1
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Young R, Ahmed KA, Court L, Castro-Vargas C, Marcora A, Boctor J, Paull C, Wijffels G, Rane R, Edwards O, Walsh T, Pandey G. Improved reference quality genome sequence of the plastic-degrading greater wax moth, Galleria mellonella. G3 (BETHESDA, MD.) 2024; 14:jkae070. [PMID: 38564250 DOI: 10.1093/g3journal/jkae070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 12/19/2023] [Accepted: 03/22/2024] [Indexed: 04/04/2024]
Abstract
Galleria mellonella is a pest of honeybees in many countries because its larvae feed on beeswax. However, G. mellonella larvae can also eat various plastics, including polyethylene, polystyrene, and polypropylene, and therefore, the species is garnering increasing interest as a tool for plastic biodegradation research. This paper presents an improved genome (99.3% completed lepidoptera_odb10 BUSCO; genome mode) for G. mellonella. This 472 Mb genome is in 221 contigs with an N50 of 6.4 Mb and contains 13,604 protein-coding genes. Genes that code for known and putative polyethylene-degrading enzymes and their similarity to proteins found in other Lepidoptera are highlighted. An analysis of secretory proteins more likely to be involved in the plastic catabolic process has also been carried out.
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Affiliation(s)
| | | | - Leon Court
- CSIRO Environment, Acton, ACT 2601, Australia
| | | | - Anna Marcora
- CSIRO Agriculture and Food, Dutton Park, QLD 4102, Australia
| | - Joseph Boctor
- Bioplastics Innovation Hub, Food Futures Institute, Murdoch University, Murdoch, WA 6150, Australia
| | - Cate Paull
- CSIRO Agriculture and Food, Dutton Park, QLD 4102, Australia
| | - Gene Wijffels
- CSIRO Agriculture and Food, St Lucia, QLD 4067, Australia
| | - Rahul Rane
- CSIRO Health and Biosecurity, Parkville, VIC 3052, Australia
| | | | - Tom Walsh
- CSIRO Environment, Acton, ACT 2601, Australia
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2
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Du Z, Weng H, Jia H, Zhang B, Wu B, Chen W, Liu T, Gao L. Characterization of a Small Cysteine-Rich Secreted Effector, TcSCP_9014, in Tilletia controversa. PLANTS (BASEL, SWITZERLAND) 2024; 13:1523. [PMID: 38891331 PMCID: PMC11174917 DOI: 10.3390/plants13111523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 05/20/2024] [Accepted: 05/23/2024] [Indexed: 06/21/2024]
Abstract
Tilletia controversa J. G. Kühn is the causal agent of wheat dwarf bunt (DB), a destructive disease causing tremendous economic losses. Small cysteine-rich secreted proteins (SCPs) of plant fungi are crucial in modulating host immunity and promoting infection. Little is known about the virulence effectors of T. controversa. Here, we characterized TcSCP_9014, a novel effector of SCPs, in T. controversa which suppressed programmed cell death triggered by BAX without relying on its signal peptide (SP). The SP in the N-terminus of TcSCP_9014 was functional in the secretory process. Live-cell imaging in the epidermal cells of Nicothiana benthamiana suggested that TcSCP_9014 localized to the plasma membrane, cytoplasm, and nucleus. Furthermore, yeast cDNA library screening was performed to obtain the interacting proteins in wheat. Yeast two-hybrid and BiFC assays were applied to validate the interaction of TcSCP_9014 with TaMTAN and TaGAPDH. Our work revealed that the novel effector TcSCP_9014 is vital in modulating plant immunity, which opens up new avenues for plant-pathogen interactions in the T. controversa infection process.
