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Payá G, Bautista V, Pastor-Soler S, Camacho M, Esclapez J, Bonete MJ. Analysis of Lsm Protein-Mediated Regulation in the Haloarchaeon Haloferax mediterranei. Int J Mol Sci 2024; 25:580. [PMID: 38203750 PMCID: PMC10779274 DOI: 10.3390/ijms25010580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 12/20/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024] Open
Abstract
The Sm protein superfamily includes Sm, like-Sm (Lsm), and Hfq found in the Eukarya, Archaea, and Bacteria domains. Archaeal Lsm proteins have been shown to bind sRNAs and are probably involved in various cellular processes, suggesting a similar function in regulating sRNAs by Hfq in bacteria. Moreover, archaeal Lsm proteins probably represent the ancestral Lsm domain from which eukaryotic Sm proteins have evolved. In this work, Haloferax mediterranei was used as a model organism because it has been widely used to investigate the nitrogen cycle and its regulation in Haloarchaea. Predicting this protein's secondary and tertiary structures has resulted in a three-dimensional model like the solved Lsm protein structure of Archaeoglobus fulgidus. To obtain information on the oligomerization state of the protein, homologous overexpression and purification by means of molecular exclusion chromatography have been performed. The results show that this protein can form hexameric complexes, which can aggregate into 6 or 12 hexameric rings depending on the NaCl concentration and without RNA. In addition, the study of transcriptional expression via microarrays has allowed us to obtain the target genes regulated by the Lsm protein under nutritional stress conditions: nitrogen or carbon starvation. Microarray analysis has shown the first universal stress proteins (USP) in this microorganism that mediate survival in situations of nitrogen deficiency.
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Affiliation(s)
| | | | | | | | | | - María-José Bonete
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, Ap 99, 03080 Alicante, Spain; (G.P.); (V.B.); (S.P.-S.); (M.C.); (J.E.)
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Joseph J, Mathew J, Alexander J. Scaffold Proteins in Autoimmune Disorders. Curr Rheumatol Rev 2024; 20:14-26. [PMID: 37670692 DOI: 10.2174/1573397119666230904151024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/26/2023] [Accepted: 08/10/2023] [Indexed: 09/07/2023]
Abstract
Cells transmit information to the external environment and within themselves through signaling molecules that modulate cellular activities. Aberrant cell signaling disturbs cellular homeostasis causing a number of different diseases, including autoimmunity. Scaffold proteins, as the name suggests, serve as the anchor for binding and stabilizing signaling proteins at a particular locale, allowing both intra and intercellular signal amplification and effective signal transmission. Scaffold proteins play a critical role in the functioning of tight junctions present at the intersection of two cells. In addition, they also participate in cleavage formation during cytokinesis, and in the organization of neural synapses, and modulate receptor management outcomes. In autoimmune settings such as lupus, scaffold proteins can lower the cell activation threshold resulting in uncontrolled signaling and hyperactivity. Scaffold proteins, through their binding domains, mediate protein- protein interaction and play numerous roles in cellular communication and homeostasis. This review presents an overview of scaffold proteins, their influence on the different signaling pathways, and their role in the pathogenesis of autoimmune and auto inflammatory diseases. Since these proteins participate in many roles and interact with several other signaling pathways, it is necessary to gain a thorough understanding of these proteins and their nuances to facilitate effective target identification and therapeutic design for the treatment of autoimmune disorders.
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Affiliation(s)
- Josna Joseph
- Department of Clinical Immunology & Rheumatology, CMC Vellore, Tamil Nadu, India
| | - John Mathew
- Department of Clinical Immunology & Rheumatology, CMC Vellore, Tamil Nadu, India
| | - Jessy Alexander
- Department of Medicine, Jacobs School of Medicine & Biomedical Sciences, University of Buffalo, New York, USA
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3
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Payá G, Bautista V, Camacho M, Esclapez J, Bonete MJ. Comprehensive Bioinformatics Analysis of the Biodiversity of Lsm Proteins in the Archaea Domain. Microorganisms 2023; 11:1196. [PMID: 37317170 DOI: 10.3390/microorganisms11051196] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/25/2023] [Accepted: 04/27/2023] [Indexed: 06/16/2023] Open
Abstract
The Sm protein superfamily includes Sm, like-Sm (Lsm), and Hfq proteins. Sm and Lsm proteins are found in the Eukarya and Archaea domains, respectively, while Hfq proteins exist in the Bacteria domain. Even though Sm and Hfq proteins have been extensively studied, archaeal Lsm proteins still require further exploration. In this work, different bioinformatics tools are used to understand the diversity and distribution of 168 Lsm proteins in 109 archaeal species to increase the global understanding of these proteins. All 109 archaeal species analyzed encode one to three Lsm proteins in their genome. Lsm proteins can be classified into two groups based on molecular weight. Regarding the gene environment of lsm genes, many of these genes are located adjacent to transcriptional regulators of the Lrp/AsnC and MarR families, RNA-binding proteins, and ribosomal protein L37e. Notably, only proteins from species of the class Halobacteria conserved the internal and external residues of the RNA-binding site identified in Pyrococcus abyssi, despite belonging to different taxonomic orders. In most species, the Lsm genes show associations with 11 genes: rpl7ae, rpl37e, fusA, flpA, purF, rrp4, rrp41, hel308, rpoD, rpoH, and rpoN. We propose that most archaeal Lsm proteins are related to the RNA metabolism, and the larger Lsm proteins could perform different functions and/or act through other mechanisms of action.
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Affiliation(s)
- Gloria Payá
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, Ap 99, 03080 Alicante, Spain
| | - Vanesa Bautista
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, Ap 99, 03080 Alicante, Spain
| | - Mónica Camacho
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, Ap 99, 03080 Alicante, Spain
| | - Julia Esclapez
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, Ap 99, 03080 Alicante, Spain
| | - María-José Bonete
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, Ap 99, 03080 Alicante, Spain
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van Rooijen LE, Tromer EC, van Hooff JJE, Kops GJPL, Snel B. Increased Sampling and Intracomplex Homologies Favor Vertical Over Horizontal Inheritance of the Dam1 Complex. Genome Biol Evol 2023; 15:evad017. [PMID: 36790109 PMCID: PMC9998035 DOI: 10.1093/gbe/evad017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/23/2022] [Accepted: 01/21/2023] [Indexed: 02/16/2023] Open
Abstract
Kinetochores connect chromosomes to spindle microtubules to ensure their correct segregation during cell division. Kinetochores of human and yeasts are largely homologous, their ability to track depolymerizing microtubules, however, is carried out by the nonhomologous complexes Ska1-C and Dam1-C, respectively. We previously reported the unique anti-correlating phylogenetic profiles of Dam1-C and Ska-C found among a wide variety of eukaryotes. Based on these profiles and the limited presence of Dam1-C, we speculated that horizontal gene transfer could have played a role in the evolutionary history of Dam1-C. Here, we present an expanded analysis of Dam1-C evolution, using additional genome as well as transcriptome sequences and recently published 3D structures. This analysis revealed a wider and more complete presence of Dam1-C in Cryptista, Rhizaria, Ichthyosporea, CRuMs, and Colponemidia. The fungal Dam1-C cryo-EM structure supports earlier hypothesized intracomplex homologies, which enables the reconstruction of rooted and unrooted phylogenies. The rooted tree of concatenated Dam1-C subunits is statistically consistent with the species tree of eukaryotes, suggesting that Dam1-C is ancient, and that the present-day phylogenetic distribution is best explained by multiple, independent losses and no horizontal gene transfer was involved. Furthermore, we investigated the ancient origin of Dam1-C via profile-versus-profile searches. Homology among 8 out of the 10 Dam1-C subunits suggests that the complex largely evolved from a single multimerizing subunit that diversified into a hetero-octameric core via stepwise subunit duplication and subfunctionalization of the subunits before the origin of the last eukaryotic common ancestor.
