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Zhao ST, Ran XT, Huang YY, Sang W, Derrick BE, Qiu BL. Transcriptomic response of citrus psyllid salivary glands to the infection of citrus Huanglongbing pathogen. BULLETIN OF ENTOMOLOGICAL RESEARCH 2024:1-20. [PMID: 38444234 DOI: 10.1017/s0007485324000038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
The Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Psyllidae), is the key vector insect transmitting the Candidatus Liberibacter asiaticus (CLas) bacterium that causes the devastating citrus greening disease (Huanglongbing, HLB) worldwide. The D. citri salivary glands (SG) exhibit an important barrier against the transmission of HLB pathogen. However, knowledge on the molecular mechanism of SG defence against CLas infection is still limited. In the present study, we compared the SG transcriptomic response of CLas-free and CLas-infected D. citri using an illumine paired-end RNA sequencing. In total of 861 differentially expressed genes (DEGs) in the SG upon CLas infection, including 202 upregulated DEGs and 659 downregulated DEGs were identified. Functional annotation analysis showed that most of the DEGs were associated with cellular processes, metabolic processes, and the immune response. Gene ontology and Kyoto Encyclopaedia of Genes and Genomes enrichment analyses revealed that these DEGs were enriched in pathways involving carbohydrate metabolism, amino acid metabolism, the immune system, the digestive system, the lysosome, and endocytosis. A total of 16 DEGs were randomly selected to further validate the accuracy of RNA-Seq dataset by reverse-transcription quantitative polymerase chain reaction. This study provides substantial transcriptomic information regarding the SG of D. citri in response to CLas infection, which may shed light on the molecular interaction between D. citri and CLas, and provides new ideas for the prevention and control of citrus psyllid.
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Affiliation(s)
- San-Tao Zhao
- Engineering Research Centre of Biological Control, Ministry of Education, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Engineering Research Center of Biotechnology for Active Substances, Ministry of Education, Chongqing Normal University, Chongqing 401331, China
| | - Xiao-Tong Ran
- Engineering Research Centre of Biological Control, Ministry of Education, South China Agricultural University, Guangzhou 510642, China
- Engineering Research Center of Biotechnology for Active Substances, Ministry of Education, Chongqing Normal University, Chongqing 401331, China
| | - Yu-Yang Huang
- Engineering Research Centre of Biological Control, Ministry of Education, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Wen Sang
- Engineering Research Centre of Biological Control, Ministry of Education, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | | | - Bao-Li Qiu
- Engineering Research Centre of Biological Control, Ministry of Education, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Engineering Research Center of Biotechnology for Active Substances, Ministry of Education, Chongqing Normal University, Chongqing 401331, China
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Niu Y, Fu S, Chen G, Wang H, Wang Y, Hu J, Jin X, Zhang M, Lu M, He Y, Wang D, Chen Y, Zhang Y, Coll NS, Valls M, Zhao C, Chen Q, Lu H. Different epitopes of Ralstonia solanacearum effector RipAW are recognized by two Nicotiana species and trigger immune responses. MOLECULAR PLANT PATHOLOGY 2022; 23:188-203. [PMID: 34719088 PMCID: PMC8743020 DOI: 10.1111/mpp.13153] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 09/27/2021] [Accepted: 09/27/2021] [Indexed: 05/17/2023]
Abstract
Diverse pathogen effectors convergently target conserved components in plant immunity guarded by intracellular nucleotide-binding domain leucine-rich repeat receptors (NLRs) and activate effector-triggered immunity (ETI), often causing cell death. Little is known of the differences underlying ETI in different plants triggered by the same effector. In this study, we demonstrated that effector RipAW triggers ETI on Nicotiana benthamiana and Nicotiana tabacum. Both the first 107 amino acids (N1-107 ) and RipAW E3-ligase activity are required but not sufficient for triggering ETI on N. benthamiana. However, on N. tabacum, the N1-107 fragment is essential and sufficient for inducing cell death. The first 60 amino acids of the protein are not essential for RipAW-triggered cell death on either N. benthamiana or N. tabacum. Furthermore, simultaneous mutation of both R75 and R78 disrupts RipAW-triggered ETI on N. tabacum, but not on N. benthamiana. In addition, N. tabacum recognizes more RipAW orthologs than N. benthamiana. These data showcase the commonalities and specificities of RipAW-activated ETI in two evolutionally related species, suggesting Nicotiana species have acquired different abilities to perceive RipAW and activate plant defences during plant-pathogen co-evolution.
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Affiliation(s)
- Yang Niu
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingChina
| | - Shouyang Fu
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingChina
| | - Gong Chen
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingChina
| | - Huijuan Wang
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingChina
| | - Yisa Wang
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingChina
| | - JinXue Hu
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingChina
| | - Xin Jin
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingChina
| | - Mancang Zhang
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingChina
| | - Mingxia Lu
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingChina
| | - Yizhe He
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingChina
| | - Dongdong Wang
- Shaanxi Key State Laboratory of Crop HeterosisNorthwest A&F UniversityYanglingChina
| | - Yue Chen
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingChina
| | - Yong Zhang
- College of Food Science and EngineeringNorthwest A&F UniversityYanglingChina
- College of Resources and EnvironmentSouthwest UniversityChongqingChina
| | - Núria S. Coll
- Interdisciplinary Research Center for Agriculture Green Development in Yangtze River BasinSoutheast UniversityChongqingChina
| | - Marc Valls
- Interdisciplinary Research Center for Agriculture Green Development in Yangtze River BasinSoutheast UniversityChongqingChina
- Centre for Research in Agricultural GenomicsCSIC‐IRTA‐UAB‐UBBellaterraCataloniaSpain
| | - Cuizhu Zhao
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingChina
| | - Qin Chen
- Shaanxi Key State Laboratory of Crop HeterosisNorthwest A&F UniversityYanglingChina
| | - Haibin Lu
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingChina
- Department of GeneticsUniversity of BarcelonaBarcelonaSpain
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3
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Wang J, Jiang N, Sang X, Yang N, Feng Y, Chen R, Wang X, Chen Q. Protein Modification Characteristics of the Malaria Parasite Plasmodium falciparum and the Infected Erythrocytes. Mol Cell Proteomics 2020; 20:100001. [PMID: 33517144 PMCID: PMC7857547 DOI: 10.1074/mcp.ra120.002375] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 11/04/2020] [Indexed: 12/14/2022] Open
Abstract
Malaria elimination is still pending on the development of novel tools that rely on a deep understanding of parasite biology. Proteins of all living cells undergo myriad posttranslational modifications (PTMs) that are critical to multifarious life processes. An extensive proteome-wide dissection revealed a fine PTM map of most proteins in both Plasmodium falciparum, the causative agent of severe malaria, and the infected red blood cells. More than two-thirds of proteins of the parasite and its host cell underwent extensive and dynamic modification throughout the erythrocytic developmental stage. PTMs critically modulate the virulence factors involved in the host-parasite interaction and pathogenesis. Furthermore, P. falciparum stabilized the supporting proteins of erythrocyte origin by selective demodification. Collectively, our multiple omic analyses, apart from having furthered a deep understanding of the systems biology of P. falciparum and malaria pathogenesis, provide a valuable resource for mining new antimalarial targets.
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Affiliation(s)
- Jianhua Wang
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Shenyang Agricultural University, Shengyang, China; The Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang, China; College of Food Science, Shenyang Agricultural Sciences, Shenyang, China
| | - Ning Jiang
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Shenyang Agricultural University, Shengyang, China; The Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang, China
| | - Xiaoyu Sang
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Shenyang Agricultural University, Shengyang, China; The Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang, China
| | - Na Yang
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Shenyang Agricultural University, Shengyang, China; The Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang, China
| | - Ying Feng
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Shenyang Agricultural University, Shengyang, China; The Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang, China
| | - Ran Chen
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Shenyang Agricultural University, Shengyang, China; The Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang, China
| | - Xinyi Wang
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Shenyang Agricultural University, Shengyang, China; College of Basic Sciences, Shenyang Agricultural University, Shenyang, China
| | - Qijun Chen
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Shenyang Agricultural University, Shengyang, China; The Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang, China.
