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Sun X, Shen J, Perrimon N, Kong X, Wang D. The endoribonuclease Arlr is required to maintain lipid homeostasis by downregulating lipolytic genes during aging. Nat Commun 2023; 14:6254. [PMID: 37803019 PMCID: PMC10558556 DOI: 10.1038/s41467-023-42042-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 09/28/2023] [Indexed: 10/08/2023] Open
Abstract
While disorders in lipid metabolism have been associated with aging and age-related diseases, how lipid metabolism is regulated during aging is poorly understood. Here, we characterize the Drosophila endoribonuclease CG2145, an ortholog of mammalian EndoU that we named Age-related lipid regulator (Arlr), as a regulator of lipid homeostasis during aging. In adult adipose tissues, Arlr is necessary for maintenance of lipid storage in lipid droplets (LDs) as flies age, a phenotype that can be rescued by either high-fat or high-glucose diet. Interestingly, RNA-seq of arlr mutant adipose tissues and RIP-seq suggest that Arlr affects lipid metabolism through the degradation of the mRNAs of lipolysis genes - a model further supported by the observation that knockdown of Lsd-1, regucalcin, yip2 or CG5162, which encode genes involved in lipolysis, rescue the LD defects of arlr mutants. In addition, we characterize DendoU as a functional paralog of Arlr and show that human ENDOU can rescue arlr mutants. Altogether, our study reveals a role of ENDOU-like endonucleases as negative regulator of lipolysis.
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Affiliation(s)
- Xiaowei Sun
- Department of Plant Biosecurity and MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing, China
| | - Jie Shen
- Department of Plant Biosecurity and MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing, China
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Xue Kong
- Department of Plant Biosecurity and MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing, China
| | - Dan Wang
- Department of Plant Biosecurity and MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing, China.
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2
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Droujinine IA, Meyer AS, Wang D, Udeshi ND, Hu Y, Rocco D, McMahon JA, Yang R, Guo J, Mu L, Carey DK, Svinkina T, Zeng R, Branon T, Tabatabai A, Bosch JA, Asara JM, Ting AY, Carr SA, McMahon AP, Perrimon N. Proteomics of protein trafficking by in vivo tissue-specific labeling. Nat Commun 2021; 12:2382. [PMID: 33888706 PMCID: PMC8062696 DOI: 10.1038/s41467-021-22599-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 03/19/2021] [Indexed: 02/06/2023] Open
Abstract
Conventional approaches to identify secreted factors that regulate homeostasis are limited in their abilities to identify the tissues/cells of origin and destination. We established a platform to identify secreted protein trafficking between organs using an engineered biotin ligase (BirA*G3) that biotinylates, promiscuously, proteins in a subcellular compartment of one tissue. Subsequently, biotinylated proteins are affinity-enriched and identified from distal organs using quantitative mass spectrometry. Applying this approach in Drosophila, we identify 51 muscle-secreted proteins from heads and 269 fat body-secreted proteins from legs/muscles, including CG2145 (human ortholog ENDOU) that binds directly to muscles and promotes activity. In addition, in mice, we identify 291 serum proteins secreted from conditional BirA*G3 embryo stem cell-derived teratomas, including low-abundance proteins with hormonal properties. Our findings indicate that the communication network of secreted proteins is vast. This approach has broad potential across different model systems to identify cell-specific secretomes and mediators of interorgan communication in health or disease.
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Affiliation(s)
- Ilia A Droujinine
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA.
| | - Amanda S Meyer
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA, USA
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA, USA
| | - Dan Wang
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Entomology, China Agricultural University, Beijing, China
| | | | - Yanhui Hu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - David Rocco
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Jill A McMahon
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA, USA
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA, USA
| | - Rui Yang
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA, USA
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA, USA
| | - JinJin Guo
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA, USA
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA, USA
| | - Luye Mu
- Department of Electrical Engineering, Yale University, New Haven, CT, USA
| | | | | | - Rebecca Zeng
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Tess Branon
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Areya Tabatabai
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Justin A Bosch
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - John M Asara
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Alice Y Ting
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Departments of Genetics, Biology, and Chemistry, Stanford University, Stanford, CA, USA
| | - Steven A Carr
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Andrew P McMahon
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA, USA
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA, USA
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
- Howard Hughes Medical Institute, Boston, MA, USA.
