studies (GWAS) to detect genetic variants affecting multiple traits with correlations and/or different plant growth stages. Subsets of multiple sorghum populations, including the Sorghum Association Panel (SAP), the Sorghum Mini Core Collection and the Senegalese sorghum population, have been screened against various sorghum diseases such as anthracnose, downy mildew, grain mold and head smut. Still, these studies were generally performed in a univariate framework. In this study, we performed GWAS based on the principal components of defense-related multi-traits against the fungal diseases, identifying new potential SNPs (S04_51771351, S02_66200847, S09_47938177, S08_7370058, S03_72625166, S07_17951013, S04_66666642 and S08_51886715) associated with sorghum's defense against these diseases.
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Affiliation(s)
- Ezekiel Ahn
- USDA-ARS Plant Science Research Unit, St. Paul, MN 55108, USA
| | - Louis K Prom
- USDA-ARS Southern Plains Agricultural Research Center, College Station, TX 77845, USA
| | - Clint Magill
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA
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Ma Y, Yu H, Lu Y, Gao S, Fatima M, Ming R, Yue J. Transcriptome analysis of sugarcane reveals rapid defense response of SES208 to Xanthomonas albilineans in early infection. BMC PLANT BIOLOGY 2023; 23:52. [PMID: 36694139 PMCID: PMC9872421 DOI: 10.1186/s12870-023-04073-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 01/18/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Diseases are the major factor affecting the quality and yield of sugarcane during its growth and development. However, our knowledge about the factors regulating disease responses remain limited. The present study focuses on identifying genes regulating transcriptional mechanisms responsible for resistance to leaf scald caused by Xanthomonas albilineans in S. spontaneum and S. officinarum. RESULTS After inoculation of the two sugarcane varieties SES208 (S. spontaneum) and LA Purple (S. officinarum) with Xanthomonas albilineans, SES208 exhibited significantly greater resistance to leaf scald caused by X. albilineans than did LA Purple. Using transcriptome analysis, we identified a total of 4323 and 1755 differentially expressed genes (DEGs) in inoculated samples of SES208 and LA Purple, respectively. Significantly, 262 DEGs were specifically identified in SES208 that were enriched for KEGG pathway terms such as plant-pathogen interaction, MAPK signaling pathway, and plant hormone signal transduction. Furthermore, we built a transcriptional regulatory co-expression network that specifically identified 16 and 25 hub genes in SES208 that were enriched for putative functions in plant-pathogen interactions, MAPK signaling, and plant hormone signal transduction. All of these essential genes might be significantly involved in resistance-regulating responses in SES208 after X. albilineans inoculation. In addition, we found allele-specific expression in SES208 that was associated with the resistance phenotype of SES208 when infected by X. albilineans. After infection with X. albilineans, a great number of DEGs associated with the KEGG pathways 'phenylpropanoid biosynthesis' and 'flavonoid biosynthesis' exhibited significant expression changes in SES208 compared to LA Purple that might contribute to superior leaf scald resistance in SES208. CONCLUSIONS We provided the first systematical transcriptome map that the higher resistance of SES208 is associated with and elicited by the rapid activation of multiple clusters of defense response genes after infection by X. albilineans and not merely due to changes in the expression of genes generically associated with stress resistance. These results will serve as the foundation for further understanding of the molecular mechanisms of resistance against X. albilineans in S. spontaneum.
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Affiliation(s)
- Yaying Ma
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hongying Yu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Yijing Lu
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Sanji Gao
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Mahpara Fatima
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ray Ming
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Jingjing Yue
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Ishida K, Noutoshi Y. The function of the plant cell wall in plant-microbe interactions. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 192:273-284. [PMID: 36279746 DOI: 10.1016/j.plaphy.2022.10.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 09/07/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
The plant cell wall is an interface of plant-microbe interactions. The ability of microbes to decompose cell wall polysaccharides contributes to microbial pathogenicity. Plants have evolved mechanisms to prevent cell wall degradation. However, the role of the cell wall in plant-microbe interactions is not well understood. Here, we discuss four functions of the plant cell wall-physical defence, storage of antimicrobial compounds, production of cell wall-derived elicitors, and provision of carbon sources-in the context of plant-microbe interactions. In addition, we discuss the four families of cell surface receptors associated with plant cell walls (malectin-like receptor kinase family, wall-associated kinase family, leucine-rich repeat receptor-like kinase family, and lysin motif receptor-like kinase family) that have been the subject of several important studies in recent years. This review summarises the findings on both plant cell wall and plant immunity, improving our understanding and may provide impetus to various researchers.
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Affiliation(s)
- Konan Ishida
- Department of Biochemistry, University of Cambridge, Hopkins Building, The Downing Site, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Yoshiteru Noutoshi
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan.