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McDermott JE, Cort JR, Nakayasu ES, Pruneda JN, Overall C, Adkins JN. Prediction of bacterial E3 ubiquitin ligase effectors using reduced amino acid peptide fingerprinting. PeerJ 2019; 7:e7055. [PMID: 31211016 PMCID: PMC6557245 DOI: 10.7717/peerj.7055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 05/02/2019] [Indexed: 11/20/2022] Open
Abstract
Background Although pathogenic Gram-negative bacteria lack their own ubiquitination machinery, they have evolved or acquired virulence effectors that can manipulate the host ubiquitination process through structural and/or functional mimicry of host machinery. Many such effectors have been identified in a wide variety of bacterial pathogens that share little sequence similarity amongst themselves or with eukaryotic ubiquitin E3 ligases. Methods To allow identification of novel bacterial E3 ubiquitin ligase effectors from protein sequences we have developed a machine learning approach, the SVM-based Identification and Evaluation of Virulence Effector Ubiquitin ligases (SIEVE-Ub). We extend the string kernel approach used previously to sequence classification by introducing reduced amino acid (RED) alphabet encoding for protein sequences. Results We found that 14mer peptides with amino acids represented as simply either hydrophobic or hydrophilic provided the best models for discrimination of E3 ligases from other effector proteins with a receiver-operator characteristic area under the curve (AUC) of 0.90. When considering a subset of E3 ubiquitin ligase effectors that do not fall into known sequence based families we found that the AUC was 0.82, demonstrating the effectiveness of our method at identifying novel functional family members. Feature selection was used to identify a parsimonious set of 10 RED peptides that provided good discrimination, and these peptides were found to be located in functionally important regions of the proteins involved in E2 and host target protein binding. Our general approach enables construction of models based on other effector functions. We used SIEVE-Ub to predict nine potential novel E3 ligases from a large set of bacterial genomes. SIEVE-Ub is available for download at https://doi.org/10.6084/m9.figshare.7766984.v1 or https://github.com/biodataganache/SIEVE-Ub for the most current version.
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Affiliation(s)
- Jason E McDermott
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States of America.,Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, United States of America
| | - John R Cort
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States of America
| | - Ernesto S Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States of America
| | - Jonathan N Pruneda
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, United States of America
| | - Christopher Overall
- Center for Brain Immunology and Glia, University of Virginia, Charlottesville, United States of America
| | - Joshua N Adkins
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States of America
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Santos C, Nogueira FCS, Domont GB, Fontes W, Prado GS, Habibi P, Santos VO, Oliveira-Neto OB, Grossi-de-Sá MF, Jorrín-Novo JV, Franco OL, Mehta A. Proteomic Analysis and Functional Validation of a Brassica oleracea Endochitinase Involved in Resistance to Xanthomonas campestris. FRONTIERS IN PLANT SCIENCE 2019; 10:414. [PMID: 31031780 PMCID: PMC6473119 DOI: 10.3389/fpls.2019.00414] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 03/19/2019] [Indexed: 05/02/2023]
Abstract
Black rot is a severe disease caused by the bacterium Xanthomonas campestris pv. campestris (Xcc), which can lead to substantial losses in cruciferous vegetable production worldwide. Although the use of resistant cultivars is the main strategy to control this disease, there are limited sources of resistance. In this study, we used the LC-MS/MS technique to analyze young cabbage leaves and chloroplast-enriched samples at 24 h after infection by Xcc, using both susceptible (Veloce) and resistant (Astrus) cultivars. A comparison between susceptible Xcc-inoculated plants and the control condition, as well as between resistant Xcc-inoculated plants with the control was performed and more than 300 differentially abundant proteins were identified in each comparison. The chloroplast enriched samples contributed with the identification of 600 additional protein species in the resistant interaction and 900 in the susceptible one, which were not detected in total leaf sample. We further determined the expression levels for 30 genes encoding the identified differential proteins by qRT-PCR. CHI-B4 like gene, encoding an endochitinase showing a high increased abundance in resistant Xcc-inoculated leaves, was selected for functional validation by overexpression in Arabidopsis thaliana. Compared to the wild type (Col-0), transgenic plants were highly resistant to Xcc indicating that CHI-B4 like gene could be an interesting candidate to be used in genetic breeding programs aiming at black rot resistance.
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Affiliation(s)
- Cristiane Santos
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brazil
- Departamento de Biologia, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | - Fábio C. S. Nogueira
- Proteomics Unit, Chemistry Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gilberto B. Domont
- Proteomics Unit, Chemistry Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Wagner Fontes
- Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil
| | | | - Peyman Habibi
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brazil
- Department of Bioprocess Engineering and Biotechnology, Universidade Federal do Paraná, Curitiba, Brazil
| | | | - Osmundo B. Oliveira-Neto
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brazil
- Departamento de Bioquímica e Biologia Molecular, Escola de Medicina, Faculdades Integradas da União Educacional do Planalto Central, Brasília, Brazil
| | - Maria Fatima Grossi-de-Sá
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brazil
- Centro de Analises Proteomicas e Bioquimica, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brazil
| | - Jesus V. Jorrín-Novo
- Department of Biochemistry and Molecular Biology, Universidad de Córdoba, Córdoba, Spain
| | - Octavio L. Franco
- Departamento de Biologia, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
- Centro de Analises Proteomicas e Bioquimica, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brazil
- S-Inova Biotech, Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
| | - Angela Mehta
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brazil
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6
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Bai P, Park C, Shirsekar G, Songkumarn P, Bellizzi M, Wang G. Role of lysine residues of the Magnaporthe oryzae effector AvrPiz-t in effector- and PAMP-triggered immunity. MOLECULAR PLANT PATHOLOGY 2019; 20:599-608. [PMID: 30548752 PMCID: PMC6637882 DOI: 10.1111/mpp.12779] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Magnaporthe oryzae is an important fungal pathogen of both rice and wheat. However, how M. oryzae effectors modulate plant immunity is not fully understood. Previous studies have shown that the M. oryzae effector AvrPiz-t targets the host ubiquitin-proteasome system to manipulate plant defence. In return, two rice ubiquitin E3 ligases, APIP6 and APIP10, ubiquitinate AvrPiz-t for degradation. To determine how lysine residues contribute to the stability and function of AvrPiz-t, we generated double (K1,2R-AvrPiz-t), triple (K1,2,3R-AvrPiz-t) and lysine-free (LF-AvrPiz-t) mutants by mutating lysines into arginines in AvrPiz-t. LF-AvrPiz-t showed the highest protein accumulation when transiently expressed in rice protoplasts. When co-expressed with APIP10 in Nicotiana benthamiana, LF-AvrPiz-t was more stable than AvrPiz-t and was less able to degrade APIP10. The avirulence of LF-AvrPiz-t on Piz-t:HA plants was less than that of AvrPiz-t, which led to resistance reduction and lower accumulation of the Piz-t:HA protein after inoculation with the LF-AvrPiz-t-carrying isolate. Chitin- and flg22-induced production of reactive oxygen species (ROS) was higher in LF-AvrPiz-t than in AvrPiz-t transgenic plants. In addition, LF-AvrPiz-t transgenic plants were less susceptible than AvrPiz-t transgenic plants to a virulent isolate. Furthermore, both AvrPiz-t and LF-AvrPiz-t interacted with OsRac1, but the suppression of OsRac1-mediated ROS generation by LF-AvrPiz-t was significantly lower than that by AvrPiz-t. Together, these results suggest that the lysine residues of AvrPiz-t are required for its avirulence and virulence functions in rice.
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Affiliation(s)
- Pengfei Bai
- Department of Plant PathologyOhio State UniversityColumbusOH43210
| | - Chan‐Ho Park
- Department of Plant PathologyOhio State UniversityColumbusOH43210
| | - Gautam Shirsekar
- Department of Plant PathologyOhio State UniversityColumbusOH43210
| | | | - Maria Bellizzi
- Department of Plant PathologyOhio State UniversityColumbusOH43210
| | - Guo‐Liang Wang
- Department of Plant PathologyOhio State UniversityColumbusOH43210
- State Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing100193China
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7
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Wu SH, Huang BH, Gao J, Wang S, Liao PC. The effects of afforestation on soil bacterial communities in temperate grassland are modulated by soil chemical properties. PeerJ 2019; 7:e6147. [PMID: 30648012 PMCID: PMC6330960 DOI: 10.7717/peerj.6147] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 11/21/2018] [Indexed: 02/01/2023] Open
Abstract
Grassland afforestation dramatically affects the abiotic, biotic, and ecological function properties of the original ecosystems. Interference from afforestation might disrupt the stasis of soil physicochemical properties and the dynamic balance of microbiota. Some studies have suggested low sensitivity of soil properties and bacterial community to afforestation, but the apparent lack of a significant relationship is probably due to the confounding effects of the generalist habitat and rare bacterial communities. In this study, soil chemical and prokaryotic properties in a 30-year-old Mongolia pine (Pinus sylvestris var. mongolica Litv.) afforested region and adjacent grassland in Inner Mongolia were classified and quantified. Our results indicate that the high richness of rare microbes accounts for the alpha-diversity of the soil microbiome. Few OTUs of generalist (core bacteria) and habitat-specialist bacteria are present. However, the high abundance of this small number of OTUs governs the beta-diversity of the grassland and afforested land bacterial communities. Afforestation has changed the soil chemical properties, thus indirectly affecting the soil bacterial composition rather than richness. The contents of soil P, Ca2+, and Fe3+ account for differentially abundant OTUs such as Planctomycetes and subsequent changes in the ecologically functional potential of soil bacterial communities due to grassland afforestation. We conclude that grassland afforestation has changed the chemical properties and composition of the soil and ecological functions of the soil bacterial community and that these effects of afforestation on the microbiome have been modulated by changes in soil chemical properties.