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Affiliation(s)
- Zhenzhen Du
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Han Weng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Huanyu Jia
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Bin Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Boming Wu
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Wanquan Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Taiguo Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Li Gao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Key Laboratory of Integrated Pest Management on Crop in Northwestern Oasis, Ministry of China, Scientific Observing and Experimental Station of Korla, Ministry of Agriculture, Urumqi 830091, China
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3
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Del Corpo D, Coculo D, Greco M, De Lorenzo G, Lionetti V. Pull the fuzes: Processing protein precursors to generate apoplastic danger signals for triggering plant immunity. PLANT COMMUNICATIONS 2024:100931. [PMID: 38689495 DOI: 10.1016/j.xplc.2024.100931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/29/2024] [Accepted: 04/26/2024] [Indexed: 05/02/2024]
Abstract
The apoplast is one of the first cellular compartments outside the plasma membrane encountered by phytopathogenic microbes in the early stages of plant tissue invasion. Plants have developed sophisticated surveillance mechanisms to sense danger events at the cell surface and promptly activate immunity. However, a fine tuning of the activation of immune pathways is necessary to mount a robust and effective defense response. Several endogenous proteins and enzymes are synthesized as inactive precursors, and their post-translational processing has emerged as a critical mechanism for triggering alarms in the apoplast. In this review, we focus on the precursors of phytocytokines, cell wall remodeling enzymes, and proteases. The physiological events that convert inactive precursors into immunomodulatory active peptides or enzymes are described. This review also explores the functional synergies among phytocytokines, cell wall damage-associated molecular patterns, and remodeling, highlighting their roles in boosting extracellular immunity and reinforcing defenses against pests.
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Affiliation(s)
- Daniele Del Corpo
- Department of Biology and Biotechnology "Charles Darwin," Sapienza University of Rome, Rome, Italy
| | - Daniele Coculo
- Department of Biology and Biotechnology "Charles Darwin," Sapienza University of Rome, Rome, Italy
| | - Marco Greco
- Department of Biology and Biotechnology "Charles Darwin," Sapienza University of Rome, Rome, Italy
| | - Giulia De Lorenzo
- Department of Biology and Biotechnology "Charles Darwin," Sapienza University of Rome, Rome, Italy
| | - Vincenzo Lionetti
- Department of Biology and Biotechnology "Charles Darwin," Sapienza University of Rome, Rome, Italy.
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4
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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] [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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5
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Jansson MK, Nguyen DT, Mikkat S, Warnke C, Janssen MB, Warnke P, Kreikemeyer B, Patenge N. Synthetic mRNA delivered to human cells leads to expression of Cpl-1 bacteriophage-endolysin with activity against Streptococcus pneumoniae. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102145. [PMID: 38435119 PMCID: PMC10907214 DOI: 10.1016/j.omtn.2024.102145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 02/06/2024] [Indexed: 03/05/2024]
Abstract
Endolysins are bacteriophage-encoded hydrolases that show high antibacterial activity and a narrow substrate spectrum. We hypothesize that an mRNA-based approach to endolysin therapy can overcome some challenges of conventional endolysin therapy, namely organ targeting and bioavailability. We show that synthetic mRNA applied to three human cell lines (HEK293T, A549, HepG2 cells) leads to expression and cytosolic accumulation of the Cpl-1 endolysin with activity against Streptococcus pneumoniae. Addition of a human lysozyme signal peptide sequence translocates the Cpl-1 to the endoplasmic reticulum leading to secretion (hlySP-sCpl-1). The pneumococcal killing effect of hlySP-sCpl-1 was enhanced by introduction of a point mutation to avoid N-linked-glycosylation. hlySP-sCpl-1N215D, collected from the culture supernatant of A549 cells 6 h post-transfection showed a significant killing effect and was active against nine pneumococcal strains. mRNA-based cytosolic Cpl-1 and secretory hlySP-sCpl-1N215D show potential for innovative treatment strategies against pneumococcal disease and, to our best knowledge, represent the first approach to mRNA-based endolysin therapy. We assume that many other bacterial pathogens could be targeted with this novel approach.
