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Li W, Zhou Q, Xu J, Zhu S, Lv S, Yu Z, Yang Y, Liu Y, Zhou Y, Sui X, Zhang Q, Xiao Y. Insight into the solubilization mechanism of wheat gluten by protease modification from conformational change and molecular interaction perspective. Food Chem 2024; 447:138992. [PMID: 38503066 DOI: 10.1016/j.foodchem.2024.138992] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 01/29/2024] [Accepted: 03/09/2024] [Indexed: 03/21/2024]
Abstract
The low solubility limits the utilization of other functional characteristics of wheat gluten (WG). This study effectively improved the solubility of WG through protease modification and explored the potential mechanism of protease modification to enhance the solubility of WG, further stimulating the potential application of WG in the food industry. Solubility of WG modified with alkaline protease, complex protease, and neutral protease was enhanced by 98.99%, 54.59%, and 51.68%, respectively. Notably, the content of β-sheet was reduced while the combined effect of hydrogen bond and ionic bond were increased after protease modification. Meanwhile, the reduced molecular size and viscoelasticity as well as the elevated surface hydrophobicity, thermostability, water absorption capacity, and crystallinity were observed in modified WG. Moreover, molecular docking indicated that protease was specifically bound to the amino acid residues of WG through hydrogen bonding, hydrophobic interaction, and salt bridge.
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Affiliation(s)
- Weixiao Li
- Key Laboratory of Jianghuai Agricultural Product Fine Processing and Resource Utilization of Ministry of Agriculture and Rural Affairs, State Key Laboratory of Tea Plant Biology and Utilization, School of Tea and Food Science & Technology, Anhui Agricultural University, Hefei 230036, China
| | - Qianxin Zhou
- Key Laboratory of Jianghuai Agricultural Product Fine Processing and Resource Utilization of Ministry of Agriculture and Rural Affairs, State Key Laboratory of Tea Plant Biology and Utilization, School of Tea and Food Science & Technology, Anhui Agricultural University, Hefei 230036, China
| | - Jianxia Xu
- Key Laboratory of Jianghuai Agricultural Product Fine Processing and Resource Utilization of Ministry of Agriculture and Rural Affairs, State Key Laboratory of Tea Plant Biology and Utilization, School of Tea and Food Science & Technology, Anhui Agricultural University, Hefei 230036, China
| | - Shanlong Zhu
- Key Laboratory of Jianghuai Agricultural Product Fine Processing and Resource Utilization of Ministry of Agriculture and Rural Affairs, State Key Laboratory of Tea Plant Biology and Utilization, School of Tea and Food Science & Technology, Anhui Agricultural University, Hefei 230036, China
| | - Sixu Lv
- Key Laboratory of Jianghuai Agricultural Product Fine Processing and Resource Utilization of Ministry of Agriculture and Rural Affairs, State Key Laboratory of Tea Plant Biology and Utilization, School of Tea and Food Science & Technology, Anhui Agricultural University, Hefei 230036, China
| | - Zhenyu Yu
- Key Laboratory of Jianghuai Agricultural Product Fine Processing and Resource Utilization of Ministry of Agriculture and Rural Affairs, State Key Laboratory of Tea Plant Biology and Utilization, School of Tea and Food Science & Technology, Anhui Agricultural University, Hefei 230036, China
| | - Yin Yang
- Anhui Bi Lv Chun Biotechnology Co., Ltd., Chuzhou 239200, China
| | - Yingnan Liu
- Key Laboratory of Jianghuai Agricultural Product Fine Processing and Resource Utilization of Ministry of Agriculture and Rural Affairs, State Key Laboratory of Tea Plant Biology and Utilization, School of Tea and Food Science & Technology, Anhui Agricultural University, Hefei 230036, China
| | - Yibin Zhou
- Key Laboratory of Jianghuai Agricultural Product Fine Processing and Resource Utilization of Ministry of Agriculture and Rural Affairs, State Key Laboratory of Tea Plant Biology and Utilization, School of Tea and Food Science & Technology, Anhui Agricultural University, Hefei 230036, China
| | - Xiaonan Sui
- College of Food Science, Northeast Agricultural University, Harbin 150030, China.
| | - Qiang Zhang
- Key Laboratory of Jianghuai Agricultural Product Fine Processing and Resource Utilization of Ministry of Agriculture and Rural Affairs, State Key Laboratory of Tea Plant Biology and Utilization, School of Tea and Food Science & Technology, Anhui Agricultural University, Hefei 230036, China.
| | - Yaqing Xiao
- Key Laboratory of Jianghuai Agricultural Product Fine Processing and Resource Utilization of Ministry of Agriculture and Rural Affairs, State Key Laboratory of Tea Plant Biology and Utilization, School of Tea and Food Science & Technology, Anhui Agricultural University, Hefei 230036, China.
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Zhang H, Liu Y, Gao L, Wang J. Analysis of flavor changes in Huangshan floral mushroom hydrolysates obtained by different enzyme treatments. Food Chem 2024; 443:138554. [PMID: 38306912 DOI: 10.1016/j.foodchem.2024.138554] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/21/2024] [Accepted: 01/21/2024] [Indexed: 02/04/2024]
Abstract
This study aimed to investigate the flavor changes in Huangshan floral mushroom by different enzyme treatments. Seven enzyme groups were used to hydrolyze its protein to obtain protein hydrolysates (FPHs). Flavourzyme composite with dispase hydrolysates (FDHs) were selected for ultrafiltration to obtain peptides (FPs) with different molecular weights (Mw). Changes in flavor were investigated using HPLC, LC-MS, GC-MS, amino acid analysis and sensory evaluation. Color parameters and DPPH-scavenging activity were also determined. The results revealed that flavor characteristics of FPHs obtained from different enzyme treatments varied. FDHs presented the highest degree of hydrolysis (DH) (58.61 ± 1.55) %, rich 5'-nucleotides (8.61 ± 0.43 mg/mL), volatile compounds (28.54 ± 0.11 μg/g) and free amino acids (FAAs) (7.73 ± 0.51 mg/g). Further tests suggested that FPs with small Mw (<1K, 1-3 K) were optimal for the development of novel flavors, thus providing application value for rational utilization of Huangshan floral mushroom.
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Affiliation(s)
- Hui Zhang
- Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230601, China; Key Laboratory for Agricultural Products Processing of Anhui Province, Hefei University of Technology, Hefei 230009, China; School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China
| | - Yong Liu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China
| | - Li Gao
- Key Laboratory for Agricultural Products Processing of Anhui Province, Hefei University of Technology, Hefei 230009, China; School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China
| | - Junhui Wang
- Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230601, China; Key Laboratory for Agricultural Products Processing of Anhui Province, Hefei University of Technology, Hefei 230009, China; School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China.
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Yolandani, Liu D, Raynaldo FA, Dabbour M, Zhang X, Chen Z, Ding Q, Luo L, Ma H. Comparison of prediction models for soy protein isolate hydrolysates bitterness built using sensory, spectrofluorometric and chromatographic data from varying enzymes and degree of hydrolysis. Food Chem 2024; 442:138428. [PMID: 38241997 DOI: 10.1016/j.foodchem.2024.138428] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 12/09/2023] [Accepted: 01/10/2024] [Indexed: 01/21/2024]
Abstract
The bitterness of soy protein isolate hydrolysates prepared using five proteases at varying degree of hydrolysis (DH) and its relation to physicochemical properties, i.e., surface hydrophobicity (H0), relative hydrophobicity (RH), and molecular weight (MW), were studied and developed for predictive modelling using machine learning. Bitter scores were collected from sensory analysis and assigned as the target, while the physicochemical properties were assigned as the features. The modelling involved data pre-processing with local outlier factor; model development with support vector machine, linear regression, adaptive boosting, and K-nearest neighbors algorithms; and performance evaluation by 10-fold stratified cross-validation. The results indicated that alcalase hydrolysates were the most bitter, followed by protamex, flavorzyme, papain, and bromelain. Distinctive correlation results were found among the physicochemical properties, influenced by the disparity of each protease. Among the features, the combination of RH-MW fitted various classification models and resulted in the best prediction performance.
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Affiliation(s)
- Yolandani
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, People's Republic of China
| | - Dandan Liu
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, People's Republic of China
| | - Fredy Agil Raynaldo
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, People's Republic of China; College of Biosystems Engineering and Food Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Mokhtar Dabbour
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, People's Republic of China; Department of Agricultural and Biosystems Engineering, Faculty of Agriculture, Benha University, P.O. Box 13736, Moshtohor, Qaluobia, Egypt
| | - Xueli Zhang
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, People's Republic of China
| | - Zhongyuan Chen
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, People's Republic of China
| | - Qingzhi Ding
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, People's Republic of China; Institute of Food Physical Processing, Jiangsu University, Zhenjiang 212013, People's Republic of China
| | - Lin Luo
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, People's Republic of China; Institute of Food Physical Processing, Jiangsu University, Zhenjiang 212013, People's Republic of China
| | - Haile Ma
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, People's Republic of China; Institute of Food Physical Processing, Jiangsu University, Zhenjiang 212013, People's Republic of China.
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Metkar SK, Girigoswami A, Bondage DD, Shinde UG, Girigoswami K. The potential of lumbrokinase and serratiopeptidase for the degradation of Aβ 1-42 peptide - an in vitro and in silico approach. Int J Neurosci 2024; 134:112-123. [PMID: 35694981 DOI: 10.1080/00207454.2022.2089137] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 05/27/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND Alzheimer's disease (AD) is diagnosed with the deposition of insoluble β-amyloid (Aβ) peptides in the neuropil of the brain leading to dementia. The extracellular deposition of the fibrillar Aβ peptide on the neurons is known as senile plaques. Therefore, Aβ degradation and clearance from the human body is a promising therapeutic approach in the medication of AD. METHODS In the current study, the enzyme lumbrokinase (LK) was extracted and purified from earthworm and its activity was utilized toward Aβ 1-42 amyloids degradation in vitro alongside with an additional enzyme serratiopeptidase (SP) considering nattokinase (NK) as a standard. RESULTS The output of this study revealed that preformed Aβ 1-42 amyloids was disintegrated by both LK and SP, as demonstrated from fluorescence assay using Thioflavin T dye. In addition, dynamic light scattering study revealed the lower size of the preformed fibrils Aβ 1-42 at various time intervals after incubation with the enzymes LK and SP. Furthermore, in silico approach showed high affinity thermodynamically favorable interaction of LK as well as SP toward Aβ 1-42 amyloid. Finally, the toxicity of degraded preformed Aβ 1-42 amyloid was assessed by MTT assay which showed reduced toxicity of enzyme treated Aβ 1-42 amyloid compared to only Aβ 1-42 amyloid. CONCLUSION The findings of the present study indicated that LK and SP, not only had Aβ 1-42 amyloid degrading potential, but also could reduce the toxicity which can make them a suitable drug candidate for AD. Furthermore, the in vivo studies are needed to be executed in future.
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Affiliation(s)
- Sanjay Kisan Metkar
- Medical Bionanotechnology, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute (CHRI), Chettinad Academy of Research and Education (CARE), Chettinad Health City, Chennai, India
| | - Agnishwar Girigoswami
- Medical Bionanotechnology, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute (CHRI), Chettinad Academy of Research and Education (CARE), Chettinad Health City, Chennai, India
| | - Devanand D Bondage
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Umakant G Shinde
- Centre for Advanced Life Sciences (CFALS), Deogiri College, Aurangabad, Maharashtra, India
| | - Koyeli Girigoswami
- Medical Bionanotechnology, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute (CHRI), Chettinad Academy of Research and Education (CARE), Chettinad Health City, Chennai, India
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Xiang Q, Xia Y, Fang S, Zhong F. Enzymatic debittering of cheese flavoring and bitterness characterization of peptide mixture using sensory and peptidomics approach. Food Chem 2024; 440:138229. [PMID: 38159315 DOI: 10.1016/j.foodchem.2023.138229] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 12/09/2023] [Accepted: 12/15/2023] [Indexed: 01/03/2024]
Abstract
Peptides in cheese flavoring produced through proteolysis plus fermentation generated bitterness. Bitterness of individual peptide can be quantified using quantitative structure-activity relationship, where molecular mass (M), hydrophobicity, residues, C-terminal hydrophobic amino acids (C-HAAs), and N-terminal basic ones (N-BAAs) are crucial. However, their accumulative influence on the overall bitterness of peptide mixture remains unknown. This study delved into extensive proteolysis to debitter and to correlate the multi-influencing factors of peptides and the collective bitterness. As hydrolysis increased from 7.5 % to 28.0 %, bitterness reduced from 5.0 to 0.3-2.7 scores, contingent on proteases used, in which FU was optimal. The overall bitterness cannot be predicted through the summation of individual peptide bitterness, which depended on M (0.5-3 kDa) and 5-23 residues, followed by N-BAAs and C-HAAs. Analysis of enzymatic cleavage sites and substrate characteristics revealed, to more effectively debitter bovine milk protein hydrolysates, proteases specifically cleaving Pro, Leu, Phe, and Val were desired.
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Affiliation(s)
- Qin Xiang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; International Joint Laboratory for Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Yixun Xia
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; Jiaxing Institute of Future Food, Jiaxing 314015, China
| | - Sicong Fang
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Fang Zhong
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; International Joint Laboratory for Food Safety, Jiangnan University, Wuxi, 214122, China.
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6
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Chen J, Sun X, Liu Y, Zhang Y, Zhao M, Shao L. SENP3 attenuates foam cell formation by deSUMOylating NLRP3 in macrophages stimulated with ox-LDL. Cell Signal 2024; 117:111092. [PMID: 38331013 DOI: 10.1016/j.cellsig.2024.111092] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 01/22/2024] [Accepted: 02/05/2024] [Indexed: 02/10/2024]
Abstract
SUMO-specific protease 3 (SENP3) participates in the removal of SUMOylation and maintains the balance of the SUMO system, which ensures normal functioning of substrates and cellular activities. In the present study, we found that SENP3 expression was significantly reduced in ox-LDL-stimulated macrophages. SENP3 overexpression suppressed and SENP3 knockdown promoted macrophage foam cell formation. Moreover, SENP3 inhibited cholesterol uptake, CD36 expression, and NOD-like receptor thermal protein domain-associated protein 3 (NLRP3) inflammasome activation in ox-LDL-stimulated macrophages. Ox-LDL-stimulated NLRP3 SUMOylation was reduced by SENP3. Blocking NLRP3 SUMOylation inhibited foam cell formation and NLRP3 inflammasome activation. Thus, this study revealed that SENP3 inhibits macrophage foam cell formation by deSUMOylating NLRP3 and regulating NLRP3 inflammasome activation, which may provide a potentially innovative approach to treatment of atherosclerosis.
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Affiliation(s)
- Jiaojiao Chen
- Department of Pathogen Biology, School of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan, China
| | - Xuan Sun
- Department of Pathogen Biology, School of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan, China
| | - Yuan Liu
- Department of Pathogen Biology, School of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan, China
| | - Yuze Zhang
- Department of Pathogen Biology, School of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan, China
| | - Min Zhao
- Department of Biochemistry, School of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan, China.
| | - Luyao Shao
- Department of Pathogen Biology, School of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan, China.
