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Gupta MN, Uversky VN. Moonlighting enzymes: when cellular context defines specificity. Cell Mol Life Sci 2023; 80:130. [PMID: 37093283 PMCID: PMC11073002 DOI: 10.1007/s00018-023-04781-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/13/2023] [Accepted: 04/15/2023] [Indexed: 04/25/2023]
Abstract
It is not often realized that the absolute protein specificity is an exception rather than a rule. Two major kinds of protein multi-specificities are promiscuity and moonlighting. This review discusses the idea of enzyme specificity and then focusses on moonlighting. Some important examples of protein moonlighting, such as crystallins, ceruloplasmin, metallothioniens, macrophage migration inhibitory factor, and enzymes of carbohydrate metabolism are discussed. How protein plasticity and intrinsic disorder enable the removing the distinction between enzymes and other biologically active proteins are outlined. Finally, information on important roles of moonlighting in human diseases is updated.
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Affiliation(s)
- Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Hauz Khas, New Delhi, 110016, India
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd., MDC07, Tampa, FL, 33612-4799, USA.
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Wu N, Wei J, Wang Y, Yan J, Qin Y, Tong D, Pang B, Sun D, Sun H, Yu Y, Sun W, Meng X, Zhang C, Bai J, Chen F, Geng J, Lee KY, Fu S, Jin Y. Ribosomal L22-like1 (RPL22L1) Promotes Ovarian Cancer Metastasis by Inducing Epithelial-to-Mesenchymal Transition. PLoS One 2015; 10:e0143659. [PMID: 26618703 PMCID: PMC4664398 DOI: 10.1371/journal.pone.0143659] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 11/06/2015] [Indexed: 12/30/2022] Open
Abstract
Double minute chromosomes (DMs) have important implications for cancer progression because oncogenes frequently amplified on them. We previously detected a functionally undefined gene amplified on DMs, Ribosomal L22-like1 (RPL22L1). The relationship between RPL22L1 and cancer progression is unknown. Here, RPL22L1 was characterized for its role in ovarian cancer (OC) metastasis and its underlying mechanism was examined. DNA copy number and mRNA expression of RPL22L1 in OC cells was analyzed using data obtained from The Cancer Genome Atlas and the Gene Expression Omnibus database. An immunohistochemical analysis of clinical OC specimens was performed and the relationships between expression level and clinicopathological factors were evaluated. Additionally, in vivo and in vitro assays were performed to understand the role of RPL22L1 in OC. RPL22L1 expression was higher in OC specimens than in normal tissues, and its expression level was highly positively correlated with invasion and lymph node metastasis (P < 0.05). RPL22L1 over-expression significantly enhanced intraperitoneal xenograft tumor development in nude mice and promoted invasion and migration in vitro. Additionally, RPL22L1 knockdown remarkably inhibited UACC-1598 cells invasion and migration. Further, RPL22L1 over-expression up-regulated the mesenchymal markers vimentin, fibronectin, and α-SMA, reduced expression of the epithelial markers E-cadherin, α-catenin, and β-catenin. RPL22L1 inhibition reduced expression of vimentin and N-cadherin. These results suggest that RPL22L1 induces epithelial-to-mesenchymal transition (EMT). Our data showed that the DMs amplified gene RPL22L1 is critical in maintaining the aggressive phenotype of OC and in triggering cell metastasis by inducing EMT. It could be employed as a novel prognostic marker and/or effective therapeutic target for OC.
