1
|
Hofman DA, Ruiz-Orera J, Yannuzzi I, Murugesan R, Brown A, Clauser KR, Condurat AL, van Dinter JT, Engels SAG, Goodale A, van der Lugt J, Abid T, Wang L, Zhou KN, Vogelzang J, Ligon KL, Phoenix TN, Roth JA, Root DE, Hubner N, Golub TR, Bandopadhayay P, van Heesch S, Prensner JR. Translation of non-canonical open reading frames as a cancer cell survival mechanism in childhood medulloblastoma. Mol Cell 2024; 84:261-276.e18. [PMID: 38176414 PMCID: PMC10872554 DOI: 10.1016/j.molcel.2023.12.003] [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: 05/16/2023] [Revised: 08/30/2023] [Accepted: 12/01/2023] [Indexed: 01/06/2024]
Abstract
A hallmark of high-risk childhood medulloblastoma is the dysregulation of RNA translation. Currently, it is unknown whether medulloblastoma dysregulates the translation of putatively oncogenic non-canonical open reading frames (ORFs). To address this question, we performed ribosome profiling of 32 medulloblastoma tissues and cell lines and observed widespread non-canonical ORF translation. We then developed a stepwise approach using multiple CRISPR-Cas9 screens to elucidate non-canonical ORFs and putative microproteins implicated in medulloblastoma cell survival. We determined that multiple lncRNA-ORFs and upstream ORFs (uORFs) exhibited selective functionality independent of main coding sequences. A microprotein encoded by one of these ORFs, ASNSD1-uORF or ASDURF, was upregulated, associated with MYC-family oncogenes, and promoted medulloblastoma cell survival through engagement with the prefoldin-like chaperone complex. Our findings underscore the fundamental importance of non-canonical ORF translation in medulloblastoma and provide a rationale to include these ORFs in future studies seeking to define new cancer targets.
Collapse
Affiliation(s)
- Damon A Hofman
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Jorge Ruiz-Orera
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Ian Yannuzzi
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Adam Brown
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Karl R Clauser
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alexandra L Condurat
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jip T van Dinter
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Sem A G Engels
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Amy Goodale
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jasper van der Lugt
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Tanaz Abid
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Li Wang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kevin N Zhou
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jayne Vogelzang
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02215, USA
| | - Keith L Ligon
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02215, USA; Department of Pathology, Boston Children's Hospital, Boston MA 02115, USA
| | - Timothy N Phoenix
- Division of Pharmaceutical Sciences, James L. Winkle College of Pharmacy, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Jennifer A Roth
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - David E Root
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; Charité-Universitätsmedizin, 10117 Berlin, Germany; German Centre for Cardiovascular Research, Partner Site Berlin, 13347 Berlin, Germany
| | - Todd R Golub
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Pratiti Bandopadhayay
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Sebastiaan van Heesch
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands.
| | - John R Prensner
- Department of Pediatrics, Division of Pediatric Hematology/Oncology and Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| |
Collapse
|
2
|
Tahmaz I, Shahmoradi Ghahe S, Stasiak M, Liput KP, Jonak K, Topf U. Prefoldin 2 contributes to mitochondrial morphology and function. BMC Biol 2023; 21:193. [PMID: 37697385 PMCID: PMC10496292 DOI: 10.1186/s12915-023-01695-y] [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: 02/27/2023] [Accepted: 08/31/2023] [Indexed: 09/13/2023] Open
Abstract
BACKGROUND Prefoldin is an evolutionarily conserved co-chaperone of the tailless complex polypeptide 1 ring complex (TRiC)/chaperonin containing tailless complex 1 (CCT). The prefoldin complex consists of six subunits that are known to transfer newly produced cytoskeletal proteins to TRiC/CCT for folding polypeptides. Prefoldin function was recently linked to the maintenance of protein homeostasis, suggesting a more general function of the co-chaperone during cellular stress conditions. Prefoldin acts in an adenosine triphosphate (ATP)-independent manner, making it a suitable candidate to operate during stress conditions, such as mitochondrial dysfunction. Mitochondrial function depends on the production of mitochondrial proteins in the cytosol. Mechanisms that sustain cytosolic protein homeostasis are vital for the quality control of proteins destined for the organelle and such mechanisms among others include chaperones. RESULTS We analyzed consequences of the loss of prefoldin subunits on the cell proliferation and survival of Saccharomyces cerevisiae upon exposure to various cellular stress conditions. We found that prefoldin subunits support cell growth under heat stress. Moreover, prefoldin facilitates the growth of cells under respiratory growth conditions. We showed that mitochondrial morphology and abundance of some respiratory chain complexes was supported by the prefoldin 2 (Pfd2/Gim4) subunit. We also found that Pfd2 interacts with Tom70, a receptor of mitochondrial precursor proteins that are targeted into mitochondria. CONCLUSIONS Our findings link the cytosolic prefoldin complex to mitochondrial function. Loss of the prefoldin complex subunit Pfd2 results in adaptive cellular responses on the proteome level under physiological conditions suggesting a continuous need of Pfd2 for maintenance of cellular homeostasis. Within this framework, Pfd2 might support mitochondrial function directly as part of the cytosolic quality control system of mitochondrial proteins or indirectly as a component of the protein homeostasis network.
Collapse
Affiliation(s)
- Ismail Tahmaz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Somayeh Shahmoradi Ghahe
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Monika Stasiak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Kamila P Liput
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Katarzyna Jonak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Ulrike Topf
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland.
| |
Collapse
|
3
|
Hofman DA, Ruiz-Orera J, Yannuzzi I, Murugesan R, Brown A, Clauser KR, Condurat AL, van Dinter JT, Engels SA, Goodale A, van der Lugt J, Abid T, Wang L, Zhou KN, Vogelzang J, Ligon KL, Phoenix TN, Roth JA, Root DE, Hubner N, Golub TR, Bandopadhayay P, van Heesch S, Prensner JR. Translation of non-canonical open reading frames as a cancer cell survival mechanism in childhood medulloblastoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.04.539399. [PMID: 37205492 PMCID: PMC10187264 DOI: 10.1101/2023.05.04.539399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
A hallmark of high-risk childhood medulloblastoma is the dysregulation of RNA translation. Currently, it is unknown whether medulloblastoma dysregulates the translation of putatively oncogenic non-canonical open reading frames. To address this question, we performed ribosome profiling of 32 medulloblastoma tissues and cell lines and observed widespread non-canonical ORF translation. We then developed a step-wise approach to employ multiple CRISPR-Cas9 screens to elucidate functional non-canonical ORFs implicated in medulloblastoma cell survival. We determined that multiple lncRNA-ORFs and upstream open reading frames (uORFs) exhibited selective functionality independent of the main coding sequence. One of these, ASNSD1-uORF or ASDURF, was upregulated, associated with the MYC family oncogenes, and was required for medulloblastoma cell survival through engagement with the prefoldin-like chaperone complex. Our findings underscore the fundamental importance of non-canonical ORF translation in medulloblastoma and provide a rationale to include these ORFs in future cancer genomics studies seeking to define new cancer targets.
Collapse
Affiliation(s)
- Damon A. Hofman
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, the Netherlands
- These authors contributed equally
| | - Jorge Ruiz-Orera
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
- These authors contributed equally
| | - Ian Yannuzzi
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | | | - Adam Brown
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Current address: Arbor Biotechnologies, Cambridge, MA, 02140, USA
| | - Karl R. Clauser
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Alexandra L. Condurat
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jip T. van Dinter
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, the Netherlands
| | - Sem A.G. Engels
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, the Netherlands
| | - Amy Goodale
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Jasper van der Lugt
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, the Netherlands
| | - Tanaz Abid
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Li Wang
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Kevin N. Zhou
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Current address: Kaiser Permanente Bernard J. Tyson School of Medicine, Pasadena, CA, 91101, USA
| | - Jayne Vogelzang
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, 02215, USA
| | - Keith L. Ligon
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, 02215, USA
- Department of Pathology, Boston Children’s Hospital, Boston MA 02115
| | - Timothy N. Phoenix
- Division of Pharmaceutical Sciences, James L. Winkle College of Pharmacy, University of Cincinnati, Cincinnati, OH, 45229, USA
| | | | - David E. Root
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
- Charité-Universitätsmedizin, 10117 Berlin, Germany
- German Centre for Cardiovascular Research, Partner Site Berlin, 13347 Berlin, Germany
| | - Todd R. Golub
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Division of Pediatric Hematology/Oncology, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Pratiti Bandopadhayay
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Division of Pediatric Hematology/Oncology, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Sebastiaan van Heesch
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, the Netherlands
| | - John R. Prensner
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Division of Pediatric Hematology/Oncology, Boston Children’s Hospital, Boston, MA, 02115, USA
- Current address: Department of Pediatrics, Division of Pediatric Hematology/Oncology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| |
Collapse
|
4
|
Hurst Z, Liu W, Shi Q, Herman PK. A distinct P-body-like granule is induced in response to the disruption of microtubule integrity in Saccharomyces cerevisiae. Genetics 2022; 222:6649695. [PMID: 35876801 PMCID: PMC9434292 DOI: 10.1093/genetics/iyac105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/08/2022] [Indexed: 11/12/2022] Open
Abstract
The Processing-body (P-body) is a conserved membraneless organelle that has been implicated in the storage and/or decay of mRNAs. Although P-bodies have been shown to be induced by a variety of conditions, the mechanisms controlling their assembly and their precise physiological roles in eukaryotic cells are still being worked out. In this study, we find that a distinct subtype of P-body is induced in response to conditions that disrupt microtubule integrity in the budding yeast, Saccharomyces cerevisiae. For example, treatment with the microtubule-destabilizing agent, benomyl, led to the induction of these novel ribonucleoprotein (RNP) granules. A link to microtubules had been noted previously and the observations here extend our understanding by demonstrating that the induced foci differ from traditional P-bodies in a number of significant ways. These include differences in overall granule morphology, protein composition and the manner in which their induction is regulated. Of particular note, several key P-body constituents are absent from these Benomyl-Induced Granules (BIGs), including the Pat1 protein that is normally required for efficient P-body assembly. However, these novel RNP structures still contain many known P-body proteins and exhibit similar hallmarks of a liquid-like compartment. In all, the data suggest that the disruption of microtubule integrity leads to the formation of a novel type of P-body granule that may have distinct biological activities in the cell. Future work will aim to identify the biological activities of these BIGs and to determine, in turn, whether these P-body-like granules have any role in the regulation of microtubule dynamics.
