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Lee YO, Do SH, Won JY, Chin YW, Chewaka LS, Park BR, Kim SJ, Kim SK. Inverse metabolic engineering for improving protein content in Saccharomyces cerevisiae. Biotechnol J 2023; 18:e2300014. [PMID: 37272298 DOI: 10.1002/biot.202300014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 05/09/2023] [Accepted: 05/31/2023] [Indexed: 06/06/2023]
Abstract
Production of Saccharomyces cerevisiae-based single cell protein (SCP) has recently received great attention due to the steady increase in the world's population and environmental issues. In this study, an inverse metabolic engineering approach was applied to improve the production of yeast SCP. Specifically, an S. cerevisiae mutant library, generated using UV-random mutagenesis, was screened for three rounds to isolate mutants with improved protein content and/or concentration. The #1021 mutant strain exhibited a respective 31% and 23% higher amino acid content and concentration than the parental S. cerevisiae D452-2 strain. Notably, the content, concentration, and composition of amino acids produced by the PAN2* strain, with a single nucleotide polymorphism in PAN2 coding for a catalytic subunit of the poly(A)-nuclease (PAN) deadenylation complex, were virtually identical to those produced by the #1021 mutant strain. In a glucose-limited fed-batch fermentation, the PAN2* strain produced 19.5 g L-1 amino acids in 89 h, which was 16% higher than that produced by the parental D452-2 strain. This study highlights the benefits of inverse metabolic engineering for enhancing the production titer and yield of target molecules without prior knowledge of rate-limiting steps involved in their biosynthetic pathways.
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Affiliation(s)
- Young-Oh Lee
- Department of Food Science and Technology, Chung-Ang University, Anseong, Gyeonggi, Republic of Korea
| | - Sang-Hun Do
- Department of Food Science and Technology, Chung-Ang University, Anseong, Gyeonggi, Republic of Korea
| | - Jae Yoon Won
- Department of Food Science and Technology, Chung-Ang University, Anseong, Gyeonggi, Republic of Korea
| | - Young-Wook Chin
- Traditional Food Research Group, Korea Food Research Institute, Wanju, Republic of Korea
| | - Legesse S Chewaka
- Department of Agro-food Resources, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, Republic of Korea
| | - Bo-Ram Park
- Department of Agro-food Resources, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, Republic of Korea
| | - Soo-Jung Kim
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, Republic of Korea
| | - Sun-Ki Kim
- Department of Food Science and Technology, Chung-Ang University, Anseong, Gyeonggi, Republic of Korea
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Zheng L, Chen X, Zhang L, Qin N, An J, Zhu J, Jin H, Tuo B. A potential tumor marker: Chaperonin containing TCP‑1 controls the development of malignant tumors (Review). Int J Oncol 2023; 63:106. [PMID: 37539774 PMCID: PMC10552740 DOI: 10.3892/ijo.2023.5554] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 07/21/2023] [Indexed: 08/05/2023] Open
Abstract
Due to concealment, high invasiveness and a lack of indicators, malignant tumors have emerged as one of the deadliest diseases worldwide and their incidence is rising yearly. Research has revealed that the chaperonin family member, chaperonin containing TCP‑1 (CCT), serves a crucial role in malignant tumors. CCT is involved in the growth of numerous malignant tumors such as lung cancer, breast cancer, hepatocellular carcinoma and colorectal cancer and assists the folding of a number of proteins linked to cancer, such as KRAS, p53 and STAT3. According to clinical data, CCT is highly expressed in a range of tumor cells and is associated with poor patient prognosis. In addition, through controlling the cell cycle or interacting with other proteins (including YAP1, HoXB2 and SMAD2), CCT has an effect on the proliferation, invasion and migration of cancer cells. As a result, it is possible that CCT will become a new tumor marker or therapeutic target, which will provide some guidance for early tumor screening or late tumor prognosis. In the present review, the molecular properties of CCT are introduced, alongside a summary of its interactions with other cancer‑related proteins and a discussion of its function in common malignant tumors. It is expected that the present review will offer fresh approaches to the treatment of cancer.
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Affiliation(s)
- Liming Zheng
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563003
| | - Xingyue Chen
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563003
| | - Li Zhang
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563003
| | - Nannan Qin
- Department of Critical Care Medicine of the First People's Hospital of Zunyi (The Third Affiliated Hospital), Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
| | - Jiaxing An
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563003
| | - Jiaxing Zhu
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563003
| | - Hai Jin
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563003
| | - Biguang Tuo
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563003
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Haarer BK, Pimm ML, de Jong EP, Amberg DC, Henty-Ridilla JL. Purification of human β- and γ-actin from budding yeast. J Cell Sci 2023; 136:jcs260540. [PMID: 37070275 PMCID: PMC10184827 DOI: 10.1242/jcs.260540] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 04/04/2023] [Indexed: 04/19/2023] Open
Abstract
Biochemical studies of human actin and its binding partners rely heavily on abundant and easily purified α-actin from skeletal muscle. Therefore, muscle actin has been used to evaluate and determine the activities of most actin regulatory proteins but there is an underlying concern that these proteins perform differently from actin present in non-muscle cells. To provide easily accessible and relatively abundant sources of human β- or γ-actin (i.e. cytoplasmic actins), we developed Saccharomyces cerevisiae strains that express each as their sole source of actin. Both β- or γ-actin purified in this system polymerize and interact with various binding partners, including profilin, mDia1 (formin), fascin and thymosin-β4 (Tβ4). Notably, Tβ4 and profilin bind to β- or γ-actin with higher affinity than to α-actin, emphasizing the value of testing actin ligands with specific actin isoforms. These reagents will make specific isoforms of actin more accessible for future studies on actin regulation.
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Affiliation(s)
- Brian K. Haarer
- Department of Biochemistry and Molecular Biology, State University of New York (SUNY) Upstate Medical University, Syracuse, NY 13210, USA
| | - Morgan L. Pimm
- Department of Biochemistry and Molecular Biology, State University of New York (SUNY) Upstate Medical University, Syracuse, NY 13210, USA
| | | | - David C. Amberg
- Department of Biochemistry and Molecular Biology, State University of New York (SUNY) Upstate Medical University, Syracuse, NY 13210, USA
| | - Jessica L. Henty-Ridilla
- Department of Biochemistry and Molecular Biology, State University of New York (SUNY) Upstate Medical University, Syracuse, NY 13210, USA
- Department of Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
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Estêvão J, Osorio H, Costas B, Cruz A, Fernández-Boo S. Search for new biomarkers of tolerance to Perkinsus olseni parasite infection in Ruditapes decussatus clams. FISH & SHELLFISH IMMUNOLOGY 2023; 134:108566. [PMID: 36736640 DOI: 10.1016/j.fsi.2023.108566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/23/2023] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
The grooved carpet shell (Ruditapes decussatus) is a clam species with high economic and social importance in several European and Mediterranean countries. Production of this species suffered a decline caused by biotic (parasite infection) and abiotic factors (environmental factors, stress, poor management methods and intensive culture of the introduced species Ruditapes philippinarum). The protozoan parasite Perkinsus olseni is also responsible for the decline of production, being nowadays one of the major issues for clam culture. Molecular biomarkers that might represent tolerance of R. decussatus to P. olseni have already been uncovered, shedding light in a possible production improvement by selecting those clams with a strongest immune response. In the present study, new tolerance biomarkers to P. olseni infection in R. decussatus were identified. The haemolymph proteomic profiles of naturally non/low-infected (tolerant) and highly-infected (susceptible) clams by the parasite across several heavy affected areas of Europe were characterized through a shotgun proteomics approach. Also, the mechanisms that might be involved in the responses against the disease in chronic infections were explored. Proteins related to energy restoration and balance, metabolic regulation, energy accumulation, ROS production, lysosomal activity, amino acid synthesis, proteolytic activity, iron regulation, iron withholding, and immune response modulation were significantly regulated in susceptible clams. In the tolerant group, proteins related to phagocytosis regulation, control of cell growth and proliferation, gonadal maturation, regulation of apoptosis, growth modulation, response to oxidative stress, iron regulation, shell development and metabolic regulation were significantly expressed. In summary, the protein expression profile of tolerant individuals suggests that an efficient pathogen elimination mechanism coupled to a better metabolic regulation leads to a tolerance to the parasite infection by limiting the spread through the tissues.
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Affiliation(s)
- João Estêvão
- Animal Health and Aquaculture (A2S), CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, University of Porto, Porto, Portugal; Instituto de Ciências Biomédicas Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Hugo Osorio
- i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal; Ipatimup-Institute of Molecular Pathology and Immunology of the University of Porto, University of Porto, Porto, Portugal
| | - Benjamin Costas
- Animal Health and Aquaculture (A2S), CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, University of Porto, Porto, Portugal; Instituto de Ciências Biomédicas Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Andreia Cruz
- Oceano Fresco S.A, Porto de Abrigo, 2450-075, Nazaré, Portugal
| | - Sergio Fernández-Boo
- Animal Health and Aquaculture (A2S), CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, University of Porto, Porto, Portugal.
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Smith TM, Willardson BM. Mechanistic insights into protein folding by the eukaryotic chaperonin complex CCT. Biochem Soc Trans 2022; 50:1403-1414. [PMID: 36196890 PMCID: PMC9704529 DOI: 10.1042/bst20220591] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 11/17/2022]
Abstract
The cytosolic chaperonin CCT is indispensable to eukaryotic life, folding the cytoskeletal proteins actin and tubulin along with an estimated 10% of the remaining proteome. However, it also participates in human diseases such as cancer and viral infections, rendering it valuable as a potential therapeutic target. CCT consists of two stacked rings, each comprised of eight homologous but distinct subunits, that assists the folding of a remarkable substrate clientele that exhibits both broad diversity and specificity. Much of the work in recent years has been aimed at understanding the mechanisms of CCT substrate recognition and folding. These studies have revealed new binding sites and mechanisms by which CCT uses its distinctive subunit arrangement to fold structurally unrelated substrates. Here, we review recent structural insights into CCT-substrate interactions and place them into the broader context of CCT function and its implications for human health.
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Affiliation(s)
- Theresa M. Smith
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, U.S.A
| | - Barry M. Willardson
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, U.S.A
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Ma J, Song P, Liu X, Ma C, Zheng M, Ren X, Wang R, Liu W, Lu Z, Li J. Insights into the roles and driving forces of CCT3 in human tumors. Front Pharmacol 2022; 13:1005855. [PMID: 36313331 PMCID: PMC9596777 DOI: 10.3389/fphar.2022.1005855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/28/2022] [Indexed: 11/22/2022] Open
Abstract
CCT3 played a key role in many cancers. This study aimed to further explore the characteristics of CCT3 from a pan-cancer perspective and reveal the driving forces for CCT3. By bioinformatic analysis, we found that the mRNA and protein levels of CCT3 were abnormally elevated in most tumor types and were correlated with poor prognosis. Single-cell sequencing data indicated an abnormal increase of CCT3 expression in both malignant cells and multiple immune cells. In the tumor microenvironment, CCT3 expression was negatively relevant with immune cell infiltration and immune checkpoint genes expression. In colon cancer, knockdown of CCT3 inhibited cell proliferation. Gene set enrichment analysis showed that CCT3 may be oncogenic by regulating amino acid metabolism. Furthermore, we predicted sensitive drugs for CCT3 by virtual screening and sensitivity analysis. Many driver genes such as TP53 and KRAS were essential for CCT3 overexpression. Epigenetic factors, enhancers in particular, were also critical for CCT3 expression. Additionally, we constructed the lncRNA/circRNA-miRNA-CCT3 regulatory network. Collectively, CCT3 had the potential to be a diagnostic and prognostic biomarker for multiple tumor types. CCT3 expression was relevant with an immunosuppressive tumor microenvironment. CCT3 could be a new molecular target for colon cancer. Both genetic and epigenetic factors were responsible for CCT3 expression in tumors.