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Périco LL, Vegso AJ, Baggio CH, MacNaughton WK. Protease-activated receptor 2 drives migration in a colon cancer cell line but not in noncancerous human epithelial cells. Am J Physiol Gastrointest Liver Physiol 2024; 326:G525-G542. [PMID: 38440826 DOI: 10.1152/ajpgi.00284.2023] [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: 11/27/2023] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 03/06/2024]
Abstract
The inflamed mucosa contains a complex assortment of proteases that may participate in wound healing or the development of inflammation-associated colon cancer. We sought to determine the role of protease-activated receptor 2 (PAR2) in epithelial wound healing in both untransformed and transformed colonic epithelial cells. Monolayers of primary epithelial cells derived from organoids cultivated from patient colonic biopsies and of the T84 colon cancer cell line were grown to confluence, wounded in the presence of a selective PAR2-activating peptide, and healing was visualized by live cell microscopy. Inhibitors of various signaling molecules were used to assess the relevant pathways responsible for wound healing. Activation of PAR2 induced an enhanced wound-healing response in T84 cells but not primary cells. The PAR2-enhanced wound-healing response was associated with the development of lamellipodia in cells at the wound edge, consistent with sheet migration. The response to PAR2 activation in T84 cells was completely dependent on Src kinase activity and partially dependent on Rac1 activity. The Src-associated signaling molecules, focal adhesion kinase, and epidermal growth factor receptor, which typically mediate wound-healing responses, were not involved in the PAR2 response. Experiments repeated in the presence of the inflammatory cytokines TNF and IFNγ revealed a synergistically enhanced PAR2 wound-healing response in T84s but not primary cells. The epithelial response to proteases may be different between primary and cancer cells and is accentuated in the presence of inflammatory cytokines. Our findings have implications for understanding epithelial restitution in the context of inflammatory bowel disease (IBD) and inflammation-associated colon cancer.NEW & NOTEWORTHY Protease-activated receptor 2 enhances wound healing in the T84 colon cancer cell line, but not in primary cells derived from patient biopsies, an effect that is synergistically enhanced in the presence of the inflammatory cytokines TNF and IFNγ.
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Affiliation(s)
- Larissa Lucena Périco
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Andrew J Vegso
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Cristiane H Baggio
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Wallace K MacNaughton
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
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8
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Miskin RP, DiPersio CM. Roles for epithelial integrin α3β1 in regulation of the microenvironment during normal and pathological tissue remodeling. Am J Physiol Cell Physiol 2024; 326:C1308-C1319. [PMID: 38497112 DOI: 10.1152/ajpcell.00128.2024] [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: 02/23/2024] [Revised: 03/08/2024] [Accepted: 03/08/2024] [Indexed: 03/19/2024]
Abstract
Integrin receptors for the extracellular matrix activate intracellular signaling pathways that are critical for tissue development, homeostasis, and regeneration/repair, and their loss or dysregulation contributes to many developmental defects and tissue pathologies. This review will focus on tissue remodeling roles for integrin α3β1, a receptor for laminins found in the basement membranes (BMs) that underlie epithelial cell layers. As a paradigm, we will discuss literature that supports a role for α3β1 in promoting ability of epidermal keratinocytes to modify their tissue microenvironment during skin development, wound healing, or tumorigenesis. Preclinical and clinical studies have shown that this role depends largely on ability of α3β1 to govern the keratinocyte's repertoire of secreted proteins, or the "secretome," including 1) matrix proteins and proteases involved in matrix remodeling and 2) paracrine-acting growth factors/cytokines that stimulate other cells with important tissue remodeling functions (e.g., endothelial cells, fibroblasts, inflammatory cells). Moreover, α3β1 signaling controls gene expression that helps epithelial cells carry out these functions, including genes that encode secreted matrix proteins, proteases, growth factors, or cytokines. We will review what is known about α3β1-dependent gene regulation through both transcription and posttranscriptional mRNA stability. Regarding the latter, we will discuss examples of α3β1-dependent alternative splicing (AS) or alternative polyadenylation (APA) that prevents inclusion of cis-acting mRNA sequences that would otherwise target the transcript for degradation via nonsense-mediated decay or destabilizing AU-rich elements (AREs) in the 3'-untranslated region (3'-UTR). Finally, we will discuss prospects and anticipated challenges of exploiting α3β1 as a clinical target for the treatment of cancer or wound healing.
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Affiliation(s)
| | - C Michael DiPersio
- Department of Surgery, Albany Medical College, Albany, New York, United States
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, New York, United States
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9
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Naumann TA, Dowling NV, Price NPJ, Rose DR. In vitro functional analysis and in silico structural modelling of pathogen-secreted polyglycine hydrolases. Biochem Biophys Res Commun 2024; 706:149746. [PMID: 38461646 DOI: 10.1016/j.bbrc.2024.149746] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/16/2024] [Accepted: 03/01/2024] [Indexed: 03/12/2024]
Abstract
Polyglycine hydrolases are fungal effectors composed of an N-domain with unique sequence and structure and a C-domain that resembles β-lactamases, with serine protease activity. These secreted fungal proteins cleave Gly-Gly bonds within a polyglycine sequence in corn ChitA chitinase. The polyglycine hydrolase N-domain (PND) function is unknown. In this manuscript we provide evidence that the PND does not directly participate in ChitA cleavage. In vitro analysis of site-directed mutants in conserved residues of the PND of polyglycine hydrolase Es-cmp did not specifically impair protease activity. Furthermore, in silico structural models of three ChitA-bound polyglycine hydrolases created by High Ambiguity Driven protein-protein DOCKing (HADDOCK) did not predict significant interactions between the PND and ChitA. Together these results suggest that the PND has another function. To determine what types of PND-containing proteins exist in nature we performed a computational analysis of Foldseek-identified PND-containing proteins. The analysis showed that proteins with PNDs are present throughout biology as either single domain proteins or fused to accessory domains that are diverse but are usually proteases or kinases.
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Affiliation(s)
- Todd A Naumann
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, 1815 N. University, Peoria, IL, 61604, USA.
| | - Nicole V Dowling
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Neil P J Price
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Renewable Product Technologies Research Unit, 1815 N. University, Peoria, IL, 61604, USA
| | - David R Rose
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
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10
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Fagernäs Z, Troché G, Olsen JV, Welker F. Digging deeper into ancient skeletal proteomes through consecutive digestion with multiple proteases. J Proteomics 2024; 298:105143. [PMID: 38423353 DOI: 10.1016/j.jprot.2024.105143] [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: 12/15/2023] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/02/2024]
Abstract
An increasing number of studies utilise the recovery of ancient skeletal proteomes for phylogenetic and evolutionary analysis. Although these studies manage to extract and analyse ancient peptides, the recovered proteomes are generally small in size and with low protein sequence coverage. We expand on previous observations which have shown that the parallel digestion and analysis of Pleistocene skeletal proteomes increases overall proteome size and protein sequence coverage. Furthermore, we demonstrate that the consecutive digestion of a skeletal proteome using two proteases, particularly the combination of Glu-C or chymotrypsin followed by trypsin digestion, enables the recovery of alternative proteome components not reachable through trypsin digestion alone. The proteomes preserved in Pleistocene skeletal specimens are larger than previously anticipated, but unlocking this protein sequence information requires adaptation of extraction and protein digestion protocols. The sequential utilisation of several proteases is, in this regard, a promising avenue for the study of highly degraded but unique hominin proteomes for phylogenetic purposes. SIGNIFICANCE: Palaeoproteomic analysis of archaeological materials, such as hominin skeletal elements, show great promise in studying past organisms and evolutionary relationships. However, as most proteomic methods are inherently destructive, it is essential to aim to recover as much information as possible from every sample. Currently, digestion with trypsin is the standard approach in most palaeoproteomic studies. We find that parallel or consecutive digestion with multiple proteases can improve proteome size and coverage for both Holocene and Pleistocene bone specimens. This allows for recovery of more proteomic data from a sample and maximises the chance of recovering phylogenetically relevant information.
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Affiliation(s)
- Zandra Fagernäs
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Gaudry Troché
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Frido Welker
- Globe Institute, University of Copenhagen, Copenhagen, Denmark.
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11
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Lin X, Wang W, He F, Hou H, Guo F. Molecular level toxicity effects of As(V) on Folsomia candida: Integrated transcriptomics and metabolomics analyses. Sci Total Environ 2024; 922:171409. [PMID: 38432367 DOI: 10.1016/j.scitotenv.2024.171409] [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] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 02/19/2024] [Accepted: 02/29/2024] [Indexed: 03/05/2024]
Abstract
Arsenic (As) is a widespread metalloid with well-known toxicity. To date, numerous studies have focused on individual level toxicity (e.g., growth and reproduction) of As to typical invertebrate springtails in soils, however, the molecular level toxicity and mechanism was poorly understood. Here, an integrated transcriptomics and metabolomics approach was used to reveal responses of Folsomia candida exposed to As(V) of 10 and 60 mg kg-1 at which the individual level endpoints were influenced. Transcriptomics identified 5349 and 4020 differentially expressed genes (DEGs) in low and high concentration groups, respectively, and the most DEGs were down-regulated. Enrichment analysis showed that low and high concentrations of As(V) significantly inhibited chromatin/chromosome-related biological processes (chromatin/chromosome organization, nucleosome assembly and organization, etc.) in springtails. At high concentration treatment, structural constituent of cuticle, chitin metabolic process and peptidase activity (serine-type peptidase activity, endopeptidase activity, etc.) were inhibited or disturbed. Moreover, the apoptosis pathway was significantly induced. Metabolomics analysis identified 271 differential changed metabolites (DCMs) in springtails exposed to high concentration of As. Steroid hormone biosynthesis was the most significantly affected pathway. Several DCMs that related to chitin metabolism could further support above transcriptomic results. These findings further extended the knowledge of As toxic mechanisms to soil fauna and offer important information for the environmental risk assessment.
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Affiliation(s)
- Xianglong Lin
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Weiran Wang
- School of Chemical and Environmental Engineering, China University of Mining and Technology-Beijing, Beijing 100083, China
| | - Fei He
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Hong Hou
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Fei Guo
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
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12
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Strange N, Luu L, Ong V, Wee BA, Phillips MJA, McCaughey L, Steele JR, Barlow CK, Cranfield CG, Myers G, Mazraani R, Rock C, Timms P, Huston WM. HtrA, fatty acids, and membrane protein interplay in Chlamydia trachomatis to impact stress response and trigger early cellular exit. J Bacteriol 2024; 206:e0037123. [PMID: 38445896 PMCID: PMC11025325 DOI: 10.1128/jb.00371-23] [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: 11/02/2023] [Accepted: 02/15/2024] [Indexed: 03/07/2024] Open
Abstract
Chlamydia trachomatis is an intracellular bacterial pathogen that undergoes a biphasic developmental cycle, consisting of intracellular reticulate bodies and extracellular infectious elementary bodies. A conserved bacterial protease, HtrA, was shown previously to be essential for Chlamydia during the reticulate body phase, using a novel inhibitor (JO146). In this study, isolates selected for the survival of JO146 treatment were found to have polymorphisms in the acyl-acyl carrier protein synthetase gene (aasC). AasC encodes the enzyme responsible for activating fatty acids from the host cell or synthesis to be incorporated into lipid bilayers. The isolates had distinct lipidomes with varied fatty acid compositions. A reduction in the lipid compositions that HtrA prefers to bind to was detected, yet HtrA and MOMP (a key outer membrane protein) were present at higher levels in the variants. Reduced progeny production and an earlier cellular exit were observed. Transcriptome analysis identified that multiple genes were downregulated in the variants especially stress and DNA processing factors. Here, we have shown that the fatty acid composition of chlamydial lipids, HtrA, and membrane proteins interplay and, when disrupted, impact chlamydial stress response that could trigger early cellular exit. IMPORTANCE Chlamydia trachomatis is an important obligate intracellular pathogen that has a unique biphasic developmental cycle. HtrA is an essential stress or virulence protease in many bacteria, with many different functions. Previously, we demonstrated that HtrA is critical for Chlamydia using a novel inhibitor. In the present study, we characterized genetic variants of Chlamydia trachomatis with reduced susceptibility to the HtrA inhibitor. The variants were changed in membrane fatty acid composition, outer membrane proteins, and transcription of stress genes. Earlier and more synchronous cellular exit was observed. Combined, this links stress response to fatty acids, membrane proteins, and HtrA interplay with the outcome of disrupted timing of chlamydial cellular exit.
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Affiliation(s)
- Natalie Strange
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Laurence Luu
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Vanissa Ong
- Faculty of Health, Queensland University of Technology, Kelvin Grove, Queensland, Australia
| | - Bryan A. Wee
- Faculty of Health, Queensland University of Technology, Kelvin Grove, Queensland, Australia
- The Roslin Institute, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Matthew J. A. Phillips
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Laura McCaughey
- Australian Institute for Microbiology and Infection, Faculty of Science, University of Technology Sydney, Ultimo, New South Wales, Australia
- School of Infection and Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Joel R. Steele
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, New South Wales, Australia
- Department of Biochemistry and Molecular Biology, Monash Proteomics and Metabolomics Platform, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Christopher K. Barlow
- Department of Biochemistry and Molecular Biology, Monash Proteomics and Metabolomics Platform, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Charles G. Cranfield
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Garry Myers
- Australian Institute for Microbiology and Infection, Faculty of Science, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Rami Mazraani
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Charles Rock
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Peter Timms
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, Queensland, Australia
| | - Wilhelmina M. Huston
- Faculty of Science, University of Technology Sydney, Ultimo, New South Wales, Australia
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13
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Paulay A, Grimaud GM, Caballero R, Laroche B, Leclerc M, Labarthe S, Maguin E. Design of a proteolytic module for improved metabolic modeling of Bacteroides caccae. mSystems 2024; 9:e0015324. [PMID: 38517169 PMCID: PMC11019848 DOI: 10.1128/msystems.00153-24] [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: 02/14/2024] [Accepted: 02/27/2024] [Indexed: 03/23/2024] Open
Abstract
The gut microbiota plays a crucial role in health and is significantly modulated by human diets. In addition to Western diets which are rich in proteins, high-protein diets are used for specific populations or indications, mainly weight loss. In this study, we investigated the effect of protein supplementation on Bacteroides caccae, a Gram-negative gut symbiont. The supplementation with whey proteins led to a significant increase in growth rate, final biomass, and short-chain fatty acids production. A comprehensive genomic analysis revealed that B. caccae possesses a set of 156 proteases with putative intracellular and extracellular localization and allowed to identify amino acid transporters and metabolic pathways. We developed a fully curated genome-scale metabolic model of B. caccae that incorporated its proteolytic activity and simulated its growth and production of fermentation-related metabolites in response to the different growth media. We validated the model by comparing the predicted phenotype to experimental data. The model accurately predicted B. caccae's growth and metabolite production (R2 = 0.92 for the training set and R2 = 0.89 for the validation set). We found that accounting for both ATP consumption related to proteolysis, and whey protein accessibility is necessary for accurate predictions of metabolites production. These results provide insights into B. caccae's adaptation to a high-protein diet and its ability to utilize proteins as a source of nutrition. The proposed model provides a useful tool for understanding the feeding mechanism of B. caccae in the gut microbiome.IMPORTANCEMicrobial proteolysis is understudied despite the availability of dietary proteins for the gut microbiota. Here, the proteolytic potential of the gut symbiont Bacteroides caccae was analyzed for the first time using pan-genomics. This sketches a well-equipped bacteria for protein breakdown, capable of producing 156 different proteases with a broad spectrum of cleavage targets. This functional potential was confirmed by the enhancement of growth and metabolic activities at high protein levels. Proteolysis was included in a B. caccae metabolic model which was fitted with the experiments and validated on external data. This model pinpoints the links between protein availability and short-chain fatty acids production, and the importance for B. caccae to gain access to glutamate and asparagine to promote growth. This integrated approach can be generalized to other symbionts and upscaled to complex microbiota to get insights into the ecological impact of proteins on the gut microbiota.