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Affiliation(s)
- Nan Wu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Jia Wei
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Yuhui Wang
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Jinyan Yan
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Ying Qin
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Dandan Tong
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Bo Pang
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Donglin Sun
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Haiming Sun
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Yang Yu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Wenjing Sun
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Xiangning Meng
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Chunyu Zhang
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Jing Bai
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Feng Chen
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Jingshu Geng
- Department of Pathology, Third Affiliated Clinical Hospital, Harbin Medical University, Harbin, China
| | - Ki-Young Lee
- Department of Cell Biology & Anatomy, University of Calgary, Alberta, Canada
| | - Songbin Fu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
- * E-mail: (YJ); , (SF)
| | - Yan Jin
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
- * E-mail: (YJ); , (SF)
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Wang W, Wu X, Liu Z, Zheng H, Cheng Y. Insights into hepatopancreatic functions for nutrition metabolism and ovarian development in the crab Portunus trituberculatus: gene discovery in the comparative transcriptome of different hepatopancreas stages. PLoS One 2014; 9:e84921. [PMID: 24454766 PMCID: PMC3890295 DOI: 10.1371/journal.pone.0084921] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2013] [Accepted: 11/20/2013] [Indexed: 11/18/2022] Open
Abstract
The crustacean hepatopancreas has different functions including absorption, storage of nutrients and vitellogenesis during growth, and ovarian development. However, genetic information on the biological functions of the crustacean hepatopancreas during such processes is limited. The swimming crab, Portunus trituberculatus, is a commercially important species for both aquaculture and fisheries in the Asia-Pacific region. This study compared the transcriptome in the hepatopancreas of female P. trituberculatus during the growth and ovarian maturation stages by 454 high-throughput pyrosequencing and bioinformatics. The goal was to discover genes in the hepatopancreas involved in food digestion, nutrition metabolism and ovarian development, and to identify patterns of gene expression during growth and ovarian maturation. Our transcriptome produced 303,450 reads with an average length of 351 bp, and the high quality reads were assembled into 21,635 contigs and 31,844 singlets. Based on BLASTP searches of the deduced protein sequences, there were 7,762 contigs and 4,098 singlets with functional annotation. Further analysis revealed 33,427 unigenes with ORFs, including 17,388 contigs and 16,039 singlets in the hepatopancreas, while only 7,954 unigenes (5,691 contigs and 2,263 singlets) with the predicted protein sequences were annotated with biological functions. The deduced protein sequences were assigned to 3,734 GO terms, 25 COG categories and 294 specific pathways. Furthermore, there were 14, 534, and 22 identified unigenes involved in food digestion, nutrition metabolism and ovarian development, respectively. 212 differentially expressed genes (DEGs) were found between the growth and endogenous stage of the hepatopancreas, while there were 382 DEGs between the endogenous and exogenous stage hepatopancreas. Our results not only enhance the understanding of crustacean hepatopancreatic functions during growth and ovarian development, but also represent a basis for further research on new genes and functional genomics of P. trituberculatus or closely related species.
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Affiliation(s)
- Wei Wang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, China
| | - Xugan Wu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, China
| | - Zhijun Liu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, China
| | - Huajun Zheng
- Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Yongxu Cheng
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, China
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Li Y, Wang ZK, Chen H, Feng EY, Yin YP. Identification and expression analysis of QM-like gene from Spodoptera litura after challenge by the entomopathogenic fungus Nomuraea rileyi. JOURNAL OF INSECT SCIENCE (ONLINE) 2014; 14:ieu062. [PMID: 25528750 PMCID: PMC5443418 DOI: 10.1093/jisesa/ieu062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 06/05/2013] [Indexed: 06/04/2023]
Abstract
A partial sequence of QM homologue was isolated from a Spodoptera litura fatbody suppression subtractive hybridization library. The full-length Spodoptera litura QM (SpLQM) cDNA of 838 bp contains a 5' untranslated region (UTR) of 112 bp, a 3' UTR of 66 bp, and an open reading frame of 660 nucleotides coding for a 219 amino acid peptide with a molecular weight of 25.5 kDa. Analysis of SpLQM sequence revealed the presence of characteristic motifs, including the ribosomal protein L10 signature and SH3-binding motif. Multiple alignment analysis revealed that SpLQM shares an overall identity of 57.1-99.1% with other members of QM family. Phylogenetic analysis confirmed that SpLQM is closely related to other insect QMs. Analysis of the tissue expression pattern showed that the SpLQM mRNA was expressed in all tissues tested, with highest levels measured in hemocytes, followed by fat bodies. Upon Nomuraea rileyi challenge, SpLQM showed significant upregulation in fat bodies and hemocytes, while slightly upregulation in midguts. The results suggest that SpLQM might play an important role in the innate immunity of S. litura in response to N. rileyi infection. SpLQM was also successfully overexpressed in Escherichia coli, and the recombinant fusion protein SpLQM-His has a molecular weight of 32 kDa.