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3
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Pascale M, Laurino S, Vogel H, Grimaldi A, Monné M, Riviello L, Tettamanti G, Falabella P. The Lepidopteran endoribonuclease-U domain protein P102 displays dramatically reduced enzymatic activity and forms functional amyloids. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2014; 47:129-39. [PMID: 25043263 PMCID: PMC7124382 DOI: 10.1016/j.dci.2014.07.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 07/08/2014] [Accepted: 07/09/2014] [Indexed: 06/03/2023]
Abstract
Hemocytes of Heliothis virescens (F.) (Lepidoptera, Noctuidae) larvae produce a protein, P102, with a putative endoribonuclease-U domain. In previous works we have shown that P102 is involved in Lepidopteran immune response by forming amyloid fibrils, which catalyze and localize melanin deposition around non-self intruders during encapsulation, preventing harmful systemic spreading. Here we demonstrate that P102 belongs to a new class of proteins that, at least in Lepidoptera, has a diminished endoribonuclease-U activity probably due to the lack of two out of five catalytically essential residues. We show that the P102 homolog from Trichoplusia ni (Lepidoptera, Noctuidae) displays catalytic site residues identical to P102, a residual endoribonuclease-U activity and the ability to form functional amyloids. On the basis of these results as well as sequence and structural analyses, we hypothesize that all the Lepidoptera endoribonuclease-U orthologs with catalytic site residues identical to P102 form a subfamily with similar function.
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Affiliation(s)
- Mariarosa Pascale
- Università della Basilicata, Dipartimento di Scienze, via dell'Ateneo Lucano 10, 85100 Potenza, Italy
| | - Simona Laurino
- Università della Basilicata, Dipartimento di Scienze, via dell'Ateneo Lucano 10, 85100 Potenza, Italy
| | - Heiko Vogel
- Department of Entomology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Strasse 8, 07745 Jena, Germany
| | - Annalisa Grimaldi
- Università dell'Insubria, Dipartimento di Biotecnologie e Scienze della Vita, via Dunant 3, 21100 Varese, Italy
| | - Magnus Monné
- Università della Basilicata, Dipartimento di Scienze, via dell'Ateneo Lucano 10, 85100 Potenza, Italy
| | - Lea Riviello
- Università della Basilicata, Dipartimento di Scienze, via dell'Ateneo Lucano 10, 85100 Potenza, Italy
| | - Gianluca Tettamanti
- Università dell'Insubria, Dipartimento di Biotecnologie e Scienze della Vita, via Dunant 3, 21100 Varese, Italy
| | - Patrizia Falabella
- Università della Basilicata, Dipartimento di Scienze, via dell'Ateneo Lucano 10, 85100 Potenza, Italy.
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4
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Ragno R, Gioia U, Laneve P, Bozzoni I, Mai A, Caffarelli E. Identification of small-molecule inhibitors of the XendoU endoribonucleases family. ChemMedChem 2011; 6:1797-805. [PMID: 21805647 PMCID: PMC7162399 DOI: 10.1002/cmdc.201100281] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2011] [Indexed: 01/12/2023]
Abstract
The XendoU family of enzymes includes several proteins displaying high sequence homology. The members characterized so far are endoribonucleases sharing similar biochemical properties and a common architecture in their active sites. Despite their similarities, these proteins are involved in distinct RNA‐processing pathways in different organisms. The amphibian XendoU participates in the biosynthesis of small nucleolar RNAs, the human PP11 is supposed to play specialized roles in placental tissue, and NendoU has critical function in coronavirus replication. Notably, XendoU family members have been implicated in human pathologies such as cancer and respiratory diseases: PP11 is aberrantly expressed in various tumors, while NendoU activity has been associated with respiratory infections by pathogenic coronaviruses. The present study is aimed at identifying small molecules that may selectively interfere with these enzymatic activities. Combining structure‐based virtual screening and experimental approaches, we identified four molecules that specifically inhibited the catalytic activity of XendoU and PP11 in the low micromolar range. Moreover, docking experiments strongly suggested that these compounds might also bind to the active site of NendoU, thus impairing the catalytic activity essential for the coronavirus life cycle. The identified compounds, while allowing deep investigation of the molecular functions of this enzyme family, may also represent leads for the development of new therapeutic tools.