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Affiliation(s)
- Laura E van Rooijen
- Theoretical Biology and Bioinformatics, Department of Biology, Science Faculty, Utrecht University, Utrecht, The Netherlands
| | - Eelco C Tromer
- Cell Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, Faculty of Science and Engineering, University of Groningen, Groningen, The Netherlands
| | - Jolien J E van Hooff
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Geert J P L Kops
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, Utrecht, The Netherlands
- Molecular Cancer Research, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Berend Snel
- Theoretical Biology and Bioinformatics, Department of Biology, Science Faculty, Utrecht University, Utrecht, The Netherlands
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Yang Y, Huang T, Fan Y, Lu H, Shao J, Wang Y, Shen A. Significance of Spliceosome-Related Genes in the Prediction of Prognosis and Treatment Strategies for Lung Adenocarcinoma. BIOMED RESEARCH INTERNATIONAL 2022; 2022:1753563. [PMID: 36389112 PMCID: PMC9652092 DOI: 10.1155/2022/1753563] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 10/18/2022] [Indexed: 08/25/2023]
Abstract
BACKGROUND The leading cause of cancer-related fatalities globally is lung cancer; lung adenocarcinoma (LUAD) is the most common histological type in it. The spliceosome plays an important role in a majority of malignancies. However, it is yet unclear how spliceosome-related genes affect patients with LUAD in terms of treatment course and prognosis. METHODS Spliceosome-related genes were assessed from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database to obtain clinical information and gene expression in patients with LUAD. A spliceosome-related gene signature and prognostic model were constructed by using the least absolute shrinkage and selection operator (LASSO), time-dependent receiver operating characteristic (ROC), and nomogram. Immune infiltrate levels, mutation analysis, and pathway enrichment were predicted potential mechanisms of the signature by using single-sample gene set enrichment analysis (ssGSEA), Gene Set Cancer Analysis (GSCA) database, Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Ontology (GO) database. Then, a protein-protein interaction (PPI) network and transcription factor- (TF-) hub gene and drug mining network were also established by Cytoscape software. RESULTS Firstly, we constructed a prognostic model for 11 spliceosome signature genes. Based on the prognostic risk score, we stratified patients with LUAD into high- and low-risk groups. The high- and low-risk groups were closely related to the OS, tumor immune infiltration level, immune checkpoint molecules, and tumor mutation burden (TMB) of LUAD patients. Based on PPI networks, we also predict relevant TF genes that may regulate signature prognostic genes. Finally, drugs including oxaliplatin, arsenic trioxide, cisplatin, and sunitinib were excavated for the treatment of the 11 spliceosome signature genes in LUAD patients. CONCLUSION In conclusion, this study is the first to explore the importance of spliceosome-related genes in the prognosis and treatment of LUAD. Through our study, we have innovatively provided potential prognosis genes and new therapeutic drug targets for the treatment of LUAD patients.
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Affiliation(s)
- Ying Yang
- Cancer Research Center Nantong, Nantong Tumor Hospital, The Affiliated Tumor Hospital of Nantong University, Nantong University, Nantong, China
| | - Tianyi Huang
- Department of Pharmacy, Nantong University Xinling College, Nantong, China
| | - Yihui Fan
- Department of Thoracic Surgery, Nantong Tumor Hospital, The Affiliated Tumor Hospital of Nantong University, Nantong University, Nantong, China
| | - Haimin Lu
- Department of Thoracic Surgery, Nantong Tumor Hospital, The Affiliated Tumor Hospital of Nantong University, Nantong University, Nantong, China
| | - Jingjing Shao
- Cancer Research Center Nantong, Nantong Tumor Hospital, The Affiliated Tumor Hospital of Nantong University, Nantong University, Nantong, China
| | - Yilang Wang
- Department of Oncology, Nantong Tumor Hospital, The Affiliated Tumor Hospital of Nantong University, Nantong University, Nantong, China
| | - Aiguo Shen
- Cancer Research Center Nantong, Nantong Tumor Hospital, The Affiliated Tumor Hospital of Nantong University, Nantong University, Nantong, China
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Wu J, Lu F, Yu B, Wang W, Ye X. The oncogenic role of SNRPB in human tumors: A pan-cancer analysis. Front Mol Biosci 2022; 9:994440. [PMID: 36275630 PMCID: PMC9582665 DOI: 10.3389/fmolb.2022.994440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 09/20/2022] [Indexed: 11/19/2022] Open
Abstract
Purpose: The purpose of this study was to explore the oncogenic role of small nuclear ribonucleoprotein polypeptides B and B1 (SNRPB) in human tumors. Materials and methods: Study cases were acquired from The Cancer Genome Atlas database, the Gene Expression Omnibus database, The Human Protein Atlas, and the Clinical Proteomic Tumor Analysis Consortium. We then used the R package and several online tools to analyze and visualize the role of SNRPB across tumors. Results: We found that the expression of SNRPB was significantly increased in 28 of 33 tumors, and higher expression was observed in late pathological and TNM stages. Significantly decreased levels of SNRPB promoter methylation were observed in 12 tumors. SNRPB was found to be a risk factor for decreased overall survival in 10 tumors (p < 0.05), a risk factor for decreased disease-specific survival in 8 tumors (p < 0.05), and a risk factor for decreased progression-free interval in 7 tumors (p < 0.05). The PPI network of SNRPB and the top 100 coexpressed genes revealed that CDK1, CDC6, AURKB, CCNB1, CCNA2, and CDC45 were the most closely interacting genes across tumors. The GO and KEGG enrichment analyses revealed that SNRPB and the above genes were mainly enriched with respect to functions in cell cycle-related genetic material replication, assembly, and distribution. SNRPB was significantly associated with immune cell infiltration and the expression of immunomodulation-related genes in several but not all tumors. Conclusion and limitations: The expression of SNRPB was significantly elevated in almost all tumors, and the decreased promoter methylation level may contribute to the elevated expression of SNRPB. SNRPB may facilitate the progression of pathological and TNM stages and is a risk factor for unfavorable prognosis across tumors. However, our research was based on data obtained from public databases, without further validation of our findings at the cellular and animal levels. Therefore, further studies are needed to clarify the oncogenic mechanism of SNRPB and its potential as a therapeutic target.