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Affiliation(s)
- Yan Li
- Chongqing Engineering Research Center for Fungal Insecticides, School of Life Science, Chongqing University, Chongqing 400030, China
| | - Zhong-Kang Wang
- Chongqing Engineering Research Center for Fungal Insecticides, School of Life Science, Chongqing University, Chongqing 400030, China
| | - Huan Chen
- Chongqing Engineering Research Center for Fungal Insecticides, School of Life Science, Chongqing University, Chongqing 400030, China
| | - Er-Yan Feng
- Chongqing Engineering Research Center for Fungal Insecticides, School of Life Science, Chongqing University, Chongqing 400030, China
| | - You-Ping Yin
- Chongqing Engineering Research Center for Fungal Insecticides, School of Life Science, Chongqing University, Chongqing 400030, China
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Yang M, Sun H, Wang H, Zhang S, Yu X, Zhang L. Down-regulation of ribosomal protein L22 in non-small cell lung cancer. Med Oncol 2013; 30:646. [DOI: 10.1007/s12032-013-0646-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2013] [Accepted: 06/14/2013] [Indexed: 11/30/2022]
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Hummel M, Cordewener JHG, de Groot JCM, Smeekens S, America AHP, Hanson J. Dynamic protein composition of Arabidopsis thaliana cytosolic ribosomes in response to sucrose feeding as revealed by label free MSE proteomics. Proteomics 2012; 12:1024-38. [PMID: 22522809 DOI: 10.1002/pmic.201100413] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Cytosolic ribosomes are among the largest multisubunit cellular complexes. Arabidopsis thaliana ribosomes consist of 79 different ribosomal proteins (r-proteins) that each are encoded by two to six (paralogous) genes. It is unknown whether the paralogs are incorporated into the ribosome and whether the relative incorporation of r-protein paralogs varies in response to environmental cues. Immunopurified ribosomes were isolated from A. thaliana rosette leaves fed with sucrose. Trypsin digested samples were analyzed by qTOF-LC-MS using both MS(E) and classical MS/MS. Peptide features obtained by using these two methods were identified using MASCOT and Proteinlynx Global Server searching the theoretical sequences of A. thaliana proteins. The A. thaliana genome encodes 237 r-proteins and 69% of these were identified with proteotypic peptides for most of the identified proteins. These r-proteins were identified with average protein sequence coverage of 32% observed by MS(E) . Interestingly, the analysis shows that the abundance of r-protein paralogs in the ribosome changes in response to sucrose feeding. This is particularly evident for paralogous RPS3aA, RPS5A, RPL8B, and RACK1 proteins. These results show that protein synthesis in the A. thaliana cytosol involves a heterogeneous ribosomal population. The implications of these findings in the regulation of translation are discussed.
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Affiliation(s)
- Maureen Hummel
- Molecular Plant Physiology, Utrecht University, Utrecht, The Netherlands
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A genome-wide over-expression screen identifies genes involved in phagocytosis in the human protozoan parasite, Entamoeba histolytica. PLoS One 2012; 7:e43025. [PMID: 22905196 PMCID: PMC3419234 DOI: 10.1371/journal.pone.0043025] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Accepted: 07/16/2012] [Indexed: 11/23/2022] Open
Abstract
Functional genomics and forward genetics seek to assign function to all known genes in a genome. Entamoeba histolytica is a protozoan parasite for which forward genetics approaches have not been extensively applied. It is the causative agent of amoebic dysentery and liver abscess, and infection is prevalent in developing countries that cannot prevent its fecal-oral spread. It is responsible for considerable global morbidity and mortality. Given that the E. histolytica genome has been sequenced, it should be possible to apply genomic approaches to discover gene function. We used a genome-wide over-expression screen to uncover genes regulating an important virulence function of E. histolytica, namely phagocytosis. We developed an episomal E. histolytica cDNA over-expression library, transfected the collection of plasmids into trophozoites, and applied a high-throughput screen to identify phagocytosis mutants in the population of over-expressing cells. The screen was based on the phagocytic uptake of human red blood cells loaded with the metabolic toxin, tubercidin. Expression plasmids were isolated from trophozoites that survived exposure to tubercidin-charged erythrocytes (phagocytosis mutants), and the cDNAs were sequenced. We isolated the gene encoding profilin, a well-characterized cytoskeleton-regulating protein with a known role in phagocytosis. This supports the validity of our approach. Furthermore, we assigned a phagocytic role to several genes not previously known to function in this manner. To our knowledge, this is the first genome-wide forward genetics screen to be applied to this pathogen. The study demonstrates the power of forward genetics in revealing genes regulating virulence in E. histolytica. In addition, the study validates an E. histolytica cDNA over-expression library as a valuable tool for functional genomics.