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Affiliation(s)
- Moritz K. Jansson
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Dat Tien Nguyen
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Stefan Mikkat
- Core Facility Proteome Analysis, University Medicine Rostock, Rostock, Germany
| | - Carolin Warnke
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Marc Benjamin Janssen
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Philipp Warnke
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Bernd Kreikemeyer
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Nadja Patenge
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
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6
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Fonseca Ó, Ramos AS, Gomes LTS, Gomes MS, Moreira AC. New Perspectives on Circulating Ferritin: Its Role in Health and Disease. Molecules 2023; 28:7707. [PMID: 38067440 PMCID: PMC10708148 DOI: 10.3390/molecules28237707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 11/16/2023] [Accepted: 11/19/2023] [Indexed: 12/18/2023] Open
Abstract
The diagnosis of iron disturbances usually includes the evaluation of serum parameters. Serum iron is assumed to be entirely bound to transferrin, and transferrin saturation-the ratio between the serum iron concentration and serum transferrin-usually reflects iron availability. Additionally, serum ferritin is commonly used as a surrogate of tissue iron levels. Low serum ferritin values are interpreted as a sign of iron deficiency, and high values are the main indicator of pathological iron overload. However, in situations of inflammation, serum ferritin levels may be very high, independently of tissue iron levels. This presents a particularly puzzling challenge for the clinician evaluating the overall iron status of the patient in the presence of an inflammatory condition. The increase in serum ferritin during inflammation is one of the enigmas regarding iron metabolism. Neither the origin, the mechanism of release, nor the effects of serum ferritin are known. The use of serum ferritin as a biomarker of disease has been rising, and it has become increasingly diverse, but whether or not it contributes to controlling the disease or host pathology, and how it would do it, are important, open questions. These will be discussed here, where we spotlight circulating ferritin and revise the recent clinical and preclinical data regarding its role in health and disease.
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Affiliation(s)
- Óscar Fonseca
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (Ó.F.); (A.S.R.); (L.T.S.G.); (M.S.G.)
| | - Ana S. Ramos
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (Ó.F.); (A.S.R.); (L.T.S.G.); (M.S.G.)
- FCUP—Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Leonor T. S. Gomes
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (Ó.F.); (A.S.R.); (L.T.S.G.); (M.S.G.)
- FCUP—Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Maria Salomé Gomes
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (Ó.F.); (A.S.R.); (L.T.S.G.); (M.S.G.)
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Ana C. Moreira
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (Ó.F.); (A.S.R.); (L.T.S.G.); (M.S.G.)
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
- IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
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7
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Stuer N, Van Damme P, Goormachtig S, Van Dingenen J. Seeking the interspecies crosswalk for filamentous microbe effectors. TRENDS IN PLANT SCIENCE 2023; 28:1045-1059. [PMID: 37062674 DOI: 10.1016/j.tplants.2023.03.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 03/02/2023] [Accepted: 03/18/2023] [Indexed: 06/19/2023]
Abstract
Both pathogenic and symbiotic microorganisms modulate the immune response and physiology of their host to establish a suitable niche. Key players in mediating colonization outcome are microbial effector proteins that act either inside (cytoplasmic) or outside (apoplastic) the plant cells and modify the abundance or activity of host macromolecules. We compile novel insights into the much-disputed processes of effector secretion and translocation of filamentous organisms, namely fungi and oomycetes. We report how recent studies that focus on unconventional secretion and effector structure challenge the long-standing image of effectors as conventionally secreted proteins that are translocated with the aid of primary amino acid sequence motifs. Furthermore, we emphasize the potential of diverse, unbiased, state-of-the-art proteomics approaches in the holistic characterization of fungal and oomycete effectomes.
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Affiliation(s)
- Naomi Stuer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), 9052 Ghent, Belgium
| | - Petra Van Damme
- iRIP Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Karel Lodewijk Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), 9052 Ghent, Belgium.
| | - Judith Van Dingenen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), 9052 Ghent, Belgium.