Collapse
Affiliation(s)
- Zachary Hurst
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210 USA
| | - Wenfang Liu
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210 USA
| | - Qian Shi
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210 USA
| | - Paul K Herman
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210 USA
| |
Collapse
|
5
|
Tahmaz I, Shahmoradi Ghahe S, Topf U. Prefoldin Function in Cellular Protein Homeostasis and Human Diseases. Front Cell Dev Biol 2022; 9:816214. [PMID: 35111762 PMCID: PMC8801880 DOI: 10.3389/fcell.2021.816214] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 12/29/2021] [Indexed: 01/05/2023] Open
Abstract
Cellular functions are largely performed by proteins. Defects in the production, folding, or removal of proteins from the cell lead to perturbations in cellular functions that can result in pathological conditions for the organism. In cells, molecular chaperones are part of a network of surveillance mechanisms that maintains a functional proteome. Chaperones are involved in the folding of newly synthesized polypeptides and assist in refolding misfolded proteins and guiding proteins for degradation. The present review focuses on the molecular co-chaperone prefoldin. Its canonical function in eukaryotes involves the transfer of newly synthesized polypeptides of cytoskeletal proteins to the tailless complex polypeptide 1 ring complex (TRiC/CCT) chaperonin which assists folding of the polypeptide chain in an energy-dependent manner. The canonical function of prefoldin is well established, but recent research suggests its broader function in the maintenance of protein homeostasis under physiological and pathological conditions. Interestingly, non-canonical functions were identified for the prefoldin complex and also for its individual subunits. We discuss the latest findings on the prefoldin complex and its subunits in the regulation of transcription and proteasome-dependent protein degradation and its role in neurological diseases, cancer, viral infections and rare anomalies.
Collapse
Affiliation(s)
- Ismail Tahmaz
- Laboratory of Molecular Basis of Aging and Rejuvenation, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Somayeh Shahmoradi Ghahe
- Laboratory of Molecular Basis of Aging and Rejuvenation, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Ulrike Topf
- Laboratory of Molecular Basis of Aging and Rejuvenation, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| |
Collapse
|
6
|
Herranz-Montoya I, Park S, Djouder N. A comprehensive analysis of prefoldins and their implication in cancer. iScience 2021; 24:103273. [PMID: 34761191 PMCID: PMC8567396 DOI: 10.1016/j.isci.2021.103273] [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] [Indexed: 01/14/2023] Open
Abstract
Prefoldins (PFDNs) are evolutionary conserved co-chaperones, initially discovered in archaea but universally present in eukaryotes. PFDNs are prevalently organized into hetero-hexameric complexes. Although they have been overlooked since their discovery and their functions remain elusive, several reports indicate they act as co-chaperones escorting misfolded or non-native proteins to group II chaperonins. Unlike the eukaryotic PFDNs which interact with cytoskeletal components, the archaeal PFDNs can bind and stabilize a wide range of substrates, possibly due to their great structural diversity. The discovery of the unconventional RPB5 interactor (URI) PFDN-like complex (UPC) suggests that PFDNs have versatile functions and are required for different cellular processes, including an important role in cancer. Here, we summarize their functions across different species. Moreover, a comprehensive analysis of PFDNs genomic alterations across cancer types by using large-scale cancer genomic data indicates that PFDNs are a new class of non-mutated proteins significantly overexpressed in some cancer types.
Collapse
Affiliation(s)
- Irene Herranz-Montoya
- Growth Factors, Nutrients and Cancer Group, Molecular Oncology Programme, Centro Nacional de Investigaciones Oncológicas, CNIO, Madrid 28029, Spain
| | - Solip Park
- Computational Cancer Genomics Group, Structural Biology Programme, Centro Nacional de Investigaciones Oncológicas, CNIO, Madrid 28029, Spain
| | - Nabil Djouder
- Growth Factors, Nutrients and Cancer Group, Molecular Oncology Programme, Centro Nacional de Investigaciones Oncológicas, CNIO, Madrid 28029, Spain
| |
Collapse
|
7
|
Variants in the Enteric Smooth Muscle Actin γ-2 Cause Pediatric Intestinal Pseudo-obstruction in Chinese Patients. J Pediatr Gastroenterol Nutr 2021; 72:36-42. [PMID: 32810037 DOI: 10.1097/mpg.0000000000002897] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
OBJECTIVES Pediatric intestinal pseudo-obstruction (PIPO) is a severe gastrointestinal disorder occurring in children, leading to failure to thrive, malnutrition, and long-term parenteral nutrition dependence. Enteric smooth muscle actin γ-2 (ACTG2) variants have been reported to be related to the pathogenesis of PIPO. This study aimed to determine the presence of ACTG2 variants in Chinese PIPO patients. METHODS Whole-exome sequencing was performed using samples from 39 recruited patients, whereas whole ACTG2 Sanger sequencing was performed using samples from 2 patients. Published data was reviewed to determine the number of pathogenic variants and the genotype related to ACTG2 variants in the Chinese population. RESULTS A total of 21 Chinese probands were found to carry heterozygous missense variants of ACTG2, among which 20 were de novo. Fifteen probands had p.Arg257 variants (c.770G>A and c.769C>T), and the other 2 probands had c.533G>A (p.Arg178His) and c.443G>T (p.Arg148Leu) variants. Four probands had novel variants c.337C>T (p.Pro113Ser), c.588G>C (p.Glu196Asp), c.734A>G (p.Asp245Gly), and c.553G>T (p.Asp185Tyr). CONCLUSIONS Variants affecting codon 257 of ACTG2 protein sequence appeared to be frequent in both Chinese and Caucasian PIPO patients, whereas p.Arg178 variants were less common in Chinese patients compared with Caucasian patients. The 4 novel variants in ACTG2 were also found to be related to Chinese PIPO.
Collapse
|
8
|
Kumar V, Behl A, Shoaib R, Abid M, Shevtsov M, Singh S. Comparative structural insight into prefoldin subunints of archaea and eukaryotes with special emphasis on unexplored prefoldin of Plasmodium falciparum. J Biomol Struct Dyn 2020; 40:3804-3818. [PMID: 33272134 DOI: 10.1080/07391102.2020.1850527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Prefoldin (PFD) is a heterohexameric molecular chaperone which bind unfolded proteins and subsequently deliver them to a group II chaperonin for correct folding. Although there is structural and functional information available for humans and archaea PFDs, their existence and functions in malaria parasite remains uncharacterized. In the present review, we have collected the available information on prefoldin family members of archaea and humans and attempted to analyze unexplored PFD subunits of Plasmodium falciparum (Pf). Our review enhances the understanding of probable functions, structure and mechanism of substrate binding of Pf prefoldin by comparing with the available information of its homologs in archaea and H. sapiens. Three PfPFD out of six and a Pf prefoldin-like protein are reported to be essential for parasite survival that signifies their importance in malaria parasite biology. Transcriptome analyses suggest that PfPFD subunits are up-regulated at the mRNA level during asexual and sexual stages of parasite life cycle. Our in silico analysis suggested several pivotal proteins like myosin E, cytoskeletal protein (tubulin), merozoite surface protein and ring exported protein 3 as their interacting partners. Based on structural information of archaeal and H. sapiens PFDs, P. falciparum counterparts have been modelled and key interface residues were identified that are critical for oligomerization of PfPFD subunits. We collated information on PFD-substrate binding and PFD-chaperonin interaction in detail to understand the mechanism of substrate delivery in archaea and humans. Overall, our review enables readers to view the PFD family comprehensively. Communicated by Ramaswamy H. SarmaAbbreviations: HSP: Heat shock proteins; CCT: Chaperonin containing TCP-1; PFD: Prefoldin; PFLP: Prefoldin like protein; PfPFD: Plasmodium falciparum prefoldin; Pf: Plasmodium falciparum; H. sapiens: Homo sapiens; M. thermoautotrophicus: Methanobacterium thermoautotrophicus; P. horikoshii: Pyrococcus horikoshii.
Collapse
Affiliation(s)
- Vikash Kumar
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Ankita Behl
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Rumaisha Shoaib
- Medicinal Chemistry Laboratory, Department of Biosciences, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi, India
| | - Mohammad Abid
- Medicinal Chemistry Laboratory, Department of Biosciences, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi, India
| | - Maxim Shevtsov
- Center for Translational Cancer Research Technische, Universität München (TranslaTUM), Radiation Immuno Oncology group, Klinikum rechts der Isar, Munich, Germany.,Institute of Cytology of the Russian Academy of Sciences (RAS), St. Petersburg, Russia.,Department of General Surgery, Pavlov First Saint Petersburg State Medical University, Petersburg, Russia.,Almazov National Medical Research Centre, Polenov Russian Scientific Research Institute of Neurosurgery, St. Petersburg, Russia.,National Center for Neurosurgery, Nur-Sultan, Kazakhstan.,Department of Biomedical Cell Technologies, Far Eastern Federal University, Vladivostok, Russia
| | - Shailja Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| |
Collapse
|
9
|
Kumar V, Rumaisha, Behl A, Munjal A, Abid M, Singh S. Prefoldin subunit 6 of Plasmodium falciparum binds merozoite surface protein-1 (MSP-1). FEBS Open Bio 2020; 12:1050-1060. [PMID: 33145997 PMCID: PMC9063436 DOI: 10.1002/2211-5463.13022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/21/2020] [Accepted: 11/02/2020] [Indexed: 11/23/2022] Open
Abstract
Malaria is a human disease caused by eukaryotic protozoan parasites of the Plasmodium genus. Plasmodium falciparum (Pf) causes the most lethal form of human malaria and is responsible for widespread mortality worldwide. Prefoldin is a heterohexameric molecular complex that binds and delivers unfolded proteins to chaperonin for correct folding. The prefoldin PFD6 is predicted to interact with merozoite surface protein‐1 (MSP‐1), a protein well known to play a pivotal role in erythrocyte binding and invasion by Plasmodium merozoites. We previously found that the P. falciparum (Pf) genome contains six prefoldin genes and a prefoldin‐like gene whose molecular functions are unidentified. Here, we analyzed the expression of PfPFD‐6 during the asexual blood stages of the parasite and investigated its interacting partners. PfPFD‐6 was found to be significantly expressed at the trophozoite and schizont stages. Pull‐down assays suggest PfPFD‐6 interacts with MSP‐1. In silico analysis suggested critical residues involved in the PfPFD‐6‐MSP‐1 interaction. Our data suggest PfPFD‐6 may play a role in stabilizing or trafficking MSP‐1.
