1
|
Izaz A, Pan T, Wang L, Zhang H, Duan S, Li E, Yan P, Wu X. Molecular cloning, characterization, and gene expression behavior of glucocorticoid and mineralocorticoid receptors from the Chinese alligator (Alligator sinensis). JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2020; 336:50-72. [PMID: 33306860 DOI: 10.1002/jez.b.23015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 11/01/2020] [Accepted: 11/09/2020] [Indexed: 12/16/2022]
Abstract
The Chinese alligator is an endemic crocodilian species in China. We isolated and obtained the glucocorticoid and mineralocorticoid receptor genes coding from the kidney of Alligator sinensis by nested polymerase chain reaction (PCR) and rapid amplification of cDNA ends (RACE). The glucocorticoid receptor (GR) gene has 2343 base pairs encoding 780 amino acids, while the mineralocorticoid receptor (MR) gene is 2958 bp in length encoding 985 amino acids. Quantitative real-time PCR was used to detect the distribution of messenger RNA (mRNA) levels. The maximum mRNA expressions were observed in the ovary and kidney, suggesting that these receptors may be involved in basic cellular functions or stress response of alligators. Besides this, RT-qPCR was performed to analyze the abundance of GR and MR mRNA transcripts in early embryonic development of the Chinese alligator in the kidney, liver, and heart. The mRNA levels of GR and MR at earlier stages in kidney, liver, and heart indicates that they might involve in the transcriptional regulation of early embryos and activate many precise developmental effects in fetal tissues. We also measured the protein expression in the liver embryonic developmental stages and found that the GR and MR proteins were restricted to both the nuclei and cytoplasm. The protein expression levels in the liver at different embryonic developmental stages have extremely prominent differences. Taken together, our results showed the full coding regions of GR and MR, their characteristics, and embryonic developmental mRNA and protein expressions of both genes in A. sinensis. This study could provide the necessary information for further investigating the diverse functions of GR and MR in A. sinensis.
Collapse
Affiliation(s)
- Ali Izaz
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Tao Pan
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Lin Wang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Huabin Zhang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Shulong Duan
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - En Li
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Peng Yan
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Xiaobing Wu
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, China
| |
Collapse
|
2
|
González-Mera L, Ravenscroft G, Cabrera-Serrano M, Ermolova N, Domínguez-González C, Arteche-López A, Soltanzadeh P, Evesson F, Navas C, Mavillard F, Clayton J, Rodrigo P, Servián-Morilla E, Cooper ST, Waddell L, Reardon K, Corbett A, Hernandez-Laín A, Sanchez A, Esteban Perez J, Paradas-Lopez C, Rivas-Infante E, Spencer M, Laing N, Olivé M. Heterozygous CAPN3 missense variants causing autosomal-dominant calpainopathy in seven unrelated families. Neuropathol Appl Neurobiol 2020; 47:283-296. [PMID: 32896923 DOI: 10.1111/nan.12663] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 08/03/2020] [Accepted: 08/22/2020] [Indexed: 01/05/2023]
Abstract
AIMS Recessive variants in CAPN3 gene are the cause of the commonest form of autosomal recessive limb girdle muscle dystrophy. However, two distinct in-frame deletions in CAPN3 (NM_000070.3:c.643_663del21 and c.598_621del15) and more recently, Gly445Arg and Arg572Pro substitutions have been linked to autosomal dominant (AD) forms of calpainopathy. We report 21 affected individuals from seven unrelated families presenting with an autosomal dominant form of muscular dystrophy associated with five different heterozygous missense variants in CAPN. METHODS We have used massively parallel gene sequencing (MPS) to determine the genetic basis of a dominant form of limb girdle muscular dystrophy in affected individuals from seven unrelated families. RESULTS The c.700G> A, [p.(Gly234Arg)], c.1327T> C [p.(Ser443Pro], c.1333G> A [p.(Gly445Arg)], c.1661A> C [p.(Tyr554Ser)] and c.1706T> C [p.(Phe569Ser)] CAPN3 variants were identified. Affected individuals presented in young adulthood with progressive proximal and axial weakness, waddling walking and scapular winging or with isolated hyperCKaemia. Muscle imaging showed fatty replacement of paraspinal muscles, variable degrees of involvement of the gluteal muscles, and the posterior compartment of the thigh and minor changes at the mid-leg level. Muscle biopsies revealed mild myopathic changes. Western blot analysis revealed a clear reduction in calpain 3 in skeletal muscle relative to controls. Protein modelling of these variants on the predicted structure of calpain 3 revealed that all variants are located in proximity to the calmodulin-binding site and are predicted to interfere with proteolytic activation. CONCLUSIONS We expand the genotypic spectrum of CAPN3-associated muscular dystrophy due to autosomal dominant missense variants.