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8
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Chen X, Pan S, Bai H, Fan J, Batool W, Shabbir A, Han Y, Zheng H, Lu G, Lin L, Tang W, Wang Z. A nonclassically secreted effector of Magnaporthe oryzae targets host nuclei and plays important roles in fungal growth and plant infection. MOLECULAR PLANT PATHOLOGY 2023; 24:1093-1106. [PMID: 37306516 PMCID: PMC10423324 DOI: 10.1111/mpp.13356] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 04/05/2023] [Accepted: 05/08/2023] [Indexed: 06/13/2023]
Abstract
Rice blast caused by Magnaporthe oryzae is one of the most destructive diseases and poses a growing threat to food security worldwide. Like many other filamentous pathogens, rice blast fungus releases multiple types of effector proteins to facilitate fungal infection and modulate host defence responses. However, most of the characterized effectors contain an N-terminal signal peptide. Here, we report the results of the functional characterization of a nonclassically secreted nuclear targeting effector in M. oryzae (MoNte1). MoNte1 has no signal peptide, but can be secreted and translocated into plant nuclei driven by a nuclear targeting peptide. It could also induce hypersensitive cell death when transiently expressed in Nicotiana benthamiana. Deletion of the MoNTE1 gene caused a significant reduction of fungal growth and conidiogenesis, partially impaired appressorium formation and host colonization, and also dramatically attenuated the pathogenicity. Taken together, these findings reveal a novel effector secretion pathway and deepen our understanding of rice-M. oryzae interactions.
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Affiliation(s)
- Xiaomin Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsCollege of Plant Protection, Fujian Agriculture and Forestry UniversityFuzhouChina
| | - Su Pan
- Fujian University Key Laboratory for Plant Microbe InteractionCollege of Life Sciences, Fujian Agriculture and Forestry UniversityFuzhouChina
| | - Huimin Bai
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsCollege of Plant Protection, Fujian Agriculture and Forestry UniversityFuzhouChina
| | - Jiaxin Fan
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsCollege of Plant Protection, Fujian Agriculture and Forestry UniversityFuzhouChina
| | - Wajjiha Batool
- Fujian University Key Laboratory for Plant Microbe InteractionCollege of Life Sciences, Fujian Agriculture and Forestry UniversityFuzhouChina
| | - Ammarah Shabbir
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsCollege of Plant Protection, Fujian Agriculture and Forestry UniversityFuzhouChina
| | - Yijuan Han
- Institute of OceanographyMinjiang UniversityFuzhouChina
| | - Huakun Zheng
- National Engineering Research Center of JUNCAO TechnologyCollege of Life Science, Fujian Agriculture and Forestry UniversityFuzhouChina
| | - Guodong Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsCollege of Plant Protection, Fujian Agriculture and Forestry UniversityFuzhouChina
| | - Lili Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsCollege of Plant Protection, Fujian Agriculture and Forestry UniversityFuzhouChina
| | - Wei Tang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsCollege of Plant Protection, Fujian Agriculture and Forestry UniversityFuzhouChina
| | - Zonghua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsCollege of Plant Protection, Fujian Agriculture and Forestry UniversityFuzhouChina
- Institute of OceanographyMinjiang UniversityFuzhouChina
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9
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Deol S, Donahue PS, Mitrut RE, Hammitt-Kess IJ, Ahn J, Zhang B, Leonard JN. Comparative Evaluation of Synthetic Cytokines for Enhancing Production and Performance of NK92 Cell-Based Therapies. GEN BIOTECHNOLOGY 2023; 2:228-246. [PMID: 37363412 PMCID: PMC10286265 DOI: 10.1089/genbio.2023.0024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 05/29/2023] [Indexed: 06/28/2023]
Abstract
Off-the shelf immune cell therapies are potentially curative and may offer cost and manufacturing advantages over autologous products, but further development is needed. The NK92 cell line has a natural killer-like phenotype, has efficacy in cancer clinical trials, and is safe after irradiation. However, NK92 cells lose activity post-injection, limiting efficacy. This may be addressed by engineering NK92 cells to express stimulatory factors, and comparative analysis is needed. Thus, we systematically explored the expression of synthetic cytokines for enhancing NK92 cell production and performance. All synthetic cytokines evaluated (membrane-bound IL2 and IL15, and engineered versions of Neoleukin-2/15, IL15, IL12, and decoy resistant IL18) enhanced NK92 cell cytotoxicity. Engineered cells were preferentially expanded by expressing membrane-bound but not soluble synthetic cytokines, without compromising the radiosensitivity required for safety. Some membrane-bound cytokines conferred cell-contact independent paracrine activity, partly attributable to extracellular vesicles. Finally, we characterized interactions within consortia of differently engineered NK92 cells.