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Affiliation(s)
- Jingang Ma
- Department of Oncology, Affiliated Hospital of Weifang Medical University, School of Clinical Medicine, Weifang Medical University, Weifang, China
| | - Ping Song
- Department of Gastroenterology, Affiliated Hangzhou First People’s Hospital, Medical School of Zhejiang University, Hangzhou, China
| | - Xinling Liu
- Department of Hematology, Laboratory for Stem Cell and Regenerative Medicine, Clinical Research Center, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Changgeng Ma
- Department of Radiotherapy, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Mingzhu Zheng
- Department of Oncology, Affiliated Hospital of Weifang Medical University, School of Clinical Medicine, Weifang Medical University, Weifang, China
| | - Xiaomin Ren
- Department of Oncology, Affiliated Hospital of Weifang Medical University, School of Clinical Medicine, Weifang Medical University, Weifang, China
| | - Rui Wang
- Department of Oncology, Affiliated Hospital of Weifang Medical University, School of Clinical Medicine, Weifang Medical University, Weifang, China
| | - Wenshan Liu
- Shandong Key Laboratory of Clinical Applied Pharmacology, Department of Pharmacy, Affiliated Hospital of Weifang Medical University, Weifang, China
- *Correspondence: Wenshan Liu, ; Zhong Lu, ; Jiaqiu Li,
| | - Zhong Lu
- Department of Oncology, Affiliated Hospital of Weifang Medical University, School of Clinical Medicine, Weifang Medical University, Weifang, China
- *Correspondence: Wenshan Liu, ; Zhong Lu, ; Jiaqiu Li,
| | - Jiaqiu Li
- Department of Oncology, Affiliated Hospital of Weifang Medical University, School of Clinical Medicine, Weifang Medical University, Weifang, China
- *Correspondence: Wenshan Liu, ; Zhong Lu, ; Jiaqiu Li,
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Wang K, He J, Tu C, Xu H, Zhang X, Lv Y, Song C. Upregulation of CCT3 predicts poor prognosis and promotes cell proliferation via inhibition of ferroptosis and activation of AKT signaling in lung adenocarcinoma. BMC Mol Cell Biol 2022; 23:25. [PMID: 35773623 PMCID: PMC9245217 DOI: 10.1186/s12860-022-00424-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 06/06/2022] [Indexed: 01/21/2023] Open
Abstract
Background Chaperonin containing TCP1 subunit 3 (CCT3) acts as an oncogene in cancers, whereas its role and underlying mechanisms in lung adenocarcinoma (LUAD) are poorly understood. This study investigated the clinical relevance and function of CCT3 in LUAD. Methods Clinical relevance of CCT3 in LUAD and lung squamous cell carcinoma (LUSC) was analyzed based on TCGA database. qRT-PCR and Western blot were used to detect mRNA and protein expression, respectively. CCK8 and colony formation were performed to measure cell viability. PI and PI/Annexin V-FITC assay kit was used to determine cell cycle and cell death, respectively. Luciferase activity was performed to check whether CCT3 regulated slc7a11’s transcription activity. Ferroptosis was determined by incubating the cells with ferroptosis and apoptosis inducer, their inhibitor and autophagy inhibitor, followed by cell viability examination. Results We found that CCT3 was overexpressed in LUAD and LUSC tissues. Overexpression of CCT3 predicted the poor prognosis of LUAD patients. Loss-of-function and gain-of-function experiments demonstrated that CCT3 promoted the proliferation and colony formation of LUAD cells. In addition, CCT3 promoted cell cycle progression and suppressed slc7a11-mediated cell ferroptosis, but not apoptosis. We also found that CCT3 activated AKT. MK2206 significantly reduced the viability of CCT3 overexpressed LUAD cells, while had smaller inhibitory effect on the proliferation of control cells, suggesting that CCT3 dictates the sensitivity of LUAD cells to AKT inhibition. Conclusion Our study demonstrates that CCT3 contributes to the proliferation and growth of LUAD cells through inhibition of ferroptosis and activation of AKT. Supplementary Information The online version contains supplementary material available at 10.1186/s12860-022-00424-7.
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Affiliation(s)
- Kun Wang
- Yunnan Kungang Hospital, Kunming Fourth People's Hospital, Seventh Affiliated Hospital of Dali University, No 9. Ganghe south Road, Anning City, Kunming, 650301, China
| | - Jian He
- Yunnan Kungang Hospital, Kunming Fourth People's Hospital, Seventh Affiliated Hospital of Dali University, No 9. Ganghe south Road, Anning City, Kunming, 650301, China
| | - Changling Tu
- The Third Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Hui Xu
- Yunnan Kungang Hospital, Kunming Fourth People's Hospital, Seventh Affiliated Hospital of Dali University, No 9. Ganghe south Road, Anning City, Kunming, 650301, China
| | - Xugang Zhang
- Yunnan Kungang Hospital, Kunming Fourth People's Hospital, Seventh Affiliated Hospital of Dali University, No 9. Ganghe south Road, Anning City, Kunming, 650301, China
| | - Yongchang Lv
- Yunnan Kungang Hospital, Kunming Fourth People's Hospital, Seventh Affiliated Hospital of Dali University, No 9. Ganghe south Road, Anning City, Kunming, 650301, China
| | - Chao Song
- Yunnan Kungang Hospital, Kunming Fourth People's Hospital, Seventh Affiliated Hospital of Dali University, No 9. Ganghe south Road, Anning City, Kunming, 650301, China.
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Ghozlan H, Cox A, Nierenberg D, King S, Khaled AR. The TRiCky Business of Protein Folding in Health and Disease. Front Cell Dev Biol 2022; 10:906530. [PMID: 35602608 PMCID: PMC9117761 DOI: 10.3389/fcell.2022.906530] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 04/20/2022] [Indexed: 01/03/2023] Open
Abstract
Maintenance of the cellular proteome or proteostasis is an essential process that when deregulated leads to diseases like neurological disorders and cancer. Central to proteostasis are the molecular chaperones that fold proteins into functional 3-dimensional (3D) shapes and prevent protein aggregation. Chaperonins, a family of chaperones found in all lineages of organisms, are efficient machines that fold proteins within central cavities. The eukaryotic Chaperonin Containing TCP1 (CCT), also known as Tailless complex polypeptide 1 (TCP-1) Ring Complex (TRiC), is a multi-subunit molecular complex that folds the obligate substrates, actin, and tubulin. But more than folding cytoskeletal proteins, CCT differs from most chaperones in its ability to fold proteins larger than its central folding chamber and in a sequential manner that enables it to tackle proteins with complex topologies or very large proteins and complexes. Unique features of CCT include an asymmetry of charges and ATP affinities across the eight subunits that form the hetero-oligomeric complex. Variable substrate binding capacities endow CCT with a plasticity that developed as the chaperonin evolved with eukaryotes and acquired functional capacity in the densely packed intracellular environment. Given the decades of discovery on the structure and function of CCT, much remains unknown such as the scope of its interactome. New findings on the role of CCT in disease, and potential for diagnostic and therapeutic uses, heighten the need to better understand the function of this essential molecular chaperone. Clues as to how CCT causes cancer or neurological disorders lie in the early studies of the chaperonin that form a foundational knowledgebase. In this review, we span the decades of CCT discoveries to provide critical context to the continued research on the diverse capacities in health and disease of this essential protein-folding complex.
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Affiliation(s)
- Heba Ghozlan
- Division of Cancer Research, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, United States
- Department of Physiology and Biochemistry, Jordan University of Science and Technology, Irbid, Jordan
| | - Amanda Cox
- Division of Cancer Research, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, United States
| | - Daniel Nierenberg
- Division of Cancer Research, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, United States
| | - Stephen King
- Division of Neuroscience, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, United States
| | - Annette R. Khaled
- Division of Cancer Research, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, United States
- *Correspondence: Annette R. Khaled,
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Lim Y, Gang DY, Lee WY, Yun SH, Cho YB, Huh JW, Park YA, Kim HC. Proteomic identification of arginine-methylated proteins in colon cancer cells and comparison of messenger RNA expression between colorectal cancer and adjacent normal tissues. Ann Coloproctol 2022:ac.2020.00899.0128. [PMID: 35081685 PMCID: PMC8898628 DOI: 10.3393/ac.2020.00899.0128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 06/29/2021] [Indexed: 11/12/2022] Open
Abstract
Purpose Identification of type I protein arginine methyltransferase (PRMT) substrates and their functional significance during tumorigenesis is becoming more important. The present study aimed to identify target substrates for type I PRMT using 2-dimensional (2D) gel electrophoresis (GE) and 2D Western blotting (WB). Methods Using immunoblot analysis, we compared the expression of type I PRMTs and endogenous levels of arginine methylation between the primary colorectal cancer (CRC) and adjacent noncancerous tissues paired from the same patient. To identify arginine-methylated proteins in HCT116 cells, we carried out 2D-GE and 2D-WB with a type I PRMT product-specific antibody (anti-dimethyl-arginine antibody, asymmetric [ASYM24]). Arginine-methylated protein spots were identified by mass spectrometry, and messenger RNA (mRNA) levels corresponding to the identified proteins were analyzed using National Center for Biotechnology Information (NCBI) microarray datasets between the primary CRC and noncancerous tissues. Results Type I PRMTs and methylarginine-containing proteins were highly maintained in CRC tissues compared to noncancerous tissues. We matched 142 spots using spot analysis software between a Coomassie blue (CBB)-stained 2D gel and 2D-WB, and we successfully identified 7 proteins that reacted with the ASYM24 antibody: CACYBP, GLOD4, MAPRE1, CCT7, TKT, CK8, and HSPA8. Among these proteins, the levels of 4 mRNAs including MAPRE1, CCT7, TKT, and HSPA8 in CRC tissues showed a statistically significant increase compared to noncancerous tissues from patients using the NCBI microarray datasets. Conclusion Our results indicate that the method shown here is useful in identifying arginine-methylated proteins, and significance of arginine modification in the proteins identified here should be further identified during CRC development.
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Affiliation(s)
- Yongchul Lim
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Da Young Gang
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Woo Yong Lee
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Seong Hyeon Yun
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Yong Beom Cho
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jung Wook Huh
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Yoon Ah Park
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hee Cheol Kim
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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Horovitz A, Reingewertz TH, Cuéllar J, Valpuesta JM. Chaperonin Mechanisms: Multiple and (Mis)Understood? Annu Rev Biophys 2022; 51:115-133. [DOI: 10.1146/annurev-biophys-082521-113418] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The chaperonins are ubiquitous and essential nanomachines that assist in protein folding in an ATP-driven manner. They consist of two back-to-back stacked oligomeric rings with cavities in which protein (un)folding can take place in a shielding environment. This review focuses on GroEL from Escherichia coli and the eukaryotic chaperonin-containing t-complex polypeptide 1, which differ considerably in their reaction mechanisms despite sharing a similar overall architecture. Although chaperonins feature in many current biochemistry textbooks after being studied intensively for more than three decades, key aspects of their reaction mechanisms remain under debate and are discussed in this review. In particular, it is unclear whether a universal reaction mechanism operates for all substrates and whether it is passive, i.e., aggregation is prevented but the folding pathway is unaltered, or active. It is also unclear how chaperonin clients are distinguished from nonclients and what are the precise roles of the cofactors with which chaperonins interact. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Amnon Horovitz
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel; Amnon.H
| | - Tali Haviv Reingewertz
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel; Amnon.H
| | - Jorge Cuéllar
- Department of Macromolecular Structure, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - José María Valpuesta
- Department of Macromolecular Structure, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
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Pandey A, Rajesh M, Baral P, Sarma D, Tripathi PH, Akhtar MS, Ciji A, Dubey MK, Pande V, Sharma P, Kamalam BS. Concurrent changes in thermal tolerance thresholds and cellular heat stress response reveals novel molecular signatures and markers of high temperature acclimation in rainbow trout. J Therm Biol 2021; 102:103124. [PMID: 34863487 DOI: 10.1016/j.jtherbio.2021.103124] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 10/27/2021] [Accepted: 10/30/2021] [Indexed: 01/31/2023]
Abstract
The objective of this study was to better understand the molecular mechanisms which regulate acclimatory responses and thermal safety margins of rainbow trout (Oncorhynchus mykiss) at temperatures above physiological optimum. For this, we investigated the time course of changes in critical thermal tolerance thresholds and associated hepatic and renal transcript abundance of molecular markers related to cellular stress response, during high temperature acclimation. The experimental fish were initially acclimated to 17 °C and later exposed to a gradually raised elevated temperature regime (22 °C) for a period of 30 days. CTmax, CTmin and mRNA expression of candidate markers were examined before the thermal challenge (T0) and over the time-course (days) of high temperature exposure (T1, T3, T7, T15 and T30). With respect to organismal response, CTmax was significantly elevated at T3, but the degree of gain in heat tolerance was not persistent. Contrarily, we observed a gradual loss in cold tolerance with highest CTmin estimate at T30. Based on the time-course of mRNA expression, the studied markers could be categorized into those which were persistently elevated (hsp70a, hsp70b, hspa5, hsp90a, hsp90b, stip1 and serpinh1 in kidney and hsp90b in liver); those which concurred with changes in CTmin (hspbp1, hsp90b, stip1, gr1, hif1a, hyou1, tnfa and tlr5 in kidney); and those which concurred with changes in CTmax (hsp90a, serpinh1, tlr5 and lmo2 in liver). Apparently, transcriptional changes in kidney and liver reflected CTmin and CTmax trend, respectively. Expression profile of stip1 and tlr5 suggest that they are potential novel markers which could reflect thermal limits in rainbow trout. Hepatic metabolic markers were either initially elevated (alt, glud, g6pase1) or down-regulated at different time-points (ast2, gls1, fas, cpt1b, mtor), linked to gluconeogenesis and metabolic depression, respectively. Whereas, growth-axis markers showed no significant differences. Overall, this time-course analysis has revealed potential associations in organismal and tissue-specific cellular response to high temperature acclimation in a thermally sensitive coldwater ectotherm.