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Affiliation(s)
- Shu-Hong Wu
- School of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Bing-Hong Huang
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Jian Gao
- Faculty of Resources and Environment, Baotou Teachers' College, Inner Mongolia University of Science and Technology, Inner Mongolia, China
| | - Siqi Wang
- School of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Pei-Chun Liao
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
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8
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Rajaraman J, Douchkov D, Lück S, Hensel G, Nowara D, Pogoda M, Rutten T, Meitzel T, Brassac J, Höfle C, Hückelhoven R, Klinkenberg J, Trujillo M, Bauer E, Schmutzer T, Himmelbach A, Mascher M, Lazzari B, Stein N, Kumlehn J, Schweizer P. Evolutionarily conserved partial gene duplication in the Triticeae tribe of grasses confers pathogen resistance. Genome Biol 2018; 19:116. [PMID: 30111359 PMCID: PMC6092874 DOI: 10.1186/s13059-018-1472-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 07/04/2018] [Indexed: 11/11/2022] Open
Abstract
Background The large and highly repetitive genomes of the cultivated species Hordeum vulgare (barley), Triticum aestivum (wheat), and Secale cereale (rye) belonging to the Triticeae tribe of grasses appear to be particularly rich in gene-like sequences including partial duplicates. Most of them have been classified as putative pseudogenes. In this study we employ transient and stable gene silencing- and over-expression systems in barley to study the function of HvARM1 (for H. vulgare Armadillo 1), a partial gene duplicate of the U-box/armadillo-repeat E3 ligase HvPUB15 (for H. vulgare Plant U-Box 15). Results The partial ARM1 gene is derived from a gene-duplication event in a common ancestor of the Triticeae and contributes to quantitative host as well as nonhost resistance to the biotrophic powdery mildew fungus Blumeria graminis. In barley, allelic variants of HvARM1 but not of HvPUB15 are significantly associated with levels of powdery mildew infection. Both HvPUB15 and HvARM1 proteins interact in yeast and plant cells with the susceptibility-related, plastid-localized barley homologs of THF1 (for Thylakoid formation 1) and of ClpS1 (for Clp-protease adaptor S1) of Arabidopsis thaliana. A genome-wide scan for partial gene duplicates reveals further events in barley resulting in stress-regulated, potentially neo-functionalized, genes. Conclusion The results suggest neo-functionalization of the partial gene copy HvARM1 increases resistance against powdery mildew infection. It further links plastid function with susceptibility to biotrophic pathogen attack. These findings shed new light on a novel mechanism to employ partial duplication of protein-protein interaction domains to facilitate the expansion of immune signaling networks. Electronic supplementary material The online version of this article (10.1186/s13059-018-1472-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jeyaraman Rajaraman
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK Gatersleben), Corrensstrasse 3, D-06466, Stadt Seeland, Germany.
| | - Dimitar Douchkov
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK Gatersleben), Corrensstrasse 3, D-06466, Stadt Seeland, Germany.
| | - Stefanie Lück
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK Gatersleben), Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Götz Hensel
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK Gatersleben), Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Daniela Nowara
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK Gatersleben), Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Maria Pogoda
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK Gatersleben), Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Twan Rutten
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK Gatersleben), Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Tobias Meitzel
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK Gatersleben), Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Jonathan Brassac
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK Gatersleben), Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Caroline Höfle
- Technische Universität München, Emil-Ramann-Straße 2, D-85354, Freising, Germany
| | - Ralph Hückelhoven
- Technische Universität München, Emil-Ramann-Straße 2, D-85354, Freising, Germany
| | - Jörn Klinkenberg
- Leibniz Institut für Pflanzenbiochemie, Weinberg 3, D-06120, Halle (Saale), Germany
| | - Marco Trujillo
- Leibniz Institut für Pflanzenbiochemie, Weinberg 3, D-06120, Halle (Saale), Germany.,Albert-Ludwigs-Universität Freiburg, Institut für Biologie II, Zellbiologie, D-79104, Freiburg, Germany
| | - Eva Bauer
- Technische Universität München, Liesel-Beckmann-Straße 2, D-85354, Freising, Germany
| | - Thomas Schmutzer
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK Gatersleben), Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Axel Himmelbach
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK Gatersleben), Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Martin Mascher
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK Gatersleben), Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Barbara Lazzari
- Parco Technologico Padano, Via Einstein, Loc. Cascina Codazza, 26900, Lodi, Italy
| | - Nils Stein
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK Gatersleben), Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Jochen Kumlehn
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK Gatersleben), Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Patrick Schweizer
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK Gatersleben), Corrensstrasse 3, D-06466, Stadt Seeland, Germany
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9
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García-Cano E, Hak H, Magori S, Lazarowitz SG, Citovsky V. The Agrobacterium F-Box Protein Effector VirF Destabilizes the Arabidopsis GLABROUS1 Enhancer/Binding Protein-Like Transcription Factor VFP4, a Transcriptional Activator of Defense Response Genes. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:576-586. [PMID: 29264953 PMCID: PMC5953515 DOI: 10.1094/mpmi-07-17-0188-fi] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Agrobacterium-mediated genetic transformation not only represents a technology of choice to genetically manipulate plants, but it also serves as a model system to study mechanisms employed by invading pathogens to counter the myriad defenses mounted against them by the host cell. Here, we uncover a new layer of plant defenses that is targeted by A. tumefaciens to facilitate infection. We show that the Agrobacterium F-box effector VirF, which is exported into the host cell, recognizes an Arabidopsis transcription factor VFP4 and targets it for proteasomal degradation. We hypothesize that VFP4 resists Agrobacterium infection and that the bacterium utilizes its VirF effector to degrade VFP4 and thereby mitigate the VFP4-based defense. Indeed, loss-of-function mutations in VFP4 resulted in differential expression of numerous biotic stress-response genes, suggesting that one of the functions of VFP4 is to control a spectrum of plant defenses, including those against Agrobacterium tumefaciens. We identified one such gene, ATL31, known to mediate resistance to bacterial pathogens. ATL31 was transcriptionally repressed in VFP4 loss-of-function plants and activated in VFP4 gain-of-function plants. Gain-of-function lines of VFP4 and ATL31 exhibited recalcitrance to Agrobacterium tumorigenicity, suggesting that A. tumefaciens may utilize the host ubiquitin/proteasome system to destabilize transcriptional regulators of the host disease response machinery.
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Affiliation(s)
- Elena García-Cano
- Department of Biochemistry and Cell Biology, State University of New York, Stony Brook, NY 11794-5215, USA
| | - Hagit Hak
- Department of Biochemistry and Cell Biology, State University of New York, Stony Brook, NY 11794-5215, USA
- Corresponding author: Hagit Hak;
| | - Shimpei Magori
- Department of Biochemistry and Cell Biology, State University of New York, Stony Brook, NY 11794-5215, USA
| | - Sondra G. Lazarowitz
- Department of Biochemistry and Cell Biology, State University of New York, Stony Brook, NY 11794-5215, USA
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
| | - Vitaly Citovsky
- Department of Biochemistry and Cell Biology, State University of New York, Stony Brook, NY 11794-5215, USA
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10
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Bègue H, Jeandroz S, Blanchard C, Wendehenne D, Rosnoblet C. Structure and functions of the chaperone-like p97/CDC48 in plants. Biochim Biophys Acta Gen Subj 2016; 1861:3053-3060. [PMID: 27717811 DOI: 10.1016/j.bbagen.2016.10.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 09/29/2016] [Accepted: 10/01/2016] [Indexed: 12/15/2022]
Abstract
BACKGROUND The chaperone-like p97 is a member of the AAA+ ATPase enzyme family that contributes to numerous cellular activities. P97 has been broadly studied in mammals (VCP/p97) and yeasts (CDC48: Cell Division Cycle 48/p97) and numerous investigations highlighted that this protein is post-translationally regulated, is structured in homohexamer and interacts with partners and cofactors that direct it to distinct cellular signalization pathway including protein quality control and degradation, cell cycle regulation, genome stability, vesicular trafficking, autophagy and immunity. SCOPE OF REVIEW p97 is also conserved in plants (CDC48) but its functions are less understood. In the present review we intended to present the state of the art of the structure, regulation and functions of CDC48 in plants. MAJOR CONCLUSIONS Evidence accumulated underline that CDC48 plays a crucial role in development, cell cycle regulation and protein turnover in plants. Furthermore, its involvement in plant immunity has recently emerged and first interacting partners have been identified, shedding light on its putative cellular activities. GENERAL SIGNIFICANCE Identification of emerging functions of CDC48 in plants opens new roads of research in immunity and provides new insights into the mechanisms of protein quality control.