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Vranic M, Perochon A, Benbow H, Doohan FM. Comprehensive analysis of pathogen-responsive wheat NAC transcription factors: new candidates for crop improvement. G3 (BETHESDA, MD.) 2022; 12:jkac247. [PMID: 36130261 PMCID: PMC9635653 DOI: 10.1093/g3journal/jkac247] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 08/03/2022] [Indexed: 11/26/2022]
Abstract
Wheat NAC (TaNAC) transcription factors are important regulators of stress responses and developmental processes. This study proposes a new TaNAC nomenclature and identified defense-associated TaNACs based on the analysis of RNA-sequencing datasets of wheat tissue infected with major fungal pathogens. A total of 146 TaNACs were pathogen-responsive, of which 52 were orthologous with functionally characterized defense-associated NACs from barley, rice, and Arabidopsis, as deduced via phylogenetic analysis. Next, we focused on the phylogenetic relationship of the pathogen-responsive TaNACs and their expression profiles in healthy and diseased tissues. Three subfamilies ("a," "e," and "f") were significantly enriched in pathogen-responsive TaNACs, of which the majority were responsive to at least 2 pathogens (universal pathogen response). Uncharacterized TaNACs from subfamily "a" enriched with defense-associated NACs are promising candidates for functional characterization in pathogen defense. In general, pathogen-responsive TaNACs were expressed in at least 2 healthy organs. Lastly, we showed that the wheat NAM domain is significantly divergent in sequence in subfamilies "f," "g," and "h" based on HMMER and motif analysis. New protein motifs were identified in both the N- and C-terminal parts of TaNACs. Three of those identified in the C-terminal part were linked to pathogen responsiveness of the TaNACs and 2 were linked to expression in grain tissue. Future studies should benefit from this comprehensive in silico analysis of pathogen-responsive TaNACs as a basis for selecting the most promising candidates for functional validation and crop improvement.
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Affiliation(s)
- Monika Vranic
- UCD School of Biology and Environmental Science and Earth Institute, College of Science, University College Dublin, Dublin 4, Ireland
| | - Alexandre Perochon
- UCD School of Biology and Environmental Science and Earth Institute, College of Science, University College Dublin, Dublin 4, Ireland
| | - Harriet Benbow
- UCD School of Biology and Environmental Science and Earth Institute, College of Science, University College Dublin, Dublin 4, Ireland
| | - Fiona M Doohan
- UCD School of Biology and Environmental Science and Earth Institute, College of Science, University College Dublin, Dublin 4, Ireland
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Isoprene Emission Influences the Proteomic Profile of Arabidopsis Plants under Well-Watered and Drought-Stress Conditions. Int J Mol Sci 2022; 23:ijms23073836. [PMID: 35409196 PMCID: PMC8998555 DOI: 10.3390/ijms23073836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/25/2022] [Accepted: 03/29/2022] [Indexed: 02/06/2023] Open
Abstract
Isoprene is a small lipophilic molecule synthesized in plastids and abundantly released into the atmosphere. Isoprene-emitting plants are better protected against abiotic stresses, but the mechanism of action of isoprene is still under debate. In this study, we compared the physiological responses and proteomic profiles of Arabidopsis which express the isoprene synthase (ISPS) gene and emit isoprene with those of non-emitting plants under both drought-stress (DS) and well-watered (WW) conditions. We aimed to investigate whether isoprene-emitting plants displayed a different proteomic profile that is consistent with the metabolic changes already reported. Only ISPS DS plants were able to maintain the same photosynthesis and fresh weight of WW plants. LC-MS/MS-based proteomic analysis revealed changes in protein abundance that were dependent on the capacity for emitting isoprene in addition to those caused by the DS. The majority of the proteins changed in response to the interaction between DS and isoprene emission. These include proteins that are associated with the activation of secondary metabolisms leading to ABA, trehalose, and proline accumulations. Overall, our proteomic data suggest that isoprene exerts its protective mechanism at different levels: under drought stress, isoprene affects the abundance of chloroplast proteins, confirming a strong direct or indirect antioxidant action and also modulates signaling and hormone pathways, especially those controlling ABA synthesis. Unexpectedly, isoprene also alters membrane trafficking.
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Zaidi S, Bhardwaj T, Somvanshi P, Khan AU. Proteomic Characterization and Target Identification Against Streptococcus mutans Under Bacitracin Stress Conditions Using LC-MS and Subtractive Proteomics. Protein J 2022; 41:166-178. [PMID: 34989956 PMCID: PMC8733428 DOI: 10.1007/s10930-021-10038-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/25/2021] [Indexed: 11/24/2022]
Abstract
The aim of the present study, is to identify potential targets against the highly pathogenic bacteria Streptococcus mutans that causes dental caries as well as the deadly infection of endocarditis. The powerful and highly sensitive technique of liquid chromatography-mass spectrometry (LC–MS/MS) identified 321 proteins of S. mutans when grown under stressful conditions induced by the antibiotic bacitracin. These 321 proteins were subjected to the insilico method of subtractive proteomics to screen out potential targets by utilizing different analyses like CD-HIT, non-homologous sequence screening, KEGG pathway, essentiality screening, gut-flora non-homology, and codon usage analysis. A database of essential proteins was employed to find sequence homology of non-paralogous proteins to determine proteins which are essential for bacterial survival. Cellular localization analysis of the selected proteins was done to localize them inside the cell along with physico-chemical characterization and druggability analysis. Using computational tools, 22 proteins out of 321, that are functionally distinguishable from their human counterparts and passed the criterion of a potential therapeutic candidate were identified. The selected proteins comprise central energy metabolic proteins, virulence factors, proteins of the sortase family, and essentiality factors. The presented analyses identified proteins of the sortase family, which appear as key therapeutic targets against caries infection. These proteins regulate a number of virulence factors, thus can be simultaneously inhibited to obstruct multiple virulence pathways.