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Affiliation(s)
- Anupam Pandey
- ICAR-Directorate of Coldwater Fisheries Research, Bhimtal, 263136, Uttarakhand, India; Department of Biotechnology, Kumaun University, Bhimtal, 263136, Uttarakhand, India
| | - Manchi Rajesh
- ICAR-Directorate of Coldwater Fisheries Research, Bhimtal, 263136, Uttarakhand, India
| | - Pratibha Baral
- ICAR-Directorate of Coldwater Fisheries Research, Bhimtal, 263136, Uttarakhand, India
| | - Debajit Sarma
- ICAR-Directorate of Coldwater Fisheries Research, Bhimtal, 263136, Uttarakhand, India
| | - Priyanka H Tripathi
- ICAR-Directorate of Coldwater Fisheries Research, Bhimtal, 263136, Uttarakhand, India; Department of Biotechnology, Kumaun University, Bhimtal, 263136, Uttarakhand, India
| | - Md Shahbaz Akhtar
- ICAR-Directorate of Coldwater Fisheries Research, Bhimtal, 263136, Uttarakhand, India
| | - Alexander Ciji
- ICAR-Directorate of Coldwater Fisheries Research, Bhimtal, 263136, Uttarakhand, India
| | - Maneesh Kumar Dubey
- ICAR-Directorate of Coldwater Fisheries Research, Bhimtal, 263136, Uttarakhand, India
| | - Veena Pande
- Department of Biotechnology, Kumaun University, Bhimtal, 263136, Uttarakhand, India
| | - Prakash Sharma
- ICAR-Directorate of Coldwater Fisheries Research, Bhimtal, 263136, Uttarakhand, India
| | - Biju Sam Kamalam
- ICAR-Directorate of Coldwater Fisheries Research, Bhimtal, 263136, Uttarakhand, India.
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Identification of CCT3 as a prognostic factor and correlates with cell survival and invasion of head and neck squamous cell carcinoma. Biosci Rep 2021; 41:229752. [PMID: 34505628 PMCID: PMC8529339 DOI: 10.1042/bsr20211137] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 08/24/2021] [Accepted: 08/26/2021] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Recurrent locally advanced or metastatic head and neck squamous cell carcinoma (HNSCC) is associated with dismal prognosis because of its highly invasive behavior and resistance to conventional intensive chemotherapy. The identification of effective markers for early diagnosis and prognosis is important for reducing mortality and ensuring that therapy for HNSCC is effective. Chaperonin-containing TCP-1 3 (CCT3) folds cancer-related proteins to control carcinogenesis. The prognostic value and growth association of CCT3 and HNSCC remain unknown. METHODS The GEO, Oncomine and UALCAN databases were used to examine CCT3 expression in HNSCC. A few clinical HNSCC samples with normal tissues were used to detect CCT3 expression by using immunohistochemistry method. The TCGA-HNSC dataset was used to evaluate the association between expression of CCT3 and prognosis. The molecular mechanism was investigated with gene set enrichment analysis (GSEA). CCK-8 and wound healing assays were used to detect cell growth and invasion of HNSCC, respectively. RESULTS CCT3 expression was significantly up-regulated in HNSCC in both mRNA and protein levels. In addition, up-regulated CCT3 expression was associated with various clinicopathological parameters. High expression of CCT3 was significantly correlated with inferior survival of HNSCC patients. Knockdown of CCT3 significantly inhibited cell growth and invasion of HNSCC cell lines. GSEA analysis indicated that CCT3 was closely correlated with tumor-related signaling pathways and HNSCC cell survival. CONCLUSION Our findings suggest that CCT3 is a biomarker of poor prognosis and related to the process of HNSCC.
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Novel Binding Partners for CCT and PhLP1 Suggest a Common Folding Mechanism for WD40 Proteins with a 7-Bladed Beta-Propeller Structure. Proteomes 2021; 9:proteomes9040040. [PMID: 34698247 PMCID: PMC8544692 DOI: 10.3390/proteomes9040040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 09/15/2021] [Accepted: 09/27/2021] [Indexed: 11/25/2022] Open
Abstract
This study investigates whether selected WD40 proteins with a 7-bladed β-propeller structure, similar to that of the β subunit of the G protein heterotrimer, interact with the cytosolic chaperonin CCT and its known binding partner, PhLP1. Previous studies have shown that CCT is required for the folding of the Gβ subunit and other WD40 proteins. The role of PhLP1 in the folding of Gβ has also been established, but it is unknown if PhLP1 assists in the folding of other Gβ-like proteins. The binding of three Gβ-like proteins, TBL2, MLST8 and CDC20, to CCT and PhLP1, was demonstrated in this study. Co-immunoprecipitation assays identified one novel binding partner for CCT and three new interactors for PhLP1. All three of the studied proteins interact with CCT and PhLP1, suggesting that these proteins may have a folding machinery in common with that of Gβ and that the well-established Gβ folding mechanism may have significantly broader biological implications than previously thought. These findings contribute to continuous efforts to determine common traits and unique differences in the folding mechanism of the WD40 β-propeller protein family, and the role PhLP1 has in this process.
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Yang P, Tang W, Li H, Hua R, Yuan Y, Zhang Y, Zhu Y, Cui Y, Sha J. T-complex protein 1 subunit zeta-2 (CCT6B) deficiency induces murine teratospermia. PeerJ 2021; 9:e11545. [PMID: 34141486 PMCID: PMC8176918 DOI: 10.7717/peerj.11545] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/11/2021] [Indexed: 12/13/2022] Open
Abstract
Background The CCT complex is an important mediator of microtubule assembly and intracellular protein folding. Owing to its high expression in spermatids, CCT knockdown can disrupt spermatogenesis. In the present report, we therefore evaluated the in vivo functionality of the testis-specific CCT complex component CCT6B using a murine knockout model system. Methods A CRISPR/Cas9 approach was used to generate Cct6b−/− mice, after which candidate gene expression in these animals was evaluated via qPCR and Western blotting. Testicular and epididymal phenotypes were assessed through histological and immunofluorescent staining assays, while a computer-assisted sperm analyzer was employed to assess semen quality. Results Cct6b−/− mice were successfully generated, and exhibited no differences in development, fertility, appearance, testis weight, or sperm counts relative to control littermates. In addition, no differences in spermatogenesis were detected when comparingCct6b+/+ and Cct6b−/− testes. However, when progressive motility was analyzed, the ratio of normal sperm was significantly decreased in Cct6b−/− male mice, with nuclear base bending being the primary detected abnormality. In addition, slight decreases in Cct4 and Cct7 expression were detected. Conclusion These data indicated that CCT6B is an important regulator of murine spermatogenesis, with the loss of this protein resulting in CCT complex dysfunction, providing a foundation for further studies.
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Affiliation(s)
- Peiyin Yang
- Department of Histology and Embryology, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Wenjing Tang
- Department of Histology and Embryology, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Huiling Li
- Department of Histology and Embryology, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Rong Hua
- Department of Histology and Embryology, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yan Yuan
- Department of Histology and Embryology, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yue Zhang
- Department of Histology and Embryology, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yunfei Zhu
- Department of Histology and Embryology, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yiqiang Cui
- Department of Histology and Embryology, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jiahao Sha
- Department of Histology and Embryology, Nanjing Medical University, Nanjing, Jiangsu, China
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Contu L, Balistreri G, Domanski M, Uldry AC, Mühlemann O. Characterisation of the Semliki Forest Virus-host cell interactome reveals the viral capsid protein as an inhibitor of nonsense-mediated mRNA decay. PLoS Pathog 2021; 17:e1009603. [PMID: 34019569 PMCID: PMC8174725 DOI: 10.1371/journal.ppat.1009603] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 06/03/2021] [Accepted: 05/03/2021] [Indexed: 01/08/2023] Open
Abstract
The positive-sense, single-stranded RNA alphaviruses pose a potential epidemic threat. Understanding the complex interactions between the viral and the host cell proteins is crucial for elucidating the mechanisms underlying successful virus replication strategies and for developing specific antiviral interventions. Here we present the first comprehensive protein-protein interaction map between the proteins of Semliki Forest Virus (SFV), a mosquito-borne member of the alphaviruses, and host cell proteins. Among the many identified cellular interactors of SFV proteins, the enrichment of factors involved in translation and nonsense-mediated mRNA decay (NMD) was striking, reflecting the virus' hijacking of the translation machinery and indicating viral countermeasures for escaping NMD by inhibiting NMD at later time points during the infectious cycle. In addition to observing a general inhibition of NMD about 4 hours post infection, we also demonstrate that transient expression of the SFV capsid protein is sufficient to inhibit NMD in cells, suggesting that the massive production of capsid protein during the SFV reproduction cycle is responsible for NMD inhibition.
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Affiliation(s)
- Lara Contu
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Giuseppe Balistreri
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Michal Domanski
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Anne-Christine Uldry
- Proteomics & Mass Spectrometry Core Facility, Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Oliver Mühlemann
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
- * E-mail:
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Wang L, Zhou W, Li H, Yang H, Shan N. Clinical Significance, Cellular Function, and Potential Molecular Pathways of CCT7 in Endometrial Cancer. Front Oncol 2020; 10:1468. [PMID: 32983981 PMCID: PMC7483479 DOI: 10.3389/fonc.2020.01468] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 07/09/2020] [Indexed: 12/24/2022] Open
Abstract
Objective: Endometrial cancer (EC) is a common gynecologic malignancy; myometrial invasion (MI) is a typical approach of EC spreads and an important index to assess tumor metastasis and outcome in EC patients. CCT7 is a member of the TCP1 chaperone family, involved in cytoskeletal protein folding and unfolding. In this study, the role of CCT7 in EC development was investigated. Methods: Clinical data for 87 EC cases and expression of CCT7 were analyzed. CCT7 was knocked out using siRNA-CCT7 in Ishikawa and RL95-2 cells, and their function about proliferation, apoptosis, and invasion was further tested. Bioinformatics methods were used to predict the potential pathways of CCT7 in EC development. Results: The rates of CCT7-positive cells in EC and adjacent normal endometrium tissues had a significant difference (67.8 vs. 51.4%, p = 0.035), and the expression rate increased from low to high pathological stage (39.7% in the I/II stage, 71.4% in the III/IV stage, p = 0.029). A similar change was found in protein level. CCT7 expression differed significantly between the deep MI group (>1/2) and the superficial MI group (≤1/2) (p = 0.039). However, there were no differences with respect to age, pathological type, and histological grade. CCT7 suppression induced a function loss in both Ishikawa and RL95-2 cells. Bioinformatics analysis demonstrated that EC patients with lower-level CCT7 expression had better overall survival (p = 0.0081). Gene ontology enrichment indicated that "RNA binding," "Mitochondrion," "Translation," and "Spliceosome" were most significantly enriched potential pathways. Five hub genes, PSMA5, PSMD14, SNRPB, SNRPG, and TXNL4A, were all significantly upregulated in EC and had a positive correlation with CCT7. Conclusions: CCT7 may be involved in EC development by excessively activating tumor cell function to promote MI or distant/nodal metastasis, which may contribute to the prognosis of EC patients.
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Affiliation(s)
- Liwen Wang
- Department of Gynecology and Obstetrics, Xiangya Hospital, Central South University, Changsha, China
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Wei Zhou
- Department of Gynecology and Obstetrics, Xiangya Hospital, Central South University, Changsha, China
| | - Hui Li
- Xiangya School of Medicine, Central South University, Changsha, China
- Department of Reproductive, Xiangya Hospital, Central South University, Changsha, China
| | - Hui Yang
- Department of Gynecology and Obstetrics, Xiangya Hospital, Central South University, Changsha, China
| | - Nianchun Shan
- Department of Gynecology and Obstetrics, Xiangya Hospital, Central South University, Changsha, China
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Suppression of CCT3 inhibits the proliferation and migration in breast cancer cells. Cancer Cell Int 2020; 20:218. [PMID: 32518527 PMCID: PMC7275521 DOI: 10.1186/s12935-020-01314-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 06/01/2020] [Indexed: 12/12/2022] Open
Abstract
Background CCT3 is a subunit of chaperonin-containing TCP-1 (CCT), which folds many proteins involved in cancer development and plays an important role in many cancers. However, the role of CCT3 in breast cancer is still unclear. Methods CCT3 expression was knocked down by transfecting breast cancer cells with lentiviral shRNA. The proliferation of breast cancer cells (HCC1937 and MDA-MB-231) was detected by Celigo image cytometry and MTT assay, the migration of the cells was measured by Transwell analysis, cell cycle distribution and apoptosis was detected by flow cytometry, and changes in signal transduction proteins were detected by western blot analysis. Results The expression of CCT3 was significantly suppressed by transduction with lentiviral shRNA; CCT3 knockdown significantly reduced the proliferation and metastasis ability of breast cancer cells (HCC 1937 and MDA-MB-231), increased the proportion of cells in S phase, and decreased the proportion of cells in G1 phase compared to those in shControl cells. There was no significant change in the number of cells in the G2/M phase. Apoptosis analysis showed that knockdown of CCT3 induced apoptosis in breast cancer cells. Western blot analysis showed that the expression of many signal transduction proteins was changed after suppression of CCT3. A rescue experiment showed that overexpression of NFκB-p65 rescued the cell proliferation and migration affected by CCT3 in breast cancer cells. Conclusion CCT3 is closely related to the proliferation and migration of breast cancer and may be a novel therapeutic target.