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Affiliation(s)
- Juan Wu
- Department of Respiratory Diseases, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Feng Lu
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Bin Yu
- Department of Respiratory Diseases, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Wenjun Wang
- Department of Respiratory Diseases, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xiaoqun Ye
- Department of Respiratory Diseases, The Second Affiliated Hospital of Nanchang University, Nanchang, China
- *Correspondence: Xiaoqun Ye,
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Singh G, Gupta D. In-Silico Functional Annotation of Plasmodium falciparum Hypothetical Proteins to Identify Novel Drug Targets. Front Genet 2022; 13:821516. [PMID: 35444689 PMCID: PMC9013929 DOI: 10.3389/fgene.2022.821516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 03/07/2022] [Indexed: 11/16/2022] Open
Abstract
Plasmodium falciparum is one of the plasmodium species responsible for the majority of life-threatening malaria cases. The current antimalarial therapies are becoming less effective due to growing drug resistance, leading to the urgent requirement for alternative and more effective antimalarial drugs or vaccines. To facilitate the novel drug discovery or vaccine development efforts, recent advances in sequencing technologies provide valuable information about the whole genome of the parasite, yet a lot more needs to be deciphered due to its incomplete proteome annotation. Surprisingly, out of the 5,389 proteins currently annotated in the Plasmodium falciparum 3D7 strain, 1,626 proteins (∼30% data) are annotated as hypothetical proteins. In parasite genomic studies, the challenge to annotate hypothetical proteins is often ignored, which may obscure the crucial information related to the pathogenicity of the parasite. In this study, we attempt to characterize hypothetical proteins of the parasite to identify novel drug targets using a computational pipeline. The study reveals that out of the overall pool of the hypothetical proteins, 266 proteins have conserved functional signatures. Furthermore, the pathway analysis of these proteins revealed that 23 proteins have an essential role in various biochemical, signalling and metabolic pathways. Additionally, all the proteins (266) were subjected to computational structure analysis. We could successfully model 11 proteins. We validated and checked the structural stability of the models by performing molecular dynamics simulation. Interestingly, eight proteins show stable conformations, and seven proteins are specific for Plasmodium falciparum, based on homology analysis. Lastly, mapping the seven shortlisted hypothetical proteins on the Plasmodium falciparum protein-protein interaction network revealed 3,299 nodes and 2,750,692 edges. Our study revealed interesting functional details of seven hypothetical proteins of the parasite, which help learn more about the less-studied molecules and their interactions, providing valuable clues to unravel the role of these proteins via future experimental validation.
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Affiliation(s)
- Gagandeep Singh
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
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8
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Specific and Global RNA Regulators in Pseudomonas aeruginosa. Int J Mol Sci 2021; 22:ijms22168632. [PMID: 34445336 PMCID: PMC8395346 DOI: 10.3390/ijms22168632] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/05/2021] [Accepted: 08/08/2021] [Indexed: 01/20/2023] Open
Abstract
Pseudomonas aeruginosa (Pae) is an opportunistic pathogen showing a high intrinsic resistance to a wide variety of antibiotics. It causes nosocomial infections that are particularly detrimental to immunocompromised individuals and to patients suffering from cystic fibrosis. We provide a snapshot on regulatory RNAs of Pae that impact on metabolism, pathogenicity and antibiotic susceptibility. Different experimental approaches such as in silico predictions, co-purification with the RNA chaperone Hfq as well as high-throughput RNA sequencing identified several hundreds of regulatory RNA candidates in Pae. Notwithstanding, using in vitro and in vivo assays, the function of only a few has been revealed. Here, we focus on well-characterized small base-pairing RNAs, regulating specific target genes as well as on larger protein-binding RNAs that sequester and thereby modulate the activity of translational repressors. As the latter impact large gene networks governing metabolism, acute or chronic infections, these protein-binding RNAs in conjunction with their cognate proteins are regarded as global post-transcriptional regulators.
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Payá G, Bautista V, Camacho M, Bonete MJ, Esclapez J. Functional analysis of Lsm protein under multiple stress conditions in the extreme haloarchaeon Haloferax mediterranei. Biochimie 2021; 187:33-47. [PMID: 33992715 DOI: 10.1016/j.biochi.2021.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 05/03/2021] [Accepted: 05/04/2021] [Indexed: 01/24/2023]
Abstract
The Sm, like-Sm, and Hfq proteins belonging to the Sm superfamily of proteins are represented in all domains of life. These proteins are involved in several RNA metabolism pathways. The functions of bacterial Hfq and eukaryotic Sm proteins have been described, but knowledge about the in vivo functions of archaeal Sm proteins remains limited. This study aims to improve the understanding of Lsm proteins and their role using the haloarchaeon Haloferax mediterranei as a model microorganism. The Haloferax mediterranei genome contains one lsm gene that overlaps with the rpl37e gene. To determine the expression of lsm and rpl37e genes and the co-transcription of both, reverse transcription-polymerase chain reaction (RT-PCR) analyses were performed under different standard and stress conditions. The results suggest that the expression of lsm and rpl37e is constitutive. Co-transcription occurs at sub-optimal salt concentrations and temperatures, depending on the growth phase. The halophilic Lsm protein contains two Sm motifs, Sm1 and Sm2, and the sequence encoding the Sm2 motif also constitutes the promoter of the rpl37e gene. To investigate their biological functions, the lsm deletion mutant and the Sm1 motif deletion mutant, where the Sm2 motif remained intact, were generated and characterised. Comparison of the lsm deletion mutant, Sm1 deletion mutant, and the parental strain HM26 under standard and stress growth conditions revealed growth differences. Finally, swarming assays in complex and defined media showed greater swarming capacity in the deletion mutants.
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Affiliation(s)
- Gloria Payá
- Agrochemistry and Biochemistry Department, Biochemistry and Molecular Biology Area, Faculty of Science, University of Alicante, Ap 99, 03080, Alicante, Spain.
| | - Vanesa Bautista
- Agrochemistry and Biochemistry Department, Biochemistry and Molecular Biology Area, Faculty of Science, University of Alicante, Ap 99, 03080, Alicante, Spain.
| | - Mónica Camacho
- Agrochemistry and Biochemistry Department, Biochemistry and Molecular Biology Area, Faculty of Science, University of Alicante, Ap 99, 03080, Alicante, Spain.
| | - María-José Bonete
- Agrochemistry and Biochemistry Department, Biochemistry and Molecular Biology Area, Faculty of Science, University of Alicante, Ap 99, 03080, Alicante, Spain.
| | - Julia Esclapez
- Agrochemistry and Biochemistry Department, Biochemistry and Molecular Biology Area, Faculty of Science, University of Alicante, Ap 99, 03080, Alicante, Spain.
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The Autoantigen Repertoire and the Microbial RNP World. Trends Mol Med 2021; 27:422-435. [PMID: 33722441 DOI: 10.1016/j.molmed.2021.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/30/2021] [Accepted: 02/13/2021] [Indexed: 02/08/2023]
Abstract
Although autoimmunity and autoimmune disease (AID) are relatively common, the repertoire of autoantigens is paradoxically very limited. Highly enriched in this autoantigen repertoire are nucleic acids and their binding proteins, which together form large macromolecular structures. Most of these complexes are of ancient evolutionary origin, with homologs throughout multiple kingdoms of life. Why and if these nucleic acid-protein particles drive the development of autoimmunity remains unresolved. Recent advances in our understanding of the microbiome may provide clues about the origins of autoimmunity - and the particular puzzle of why the autoantigen repertoire is so particularly enriched in ribonucleoprotein particles (RNPs). We discuss the possibility that autoimmunity to some RNPs may arise from molecular mimicry to microbial orthologs.
