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Zhang Y, Yu L, Yang M, Han B, Luo J, Jing R. Model fusion for predicting unconventional proteins secreted by exosomes using deep learning. Proteomics 2024:e2300184. [PMID: 38643383 DOI: 10.1002/pmic.202300184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/22/2024]
Abstract
Unconventional secretory proteins (USPs) are vital for cell-to-cell communication and are necessary for proper physiological processes. Unlike classical proteins that follow the conventional secretory pathway via the Golgi apparatus, these proteins are released using unconventional pathways. The primary modes of secretion for USPs are exosomes and ectosomes, which originate from the endoplasmic reticulum. Accurate and rapid identification of exosome-mediated secretory proteins is crucial for gaining valuable insights into the regulation of non-classical protein secretion and intercellular communication, as well as for the advancement of novel therapeutic approaches. Although computational methods based on amino acid sequence prediction exist for predicting unconventional proteins secreted by exosomes (UPSEs), they suffer from significant limitations in terms of algorithmic accuracy. In this study, we propose a novel approach to predict UPSEs by combining multiple deep learning models that incorporate both protein sequences and evolutionary information. Our approach utilizes a convolutional neural network (CNN) to extract protein sequence information, while various densely connected neural networks (DNNs) are employed to capture evolutionary conservation patterns.By combining six distinct deep learning models, we have created a superior framework that surpasses previous approaches, achieving an ACC score of 77.46% and an MCC score of 0.5406 on an independent test dataset.
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Affiliation(s)
- Yonglin Zhang
- Department of Clinical Pharmacy and Pharmacy Management, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
| | - Lezheng Yu
- School of Chemistry and Materials Science, Guizhou Education University, Guiyang, Guizhou, China
| | - Ming Yang
- Department of Clinical Pharmacy and Pharmacy Management, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
| | - Bin Han
- GCP Center/Institute of Drug Clinical Trials, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Jiesi Luo
- Basic Medical College, Southwest Medical University, Luzhou, Sichuan, China
| | - Runyu Jing
- School of Cyber Science and Engineering, Sichuan University, Chengdu, Sichuan, China
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Ostan NKH, Cole GB, Wang FZ, Reichheld SE, Moore G, Pan C, Yu R, Lai CCL, Sharpe S, Lee HO, Schryvers AB, Moraes TF. A secreted bacterial protein protects bacteria from cationic antimicrobial peptides by entrapment in phase-separated droplets. PNAS Nexus 2024; 3:pgae139. [PMID: 38633880 PMCID: PMC11022072 DOI: 10.1093/pnasnexus/pgae139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 03/26/2024] [Indexed: 04/19/2024]
Abstract
Mammalian hosts combat bacterial infections through the production of defensive cationic antimicrobial peptides (CAPs). These immune factors are capable of directly killing bacterial invaders; however, many pathogens have evolved resistance evasion mechanisms such as cell surface modification, CAP sequestration, degradation, or efflux. We have discovered that several pathogenic and commensal proteobacteria, including the urgent human threat Neisseria gonorrhoeae, secrete a protein (lactoferrin-binding protein B, LbpB) that contains a low-complexity anionic domain capable of inhibiting the antimicrobial activity of host CAPs. This study focuses on a cattle pathogen, Moraxella bovis, that expresses the largest anionic domain of the LbpB homologs. We used an exhaustive biophysical approach employing circular dichroism, biolayer interferometry, cross-linking mass spectrometry, microscopy, size-exclusion chromatography with multi-angle light scattering coupled to small-angle X-ray scattering (SEC-MALS-SAXS), and NMR to understand the mechanisms of LbpB-mediated protection against CAPs. We found that the anionic domain of this LbpB displays an α-helical secondary structure but lacks a rigid tertiary fold. The addition of antimicrobial peptides derived from lactoferrin (i.e. lactoferricin) to the anionic domain of LbpB or full-length LbpB results in the formation of phase-separated droplets of LbpB together with the antimicrobial peptides. The droplets displayed a low rate of diffusion, suggesting that CAPs become trapped inside and are no longer able to kill bacteria. Our data suggest that pathogens, like M. bovis, leverage anionic intrinsically disordered domains for the broad recognition and neutralization of antimicrobials via the formation of biomolecular condensates.
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Affiliation(s)
- Nicholas K H Ostan
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Gregory B Cole
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Flora Zhiqi Wang
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Sean E Reichheld
- Molecular Medicine Program, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Gaelen Moore
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Chuxi Pan
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Ronghua Yu
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB T2N 4N1, Canada
| | | | - Simon Sharpe
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
- Molecular Medicine Program, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Hyun O Lee
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Anthony B Schryvers
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Trevor F Moraes
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
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Park DD, Xu G, Park SS, Haigh NE, Phoomak C, Wongkham S, Maverakis E, Lebrilla CB. Combined analysis of secreted proteins and glycosylation identifies prognostic features in cholangiocarcinoma. J Cell Physiol 2024; 239:e31147. [PMID: 37921263 PMCID: PMC10939962 DOI: 10.1002/jcp.31147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 09/05/2023] [Accepted: 10/16/2023] [Indexed: 11/04/2023]
Abstract
Secreted proteins are overexpressed in cholangiocarcinoma (CCA) and actively involved in promoting metastatic spread. Many of these proteins possess one or more sites of glycosylation and their various glycoforms have potential utility as prognostic or diagnostic biomarkers. To evaluate the effects of secretome glycosylation on patient outcome, we elucidated the glycosylation patterns of proteins secreted by parental and metastatic CCA cells using liquid chromatography-mass spectrometry. Our analysis showed that the secretome of CCA cells was dominated by fucosylated and fucosialylated glycoforms. Based on the glycan and protein profiles, we evaluated the combined prognostic significance of glycosyltransferases and secretory proteins. Significantly, genes encoding fucosyltransferases and sialyltransferases showed favorable prognostic effects when combined with secretory protein-coding gene expression, particularly thrombospondin-1. Combining these measures may provide improved risk assessment for CCA and be used to indicate stages of disease progression.
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Affiliation(s)
| | - Gege Xu
- Department of Chemistry, University of California, Davis, CA, 95616 USA
| | - Simon S. Park
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215 USA
| | - Nathan E. Haigh
- Department of Dermatology, University of California, Davis School of Medicine, Sacramento, CA, 95817 USA
| | - Chatchai Phoomak
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Thailand
| | - Sopit Wongkham
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Thailand
| | - Emanual Maverakis
- Department of Dermatology, University of California, Davis School of Medicine, Sacramento, CA, 95817 USA
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Du Y, Li J, Chen S, Xia Y, Jin K. Pathogenicity analysis and comparative genomics reveal the different infection strategies between the generalist Metarhizium anisopliae and the specialist Metarhizium acridum. Pest Manag Sci 2024; 80:820-836. [PMID: 37794279 DOI: 10.1002/ps.7812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 08/28/2023] [Accepted: 09/30/2023] [Indexed: 10/06/2023]
Abstract
BACKGROUND The fungal genera Metarhizium contain many important multiple species that are used as biocontrol agents and as model organisms for exploring insect-fungal interactions. Metarhizium spp. exhibit different traits of pathogenicity, suggesting that the pathogenesis can be quite distinctive. However, the underlying differences in their pathogenesis remain poorly understood. RESULTS Pathogenicity analysis showed that Metarhizium anisopliae (strain CQMa421) displayed higher virulence against oriental migratory locusts, Locusta migratoria manilensis (Meyen), than the acridid-specific specie Metarhizium acridum (strain CQMa102). Relative to M. acridum, M. anisopliae possessed a higher conidial hydrophobicity, increased ability to penetrate the host, accelerated growth under hypoxia and enhanced ability for the utilization of different carbon sources. Different distributions of carbohydrate epitopes at cell wall surface of M. anisopliae might also contribute to successful evasion of host immune defenses. Comparative genomics showed that M. anisopliae has 98 more virulence-related secreted proteins (133) than M. acridum (35), which can be functionally classified as hydrolases, virulence effectors, cell wall degradation and stress tolerance-related proteins, and helpful to the cuticle penetration and host internal environment adaption. In addition, differences in genomic clusters specifically related to secondary metabolites, including the clusters of Indole-NRPS hybrid, T1PKS-NRPS like hybrid, Betalactone, Fungal-Ripp and NRPS-Terpene hybrid, may lead to differences in core virulence-related secondary metabolite genes in M. acridum (18) and M. anisopliae (36). CONCLUSION The comparative study provided new insights into the different infection strategies between M. anisopliae and M. acridum, and further facilitate the identification of virulence-related genes for the improvement of mycoinsecticides. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Yanru Du
- School of Life Sciences, Chongqing University, Chongqing, P. R. China
- Chongqing Engineering Research Center for Fungal Insecticide, Chongqing, P. R. China
- Key Laboratory of Gene Function and Regulation Technologies under Chongqing Municipal Education Commission, Chongqing, P. R. China
| | - Jun Li
- School of Life Sciences, Chongqing University, Chongqing, P. R. China
- Chongqing Engineering Research Center for Fungal Insecticide, Chongqing, P. R. China
- Key Laboratory of Gene Function and Regulation Technologies under Chongqing Municipal Education Commission, Chongqing, P. R. China
| | - Shaopeng Chen
- Tobacco Leaf Branch of Chongqing Tobacco Company of China Tobacco Corporation, Chongqing, P. R. China
| | - Yuxian Xia
- School of Life Sciences, Chongqing University, Chongqing, P. R. China
- Chongqing Engineering Research Center for Fungal Insecticide, Chongqing, P. R. China
- Key Laboratory of Gene Function and Regulation Technologies under Chongqing Municipal Education Commission, Chongqing, P. R. China
| | - Kai Jin
- School of Life Sciences, Chongqing University, Chongqing, P. R. China
- Chongqing Engineering Research Center for Fungal Insecticide, Chongqing, P. R. China
- Key Laboratory of Gene Function and Regulation Technologies under Chongqing Municipal Education Commission, Chongqing, P. R. China
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5
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Hou G, Wang X, Wang A, Yuan L, Zheng Q, Xiao H, Wang H. The role of secreted proteins in efferocytosis. Front Cell Dev Biol 2024; 11:1332482. [PMID: 38259511 PMCID: PMC10800375 DOI: 10.3389/fcell.2023.1332482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
The clearance of apoptotic cells known as efferocytosis is the final stage of apoptosis, and includes the recognition, phagocytosis, and degradation of apoptotic cells. The maintenance of tissue homeostasis requires the daily elimination of billions of apoptotic cells from the human body via the process of efferocytosis. Accordingly, aberrations in efferocytosis underlie a growing list of diseases, including atherosclerosis, cancer, and infections. During the initial phase of apoptosis, "Eat-Me" signals are exposed and recognized by phagocytes either directly through phagocyte receptors or indirectly through secreted proteins that function as bridge molecules that cross-link dying cells to phagocytes. Here, we set out to provide a comprehensive review of the molecular mechanisms and biological significance of secreted proteins in apoptotic cell clearance. Specifically, it focuses on how these secreted proteins act as bridging molecules to facilitate the clearance process.
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Affiliation(s)
| | | | | | | | | | - Hui Xiao
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Hui Wang
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
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Zhou Y, Chen H, Jiang H, Yao Q, Zhu H. Characteristics of a lipase ArEstA with lytic activity against drug-resistant pathogen from a novel myxobacterium, Archangium lipolyticum sp. nov. Front Microbiol 2024; 14:1320827. [PMID: 38239728 PMCID: PMC10794672 DOI: 10.3389/fmicb.2023.1320827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 12/04/2023] [Indexed: 01/22/2024] Open
Abstract
Bacteriolytic myxobacteria are versatile micropredators and are proposed as potential biocontrol agents against diverse bacterial and fungal pathogens. Isolation of new myxobacteria species and exploration of effective predatory products are necessary for successful biocontrol of pathogens. In this study, a myxobacterium strain CY-1 was isolated from a soil sample of a pig farm using the Escherichia coli baiting method. Based on the morphological observation, physiological test, 16S rRNA gene sequence, and genomic data, strain CY-1 was identified as a novel species of the myxobacterial genus Archangium, for which the name Archangium lipolyticum sp. nov. was proposed. Subsequent predation tests indicated that the strain efficiently lysed drug-resistant pathogens, with a higher predatory activity against E. coli 64 than Staphylococcus aureus GDMCC 1.771 (MRSA). The lysis of extracellular proteins against ester-bond-containing substrates (tributyrin, tween 80, egg-yolk, and autoclaved drug-resistant pathogens) inspired the mining of secreted predatory products with lipolytic activity. Furthermore, a lipase ArEstA was identified from the genome of CY-1, and the heterologously expressed and purified enzyme showed bacteriolytic activity against Gram-negative bacteria E. coli 64 but not against Gram-positive MRSA, possibly due to different accessibility of enzyme to lipid substrates in different preys. Our research not only provided a novel myxobacterium species and a candidate enzyme for the development of new biocontrol agents but also reported an experimental basis for further study on different mechanisms of secreted predatory products in myxobacterial killing and degrading of Gram-negative and Gram-positive preys.
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Affiliation(s)
- Yang Zhou
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Haixin Chen
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- Guangdong Key Laboratory for Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Hongxia Jiang
- Guangdong Key Laboratory for Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Qing Yao
- College of Horticulture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangdong Engineering Research Center for Litchi, South China Agricultural University, Guangzhou, China
| | - Honghui Zhu
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
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7
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Dawood AS, Zhao G, He Y, Lu D, Wang S, Zhang H, Chen Y, Hu C, Chen H, Schieck E, Guo A. Comparative Proteomic Analysis of Secretory Proteins of Mycoplasma bovis and Mycoplasma mycoides subsp. mycoides Investigates Virulence and Discovers Important Diagnostic Biomarkers. Vet Sci 2023; 10:685. [PMID: 38133236 PMCID: PMC10748157 DOI: 10.3390/vetsci10120685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/24/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023] Open
Abstract
The most important pathogenic Mycoplasma species in bovines are Mycoplasma bovis (M. bovis) and Mycoplasma mycoides subsp. mycoides (Mmm). Mmm causes contagious bovine pleuropneumonia (CBPP), which is a severe respiratory disease widespread in sub-Saharan Africa but eradicated in several countries, including China. M. bovis is an important cause of the bovine respiratory disease complex (BRD), characterized worldwide by pneumonia, arthritis, and mastitis. Secreted proteins of bacteria are generally considered virulence factors because they can act as toxins, adhesins, and virulent enzymes in infection. Therefore, this study performed a comparative proteomic analysis of the secreted proteins of M. bovis and Mmm in order to find some virulence-related factors as well as discover differential diagnostic biomarkers for these bovine mycoplasmas. The secretome was extracted from both species, and liquid chromatography-tandem mass spectrometry was used, which revealed 55 unique secreted proteins of M. bovis, 44 unique secreted proteins of Mmm, and 4 homologous proteins. In the M. bovis secretome, 19 proteins were predicted to be virulence factors, while 4 putative virulence factors were identified in the Mmm secretome. In addition, five unique secreted proteins of Mmm were expressed and purified, and their antigenicity was confirmed by Western blotting assay and indirect ELISA. Among them, Ts1133 and Ts0085 were verified as potential candidates for distinguishing Mmm infection from M. bovis infection.
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Affiliation(s)
- Ali Sobhy Dawood
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (A.S.D.); (Y.H.); (D.L.); (S.W.); (H.Z.); (Y.C.); (C.H.); (H.C.)