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Nucleus-specific linker histones Hho1 and Mlh1 form distinct protein interactions during growth, starvation and development in Tetrahymena thermophila. Sci Rep 2020; 10:168. [PMID: 31932604 PMCID: PMC6957481 DOI: 10.1038/s41598-019-56867-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 11/14/2019] [Indexed: 02/07/2023] Open
Abstract
Chromatin organization influences most aspects of gene expression regulation. The linker histone H1, along with the core histones, is a key component of eukaryotic chromatin. Despite its critical roles in chromatin structure and function and gene regulation, studies regarding the H1 protein-protein interaction networks, particularly outside of Opisthokonts, are limited. The nuclear dimorphic ciliate protozoan Tetrahymena thermophila encodes two distinct nucleus-specific linker histones, macronuclear Hho1 and micronuclear Mlh1. We used a comparative proteomics approach to identify the Hho1 and Mlh1 protein-protein interaction networks in Tetrahymena during growth, starvation, and sexual development. Affinity purification followed by mass spectrometry analysis of the Hho1 and Mlh1 proteins revealed a non-overlapping set of co-purifying proteins suggesting that Tetrahymena nucleus-specific linker histones are subject to distinct regulatory pathways. Furthermore, we found that linker histones interact with distinct proteins under the different stages of the Tetrahymena life cycle. Hho1 and Mlh1 co-purified with several Tetrahymena-specific as well as conserved interacting partners involved in chromatin structure and function and other important cellular pathways. Our results suggest that nucleus-specific linker histones might be subject to nucleus-specific regulatory pathways and are dynamically regulated under different stages of the Tetrahymena life cycle.
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Structural and functional analysis of the role of the chaperonin CCT in mTOR complex assembly. Nat Commun 2019; 10:2865. [PMID: 31253771 PMCID: PMC6599039 DOI: 10.1038/s41467-019-10781-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 06/01/2019] [Indexed: 01/01/2023] Open
Abstract
The mechanistic target of rapamycin (mTOR) kinase forms two multi-protein signaling complexes, mTORC1 and mTORC2, which are master regulators of cell growth, metabolism, survival and autophagy. Two of the subunits of these complexes are mLST8 and Raptor, β-propeller proteins that stabilize the mTOR kinase and recruit substrates, respectively. Here we report that the eukaryotic chaperonin CCT plays a key role in mTORC assembly and signaling by folding both mLST8 and Raptor. A high resolution (4.0 Å) cryo-EM structure of the human mLST8-CCT intermediate isolated directly from cells shows mLST8 in a near-native state bound to CCT deep within the folding chamber between the two CCT rings, and interacting mainly with the disordered N- and C-termini of specific CCT subunits of both rings. These findings describe a unique function of CCT in mTORC assembly and a distinct binding site in CCT for mLST8, far from those found for similar β-propeller proteins. β-propeller domains are an important class of folding substrates for the eukaryotic cytosolic chaperonin CTT. Here the authors find that CTT contributes to the folding and assembly of two β-propeller proteins from mTOR complexes, mLST8 and Raptor, and determine the 4.0 Å cryoEM structure of a human mLST8-CCT intermediate that shows mLST8 in a near-native state.
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Si FL, Qiao L, He QY, Zhou Y, Yan ZT, Chen B. HSP superfamily of genes in the malaria vector Anopheles sinensis: diversity, phylogenetics and association with pyrethroid resistance. Malar J 2019; 18:132. [PMID: 30975215 PMCID: PMC6460852 DOI: 10.1186/s12936-019-2770-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 04/06/2019] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Heat shock proteins (HSPs) are molecular chaperones that are involved in many normal cellular processes and various kinds of environmental stress. There is still no report regarding the diversity and phylogenetics research of HSP superfamily of genes at whole genome level in insects, and the HSP gene association with pyrethroid resistance is also not well known. The present study investigated the diversity, classification, scaffold location, characteristics, and phylogenetics of the superfamily of genes in Anopheles sinensis genome, and the HSP genes associated with pyrethroid resistance. METHODS The present study identified the HSP genes in the An. sinensis genome, analysed their characteristics, and deduced phylogenetic relationships of all HSPs in An. sinensis, Anopheles gambiae, Culex quinquefasciatus and Aedes aegypti by bioinformatic methods. Importantly, the present study screened the HSPs associated with pyrethroid resistance using three field pyrethroid-resistant populations with RNA-seq and RT-qPCR, and looked over the HSP gene expression pattern for the first time in An. sinensis on the time-scale post insecticide treatment with RT-qPCR. RESULTS There are 72 HSP genes in An. sinensis genome, and they are classified into five families and 11 subfamilies based on their molecular weight, homology and phylogenetics. Both RNA-seq and qPCR analysis revealed that the expression of AsHSP90AB, AsHSP70-2 and AsHSP21.7 are significantly upregulated in at least one field pyrethroid-resistant population. Eleven genes are significantly upregulated in different period after pyrethroid exposure. The HSP90, sHSP and HSP70 families are proposed to be involved in pyrethroid stress response based in expression analyses of three field pyrethroid-resistant populations, and expression pattern on the time scale post insecticide treatment. The AsHSP90AB gene is proposed to be the essential HSP gene for pyrethroid stress response in An. sinensis. CONCLUSIONS This study provides the information frame for HSP superfamily of genes, and lays an important basis for the better understanding and further research of HSP function in insect adaptability to diverse environments.
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Affiliation(s)
- Feng-Ling Si
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Chongqing Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, Chongqing Normal University, Chongqing, 401331, China
| | - Liang Qiao
- Chongqing Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, Chongqing Normal University, Chongqing, 401331, China
| | - Qi-Yi He
- Chongqing Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, Chongqing Normal University, Chongqing, 401331, China
| | - Yong Zhou
- Chongqing Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, Chongqing Normal University, Chongqing, 401331, China
| | - Zhen-Tian Yan
- Chongqing Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, Chongqing Normal University, Chongqing, 401331, China
| | - Bin Chen
- Chongqing Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, Chongqing Normal University, Chongqing, 401331, China.
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Willison KR. The substrate specificity of eukaryotic cytosolic chaperonin CCT. Philos Trans R Soc Lond B Biol Sci 2019; 373:rstb.2017.0192. [PMID: 29735743 DOI: 10.1098/rstb.2017.0192] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/12/2018] [Indexed: 12/22/2022] Open
Abstract
The cytosolic chaperonin CCT (chaperonin containing TCP-1) is an ATP-dependent double-ring protein machine mediating the folding of members of the eukaryotic cytoskeletal protein families. The actins and tubulins are obligate substrates of CCT because they are completely dependent on CCT activity to reach their native states. Genetic and proteomic analysis of the CCT interactome in the yeast Saccharomyces cerevisiae revealed a CCT network of approximately 300 genes and proteins involved in many fundamental biological processes. We classified network members into sets such as substrates, CCT cofactors and CCT-mediated assembly processes. Many members of the 7-bladed propeller family of proteins are commonly found tightly bound to CCT isolated from human and plant cells and yeasts. The anaphase promoting complex (APC/C) cofactor propellers, Cdh1p and Cdc20p, are also obligate substrates since they both require CCT for folding and functional activation. In vitro translation analysis in prokaryotic and eukaryotic cell extracts of a set of yeast propellers demonstrates their highly differential interactions with CCT and GroEL (another chaperonin). Individual propeller proteins have idiosyncratic interaction modes with CCT because they emerged independently with neo-functions many times throughout eukaryotic evolution. We present a toy model in which cytoskeletal protein biogenesis and folding flux through CCT couples cell growth and size control to time dependent cell cycle mechanisms.This article is part of a discussion meeting issue 'Allostery and molecular machines'.
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Affiliation(s)
- Keith R Willison
- Department of Chemistry, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
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Yusof NA, Kamaruddin S, Abu Bakar FD, Mahadi NM, Abdul Murad AM. Structural and functional insights into TRiC chaperonin from a psychrophilic yeast, Glaciozyma antarctica. Cell Stress Chaperones 2019; 24:351-368. [PMID: 30649671 PMCID: PMC6439030 DOI: 10.1007/s12192-019-00969-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 01/04/2019] [Accepted: 01/08/2019] [Indexed: 12/29/2022] Open
Abstract
Studies on TCP1-1 ring complex (TRiC) chaperonin have shown its indispensable role in folding cytosolic proteins in eukaryotes. In a psychrophilic organism, extreme cold temperature creates a low-energy environment that potentially causes protein denaturation with loss of activity. We hypothesized that TRiC may undergo evolution in terms of its structural molecular adaptation in order to facilitate protein folding in low-energy environment. To test this hypothesis, we isolated G. antarctica TRiC (GaTRiC) and found that the expression of GaTRiC mRNA in G. antarctica was consistently expressed at all temperatures indicating their importance in cell regulation. Moreover, we showed GaTRiC has the ability of a chaperonin whereby denatured luciferase can be folded to the functional stage in its presence. Structurally, three categories of residue substitutions were found in α, β, and δ subunits: (i) bulky/polar side chains to alanine or valine, (ii) charged residues to alanine, and (iii) isoleucine to valine that would be expected to increase intramolecular flexibility within the GaTRiC. The residue substitutions observed in the built structures possibly affect the hydrophobic, hydrogen bonds, and ionic and aromatic interactions which lead to an increase in structural flexibility. Our structural and functional analysis explains some possible structural features which may contribute to cold adaptation of the psychrophilic TRiC folding chamber.
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Affiliation(s)
- Nur Athirah Yusof
- Biotechnology Research Institute, Universiti Malaysia Sabah, 88400, Kota Kinabalu, Sabah, Malaysia.
| | - Shazilah Kamaruddin
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Farah Diba Abu Bakar
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Nor Muhammad Mahadi
- Malaysia Genome Institute, Jalan Bangi, 43000, Kajang, Selangor Darul Ehsan, Malaysia
| | - Abdul Munir Abdul Murad
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
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Proteomic analysis of protein homeostasis and aggregation. J Proteomics 2018; 198:98-112. [PMID: 30529741 DOI: 10.1016/j.jprot.2018.12.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 11/24/2018] [Accepted: 12/05/2018] [Indexed: 12/13/2022]
Abstract
Protein homeostasis (proteostasis) refers to the ability of cells to preserve the correct balance between protein synthesis, folding and degradation. Proteostasis is essential for optimal cell growth and survival under stressful conditions. Various extracellular and intracellular stresses including heat shock, oxidative stress, proteasome malfunction, mutations and aging-related modifications can result in disturbed proteostasis manifested by enhanced misfolding and aggregation of proteins. To limit protein misfolding and aggregation cells have evolved various strategies including molecular chaperones, proteasome system and autophagy. Molecular chaperones assist folding of proteins, protect them from denaturation and facilitate renaturation of the misfolded polypeptides, whereas proteasomes and autophagosomes remove the irreversibly damaged proteins. The impairment of proteostasis results in protein aggregation that is a major pathological hallmark of numerous age-related disorders, such as cataract, Alzheimer's, Parkinson's, Huntington's, and prion diseases. To discover protein markers and speed up diagnosis of neurodegenerative diseases accompanied by protein aggregation, proteomic tools have increasingly been used in recent years. Systematic and exhaustive analysis of the changes that occur in the proteomes of affected tissues and biofluids in humans or in model organisms is one of the most promising approaches to reveal mechanisms underlying protein aggregation diseases, improve their diagnosis and develop therapeutic strategies. Significance: In this review we outline the elements responsible for maintaining cellular proteostasis and present the overview of proteomic studies focused on protein-aggregation diseases. These studies provide insights into the mechanisms responsible for age-related disorders and reveal new potential biomarkers for Alzheimer's, Parkinson's, Huntigton's and prion diseases.
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Sokolov M, Yadav RP, Brooks C, Artemyev NO. Chaperones and retinal disorders. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2018; 114:85-117. [PMID: 30635087 DOI: 10.1016/bs.apcsb.2018.09.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Defects in protein folding and trafficking are a common cause of photoreceptor degeneration, causing blindness. Photoreceptor cells present an unusual challenge to the protein folding and transport machinery due to the high rate of protein synthesis, trafficking and the renewal of the outer segment, a primary cilium that has been modified into a specialized light-sensing compartment. Phototransduction components, such as rhodopsin and cGMP-phosphodiesterase, and multimeric ciliary transport complexes, such as the BBSome, are hotspots for mutations that disrupt proteostasis and lead to the death of photoreceptors. In this chapter, we review recent studies that advance our understanding of the chaperone and transport machinery of phototransduction proteins.
