1
|
Lamsal M, Luker HA, Pinch M, Hansen IA. RNAi-Mediated Knockdown of Acidic Ribosomal Stalk Protein P1 Arrests Egg Development in Adult Female Yellow Fever Mosquitoes, Aedes aegypti. INSECTS 2024; 15:84. [PMID: 38392504 PMCID: PMC10889338 DOI: 10.3390/insects15020084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/10/2024] [Accepted: 01/20/2024] [Indexed: 02/24/2024]
Abstract
After taking a blood meal, the fat body of the adult female yellow fever mosquito, Aedes aegypti, switches from a previtellogenic state of arrest to an active state of synthesizing large quantities of yolk protein precursors (YPPs) that are crucial for egg development. The synthesis of YPPs is regulated at both the transcriptional and translational levels. Previously, we identified the cytoplasmic protein general control nonderepressible 1 (GCN1) as a part of the translational regulatory pathway for YPP synthesis. In the current study, we used the C-terminal end of GCN1 to screen for protein-protein interactions and identified 60S acidic ribosomal protein P1 (P1). An expression analysis and RNAi-mediated knockdown of P1 was performed to further investigate the role of P1 in mosquito reproduction. We showed that in unfed (absence of a blood meal) adult A. aegypti mosquitoes, P1 was expressed ubiquitously in the mosquito organs and tissues tested. We also showed that the RNAi-mediated knockdown of P1 in unfed adult female mosquitoes resulted in a strong, transient knockdown with observable phenotypic changes in ovary length and egg deposition. Our results suggest that 60S acidic ribosomal protein P1 is necessary for mosquito reproduction and is a promising target for mosquito population control.
Collapse
Affiliation(s)
- Mahesh Lamsal
- Molecular Vector Physiology Laboratory, Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA
| | - Hailey A Luker
- Molecular Vector Physiology Laboratory, Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA
| | - Matthew Pinch
- Department of Biology, University of Texas El Paso, El Paso, TX 79968, USA
| | - Immo A Hansen
- Molecular Vector Physiology Laboratory, Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA
| |
Collapse
|
2
|
Chang Z, Wang X, Pan X, Yan W, Wu W, Zhuang Y, Li Z, Wang D, Yuan S, Xu C, Chen Z, Liu D, Chen ZS, Tang X, Wu J. The ribosomal protein P0A is required for embryo development in rice. BMC PLANT BIOLOGY 2023; 23:465. [PMID: 37798654 PMCID: PMC10552409 DOI: 10.1186/s12870-023-04445-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 09/06/2023] [Indexed: 10/07/2023]
Abstract
BACKGROUND The P-stalk is a conserved and vital structural element of ribosome. The eukaryotic P-stalk exists as a P0-(P1-P2)2 pentameric complex, in which P0 function as a base structure for incorporating the stalk onto 60S pre-ribosome. Prior studies have suggested that P0 genes are indispensable for survival in yeast and animals. However, the functions of P0 genes in plants remain elusive. RESULTS In the present study, we show that rice has three P0 genes predicted to encode highly conserved proteins OsP0A, OsP0B and OsP0C. All of these P0 proteins were localized both in cytoplasm and nucleus, and all interacted with OsP1. Intriguingly, the transcripts of OsP0A presented more than 90% of the total P0 transcripts. Moreover, knockout of OsP0A led to embryo lethality, while single or double knockout of OsP0B and OsP0C did not show any visible defects in rice. The genomic DNA of OsP0A could well complement the lethal phenotypes of osp0a mutant. Finally, sequence and syntenic analyses revealed that OsP0C evolved from OsP0A, and that duplication of genomic fragment harboring OsP0C further gave birth to OsP0B, and both of these duplication events might happen prior to the differentiation of indica and japonica subspecies in rice ancestor. CONCLUSION These data suggested that OsP0A functions as the predominant P0 gene, playing an essential role in embryo development in rice. Our findings highlighted the importance of P0 genes in plant development.
Collapse
Affiliation(s)
- Zhenyi Chang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Xia Wang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Xiaoying Pan
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Wei Yan
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Wenshi Wu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Yi Zhuang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Zhiai Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Dan Wang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Shuting Yuan
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Chunjue Xu
- Shenzhen Institute of Molecular Crop Design, Shenzhen, 518107, China
| | - Zhufeng Chen
- Shenzhen Institute of Molecular Crop Design, Shenzhen, 518107, China
| | - Dongfeng Liu
- Shenzhen Agricultural Technology Promotion Center, Shenzhen, 518055, China
| | - Zi Sheng Chen
- Shenzhen Agricultural Technology Promotion Center, Shenzhen, 518055, China.
| | - Xiaoyan Tang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.
- Shenzhen Institute of Molecular Crop Design, Shenzhen, 518107, China.
| | - Jianxin Wu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.
| |
Collapse
|
3
|
Yadav R, Li QZ, Huang H, Bridges SL, Kahlenberg JM, Stecenko AA, Rada B. Cystic fibrosis autoantibody signatures associate with Staphylococcus aureus lung infection or cystic fibrosis-related diabetes. Front Immunol 2023; 14:1151422. [PMID: 37767091 PMCID: PMC10519797 DOI: 10.3389/fimmu.2023.1151422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 08/18/2023] [Indexed: 09/29/2023] Open
Abstract
Introduction While cystic fibrosis (CF) lung disease is characterized by persistent inflammation and infections and chronic inflammatory diseases are often accompanied by autoimmunity, autoimmune reactivity in CF has not been studied in depth. Methods In this work we undertook an unbiased approach to explore the systemic autoantibody repertoire in CF using autoantibody microarrays. Results and discussion Our results show higher levels of several new autoantibodies in the blood of people with CF (PwCF) compared to control subjects. Some of these are IgA autoantibodies targeting neutrophil components or autoantigens linked to neutrophil-mediated tissue damage in CF. We also found that people with CF with higher systemic IgM autoantibody levels have lower prevalence of S. aureus infection. On the other hand, IgM autoantibody levels in S. aureus-infected PwCF correlate with lung disease severity. Diabetic PwCF have significantly higher levels of IgA autoantibodies in their circulation compared to nondiabetic PwCF and several of their IgM autoantibodies associate with worse lung disease. In contrast, in nondiabetic PwCF blood levels of IgA autoantibodies correlate with lung disease. We have also identified other autoantibodies in CF that associate with P. aeruginosa airway infection. In summary, we have identified several new autoantibodies and associations of autoantibody signatures with specific clinical features in CF.
Collapse
Affiliation(s)
- Ruchi Yadav
- Department of Infectious Diseases, College of Veterinary Medicine, The University of Georgia, Athens, GA, United States
| | - Quan-Zhen Li
- Department of Immunology and Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Hanwen Huang
- Department of Epidemiology & Biostatistics, College of Public Health, The University of Georgia, Athens, GA, United States
| | - S. Louis Bridges
- Department of Medicine, Hospital for Special Surgery, Division of Rheumatology, Weill Cornell Medical College, New York, NY, United States
| | - J. Michelle Kahlenberg
- Division of Rheumatology, University of Michigan, School of Medicine, Ann Arbor, MI, United States
| | - Arlene A. Stecenko
- Division of Pulmonology, Asthma, Cystic Fibrosis and Sleep, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, United States
| | - Balázs Rada
- Department of Infectious Diseases, College of Veterinary Medicine, The University of Georgia, Athens, GA, United States
| |
Collapse
|
4
|
Levi O, Mallik M, Arava YS. ThrRS-Mediated Translation Regulation of the RNA Polymerase III Subunit RPC10 Occurs through an Element with Similarity to Cognate tRNA ASL and Affects tRNA Levels. Genes (Basel) 2023; 14:462. [PMID: 36833389 PMCID: PMC9956033 DOI: 10.3390/genes14020462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023] Open
Abstract
Aminoacyl tRNA synthetases (aaRSs) are a well-studied family of enzymes with a canonical role in charging tRNAs with a specific amino acid. These proteins appear to also have non-canonical roles, including post-transcriptional regulation of mRNA expression. Many aaRSs were found to bind mRNAs and regulate their translation into proteins. However, the mRNA targets, mechanism of interaction, and regulatory consequences of this binding are not fully resolved. Here, we focused on yeast cytosolic threonine tRNA synthetase (ThrRS) to decipher its impact on mRNA binding. Affinity purification of ThrRS with its associated mRNAs followed by transcriptome analysis revealed a preference for mRNAs encoding RNA polymerase subunits. An mRNA that was significantly bound compared to all others was the mRNA encoding RPC10, a small subunit of RNA polymerase III. Structural modeling suggested that this mRNA includes a stem-loop element that is similar to the anti-codon stem loop (ASL) structure of ThrRS cognate tRNA (tRNAThr). We introduced random mutations within this element and found that almost every change from the normal sequence leads to reduced binding by ThrRS. Furthermore, point mutations at six key positions that abolish the predicted ASL-like structure showed a significant decrease in ThrRS binding with a decrease in RPC10 protein levels. Concomitantly, tRNAThr levels were reduced in the mutated strain. These data suggest a novel regulatory mechanism in which cellular tRNA levels are regulated through a mimicking element within an RNA polymerase III subunit in a manner that involves the tRNA cognate aaRS.
Collapse
Affiliation(s)
| | | | - Yoav S. Arava
- Faculty of Biology, Technion—Israel Institute of Technology, Haifa 3200003, Israel
| |
Collapse
|
5
|
Archaea/eukaryote-specific ribosomal proteins - guardians of a complex structure. Comput Struct Biotechnol J 2023; 21:1249-1261. [PMID: 36817958 PMCID: PMC9932298 DOI: 10.1016/j.csbj.2023.01.037] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 01/09/2023] [Accepted: 01/26/2023] [Indexed: 01/29/2023] Open
Abstract
In three domains of life, proteins are synthesized by large ribonucleoprotein particles called ribosomes. All ribosomes are composed of ribosomal RNAs (rRNA) and numerous ribosomal proteins (r-protein). The three-dimensional shape of ribosomes is mainly defined by a tertiary structure of rRNAs. In addition, rRNAs have a major role in decoding the information carried by messenger RNAs and catalyzing the peptide bond formation. R-proteins are essential for shaping the network of interactions that contribute to a various aspects of the protein synthesis machinery, including assembly of ribosomes and interaction of ribosomal subunits. Structural studies have revealed that many key components of ribosomes are conserved in all life domains. Besides the core structure, ribosomes contain domain-specific structural features that include additional r-proteins and extensions of rRNA and r-proteins. This review focuses specifically on those r-proteins that are found only in archaeal and eukaryotic ribosomes. The role of these archaea/eukaryote specific r-proteins in stabilizing the ribosome structure is discussed. Several examples illustrate their functions in the formation of the internal network of ribosomal subunits and interactions between the ribosomal subunits. In addition, the significance of these r-proteins in ribosome biogenesis and protein synthesis is highlighted.