Collapse
Affiliation(s)
- Vikash Kumar
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Rumaisha
- Medicinal Chemistry laboratory, Department of Biosciences, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi, India
| | - Ankita Behl
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Akshay Munjal
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Mohammad Abid
- Medicinal Chemistry laboratory, Department of Biosciences, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi, India
| | - Shailja Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| |
Collapse
|
10
|
Chesnel F, Couturier A, Alusse A, Gagné JP, Poirier GG, Jean D, Boisvert FM, Hascoet P, Paillard L, Arlot-Bonnemains Y, Le Goff X. The prefoldin complex stabilizes the von Hippel-Lindau protein against aggregation and degradation. PLoS Genet 2020; 16:e1009183. [PMID: 33137104 PMCID: PMC7660911 DOI: 10.1371/journal.pgen.1009183] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 11/12/2020] [Accepted: 10/07/2020] [Indexed: 11/18/2022] Open
Abstract
Loss of von Hippel-Lindau protein pVHL function promotes VHL diseases, including sporadic and inherited clear cell Renal Cell Carcinoma (ccRCC). Mechanisms controlling pVHL function and regulation, including folding and stability, remain elusive. Here, we have identified the conserved cochaperone prefoldin complex in a screen for pVHL interactors. The prefoldin complex delivers non-native proteins to the chaperonin T-complex-protein-1-ring (TRiC) or Cytosolic Chaperonin containing TCP-1 (CCT) to assist folding of newly synthesized polypeptides. The pVHL-prefoldin interaction was confirmed in human cells and prefoldin knock-down reduced pVHL expression levels. Furthermore, when pVHL was expressed in Schizosaccharomyces pombe, all prefoldin mutants promoted its aggregation. We mapped the interaction of prefoldin with pVHL at the exon2-exon3 junction encoded region. Low levels of the PFDN3 prefoldin subunit were associated with poor survival in ccRCC patients harboring VHL mutations. Our results link the prefoldin complex with pVHL folding and this may impact VHL diseases progression.
Collapse
Affiliation(s)
- Franck Chesnel
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes)—UMR 6290, France
| | - Anne Couturier
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes)—UMR 6290, France
| | - Adrien Alusse
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes)—UMR 6290, France
| | - Jean-Philippe Gagné
- Department of Molecular Biology, Medical Biochemistry and Pathology; Université Laval, Québec City, Québec, Canada
- CHU de Québec Research Center, CHUL Pavilion, Oncology Axis, Québec City, Québec, Canada
| | - Guy G. Poirier
- Department of Molecular Biology, Medical Biochemistry and Pathology; Université Laval, Québec City, Québec, Canada
- CHU de Québec Research Center, CHUL Pavilion, Oncology Axis, Québec City, Québec, Canada
| | - Dominique Jean
- Department of Anatomy and Cell Biology, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | | | - Pauline Hascoet
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes)—UMR 6290, France
| | - Luc Paillard
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes)—UMR 6290, France
| | - Yannick Arlot-Bonnemains
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes)—UMR 6290, France
- * E-mail: (YA-B); (XLG)
| | - Xavier Le Goff
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes)—UMR 6290, France
- * E-mail: (YA-B); (XLG)
| |
Collapse
|
11
|
Cloutier P, Poitras C, Faubert D, Bouchard A, Blanchette M, Gauthier MS, Coulombe B. Upstream ORF-Encoded ASDURF Is a Novel Prefoldin-like Subunit of the PAQosome. J Proteome Res 2019; 19:18-27. [PMID: 31738558 DOI: 10.1021/acs.jproteome.9b00599] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The PAQosome is an 11-subunit chaperone involved in the biogenesis of several human protein complexes. We show that ASDURF, a recently discovered upstream open reading frame (uORF) in the 5' UTR of ASNSD1 mRNA, encodes the 12th subunit of the PAQosome. ASDURF displays significant structural homology to β-prefoldins and assembles with the five known subunits of the prefoldin-like module of the PAQosome to form a heterohexameric prefoldin-like complex. A model of the PAQosome prefoldin-like module is presented. The data presented here provide an example of a eukaryotic uORF-encoded polypeptide whose function is not limited to cis-acting translational regulation of downstream coding sequence and highlights the importance of including alternative ORF products in proteomic studies.
Collapse
Affiliation(s)
- Philippe Cloutier
- Institut de Recherches Cliniques de Montréal , 110 Avenue des Pins Ouest , Montréal , Quebec H2W 1R7 , Canada
| | - Christian Poitras
- Institut de Recherches Cliniques de Montréal , 110 Avenue des Pins Ouest , Montréal , Quebec H2W 1R7 , Canada
| | - Denis Faubert
- Institut de Recherches Cliniques de Montréal , 110 Avenue des Pins Ouest , Montréal , Quebec H2W 1R7 , Canada
| | - Annie Bouchard
- Institut de Recherches Cliniques de Montréal , 110 Avenue des Pins Ouest , Montréal , Quebec H2W 1R7 , Canada
| | - Mathieu Blanchette
- School of Computer Science , McGill University , 3480 University Street , Montréal , Quebec H3A 0E9 , Canada
| | - Marie-Soleil Gauthier
- Institut de Recherches Cliniques de Montréal , 110 Avenue des Pins Ouest , Montréal , Quebec H2W 1R7 , Canada
| | - Benoit Coulombe
- Institut de Recherches Cliniques de Montréal , 110 Avenue des Pins Ouest , Montréal , Quebec H2W 1R7 , Canada.,Département de Biochimie et Médecine Moléculaire, Faculté de Médecine , Université de Montréal , 2900 Boulevard Édouart-Montpetit , Montréal , Quebec H3T 1J4 , Canada
| |
Collapse
|
12
|
Abstract
Molecular chaperones promote the correct folding of proteins in aggregation-prone cellular environments by stabilizing nascent polypeptide chains and providing appropriate folding conditions. Prefoldins (PFDs) are molecular chaperones found in archaea and eukaryotes, generally characterized by a unique jellyfish-like hexameric structure consisting of a rigid beta-barrel backbone with protruding flexible coiled-coils. Unlike eukaryotic PFDs that mainly interact with cytoskeletal components, archaeal PFDs can stabilize a wide range of substrates; such versatility reflects PFD's role as a key element in archaeal chaperone systems, which often lack general nascent-chain binding chaperone components such as Hsp70. While archaeal PFDs mainly exist as hexameric complexes, their structural diversity ranges from tetramers to filamentous oligomers. PFDs bind and stabilize nonnative proteins using varying numbers of coiled-coils, and subsequently transfer the substrate to a group II chaperonin (CPN) for refolding. The distinct structure and specific function of archaeal PFDs have been exploited for a broad range of applications in biotechnology; furthermore, a filament-forming variant of PFD has been used to fabricate nanoscale architectures of defined shapes, demonstrating archaeal PFDs' potential applicability in nanotechnology.
Collapse
Affiliation(s)
- Samuel Lim
- Department of Chemical and Biological Engineering, University of California, Berkeley, CA, USA
| | - Dominic J Glover
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Douglas S Clark
- Department of Chemical and Biological Engineering, University of California, Berkeley, CA, USA.
| |
Collapse
|
13
|
Lynham J, Houry WA. The Multiple Functions of the PAQosome: An R2TP- and URI1 Prefoldin-Based Chaperone Complex. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1106:37-72. [DOI: 10.1007/978-3-030-00737-9_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
14
|
Expression, Functional Characterization, and Preliminary Crystallization of the Cochaperone Prefoldin from the Thermophilic Fungus Chaetomium thermophilum. Int J Mol Sci 2018; 19:ijms19082452. [PMID: 30126249 PMCID: PMC6121465 DOI: 10.3390/ijms19082452] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 08/15/2018] [Accepted: 08/15/2018] [Indexed: 02/07/2023] Open
Abstract
Prefoldin is a hexameric molecular chaperone found in the cytosol of archaea and eukaryotes. Its hexameric complex is built from two related classes of subunits, and has the appearance of a jellyfish: Its body consists of a double β-barrel assembly with six long tentacle-like coiled coils protruding from it. Using the tentacles, prefoldin captures an unfolded protein substrate and transfers it to a group II chaperonin. Based on structural information from archaeal prefoldins, mechanisms of substrate recognition and prefoldin-chaperonin cooperation have been investigated. In contrast, the structure and mechanisms of eukaryotic prefoldins remain unknown. In this study, we succeeded in obtaining recombinant prefoldin from a thermophilic fungus, Chaetomium thermophilum (CtPFD). The recombinant CtPFD could not protect citrate synthase from thermal aggregation. However, CtPFD formed a complex with actin from chicken muscle and tubulin from porcine brain, suggesting substrate specificity. We succeeded in observing the complex formation of CtPFD and the group II chaperonin of C. thermophilum (CtCCT) by atomic force microscopy and electron microscopy. These interaction kinetics were analyzed by surface plasmon resonance using Biacore. Finally, we have shown the transfer of actin from CtPFD to CtCCT. The study of the folding pathway formed by CtPFD and CtCCT should provide important information on mechanisms of the eukaryotic prefoldin–chaperonin system.
Collapse
|
15
|
Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane. Proc Natl Acad Sci U S A 2018; 115:3716-3721. [PMID: 29463731 PMCID: PMC5889667 DOI: 10.1073/pnas.1721760115] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
This study identifies and outlines a nontranscriptional branch of the canonical GA signaling pathway that redirects protein traffic from the vacuolar degradation route to the plasma membrane. As a result, the amount of receptors and transporters, such as PIN transporters for the plant hormone auxin, is functionally regulated at the cell surface. The identified branching occurs at the level of DELLA proteins that, besides transcriptional regulation, also target the microtubule (MT) network and protein trafficking. In this work, we provide multiple lines of evidence that DELLA proteins act via their interacting partners Prefoldins and that a downstream MT/CLASP1 module regulates the activity of the retromer complex that directs protein trafficking at the intersection of the vacuolar and recycling pathways. The plant hormone gibberellic acid (GA) is a crucial regulator of growth and development. The main paradigm of GA signaling puts forward transcriptional regulation via the degradation of DELLA transcriptional repressors. GA has also been shown to regulate tropic responses by modulation of the plasma membrane incidence of PIN auxin transporters by an unclear mechanism. Here we uncovered the cellular and molecular mechanisms by which GA redirects protein trafficking and thus regulates cell surface functionality. Photoconvertible reporters revealed that GA balances the protein traffic between the vacuole degradation route and recycling back to the cell surface. Low GA levels promote vacuolar delivery and degradation of multiple cargos, including PIN proteins, whereas high GA levels promote their recycling to the plasma membrane. This GA effect requires components of the retromer complex, such as Sorting Nexin 1 (SNX1) and its interacting, microtubule (MT)-associated protein, the Cytoplasmic Linker-Associated Protein (CLASP1). Accordingly, GA regulates the subcellular distribution of SNX1 and CLASP1, and the intact MT cytoskeleton is essential for the GA effect on trafficking. This GA cellular action occurs through DELLA proteins that regulate the MT and retromer presumably via their interaction partners Prefoldins (PFDs). Our study identified a branching of the GA signaling pathway at the level of DELLA proteins, which, in parallel to regulating transcription, also target by a nontranscriptional mechanism the retromer complex acting at the intersection of the degradation and recycling trafficking routes. By this mechanism, GA can redirect receptors and transporters to the cell surface, thus coregulating multiple processes, including PIN-dependent auxin fluxes during tropic responses.