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Affiliation(s)
- Rino Ragno
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza Università di Roma, P.le A. Moro 5, 00185 Roma, Italy
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5
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Abstract
The efficient turnover of messenger RNA represents an important mechanism that allows the cell to control gene expression. Until recently, the mechanism of mRNA decay was mainly attributed to exonucleases, comprising enzymes that degrade RNAs from the ends of the molecules. This article summarizes the endoribonucleases, comprising enzymes that cleave RNA molecules internally, which were identified in more recent years in eukaryotic mRNA metabolism. Endoribonucleases have received little attention in the past, based on the difficulty in their identification and a lack of understanding of their physiological significance. This review aims to compare the similarities and differences among this group of enzymes, as well as their known cellular functions. Despite the many differences in protein structure, and thus difficulties in identifying them based on amino acid sequence, most endoribonucleases possess essential cellular functions and have been shown to play an important role in mRNA turnover.
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Affiliation(s)
- Wai Ming Li
- Chemistry Program, University of Northern British Columbia, Prince George, BC, Canada
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Laneve P, Gioia U, Ragno R, Altieri F, Di Franco C, Santini T, Arceci M, Bozzoni I, Caffarelli E. The tumor marker human placental protein 11 is an endoribonuclease. J Biol Chem 2008; 283:34712-9. [PMID: 18936097 PMCID: PMC3259861 DOI: 10.1074/jbc.m805759200] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2008] [Revised: 10/16/2008] [Indexed: 01/19/2023] Open
Abstract
Human PP11 (placental protein 11) was previously described as a serine protease specifically expressed in the syncytiotrophoblast and in numerous tumor tissues. Several PP11-like proteins were annotated in distantly related organisms, such as worms and mammals, suggesting their involvement in evolutionarily conserved processes. Based on sequence similarity, human PP11 was included in a protein family whose characterized members are XendoU, a Xenopus laevis endoribonuclease involved in small nucleolar RNA processing, and Nsp15, an endoribonuclease essential for coronavirus replication. Here we show that the bacterially expressed human PP11 displays RNA binding capability and cleaves single stranded RNA in a Mn(2+)-dependent manner at uridylates, to produce molecules with 2',3'-cyclic phosphate ends. These features, together with structural and mutagenesis analyses, which identified the potential active site residues, reveal striking parallels to the amphibian XendoU and assign a ribonuclease function to PP11. This newly discovered enzymatic activity places PP11-like proteins in a completely new perspective.
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Affiliation(s)
- Pietro Laneve
- Istituto di Biologia e Patologia
Molecolari, Consiglio Nazionale delle Ricerche, the
Dipartimento di Genetica e Biologia Molecolare,
the Dipartimento di Chimica e Tecnologie del
Farmaco, the Dipartimento di Biochimica, and the
Istituto Pasteur Fondazione Cenci-Bolognetti,
“Sapienza” Università di Roma, Piazzale Aldo Moro 5, 00185
Rome, Italy
| | - Ubaldo Gioia
- Istituto di Biologia e Patologia
Molecolari, Consiglio Nazionale delle Ricerche, the
Dipartimento di Genetica e Biologia Molecolare,
the Dipartimento di Chimica e Tecnologie del
Farmaco, the Dipartimento di Biochimica, and the
Istituto Pasteur Fondazione Cenci-Bolognetti,
“Sapienza” Università di Roma, Piazzale Aldo Moro 5, 00185
Rome, Italy
| | - Rino Ragno
- Istituto di Biologia e Patologia
Molecolari, Consiglio Nazionale delle Ricerche, the
Dipartimento di Genetica e Biologia Molecolare,
the Dipartimento di Chimica e Tecnologie del
Farmaco, the Dipartimento di Biochimica, and the
Istituto Pasteur Fondazione Cenci-Bolognetti,
“Sapienza” Università di Roma, Piazzale Aldo Moro 5, 00185
Rome, Italy
| | - Fabio Altieri
- Istituto di Biologia e Patologia
Molecolari, Consiglio Nazionale delle Ricerche, the
Dipartimento di Genetica e Biologia Molecolare,
the Dipartimento di Chimica e Tecnologie del
Farmaco, the Dipartimento di Biochimica, and the