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan 430070, China
- International Research Center for Animal Disease, Ministry of Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Infectious Diseases, Faculty of Veterinary Medicine, University of Sadat City, Sadat City 32897, Egypt
| | - Gang Zhao
- Key Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources in the Western China, School of Life Sciences, Ningxia University, Yinchuan 750021, China;
| | - Yujia He
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (A.S.D.); (Y.H.); (D.L.); (S.W.); (H.Z.); (Y.C.); (C.H.); (H.C.)
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan 430070, China
- International Research Center for Animal Disease, Ministry of Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Doukun Lu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (A.S.D.); (Y.H.); (D.L.); (S.W.); (H.Z.); (Y.C.); (C.H.); (H.C.)
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan 430070, China
- International Research Center for Animal Disease, Ministry of Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Shujuan Wang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (A.S.D.); (Y.H.); (D.L.); (S.W.); (H.Z.); (Y.C.); (C.H.); (H.C.)
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan 430070, China
- International Research Center for Animal Disease, Ministry of Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hui Zhang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (A.S.D.); (Y.H.); (D.L.); (S.W.); (H.Z.); (Y.C.); (C.H.); (H.C.)
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan 430070, China
- International Research Center for Animal Disease, Ministry of Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yingyu Chen
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (A.S.D.); (Y.H.); (D.L.); (S.W.); (H.Z.); (Y.C.); (C.H.); (H.C.)
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan 430070, China
- International Research Center for Animal Disease, Ministry of Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Changmin Hu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (A.S.D.); (Y.H.); (D.L.); (S.W.); (H.Z.); (Y.C.); (C.H.); (H.C.)
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan 430070, China
- International Research Center for Animal Disease, Ministry of Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Huanchun Chen
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (A.S.D.); (Y.H.); (D.L.); (S.W.); (H.Z.); (Y.C.); (C.H.); (H.C.)
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan 430070, China
- International Research Center for Animal Disease, Ministry of Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Elise Schieck
- International Livestock Research Institute, Nairobi 00100, Kenya
| | - Aizhen Guo
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (A.S.D.); (Y.H.); (D.L.); (S.W.); (H.Z.); (Y.C.); (C.H.); (H.C.)
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan 430070, China
- International Research Center for Animal Disease, Ministry of Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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Saruuljavkhlan B, Alfaray RI, Oyuntsetseg K, Gantuya B, Khangai A, Renchinsengee N, Matsumoto T, Akada J, Azzaya D, Davaadorj D, Yamaoka Y. Study of Helicobacter pylori Isolated from a High-Gastric-Cancer-Risk Population: Unveiling the Comprehensive Analysis of Virulence-Associated Genes including Secretion Systems, and Genome-Wide Association Study. Cancers (Basel) 2023; 15:4528. [PMID: 37760497 PMCID: PMC10526929 DOI: 10.3390/cancers15184528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/25/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND The prevalence of gastric cancer in Mongolia, in East Asia, remains the highest in the world. However, most Helicobacter pylori strains in Mongolia have a less virulent Western-type CagA. We aimed to determine how H. pylori genomic variation affected gastric diseases, especially gastric cancer, based on comprehensive genome analysis. METHODS We identified a set of 274 virulence-associated genes in H. pylori, including virulence factor and outer membrane protein (OMP) genes, the type four secretion system gene cluster, and 13 well-known virulence gene genotypes in 223 H. pylori strains and their associations with gastric cancer and other gastric diseases. We conducted a genome-wide association study on 158 H. pylori strains (15 gastric cancer and 143 non-gastric cancer strains). RESULTS Out of 274 genes, we found 13 genes were variable depending on disease outcome, especially iron regulating OMP genes. H. pylori strains from Mongolia were divided into two main subgroups: subgroup (Sg1) with high risk and Sg2 with low risk for gastric cancer. The general characteristics of Sg1 strains are that they possess more virulence genotype genes. We found nine non-synonymous single nucleotide polymorphisms in seven genes that are linked with gastric cancer strains. CONCLUSIONS Highly virulent H. pylori strains may adapt through host-influenced genomic variations, potentially impacting gastric carcinogenesis.
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Grants
- 18KK0266, 19H03473, 21H00346, 22H02871, 17K09353, 21K07898, 18K16182, 21K08010 Grants-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 2021B13 Research Center for GLOBAL and LOCAL Infectious Diseases, Oita University
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Affiliation(s)
- Batsaikhan Saruuljavkhlan
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu 879-5593, Oita, Japan; (B.S.); (R.I.A.); (A.K.); (N.R.); (T.M.); (J.A.)
| | - Ricky Indra Alfaray
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu 879-5593, Oita, Japan; (B.S.); (R.I.A.); (A.K.); (N.R.); (T.M.); (J.A.)
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya 60286, East Java, Indonesia
| | - Khasag Oyuntsetseg
- Endoscopy Center, Mongolia Japan Hospital, Mongolian National University of Medical Sciences, Ulaanbaatar 14210, Mongolia; (K.O.); (B.G.)
| | - Boldbaatar Gantuya
- Endoscopy Center, Mongolia Japan Hospital, Mongolian National University of Medical Sciences, Ulaanbaatar 14210, Mongolia; (K.O.); (B.G.)
- Department of Gastroenterology and Hepatology, Mongolian National University of Medical Sciences, Ulaanbaatar 14210, Mongolia; (D.A.); (D.D.)
| | - Ayush Khangai
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu 879-5593, Oita, Japan; (B.S.); (R.I.A.); (A.K.); (N.R.); (T.M.); (J.A.)
| | - Namsrai Renchinsengee
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu 879-5593, Oita, Japan; (B.S.); (R.I.A.); (A.K.); (N.R.); (T.M.); (J.A.)
| | - Takashi Matsumoto
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu 879-5593, Oita, Japan; (B.S.); (R.I.A.); (A.K.); (N.R.); (T.M.); (J.A.)
| | - Junko Akada
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu 879-5593, Oita, Japan; (B.S.); (R.I.A.); (A.K.); (N.R.); (T.M.); (J.A.)
| | - Dashdorj Azzaya
- Department of Gastroenterology and Hepatology, Mongolian National University of Medical Sciences, Ulaanbaatar 14210, Mongolia; (D.A.); (D.D.)
| | - Duger Davaadorj
- Department of Gastroenterology and Hepatology, Mongolian National University of Medical Sciences, Ulaanbaatar 14210, Mongolia; (D.A.); (D.D.)
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu 879-5593, Oita, Japan; (B.S.); (R.I.A.); (A.K.); (N.R.); (T.M.); (J.A.)
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya 60286, East Java, Indonesia
- The Research Center for GLOBAL and LOCAL Infectious Diseases (RCGLID), Oita University, Yufu 870-1192, Oita, Japan
- Department of Medicine, Gastroenterology and Hepatology Section, Baylor College of Medicine, Houston, TX 77030, USA
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9
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Oh Y, Ingram T, Shekasteband R, Adhikari T, Louws FJ, Dean RA. Tissues and mechanisms associated with Verticillium wilt resistance in tomato using bi-grafted near-isogenic lines. J Exp Bot 2023; 74:4685-4706. [PMID: 37184211 PMCID: PMC10433936 DOI: 10.1093/jxb/erad182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 05/12/2023] [Indexed: 05/16/2023]
Abstract
Host resistance is the primary means to control Verticillium dahliae, a soil-borne pathogen causing major losses on a broad range of plants, including tomato. The tissues and mechanisms responsible for resistance remain obscure. In the field, resistant tomato used as rootstocks does not confer resistance. Here, we created bi-grafted plants with near-isogenic lines (NILs) exhibiting (Ve1) or lacking (ve1) resistance to V. dahliae race 1. Ten days after inoculation, scion and rootstock tissues were subjected to differential gene expression and co-expression network analyses. Symptoms only developed in susceptible scions regardless of the rootstock. Infection caused more dramatic alteration of tomato gene expression in susceptible compared with resistant tissues, including pathogen receptor, signaling pathway, pathogenesis-related protein, and cell wall modification genes. Differences were observed between scions and rootstocks, primarily related to physiological processes in these tissues. Gene expression in scions was influenced by the rootstock genotype. A few genes were associated with the Ve1 genotype, which was independent of infection or tissue type. Several were physically clustered, some near the Ve1 locus on chromosome 9. Transcripts mapped to V. dahliae were dominated by secreted candidate effector proteins. These findings advance knowledge of molecular mechanisms underlying the tomato-V. dahliae interaction.
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Affiliation(s)
- Yeonyee Oh
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
| | - Thomas Ingram
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
| | - Reza Shekasteband
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695, USA
| | - Tika Adhikari
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
| | - Frank J Louws
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695, USA
| | - Ralph A Dean
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
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10
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Mittenbühler MJ, Jedrychowski MP, Van Vranken JG, Sprenger HG, Wilensky S, Dumesic PA, Sun Y, Tartaglia A, Bogoslavski D, A M, Xiao H, Blackmore KA, Reddy A, Gygi SP, Chouchani ET, Spiegelman BM. Isolation of extracellular fluids reveals novel secreted bioactive proteins from muscle and fat tissues. Cell Metab 2023; 35:535-549.e7. [PMID: 36681077 PMCID: PMC9998376 DOI: 10.1016/j.cmet.2022.12.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 10/24/2022] [Accepted: 12/21/2022] [Indexed: 01/21/2023]
Abstract
Proteins are secreted from cells to send information to neighboring cells or distant tissues. Because of the highly integrated nature of energy balance systems, there has been particular interest in myokines and adipokines. These are challenging to study through proteomics because serum or plasma contains highly abundant proteins that limit the detection of proteins with lower abundance. We show here that extracellular fluid (EF) from muscle and fat tissues of mice shows a different protein composition than either serum or tissues. Mass spectrometry analyses of EFs from mice with physiological perturbations, like exercise or cold exposure, allowed the quantification of many potentially novel myokines and adipokines. Using this approach, we identify prosaposin as a secreted product of muscle and fat. Prosaposin expression stimulates thermogenic gene expression and induces mitochondrial respiration in primary fat cells. These studies together illustrate the utility of EF isolation as a discovery tool for adipokines and myokines.
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Affiliation(s)
- Melanie J Mittenbühler
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Mark P Jedrychowski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Hans-Georg Sprenger
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Sarah Wilensky
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Phillip A Dumesic
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Yizhi Sun
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Andrea Tartaglia
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Dina Bogoslavski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Mu A
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Haopeng Xiao
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Katherine A Blackmore
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Anita Reddy
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Edward T Chouchani
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Bruce M Spiegelman
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
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11
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Abstract
Owing to its high disability and mortality rates, stroke has been the second leading cause of death worldwide. Since the pathological mechanisms of stroke are not fully understood, there are few clinical treatment strategies available with an exception of tissue plasminogen activator (tPA), the only FDA-approved drug for the treatment of ischemic stroke. Angiogenesis is an important protective mechanism that promotes neural regeneration and functional recovery during the pathophysiological process of stroke. Thus, inducing angiogenesis in the peri-infarct area could effectively improve hemodynamics, and promote vascular remodeling and recovery of neurovascular function after ischemic stroke. In this review, we summarize the cellular and molecular mechanisms affecting angiogenesis after cerebral ischemia registered in PubMed, and provide pro-angiogenic strategies for exploring the treatment of ischemic stroke, including endothelial progenitor cells, mesenchymal stem cells, growth factors, cytokines, non-coding RNAs, etc.
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12
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Liu J, Maxwell M, Cuddihy T, Crawford T, Bassetti M, Hyde C, Peigneur S, Tytgat J, Undheim EAB, Mobli M. ScrepYard: An online resource for disulfide-stabilized tandem repeat peptides. Protein Sci 2023; 32:e4566. [PMID: 36644825 PMCID: PMC9885460 DOI: 10.1002/pro.4566] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 01/05/2023] [Accepted: 01/12/2023] [Indexed: 01/17/2023]
Abstract
Receptor avidity through multivalency is a highly sought-after property of ligands. While readily available in nature in the form of bivalent antibodies, this property remains challenging to engineer in synthetic molecules. The discovery of several bivalent venom peptides containing two homologous and independently folded domains (in a tandem repeat arrangement) has provided a unique opportunity to better understand the underpinning design of multivalency in multimeric biomolecules, as well as how naturally occurring multivalent ligands can be identified. In previous work, we classified these molecules as a larger class termed secreted cysteine-rich repeat-proteins (SCREPs). Here, we present an online resource; ScrepYard, designed to assist researchers in identification of SCREP sequences of interest and to aid in characterizing this emerging class of biomolecules. Analysis of sequences within the ScrepYard reveals that two-domain tandem repeats constitute the most abundant SCREP domain architecture, while the interdomain "linker" regions connecting the functional domains are found to be abundant in amino acids with short or polar sidechains and contain an unusually high abundance of proline residues. Finally, we demonstrate the utility of ScrepYard as a virtual screening tool for discovery of putatively multivalent peptides, by using it as a resource to identify a previously uncharacterized serine protease inhibitor and confirm its predicted activity using an enzyme assay.
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Affiliation(s)
- Junyu Liu
- Centre for Advanced ImagingThe University of QueenslandSt. LuciaQueenslandAustralia
| | - Michael Maxwell
- Centre for Advanced ImagingThe University of QueenslandSt. LuciaQueenslandAustralia
| | - Thom Cuddihy
- Queensland Cyber Infrastructure Foundation Ltd.The University of QueenslandSt. LuciaQueenslandAustralia,Centre for Clinical ResearchThe University of QueenslandSt. LuciaQueenslandAustralia
| | - Theo Crawford
- Centre for Advanced ImagingThe University of QueenslandSt. LuciaQueenslandAustralia
| | - Madeline Bassetti
- Queensland Cyber Infrastructure Foundation Ltd.The University of QueenslandSt. LuciaQueenslandAustralia
| | - Cameron Hyde
- Queensland Cyber Infrastructure Foundation Ltd.The University of QueenslandSt. LuciaQueenslandAustralia,University of the Sunshine CoastMaroochydoreQueenslandAustralia
| | - Steve Peigneur
- Toxicology and PharmacologyUniversity of Leuven (KU Leuven)LeuvenBelgium
| | - Jan Tytgat
- Toxicology and PharmacologyUniversity of Leuven (KU Leuven)LeuvenBelgium
| | - Eivind A. B. Undheim
- Centre for Advanced ImagingThe University of QueenslandSt. LuciaQueenslandAustralia,Centre for Ecological and Evolutionary Synthesis, Department of BiosciencesUniversity of OsloOsloNorway
| | - Mehdi Mobli
- Centre for Advanced ImagingThe University of QueenslandSt. LuciaQueenslandAustralia
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13
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Khajuria YP, Akhoon BA, Kaul S, Dhar MK. Secretomic Insights into the Pathophysiology of Venturia inaequalis: The Causative Agent of Scab, a Devastating Apple Tree Disease. Pathogens 2022; 12. [PMID: 36678413 DOI: 10.3390/pathogens12010066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 12/10/2022] [Accepted: 12/27/2022] [Indexed: 01/04/2023] Open
Abstract
Apple scab, caused by Venturia inaequalis, is one of the world's most commercially significant apple diseases. The fungi have a catastrophic impact on apples, causing considerable losses in fruit quality and productivity in many apple-growing locations despite numerous control agents. Fungi secrete various effectors and other virulence-associated proteins that suppress or alter the host's immune system, and several such proteins were discovered in this work. Using state-of-the-art bioinformatics techniques, we examined the V. inaequalis reference genome (EU-B04), resulting in the identification of 647 secreted proteins, of which 328 were classified as small secreted proteins (SSPs), with 76.52% of SSPs identified as anticipated effector proteins. The more prevalent CAZyme proteins were the enzymes engaged in plant cell wall disintegration (targeting pectin and xylanase), adhesion and penetration (Cutinases/acetyl xylan esterase), and reactive oxygen species formation (multicopper oxidases). Furthermore, members of the S9 prolyl oligopeptidase family were identified as the most abundant host defense peptidases. Several known effector proteins were discovered to be expressed during the V. inaequalis infection process on apple leaves. The present study provides valuable data that can be used to develop new strategies for controlling apple scab.