Collapse
|
16
|
Sahlan M, Zako T, Yohda M. Prefoldin, a jellyfish-like molecular chaperone: functional cooperation with a group II chaperonin and beyond. Biophys Rev 2018; 10:339-345. [PMID: 29427249 DOI: 10.1007/s12551-018-0400-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 01/23/2018] [Indexed: 01/04/2023] Open
Abstract
Prefoldin is a hexameric molecular chaperone found in the cytosol of archaea and eukaryotes. Its hexameric complex is built from two related classes of subunits and has the appearance of a jellyfish: its body consists of a double beta-barrel assembly with six long tentacle-like coiled coils protruding from it. Using the tentacles, prefoldin captures an unfolded protein substrate and transfers it to a group II chaperonin. The prefoldin-group II chaperonin system is thought to be important for the folding of newly synthesized proteins and for their maintenance, or proteostasis, in the cytosol. Based on structural information of archaeal prefoldins, the mechanisms of substrate recognition and prefoldin-chaperonin cooperation have been investigated. In contrast, the role and mechanism of eukaryotic PFDs remain unknown. Recent studies have shown that prefoldin plays an important role in proteostasis and is involved in various diseases. In this paper, we review a series of studies on the molecular mechanisms of archaeal prefoldins and introduce recent findings about eukaryotic prefoldin.
Collapse
Affiliation(s)
- Muhamad Sahlan
- Department of Chemical Engineering, Universitas Indonesia, Depok, Indonesia
- Research Centre for Biomedical Engineering, Faculty of Engineering, Universitas Indonesia, Depok, Indonesia
| | - Tamotsu Zako
- Department of Chemistry and Biology, Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime, Japan
| | - Masafumi Yohda
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-4-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan.
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan.
| |
Collapse
|
17
|
Arranz R, Martín-Benito J, Valpuesta JM. Structure and Function of the Cochaperone Prefoldin. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1106:119-131. [PMID: 30484157 DOI: 10.1007/978-3-030-00737-9_9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Molecular chaperones are key players in proteostasis, the balance between protein synthesis, folding, assembly and degradation. They are helped by a plethora of cofactors termed cochaperones, which direct chaperones towards any of these different, sometime opposite pathways. One of these is prefoldin (PFD), present in eukaryotes and in archaea, a heterohexamer whose best known role is the assistance to group II chaperonins (the Hsp60 chaperones found in archaea and the eukaryotic cytosolic) in the folding of proteins in the cytosol, in particular cytoskeletal proteins. However, over the last years it has become evident a more complex role for this cochaperone, as it can adopt different oligomeric structures, form complexes with other proteins and be involved in many other processes, both in the cytosol and in the nucleus, different from folding. This review intends to describe the structure and the many functions of this interesting macromolecular complex.
Collapse
Affiliation(s)
- Rocío Arranz
- Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | | | | |
Collapse
|
18
|
Silva-Rocha WP, de Azevedo MF, Ferreira MRA, da Silva JDF, Svidzinski TIE, Milan EP, Soares LAL, Rocha KBF, Uchôa AF, Mendes-Giannini MJS, Fusco Almeida AM, Chaves GM. Effect of the Ethyl Acetate Fraction of Eugenia uniflora on Proteins Global Expression during Morphogenesis in Candida albicans. Front Microbiol 2017; 8:1788. [PMID: 29018413 PMCID: PMC5622941 DOI: 10.3389/fmicb.2017.01788] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 09/05/2017] [Indexed: 12/18/2022] Open
Abstract
Candida albicans is able to switch from yeast to hyphal growth and this is an essential step for tissue invasion and establishment of infection. Due to the limited drug arsenal used to treat fungal infections and the constant emergence of resistant strains, it is important to search for new therapeutic candidates. Therefore, this study aimed to investigate by proteomic analysis the role of a natural product (Eugenia uniflora) in impairing hypha formation in C. albicans. We also tested the potential action of E. uniflora to prevent and treat oral candidiasis induced in a murine model of oral infection and the ability of polymorphonuclear neutrophils to phagocytize C. albicans cells treated with the ethyl acetate fraction of the extract. We found that this fraction greatly reduced hypha formation after morphogenesis induction in the presence of serum. Besides, several proteins were differentially expressed in cells treated with the fraction. Surprisingly, the ethyl acetate fraction significantly reduced phagocytosis in C. albicans (Mean 120.36 ± 36.71 yeasts/100 PMNs vs. 44.68 ± 19.84 yeasts/100 PMNs). Oral candidiasis was attenuated when C. albicans cells were either pre-incubated in the presence of E. uniflora or when the fraction was applied to the surface of the oral cavity after infection. These results were consistent with the reduction in CFU counts (2.36 vs. 1.85 Log10 CFU/ml) and attenuation of tissue damage observed with histopathological analysis of animals belonging to treated group. We also observed shorter true hyphae by direct examination and histopathological analysis, when cells were treated with the referred natural product. The E. uniflora ethyl acetate fraction was non-toxic to human cells. E. uniflora may act on essential proteins mainly related to cellular structure, reducing the capacity of filamentation and attenuating infection in a murine model, without causing any toxic effect on human cells, suggesting that it may be a future therapeutic alternative for the treatment of Candida infections.
Collapse
Affiliation(s)
- Walicyranison P Silva-Rocha
- Laboratório de Micologia Médica e Molecular, Departamento de Análises Clínicas e Toxicológicas, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - Matheus F de Azevedo
- Laboratório de Micologia Médica e Molecular, Departamento de Análises Clínicas e Toxicológicas, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - Magda R A Ferreira
- Departamento de Farmácia, Centro de Ciências da Saúde, Universidade Federal de Pernambuco, Recife, Brazil
| | | | - Terezinha I E Svidzinski
- Departamento de Análise Clínicas, Centro de Ciências Biológicas, Universidade Estadual de Maringá, Maringá, Brazil
| | - Eveline P Milan
- Departamento de Infectologia, Centro de Ciências da Saúde, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - Luiz A L Soares
- Departamento de Farmácia, Centro de Ciências da Saúde, Universidade Federal de Pernambuco, Recife, Brazil
| | - Keyla B F Rocha
- Departamento de Patologia, Centro de Ciências da Saúde, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - Adriana F Uchôa
- Departamento de Biologia Celular e Genética, Centro de Biociências, Instituto de Medicina Tropical do RN, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | | | - Ana M Fusco Almeida
- Faculdade de Ciências Farmacêuticas, Universidade Estadual Paulista, São Paulo, Brazil
| | - Guilherme M Chaves
- Laboratório de Micologia Médica e Molecular, Departamento de Análises Clínicas e Toxicológicas, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| |
Collapse
|
19
|
Printz B, Guerriero G, Sergeant K, Renaut J, Lutts S, Hausman JF. Ups and downs in alfalfa: Proteomic and metabolic changes occurring in the growing stem. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 238:13-25. [PMID: 26259170 DOI: 10.1016/j.plantsci.2015.05.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 05/16/2015] [Indexed: 05/05/2023]
Abstract
The expanding interest for using lignocellulosic biomass in industry spurred the study of the mechanisms underlying plant cell-wall synthesis. Efforts using genetic approaches allowed the disentanglement of major steps governing stem fibre synthesis. Nonetheless, little is known about the relations between the stem maturation and the evolution of its proteome. During Medicago sativa L. maturation, the different internodes grow asynchronously allowing the discrimination of various developmental stages on a same stem. In this study, the proteome of three selected regions of the stem of alfalfa (apical, intermediate and basal) was analyzed and combined with a compositional analysis of the different stem parts. Interestingly, the apical and the median regions share many similarities: high abundance of chloroplast- and mitochondrial-related proteins together with the accumulation of proteins acting in the early steps of fibre production. In the mature basal region, forisomes and stress-related proteins accumulate. The RT-qPCR assessment of the expression of genes coding for members of the cellulose synthase family likewise indicates that fibres and the machinery responsible for the deposition of secondary cell walls are predominantly formed in the apical section. Altogether, this study reflects the metabolic change from the fibre production in the upper stem regions to the acquisition of defence-related functions in the fibrous basal part.
Collapse
Affiliation(s)
- Bruno Printz
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 5, Avenue des Hauts-Fourneaux, L-4362 Esch/Alzette, Luxembourg; Groupe de Recherche en Physiologie végétale (GRPV), Earth and Life Institute Agronomy (ELI-A), Université catholique de Louvain, 5 (bte 7.07.13) Place Croix du Sud, B-1348 Louvain-la-Neuve, Belgium
| | - Gea Guerriero
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 5, Avenue des Hauts-Fourneaux, L-4362 Esch/Alzette, Luxembourg
| | - Kjell Sergeant
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 5, Avenue des Hauts-Fourneaux, L-4362 Esch/Alzette, Luxembourg.
| | - Jenny Renaut
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 5, Avenue des Hauts-Fourneaux, L-4362 Esch/Alzette, Luxembourg
| | - Stanley Lutts
- Groupe de Recherche en Physiologie végétale (GRPV), Earth and Life Institute Agronomy (ELI-A), Université catholique de Louvain, 5 (bte 7.07.13) Place Croix du Sud, B-1348 Louvain-la-Neuve, Belgium
| | - Jean-Francois Hausman
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 5, Avenue des Hauts-Fourneaux, L-4362 Esch/Alzette, Luxembourg
| |
Collapse
|
20
|
Abstract
Prefoldin is a cochaperone, present in all eukaryotes, that cooperates with the chaperonin CCT. It is known mainly for its functional relevance in the cytoplasmic folding of actin and tubulin monomers during cytoskeleton assembly. However, both canonical and prefoldin-like subunits of this heterohexameric complex have also been found in the nucleus, and are functionally connected with nuclear processes in yeast and metazoa. Plant prefoldin has also been detected in the nucleus and physically associated with a gene regulator. In this review, we summarize the information available on the involvement of prefoldin in nuclear phenomena, place special emphasis on gene transcription, and discuss the possibility of a global coordination between gene regulation and cytoplasmic dynamics mediated by prefoldin.