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Affiliation(s)
- Maxim Sokolov
- Department of Ophthalmology, West Virginia University, Morgantown, WV, United States
| | - Ravi P Yadav
- Department of Molecular Physiology and Biophysics, The University of Iowa Carver College of Medicine, Iowa City, IA, United States
| | - Celine Brooks
- Department of Ophthalmology, West Virginia University, Morgantown, WV, United States
| | - Nikolai O Artemyev
- Department of Molecular Physiology and Biophysics, The University of Iowa Carver College of Medicine, Iowa City, IA, United States; Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA, United States.
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26
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Wang H, Han W, Takagi J, Cong Y. Yeast Inner-Subunit PA–NZ-1 Labeling Strategy for Accurate Subunit Identification in a Macromolecular Complex through Cryo-EM Analysis. J Mol Biol 2018; 430:1417-1425. [DOI: 10.1016/j.jmb.2018.03.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 03/14/2018] [Accepted: 03/25/2018] [Indexed: 12/25/2022]
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27
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Zang Y, Wang H, Cui Z, Jin M, Liu C, Han W, Wang Y, Cong Y. Development of a yeast internal-subunit eGFP labeling strategy and its application in subunit identification in eukaryotic group II chaperonin TRiC/CCT. Sci Rep 2018; 8:2374. [PMID: 29403048 PMCID: PMC5799240 DOI: 10.1038/s41598-017-18962-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/18/2017] [Indexed: 11/23/2022] Open
Abstract
Unambiguous subunit assignment in a multicomponent complex is critical for thorough understanding of the machinery and its functionality. The eukaryotic group II chaperonin TRiC/CCT folds approximately 10% of cytosolic proteins and is important for the maintenance of cellular homeostasis. TRiC consists of two rings and each ring has eight homologous but distinct subunits. Unambiguous subunit identification of a macromolecular machine such as TRiC through intermediate or low-resolution cryo-EM map remains challenging. Here we present a yeast internal-subunit eGFP labeling strategy termed YISEL, which can quickly introduce an eGFP tag in the internal position of a target subunit by homologous recombination, and the tag labeled protein can be expressed in endogenous level. Through this method, the labeling efficiency and tag-occupancy is ensured, and the inserted tag is usually less mobile compared to that fused to the terminus. It can also be used to bio-engineer other tag in the internal position of a protein in yeast. By applying our YISEL strategy and combined with cryo-EM 3D reconstruction, we unambiguously identified all the subunits in the cryo-EM map of TRiC, demonstrating the potential for broad application of this strategy in accurate and efficient subunit identification in other challenging complexes.
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Affiliation(s)
- Yunxiang Zang
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Huping Wang
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Zhicheng Cui
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Mingliang Jin
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Caixuan Liu
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Wenyu Han
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yanxing Wang
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.,Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Yao Cong
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China. .,Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai, China.
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28
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Nusrat S, Khan RH. Exploration of ligand-induced protein conformational alteration, aggregate formation, and its inhibition: A biophysical insight. Prep Biochem Biotechnol 2018; 48:43-56. [PMID: 29106330 DOI: 10.1080/10826068.2017.1387561] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The association of protein aggregates with plentiful human diseases has fascinated studies regarding the biophysical characterization of protein misfolding and ultimately their aggregate formation mechanism. Protein-ligand interaction, their mechanism, conformational changes by ligands, and protein aggregate formation have been studied upon exploiting experimental techniques and computational methodologies. Such studies for the exploration of ligand-induced conformational changes in protein, misfolding and aggregation, has confirmed drastic progresses in the study of aggregate formation pathways. This review comprises of an inclusive description of contemporary experimental techniques as well as theoretical improvements in the interpretation of the conformational properties of protein. We have also discussed various factors responsible for the microenvironment change around protein that sequentially causes amyloidoses. Biophysical techniques and cell-based assays to gain comprehensive understandings of protein-ligand interaction, protein folding, and aggregation pathways have also been described. The promising therapeutic methods used to inhibit the protein fibrillogenesis have also been discussed.
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Affiliation(s)
- Saima Nusrat
- a Interdisciplinary Biotechnology Unit , Aligarh Muslim University , Aligarh , Uttar Pradesh , India
| | - Rizwan Hasan Khan
- a Interdisciplinary Biotechnology Unit , Aligarh Muslim University , Aligarh , Uttar Pradesh , India
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29
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Counts JT, Hester TM, Rouhana L. Genetic expansion of chaperonin-containing TCP-1 (CCT/TRiC) complex subunits yields testis-specific isoforms required for spermatogenesis in planarian flatworms. Mol Reprod Dev 2017; 84:1271-1284. [PMID: 29095551 DOI: 10.1002/mrd.22925] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 10/16/2017] [Indexed: 12/23/2022]
Abstract
Chaperonin-containing Tail-less complex polypeptide 1 (CCT) is a highly conserved, hetero-oligomeric complex that ensures proper folding of actin, tubulin, and regulators of mitosis. Eight subunits (CCT1-8) make up this complex, and every subunit has a homolog expressed in the testes and somatic tissue of the planarian flatworm Schmidtea mediterranea. Gene duplications of four subunits in the genomes of S. mediterranea and other planarian flatworms created paralogs to CCT1, CCT3, CCT4, and CCT8 that are expressed exclusively in the testes. Functional analyses revealed that each CCT subunit expressed in the S. mediterranea soma is essential for homeostatic integrity and survival, whereas sperm elongation defects were observed upon knockdown of each individual testis-specific paralog (Smed-cct1B; Smed-cct3B; Smed-cct4A; and Smed-cct8B), regardless of potential redundancy with paralogs expressed in both testes and soma (Smed-cct1A; Smed-cct3A; Smed-cct4B; and Smed-cct8A). Yet, no detriment was observed in the number of adult somatic stem cells (neoblasts) that maintain differentiated tissue in planarians. Thus, expression of all eight CCT subunits is required to execute the essential functions of the CCT complex. Furthermore, expression of the somatic paralogs in planarian testes is not sufficient to complete spermatogenesis when testis-specific paralogs are knocked down, suggesting that the evolution of chaperonin subunits may drive changes in the development of sperm structure and that correct CCT subunit stoichiometry is crucial for spermiogenesis.
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Affiliation(s)
- Jenna T Counts
- Department of Biological Sciences, Wright State University, Dayton, Ohio
| | - Tasha M Hester
- Department of Biological Sciences, Wright State University, Dayton, Ohio
| | - Labib Rouhana
- Department of Biological Sciences, Wright State University, Dayton, Ohio
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30
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Zhao M, Spiess M, Johansson HJ, Olofsson H, Hu J, Lehtiö J, Strömblad S. Identification of the PAK4 interactome reveals PAK4 phosphorylation of N-WASP and promotion of Arp2/3-dependent actin polymerization. Oncotarget 2017; 8:77061-77074. [PMID: 29100370 PMCID: PMC5652764 DOI: 10.18632/oncotarget.20352] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Accepted: 07/25/2017] [Indexed: 12/14/2022] Open
Abstract
p21-activated kinase 4 (PAK4) regulates cell proliferation, apoptosis, cell motility and F-actin remodeling, but the PAK4 interactome has not been systematically analyzed. Here, we comprehensively characterized the human PAK4 interactome by iTRAQ quantitative mass spectrometry of PAK4-immunoprecipitations. Consistent with its multiple reported functions, the PAK4 interactome was enriched in diverse protein networks, including the 14-3-3, proteasome, replication fork, CCT and Arp2/3 complexes. Because PAK4 co-immunoprecipitated most subunits of the Arp2/3 complex, we hypothesized that PAK4 may play a role in Arp2/3 dependent actin regulation. Indeed, we found that PAK4 interacts with and phosphorylates the nucleation promoting factor N-WASP at Ser484/Ser485 and promotes Arp2/3-dependent actin polymerization in vitro. Also, PAK4 ablation in vivo reduced N-WASP Ser484/Ser485 phosphorylation and altered the cellular balance between G- and F-actin as well as the actin organization. By presenting the PAK4 interactome, we here provide a powerful resource for further investigations and as proof of principle, we also indicate a novel mechanism by which PAK4 regulates actin cytoskeleton remodeling.
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Affiliation(s)
- Miao Zhao
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Matthias Spiess
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Henrik J Johansson
- Cancer Proteomics Mass Spectrometry, Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Helene Olofsson
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Jianjiang Hu
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Janne Lehtiö
- Cancer Proteomics Mass Spectrometry, Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Staffan Strömblad
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
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31
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Rouhana L, Tasaki J, Saberi A, Newmark PA. Genetic dissection of the planarian reproductive system through characterization of Schmidtea mediterranea CPEB homologs. Dev Biol 2017; 426:43-55. [PMID: 28434803 PMCID: PMC5544531 DOI: 10.1016/j.ydbio.2017.04.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 03/30/2017] [Accepted: 04/18/2017] [Indexed: 01/30/2023]
Abstract
Cytoplasmic polyadenylation is a mechanism of mRNA regulation prevalent in metazoan germ cells; it is largely dependent on Cytoplasmic Polyadenylation Element Binding proteins (CPEBs). Two CPEB homologs were identified in the planarian Schmidtea mediterranea. Smed-CPEB1 is expressed in ovaries and yolk glands of sexually mature planarians, and required for oocyte and yolk gland development. In contrast, Smed-CPEB2 is expressed in the testes and the central nervous system; its function is required for spermatogenesis as well as non-autonomously for development of ovaries and accessory reproductive organs. Transcriptome analysis of CPEB knockdown animals uncovered a comprehensive collection of molecular markers for reproductive structures in S. mediterranea, including ovaries, testes, yolk glands, and the copulatory apparatus. Analysis by RNA interference revealed contributions for a dozen of these genes during oogenesis, spermatogenesis, or capsule formation. We also present evidence suggesting that Smed-CPEB2 promotes translation of Neuropeptide Y-8, a prohormone required for planarian sexual maturation. These findings provide mechanistic insight into potentially conserved processes of germ cell development, as well as events involved in capsule deposition by flatworms.
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Affiliation(s)
- Labib Rouhana
- Department of Biological Sciences, Wright State University, 3640 Colonel Glenn Highway, Dayton, OH 45435, USA; Howard Hughes Medical Institute and Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave., Urbana, IL 61801, USA.
| | - Junichi Tasaki
- Department of Biological Sciences, Wright State University, 3640 Colonel Glenn Highway, Dayton, OH 45435, USA
| | - Amir Saberi
- Howard Hughes Medical Institute and Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave., Urbana, IL 61801, USA
| | - Phillip A Newmark
- Howard Hughes Medical Institute and Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave., Urbana, IL 61801, USA
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32
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Génier S, Degrandmaison J, Moreau P, Labrecque P, Hébert TE, Parent JL. Regulation of GPCR expression through an interaction with CCT7, a subunit of the CCT/TRiC complex. Mol Biol Cell 2016; 27:3800-3812. [PMID: 27708139 PMCID: PMC5170604 DOI: 10.1091/mbc.e16-04-0224] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 09/22/2016] [Accepted: 09/26/2016] [Indexed: 12/25/2022] Open
Abstract
A direct and functional interaction between a subunit of the CCT/TCP-1 ring complex (TRiC) chaperonin complex and G protein–coupled receptor (GPCRs) is shown. Evidence is provided that distinct nascent GPCRs can undergo alternative folding pathways and that CCT/TRiC is critical in preventing aggregation of some GPCRs and in promoting their proper maturation and expression. Mechanisms that prevent aggregation and promote folding of nascent G protein–coupled receptors (GPCRs) remain poorly understood. We identified chaperonin containing TCP-1 subunit eta (CCT7) as an interacting partner of the β-isoform of thromboxane A2 receptor (TPβ) by yeast two-hybrid screening. CCT7 coimmunoprecipitated with overexpressed TPβ and β2-adrenergic receptor (β2AR) in HEK 293 cells, but also with endogenous β2AR. CCT7 depletion by small interfering RNA reduced total and cell-surface expression of both receptors and caused redistribution of the receptors to juxtanuclear aggresomes, significantly more so for TPβ than β2AR. Interestingly, Hsp90 coimmunoprecipitated with β2AR but virtually not with TPβ, indicating that nascent GPCRs can adopt alternative folding pathways. In vitro pull-down assays showed that both receptors can interact directly with CCT7 through their third intracellular loops and C-termini. We demonstrate that Trp334 in the TPβ C-terminus is critical for the CCT7 interaction and plays an important role in TPβ maturation and cell-surface expression. Of note, introducing a tryptophan in the corresponding position of the TPα isoform confers the CCT7-binding and maturation properties of TPβ. We show that an interaction with a subunit of the CCT/TCP-1 ring complex (TRiC) chaperonin complex is involved in regulating aggregation of nascent GPCRs and in promoting their proper maturation and expression.