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14
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Bao J, Wang Z, Chen M, Chen S, Chen X, Xie J, Tang W, Zheng H, Wang Z. Pan-Genomics Reveals a New Variation Pattern of Secreted Proteins in Pyricularia oryzae. J Fungi (Basel) 2022; 8. [PMID: 36547571 DOI: 10.3390/jof8121238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/19/2022] [Accepted: 11/20/2022] [Indexed: 11/24/2022] Open
Abstract
(1) Background: Pyricularia oryzae, the causal agent of rice blast disease, is one of the major rice pathogens. The complex population structure of P. oryzae facilitates the rapid virulence variations, which make the blast disease a serious challenge for global food security. There is a large body of existing genomics research on P. oryzae, however the population structure at the pan-genome level is not clear, and the mechanism of genetic divergence and virulence variations of different sub-populations is also unknown. (2) Methods: Based on the genome data published in the NCBI, we constructed a pan-genome database of P. oryzae, which consisted of 156 strains (117 isolated from rice and 39 isolated from other hosts). (3) Results: The pan-genome contained a total of 24,100 genes (12,005 novel genes absent in the reference genome 70-15), including 16,911 (~70%) core genes (population frequency ≥95%) and 1378 (~5%) strain-specific genes (population frequency ≤5%). Gene presence-absence variation (PAV) based clustering analysis of the population structure of P. oryzae revealed four subgroups (three from rice and one from other hosts). Interestingly, the cloned avirulence genes and conventional secreted proteins (SPs, with signal peptides) were enriched in the high-frequency regions and significantly associated with transposable elements (TEs), while the unconventional SPs (without signal peptides) were enriched in the low-frequency regions and not associated significantly with TEs. This pan-genome will expand the breadth and depth of the rice blast fungus reference genome, and also serve as a new blueprint for scientists to further study the pathogenic mechanism and virulence variation of the rice blast fungus.
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15
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Cheng X, Zhao C, Gao L, Zeng L, Xu Y, Liu F, Huang J, Liu L, Liu S, Zhang X. Alternative splicing reprogramming in fungal pathogen Sclerotinia sclerotiorum at different infection stages on Brassica napus. Front Plant Sci 2022; 13:1008665. [PMID: 36311105 PMCID: PMC9597501 DOI: 10.3389/fpls.2022.1008665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Alternative splicing (AS) is an important post-transcriptional mechanism promoting the diversity of transcripts and proteins to regulate various life processes in eukaryotes. Sclerotinia stem rot is a major disease of Brassica napus caused by Sclerotinia sclerotiorum, which causes severe yield loss in B. napus production worldwide. Although many transcriptome studies have been carried out on the growth, development, and infection of S. sclerotiorum, the genome-wide AS events of S. sclerotiorum remain poorly understood, particularly at the infection stage. In this study, transcriptome sequencing was performed to systematically explore the genome-scale AS events of S. sclerotiorum at five important infection stages on a susceptible oilseed rape cultivar. A total of 130 genes were predicted to be involved in AS from the S. sclerotiorum genome, among which 98 genes were differentially expressed and may be responsible for AS reprogramming for its successful infection. In addition, 641 differential alternative splicing genes (DASGs) were identified during S. sclerotiorum infection, accounting for 5.76% of all annotated S. sclerotiorum genes, and 71 DASGs were commonly found at all the five infection stages. The most dominant AS type of S. sclerotiorum was found to be retained introns or alternative 3' splice sites. Furthermore, the resultant AS isoforms of 21 DASGs became pseudogenes, and 60 DASGs encoded different putative proteins with different domains. More importantly, 16 DASGs of S. sclerotiorum were found to have signal peptides and possibly encode putative effectors to facilitate the infection of S. sclerotiorum. Finally, about 69.27% of DASGs were found to be non-differentially expressed genes, indicating that AS serves as another important way to regulate the infection of S. sclerotiorum on plants besides the gene expression level. Taken together, this study provides a genome-wide landscape for the AS of S. sclerotiorum during infection as well as an important resource for further elucidating the pathogenic mechanisms of S. sclerotiorum.
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Affiliation(s)
- Xiaohui Cheng
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the People’s Republic of China (PRC), Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Chuanji Zhao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the People’s Republic of China (PRC), Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Lixia Gao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Lingyi Zeng
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the People’s Republic of China (PRC), Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yu Xu
- Hebei Provincial Academy of Ecological and Environmental Sciences, Shijiazhuang, China
| | - Fan Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the People’s Republic of China (PRC), Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Junyan Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the People’s Republic of China (PRC), Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Lijiang Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the People’s Republic of China (PRC), Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Shengyi Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the People’s Republic of China (PRC), Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiong Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the People’s Republic of China (PRC), Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
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16
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Robles J, Pintado‐Berninches L, Boukich I, Escudero B, de los Rios V, Bartolomé RA, Jaén M, Martín‐Regalado Á, Fernandez‐Aceñero MJ, Imbaud JI, Casal JI. A prognostic six-gene expression risk-score derived from proteomic profiling of the metastatic colorectal cancer secretome. J Pathol Clin Res 2022; 8:495-508. [PMID: 36134447 PMCID: PMC9535096 DOI: 10.1002/cjp2.294] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 07/20/2022] [Accepted: 08/05/2022] [Indexed: 12/29/2022]
Abstract
The necessity to accurately predict recurrence and clinical outcome in early stage colorectal cancer (CRC) is critical to identify those patients who may benefit from adjuvant chemotherapy. Here, we developed and validated a gene-based risk-score algorithm for patient stratification and personalised treatment in early stage disease based on alterations in the secretion of metastasis-related proteins. A quantitative label-free proteomic analysis of the secretome of highly and poorly metastatic CRC cell lines with different genetic backgrounds revealed 153 differentially secreted proteins (fold-change >5). These changes in the secretome were validated at the transcriptomic level. Starting from 119 up-regulated proteins, a six-gene/protein-based prognostic signature composed of IGFBP3, CD109, LTBP1, PSAP, BMP1, and NPC2 was identified after sequential discovery, training, and validation in four different cohorts. This signature was used to develop a risk-score algorithm, named SEC6, for patient stratification. SEC6 risk-score components showed higher expression in the poor prognosis CRC subtypes: consensus molecular subtype 4 (CMS4), CRIS-B, and stem-like. High expression of the signature was also associated with patients showing dMMR, CIMP+ status, and BRAF mutations. In addition, the SEC6 signature was associated with lower overall survival, progression-free interval, and disease-specific survival in stage II and III patients. SEC6-based risk stratification indicated that 5-FU treatment was beneficial for low-risk patients, whereas only aggressive treatments (FOLFOX and FOLFIRI) provided benefits to high-risk patients in stages II and III. In summary, this novel risk-score demonstrates the value of the secretome compartment as a reliable source for the retrieval of biomarkers with high prognostic and chemotherapy-predictive capacity, providing a potential new tool for tailoring decision-making in patient care.
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Affiliation(s)
- Javier Robles
- Protein Alternatives SLMadridSpain,Department of Molecular BiomedicineCentro de Investigaciones Biológicas Margarita Salas, CSICMadridSpain
| | - Laura Pintado‐Berninches
- Department of Molecular BiomedicineCentro de Investigaciones Biológicas Margarita Salas, CSICMadridSpain,Present address:
Biochemistry DepartmentUniversidad Autónoma de MadridMadridSpain
| | - Issam Boukich
- Department of Molecular BiomedicineCentro de Investigaciones Biológicas Margarita Salas, CSICMadridSpain
| | - Beatriz Escudero
- Department of Molecular BiomedicineCentro de Investigaciones Biológicas Margarita Salas, CSICMadridSpain
| | - Vivian de los Rios
- Proteomics Core FacilityCentro de Investigaciones Biológicas Margarita Salas, CSICMadridSpain
| | - Rubén A Bartolomé
- Department of Molecular BiomedicineCentro de Investigaciones Biológicas Margarita Salas, CSICMadridSpain
| | - Marta Jaén
- Department of Molecular BiomedicineCentro de Investigaciones Biológicas Margarita Salas, CSICMadridSpain
| | - Ángela Martín‐Regalado
- Department of Molecular BiomedicineCentro de Investigaciones Biológicas Margarita Salas, CSICMadridSpain
| | - María Jesús Fernandez‐Aceñero
- Pathology DepartmentHospital Clínico San Carlos (HCSC)MadridSpain,Fundación de Investigación Biomédica del HCSC (FIBHCSC)MadridSpain
| | | | - José Ignacio Casal
- Department of Molecular BiomedicineCentro de Investigaciones Biológicas Margarita Salas, CSICMadridSpain
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17
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Rethi-Nagy Z, Abraham E, Udvardy K, Klement E, Darula Z, Pal M, Katona RL, Tubak V, Pali T, Kota Z, Sinka R, Udvardy A, Lipinszki Z. STABILON, a Novel Sequence Motif That Enhances the Expression and Accumulation of Intracellular and Secreted Proteins. Int J Mol Sci 2022; 23:ijms23158168. [PMID: 35897744 PMCID: PMC9332151 DOI: 10.3390/ijms23158168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/17/2022] [Accepted: 07/22/2022] [Indexed: 12/10/2022] Open
Abstract
The dynamic balance of transcriptional and translational regulation together with degron-controlled proteolysis shapes the ever-changing cellular proteome. While a large variety of degradation signals has been characterized, our knowledge of cis-acting protein motifs that can in vivo stabilize otherwise short-lived proteins is very limited. We have identified and characterized a conserved 13-mer protein segment derived from the p54/Rpn10 ubiquitin receptor subunit of the Drosophila 26S proteasome, which fulfills all the characteristics of a protein stabilization motif (STABILON). Attachment of STABILON to various intracellular as well as medically relevant secreted model proteins resulted in a significant increase in their cellular or extracellular concentration in mammalian cells. We demonstrate that STABILON acts as a universal and dual function motif that, on the one hand, increases the concentration of the corresponding mRNAs and, on the other hand, prevents the degradation of short-lived fusion proteins. Therefore, STABILON may lead to a breakthrough in biomedical recombinant protein production.
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Affiliation(s)
- Zsuzsanna Rethi-Nagy
- Biological Research Centre, Institute of Biochemistry, MTA SZBK Lendület Laboratory of Cell Cycle Regulation, ELKH, H-6726 Szeged, Hungary; (Z.R.-N.); (E.A.); (K.U.); (M.P.)
- Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary
| | - Edit Abraham
- Biological Research Centre, Institute of Biochemistry, MTA SZBK Lendület Laboratory of Cell Cycle Regulation, ELKH, H-6726 Szeged, Hungary; (Z.R.-N.); (E.A.); (K.U.); (M.P.)
| | - Katalin Udvardy
- Biological Research Centre, Institute of Biochemistry, MTA SZBK Lendület Laboratory of Cell Cycle Regulation, ELKH, H-6726 Szeged, Hungary; (Z.R.-N.); (E.A.); (K.U.); (M.P.)
| | - Eva Klement
- Single Cell Omics Advanced Core Facility, Hungarian Centre of Excellence for Molecular Medicine (HCEMM), H-6726 Szeged, Hungary; (E.K.); (Z.D.)
- Biological Research Centre, Laboratory of Proteomics Research, ELKH, H-6726 Szeged, Hungary
| | - Zsuzsanna Darula
- Single Cell Omics Advanced Core Facility, Hungarian Centre of Excellence for Molecular Medicine (HCEMM), H-6726 Szeged, Hungary; (E.K.); (Z.D.)
- Biological Research Centre, Laboratory of Proteomics Research, ELKH, H-6726 Szeged, Hungary
| | - Margit Pal
- Biological Research Centre, Institute of Biochemistry, MTA SZBK Lendület Laboratory of Cell Cycle Regulation, ELKH, H-6726 Szeged, Hungary; (Z.R.-N.); (E.A.); (K.U.); (M.P.)
| | | | - Vilmos Tubak
- Creative Laboratory Ltd., H-6726 Szeged, Hungary;
| | - Tibor Pali
- Biological Research Centre, Institute of Biophysics, ELKH, H-6726 Szeged, Hungary; (T.P.); (Z.K.)
| | - Zoltan Kota
- Biological Research Centre, Institute of Biophysics, ELKH, H-6726 Szeged, Hungary; (T.P.); (Z.K.)
| | - Rita Sinka
- Department of Genetics, University of Szeged, H-6726 Szeged, Hungary
- Correspondence: (R.S.); (A.U.); (Z.L.)
| | - Andor Udvardy
- Biological Research Centre, Institute of Biochemistry, MTA SZBK Lendület Laboratory of Cell Cycle Regulation, ELKH, H-6726 Szeged, Hungary; (Z.R.-N.); (E.A.); (K.U.); (M.P.)
- Correspondence: (R.S.); (A.U.); (Z.L.)
| | - Zoltan Lipinszki
- Biological Research Centre, Institute of Biochemistry, MTA SZBK Lendület Laboratory of Cell Cycle Regulation, ELKH, H-6726 Szeged, Hungary; (Z.R.-N.); (E.A.); (K.U.); (M.P.)
- Correspondence: (R.S.); (A.U.); (Z.L.)
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Millar-Haskell CS, Sperduto JL, Slater JH, Thorpe C, Gleghorn JP. Secretion of the disulfide bond generating catalyst QSOX1 from pancreatic tumor cells into the extracellular matrix: association with extracellular vesicles and matrix proteins. J Extracell Biol 2022; 1:e48. [PMID: 36590238 PMCID: PMC9797115 DOI: 10.1002/jex2.48] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Quiescin sulfhydryl oxidase 1 (QSOX1) is a disulfide bond generating catalyst that is overexpressed in solid tumors. Expression of QSOX1 is linked to cancer cell invasion, tumor grade, and extracellular matrix (ECM) protein deposition. While the secreted version of QSOX1 is known to be present in various fluids and secretory tissues, its presence in the ECM of cancer is less understood. To characterize secreted QSOX1, we separated conditioned media based on size and density. We discovered that the majority of secreted QSOX1 resides in the EV-depleted fraction and in the soluble protein fraction. Very little QSOX1 could be detected in the EVP fraction. We used immunofluorescence to image subpopulations of EVs and found QSOX1 in Golgi-derived vesicles and medium/large vesicles, but in general, most extracellular QSOX1 was not attributed to these vesicles. Next, we quantified QSOX1 co-localization with the EV marker Alix. For the medium/large EVs, ~98% contained QSOX1 when fibronectin was used as a coating. However, on collagen coatings, only ~60% of these vesicles contained QSOX1, suggesting differences in EV cargo based on ECM coated surfaces. About 10% of small EVs co-localized with QSOX1 on every ECM protein surface except for collagen (0.64%). We next investigated adhesion of QSOX1 to ECM proteins in vitro and in situ and found that QSOX1 preferentially adheres to fibronectin, laminins, and Matrigel compared to gelatin and collagen. This mechanism was found to be, in part, mediated by the formation of mixed disulfides between QSOX1 and cysteine-rich ECM proteins. In summary, we found that QSOX1 (1) is in subpopulations of medium/large EVs, (2) seems to interact with small Alix+ EVs, and (3) adheres to cysteine-rich ECM proteins, potentially through the formation of intermediate disulfides. These observations offer significant insight into how enzymes, such as QSOX1, can facilitate matrix remodeling events in solid tumor progression.