Collapse
Affiliation(s)
- Gonzalo Millán-Zambrano
- Instituto de Biomedicina de Sevilla, Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, 41013 Seville, Spain Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Sebastián Chávez
- Instituto de Biomedicina de Sevilla, Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, 41013 Seville, Spain Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| |
Collapse
|
21
|
Na I, Reddy KD, Breydo L, Xue B, Uversky VN. A putative role of the Sup35p C-terminal domain in the cytoskeleton organization during yeast mitosis. ACTA ACUST UNITED AC 2014; 10:925-40. [DOI: 10.1039/c3mb70515c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Based on structural analysis of several effectors and partners, Sup35pC is proposed to serve as actin modulator during mitosis.
Collapse
Affiliation(s)
- Insung Na
- Department of Molecular Medicine
- Morsani College of Medicine
- University of South Florida
- Tampa, USA
| | - Krishna D. Reddy
- Department of Molecular Medicine
- Morsani College of Medicine
- University of South Florida
- Tampa, USA
| | - Leonid Breydo
- Department of Molecular Medicine
- Morsani College of Medicine
- University of South Florida
- Tampa, USA
| | - Bin Xue
- Department of Cell Biology
- Microbiology, and Molecular Biology
- College of Arts and Science
- University of South Florida
- Tampa, USA
| | - Vladimir N. Uversky
- Department of Molecular Medicine
- Morsani College of Medicine
- University of South Florida
- Tampa, USA
- USF Health Byrd Alzheimer's Research Institute
| |
Collapse
|
22
|
Millán-Zambrano G, Rodríguez-Gil A, Peñate X, de Miguel-Jiménez L, Morillo-Huesca M, Krogan N, Chávez S. The prefoldin complex regulates chromatin dynamics during transcription elongation. PLoS Genet 2013; 9:e1003776. [PMID: 24068951 PMCID: PMC3777993 DOI: 10.1371/journal.pgen.1003776] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 07/23/2013] [Indexed: 12/13/2022] Open
Abstract
Transcriptional elongation requires the concerted action of several factors that allow RNA polymerase II to advance through chromatin in a highly processive manner. In order to identify novel elongation factors, we performed systematic yeast genetic screening based on the GLAM (Gene Length-dependent Accumulation of mRNA) assay, which is used to detect defects in the expression of long transcription units. Apart from well-known transcription elongation factors, we identified mutants in the prefoldin complex subunits, which were among those that caused the most dramatic phenotype. We found that prefoldin, so far involved in the cytoplasmic co-translational assembly of protein complexes, is also present in the nucleus and that a subset of its subunits are recruited to chromatin in a transcription-dependent manner. Prefoldin influences RNA polymerase II the elongation rate in vivo and plays an especially important role in the transcription elongation of long genes and those whose promoter regions contain a canonical TATA box. Finally, we found a specific functional link between prefoldin and histone dynamics after nucleosome remodeling, which is consistent with the extensive network of genetic interactions between this factor and the machinery regulating chromatin function. This study establishes the involvement of prefoldin in transcription elongation, and supports a role for this complex in cotranscriptional histone eviction. Transcription is the biological process that allows genes to be copied into RNA; the molecule that can be read by the cell in order to fabricate its structural components, proteins. Transcription is carried out by RNA polymerases, but these molecular machines need auxiliary factors to guide them through the genome and to help them during the RNA synthesis process. We searched for novel auxiliary factors using a genetic procedure and found a set of potential novel transcriptional players. Among them, we encountered a highly unexpected result: a factor, called prefoldin, so far exclusively involved in the folding of proteins during their fabrication. We confirmed that prefoldin binds transcribed genes and plays an important role during gene transcription. We also further investigated this transcriptional role and found that prefoldin is important for unpacking genes, thus facilitating the advance of the RNA polymerases along them.
Collapse
Affiliation(s)
- Gonzalo Millán-Zambrano
- Departmento de Genética, Universidad de Sevilla, and Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
| | - Alfonso Rodríguez-Gil
- Departmento de Genética, Universidad de Sevilla, and Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
| | - Xenia Peñate
- Departmento de Genética, Universidad de Sevilla, and Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
| | - Lola de Miguel-Jiménez
- Departmento de Genética, Universidad de Sevilla, and Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
| | - Macarena Morillo-Huesca
- Departmento de Genética, Universidad de Sevilla, and Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
| | - Nevan Krogan
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, United States of America
| | - Sebastián Chávez
- Departmento de Genética, Universidad de Sevilla, and Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
- * E-mail:
| |
Collapse
|
23
|
Abe A, Takahashi-Niki K, Takekoshi Y, Shimizu T, Kitaura H, Maita H, Iguchi-Ariga SMM, Ariga H. Prefoldin plays a role as a clearance factor in preventing proteasome inhibitor-induced protein aggregation. J Biol Chem 2013; 288:27764-76. [PMID: 23946485 DOI: 10.1074/jbc.m113.476358] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Prefoldin is a molecular chaperone composed of six subunits, PFD1-6, and prevents misfolding of newly synthesized nascent polypeptides. Although it is predicted that prefoldin, like other chaperones, modulates protein aggregation, the precise function of prefoldin against protein aggregation under physiological conditions has never been elucidated. In this study, we first established an anti-prefoldin monoclonal antibody that recognizes the prefoldin complex but not its subunits. Using this antibody, it was found that prefoldin was localized in the cytoplasm with dots in co-localization with polyubiquitinated proteins and that the number and strength of dots were increased in cells that had been treated with lactacystin, a proteasome inhibitor, and thapsigargin, an inducer of endoplasmic reticulum stress. Knockdown of prefoldin increased the level of SDS-insoluble ubiquitinated protein and reduced cell viability in lactacystin and thapsigargin-treated cells. Opposite results were obtained in prefoldin-overexpressed cells. It has been reported that mice harboring a missense mutation L110R of MM-1α/PFD5 exhibit neurodegeneration in the cerebellum. Although the prefoldin complex containing L110R MM-1α was properly formed in vitro and in cells derived from L110R MM-1α mice, the levels of ubiquitinated proteins and cytotoxicity were higher in L110R MM-1α cells than in wild-type cells under normal conditions and were increased by lactacystin and thapsigargin treatment, and growth of L110R MM-1α cells was attenuated. Furthermore, the polyubiquitinated protein aggregation level was increased in the brains of L110R MM-1α mice. These results suggest that prefoldin plays a role in quality control against protein aggregation and that dysfunction of prefoldin is one of the causes of neurodegenerative diseases.
Collapse
Affiliation(s)
- Akira Abe
- From the Graduate School of Pharmaceutical Sciences, Hokkaido University, Kita-ku, Sapporo 060-0812 and
| | | | | | | | | | | | | | | |
Collapse
|
24
|
Identification of dynamic changes in proteins associated with the cellular cytoskeleton after exposure to okadaic acid. Mar Drugs 2013; 11:1763-82. [PMID: 23708184 PMCID: PMC3721204 DOI: 10.3390/md11061763] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 04/16/2013] [Accepted: 05/06/2013] [Indexed: 01/02/2023] Open
Abstract
Exposure of cells to the diarrhetic shellfish poison, okadaic acid, leads to a dramatic reorganization of cytoskeletal architecture and loss of cell-cell contact. When cells are exposed to high concentrations of okadaic acid (100–500 nM), the morphological rearrangement is followed by apoptotic cell death. Okadaic acid inhibits the broad acting Ser/Thr protein phosphatases 1 and 2A, which results in hyperphosphorylation of a large number of proteins. Some of these hyperphosphorylated proteins are most likely key players in the reorganization of the cell morphology induced by okadaic acid. We wanted to identify these phosphoproteins and searched for them in the cellular lipid rafts, which have been found to contain proteins that regulate cytoskeletal dynamics and cell adhesion. By using stable isotope labeling by amino acids in cell culture cells treated with okadaic acid (400 nM) could be combined with control cells before the isolation of lipid rafts. Protein phosphorylation events and translocations induced by okadaic acid were identified by mass spectrometry. Okadaic acid was shown to regulate the phosphorylation status and location of proteins associated with the actin cytoskeleton, microtubules and cell adhesion structures. A large number of these okadaic acid-regulated proteins have previously also been shown to be similarly regulated prior to cell proliferation and migration. Our results suggest that okadaic acid activates general cell signaling pathways that induce breakdown of the cortical actin cytoskeleton and cell detachment.
Collapse
|
25
|
Tashiro E, Zako T, Muto H, Itoo Y, Sörgjerd K, Terada N, Abe A, Miyazawa M, Kitamura A, Kitaura H, Kubota H, Maeda M, Momoi T, Iguchi-Ariga SMM, Kinjo M, Ariga H. Prefoldin protects neuronal cells from polyglutamine toxicity by preventing aggregation formation. J Biol Chem 2013; 288:19958-72. [PMID: 23720755 DOI: 10.1074/jbc.m113.477984] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Huntington disease is caused by cell death after the expansion of polyglutamine (polyQ) tracts longer than ∼40 repeats encoded by exon 1 of the huntingtin (HTT) gene. Prefoldin is a molecular chaperone composed of six subunits, PFD1-6, and prevents misfolding of newly synthesized nascent polypeptides. In this study, we found that knockdown of PFD2 and PFD5 disrupted prefoldin formation in HTT-expressing cells, resulting in accumulation of aggregates of a pathogenic form of HTT and in induction of cell death. Dead cells, however, did not contain inclusions of HTT, and analysis by a fluorescence correlation spectroscopy indicated that knockdown of PFD2 and PFD5 also increased the size of soluble oligomers of pathogenic HTT in cells. In vitro single molecule observation demonstrated that prefoldin suppressed HTT aggregation at the small oligomer (dimer to tetramer) stage. These results indicate that prefoldin inhibits elongation of large oligomers of pathogenic Htt, thereby inhibiting subsequent inclusion formation, and suggest that soluble oligomers of polyQ-expanded HTT are more toxic than are inclusion to cells.
Collapse
Affiliation(s)
- Erika Tashiro
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Sörgjerd KM, Zako T, Sakono M, Stirling PC, Leroux MR, Saito T, Nilsson P, Sekimoto M, Saido TC, Maeda M. Human prefoldin inhibits amyloid-β (Aβ) fibrillation and contributes to formation of nontoxic Aβ aggregates. Biochemistry 2013; 52:3532-42. [PMID: 23614719 DOI: 10.1021/bi301705c] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Amyloid-β (Aβ) peptides represent key players in the pathogenesis of Alzheimer's disease (AD), and mounting evidence indicates that soluble Aβ oligomers mediate the toxicity. Prefoldin (PFD) is a molecular chaperone that prevents aggregation of misfolded proteins. Here we investigated the role of PFD in Aβ aggregation. First, we demonstrated that PFD is expressed in mouse brain by Western blotting and immunohistochemistry and found that PFD is upregulated in AD model APP23 transgenic mice. Then we investigated the effect of recombinant human PFD (hPFD) on Aβ(1-42) aggregation in vitro and found that hPFD inhibited Aβ fibrillation and induced formation of soluble Aβ oligomers. Interestingly, cell viability measurements using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay showed that Aβ oligomers formed by hPFD were 30-40% less toxic to cultured rat pheochromocytoma (PC12) cells or primary cortical neurons from embryonic C57BL/6CrSlc mice than previously reported Aβ oligomers (formed by archaeal PFD) and Aβ fibrils (p < 0.001). Thioflavin T measurements and immunoblotting indicated different structural properties for the different Aβ oligomers. Our findings show a relation between cytotoxicity of Aβ oligomers and structure and suggest a possible protective role of PFD in AD.