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Affiliation(s)
- Amandine Paulay
- Université Paris-Saclay, INRAE, AgroParisTech, UMR1319 Micalis Institute, Jouy-en-Josas, France
- Biomathematica, Ajaccio, France
- Université Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France
| | | | - Raphaël Caballero
- Université Paris-Saclay, INRAE, AgroParisTech, UMR1319 Micalis Institute, Jouy-en-Josas, France
| | - Béatrice Laroche
- Université Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France
- Université Paris-Saclay, Inria, Centre Inria de Saclay, Palaiseau, France
| | - Marion Leclerc
- Université Paris-Saclay, INRAE, AgroParisTech, UMR1319 Micalis Institute, Jouy-en-Josas, France
- Pendulum Therapeutics, San Francisco, California, USA
| | - Simon Labarthe
- Université Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France
- University of Bordeaux, INRAE, BIOGECO, Cestas, France
- Inria, Univ. Bordeaux, INRAE, Talence, France
| | - Emmanuelle Maguin
- Université Paris-Saclay, INRAE, AgroParisTech, UMR1319 Micalis Institute, Jouy-en-Josas, France
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14
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Mohebbi A, Eskandarzadeh M, Zangi H, Fatehi M. In silico study of alkaloids with quercetin nucleus for inhibition of SARS-CoV-2 protease and receptor cell protease. PLoS One 2024; 19:e0298201. [PMID: 38626042 PMCID: PMC11020608 DOI: 10.1371/journal.pone.0298201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 01/21/2024] [Indexed: 04/18/2024] Open
Abstract
Covid-19 disease caused by the deadly SARS-CoV-2 virus is a serious and threatening global health issue declared by the WHO as an epidemic. Researchers are studying the design and discovery of drugs to inhibit the SARS-CoV-2 virus due to its high mortality rate. The main Covid-19 virus protease (Mpro) and human transmembrane protease, serine 2 (TMPRSS2) are attractive targets for the study of antiviral drugs against SARS-2 coronavirus. Increasing consumption of herbal medicines in the community and a serious approach to these drugs have increased the demand for effective herbal substances. Alkaloids are one of the most important active ingredients in medicinal plants that have wide applications in the pharmaceutical industry. In this study, seven alkaloid ligands with Quercetin nucleus for the inhibition of Mpro and TMPRSS2 were studied using computational drug design including molecular docking and molecular dynamics simulation (MD). Auto Dock software was used to evaluate molecular binding energy. Three ligands with the most negative docking score were selected to be entered into the MD simulation procedure. To evaluate the protein conformational changes induced by tested ligands and calculate the binding energy between the ligands and target proteins, GROMACS software based on AMBER03 force field was used. The MD results showed that Phyllospadine and Dracocephin-A form stable complexes with Mpro and TMPRSS2. Prolinalin-A indicated an acceptable inhibitory effect on Mpro, whereas it resulted in some structural instability of TMPRSS2. The total binding energies between three ligands, Prolinalin-A, Phyllospadine and Dracocephin-A and two proteins MPro and TMRPSS2 are (-111.235 ± 15.877, - 75.422 ± 11.140), (-107.033 ± 9.072, -84.939 ± 10.155) and (-102.941 ± 9.477, - 92.451 ± 10.539), respectively. Since the binding energies are at a minimum, this indicates confirmation of the proper binding of the ligands to the proteins. Regardless of some Prolinalin-A-induced TMPRSS2 conformational changes, it may properly bind to TMPRSS2 binding site due to its acceptable binding energy. Therefore, these three ligands can be promising candidates for the development of drugs to treat infections caused by the SARS-CoV-2 virus.
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Affiliation(s)
- Ali Mohebbi
- Department of Chemical Engineering, Faculty of Engineering, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Marzieh Eskandarzadeh
- Research Committee of Faculty of Pharmacy, Lorestan University of Medical Science, Khorramabad, Iran
| | - Hanieh Zangi
- Department of Chemical Engineering, Faculty of Engineering, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Marzie Fatehi
- Department of Chemical Engineering, Faculty of Engineering, Shahid Bahonar University of Kerman, Kerman, Iran
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15
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Coene J, Wilms S, Verhelst SHL. Photopharmacology of Protease Inhibitors: Current Status and Perspectives. Chemistry 2024; 30:e202303999. [PMID: 38224181 DOI: 10.1002/chem.202303999] [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: 11/30/2023] [Revised: 01/10/2024] [Accepted: 01/15/2024] [Indexed: 01/16/2024]
Abstract
Proteases are involved in many essential biological processes. Dysregulation of their activity underlies a wide variety of human diseases. Photopharmacology, as applied on various classes of proteins, has the potential to assist protease research by enabling spatiotemporal control of protease activity. Moreover, it may be used to decrease side-effects of protease-targeting drugs. In this review, we discuss the current status of the chemical design of photoactivatable proteases inhibitors and their biological application. Additionally, we give insight into future possibilities for further development of this field of research.
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Affiliation(s)
- Jonathan Coene
- Department of Cellular and Molecular Medicine, KU Leuven - University of Leuven, Herestraat 49, box 901b, 3000, Leuven, Belgium
| | - Simon Wilms
- Department of Cellular and Molecular Medicine, KU Leuven - University of Leuven, Herestraat 49, box 901b, 3000, Leuven, Belgium
| | - Steven H L Verhelst
- Department of Cellular and Molecular Medicine, KU Leuven - University of Leuven, Herestraat 49, box 901b, 3000, Leuven, Belgium
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16
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Shevalev R, Bischof L, Sapegin A, Bunev A, Olga G, Kantin G, Kalinin S, Hartmann MD. Discovery and characterization of potent spiro-isoxazole-based cereblon ligands with a novel binding mode. Eur J Med Chem 2024; 270:116328. [PMID: 38552426 DOI: 10.1016/j.ejmech.2024.116328] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 03/05/2024] [Accepted: 03/10/2024] [Indexed: 04/21/2024]
Abstract
The vast majority of current cereblon (CRBN) ligands is based on the thalidomide scaffold, relying on glutarimide as the core binding moiety. With this architecture, most of these ligands inherit the overall binding mode, interactions with neo-substrates, and thereby potentially also the cytotoxic and teratogenic properties of the parent thalidomide. In this work, by incorporating a spiro-linker to the glutarimide moiety, we have generated a new chemotype that exhibits an unprecedented binding mode for glutarimide-based CRBN ligands. In total, 16 spirocyclic glutarimide derivatives incorporating an isoxazole moiety were synthesized and tested for different criteria. In particular, all ligands showed a favorable lipophilicity, and several were able to outperform the binding affinity of thalidomide as a reference. In addition, all compounds showed favorable cytotoxicity profiles in myeloma cell lines and human peripheral blood mononuclear cells. The novel binding mode, which we determined in co-crystal structures, provides explanations for these improved properties: The incorporation of the spiro-isoxazole changes both the conformation of the glutarimide moiety within the canonical tri-trp pocket and the orientation of the protruding moiety. In this new orientation it forms additional hydrophobic interactions and is not available for direct interactions with the canonical neo-substrates. We therefore propose this chemotype as an attractive building block for the design of PROTACs.
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Affiliation(s)
- Robert Shevalev
- Institute of Chemistry, Saint Petersburg State University, Saint Petersburg, Russia
| | - Luca Bischof
- Department of Protein Evolution, Max Planck Institute for Biology, Tübingen, Germany
| | - Alexander Sapegin
- Institute of Chemistry, Saint Petersburg State University, Saint Petersburg, Russia
| | - Alexander Bunev
- Medicinal Chemistry Center, Togliatti State University, Togliatti, Russia
| | - Grigor'eva Olga
- Medicinal Chemistry Center, Togliatti State University, Togliatti, Russia
| | - Grigory Kantin
- Institute of Chemistry, Saint Petersburg State University, Saint Petersburg, Russia
| | - Stanislav Kalinin
- Institute of Chemistry, Saint Petersburg State University, Saint Petersburg, Russia.
| | - Marcus D Hartmann
- Department of Protein Evolution, Max Planck Institute for Biology, Tübingen, Germany.
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17
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Kang W, Xiao F, Zhu X, Ling X, Xie S, Li R, Yu P, Cao L, Lei C, Qiu Y, Liu T, Nie Z. Engineering Anti-CRISPR Proteins to Create CRISPR-Cas Protein Switches for Activatable Genome Editing and Viral Protease Detection. Angew Chem Int Ed Engl 2024; 63:e202400599. [PMID: 38407550 DOI: 10.1002/anie.202400599] [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: 01/09/2024] [Revised: 02/07/2024] [Accepted: 02/26/2024] [Indexed: 02/27/2024]
Abstract
Proteins capable of switching between distinct active states in response to biochemical cues are ideal for sensing and controlling biological processes. Activatable CRISPR-Cas systems are significant in precise genetic manipulation and sensitive molecular diagnostics, yet directly controlling Cas protein function remains challenging. Herein, we explore anti-CRISPR (Acr) proteins as modules to create synthetic Cas protein switches (CasPSs) based on computational chemistry-directed rational protein interface engineering. Guided by molecular fingerprint analysis, electrostatic potential mapping, and binding free energy calculations, we rationally engineer the molecular interaction interface between Cas12a and its cognate Acr proteins (AcrVA4 and AcrVA5) to generate a series of orthogonal protease-responsive CasPSs. These CasPSs enable the conversion of specific proteolytic events into activation of Cas12a function with high switching ratios (up to 34.3-fold). These advancements enable specific proteolysis-inducible genome editing in mammalian cells and sensitive detection of viral protease activities during virus infection. This work provides a promising strategy for developing CRISPR-Cas tools for controllable gene manipulation and regulation and clinical diagnostics.
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Affiliation(s)
- Wenyuan Kang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
- Key Laboratory of Tropical Medicinal Resource Chemistry of Ministry of Education & Key Laboratory of Tropical Medicinal Plant Chemistry of Hainan Province, College of Chemistry and Chemical Engineering, Hainan Normal University, Haikou, 571158, P. R. China
| | - Fei Xiao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
| | - Xi Zhu
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, Changsha, 410082, P. R. China
| | - Xinyu Ling
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, P. R. China
| | - Shiyi Xie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
| | - Ruimiao Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
| | - Peihang Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
| | - Linxin Cao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
| | - Chunyang Lei
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
| | - Ye Qiu
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, Changsha, 410082, P. R. China
| | - Tao Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, P. R. China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
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18
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Campbell MJ, Beenken KE, Ramirez AM, Smeltzer MS. Increased production of aureolysin and staphopain A is a primary determinant of the reduced virulence of Staphylococcus aureus sarA mutants in osteomyelitis. mBio 2024; 15:e0338323. [PMID: 38415646 PMCID: PMC11005355 DOI: 10.1128/mbio.03383-23] [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: 12/12/2023] [Accepted: 02/09/2024] [Indexed: 02/29/2024] Open
Abstract
We previously demonstrated that mutation of sarA in Staphylococcus aureus limits biofilm formation, cytotoxicity for osteoblasts and osteoclasts, and virulence in osteomyelitis, and that all of these phenotypes can be attributed to the increased production of extracellular proteases. Here we extend these studies to assess the individual importance of these proteases alone and in combination with each other using the methicillin-resistant USA300 strain LAC, the methicillin-susceptible USA200 strain UAMS-1, and isogenic sarA mutants that were also unable to produce aureolysin (Aur), staphopain A (ScpA), staphylococcal serine protease A (subsp.), staphopain B (SspB), and the staphylococcal serine protease-like proteins A-F (SplA-F). Biofilm formation was restored in LAC and UAMS-1 sarA mutants by subsequent mutation of aur and scpA, while mutation of aur had the greatest impact on cytotoxicity to mammalian cells, particularly with conditioned medium (CM) from the more cytotoxic strain LAC. However, SDS-PAGE and western blot analysis of CM confirmed that mutation of sspAB was also required to mimic the phenotype of sarA mutants unable to produce any extracellular proteases. Nevertheless, in a murine model of post-traumatic osteomyelitis, mutation of aur and scpA had the greatest impact on restoring the virulence of LAC and UAMS-1 sarA mutants, with concurrent mutation of sspAB and the spl operon having relatively little effect. These results demonstrate that the increased production of Aur and ScpA in combination with each other is a primary determinant of the reduced virulence of S. aureus sarA mutants in diverse clinical isolates including both methicillin-resistant and methicillin-susceptible strains.IMPORTANCEPrevious work established that SarA plays a primary role in limiting the production of extracellular proteases to prevent them from limiting the abundance of S. aureus virulence factors. Eliminating the production of all 10 extracellular proteases in the methicillin-resistant strain LAC has also been shown to enhance virulence in a murine sepsis model, and this has been attributed to the specific proteases Aur and ScpA. The importance of this work lies in our demonstration that the increased production of these same proteases largely accounts for the decreased virulence of sarA mutants in a murine model of post-traumatic osteomyelitis not only in LAC but also in the methicillin-susceptible human osteomyelitis isolate UAMS-1. This confirms that sarA-mediated repression of Aur and ScpA production plays a critical role in the posttranslational regulation of S. aureus virulence factors in diverse clinical isolates and diverse forms of S. aureus infection.
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Affiliation(s)
- Mara J. Campbell
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Karen E. Beenken
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Aura M. Ramirez
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Mark S. Smeltzer
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
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19
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Xu X, Wang Y, Huang W, Li D, Deng Z, Long F. Structural insights into the Clp protein degradation machinery. mBio 2024; 15:e0003124. [PMID: 38501868 PMCID: PMC11005422 DOI: 10.1128/mbio.00031-24] [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: 01/10/2024] [Accepted: 02/27/2024] [Indexed: 03/20/2024] Open
Abstract
The Clp protease system is important for maintaining proteostasis in bacteria. It consists of ClpP serine proteases and an AAA+ Clp-ATPase such as ClpC1. The hexameric ATPase ClpC1 utilizes the energy of ATP binding and hydrolysis to engage, unfold, and translocate substrates into the proteolytic chamber of homo- or hetero-tetradecameric ClpP for degradation. The assembly between the hetero-tetradecameric ClpP1P2 chamber and the Clp-ATPases containing tandem ATPase domains from the same species has not been studied in depth. Here, we present cryo-EM structures of the substrate-bound ClpC1:shClpP1P2 from Streptomyces hawaiiensis, and shClpP1P2 in complex with ADEP1, a natural compound produced by S. hawaiiensis and known to cause over-activation and dysregulation of the ClpP proteolytic core chamber. Our structures provide detailed information on the shClpP1-shClpP2, shClpP2-ClpC1, and ADEP1-shClpP1/P2 interactions, reveal conformational transition of ClpC1 during the substrate translocation, and capture a rotational ATP hydrolysis mechanism likely dominated by the D1 ATPase activity of chaperones.IMPORTANCEThe Clp-dependent proteolysis plays an important role in bacterial homeostasis and pathogenesis. The ClpP protease system is an effective drug target for antibacterial therapy. Streptomyces hawaiiensis can produce a class of potent acyldepsipeptide antibiotics such as ADEP1, which could affect the ClpP protease activity. Although S. hawaiiensis hosts one of the most intricate ClpP systems in nature, very little was known about its Clp protease mechanism and the impact of ADEP molecules on ClpP. The significance of our research is in dissecting the functional mechanism of the assembled Clp degradation machinery, as well as the interaction between ADEP1 and the ClpP proteolytic chamber, by solving high-resolution structures of the substrate-bound Clp system in S. hawaiiensis. The findings shed light on our understanding of the Clp-dependent proteolysis in bacteria, which will enhance the development of antimicrobial drugs targeting the Clp protease system, and help fighting against bacterial multidrug resistance.
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Affiliation(s)
- Xiaolong Xu
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Yanhui Wang
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Wei Huang
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Danyang Li
- Cryo-EM Center and the Core Facility of Wuhan University, Wuhan, China
| | - Zixin Deng
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Feng Long
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
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20
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Foster BM, Wang Z, Schmidt CK. DoUBLing up: ubiquitin and ubiquitin-like proteases in genome stability. Biochem J 2024; 481:515-545. [PMID: 38572758 DOI: 10.1042/bcj20230284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/05/2024] [Accepted: 03/18/2024] [Indexed: 04/05/2024]
Abstract
Maintaining stability of the genome requires dedicated DNA repair and signalling processes that are essential for the faithful duplication and propagation of chromosomes. These DNA damage response (DDR) mechanisms counteract the potentially mutagenic impact of daily genotoxic stresses from both exogenous and endogenous sources. Inherent to these DNA repair pathways is the activity of protein factors that instigate repair processes in response to DNA lesions. The regulation, coordination, and orchestration of these DDR factors is carried out, in a large part, by post-translational modifications, such as phosphorylation, ubiquitylation, and modification with ubiquitin-like proteins (UBLs). The importance of ubiquitylation and UBLylation with SUMO in DNA repair is well established, with the modified targets and downstream signalling consequences relatively well characterised. However, the role of dedicated erasers for ubiquitin and UBLs, known as deubiquitylases (DUBs) and ubiquitin-like proteases (ULPs) respectively, in genome stability is less well established, particularly for emerging UBLs such as ISG15 and UFM1. In this review, we provide an overview of the known regulatory roles and mechanisms of DUBs and ULPs involved in genome stability pathways. Expanding our understanding of the molecular agents and mechanisms underlying the removal of ubiquitin and UBL modifications will be fundamental for progressing our knowledge of the DDR and likely provide new therapeutic avenues for relevant human diseases, such as cancer.