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Affiliation(s)
- Hervé Bègue
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Sylvain Jeandroz
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Cécile Blanchard
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - David Wendehenne
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Claire Rosnoblet
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France.
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11
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Sahu PP, Sharma N, Puranik S, Chakraborty S, Prasad M. Tomato 26S Proteasome subunit RPT4a regulates ToLCNDV transcription and activates hypersensitive response in tomato. Sci Rep 2016; 6:27078. [PMID: 27252084 PMCID: PMC4890432 DOI: 10.1038/srep27078] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 05/09/2016] [Indexed: 01/05/2023] Open
Abstract
Involvement of 26S proteasomal subunits in plant pathogen-interactions, and the roles of each subunit in independently modulating the activity of many intra- and inter-cellular regulators controlling physiological and defense responses of a plant were well reported. In this regard, we aimed to functionally characterize a Solanum lycopersicum 26S proteasomal subunit RPT4a (SlRPT4) gene, which was differentially expressed after Tomato leaf curl New Delhi virus (ToLCNDV) infection in tolerant cultivar H-88-78-1. Molecular analysis revealed that SlRPT4 protein has an active ATPase activity. SlRPT4 could specifically bind to the stem-loop structure of intergenic region (IR), present in both DNA-A and DNA-B molecule of the bipartite viral genome. Lack of secondary structure in replication-associated gene fragment prevented formation of DNA-protein complex suggesting that binding of SlRPT4 with DNA is secondary structure specific. Interestingly, binding of SlRPT4 to IR inhibited the function of RNA Pol-II and subsequently reduced the bi-directional transcription of ToLCNDV genome. Virus-induced gene silencing of SlRPT4 gene incited conversion of tolerant attributes of cultivar H-88-78-1 into susceptibility. Furthermore, transient overexpression of SlRPT4 resulted in activation of programmed cell death and antioxidant enzymes system. Overall, present study highlights non-proteolytic function of SlRPT4 and their participation in defense pathway against virus infection in tomato.
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Affiliation(s)
- Pranav Pankaj Sahu
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
- School of Life Sciences, Jawaharlal Nehru University, New Delhi-110067, India
| | - Namisha Sharma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Swati Puranik
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Supriya Chakraborty
- School of Life Sciences, Jawaharlal Nehru University, New Delhi-110067, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
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12
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Mata-Cantero L, Azkargorta M, Aillet F, Xolalpa W, LaFuente MJ, Elortza F, Carvalho AS, Martin-Plaza J, Matthiesen R, Rodriguez MS. New insights into host-parasite ubiquitin proteome dynamics in P. falciparum infected red blood cells using a TUBEs-MS approach. J Proteomics 2016; 139:45-59. [PMID: 26972027 DOI: 10.1016/j.jprot.2016.03.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 02/11/2016] [Accepted: 03/02/2016] [Indexed: 02/06/2023]
Abstract
UNLABELLED Malaria, caused by Plasmodium falciparum (P. falciparum), ranks as one of the most baleful infectious diseases worldwide. New antimalarial treatments are needed to face existing or emerging drug resistant strains. Protein degradation appears to play a significant role during the asexual intraerythrocytic developmental cycle (IDC) of P. falciparum. Inhibition of the ubiquitin proteasome system (UPS), a major intracellular proteolytic pathway, effectively reduces infection and parasite replication. P. falciparum and erythrocyte UPS coexist during IDC but the nature of their relationship is largely unknown. We used an approach based on Tandem Ubiquitin-Binding Entities (TUBEs) and 1D gel electrophoresis followed by mass spectrometry to identify major components of the TUBEs-associated ubiquitin proteome of both host and parasite during ring, trophozoite and schizont stages. Ring-exported protein (REX1), a P. falciparum protein located in Maurer's clefts and important for parasite nutrient import, was found to reach a maximum level of ubiquitylation in trophozoites stage. The Homo sapiens (H. sapiens) TUBEs associated ubiquitin proteome decreased during the infection, whereas the equivalent P. falciparum TUBEs-associated ubiquitin proteome counterpart increased. Major cellular processes such as DNA repair, replication, stress response, vesicular transport and catabolic events appear to be regulated by ubiquitylation along the IDC P. falciparum infection. BIOLOGICAL SIGNIFICANCE In this work we analyze for the first time the interconnection between Plasmodium and human red blood cells ubiquitin-regulated proteins in the context of infection. We identified a number of human and Plasmodium proteins whose ubiquitylation pattern changes during the asexual infective stage. We demonstrate that ubiquitylation of REX1, a P. falciparum protein located in Maurer's clefts and important for parasite nutrient import, peaks in trophozoites stage. The ubiquitin-proteome from P. falciparum infected red blood cells (iRBCs) revealed a significant host-parasite crosstalk, underlining the importance of ubiquitin-regulated proteolytic activities during the intraerythrocytic developmental cycle (IDC) of P. falciparum. Major cellular processes defined from gene ontology such as DNA repair, replication, stress response, vesicular transport and catabolic events appear to be regulated by ubiquitylation along the IDC P. falciparum infection. Given the importance of ubiquitylation in the development of infectious diseases, this work provides a number of potential drug-target candidates that should be further explored.
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Affiliation(s)
- Lydia Mata-Cantero
- Medicines Development Campus, Diseases of the Developing World, GlaxoSmithKline Tres Cantos, Madrid, Spain; Proteomics Platform CICbioGUNE, CIBERehd, ProteoRed-ISCIII, Parque Tecnologico de Bizkaia, Derio, Spain; Ubiquitylation and Cancer Molecular Biology, Inbiomed, San Sebastian, Spain
| | - Mikel Azkargorta
- Proteomics Platform CICbioGUNE, CIBERehd, ProteoRed-ISCIII, Parque Tecnologico de Bizkaia, Derio, Spain
| | - Fabienne Aillet
- Ubiquitylation and Cancer Molecular Biology, Inbiomed, San Sebastian, Spain
| | - Wendy Xolalpa
- Proteomics Platform CICbioGUNE, CIBERehd, ProteoRed-ISCIII, Parque Tecnologico de Bizkaia, Derio, Spain
| | - Maria J LaFuente
- Medicines Development Campus, Diseases of the Developing World, GlaxoSmithKline Tres Cantos, Madrid, Spain
| | - Felix Elortza
- Proteomics Platform CICbioGUNE, CIBERehd, ProteoRed-ISCIII, Parque Tecnologico de Bizkaia, Derio, Spain
| | - Ana Sofia Carvalho
- Computational and Experimental Biology Group, Health Promotion and Chronic Diseases Department, National Institute of Health Dr Ricardo Jorge, Lisbon, Portugal
| | - Julio Martin-Plaza
- Centro de Investigación Básica, GlaxoSmithKline, Tres Cantos, Madrid, Spain
| | - Rune Matthiesen
- Computational and Experimental Biology Group, Health Promotion and Chronic Diseases Department, National Institute of Health Dr Ricardo Jorge, Lisbon, Portugal.
| | - Manuel S Rodriguez
- Proteomics Platform CICbioGUNE, CIBERehd, ProteoRed-ISCIII, Parque Tecnologico de Bizkaia, Derio, Spain; Ubiquitylation and Cancer Molecular Biology, Inbiomed, San Sebastian, Spain; Institut des Technologies Avancées en sciences du Vivant (ITAV), Université de Toulouse, CNRS, UPS, France; University of Toulouse III-Paul Sabatier, 31077 Toulouse, France; Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, France.
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13
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Ben Khaled S, Postma J, Robatzek S. A moving view: subcellular trafficking processes in pattern recognition receptor-triggered plant immunity. ANNUAL REVIEW OF PHYTOPATHOLOGY 2015; 53:379-402. [PMID: 26243727 DOI: 10.1146/annurev-phyto-080614-120347] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
A significant challenge for plants is to induce localized defense responses at sites of pathogen attack. Therefore, host subcellular trafficking processes enable accumulation and exchange of defense compounds, which contributes to the plant on-site defenses in response to pathogen perception. This review summarizes our current understanding of the transport processes that facilitate immunity, the significance of which is highlighted by pathogens reprogramming membrane trafficking through host cell translocated effectors. Prominent immune-related cargos of plant trafficking pathways are the pattern recognition receptors (PRRs), which must be present at the plasma membrane to sense microbes in the apoplast. We focus on the dynamic localization of the FLS2 receptor and discuss the pathways that regulate receptor transport within the cell and their link to FLS2-mediated immunity. One emerging theme is that ligand-induced late endocytic trafficking is conserved across different PRR protein families as well as across different plant species.