Istituto Pasteur Fondazione Cenci-Bolognetti,
“Sapienza” Università di Roma, Piazzale Aldo Moro 5, 00185
Rome, Italy
| | - Carmen Di Franco
- Istituto di Biologia e Patologia
Molecolari, Consiglio Nazionale delle Ricerche, the
Dipartimento di Genetica e Biologia Molecolare,
the Dipartimento di Chimica e Tecnologie del
Farmaco, the Dipartimento di Biochimica, and the
Istituto Pasteur Fondazione Cenci-Bolognetti,
“Sapienza” Università di Roma, Piazzale Aldo Moro 5, 00185
Rome, Italy
| | - Tiziana Santini
- Istituto di Biologia e Patologia
Molecolari, Consiglio Nazionale delle Ricerche, the
Dipartimento di Genetica e Biologia Molecolare,
the Dipartimento di Chimica e Tecnologie del
Farmaco, the Dipartimento di Biochimica, and the
Istituto Pasteur Fondazione Cenci-Bolognetti,
“Sapienza” Università di Roma, Piazzale Aldo Moro 5, 00185
Rome, Italy
| | - Massimo Arceci
- Istituto di Biologia e Patologia
Molecolari, Consiglio Nazionale delle Ricerche, the
Dipartimento di Genetica e Biologia Molecolare,
the Dipartimento di Chimica e Tecnologie del
Farmaco, the Dipartimento di Biochimica, and the
Istituto Pasteur Fondazione Cenci-Bolognetti,
“Sapienza” Università di Roma, Piazzale Aldo Moro 5, 00185
Rome, Italy
| | - Irene Bozzoni
- Istituto di Biologia e Patologia
Molecolari, Consiglio Nazionale delle Ricerche, the
Dipartimento di Genetica e Biologia Molecolare,
the Dipartimento di Chimica e Tecnologie del
Farmaco, the Dipartimento di Biochimica, and the
Istituto Pasteur Fondazione Cenci-Bolognetti,
“Sapienza” Università di Roma, Piazzale Aldo Moro 5, 00185
Rome, Italy
| | - Elisa Caffarelli
- Istituto di Biologia e Patologia
Molecolari, Consiglio Nazionale delle Ricerche, the
Dipartimento di Genetica e Biologia Molecolare,
the Dipartimento di Chimica e Tecnologie del
Farmaco, the Dipartimento di Biochimica, and the
Istituto Pasteur Fondazione Cenci-Bolognetti,
“Sapienza” Università di Roma, Piazzale Aldo Moro 5, 00185
Rome, Italy
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7
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Toulza E, Mattiuzzo NR, Galliano MF, Jonca N, Dossat C, Jacob D, de Daruvar A, Wincker P, Serre G, Guerrin M. Large-scale identification of human genes implicated in epidermal barrier function. Genome Biol 2008; 8:R107. [PMID: 17562024 PMCID: PMC2394760 DOI: 10.1186/gb-2007-8-6-r107] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2007] [Revised: 05/24/2007] [Accepted: 06/11/2007] [Indexed: 11/19/2022] Open
Abstract
Identification of genes expressed in epidermal granular keratinocytes by ORESTES, including a number that are highly specific for these cells. Background During epidermal differentiation, keratinocytes progressing through the suprabasal layers undergo complex and tightly regulated biochemical modifications leading to cornification and desquamation. The last living cells, the granular keratinocytes (GKs), produce almost all of the proteins and lipids required for the protective barrier function before their programmed cell death gives rise to corneocytes. We present here the first analysis of the transcriptome of human GKs, purified from healthy epidermis by an original approach. Results Using the ORESTES method, 22,585 expressed sequence tags (ESTs) were produced that matched 3,387 genes. Despite normalization provided by this method (mean 4.6 ORESTES per gene), some highly transcribed genes, including that encoding dermokine, were overrepresented. About 330 expressed genes displayed less than 100 ESTs in UniGene clusters and are most likely to be specific for GKs and potentially involved in barrier function. This hypothesis was tested by comparing the relative expression of 73 genes in the basal and granular layers of epidermis by quantitative RT-PCR. Among these, 33 were identified as new, highly specific markers of GKs, including those encoding a protease, protease inhibitors and proteins involved in lipid metabolism and transport. We identified filaggrin 2 (also called ifapsoriasin), a poorly characterized member of the epidermal differentiation complex, as well as three new lipase genes clustered with paralogous genes on chromosome 10q23.31. A new gene of unknown function, C1orf81, is specifically disrupted in the human genome by a frameshift mutation. Conclusion These data increase the present knowledge of genes responsible for the formation of the skin barrier and suggest new candidates for genodermatoses of unknown origin.