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Affiliation(s)
| | - John L. Sperduto
- Departments of Biomedical Engineering, University of Delaware, Newark, DE 19716
| | - John H. Slater
- Departments of Biomedical Engineering, University of Delaware, Newark, DE 19716
| | - Colin Thorpe
- Chemistry & Biochemistry, University of Delaware, Newark, DE 19716
| | - Jason P. Gleghorn
- Departments of Biomedical Engineering, University of Delaware, Newark, DE 19716,Address correspondence to J.P.G., 590 Avenue 1743, Newark, DE 19713, Tel:
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Fu Y, Maaβ S, du Teil Espina M, Wolters AHG, Gong Y, de Jong A, Raangs E, Buist G, Westra J, Becher D, van Dijl JM. Connections between Exoproteome Heterogeneity and Virulence in the Oral Pathogen Aggregatibacter actinomycetemcomitans. mSystems 2022; 7:e0025422. [PMID: 35695491 DOI: 10.1128/msystems.00254-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Aggregatibacter actinomycetemcomitans is a Gram-negative bacterial pathogen associated with severe periodontitis and nonoral diseases. Clinical isolates of A. actinomycetemcomitans display a rough (R) colony phenotype with strong adherent properties. Upon prolonged culturing, nonadherent strains with a smooth (S) colony phenotype emerge. To date, most virulence studies on A. actinomycetemcomitans have been performed with S strains of A. actinomycetemcomitans, whereas the virulence of clinical R isolates has received relatively little attention. Since the extracellular proteome is the main bacterial reservoir of virulence factors, the present study was aimed at a comparative analysis of this subproteome fraction for a collection of R isolates and derivative S strains, in order to link particular proteins to the virulence of A. actinomycetemcomitans with serotype b. To assess the bacterial virulence, we applied different infection models based on larvae of the greater wax moth Galleria mellonella, a human salivary gland-derived epithelial cell line, and freshly isolated neutrophils from healthy human volunteers. A total number of 351 extracellular A. actinomycetemcomitans proteins was identified by mass spectrometry, with the S strains consistently showing more extracellular proteins than their parental R isolates. A total of 50 known extracellular virulence factors was identified, of which 15 were expressed by all investigated bacteria. Importantly, the comparison of differences in exoproteome composition and virulence highlights critical roles of 10 extracellular proteins in the different infection models. Together, our findings provide novel clues for understanding the virulence of A. actinomycetemcomitans and for development of potential preventive or therapeutic avenues to neutralize this important oral pathogen. IMPORTANCE Periodontitis is one of the most common inflammatory diseases worldwide, causing high morbidity and decreasing the quality of life of millions of people. The bacterial pathogen Aggregatibacter actinomycetemcomitans is strongly associated with aggressive forms of periodontitis. Moreover, it has been implicated in serious nonoral infections, including endocarditis and brain abscesses. Therefore, it is important to investigate how A. actinomycetemcomitans can cause disease. In the present study, we applied a mass spectrometry approach to make an inventory of the virulence factors secreted by different clinical A. actinomycetemcomitans isolates and derivative strains that emerged upon culturing. We subsequently correlated the secreted virulence factors to the pathogenicity of the investigated bacteria in different infection models. The results show that a limited number of extracellular virulence factors of A. actinomycetemcomitans have central roles in pathogenesis, indicating that they could be druggable targets to prevent or treat oral disease.
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Lu D, Zhang H, Zhang Y, Zhao G, Anwar Khan F, Chen Y, Hu C, Yang L, Chen H, Guo A. Secreted MbovP0145 Promotes IL-8 Expression through Its Interactive β-Actin and MAPK Activation and Contributes to Neutrophil Migration. Pathogens 2021; 10:pathogens10121628. [PMID: 34959583 PMCID: PMC8707762 DOI: 10.3390/pathogens10121628] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/10/2021] [Accepted: 12/11/2021] [Indexed: 11/16/2022] Open
Abstract
Mycoplasma bovis (M. bovis) is an important pathogen of cattle responsible for huge economic losses in the dairy and beef industries worldwide. The proteins secreted by M. bovis are mainly related to its adhesion, invasion, virulence, and intracellular survival and play a role in mycoplasma-host interactions. In our previous study, we found MbovP0145, a secreted protein present in the M. bovis secretome, but little is known about its function. In this study, we assessed the inflammatory characteristics and underlined mechanism of this inflammation of recombinant MbovP0145 (rMbovP0145). For this, bovine lung epithelial cells (EBL) were stimulated by rMbovP0145 to see the IL-8 production in a time- and dose-dependent manner. We observed that rMbovP0145 increased the production of IL-8 via ERK1/2 and P38 pathway activation. Further, the effect of the M. bovis ΔMbov_0145 mutant and its complementary strain on IL-8 mRNA expression was also confirmed. A pulldown assay of the GST-tagged MbovP0145 protein with mass spectrometry demonstrated that β-actin could specifically interact with rMbovP0145 to mediate the IL-8 signaling. As knockdown of β-actin expression with RNA interference in EBL cells decreased the mRNA expression of IL-8 and the phosphorylated ERK1/2 and P38 proteins, whereas disrupted actin polymerization by cytochalasin D led to a significantly higher IL-8 expression and MAPK phosphorylation in rMbovP0145-stimulated cells. Compared to M. bovis HB0801 and its complementary strain, the culture supernatant of EBL cells infected with the M. bovis ΔMbov_0145 mutant induced less neutrophil migration to the lower chamber in a transwell system. In conclusion, MbovP0145 promoted IL-8 expression by interacting with β-actin through activation of the MAPK pathway, thus contributing to neutrophil migration.
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Affiliation(s)
- Doukun Lu
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (D.L.); (H.Z.); (Y.Z.); (G.Z.); (Y.C.); (C.H.); (H.C.)
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Hui Zhang
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (D.L.); (H.Z.); (Y.Z.); (G.Z.); (Y.C.); (C.H.); (H.C.)
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Yiqiu Zhang
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (D.L.); (H.Z.); (Y.Z.); (G.Z.); (Y.C.); (C.H.); (H.C.)
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Gang Zhao
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (D.L.); (H.Z.); (Y.Z.); (G.Z.); (Y.C.); (C.H.); (H.C.)
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Farhan Anwar Khan
- Department of Animal Health, The University of Agriculture, Peshawar 25120, Pakistan;
| | - Yingyu Chen
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (D.L.); (H.Z.); (Y.Z.); (G.Z.); (Y.C.); (C.H.); (H.C.)
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Changmin Hu
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (D.L.); (H.Z.); (Y.Z.); (G.Z.); (Y.C.); (C.H.); (H.C.)
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Liguo Yang
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Huanchun Chen
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (D.L.); (H.Z.); (Y.Z.); (G.Z.); (Y.C.); (C.H.); (H.C.)
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan 430070, China
| | - Aizhen Guo
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (D.L.); (H.Z.); (Y.Z.); (G.Z.); (Y.C.); (C.H.); (H.C.)
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan 430070, China
- Correspondence: ; Tel.: +86-27-87287115
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Labois C, Stempien E, Schneider J, Schaeffer-Reiss C, Bertsch C, Goddard ML, Chong J. Comparative Study of Secreted Proteins, Enzymatic Activities of Wood Degradation and Stilbene Metabolization in Grapevine Botryosphaeria Dieback Fungi. J Fungi (Basel) 2021; 7:568. [PMID: 34356948 PMCID: PMC8303417 DOI: 10.3390/jof7070568] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/08/2021] [Accepted: 07/08/2021] [Indexed: 02/01/2023] Open
Abstract
Botryosphaeriaceae fungi are plant pathogens associated with Botryosphaeria dieback. To better understand the virulence factors of these fungi, we investigated the diversity of secreted proteins and extracellular enzyme activities involved in wood degradation and stilbene metabolization in Neofusicoccumparvum and Diplodiaseriata, which are two major fungi associated with grapevine B. dieback. Regarding the analysis of proteins secreted by the two fungi, our study revealed that N. parvum, known to be more aggressive than D. seriata, was characterized by a higher quantity and diversity of secreted proteins, especially hydrolases and oxidoreductases that are likely involved in cell wall and lignin degradation. In addition, when fungi were grown with wood powder, the extracellular laccase and Mn peroxidase enzyme activities were significantly higher in D. seriata compared to N.parvum. Importantly, our work also showed that secreted Botryosphaeriaceae proteins produced after grapevine wood addition are able to rapidly metabolize the grapevine stilbenes. Overall, a higher diversity of resveratrol and piceatannol metabolization products was found with enzymes of N. parvum compared to D. seriata. This study emphasizes the diversity of secreted virulence factors found in B. dieback fungi and suggests that some resveratrol oligomers produced in grapevine wood after pathogen attack could be formed via pathogenic fungal oxidases.
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Affiliation(s)
- Clément Labois
- Laboratoire Vigne, Biotechnologies et Environnement (LVBE, UPR 3991), Université de Haute Alsace, 68000 Colmar, France; (C.L.); (E.S.); (C.B.)
- Laboratoire d’Innovation Moléculaire et Applications, Université de Haute-Alsace, Université de Strasbourg, CNRS, LIMA, UMR 7042, CEDEX, 68093 Mulhouse, France
| | - Elodie Stempien
- Laboratoire Vigne, Biotechnologies et Environnement (LVBE, UPR 3991), Université de Haute Alsace, 68000 Colmar, France; (C.L.); (E.S.); (C.B.)
| | - Justine Schneider
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, Université de Strasbourg, CNRS, UMR7178, 25 Rue Becquerel, 67087 Strasbourg, France; (J.S.); (C.S.-R.)
| | - Christine Schaeffer-Reiss
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, Université de Strasbourg, CNRS, UMR7178, 25 Rue Becquerel, 67087 Strasbourg, France; (J.S.); (C.S.-R.)
| | - Christophe Bertsch
- Laboratoire Vigne, Biotechnologies et Environnement (LVBE, UPR 3991), Université de Haute Alsace, 68000 Colmar, France; (C.L.); (E.S.); (C.B.)
| | - Mary-Lorène Goddard
- Laboratoire Vigne, Biotechnologies et Environnement (LVBE, UPR 3991), Université de Haute Alsace, 68000 Colmar, France; (C.L.); (E.S.); (C.B.)
- Laboratoire d’Innovation Moléculaire et Applications, Université de Haute-Alsace, Université de Strasbourg, CNRS, LIMA, UMR 7042, CEDEX, 68093 Mulhouse, France
| | - Julie Chong
- Laboratoire Vigne, Biotechnologies et Environnement (LVBE, UPR 3991), Université de Haute Alsace, 68000 Colmar, France; (C.L.); (E.S.); (C.B.)
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22
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Vaz C, Pitarch A, Gómez-Molero E, Amador-García A, Weig M, Bader O, Monteoliva L, Gil C. Mass Spectrometry-Based Proteomic and Immunoproteomic Analyses of the Candida albicans Hyphal Secretome Reveal Diagnostic Biomarker Candidates for Invasive Candidiasis. J Fungi (Basel) 2021; 7:501. [PMID: 34201883 DOI: 10.3390/jof7070501] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/18/2021] [Accepted: 06/18/2021] [Indexed: 01/08/2023] Open
Abstract
Invasive candidiasis (IC) is associated with high morbidity and mortality in hospitalized patients if not diagnosed early. Long-term use of central venous catheters is a predisposing factor for IC. Hyphal forms of Candida albicans (the major etiological agent of IC) are related to invasion of host tissues. The secreted proteins of hyphae are involved in virulence, host interaction, immune response, and immune evasion. To identify IC diagnostic biomarker candidates, we characterized the C. albicans hyphal secretome by gel-free proteomic analysis, and further assessed the antibody-reactivity patterns to this subproteome in serum pools from 12 patients with non-catheter-associated IC (ncIC), 11 patients with catheter-associated IC (cIC), and 11 non-IC patients. We identified 301 secreted hyphal proteins stratified to stem from the extracellular region, cell wall, cell surface, or intracellular compartments. ncIC and cIC patients had higher antibody levels to the hyphal secretome than non-IC patients. Seven secreted hyphal proteins were identified to be immunogenic (Bgl2, Eno1, Pgk1, Glx3, Sap5, Pra1 and Tdh3). Antibody-reactivity patterns to Bgl2, Eno1, Pgk1 and Glx3 discriminated IC patients from non-IC patients, while those to Sap5, Pra1 and Tdh3 differentiated between cIC and non-IC patients. These proteins may be useful for development of future IC diagnostic tests.
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de la Torre EP, Rodríguez-Franco A, Rodríguez-Ortega MJ. Comparative Exoproteome Analysis of Streptococcus suis Human Isolates. Microorganisms 2021; 9:1287. [PMID: 34204746 DOI: 10.3390/microorganisms9061287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 06/03/2021] [Accepted: 06/09/2021] [Indexed: 11/23/2022] Open
Abstract
The swine pathogen Streptococcus suis is a Gram-positive bacterium which causes infections in pigs, with an impact in animal health and in the livestock industry, and it is also an important zoonotic agent. During the infection process, surface and secreted proteins are essential in the interaction between microorganisms and their hosts. Here, we report a comparative proteomic analysis of the proteins released to the extracellular milieu in six human clinical isolates belonging to the highly prevalent and virulent serotype 2. The total secreted content was precipitated and analyzed by GeLC-MS/MS. In the six strains, 144 proteins assigned to each of the categories of extracellular or surface proteins were identified, as well as 680 predicted cytoplasmic proteins, many of which are putative moonlighting proteins. Of the nine predicted signal peptide-I secreted proteins, seven had relevant antigenic potential when they were analyzed through bioinformatic analysis. This is the first work comparing the exoproteome fraction of several human isolates of this important pathogen.
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Marcet-Houben M, Villarino M, Vilanova L, De Cal A, van Kan JAL, Usall J, Gabaldón T, Torres R. Comparative Genomics Used to Predict Virulence Factors and Metabolic Genes among Monilinia Species. J Fungi (Basel) 2021; 7:464. [PMID: 34201288 DOI: 10.3390/jof7060464] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 02/07/2023] Open
Abstract
Brown rot, caused by Monilinia spp., is among the most important diseases in stone fruits, and some pome fruits (mainly apples). This disease is responsible for significant yield losses, particularly in stone fruits, when weather conditions favorable for disease development appear. To achieve future sustainable strategies to control brown rot on fruit, one potential approach will be to characterize genomic variation among Monilinia spp. to define, among others, the capacity to infect fruit in this genus. In the present work, we performed genomic and phylogenomic comparisons of five Monilinia species and inferred differences in numbers of secreted proteins, including CAZy proteins and other proteins important for virulence. Duplications specific to Monilinia were sparse and, overall, more genes have been lost than gained. Among Monilinia spp., low variability in the CAZome was observed. Interestingly, we identified several secondary metabolism clusters based on similarity to known clusters, and among them was a cluster with homology to pyriculol that could be responsible for the synthesis of chloromonilicin. Furthermore, we compared sequences of all strains available from NCBI of these species to assess their MAT loci and heterokaryon compatibility systems. Our comparative analyses provide the basis for future studies into understanding how these genomic differences underlie common or differential abilities to interact with the host plant.