Collapse
Affiliation(s)
- L González-Mera
- Neuropathology Unit, Department of Pathology, IDIBELL-Hospital Universitari de Bellvitge, Hospitalet de Llobregat, Barcelona, Spain.,Neuromuscular Unit, Department of Neurology, IDIBELL-Hospital Universitari de Bellvitge, Hospitalet de Llobregat, Barcelona, Spain
| | - G Ravenscroft
- Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, Perth, WA, Australia
| | - M Cabrera-Serrano
- Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, Perth, WA, Australia.,Neurology Department, Hospital Universitario Virgen del Rocío, Seville, Spain.,Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocıo/CSIC, Universidad de Sevilla, Sevilla, Spain.,Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - N Ermolova
- Department of Physiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - C Domínguez-González
- Neuromuscular Unit, Department of Neurology, Hospital Universitario 12 de Octubre, Research Institute imas12, Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - A Arteche-López
- Department of Genetic, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - P Soltanzadeh
- Departments of Neurology and Physiology, David Geffen School of Medicine, UCLA, University of California, Los Angeles, CA, USA
| | - F Evesson
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, NSW, Australia.,The Children's Medical Research Institute, Westmead, NSW, Australia
| | - C Navas
- Neuropathology Unit, Department of Pathology, IDIBELL-Hospital Universitari de Bellvitge, Hospitalet de Llobregat, Barcelona, Spain
| | - F Mavillard
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocıo/CSIC, Universidad de Sevilla, Sevilla, Spain.,Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - J Clayton
- Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, Perth, WA, Australia
| | - P Rodrigo
- Neuropathology Unit, Department of Pathology, IDIBELL-Hospital Universitari de Bellvitge, Hospitalet de Llobregat, Barcelona, Spain.,Neuromuscular Unit, Department of Neurology, IDIBELL-Hospital Universitari de Bellvitge, Hospitalet de Llobregat, Barcelona, Spain
| | - E Servián-Morilla
- Neurology Department, Hospital Universitario Virgen del Rocío, Seville, Spain.,Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocıo/CSIC, Universidad de Sevilla, Sevilla, Spain.,Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - S T Cooper
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, NSW, Australia.,The Children's Medical Research Institute, Westmead, NSW, Australia.,Discipline of Child and Adolescent Health, Faculty of Health and Medicine, University of Sydney, Westmead, NSW, Australia
| | - L Waddell
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, NSW, Australia.,Discipline of Child and Adolescent Health, Faculty of Health and Medicine, University of Sydney, Westmead, NSW, Australia
| | - K Reardon
- St. Vincent's Melbourne Neuromuscular Diagnostic Laboratory, Department of Clinical Neurosciences and Neurological Research, St Vincent's Hospital, Melbourne, VIC, Australia
| | - A Corbett
- Department of Neurology, Concord General Repatriation Hospital, Sydney, NSW, Australia
| | - A Hernandez-Laín
- Department of Pathology, Neuropathology Unit. Hospital Universitario 12 de Octubre, Madrid, Spain
| | - A Sanchez
- Institut de Diagnòstic per la imatge (IDI), IDIBELL-Hospital de Bellvitge, Hospitalet de Llobregat, Barcelona, Spain
| | - J Esteban Perez
- Neuromuscular Unit, Department of Neurology, Hospital Universitario 12 de Octubre, Research Institute imas12, Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - C Paradas-Lopez
- Neurology Department, Hospital Universitario Virgen del Rocío, Seville, Spain.,Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocıo/CSIC, Universidad de Sevilla, Sevilla, Spain.,Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - E Rivas-Infante
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain.,Department of Neuropathology, Hospital U. Virgen del Rocío/Instituto de Biomedicina de Sevilla (IBiS), Sevilla, Spain
| | - M Spencer
- Department of Neurology, Neuromuscular Program, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - N Laing
- Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, Perth, WA, Australia
| | - M Olivé
- Neuropathology Unit, Department of Pathology, IDIBELL-Hospital Universitari de Bellvitge, Hospitalet de Llobregat, Barcelona, Spain.,Neuromuscular Unit, Department of Neurology, IDIBELL-Hospital Universitari de Bellvitge, Hospitalet de Llobregat, Barcelona, Spain
| |
Collapse
|
3
|
Laskowski RA, Jabłońska J, Pravda L, Vařeková RS, Thornton JM. PDBsum: Structural summaries of PDB entries. Protein Sci 2017; 27:129-134. [PMID: 28875543 PMCID: PMC5734310 DOI: 10.1002/pro.3289] [Citation(s) in RCA: 739] [Impact Index Per Article: 105.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 08/29/2017] [Accepted: 08/29/2017] [Indexed: 12/11/2022]
Abstract
PDBsum is a web server providing structural information on the entries in the Protein Data Bank (PDB). The analyses are primarily image‐based and include protein secondary structure, protein‐ligand and protein‐DNA interactions, PROCHECK analyses of structural quality, and many others. The 3D structures can be viewed interactively in RasMol, PyMOL, and a JavaScript viewer called 3Dmol.js. Users can upload their own PDB files and obtain a set of password‐protected PDBsum analyses for each. The server is freely accessible to all at: http://www.ebi.ac.uk/pdbsum.
Collapse
Affiliation(s)
- Roman A Laskowski
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Jagoda Jabłońska
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, 02-089, Warsaw, Poland
| | - Lukáš Pravda
- National Centre for Biomolecular Research, Faculty of Science and CEITEC - Central European Institute of Technology, Masaryk University Brno, 625 00, Brno-Bohunice, Czech Republic
| | - Radka Svobodová Vařeková
- National Centre for Biomolecular Research, Faculty of Science and CEITEC - Central European Institute of Technology, Masaryk University Brno, 625 00, Brno-Bohunice, Czech Republic
| | - Janet M Thornton
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| |
Collapse
|
4
|
Molecular cloning of ESR2 and gene expression analysis of ESR1 and ESR2 in the pituitary gland of the Chinese alligator ( Alligator sinensis ) during female reproductive cycle. Gene 2017; 623:15-23. [DOI: 10.1016/j.gene.2017.04.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 01/04/2017] [Accepted: 04/12/2017] [Indexed: 02/02/2023]
|
5
|
Faria J, Loureiro I, Santarém N, Macedo-Ribeiro S, Tavares J, Cordeiro-da-Silva A. Leishmania infantum Asparagine Synthetase A Is Dispensable for Parasites Survival and Infectivity. PLoS Negl Trop Dis 2016; 10:e0004365. [PMID: 26771178 PMCID: PMC4714757 DOI: 10.1371/journal.pntd.0004365] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 12/15/2015] [Indexed: 11/19/2022] Open
Abstract
A growing interest in asparagine (Asn) metabolism has currently been observed in cancer and infection fields. Asparagine synthetase (AS) is responsible for the conversion of aspartate into Asn in an ATP-dependent manner, using ammonia or glutamine as a nitrogen source. There are two structurally distinct AS: the strictly ammonia dependent, type A, and the type B, which preferably uses glutamine. Absent in humans and present in trypanosomatids, AS-A was worthy of exploring as a potential drug target candidate. Appealingly, it was reported that AS-A was essential in Leishmania donovani, making it a promising drug target. In the work herein we demonstrate that Leishmania infantum AS-A, similarly to Trypanosoma spp. and L. donovani, is able to use both ammonia and glutamine as nitrogen donors. Moreover, we have successfully generated LiASA null mutants by targeted gene replacement in L. infantum, and these parasites do not display any significant growth or infectivity defect. Indeed, a severe impairment of in vitro growth was only observed when null mutants were cultured in asparagine limiting conditions. Altogether our results demonstrate that despite being important under asparagine limitation, LiAS-A is not essential for parasite survival, growth or infectivity in normal in vitro and in vivo conditions. Therefore we exclude AS-A as a suitable drug target against L. infantum parasites.