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Affiliation(s)
- Eve Toulza
- UMR 5165 "Epidermis Differentiation and Rheumatoid Autoimmunity", CNRS - Toulouse III University (IFR 30, INSERM - CNRS - Toulouse III University - CHU), allées Jules Guesde, 31073 Toulouse, France
| | - Nicolas R Mattiuzzo
- UMR 5165 "Epidermis Differentiation and Rheumatoid Autoimmunity", CNRS - Toulouse III University (IFR 30, INSERM - CNRS - Toulouse III University - CHU), allées Jules Guesde, 31073 Toulouse, France
| | - Marie-Florence Galliano
- UMR 5165 "Epidermis Differentiation and Rheumatoid Autoimmunity", CNRS - Toulouse III University (IFR 30, INSERM - CNRS - Toulouse III University - CHU), allées Jules Guesde, 31073 Toulouse, France
| | - Nathalie Jonca
- UMR 5165 "Epidermis Differentiation and Rheumatoid Autoimmunity", CNRS - Toulouse III University (IFR 30, INSERM - CNRS - Toulouse III University - CHU), allées Jules Guesde, 31073 Toulouse, France
| | - Carole Dossat
- Genoscope and CNRS UMR 8030, rue Gaston Crémieux, 91057 Evry, France
| | - Daniel Jacob
- Centre de Bioinformatique Bordeaux, Université V. Segalen Bordeaux 2, rue Léo Saignat, 33076 Bordeaux Cedex, France
| | - Antoine de Daruvar
- Centre de Bioinformatique Bordeaux, Université V. Segalen Bordeaux 2, rue Léo Saignat, 33076 Bordeaux Cedex, France
| | - Patrick Wincker
- Genoscope and CNRS UMR 8030, rue Gaston Crémieux, 91057 Evry, France
| | - Guy Serre
- UMR 5165 "Epidermis Differentiation and Rheumatoid Autoimmunity", CNRS - Toulouse III University (IFR 30, INSERM - CNRS - Toulouse III University - CHU), allées Jules Guesde, 31073 Toulouse, France
| | - Marina Guerrin
- UMR 5165 "Epidermis Differentiation and Rheumatoid Autoimmunity", CNRS - Toulouse III University (IFR 30, INSERM - CNRS - Toulouse III University - CHU), allées Jules Guesde, 31073 Toulouse, France
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8
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Renzi F, Caffarelli E, Laneve P, Bozzoni I, Brunori M, Vallone B. The structure of the endoribonuclease XendoU: From small nucleolar RNA processing to severe acute respiratory syndrome coronavirus replication. Proc Natl Acad Sci U S A 2006; 103:12365-70. [PMID: 16895992 PMCID: PMC1567885 DOI: 10.1073/pnas.0602426103] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Small nucleolar RNAs (snoRNAs) play a key role in eukaryotic ribosome biogenesis. In most cases, snoRNAs are encoded in introns and are released through the splicing reaction. Some snoRNAs are, instead, produced by an alternative pathway consisting of endonucleolytic processing of pre-mRNA. XendoU, the endoribonuclease responsible for this activity, is a U-specific, metal-dependent enzyme that releases products with 2'-3' cyclic phosphate termini. XendoU is broadly conserved among eukaryotes, and it is a genetic marker of nidoviruses, including the severe acute respiratory syndrome coronavirus, where it is essential for replication and transcription. We have determined by crystallography the structure of XendoU that, by refined search methodologies, appears to display a unique fold. Based on sequence conservation, mutagenesis, and docking simulations, we have identified the active site. The conserved structural determinants of this site may provide a framework for attempting to design antiviral drugs to interfere with the infectious nidovirus life cycle.