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25
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Nakamura R, Nakajima D, Sato H, Endo Y, Ohara O, Kawashima Y. A Simple Method for In-Depth Proteome Analysis of Mammalian Cell Culture Conditioned Media Containing Fetal Bovine Serum. Int J Mol Sci 2021; 22:ijms22052565. [PMID: 33806404 PMCID: PMC7961985 DOI: 10.3390/ijms22052565] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 02/26/2021] [Accepted: 02/27/2021] [Indexed: 12/02/2022] Open
Abstract
A conditioned medium of a cell culture is widely used for various biological applications and frequently analyzed to characterize the functional proteins responsible for observed biological functions. However, a large number of abundant proteins in fetal bovine serum (FBS), usually included in the conditioned medium of a mammalian cell culture medium, hampers in-depth proteomic analysis by liquid chromatography–tandem mass spectrometry (LC-MS/MS). For a deep proteomic analysis of a conditioned medium by LC-MS/MS, we developed a simple albumin depletion approach coupled with data-independent acquisition (DIA)-mode LC-MS/MS for the conditioned medium of mammalian cells in this study. The results showed that this approach enabled the detection of more than 3700 cell-derived proteins in the cell culture supernatant containing FBS. We further demonstrated the potency of this approach by analyzing proteins in the conditioned media of HeLa cells with and without tumor necrosis factor (TNF) stimulation: >40 differentially accumulated proteins, including four cytokines, upon TNF stimulation were identified in the culture media, which were hardly detected by conventional proteome approaches in the literature.
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Affiliation(s)
- Ren Nakamura
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan; (R.N.); (D.N.); (H.S.); (O.O.)
| | - Daisuke Nakajima
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan; (R.N.); (D.N.); (H.S.); (O.O.)
| | - Hironori Sato
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan; (R.N.); (D.N.); (H.S.); (O.O.)
| | - Yusuke Endo
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan;
| | - Osamu Ohara
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan; (R.N.); (D.N.); (H.S.); (O.O.)
| | - Yusuke Kawashima
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan; (R.N.); (D.N.); (H.S.); (O.O.)
- Correspondence: ; Tel.: +81-438-52-3580
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Maarof M, Mohd Nadzir M, Sin Mun L, Fauzi MB, Chowdhury SR, Idrus RBH, Lokanathan Y. Hybrid Collagen Hydrogel/Chondroitin-4-Sulphate Fortified with Dermal Fibroblast Conditioned Medium for Skin Therapeutic Application. Polymers (Basel) 2021; 13:508. [PMID: 33567703 DOI: 10.3390/polym13040508] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/03/2021] [Accepted: 02/04/2021] [Indexed: 12/30/2022] Open
Abstract
The current strategy for rapid wound healing treatment involves combining a biomaterial and cell-secreted proteins or biomolecules. This study was aimed at characterizing 3-dimensional (3D) collagen hydrogels fortified with dermal fibroblast-conditioned medium (DFCM) as a readily available acellular skin substitute. Confluent fibroblasts were cultured with serum-free keratinocyte-specific medium (KM1 and KM2) and fibroblast-specific medium (FM) to obtain DFCM. Subsequently, the DFCM was mixed with collagen (Col) hydrogel and chondroitin-4-sulphate (C4S) to fabricate 3D constructs termed Col/C4S/DFCM-KM1, Col/C4S/DFCM-KM2, and Col/C4S/DFCM-FM. The constructs successfully formed soft, semi-solid and translucent hydrogels within 1 h of incubation at 37 °C with strength of <2.5 Newton (N). The Col/C4S/DFCM demonstrated significantly lower turbidity compared to the control groups. The Col/C4S/DFCM also showed a lower percentage of porosity (KM1: 35.15 ± 9.76%; KM2: 6.85 ± 1.60%; FM: 14.14 ± 7.65%) compared to the Col (105.14 ± 11.87%) and Col/C4S (143.44 ± 27.72%) constructs. There were no changes in both swelling and degradation among all constructs. Fourier transform infrared spectrometry showed that all groups consisted of oxygen–hydrogen bonds (O-H) and amide I, II, and III. In conclusion, the Col/C4S/DFCM constructs maintain the characteristics of native collagen and can synergistically deliver essential biomolecules for future use in skin therapeutic applications.
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Ngcala MG, Goche T, Brown AP, Chivasa S, Ngara R. Heat Stress Triggers Differential Protein Accumulation in the Extracellular Matrix of Sorghum Cell Suspension Cultures. Proteomes 2020; 8:29. [PMID: 33105781 PMCID: PMC7709130 DOI: 10.3390/proteomes8040029] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/15/2020] [Accepted: 10/19/2020] [Indexed: 01/13/2023] Open
Abstract
Plants reprogram gene expression as an adaptive response to survive high temperatures. While the identity and functions of intracellular heat stress-responsive proteins have been extensively studied, the heat response of proteins secreted to the extracellular matrix is unknown. Here, we used Sorghum bicolor, a species adapted for growth in hot climates, to investigate the extracellular heat-induced responses. When exposed to 40 C for 72 h, heat-sensitive Arabidopsis cell suspension cultures died, while ICSB338 sorghum cell cultures survived by activation of a transcriptional response characterized by the induction of HSP70 and HSP90 genes. Quantitative proteomic analysis of proteins recovered from cell culture medium revealed specific heat stress-induced protein accumulation within the sorghum secretome. Of the 265 secreted proteins identified, 31 responded to heat (2-fold change), with 84% possessing a predicted signal peptide for targeting to the classical secretory pathway. The differentially accumulated proteins have putative functions in metabolism, detoxification, and protein modifications. A germin (SORBI_3003G427700) was highly heat-inducible at both protein and gene level. Overall, our study reveals new insights into sorghum responses to heat and provides a useful resource of extracellular proteins that could serve as targets for developing thermotolerant crops. Data are available via ProteomeXchange with identifier PXD021536.
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Affiliation(s)
- Mamosa G. Ngcala
- Department of Plant Sciences, Qwaqwa campus, University of the Free State, Phuthadithjaba 9866, South Africa;
| | - Tatenda Goche
- Department of Crop Sciences, Epoch Mine Campus, Gwanda State University, Filabusi, Zimbabwe;
| | - Adrian P. Brown
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK; (A.P.B.); (S.C.)
| | - Stephen Chivasa
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK; (A.P.B.); (S.C.)
| | - Rudo Ngara
- Department of Plant Sciences, Qwaqwa campus, University of the Free State, Phuthadithjaba 9866, South Africa;
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Barger PC, Liles MR, Newton JC. Type II Secretion Is Essential for Virulence of the Emerging Fish Pathogen, Hypervirulent Aeromonas hydrophila. Front Vet Sci 2020; 7:574113. [PMID: 33088835 PMCID: PMC7544816 DOI: 10.3389/fvets.2020.574113] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 08/24/2020] [Indexed: 11/18/2022] Open
Abstract
Hypervirulent Aeromonas hydrophila (vAh) is an emerging pathogen in freshwater aquaculture systems. In the U.S.A., outbreaks of motile aeromonad septicemia associated with vAh result in the loss of over 3 million pounds of channel catfish from Southeastern production systems each year. A. hydrophila is a well-known opportunistic pathogen that secretes degradative and potentially toxigenic proteins, and the rapid mortality that occurs when catfish are challenged with vAh by intraperitoneal injection suggests that vAh-induced motile aeromonad septicemia may be, in part, a toxin-mediated disease. While vAh isolates from carp isolated in China possess complete Type I, Type II, and Type VI secretion systems, many of the US catfish isolates only possess complete Type I and Type II secretions systems. In order to determine the role of secreted proteins in vAh-induced disease, and to determine the extent of protein secretion by the Type II secretion pathway, an exeD secretin mutant was constructed using a recombineering method in the well-characterized US vAh strain, ML09-119. Wild-type and mutant secretomes were analyzed for protein content by SDS-PAGE and by assays for specific enzymes and toxins. Type II secretion-deficient mutants had a near complete loss of secreted proteins and enzyme/toxin activity, including hemolytic and proteolytic activity. The intact Type II secretion system was cloned and used to complement the deletion mutant, ML09-119 exeD, which restored protein secretion and the degradative and toxigenic potential. In vivo challenges in channel catfish resulted in complete attenuation of virulence in ML09-119 exeD, while the complemented mutant was observed to have restored virulence. These results indicate that secreted proteins are critical to vAh virulence, and that the Type II secretion system is the primary secretory pathway utilized for multiple effectors of vAh pathogenesis.
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Affiliation(s)
- Priscilla C. Barger
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
- Biological Sciences, College of Sciences and Math, Auburn University, Auburn, AL, United States
| | - Mark R. Liles
- Biological Sciences, College of Sciences and Math, Auburn University, Auburn, AL, United States
| | - Joseph C. Newton
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
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29
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Sauvage S, Hardouin J. Exoproteomics for Better Understanding Pseudomonas aeruginosa Virulence. Toxins (Basel) 2020; 12:E571. [PMID: 32899849 PMCID: PMC7551764 DOI: 10.3390/toxins12090571] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/25/2020] [Accepted: 09/01/2020] [Indexed: 12/12/2022] Open
Abstract
Pseudomonas aeruginosa is the most common human opportunistic pathogen associated with nosocomial diseases. In 2017, the World Health Organization has classified P. aeruginosa as a critical agent threatening human health, and for which the development of new treatments is urgently necessary. One interesting avenue is to target virulence factors to understand P. aeruginosa pathogenicity. Thus, characterising exoproteins of P. aeruginosa is a hot research topic and proteomics is a powerful approach that provides important information to gain insights on bacterial virulence. The aim of this review is to focus on the contribution of proteomics to the studies of P. aeruginosa exoproteins, highlighting its relevance in the discovery of virulence factors, post-translational modifications on exoproteins and host-pathogen relationships.
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Affiliation(s)
- Salomé Sauvage
- Polymers, Biopolymers, Surface Laboratory, UMR 6270 CNRS, University of Rouen, CEDEX, F-76821 Mont-Saint-Aignan, France;
- PISSARO Proteomics Facility, IRIB, F-76820 Mont-Saint-Aignan, France
| | - Julie Hardouin
- Polymers, Biopolymers, Surface Laboratory, UMR 6270 CNRS, University of Rouen, CEDEX, F-76821 Mont-Saint-Aignan, France;
- PISSARO Proteomics Facility, IRIB, F-76820 Mont-Saint-Aignan, France
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30
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M Alreshidi M, Dunstan RH, M Macdonald M, K Singh V, K Roberts T. Analysis of Cytoplasmic and Secreted Proteins of Staphylococcus aureus Revealed Adaptive Metabolic Homeostasis in Response to Changes in the Environmental Conditions Representative of the Human Wound Site. Microorganisms 2020; 8:E1082. [PMID: 32698515 DOI: 10.3390/microorganisms8071082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/11/2020] [Accepted: 07/15/2020] [Indexed: 11/16/2022] Open
Abstract
The pathogenesis of Staphylococcus aureus is mainly attributed to its capability to adjust to changes in environmental conditions, including those present on human skin or within a wound site. This study investigated the changes in the cytoplasmic and secreted proteins in S. aureus that occurred in response to alterations in the environmental parameters that could be found in the human wound site. In total, sixty differentially regulated cytoplasmic proteins were detected using a label-free quantification approach, and these proteins were classified into ten molecular functions: protein biosynthesis, glycolysis, signal transduction, metabolism, cell cycle, transport, energy generation, cell anchorage, nucleotide biosynthesis and unknown. These changes represented characteristic protein profiles when evaluated by principal component analysis. The bacterium responded to elevated NaCl at pH 6 by decreasing the abundance of the majority of cytoplasmic proteins, while at pH 8 there was an increase in the levels of cytoplasmic proteins in comparison to the untreated cells. The analysis of the secreted proteins showed that there was a high degree of difference in both the intensity and the distribution of many individual protein bands in response to environmental challenges. From these results, it was deduced that specific metabolic homeostasis occurred under each combination of defined environmental conditions.
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31
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Chung YW, Cha J, Han S, Chen Y, Gucek M, Cho HJ, Nakahira K, Choi AMK, Ryu JH, Yoon JH. Apolipoprotein E and Periostin Are Potential Biomarkers of Nasal Mucosal Inflammation. A Parallel Approach of In Vitro and In Vivo Secretomes. Am J Respir Cell Mol Biol 2020; 62:23-34. [PMID: 31194918 DOI: 10.1165/rcmb.2018-0248oc] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
No previously suggested biomarkers of nasal mucosal inflammation have been practically applied in clinical fields, and nasal epithelium-derived secreted proteins as biomarkers have not specifically been investigated. The goal of this study was to identify secreted proteins that dynamically change during the differentiation from basal cells to fully differentiated cells and examine whether nasal epithelium-derived proteins can be used as biomarkers of nasal mucosal inflammation, such as chronic rhinosinusitis. To achieve this goal, we analyzed two secretomes using the isobaric tag for relative and absolute quantification technique. From in vitro secretomes, we identified the proteins altered in apical secretions of primary human nasal epithelial cells according to the degree of differentiation; from in vivo secretomes, we identified the increased proteins in nasal lavage fluids obtained from patients 2 weeks after endoscopic sinus surgery for chronic sinusitis. We then used a parallel approach to identify specific biomarkers of nasal mucosal inflammation; first, we selected apolipoprotein E as a nasal epithelial cell-derived biomarker through screening proteins that were upregulated in both in vitro and in vivo secretomes, and verified highly secreted apolipoprotein E in nasal lavage fluids of the patients by Western blotting. Next, we selected periostin as an inflammatory mediator-inducible biomarker from in vivo secretomes, the secretion of which was not induced under in vitro culture conditions. We demonstrated that those two nasal epithelium-derived proteins are possible biomarkers of nasal mucosal inflammation.