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Affiliation(s)
- Simrita Deol
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois, USA
- Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois, USA
| | - Patrick S. Donahue
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois, USA
- Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Roxana E. Mitrut
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois, USA
| | - Iva J. Hammitt-Kess
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, USA
| | - Jihae Ahn
- Division of Hematology/Oncology, Department of Medicine, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Bin Zhang
- Division of Hematology/Oncology, Department of Medicine, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Joshua N. Leonard
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois, USA
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, Illinois, USA
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10
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Priester J, Meier-Soelch J, Weiser H, Heylmann D, Weber A, Linne U, Kracht M. Metabolic labeling and LC-MS/MS-based identification of interleukin-1α-induced secreted proteomes from epithelial cells in the presence or absence of serum. STAR Protoc 2023; 4:102195. [PMID: 37004159 PMCID: PMC10090805 DOI: 10.1016/j.xpro.2023.102195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/11/2023] [Accepted: 03/03/2023] [Indexed: 04/03/2023] Open
Abstract
The unbiased identification of cytokine-induced, secreted proteins from cells cultured in serum-containing medium is challenging. Here, we describe an experimental and bioinformatics workflow to label interleukin-1α-regulated proteins in living cells with the methionine analogue L-homopropargylglycine. We detail their purification and identification by means of CLICK-chemistry-based biotinylation followed by nanoHPLC-MS/MS. A side-by-side comparison of enriched proteins and their ontologies to serum-free conditions demonstrates the sensitivity and specificity of this approach to study the inducible secreted proteomes of epithelial cells.
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Affiliation(s)
- Jasmin Priester
- Rudolf Buchheim Institute of Pharmacology, Justus Liebig University, 35392 Giessen, Germany
| | - Johanna Meier-Soelch
- Rudolf Buchheim Institute of Pharmacology, Justus Liebig University, 35392 Giessen, Germany
| | - Hendrik Weiser
- Rudolf Buchheim Institute of Pharmacology, Justus Liebig University, 35392 Giessen, Germany
| | - Daniel Heylmann
- Rudolf Buchheim Institute of Pharmacology, Justus Liebig University, 35392 Giessen, Germany
| | - Axel Weber
- Rudolf Buchheim Institute of Pharmacology, Justus Liebig University, 35392 Giessen, Germany
| | - Uwe Linne
- Mass Spectrometry Facility of the Department of Chemistry, Philipps University, 35032 Marburg, Germany.
| | - Michael Kracht
- Rudolf Buchheim Institute of Pharmacology, Justus Liebig University, 35392 Giessen, Germany; Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany; Cardio-Pulmonary Institute (CPI), Giessen, Germany.