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Affiliation(s)
- Sahar Zaidi
- Medical Microbiology and Molecular Biology Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, UP, 202002, India
| | - Tulika Bhardwaj
- School of Computational & Integrative Sciences (SC&IS), Jawaharlal Nehru University, New Delhi, 110067, India
| | - Pallavi Somvanshi
- School of Computational & Integrative Sciences (SC&IS), Jawaharlal Nehru University, New Delhi, 110067, India.,Special Centre of Systems Medicine (SCSM), Jawaharlal Nehru University, New Delhi, 110067, India
| | - Asad U Khan
- Medical Microbiology and Molecular Biology Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, UP, 202002, India.
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Dynamic Diversity of NLR Genes in Triticum and Mining of Promising NLR Alleles for Disease Resistance. Curr Issues Mol Biol 2021; 43:965-977. [PMID: 34449534 PMCID: PMC8929112 DOI: 10.3390/cimb43020069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/12/2021] [Accepted: 08/14/2021] [Indexed: 11/17/2022] Open
Abstract
Bread wheat is an essential crop with the second-highest global production after maize. Currently, wheat diseases are a serious threat to wheat production. Therefore, efficient breeding for disease resistance is extremely urgent in modern wheat. Here, we identified 2012 NLR genes from hexaploid wheat, and Ks values of paired syntenic NLRs showed a significant peak at 3.1–6.3 MYA, which exactly coincided with the first hybridization event between A and B genome lineages at ~5.5 MYA. We provided a landscape of dynamic diversity of NLRs from Triticum and Aegilops and found that NLR genes have higher diversity in wild progenitors and relatives. Further, most NLRs had opposite diversity patterns between genic and 2 Kb-promoter regions, which might respectively link sub/neofunctionalization and loss of duplicated NLR genes. Additionally, we identified an alien introgression of chromosome 4A in tetraploid emmer wheat, which was similar to that in hexaploid wheat. Transcriptome data from four experiments of wheat disease resistance helped to profile the expression pattern of NLR genes and identified promising NLRs involved in broad-spectrum disease resistance. Our study provided insights into the diversity evolution of NLR genes and identified beneficial NLRs to deploy into modern wheat in future wheat disease-resistance breeding.
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Vannini C, Domingo G, Fiorilli V, Seco DG, Novero M, Marsoni M, Wisniewski-Dye F, Bracale M, Moulin L, Bonfante P. Proteomic analysis reveals how pairing of a Mycorrhizal fungus with plant growth-promoting bacteria modulates growth and defense in wheat. PLANT, CELL & ENVIRONMENT 2021; 44:1946-1960. [PMID: 33675052 DOI: 10.1111/pce.14039] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 02/17/2021] [Accepted: 02/23/2021] [Indexed: 06/12/2023]
Abstract
Plants rely on their microbiota for improving the nutritional status and environmental stress tolerance. Previous studies mainly focused on bipartite interactions (a plant challenged by a single microbe), while plant responses to multiple microbes have received limited attention. Here, we investigated local and systemic changes induced in wheat by two plant growth-promoting bacteria (PGPB), Azospirillum brasilense and Paraburkholderia graminis, either alone or together with an arbuscular mycorrhizal fungus (AMF). We conducted phenotypic, proteomic, and biochemical analyses to investigate bipartite (wheat-PGPB) and tripartite (wheat-PGPB-AMF) interactions, also upon a leaf pathogen infection. Results revealed that only AMF and A. brasilense promoted plant growth by activating photosynthesis and N assimilation which led to increased glucose and amino acid content. The bioprotective effect of the PGPB-AMF interactions on infected wheat plants depended on the PGPB-AMF combinations, which caused specific phenotypic and proteomic responses (elicitation of defense related proteins, immune response and jasmonic acid biosynthesis). In the whole, wheat responses strongly depended on the inoculum composition (single vs. multiple microbes) and the investigated organs (roots vs. leaf). Our findings showed that AMF is the best-performing microbe, suggesting its presence as the crucial one for synthetic microbial community development.