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Affiliation(s)
- Fabiana Renzi
- *Dipartimento di Scienze Biochimiche, University of Rome “La Sapienza,” Piazzale A. Moro 5, 00185 Rome, Italy
| | - Elisa Caffarelli
- Istituto di Biologia e Patologia Molecolari del Consiglio Nazionale delle Ricerche
| | - Pietro Laneve
- Istituto di Biologia e Patologia Molecolari del Consiglio Nazionale delle Ricerche
- Dipartimento di Genetica e Biologia Molecolare, and
| | - Irene Bozzoni
- Istituto di Biologia e Patologia Molecolari del Consiglio Nazionale delle Ricerche
- Istituto Pasteur-Fondazione Cenci Bolognetti
- Dipartimento di Genetica e Biologia Molecolare, and
| | - Maurizio Brunori
- Istituto Pasteur-Fondazione Cenci Bolognetti
- *Dipartimento di Scienze Biochimiche, University of Rome “La Sapienza,” Piazzale A. Moro 5, 00185 Rome, Italy
- To whom correspondence should be addressed. E-mail:
| | - Beatrice Vallone
- *Dipartimento di Scienze Biochimiche, University of Rome “La Sapienza,” Piazzale A. Moro 5, 00185 Rome, Italy
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9
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Gioia U, Laneve P, Dlakic M, Arceci M, Bozzoni I, Caffarelli E. Functional characterization of XendoU, the endoribonuclease involved in small nucleolar RNA biosynthesis. J Biol Chem 2005; 280:18996-9002. [PMID: 15755742 DOI: 10.1074/jbc.m501160200] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
XendoU is the endoribonuclease involved in the biosynthesis of a specific subclass of Xenopus laevis intron-encoded small nucleolar RNAs. XendoU has no homology to any known cellular RNase, although it has sequence similarity with proteins tentatively annotated as serine proteases. It has been recently shown that XendoU represents the cellular counterpart of a nidovirus replicative endoribonuclease (NendoU), which plays a critical role in viral replication and transcription. In this paper, we combined prediction and experimental data to define the amino acid residues directly involved in XendoU catalysis. Specifically, we find that XendoU residues Glu-161, Glu-167, His-162, His-178, and Lys-224 are essential for RNA cleavage, which occurs in the presence of manganese ions. Furthermore, we identified the RNA sequence required for XendoU binding and showed that the formation of XendoU-RNA complex is Mn2+-independent.
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Affiliation(s)
- Ubaldo Gioia
- Institute Pasteur-Fondazione Cenci Bolognetti, Department of Genetics and Molecular Biology, University La Sapienza, p.le A. Moro 5, 00185 Rome, Italy
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10
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Laneve P, Altieri F, Fiori ME, Scaloni A, Bozzoni I, Caffarelli E. Purification, cloning, and characterization of XendoU, a novel endoribonuclease involved in processing of intron-encoded small nucleolar RNAs in Xenopus laevis. J Biol Chem 2003; 278:13026-32. [PMID: 12571235 DOI: 10.1074/jbc.m211937200] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Here we report the purification, from Xenopus laevis oocyte nuclear extracts, of a new endoribonuclease, XendoU, that is involved in the processing of the intron-encoded box C/D U16 small nucleolar RNA (snoRNA) from its host pre-mRNA. Such an activity has never been reported before and has several uncommon features that make it quite a novel enzyme: it is poly(U)-specific, it requires Mn(2+) ions, and it produces molecules with 2'-3'-cyclic phosphate termini. Even if XendoU cleaves U-stretches, it displays some preferential cleavage on snoRNA precursor molecules. XendoU also participates in the biosynthesis of another intron-encoded snoRNA, U86, which is contained in the NOP56 gene of Xenopus laevis. A common feature of these snoRNAs is that their production is alternative to that of the mRNA, suggesting an important regulatory role for all the factors involved in the processing reaction.
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Affiliation(s)
- Pietro Laneve
- Institute Pasteur Fondazione Cenci-Bolognetti, Department of Genetics and Molecular Biology, University La Sapienza Piazzale Aldo Moro 5, 00185 Rome, Italy
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11
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Sogame A, Hayata T, Asashima M. Screening for novel pancreatic genes from in vitro-induced pancreas in Xenopus. Dev Growth Differ 2003; 45:143-52. [PMID: 12752502 DOI: 10.1034/j.1600-0854.2004.00683.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The processes of development and differentiation of the pancreas, an endoderm-derived vital organ that consists of both endocrine and exocrine cells, are highly conserved across most vertebrates. Recently, an in vitro system has been reported to induce embryonic pancreas using multipotent Xenopus ectodermal cells treated with activin and retinoic acid. In this study, this system was first modified to eliminate the mesoderm-derived pronephros. It was found that pronephros, which appeared with the use of low concentrations of activin, was eliminated at higher concentrations (400 ng/mL), while pancreas developed at a high frequency. Using this modified system, subtractive hybridization screening for novel pancreatic genes was done to better understand the molecular mechanisms of pancreas formation. Four novel genes were identified and characterized that were also found to be specifically expressed in the developing pancreas: carboxyl ester lipase, pancreatic elastase2, placental protein11 and protein disulfide isomerase A2 precursor. This in vitro pancreas-induction system may provide a useful model for analysis of the molecular mechanisms that function during pancreas development.