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Affiliation(s)
- Benjamin M Foster
- Manchester Cancer Research Centre (MCRC), Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, U.K
| | - Zijuan Wang
- Manchester Cancer Research Centre (MCRC), Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, U.K
| | - Christine K Schmidt
- Manchester Cancer Research Centre (MCRC), Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, U.K
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21
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Crosby HA, Keim K, Kwiecinski JM, Langouët-Astrié CJ, Oshima K, LaRivière WB, Schmidt EP, Horswill AR. Host-derived protease promotes aggregation of Staphylococcus aureus by cleaving the surface protein SasG. mBio 2024; 15:e0348323. [PMID: 38511930 PMCID: PMC11005337 DOI: 10.1128/mbio.03483-23] [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: 01/11/2024] [Accepted: 02/21/2024] [Indexed: 03/22/2024] Open
Abstract
Staphylococcus aureus is one of the leading causes of hospital-acquired infections, many of which begin following attachment and accumulation on indwelling medical devices or diseased tissue. These infections are often linked to the establishment of biofilms, but another often overlooked key characteristic allowing S. aureus to establish persistent infection is the formation of planktonic aggregates. Such aggregates are physiologically similar to biofilms and protect pathogens from innate immune clearance and increase antibiotic tolerance. The cell-wall-associated protein SasG has been implicated in biofilm formation via mechanisms of intercellular aggregation but the mechanism in the context of disease is largely unknown. We have previously shown that the expression of cell-wall-anchored proteins involved in biofilm formation is controlled by the ArlRS-MgrA regulatory cascade. In this work, we demonstrate that the ArlRS two-component system controls aggregation, by repressing the expression of sasG by activation of the global regulator MgrA. We also demonstrate that SasG must be proteolytically processed by a non-staphylococcal protease to induce aggregation and that strains expressing functional full-length sasG aggregate significantly upon proteolysis by a mucosal-derived host protease found in human saliva. We used fractionation and N-terminal sequencing to demonstrate that human trypsin within saliva cleaves within the A domain of SasG to expose the B domain and induce aggregation. Finally, we demonstrated that SasG is involved in virulence during mouse lung infection. Together, our data point to SasG, its processing by host proteases, and SasG-driven aggregation as important elements of S. aureus adaptation to the host environment.IMPORTANCEHere, we demonstrate that the Staphylococcus aureus surface protein SasG is important for cell-cell aggregation in the presence of host proteases. We show that the ArlRS two-component regulatory system controls SasG levels through the cytoplasmic regulator MgrA. We identified human trypsin as the dominant protease triggering SasG-dependent aggregation and demonstrated that SasG is important for S. aureus lung infection. The discovery that host proteases can induce S. aureus aggregation contributes to our understanding of how this pathogen establishes persistent infections. The observations in this study demonstrate the need to strengthen our knowledge of S. aureus surface adhesin function and processing, regulation of adhesin expression, and the mechanisms that promote biofilm formation to develop strategies for preventing chronic infections.
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Affiliation(s)
- Heidi A. Crosby
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Klara Keim
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Jakub M. Kwiecinski
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Christophe J. Langouët-Astrié
- Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Kaori Oshima
- Division of Pulmonary Sciences and Critical Care, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Wells B. LaRivière
- Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Eric P. Schmidt
- Division of Pulmonary Sciences and Critical Care, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Alexander R. Horswill
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
- Department of Veterans Affairs Eastern Colorado Health Care System, Denver, Colorado, USA
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22
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Jiang X, Yeung D, Liu Y, Spicer V, Afshari H, Lao Y, Lin F, Krokhin O, Zahedi RP. Accelerating Proteomics Using Broad Specificity Proteases. J Proteome Res 2024; 23:1360-1369. [PMID: 38457694 DOI: 10.1021/acs.jproteome.3c00852] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2024]
Abstract
Trypsin is the gold-standard protease in bottom-up proteomics, but many sequence stretches of the proteome are inaccessible to trypsin and standard LC-MS approaches. Thus, multienzyme strategies are used to maximize sequence coverage in post-translational modification profiling. We present fast and robust SP3- and STRAP-based protocols for the broad-specificity proteases subtilisin, proteinase K, and thermolysin. All three enzymes are remarkably fast, producing near-complete digests in 1-5 min, and cost 200-1000× less than proteomics-grade trypsin. Using FragPipe resolved a major challenge by drastically reducing the duration of the required "unspecific" searches. In-depth analyses of proteinase K, subtilisin, and thermolysin Jurkat digests identified 7374, 8178, and 8753 unique proteins with average sequence coverages of 21, 29, and 37%, including 10,000s of amino acids not reported in PeptideAtlas' >2400 experiments. While we could not identify distinct cleavage patterns, machine learning could distinguish true protease products from random cleavages, potentially enabling the prediction of cleavage products. Finally, proteinase K, subtilisin, and thermolysin enabled label-free quantitation of 3111, 3659, and 4196 unique Jurkat proteins, which in our hands is comparable to trypsin. Our data demonstrate that broad-specificity proteases enable quantitative proteomics of uncharted areas of the proteome. Their fast kinetics may allow "on-the-fly" digestion of samples in the future.
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Affiliation(s)
- Xuehui Jiang
- Manitoba Centre for Proteomics and Systems Biology, Health Science Centre, Winnipeg, Manitoba R3E 3P4, Canada
| | - Darien Yeung
- Manitoba Centre for Proteomics and Systems Biology, Health Science Centre, Winnipeg, Manitoba R3E 3P4, Canada
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada
| | - Yang Liu
- Department of Physics and Astronomy, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Victor Spicer
- Manitoba Centre for Proteomics and Systems Biology, Health Science Centre, Winnipeg, Manitoba R3E 3P4, Canada
| | - Havva Afshari
- Manitoba Centre for Proteomics and Systems Biology, Health Science Centre, Winnipeg, Manitoba R3E 3P4, Canada
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada
| | - Ying Lao
- Manitoba Centre for Proteomics and Systems Biology, Health Science Centre, Winnipeg, Manitoba R3E 3P4, Canada
| | - Francis Lin
- Department of Physics and Astronomy, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Oleg Krokhin
- Manitoba Centre for Proteomics and Systems Biology, Health Science Centre, Winnipeg, Manitoba R3E 3P4, Canada
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada
- Department of Internal Medicine, University of Manitoba, Winnipeg, Manitoba R3A 1R9, Canada
| | - René P Zahedi
- Manitoba Centre for Proteomics and Systems Biology, Health Science Centre, Winnipeg, Manitoba R3E 3P4, Canada
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada
- Department of Internal Medicine, University of Manitoba, Winnipeg, Manitoba R3A 1R9, Canada
- Paul Albrechtsen Research Institute, Cancer Care Manitoba, Winnipeg, Manitoba R3E 0 V9, Canada
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23
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Rachedi R, Risoul V, Foglino M, Aoudache Y, Lang K, Champ S, Kaplan E, Orelle C, Douzi B, Jault JM, Latifi A. Unravelling HetC as a peptidase-based ABC exporter driving functional cell differentiation in the cyanobacterium Nostoc PCC 7120. Microbiol Spectr 2024; 12:e0405823. [PMID: 38358282 DOI: 10.1128/spectrum.04058-23] [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: 11/30/2023] [Accepted: 01/30/2024] [Indexed: 02/16/2024] Open
Abstract
The export of peptides or proteins is essential for a variety of important functions in bacteria. Among the diverse protein-translocation systems, peptidase-containing ABC transporters (PCAT) are involved in the maturation and export of quorum-sensing or antimicrobial peptides in Gram-positive bacteria and of toxins in Gram-negative organisms. In the multicellular and diazotrophic cyanobacterium Nostoc PCC 7120, the protein HetC is essential for the differentiation of functional heterocysts, which are micro-oxic and non-dividing cells specialized in atmospheric nitrogen fixation. HetC shows similarities to PCAT systems, but whether it actually acts as a peptidase-based exporter remains to be established. In this study, we show that the N-terminal part of HetC, encompassing the peptidase domain, displays a cysteine-type protease activity. The conserved catalytic residues conserved in this family of proteases are essential for the proteolytic activity of HetC and the differentiation of heterocysts. Furthermore, we show that the catalytic residue of the ATPase domain of HetC is also essential for cell differentiation. Interestingly, HetC has a cyclic nucleotide-binding domain at its N-terminus which can bind ppGpp in vitro and which is required for its function in vivo. Our results indicate that HetC is a peculiar PCAT that might be regulated by ppGpp to potentially facilitate the export of a signaling peptide essential for cell differentiation, thereby broadening the scope of PCAT role in Gram-negative bacteria.IMPORTANCEBacteria have a great capacity to adapt to various environmental and physiological conditions; it is widely accepted that their ability to produce extracellular molecules contributes greatly to their fitness. Exported molecules are used for a variety of purposes ranging from communication to adjust cellular physiology, to the production of toxins that bacteria secrete to fight for their ecological niche. They use export machineries for this purpose, the most common of which energize transport by hydrolysis of adenosine triphosphate. Here, we demonstrate that such a mechanism is involved in cell differentiation in the filamentous cyanobacterium Nostoc PCC 7120. The HetC protein belongs to the ATP-binding cassette transporter superfamily and presumably ensures the maturation of a yet unknown substrate during export. These results open interesting perspectives on cellular signaling pathways involving the export of regulatory peptides, which will broaden our knowledge of how these bacteria use two cell types to conciliate photosynthesis and nitrogen fixation.
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Affiliation(s)
- Raphaël Rachedi
- Aix-Marseille Université, CNRS, Laboratoire de Chimie Bactérienne LCB, IMM, Marseille, France
| | - Véronique Risoul
- Aix-Marseille Université, CNRS, Laboratoire de Chimie Bactérienne LCB, IMM, Marseille, France
| | - Maryline Foglino
- Aix-Marseille Université, CNRS, Laboratoire de Chimie Bactérienne LCB, IMM, Marseille, France
| | | | - Kevin Lang
- Microbiologie Moléculaire et Biochimie Structurale, UMR5086 Université de Lyon/CNRS, IBCP, Lyon, France
| | - Stéphanie Champ
- Aix-Marseille Université, CNRS, Laboratoire de Chimie Bactérienne LCB, IMM, Marseille, France
| | - Elise Kaplan
- Microbiologie Moléculaire et Biochimie Structurale, UMR5086 Université de Lyon/CNRS, IBCP, Lyon, France
| | - Cédric Orelle
- Microbiologie Moléculaire et Biochimie Structurale, UMR5086 Université de Lyon/CNRS, IBCP, Lyon, France
| | | | - Jean-Michel Jault
- Microbiologie Moléculaire et Biochimie Structurale, UMR5086 Université de Lyon/CNRS, IBCP, Lyon, France
| | - Amel Latifi
- Aix-Marseille Université, CNRS, Laboratoire de Chimie Bactérienne LCB, IMM, Marseille, France
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24
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Kim Y, Pool E, Kim E, Dampalla CS, Nguyen HN, Johnson DK, Lovell S, Groutas WC, Chang KO. Potent small molecule inhibitors against the 3C protease of foot-and-mouth disease virus. Microbiol Spectr 2024; 12:e0337223. [PMID: 38466127 DOI: 10.1128/spectrum.03372-23] [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: 09/14/2023] [Accepted: 01/18/2024] [Indexed: 03/12/2024] Open
Abstract
Foot-and-mouth disease (FMD) is one of the most devastating diseases of livestock which can cause significant economic losses, especially when introduced to FMD-free countries. FMD virus (FMDV) belongs to the family Picornaviridae and is antigenically heterogeneous with seven established serotypes. The prevailing preventive and control strategies are limited to restriction of animal movement and elimination of infected or exposed animals, which can be potentially combined with vaccination. However, FMD vaccination has limitations including delayed protection and lack of cross-protection against different serotypes. Recently, antiviral drug use for FMD outbreaks has increasingly been recognized as a potential tool to augment the existing early response strategies, but limited research has been reported on potential antiviral compounds for FMDV. FMDV 3C protease (3Cpro) cleaves the viral-encoded polyprotein into mature and functional proteins during viral replication. The essential role of viral 3Cpro in viral replication and the high conservation of 3Cpro among different FMDV serotypes make it an excellent target for antiviral drug development. We have previously reported multiple series of inhibitors against picornavirus 3Cpro or 3C-like proteases (3CLpros) encoded by coronaviruses or caliciviruses. In this study, we conducted structure-activity relationship studies for our in-house focused compound library containing 3Cpro or 3CLpro inhibitors against FMDV 3Cpro using enzyme and cell-based assays. Herein, we report the discovery of aldehyde and α-ketoamide inhibitors of FMDV 3Cpro with high potency. These data inform future preclinical studies that are related to the advancement of these compounds further along the drug development pathway.IMPORTANCEFood-and-mouth disease (FMD) virus (FMDV) causes devastating disease in cloven-hoofed animals with a significant economic impact. Emergency response to FMD outbreaks to limit FMD spread is critical, and the use of antivirals may overcome the limitations of existing control measures by providing immediate protection for susceptible animals. FMDV encodes 3C protease (3Cpro), which is essential for virus replication and an attractive target for antiviral drug discovery. Here, we report a structure-activity relationship study on multiple series of protease inhibitors and identified potent inhibitors of FMDV 3Cpro. Our results suggest that these compounds have the potential for further development as FMD antivirals.
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Affiliation(s)
- Yunjeong Kim
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Emma Pool
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Eunji Kim
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | | | - Harry Nhat Nguyen
- Department of Chemistry, Wichita State University, Wichita, Kansas, USA
| | - David K Johnson
- Computational Chemical Biology Core, The University of Kansas, Lawrence, Kansas, USA
| | - Scott Lovell
- Protein Structure and X-ray Crystallography Laboratory, The University of Kansas, Lawrence, Kansas, USA
| | - William C Groutas
- Department of Chemistry, Wichita State University, Wichita, Kansas, USA
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
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25
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Santana RDS, Mendes FDS, Paula da Silva BJ, Lima ES, Nascimento TP, Carneiro da Cunha MN, Porto ALF, Teixeira MFS, Carvalho RP, Gomes WR. Recovery and partial purification of fibrinolytic protease from Pleurotus ostreatus and P. eryngii and cytotoxic and antioxidant activity of their extracts. Prep Biochem Biotechnol 2024; 54:545-552. [PMID: 37667995 DOI: 10.1080/10826068.2023.2253466] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
Mushrooms are a source of primary and secondary metabolites. Little is known about the most suitable conditions for production of mushrooms by submerged fermentation. This article reports antioxidant and cytotoxic assays, in addition to quantitatively evaluating the content of proteases with fibrinolytic action in the crude extracts of two species of edible mushrooms produced in different formulations, as well as evaluating the recovery of these enzymes by aqueous two-phase systems (ATPS). The mushrooms Pleurotus ostreatus and Pleurotus eryngii, at concentration of 100 µg/mL, displayed inhibition of DPPH and ABTS radicals below 50%. In the cytotoxicity test, the cells human fibroblast cell lines (MRC-5) showed cell viability greater than 80%. Concerning fibrinolytic activity, P. eryngii presented 226.47 ± 7.26 U/mL, therefore being more efficient than P. ostreatus (71.5 ± 0.56 U/mL). In the recovery of the P. eryngii extract by ATPS, the fibrinolytic protease was partitioned in the salt phase (30.25 U/mL). The molecular mass of the proteases was between 75 and 100 kDa. These results prove the low cytotoxicity of the extracts produced and that fermentation in supplemented malt broth favored the excretion of fibrinolytic proteases compared to the other evaluated media.