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11
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Mahapatra KK, Patra S, Mishra SR, Behera BP, Patil S, Bhutia SK. Autophagy for secretory protein: Therapeutic targets in cancer. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 133:159-180. [PMID: 36707200 DOI: 10.1016/bs.apcsb.2022.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Autophagy, a classical cellular degradative catabolic process, also involves a functionally discrete non-degradative role in eukaryotic cells. It imparts critical regulatory function on conventional and unconventional protein secretion (degradative and secretory autophagy with distinct lysosomal degradation and extracellular expulsion, respectively) pathways. The N-amino terminal leader sequence containing proteins follows a conventional secretion pathway, while the leader-less proteins opt for secretory autophagy. The secretory autophagic process ensembles core autophagy machinery proteins, specifically ULK1/2, Beclin 1, LC3, and GABARAP, in coordination with Golgi re-assembly and stacking proteins (GRASPs). The secretory omegasomes fuse with the plasma membrane for the expulsion of cytosolic cargos to the extracellular environment. Alternatively, the secretory omegasomes also fuse with multi-vesicular bodies (MVBs) and harmonize ESCRTs (Complex I; TSG101) and Rab GTPase for their release to extracellular space. Autophagy has been associated with the secretion of diverse proteins involved in cellular signaling, inflammation, and carcinogenesis. Secreted proteins play an essential role in cancer by sustaining cell proliferation, inhibiting apoptosis, enhancing angiogenesis and metastasis, immune cell regulation, modulation of cellular energy metabolism, and resistance to anticancer drugs. The complexity of autophagy regulation during tumorigenesis is dependent on protein secretion pathways. Autophagy-regulated TOR-autophagy spatial coupling compartment complex energizes enhanced secretion of pro-inflammatory cytokines and leaderless proteins such as HMGB1. In conclusion, the chapter reviews the role of autophagy in regulating conventional and unconventional protein secretion pathways and its possible role in cancer.
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Affiliation(s)
- Kewal Kumar Mahapatra
- Cancer and Cell Death Laboratory, Department of Life Science, National Institute of Technology, Rourkela, Odisha, India
| | - Srimanta Patra
- Cancer and Cell Death Laboratory, Department of Life Science, National Institute of Technology, Rourkela, Odisha, India
| | - Soumya Ranjan Mishra
- Cancer and Cell Death Laboratory, Department of Life Science, National Institute of Technology, Rourkela, Odisha, India
| | - Bishnu Prasad Behera
- Cancer and Cell Death Laboratory, Department of Life Science, National Institute of Technology, Rourkela, Odisha, India
| | - Shankargouda Patil
- College of Dental Medicine, Roseman University of Health Sciences, South Jordan, UT, United States.
| | - Sujit Kumar Bhutia
- Cancer and Cell Death Laboratory, Department of Life Science, National Institute of Technology, Rourkela, Odisha, India.
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Post-Transcriptional Control of mRNA Metabolism and Protein Secretion: The Third Level of Regulation within the NF-κB System. Biomedicines 2022; 10:biomedicines10092108. [PMID: 36140209 PMCID: PMC9495616 DOI: 10.3390/biomedicines10092108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/12/2022] [Accepted: 08/21/2022] [Indexed: 11/17/2022] Open
Abstract
The NF-κB system is a key transcriptional pathway that regulates innate and adaptive immunity because it triggers the activation and differentiation processes of lymphocytes and myeloid cells during immune responses. In most instances, binding to cytoplasmic inhibitory IκB proteins sequesters NF-κB into an inactive state, while a plethora of external triggers activate three complex signaling cascades that mediate the release and nuclear translocation of the NF-κB DNA-binding subunits. In addition to these cytosolic steps (level 1 of NF-κB regulation), NF-κB activity is also controlled in the nucleus by signaling events, cofactors and the chromatin environment to precisely determine chromatin recruitment and the specificity and timing of target gene transcription (level 2 of NF-κB regulation). Here, we discuss an additional layer of the NF-κB system that manifests in various steps of post-transcriptional gene expression and protein secretion. This less-studied regulatory level allows reduction of (transcriptional) noise and signal integration and endows time-shifted control of the secretion of inflammatory mediators. Detailed knowledge of these steps is important, as dysregulated post-transcriptional NF-κB signaling circuits are likely to foster chronic inflammation and contribute to the formation and maintenance of a tumor-promoting microenvironment.
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