Collapse
Affiliation(s)
- Joana Faria
- Parasite Disease Group, Instituto de Biologia Molecular e Celular da Universidade do Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Inês Loureiro
- Parasite Disease Group, Instituto de Biologia Molecular e Celular da Universidade do Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Nuno Santarém
- Parasite Disease Group, Instituto de Biologia Molecular e Celular da Universidade do Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Sandra Macedo-Ribeiro
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Protein Crystallography Group, Instituto de Biologia Molecular e Celular da Universidade do Porto, Porto, Portugal
| | - Joana Tavares
- Parasite Disease Group, Instituto de Biologia Molecular e Celular da Universidade do Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Anabela Cordeiro-da-Silva
- Parasite Disease Group, Instituto de Biologia Molecular e Celular da Universidade do Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| |
Collapse
|
6
|
Pilecki B, Holm AT, Schlosser A, Moeller JB, Wohl AP, Zuk AV, Heumüller SE, Wallis R, Moestrup SK, Sengle G, Holmskov U, Sorensen GL. Characterization of Microfibrillar-associated Protein 4 (MFAP4) as a Tropoelastin- and Fibrillin-binding Protein Involved in Elastic Fiber Formation. J Biol Chem 2015; 291:1103-14. [PMID: 26601954 DOI: 10.1074/jbc.m115.681775] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Indexed: 11/06/2022] Open
Abstract
MFAP4 (microfibrillar-associated protein 4) is an extracellular glycoprotein found in elastic fibers without a clearly defined role in elastic fiber assembly. In the present study, we characterized molecular interactions between MFAP4 and elastic fiber components. We established that MFAP4 primarily assembles into trimeric and hexameric structures of homodimers. Binding analysis revealed that MFAP4 specifically binds tropoelastin and fibrillin-1 and -2, as well as the elastin cross-linking amino acid desmosine, and that it co-localizes with fibrillin-1-positive fibers in vivo. Site-directed mutagenesis disclosed residues Phe(241) and Ser(203) in MFAP4 as being crucial for type I collagen, elastin, and tropoelastin binding. Furthermore, we found that MFAP4 actively promotes tropoelastin self-assembly. In conclusion, our data identify MFAP4 as a new ligand of microfibrils and tropoelastin involved in proper elastic fiber organization.