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Affiliation(s)
- Romário da S Santana
- Postgraduate Program in Biotechnology, Federal University of Amazonas, Manaus, Brazil
| | - Felipe de S Mendes
- Postgraduate Program in Biotechnology, Federal University of Amazonas, Manaus, Brazil
| | | | - Emerson S Lima
- Faculty of Pharmaceutical Sciences, Federal University of Amazonas (UFAM), Manaus, Brazil
| | - Thiago P Nascimento
- Campus Professora Cinobelina Elvas, Federal University of Piaui, Bom Jesus, Brazil
| | | | - Ana Lúcia F Porto
- Department of Animal Morphology and Physiology, Rural Federal University of Pernambuco, Recife, Brazil
| | | | - Rosany P Carvalho
- Department of Physiological Sciences, Federal University of Amazonas, Manaus, Brazil
| | - Waldireny R Gomes
- Faculty of Pharmaceutical Sciences, Federal University of Amazonas (UFAM), Manaus, Brazil
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26
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Yang H, Zhou JN, Zhang XM, Ling DD, Sun YB, Li CY, Zhou QQ, Shi GN, Wang SH, Lin XS, Fan T, Wang HY, Zeng Q, Jia YL, Xi JF, Jin YG, Pei XT, Yue W. Nanoengineered Red Blood Cells Loaded with TMPRSS2 and Cathepsin L Inhibitors Block SARS-CoV-2 Pseudovirus Entry into Lung ACE2 + Cells. Adv Mater 2024; 36:e2310306. [PMID: 38194699 DOI: 10.1002/adma.202310306] [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: 10/05/2023] [Revised: 12/27/2023] [Indexed: 01/11/2024]
Abstract
The enzymatic activities of Furin, Transmembrane serine proteinase 2 (TMPRSS2), Cathepsin L (CTSL), and Angiotensin-converting enzyme 2 (ACE2) receptor binding are necessary for the entry of coronaviruses into host cells. Precise inhibition of these key proteases in ACE2+ lung cells during a viral infection cycle shall prevent viral Spike (S) protein activation and its fusion with a host cell membrane, consequently averting virus entry to the cells. In this study, dual-drug-combined (TMPRSS2 inhibitor Camostat and CTSL inhibitor E-64d) nanocarriers (NCs) are constructed conjugated with an anti-human ACE2 (hACE2) antibody and employ Red Blood Cell (RBC)-hitchhiking, termed "Nanoengineered RBCs," for targeting lung cells. The significant therapeutic efficacy of the dual-drug-loaded nanoengineered RBCs in pseudovirus-infected K18-hACE2 transgenic mice is reported. Notably, the modular nanoengineered RBCs (anti-receptor antibody+NCs+RBCs) precisely target key proteases of host cells in the lungs to block the entry of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), regardless of virus variations. These findings are anticipated to benefit the development of a series of novel and safe host-cell-protecting antiviral therapies.
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Affiliation(s)
- Hui Yang
- Stem Cell and Regenerative Medicine Lab, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Jun-Nian Zhou
- Stem Cell and Regenerative Medicine Lab, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Xue-Mei Zhang
- Stem Cell and Regenerative Medicine Lab, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Dan-Dan Ling
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Ying-Bao Sun
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Chen-Yan Li
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China
| | - Qian-Qian Zhou
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China
| | - Gao-Na Shi
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Si-Han Wang
- Stem Cell and Regenerative Medicine Lab, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Xiao-Song Lin
- Stem Cell and Regenerative Medicine Lab, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Tao Fan
- Stem Cell and Regenerative Medicine Lab, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Hai-Yang Wang
- Stem Cell and Regenerative Medicine Lab, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Quan Zeng
- Stem Cell and Regenerative Medicine Lab, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Ya-Li Jia
- Stem Cell and Regenerative Medicine Lab, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Jia-Fei Xi
- Stem Cell and Regenerative Medicine Lab, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Yi-Guang Jin
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Xue-Tao Pei
- Stem Cell and Regenerative Medicine Lab, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Wen Yue
- Stem Cell and Regenerative Medicine Lab, Beijing Institute of Radiation Medicine, Beijing, 100850, China
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27
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Wang X, Kang L, Kong D, Wu X, Zhou Y, Yu G, Dai D, Ye H. A programmable protease-based protein secretion platform for therapeutic applications. Nat Chem Biol 2024; 20:432-442. [PMID: 37872400 DOI: 10.1038/s41589-023-01433-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 09/02/2023] [Indexed: 10/25/2023]
Abstract
Cell-based therapies represent potent enabling technologies in biomedical science. However, current genetic control systems for engineered-cell therapies are predominantly based on the transcription or translation of therapeutic outputs. Here we report a protease-based rapid protein secretion system (PASS) that regulates the secretion of pretranslated proteins retained in the endoplasmic reticulum (ER) owing to an ER-retrieval signal. Upon cleavage by inducible proteases, these proteins are secreted. Three PASS variants (chemPASS, antigenPASS and optoPASS) are developed. With chemPASS, we demonstrate the reversal of hyperglycemia in diabetic mice within minutes via drug-induced insulin secretion. AntigenPASS-equipped cells recognize the tumor antigen and secrete granzyme B and perforin, inducing targeted cell apoptosis. Finally, results from mouse models of diabetes, hypertension and inflammatory pain demonstrate light-induced, optoPASS-mediated therapeutic peptide secretion within minutes, conferring anticipated therapeutic benefits. PASS is a flexible platform for rapid delivery of therapeutic proteins that can facilitate the development and adoption of cell-based precision therapies.
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Affiliation(s)
- Xinyi Wang
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Liping Kang
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Deqiang Kong
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Xin Wu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Yang Zhou
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
- Wuhu Hospital, Health Science Center, East China Normal University, Wuhu City, China
| | - Guiling Yu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Di Dai
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Haifeng Ye
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China.
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Liu H, Wang S, Sorbara JO, Umar-Faruk M, Cowieson AJ. Novel sfericase protease improves amino acid digestibility of soybean meal and rapeseed meal in broiler chickens. Br Poult Sci 2024; 65:137-143. [PMID: 38265055 DOI: 10.1080/00071668.2023.2295348] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 11/20/2023] [Indexed: 01/25/2024]
Abstract
1. Two experiments were conducted to explore the effects of an exogenous sfericase protease on the apparent ileal nutrient digestibility of soybean meal (SBM) and rapeseed meal (RSM) in broiler chickens.2. In each experiment, a total of 256 sixteen-day-old male Cobb 500 broilers were fed one of four semi-purified experimental diets, comprising two different batches (A and B) of samples for either SBM (Exp. 1) or RSM (Exp. 2) without or with an exogenous sfericase (0 or 30,000 NFP/kg). Each experimental diet was fed to eight replicate pens of broiler chickens from 16 to 21 d of age (eight birds per cage), and ileal digesta were collected for measuring the digestibility coefficients.3. In Exp. 1, the amino acid digestibility was greater (P < 0.05) in SBM B compared with SBM A for Arg and Val, and a similar trend (P < 0.1) was observed for Tyr, Leu and Thr. Exogenous sfericase increased (P < 0.10) digestibility of most of amino acids except Gly, His and Trp. There was an interaction between SBM source and sfericase, whereby digestibility of P, N and Asp was increased by sfericase for SBM B but not for SBM A. In Exp. 2, there was no interaction (P > 0.05) between RSM source and sfericase for ileal nutrient digestibility. Digestibility was greater in RSM A compared to RSM B for all non-essential AA and most essential AA (except for Trp), while the reverse was noted for Ca and P (P < 0.05). Exogenous sfericase increased (P < 0.1) digestibility for all amino acids except Cys and Met.4. In conclusion, the current studies showed that both SBM and RSM batches influenced amino acid digestibility. Sfericase protease supplementation increased amino acid digestibility for both SBM and RSM. The digestibility effects were greater in the SBM batch with low digestibility for N and Asp which was in line with an increase in P digestibility.
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Affiliation(s)
- H Liu
- DSM (China) Animal Nutrition Research Center Co. Ltd, Bazhou, P. R. China
| | - S Wang
- DSM (China) Animal Nutrition Research Center Co. Ltd, Bazhou, P. R. China
| | - J-O Sorbara
- DSM Nutritional Products, Kaiseraugst, Switzerland
| | - M Umar-Faruk
- DSM Nutritional Products, Kaiseraugst, Switzerland
| | - A J Cowieson
- DSM Nutritional Products, Kaiseraugst, Switzerland
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Zhang Y, Guo J, Liu Y, Qu Y, Li YQ, Mu Y, Li W. An allosteric mechanism for potent inhibition of SARS-CoV-2 main proteinase. Int J Biol Macromol 2024; 265:130644. [PMID: 38462102 DOI: 10.1016/j.ijbiomac.2024.130644] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 02/25/2024] [Accepted: 03/04/2024] [Indexed: 03/12/2024]
Abstract
The main proteinase (Mpro) of SARS-CoV-2 plays a critical role in cleaving viral polyproteins into functional proteins required for viral replication and assembly, making it a prime drug target for COVID-19. It is well known that noncompetitive inhibition offers potential therapeutic options for treating COVID-19, which can effectively reduce the likelihood of cross-reactivity with other proteins and increase the selectivity of the drug. Therefore, the discovery of allosteric sites of Mpro has both scientific and practical significance. In this study, we explored the binding characteristics and inhibiting process of Mpro activity by two recently reported allosteric inhibitors, pelitinib and AT7519 which were obtained by the X-ray screening experiments, to probe the allosteric mechanism via molecular dynamic (MD) simulations. We found that pelitinib and AT7519 can stably bind to Mpro far from the active site. The binding affinity is estimated to be -24.37 ± 4.14 and - 26.96 ± 4.05 kcal/mol for pelitinib and AT7519, respectively, which is considerably stable compared with orthosteric drugs. Furthermore, the strong binding caused clear changes in the catalytic site of Mpro, thus decreasing the substrate accessibility. The community network analysis also validated that pelitinib and AT7519 strengthened intra- and inter-domain communication of Mpro dimer, resulting in a rigid Mpro, which could negatively impact substrate binding. In summary, our findings provide the detailed working mechanism for the two experimentally observed allosteric sites of Mpro. These allosteric sites greatly enhance the 'druggability' of Mpro and represent attractive targets for the development of new Mpro inhibitors.
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Affiliation(s)
- Yunju Zhang
- School of Physics, Shandong University, China
| | - Jingjing Guo
- Centre in Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, 999078, Macao
| | - Yang Liu
- School of Physics, Shandong University, China
| | - Yuanyuan Qu
- School of Physics, Shandong University, China
| | | | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
| | - Weifeng Li
- School of Physics, Shandong University, China.
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30
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Pedram K, Shon DJ, Tender GS, Mantuano NR, Northey JJ, Metcalf KJ, Wisnovsky SP, Riley NM, Forcina GC, Malaker SA, Kuo A, George BM, Miller CL, Casey KM, Vilches-Moure JG, Ferracane MJ, Weaver VM, Läubli H, Bertozzi CR. Design of a mucin-selective protease for targeted degradation of cancer-associated mucins. Nat Biotechnol 2024; 42:597-607. [PMID: 37537499 PMCID: PMC11018308 DOI: 10.1038/s41587-023-01840-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [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: 06/15/2022] [Accepted: 05/22/2023] [Indexed: 08/05/2023]
Abstract
Targeted protein degradation is an emerging strategy for the elimination of classically undruggable proteins. Here, to expand the landscape of targetable substrates, we designed degraders that achieve substrate selectivity via recognition of a discrete peptide and glycan motif and achieve cell-type selectivity via antigen-driven cell-surface binding. We applied this approach to mucins, O-glycosylated proteins that drive cancer progression through biophysical and immunological mechanisms. Engineering of a bacterial mucin-selective protease yielded a variant for fusion to a cancer antigen-binding nanobody. The resulting conjugate selectively degraded mucins on cancer cells, promoted cell death in culture models of mucin-driven growth and survival, and reduced tumor growth in mouse models of breast cancer progression. This work establishes a blueprint for the development of biologics that degrade specific protein glycoforms on target cells.
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Affiliation(s)
- Kayvon Pedram
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - D Judy Shon
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Gabrielle S Tender
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Natalia R Mantuano
- Cancer Immunotherapy Laboratory, Department of Biomedicine, University of Basel, Basel, Switzerland
- Division of Oncology, Department of Theragnostics, University Hospital, Basel, Switzerland
| | - Jason J Northey
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Kevin J Metcalf
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Simon P Wisnovsky
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nicholas M Riley
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Giovanni C Forcina
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Stacy A Malaker
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Angel Kuo
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Benson M George
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | - Caitlyn L Miller
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Kerriann M Casey
- Department of Comparative Medicine, Stanford University, Stanford, CA, USA
| | | | | | - Valerie M Weaver
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco (UCSF), San Francisco, CA, USA
- Departments of Radiation Oncology and Bioengineering and Therapeutic Sciences, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, and Helen Diller Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Heinz Läubli
- Cancer Immunotherapy Laboratory, Department of Biomedicine, University of Basel, Basel, Switzerland
- Division of Oncology, Department of Theragnostics, University Hospital, Basel, Switzerland
| | - Carolyn R Bertozzi
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford, CA, USA.
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31
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Xie S, Zou W, Liu S, Yang Q, Hu T, Zhu WP, Tang H, Wang C. Site 1 protease aggravates acute kidney injury by promoting tubular epithelial cell ferroptosis through SIRT3-SOD2-mtROS signaling. FEBS J 2024; 291:1575-1592. [PMID: 38243371 DOI: 10.1111/febs.17057] [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: 05/30/2023] [Revised: 11/21/2023] [Accepted: 01/08/2024] [Indexed: 01/21/2024]
Abstract
Ischemia/reperfusion (I/R)-induced acute kidney injury (AKI) is a common clinical syndrome with high morbidity and mortality. Ferroptosis, a newly discovered form of oxidative cell death, is involved in the pathogenesis of renal I/R injury; however, the underlying mechanism remains to be explored. Here, we reported that site 1 protease (S1P) promotes ischemic kidney injury by regulating ferroptotic cell death of tubular epithelial cells. S1P abundance was measured in hypoxia/reoxygenation (H/R)-treated Boston University mouse proximal tubular (BUMPT) cells and I/R-induced murine kidney tissue. S1P expression in BUMPT cells and kidneys was initially activated by hypoxic stimulation, accompanied by the ferroptotic response. Blocking S1P blunted H/R-induced ferroptotic cell death, which also restored sirtuin 3 (SIRT3) expression and superoxide dismutase 2 (SOD2) activity in BUMPT cells. Next, inhibition of S1P expression restored I/R-suppressed SIRT3 abundance, SOD2 activity and reduced the elevated level of mitochondria reactive oxygen species (mtROS), which attenuated tubular cell ferroptosis and renal I/R injury. In conclusion, S1P promoted renal tubular epithelial cell ferroptosis under I/R status by activating SIRT3-SOD2-mtROS signaling, thereby accelerating kidney injury. Thus, targeting S1P signaling may serve as a promising strategy for I/R kidney injury.