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Affiliation(s)
- Youn Wook Chung
- The Airway Mucus Institute.,Global Research Laboratory for Allergic Airway Disease.,Severance Biomedical Science Institute
| | - Jimin Cha
- Severance Biomedical Science Institute.,Brain Korea 21 PLUS Project for Medical Science, and
| | - Seunghan Han
- Severance Biomedical Science Institute.,Brain Korea 21 PLUS Project for Medical Science, and
| | - Yong Chen
- Proteomics Core Facility, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland; and
| | - Marjan Gucek
- Proteomics Core Facility, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland; and
| | - Hyung-Ju Cho
- The Airway Mucus Institute.,Global Research Laboratory for Allergic Airway Disease.,Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Korea
| | - Kiichi Nakahira
- Division of Pulmonary and Critical Care Medicine, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Augustine M K Choi
- Division of Pulmonary and Critical Care Medicine, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Ji-Hwan Ryu
- Severance Biomedical Science Institute.,Brain Korea 21 PLUS Project for Medical Science, and
| | - Joo-Heon Yoon
- The Airway Mucus Institute.,Global Research Laboratory for Allergic Airway Disease.,Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Korea
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Blango MG, Pschibul A, Rivieccio F, Krüger T, Rafiq M, Jia LJ, Zheng T, Goldmann M, Voltersen V, Li J, Panagiotou G, Kniemeyer O, Brakhage AA. Dynamic Surface Proteomes of Allergenic Fungal Conidia. J Proteome Res 2020; 19:2092-2104. [PMID: 32233371 DOI: 10.1021/acs.jproteome.0c00013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Fungal spores and hyphal fragments play an important role as allergens in respiratory diseases. In this study, we performed trypsin shaving and secretome analyses to identify the surface-exposed proteins and secreted/shed proteins of Aspergillus fumigatus conidia, respectively. We investigated the surface proteome under different conditions, including temperature variation and germination. We found that the surface proteome of resting A. fumigatus conidia is not static but instead unexpectedly dynamic, as evidenced by drastically different surface proteomes under different growth conditions. Knockouts of two abundant A. fumigatus surface proteins, ScwA and CweA, were found to function only in fine-tuning the cell wall stress response, implying that the conidial surface is very robust against perturbations. We then compared the surface proteome of A. fumigatus to other allergy-inducing molds, including Alternaria alternata, Penicillium rubens, and Cladosporium herbarum, and performed comparative proteomics on resting and swollen conidia, as well as secreted proteins from germinating conidia. We detected 125 protein ortholog groups, including 80 with putative catalytic activity, in the extracellular region of all four molds, and 42 nonorthologous proteins produced solely by A. fumigatus. Ultimately, this study highlights the dynamic nature of the A. fumigatus conidial surface and provides targets for future diagnostics and immunotherapy.
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Affiliation(s)
- Matthew G Blango
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (Leibniz-HKI), Jena 07745, Germany
| | - Annica Pschibul
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (Leibniz-HKI), Jena 07745, Germany.,Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University, Jena 07745, Germany
| | - Flora Rivieccio
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (Leibniz-HKI), Jena 07745, Germany.,Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University, Jena 07745, Germany
| | - Thomas Krüger
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (Leibniz-HKI), Jena 07745, Germany
| | - Muhammad Rafiq
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (Leibniz-HKI), Jena 07745, Germany.,Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University, Jena 07745, Germany
| | - Lei-Jie Jia
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (Leibniz-HKI), Jena 07745, Germany
| | - Tingting Zheng
- Department of Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (Leibniz-HKI), Jena 07745, Germany
| | - Marie Goldmann
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (Leibniz-HKI), Jena 07745, Germany.,Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University, Jena 07745, Germany
| | - Vera Voltersen
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (Leibniz-HKI), Jena 07745, Germany
| | - Jun Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong S.A.R., China.,School of Data Science, City University of Hong Kong, Kowloon, Hong Kong S.A.R., China
| | - Gianni Panagiotou
- Department of Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (Leibniz-HKI), Jena 07745, Germany
| | - Olaf Kniemeyer
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (Leibniz-HKI), Jena 07745, Germany.,Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University, Jena 07745, Germany
| | - Axel A Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (Leibniz-HKI), Jena 07745, Germany.,Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University, Jena 07745, Germany
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33
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Tao SQ, Auer L, Morin E, Liang YM, Duplessis S. Transcriptome Analysis of Apple Leaves Infected by the Rust Fungus Gymnosporangium yamadae at Two Sporulation Stages. Mol Plant Microbe Interact 2020; 33:444-461. [PMID: 31765287 DOI: 10.1094/mpmi-07-19-0208-r] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Apple rust disease caused by Gymnosporangium yamadae is one of the major threats to apple orchards. In this study, dual RNA-seq analysis was conducted to simultaneously monitor gene expression profiles of G. yamadae and infected apple leaves during the formation of rust spermogonia and aecia. The molecular mechanisms underlying this compatible interaction at 10 and 30 days postinoculation (dpi) indicate a significant reaction from the host plant and comprise detoxication pathways at the earliest stage and the induction of secondary metabolism pathways at 30 dpi. Such host reactions have been previously reported in other rust pathosystems and may represent a general reaction to rust infection. G. yamadae transcript profiling indicates a conserved genetic program in spermogonia and aecia that is shared with other rust fungi, whereas secretome prediction reveals the presence of specific secreted candidate effector proteins expressed during apple infection. Unexpectedly, the survey of fungal unigenes in the transcriptome assemblies of inoculated and mock-inoculated apple leaves reveals that G. yamadae infection may modify the fungal community composition in the apple phyllosphere at 30 dpi. Collectively, our results provide novel insights into the compatible apple-G. yamadae interaction and advance the knowledge of this heteroecious demicyclic rust fungus.
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Affiliation(s)
- Si-Qi Tao
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing 100083, China
- Université de Lorraine, INRAE, Unité Mixte de Recherche 1136 Interactions Arbres-Microorganismes, 54280, Champenoux, France
| | - Lucas Auer
- Université de Lorraine, INRAE, Unité Mixte de Recherche 1136 Interactions Arbres-Microorganismes, 54280, Champenoux, France
| | - Emmanuelle Morin
- Université de Lorraine, INRAE, Unité Mixte de Recherche 1136 Interactions Arbres-Microorganismes, 54280, Champenoux, France
| | - Ying-Mei Liang
- Museum of Beijing Forestry University, Beijing Forestry University
| | - Sébastien Duplessis
- Université de Lorraine, INRAE, Unité Mixte de Recherche 1136 Interactions Arbres-Microorganismes, 54280, Champenoux, France
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Mazzeo MF, Luongo D, Sashihara T, Rossi M, Siciliano RA. Secretome Analysis of Mouse Dendritic Cells Interacting with a Probiotic Strain of Lactobacillus gasseri. Nutrients 2020; 12:E555. [PMID: 32093322 DOI: 10.3390/nu12020555] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/12/2020] [Accepted: 02/14/2020] [Indexed: 12/18/2022] Open
Abstract
Probiotics play a key role in the modulation of the gut immune system in health and disease and their action is mediated by molecules exposed on the microorganism surface or secreted probiotic-derived factors. In particular, Lactobacillus gasseri OLL2809, a probiotic microorganism isolated from human feces, has the potential to modulate various immune responses. The dendritic cells (DCs) are considered the main players in orchestrating the immune response, and their contact with intestinal microbiota is crucial for the development and homeostasis of gut immunity. To gain a perspective on the molecular mechanisms involved in the maturation process of DCs and investigate factors that could modulate these processes, a differential proteomic analysis was performed on the secretome of immature DCs, mature DCs (mDCs, induced by lipopolysaccharide (LPS)), and immature DCs challenged with L. gasseri OLL2809 before treatment with LPS (LGmDCs). The maturation process of DCs was associated to profound changes in the protein secretome and probiotic pre-treatment led to a dramatic modulation of several secreted proteins of mDC, not only classical immune mediators (i.e., cytokines, complement factors, T cell Receptor ligands) but also proteins involved in the contractile and desmosome machineries. The latter data highlight a novel mechanism by which L. gasseri can modulate the maturation process of DCs, reinforcing the concept of a protective anti-inflammatory role ascribed to this probiotic strain.
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35
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Wang M, Liu B, Ruan R, Zeng Y, Luo J, Li H. Genomic Sequencing of Phyllosticta citriasiana Provides Insight Into Its Conservation and Diversification With Two Closely Related Phyllosticta Species Associated With Citrus. Front Microbiol 2020; 10:2979. [PMID: 31998266 PMCID: PMC6965161 DOI: 10.3389/fmicb.2019.02979] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 12/10/2019] [Indexed: 11/25/2022] Open
Abstract
Phyllosticta capitalensis, Phyllosticta citricarpa, and Phyllosticta citriasiana are three very important Phyllosticta species associated with citrus. P. capitalensis is an endophyte fungus of citrus while P. citricarpa can cause black spot of citrus (e.g., oranges and mandarins). P. citriasiana was identified recently which is the causal agent of the pomelo tan spot. Here, we present the ∼34 Mb genome of P. citriasiana. The genome is organized in 92 contigs, encompassing 9202 predicted genes. Comparative genomic analyses with two other Phyllosticta species (P. citricarpa and P. capitalensis) associated with citrus was conducted to understand their evolutionary conservation and diversification. Pair-wise genome alignments revealed that these species are highly syntenic. All species encode similar numbers of CAZymes and secreted proteins. However, the molecular functions of the secretome showed that each species contains some enzymes with distinct activities. The three Phyllosticta species investigated shared a core set of 7261 protein families. P. capitalensis had the largest set of orphan genes (1991), in complete contrast to that of P. citriasiana (364) and P. citricarpa (262). Most of the orphan genes are functionally unknown, but they contain a certain number of species-specific secreted proteins. A total of 23 secondary metabolites biosynthesis clusters were identified in the three Phyllosticta species, 21 of them being highly conserved among these species while the remaining two showed whole cluster gain and loss polymorphisms or gene content polymorphisms. Taken together, our study reveals insights into the genetic mechanisms of host adaptation of three species of Phyllosticta associated with citrus and paves the way to identify effectors that function in infection of citrus plants.
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Affiliation(s)
- Mingshuang Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Bei Liu
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Ruoxin Ruan
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou, China
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Yibing Zeng
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Jinshui Luo
- Fujian Institute of Tropical Crops, Zhangzhou, China
| | - Hongye Li
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou, China
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36
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Chen G, Chen J, Liu H, Chen S, Zhang Y, Li P, Thierry-Mieg D, Thierry-Mieg J, Mattes W, Ning B, Shi T. Comprehensive Identification and Characterization of Human Secretome Based on Integrative Proteomic and Transcriptomic Data. Front Cell Dev Biol 2019; 7:299. [PMID: 31824949 PMCID: PMC6881247 DOI: 10.3389/fcell.2019.00299] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 11/07/2019] [Indexed: 12/25/2022] Open
Abstract
Secreted proteins (SPs) play important roles in diverse important biological processes; however, a comprehensive and high-quality list of human SPs is still lacking. Here we identified 6,943 high-confidence human SPs (3,522 of them are novel) based on 330,427 human proteins derived from databases of UniProt, Ensembl, AceView, and RefSeq. Notably, 6,267 of 6,943 (90.3%) SPs have the supporting evidences from a large amount of mass spectrometry (MS) and RNA-seq data. We found that the SPs were broadly expressed in diverse tissues as well as human body fluid, and a significant portion of them exhibited tissue-specific expression. Moreover, 14 cancer-specific SPs that their expression levels were significantly associated with the patients’ survival of eight different tumors were identified, which could be potential prognostic biomarkers. Strikingly, 89.21% of 6,943 SPs (2,927 novel SPs) contain known protein domains. Those novel SPs we mainly enriched with the known domains regarding immunity, such as Immunoglobulin V-set and C1-set domain. Specifically, we constructed a user-friendly and freely accessible database, SPRomeDB (www.unimd.org/SPRomeDB), to catalog those SPs. Our comprehensive SP identification and characterization gain insights into human secretome and provide valuable resource for future researches.
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Affiliation(s)
- Geng Chen
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Jiwei Chen
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Huanlong Liu
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Shuangguan Chen
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Yang Zhang
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Peng Li
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Danielle Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
| | - Jean Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
| | - William Mattes
- National Center for Toxicological Research, Food and Drug Administration, Jefferson City, AR, United States
| | - Baitang Ning
- National Center for Toxicological Research, Food and Drug Administration, Jefferson City, AR, United States
| | - Tieliu Shi
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
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Messal M, Slippers B, Naidoo S, Bezuidt O, Kemler M. Active Fungal Communities in Asymptomatic Eucalyptus grandis Stems Differ between a Susceptible and Resistant Clone. Microorganisms 2019; 7:E375. [PMID: 31547186 DOI: 10.3390/microorganisms7100375] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 08/06/2019] [Accepted: 08/09/2019] [Indexed: 11/20/2022] Open
Abstract
Fungi represent a common and diverse part of the microbial communities that associate with plants. They also commonly colonise various plant parts asymptomatically. The molecular mechanisms of these interactions are, however, poorly understood. In this study we use transcriptomic data from Eucalyptus grandis, to demonstrate that RNA-seq data are a neglected source of information to study fungal–host interactions, by exploring the fungal transcripts they inevitably contain. We identified fungal transcripts from E. grandis data based on their sequence dissimilarity to the E. grandis genome and predicted biological functions. Taxonomic classifications identified, amongst other fungi, many well-known pathogenic fungal taxa in the asymptomatic tissue of E. grandis. The comparison of a clone of E. grandis resistant to Chrysoporthe austroafricana with a susceptible clone revealed a significant difference in the number of fungal transcripts, while the number of fungal taxa was not substantially affected. Classifications of transcripts based on their respective biological functions showed that the fungal communities of the two E. grandis clones associate with fundamental biological processes, with some notable differences. To shield the greater host defence machinery in the resistant E. grandis clone, fungi produce more secondary metabolites, whereas the environment for fungi associated with the susceptible E. grandis clone is more conducive for building fungal cellular structures and biomass growth. Secreted proteins included carbohydrate active enzymes that potentially are involved in fungal–plant and fungal–microbe interactions. While plant transcriptome datasets cannot replace the need for designed experiments to probe plant–microbe interactions at a molecular level, they clearly hold potential to add to the understanding of the diversity of plant–microbe interactions.
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38
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Xu Q, Biancalana M, Grant JC, Chiu H, Jaroszewski L, Knuth MW, Lesley SA, Godzik A, Elsliger M, Deacon AM, Wilson IA. Structures of single-layer β-sheet proteins evolved from β-hairpin repeats. Protein Sci 2019; 28:1676-1689. [PMID: 31306512 PMCID: PMC6699103 DOI: 10.1002/pro.3683] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 07/08/2019] [Accepted: 07/08/2019] [Indexed: 11/09/2022]
Abstract
Free-standing single-layer β-sheets are extremely rare in naturally occurring proteins, even though β-sheet motifs are ubiquitous. Here we report the crystal structures of three homologous, single-layer, anti-parallel β-sheet proteins, comprised of three or four twisted β-hairpin repeats. The structures reveal that, in addition to the hydrogen bond network characteristic of β-sheets, additional hydrophobic interactions mediated by small clusters of residues adjacent to the turns likely play a significant role in the structural stability and compensate for the lack of a compact hydrophobic core. These structures enabled identification of a family of secreted proteins that are broadly distributed in bacteria from the human gut microbiome and are putatively involved in the metabolism of complex carbohydrates. A conserved surface patch, rich in solvent-exposed tyrosine residues, was identified on the concave surface of the β-sheet. These new modular single-layer β-sheet proteins may serve as a new model system for studying folding and design of β-rich proteins.