Collapse
|
6
|
García-Pérez R, Ramirez JM, Ripoll-Cladellas A, Chazarra-Gil R, Oliveros W, Soldatkina O, Bosio M, Rognon PJ, Capella-Gutierrez S, Calvo M, Reverter F, Guigó R, Aguet F, Ferreira PG, Ardlie KG, Melé M. The landscape of expression and alternative splicing variation across human traits. CELL GENOMICS 2022; 3:100244. [PMID: 36777183 PMCID: PMC9903719 DOI: 10.1016/j.xgen.2022.100244] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 11/08/2022] [Accepted: 12/07/2022] [Indexed: 12/31/2022]
Abstract
Understanding the consequences of individual transcriptome variation is fundamental to deciphering human biology and disease. We implement a statistical framework to quantify the contributions of 21 individual traits as drivers of gene expression and alternative splicing variation across 46 human tissues and 781 individuals from the Genotype-Tissue Expression project. We demonstrate that ancestry, sex, age, and BMI make additive and tissue-specific contributions to expression variability, whereas interactions are rare. Variation in splicing is dominated by ancestry and is under genetic control in most tissues, with ribosomal proteins showing a strong enrichment of tissue-shared splicing events. Our analyses reveal a systemic contribution of types 1 and 2 diabetes to tissue transcriptome variation with the strongest signal in the nerve, where histopathology image analysis identifies novel genes related to diabetic neuropathy. Our multi-tissue and multi-trait approach provides an extensive characterization of the main drivers of human transcriptome variation in health and disease.
Collapse
Affiliation(s)
- Raquel García-Pérez
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Jose Miguel Ramirez
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Aida Ripoll-Cladellas
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Ruben Chazarra-Gil
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Winona Oliveros
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Oleksandra Soldatkina
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Mattia Bosio
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Paul Joris Rognon
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain,Department of Economics and Business, Universitat Pompeu Fabra, Barcelona, Catalonia 08005, Spain,Department of Statistics and Operations Research, Universitat Politècnica de Catalunya, Barcelona, Catalonia 08034, Spain
| | - Salvador Capella-Gutierrez
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Miquel Calvo
- Statistics Section, Faculty of Biology, Universitat de Barcelona (UB), Barcelona, Catalonia 08028, Spain
| | - Ferran Reverter
- Statistics Section, Faculty of Biology, Universitat de Barcelona (UB), Barcelona, Catalonia 08028, Spain
| | - Roderic Guigó
- Bioinformatics and Genomics, Center for Genomic Regulation, Barcelona, Catalonia 08003, Spain
| | | | - Pedro G. Ferreira
- Department of Computer Science, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal,Laboratory of Artificial Intelligence and Decision Support, INESC TEC, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal,Institute of Molecular Pathology and Immunology of the University of Porto, Institute for Research and Innovation in Health (i3s), R. Alfredo Allen 208, 4200-135 Porto, Portugal
| | | | - Marta Melé
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain,Corresponding author
| |
Collapse
|
7
|
Chen F, Wang N, He X. Identification of Differential Genes of DNA Methylation Associated With Alzheimer's Disease Based on Integrated Bioinformatics and Its Diagnostic Significance. Front Aging Neurosci 2022; 14:884367. [PMID: 35615586 PMCID: PMC9125150 DOI: 10.3389/fnagi.2022.884367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 04/19/2022] [Indexed: 12/16/2022] Open
Abstract
Background Alzheimer's disease (AD) is a common neurodegenerative disease. The pathogenesis is complex and has not been clearly elucidated, and there is no effective treatment. Recent studies have demonstrated that DNA methylation is closely associated with the pathogenesis of AD, which sheds light on investigating potential biomarkers for the diagnosis of early AD and related possible therapeutic approaches. Methods Alzheimer's disease patients samples and healthy controls samples were collected from two datasets in the GEO database. Using LIMMA software package in R language to find differentially expressed genes (DEGs). Afterward, DEGs have been subjected to enrichment analysis of GO and KEGG pathways. The PPI networks and Hub genes were created and visualized based on the STRING database and Cytoscape. ROC curves were further constructed to analyze the accuracy of these genes for AD diagnosis. Results Analysis of the GSE109887 and GSE97760 datasets showed 477 significant DEGs. GO and KEGG enrichment analysis showed terms related to biological processes related to these genes. The top ten Hub genes were found on the basis of the PPI network using the CytoHubba plugin, and the AUC areas of these top ranked genes were all greater than 0.7, showing satisfactory diagnostic accuracy. Conclusion The study identified the top 10 Hub genes associated with AD-related DNA methylation, of which RPSA, RPS23, and RPLP0 have high diagnostic accuracy and excellent AD biomarker potential.
Collapse
Affiliation(s)
| | | | - Xiaping He
- School of Basic Medical Sciences, Dali University, Dali, China
| |
Collapse
|
8
|
Ahn HR, Baek GO, Yoon MG, Son JA, You D, Yoon JH, Cho HJ, Kim SS, Cheong JY, Eun JW. HMBS is the most suitable reference gene for RT-qPCR in human HCC tissues and blood samples. Oncol Lett 2021; 22:791. [PMID: 34584568 PMCID: PMC8461756 DOI: 10.3892/ol.2021.13052] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 08/17/2021] [Indexed: 12/15/2022] Open
Abstract
Reverse transcription-quantitative (RT-q) PCR is the most feasible and useful technique for identifying and evaluating cancer biomarkers; however, the method requires suitable reference genes for gene expression analysis. The aim of the present study was to identify the most suitable reference gene for the normalization of relative gene expression in human hepatocellular carcinoma (HCC) tissue and blood samples. First, 14 candidate reference genes were selected through a systematic literature search. The expression levels of these genes (ACTB, B2M, GAPDH, GUSB, HMBS, HPRT1, PGK1, PPIA, RPLP0, RPL13A, SDHA, TBP, TFRC and YWHAZ) were evaluated using human multistage HCC transcriptome data (dataset GSE114564), which included normal liver (n=15), chronic hepatitis (n=20), liver cirrhosis (n=10), and early (n=18) and advanced HCC (n=45). From the 14 selected genes, five genes, whose expression levels were stable in all liver disease statuses (ACTB, GAPDH, HMBS, PPIA and RPLP0), were further assessed using RT-qPCR in 40 tissues (20 paired healthy tissues and 20 tissues from patients with HCC) and 40 blood samples (20 healthy controls and 20 samples from patients with HCC). BestKeeper statistical algorithms were used to identify the most stable reference genes, of which HMBS was found to be the most stable in both HCC tissues and blood samples. Therefore, the results of the present study suggest HMBS as a promising reference gene for the normalization of relative RT-qPCR techniques in HCC-related studies.
Collapse
Affiliation(s)
- Hye Ri Ahn
- Department of Gastroenterology, Ajou University School of Medicine, Suwon 16499, Republic of Korea.,Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon 16499, Republic of Korea
| | - Geum Ok Baek
- Department of Gastroenterology, Ajou University School of Medicine, Suwon 16499, Republic of Korea
| | - Moon Gyeong Yoon
- Department of Gastroenterology, Ajou University School of Medicine, Suwon 16499, Republic of Korea
| | - Ju A Son
- Department of Gastroenterology, Ajou University School of Medicine, Suwon 16499, Republic of Korea.,Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon 16499, Republic of Korea
| | - Donglim You
- Department of Gastroenterology, Ajou University School of Medicine, Suwon 16499, Republic of Korea.,Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon 16499, Republic of Korea
| | - Jung Hwan Yoon
- Department of Pathology, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Hyo Jung Cho
- Department of Gastroenterology, Ajou University School of Medicine, Suwon 16499, Republic of Korea
| | - Soon Sun Kim
- Department of Gastroenterology, Ajou University School of Medicine, Suwon 16499, Republic of Korea
| | - Jae Yeon Cheong
- Department of Gastroenterology, Ajou University School of Medicine, Suwon 16499, Republic of Korea
| | - Jung Woo Eun
- Department of Gastroenterology, Ajou University School of Medicine, Suwon 16499, Republic of Korea
| |
Collapse
|
9
|
Das S, Roy B, Chakrabarty S. Non-ribosomal insights into ribosomal P2 protein in Plasmodium falciparum-infected erythrocytes. Microbiologyopen 2021; 10:e1188. [PMID: 34459544 PMCID: PMC8380560 DOI: 10.1002/mbo3.1188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 04/10/2021] [Indexed: 11/12/2022] Open
Abstract
The enormous complexity of the eukaryotic ribosome has been a real challenge in unlocking the mechanistic aspects of its amazing molecular function during mRNA translation and many non‐canonical activities of ribosomal proteins in eukaryotic cells. While exploring the uncanny nature of ribosomal P proteins in malaria parasites Plasmodium falciparum, the 60S stalk ribosomal P2 protein has been shown to get exported to the infected erythrocyte (IE) surface as an SDS‐resistant oligomer during the early to the mid‐trophozoite stage. Inhibiting IE surface P2 either by monoclonal antibody or through genetic knockdown resulted in nuclear division arrest of the parasite. This strange and serendipitous finding has led us to explore more about un‐canonical cell biology and the structural involvement of P2 protein in Plasmodium in the search for a novel biochemical role during parasite propagation in the human host.
Collapse
Affiliation(s)
- Sudipta Das
- Asymmetric Cell Division Laboratory, Division of Infectious Disease and Immunology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Bhaskar Roy
- Asymmetric Cell Division Laboratory, Division of Infectious Disease and Immunology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Saswata Chakrabarty
- Asymmetric Cell Division Laboratory, Division of Infectious Disease and Immunology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| |
Collapse
|
10
|
The Importance of Protein Phosphorylation for Signaling and Metabolism in Response to Diel Light Cycling and Nutrient Availability in a Marine Diatom. BIOLOGY 2020; 9:biology9070155. [PMID: 32640597 PMCID: PMC7408324 DOI: 10.3390/biology9070155] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 07/01/2020] [Accepted: 07/03/2020] [Indexed: 01/23/2023]
Abstract
Diatoms are major contributors to global primary production and their populations in the modern oceans are affected by availability of iron, nitrogen, phosphate, silica, and other trace metals, vitamins, and infochemicals. However, little is known about the role of phosphorylation in diatoms and its role in regulation and signaling. We report a total of 2759 phosphorylation sites on 1502 proteins detected in Phaeodactylum tricornutum. Conditionally phosphorylated peptides were detected at low iron (n = 108), during the diel cycle (n = 149), and due to nitrogen availability (n = 137). Through a multi-omic comparison of transcript, protein, phosphorylation, and protein homology, we identify numerous proteins and key cellular processes that are likely under control of phospho-regulation. We show that phosphorylation regulates: (1) carbon retrenchment and reallocation during growth under low iron, (2) carbon flux towards lipid biosynthesis after the lights turn on, (3) coordination of transcription and translation over the diel cycle and (4) in response to nitrogen depletion. We also uncover phosphorylation sites for proteins that play major roles in diatom Fe sensing and utilization, including flavodoxin and phytotransferrin (ISIP2A), as well as identify phospho-regulated stress proteins and kinases. These findings provide much needed insight into the roles of protein phosphorylation in diel cycling and nutrient sensing in diatoms.