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Affiliation(s)
- Samuel Génier
- Service de Rhumatologie, Département de Médecine, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CR-CHUS), and Institut de Pharmacologie de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| | - Jade Degrandmaison
- Service de Rhumatologie, Département de Médecine, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CR-CHUS), and Institut de Pharmacologie de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| | - Pierrick Moreau
- Service de Rhumatologie, Département de Médecine, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CR-CHUS), and Institut de Pharmacologie de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| | - Pascale Labrecque
- Service de Rhumatologie, Département de Médecine, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CR-CHUS), and Institut de Pharmacologie de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| | - Terence E Hébert
- Department of Pharmacology and Therapeutics, McGill University, Montréal, QC H3G 1Y6, Canada
| | - Jean-Luc Parent
- Service de Rhumatologie, Département de Médecine, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CR-CHUS), and Institut de Pharmacologie de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
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Hwang J, Lee JA, Pallas DC. Leucine Carboxyl Methyltransferase 1 (LCMT-1) Methylates Protein Phosphatase 4 (PP4) and Protein Phosphatase 6 (PP6) and Differentially Regulates the Stable Formation of Different PP4 Holoenzymes. J Biol Chem 2016; 291:21008-21019. [PMID: 27507813 DOI: 10.1074/jbc.m116.739920] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Indexed: 11/06/2022] Open
Abstract
The protein phosphatase 2A (PP2A) subfamily of phosphatases, PP2A, PP4, and PP6, are multifunctional serine/threonine protein phosphatases involved in many cellular processes. Carboxyl methylation of the PP2A catalytic subunit (PP2Ac) C-terminal leucine is regulated by the opposing activities of leucine carboxyl methyltransferase 1 (LCMT-1) and protein phosphatase methylesterase 1 (PME-1) and regulates PP2A holoenzyme formation. The site of methylation on PP2Ac is conserved in the catalytic subunits of PP4 and PP6, and PP4 is also methylated on that site, but the identities of the methyltransferase enzyme for PP4 are not known. Whether PP6 is methylated is also not known. Here we use antibodies specific for the unmethylated phosphatases to show that PP6 is carboxyl-methylated and that LCMT-1 is the major methyltransferase for PP2A, PP4, and PP6 in mouse embryonic fibroblasts (MEFs). Analysis of PP2A and PP4 complexes by blue native polyacrylamide gel electrophoresis (BN-PAGE) indicates that PP4 holoenzyme complexes, like those of PP2A, are differentially regulated by LCMT-1, with the PP4 regulatory subunit 1 (PP4R1)-containing PP4 complex being the most dramatically affected by the LCMT-1 loss. MEFs derived from LCMT-1 knock-out mouse embryos have reduced levels of PP2A B regulatory subunit and PP4R1 relative to control MEFs, indicating that LCMT-1 is important for maintaining normal levels of these subunits. Finally, LCMT-1 homozygous knock-out MEFs exhibited hyperphosphorylation of HDAC3, a reported target of the methylation-dependent PP4R1-PP4c complex. Collectively, our data suggest that LCMT-1 coordinately regulates the carboxyl methylation of PP2A-related phosphatases and, consequently, their holoenzyme assembly and function.
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Affiliation(s)
- Juyeon Hwang
- From the Department of Biochemistry, Winship Cancer Center, and the Biochemistry, Cell, and Developmental Graduate Program, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Jocelyn A Lee
- From the Department of Biochemistry, Winship Cancer Center, and the Biochemistry, Cell, and Developmental Graduate Program, Emory University School of Medicine, Atlanta, Georgia 30322
| | - David C Pallas
- From the Department of Biochemistry, Winship Cancer Center, and the Biochemistry, Cell, and Developmental Graduate Program, Emory University School of Medicine, Atlanta, Georgia 30322
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Chen H, You H, Wang L, Zhang X, Zhang J, He W. Chaperonin-containing T-complex Protein 1 Subunit ζ Serves as an Autoantigen Recognized by Human Vδ2 γδ T Cells in Autoimmune Diseases. J Biol Chem 2016; 291:19985-93. [PMID: 27489109 DOI: 10.1074/jbc.m115.700070] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Indexed: 01/20/2023] Open
Abstract
Human γδ T cells recognize conserved endogenous and stress-induced antigens typically associated with autoimmune diseases. However, the role of γδ T cells in autoimmune diseases is not clear. Few autoimmune disease-related antigens recognized by T cell receptor (TCR) γδ have been defined. In this study, we compared Vδ2 TCR complementarity-determining region 3 (CDR3) between systemic lupus erythematosus (SLE) patients and healthy donors. Results show that CDR3 length distribution differed significantly and displayed oligoclonal characteristics in SLE patients when compared with healthy donors. We found no difference in the frequency of Jδ gene fragment usage between these two groups. According to the dominant CDR3δ sequences in SLE patients, synthesized SL2 peptides specifically bound to human renal proximal tubular epithelial cell line HK-2; SL2-Vm, a mutant V sequence of SL2, did not bind. We identified the putative protein ligand chaperonin-containing T-complex protein 1 subunit ζ (CCT6A) using SL2 as a probe in HK-2 cell protein extracts by affinity chromatography and liquid chromatography-electrospray ionization-tandem mass spectrometry analysis. We found CCT6A expression on the surface of HK-2 cells. Cytotoxicity of only Vδ2 γδ T cells to HK-2 cells was blocked by anti-CCT6A antibody. Finally, we note that CCT6A concentration was significantly increased in plasma of SLE and rheumatoid arthritis patients. These data suggest that CCT6A is a novel autoantigen recognized by Vδ2 γδ T cells, which deepens our understanding of mechanisms in autoimmune diseases.
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Affiliation(s)
- Hui Chen
- From the Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, State Key Laboratory of Medical Molecular Biology, Beijing 100005, China and
| | - Hongqin You
- From the Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, State Key Laboratory of Medical Molecular Biology, Beijing 100005, China and
| | - Lifang Wang
- From the Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, State Key Laboratory of Medical Molecular Biology, Beijing 100005, China and
| | - Xuan Zhang
- the Department of Rheumatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100730, China
| | - Jianmin Zhang
- From the Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, State Key Laboratory of Medical Molecular Biology, Beijing 100005, China and
| | - Wei He
- From the Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, State Key Laboratory of Medical Molecular Biology, Beijing 100005, China and
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35
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Beers JM, Jayasundara N. Antarctic notothenioid fish: what are the future consequences of 'losses' and 'gains' acquired during long-term evolution at cold and stable temperatures? ACTA ACUST UNITED AC 2016; 218:1834-45. [PMID: 26085661 DOI: 10.1242/jeb.116129] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Antarctic notothenioids dominate the fish fauna of the Southern Ocean. Evolution for millions of years at cold and stable temperatures has led to the acquisition of numerous biochemical traits that allow these fishes to thrive in sub-zero waters. The gain of antifreeze glycoproteins has afforded notothenioids the ability to avert freezing and survive at temperatures often hovering near the freezing point of seawater. Additionally, possession of cold-adapted proteins and membranes permits them to sustain appropriate metabolic rates at exceptionally low body temperatures. The notothenioid genome is also distinguished by the disappearance of traits in some species, losses that might prove costly in a warmer environment. Perhaps the best-illustrated example is the lack of expression of hemoglobin in white-blooded icefishes from the family Channichthyidae. Loss of key elements of the cellular stress response, notably the heat shock response, has also been observed. Along with their attainment of cold tolerance, notothenioids have developed an extreme stenothermy and many species perish at temperatures only a few degrees above their habitat temperatures. Thus, in light of today's rapidly changing climate, it is critical to evaluate how these extreme stenotherms will respond to rising ocean temperatures. It is conceivable that the remarkable cold specialization of notothenioids may ultimately leave them vulnerable to future thermal increases and threaten their fitness and survival. Within this context, our review provides a current summary of the biochemical losses and gains that are known for notothenioids and examines these cold-adapted traits with a focus on processes underlying thermal tolerance and acclimation capacity.
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Affiliation(s)
- Jody M Beers
- Hopkins Marine Station, Stanford University, 120 Ocean View Boulevard, Pacific Grove, CA 93950, USA
| | - Nishad Jayasundara
- Nicholas School of the Environment, Duke University, 450 Research Drive, Durham, NC 27708, USA
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36
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Shan N, Zhou W, Zhang S, Zhang Y. Identification of HSPA8 as a candidate biomarker for endometrial carcinoma by using iTRAQ-based proteomic analysis. Onco Targets Ther 2016; 9:2169-79. [PMID: 27110132 PMCID: PMC4835145 DOI: 10.2147/ott.s97983] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Although there are advances in diagnostic, predictive, and therapeutic strategies, discovering protein biomarker for early detection is required for improving the survival rate of the patients with endometrial carcinoma. In this study, we identify proteins that are differentially expressed between the Stage I endometrial carcinoma and the normal pericarcinous tissues by using isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomic analysis. Totally, we screened 1,266 proteins. Among them, 103 proteins were significantly overexpressed, and 30 were significantly downexpressed in endometrial carcinoma. Using the bioinformatics analysis, we identified a list of proteins that might be closely associated with endometrial carcinoma, including CCT7, HSPA8, PCBP2, LONP1, PFN1, and EEF2. We validated the gene overexpression of these molecules in the endometrial carcinoma tissues and found that HSPA8 was most significantly upregulated. We further validated the overexpression of HSPA8 by using immunoblot analysis. Then, HSPA8 siRNA was transferred into the endometrial cancer cells RL-95-2 and HEC-1B. The depletion of HSPA8 siRNAs significantly reduced cell proliferation, promoted cell apoptosis, and suppressed cell growth in both cell lines. Taken together, HSPA8 plays a vital role in the development of endometrial carcinoma. HSPA8 is a candidate biomarker for early diagnosis and therapy of Stage I endometrial carcinoma.
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Affiliation(s)
- Nianchun Shan
- Department of Obstetric and Gynecology, Central South University, Changsha, Hunan, People's Republic of China
| | - Wei Zhou
- Health Management Center, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Shufen Zhang
- Department of Obstetric and Gynecology, Central South University, Changsha, Hunan, People's Republic of China
| | - Yu Zhang
- Department of Obstetric and Gynecology, Central South University, Changsha, Hunan, People's Republic of China
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37
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Bassiouni R, Nemec KN, Iketani A, Flores O, Showalter A, Khaled AS, Vishnubhotla P, Sprung RW, Kaittanis C, Perez JM, Khaled AR. Chaperonin Containing TCP-1 Protein Level in Breast Cancer Cells Predicts Therapeutic Application of a Cytotoxic Peptide. Clin Cancer Res 2016; 22:4366-79. [PMID: 27012814 DOI: 10.1158/1078-0432.ccr-15-2502] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 02/21/2016] [Indexed: 01/01/2023]
Abstract
PURPOSE Metastatic disease is a leading cause of death for patients with breast cancer, driving the need for new therapies. CT20p is a peptide previously discovered by our group that displays cancer-specific cytotoxicity. To design the optimal therapeutic use of the peptide, we identified the intracellular target of CT20p in breast cancer cells, correlating expression patterns of the target with susceptibility to CT20p. EXPERIMENTAL DESIGN Using polymeric nanoparticles to deliver CT20p, we assessed cytoskeletal changes, cell migration, adhesion, and viability in cells treated with the peptide. Protein pull-down experiments, coupled to mass spectrometry, enabled identification of the peptide's intracellular target. Biochemical and histologic techniques validated target identity in human cell lines and breast cancer tissue microarrays and revealed susceptibility patterns to CT20p. RESULTS Chaperonin containing TCP-1 (CCT) was identified as the intracellular target of CT20p. Cancer cells susceptible to CT20p had increased CCT, and overexpression of CCTβ, a subunit of the CCT complex, enhanced susceptibility to CT20p. Susceptible cells displayed reduced tubulin, a substrate of CCT, and inhibition of migration upon CT20p treatment. CCTβ levels were higher in invasive ductal carcinomas than in cancer adjacent tissues and increased with breast cancer stage. Decreased breast cancer patient survival correlated with genomic alternations in CCTβ and higher levels of the chaperone. CONCLUSIONS Increased CCT protein in breast cancer cells underlies the cytotoxicity of CT20p. CCT is thus a potential target for therapeutic intervention and serves as a companion diagnostic to personalize the therapeutic use of CT20p for breast cancer treatment. Clin Cancer Res; 22(17); 4366-79. ©2016 AACR.