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Affiliation(s)
- Qingping Xu
- Joint Center for Structural Genomics, www.jcsg.org
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator LaboratoryMenlo ParkCalifornia
- GMCA@APS, Argonne National LaboratoryLemontIllinois
| | - Matthew Biancalana
- Perlmutter Cancer Center, New York University Langone Medical Center, Smilow Research CenterNew YorkNew York
| | | | - Hsiu‐Ju Chiu
- Joint Center for Structural Genomics, www.jcsg.org
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator LaboratoryMenlo ParkCalifornia
| | - Lukasz Jaroszewski
- Joint Center for Structural Genomics, www.jcsg.org
- Center for Research in Biological SystemsUniversity of CaliforniaLa JollaCalifornia
- Program on Bioinformatics and Systems BiologySanford‐Burnham Medical Research InstituteLa JollaCalifornia
- Division of Biomedical SciencesUniversity of CaliforniaRiversideCalifornia
| | - Mark W. Knuth
- Joint Center for Structural Genomics, www.jcsg.org
- Protein Sciences DepartmentGenomics Institute of the Novartis Research FoundationSan DiegoCalifornia
| | - Scott A. Lesley
- Joint Center for Structural Genomics, www.jcsg.org
- Protein Sciences DepartmentGenomics Institute of the Novartis Research FoundationSan DiegoCalifornia
- Department of Integrative Structural and Computational BiologyThe Scripps Research InstituteLa JollaCalifornia
- Merck & Co., Inc.South San FranciscoCalifornia
| | - Adam Godzik
- Joint Center for Structural Genomics, www.jcsg.org
- Center for Research in Biological SystemsUniversity of CaliforniaLa JollaCalifornia
- Program on Bioinformatics and Systems BiologySanford‐Burnham Medical Research InstituteLa JollaCalifornia
- Division of Biomedical SciencesUniversity of CaliforniaRiversideCalifornia
| | - Marc‐André Elsliger
- Joint Center for Structural Genomics, www.jcsg.org
- Department of Integrative Structural and Computational BiologyThe Scripps Research InstituteLa JollaCalifornia
| | - Ashley M. Deacon
- Joint Center for Structural Genomics, www.jcsg.org
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator LaboratoryMenlo ParkCalifornia
- Accelero BiostructuresSan CarlosCalifornia
| | - Ian A. Wilson
- Joint Center for Structural Genomics, www.jcsg.org
- Department of Integrative Structural and Computational BiologyThe Scripps Research InstituteLa JollaCalifornia
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Häussler RS, Bendes A, Iglesias M, Sanchez-Rivera L, Dodig-Crnković T, Byström S, Fredolini C, Birgersson E, Dale M, Edfors F, Fagerberg L, Rockberg J, Tegel H, Uhlén M, Qundos U, Schwenk JM. Systematic Development of Sandwich Immunoassays for the Plasma Secretome. Proteomics 2019; 19:e1900008. [PMID: 31278833 DOI: 10.1002/pmic.201900008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 06/17/2019] [Indexed: 12/15/2022]
Abstract
The plasma proteome offers a clinically useful window into human health. Recent advances from highly multiplexed assays now call for appropriate pipelines to validate individual candidates. Here, a workflow is developed to build dual binder sandwich immunoassays (SIA) and for proteins predicted to be secreted into plasma. Utilizing suspension bead arrays, ≈1800 unique antibody pairs are first screened against 209 proteins with recombinant proteins as well as EDTA plasma. Employing 624 unique antibodies, dilution-dependent curves in plasma and concentration-dependent curves of full-length proteins for 102 (49%) of the targets are obtained. For 22 protein assays, the longitudinal, interindividual, and technical performance is determined in a set of plasma samples collected from 18 healthy subjects every third month over 1 year. Finally, 14 of these assays are compared with with SIAs composed of other binders, proximity extension assays, and affinity-free targeted mass spectrometry. The workflow provides a multiplexed approach to screen for SIA pairs that suggests using at least three antibodies per target. This design is applicable for a wider range of targets of the plasma proteome, and the assays can be applied for discovery but also to validate emerging candidates derived from other platforms.
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Affiliation(s)
- Ragna S Häussler
- Division of Affinity Proteomics, Science for Life Laboratory, KTH - Royal Institute of Technology, Box 1031, 171 21, Solna, Sweden
| | - Annika Bendes
- Division of Affinity Proteomics, Science for Life Laboratory, KTH - Royal Institute of Technology, Box 1031, 171 21, Solna, Sweden
| | - MariaJesus Iglesias
- Division of Cellular and Clinical Proteomics, Science for Life Laboratory, KTH - Royal Institute of Technology, Box 1031, 171 21, Solna, Sweden
- K.G. Jebsen - Thrombosis Research and Expertise Center (TREC), Department of Clinical Medicine, UiT - The Arctic University of Norway, 9010, Tromsø, Norway
- Division of Internal Medicine, University Hospital of North Norway, 9010, Tromsø, Norway
| | - Laura Sanchez-Rivera
- Division of Cellular and Clinical Proteomics, Science for Life Laboratory, KTH - Royal Institute of Technology, Box 1031, 171 21, Solna, Sweden
| | - Tea Dodig-Crnković
- Division of Affinity Proteomics, Science for Life Laboratory, KTH - Royal Institute of Technology, Box 1031, 171 21, Solna, Sweden
| | - Sanna Byström
- Division of Affinity Proteomics, Science for Life Laboratory, KTH - Royal Institute of Technology, Box 1031, 171 21, Solna, Sweden
| | - Claudia Fredolini
- Division of Affinity Proteomics, Science for Life Laboratory, KTH - Royal Institute of Technology, Box 1031, 171 21, Solna, Sweden
| | - Elin Birgersson
- Division of Affinity Proteomics, Science for Life Laboratory, KTH - Royal Institute of Technology, Box 1031, 171 21, Solna, Sweden
| | - Matilda Dale
- Division of Affinity Proteomics, Science for Life Laboratory, KTH - Royal Institute of Technology, Box 1031, 171 21, Solna, Sweden
| | - Fredrik Edfors
- Division of Systems Biology, Science for Life Laboratory, KTH - Royal Institute of Technology, Box 1031, 171 21, Solna, Sweden
| | - Linn Fagerberg
- Division of Systems Biology, Science for Life Laboratory, KTH - Royal Institute of Technology, Box 1031, 171 21, Solna, Sweden
| | - Johan Rockberg
- Division of Protein Technology, Department of Protein Science, KTH - Royal Institute of Technology, 106 91, Stockholm, Sweden
| | - Hanna Tegel
- Division of Protein Technology, Department of Protein Science, KTH - Royal Institute of Technology, 106 91, Stockholm, Sweden
| | - Mathias Uhlén
- Division of Systems Biology, Science for Life Laboratory, KTH - Royal Institute of Technology, Box 1031, 171 21, Solna, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970, Hørsholm, Denmark
| | | | - Jochen M Schwenk
- Division of Affinity Proteomics, Science for Life Laboratory, KTH - Royal Institute of Technology, Box 1031, 171 21, Solna, Sweden
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40
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Li T, Wu Y, Wang Y, Gao H, Gupta VK, Duan X, Qu H, Jiang Y. Secretome Profiling Reveals Virulence-Associated Proteins of Fusarium proliferatum during Interaction with Banana Fruit. Biomolecules 2019; 9:biom9060246. [PMID: 31234604 PMCID: PMC6628180 DOI: 10.3390/biom9060246] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 06/19/2019] [Accepted: 06/22/2019] [Indexed: 12/12/2022] Open
Abstract
Secreted proteins are vital for the pathogenicity of many fungi through manipulating their hosts for efficient colonization. Fusarium proliferatum is a phytopathogenic fungus infecting many crops, vegetables, and fruit, including banana fruit. To access the proteins involved in pathogen–host interaction, we used label-free quantitative proteomics technology to comparatively analyze the secretomes of F. proliferatum cultured with and without banana peel in Czapek’s broth medium. By analyzing the secretomes of F. proliferatum, we have identified 105 proteins with 40 exclusively secreted and 65 increased in abundance in response to a banana peel. These proteins were involved in the promotion of invasion of banana fruit, and they were mainly categorized into virulence factors, cell wall degradation, metabolic process, response to stress, regulation, and another unknown biological process. The expressions of corresponding genes confirmed the existence of these secreted proteins in the banana peel. Furthermore, expression pattern suggested variable roles for these genes at different infection stages. This study expanded the current database of F. proliferatum secreted proteins which might be involved in the infection strategy of this fungus. Additionally, this study warranted the further attention of some secreted proteins that might initiate infection of F. proliferatum on banana fruit.
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Affiliation(s)
- Taotao Li
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
| | - Yu Wu
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
- University of Chinese Academy of Sciences, Beijing 100039, China.
| | - Yong Wang
- Zhongshan Entry-Exit Inspection and Quarantine Bureau, Zhongshan 528403, China.
| | - Haiyan Gao
- Key Laboratory of Post-Harvest Handling of Fruits, Ministry of Agriculture, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Vijai Kumar Gupta
- Department of Chemistry and Biotechnology, ERA Chair of Green Chemistry, Tallinn University of Technology, 12618 Tallinn, Estonia.
| | - Xuewu Duan
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
| | - Hongxia Qu
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
| | - Yueming Jiang
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
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41
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Li Y, Liu J, Díaz-Cruz G, Cheng Z, Bignell DRD. Virulence mechanisms of plant-pathogenic Streptomyces species: an updated review. Microbiology (Reading) 2019; 165:1025-1040. [PMID: 31162023 DOI: 10.1099/mic.0.000818] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Gram-positive Actinobacteria from the genus Streptomyces are best known for their morphological complexity and for their ability to produce numerous bioactive specialized metabolites with useful applications in human and veterinary medicine and in agriculture. In contrast, the ability to infect living plant tissues and to cause diseases of root and tuber crops such as potato common scab (CS) is a rare attribute among members of this genus. Research on the virulence mechanisms of plant-pathogenic Streptomyces spp. has revealed the importance of the thaxtomin phytotoxins as key pathogenicity determinants produced by several species. In addition, other phytotoxic specialized metabolites may contribute to the development or severity of disease caused by Streptomyces spp., along with the production of phytohormones and secreted proteins. A thorough understanding of the molecular mechanisms of plant pathogenicity will enable the development of better management procedures for controlling CS and other plant diseases caused by the Streptomyces.
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Affiliation(s)
- Yuting Li
- Department of Biology, Memorial University of Newfoundland, St John's, NL A1B 3X9, Canada
| | - Jingyu Liu
- Department of Biology, Memorial University of Newfoundland, St John's, NL A1B 3X9, Canada
| | - Gustavo Díaz-Cruz
- Department of Biology, Memorial University of Newfoundland, St John's, NL A1B 3X9, Canada
| | - Zhenlong Cheng
- Department of Biology, Memorial University of Newfoundland, St John's, NL A1B 3X9, Canada
| | - Dawn R D Bignell
- Department of Biology, Memorial University of Newfoundland, St John's, NL A1B 3X9, Canada
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42
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Kong L, Zhang L. An ensemble method for multi-type Gram-negative bacterial secreted protein prediction by integrating different PSSM-based features. SAR QSAR Environ Res 2019; 30:181-194. [PMID: 30739484 DOI: 10.1080/1062936x.2019.1573438] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 01/20/2019] [Indexed: 06/09/2023]
Abstract
In Gram-negative bacteria, a wide range of proteins are secreted by highly specialized secretion systems. These secreted proteins play essential roles in the response of bacteria to their environment and also in several physiological processes such as adhesion, pathogenicity, adaptation and survival. Therefore, identifying secreted proteins in Gram-negative bacteria may assist in understanding the secretion mechanism and development of new antimicrobial strategies. Considering that a single-feature model is less likely to comprehensively cover this information, three kinds of feature models were used in this paper to represent protein samples by composition analysis, correlation analysis and smoothing encoding method on position-specific scoring matrix profiles. A support vector machine-based ensemble method with these hybrid features was developed to predict multi-type Gram-negative bacterial secreted proteins. Finally, our method achieves overall accuracies of 97.09% and 96.51% using an independent dataset test and jackknife test on a public test dataset, which are 3.49% and 2.32% higher, respectively, than results obtained by other methods. These results show the effectiveness and stability of the proposed ensemble method. It is anticipated that our method will provide useful information for further research on bacterial secreted proteins and secreted systems.
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Affiliation(s)
- L Kong
- a School of Mathematics and Information Science & Technology , Hebei Normal University of Science & Technology , Qinhuangdao , PR China
| | - L Zhang
- b School of Mathematics and Statistics , Northeastern University at Qinhuangdao , Qinhuangdao , PR China
- c College of Science , Northeastern University , Shenyang , PR China
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43
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Song W, Kir S, Hong S, Hu Y, Wang X, Binari R, Tang HW, Chung V, Banks AS, Spiegelman B, Perrimon N. Tumor-Derived Ligands Trigger Tumor Growth and Host Wasting via Differential MEK Activation. Dev Cell 2019; 48:277-286.e6. [PMID: 30639055 DOI: 10.1016/j.devcel.2018.12.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 11/21/2018] [Accepted: 12/04/2018] [Indexed: 12/19/2022]
Abstract
Interactions between tumors and host tissues play essential roles in tumor-induced systemic wasting and cancer cachexia, including muscle wasting and lipid loss. However, the pathogenic molecular mechanisms of wasting are still poorly understood. Using a fly model of tumor-induced organ wasting, we observed aberrant MEK activation in both tumors and host tissues of flies bearing gut-yki3SA tumors. We found that host MEK activation results in muscle wasting and lipid loss, while tumor MEK activation is required for tumor growth. Strikingly, host MEK suppression alone is sufficient to abolish the wasting phenotypes without affecting tumor growth. We further uncovered that yki3SA tumors produce the vein (vn) ligand to trigger autonomous Egfr/MEK-induced tumor growth and produce the PDGF- and VEGF-related factor 1 (Pvf1) ligand to non-autonomously activate host Pvr/MEK signaling and wasting. Altogether, our results demonstrate the essential roles and molecular mechanisms of differential MEK activation in tumor-induced host wasting.
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44
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Zhang J, Chai H, Guo S, Guo H, Li Y. High-Throughput Identification of Mammalian Secreted Proteins Using Species-Specific Scheme and Application to Human Proteome. Molecules 2018; 23:molecules23061448. [PMID: 29903999 PMCID: PMC6099666 DOI: 10.3390/molecules23061448] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 05/29/2018] [Accepted: 05/30/2018] [Indexed: 02/02/2023] Open
Abstract
Secreted proteins are widely spread in living organisms and cells. Since secreted proteins are easy to be detected in body fluids, urine, and saliva in clinical diagnosis, they play important roles in biomarkers for disease diagnosis and vaccine production. In this study, we propose a novel predictor for accurate high-throughput identification of mammalian secreted proteins that is based on sequence-derived features. We combine the features of amino acid composition, sequence motifs, and physicochemical properties to encode collected proteins. Detailed feature analyses prove the effectiveness of the considered features. Based on the differences across various species of secreted proteins, we introduce the species-specific scheme, which is expected to further explore the intrinsic attributes of specific secreted proteins. Experiments on benchmark datasets prove the effectiveness of our proposed method. The test on independent testing dataset also promises a good generalization capability. When compared with the traditional universal model, we experimentally demonstrate that the species-specific scheme is capable of significantly improving the prediction performance. We use our method to make predictions on unreviewed human proteome, and find 272 potential secreted proteins with probabilities that are higher than 99%. A user-friendly web server, named iMSPs (identification of Mammalian Secreted Proteins), which implements our proposed method, is designed and is available for free for academic use at: http://www.inforstation.com/webservers/iMSP/.
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Affiliation(s)
- Jian Zhang
- School of Computer and Information Technology, Xinyang Normal University, Xinyang 464000, China.
| | - Haiting Chai
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK.
| | - Song Guo
- School of Computer and Information Technology, Xinyang Normal University, Xinyang 464000, China.
| | - Huaping Guo
- School of Computer and Information Technology, Xinyang Normal University, Xinyang 464000, China.
| | - Yanling Li
- School of Computer and Information Technology, Xinyang Normal University, Xinyang 464000, China.