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Hyjek‐Składanowska M, Bajczyk M, Gołębiewski M, Nuc P, Kołowerzo‐Lubnau A, Jarmołowski A, Smoliński DJ. Core spliceosomal Sm proteins as constituents of cytoplasmic mRNPs in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1155-1173. [PMID: 32369637 PMCID: PMC7540296 DOI: 10.1111/tpj.14792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 04/13/2020] [Accepted: 04/21/2020] [Indexed: 05/15/2023]
Abstract
In recent years, research has increasingly focused on the key role of post-transcriptional regulation of messenger ribonucleoprotein (mRNP) function and turnover. As a result of the complexity and dynamic nature of mRNPs, the full composition of a single mRNP complex remains unrevealed and mRNPs are poorly described in plants. Here we identify canonical Sm proteins as part of the cytoplasmic mRNP complex, indicating their function in the post-transcriptional regulation of gene expression in plants. Sm proteins comprise an evolutionarily ancient family of small RNA-binding proteins involved in pre-mRNA splicing. The latest research indicates that Sm could also impact on mRNA at subsequent stages of its life cycle. In this work we show that in the microsporocyte cytoplasm of Larix decidua, the European larch, Sm proteins accumulate within distinct cytoplasmic bodies, also containing polyadenylated RNA. To date, several types of cytoplasmic bodies involved in the post-transcriptional regulation of gene expression have been described, mainly in animal cells. Their role and molecular composition in plants remain less well established, however. A total of 222 mRNA transcripts have been identified as cytoplasmic partners for Sm proteins. The specific colocalization of these mRNAs with Sm proteins within cytoplasmic bodies has been confirmed via microscopic analysis. The results from this work support the hypothesis, that evolutionarily conserved Sm proteins have been adapted to perform a whole repertoire of functions related to the post-transcriptional regulation of gene expression in Eukaryota. This adaptation presumably enabled them to coordinate the interdependent processes of splicing element assembly, mRNA maturation and processing, and mRNA translation regulation, and its degradation.
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Affiliation(s)
- Malwina Hyjek‐Składanowska
- Department of Cellular and Molecular BiologyNicolaus Copernicus UniveristyLwowska 187‐100TorunPoland
- Centre For Modern Interdisciplinary TechnologiesNicolaus Copernicus UniversityWilenska 487‐100TorunPoland
- Present address:
Laboratory of Protein StructureInternational Institute of Molecular and Cell Biology4 Trojdena St.02‐109WarsawPoland
| | - Mateusz Bajczyk
- Department of Gene ExpressionInstitute of Molecular Biology and BiotechnologyAdam Mickiewicz UniversityUmultowska 89Poznan61‐614Poland
| | - Marcin Gołębiewski
- Centre For Modern Interdisciplinary TechnologiesNicolaus Copernicus UniversityWilenska 487‐100TorunPoland
- Department of Plant Physiology and BiotechnologyNicolaus Copernicus UniveristyLwowska 187‐100TorunPoland
| | - Przemysław Nuc
- Department of Gene ExpressionInstitute of Molecular Biology and BiotechnologyAdam Mickiewicz UniversityUmultowska 89Poznan61‐614Poland
| | - Agnieszka Kołowerzo‐Lubnau
- Department of Cellular and Molecular BiologyNicolaus Copernicus UniveristyLwowska 187‐100TorunPoland
- Centre For Modern Interdisciplinary TechnologiesNicolaus Copernicus UniversityWilenska 487‐100TorunPoland
| | - Artur Jarmołowski
- Department of Gene ExpressionInstitute of Molecular Biology and BiotechnologyAdam Mickiewicz UniversityUmultowska 89Poznan61‐614Poland
| | - Dariusz Jan Smoliński
- Department of Cellular and Molecular BiologyNicolaus Copernicus UniveristyLwowska 187‐100TorunPoland
- Centre For Modern Interdisciplinary TechnologiesNicolaus Copernicus UniversityWilenska 487‐100TorunPoland
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Gangras P, Gallagher TL, Parthun MA, Yi Z, Patton RD, Tietz KT, Deans NC, Bundschuh R, Amacher SL, Singh G. Zebrafish rbm8a and magoh mutants reveal EJC developmental functions and new 3'UTR intron-containing NMD targets. PLoS Genet 2020; 16:e1008830. [PMID: 32502192 PMCID: PMC7310861 DOI: 10.1371/journal.pgen.1008830] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 06/23/2020] [Accepted: 05/05/2020] [Indexed: 12/11/2022] Open
Abstract
Many post-transcriptional mechanisms operate via mRNA 3'UTRs to regulate protein expression, and such controls are crucial for development. We show that homozygous mutations in two zebrafish exon junction complex (EJC) core genes rbm8a and magoh leads to muscle disorganization, neural cell death, and motor neuron outgrowth defects, as well as dysregulation of mRNAs subjected to nonsense-mediated mRNA decay (NMD) due to translation termination ≥ 50 nts upstream of the last exon-exon junction. Intriguingly, we find that EJC-dependent NMD also regulates a subset of transcripts that contain 3'UTR introns (3'UI) < 50 nts downstream of a stop codon. Some transcripts containing such stop codon-proximal 3'UI are also NMD-sensitive in cultured human cells and mouse embryonic stem cells. We identify 167 genes that contain a conserved proximal 3'UI in zebrafish, mouse and humans. foxo3b is one such proximal 3'UI-containing gene that is upregulated in zebrafish EJC mutant embryos, at both mRNA and protein levels, and loss of foxo3b function in EJC mutant embryos significantly rescues motor axon growth defects. These data are consistent with EJC-dependent NMD regulating foxo3b mRNA to control protein expression during zebrafish development. Our work shows that the EJC is critical for normal zebrafish development and suggests that proximal 3'UIs may serve gene regulatory function in vertebrates.
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Affiliation(s)
- Pooja Gangras
- Department of Molecular Genetics, The Ohio State University, Ohio, United States of America
- Center for RNA Biology, The Ohio State University, Ohio, United States of America
| | - Thomas L. Gallagher
- Department of Molecular Genetics, The Ohio State University, Ohio, United States of America
- Center for RNA Biology, The Ohio State University, Ohio, United States of America
| | - Michael A. Parthun
- Department of Molecular Genetics, The Ohio State University, Ohio, United States of America
- Center for RNA Biology, The Ohio State University, Ohio, United States of America
| | - Zhongxia Yi
- Department of Molecular Genetics, The Ohio State University, Ohio, United States of America
- Center for RNA Biology, The Ohio State University, Ohio, United States of America
| | - Robert D. Patton
- Center for RNA Biology, The Ohio State University, Ohio, United States of America
- Department of Physics, The Ohio State University, Ohio, United States of America
| | - Kiel T. Tietz
- Department of Molecular Genetics, The Ohio State University, Ohio, United States of America
- Center for RNA Biology, The Ohio State University, Ohio, United States of America
| | - Natalie C. Deans
- Department of Molecular Genetics, The Ohio State University, Ohio, United States of America
- Center for RNA Biology, The Ohio State University, Ohio, United States of America
| | - Ralf Bundschuh
- Center for RNA Biology, The Ohio State University, Ohio, United States of America
- Department of Physics, The Ohio State University, Ohio, United States of America
- Department of Chemistry and Biochemistry, The Ohio State University, Ohio, United States of America
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Ohio, United States of America
| | - Sharon L. Amacher
- Department of Molecular Genetics, The Ohio State University, Ohio, United States of America
- Center for RNA Biology, The Ohio State University, Ohio, United States of America
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Ohio, United States of America
- Center for Muscle Health and Neuromuscular Disorders, The Ohio State University and Nationwide Children’s Hospital, Ohio, United States of America
| | - Guramrit Singh
- Department of Molecular Genetics, The Ohio State University, Ohio, United States of America
- Center for RNA Biology, The Ohio State University, Ohio, United States of America
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13
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A journey through the evolutionary diversification of archaeal Lsm and Hfq proteins. Emerg Top Life Sci 2018; 2:647-657. [PMID: 33525833 DOI: 10.1042/etls20180034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 10/09/2018] [Accepted: 10/12/2018] [Indexed: 11/17/2022]
Abstract
Sm-like (Lsm) proteins are found in all three domains of life. They are crucially involved in the RNA metabolism of prokaryotic organisms. To exert their function, they assemble into hexa- or heptameric rings and bind RNA via a conserved binding pocket for uridine stretches in the inner pore of the ring. Despite the conserved secondary structure of Lsm proteins, there are several features that lead to a structural diversification of this protein family that mediates their participation in a variety of processes related to RNA metabolism. Until recently, the cellular function of archaeal Sm-like proteins was not well understood. In this review, we discuss structural features of Lsm proteins with a strong focus on archaeal variants, reflect on the evolutionary development of archaeal Lsm proteins and present recent insights into their biological function.