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Ferreyra MLF, Biarc J, Burlingame AL, Casati P. Arabidopsis L10 ribosomal proteins in UV-B responses. PLANT SIGNALING & BEHAVIOR 2010; 5:1222-5. [PMID: 20855946 PMCID: PMC3115351 DOI: 10.4161/psb.5.10.12758] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Ribosomal protein L10 (RPL10) is an ubiquitous protein that participates in joining the 40S and 60S ribosomal subunits into a functional 80S ribosome; however, increasing evidences indicate that RPL10 from various organisms has multiple extra ribosomal functions, besides being a constituent of ribosome and its role in translation. Arabidopsis thaliana contains in its genome three genes encoding RPL10, named RPL10A, RPL10B and RPL10C. Previously, we found that in maize and in A. thaliana, UV-B induces a reduction in protein biosynthesis, probably as a consequence of ribosomal damage; however, cellular recovery occurs in the absence of UV-B. Here, we show that RPL10s are differentially regulated by UV-B in a dosage and time dependent manner: RPL10C is induced, RPL10B is down regulated at high UV-B intensity, and RPL10A is not UV-B regulated. In addition, by coimmunoprecipitation studies using RPL10 antibodies and proteins from control and UV-B irradiated Arabidopsis plants, we demonstrate that RPL10 associates with different proteins under the two different conditions, including nuclear proteins, suggesting that at least one isoform may have extra-ribosomal roles.
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Affiliation(s)
| | - Jordane Biarc
- Department of Pharmaceutical Chemistry; University of California; San Francisco, CA USA
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry; University of California; San Francisco, CA USA
| | - Paula Casati
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI); Universidad Nacional de Rosario; Rosario, Argentina
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Santos AA, Lopes KVG, Apfata JAC, Fontes EPB. NSP-interacting kinase, NIK: a transducer of plant defence signalling. JOURNAL OF EXPERIMENTAL BOTANY 2010; 61:3839-45. [PMID: 20624762 DOI: 10.1093/jxb/erq219] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The NSP-interacting kinase, NIK, belongs to the five leucine-rich repeats-containing receptor-like serine/threonine kinase subfamily that includes members involved in plant development and defence. NIK was first identified by its capacity to interact with the geminivirus nuclear shuttle protein (NSP) and has been strongly associated with plant defence against geminivirus. Recent studies corroborate its function in transducing a defence signal against virus infection and describe components of the NIK-mediated antiviral signalling pathway. This mini-review describes the role of NIK as a transducer of a novel layer of plant innate defence, presents new data on NIK function, and discusses its possible involvement in plant development.
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Affiliation(s)
- Anésia A Santos
- Departamento de Bioquímica e Biologia Molecular, BIOAGRO, Universidade Federal de Viçosa, 36571.000, Viçosa, MG, Brazil
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Ferreyra MLF, Pezza A, Biarc J, Burlingame AL, Casati P. Plant L10 ribosomal proteins have different roles during development and translation under ultraviolet-B stress. PLANT PHYSIOLOGY 2010; 153:1878-94. [PMID: 20516338 PMCID: PMC2923885 DOI: 10.1104/pp.110.157057] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Accepted: 05/30/2010] [Indexed: 05/19/2023]
Abstract
Ribosomal protein L10 (RPL10) proteins are ubiquitous in the plant kingdom. Arabidopsis (Arabidopsis thaliana) has three RPL10 genes encoding RPL10A to RPL10C proteins, while two genes are present in the maize (Zea mays) genome (rpl10-1 and rpl10-2). Maize and Arabidopsis RPL10s are tissue-specific and developmentally regulated, showing high levels of expression in tissues with active cell division. Coimmunoprecipitation experiments indicate that RPL10s in Arabidopsis associate with translation proteins, demonstrating that it is a component of the 80S ribosome. Previously, ultraviolet-B (UV-B) exposure was shown to increase the expression of a number of maize ribosomal protein genes, including rpl10. In this work, we demonstrate that maize rpl10 genes are induced by UV-B while Arabidopsis RPL10s are differentially regulated by this radiation: RPL10A is not UV-B regulated, RPL10B is down-regulated, while RPL10C is up-regulated by UV-B in all organs studied. Characterization of Arabidopsis T-DNA insertional mutants indicates that RPL10 genes are not functionally equivalent. rpl10A and rpl10B mutant plants show different phenotypes: knockout rpl10A mutants are lethal, rpl10A heterozygous plants are deficient in translation under UV-B conditions, and knockdown homozygous rpl10B mutants show abnormal growth. Based on the results described here, RPL10 genes are not redundant and participate in development and translation under UV-B stress.