Collapse
Affiliation(s)
- Bartosz Pilecki
- From the Department of Cancer and Inflammation Research, Institute of Molecular Medicine, Faculty of Health Sciences, University of Southern Denmark, 5000 Odense C, Denmark
| | - Anne T Holm
- From the Department of Cancer and Inflammation Research, Institute of Molecular Medicine, Faculty of Health Sciences, University of Southern Denmark, 5000 Odense C, Denmark
| | - Anders Schlosser
- From the Department of Cancer and Inflammation Research, Institute of Molecular Medicine, Faculty of Health Sciences, University of Southern Denmark, 5000 Odense C, Denmark
| | - Jesper B Moeller
- From the Department of Cancer and Inflammation Research, Institute of Molecular Medicine, Faculty of Health Sciences, University of Southern Denmark, 5000 Odense C, Denmark
| | | | | | - Stefanie E Heumüller
- the Center for Biochemistry, Faculty of Medicine and the Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
| | - Russell Wallis
- the Department of Infection, Immunity and Inflammation, and Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 9HN, United Kingdom, and
| | - Soren K Moestrup
- From the Department of Cancer and Inflammation Research, Institute of Molecular Medicine, Faculty of Health Sciences, University of Southern Denmark, 5000 Odense C, Denmark, the Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, 5000 Odense C, Denmark
| | - Gerhard Sengle
- the Center for Biochemistry, Faculty of Medicine and the Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
| | - Uffe Holmskov
- From the Department of Cancer and Inflammation Research, Institute of Molecular Medicine, Faculty of Health Sciences, University of Southern Denmark, 5000 Odense C, Denmark
| | - Grith L Sorensen
- From the Department of Cancer and Inflammation Research, Institute of Molecular Medicine, Faculty of Health Sciences, University of Southern Denmark, 5000 Odense C, Denmark,
| |
Collapse
|
7
|
Beinsteiner B, Michalon J, Klaholz BP. IBiSS, a versatile and interactive tool for integrated sequence and 3D structure analysis of large macromolecular complexes. Bioinformatics 2015; 31:3339-44. [DOI: 10.1093/bioinformatics/btv347] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 05/30/2015] [Indexed: 11/13/2022] Open
|
8
|
Thomas S, Cantagrel V, Mariani L, Serre V, Lee JE, Elkhartoufi N, de Lonlay P, Desguerre I, Munnich A, Boddaert N, Lyonnet S, Vekemans M, Lisgo SN, Caspary T, Gleeson J, Attié-Bitach T. Identification of a novel ARL13B variant in a Joubert syndrome-affected patient with retinal impairment and obesity. Eur J Hum Genet 2015; 23:621-7. [PMID: 25138100 PMCID: PMC4402632 DOI: 10.1038/ejhg.2014.156] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 06/27/2014] [Accepted: 07/09/2014] [Indexed: 12/29/2022] Open
Abstract
Joubert syndrome (JS) is a genetically heterogeneous autosomal recessive ciliopathy with 22 genes implicated to date, including a small, ciliary GTPase, ARL13B. ARL13B is required for cilia formation in vertebrates. JS patients display multiple symptoms characterized by ataxia due to the cerebellar vermis hypoplasia, and that can also include ocular abnormalities, renal cysts, liver fibrosis or polydactyly. These symptoms are shared with other ciliopathies, some of which display additional phenotypes, such as obesity. Here we identified a novel homozygous missense variant in ARL13B/JBTS8 in a JS patient who displayed retinal defects and obesity. We demonstrate the variant disrupts ARL13B function, as its expression did not rescue the mutant phenotype either in Arl13b(scorpion) zebrafish or in Arl13b(hennin) mouse embryonic fibroblasts, while the wild-type ARL13B did. Finally, we show that ARL13B is localized within the primary cilia of neonatal mouse hypothalamic neurons consistent with the known link between hypothalamic ciliary function and obesity. Thus our data identify a novel ARL13B variant that causes JS and retinopathy and suggest an extension of the phenotypic spectrum of ARL13B mutations to obesity.