Collapse
|
27
|
Ludueña RF. A Hypothesis on the Origin and Evolution of Tubulin. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2013; 302:41-185. [DOI: 10.1016/b978-0-12-407699-0.00002-9] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
28
|
[Molecular cloning, sequence analysis and stress-related changes of the heat shock protein 60 gene in Neobenedenia melleni]. DONG WU XUE YAN JIU = ZOOLOGICAL RESEARCH 2012; 33:603-8. [PMID: 23266980 DOI: 10.3724/sp.j.1141.2012.06603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Heat shock protein 60 is an essential chaperone that can maintain the natural structure and function of mitochondrial proteins. Here, we successfully cloned the full length cDNA of HSP60 from Neobenedenia melleni, designated as NmHSP60. Real-time quantitative PCR and Western blot were used to analyze the expression change of NmHSP60 under different temperature and salinity. Compared with the typical 25 Degrees Celsius, expressions decreased dramatically in eggs and adults at 18 Degrees Celsius. Conversely, at 32 Degrees Celsius, expression increase dramatically in adults. Compared with salinity 24, expressions were significantly down-regulated in adults at salinity 18, and up-regulated in eggs at salinity 30. Experimental results suggest that NmHSP60 may play an significant role in N. melleni's adaptation to adverse environmental conditions.
Collapse
|
29
|
A multi-omics analysis of recombinant protein production in Hek293 cells. PLoS One 2012; 7:e43394. [PMID: 22937046 PMCID: PMC3427347 DOI: 10.1371/journal.pone.0043394] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Accepted: 07/19/2012] [Indexed: 11/19/2022] Open
Abstract
Hek293 cells are the predominant hosts for transient expression of recombinant proteins and are used for stable expression of proteins where post-translational modifications performed by CHO cells are inadequate. Nevertheless, there is little information available on the key cellular features underpinning recombinant protein production in Hek293 cells. To improve our understanding of recombinant protein production in Hek293 cells and identify targets for the engineering of an improved host cell line, we have compared a stable, recombinant protein producing Hek293 cell line and its parental cell line using a combination of transcriptomics, metabolomics and fluxomics. Producer cultures consumed less glucose than non-producer cultures while achieving the same growth rate, despite the additional burden of recombinant protein production. Surprisingly, there was no indication that producer cultures compensated for the reduction in glycolytic energy by increasing the efficiency of glucose utilization or increasing glutamine consumption. In contrast, glutamine consumption was lower and the majority of genes involved in oxidative phosphorylation were downregulated in producer cultures. We observed an overall downregulation of a large number of genes associated with broad cellular functions (e.g., cell growth and proliferation) in producer cultures, and therefore speculate that a broad adaptation of the cellular network freed up resources for recombinant protein production while maintaining the same growth rate. Increased abundance of genes associated with endoplasmic reticulum stress indicated a possible bottleneck at the point of protein folding and assembly.
Collapse
|
30
|
Dingus J, Hildebrandt JD. Synthesis and assembly of G protein βγ dimers: comparison of in vitro and in vivo studies. Subcell Biochem 2012; 63:155-80. [PMID: 23161138 DOI: 10.1007/978-94-007-4765-4_9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The heterotrimeric GTP-binding proteins (G proteins) are the canonical cellular machinery used with the approximately 700 G protein-coupled receptors (GPCRs) in the human genome to transduce extracellular signals across the plasma membrane. The synthesis of the constituent G protein subunits, and their assembly into Gβγ dimers and G protein heterotrimers, determines the signaling repertoire for G-protein/GPCR signaling in cells. These synthesis/assembly -processes are intimately related to two other overlapping events in the intricate pathway leading to formation of G protein signaling complexes, posttranslational modification and intracellular trafficking of G proteins. The assembly of the Gβγ dimer is a complex process involving multiple accessory proteins and organelles. The mechanisms involved are becoming increasingly appreciated, but are still incompletely understood. In vitro and in vivo (cellular) studies provide different perspectives of these processes, and a comparison of them can provide insight into both our current level of understanding and directions to be taken in future investigations.
Collapse
Affiliation(s)
- Jane Dingus
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, Charleston, SC, 29425, USA
| | | |
Collapse
|
31
|
Miyazawa M, Tashiro E, Kitaura H, Maita H, Suto H, Iguchi-Ariga SMM, Ariga H. Prefoldin subunits are protected from ubiquitin-proteasome system-mediated degradation by forming complex with other constituent subunits. J Biol Chem 2011; 286:19191-203. [PMID: 21478150 DOI: 10.1074/jbc.m110.216259] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The molecular chaperone prefoldin (PFD) is a complex comprised of six different subunits, PFD1-PFD6, and delivers newly synthesized unfolded proteins to cytosolic chaperonin TRiC/CCT to facilitate the folding of proteins. PFD subunits also have functions different from the function of the PFD complex. We previously identified MM-1α/PFD5 as a novel c-Myc-binding protein and found that MM-1α suppresses transformation activity of c-Myc. However, it remains unclear how cells regulate protein levels of individual subunits and what mechanisms alter the ratio of their activities between subunits and their complex. In this study, we found that knockdown of one subunit decreased protein levels of other subunits and that transfection of five subunits other than MM-1α into cells increased the level of endogenous MM-1α. We also found that treatment of cells with MG132, a proteasome inhibitor, increased the level of transfected/overexpressed MM-1α but not that of endogenous MM-1α, indicating that overexpressed MM-1α, but not endogenous MM-1α, was degraded by the ubiquitin proteasome system (UPS). Experiments using other PFD subunits showed that the UPS degraded a monomer of PFD subunits, though extents of degradation varied among subunits. Furthermore, the level of one subunit was increased after co-transfection with the respective subunit, indicating that there are specific combinations between subunits to be stabilized. These results suggest mutual regulation of protein levels among PFD subunits and show how individual subunits form the PFD complex without degradation.
Collapse
Affiliation(s)
- Makoto Miyazawa
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Kita-ku, Sapporo, Japan
| | | | | | | | | | | | | |
Collapse
|
32
|
Faustino RS, Chiriac A, Niederlander NJ, Nelson TJ, Behfar A, Mishra PK, Macura S, Michalak M, Terzic A, Perez-Terzic C. Decoded calreticulin-deficient embryonic stem cell transcriptome resolves latent cardiophenotype. Stem Cells 2010; 28:1281-91. [PMID: 20506533 DOI: 10.1002/stem.447] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Genomic perturbations that challenge normal signaling at the pluripotent stage may trigger unforeseen ontogenic aberrancies. Anticipatory systems biology identification of transcriptome landscapes that underlie latent phenotypes would offer molecular diagnosis before the onset of symptoms. The purpose of this study was to assess the impact of calreticulin-deficient embryonic stem cell transcriptomes on molecular functions and physiological systems. Bioinformatic surveillance of calreticulin-null stem cells, a monogenic insult model, diagnosed a disruption in transcriptome dynamics, which re-prioritized essential cellular functions. Calreticulin-calibrated signaling axes were uncovered, and network-wide cartography of undifferentiated stem cell transcripts suggested cardiac manifestations. Calreticulin-deficient stem cell-derived cardiac cells verified disorganized sarcomerogenesis, mitochondrial paucity, and cytoarchitectural aberrations to validate calreticulin-dependent network forecasts. Furthermore, magnetic resonance imaging and histopathology detected a ventricular septal defect, revealing organogenic manifestation of calreticulin deletion. Thus, bioinformatic deciphering of a primordial calreticulin-deficient transcriptome decoded at the pluripotent stem cell stage a reconfigured multifunctional molecular registry to anticipate predifferentiation susceptibility toward abnormal cardiophenotype.
Collapse
Affiliation(s)
- Randolph S Faustino
- Marriott Heart Disease Research Program, Division of Cardiovascular Diseases, Departments of Medicine, Molecular Pharmacology and Experimental Therapeutics, and Medical Genetics, Mayo Clinic, Rochester, Minnesota 55905, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Lee Y, Smith RS, Jordan W, King BL, Won J, Valpuesta JM, Naggert JK, Nishina PM. Prefoldin 5 is required for normal sensory and neuronal development in a murine model. J Biol Chem 2010; 286:726-36. [PMID: 20956523 DOI: 10.1074/jbc.m110.177352] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Molecular chaperones and co-chaperones are crucial for cellular development and maintenance as they assist in protein folding and stabilization of unfolded or misfolded proteins. Prefoldin (PFDN), a ubiquitously expressed heterohexameric co-chaperone, is necessary for proper folding of nascent proteins, in particular, tubulin and actin. Here we show that a genetic disruption in the murine Pfdn5 gene, a subunit of prefoldin, causes a syndrome characterized by photoreceptor degeneration, central nervous system abnormalities, and male infertility. Our data indicate that a missense mutation in Pfdn5, may cause these phenotypes through a reduction in formation of microtubules and microfilaments, which are necessary for the development of cilia and cytoskeletal structures, respectively. The diversity of phenotypes demonstrated by models carrying mutations in different PFDN subunits suggests that each PFDN subunit must confer a distinct substrate specificity to the prefoldin holocomplex.