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Affiliation(s)
| | | | | | | | - Paula Casati
- Centro de Estudios Fotosintéticos y Bioquímicos, Universidad Nacional de Rosario, Suipacha 531, Rosario, Argentina (M.L.F.F., A.P., P.C.); Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158–2517 (J.B., A.L.B.)
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RPL41, a small ribosomal peptide deregulated in tumors, is essential for mitosis and centrosome integrity. Neoplasia 2010; 12:284-93. [PMID: 20234822 DOI: 10.1593/neo.91610] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2009] [Revised: 12/08/2009] [Accepted: 12/09/2009] [Indexed: 11/18/2022]
Abstract
Ribosomal large subunit protein RPL41 is a basic (positively charged) peptide consisting of only 25 amino acids. An antisense-based functional screening revealed that the down-regulation of RPL41 led to an anchorage-independent growth of NIH3T3 cells in soft agar plates. RPL41 depletion with gene-specific small interfering RNA also resulted in malignant transformation of NIH3T3 cells including increased tumor growth in mice. RPL41 deletion was detected in 59% of tumor cell lines by fluorescence in situ hybridization analyses and RPL41 down-regulation in 75% of primary breast cancers by real-time quantitative reverse transcription-polymerase chain reaction. These studies suggest a tumor suppression role for RPL41. By mass spectrometry, RPL41 was associated with several cytoskeleton components including tubulin beta, gamma, and myosin IIA, which was confirmed by Western blot analysis on both cellular lysis and individually in vitro-expressed proteins. RPL41 also bound directly to polymerized tubulins. Cells overexpressing a GFP-RPL41 were resistant to nocodazole-induced microtubule depolymerization. A synthetic RPL41 induced cellular alpha-tubulin acetylation and G(2)/M cell cycle arrest. These results indicate a stabilizing role of RPL41 on microtubule. Microtubule spindles are essential for chromosome segregation during mitosis. Cells with RPL41 knock-down showed abnormal spindles, frequent failure of cytokinesis, and formation of polynuclear cells. In interphase cells, RPL41-depleted cells had premature splitting of centrosome. Our results provide evidence that RPL41 is a microtubule-associated protein essential for functional spindles and for the integrity of centrosome and that the abnormal mitosis and disrupted centrosome associated with the RPL41 down-regulation may be related to malignant transformation.