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Affiliation(s)
- Candida Vannini
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, Varese, Italy
| | - Guido Domingo
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, Varese, Italy
| | - Valentina Fiorilli
- Department of Life Sciences and Systems Biology, Università degli Studi di Torino, Torino, Italy
| | | | - Mara Novero
- Department of Life Sciences and Systems Biology, Università degli Studi di Torino, Torino, Italy
| | - Milena Marsoni
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, Varese, Italy
| | - Florence Wisniewski-Dye
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgroSup, UMR Ecologie Microbienne, Villeurbanne, France
| | - Marcella Bracale
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, Varese, Italy
| | - Lionel Moulin
- IRD, CIRAD, University of Montpellier, IPME, Montpellier, France
| | - Paola Bonfante
- Department of Life Sciences and Systems Biology, Università degli Studi di Torino, Torino, Italy
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Deng L, Handler DCL, Multari DH, Haynes PA. Comparison of protein and peptide fractionation approaches in protein identification and quantification from Saccharomyces cerevisiae. J Chromatogr B Analyt Technol Biomed Life Sci 2021; 1162:122453. [PMID: 33279813 DOI: 10.1016/j.jchromb.2020.122453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 11/09/2020] [Accepted: 11/12/2020] [Indexed: 11/29/2022]
Abstract
Shotgun proteomics is a high-throughput technology which has been developed with the aim of investigating the maximum number of proteins in cells in a given experiment. However, protein discovery and data generation vary in depth and coverage when different technical strategies are selected. In this study, three different sample preparation approaches, and peptide or protein fractionation methods, were applied to identify and quantify proteins from log-phase yeast lysate: sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), filter-aided sample preparation coupled with gas phase fractionation (FASP-GPF), and FASP - high pH reversed phase fractionation (HpH). Fractions were initially analyzed and compared using nanoflow liquid chromatography - tandem mass spectrometry (nanoLC-MS/MS) employing data dependent acquisition on a linear ion trap instrument. The number of fractions and analytical replicates was adjusted so that each experiment used a similar amount of mass spectrometric instrument time. A second set of experiments was performed, comparing FASP-GPF, SDS-PAGE and FASP-HpH using a Q Exactive Orbitrap mass spectrometer. Compared with results from the linear ion trap mass spectrometer, the use of a Q Exactive Orbitrap mass spectrometer enabled a substantial increase in protein identifications, and an even greater increase in peptide identifications. This shows that the main advantage of using the higher resolution instrument is in increased proteome coverage. A total of 1035, 1357 and 2134 proteins were separately identified by FASP-GPF, SDS-PAGE and FASP-HpH. Combining results from the Orbitrap experiments, there were a total of 2269 proteins found, with 94% of them identified using the FASP-HpH method. Therefore, the FASP-HpH method is the optimal choice among these approaches, when applied to this type of sample.
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Affiliation(s)
- Liting Deng
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
| | - David C L Handler
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
| | - Dylan H Multari
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
| | - Paul A Haynes
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia; Biomolecular Discovery Research Centre, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia.
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Balkenhol J, Kaltdorf KV, Mammadova-Bach E, Braun A, Nieswandt B, Dittrich M, Dandekar T. Comparison of the central human and mouse platelet signaling cascade by systems biological analysis. BMC Genomics 2020; 21:897. [PMID: 33353544 PMCID: PMC7756956 DOI: 10.1186/s12864-020-07215-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 11/08/2020] [Indexed: 12/12/2022] Open
Abstract
Background Understanding the molecular mechanisms of platelet activation and aggregation is of high interest for basic and clinical hemostasis and thrombosis research. The central platelet protein interaction network is involved in major responses to exogenous factors. This is defined by systemsbiological pathway analysis as the central regulating signaling cascade of platelets (CC). Results The CC is systematically compared here between mouse and human and major differences were found. Genetic differences were analysed comparing orthologous human and mouse genes. We next analyzed different expression levels of mRNAs. Considering 4 mouse and 7 human high-quality proteome data sets, we identified then those major mRNA expression differences (81%) which were supported by proteome data. CC is conserved regarding genetic completeness, but we observed major differences in mRNA and protein levels between both species. Looking at central interactors, human PLCB2, MMP9, BDNF, ITPR3 and SLC25A6 (always Entrez notation) show absence in all murine datasets. CC interactors GNG12, PRKCE and ADCY9 occur only in mice. Looking at the common proteins, TLN1, CALM3, PRKCB, APP, SOD2 and TIMP1 are higher abundant in human, whereas RASGRP2, ITGB2, MYL9, EIF4EBP1, ADAM17, ARRB2, CD9 and ZYX are higher abundant in mouse. Pivotal kinase SRC shows different regulation on mRNA and protein level as well as ADP receptor P2RY12. Conclusions Our results highlight species-specific differences in platelet signaling and points of specific fine-tuning in human platelets as well as murine-specific signaling differences. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07215-4.
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Affiliation(s)
- Johannes Balkenhol
- Functional Genomics and Systems Biology Group, Department of Bioinformatics, Biocenter, Am Hubland, University of Würzburg, D-97074, Würzburg, Germany
| | - Kristin V Kaltdorf
- Functional Genomics and Systems Biology Group, Department of Bioinformatics, Biocenter, Am Hubland, University of Würzburg, D-97074, Würzburg, Germany
| | - Elmina Mammadova-Bach
- Institute of Experimental Biomedicine, University Hospital and Rudolf Virchow Centre, University of Würzburg, Würzburg, Germany.,Present address: Division of Nephrology, Department of Medicine IV, Hospital of the Ludwig, Maximilian University of Munich, D-80336, Munich, Germany
| | - Attila Braun
- Member of the German Center for Lung Research (DZL), Walther-Straub-Institute for Pharmacology and Toxicology, Ludwig-Maximilians University Munich, Munich, Germany
| | - Bernhard Nieswandt
- Institute of Experimental Biomedicine, University Hospital and Rudolf Virchow Centre, University of Würzburg, Würzburg, Germany
| | - Marcus Dittrich
- Functional Genomics and Systems Biology Group, Department of Bioinformatics, Biocenter, Am Hubland, University of Würzburg, D-97074, Würzburg, Germany.,Dept of Genetics, Biocenter, Am Hubland, University of Würzburg, Am Hubland, D 97074, Würzburg, Germany
| | - Thomas Dandekar
- Functional Genomics and Systems Biology Group, Department of Bioinformatics, Biocenter, Am Hubland, University of Würzburg, D-97074, Würzburg, Germany.