Collapse
|
11
|
Yang HW, Kim HD, Kim TS, Kim J. Senescent Cells Differentially Translate Senescence-Related mRNAs Via Ribosome Heterogeneity. J Gerontol A Biol Sci Med Sci 2020; 74:1015-1024. [PMID: 30285098 DOI: 10.1093/gerona/gly228] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Indexed: 12/15/2022] Open
Abstract
The ribosome has a lateral stalk which consists of rpLP0, rpLP1, and rpLP2. One of these proteins, rpLP2, is decreased in translating ribosome when cellular senescence is induced. Y-box binding protein-1 (YB-1) is also reduced in polysomal fraction of senescent cells. We discovered that rpLP2 depletion in the ribosome can cause the detachment of YB-1 in polysomes and that it is linked to cellular senescence. Our results also revealed that a decrement of CK2α or GRK2 in senescent cells induced an increment of unphosphorylated rpLP2, resulting in release of YB-1 from polysomes. This heterogeneous senescent ribosome has different translational efficiencies for some senescence-related genes. We also showed that the decrease of rpLP1/rpLP2 and YB-1 in senescent ribosomes was not specific to cell type or stress type and the same phenomenon was also observed in aged mouse livers regardless of gender. Taken together, our results suggest that the senescent ribosome complex appears to have low levels of rpLP1/rpLP2 and YB-1, resulting in altered translational efficiency for senescence-related genes.
Collapse
Affiliation(s)
- Hee Woong Yang
- Laboratory of Biochemistry, Division of Life Sciences, Korea University, Seoul, Republic of Korea
| | - Hag Dong Kim
- Laboratory of Biochemistry, Division of Life Sciences, Korea University, Seoul, Republic of Korea.,HAEL Lab, TechnoComplex Building, Korea University, Seoul, Republic of Korea
| | - Tae-Sung Kim
- Laboratory of Biochemistry, Division of Life Sciences, Korea University, Seoul, Republic of Korea
| | - Joon Kim
- Laboratory of Biochemistry, Division of Life Sciences, Korea University, Seoul, Republic of Korea.,HAEL Lab, TechnoComplex Building, Korea University, Seoul, Republic of Korea
| |
Collapse
|
12
|
Scollo E, Neville DC, Oruna-Concha MJ, Trotin M, Cramer R. UHPLC–MS/MS analysis of cocoa bean proteomes from four different genotypes. Food Chem 2020; 303:125244. [DOI: 10.1016/j.foodchem.2019.125244] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 07/18/2019] [Accepted: 07/23/2019] [Indexed: 01/01/2023]
|
13
|
Choi KHA, Yang L, Lee KM, Yu CWH, Banfield DK, Ito K, Uchiumi T, Wong KB. Structural and Mutagenesis Studies Evince the Role of the Extended Protuberant Domain of Ribosomal Protein uL10 in Protein Translation. Biochemistry 2019; 58:3744-3754. [PMID: 31419120 DOI: 10.1021/acs.biochem.9b00528] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The lateral stalk of ribosomes constitutes the GTPase-associated center and is responsible for recruiting translation factors to the ribosomes. The eukaryotic stalk contains a P-complex, in which one molecule of uL10 (formerly known as P0) protein binds two copies of P1/P2 heterodimers. Unlike bacterial uL10, eukaryotic uL10 has an extended protuberant (uL10ext) domain inserted into the N-terminal RNA-binding domain. Here, we determined the solution structure of the extended protuberant domain of Bombyx mori uL10 by nuclear magnetic resonance spectroscopy. Comparison of the structures of the B. mori uL10ext domain with eRF1-bound and eEF2-bound ribosomes revealed significant structural rearrangement in a "hinge" region surrounding Phe183, a residue conserved in eukaryotic but not in archaeal uL10. 15N relaxation analyses showed that residues in the hinge region have significantly large values of transverse relaxation rates. To test the role of the conserved phenylalanine residue, we created a yeast mutant strain expressing an F181A variant of uL10. An in vitro translation assay showed that the alanine substitution increased the level of polyphenylalanine synthesis by ∼33%. Taken together, our results suggest that the hinge motion of the uL10ext domain facilitates the binding of different translation factors to the GTPase-associated center during protein synthesis.
Collapse
Affiliation(s)
- Kwok-Ho Andrew Choi
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology , The Chinese University of Hong Kong , Shatin , Hong Kong, China
| | - Lei Yang
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology , The Chinese University of Hong Kong , Shatin , Hong Kong, China
| | - Ka-Ming Lee
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology , The Chinese University of Hong Kong , Shatin , Hong Kong, China
| | - Conny Wing-Heng Yu
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology , The Chinese University of Hong Kong , Shatin , Hong Kong, China
| | - David K Banfield
- Division of Life Science , Hong Kong University of Science and Technology , Clear Water Bay , Hong Kong , China
| | - Kosuke Ito
- Department of Biology, Faculty of Science , Niigata University , Ikarashi 2-8050 , Nishi-ku, Niigata 950-2191 , Japan
| | - Toshio Uchiumi
- Department of Biology, Faculty of Science , Niigata University , Ikarashi 2-8050 , Nishi-ku, Niigata 950-2191 , Japan
| | - Kam-Bo Wong
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology , The Chinese University of Hong Kong , Shatin , Hong Kong, China
| |
Collapse
|
14
|
Li XM, Li ZY, Wang YD, Wang JQ, Yang PL. Quercetin Inhibits the Proliferation and Aflatoxins Biosynthesis of Aspergillus flavus. Toxins (Basel) 2019; 11:toxins11030154. [PMID: 30857280 PMCID: PMC6468572 DOI: 10.3390/toxins11030154] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 03/03/2019] [Accepted: 03/05/2019] [Indexed: 01/10/2023] Open
Abstract
In this work of quercetin’s anti-proliferation action on A. flavus, we revealed that quercetin can effectively hamper the proliferation of A. flavus in dose-effect and time-effect relationships. We tested whether quercetin induced apoptosis in A. flavus via various detection methods, such as phosphatidylserine externalization and Hoechst 33342 staining. The results showed that quercetin had no effect on phosphatidylserine externalization and cell nucleus in A. flavus. Simultaneously, quercetin reduced the levels of reactive oxygen species (ROS). For a better understanding of the molecular mechanism of the A. flavus response to quercetin, the RNA-Seq was used to explore the transcriptomic profiles of A. flavus. According to transcriptome sequencing data, quercetin inhibits the proliferation and aflatoxin biosynthesis by regulating the expression of development-related genes and aflatoxin production-related genes. These results will provide some theoretical basis for quercetin as an anti-mildew agent resource.
Collapse
Affiliation(s)
- Xiu-Mei Li
- Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
- National Engineering Research Center of Biological Feed, Beijing 100081, China.
| | - Zhong-Yuan Li
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education & Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China.
| | - Ya-Dong Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education & Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China.
| | - Jin-Quan Wang
- Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Pei-Long Yang
- Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
- National Engineering Research Center of Biological Feed, Beijing 100081, China.
| |
Collapse
|
15
|
Yang M, Sun Y, Sun J, Wang Z, Zhou Y, Yao G, Gu Y, Zhang H, Zhao H. Differentially expressed and survival-related proteins of lung adenocarcinoma with bone metastasis. Cancer Med 2018. [PMID: 29522283 PMCID: PMC5911611 DOI: 10.1002/cam4.1363] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Despite recent advances in targeted and immune‐based therapies, the poor prognosis of lung adenocarcinoma (LUAD) with bone metastasis (BM) remains a challenge. First, two‐dimensional gel electrophoresis (2‐DE) was used to identify proteins that were differentially expressed in LUAD with BM, and then matrix‐assisted laser desorption/ionization time of flight mass spectrometry (MALDI‐TOF‐MS) was used to identify these proteins. Second, the Cancer Genome Atlas (TCGA) was used to identify mutations in these differentially expressed proteins and Kaplan–Meier plotter (KM Plotter) was used to generate survival curves for the analyzed cases. Immunohistochemistry (IHC) was used to check the expression of proteins in 28 patients with BM and nine patients with LUAD. Lastly, the results were analyzed with respect to clinical features and patient's follow‐up. We identified a number of matched proteins from 2‐DE. High expression of enolase 1 (ENO1) (HR = 1.67, logrank P = 1.9E‐05), ribosomal protein lateral stalk subunit P2 (RPLP2) (HR = 1.77, logrank P = 2.9e‐06), and NME/NM23 nucleoside diphosphate kinase 2 (NME1‐NME2) (HR = 2.65, logrank P = 3.9E‐15) was all significantly associated with poor survival (P < 0.05). Further, ENO1 was upregulated (P = 0.0004) and calcyphosine (CAPS1) was downregulated (P = 5.34E‐07) in TCGA LUAD RNA‐seq expression data. IHC revealed that prominent ENO1 staining (OR = 7.5, P = 0.034) and low levels of CAPS1 (OR = 0.01, P < 0.0001) staining were associated with BM incidence. Finally, we found that LUAD patients with high expression of ENO1 and RPLP2 had worse overall survival. This is the first instance where the genes ENO1, RPLP2, NME1‐NME2 and CAPS1 were associated with disease severity and progression in LUAD patients with BM. Thus, with this study, we have identified potential biomarkers and therapeutic targets for this disease.