Collapse
Affiliation(s)
- YongSuk Lee
- The Jackson Laboratory, Bar Harbor, Maine 04609, USA
| | | | | | | | | | | | | | | |
Collapse
|
34
|
Sahlan M, Zako T, Tai PT, Ohtaki A, Noguchi K, Maeda M, Miyatake H, Dohmae N, Yohda M. Thermodynamic characterization of the interaction between prefoldin and group II chaperonin. J Mol Biol 2010; 399:628-36. [PMID: 20434454 DOI: 10.1016/j.jmb.2010.04.046] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2010] [Revised: 04/20/2010] [Accepted: 04/23/2010] [Indexed: 11/16/2022]
Abstract
Prefoldin (PFD) is a hexameric chaperone that captures a protein substrate and transfers it to a group II chaperonin (CPN) to complete protein folding. We have studied the interaction between PFD and CPN using those from a hyperthermophilic archaeon, Thermococcus strain KS-1 (T. KS-1). In this study, we determined the crystal structure of the T. KS-1 PFDbeta2 subunit and characterized the interactions between T. KS-1 CPNs (CPNalpha and CPNbeta) and T. KS-1 PFDs (PFDalpha1-beta1 and PFDalpha2-beta2). As predicted from its amino acid sequence, the PFDbeta2 subunit conforms to a structure similar to those of the PFDbeta1 subunit and the Pyrococcus horikoshii OT3 PFDbeta subunit, with the exception of the tip of its coiled-coil domain, which is thought to be the CPN interaction site. The interactions between T. KS-1 CPNs and PFDs (CPNalpha and PFDalpha1-beta1; CPNalpha and PFDalpha2-beta2; CPNbeta and PFDalpha1-beta1; and CPNbeta and PFDalpha2-beta2) were analyzed using the Biacore T100 system at various temperatures ranging from 20 to 45 degrees C. The affinities between PFDs and CPNs increased with an increase in temperature. The thermodynamic parameters calculated from association constants showed that the interaction between PFD and CPN is entropy driven. Among the four combinations of PFD-CPN interactions, the entropy difference in binding between CPNbeta and PFDalpha2-beta2 was the largest, and affinity significantly increased at higher temperatures. Considering that expression of PFDalpha2-beta2 and CPNbeta subunit is induced upon heat shock, our results suggest that PFDalpha1-beta1 is a general PFD for T. KS-1 CPNs, whereas PFDalpha2-beta2 is specific for CPNbeta.
Collapse
Affiliation(s)
- Muhamad Sahlan
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo 184-8588, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Rodríguez-Milla MA, Salinas J. Prefoldins 3 and 5 play an essential role in Arabidopsis tolerance to salt stress. MOLECULAR PLANT 2009; 2:526-34. [PMID: 19825635 DOI: 10.1093/mp/ssp016] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
During the last years, our understanding of the mechanisms that control plant response to salt stress has been steadily progressing. Pharmacological studies have allowed the suggestion that the cytoskeleton may be involved in regulating such a response. Nevertheless, genetic evidence establishing that the cytoskeleton has a role in plant tolerance to salt stress has not been reported yet. Here, we have characterized Arabidopsis T-DNA mutants for genes encoding proteins orthologous to prefoldin (PFD) subunits 3 and 5 from yeast and mammals. In these organisms, PFD subunits, also known as Genes Involved in Microtubule biogenesis (GIM), form a heterohexameric PFD complex implicated in tubulin and actin folding. We show that, indeed, PFD3 and PFD5 can substitute for the loss of their yeast orthologs, as they are able to complement yeast gim2Delta and gim5Delta mutants, respectively. Our results indicate that pfd3 and pfd5 mutants have reduced levels of alpha- and beta-tubulin compared to the wild-type plants when growing under both control and salt-stress conditions. In addition, pfd3 and pfd5 mutants display alterations in their developmental patterns and microtubule organization, and, more importantly, are hypersensitive to high concentrations of NaCl but not of LiCl or mannitol. These results demonstrate that the cytoskeleton plays an essential role in plant tolerance to salt stress.
Collapse
Affiliation(s)
- Miguel A Rodríguez-Milla
- Departamento de Biología de Plantas, Centro de Investigaciones Biológicas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | | |
Collapse
|
36
|
Wang S, Haynes C, Barany F, Ott J. Genome-wide autozygosity mapping in human populations. Genet Epidemiol 2009; 33:172-80. [PMID: 18814273 DOI: 10.1002/gepi.20344] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Individuals are frequently observed to have long segments of uninterrupted sequences of homozygous markers. One of the major mechanisms that gives rise to such long homozygous segments is consanguineous marriages, where parents pass shared chromosomal segments to their child. Such chromosomal segments are also known as autozygous segments. The clinical evidence that progeny from inbred individuals may have reduced health and fitness because of homozygosity of recessive alleles is well known. As the length of such homozygous segments depends on the degree of parental consanguinity, it would be logical to observe shorter homozygous segments in more outbred populations. However, a recent study identified long homozygous regions, thus likely to be autozygous segments in the HapMap populations. While an abundance of homozygous segments may significantly reduce the ability to fine map disease genes using association studies, detecting tracts of extended homozygosity related to disease status seems the natural next step in genome-wide association studies beyond allele, genotype and haplotype association analyses. In this study, we propose a new algorithm to map disease-related segments based on autozygosity using case-control data. The underlying rationale for the proposed method is that shared autozygosity regions that differ between diseased and healthy individuals may harbor mutations underlying diseases. Specifically, our algorithm uses a sliding-window framework and employs a logarithm of the odds score measure of autozygosity coupled with permutation-based methods to identify disease-related regions. We illustrate the advantage of the algorithm with its application to a genome-wide association study on Parkinson's disease.
Collapse
Affiliation(s)
- Shuang Wang
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, New York 10032, USA.
| | | | | | | |
Collapse
|
37
|
Malta-Vacas J, Nolasco S, Monteiro C, Soares H, Brito M. Translation termination and protein folding pathway genes are not correlated in gastric cancer. Clin Chem Lab Med 2009; 47:427-31. [DOI: 10.1515/cclm.2009.091] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
38
|
Iizuka R, Sugano Y, Ide N, Ohtaki A, Yoshida T, Fujiwara S, Imanaka T, Yohda M. Functional Characterization of Recombinant Prefoldin Complexes from a Hyperthermophilic Archaeon, Thermococcus sp. Strain KS-1. J Mol Biol 2008; 377:972-83. [DOI: 10.1016/j.jmb.2008.01.070] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2007] [Revised: 01/07/2008] [Accepted: 01/22/2008] [Indexed: 11/30/2022]
|
39
|
Lundin VF, Srayko M, Hyman AA, Leroux MR. Efficient chaperone-mediated tubulin biogenesis is essential for cell division and cell migration in C. elegans. Dev Biol 2007; 313:320-34. [PMID: 18062952 DOI: 10.1016/j.ydbio.2007.10.022] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2007] [Revised: 10/17/2007] [Accepted: 10/18/2007] [Indexed: 11/29/2022]
Abstract
The efficient folding of actin and tubulin in vitro and in Saccharomyces cerevisiae is known to require the molecular chaperones prefoldin and CCT, yet little is known about the functions of these chaperones in multicellular organisms. Whereas none of the six prefoldin genes are essential in yeast, where prefoldin-independent folding of actin and tubulin is sufficient for viability, we demonstrate that reducing prefoldin function by RNAi in Caenorhabditis elegans causes defects in cell division that result in embryonic lethality. Our analyses suggest that these defects result mainly from a decrease in alpha-tubulin levels and a subsequent reduction in the microtubule growth rate. Prefoldin subunit 1 (pfd-1) mutant animals with maternally contributed PFD-1 develop to the L4 larval stage with gonadogenesis defects that include aberrant distal tip cell migration. Importantly, RNAi knockdown of prefoldin, CCT or tubulin in developing animals phenocopy the pfd-1 cell migration phenotype. Furthermore, reducing CCT function causes more severe phenotypes (compared with prefoldin knockdown) in the embryo and developing gonad, consistent with a broader role for CCT in protein folding. Overall, our results suggest that efficient chaperone-mediated tubulin biogenesis is essential in C. elegans, owing to the critical role of the microtubule cytoskeleton in metazoan development.
Collapse
Affiliation(s)
- Victor F Lundin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | | | | | | |
Collapse
|
40
|
Martín-Benito J, Gómez-Reino J, Stirling PC, Lundin VF, Gómez-Puertas P, Boskovic J, Chacón P, Fernández JJ, Berenguer J, Leroux MR, Valpuesta JM. Divergent substrate-binding mechanisms reveal an evolutionary specialization of eukaryotic prefoldin compared to its archaeal counterpart. Structure 2007; 15:101-10. [PMID: 17223536 DOI: 10.1016/j.str.2006.11.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2006] [Revised: 11/28/2006] [Accepted: 11/28/2006] [Indexed: 11/24/2022]
Abstract
Prefoldin (PFD) is a molecular chaperone that stabilizes and then delivers unfolded proteins to a chaperonin for facilitated folding. The PFD hexamer has undergone an evolutionary change in subunit composition, from two PFDalpha and four PFDbeta subunits in archaea to six different subunits (two alpha-like and four beta-like subunits) in eukaryotes. Here, we show by electron microscopy that PFD from the archaeum Pyrococcus horikoshii (PhPFD) selectively uses an increasing number of subunits to interact with nonnative protein substrates of larger sizes. PhPFD stabilizes unfolded proteins by interacting with the distal regions of the chaperone tentacles, a mechanism different from that of eukaryotic PFD, which encapsulates its substrate inside the cavity. This suggests that although the fundamental functions of archaeal and eukaryal PFD are conserved, their mechanism of substrate interaction have diverged, potentially reflecting a narrower range of substrates stabilized by the eukaryotic PFD.
Collapse
Affiliation(s)
- Jaime Martín-Benito
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Campus de la Universidad Autónoma de Madrid, Darwin 3, 28049 Madrid, Spain
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Tsao ML, Chao CH, Yeh CT. Interaction of hepatitis C virus F protein with prefoldin 2 perturbs tubulin cytoskeleton organization. Biochem Biophys Res Commun 2006; 348:271-7. [PMID: 16876117 DOI: 10.1016/j.bbrc.2006.07.062] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2006] [Accepted: 07/12/2006] [Indexed: 12/25/2022]
Abstract
By use of the yeast two-hybrid system, hepatitis C virus (HCV) F protein was found to interact with a cellular protein named prefoldin 2. The interaction was confirmed by confocal immunofluorescence microscopy as well as coimmunoprecipitation experiments. Prefoldin 2 is a subunit of a hexameric molecular chaperone complex, named prefoldin, which delivers nascent actin and tubulin proteins to the eukaryotic cytosolic chaperonin for facilitated folding. Functional prefoldin spontaneously assembles from its six subunits (prefoldin 1-6). In the yeast three-hybrid system, it was found that expression of HCV F protein impeded the interaction between prefoldin 1 and 2. By performing immunofluorescence experiment and non-denaturing gel electrophoresis, it was shown that expression of HCV F protein resulted in aberrant organization of tubulin cytoskeleton. Since HCV replication requires intact microtubule and actin polymerization, HCV F protein may serve as a modulator to prevent high level of HCV replication and thus contributes to viral persistence in chronic HCV infection.