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Affiliation(s)
- Rania Bassiouni
- Burnett School of Biomedical Science, College of Medicine, University of Central Florida, Orlando, Florida
| | - Kathleen N Nemec
- Burnett School of Biomedical Science, College of Medicine, University of Central Florida, Orlando, Florida
| | - Ashley Iketani
- Burnett School of Biomedical Science, College of Medicine, University of Central Florida, Orlando, Florida
| | - Orielyz Flores
- Nanoscience Technology Center, University of Central Florida, Orlando, Florida
| | - Anne Showalter
- Burnett School of Biomedical Science, College of Medicine, University of Central Florida, Orlando, Florida
| | | | | | | | - Charalambos Kaittanis
- Gordon Center for Medical Imaging, Department of Radiology, Massachusetts General Hospital, Boston, Massachusetts
| | - Jesus M Perez
- Cedars-Sinai Medical Center, Los Angeles, California
| | - Annette R Khaled
- Burnett School of Biomedical Science, College of Medicine, University of Central Florida, Orlando, Florida.
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38
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Wang L, Delahunty C, Fritz-Wolf K, Rahlfs S, Helena Prieto J, Yates JR, Becker K. Characterization of the 26S proteasome network in Plasmodium falciparum. Sci Rep 2015; 5:17818. [PMID: 26639022 PMCID: PMC4671066 DOI: 10.1038/srep17818] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 11/06/2015] [Indexed: 11/09/2022] Open
Abstract
In eukaryotic cells, the ubiquitin-proteasome system as a key regulator of protein quality control is an excellent drug target. We therefore aimed to analyze the 26S proteasome complex in the malaria parasite Plasmodium falciparum, which still threatens almost half of the world’s population. First, we established an affinity purification protocol allowing for the isolation of functional 26S proteasome complexes from the parasite. Subunit composition of the proteasome and component stoichiometry were studied and physiologic interacting partners were identified via in situ protein crosslinking. Furthermore, intrinsic ubiquitin receptors of the plasmodial proteasome were determined and their roles in proteasomal substrate recognition were analyzed. Notably, PfUSP14 was characterized as a proteasome-associated deubiquitinase resulting in the concept that targeting proteasomal deubiquitinating activity in P. falciparum may represent a promising antimalarial strategy. The data provide insights into a profound network orchestrated by the plasmodial proteasome and identified novel drug target candidates in the ubiquitin-proteasome system.
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Affiliation(s)
- Lihui Wang
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University, Giessen, Germany
| | - Claire Delahunty
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California
| | | | - Stefan Rahlfs
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University, Giessen, Germany
| | - Judith Helena Prieto
- Department of Chemistry, Western Connecticut State University, Danbury, Connecticut
| | - John R Yates
- Max-Planck Institute for Medical Research, Heidelberg, Germany
| | - Katja Becker
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University, Giessen, Germany
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39
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Skjærven L, Cuellar J, Martinez A, Valpuesta JM. Dynamics, flexibility, and allostery in molecular chaperonins. FEBS Lett 2015; 589:2522-32. [PMID: 26140986 DOI: 10.1016/j.febslet.2015.06.019] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Revised: 06/18/2015] [Accepted: 06/23/2015] [Indexed: 12/26/2022]
Abstract
The chaperonins are a family of molecular chaperones present in all three kingdoms of life. They are classified into Group I and Group II. Group I consists of the bacterial variants (GroEL) and the eukaryotic ones from mitochondria and chloroplasts (Hsp60), while Group II consists of the archaeal (thermosomes) and eukaryotic cytosolic variants (CCT or TRiC). Both groups assemble into a dual ring structure, with each ring providing a protective folding chamber for nascent and denatured proteins. Their functional cycle is powered by ATP binding and hydrolysis, which drives a series of structural rearrangements that enable encapsulation and subsequent release of the substrate protein. Chaperonins have elaborate allosteric mechanisms to regulate their functional cycle. Long-range negative cooperativity between the two rings ensures alternation of the folding chambers. Positive intra-ring cooperativity, which facilitates concerted conformational transitions within the protein subunits of one ring, has only been demonstrated for Group I chaperonins. In this review, we describe our present understanding of the underlying mechanisms and the structure-function relationships in these complex protein systems with a particular focus on the structural dynamics, allostery, and associated conformational rearrangements.
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Affiliation(s)
- Lars Skjærven
- Department of Biomedicine, University of Bergen, Bergen, Norway.
| | - Jorge Cuellar
- Department of Macromolecular Structure, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Aurora Martinez
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - José María Valpuesta
- Department of Macromolecular Structure, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
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40
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Molecular Chaperones of Leishmania: Central Players in Many Stress-Related and -Unrelated Physiological Processes. BIOMED RESEARCH INTERNATIONAL 2015; 2015:301326. [PMID: 26167482 PMCID: PMC4488524 DOI: 10.1155/2015/301326] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Accepted: 05/24/2015] [Indexed: 12/12/2022]
Abstract
Molecular chaperones are key components in the maintenance of cellular homeostasis and survival, not only during stress but also under optimal growth conditions. Folding of nascent polypeptides is supported by molecular chaperones, which avoid the formation of aggregates by preventing nonspecific interactions and aid, when necessary, the translocation of proteins to their correct intracellular localization. Furthermore, when proteins are damaged, molecular chaperones may also facilitate their refolding or, in the case of irreparable proteins, their removal by the protein degradation machinery of the cell. During their digenetic lifestyle, Leishmania parasites encounter and adapt to harsh environmental conditions, such as nutrient deficiency, hypoxia, oxidative stress, changing pH, and shifts in temperature; all these factors are potential triggers of cellular stress. We summarize here our current knowledge on the main types of molecular chaperones in Leishmania and their functions. Among them, heat shock proteins play important roles in adaptation and survival of this parasite against temperature changes associated with its passage from the poikilothermic insect vector to the warm-blooded vertebrate host. The study of structural features and the function of chaperones in Leishmania biology is providing opportunities (and challenges) for drug discovery and improving of current treatments against leishmaniasis.
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41
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Alonso-Morales A, González-López L, Cázares-Raga FE, Cortés-Martínez L, Torres-Monzón JA, Gallegos-Pérez JL, Rodríguez MH, James AA, Hernández-Hernández FDLC. Protein phosphorylation during Plasmodium berghei gametogenesis. Exp Parasitol 2015; 156:49-60. [PMID: 26008612 DOI: 10.1016/j.exppara.2015.05.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 05/08/2015] [Accepted: 05/18/2015] [Indexed: 10/23/2022]
Abstract
Plasmodium gametogenesis within the mosquito midgut is a complex differentiation process involving signaling mediated by phosphorylation, which modulate metabolic routes and protein synthesis required to complete this development. However, the mechanisms leading to gametogenesis activation are poorly understood. We analyzed protein phosphorylation during Plasmodium berghei gametogenesis in vitro in serum-free medium using bidimensional electrophoresis (2-DE) combined with immunoblotting (IB) and antibodies specific to phosphorylated serine, threonine and tyrosine. Approximately 75 protein exhibited phosphorylation changes, of which 23 were identified by mass spectrometry. These included components of the cytoskeleton, heat shock proteins, and proteins involved in DNA synthesis and signaling pathways among others. Novel phosphorylation events support a role for these proteins during gametogenesis. The phosphorylation sites of six of the identified proteins, HSP70, WD40 repeat protein msi1, enolase, actin-1 and two isoforms of large subunit of ribonucleoside reductase were investigated using TiO2 phosphopeptides enrichment and tandem mass spectrometry. In addition, transient exposure to hydroxyurea, an inhibitor of ribonucleoside reductase, impaired male gametocytes exflagellation in a dose-dependent manner, and provides a resource for functional studies.
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Affiliation(s)
- Alberto Alonso-Morales
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Avenida Instituto Politécnico Nacional # 2508, Colonia San Pedro Zacatenco, Delegación Gustavo A. Madero, C.P. 07360, México, D.F., México
| | - Lorena González-López
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Avenida Instituto Politécnico Nacional # 2508, Colonia San Pedro Zacatenco, Delegación Gustavo A. Madero, C.P. 07360, México, D.F., México
| | - Febe Elena Cázares-Raga
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Avenida Instituto Politécnico Nacional # 2508, Colonia San Pedro Zacatenco, Delegación Gustavo A. Madero, C.P. 07360, México, D.F., México
| | - Leticia Cortés-Martínez
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Avenida Instituto Politécnico Nacional # 2508, Colonia San Pedro Zacatenco, Delegación Gustavo A. Madero, C.P. 07360, México, D.F., México
| | - Jorge Aurelio Torres-Monzón
- Centro Regional de Investigación en Salud Pública, Instituto Nacional de Salud Pública, Avenida 19 Poniente esquina 4a Norte s/n, Colonia Centro, C.P. 62100 Tapachula, Chiapas, Mexico
| | | | - Mario Henry Rodríguez
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Avenida Universidad # 655, Colonia Santa María Ahuacatitlán, C.P. 62100, Cuernavaca, Morelos, México
| | - Anthony A James
- Departments of Molecular Biology and Biochemistry, and Microbiology and Molecular Genetics, University of California, Irvine, CA 92697, USA
| | - Fidel de la Cruz Hernández-Hernández
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Avenida Instituto Politécnico Nacional # 2508, Colonia San Pedro Zacatenco, Delegación Gustavo A. Madero, C.P. 07360, México, D.F., México.
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42
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Barrack KL, Fyfe PK, Finney AJ, Hunter WN. Crystal structure of the C-terminal domain of tubulin-binding cofactor C from Leishmania major. Mol Biochem Parasitol 2015; 201:26-30. [PMID: 25982270 PMCID: PMC4539340 DOI: 10.1016/j.molbiopara.2015.05.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 05/01/2015] [Accepted: 05/08/2015] [Indexed: 01/23/2023]
Abstract
Tubulin-binding cofactor C stimulates GTPase activity and contributes to the release of the heterodimeric α/β-tubulin from a super-complex of tubulin monomers and two ancillary cofactors. We have determined the 2.2 Å resolution crystal structure of the C-terminal domain of tubulin-binding cofactor C from Leishmania major based on single wavelength anomalous dispersion measurements targeting a selenomethionine derivative. Although previously predicted to consist of two domains the structure is best described as a single domain dominated by a right-handed β-helix of five turns that form a triangular prism. One face of the prism is covered by the C-terminal residues leaving another face solvent exposed. Comparisons with an orthologous human GTPase activating protein match key residues involved in binding nucleotide and identify the face of the β-helix fold likely involved in interacting with the β-tubulin:GTP complex.
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Affiliation(s)
- Keri L Barrack
- Division of Biological Chemistry & Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Paul K Fyfe
- Division of Biological Chemistry & Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Alex J Finney
- Division of Biological Chemistry & Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - William N Hunter
- Division of Biological Chemistry & Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK.
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43
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Mbengue A, Vialla E, Berry L, Fall G, Audiger N, Demettre-Verceil E, Boteller D, Braun-Breton C. New Export Pathway inPlasmodium falciparum-Infected Erythrocytes: Role of the Parasite Group II Chaperonin, PfTRiC. Traffic 2015; 16:461-75. [DOI: 10.1111/tra.12266] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 01/20/2015] [Accepted: 01/21/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Alassane Mbengue
- University Montpellier II; CNRS UMR 5235, University Montpellier I; Dynamique des Interactions Membranaires Normales et Pathologiques 34095 Montpellier Cedex 5 France
| | - Emilie Vialla
- University Montpellier II; CNRS UMR 5235, University Montpellier I; Dynamique des Interactions Membranaires Normales et Pathologiques 34095 Montpellier Cedex 5 France
| | - Laurence Berry
- University Montpellier II; CNRS UMR 5235, University Montpellier I; Dynamique des Interactions Membranaires Normales et Pathologiques 34095 Montpellier Cedex 5 France
| | - Gamou Fall
- University Montpellier II; CNRS UMR 5235, University Montpellier I; Dynamique des Interactions Membranaires Normales et Pathologiques 34095 Montpellier Cedex 5 France
| | - Nicolas Audiger
- University Montpellier II; CNRS UMR 5235, University Montpellier I; Dynamique des Interactions Membranaires Normales et Pathologiques 34095 Montpellier Cedex 5 France
| | - Edith Demettre-Verceil
- Plate-forme de Protéomique Fonctionnelle - FPP; UMS CNRS 3426 - US 009 INSERM - UMI - UMII, IGF; 141 rue de la Cardonille 34094 Montpellier Cedex 5 France
| | - David Boteller
- University Montpellier II; CNRS UMR 5235, University Montpellier I; Dynamique des Interactions Membranaires Normales et Pathologiques 34095 Montpellier Cedex 5 France
| | - Catherine Braun-Breton
- University Montpellier II; CNRS UMR 5235, University Montpellier I; Dynamique des Interactions Membranaires Normales et Pathologiques 34095 Montpellier Cedex 5 France
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44
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Structures of the Gβ-CCT and PhLP1-Gβ-CCT complexes reveal a mechanism for G-protein β-subunit folding and Gβγ dimer assembly. Proc Natl Acad Sci U S A 2015; 112:2413-8. [PMID: 25675501 DOI: 10.1073/pnas.1419595112] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
G-protein signaling depends on the ability of the individual subunits of the G-protein heterotrimer to assemble into a functional complex. Formation of the G-protein βγ (Gβγ) dimer is particularly challenging because it is an obligate dimer in which the individual subunits are unstable on their own. Recent studies have revealed an intricate chaperone system that brings Gβ and Gγ together. This system includes cytosolic chaperonin containing TCP-1 (CCT; also called TRiC) and its cochaperone phosducin-like protein 1 (PhLP1). Two key intermediates in the Gβγ assembly process, the Gβ-CCT and the PhLP1-Gβ-CCT complexes, were isolated and analyzed by a hybrid structural approach using cryo-electron microscopy, chemical cross-linking coupled with mass spectrometry, and unnatural amino acid cross-linking. The structures show that Gβ interacts with CCT in a near-native state through interactions of the Gγ-binding region of Gβ with the CCTγ subunit. PhLP1 binding stabilizes the Gβ fold, disrupting interactions with CCT and releasing a PhLP1-Gβ dimer for assembly with Gγ. This view provides unique insight into the interplay between CCT and a cochaperone to orchestrate the folding of a protein substrate.