Collapse
Affiliation(s)
- Mengdi Yang
- Department of Internal Oncology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiaotong University, Shanghai, 200233, China
| | - Yi Sun
- Department of Radiology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiaotong University, Shanghai, 200233, China
| | - Jing Sun
- Department of Internal Oncology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiaotong University, Shanghai, 200233, China
| | - Zhiyu Wang
- Department of Internal Oncology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiaotong University, Shanghai, 200233, China
| | - Yiyi Zhou
- Department of Internal Oncology, Shanghai Sixth People's Hospital, Soochow University, Shanghai, 200233, China
| | - Guangyu Yao
- Department of Internal Oncology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiaotong University, Shanghai, 200233, China
| | - Yifeng Gu
- Department of Radiology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiaotong University, Shanghai, 200233, China
| | - Huizhen Zhang
- Department of Pathology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiaotong University, Shanghai, 200233, China
| | - Hui Zhao
- Department of Internal Oncology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiaotong University, Shanghai, 200233, China
| |
Collapse
|
16
|
The uL10 protein, a component of the ribosomal P-stalk, is released from the ribosome in nucleolar stress. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2018; 1865:34-47. [DOI: 10.1016/j.bbamcr.2017.10.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Revised: 09/20/2017] [Accepted: 10/02/2017] [Indexed: 01/05/2023]
|
17
|
Preribosomes escaping from the nucleus are caught during translation by cytoplasmic quality control. Nat Struct Mol Biol 2017; 24:1107-1115. [PMID: 29083413 DOI: 10.1038/nsmb.3495] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 10/04/2017] [Indexed: 12/28/2022]
Abstract
Assembly of fully functional ribosomes is a prerequisite for failsafe translation. This explains why maturing preribosomal subunits have to pass through an array of quality-control checkpoints, including nuclear export, to ensure that only properly assembled ribosomes engage in translation. Despite these safeguards, we found that nuclear pre-60S particles unable to remove a transient structure composed of ITS2 pre-rRNA and associated assembly factors, termed the 'foot', escape to the cytoplasm, where they can join with mature 40S subunits to catalyze protein synthesis. However, cells harboring these abnormal ribosomes show translation defects indicated by the formation of 80S ribosomes poised with pre-60S subunits carrying tRNAs in trapped hybrid states. To overcome this translational stress, the cytoplasmic surveillance machineries RQC and Ski-exosome target these malfunctioning ribosomes. Thus, pre-60S subunits that escape nuclear quality control can enter translation, but are caught by cytoplasmic surveillance mechanisms.
Collapse
|
18
|
Song J, Che J, You Z, Ye L, Li J, Zhang Y, Qian Q, Zhong B. Phosphoproteomic analysis of the posterior silk gland of Bombyx mori provides novel insight into phosphorylation regulating the silk production. J Proteomics 2016; 148:194-201. [DOI: 10.1016/j.jprot.2016.08.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 08/03/2016] [Accepted: 08/09/2016] [Indexed: 11/28/2022]
|
19
|
Jetzt AE, Li XP, Tumer NE, Cohick WS. Toxicity of ricin A chain is reduced in mammalian cells by inhibiting its interaction with the ribosome. Toxicol Appl Pharmacol 2016; 310:120-128. [PMID: 27639428 DOI: 10.1016/j.taap.2016.09.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 09/08/2016] [Accepted: 09/10/2016] [Indexed: 01/11/2023]
Abstract
Ricin is a potent ribotoxin that is considered a bioterror threat due to its ease of isolation and possibility of aerosolization. In yeast, mutation of arginine residues away from the active site results in a ricin toxin A chain (RTA) variant that is unable to bind the ribosome and exhibits reduced cytotoxicity. The goal of the present work was to determine if these residues contribute to ribosome binding and cytotoxicity of RTA in mammalian cells. The RTA mutant R193A/R235A did not interact with mammalian ribosomes, while a G212E variant with a point mutation near its active site bound ribosomes similarly to wild-type (WT) RTA. R193A/R235A retained full catalytic activity on naked RNA but had reduced activity on mammalian ribosomes. To determine the effect of this mutant in intact cells, pre R193A/R235A containing a signal sequence directing it to the endoplasmic reticulum and mature R193A/R235A that directly targeted cytosolic ribosomes were each expressed. Depurination and protein synthesis inhibition were reduced by both pre- and mature R193A/R235A relative to WT. Protein synthesis inhibition was reduced to a greater extent by R193A/R235A than by G212E. Pre R193A/R235A caused a greater reduction in caspase activation and loss of mitochondrial membrane potential than G212E relative to WT RTA. These findings indicate that an RTA variant with reduced ribosome binding is less toxic than a variant with less catalytic activity but normal ribosome binding activity. The toxin-ribosome interaction represents a novel target for the development of therapeutics to prevent or treat ricin intoxication.
Collapse
Affiliation(s)
- Amanda E Jetzt
- Department of Animal Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901-8520, United States
| | - Xiao-Ping Li
- Department of Plant Biology and Pathology, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901-8520, United States
| | - Nilgun E Tumer
- Department of Plant Biology and Pathology, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901-8520, United States
| | - Wendie S Cohick
- Department of Animal Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901-8520, United States.
| |
Collapse
|
20
|
Pagano GJ, King RS, Martin LM, Hufnagel LA. The unique N-terminal insert in the ribosomal protein, phosphoprotein P0, of Tetrahymena thermophila: Bioinformatic evidence for an interaction with 26S rRNA. Proteins 2015; 83:1078-90. [PMID: 25820769 DOI: 10.1002/prot.24800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 02/27/2015] [Accepted: 03/20/2015] [Indexed: 11/11/2022]
Abstract
Phosphoprotein P0 (P0) is part of the stalk complex of the eukaryotic large ribosomal subunit necessary for recruiting elongation factors. While the P0 sequence is highly conserved, our group noted a 15-16 residue insert exclusive to the P0s of ciliated protists, including Tetrahymena thermophila. We hypothesized that this insert may have a function unique in ciliated protists, such as stalk regulation via phosphorylation of the insert. Almost no mention of this insert exists in the literature, and although the T. thermophila ribosome has been crystallized, there is limited structural data for Tetrahymena's P0 (TtP0) and its insert. To investigate the structure and function of the TtP0 insert, we performed in silico analyses. The TtP0 sequence was scanned with phosphorylation site prediction tools to detect the likelihood of phosphorylation in the insert. TtP0's sequence was also used to produce a homology model of the N-terminal domain of TtP0, including the insert. When the insert was modeled in the context of the 26S rRNA, it associated with a region identified as expansion segment 7B (ES7B), suggesting a potential functional interaction between ES7B and the insert in T. thermophila. We were not able to obtain sufficient data to determine whether a similar relationship exists in other ciliated protists. This study lays the groundwork for future experimental studies to verify the presence of TtP0 insert/ES7 interactions in Tetrahymena, and to explore their functional significance during protein synthesis.
Collapse
Affiliation(s)
- Giovanni J Pagano
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, Rhode Island, 02881
| | - Roberta S King
- Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, Rhode Island, 02881
| | - Lenore M Martin
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, Rhode Island, 02881
| | - Linda A Hufnagel
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, Rhode Island, 02881
| |
Collapse
|
21
|
Benvenuto M, Sileri P, Rossi P, Masuelli L, Fantini M, Nanni M, Franceschilli L, Sconocchia G, Lanzilli G, Arriga R, Faggioni G, Lista F, Orlandi A, Manzari V, Gaspari AL, Modesti A, Bei R. Natural humoral immune response to ribosomal P0 protein in colorectal cancer patients. J Transl Med 2015; 13:101. [PMID: 25889931 PMCID: PMC4411786 DOI: 10.1186/s12967-015-0455-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 03/09/2015] [Indexed: 01/19/2023] Open
Abstract
Background Tumor associated antigens are useful in colorectal cancer (CRC) management. The ribosomal P proteins (P0, P1, P2) play an important role in protein synthesis and tumor formation. The immunogenicity of the ribosomal P0 protein in head and neck, in breast and prostate cancer patients and the overexpression of the carboxyl-terminal P0 epitope (C-22 P0) in some tumors were reported. Methods Sera from 72 colorectal tumor patients (67 malignant and 5 benign tumors) were compared with 73 healthy donor sera for the presence of antibodies to CEA, EGFR, ErbB2 and ribosomal P proteins by western blotting or ELISA. Expression of the C-22 P0 epitope on tissues and colon cancer cells was determined by immunoperoxidase staining and indirect immunofluorescence/western blotting, respectively, employing MAb 2B2. Biological effects of MAb 2B2 on colon cancer cells were assessed by the Sulforhodamine B cell proliferation assay, trypan blue exclusion test and cleaved caspase-3 detection. Fisher’s exact test was used to compare the number of auto-antibodies positive patients with healthy donors. Variation in the C-22 P0 expression, and in the number of apoptotic cells was evaluated by Student’s t-test. Variation in cell survival and cell death was evaluated by Newman-Keuls test. Results No significant humoral response was observed to CEA, EGFR and ErbB2 in CRC patients. Conversely, 7 out of 67 CRC patient sera reacted to ribosomal P proteins. The prevalence of P proteins auto-antibodies in CRC patients was significant. Five patients showed restricted P0 immunoreactivity, while two patients reacted simultaneously to all P proteins. The C-22 P0 epitope was homogenously expressed both in malignant tumors and the adjacent mucosa, but the intensity of expression was higher in the tumor. Starved colon cancer cells showed a higher C-22 P0 epitope plasma membrane expression compared to control cells. MAb 2B2 inhibited colon cancer cell growth and induced cell death in a dose dependent manner. Conclusions Our study shows a spontaneous humoral immune response to ribosomal P0 protein in CRC patients and the inhibition of in vitro cancer cell growth after C-22 P0 epitope targeting. The ribosomal P0 protein might be a useful immunological target in CRC patients.