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Jiao Z, Zhu X, Li H, Liu Z, Huang X, Wu N, An J, Li J, Zhang J, Jiang Y, Li Q, Qi Z, Niu J. Cytological and molecular characterizations of a novel 2A nullisomic line derived from a widely-grown wheat cultivar Zhoumai 18 conferring male sterility. PeerJ 2020; 8:e10275. [PMID: 33194433 PMCID: PMC7605228 DOI: 10.7717/peerj.10275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 10/08/2020] [Indexed: 11/20/2022] Open
Abstract
A dwarf, multi-pistil and male sterile dms mutant was previously reported by us. However, the genetic changes in this dms are unclear. To examine the genetic changes, single nucleotide polymorphism (SNP) association, chromosome counting, and high-resolution chromosome fluorescence in situ hybridization (FISH) techniques were employed. By comparing tall plants (T) with dwarf plants (D) in the offspring of dms mutant plants, SNP association analysis indicated that most SNPs were on chromosome 2A. There were three types in offspring of dms plants, with 42, 41 and 40 chromosomes respectively. High-resolution chromosome painting analysis demonstrated that T plants had all 42 wheat chromosomes; the medium plants (M) had 41 chromosomes, lacking one chromosome 2A; while D plants had 40 wheat chromosomes, and lacked both 2A chromosomes. These data demonstrated that dms resulted from a loss of chromosome 2A. We identified 23 genes on chromosome 2A which might be involved in the development of stamens or pollen grains. These results lay a solid foundation for further analysis of the molecular mechanisms of wheat male sterility. Because D plants can be used as a female parent to cross with other wheat genotypes, dms is a unique germplasm for any functional study of chromosome 2A and wheat breeding specifically targeting genes on 2A.
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Affiliation(s)
- Zhixin Jiao
- Henan Agricultural University, National Centre of Engineering and Technological Research for Wheat / National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, Henan, China
| | - Xinxin Zhu
- Henan Agricultural University, National Centre of Engineering and Technological Research for Wheat / National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, Henan, China
| | - Huijuan Li
- Henan Agricultural University, National Centre of Engineering and Technological Research for Wheat / National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, Henan, China
| | - Zhitao Liu
- Nanjing Agricultural University, State key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing, Jiangsu, China.,Sichuan Academy of Agricultural Sciences, Crop Research Institue, Chengdu, Sichuan, China
| | - Xinyi Huang
- Nanjing Agricultural University, State key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing, Jiangsu, China
| | - Nan Wu
- Nanjing Agricultural University, State key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing, Jiangsu, China
| | - Junhang An
- Henan Agricultural University, National Centre of Engineering and Technological Research for Wheat / National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, Henan, China
| | - Junchang Li
- Henan Agricultural University, National Centre of Engineering and Technological Research for Wheat / National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, Henan, China
| | - Jing Zhang
- Henan Agricultural University, National Centre of Engineering and Technological Research for Wheat / National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, Henan, China
| | - Yumei Jiang
- Henan Agricultural University, National Centre of Engineering and Technological Research for Wheat / National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, Henan, China
| | - Qiaoyun Li
- Henan Agricultural University, National Centre of Engineering and Technological Research for Wheat / National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, Henan, China
| | - Zengjun Qi
- Nanjing Agricultural University, State key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing, Jiangsu, China
| | - Jishan Niu
- Henan Agricultural University, National Centre of Engineering and Technological Research for Wheat / National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, Henan, China
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Tao GY, Ramakrishnan M, Vinod KK, Yrjälä K, Satheesh V, Cho J, Fu Y, Zhou M. Multi-omics analysis of cellular pathways involved in different rapid growth stages of moso bamboo. TREE PHYSIOLOGY 2020; 40:1487-1508. [PMID: 32705116 DOI: 10.1093/treephys/tpaa090] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 04/29/2020] [Accepted: 07/09/2020] [Indexed: 06/11/2023]
Abstract
Moso bamboo (Phyllostachys edulis (Carriere) J. Houzeau) is a rapidly growing grass of industrial and ecological importance. However, the molecular mechanisms of its remarkable growth are not well understood. In this study, we investigated the early-stage growth of moso bamboo shoots and defined three different growth stages based on histological and biochemical analyses, namely, starting of cell division (SD), rapid division (RD) and rapid elongation (RE). Further analyses on potentially relevant cellular pathways in these growth stages using multi-omics approaches such as transcriptomics and proteomics revealed the involvement of multiple cellular pathways, including DNA replication, repair and ribosome biogenesis. A total of 8045 differentially expressed genes (DEGs) and 1053 differentially expressed proteins (DEPs) were identified in our analyses. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses of detected DEGs identified several key biological pathways such as phytohormone metabolism, signal transduction, cell wall development and carbohydrate metabolism. The comparative analysis of proteins displayed that a total of 213 DEPs corresponded with DEGs and 3 significant expression profiles that could be promoting the fast growth of bamboo internodes. Moreover, protein-protein interaction network prediction analysis is suggestive of the involvement of five major proteins of signal transduction, DNA synthesis and RNA transcription, and may act as key elements responsible for the rapid shoot growth. Our work exploits multi-omics and bioinformatic approaches to unfurl the complexity of molecular networks involved in the rapid growth of moso bamboo and opens up questions related to the interactions between the functions played by individual molecular pathway.