Collapse
Affiliation(s)
- Mei-Ling Tsao
- Liver Research Unit, Chang Gung Memorial Hospital, Taipei, Taiwan
| | | | | |
Collapse
|
42
|
Wang P, Wang X, Wang F, Cai T, Luo Y. Interaction between Mnk2 and CBC(VHL) ubiquitin ligase E3 complex. SCIENCE IN CHINA. SERIES C, LIFE SCIENCES 2006; 49:265-73. [PMID: 16856496 DOI: 10.1007/s11427-006-0265-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
MAP kinase-interacting kinase-2 (Mnk2) is one of the downstream kinases activated by MAP kinases. It phosphorylates the eukaryotic initiation factor 4E (eIF4E), although the role of eIF4E phosphorylation and the role of Mnk2 in the process of protein translation are not well understood. Except for eIF4E, other physiological substrates of Mnk2 are still unidentified. To look for these unidentified substrates and to reveal the physiological function of Mnk2, we performed a yeast two-hybrid screening with Mnk2 as the bait. The results demonstrated Mnk2 could interact with VHL (von Hippel-Lindau tumor suppressor), Rbx1 (ring-box 1) and Cul2 (Cullin2) proteins in yeast cells. Furthermore, we validated the interaction between Mnk2 and VHL proteins in mammalian cells by co-immunoprecipitation analysis. Because the three proteins VHL, Rbx1 and Cul2 are all components of the CBC(VHL) ubiquitin ligase E3 complex, it has been shown that Mnk2 can interact with CBC(VHL) complex, and is probably one of the new substrates of the CBC(VHL) complex. Furthermore, during the interaction of Mnk2 with von Hippel-Lindau (VHL) tumor suppressor- binding protein 1 (VBP1), it appears that Mnk2 also joins to modulate cell shape as VBP1 plays an important role in the process of the maturation of the cytoskeleton and in the process of morphogenesis.
Collapse
Affiliation(s)
- Pingzhang Wang
- Chinese National Human Genome Center, Beijing 100176, China.
| | | | | | | | | |
Collapse
|
43
|
Zhang J, Liu L, Zhang X, Jin F, Chen J, Ji C, Gu S, Xie Y, Mao Y. Cloning and Characterization of a Novel Human Prefoldin and SPEC Domain Protein Gene (PFD6L) From the Fetal Brain. Biochem Genet 2006; 44:69-74. [PMID: 16710767 DOI: 10.1007/s10528-006-9008-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2005] [Accepted: 08/16/2005] [Indexed: 10/24/2022]
Affiliation(s)
- Jiayi Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, P.R. China
| | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Pappenberger G, McCormack EA, Willison KR. Quantitative actin folding reactions using yeast CCT purified via an internal tag in the CCT3/gamma subunit. J Mol Biol 2006; 360:484-96. [PMID: 16762366 DOI: 10.1016/j.jmb.2006.05.003] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2006] [Revised: 04/28/2006] [Accepted: 05/01/2006] [Indexed: 11/16/2022]
Abstract
The eukaryotic cytosolic chaperonin CCT is an essential ATP-dependent protein folding machine whose action is required for folding the cytoskeletal proteins actin and tubulin, and a small number of other substrates, including members of the WD40-propellor repeat-containing protein family. An efficient purification protocol for CCT from Saccharomyces cerevisiae has been developed. It uses the calmodulin binding peptide as an affinity tag in an internal loop in the apical domain of the CCT3 subunit, which is predicted to be located on the outside of the double-ring assembly. This purified yeast CCT was used for a novel quantitative actin-folding assay with human beta-actin or yeast ACT1p protein folding intermediates, Ac(I), pre-synthesised in an Escherichia coli translation system. The formation of native actin follows approximately a first-order reaction with a rate constant of about 0.03 min(-1). Yeast CCT catalyses the folding of yeast ACT1p and human beta-actin with nearly identical rate constants and yields. The results from this controlled CCT-actin folding assay are consistent with a model where CCT and Ac(I) are in a binding pre-equilibrium with a rate-limiting binding step, followed by a faster ATP-driven processing to native actin. In this pure in vitro system, the human beta-actin mutants, D244S and G150P, show impaired folding behaviour in the manner predicted by our sequence-specific recognition model for CCT-actin interaction.
Collapse
Affiliation(s)
- Günter Pappenberger
- Cancer Research U.K., Centre for Cell and Molecular Biology, Chester Beatty Laboratories, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | | | | |
Collapse
|
45
|
Gangemi RMR, Daga A, Muzio L, Marubbi D, Cocozza S, Perera M, Verardo S, Bordo D, Griffero F, Capra MC, Mallamaci A, Corte G. Effects of Emx2 inactivation on the gene expression profile of neural precursors. Eur J Neurosci 2006; 23:325-34. [PMID: 16420441 DOI: 10.1111/j.1460-9568.2005.04559.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Emx2 plays a crucial role in the development of the diencephalon and dorsal telencephalon. Thus, Emx2-null mutants have abnormal cortical lamination and a reduction in size of the caudal and medial areas of the prosencephalon. Emx2 is expressed in neural precursors of the subventricular zone in vivo and in cultured neurospheres in vitro where it controls the size of the transit-amplifying population, affecting proliferation and clonal efficiency of neural stem cells. To identify the cellular processes mastered by Emx2, and possibly the molecular mechanisms by which the gene exerts its action, we compared the expression profile of cultured neurospheres derived from wild-type and Emx2-null mouse embryos. The differential expression of several genes was also confirmed by semiquantitative RT-PCR, real-time PCR and cytofluorimetric analysis in different preparations of neurospheres, and by in situ hybridization. The gene expression profile suggested a role for Emx2 in regulating the differentiation and migration properties of neural precursor cells. This involvement was confirmed in vitro, where the altered clonogenicity and impaired migration of Emx2-null cells were partially corrected by transduction of the Emx2 gene. Taken together, our results indicate that Emx2 is indeed involved in the transition between resident early progenitors (perhaps stem cells) and more mature precursors capable of migrating out of the ventricular zone, becoming postmitotic and differentiating into the appropriate cell type, and help explain the alterations observed in the brains of knock-out mice.
Collapse
|
46
|
Zhao H, Wang Q, Zhang H, Liu Q, Du X, Richter M, Greene MI. UXT is a novel centrosomal protein essential for cell viability. Mol Biol Cell 2005; 16:5857-65. [PMID: 16221885 PMCID: PMC1289427 DOI: 10.1091/mbc.e05-08-0705] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Ubiquitously expressed transcript (UXT) is a prefoldinlike protein that has been suggested to be involved in human tumorigenesis. Here, we have found that UXT is overexpressed in a number of human tumor tissues but not in the matching normal tissues. We demonstrate that UXT is located in human centrosomes and is associated with gamma-tubulin. In addition, overexpression of UXT disrupts centrosome structure. Furthermore, abrogation of UXT protein expression by small interfering RNA knockdown leads to cell death. Together, our findings suggest that UXT is a component of centrosome and is essential for cell viability. We propose that UXT may facilitate transformation by corrupting regulated centrosome functions.
Collapse
Affiliation(s)
- Huiwu Zhao
- Department of Pathology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | | | | | | | | | | |
Collapse
|
47
|
Young JC, Agashe VR, Siegers K, Hartl FU. Pathways of chaperone-mediated protein folding in the cytosol. Nat Rev Mol Cell Biol 2004; 5:781-91. [PMID: 15459659 DOI: 10.1038/nrm1492] [Citation(s) in RCA: 827] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cells are faced with the task of folding thousands of different polypeptides into a wide range of conformations. For many proteins, the folding process requires the action of molecular chaperones. In the cytosol of prokaryotic and eukaryotic cells, molecular chaperones of different structural classes form a network of pathways that can handle substrate polypeptides from the point of initial synthesis on ribosomes to the final stages of folding.
Collapse
Affiliation(s)
- Jason C Young
- Department of Biochemistry, McIntyre Medical Sciences Building, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec H3G 1Y6, Canada
| | | | | | | |
Collapse
|
48
|
Okochi M, Nomura T, Zako T, Arakawa T, Iizuka R, Ueda H, Funatsu T, Leroux M, Yohda M. Kinetics and Binding Sites for Interaction of the Prefoldin with a Group II Chaperonin. J Biol Chem 2004; 279:31788-95. [PMID: 15145959 DOI: 10.1074/jbc.m402889200] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Prefoldin is a jellyfish-shaped hexameric co-chaperone of the group II chaperonins. It captures a protein folding intermediate and transfers it to a group II chaperonin for completion of folding. The manner in which prefoldin interacts with its substrates and cooperates with the chaperonin is poorly understood. In this study, we have examined the interaction between a prefoldin and a chaperonin from hyperthermophilic archaea by immunoprecipitation, single molecule observation, and surface plasmon resonance. We demonstrate that Pyrococcus prefoldin interacts most tightly with its cognate chaperonin, and vice versa, suggesting species specificity in the interaction. Using truncation mutants, we uncovered by kinetic analyses that this interaction is multivalent in nature, consistent with multiple binding sites between the two chaperones. We present evidence that both N- and C-terminal regions of the prefoldin beta sub-unit are important for molecular chaperone activity and for the interaction with a chaperonin. Our data are consistent with substrate and chaperonin binding sites on prefoldin that are different but in close proximity, which suggests a possible handover mechanism of prefoldin substrates to the chaperonin.
Collapse
Affiliation(s)
- Mina Okochi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo 184-8588, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Lundin VF, Stirling PC, Gomez-Reino J, Mwenifumbo JC, Obst JM, Valpuesta JM, Leroux MR. Molecular clamp mechanism of substrate binding by hydrophobic coiled-coil residues of the archaeal chaperone prefoldin. Proc Natl Acad Sci U S A 2004; 101:4367-72. [PMID: 15070724 PMCID: PMC384753 DOI: 10.1073/pnas.0306276101] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Prefoldin (PFD) is a jellyfish-shaped molecular chaperone that has been proposed to play a general role in de novo protein folding in archaea and is known to assist the biogenesis of actins, tubulins, and potentially other proteins in eukaryotes. Using point mutants, chimeras, and intradomain swap variants, we show that the six coiled-coil tentacles of archaeal PFD act in concert to bind and stabilize nonnative proteins near the opening of the cavity they form. Importantly, the interaction between chaperone and substrate depends on the mostly buried interhelical hydrophobic residues of the coiled coils. We also show by electron microscopy that the tentacles can undergo an en bloc movement to accommodate an unfolded substrate. Our data reveal how archael PFD uses its unique architecture and intrinsic coiled-coil properties to interact with nonnative polypeptides.
Collapse
Affiliation(s)
- Victor F Lundin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, Canada V5A 1S6
| | | | | | | | | | | | | |
Collapse
|