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Affiliation(s)
- Sara Ben Khaled
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, United Kingdom;
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14
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Grau-Bové X, Sebé-Pedrós A, Ruiz-Trillo I. The eukaryotic ancestor had a complex ubiquitin signaling system of archaeal origin. Mol Biol Evol 2014; 32:726-39. [PMID: 25525215 PMCID: PMC4327156 DOI: 10.1093/molbev/msu334] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The origin of the eukaryotic cell is one of the most important transitions in the history of life. However, the emergence and early evolution of eukaryotes remains poorly understood. Recent data have shown that the last eukaryotic common ancestor (LECA) was much more complex than previously thought. The LECA already had the genetic machinery encoding the endomembrane apparatus, spliceosome, nuclear pore, and myosin and kinesin cytoskeletal motors. It is unclear, however, when the functional regulation of these cellular components evolved. Here, we address this question by analyzing the origin and evolution of the ubiquitin (Ub) signaling system, one of the most important regulatory layers in eukaryotes. We delineated the evolution of the whole Ub, Small-Ub-related MOdifier (SUMO), and Ub-fold modifier 1 (Ufm1) signaling networks by analyzing representatives from all major eukaryotic, bacterial, and archaeal lineages. We found that the Ub toolkit had a pre-eukaryotic origin and is present in three extant archaeal groups. The pre-eukaryotic Ub toolkit greatly expanded during eukaryogenesis, through massive gene innovation and diversification of protein domain architectures. This resulted in a LECA with essentially all of the Ub-related genes, including the SUMO and Ufm1 Ub-like systems. Ub and SUMO signaling further expanded during eukaryotic evolution, especially labeling and delabeling enzymes responsible for substrate selection. Additionally, we analyzed protein domain architecture evolution and found that multicellular lineages have the most complex Ub systems in terms of domain architectures. Together, we demonstrate that the Ub system predates the origin of eukaryotes and that a burst of innovation during eukaryogenesis led to a LECA with complex posttranslational regulation.
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Affiliation(s)
- Xavier Grau-Bové
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Arnau Sebé-Pedrós
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain Departament de Genètica, Universitat de Barcelona, Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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15
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Banfield MJ. Perturbation of host ubiquitin systems by plant pathogen/pest effector proteins. Cell Microbiol 2014; 17:18-25. [PMID: 25339602 PMCID: PMC4312480 DOI: 10.1111/cmi.12385] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 09/26/2014] [Accepted: 10/09/2014] [Indexed: 12/26/2022]
Abstract
Microbial pathogens and pests of animals and plants secrete effector proteins into host cells, altering cellular physiology to the benefit of the invading parasite. Research in the past decade has delivered significant new insights into the molecular mechanisms of how these effector proteins function, with a particular focus on modulation of host immunity-related pathways. One host system that has emerged as a common target of effectors is the ubiquitination system in which substrate proteins are post-translationally modified by covalent conjugation with the small protein ubiquitin. This modification, typically via isopeptide bond formation through a lysine side chain of ubiquitin, can result in target degradation, relocalization, altered activity or affect protein–protein interactions. In this review, I focus primarily on how effector proteins from bacterial and filamentous pathogens of plants and pests perturb host ubiquitination pathways that ultimately include the 26S proteasome. The activities of these effectors, in how they affect ubiquitin pathways in plants, reveal how pathogens have evolved to identify and exploit weaknesses in this system that deliver increased pathogen fitness.
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Affiliation(s)
- Mark J Banfield
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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16
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Lozano-Durán R, Bourdais G, He SY, Robatzek S. The bacterial effector HopM1 suppresses PAMP-triggered oxidative burst and stomatal immunity. THE NEW PHYTOLOGIST 2014; 202:259-269. [PMID: 24372399 DOI: 10.1111/nph.12651] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 11/08/2013] [Indexed: 05/19/2023]
Abstract
Successful pathogens counter immunity at multiple levels, mostly through the action of effectors. Pseudomonas syringae secretes c. 30 effectors, some of which have been shown to inhibit plant immunity triggered upon perception of conserved pathogen-associated molecular patterns (PAMPs). One of these is HopM1, which impairs late immune responses through targeting the vesicle trafficking-related AtMIN7 for degradation. Here, we report that in planta expressed HopM1 suppresses two early PAMP-triggered responses, the oxidative burst and stomatal immunity, both of which seem to require proteasomal function but are independent of AtMIN7. Notably, a 14-3-3 protein, GRF8/AtMIN10, was found previously to be a target of HopM1 in vivo, and expression of HopM1 mimics the effect of chemically and genetically disrupting 14-3-3 function. Our data further show that the function of 14-3-3 proteins is required for PAMP-triggered oxidative burst and stomatal immunity, and chemical-mediated disruption of the 14-3-3 interactions with their client proteins restores virulence of a HopM1-deficient P. syringae mutant, providing a link between HopM1 and the involvement of 14-3-3 proteins in plant immunity. Taken together, these results unveil the impact of HopM1 on the PAMP-triggered oxidative burst and stomatal immunity in an AtMIN7-independent manner, most likely acting at the function of (a) 14-3-3 protein(s).
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Affiliation(s)
- Rosa Lozano-Durán
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Gildas Bourdais
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Sheng Yang He
- Department of Energy Plant Research Laboratory, Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, Michigan State University, East Lansing, MI, 48824, USA
| | - Silke Robatzek
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
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17
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Salomon D, Orth K. What pathogens have taught us about posttranslational modifications. Cell Host Microbe 2014; 14:269-79. [PMID: 24034613 DOI: 10.1016/j.chom.2013.07.008] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Pathogens use various mechanisms to manipulate host processes to promote infection. Decades of research on pathogens have revealed not only the molecular mechanisms that these microbes use to replicate and survive within host cells, but also seminal information on how host signaling machinery regulates cellular processes. Among these discoveries are mechanisms involving posttranslational modifications that alter the activity, localization, or interactions of the modified protein. Herein, we examine how pathogens have contributed to our basic understanding of three posttranslational modifications: phosphorylation, NMPylation, and ubiquitylation. Over the years, technologies, techniques and research tools have developed side by side with the study of pathogens, facilitating the discovery of protein modifications and furthering our understanding of how they contribute to both infection and cellular functions.
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Affiliation(s)
- Dor Salomon
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
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18
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Lin AE, Guttman JA. The Escherichia coli adherence factor plasmid of enteropathogenic Escherichia coli causes a global decrease in ubiquitylated host cell proteins by decreasing ubiquitin E1 enzyme expression through host aspartyl proteases. Int J Biochem Cell Biol 2012; 44:2223-32. [PMID: 22999844 DOI: 10.1016/j.biocel.2012.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 08/08/2012] [Accepted: 09/06/2012] [Indexed: 01/04/2023]
Abstract
Ubiquitylation is a widespread post-translational global regulatory system that is essential for the proper functioning of various cellular events. Recent studies have shown that certain types of Escherichia coli can exploit specific aspects of the ubiquitylation system to influence downstream targets. Despite these findings, examination of the effects pathogenic E. coli have on the overall host ubiquitylation system remain unexplored. To study the impact that pathogenic E. coli have on the ubiquitylation levels of host proteins during infections, we analyzed the entire ubiquitylation system during enteropathogenic E. coli infections of cultured cells. We found that these microbes caused a dramatic decrease in ubiquitylated host proteins during these infections. This occurred with a concomitant reduction in the expression of essential E1 activating enzymes in the host, which are integral for the initiation of the ubiquitylation cascade. Control of host E1 enzyme levels was dependent on the E. coli adherence factor plasmid which acted on host aspartyl proteases within enteropathogenic E. coli. Hijacking of the ubiquitylation system did not require the plasmid-encoded regulator or bundle forming pilus expression, as enteropathogenic E. coli mutated in those factors did not revert the ubiquitylation of host proteins or the abundance of E1 enzyme proteins to uninfected levels. Our work shows that E. coli have developed strategies to usurp post-translational systems by targeting crucial enzymes. The ability of enteropathogenic E. coli to inactivate host protein ubiquitylation could enable more efficient effector protein functionality, providing increased bacterial control of host cells during enteropathogenic E. coli pathogenesis.