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14
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Vosseberg J, Snel B. Domestication of self-splicing introns during eukaryogenesis: the rise of the complex spliceosomal machinery. Biol Direct 2017; 12:30. [PMID: 29191215 PMCID: PMC5709842 DOI: 10.1186/s13062-017-0201-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 11/20/2017] [Indexed: 12/31/2022] Open
Abstract
ᅟ The spliceosome is a eukaryote-specific complex that is essential for the removal of introns from pre-mRNA. It consists of five small nuclear RNAs (snRNAs) and over a hundred proteins, making it one of the most complex molecular machineries. Most of this complexity has emerged during eukaryogenesis, a period that is characterised by a drastic increase in cellular and genomic complexity. Although not fully resolved, recent findings have started to shed some light on how and why the spliceosome originated. In this paper we review how the spliceosome has evolved and discuss its origin and subsequent evolution in light of different general hypotheses on the evolution of complexity. Comparative analyses have established that the catalytic core of this ribonucleoprotein (RNP) complex, as well as the spliceosomal introns, evolved from self-splicing group II introns. Most snRNAs evolved from intron fragments and the essential Prp8 protein originated from the protein that is encoded by group II introns. Proteins that functioned in other RNA processes were added to this core and extensive duplications of these proteins substantially increased the complexity of the spliceosome prior to the eukaryotic diversification. The splicing machinery became even more complex in animals and plants, yet was simplified in eukaryotes with streamlined genomes. Apparently, the spliceosome did not evolve its complexity gradually, but in rapid bursts, followed by stagnation or even simplification. We argue that although both adaptive and neutral evolution have been involved in the evolution of the spliceosome, especially the latter was responsible for the emergence of an enormously complex eukaryotic splicing machinery from simple self-splicing sequences. Reviewers This article was reviewed by W. Ford Doolittle, Eugene V. Koonin and Vivek Anantharaman.
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Affiliation(s)
- Julian Vosseberg
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands.
| | - Berend Snel
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
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15
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Hyjek M, Wojciechowska N, Rudzka M, Kołowerzo-Lubnau A, Smoliński DJ. Spatial regulation of cytoplasmic snRNP assembly at the cellular level. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:7019-30. [PMID: 26320237 PMCID: PMC4765780 DOI: 10.1093/jxb/erv399] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Small nuclear ribonucleoproteins (snRNPs) play a crucial role in pre-mRNA splicing in all eukaryotic cells. In contrast to the relatively broad knowledge on snRNP assembly within the nucleus, the spatial organization of the cytoplasmic stages of their maturation remains poorly understood. Nevertheless, sparse research indicates that, similar to the nuclear steps, the crucial processes of cytoplasmic snRNP assembly may also be strictly spatially regulated. In European larch microsporocytes, it was determined that the cytoplasmic assembly of snRNPs within a cell might occur in two distinct spatial manners, which depend on the rate of de novo snRNP formation in relation to the steady state of these particles within the nucleus. During periods of moderate expression of splicing elements, the cytoplasmic assembly of snRNPs occurred diffusely throughout the cytoplasm. Increased expression of both Sm proteins and U snRNA triggered the accumulation of these particles within distinct, non-membranous RNP-rich granules, which are referred to as snRNP-rich cytoplasmic bodies.
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Affiliation(s)
- Malwina Hyjek
- Department of Cell Biology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University, Lwowska 1, Toruń, 87-100, Poland Centre For Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4, 87-100 Toruń Poland
| | - Natalia Wojciechowska
- Department of Cell Biology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University, Lwowska 1, Toruń, 87-100, Poland Department of General Botany, Institute of Experimental Biology, Faculty of Biology, A. Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Magda Rudzka
- Department of Cell Biology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University, Lwowska 1, Toruń, 87-100, Poland Centre For Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4, 87-100 Toruń Poland
| | - Agnieszka Kołowerzo-Lubnau
- Department of Cell Biology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University, Lwowska 1, Toruń, 87-100, Poland Centre For Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4, 87-100 Toruń Poland
| | - Dariusz Jan Smoliński
- Department of Cell Biology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University, Lwowska 1, Toruń, 87-100, Poland Centre For Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4, 87-100 Toruń Poland
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16
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Maier LK, Benz J, Fischer S, Alstetter M, Jaschinski K, Hilker R, Becker A, Allers T, Soppa J, Marchfelder A. Deletion of the Sm1 encoding motif in the lsm gene results in distinct changes in the transcriptome and enhanced swarming activity of Haloferax cells. Biochimie 2015; 117:129-37. [DOI: 10.1016/j.biochi.2015.02.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 02/26/2015] [Indexed: 01/08/2023]
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17
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Seng CO, Magee C, Young PJ, Lorson CL, Allen JP. The SMN structure reveals its crucial role in snRNP assembly. Hum Mol Genet 2015; 24:2138-46. [PMID: 25561692 DOI: 10.1093/hmg/ddu734] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The spliceosome plays a fundamental role in RNA metabolism by facilitating pre-RNA splicing. To understand how this essential complex is formed, we have used protein crystallography to determine the first complete structures of the key assembler protein, SMN, and the truncated isoform, SMNΔ7, which is found in patients with the disease spinal muscular atrophy (SMA). Comparison of the structures of SMN and SMNΔ7 shows many similar features, including the presence of two Tudor domains, but significant differences are observed in the C-terminal domain, including 12 additional amino acid residues encoded by exon 7 in SMN compared with SMNΔ7. Mapping of missense point mutations found in some SMA patients reveals clustering around three spatial locations, with the largest cluster found in the C-terminal domain. We propose a structural model of SMN binding with the Gemin2 protein and a heptameric Sm ring, revealing a critical assembly role of the residues 260-294, with the differences at the C-terminus of SMNΔ7 compared with SMN likely leading to loss of small nuclear ribonucleoprotein (snRNP) assembly. The SMN complex is proposed to form a dimer driven by formation of a glycine zipper involving α helix formed by amino acid residues 263-294. These results explain how structural changes of SMN give rise to loss of SMN-mediated snRNP assembly and support the hypothesis that this loss results in atrophy of neurons in SMA.
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Affiliation(s)
- Chenda O Seng
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA and
| | - Craig Magee
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA and
| | - Philip J Young
- Department of Veterinary Pathology, Bond Life Sciences Center, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA
| | - Christian L Lorson
- Department of Veterinary Pathology, Bond Life Sciences Center, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA
| | - James P Allen
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA and
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18
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Chen Y, Cao J. Comparative genomic analysis of the Sm gene family in rice and maize. Gene 2014; 539:238-49. [PMID: 24525402 DOI: 10.1016/j.gene.2014.02.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Revised: 02/03/2014] [Accepted: 02/06/2014] [Indexed: 10/25/2022]
Abstract
Sm proteins are a group of ubiquitous ring-shaped oligomers that function in multiple aspects of RNA metabolism. However, until this study, no comprehensive study incorporating phylogeny, chromosomal location, gene organization, adaptive evolution, expression profiling and functional networks has been reported for rice and maize. In this study, twenty-five and thirty-three Sm genes have been identified in rice and maize, respectively. Phylogenetic analyses identified eighteen gene groups. Results by gene locations indicated that segmental duplication contributes to the expansion of this gene family in rice and maize. Gene organization and motif compositions of the Sm members are highly conserved in each group, indicative of their functional conservation. Expression profiles have provided insights into the possible functional divergence among members of the Sm gene family. Adaptive evolution analyses suggested that purifying selection was the main force driving Sm evolution, but some critical sites might be responsible for functional divergence. In addition, four hundred and seventy-nine interactions were identified by functional network analyses, and most of which were associated with binding, cellular macromolecule biosynthesis, pre-mRNA processing and transferase activity. Overall, the data contribute to a better understanding of the complexity of Sm gene family in rice and maize and will provide a solid foundation for future functional studies.