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Kang B, Guo J, Yang H, Zhou R, Liu J, Li S, Dong C. Differential expression profiling of ovarian genes in prelaying and laying geese. Poult Sci 2009; 88:1975-83. [DOI: 10.3382/ps.2008-00519] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Regulated nuclear trafficking of rpL10A mediated by NIK1 represents a defense strategy of plant cells against virus. PLoS Pathog 2008; 4:e1000247. [PMID: 19112492 PMCID: PMC2597721 DOI: 10.1371/journal.ppat.1000247] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2008] [Accepted: 11/25/2008] [Indexed: 11/24/2022] Open
Abstract
The NSP-interacting kinase (NIK) receptor-mediated defense pathway has been identified recently as a virulence target of the geminivirus nuclear shuttle protein (NSP). However, the NIK1–NSP interaction does not fit into the elicitor–receptor model of resistance, and hence the molecular mechanism that links this antiviral response to receptor activation remains obscure. Here, we identified a ribosomal protein, rpL10A, as a specific partner and substrate of NIK1 that functions as an immediate downstream effector of NIK1-mediated response. Phosphorylation of cytosolic rpL10A by NIK1 redirects the protein to the nucleus where it may act to modulate viral infection. While ectopic expression of normal NIK1 or a hyperactive NIK1 mutant promotes the accumulation of phosphorylated rpL10A within the nuclei, an inactive NIK1 mutant fails to redirect the protein to the nuclei of co-transfected cells. Likewise, a mutant rpL10A defective for NIK1 phosphorylation is not redirected to the nucleus. Furthermore, loss of rpL10A function enhances susceptibility to geminivirus infection, resembling the phenotype of nik1 null alleles. We also provide evidence that geminivirus infection directly interferes with NIK1-mediated nuclear relocalization of rpL10A as a counterdefensive measure. However, the NIK1-mediated defense signaling neither activates RNA silencing nor promotes a hypersensitive response but inhibits plant growth and development. Although the virulence function of the particular geminivirus NSP studied here overcomes this layer of defense in Arabidopsis, the NIK1-mediated signaling response may be involved in restricting the host range of other viruses. Plants are constantly exposed to microorganisms and, like animals, developed innate immune systems to prevent infections. Although these immune systems protect plants against most potential pathogens, the molecular mechanisms underlying nonhost immunity remain obscure. Here, we describe a novel strategy of plant defenses identified as a target of the geminivirus nuclear shuttle protein (NSP) that suppresses the activity of the transmembrane receptor NIK (NSP-interacting kinase). In addition, we identified a ribosomal protein, rpL10A, as the immediate downstream component of the pathway. Based on our findings, we propose that this pathway is elicited by activation of the receptor NIK1, which results in phosphorylation and translocation of rpL10A to the nucleus. We also provided genetic and biochemical evidence that this regulated trafficking of rpL10A may effectively mount a defense strategy that negatively impacts geminivirus proliferation or movement. Nevertheless, the virulence function of NSP from the bipartite geminivirus CaLCuV (Cabbage leaf curl virus) is capable of overcoming the NIK1-mediated defense and thereby enhances the pathogenicity of CaLCuV in Arabidopsis. The NIK1-mediated signaling response may be involved in restricting the host range of other viruses.
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The ribosomal protein L10/QM-like protein is a component of the NIK-mediated antiviral signaling. Virology 2008; 380:165-9. [DOI: 10.1016/j.virol.2008.08.005] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2008] [Revised: 07/13/2008] [Accepted: 08/02/2008] [Indexed: 11/18/2022]
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Marlétaz F, Le Parco Y. Careful with understudied phyla: the case of chaetognath. BMC Evol Biol 2008; 8:251. [PMID: 18798978 PMCID: PMC2566580 DOI: 10.1186/1471-2148-8-251] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2007] [Accepted: 09/17/2008] [Indexed: 11/10/2022] Open
Abstract
Background A recent study by Barthélémy et al. described a set of ribosomal protein (RP) genes extracted from a collection of expressed sequence tags (ESTs) of the chaetognath (arrow worm) Spadella cephaloptera. Three main conclusions were drawn in this paper. First, the authors stated that RP genes present paralogous copies, which have arisen through allopolyploidization. Second, they reported two alternate nucleotide stretches conserved within the 5' untranslated regions (UTR) of multiple ribosomal cDNAs and they suggested that these motifs are involved in the differential transcriptional regulation of paralogous RP genes. Third, they claimed that the phylogenetic position of chaetognaths could not be accurately inferred from a RP dataset because of the persistence of two problems: a long branch attraction (LBA) artefact and a compositional bias. Results We reconsider here the results described in Barthélémy et al. and question the evidence on which they are based. We find that their evidence for paralogous copies relies on faulty PCR experiments since they attempted to amplify DNA fragments absent from the genomic template. Our PCR experiments proved that the conserved motifs in 5'UTRs that they targeted in their amplifications are added post-transcriptionally by a trans-splicing mechanism. Then, we showed that the lack of phylogenetic resolution observed by these authors is due to limited taxon sampling and not to LBA or to compositional bias. A ribosomal protein dataset thus fully supports the position of chaetognaths as sister group of all other protostomes. This reinterpretation demonstrates that the statements of Barthélémy et al. should be taken with caution because they rely on inaccurate evidence. Conclusion The genomic study of an unconventional model organism is a meaningful approach to understand the evolution of animals. However, the previous study came to incorrect conclusions on the basis of experiments that omitted validation procedures.