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Affiliation(s)
- Shiying Xie
- Division of Nephrology, Department of Medicine, The Fifth Affiliated Hospital Sun Yat-Sen University, Zhuhai, China
- Guangdong Provincial Engineering Research Center of Molecular Imaging Center, The Fifth Affiliated Hospital Sun Yat-Sen University, Zhuhai, China
| | - Wei Zou
- Division of Nephrology, Department of Medicine, The Fifth Affiliated Hospital Sun Yat-Sen University, Zhuhai, China
- Guangdong Provincial Engineering Research Center of Molecular Imaging Center, The Fifth Affiliated Hospital Sun Yat-Sen University, Zhuhai, China
| | - Sirui Liu
- Division of Nephrology, Department of Medicine, The Fifth Affiliated Hospital Sun Yat-Sen University, Zhuhai, China
- Guangdong Provincial Engineering Research Center of Molecular Imaging Center, The Fifth Affiliated Hospital Sun Yat-Sen University, Zhuhai, China
| | - Qinglan Yang
- Division of Nephrology, Department of Medicine, The Fifth Affiliated Hospital Sun Yat-Sen University, Zhuhai, China
- Guangdong Provincial Engineering Research Center of Molecular Imaging Center, The Fifth Affiliated Hospital Sun Yat-Sen University, Zhuhai, China
| | - Tiantian Hu
- Division of Nephrology, Department of Medicine, The Fifth Affiliated Hospital Sun Yat-Sen University, Zhuhai, China
- Guangdong Provincial Engineering Research Center of Molecular Imaging Center, The Fifth Affiliated Hospital Sun Yat-Sen University, Zhuhai, China
| | - Wei-Ping Zhu
- Division of Nephrology, Department of Medicine, The Fifth Affiliated Hospital Sun Yat-Sen University, Zhuhai, China
- Guangdong Provincial Engineering Research Center of Molecular Imaging Center, The Fifth Affiliated Hospital Sun Yat-Sen University, Zhuhai, China
| | - Hua Tang
- Division of Nephrology, Department of Medicine, The Third Affiliated Hospital of Sun Yat-Sen University, Zhuhai, China
| | - Cheng Wang
- Division of Nephrology, Department of Medicine, The Fifth Affiliated Hospital Sun Yat-Sen University, Zhuhai, China
- Guangdong Provincial Engineering Research Center of Molecular Imaging Center, The Fifth Affiliated Hospital Sun Yat-Sen University, Zhuhai, China
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Zhu J, Lu F, Liu D, Zhao X, Chao J, Wang Y, Luan Y, Ma H. The process of solid-state fermentation of soybean meal: antimicrobial activity, fermentation heat generation and nitrogen solubility index. J Sci Food Agric 2024; 104:3228-3234. [PMID: 38072810 DOI: 10.1002/jsfa.13209] [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: 07/13/2023] [Revised: 12/01/2023] [Accepted: 12/11/2023] [Indexed: 01/18/2024]
Abstract
BACKGROUND Bacillus amyloliquefaciens has excellent protease production ability and holds great prospects for application in the solid-state fermentation of soybean meal (SBM). RESULTS Among eight strains of bacteria, Bacillus amyloliquefaciens subsp. plantarum CICC 10265, which exhibited higher protease production, was selected as the fermentation strain. The protease activity secreted by this strain reached 106.41 U mL-1 . The microbial community structure differed significantly between natural fermentation and inoculation-enhanced fermented soybean meal (FSBM), with the latter showing greater stability and inhibition of miscellaneous bacterial growth. During fermentation, the temperature inside the soybean meal increased, and the optimal environmental temperature for FSBM was found to be between 35 and 40 °C. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis and nitrogen solubility index (NSI) results demonstrated that solid-state fermentation had a degrading effect on highly denatured proteins in SBM, resulting in an NSI of 67.1%. CONCLUSION Bacillus amyloliquefaciens subsp. plantarum CICC 10265 can enhance the NSI of SBM in solid-state fermentation and inhibit the growth of miscellaneous bacteria. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Junsong Zhu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
- Institute of Food Physical Processing, Jiangsu University, Zhenjiang, China
| | - Feng Lu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
- Institute of Food Physical Processing, Jiangsu University, Zhenjiang, China
| | - Dandan Liu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
- Institute of Food Physical Processing, Jiangsu University, Zhenjiang, China
| | - Xiaoxue Zhao
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Jiapin Chao
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Yucheng Wang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
- Institute of Food Physical Processing, Jiangsu University, Zhenjiang, China
| | - Yu Luan
- Zhenjiang Food and Drug Supervision and Inspection Center, Zhenjiang, China
| | - Haile Ma
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
- Institute of Food Physical Processing, Jiangsu University, Zhenjiang, China
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Purohit P, Barik D, Agasti S, Panda M, Meher BR. Evaluation of the inhibitory potency of anti-dengue phytocompounds against DENV-2 NS2B-NS3 protease: virtual screening, ADMET profiling and molecular dynamics simulation investigations. J Biomol Struct Dyn 2024; 42:2990-3009. [PMID: 37194462 DOI: 10.1080/07391102.2023.2212798] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 04/28/2023] [Indexed: 05/18/2023]
Abstract
Dengue fever has been a worldwide concern, with 50-100 million new infections each year mainly due to five different serotypes of the Dengue virus (DENV). Designing a perfect anti-dengue agent that can inhibit all the serotypes by distinguishing antigenic differences is quite difficult. Previous anti-dengue researches have included chemical compounds screening against DENV enzymes. The ongoing analysis is meant for investigation of the plant-based compounds as antagonistic to DENV-2 focusing on the specific NS2B-NS3Pro target, a trypsin like serine protease that cuts the DENV polyprotein into separate proteins crucial for viral reproduction. Initially, a virtual library of more than 130 phytocompounds was prepared from previously published reports of plants with anti-dengue properties, which were then virtually screened and shortlisted against the WT, H51N and S135A mutant of DENV-2 NS2B-NS3Pro. The three top-most compounds were viewed as Gallocatechin (GAL), Flavokawain-C (FLV), and Isorhamnetin (ISO) showing docking scores of -5.8, -5.7, -5.7 kcal/mol for WT, -7.5, -6.8, -7.6 kcal/mol for the H51N, and -6.9, -6.5, -6.1 kcal/mol for the S135A mutant protease, respectively. 100 ns long MD simulations and MM-GBSA based free energy calculations were performed on the NS2B-NS3Pro complexes to witness the relative binding affinity of the compounds and favourable molecular interactions network. A comprehensive analysis of the study reveals some promising outcomes with ISO as the topmost compound with favourable pharmacokinetic properties for the WT and mutants (H51N and S135A) as well, suggesting as a novel anti-NS2B-NS3Pro agent with better adapting characters in both the mutants.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Priyanka Purohit
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, Odisha, India
| | - Debashis Barik
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, Odisha, India
| | - Sidhartha Agasti
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, Odisha, India
| | - Madhusmita Panda
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, Odisha, India
| | - Biswa Ranjan Meher
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, Odisha, India
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Mei M, Fan X, Zhou Y, Zhang F, Zhang G, Yi L. A combinatorial strategy for HRV 3C protease engineering to achieve the N-terminal free cleavage. Int J Biol Macromol 2024; 265:131066. [PMID: 38521339 DOI: 10.1016/j.ijbiomac.2024.131066] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 03/07/2024] [Accepted: 03/20/2024] [Indexed: 03/25/2024]
Abstract
Human rhinovirus 3C protease (HRV 3CP) has a high specificity against the substrate of LEVLFQ↓G at P1' site, which plays an important role in biotechnology and academia as a fusion tag removal tool. However, a non-ignorable limitation is that an extra residue of Gly would remain at the N terminus of the recombinant target protein after cleavage with HRV 3CP, thus potentially causing protein mis-functionality or immunogenicity. Here, we developed a combinatorial strategy by integrating structure-guided library design and high-throughput screening of eYESS approach for HRV 3CP engineering to expand its P1' specificity. Finally, a C3 variant was obtained, exhibiting a broad substrate P1' specificity to recognize 20 different amino acids with the highest activity against LEVLFQ↓M (kcat/KM = 3.72 ± 0.04 mM-1∙s-1). Further biochemical and NGS-mediated substrate profiling analysis showed that C3 variant still kept its substrate stringency at P1 site and good residue tolerance at P2' site, but with an expanded P1' specificity. Structural simulation of C3 indicated a reconstructed S1' binding pocket as well as new interactions with the substrates. Overall, our studies here prompt not only the practical applications and understanding of substrate recognition mechanisms of HRV 3CP, also provide new tools for other enzyme engineering.
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Affiliation(s)
- Meng Mei
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Xian Fan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Yu Zhou
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Faying Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Guimin Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Li Yi
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China.
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35
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Pei XD, Fan HL, Jiao DQ, Li F, He YN, Wu QL, Liu XL, Wang CH. Rational engineering S1' substrate binding pocket to enhance substrate specificity and catalytic activity of thermal-stable keratinase for efficient keratin degradation. Int J Biol Macromol 2024; 263:130688. [PMID: 38458294 DOI: 10.1016/j.ijbiomac.2024.130688] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/24/2024] [Accepted: 03/05/2024] [Indexed: 03/10/2024]
Abstract
This study reports the rational engineering of the S1' substrate-binding pocket of a thermally-stable keratinase from Pseudomonas aeruginosa 4-3 (4-3Ker) to improve substrate specificity to typical keratinase (K/C > 0.5) and catalytic activity without compromising thermal stability for efficient keratin degradation. Of 10 chosen mutation hotspots in the S1' substrate-binding pocket, the top three mutations M128R, A138V, and V142I showing the best catalytic activity and substrate specificity were identified. Their double and triple combinatorial mutants synergistically overcame limitations of single mutants, fabricating an excellent M128R/A138V/V142I triple mutant which displayed a 1.21-fold increase in keratin catalytic activity, 1.10-fold enhancement in keratin/casein activity ratio, and a 3.13 °C increase in half-inactivation temperature compared to 4-3Ker. Molecular dynamics simulations revealed enhanced flexibility of critical amino acid residues at the substrate access tunnel, improved global protein rigidity, and heightened hydrophobicity within the active site likely underpinned the increased catalytic activity and substrate specificity. Additionally, the triple mutant improved the feather degradation rate by 32.86 % over the wild-type, far exceeding commercial keratinase in substrate specificity and thermal stability. This study exemplified engineering a typical keratinase with enhanced substrate specificity, catalytic activity, and thermal stability from thermally-stable 4-3Ker, providing a more robust tool for feather degradation.
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Affiliation(s)
- Xiao-Dong Pei
- College of Light Industry and Food Engineering, Guangxi University, Nanning 530004, People's Republic of China; Key Laboratory of Deep Processing and Safety Control for Specialty Agricultural Products in Guangxi Universities, Education Department of Guangxi Zhuang Autonomous Region, Nanning 530004, People's Republic of China
| | - He-Liang Fan
- College of Light Industry and Food Engineering, Guangxi University, Nanning 530004, People's Republic of China; Guangxi College and University Key Laboratory of High-value Utilization of Seafood and Prepared Food in Beibu Gulf, Qinzhou 535011, People's Republic of China
| | - Dao-Quan Jiao
- College of Light Industry and Food Engineering, Guangxi University, Nanning 530004, People's Republic of China
| | - Fan Li
- College of Light Industry and Food Engineering, Guangxi University, Nanning 530004, People's Republic of China
| | - Yi-Ning He
- College of Light Industry and Food Engineering, Guangxi University, Nanning 530004, People's Republic of China
| | - Qing-Ling Wu
- College of Light Industry and Food Engineering, Guangxi University, Nanning 530004, People's Republic of China
| | - Xiao-Ling Liu
- College of Light Industry and Food Engineering, Guangxi University, Nanning 530004, People's Republic of China
| | - Cheng-Hua Wang
- College of Light Industry and Food Engineering, Guangxi University, Nanning 530004, People's Republic of China; Key Laboratory of Deep Processing and Safety Control for Specialty Agricultural Products in Guangxi Universities, Education Department of Guangxi Zhuang Autonomous Region, Nanning 530004, People's Republic of China.
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36
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Akiyama H, Zhao R, Ostermann LB, Li Z, Tcheng M, Yazdani SJ, Moayed A, Pryor ML, Slngh S, Baran N, Ayoub E, Nishida Y, Mak PY, Ruvolo VR, Carter BZ, Schimmer AD, Andreeff M, Ishizawa J. Mitochondrial regulation of GPX4 inhibition-mediated ferroptosis in acute myeloid leukemia. Leukemia 2024; 38:729-740. [PMID: 38148395 DOI: 10.1038/s41375-023-02117-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 12/02/2023] [Accepted: 12/08/2023] [Indexed: 12/28/2023]
Abstract
Resistance to apoptosis in acute myeloid leukemia (AML) cells causes refractory or relapsed disease, associated with dismal clinical outcomes. Ferroptosis, a mode of non-apoptotic cell death triggered by iron-dependent lipid peroxidation, has been investigated as potential therapeutic modality against therapy-resistant cancers, but our knowledge of its role in AML is limited. We investigated ferroptosis in AML cells and identified its mitochondrial regulation as a therapeutic vulnerability. GPX4 knockdown induced ferroptosis in AML cells, accompanied with characteristic mitochondrial lipid peroxidation, exerting anti-AML effects in vitro and in vivo. Electron transport chains (ETC) are primary sources of coenzyme Q10 (CoQ) recycling for its function of anti-lipid peroxidation in mitochondria. We found that the mitochondria-specific CoQ potently inhibited GPX4 inhibition-mediated ferroptosis, suggesting that mitochondrial lipid redox regulates ferroptosis in AML cells. Consistently, Rho0 cells, which lack functional ETC, were more sensitive to GPX4 inhibition-mediated mitochondrial lipid peroxidation and ferroptosis than control cells. Furthermore, degradation of ETC through hyperactivation of a mitochondrial protease, caseinolytic protease P (ClpP), synergistically enhanced the anti-AML effects of GPX4 inhibition. Collectively, our findings indicate that in AML cells, GPX4 inhibition induces ferroptosis, which is regulated by mitochondrial lipid redox and ETC.
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Affiliation(s)
- Hiroki Akiyama
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ran Zhao
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lauren B Ostermann
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ziyi Li
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Matthew Tcheng
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Samar J Yazdani
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Arman Moayed
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Malcolm L Pryor
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sandeep Slngh
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Natalia Baran
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Edward Ayoub
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yuki Nishida
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Po Yee Mak
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vivian R Ruvolo
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bing Z Carter
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Aaron D Schimmer
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Michael Andreeff
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jo Ishizawa
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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Kespohl B, Hegele AL, Düsterhöft S, Bakker H, Buettner FFR, Hartig R, Lokau J, Garbers C. Molecular characterization of the craniosynostosis-associated interleukin-11 receptor variants p.T306_S308dup and p.E364_V368del. FEBS J 2024; 291:1667-1683. [PMID: 37994264 DOI: 10.1111/febs.17015] [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: 09/08/2023] [Revised: 11/02/2023] [Accepted: 11/21/2023] [Indexed: 11/24/2023]
Abstract
Interleukin-11 (IL-11) is a member of the IL-6 family of cytokines and is an important factor for bone homeostasis. IL-11 binds to and signals via the membrane-bound IL-11 receptor (IL-11R, classic signaling) or soluble forms of the IL-11R (sIL-11R, trans-signaling). Mutations in the IL11RA gene, which encodes the IL-11R, are associated with craniosynostosis, a human condition in which one or several of the sutures close prematurely, resulting in malformation of the skull. The biological mechanisms of how mutations within the IL-11R are linked to craniosynostosis are mostly unexplored. In this study, we analyze two variants of the IL-11R described in craniosynostosis patients: p.T306_S308dup, which results in a duplication of three amino-acid residues within the membrane-proximal fibronectin type III domain, and p.E364_V368del, which results in a deletion of five amino-acid residues in the so-called stalk region adjacent to the plasma membrane. The stalk region connects the three extracellular domains to the transmembrane and intracellular region of the IL-11R and contains cleavage sites for different proteases that generate sIL-11R variants. Using a combination of bioinformatics and different biochemical, molecular, and cell biology methods, we show that the IL-11R-T306_S308dup variant does not mature correctly, is intracellularly retained, and does not reach the cell surface. In contrast, the IL-11R-E364_V368del variant is fully biologically active and processed normally by proteases, thus allowing classic and trans-signaling of IL-11. Our results provide evidence that mutations within the IL11RA gene may not be causative for craniosynostosis and suggest that other regulatory mechanism(s) are involved but remain to be identified.