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Affiliation(s)
- Ann E Lin
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
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19
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Anand A, Rojas CM, Tang Y, Mysore KS. Several components of SKP1/Cullin/F-box E3 ubiquitin ligase complex and associated factors play a role in Agrobacterium-mediated plant transformation. THE NEW PHYTOLOGIST 2012; 195:203-16. [PMID: 22486382 DOI: 10.1111/j.1469-8137.2012.04133.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
• Successful genetic transformation of plants by Agrobacterium tumefaciens requires the import of bacterial T-DNA and virulence proteins into the plant cell that eventually form a complex (T-complex). The essential components of the T-complex include the single stranded T-DNA, bacterial virulence proteins (VirD2, VirE2, VirE3 and VirF) and associated host proteins that facilitate the transfer and integration of T-DNA. The removal of the proteins from the T-complex is likely achieved by targeted proteolysis mediated by VirF and the plant ubiquitin proteasome complex. • We evaluated the involvement of the host SKP1/culin/F-box (SCF)-E3 ligase complex and its role in plant transformation. Gene silencing, mutant screening and gene expression studies suggested that the Arabidopsis homologs of yeast SKP1 (suppressor of kinetochore protein 1) protein, ASK1 and ASK2, are required for Agrobacterium-mediated plant transformation. • We identified the role for SGT1b (suppressor of the G2 allele of SKP1), an accessory protein that associates with SCF-complex, in plant transformation. We also report the differential expression of many genes that encode F-box motif containing SKP1-interacting proteins (SKIP) upon Agrobacterium infection. • We speculate that these SKIP genes could encode the plant specific F-box proteins that target the T-complex associated proteins for polyubiquitination and subsequent degradation by the 26S proteasome.
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Affiliation(s)
- Ajith Anand
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73402, USA
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20
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Üstün Ş, Müller P, Palmisano R, Hensel M, Börnke F. SseF, a type III effector protein from the mammalian pathogen Salmonella enterica, requires resistance-gene-mediated signalling to activate cell death in the model plant Nicotiana benthamiana. THE NEW PHYTOLOGIST 2012; 194:1046-1060. [PMID: 22471508 DOI: 10.1111/j.1469-8137.2012.04124.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Type III effector proteins (T3Es) of many Gram-negative pathogenic bacteria manipulate highly conserved cellular processes, indicating conservation in virulence mechanisms during the infection of hosts of divergent evolutionary origin. In order to identify conserved effector functions, we used a cross-kingdom approach in which we expressed selected T3Es from the mammalian pathogen Salmonella enterica in leaves of Nicotiana benthamiana and searched for possible virulence or avirulence phenotypes. We show that the T3E SseF of S. enterica triggers hypersensitive response (HR)-like symptoms, a hallmark of effector-triggered immunity in plants, either when transiently expressed in leaves of N. benthamiana by Agrobacterium tumefaciens infiltration or when delivered by Xanthomonas campestris pv vesicatoria (Xcv) through the type III secretion system. The ability of SseF to elicit HR-like symptoms was lost upon silencing of suppressor of G2 allele of skp1 (SGT1), indicating that the S. enterica T3E is probably recognized by an R protein in N. benthamiana. Xcv translocating an AvrRpt2-SseF fusion protein was restricted in multiplication within leaves of N. benthamiana. Bacterial growth was not impaired but symptom development was rather accelerated in a compatible interaction with susceptible pepper (Capsicum annuum) plants. We conclude that the S. enterica T3E SseF is probably recognized by the plant immune system in N. benthamiana, resulting in effector-triggered immunity.
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Affiliation(s)
- Şuayib Üstün
- Department Biologie, Lehrstuhl für Biochemie, Friedrich Alexander Universität Erlangen-Nürnberg, Staudtstr. 5, 91058 Erlangen, Germany
| | - Petra Müller
- Infektionsbiologische Abteilung im Mikrobiologischen Institut, Universitätsklinikum Erlangen, Wasserturmstr. 3-5, 91054 Erlangen, Germany
| | - Ralf Palmisano
- Department Biologie, Lehrstuhl für Biochemie, Friedrich Alexander Universität Erlangen-Nürnberg, Staudtstr. 5, 91058 Erlangen, Germany
| | - Michael Hensel
- Infektionsbiologische Abteilung im Mikrobiologischen Institut, Universitätsklinikum Erlangen, Wasserturmstr. 3-5, 91054 Erlangen, Germany
| | - Frederik Börnke
- Department Biologie, Lehrstuhl für Biochemie, Friedrich Alexander Universität Erlangen-Nürnberg, Staudtstr. 5, 91058 Erlangen, Germany
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21
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Gustin JK, Douglas JL, Bai Y, Moses AV. Ubiquitination of BST-2 protein by HIV-1 Vpu protein does not require lysine, serine, or threonine residues within the BST-2 cytoplasmic domain. J Biol Chem 2012; 287:14837-50. [PMID: 22383521 DOI: 10.1074/jbc.m112.349928] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The cellular protein BST-2/CD317/Tetherin has been shown to inhibit the release of HIV-1 and other enveloped viruses from infected cells. The HIV-1 accessory protein Vpu binds to both BST-2 and βTrCP, a substrate-recognition subunit for the SCF (Skip1-Cullin1-F-box protein) E3 ubiquitin ligase complex. This interaction leads to both the degradation of BST-2 and the enhancement of viral egress. Recently BST-2 was shown to be ubiquitinated in this process. Here we have confirmed the Vpu- and βTrCP-dependent multi/polyubiquitination of BST-2. Ubiquitinated BST-2 accumulated in cells treated with a lysosomal inhibitor but not a proteasomal inhibitor. Additionally, we observed that a BST-2 mutant deleted for its cytosolically exposed lysine residues is also ubiquitinated. Subsequent experiments suggested that Vpu promotes BST-2 ubiquitination upon amino acid residues bearing hydroxyl- but not thiol-bearing side chains. However, a BST-2 mutant bearing substitutions for its cytoplasmically exposed Ser, Thr, and Lys residues was still down-regulated, ubiquitinated, and degraded in a Vpu-dependent manner. Our results suggest that Vpu may target either the BST-2 cytoplasmic Tyr residues or the NH(2) terminus itself for ubiquitination.
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Affiliation(s)
- Jean K Gustin
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, Oregon 97006, USA.
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22
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Ponts N, Saraf A, Chung DWD, Harris A, Prudhomme J, Washburn MP, Florens L, Le Roch KG. Unraveling the ubiquitome of the human malaria parasite. J Biol Chem 2011; 286:40320-30. [PMID: 21930698 PMCID: PMC3220526 DOI: 10.1074/jbc.m111.238790] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Revised: 09/13/2011] [Indexed: 11/06/2022] Open
Abstract
Malaria is one of the deadliest infectious diseases worldwide. The most severe form is caused by the eukaryotic protozoan parasite Plasmodium falciparum. Recent studies have highlighted the importance of post-translational regulations for the parasite's progression throughout its life cycle, protein ubiquitylation being certainly one of the most abundant. The specificity of its components and the wide range of biological processes in which it is involved make the ubiquitylation pathway a promising source of suitable targets for anti-malarial drug development. Here, we combined immunofluorescent microscopy, biochemical assays, in silico prediction, and mass spectrometry analysis using the multidimensional protein identification technology, or MudPIT, to describe the P. falciparum ubiquitome. We found that ubiquitin conjugates are detected at every morphological stage of the parasite erythrocytic cycle. Furthermore, we detected that more than half of the parasite's proteome represents possible targets for ubiquitylation, especially proteins found to be present at the most replicative stage of the asexual cycle, the trophozoite stage. A large proportion of ubiquitin conjugates were also detected at the schizont stage, consistent with a cell activity slowdown to prepare for merozoite differentiation and invasion. Finally, for the first time in the human malaria parasite, our results strongly indicate the presence of heterologous mixed conjugations, SUMO/UB. This discovery suggests that sumoylated proteins may be regulated by ubiquitylation in P. falciparum. Altogether, our results present the first stepping stone toward a better understanding of ubiquitylation and its role(s) in the biology of the human malaria parasite.