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Affiliation(s)
- Yuzhu Chen
- Institute of Life Science, Jiangsu University, Zhenjiang, Jiangsu, PR China
| | - Jun Cao
- Institute of Life Science, Jiangsu University, Zhenjiang, Jiangsu, PR China.
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19
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Yonekura K, Watanabe M, Kageyama Y, Hirata K, Yamamoto M, Maki-Yonekura S. Post-transcriptional regulator Hfq binds catalase HPII: crystal structure of the complex. PLoS One 2013; 8:e78216. [PMID: 24223139 PMCID: PMC3819363 DOI: 10.1371/journal.pone.0078216] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Accepted: 09/18/2013] [Indexed: 12/12/2022] Open
Abstract
We report a crystal structure of Hfq and catalase HPII from Escherichia coli. The post-transcriptional regulator Hfq plays a key role in the survival of bacteria under stress. A small non-coding RNA (sRNA) DsrA is required for translation of the stationary phase sigma factor RpoS, which is the central regulator of the general stress response. Hfq facilitates efficient translation of rpoS mRNA, which encodes RpoS. Hfq helps in the function of other specific proteins involved in RNA processing, indicating its versatility in the cell. However, structural information regarding its interactions with partners is missing. Here we obtained crystals of Hfq and HPII complexes from cell lysates following attempts to overexpress a foreign membrane protein. HPII is one of two catalases in E. coli and its mRNA is transcribed by an RNA polymerase holoenzyme containing RpoS, which in turn is under positive control of small non-coding RNAs and of the RNA chaperone Hfq. This sigma factor is known to have a pronounced effect on the expression of HPII. The crystal structure reveals that a Hfq hexamer binds each subunit of a HPII tetramer. Each subunit of the Hfq hexamer exhibits a unique binding mode with HPII. The hexamer of Hfq interacts via its distal surface. The proximal and distal surfaces are known to specifically bind different sRNAs, and binding of HPII could affect Hfq function. Hfq-HPII complexation has no effect on catalase HPII activity.
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Affiliation(s)
- Koji Yonekura
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, Harima Institute, Sayo, Hyogo, Japan
| | - Masahiro Watanabe
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, Harima Institute, Sayo, Hyogo, Japan
| | - Yuko Kageyama
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, Harima Institute, Sayo, Hyogo, Japan
| | - Kunio Hirata
- Research Infrastructure Group, RIKEN SPring-8 Center, Harima Institute, Sayo, Hyogo, Japan
| | - Masaki Yamamoto
- Research Infrastructure Group, RIKEN SPring-8 Center, Harima Institute, Sayo, Hyogo, Japan
| | - Saori Maki-Yonekura
- Bio-Specimen Platform Group, RIKEN SPring-8 Center, Harima Institute, Sayo, Hyogo, Japan
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20
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Rossi A, Ross EJ, Jack A, Sánchez Alvarado A. Molecular cloning and characterization of SL3: a stem cell-specific SL RNA from the planarian Schmidtea mediterranea. Gene 2013; 533:156-67. [PMID: 24120894 DOI: 10.1016/j.gene.2013.09.101] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 08/26/2013] [Accepted: 09/26/2013] [Indexed: 01/03/2023]
Abstract
Spliced leader (SL) trans-splicing is a biological phenomenon, common among many metazoan taxa, consisting in the transfer of a short leader sequence from a small SL RNA to the 5' end of a subset of pre-mRNAs. While knowledge of the biochemical mechanisms driving this process has accumulated over the years, the functional consequences of such post-transcriptional event at the organismal level remain unclear. In addition, the fact that functional analyses have been undertaken mainly in trypanosomes and nematodes leaves a somehow fragmented picture of the possible biological significance and evolution of SL trans-splicing in eukaryotes. Here, we analyzed the spatial expression of SL RNAs in the planarian flatworm Schmidtea mediterranea, with the goal of identifying novel developmental paradigms for the study of trans-splicing in metazoans. Besides the previously identified SL1 and SL2, S. mediterranea expresses a third SL RNA described here as SL3. While, SL1 and SL2 are collectively expressed in a broad range of planarian cell types, SL3 is highly enriched in a subset of the planarian stem cells engaged in regenerative responses. Our findings provide new opportunities to study how trans-splicing may regulate the phenotype of a cell.
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Affiliation(s)
- Alessandro Rossi
- Stowers Institute for Medical Research, 1000 E 50th St., Kansas City, MO 64110, USA.
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21
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Pontes O, Vitins A, Ream TS, Hong E, Pikaard CS, Costa-Nunes P. Intersection of small RNA pathways in Arabidopsis thaliana sub-nuclear domains. PLoS One 2013; 8:e65652. [PMID: 23776518 PMCID: PMC3680462 DOI: 10.1371/journal.pone.0065652] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Accepted: 04/25/2013] [Indexed: 12/22/2022] Open
Abstract
In Arabidopsis thaliana, functionally diverse small RNA (smRNA) pathways bring about decreased RNA accumulation of target genes via several different mechanisms. Cytological experiments have suggested that the processing of microRNAs (miRNAs) and heterochromatic small interfering RNAs (hc-siRNAs) occurs within a specific nuclear domain that can present Cajal Body (CB) characteristics. It is unclear whether single or multiple smRNA-related domains are found within the same CB and how specialization of the smRNA pathways is determined within this specific sub-compartment. To ascertain whether nuclear smRNA centers are spatially related, we localized key proteins required for siRNA or miRNA biogenesis by immunofluorescence analysis. The intranuclear distribution of the proteins revealed that hc-siRNA, miRNA and trans-acting siRNA (ta-siRNA) pathway proteins accumulate and colocalize within a sub-nuclear structure in the nucleolar periphery. Furthermore, colocalization of miRNA- and siRNA-pathway members with CB markers, and reduced wild-type localization patterns in CB mutants indicates that proper nuclear localization of these proteins requires CB integrity. We hypothesize that these nuclear domains could be important for RNA silencing and may partially explain the functional redundancies and interactions among components of the same protein family. The CB may be the place in the nucleus where Dicer-generated smRNA precursors are processed and assigned to a specific pathway, and where storage, recycling or assembly of RNA interference components takes place.
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Affiliation(s)
- Olga Pontes
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States of America.
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22
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Wang W, Wang L, Wu J, Gong Q, Shi Y. Hfq-bridged ternary complex is important for translation activation of rpoS by DsrA. Nucleic Acids Res 2013; 41:5938-48. [PMID: 23605038 PMCID: PMC3675490 DOI: 10.1093/nar/gkt276] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The rpoS mRNA, which encodes the master regulator σ(S) of general stress response, requires Hfq-facilitated base pairing with DsrA small RNA for efficient translation at low temperatures. It has recently been proposed that one mechanism underlying Hfq action is to bridge a transient ternary complex by simultaneously binding to rpoS and DsrA. However, no structural evidence of Hfq simultaneously bound to different RNAs has been reported. We detected simultaneous binding of Hfq to rpoS and DsrA fragments. Crystal structures of AU6A•Hfq•A7 and Hfq•A7 complexes were resolved using 1.8- and 1.9-Å resolution, respectively. Ternary complex has been further verified in solution by NMR. In vivo, activation of rpoS translation requires intact Hfq, which is capable of bridging rpoS and DsrA simultaneously into ternary complex. This ternary complex possibly corresponds to a meta-stable transition state in Hfq-facilitated small RNA-mRNA annealing process.