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Affiliation(s)
- Gui-Yun Tao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
- Zhejiang Provincial Collaborative Innovation Centre for Bamboo Resources and High-efficiency Utilization, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
- The State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Xiangshan, Haidian District, Beijing, China
- Research Institute of Forestry, Chinese Academy of Forestry, Xiangshan, Haidian District, Beijing, China
| | - Muthusamy Ramakrishnan
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
| | | | - Kim Yrjälä
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
- Department of Forest Sciences, University of Helsinki, Helsinki P.O. Box 27 00014, Finland
| | - Viswanathan Satheesh
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jungnam Cho
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science, Chinese Academy of Sciences, Shanghai 200032, China
| | - Ying Fu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
- Zhejiang Provincial Collaborative Innovation Centre for Bamboo Resources and High-efficiency Utilization, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
| | - Mingbing Zhou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
- Zhejiang Provincial Collaborative Innovation Centre for Bamboo Resources and High-efficiency Utilization, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
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16
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Ntambo MS, Meng JY, Rott PC, Henry RJ, Zhang HL, Gao SJ. Comparative Transcriptome Profiling of Resistant and Susceptible Sugarcane Cultivars in Response to Infection by Xanthomonas albilineans. Int J Mol Sci 2019; 20:ijms20246138. [PMID: 31817492 PMCID: PMC6940782 DOI: 10.3390/ijms20246138] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/26/2019] [Accepted: 12/03/2019] [Indexed: 12/20/2022] Open
Abstract
Sugarcane (Saccharum spp. hybrids) is a major source of sugar and renewable bioenergy crop worldwide and suffers serious yield losses due to many pathogen infections. Leaf scald caused by Xanthomonas albilineans is a major bacterial disease of sugarcane in most sugarcane-planting countries. The molecular mechanisms of resistance to leaf scald in this plant are, however, still unclear. We performed a comparative transcriptome analysis between resistant (LCP 85-384) and susceptible (ROC20) sugarcane cultivars infected by X. albilineans using the RNA-seq platform. 24 cDNA libraries were generated with RNA isolated at four time points (0, 24, 48, and 72 h post inoculation) from the two cultivars with three biological replicates. A total of 105,783 differentially expressed genes (DEGs) were identified in both cultivars and the most upregulated and downregulated DEGs were annotated for the processes of the metabolic and single-organism categories, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the 7612 DEGs showed that plant-pathogen interaction, spliceosome, glutathione metabolism, protein processing in endoplasmic reticulum, and plant hormone signal transduction contributed to sugarcane's response to X. albilineans infection. Subsequently, relative expression levels of ten DEGs determined by quantitative reverse transcription-PCR (qRT-PCR), in addition to RNA-Seq data, indicated that different plant hormone (auxin and ethylene) signal transduction pathways play essential roles in sugarcane infected by X. albilineans. In conclusion, our results provide, for the first time, valuable information regarding the transcriptome changes in sugarcane in response to infection by X. albilineans, which contribute to the understanding of the molecular mechanisms underlying the interactions between sugarcane and this pathogen and provide important clues for further characterization of leaf scald resistance in sugarcane.
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Affiliation(s)
- Mbuya Sylvain Ntambo
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.N.); (H.-L.Z.)
| | - Jian-Yu Meng
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.N.); (H.-L.Z.)
| | - Philippe C. Rott
- BGPI, INRA, CIRAD, SupAgro, Univ Montpellier, 34398 Montpellier, France;
| | - Robert J. Henry
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072, Australia;
| | - Hui-Li Zhang
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.N.); (H.-L.Z.)
| | - San-Ji Gao
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.N.); (H.-L.Z.)
- Correspondence:
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Sun W, Zhu Q, Yan L, Shao F. Mesenchymal stem cells alleviate acute kidney injury via miR-107-mediated regulation of ribosomal protein S19. ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:765. [PMID: 32042781 DOI: 10.21037/atm.2019.11.89] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Background The characteristics of mesenchymal stem cells (MSCs) in the repair of acute kidney injury (AKI) have been extensively studied. However, some potential molecular mechanisms remain indistinct. The aim of this study was to combine published microRNA (miRNA) transcriptional profiling with quantitative proteomic analyses to reveal specific miRNAs or genes for MSC-based therapy in AKI. Methods Transcriptome data containing significantly changed miRNAs in renal tissue from AKI mice treated with and without MSCs were downloaded. Proteomics resources were downloaded from a human proximal renal tubule cell line (HK-2) that served as a good in vitro model for AKI treated with MSCs. We connected the proteomics data with transcriptional records based on miRNA function. Differentially expressed genes (DEGs) were sorted. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was conducted, and protein-protein interaction (PPI) chains were formed. The genes identified in the analyses were verified in a cisplatin-induced AKI rat model and in HK-2 cells exposed to cisplatin and cocultured with MSCs. Results A total of 207 specific DEGs were sorted. The ribosomal pathway was identified in pathway enrichment, and ribosomal proteins were identified from the PPI network complex. The targeting of the microRNAs, miR-107 to RPS19, was directly verified by the dual-luciferase method. miR-107 knockdown induced RPS19 expression, protected HK-2 cells from cisplatin-induced apoptosis, and promoted cell proliferation. Conclusions By analyzing comprehensive bioinformatics data, we have confirmed the DEGs and pathways in AKI treated with MSCs. Bone marrow-derived MSCs reduce miR-107 expression and increase RPS19 expression by repressing the proliferation of cisplatin-induced AKI cells and initiating apoptosis.