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Affiliation(s)
- Ferdinand Marlétaz
- Station Marine d'Endoume, CNRS UMR 6540 DIMAR, Centre d'Océanologie de Marseille, Université de Méditerranée, Marseille, France.
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Xu J, Wu S, Zhang X. Novel Function of QM Protein of Shrimp ( Penaeus Japonicus) in Regulation of Phenol Oxidase Activity by Interaction with Hemocyanin. Cell Physiol Biochem 2008; 21:473-80. [DOI: 10.1159/000129640] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2007] [Indexed: 11/19/2022] Open
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Barthélémy RM, Chenuil A, Blanquart S, Casanova JP, Faure E. Translational machinery of the chaetognath Spadella cephaloptera: a transcriptomic approach to the analysis of cytosolic ribosomal protein genes and their expression. BMC Evol Biol 2007; 7:146. [PMID: 17725830 PMCID: PMC2020476 DOI: 10.1186/1471-2148-7-146] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2006] [Accepted: 08/28/2007] [Indexed: 12/01/2022] Open
Abstract
Background Chaetognaths, or arrow worms, are small marine, bilaterally symmetrical metazoans. The objective of this study was to analyse ribosomal protein (RP) coding sequences from a published collection of expressed sequence tags (ESTs) from a chaetognath (Spadella cephaloptera) and to use them in phylogenetic studies. Results This analysis has allowed us to determine the complete primary structures of 23 out of 32 RPs from the small ribosomal subunit (SSU) and 32 out of 47 RPs from the large ribosomal subunit (LSU). Ten proteins are partially determined and 14 proteins are missing. Phylogenetic analyses of concatenated RPs from six animals (chaetognath, echinoderm, mammalian, insect, mollusc and sponge) and one fungal taxa do not resolve the chaetognath phylogenetic position, although each mega-sequence comprises approximately 5,000 amino acid residues. This is probably due to the extremely biased base composition and to the high evolutionary rates in chaetognaths. However, the analysis of chaetognath RP genes revealed three unique features in the animal Kingdom. First, whereas generally in animals one RP appeared to have a single type of mRNA, two or more genes are generally transcribed for one RP type in chaetognath. Second, cDNAs with complete 5'-ends encoding a given protein sequence can be divided in two sub-groups according to a short region in their 5'-ends: two novel and highly conserved elements have been identified (5'-TAATTGAGTAGTTT-3' and 5'-TATTAAGTACTAC-3') which could correspond to different transcription factor binding sites on paralog RP genes. And, third, the overall number of deduced paralogous RPs is very high compared to those published for other animals. Conclusion These results suggest that in chaetognaths the deleterious effects of the presence of paralogous RPs, such as apoptosis or cancer are avoided, and also that in each protein family, some of the members could have tissue-specific and extra-ribosomal functions. These results are congruent with the hypotheses of an allopolyploid origin of this phylum and of a ribosome heterogeneity.