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Affiliation(s)
- Nadia Ponts
- From the Department of Cell Biology and Neuroscience, University of California, Riverside, California 92521 and
| | - Anita Saraf
- the Stowers Institute for Medical Research, Kansas City, Missouri 64110
| | - Duk-Won D. Chung
- From the Department of Cell Biology and Neuroscience, University of California, Riverside, California 92521 and
| | - Alona Harris
- From the Department of Cell Biology and Neuroscience, University of California, Riverside, California 92521 and
| | - Jacques Prudhomme
- From the Department of Cell Biology and Neuroscience, University of California, Riverside, California 92521 and
| | | | - Laurence Florens
- the Stowers Institute for Medical Research, Kansas City, Missouri 64110
| | - Karine G. Le Roch
- From the Department of Cell Biology and Neuroscience, University of California, Riverside, California 92521 and
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23
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Cui J, Shao F. Biochemistry and cell signaling taught by bacterial effectors. Trends Biochem Sci 2011; 36:532-40. [DOI: 10.1016/j.tibs.2011.07.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Revised: 07/08/2011] [Accepted: 07/18/2011] [Indexed: 12/22/2022]
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24
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Abstract
Ubiquitination, the covalent attachment of ubiquitin molecules to proteins, is emerging as a widely utilized mechanism for rapidly regulating cell signaling. Recent studies indicate that ubiquitination plays potent roles in regulating a variety of signals in both innate and adaptive immune cells. Here, we will review recent studies of ubiquitin ligases, ubiquitin chain linkages, and ubiquitin binding proteins that highlight the diversity and specificity of ubiquitin dependent functions in immune cells. We will also review studies that shed light on how ubiquitination signals are integrated in cell-type-specific fashion to regulate the immune system in vivo.
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Affiliation(s)
- Barbara A Malynn
- Department of Medicine, Biomedical Sciences Program, University of California, San Francisco, San Francisco, CA 94143-0451, USA
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25
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How ubiquitination and autophagy participate in the regulation of the cell response to bacterial infection. Biol Cell 2011; 102:621-34. [PMID: 21077843 PMCID: PMC2975374 DOI: 10.1042/bc20100101] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Bacterial infection relies on the micro-organism's ability to orchestrate the host's cell signalling such that the immune response is not activated. Conversely, the host cell has dedicated signalling pathways for coping with intrusions by pathogens. The autophagy of foreign micro-organisms (known as xenophagy) has emerged as one of the most powerful of these pathways, although the triggering mode remains largely unknown. In the present paper, we discuss the role that certain post-translational modifications (primarily ubiquitination) may play in the activation of xenophagy and how some bacteria have evolved mechanisms to subvert or hijack this process. In particular, we address the role played by P62/SQSTM1 (sequestosome 1). Finally, we discuss how autophagy can be subverted to eliminate bacteria-induced danger signals.
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26
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Lin DYW, Diao J, Zhou D, Chen J. Biochemical and structural studies of a HECT-like ubiquitin ligase from Escherichia coli O157:H7. J Biol Chem 2011; 286:441-9. [PMID: 20980253 PMCID: PMC3013003 DOI: 10.1074/jbc.m110.167643] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Revised: 09/28/2010] [Indexed: 11/21/2022] Open
Abstract
Many microbial pathogens deliver effector proteins via the type III secretion system into infected host cells. Elucidating the function of these effectors is essential for our understanding of pathogenesis. Here, we describe biochemical and structural characterization of an effector protein (NleL) from Escherichia coli O157:H7, a widespread pathogen causing severe foodborne diseases. We show that NleL functionally and structurally mimics eukaryotic HECT E3 ligases and catalyzes formation of unanchored polyubiquitin chains using Lys(6) and Lys(48) linkage. The catalytic cysteine residue forms a thioester intermediate with ubiquitin. The structure of NleL contains two domains, a β-helix domain formed by pentapeptide repeats and a bilobed catalytic domain reminiscent of the N- and C-lobe architecture of HECT E3s. Six structures of NleL observed in two crystal forms revealed a large range of different positions of the C-lobe relative to the N-lobe, indicating that the helix linking the two lobes is extremely flexible. Comparing the structure of NleL with that of the Salmonella homolog SopA showed that the orientation of the C-lobes differ by as much as 108°, suggesting that large movements of the C-lobe may be required to facilitate the transfer of ubiquitin from E2 to the substrate. These results provide critical knowledge toward understanding the molecular mechanism by which pathogens utilize the host ubiquitination system during infection.
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Affiliation(s)
| | - Jianbo Diao
- the Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Daoguo Zhou
- From the Department of Biological Sciences, Purdue University and
| | - Jue Chen
- From the Department of Biological Sciences, Purdue University and
- Howard Hughes Medical Institute, West Lafayette, Indiana 47907 and
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27
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Abstract
A variety of bacterial intracellular pathogens target the host cell ubiquitin system during invasion, a process that involves transient but fundamental changes in the actin cytoskeleton and plasma membrane. These changes are induced by bacterial proteins, which can be surface associated, secreted or injected directly into the host cell. Here, the invasion strategies of two extensively studied intracellular bacteria, Salmonella enterica serovar Typhimurium and Listeria monocytogenes, are used to illustrate some of the diverse ways by which bacterial pathogens intersect the host cell ubiquitin pathway.
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Affiliation(s)
- Olivia Steele-Mortimer
- Laboratory of Intracellular Parasites, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, MT 59840, USA.
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28
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Jubelin G, Taieb F, Duda DM, Hsu Y, Samba-Louaka A, Nobe R, Penary M, Watrin C, Nougayrède JP, Schulman BA, Stebbins CE, Oswald E. Pathogenic bacteria target NEDD8-conjugated cullins to hijack host-cell signaling pathways. PLoS Pathog 2010; 6:e1001128. [PMID: 20941356 PMCID: PMC2947998 DOI: 10.1371/journal.ppat.1001128] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Accepted: 09/01/2010] [Indexed: 11/22/2022] Open
Abstract
The cycle inhibiting factors (Cif), produced by pathogenic bacteria isolated from vertebrates and invertebrates, belong to a family of molecules called cyclomodulins that interfere with the eukaryotic cell cycle. Cif blocks the cell cycle at both the G1/S and G2/M transitions by inducing the stabilization of cyclin-dependent kinase inhibitors p21waf1 and p27kip1. Using yeast two-hybrid screens, we identified the ubiquitin-like protein NEDD8 as a target of Cif. Cif co-compartmentalized with NEDD8 in the host cell nucleus and induced accumulation of NEDD8-conjugated cullins. This accumulation occurred early after cell infection and correlated with that of p21 and p27. Co-immunoprecipitation revealed that Cif interacted with cullin-RING ubiquitin ligase complexes (CRLs) through binding with the neddylated forms of cullins 1, 2, 3, 4A and 4B subunits of CRL. Using an in vitro ubiquitylation assay, we demonstrate that Cif directly inhibits the neddylated CUL1-associated ubiquitin ligase activity. Consistent with this inhibition and the interaction of Cif with several neddylated cullins, we further observed that Cif modulates the cellular half-lives of various CRL targets, which might contribute to the pathogenic potential of diverse bacteria. Among the arsenal of virulence factors used by bacterial pathogens to infect and manipulate their hosts, cyclomodulins are a growing family of bacterial toxins that interfere with the eukaryotic cell-cycle. Cif is one of these cyclomodulins produced by both mammalian and invertebrate pathogenic bacteria. Cif blocks the host cell cycle by inducing the accumulation of two regulators of cell cycle progression: the cyclin-dependent kinase inhibitors p21 and p27. To decipher the mode of action of Cif, we performed yeast two-hybrid screenings. We show that Cif binds to NEDD8 and induce accumulation of neddylated cullins early after infection. Cullins are scaffold components of cullin-RING ubiquitin ligases (CRLs), which ubiquitinate proteins and target them for degradation by the 26S proteasome. We demonstrate that Cif directly inhibits the ubiquitin ligase activity of these CRLs and consequently the targeting of p21 and p27 for ubiquitin-dependent degradation. Targeting at NEDD8 represents a novel strategy for modulation of host cell functions by bacterial pathogens. By inhibiting the most prominent class of ubiquitin-ligases, Cif controls the stability of a cohort of key regulators and impinge on not only cell cycle progression but also on many cellular and biological processes such as immunity, development, transcription, and cell signaling.