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Affiliation(s)
- Weiwei Wang
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, P R China
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23
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Mura C, Randolph PS, Patterson J, Cozen AE. Archaeal and eukaryotic homologs of Hfq: A structural and evolutionary perspective on Sm function. RNA Biol 2013; 10:636-51. [PMID: 23579284 PMCID: PMC3710371 DOI: 10.4161/rna.24538] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Hfq and other Sm proteins are central in RNA metabolism, forming an evolutionarily conserved family that plays key roles in RNA processing in organisms ranging from archaea to bacteria to human. Sm-based cellular pathways vary in scope from eukaryotic mRNA splicing to bacterial quorum sensing, with at least one step in each of these pathways being mediated by an RNA-associated molecular assembly built upon Sm proteins. Though the first structures of Sm assemblies were from archaeal systems, the functions of Sm-like archaeal proteins (SmAPs) remain murky. Our ignorance about SmAP biology, particularly vis-à-vis the eukaryotic and bacterial Sm homologs, can be partly reduced by leveraging the homology between these lineages to make phylogenetic inferences about Sm functions in archaea. Nevertheless, whether SmAPs are more eukaryotic (RNP scaffold) or bacterial (RNA chaperone) in character remains unclear. Thus, the archaeal domain of life is a missing link, and an opportunity, in Sm-based RNA biology.
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Affiliation(s)
- Cameron Mura
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
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24
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ncRNAs and thermoregulation: a view in prokaryotes and eukaryotes. FEBS Lett 2012; 586:4061-9. [PMID: 23098758 DOI: 10.1016/j.febslet.2012.10.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 10/09/2012] [Accepted: 10/10/2012] [Indexed: 11/24/2022]
Abstract
During cellular stress response, a widespread inhibition of transcription and blockade of splicing and other post-transcriptional processing is detected, while certain specific genes are induced. In particular, free-living cells constantly monitor temperature. When the thermal condition changes, they activate a set of genes coding for proteins that participate in the response. Non-coding RNAs, ncRNAs, and conformational changes in specific regions of mRNAs seem also to be crucial regulators that enable the cell to adjust its physiology to environmental changes. They exert their effects following the same principles in all organisms and may affect all steps of gene expression. These ncRNAs and structural elements as related to thermal stress response in bacteria are reviewed. The resemblances to eukaryotic ncRNAs are highlighted.
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Abstract
Although the mechanisms by which complex cellular features evolve constitute one of the great unsolved problems of evolutionary biology, it is clear that the emergence of new protein-protein interactions, often accompanied by the diversification of duplicate genes, is involved. Using information on the levels of protein multimerization in major phylogenetic groups as a guide to the patterns that must be explained and relying on results from population-genetic theory to define the relative plausibility of alternative evolutionary pathways, a framework for understanding the evolution of dimers is developed. The resultant theory demonstrates that the likelihoods of alternative pathways for the emergence of protein complexes depend strongly on the effective population size. Nonetheless, it is equally clear that further advancements in this area will require comparative studies on the fitness consequences of alternative monomeric and dimeric proteins.
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26
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Wang W, Wang L, Zou Y, Zhang J, Gong Q, Wu J, Shi Y. Cooperation of Escherichia coli Hfq hexamers in DsrA binding. Genes Dev 2011; 25:2106-17. [PMID: 21979921 DOI: 10.1101/gad.16746011] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Hfq is a bacterial post-transcriptional regulator. It facilitates base-pairing between sRNA and target mRNA. Hfq mediates DsrA-dependent translational activation of rpoS mRNA at low temperatures. rpoS encodes the stationary-phase σ factor σ(S), which is the central regulator in general stress response. However, structural information on Hfq-DsrA interaction is not yet available. Although Hfq is reported to hydrolyze ATP, the ATP-binding site is still unknown. Here, we report a ternary crystal complex structure of Escherichia coli Hfq bound to a major Hfq recognition region on DsrA (AU(6)A) together with ADP, and a crystal complex structure of Hfq bound to ADP. AU(6)A binds to the proximal and distal sides of two Hfq hexamers. ADP binds to a purine-selective site on the distal side and contacts conserved arginine or glutamine residues on the proximal side of another hexamer. This binding mode is different from previously postulated. The cooperation of two different Hfq hexamers upon nucleic acid binding in solution is verified by fluorescence polarization and solution nuclear magnetic resonance (NMR) experiments using fragments of Hfq and DsrA. Fluorescence resonance energy transfer conducted with full-length Hfq and DsrA also supports cooperation of Hfq hexamers upon DsrA binding. The implications of Hfq hexamer cooperation have been discussed.
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Affiliation(s)
- Weiwei Wang
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
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27
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Lynch M, Bobay LM, Catania F, Gout JF, Rho M. The repatterning of eukaryotic genomes by random genetic drift. Annu Rev Genomics Hum Genet 2011; 12:347-66. [PMID: 21756106 DOI: 10.1146/annurev-genom-082410-101412] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Recent observations on rates of mutation, recombination, and random genetic drift highlight the dramatic ways in which fundamental evolutionary processes vary across the divide between unicellular microbes and multicellular eukaryotes. Moreover, population-genetic theory suggests that the range of variation in these parameters is sufficient to explain the evolutionary diversification of many aspects of genome size and gene structure found among phylogenetic lineages. Most notably, large eukaryotic organisms that experience elevated magnitudes of random genetic drift are susceptible to the passive accumulation of mutationally hazardous DNA that would otherwise be eliminated by efficient selection. Substantial evidence also suggests that variation in the population-genetic environment influences patterns of protein evolution, with the emergence of certain kinds of amino-acid substitutions and protein-protein complexes only being possible in populations with relatively small effective sizes. These observations imply that the ultimate origins of many of the major genomic and proteomic disparities between prokaryotes and eukaryotes and among eukaryotic lineages have been molded as much by intrinsic variation in the genetic and cellular features of species as by external ecological forces.
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Affiliation(s)
- Michael Lynch
- Department of Biology, Indiana University, Bloomington, Indiana 47408, USA.
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28
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Abstract
Hfq is an RNA-binding protein that is common to diverse bacterial lineages and has key roles in the control of gene expression. By facilitating the pairing of small RNAs with their target mRNAs, Hfq affects the translation and turnover rates of specific transcripts and contributes to complex post-transcriptional networks. These functions of Hfq can be attributed to its ring-like oligomeric architecture, which presents two non-equivalent binding surfaces that are capable of multiple interactions with RNA molecules. Distant homologues of Hfq occur in archaea and eukaryotes, reflecting an ancient origin for the protein family and hinting at shared functions. In this Review, we describe the salient structural and functional features of Hfq and discuss possible mechanisms by which this protein can promote RNA interactions to catalyse specific and rapid regulatory responses in vivo.
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Affiliation(s)
- Jörg Vogel
- Institute for Molecular Infection Biology, University of Würzburg, Joseph-Schneider-Strasse 2, D-97080 Würzburg, Germany.
| | - Ben F. Luisi
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK.