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45
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Abstract
Microtubules (MTs) are highly conserved polar polymers that are key elements of the eukaryotic cytoskeleton and are essential for various cell functions. αβ-tubulin, a heterodimer containing one structural GTP and one hydrolysable and exchangeable GTP, is the building block of MTs and is formed by the sequential action of several molecular chaperones. GTP hydrolysis in the MT lattice is mechanistically coupled with MT growth, thus giving MTs a metastable and dynamic nature. MTs adopt several distinct higher-order organizations that function in cell division and cell morphogenesis. Small molecular weight compounds that bind tubulin are used as herbicides and as research tools to investigate MT functions in plant cells. The de novo formation of MTs in cells requires conserved γ-tubulin-containing complexes and targeting/activating regulatory proteins that contribute to the geometry of MT arrays. Various MT regulators and tubulin modifications control the dynamics and organization of MTs throughout the cell cycle and in response to developmental and environmental cues. Signaling pathways that converge on the regulation of versatile MT functions are being characterized.
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Affiliation(s)
- Takashi Hashimoto
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara 630-0192, Japan
- Address correspondence to
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46
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Miyata Y, Shibata T, Aoshima M, Tsubata T, Nishida E. The molecular chaperone TRiC/CCT binds to the Trp-Asp 40 (WD40) repeat protein WDR68 and promotes its folding, protein kinase DYRK1A binding, and nuclear accumulation. J Biol Chem 2014; 289:33320-32. [PMID: 25342745 PMCID: PMC4246089 DOI: 10.1074/jbc.m114.586115] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 10/18/2014] [Indexed: 11/06/2022] Open
Abstract
Trp-Asp (WD) repeat protein 68 (WDR68) is an evolutionarily conserved WD40 repeat protein that binds to several proteins, including dual specificity tyrosine phosphorylation-regulated protein kinase (DYRK1A), MAPK/ERK kinase kinase 1 (MEKK1), and Cullin4-damage-specific DNA-binding protein 1 (CUL4-DDB1). WDR68 affects multiple and diverse physiological functions, such as controlling anthocyanin synthesis in plants, tissue growth in insects, and craniofacial development in vertebrates. However, the biochemical basis and the regulatory mechanism of WDR68 activity remain largely unknown. To better understand the cellular function of WDR68, here we have isolated and identified cellular WDR68 binding partners using a phosphoproteomic approach. More than 200 cellular proteins with wide varieties of biochemical functions were identified as WDR68-binding protein candidates. Eight T-complex protein 1 (TCP1) subunits comprising the molecular chaperone TCP1 ring complex/chaperonin-containing TCP1 (TRiC/CCT) were identified as major WDR68-binding proteins, and phosphorylation sites in both WDR68 and TRiC/CCT were identified. Co-immunoprecipitation experiments confirmed the binding between TRiC/CCT and WDR68. Computer-aided structural analysis suggested that WDR68 forms a seven-bladed β-propeller ring. Experiments with a series of deletion mutants in combination with the structural modeling showed that three of the seven β-propeller blades of WDR68 are essential and sufficient for TRiC/CCT binding. Knockdown of cellular TRiC/CCT by siRNA caused an abnormal WDR68 structure and led to reduction of its DYRK1A-binding activity. Concomitantly, nuclear accumulation of WDR68 was suppressed by the knockdown of TRiC/CCT, and WDR68 formed cellular aggregates when overexpressed in the TRiC/CCT-deficient cells. Altogether, our results demonstrate that the molecular chaperone TRiC/CCT is essential for correct protein folding, DYRK1A binding, and nuclear accumulation of WDR68.
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Affiliation(s)
- Yoshihiko Miyata
- From the Department of Cell and Developmental Biology, Graduate School of Biostudies, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan and
| | | | | | | | - Eisuke Nishida
- From the Department of Cell and Developmental Biology, Graduate School of Biostudies, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan and
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47
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Trippier PC, Zhao KT, Fox SG, Schiefer IT, Benmohamed R, Moran J, Kirsch DR, Morimoto RI, Silverman RB. Proteasome activation is a mechanism for pyrazolone small molecules displaying therapeutic potential in amyotrophic lateral sclerosis. ACS Chem Neurosci 2014; 5:823-9. [PMID: 25001311 PMCID: PMC4176317 DOI: 10.1021/cn500147v] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
![]()
Amyotrophic
lateral sclerosis (ALS) is a progressive and ultimately
fatal neurodegenerative disease. Pyrazolone containing small molecules
have shown significant disease attenuating efficacy in cellular and
murine models of ALS. Pyrazolone based affinity probes were synthesized
to identify high affinity binding partners and ascertain a potential
biological mode of action. Probes were confirmed to be neuroprotective
in PC12-SOD1G93A cells. PC12-SOD1G93A cell lysates
were used for protein pull-down, affinity purification, and subsequent
proteomic analysis using LC-MS/MS. Proteomics identified the 26S proteasome
regulatory subunit 4 (PSMC1), 26S proteasome regulatory subunit 6B
(PSMC4), and T-complex protein 1 (TCP-1) as putative protein targets.
Coincubation with appropriate competitors confirmed the authenticity
of the proteomics results. Activation of the proteasome by pyrazolones
was demonstrated in the absence of exogenous proteasome inhibitor
and by restoration of cellular protein degradation of a fluorogenic
proteasome substrate in PC12-SOD1G93A cells. Importantly,
supplementary studies indicated that these molecules do not induce
a heat shock response. We propose that pyrazolones represent a rare
class of molecules that enhance proteasomal activation in the absence
of a heat shock response and may have therapeutic potential in ALS.
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Affiliation(s)
| | | | | | | | - Radhia Benmohamed
- Cambria Pharmaceuticals, Cambridge, Massachusetts 02142, United States
| | | | - Donald R. Kirsch
- Cambria Pharmaceuticals, Cambridge, Massachusetts 02142, United States
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48
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Liang XH, Shen W, Sun H, Prakash TP, Crooke ST. TCP1 complex proteins interact with phosphorothioate oligonucleotides and can co-localize in oligonucleotide-induced nuclear bodies in mammalian cells. Nucleic Acids Res 2014; 42:7819-32. [PMID: 24861627 PMCID: PMC4081088 DOI: 10.1093/nar/gku484] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Phosphorothioate (PS) antisense oligonucleotides (ASOs) have been successfully developed as drugs to reduce the expression of disease-causing genes. PS-ASOs can be designed to induce degradation of complementary RNAs via the RNase H pathway and much is understood about that process. However, interactions of PS-ASOs with other cellular proteins are not well characterized. Here we report that in cells transfected with PS-ASOs, the chaperonin T-complex 1 (TCP1) proteins interact with PS-ASOs and enhance antisense activity. The TCP1-β subunit co-localizes with PS-ASOs in distinct nuclear structures, termed phosphorothioate bodies or PS-bodies. Upon Ras-related nuclear protein (RAN) depletion, cytoplasmic PS-body-like structures were observed and nuclear concentrations of PS-ASOs were reduced, suggesting that TCP1-β can interact with PS-ASOs in the cytoplasm and that the nuclear import of PS-ASOs is at least partially through the RAN-mediated pathway. Upon free uptake, PS-ASOs co-localize with TCP1 proteins in cytoplasmic foci related to endosomes/lysosomes. Together, our results indicate that the TCP1 complex binds oligonucleotides with TCP1-β subunit being a nuclear PS-body component and suggest that the TCP1 complex may facilitate PS-ASO uptake and/or release from the endocytosis pathway.
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Affiliation(s)
- Xue-hai Liang
- Department of Core Antisense Research, ISIS Pharmaceuticals, Inc., Carlsbad, CA 92010, USA
| | - Wen Shen
- Department of Core Antisense Research, ISIS Pharmaceuticals, Inc., Carlsbad, CA 92010, USA
| | - Hong Sun
- Department of Core Antisense Research, ISIS Pharmaceuticals, Inc., Carlsbad, CA 92010, USA
| | - Thazha P Prakash
- Department of Medicinal Chemistry, ISIS Pharmaceuticals, Inc., Carlsbad, CA 92010, USA
| | - Stanley T Crooke
- Department of Core Antisense Research, ISIS Pharmaceuticals, Inc., Carlsbad, CA 92010, USA
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Rescue of embryonic stem cells from cellular transformation by proteomic stabilization of mutant p53 and conversion into WT conformation. Proc Natl Acad Sci U S A 2014; 111:7006-11. [PMID: 24778235 DOI: 10.1073/pnas.1320428111] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
p53 is a well-known tumor suppressor that is mutated in over 50% of human cancers. These mutations were shown to exhibit gain of oncogenic function compared with the deletion of the gene. Additionally, p53 has fundamental roles in differentiation and development; nevertheless, mutant p53 mice are viable and develop malignant tumors only on adulthood. We set out to reveal the mechanisms by which embryos are protected from mutant p53-induced transformation using ES cells (ESCs) that express a conformational mutant of p53. We found that, despite harboring mutant p53, the ESCs remain pluripotent and benign and have relatively normal karyotype compared with ESCs knocked out for p53. Additionally, using high-content RNA sequencing, we show that p53 is transcriptionally active in response to DNA damage in mutant ESCs and elevates p53 target genes, such as p21 and btg2. We also show that the conformation of mutant p53 protein in ESCs is stabilized to a WT conformation. Through MS-based interactome analyses, we identified a network of proteins, including the CCT complex, USP7, Aurora kinase, Nedd4, and Trim24, that bind mutant p53 and may shift its conformation to a WT form. We propose this conformational shift as a novel mechanism of maintenance of genomic integrity, despite p53 mutation. Harnessing the ability of these protein interactors to transform the oncogenic mutant p53 to the tumor suppressor WT form can be the basis for future development of p53-targeted cancer therapy.
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Cuellar J, Yébenes H, Parker SK, Carranza G, Serna M, Valpuesta JM, Zabala JC, Detrich HW. Assisted protein folding at low temperature: evolutionary adaptation of the Antarctic fish chaperonin CCT and its client proteins. Biol Open 2014; 3:261-70. [PMID: 24659247 PMCID: PMC3988795 DOI: 10.1242/bio.20147427] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Eukaryotic ectotherms of the Southern Ocean face energetic challenges to protein folding assisted by the cytosolic chaperonin CCT. We hypothesize that CCT and its client proteins (CPs) have co-evolved molecular adaptations that facilitate CCT–CP interaction and the ATP-driven folding cycle at low temperature. To test this hypothesis, we compared the functional and structural properties of CCT–CP systems from testis tissues of an Antarctic fish, Gobionotothen gibberifrons (Lönnberg) (habitat/body T = −1.9 to +2°C), and of the cow (body T = 37°C). We examined the temperature dependence of the binding of denatured CPs (β-actin, β-tubulin) by fish and bovine CCTs, both in homologous and heterologous combinations and at temperatures between −4°C and 20°C, in a buffer conducive to binding of the denatured CP to the open conformation of CCT. In homologous combination, the percentage of G. gibberifrons CCT bound to CP declined linearly with increasing temperature, whereas the converse was true for bovine CCT. Binding of CCT to heterologous CPs was low, irrespective of temperature. When reactions were supplemented with ATP, G. gibberifrons CCT catalyzed the folding and release of actin at 2°C. The ATPase activity of apo-CCT from G. gibberifrons at 4°C was ∼2.5-fold greater than that of apo-bovine CCT, whereas equivalent activities were observed at 20°C. Based on these results, we conclude that the catalytic folding cycle of CCT from Antarctic fishes is partially compensated at their habitat temperature, probably by means of enhanced CP-binding affinity and increased flexibility of the CCT subunits.
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Affiliation(s)
- Jorge Cuellar
- Centro Nacional de Biotechnología (CNB-CSIC), Campus de la Universidad Autónoma de Madrid, 28049 Madrid, Spain
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