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Affiliation(s)
- Grégory Jubelin
- INRA, UMR 1225, Toulouse, France
- Université de Toulouse; ENVT; UMR 1225; Toulouse, France
| | - Frédéric Taieb
- INRA, UMR 1225, Toulouse, France
- Université de Toulouse; ENVT; UMR 1225; Toulouse, France
| | - David M. Duda
- Howard Hughes Medical Institute, St. Jude Children's Research Hospital, Department of Structural Biology, Memphis, Tennessee, United States of America
| | - Yun Hsu
- Laboratory of Structural Microbiology, Rockefeller University, New York, New York, United States of America
| | - Ascel Samba-Louaka
- INRA, UMR 1225, Toulouse, France
- Université de Toulouse; ENVT; UMR 1225; Toulouse, France
| | - Rika Nobe
- INRA, UMR 1225, Toulouse, France
- Université de Toulouse; ENVT; UMR 1225; Toulouse, France
| | - Marie Penary
- INRA, UMR 1225, Toulouse, France
- Université de Toulouse; ENVT; UMR 1225; Toulouse, France
| | - Claude Watrin
- INRA, UMR 1225, Toulouse, France
- Université de Toulouse; ENVT; UMR 1225; Toulouse, France
| | | | - Brenda A. Schulman
- Howard Hughes Medical Institute, St. Jude Children's Research Hospital, Department of Structural Biology, Memphis, Tennessee, United States of America
| | - C. Erec Stebbins
- Laboratory of Structural Microbiology, Rockefeller University, New York, New York, United States of America
- * E-mail: (CES); (EO)
| | - Eric Oswald
- INRA, UMR 1225, Toulouse, France
- Université de Toulouse; ENVT; UMR 1225; Toulouse, France
- Université de Toulouse; UPS; Faculté de Médecine; Toulouse, France
- CHU de Toulouse; Institut Fédératif de Biologie; Laboratoire de Bactériologie-Hygiène; Toulouse, France
- * E-mail: (CES); (EO)
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29
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Camborde L, Planchais S, Tournier V, Jakubiec A, Drugeon G, Lacassagne E, Pflieger S, Chenon M, Jupin I. The ubiquitin-proteasome system regulates the accumulation of Turnip yellow mosaic virus RNA-dependent RNA polymerase during viral infection. THE PLANT CELL 2010; 22:3142-52. [PMID: 20823192 PMCID: PMC2965540 DOI: 10.1105/tpc.109.072090] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2009] [Revised: 08/01/2010] [Accepted: 08/22/2010] [Indexed: 05/19/2023]
Abstract
Replication of positive-strand RNA viruses, the largest group of plant viruses, is initiated by viral RNA-dependent RNA polymerase (RdRp). Given its essential function in viral replication, understanding the regulation of RdRp is of great importance. Here, we show that Turnip yellow mosaic virus (TYMV) RdRp (termed 66K) is degraded by the proteasome at late time points during viral infection and that the accumulation level of 66K affects viral RNA replication in infected Arabidopsis thaliana cells. We mapped the cis-determinants responsible for 66K degradation within its N-terminal noncatalytic domain, but we conclude that 66K is not a natural N-end rule substrate. Instead, we show that a proposed PEST sequence within 66K functions as a transferable degradation motif. In addition, several Lys residues that constitute target sites for ubiquitylation were mapped; mutation of these Lys residues leads to stabilization of 66K. Altogether, these results demonstrate that TYMV RdRp is a target of the ubiquitin-proteasome system in plant cells and support the idea that proteasomal degradation may constitute yet another fundamental level of regulation of viral replication.
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30
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Wu B, Skarina T, Yee A, Jobin MC, DiLeo R, Semesi A, Fares C, Lemak A, Coombes BK, Arrowsmith CH, Singer AU, Savchenko A. NleG Type 3 effectors from enterohaemorrhagic Escherichia coli are U-Box E3 ubiquitin ligases. PLoS Pathog 2010; 6:e1000960. [PMID: 20585566 PMCID: PMC2891834 DOI: 10.1371/journal.ppat.1000960] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2010] [Accepted: 05/24/2010] [Indexed: 01/11/2023] Open
Abstract
NleG homologues constitute the largest family of Type 3 effectors delivered by pathogenic E. coli, with fourteen members in the enterohaemorrhagic (EHEC) O157:H7 strain alone. Identified recently as part of the non-LEE-encoded (Nle) effector set, this family remained uncharacterised and shared no sequence homology to other proteins including those of known function. The C-terminal domain of NleG2-3 (residues 90 to 191) is the most conserved region in NleG proteins and was solved by NMR. Structural analysis of this structure revealed the presence of a RING finger/U-box motif. Functional assays demonstrated that NleG2-3 as well as NleG5-1, NleG6-2 and NleG9' family members exhibited a strong autoubiquitination activity in vitro; a characteristic usually expressed by eukaryotic ubiquitin E3 ligases. When screened for activity against a panel of 30 human E2 enzymes, the NleG2-3 and NleG5-1 homologues showed an identical profile with only UBE2E2, UBE2E3 and UBE2D2 enzymes supporting NleG activity. Fluorescence polarization analysis yielded a binding affinity constant of 56+/-2 microM for the UBE2D2/NleG5-1 interaction, a value comparable with previous studies on E2/E3 affinities. The UBE2D2 interaction interface on NleG2-3 defined by NMR chemical shift perturbation and mutagenesis was shown to be generally similar to that characterised for human RING finger ubiquitin ligases. The alanine substitutions of UBE2D2 residues Arg5 and Lys63, critical for activation of eukaryotic E3 ligases, also significantly decreased both NleG binding and autoubiquitination activity. These results demonstrate that bacteria-encoded NleG effectors are E3 ubiquitin ligases analogous to RING finger and U-box enzymes in eukaryotes.
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Affiliation(s)
- Bin Wu
- Division of Cancer Genomics and Proteomics, Ontario Cancer Institute, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Tatiana Skarina
- Banting and Best Department for Medical Research, University of Toronto, C.H. Best Institute, Toronto, Ontario, Canada
| | - Adelinda Yee
- Division of Cancer Genomics and Proteomics, Ontario Cancer Institute, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Marie-Claude Jobin
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Banting and Best Department for Medical Research, University of Toronto, C.H. Best Institute, Toronto, Ontario, Canada
| | - Rosa DiLeo
- Banting and Best Department for Medical Research, University of Toronto, C.H. Best Institute, Toronto, Ontario, Canada
| | - Anthony Semesi
- Division of Cancer Genomics and Proteomics, Ontario Cancer Institute, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Christophe Fares
- Division of Cancer Genomics and Proteomics, Ontario Cancer Institute, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Alexander Lemak
- Division of Cancer Genomics and Proteomics, Ontario Cancer Institute, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Brian K. Coombes
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Cheryl H. Arrowsmith
- Division of Cancer Genomics and Proteomics, Ontario Cancer Institute, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Banting and Best Department for Medical Research, University of Toronto, C.H. Best Institute, Toronto, Ontario, Canada
| | - Alexander U. Singer
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Banting and Best Department for Medical Research, University of Toronto, C.H. Best Institute, Toronto, Ontario, Canada
| | - Alexei Savchenko
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Banting and Best Department for Medical Research, University of Toronto, C.H. Best Institute, Toronto, Ontario, Canada
- * E-mail:
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31
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Joshi MV, Mann SG, Antelmann H, Widdick DA, Fyans JK, Chandra G, Hutchings MI, Toth I, Hecker M, Loria R, Palmer T. The twin arginine protein transport pathway exports multiple virulence proteins in the plant pathogen Streptomyces scabies. Mol Microbiol 2010; 77:252-71. [PMID: 20487278 DOI: 10.1111/j.1365-2958.2010.07206.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Summary Streptomyces scabies is one of a group of organisms that causes the economically important disease potato scab. Analysis of the S. scabies genome sequence indicates that it is likely to secrete many proteins via the twin arginine protein transport (Tat) pathway, including several proteins whose coding sequences may have been acquired through horizontal gene transfer and share a common ancestor with proteins in other plant pathogens. Inactivation of the S. scabies Tat pathway resulted in pleiotropic phenotypes including slower growth rate and increased permeability of the cell envelope. Comparison of the extracellular proteome of the wild type and DeltatatC strains identified 73 predicted secretory proteins that were present in reduced amounts in the tatC mutant strain, and 47 Tat substrates were verified using a Tat reporter assay. The DeltatatC strain was almost completely avirulent on Arabidopsis seedlings and was delayed in attaching to the root tip relative to the wild-type strain. Genes encoding 14 candidate Tat substrates were individually inactivated, and seven of these mutants were reduced in virulence compared with the wild-type strain. We conclude that the Tat pathway secretes multiple proteins that are required for full virulence.
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Affiliation(s)
- Madhumita V Joshi
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
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32
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Pajerowska-Mukhtar K, Dong X. A kiss of death--proteasome-mediated membrane fusion and programmed cell death in plant defense against bacterial infection. Genes Dev 2009; 23:2449-54. [PMID: 19884251 DOI: 10.1101/gad.1861609] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Eukaryotes have evolved various means for controlled and organized cellular destruction, known as programmed cell death (PCD). In plants, PCD is a crucial regulatory mechanism in multiple physiological processes, including terminal differentiation, senescence, and disease resistance. In this issue of Genes & Development, Hatsugai and colleagues (pp. 2496-2506) demonstrate a novel plant defense strategy to trigger bacteria-induced PCD, involving proteasome-dependent tonoplast and plasma membrane fusion followed by discharge of vacuolar antimicrobial and death-inducing contents into the apoplast.
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