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Affiliation(s)
- Weinan Sun
- Department of Nephrology, People's Hospital of Zhengzhou University, He'nan Provincial People's Hospital, He'nan Provincial Key Laboratory of Kidney Disease and Immunology, Zhengzhou 450003, China
| | - Qing Zhu
- Department of Nephrology, People's Hospital of Zhengzhou University, He'nan Provincial People's Hospital, He'nan Provincial Key Laboratory of Kidney Disease and Immunology, Zhengzhou 450003, China
| | - Lei Yan
- Department of Nephrology, People's Hospital of Zhengzhou University, He'nan Provincial People's Hospital, He'nan Provincial Key Laboratory of Kidney Disease and Immunology, Zhengzhou 450003, China
| | - Fengmin Shao
- Department of Nephrology, People's Hospital of Zhengzhou University, He'nan Provincial People's Hospital, He'nan Provincial Key Laboratory of Kidney Disease and Immunology, Zhengzhou 450003, China
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Lenk M, Wenig M, Bauer K, Hug F, Knappe C, Lange B, Häußler F, Mengel F, Dey S, Schäffner A, Vlot AC. Pipecolic Acid Is Induced in Barley upon Infection and Triggers Immune Responses Associated with Elevated Nitric Oxide Accumulation. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:1303-1313. [PMID: 31194615 DOI: 10.1094/mpmi-01-19-0013-r] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Pipecolic acid (Pip) is an essential component of systemic acquired resistance, priming resistance in Arabidopsis thaliana against (hemi)biotrophic pathogens. Here, we studied the potential role of Pip in bacteria-induced systemic immunity in barley. Exudates of barley leaves infected with the systemic immunity-inducing pathogen Pseudomonas syringae pv. japonica induced immune responses in A. thaliana. The same leaf exudates contained elevated Pip levels compared with those of mock-treated barley leaves. Exogenous application of Pip induced resistance in barley against the hemibiotrophic bacterial pathogen Xanthomonas translucens pv. cerealis. Furthermore, both a systemic immunity-inducing infection and exogenous application of Pip enhanced the resistance of barley against the biotrophic powdery mildew pathogen Blumeria graminis f. sp. hordei. In contrast to a systemic immunity-inducing infection, Pip application did not influence lesion formation by a systemically applied inoculum of the necrotrophic fungus Pyrenophora teres. Nitric oxide (NO) levels in barley leaves increased after Pip application. Furthermore, X. translucens pv. cerealis induced the accumulation of superoxide anion radicals and this response was stronger in Pip-pretreated compared with mock-pretreated plants. Thus, the data suggest that Pip induces barley innate immune responses by triggering NO and priming reactive oxygen species accumulation.
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Affiliation(s)
- Miriam Lenk
- Helmholtz Zentrum München, Department of Environmental Science, Institute of Biochemical Plant Pathology, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Marion Wenig
- Helmholtz Zentrum München, Department of Environmental Science, Institute of Biochemical Plant Pathology, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Kornelia Bauer
- Helmholtz Zentrum München, Department of Environmental Science, Institute of Biochemical Plant Pathology, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Florian Hug
- Helmholtz Zentrum München, Department of Environmental Science, Institute of Biochemical Plant Pathology, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Claudia Knappe
- Helmholtz Zentrum München, Department of Environmental Science, Institute of Biochemical Plant Pathology, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Birgit Lange
- Helmholtz Zentrum München, Department of Environmental Science, Institute of Biochemical Plant Pathology, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Finni Häußler
- Helmholtz Zentrum München, Department of Environmental Science, Institute of Biochemical Plant Pathology, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Felicitas Mengel
- Helmholtz Zentrum München, Department of Environmental Science, Institute of Biochemical Plant Pathology, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Sanjukta Dey
- Helmholtz Zentrum München, Department of Environmental Science, Institute of Biochemical Plant Pathology, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Anton Schäffner
- Helmholtz Zentrum München, Department of Environmental Science, Institute of Biochemical Plant Pathology, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - A Corina Vlot
- Helmholtz Zentrum München, Department of Environmental Science, Institute of Biochemical Plant Pathology, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
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Vannini C, Marsoni M, Scoccianti V, Ceccarini C, Domingo G, Bracale M, Crinelli R. Proteasome-mediated remodeling of the proteome and phosphoproteome during kiwifruit pollen germination. J Proteomics 2019; 192:334-345. [DOI: 10.1016/j.jprot.2018.09.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/11/2018] [Accepted: 09/20/2018] [Indexed: 01/19/2023]
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Hartmann M, Zeier J. l-lysine metabolism to N-hydroxypipecolic acid: an integral immune-activating pathway in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:5-21. [PMID: 30035374 DOI: 10.1111/tpj.14037] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 06/22/2018] [Accepted: 07/03/2018] [Indexed: 05/03/2023]
Abstract
l-lysine catabolic routes in plants include the saccharopine pathway to α-aminoadipate and decarboxylation of lysine to cadaverine. The current review will cover a third l-lysine metabolic pathway having a major role in plant systemic acquired resistance (SAR) to pathogen infection that was recently discovered in Arabidopsis thaliana. In this pathway, the aminotransferase AGD2-like defense response protein (ALD1) α-transaminates l-lysine and generates cyclic dehydropipecolic (DP) intermediates that are subsequently reduced to pipecolic acid (Pip) by the reductase SAR-deficient 4 (SARD4). l-pipecolic acid, which occurs ubiquitously in the plant kingdom, is further N-hydroxylated to the systemic acquired resistance (SAR)-activating metabolite N-hydroxypipecolic acid (NHP) by flavin-dependent monooxygenase1 (FMO1). N-hydroxypipecolic acid induces the expression of a set of major plant immune genes to enhance defense readiness, amplifies resistance responses, acts synergistically with the defense hormone salicylic acid, promotes the hypersensitive cell death response and primes plants for effective immune mobilization in cases of future pathogen challenge. This pathogen-inducible NHP biosynthetic pathway is activated at the transcriptional level and involves feedback amplification. Apart from FMO1, some cytochrome P450 monooxygenases involved in secondary metabolism catalyze N-hydroxylation reactions in plants. In specific taxa, pipecolic acid might also serve as a precursor in the biosynthesis of specialized natural products, leading to C-hydroxylated and otherwise modified piperidine derivatives, including indolizidine alkaloids. Finally, we show that NHP is glycosylated in Arabidopsis to form a hexose-conjugate, and then discuss open questions in Pip/NHP-related research.