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Affiliation(s)
- Roxane M Barthélémy
- E.R. Biodiversity and environnement, case 5, Pl. V. Hugo, Université de Provence, 13331, Marseille cedex 3, France
| | - Anne Chenuil
- UMR 6540 CNRS DIMAR, Centre d'Océanologie de Marseille, Station Marine d'Endoume, Ch. de la Batterie des Lions, 13007 Marseille, France
| | - Samuel Blanquart
- Laboratoire d'Informatique, de Robotique et de Microélectronique de Montpellier, UMR 5506, CNRS-Université de Montpellier 2, 161, rue Ada, 34392 Montpellier Cedex 5, France
| | - Jean-Paul Casanova
- E.R. Biodiversity and environnement, case 5, Pl. V. Hugo, Université de Provence, 13331, Marseille cedex 3, France
| | - Eric Faure
- E.R. Biodiversity and environnement, case 5, Pl. V. Hugo, Université de Provence, 13331, Marseille cedex 3, France
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Ishii K, Washio T, Uechi T, Yoshihama M, Kenmochi N, Tomita M. Characteristics and clustering of human ribosomal protein genes. BMC Genomics 2006; 7:37. [PMID: 16504170 PMCID: PMC1459141 DOI: 10.1186/1471-2164-7-37] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2005] [Accepted: 02/28/2006] [Indexed: 11/20/2022] Open
Abstract
Background The ribosome is a central player in the translation system, which in mammals consists of four RNA species and 79 ribosomal proteins (RPs). The control mechanisms of gene expression and the functions of RPs are believed to be identical. Most RP genes have common promoters and were therefore assumed to have a unified gene expression control mechanism. Results We systematically analyzed the homogeneity and heterogeneity of RP genes on the basis of their expression profiles, promoter structures, encoded amino acid compositions, and codon compositions. The results revealed that (1) most RP genes are coordinately expressed at the mRNA level, with higher signals in the spleen, lymph node dissection (LND), and fetal brain. However, 17 genes, including the P protein genes (RPLP0, RPLP1, RPLP2), are expressed in a tissue-specific manner. (2) Most promoters have GC boxes and possible binding sites for nuclear respiratory factor 2, Yin and Yang 1, and/or activator protein 1. However, they do not have canonical TATA boxes. (3) Analysis of the amino acid composition of the encoded proteins indicated a high lysine and arginine content. (4) The major RP genes exhibit a characteristic synonymous codon composition with high rates of G or C in the third-codon position and a high content of AAG, CAG, ATC, GAG, CAC, and CTG. Conclusion Eleven of the RP genes are still identified as being unique and did not exhibit at least some of the above characteristics, indicating that they may have unknown functions not present in other RP genes. Furthermore, we found sequences conserved between human and mouse genes around the transcription start sites and in the intronic regions. This study suggests certain overall trends and characteristic features of human RP genes.
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Affiliation(s)
- Kyota Ishii
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0035, Japan
- Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa 252-8520, Japan
| | - Takanori Washio
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0035, Japan
- Graduate School of Information Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Tamayo Uechi
- Frontier Science Research Center, University of Miyazaki, Kiyotake, Miyazaki 889-1692, Japan
| | - Maki Yoshihama
- Frontier Science Research Center, University of Miyazaki, Kiyotake, Miyazaki 889-1692, Japan
| | - Naoya Kenmochi
- Frontier Science Research Center, University of Miyazaki, Kiyotake, Miyazaki 889-1692, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0035, Japan
- Department of Environmental Information, Keio University, Fujisawa, Kanagawa 252-8520, Japan
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Wang J, Jing W, Yuan S, Sheng Y, Jiang S, Jang S. The ribosomal protein L32-2 (RPL32-2) of S. pombe exhibits a novel extraribosomal function by acting as a potential transcriptional regulator. FEBS Lett 2006; 580:1827-32. [PMID: 16516201 DOI: 10.1016/j.febslet.2006.02.040] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2006] [Revised: 02/04/2006] [Accepted: 02/14/2006] [Indexed: 11/17/2022]
Abstract
Ribosomal proteins play important roles in stabilizing the rRNA structure to facilitate protein synthesis in ribosome. In the present study, we analyzed the potential extraribosomal function of the ribosomal protein L32-2 (RPL32-2), which was expressed by a gene clone isolated from a cDNA library of Schizosaccharomyces pombe (S. pombe). RPL32-2 fused with the GAL4 DNA-bind domain or the GAL4 transcriptional activating domain could, respectively, activate transcriptions of reporter genes in yeast strain AH109. The RPL32-2 mutants with truncation of either the N- or the C-terminal domain resulted in abolishment of this regulatory effect. The DNA binding site for RPL32-2 of S. pombe was identified by using a random oligonucleotide selection strategy and gel motility shift assay and Western blotting confirmed its binding specificity. Moreover, we found RPL32-2 was also able to interact with a to-be-identified AT sequence binding protein. These data suggest that RPL32-2 of S. pombe, besides its ribosomal function, may also act as a potential transcriptional regulator in nucleus.
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Affiliation(s)
- Jing Wang
- Jiangsu Key Lab for Biodiversity and Biotechnology, NNU Key Lab of Microbial Technology, College of Life Science, Nanjing Normal University, 122 Ninghai Lu, Nanjing 210097, PR China
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