Collapse
Affiliation(s)
- Sophie Thomas
- INSERM U1163, Hôpital Necker-Enfants Malades, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Institut Imagine, Paris, France
| | - Vincent Cantagrel
- INSERM U1163, Hôpital Necker-Enfants Malades, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Institut Imagine, Paris, France
- Laboratory of Neurogenetics, Howard Hughes Medical Institute, Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Laura Mariani
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Valérie Serre
- INSERM U1163, Hôpital Necker-Enfants Malades, Paris, France
- UMR7592CNRS, Jacques Monod Institute, Paris Diderot University, Paris, France
| | - Ji-Eun Lee
- Laboratory of Neurogenetics, Howard Hughes Medical Institute, Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Nadia Elkhartoufi
- INSERM U1163, Hôpital Necker-Enfants Malades, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Institut Imagine, Paris, France
- Département de Génétique, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
| | - Pascale de Lonlay
- INSERM U1163, Hôpital Necker-Enfants Malades, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Institut Imagine, Paris, France
- Département de Génétique, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
| | - Isabelle Desguerre
- Service de neurométabolisme, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
| | - Arnold Munnich
- INSERM U1163, Hôpital Necker-Enfants Malades, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Institut Imagine, Paris, France
- Département de Génétique, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
| | - Nathalie Boddaert
- Radiologie Pédiatrique et INSERM U-797, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
| | - Stanislas Lyonnet
- INSERM U1163, Hôpital Necker-Enfants Malades, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Institut Imagine, Paris, France
- Département de Génétique, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
| | - Michel Vekemans
- INSERM U1163, Hôpital Necker-Enfants Malades, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Institut Imagine, Paris, France
- Département de Génétique, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
| | - Steven N Lisgo
- The MRC-Wellcome Trust Human Developmental Biology Resource (HDBR), Institute of Genetic Medicine, International Centre for Life, Central Parkway, Newcastle Upon Tyne, UK
| | - Tamara Caspary
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Joseph Gleeson
- Laboratory of Neurogenetics, Howard Hughes Medical Institute, Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Tania Attié-Bitach
- INSERM U1163, Hôpital Necker-Enfants Malades, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Institut Imagine, Paris, France
- Département de Génétique, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
| |
Collapse
|
9
|
Liu G, Zakharov SI, Yao Y, Marx SO, Karlin A. Positions of the cytoplasmic end of BK α S0 helix relative to S1-S6 and of β1 TM1 and TM2 relative to S0-S6. ACTA ACUST UNITED AC 2015; 145:185-99. [PMID: 25667410 PMCID: PMC4338161 DOI: 10.1085/jgp.201411337] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The BK β1 subunit displaces the unique S0 transmembrane helix on the intracellular side of BK α but not on the extracellular side, thereby altering its path through the membrane. The large-conductance, voltage- and Ca2+-gated K+ (BK) channel consists of four α subunits, which form a voltage- and Ca2+-gated channel, and up to four modulatory β subunits. The β1 subunit is expressed in smooth muscle, where it slows BK channel kinetics and shifts the conductance–voltage (G-V) curve to the left at [Ca2+] > 2 µM. In addition to the six transmembrane (TM) helices, S1–S6, conserved in all voltage-dependent K+ channels, BK α has a unique seventh TM helix, S0, which may contribute to the unusual rightward shift in the G-V curve of BK α in the absence of β1 and to a leftward shift in its presence. Such a role is supported by the close proximity of S0 to S3 and S4 in the voltage-sensing domain. Furthermore, on the extracellular side of the membrane, one of the two TM helices of β1, TM2, is adjacent to S0. We have now analyzed induced disulfide bond formation between substituted Cys residues on the cytoplasmic side of the membrane. There, in contrast, S0 is closest to the S2–S3 loop, from which position it is displaced on the addition of β1. The cytoplasmic ends of β1 TM1 and TM2 are adjacent and are located between the S2–S3 loop of one α subunit and S1 of a neighboring α subunit and are not adjacent to S0; i.e., S0 and TM2 have different trajectories through the membrane. In the absence of β1, 70% of disulfide bonding of W43C (S0) and L175C (S2–S3) has no effect on V50 for activation, implying that the cytoplasmic end of S0 and the S2–S3 loop move in concert, if at all, during activation. Otherwise, linking them together in one state would obstruct the transition to the other state, which would certainly change V50.