Collapse
Affiliation(s)
- Monica Benvenuto
- Department of Clinical Sciences and Translational Medicine, University of Rome "Tor Vergata", Rome, Italy.
| | - Pierpaolo Sileri
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, Italy.
| | - Piero Rossi
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, Italy.
| | - Laura Masuelli
- Department of Experimental Medicine, University of Rome "Sapienza", Rome, Italy.
| | - Massimo Fantini
- Department of Clinical Sciences and Translational Medicine, University of Rome "Tor Vergata", Rome, Italy.
| | - Monica Nanni
- Department of Clinical Sciences and Translational Medicine, University of Rome "Tor Vergata", Rome, Italy.
| | - Luana Franceschilli
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, Italy.
| | - Giuseppe Sconocchia
- Laboratory of Tumor Immunology and Immunotherapy, Institute of Translational Pharmacology, Department of Medicine, CNR, Rome, Italy.
| | - Giulia Lanzilli
- Laboratory of Tumor Immunology and Immunotherapy, Institute of Translational Pharmacology, Department of Medicine, CNR, Rome, Italy.
| | - Roberto Arriga
- Department of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy.
| | | | - Florigio Lista
- Centro Studi e Ricerche Sanità e Veterinaria Esercito, Rome, Italy.
| | - Augusto Orlandi
- Department of Biomedicine and Prevention, University of Rome "Tor Vergata", Rome, Italy.
| | - Vittorio Manzari
- Department of Clinical Sciences and Translational Medicine, University of Rome "Tor Vergata", Rome, Italy.
| | - Achille Lucio Gaspari
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, Italy.
| | - Andrea Modesti
- Department of Clinical Sciences and Translational Medicine, University of Rome "Tor Vergata", Rome, Italy.
| | - Roberto Bei
- Department of Clinical Sciences and Translational Medicine, University of Rome "Tor Vergata", Rome, Italy.
| |
Collapse
|
22
|
Bautista-Santos A, Zinker S. The P1/P2 protein heterodimers assemble to the ribosomal stalk at the moment when the ribosome is committed to translation but not to the native 60S ribosomal subunit in Saccharomyces cerevisiae. Biochemistry 2014; 53:4105-12. [PMID: 24922111 DOI: 10.1021/bi500341w] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The four structural acidic ribosomal proteins that dissociate from P1A/P2B and P1B/P2A heterodimers of Saccharomyces cerevisiae were searched in the 60S ribosomal subunit, the 80S monosome, and the polysomal fractions after ribosome profile centrifugation in sucrose gradients in TMN buffer, and after dissociation of monosomes and polysomes to small and large ribosomal subunits in LMS buffer. Analysis by isoelectric focusing, sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and Western blotting of these fractions or the purified acidic protein samples showed eight bands that correspond to the acidic ribosomal proteins in the 60S dissociated subunits of the 80S monosome and polysomes. After samples had been radiolabeled with (32)P, four bands were shown to correspond to the phosphorylated form of the acidic ribosomal proteins located in the 80S monosome and the polysomes. Surprisingly, native 60S subunits have no acidic ribosomal proteins. Altogether, these findings indicate that P1/P2 heterodimers bind to P0 when both ribosomal subunits are joined and committed to translation, and they detached from the stalk, just after the small and large ribosomal subunits were separated from the mRNA. Evidence that the phosphorylated and unphosphorylated P1 and P2 acidic ribosomal proteins are part of the functional stalk is also presented.
Collapse
Affiliation(s)
- A Bautista-Santos
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional , México D.F. 07360, México
| | | |
Collapse
|
23
|
Sulima SO, Gülay SP, Anjos M, Patchett S, Meskauskas A, Johnson AW, Dinman JD. Eukaryotic rpL10 drives ribosomal rotation. Nucleic Acids Res 2013; 42:2049-63. [PMID: 24214990 PMCID: PMC3919601 DOI: 10.1093/nar/gkt1107] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Ribosomes transit between two conformational states, non-rotated and rotated, through the elongation cycle. Here, we present evidence that an internal loop in the essential yeast ribosomal protein rpL10 is a central controller of this process. Mutations in this loop promote opposing effects on the natural equilibrium between these two extreme conformational states. rRNA chemical modification analyses reveals allosteric interactions involved in coordinating intersubunit rotation originating from rpL10 in the core of the large subunit (LSU) through both subunits, linking all the functional centers of the ribosome. Mutations promoting rotational disequilibria showed catalytic, biochemical and translational fidelity defects. An rpL3 mutation promoting opposing structural and biochemical effects, suppressed an rpL10 mutant, re-establishing rotational equilibrium. The rpL10 loop is also involved in Sdo1p recruitment, suggesting that rotational status is important for ensuring late-stage maturation of the LSU, supporting a model in which pre-60S subunits undergo a ‘test drive’ before final maturation.
Collapse
Affiliation(s)
- Sergey O Sulima
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA, Section of Molecular Genetics and Microbiology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA and Department of Biotechnology and Microbiology, Vilnius University, Vilnius LT-03101, Lithuania
| | | | | | | | | | | | | |
Collapse
|
24
|
Mishra P, Sharma S, Hosur RV. Residue level description of In vivo self-association ofPlasmodium falciparumP2. J Biomol Struct Dyn 2013; 32:602-12. [PMID: 23581826 DOI: 10.1080/07391102.2013.782827] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Pushpa Mishra
- a Department of Chemical Sciences , Tata Institute of Fundamental Research , Mumbai , India
| | | | | |
Collapse
|
25
|
Hafrén A, Eskelin K, Mäkinen K. Ribosomal protein P0 promotes Potato virus A infection and functions in viral translation together with VPg and eIF(iso)4E. J Virol 2013; 87:4302-12. [PMID: 23365448 PMCID: PMC3624370 DOI: 10.1128/jvi.03198-12] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 01/25/2013] [Indexed: 11/20/2022] Open
Abstract
We report here that the acidic ribosomal protein P0 is a component of the membrane-associated Potato virus A (PVA) ribonucleoprotein complex. As a constituent of the ribosomal stalk, P0 functions in translation. Although the ribosomal stalk proteins P0, P1, P2, and P3 are all important for PVA infection, P0 appears to have a distinct role from those of the other stalk proteins in infection. Our results indicate that P0 also regulates viral RNA functions as an extraribosomal protein. We reported previously that PVA RNA can be targeted by VPg to a specific gene expression pathway that protects the viral RNA from degradation and facilitates its translation. Here, we show that P0 is essential for this activity of VPg, similar to eIF4E/eIF(iso)4E. We also demonstrate that VPg, P0, and eIF(iso)4E synergistically enhance viral translation. Interestingly, the positive effects of VPg and P0 on viral translation were negatively correlated with the cell-to-cell spread of infection, suggesting that these processes may compete for viral RNA.
Collapse
Affiliation(s)
- Anders Hafrén
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | | | | |
Collapse
|
26
|
Bracht JR, Perlman DH, Landweber LF. Cytosine methylation and hydroxymethylation mark DNA for elimination in Oxytricha trifallax. Genome Biol 2012; 13:R99. [PMID: 23075511 PMCID: PMC3491425 DOI: 10.1186/gb-2012-13-10-r99] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 10/17/2012] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Cytosine methylation of DNA is conserved across eukaryotes and plays important functional roles regulating gene expression during differentiation and development in animals, plants and fungi. Hydroxymethylation was recently identified as another epigenetic modification marking genes important for pluripotency in embryonic stem cells. RESULTS Here we describe de novo cytosine methylation and hydroxymethylation in the ciliate Oxytricha trifallax. These DNA modifications occur only during nuclear development and programmed genome rearrangement. We detect methylcytosine and hydroxymethylcytosine directly by high-resolution nano-flow UPLC mass spectrometry, and indirectly by immunofluorescence, methyl-DNA immunoprecipitation and bisulfite sequencing. We describe these modifications in three classes of eliminated DNA: germline-limited transposons and satellite repeats, aberrant DNA rearrangements, and DNA from the parental genome undergoing degradation. Methylation and hydroxymethylation generally occur on the same sequence elements, modifying cytosines in all sequence contexts. We show that the DNA methyltransferase-inhibiting drugs azacitidine and decitabine induce demethylation of both somatic and germline sequence elements during genome rearrangements, with consequent elevated levels of germline-limited repetitive elements in exconjugant cells. CONCLUSIONS These data strongly support a functional link between cytosine DNA methylation/hydroxymethylation and DNA elimination. We identify a motif strongly enriched in methylated/hydroxymethylated regions, and we propose that this motif recruits DNA modification machinery to specific chromosomes in the parental macronucleus. No recognizable methyltransferase enzyme has yet been described in O. trifallax, raising the possibility that it might employ a novel cytosine methylation machinery to mark DNA sequences for elimination during genome rearrangements.
Collapse
|
27
|
Das S, Basu H, Korde R, Tewari R, Sharma S. Arrest of nuclear division in Plasmodium through blockage of erythrocyte surface exposed ribosomal protein P2. PLoS Pathog 2012; 8:e1002858. [PMID: 22912579 PMCID: PMC3415463 DOI: 10.1371/journal.ppat.1002858] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 06/27/2012] [Indexed: 12/24/2022] Open
Abstract
Malaria parasites reside inside erythrocytes and the disease manifestations are linked to the growth inside infected erythrocytes (IE). The growth of the parasite is mostly confined to the trophozoite stage during which nuclear division occurs followed by the formation of cell bodies (schizogony). The mechanism and regulation of schizogony are poorly understood. Here we show a novel role for a Plasmodium falciparum 60S stalk ribosomal acidic protein P2 (PfP2) (PFC0400w), which gets exported to the IE surface for 6-8 hrs during early schizogony, starting around 26-28 hrs post-merozoite invasion. The surface exposure is demonstrated using multiple PfP2-specific monoclonal antibodies, and is confirmed through transfection using PfP2-GFP. The IE surface-exposed PfP2-protein occurs mainly as SDS-resistant P2-homo-tetramers. Treatment with anti-PfP2 monoclonals causes arrest of IEs at the first nuclear division. Upon removal of the antibodies, about 80-85% of synchronized parasites can be released even after 24 hrs of antibody treatment. It has been reported that a tubovesicular network (TVN) is set up in early trophozoites which is used for nutrient import. Anti-P2 monoclonal antibodies cause a complete fragmentation of TVN by 36 hrs, and impairs lipid import in IEs. These may be downstream causes for the cell-cycle arrest. Upon antibody removal, the TVN is reconstituted, and the cell division progresses. Each of the above properties is observed in the rodent malaria parasite species P. yoelii and P. berghei. The translocation of the P2 protein to the IE surface is therefore likely to be of fundamental importance in Plasmodium cell division.
Collapse
Affiliation(s)
- Sudipta Das
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Himanish Basu
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Reshma Korde
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Rita Tewari
- Centre for Genetics and Genomics, Queen's Medical Centre, The University of Nottingham, Nottingham, United Kingdom
| | - Shobhona Sharma
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
- * E-mail:
| |
Collapse
|
28
|
Comparative proteomic and phosphoproteomic analysis of the silkworm (Bombyx mori) posterior silk gland under high temperature treatment. Mol Biol Rep 2012; 39:8447-56. [PMID: 22707192 DOI: 10.1007/s11033-012-1698-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Accepted: 06/06/2012] [Indexed: 10/28/2022]
Abstract
The proteins from the posterior silk gland of silkworm hybrids and their parents reared under high temperatures were studied by using comparative proteomic and phosphoproteomic analysis. A total of 82.07, 6.17 and 11.76 % protein spots showed additivity, overdominance and underdominance patterns, respectively. Fifteen differentially expressed protein spots were identified by peptide mass fingerprinting. Among these, four spots, including sHSPs and prohibitin protein that were directly relevant to heat response, were identified. Eleven protein spots were found to play an important role in silk synthesis, and nine protein spots expressed phosphorylation states. According to Gene ontology and KEGG pathway analysis, these nine spots played an important role in stress-induced signal transduction. Expression of most silk synthesis-related proteins was reduced, whereas stress-responsive proteins increased with heat exposure time in three breeds. Furthermore, most proteins showed under- or overdominance in the hybrids compared to the parents. The results suggested that high temperature could alter the expression of proteins related to silk synthesis and heat response in silkworm. Moreover, differentially expressed proteins occurring in the hybrid and its parents may be the main explanation of the observed heterosis.