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Affiliation(s)
- Michael Hartmann
- Department of Biology, Institute for Molecular Ecophysiology of Plants, Heinrich Heine University, Universitätsstraße 1, D-40225, Düsseldorf, Germany
| | - Jürgen Zeier
- Department of Biology, Institute for Molecular Ecophysiology of Plants, Heinrich Heine University, Universitätsstraße 1, D-40225, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstraße 1, D-40225, Düsseldorf, Germany
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21
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Fiorilli V, Vannini C, Ortolani F, Garcia-Seco D, Chiapello M, Novero M, Domingo G, Terzi V, Morcia C, Bagnaresi P, Moulin L, Bracale M, Bonfante P. Omics approaches revealed how arbuscular mycorrhizal symbiosis enhances yield and resistance to leaf pathogen in wheat. Sci Rep 2018; 8:9625. [PMID: 29941972 PMCID: PMC6018116 DOI: 10.1038/s41598-018-27622-8] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 05/29/2018] [Indexed: 01/27/2023] Open
Abstract
Besides improved mineral nutrition, plants colonised by arbuscular mycorrhizal (AM) fungi often display increased biomass and higher tolerance to biotic and abiotic stresses. Notwithstanding the global importance of wheat as an agricultural crop, its response to AM symbiosis has been poorly investigated. We focused on the role of an AM fungus on mineral nutrition of wheat, and on its potential protective effect against Xanthomonas translucens. To address these issues, phenotypical, molecular and metabolomic approaches were combined. Morphological observations highlighted that AM wheat plants displayed an increased biomass and grain yield, as well as a reduction in lesion area following pathogen infection. To elucidate the molecular mechanisms underlying the mycorrhizal phenotype, we investigated changes of transcripts and proteins in roots and leaves during the double (wheat-AM fungus) and tripartite (wheat-AM fungus-pathogen) interaction. Transcriptomic and proteomic profiling identified the main pathways involved in enhancing plant biomass, mineral nutrition and in promoting the bio-protective effect against the leaf pathogen. Mineral and amino acid contents in roots, leaves and seeds, and protein oxidation profiles in leaves, supported the omics data, providing new insight into the mechanisms exerted by AM symbiosis to confer stronger productivity and enhanced resistance to X. translucens in wheat.
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Affiliation(s)
- Valentina Fiorilli
- Department of Life Sciences and Systems Biology, Università degli Studi di Torino, Viale P.A. Mattioli 25, 10125, Torino, Italy.
| | - Candida Vannini
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, via J.H. Dunant 3, 21100, Varese, Italy
| | - Francesca Ortolani
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, via J.H. Dunant 3, 21100, Varese, Italy
| | - Daniel Garcia-Seco
- IRD, Cirad, Univ. Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394, Montpellier, France
| | - Marco Chiapello
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, via J.H. Dunant 3, 21100, Varese, Italy
| | - Mara Novero
- Department of Life Sciences and Systems Biology, Università degli Studi di Torino, Viale P.A. Mattioli 25, 10125, Torino, Italy
| | - Guido Domingo
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, via J.H. Dunant 3, 21100, Varese, Italy
| | - Valeria Terzi
- CREA-GB, Research Centre for Genomics and Bioinformatics, Via San Protaso 302, 29017, Fiorenzuola d'Arda, Italy
| | - Caterina Morcia
- CREA-GB, Research Centre for Genomics and Bioinformatics, Via San Protaso 302, 29017, Fiorenzuola d'Arda, Italy
| | - Paolo Bagnaresi
- CREA-GB, Research Centre for Genomics and Bioinformatics, Via San Protaso 302, 29017, Fiorenzuola d'Arda, Italy
| | - Lionel Moulin
- IRD, Cirad, Univ. Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394, Montpellier, France
| | - Marcella Bracale
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, via J.H. Dunant 3, 21100, Varese, Italy
| | - Paola Bonfante
- Department of Life Sciences and Systems Biology, Università degli Studi di Torino, Viale P.A. Mattioli 25, 10125, Torino, Italy
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