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Affiliation(s)
- Birte Kespohl
- Department of Pathology, Medical Faculty, Otto-von-Guericke-University Magdeburg, Germany
| | - Anna-Lena Hegele
- Department of Pathology, Medical Faculty, Otto-von-Guericke-University Magdeburg, Germany
| | - Stefan Düsterhöft
- Institute of Molecular Pharmacology, RWTH Aachen University, Germany
| | - Hans Bakker
- Institute of Clinical Biochemistry, Hannover Medical School, Germany
| | - Falk F R Buettner
- Institute of Clinical Biochemistry, Hannover Medical School, Germany
| | - Roland Hartig
- Institute for Molecular and Clinical Immunology and Service Unit Multiparametric Bioimaging and Cytometry, Medical Faculty, University of Magdeburg, Germany
| | - Juliane Lokau
- Department of Pathology, Medical Faculty, Otto-von-Guericke-University Magdeburg, Germany
- Institute of Clinical Biochemistry, Hannover Medical School, Germany
| | - Christoph Garbers
- Institute of Clinical Biochemistry, Hannover Medical School, Germany
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38
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Sirisena S, Chan S, Roberts N, Dal Maso S, Gras SL, J O Martin G. Influence of yeast growth conditions and proteolytic enzymes on the amino acid profiles of yeast hydrolysates: Implications for taste and nutrition. Food Chem 2024; 437:137906. [PMID: 37939420 DOI: 10.1016/j.foodchem.2023.137906] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 10/16/2023] [Accepted: 10/28/2023] [Indexed: 11/10/2023]
Abstract
This study investigated the effects of aerobic and anaerobic growth and proteolytic enzymes on the amino acid content of yeast hydrolysates in relation to taste and nutrition. Saccharomyces cerevisiae ATCC5574 was grown under fed-batch aerobic or batch anaerobic conditions. Intracellular glutamic acid (Glu) concentrations were 18-fold higher in aerobic yeast. Hydrolysis with papain and alkaline protease released more amino acids (AA) than simple autolysis or hydrolysis with bromelain, most significantly when applied to aerobic yeast (∼2-fold increase). Autolysates and bromelain hydrolysates from aerobic yeast had low levels of bitter and essential AAs, with high levels of umami Glu. Papain and alkaline protease hydrolysates of aerobic yeast had high levels of umami, bitter and essential AAs. Autolysates/hydrolysates from anaerobic yeast had moderate, high, and low levels of bitter, essential and umami AAs. Selection of both yeast growth conditions and hydrolysis enzyme can manipulate the free AA profile and yield of hydrolysates.
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Affiliation(s)
- Sameera Sirisena
- Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Sitha Chan
- Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Nic Roberts
- Bega Foods, 1 Vegemite Way, Port Melbourne, Victoria 3207, Australia
| | - Sandra Dal Maso
- Bega Foods, 1 Vegemite Way, Port Melbourne, Victoria 3207, Australia
| | - Sally L Gras
- Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia; The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Gregory J O Martin
- Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia.
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Kim DH, Chun BH, Lee JJ, Kim OC, Hyun J, Han DM, Jeon CO, Lee SH, Lee SH, Choi YH, Hong SB. Enzymatic Activity and Amino Acids Production of Predominant Fungi from Traditional Meju during Soybean Fermentation. J Microbiol Biotechnol 2024; 34:654-662. [PMID: 38213301 PMCID: PMC11016766 DOI: 10.4014/jmb.2309.09008] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/23/2023] [Accepted: 12/12/2023] [Indexed: 01/13/2024]
Abstract
To investigate the effect of the predominant fungal species from Korean traditional meju and doenjang on soybean fermentation, the enzymatic activity and amino acid production of twenty-two fungal strains were assessed through solid- and liquid-state soybean fermentation. Enzymatic activity analyses of solid-state fermented soybeans revealed different enzyme activities involving protease, leucine aminopeptidase (LAP), carboxypeptidase (CaP), glutaminase, γ-glutamyl transferase (GGT), and amylase, depending on the fungal species. These enzymatic activities significantly affected the amino acid profile throughout liquid-state fermentation. Strains belonging to Mucoromycota, including Lichtheimia, Mucor, Rhizomucor, and Rhizopus, produced smaller amounts of total amino acids and umami-producing amino acids, such as glutamic acid and aspartic acid, than strains belonging to Aspergillus subgenus circumdati. The genera Penicillium and Scopulariopsis produced large amounts of total amino acids and glutamic acid, suggesting that these genera play an essential role in producing umami and kokumi tastes in fermented soybean products. Strains belonging to Aspergillus subgenus circumdati, including A. oryzae, showed the highest amino acid content, including glutamic acid, suggesting the potential benefits of A. oryzae as a starter for soybean fermentation. This study showed the potential of traditional meju strains as starters for soybean fermentation. However, further analysis of processes such as the production of G-peptide for kokumi taste and volatile compounds for flavor and safety is needed.
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Affiliation(s)
- Dong Hyun Kim
- Korean Agricultural Culture Collection, Agricultural Microbiology Division, National Institute of Agricultural Sciences, Wanju 55365, Republic of Korea
- Department of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Byung Hee Chun
- Department of Microbiology, Pukyong University, Busan 48513, Republic of Korea
| | - Jae-Jung Lee
- Fermentation Research Lab., Fermentation R&D Center, Sempio Foods Company, Cheongju 28156, Republic of Korea
| | - Oh Cheol Kim
- Fermentation Research Lab., Fermentation R&D Center, Sempio Foods Company, Cheongju 28156, Republic of Korea
| | - Jiye Hyun
- Fermentation Research Lab., Fermentation R&D Center, Sempio Foods Company, Cheongju 28156, Republic of Korea
| | - Dong Min Han
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Sang Hun Lee
- Food and Nutrition Div., National Institute of Agricultural Sciences, Wanju 55365, Republic of Korea
| | - Sang-Han Lee
- Department of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Yong-Ho Choi
- Fermentation Research Lab., Fermentation R&D Center, Sempio Foods Company, Cheongju 28156, Republic of Korea
| | - Seung-Beom Hong
- Korean Agricultural Culture Collection, Agricultural Microbiology Division, National Institute of Agricultural Sciences, Wanju 55365, Republic of Korea
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Lv L, Mo J, Qing Y, Wang S, Chen L, Mei A, Xu R, Huang H, Tan J, Li Y, Liu J. NEMF-mediated Listerin-independent mitochondrial translational surveillance by E3 ligase Pirh2 and mitochondrial protease ClpXP. Cell Rep 2024; 43:113860. [PMID: 38412092 DOI: 10.1016/j.celrep.2024.113860] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 12/13/2023] [Accepted: 02/08/2024] [Indexed: 02/29/2024] Open
Abstract
The ribosome-associated protein quality control (RQC) pathway acts as a translational surveillance mechanism to maintain proteostasis. In mammalian cells, the cytoplasmic RQC pathway involves nuclear export mediator factor (NEMF)-dependent recruitment of the E3 ligase Listerin to ubiquitinate ribosome-stalled nascent polypeptides on the lysine residue for degradation. However, the quality control of ribosome-stalled nuclear-encoded mitochondrial nascent polypeptides remains elusive, as these peptides can be partially imported into mitochondria through translocons, restricting accessibility to the lysine by Listerin. Here, we identify a Listerin-independent organelle-specific mitochondrial RQC pathway that acts on NEMF-mediated carboxy-terminal poly-alanine modification. In the pathway, mitochondrial proteins carrying C-end poly-Ala tails are recognized by the cytosolic E3 ligase Pirh2 and the ClpXP protease in the mitochondria, which coordinately clear ribosome-stalled mitochondrial nascent polypeptides. Defects in this elimination pathway result in NEMF-mediated aggregates and mitochondrial integrity failure, thus providing a potential molecular mechanism of the RQC pathway in mitochondrial-associated human diseases.
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Affiliation(s)
- Liang Lv
- Department of Gastroenterology, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Jinyou Mo
- Center for Medical Research, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Yumin Qing
- Department of Gastroenterology, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China; Center for Medical Research, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Shuchao Wang
- Center for Medical Research, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Leijie Chen
- Department of Gastroenterology, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China; Center for Medical Research, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Anna Mei
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Ru Xu
- Department of Obstetrics and Gynecology, Reproductive Medicine Center, The Second Xiangya Hospital, Changsha, Hunan, China
| | - Hualin Huang
- Department of Obstetrics and Gynecology, Reproductive Medicine Center, The Second Xiangya Hospital, Changsha, Hunan, China
| | - Jieqiong Tan
- Center for Medical Genetics, School of Life Science, Central South University, Changsha, Hunan 410078, China
| | - Yifu Li
- Center for Medical Research, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Jia Liu
- Center for Medical Research, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China.
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Öktem A, Pranoto DA, van Dijl JM. Post-translational secretion stress regulation in Bacillus subtilis is controlled by intra- and extracellular proteases. N Biotechnol 2024; 79:71-81. [PMID: 38158017 DOI: 10.1016/j.nbt.2023.12.009] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/20/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
The Gram-positive bacterium Bacillus subtilis is a prolific producer of industrial enzymes that are effectively harvested from the fermentation broth. However, the high capacity of B. subtilis for protein secretion has so far not been exploited to the full due to particular bottlenecks, including product degradation by extracellular proteases and counterproductive secretion stress responses. To unlock the Bacillus secretion pathway for difficult-to-produce proteins, various cellular interventions have been explored, including genome engineering. Our previous research has shown a superior performance of genome-reduced B. subtilis strains in the production of staphylococcal antigens compared to the parental strain 168. This was attributed, at least in part, to redirected secretion stress responses, including the presentation of elevated levels of the quality control proteases HtrA and HtrB that also catalyse protein folding. Here we show that this relates to the elimination of two homologous serine proteases, namely the cytosolic protease AprX and the extracellular protease AprE. This unprecedented posttranslational regulation of secretion stress effectors, like HtrA and HtrB, by the concerted action of cytosolic and extracellular proteases has important implications for the biotechnological application of microbial cell factories. In B. subtilis, this conclusion is underscored by extracellular degradation of the staphylococcal antigen IsaA by both AprX and AprE. Extracellular activity of the cytosolic protease AprX is remarkable since it shows that not only extracellular, but also intracellular proteases impact extracellular product levels. We therefore conclude that intracellular proteases represent new targets for improved recombinant protein production in microbial cell factories like B. subtilis.
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Affiliation(s)
- Ayşegül Öktem
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, the Netherlands
| | - Dicky A Pranoto
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, the Netherlands
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, the Netherlands.
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42
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Bridge HN, Leiter W, Frazier CL, Weeks AM. An N terminomics toolbox combining 2-pyridinecarboxaldehyde probes and click chemistry for profiling protease specificity. Cell Chem Biol 2024; 31:534-549.e8. [PMID: 37816350 PMCID: PMC10960722 DOI: 10.1016/j.chembiol.2023.09.009] [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: 02/22/2023] [Revised: 07/10/2023] [Accepted: 09/18/2023] [Indexed: 10/12/2023]
Abstract
Proteomic profiling of protease-generated N termini provides key insights into protease function and specificity. However, current technologies have sequence limitations or require specialized synthetic reagents for N-terminal peptide isolation. Here, we introduce an N terminomics toolbox that combines selective N-terminal biotinylation using 2-pyridinecarboxaldehyde (2PCA) reagents with chemically cleavable linkers to enable efficient enrichment of protein N termini. By incorporating a commercially available alkyne-modified 2PCA in combination with Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC), our strategy eliminates the need for chemical synthesis of N-terminal probes. Using these reagents, we developed PICS2 (Proteomic Identification of Cleavage Sites with 2PCA) to profile the specificity of subtilisin/kexin-type proprotein convertases (PCSKs). We also implemented CHOPPER (chemical enrichment of protease substrates with purchasable, elutable reagents) for global sequencing of apoptotic proteolytic cleavage sites. Based on their broad applicability and ease of implementation, PICS2 and CHOPPER are useful tools that will advance our understanding of protease biology.
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Affiliation(s)
- Haley N Bridge
- Department of Biochemistry, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - William Leiter
- Department of Chemistry, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Clara L Frazier
- Department of Biochemistry, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Amy M Weeks
- Department of Biochemistry, University of Wisconsin - Madison, Madison, WI 53706, USA; Department of Chemistry, University of Wisconsin - Madison, Madison, WI 53706, USA.
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43
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Sanz MÁ, Polo M, Rodríguez-Pulido M, Huildore Bommanna R, Sáiz M. The antiviral response triggered by the cGAS/STING pathway is subverted by the foot-and-mouth disease virus proteases. Cell Mol Life Sci 2024; 81:148. [PMID: 38509419 PMCID: PMC10954996 DOI: 10.1007/s00018-024-05190-7] [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: 12/15/2023] [Revised: 02/19/2024] [Accepted: 02/29/2024] [Indexed: 03/22/2024]
Abstract
Propagation of viruses requires interaction with host factors in infected cells and repression of innate immune responses triggered by the host viral sensors. Cytosolic DNA sensing pathway of cyclic GMP-AMP synthase (cGAS) and stimulator of interferon genes (STING) is a major component of the antiviral response to DNA viruses, also known to play a relevant role in response to infection by RNA viruses, including foot-and-mouth disease virus (FMDV). Here, we provide supporting evidence of cGAS degradation in swine cells during FMDV infection and show that the two virally encoded proteases, Leader (Lpro) and 3Cpro, target cGAS for cleavage to dampen the cGAS/STING-dependent antiviral response. The specific target sequence sites on swine cGAS were identified as Q140/T141 for the FMDV 3Cpro and the KVKNNLKRQ motif at residues 322-330 for Lpro. Treatment of swine cells with inhibitors of the cGAS/STING pathway or depletion of cGAS promoted viral infection, while overexpression of a mutant cGAS defective for cGAMP synthesis, unlike wild type cGAS, failed to reduce FMDV replication. Our findings reveal a new mechanism of RNA viral antagonism of the cGAS-STING innate immune sensing pathway, based on the redundant degradation of cGAS through the concomitant proteolytic activities of two proteases encoded by an RNA virus, further proving the key role of cGAS in restricting FMDV infection.
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Affiliation(s)
| | - Miryam Polo
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Madrid, Spain
| | | | | | - Margarita Sáiz
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Madrid, Spain.
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Zhai Y, Du Y, Yuan H, Fan S, Chen X, Wang J, He W, Han S, Zhang Y, Hu M, Zhang G, Kong Z, Wan B. Ubiquitin-specific proteinase 1 stabilizes PRRSV nonstructural protein Nsp1β to promote viral replication by regulating K48 ubiquitination. J Virol 2024; 98:e0168623. [PMID: 38376196 PMCID: PMC10949481 DOI: 10.1128/jvi.01686-23] [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: 10/26/2023] [Accepted: 01/26/2024] [Indexed: 02/21/2024] Open
Abstract
The porcine reproductive and respiratory syndrome virus (PRRSV) can lead to severe reproductive problems in sows, pneumonia in weaned piglets, and increased mortality, significantly negatively impacting the economy. Post-translational changes are essential for the host-dependent replication and long-term infection of PRRSV. Uncertainty surrounds the function of the ubiquitin network in PRRSV infection. Here, we screened 10 deubiquitinating enzyme inhibitors and found that the ubiquitin-specific proteinase 1 (USP1) inhibitor ML323 significantly inhibited PRRSV replication in vitro. Importantly, we found that USP1 interacts with nonstructural protein 1β (Nsp1β) and deubiquitinates its K48 to increase protein stability, thereby improving PRRSV replication and viral titer. Among them, lysine at position 45 is essential for Nsp1β protein stability. In addition, deficiency of USP1 significantly reduced viral replication. Moreover, ML323 loses antagonism to PRRSV rSD16-K45R. This study reveals the mechanism by which PRRSV recruits the host factor USP1 to promote viral replication, providing a new target for PRRSV defense.IMPORTANCEDeubiquitinating enzymes are critical factors in regulating host innate immunity. The porcine reproductive and respiratory syndrome virus (PRRSV) nonstructural protein 1β (Nsp1β) is essential for producing viral subgenomic mRNA and controlling the host immune system. The host inhibits PRRSV proliferation by ubiquitinating Nsp1β, and conversely, PRRSV recruits the host protein ubiquitin-specific proteinase 1 (USP1) to remove this restriction. Our results demonstrate the binding of USP1 to Nsp1β, revealing a balance of antagonism between PRRSV and the host. Our research identifies a brand-new PRRSV escape mechanism from the immune response.