Collapse
|
29
|
Abstract
Ricin and Shiga toxins designated as ribosome inactivating proteins (RIPs) are RNA N-glycosidases that depurinate a specific adenine (A₄₃₂₄ in rat 28S rRNA) in the conserved α-sarcin/ricin loop of the large rRNA, inhibiting protein synthesis. Evidence obtained from a number of studies suggests that interaction with ribosomal proteins plays an important role in the catalytic activity and ribosome specificity of RIPs. This review summarizes the recent developments in identification of the ribosomal proteins that interact with ricin and Shiga toxins and the principles governing these interactions.
Collapse
Affiliation(s)
- Nilgun E Tumer
- Department of Plant Biology and Pathology, School of Environmental and Biological Sciences, Rutgers University, 59 Dudley Road, New Brunswick, NJ 08901-8520, USA.
| | | |
Collapse
|
30
|
Chiou JC, Li XP, Remacha M, Ballesta JPG, Tumer NE. Shiga toxin 1 is more dependent on the P proteins of the ribosomal stalk for depurination activity than Shiga toxin 2. Int J Biochem Cell Biol 2011; 43:1792-801. [PMID: 21907821 DOI: 10.1016/j.biocel.2011.08.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Revised: 07/27/2011] [Accepted: 08/26/2011] [Indexed: 01/01/2023]
Abstract
Shiga toxins produced by Escherichia coli O157:H7 are responsible for food poisoning and hemolytic uremic syndrome (HUS). The A subunits of Shiga toxins (Stx1A and Stx2A) inhibit translation by depurinating a specific adenine in the large rRNA. To determine if Stx1A and Stx2A require the ribosomal stalk for depurination, their activity and cytotoxicity were examined in the yeast P protein deletion mutants. Stx1A and Stx2A were less toxic and depurinated ribosomes less in a strain lacking P1/P2 on the ribosome and in the cytosol (ΔP2) than in a strain lacking P1/P2 on the ribosome, but containing free P2 in the cytosol (ΔP1). To determine if cytoplasmic P proteins facilitated depurination, Stx1A and Stx2A were expressed in the P0ΔAB mutant, in which the binding sites for P1/P2 were deleted on the ribosome, and P1/P2 accumulated in the cytosol. Stx1A was less toxic and depurinated ribosomes less in P0ΔAB, suggesting that intact binding sites for P1/P2 were critical. In contrast, Stx2A was toxic and depurinated ribosomes in P0ΔAB as in wild type, suggesting that it did not require the P1/P2 binding sites. Depurination of ΔP1, but not P0ΔAB ribosomes increased upon addition of purified P1α/P2βin vitro, and the increase was greater for Stx1 than for Stx2. We conclude that cytoplasmic P proteins stimulate depurination by Stx1 by facilitating the access of the toxin to the ribosome. Although ribosomal stalk is important for Stx1 and Stx2 to depurinate the ribosome, Stx2 is less dependent on the stalk proteins for activity than Stx1 and can depurinate ribosomes with an incomplete stalk better than Stx1.
Collapse
Affiliation(s)
- Jia-Chi Chiou
- Department of Plant Biology and Pathology, School of Environmental and Biological Sciences, Rutgers University, 59 Dudley Road, New Brunswick, NJ 08901-8520, USA
| | | | | | | | | |
Collapse
|
31
|
Camargo H, Nusspaumer G, Abia D, Briceño V, Remacha M, Ballesta JPG. The amino terminal end determines the stability and assembling capacity of eukaryotic ribosomal stalk proteins P1 and P2. Nucleic Acids Res 2011; 39:3735-43. [PMID: 21247875 PMCID: PMC3089481 DOI: 10.1093/nar/gkq1356] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The eukaryotic ribosomal proteins P1 and P2 bind to protein P0 through their N-terminal domain to form the essential ribosomal stalk. A mutational analysis points to amino acids at positions 2 and 3 as determinants for the drastic difference of Saccharomyces cerevisiae P1 and P2 half-life, and suggest different degradation mechanisms for each protein type. Moreover, the capacity to form P1/P2 heterodimers is drastically affected by mutations in the P2β four initial amino acids, while these mutations have no effect on P1β. Binding of P2β and, to a lesser extent, P1β to the ribosome is also seriously affected showing the high relevance of the amino acids in the first turn of the NTD α-helix 1 for the stalk assembly. The negative effect of some mutations on ribosome binding can be reversed by the presence of the second P1/P2 couple in the ribosome, indicating a stabilizing structural influence between the two heterodimers. Unexpectedly, some mutations totally abolish heterodimer formation but allow significant ribosome binding and, therefore, a previous P1 and P2 association seems not to be an absolute requirement for stalk assembly. Homology modeling of the protein complexes suggests that the mutated residues can affect the overall protein conformation.
Collapse
Affiliation(s)
- Hendricka Camargo
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | | | | | | | | | | |
Collapse
|
32
|
Sugiyama M, Nugroho S, Iida N, Sakai T, Kaneko Y, Harashima S. Genetic interactions of ribosome maturation factors Yvh1 and Mrt4 influence mRNA decay, glycogen accumulation, and the expression of early meiotic genes in Saccharomyces cerevisiae. J Biochem 2011; 150:103-11. [PMID: 21474464 DOI: 10.1093/jb/mvr040] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The Saccharomyces cerevisiae Yvh1, a dual-specificity protein phosphatase involved in glycogen accumulation and sporulation, is required for normal vegetative growth. To further elucidate the role of Yvh1, we generated dominant mutants suppressing the slow growth caused by YVH1 disruption. One of the mutant alleles, designated as SVH1-1 (suppressor of Δyvh1 deletion), was identical to MRT4 (mRNA turnover) that contained a single-base substitution causing an amino acid change from Gly(68) to Asp. Mrt4(G68D) restored the deficiencies in growth and rRNA biogenesis that occurs in absence of Yvh1. Here, we report that the interaction between Mrt4 and Yvh1 is also essential for normal glycogen accumulation and mRNA decay as well as the induction of sporulation genes IME2, SPO13 and HOP1. The Mrt4(G68D) could restore the plethora of phenotypes we observed in absence of Yvh1. We found that Yvh1 is not essential for wild-type induction of the transcriptional regulator of these genes, IME1, suggesting that either translation or post-translational modification to activate Ime1 has been compromised. Since a defect in ribosome biogenesis in general can be related to other various defects, the ribosome biogenesis defect caused by absence of Yvh1 might be an indirect cause of observed phenotypes.
Collapse
Affiliation(s)
- Minetaka Sugiyama
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | | | | | | | | | | |
Collapse
|
33
|
David A, Netzer N, Strader MB, Das SR, Chen CY, Gibbs J, Pierre P, Bennink JR, Yewdell JW. RNA binding targets aminoacyl-tRNA synthetases to translating ribosomes. J Biol Chem 2011; 286:20688-700. [PMID: 21460219 DOI: 10.1074/jbc.m110.209452] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Here, we examine tRNA-aminoacyl synthetase (ARS) localization in protein synthesis. Proteomics reveals that ten of the twenty cytosolic ARSs associate with ribosomes in sucrose gradients: phenylalanyl-RS (FRS), and the 9 ARSs that form the multi-ARS complex (MSC). Using the ribopuromycylation method (RPM) for localizing intracellular translation, we show that FRS and the MSC, and to a lesser extent other ARSs, localize to translating ribosomes, most strikingly when translation is restricted to poxvirus or alphavirus factories in infected cells. Immunoproximity fluorescence indicates close proximity between MSC and the ribosome. Stress induced-translational shutdown recruits the MSC to stress-granules, a depot for mRNA and translation components. MSC binding to mRNA provides a facile explanation for its delivery to translating ribosomes and stress granules. These findings, along with the abundance of the MSC (9 × 10(6) copies per cell, roughly equimolar with ribosomes), is consistent with the idea that MSC specificity, recently reported to vary with cellular stress (Netzer, N., Goodenbour, J. M., David, A., Dittmar, K. A., Jones, R. B., Schneider, J. R., Boone, D., Eves, E. M., Rosner, M. R., Gibbs, J. S., Embry, A., Dolan, B., Das, S., Hickman, H. D., Berglund, P., Bennink, J. R., Yewdell, J. W., and Pan, T. (2009) Nature 462, 522-526) can be modulated at the level of individual mRNAs to modify decoding of specific gene products.