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Affiliation(s)
- Asako Sogame
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
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12
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Suzuki T, Srivastava AS, Kurokawa T. A homologue of human placental protein, PP11, and mouse T cell-specific protein, Tcl-30, in exocrine pancreas of a teleost (Paralichthys olivaceus). Comp Biochem Physiol B Biochem Mol Biol 2002; 133:325-9. [PMID: 12431400 DOI: 10.1016/s1096-4959(02)00158-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We cloned a 1401-bp cDNA encoding a novel pancreatic protein (PPSB) with two cysteine-rich somatomedin B-like domains from Japanese flounder (Paralichthys olivaceus). PPSB is predicted to be composed of 385 amino acids, including a signal sequence. The peptide sequence shares high homology with human placental protein 11 (PP11) and mouse T-cell specific protein (Tcl-30), which both contain a single somatomedin B-like domain. PPSB shares 47% and 44% identity with PP11 and Tcl-30, respectively. The unique point of PPSB is that an additional, somatomedin B-like domain is tandemly inserted. Unlike PP11 and Tcl-30, PPSB mRNA is specifically expressed by the exocrine pancreatic acinar cells, together with trypsinogen. Since PP11 has serine protease activity, it is predicted that its teleost homologue, PPSB, may function as a pancreatic digestive enzyme.
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Affiliation(s)
- Tohru Suzuki
- Metabolism Section, National Research Institute of Aquaculture, Fisheries Research Agency, Nansei, Mie 516-0193, Japan.
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13
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Deng G, Royle G, Wang S, Crain K, Loskutoff DJ. Structural and functional analysis of the plasminogen activator inhibitor-1 binding motif in the somatomedin B domain of vitronectin. J Biol Chem 1996; 271:12716-23. [PMID: 8662688 DOI: 10.1074/jbc.271.22.12716] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Plasminogen activator inhibitor 1 (PAI-1) binds to the somatomedin B (SMB) domain of vitronectin (VN), a domain present in at least seven other proteins. In this study, we investigate the PAI-1 binding activity of these SMB homologs and attempt to more specifically localize the PAI-1 binding site within this domain. SMBVN and several of its homologs were expressed in Escherichia coli, purified, and tested for PAI-1 binding activity in a competitive ligand binding assay. Although recombinant SMBVN was fully active in this assay, none of the homologs bound to PAI-1 or competed with VN for PAI-1 binding. These inactive homologs are structurally related to SMBVN, having 33-45% sequence identity and containing all 8 cysteines at conserved positions. Thus, homolog-scanning experiments were conducted by exchanging progressively larger portions of the NH2- or COOH-terminal regions of active SMBVN with the corresponding regions of the inactive homologs. These experiments revealed that the minimum PAI-1-binding sequence was present in the central region (residues 12-30) of SMBVN. Alanine scanning mutagenesis further demonstrated that each of the 8 cysteines as well as Gly12, Asp22, Leu24, Try27, Tyr28, and Asp34 were critical for PAI-1 binding and were required to stabilize PAI-1 activity. These results indicate that the PAI-1 binding motif is localized to residues 12-30 of SMBVN and suggest that this motif is anchored in the active conformation by disulfide bonds.
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Affiliation(s)
- G Deng
- Department of Vascular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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14
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Deissler H, Lottspeich F, Rajewsky MF. Affinity purification and cDNA cloning of rat neural differentiation and tumor cell surface antigen gp130RB13-6 reveals relationship to human and murine PC-1. J Biol Chem 1995; 270:9849-55. [PMID: 7730366 DOI: 10.1074/jbc.270.17.9849] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Monoclonal antibody RB13-6 recognizes a subset of rat brain glial precursor cells that are highly susceptible to malignant conversion by the carcinogen N-ethyl-N-nitrosourea. The corresponding cell surface antigen was identified as a membrane glycoprotein (gp130RB13-6) and purified by immunoaffinity chromatography from the tumorigenic neuroectodermal rat cell line BT4Ca. Sequencing of 5 endoproteinase-generated peptides of the purified antigen permitted the specific amplification of a cDNA fragment by reverse transcription-polymerase chain reaction and subsequent isolation of the complete coding sequence from a fetal rat brain cDNA library. The derived amino acid sequence indicates that the RB13-6 antigen is related to the human and murine plasma cell membrane protein PC-1, a nucleotide pyrophosphatase/alkaline phosphodiesterase and ectoprotein kinase. Similarly, purified gp130RB13-6 possesses 5'-nucleotidase activity that can be inhibited with EDTA. Different from PC-1, gp130RB13-6 isolated from BT4Ca cells is not a disulfide-linked dimer and contains an RGD-tripeptide sequence which, together with other structural features, suggests a possible function in cell adhesion and its subversion in malignant phenotypes.