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Swaraz AM, Park YD, Hur Y. Knock-out mutations of Arabidopsis SmD3-b induce pleotropic phenotypes through altered transcript splicing. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2011; 180:661-671. [PMID: 21421416 DOI: 10.1016/j.plantsci.2011.01.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Revised: 01/13/2011] [Accepted: 01/19/2011] [Indexed: 05/30/2023]
Abstract
SmD3 is a core protein of small nuclear ribonucleoprotein (snRNP) essential for splicing of primary transcripts. To elucidate function of SmD3 protein in plants, phenotypes and gene expression of SmD3 knock-out and overexpressing mutants in Arabidopsis have been analyzed. smd3-a knock-out mutant or SmD3-a and SmD3-b overexpressors did not show phenotypic alteration. Knock-out of SmD3-b resulted in the pleotropic phenotypes of delayed flowering time and completion of life cycle, reduced root growth, partially defective leaf venation, abnormal numbers of trichome branches, and changed numbers of floral organs. Microarray data revealed that the smd3-b mutant had altered expression of genes related to the above phenotypes, indirectly suggesting that changed splicing of these genes may cause the observed phenotypes. Splicing of selected genes was either totally blocked or reduced in the smd3-b mutant, indicating the important role of SmD3-b in the process. A double knock-out mutant of smd3-a and smd3-b could not be generated, indicating possible redundant function of these two genes. All data indicate that SmD3-b may be major component of the spliceosomal snRNP in Arabidopsis, but the function of SmD3-a may be redundant.
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Affiliation(s)
- A M Swaraz
- Department of Biological Sciences, Chungnam National University, Daejeon 305-764, Republic of Korea
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Cao J, Shi F, Liu X, Jia J, Zeng J, Huang G. Genome-wide identification and evolutionary analysis of Arabidopsis sm genes family. J Biomol Struct Dyn 2011; 28:535-44. [PMID: 21142222 DOI: 10.1080/07391102.2011.10508593] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Sm proteins are members of a family of small proteins that are widespread in biosphere and found associated with RNA metabolism. To date, to our knowledge, only Arabidopsis SAD1 gene has been studied functionally in plant. In this study, 42 Sm genes are identified through comprehensive analysis in Arabidopsis. And a complete overview of this gene family is presented, including the gene structures, phylogeny, chromosome locations, selection pressure and expression. The results reveal that gene duplication contributes to the expansion of the Sm gene family in Arabidopsis genome, diverse expression patterns suggest their functional differentiation and divergence analysis indicates purifying selection as a key role in evolution. Our comparative genomics analysis of Sm genes will provide the first step towards the future experimental research on determining the functions of these genes.
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Affiliation(s)
- Jun Cao
- Institute of Life Science, Jiangsu University, Xuefu Road 301, Zhenjiang 212013, Jiangsu, PR China.
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31
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Functional organization of the Sm core in the crystal structure of human U1 snRNP. EMBO J 2010; 29:4172-84. [PMID: 21113136 DOI: 10.1038/emboj.2010.295] [Citation(s) in RCA: 104] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Accepted: 10/28/2010] [Indexed: 11/08/2022] Open
Abstract
U1 small nuclear ribonucleoprotein (snRNP) recognizes the 5'-splice site early during spliceosome assembly. It represents a prototype spliceosomal subunit containing a paradigmatic Sm core RNP. The crystal structure of human U1 snRNP obtained from natively purified material by in situ limited proteolysis at 4.4 Å resolution reveals how the seven Sm proteins, each recognize one nucleotide of the Sm site RNA using their Sm1 and Sm2 motifs. Proteins D1 and D2 guide the snRNA into and out of the Sm ring, and proteins F and E mediate a direct interaction between the Sm site termini. Terminal extensions of proteins D1, D2 and B/B', and extended internal loops in D2 and B/B' support a four-way RNA junction and a 3'-terminal stem-loop on opposite sides of the Sm core RNP, respectively. On a higher organizational level, the core RNP presents multiple attachment sites for the U1-specific 70K protein. The intricate, multi-layered interplay of proteins and RNA rationalizes the hierarchical assembly of U snRNPs in vitro and in vivo.
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32
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Anne J. Arginine methylation of SmB is required for Drosophila germ cell development. Development 2010; 137:2819-28. [PMID: 20659974 DOI: 10.1242/dev.052944] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Sm proteins constitute the common core of spliceosomal small nuclear ribonucleoproteins. Although Sm proteins are known to be methylated at specific arginine residues within the C-terminal arginine-glycine dipeptide (RG) repeats, the biological relevance of these modifications remains unknown. In this study, a tissue-specific function of arginine methylation of the SmB protein was identified in Drosophila. Analysis of the distribution of SmB during oogenesis revealed that this protein accumulates at the posterior pole of the oocyte, a cytoplasmic region containing the polar granules, which are necessary for the formation of primordial germ cells. The pole plasm localisation of SmB requires the methylation of arginine residues in its RG repeats by the Capsuléen-Valois methylosome complex. Functional studies showed that the methylation of these arginine residues is essential for distinct processes of the germline life cycle, including germ cell formation, migration and differentiation. In particular, the methylation of a subset of these arginine residues appears essential for the anchoring of the polar granules at the posterior cortex of the oocyte, whereas the methylation of another subset controls germ cell migration during embryogenesis. These results demonstrate a crucial role of arginine methylation in directing the subcellular localisation of SmB and that this modification contributes specifically to the establishment and development of germ cells.
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Affiliation(s)
- Joël Anne
- Department of Developmental Genetics, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, Heidelberg, Germany.
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An Overview of the Introns-First Theory. J Mol Evol 2009; 69:527-40. [DOI: 10.1007/s00239-009-9279-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2009] [Accepted: 09/08/2009] [Indexed: 10/20/2022]
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Das D, Kozbial P, Axelrod HL, Miller MD, McMullan D, Krishna SS, Abdubek P, Acosta C, Astakhova T, Burra P, Carlton D, Chen C, Chiu HJ, Clayton T, Deller MC, Duan L, Elias Y, Elsliger MA, Ernst D, Farr C, Feuerhelm J, Grzechnik A, Grzechnik SK, Hale J, Han GW, Jaroszewski L, Jin KK, Johnson HA, Klock HE, Knuth MW, Kumar A, Marciano D, Morse AT, Murphy KD, Nigoghossian E, Nopakun A, Okach L, Oommachen S, Paulsen J, Puckett C, Reyes R, Rife CL, Sefcovic N, Sudek S, Tien H, Trame C, Trout CV, van den Bedem H, Weekes D, White A, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA. Crystal structure of a novel Sm-like protein of putative cyanophage origin at 2.60 A resolution. Proteins 2009; 75:296-307. [PMID: 19173316 DOI: 10.1002/prot.22360] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
ECX21941 represents a very large family (over 600 members) of novel, ocean metagenome-specific proteins identified by clustering of the dataset from the Global Ocean Sampling expedition. The crystal structure of ECX21941 reveals unexpected similarity to Sm/LSm proteins, which are important RNA-binding proteins, despite no detectable sequence similarity. The ECX21941 protein assembles as a homopentamer in solution and in the crystal structure when expressed in Escherichia coli and represents the first pentameric structure for this Sm/LSm family of proteins, although the actual oligomeric form in vivo is currently not known. The genomic neighborhood analysis of ECX21941 and its homologs combined with sequence similarity searches suggest a cyanophage origin for this protein. The specific functions of members of this family are unknown, but our structure analysis of ECX21941 indicates nucleic acid-binding capabilities and suggests a role in RNA and/or DNA processing.
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Affiliation(s)
- Debanu Das
- Joint Center for Structural Genomics, 2 Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, USA
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