Collapse
Affiliation(s)
- Alexandre David
- Laboratory of Viral Diseases, NIAID, National Institutes of Health, Bethesda, Maryland 20892, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Marzocchella L, Sini V, Buonomo O, Orlandi A, Masuelli L, Bonanno E, Lista F, Turriziani M, Manzari V, Roselli M, Modesti A, Bei R. Spontaneous immunogenicity of ribosomal P0 protein in patients with benign and malignant breast lesions and delay of mammary tumor growth in P0-vaccinated mice. Cancer Sci 2010; 102:509-15. [DOI: 10.1111/j.1349-7006.2010.01814.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
|
35
|
Bai Y, Wu C, Zhao J, Liu YH, Ding W, Ling WLW. Role of iron and sodium citrate in animal protein-free CHO cell culture medium on cell growth and monoclonal antibody production. Biotechnol Prog 2010; 27:209-19. [DOI: 10.1002/btpr.513] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2010] [Revised: 08/18/2010] [Indexed: 01/04/2023]
|
36
|
Grela P, Krokowski D, Gordiyenko Y, Krowarsch D, Robinson CV, Otlewski J, Grankowski N, Tchórzewski M. Biophysical Properties of the Eukaryotic Ribosomal Stalk. Biochemistry 2010; 49:924-33. [DOI: 10.1021/bi901811s] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Przemysław Grela
- Department of Molecular Biology, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland
| | - Dawid Krokowski
- Department of Molecular Biology, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland
| | - Yuliya Gordiyenko
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB21EW, United Kingdom
| | - Daniel Krowarsch
- Laboratory of Protein Engineering, University of Wroclaw, Tamka 2, 50-137 Wroclaw, Poland
| | - Carol V. Robinson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB21EW, United Kingdom
| | - Jacek Otlewski
- Laboratory of Protein Engineering, University of Wroclaw, Tamka 2, 50-137 Wroclaw, Poland
| | - Nikodem Grankowski
- Department of Molecular Biology, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland
| | - Marek Tchórzewski
- Department of Molecular Biology, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland
| |
Collapse
|
37
|
Taylor DJ, Devkota B, Huang AD, Topf M, Narayanan E, Sali A, Harvey SC, Frank J. Comprehensive molecular structure of the eukaryotic ribosome. Structure 2009; 17:1591-1604. [PMID: 20004163 PMCID: PMC2814252 DOI: 10.1016/j.str.2009.09.015] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2009] [Revised: 09/16/2009] [Accepted: 09/18/2009] [Indexed: 01/02/2023]
Abstract
Despite the emergence of a large number of X-ray crystallographic models of the bacterial 70S ribosome over the past decade, an accurate atomic model of the eukaryotic 80S ribosome is still not available. Eukaryotic ribosomes possess more ribosomal proteins and ribosomal RNA than do bacterial ribosomes, which are implicated in extraribosomal functions in the eukaryotic cells. By combining cryo-EM with RNA and protein homology modeling, we obtained an atomic model of the yeast 80S ribosome complete with all ribosomal RNA expansion segments and all ribosomal proteins for which a structural homolog can be identified. Mutation or deletion of 80S ribosomal proteins can abrogate maturation of the ribosome, leading to several human diseases. We have localized one such protein unique to eukaryotes, rpS19e, whose mutations are associated with Diamond-Blackfan anemia in humans. Additionally, we characterize crucial interactions between the dynamic stalk base of the ribosome with eukaryotic elongation factor 2.
Collapse
Affiliation(s)
- Derek J Taylor
- Wadsworth Center, Empire State Plaza, Albany, NY 12201-0509, USA
| | - Batsal Devkota
- School of Biology and Parker H. Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA 30332-0230, USA
| | - Andrew D Huang
- School of Biology and Parker H. Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA 30332-0230, USA
| | - Maya Topf
- Department of Bioengineering and Therapeutical Sciences, Department of Pharmaceutical Chemistry, and California Institute of Quantitative Biosciences, Mission Bay Byers Hall, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Eswar Narayanan
- Department of Bioengineering and Therapeutical Sciences, Department of Pharmaceutical Chemistry, and California Institute of Quantitative Biosciences, Mission Bay Byers Hall, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Andrej Sali
- Department of Bioengineering and Therapeutical Sciences, Department of Pharmaceutical Chemistry, and California Institute of Quantitative Biosciences, Mission Bay Byers Hall, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Stephen C Harvey
- School of Biology and Parker H. Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA 30332-0230, USA
| | - Joachim Frank
- Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biology and Department of Biological Sciences, Columbia University, New York, NY 10032, USA.
| |
Collapse
|
38
|
Rodríguez-Mateos M, García-Gómez JJ, Francisco-Velilla R, Remacha M, de la Cruz J, Ballesta JPG. Role and dynamics of the ribosomal protein P0 and its related trans-acting factor Mrt4 during ribosome assembly in Saccharomyces cerevisiae. Nucleic Acids Res 2009; 37:7519-32. [PMID: 19789271 PMCID: PMC2794172 DOI: 10.1093/nar/gkp806] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2009] [Revised: 09/08/2009] [Accepted: 09/11/2009] [Indexed: 11/25/2022] Open
Abstract
Mrt4 is a nucleolar component of the ribosome assembly machinery that shares notable similarity and competes for binding to the 25S rRNA GAR domain with the ribosomal protein P0. Here, we show that loss of function of either P0 or Mrt4 results in a deficit in 60S subunits, which is apparently due to impaired rRNA processing of 27S precursors. Mrt4, which shuttles between the nucleus and the cytoplasm, defines medium pre-60S particles. In contrast, P0 is absent from medium but present in late/cytoplasmic pre-60S complexes. The absence of Mrt4 notably increased the amount of P0 in nuclear Nop7-TAP complexes and causes P0 assembly to medium pre-60S particles. Upon P0 depletion, Mrt4 is relocated to the cytoplasm within aberrant 60S subunits. We conclude that Mrt4 controls the position and timing of P0 assembly. In turn, P0 is required for the release of Mrt4 and exchanges with this factor at the cytoplasm. Our results also suggest other P0 assembly alternatives.
Collapse
Affiliation(s)
- María Rodríguez-Mateos
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Cantoblanco E-28049 Madrid and Departamento de Genética, Universidad de Sevilla, E-41012 Sevilla, Spain
| | - Juan J. García-Gómez
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Cantoblanco E-28049 Madrid and Departamento de Genética, Universidad de Sevilla, E-41012 Sevilla, Spain
| | - Rosario Francisco-Velilla
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Cantoblanco E-28049 Madrid and Departamento de Genética, Universidad de Sevilla, E-41012 Sevilla, Spain
| | - Miguel Remacha
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Cantoblanco E-28049 Madrid and Departamento de Genética, Universidad de Sevilla, E-41012 Sevilla, Spain
| | - Jesús de la Cruz
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Cantoblanco E-28049 Madrid and Departamento de Genética, Universidad de Sevilla, E-41012 Sevilla, Spain
| | - Juan P. G. Ballesta
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Cantoblanco E-28049 Madrid and Departamento de Genética, Universidad de Sevilla, E-41012 Sevilla, Spain
| |
Collapse
|
39
|
Zandi F, Eslami N, Soheili M, Fayaz A, Gholami A, Vaziri B. Proteomics analysis of BHK-21 cells infected with a fixed strain of rabies virus. Proteomics 2009; 9:2399-407. [PMID: 19322775 DOI: 10.1002/pmic.200701007] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Rabies is a neurotropic virus that causes a life threatening acute viral encephalitis. The complex relationship of rabies virus (RV) with the host leads to its replication and spreading toward the neural network, where viral pathogenic effects appeared as neuronal dysfunction. In order to better understand the molecular basis of this relationship, a proteomics study on baby hamster kidney cells infected with challenge virus standard strain of RV was performed. This cell line is an in vitro model for rabies infection and is commonly used for viral seed preparation. The direct effect of the virus on cellular protein machinery was investigated by 2-DE proteome mapping of infected versus control cells followed by LC-MS/MS identification. This analysis revealed significant changes in expression of 14 proteins, seven of these proteins were viral and the remaining were host proteins with different known functions: cytoskeletal (capping protein, vimentin), anti-oxidative stress (superoxide dismutase), regulatory (Stathmin), and protein synthesis (P0). Despite of limited changes appeared upon rabies infection, they present a set of interesting biochemical pathways for further investigation on viral-host interaction.
Collapse
Affiliation(s)
- Fatemeh Zandi
- Protein Chemistry Unit, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | | | | | | | | | | |
Collapse
|
40
|
Rodríguez-Mateos M, Abia D, García-Gómez JJ, Morreale A, de la Cruz J, Santos C, Remacha M, Ballesta JPG. The amino terminal domain from Mrt4 protein can functionally replace the RNA binding domain of the ribosomal P0 protein. Nucleic Acids Res 2009; 37:3514-21. [PMID: 19346338 PMCID: PMC2699499 DOI: 10.1093/nar/gkp209] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2009] [Revised: 03/06/2009] [Accepted: 03/14/2009] [Indexed: 11/20/2022] Open
Abstract
In Saccharomyces cerevisiae, the Mrt4 protein is a component of the ribosome assembly machinery that shares notable sequence homology to the P0 ribosomal stalk protein. Here, we show that these proteins can not bind simultaneously to ribosomes and moreover, a chimera containing the first 137 amino acids of Mrt4 and the last 190 amino acids from P0 can partially complement the absence of the ribosomal protein in a conditional P0 null mutant. This chimera is associated with ribosomes isolated from this strain when grown under restrictive conditions, although its binding is weaker than that of P0. These ribosomes contain less P1 and P2 proteins, the other ribosomal stalk components. Similarly, the interaction of the L12 protein, a stalk base component, is affected by the presence of the chimera. These results indicate that Mrt4 and P0 bind to the same site in the 25S rRNA. Indeed, molecular dynamics simulations using modelled Mrt4 and P0 complexes provide further evidence that both proteins bind similarly to rRNA, although their interaction with L12 displays notable differences. Together, these data support the participation of the Mrt4 protein in the assembly of the P0 protein into the ribosome and probably, that also of the L12 protein.
Collapse
Affiliation(s)
- María Rodríguez-Mateos
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Cantoblanco, Madrid 28049 and Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes, Sevilla
| | - David Abia
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Cantoblanco, Madrid 28049 and Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes, Sevilla
| | - Juan J. García-Gómez
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Cantoblanco, Madrid 28049 and Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes, Sevilla
| | - Antonio Morreale
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Cantoblanco, Madrid 28049 and Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes, Sevilla
| | - Jesús de la Cruz
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Cantoblanco, Madrid 28049 and Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes, Sevilla
| | - Cruz Santos
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Cantoblanco, Madrid 28049 and Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes, Sevilla
| | - Miguel Remacha
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Cantoblanco, Madrid 28049 and Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes, Sevilla
| | - Juan P. G. Ballesta
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Cantoblanco, Madrid 28049 and Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes, Sevilla
| |
Collapse
|
41
|
Artero-Castro A, Kondoh H, Fernández-Marcos P, Serrano M, y Cajal SR, LLeonart M. Rplp1 bypasses replicative senescence and contributes to transformation. Exp Cell Res 2009; 315:1372-83. [DOI: 10.1016/j.yexcr.2009.02.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2008] [Revised: 12/03/2008] [Accepted: 02/09/2009] [Indexed: 10/21/2022]
|
42
|
Briceño V, Camargo H, Remacha M, Santos C, Ballesta JPG. Structural and functional characterization of the amino terminal domain of the yeast ribosomal stalk P1 and P2 proteins. Int J Biochem Cell Biol 2008; 41:1315-22. [PMID: 19084076 DOI: 10.1016/j.biocel.2008.11.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2008] [Revised: 11/07/2008] [Accepted: 11/17/2008] [Indexed: 11/17/2022]
Abstract
The essential ribosomal stalk is formed in eukaryotes by a pentamer of two P1-P2 protein heterodimers and the P0 rRNA binding protein. In contrast to the highly stable prokaryotic complex, the P1 and P2 proteins in the eukaryotic stalk undergo a cyclic process of assembly and disassembly during translation that seems to modulate the ribosome activity. To better understand this process, the regions of the Saccharomyces cerevisiae P1alpha and P2beta proteins that are directly involved in heterodimer formation and ribosome binding have been characterized using a series of P1alpha/P2beta chimeras. The region required for a stable interaction with the ribosome is formed by the first three predicted alpha-helices in the N-terminal domain of both proteins. The same region is required for heterodimer formation in P2beta but the third helix is dispensable for this association in P1alpha. It seems, therefore, that stable ribosome binding is more structurally demanding than heterodimerization. A fourth predicted alpha-helix in the N-terminal domain of P1alpha and P2beta appears not to be involved in the assembly process but rather, it contributes to the conformation of the proteins by apparently restricting the mobility of their C-terminal domain and paradoxically, by reducing their activity. In addition, the study of P1/P2 chimeras showed that the C-terminal domains of these two types of protein are functionally identical and that their protein specificity is exclusively determined by their N-terminal domains.