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Affiliation(s)
- H Deissler
- Institute of Cell Biology (Cancer Research), University of Essen Medical School, Germany
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15
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Kingsmore SF, Bieniarz MC, Watson ML, Seldin MF. Genetic mapping of Pp11r, a thymocyte gene expressed during apoptosis, to mouse chromosome 15. Mamm Genome 1993; 4:459-60. [PMID: 8104059 DOI: 10.1007/bf00296822] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- S F Kingsmore
- Department of Medicine, Duke University Medical Center, Durham, North Carolina 27710
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16
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Lehmeier B, Amann E. Tac promoter vectors incorporating the bacteriophage T7 gene 10 translational enhancer sequence for improved expression of cloned genes in Escherichia coli. J Biotechnol 1992; 23:153-65. [PMID: 1368056 DOI: 10.1016/0168-1656(92)90089-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Two new plasmid expression vectors, pTacT7 and pTacT7L, have been constructed, which incorporate between the tac promoter and a downstream NcoI-HindIII polylinker sequence a synthetic sequence derived from the region upstream from gene 10 of bacteriophage T7 (g10-L). This sequence was recently shown to act as a translational enhancer (Olins et al., 1988) and was termed "Epsilon" (Enhancer of Protein Synthesis Initiation) element (Olins and Rangwala, 1989). In this communication we describe in detail the construction of ptacT7 and ptacT7L. Furthermore, we present evidence that the "Epsilon" element is able to enhance 3 to 20-fold the expression levels of two poorly expressed test genes encoding the human placental proteins PP9 and PP15. On the other hand, the expression levels of two highly expressed test genes encoding the human placental proteins PP4 and FXIIIa could not be further enhanced by the presence of the "Epsilon" element. These experiments show that the T7 gene 10 leader sequence can be utilized to improve the expression yields of otherwise poorly expressed heterologous genes in Escherichia coli.
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Affiliation(s)
- B Lehmeier
- Research Laboratories of Behringwerke AG, Marburg, F.R.G
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17
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Bohn H, Winckler W, Grundmann U. Immunochemically detected placental proteins and their biological functions. Arch Gynecol Obstet 1991; 249:107-18. [PMID: 1772263 DOI: 10.1007/bf02391577] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
During the last 20 years a systematic search for proteins occurring in human term placenta (afterbirth) has been performed in our laboratory. As a result more than 30 soluble placental proteins and at least 20 different solubilized antigens apparently derived from the placental membranes have been identified by immunochemical methods in extracts from human term placentas. Most of these proteins have already been isolated to purity and characterized by their physicochemical parameters. Specific antisera to these proteins were obtained by immunizing animals with the corresponding purified proteins. They were used detect and localize these antigens by immunochemical methods in the placenta and in other human tissues. Sensitive immunochemical assays have been developed to exactly quantitate the new proteins in body fluids and to find out the diagnostic significance of measurement of these proteins in pregnant women and in patients with tumors and other diseases. Another aim was to elucidate the biological functions of our immunochemically detected proteins. The results obtained thus far are reported.
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Affiliation(s)
- H Bohn
- Forschungslaboratorien, Behringwerke AG, Marburg, FRG
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18
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Abstract
Vitronectin (complement S-protein), a plasma and tissue glycoprotein of 75 kDa, shares the amino-terminal somatomedin B domain with the membrane glycoprotein PC1 of plasma cells and several hemopexin-type repeats with hemopexin and the non-catalytic carboxy-terminal domain of collagenases. It serves as a ligand for certain integrin receptors, binds to distinct members of the serpin family and inhibits the pore-forming cytolytic reaction of the terminal complement pathway. Computer-assisted data base searches revealed the presence of a single somatomedin B domain in the recently cloned placental protein 11, and four hemopexin-type repeats in the cytosolic plant protein PA2, the major albumin of pea seeds, whose function is unknown. Our finding shows that hemopexin-type repeats are present in extracellular as well as in cytosolic proteins and most likely originated before the divergence of the animal and plant kindoms.
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Affiliation(s)
- D Jenne
- Institute of Biochemistry, University of Lausanne, Epalinges, Switzerland
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