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45
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Schirrmann MK, Zoller S, Croll D, Stukenbrock EH, Leuchtmann A, Fior S. Genomewide signatures of selection in Epichloë reveal candidate genes for host specialization. Mol Ecol 2018; 27:3070-3086. [PMID: 29633410 DOI: 10.1111/mec.14585] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 02/21/2018] [Accepted: 02/23/2018] [Indexed: 12/31/2022]
Abstract
Host specialization is a key process in ecological divergence and speciation of plant-associated fungi. The underlying determinants of host specialization are generally poorly understood, especially in endophytes, which constitute one of the most abundant components of the plant microbiome. We addressed the genetic basis of host specialization in two sympatric subspecies of grass-endophytic fungi from the Epichloë typhina complex: subsp. typhina and clarkii. The life cycle of these fungi entails unrestricted dispersal of gametes and sexual reproduction before infection of a new host, implying that the host imposes a selective barrier on viability of the progeny. We aimed to detect genes under divergent selection between subspecies, experiencing restricted gene flow due to adaptation to different hosts. Using pooled whole-genome sequencing data, we combined FST and DXY population statistics in genome scans and detected 57 outlier genes showing strong differentiation between the two subspecies. Genomewide analyses of nucleotide diversity (π), Tajima's D and dN/dS ratios indicated that these genes have evolved under positive selection. Genes encoding secreted proteins were enriched among the genes showing evidence of positive selection, suggesting that molecular plant-fungus interactions are strong drivers of endophyte divergence. We focused on five genes encoding secreted proteins, which were further sequenced in 28 additional isolates collected across Europe to assess genetic variation in a larger sample size. Signature of positive selection in these isolates and putative identification of pathogenic function supports our findings that these genes represent strong candidates for host specialization determinants in Epichloë endophytes. Our results highlight the role of secreted proteins as key determinants of host specialization.
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Affiliation(s)
- Melanie K Schirrmann
- Institute of Integrative Biology (IBZ), ETH Zürich, Zürich, Switzerland.,Research Group Molecular Diagnostics, Genomics and Bioinformatics, Agroscope, Wädenswil, Switzerland
| | - Stefan Zoller
- Genetic Diversity Centre (GDC), ETH Zürich, Zürich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Eva H Stukenbrock
- Environmental Genomics, Christian-Albrechts University of Kiel, Kiel, Germany.,Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Adrian Leuchtmann
- Institute of Integrative Biology (IBZ), ETH Zürich, Zürich, Switzerland
| | - Simone Fior
- Institute of Integrative Biology (IBZ), ETH Zürich, Zürich, Switzerland
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da Silva LB, Menezes MC, Kitano ES, Oliveira AK, Abreu AG, Souza GO, Heinemann MB, Isaac L, Fraga TR, Serrano SMT, Barbosa AS. Leptospira interrogans Secreted Proteases Degrade Extracellular Matrix and Plasma Proteins From the Host. Front Cell Infect Microbiol 2018; 8:92. [PMID: 29637048 PMCID: PMC5881292 DOI: 10.3389/fcimb.2018.00092] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 03/07/2018] [Indexed: 12/30/2022] Open
Abstract
Leptospires are highly motile spirochetes equipped with strategies for efficient invasion and dissemination within the host. Our group previously demonstrated that pathogenic leptospires secrete proteases capable of cleaving and inactivating key molecules of the complement system, allowing these bacteria to circumvent host's innate immune defense mechanisms. Given the successful dissemination of leptospires during infection, we wondered if such proteases would target a broader range of host molecules. In the present study, the proteolytic activity of secreted leptospiral proteases against a panel of extracellular matrix (ECM) and plasma proteins was assessed. The culture supernatant of the virulent L. interrogans serovar Kennewicki strain Fromm (LPF) degraded human fibrinogen, plasma fibronectin, gelatin, and the proteoglycans decorin, biglycan, and lumican. Interestingly, human plasminogen was not cleaved by proteases present in the supernatants. Proteolytic activity was inhibited by 1,10-phenanthroline, suggesting the participation of metalloproteases. Moreover, production of proteases might be an important virulence determinant since culture-attenuated or saprophytic Leptospira did not display proteolytic activity against ECM or plasma components. Exoproteomic analysis allowed the identification of three metalloproteases that could be involved in the degradation of host components. The ability to cleave conjunctive tissue molecules and coagulation cascade proteins may certainly contribute to invasion and tissue destruction observed upon infection with Leptospira.
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Affiliation(s)
| | - Milene C Menezes
- Special Laboratory of Applied Toxinology, Center of Toxins, Immune-Response and Cell Signaling, Butantan Institute, São Paulo, Brazil
| | - Eduardo S Kitano
- Special Laboratory of Applied Toxinology, Center of Toxins, Immune-Response and Cell Signaling, Butantan Institute, São Paulo, Brazil
| | - Ana K Oliveira
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Afonso G Abreu
- Postgraduation Program in Parasitic Biology, CEUMA University, São Luís, Brazil.,Postgraduation Program in Health Sciences, Federal University of Maranhão, São Luís, Brazil
| | - Gisele O Souza
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Marcos B Heinemann
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Lourdes Isaac
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Tatiana R Fraga
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Solange M T Serrano
- Special Laboratory of Applied Toxinology, Center of Toxins, Immune-Response and Cell Signaling, Butantan Institute, São Paulo, Brazil
| | - Angela S Barbosa
- Laboratory of Bacteriology, Butantan Institute, São Paulo, Brazil
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47
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Chiliza TE, Pillay M, Pillay B. Identification of unique essential proteins from a Mycobacterium tuberculosis F15/LAM4/KZN phage secretome library. Pathog Dis 2017; 75:ftx001. [PMID: 28087649 DOI: 10.1093/femspd/ftx001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2017] [Indexed: 11/12/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis disease (TB), the leading cause of death from bacterial infection worldwide. Although treatable, the resurgence of multidrug-resistant and extensively drug-resistant TB is a major setback for the fight against TB globally. Consequently, there is an urgent need for new Mtb-derived biomarkers for use in the design of new drugs and rapid point-of-care diagnostic or prognostic tools for the management of TB transmission. Therefore, the present study aimed to identify unique Mtb-secreted proteins from the extensively drug-resistant Mtb F15/LAM4/KZN phage secretome library. A whole genome library was constructed using genomic DNA fragments of the Mtb F15/LAM4/KZN strain. A phage secretome sub-library of 8 × 103 clones was prepared and phage DNA was sequenced from 120 randomly selected clones. DNA sequence BLAST analysis identified 86 open reading frames. Using bioinformatics tools and databases, 10 proteins essential for in vivo growth and survival of Mtb (Nrp, PssA, MmpL5, SirA, GatB, EspA, TopA, EccCa1, Rv1634 and Rv3103c) were identified. Proteins essential for the growth and survival of Mtb during infection have potential application in the development of diagnostic tools, new drugs and vaccines. Further studies will be conducted to evaluate their potential application in the fight against TB.
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Affiliation(s)
- Thamsanqa Emmanuel Chiliza
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Westville 3630, South Africa
| | - Manormoney Pillay
- Medical Microbiology and Infection Control, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Balakrishna Pillay
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Westville 3630, South Africa
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48
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Xiang J, Cao S, Zhong L, Wang H, Pei Y, Wei Q, Wen B, Mu H, Zhang S, Yue L, Yue G, Lim B, Han J. Pluripotent stem cells secrete Activin A to improve their epiblast competency after injection into recipient embryos. Protein Cell 2017; 9:717-728. [PMID: 29027123 PMCID: PMC6053354 DOI: 10.1007/s13238-017-0470-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 08/22/2017] [Indexed: 11/10/2022] Open
Abstract
It is not fully clear why there is a higher contribution of pluripotent stem cells (PSCs) to the chimera produced by injection of PSCs into 4-cell or 8-cell stage embryos compared with blastocyst injection. Here, we show that not only embryonic stem cells (ESCs) but also induced pluripotent stem cells (iPSCs) can generate F0 nearly 100% donor cell-derived mice by 4-cell stage embryo injection, and the approach has a “dose effect”. Through an analysis of the PSC-secreted proteins, Activin A was found to impede epiblast (EPI) lineage development while promoting trophectoderm (TE) differentiation, resulting in replacement of the EPI lineage of host embryos with PSCs. Interestingly, the injection of ESCs into blastocysts cultured with Activin A (cultured from 4-cell stage to early blastocyst at E3.5) could increase the contribution of ESCs to the chimera. The results indicated that PSCs secrete protein Activin A to improve their EPI competency after injection into recipient embryos through influencing the development of mouse early embryos. This result is useful for optimizing the chimera production system and for a deep understanding of PSCs effects on early embryo development.
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Affiliation(s)
- Jinzhu Xiang
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Suying Cao
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, 102206, China
| | - Liang Zhong
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Hanning Wang
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing, 100193, China
| | - Yangli Pei
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.,State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Qingqing Wei
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Bingqiang Wen
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Haiyuan Mu
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Shaopeng Zhang
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Liang Yue
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Genhua Yue
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, 117604, Singapore
| | - Bing Lim
- Stem Cell and Developmental Biology, Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Jianyong Han
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
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Daguerre Y, Levati E, Ruytinx J, Tisserant E, Morin E, Kohler A, Montanini B, Ottonello S, Brun A, Veneault-Fourrey C, Martin F. Regulatory networks underlying mycorrhizal development delineated by genome-wide expression profiling and functional analysis of the transcription factor repertoire of the plant symbiotic fungus Laccaria bicolor. BMC Genomics 2017; 18:737. [PMID: 28923004 PMCID: PMC5604158 DOI: 10.1186/s12864-017-4114-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 09/04/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Ectomycorrhizal (ECM) fungi develop a mutualistic symbiotic interaction with the roots of their host plants. During this process, they undergo a series of developmental transitions from the running hyphae in the rhizosphere to the coenocytic hyphae forming finger-like structures within the root apoplastic space. These transitions, which involve profound, symbiosis-associated metabolic changes, also entail a substantial transcriptome reprogramming with coordinated waves of differentially expressed genes. To date, little is known about the key transcriptional regulators driving these changes, and the aim of the present study was to delineate and functionally characterize the transcription factor (TF) repertoire of the model ECM fungus Laccaria bicolor. RESULTS We curated the L. bicolor gene models coding for transcription factors and assessed their expression and regulation in Poplar and Douglas fir ectomycorrhizae. We identified 285 TFs, 191 of which share a significant similarity with known transcriptional regulators. Expression profiling of the corresponding transcripts identified TF-encoding fungal genes differentially expressed in the ECM root tips of both host plants. The L. bicolor core set of differentially expressed TFs consists of 12 and 22 genes that are, respectively, upregulated and downregulated in symbiotic tissues. These TFs resemble known fungal regulators involved in the control of fungal invasive growth, fungal cell wall integrity, carbon and nitrogen metabolism, invasive stress response and fruiting-body development. However, this core set of mycorrhiza-regulated TFs seems to be characteristic of L. bicolor and our data suggest that each mycorrhizal fungus has evolved its own set of ECM development regulators. A subset of the above TFs was functionally validated with the use of a heterologous, transcription activation assay in yeast, which also allowed the identification of previously unknown, transcriptionally active yet secreted polypeptides designated as Secreted Transcriptional Activator Proteins (STAPs). CONCLUSIONS Transcriptional regulators required for ECM symbiosis development in L. bicolor have been uncovered and classified through genome-wide analysis. This study also identifies the STAPs as a new class of potential ECM effectors, highly expressed in mycorrhizae, which may be involved in the control of the symbiotic root transcriptome.
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Affiliation(s)
- Y Daguerre
- INRA, UMR 1136, INRA-Université de Lorraine, Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, 54280, Champenoux, France
- Université de Lorraine, UMR 1136, INRA-Université de Lorraine, Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, F-54500 Vandoeuvre-lès-, Nancy, France
- Present address: Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83, Umea, Sweden
| | - E Levati
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università degli Studi di Parma, Parco Area delle Scienze 23/A, 43124, Parma, Italy
| | - J Ruytinx
- INRA, UMR 1136, INRA-Université de Lorraine, Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, 54280, Champenoux, France
- Université de Lorraine, UMR 1136, INRA-Université de Lorraine, Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, F-54500 Vandoeuvre-lès-, Nancy, France
- Present address: Hasselt University, Centre for Environmental Sciences, Agoralaan building D, 3590, Diepenbeek, Belgium
| | - E Tisserant
- INRA, UMR 1136, INRA-Université de Lorraine, Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, 54280, Champenoux, France
- Université de Lorraine, UMR 1136, INRA-Université de Lorraine, Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, F-54500 Vandoeuvre-lès-, Nancy, France
| | - E Morin
- INRA, UMR 1136, INRA-Université de Lorraine, Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, 54280, Champenoux, France
- Université de Lorraine, UMR 1136, INRA-Université de Lorraine, Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, F-54500 Vandoeuvre-lès-, Nancy, France
| | - A Kohler
- INRA, UMR 1136, INRA-Université de Lorraine, Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, 54280, Champenoux, France
- Université de Lorraine, UMR 1136, INRA-Université de Lorraine, Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, F-54500 Vandoeuvre-lès-, Nancy, France
| | - B Montanini
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università degli Studi di Parma, Parco Area delle Scienze 23/A, 43124, Parma, Italy
| | - S Ottonello
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università degli Studi di Parma, Parco Area delle Scienze 23/A, 43124, Parma, Italy
| | - A Brun
- INRA, UMR 1136, INRA-Université de Lorraine, Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, 54280, Champenoux, France
- Université de Lorraine, UMR 1136, INRA-Université de Lorraine, Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, F-54500 Vandoeuvre-lès-, Nancy, France
| | - C Veneault-Fourrey
- INRA, UMR 1136, INRA-Université de Lorraine, Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, 54280, Champenoux, France.
- Université de Lorraine, UMR 1136, INRA-Université de Lorraine, Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, F-54500 Vandoeuvre-lès-, Nancy, France.
| | - F Martin
- INRA, UMR 1136, INRA-Université de Lorraine, Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, 54280, Champenoux, France
- Université de Lorraine, UMR 1136, INRA-Université de Lorraine, Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, F-54500 Vandoeuvre-lès-, Nancy, France
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Varshney S, Stanley P. EOGT and O-GlcNAc on secreted and membrane proteins. Biochem Soc Trans 2017; 45:401-8. [PMID: 28408480 DOI: 10.1042/BST20160165] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 02/01/2017] [Accepted: 02/06/2017] [Indexed: 11/17/2022]
Abstract
Here, we describe a recently discovered O-GlcNAc transferase termed EOGT for EGF domain-specific O-GlcNAc transferase. EOGT transfers GlcNAc (N-acetylglucosamine) to Ser or Thr in secreted and membrane proteins that contain one or more epidermal growth factor-like repeats with a specific consensus sequence. Thus, EOGT is distinct from OGT, the O-GlcNAc transferase, that transfers GlcNAc to Ser/Thr in proteins of the cytoplasm or nucleus. EOGT and OGT are in separate cellular compartments and have mostly distinct substrates, although both can act on cytoplasmic (OGT) and lumenal (EOGT) domains of transmembrane proteins. The present review will describe known substrates of EOGT and biological roles for EOGT in Drosophila and humans. Mutations in EOGT that give rise to Adams-Oliver Syndrome in humans will also be discussed.
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