Collapse
Affiliation(s)
- Verónica Briceño
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid and Consejo Superior de Investigaciones Científicas, Cantoblanco, Madrid 28049, Spain
| | | | | | | | | |
Collapse
|
43
|
Abstract
The 'stalk' is a large ribosomal subunit domain that regulates translation. In the present study the role of the ribosomal stalk P proteins in modulating ribosomal activity has been investigated in human cells using RNA interference. A strong down-regulation of P2 mRNA and a drastic decrease in P2 protein in a stable human cell line was achieved using a doxycycline-inducible system. Interestingly, the amount of P1 protein was similarly decreased in these cells, in contrast with the expression of P1 mRNA. The loss of P1/P2 proteins produced a decrease in the growth rate of these cells, as well as an altered polysome pattern with reduced translation efficiency, but without affecting the free 40 S/60 S subunit ratio. A decrease in the ribosomal-subunit joining capacity was also observed. These data indicate that P1/P2 proteins modulate cytoplasmic translation by influencing the interaction between subunits, thereby regulating the rate of cell proliferation.
Collapse
|
44
|
Rowe A, Yun K, Emery D, Sangster N. Haemonchus contortus: Development of a two-step, differential-display PCR to detect differential gene expression in nematodes from immune and naïve sheep. Exp Parasitol 2008; 119:207-16. [DOI: 10.1016/j.exppara.2008.01.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2007] [Revised: 01/17/2008] [Accepted: 01/23/2008] [Indexed: 02/02/2023]
|
45
|
García-Marcos A, Sánchez SA, Parada P, Eid J, Jameson DM, Remacha M, Gratton E, Ballesta JPG. Yeast ribosomal stalk heterogeneity in vivo shown by two-photon FCS and molecular brightness analysis. Biophys J 2008; 94:2884-90. [PMID: 18096629 PMCID: PMC2267128 DOI: 10.1529/biophysj.107.121822] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2007] [Accepted: 11/26/2007] [Indexed: 11/18/2022] Open
Abstract
The stalk of Saccharomyces cerevisiae ribosomes contains, on average, five distinct proteins, namely P0 and four acidic proteins, P1alpha, P1beta, P2alpha, and P2beta. Each ribosome contains only one copy of P0, but the distribution of the acidic proteins among the ribosome population in vivo has not been determined. Using two-photon fluorescence correlation spectroscopy and scanning FCS, on cells expressing EGFP-tagged P0, P1, and P2 proteins, we show, with brightness analysis, that individual yeast ribosomes in vivo are compositionally heterogeneous in regard to P1alpha, P1beta, P2alpha, and P2beta. These results are relevant to the hypothesis, based on in vitro studies, that the overall cellular pattern of expressed proteins can be determined by the distribution of the stalk proteins among the ribosome population.
Collapse
Affiliation(s)
- Alberto García-Marcos
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | | | | | | | | | | | | | | |
Collapse
|
46
|
Impaired ribosome biogenesis disrupts the integration between morphogenesis and nuclear duplication during the germination of Aspergillus fumigatus. EUKARYOTIC CELL 2008; 7:575-83. [PMID: 18296619 DOI: 10.1128/ec.00412-07] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Aspergillus fumigatus is an important opportunistic fungal pathogen that is responsible for high mortality rates in the immunosuppressed population. CgrA, the A. fumigatus ortholog of a Saccharomyces cerevisiae nucleolar protein involved in ribosome biogenesis, contributes to the virulence of this fungus by supporting rapid growth at 37 degrees C. To determine how CgrA affects ribosome biogenesis in A. fumigatus, polysome profile and ribosomal subunit analyses were performed on both wild-type A. fumigatus and a DeltacgrA mutant. The loss of CgrA was associated with a reduction in the level of 80S monosomes as well as an imbalance in the 60S:40S subunit ratio and the appearance of half-mer ribosomes. The gene expression profile in the DeltacgrA mutant revealed increased abundance of a subset of translational machinery mRNAs relative to the wild type, suggesting a potential compensatory response to CgrA deficiency. Although DeltacgrA conidia germinated normally at 22 degrees C, they swelled excessively when incubated at 37 degrees C and accumulated abnormally high numbers of nuclei. This hypernucleated phenotype could be replicated pharmacologically by germinating wild-type conidia under conditions of reductive stress. These findings indicate that the germination process is particularly vulnerable to global disruption of protein synthesis and suggest that CgrA is involved in both ribosome biogenesis and polarized cell growth in A. fumigatus.
Collapse
|
47
|
Abolition of stress-induced protein synthesis sensitizes leukemia cells to anthracycline-induced death. Blood 2008; 111:2866-77. [PMID: 18182573 DOI: 10.1182/blood-2007-07-103242] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Anthracycline action has been thought to involve the neosynthesis of proapoptotic gene products and to therefore depend on protein synthesis for optimal effect. We found that inhibition of general, but not rapamycin-sensitive (cap-dependent), protein synthesis in the preapoptotic period enhanced anthracycline-induced acute myelogenous leukemia (AML) cell death, both in vitro and in several animal AML models. Pre-apoptotic anthracycline-exposed AML cells had altered translational specificity, with enhanced synthesis of a subset of proteins, including endoplasmatic reticulum chaperones. The altered translational specificity could be explained by perturbation (protein degradation, truncation, or dephosphorylation) of the cap-dependent translation initiation machinery and of proteins control-ing translation of specific mRNAs. We propose that judiciously timed inhibition of cap-independent translation is considered for combination therapy with anthracyclines in AML.
Collapse
|
48
|
Du YJ, Luo XY, Hao YZ, Zhang T, Hou WR. cDNA cloning and overexpression of acidic ribosomal phosphoprotein P1 gene (RPLP1) from the giant panda. Int J Biol Sci 2007; 3:428-33. [PMID: 18071584 PMCID: PMC2043164 DOI: 10.7150/ijbs.3.428] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2007] [Accepted: 10/18/2007] [Indexed: 01/23/2023] Open
Abstract
RPLP1 is one of acidic ribosomal phosphoproteins encoded by RPLP1 gene, which plays an important role in the elongation step of protein synthesis. The cDNA of RPLP1 was cloned successfully for the first time from the Giant Panda (Ailuropoda melanoleuca) using RT-PCR technology, which was also sequenced, analyzed preliminarily and expressed in E.coli. The cDNA fragment cloned is 449bp in size, containing an open reading frame of 344bp encoding 114 amino acids. Alignment analysis indicated that the nucleotide sequence and the deduced amino acid sequence are highly conserved to other five species studied, including Homo sapiens, Mus musculus, Rattus norvegicus, Bos Taurus and Sus scrofa. The homologies for nucleotide sequences of Giant Panda PPLP1 to that of these species are 92.4%, 89.8%, 89.0%, 91.3% and 87.5%, while the homologies for amino acid sequences are 96.5%, 94.7%, 95.6%, 96.5% and 88.6%. Topology prediction showed there are three Casein kinase II phosphorylation sites and two N-myristoylation sites in the RPLP1 protein of the Giant Panda (Ailuropoda melanoleuca). The RPLP1 gene was overexpressed in E. coli and the result indicated that RPLP1 fusion with the N-terminally His-tagged form gave rise to the accumulation of an expected 18kDa polypeptide, which was in accordance with the predicted protein and could also be used to purify the protein and study its function.
Collapse
Affiliation(s)
- Yu-Jie Du
- College of Life Science, China West Normal University, 44# Yuying Road, 637002, Nanchong, China
| | | | | | | | | |
Collapse
|
49
|
von der Haar T. Optimized protein extraction for quantitative proteomics of yeasts. PLoS One 2007; 2:e1078. [PMID: 17957260 PMCID: PMC2031916 DOI: 10.1371/journal.pone.0001078] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2007] [Accepted: 10/05/2007] [Indexed: 11/19/2022] Open
Abstract
Background The absolute quantification of intracellular protein levels is technically demanding, but has recently become more prominent because novel approaches like systems biology and metabolic control analysis require knowledge of these parameters. Current protocols for the extraction of proteins from yeast cells are likely to introduce artifacts into quantification procedures because of incomplete or selective extraction. Principal Findings We have developed a novel procedure for protein extraction from S. cerevisiae based on chemical lysis and simultaneous solubilization in SDS and urea, which can extract the great majority of proteins to apparent completeness. The procedure can be used for different Saccharomycetes yeast species and varying growth conditions, is suitable for high-throughput extraction in a 96-well format, and the resulting extracts can easily be post-processed for use in non-SDS compatible procedures like 2D gel electrophoresis. Conclusions An improved method for quantitative protein extraction has been developed that removes some of the sources of artefacts in quantitative proteomics experiments, while at the same time allowing novel types of applications.
Collapse
Affiliation(s)
- Tobias von der Haar
- Protein Science Group, Department of Biosciences, University of Kent, Canterbury, United Kingdom.
| |
Collapse
|
50
|
Akashi T, Yamori T. A novel method for analyzing phosphoproteins using SELDI-TOF MS in combination with a series of recombinant proteins. Proteomics 2007; 7:2350-4. [PMID: 17570519 DOI: 10.1002/pmic.200700157] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A novel SELDI-TOF MS-based method for analyzing phosphoproteins was developed using a series of recombinant wild-type and mutant ribosomal P2 proteins. We demonstrated that the phosphorylation status of the overexpressed proteins in cells was easily and rapidly confirmed using this method. The ribosomal P2 protein contained two phosphorylation sites, which were sequentially phosphorylated in vivo. We also quantitatively detected the phosphoprotein by using SELDI-TOF MS.
Collapse
Affiliation(s)
- Tetsuyuki Akashi
- Division of Molecular Pharmacology, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | | |
Collapse
|