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Affiliation(s)
- Yunyun Zhai
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
- International Joint Research Center for National Animal Immunology, Zhengzhou, Henan, China
| | - Yongkun Du
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
- International Joint Research Center for National Animal Immunology, Zhengzhou, Henan, China
| | - Hang Yuan
- Zhengzhou Shengda University of Economic Business & Management, Zhengzhou, China
| | - Shuai Fan
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
- International Joint Research Center for National Animal Immunology, Zhengzhou, Henan, China
| | - Xing Chen
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
- International Joint Research Center for National Animal Immunology, Zhengzhou, Henan, China
| | - Jiang Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
- International Joint Research Center for National Animal Immunology, Zhengzhou, Henan, China
| | - Wenrui He
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
- International Joint Research Center for National Animal Immunology, Zhengzhou, Henan, China
| | - Shichong Han
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
- International Joint Research Center for National Animal Immunology, Zhengzhou, Henan, China
| | - Yuhang Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
- International Joint Research Center for National Animal Immunology, Zhengzhou, Henan, China
| | - Man Hu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
- International Joint Research Center for National Animal Immunology, Zhengzhou, Henan, China
| | - Gaiping Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
- International Joint Research Center for National Animal Immunology, Zhengzhou, Henan, China
- Peking University, Beijing, China
- Longhu Laboratory, Zhengzhou, China
| | | | - Bo Wan
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
- International Joint Research Center for National Animal Immunology, Zhengzhou, Henan, China
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45
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Hosseini SB, Azizi M, Nojoumi SA, Valizadeh V. An up-to-date review of biomedical applications of serratiopeptidase and its biobetter derivatives as a multi-potential metalloprotease. Arch Microbiol 2024; 206:180. [PMID: 38502196 DOI: 10.1007/s00203-024-03889-6] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 02/03/2024] [Accepted: 02/06/2024] [Indexed: 03/21/2024]
Abstract
Serratiopeptidase is a bacterial metalloprotease used in a variety of medical applications. The multidimensional properties of serratiopeptidase make it noticeable as a miraculous enzyme. Anti-coagulant, anti-inflammatory and anti-biofilm activity of serratiopeptidase making it useful in reducing pain and swelling associated with various conditions including arthritis, diabetes, cancer, swelling, pain and also thrombolytic disorders. It breaks down fibrin, thins the fluids formed during inflammation and due to its anti-biofilm activity, can be used in the combination of antibiotics to reduce development of antibiotic resistance. However, some drawbacks like sensitivity to environmental conditions and low penetration into cells due to its large size have limited its usage as a potent pharmaceutical agent. To overcome such limitations, improved versions of the enzyme were introduced using protein engineering in our previous studies. Novel functional serratiopeptidases with shorter length and higher stability have seemingly created a hope for using this enzyme as a more effective therapeutic enzyme. This review explains the structural properties and functional aspects of serratiopeptidase, its main characteristics and properties, pre-clinical and clinical applications of the enzyme, improved qualities of the modified forms, different formulations of the enzyme, and the potential future developments.
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Affiliation(s)
- Seyedeh Bahareh Hosseini
- New Technologies Research Group, Nanobiotechnology Department, Pasteur Institute of Iran, Tehran, Iran
| | - Masoumeh Azizi
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Ali Nojoumi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Vahideh Valizadeh
- New Technologies Research Group, Nanobiotechnology Department, Pasteur Institute of Iran, Tehran, Iran.
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Li MD, Lu JW, Zhang F, Lei WJ, Pan F, Lin YK, Ling LJ, Myatt L, Wang WS, Sun K. ADAMTS4 is a crucial proteolytic enzyme for versican cleavage in the amnion at parturition. Commun Biol 2024; 7:301. [PMID: 38461223 PMCID: PMC10924920 DOI: 10.1038/s42003-024-06007-w] [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: 09/27/2023] [Accepted: 03/03/2024] [Indexed: 03/11/2024] Open
Abstract
Hyalectan cleavage may play an important role in extracellular matrix remodeling. However, the proteolytic enzyme responsible for hyalectan degradation for fetal membrane rupture at parturition remains unknown. Here, we reveal that versican (VCAN) is the major hyalectan in the amnion, where its cleavage increases at parturition with spontaneous rupture of membrane. We further reveal that ADAMTS4 is a crucial proteolytic enzyme for VCAN cleavage in the amnion. Inflammatory factors may enhance VCAN cleavage by inducing ADAMTS4 expression and inhibiting ADAMTS4 endocytosis in amnion fibroblasts. In turn, versikine, the VCAN cleavage product, induces inflammatory factors in amnion fibroblasts, thereby forming a feedforward loop between inflammation and VCAN degradation. Mouse studies show that intra-amniotic injection of ADAMTS4 induces preterm birth along with increased VCAN degradation and proinflammatory factors abundance in the fetal membranes. Conclusively, there is enhanced VCAN cleavage by ADAMTS4 in the amnion at parturition, which can be reenforced by inflammation.
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Affiliation(s)
- Meng-Die Li
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, PR China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, PR China
| | - Jiang-Wen Lu
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, PR China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, PR China
| | - Fan Zhang
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, PR China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, PR China
| | - Wen-Jia Lei
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, PR China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, PR China
| | - Fan Pan
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, PR China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, PR China
| | - Yi-Kai Lin
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, PR China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, PR China
| | - Li-Jun Ling
- Department of Obstetrics, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, PR China
| | - Leslie Myatt
- Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, OR, USA
| | - Wang-Sheng Wang
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, PR China.
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, PR China.
| | - Kang Sun
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, PR China.
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, PR China.
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Lu X, Wang M, Yue H, Feng X, Tian Y, Xue C, Zhang T, Wang Y. Novel peptides from sea cucumber intestines hydrolyzed by neutral protease alleviate exercise-induced fatigue via upregulating the glutaminemediated Ca 2+ /Calcineurin signaling pathway in mice. J Food Sci 2024; 89:1727-1738. [PMID: 38258958 DOI: 10.1111/1750-3841.16934] [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: 09/06/2023] [Revised: 12/15/2023] [Accepted: 12/24/2023] [Indexed: 01/24/2024]
Abstract
Sea cucumber intestines are considered a valuable resource in the sea cucumber processing industry due to their balanced amino acid composition. Studies have reported that peptides rich in glutamate and branched-chain amino acids have anti-fatigue properties. However, the function of the sea cucumber intestine in reducing exercise-induced fatigue remains unclear. In this study, we enzymatically hydrolyzed low molecular weight peptides from sea cucumber intestines (SCIP) and administered SCIP orally to mice to examine its effects on exercise-induced fatigue using swimming and pole-climbing exhaustion experiments. The results revealed that supplementation with SCIP significantly prolonged the exhaustion time of swimming in mice, decreased blood lactate and urea nitrogen levels, and increased liver and muscle glycogen levels following a weight-loaded swimming test. Immunofluorescence analysis indicated a notable increase the proportion of slow-twitch muscle fiber and a significant decrease the proportion of fast-twitch muscle fiber following SCIP supplementation. Furthermore, SCIP upregulated mRNA expression levels of Ca2+ /Calcineurin upstream and downstream regulators, thereby contributing to the promotion of skeletal muscle fiber type conversion. This study presents the initial evidence establishing SCIP as a potential enhancer of skeletal muscle fatigue resistance, consequently providing a theoretical foundation for the valuable utilization of sea cucumber intestines.
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Affiliation(s)
- Xutong Lu
- SKL of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, P. R. China
| | - Meng Wang
- SKL of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, P. R. China
| | - Hao Yue
- Institute of Food & Nutrition Science and Technology, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
| | - Xiaoxuan Feng
- SKL of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, P. R. China
| | - Yingying Tian
- SKL of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, P. R. China
| | - Changhu Xue
- SKL of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, P. R. China
| | - Tiantian Zhang
- SKL of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, P. R. China
| | - Yuming Wang
- SKL of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, P. R. China
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Nguyen HLT, Nguyen NQT, Le TT, Pham XDT, Pham HL, Le HNT, Phan TN, Dinh NT. Improved expression and purification of highly-active 3 chymotrypsin-like protease from SARS-CoV-2. Protein Expr Purif 2024; 215:106414. [PMID: 38072143 DOI: 10.1016/j.pep.2023.106414] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 12/31/2023]
Abstract
Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) is the causative pathogen of coronavirus disease-19 (COVID-19). The COVID-19 pandemic has resulted in millions of deaths and widespread socio-economic damage worldwide. Therefore, numerous studies have been conducted to identify effective measures to control the spreading of the virus. Among various potential targets, the 3 chymotrypsin-like protease (3CLpro), also known as Mpro, stands out as the key protease of SARS-CoV-2, playing an essential role in virus replication and assembly, is the most prospective. In this study, we modified the commercial vector, pETM33-Nsp5-Mpro (plasmid # 156475, Addgene, USA), by inserting an autocleavage site (AVLQ) of 3CLpro and 6 × His-tag encoding sequences before and after the Nsp5-Mpro sequence, respectively. This modification enabled the expression of 3CLpro as an authentic N terminal protease (au3CLpro), which was purified to electrophoretic homogeneity by a single-step chromatography using two tandem Glutathione- and Ni-Sepharose columns. The enzyme au3CLpro demonstrated significantly higher activity (3169 RFU/min/μg protein) and catalytic efficiency (Kcat/Km of 0.007 μM-1.s-1) than that of the 3CLpro (com3CLpro) expressed from the commercial vector (pETM33-Nsp5-Mpro) with specific activity 889 RFU/min/μg and Kcat/Km of 0.0015 μM-1.s-1, respectively. Optimal conditions for au3CLpro activity included a 50 mM Tris-HCl buffer at pH 7, containing 150 mM NaCl and 0.1 mg/ml BSA at 37 °C.
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Affiliation(s)
- Hong-Loan T Nguyen
- Key Laboratory of Enzyme and Protein Technology, VNU University of Science, 334 Nguyen Trai, Thanh Xuan, Hanoi, Viet Nam; Faculty of Biology, VNU University of Science, 334 Nguyen Trai, Thanh Xuan, Hanoi, Viet Nam
| | - Nhu-Quynh T Nguyen
- Faculty of Biology, VNU University of Science, 334 Nguyen Trai, Thanh Xuan, Hanoi, Viet Nam
| | - The-Thai Le
- Faculty of Biology, VNU University of Science, 334 Nguyen Trai, Thanh Xuan, Hanoi, Viet Nam
| | - Xuan-Dieu T Pham
- Faculty of Biology, VNU University of Science, 334 Nguyen Trai, Thanh Xuan, Hanoi, Viet Nam
| | - Hai-Long Pham
- Faculty of Biology, VNU University of Science, 334 Nguyen Trai, Thanh Xuan, Hanoi, Viet Nam
| | - Hong-Nhung T Le
- Key Laboratory of Enzyme and Protein Technology, VNU University of Science, 334 Nguyen Trai, Thanh Xuan, Hanoi, Viet Nam; Faculty of Biology, VNU University of Science, 334 Nguyen Trai, Thanh Xuan, Hanoi, Viet Nam
| | - Tuan-Nghia Phan
- Key Laboratory of Enzyme and Protein Technology, VNU University of Science, 334 Nguyen Trai, Thanh Xuan, Hanoi, Viet Nam; Faculty of Biology, VNU University of Science, 334 Nguyen Trai, Thanh Xuan, Hanoi, Viet Nam
| | - Nho-Thai Dinh
- Key Laboratory of Enzyme and Protein Technology, VNU University of Science, 334 Nguyen Trai, Thanh Xuan, Hanoi, Viet Nam; Faculty of Biology, VNU University of Science, 334 Nguyen Trai, Thanh Xuan, Hanoi, Viet Nam.
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Li R, Wang Q, Shen Y, Li M, Sun L. Integrated extraction, structural characterization, and activity assessment of squid pen protein hydrolysates and β-chitin with different protease hydrolysis. Int J Biol Macromol 2024; 262:130069. [PMID: 38340918 DOI: 10.1016/j.ijbiomac.2024.130069] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 01/21/2024] [Accepted: 02/07/2024] [Indexed: 02/12/2024]
Abstract
Squid pen (SP) is a valuable source of protein and β-chitin. However, current research has primarily focused on extracting β-chitin from SP. This study innovatively extracted both SP protein hydrolysates (SPPHs) and SP β-chitin (SPC) simultaneously using protease hydrolysis. The effects of different proteases on their structural characteristics and bioactivity were evaluated. The results showed that SP alcalase β-chitin (SPAC) had the highest degree of deproteinization (DP, 98.19 %) and SP alcalase hydrolysates (SPAH) had a degree of hydrolysis (DH) of 24.47 %. The analysis of amino acid composition suggested that aromatic amino acids accounted for 17.44 % in SPAH. Structural characterization revealed that SP flavourzyme hydrolysates (SPFH) had the sparsest structure. SPC exhibited an excellent crystallinity index (CI, over 60 %) and degree of acetylation (DA, over 70 %). During simulated gastrointestinal digestion (SGD), the hydroxyl radical scavenging activity, ABTS radical scavenging activity, Fe2+ chelating activity, and reducing power of the SPPHs remained stable or increased significantly. Additionally, SPFC exhibited substantial inhibitory effects on Staphylococcus aureus and Escherichia coli (S. aureus and E. coli), with inhibition circle diameters measuring 2.4 cm and 2.1 cm. These findings supported the potential use of SPPHs as natural antioxidant alternatives and suggested that SPC could serve as a potential antibacterial supplement.
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Affiliation(s)
- Ruimin Li
- College of Life Science, Yantai University, Yantai 264005, China
| | - Qiuting Wang
- College of Life Science, Yantai University, Yantai 264005, China
| | - Yanyan Shen
- College of Life Science, Yantai University, Yantai 264005, China
| | - Mingbo Li
- College of Life Science, Yantai University, Yantai 264005, China
| | - Leilei Sun
- College of Life Science, Yantai University, Yantai 264005, China.
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50
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Rani A, Pandey DM, Pandey JP. Biomolecular characterization of Antheraea mylitta cocoonase: A secreted protease. Anal Biochem 2024; 686:115408. [PMID: 38008303 DOI: 10.1016/j.ab.2023.115408] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 11/16/2023] [Accepted: 11/20/2023] [Indexed: 11/28/2023]
Abstract
Cocoonase is a protease secreted during the emergence of silk moths. In the present study cocoonase of Antheraea mylitta was collected, purified and secondary structure was determined using circular dichroism (CD) spectroscopy which revealed the presence of α-helix 4.3%, β-sheet 55%, turn 8% and random coil 32.7%. The thermal stability of cocoonase was studied using CD spectroscopy while the thermal property was observed using Differential Scanning Calorimetry (DSC). Furthermore, MALDI-TOF peptide mass fingerprinting (PMF) was performed for similar protein identification using the MASCOT server. Using casein as the substrate, the kinetic constants Km and Vmax were 13 × 103 mg/ml and 15.09 × 10-2 μg/mg.s1 respectively. The specific activity of cocoonase was observed to be maximum at temperature 40 °C, pH-8.0. The effect of heavy metals Hg2+, Cd2+, Co2+, Pb2+ showed inhibitory activity at higher concentrations, while few metals like Mn2+, Fe3+ enhanced the activity while the effect of Ca2+ was not much on the activity. Soybean trypsin inhibitor and PMSF showed an inhibitory effect on the activity of cocoonase. Additionally, antioxidant scavenging and fibrinolytic properties were also observed. Furthermore, the imperative information generated through the present study will serve to explore cocoonase for its prospective pharmaceutical applications.
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Affiliation(s)
- Aruna Rani
- Birla Institute of Technology, Mesra, Ranchi, 835215, Jharkhand, India; Central Tasar Research and Training Institute (Central Silk Board, MOT Govt. of India), Piska Nagri, Ranchi, 835303, Jharkhand, India
| | - Dev Mani Pandey
- Birla Institute of Technology, Mesra, Ranchi, 835215, Jharkhand, India
| | - Jay Prakash Pandey
- Central Tasar Research and Training Institute (Central Silk Board, MOT Govt. of India), Piska Nagri, Ranchi, 835303, Jharkhand, India.
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