Collapse
Affiliation(s)
- Guoxia Liu
- Department of Medicine, Division of Cardiology; Department of Pharmacology; and Department of Biochemistry, Department of Physiology, and Department of Neurology, Center for Molecular Recognition, College of Physicians and Surgeons, Columbia University, New York, NY 10032 Department of Medicine, Division of Cardiology; Department of Pharmacology; and Department of Biochemistry, Department of Physiology, and Department of Neurology, Center for Molecular Recognition, College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Sergey I Zakharov
- Department of Medicine, Division of Cardiology; Department of Pharmacology; and Department of Biochemistry, Department of Physiology, and Department of Neurology, Center for Molecular Recognition, College of Physicians and Surgeons, Columbia University, New York, NY 10032 Department of Medicine, Division of Cardiology; Department of Pharmacology; and Department of Biochemistry, Department of Physiology, and Department of Neurology, Center for Molecular Recognition, College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Yongneng Yao
- Department of Medicine, Division of Cardiology; Department of Pharmacology; and Department of Biochemistry, Department of Physiology, and Department of Neurology, Center for Molecular Recognition, College of Physicians and Surgeons, Columbia University, New York, NY 10032 Department of Medicine, Division of Cardiology; Department of Pharmacology; and Department of Biochemistry, Department of Physiology, and Department of Neurology, Center for Molecular Recognition, College of Physicians and Surgeons, Columbia University, New York, NY 10032 Department of Medicine, Division of Cardiology; Department of Pharmacology; and Department of Biochemistry, Department of Physiology, and Department of Neurology, Center for Molecular Recognition, College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Steven O Marx
- Department of Medicine, Division of Cardiology; Department of Pharmacology; and Department of Biochemistry, Department of Physiology, and Department of Neurology, Center for Molecular Recognition, College of Physicians and Surgeons, Columbia University, New York, NY 10032 Department of Medicine, Division of Cardiology; Department of Pharmacology; and Department of Biochemistry, Department of Physiology, and Department of Neurology, Center for Molecular Recognition, College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Arthur Karlin
- Department of Medicine, Division of Cardiology; Department of Pharmacology; and Department of Biochemistry, Department of Physiology, and Department of Neurology, Center for Molecular Recognition, College of Physicians and Surgeons, Columbia University, New York, NY 10032 Department of Medicine, Division of Cardiology; Department of Pharmacology; and Department of Biochemistry, Department of Physiology, and Department of Neurology, Center for Molecular Recognition, College of Physicians and Surgeons, Columbia University, New York, NY 10032 Department of Medicine, Division of Cardiology; Department of Pharmacology; and Department of Biochemistry, Department of Physiology, and Department of Neurology, Center for Molecular Recognition, College of Physicians and Surgeons, Columbia University, New York, NY 10032
| |
Collapse
|
10
|
Loureiro I, Faria J, Clayton C, Macedo-Ribeiro S, Santarém N, Roy N, Cordeiro-da-Siva A, Tavares J. Ribose 5-phosphate isomerase B knockdown compromises Trypanosoma brucei bloodstream form infectivity. PLoS Negl Trop Dis 2015; 9:e3430. [PMID: 25568941 PMCID: PMC4287489 DOI: 10.1371/journal.pntd.0003430] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 11/21/2014] [Indexed: 12/13/2022] Open
Abstract
Ribose 5-phosphate isomerase is an enzyme involved in the non-oxidative branch of the pentose phosphate pathway, and catalyzes the inter-conversion of D-ribose 5-phosphate and D-ribulose 5-phosphate. Trypanosomatids, including the agent of African sleeping sickness namely Trypanosoma brucei, have a type B ribose-5-phosphate isomerase. This enzyme is absent from humans, which have a structurally unrelated ribose 5-phosphate isomerase type A, and therefore has been proposed as an attractive drug target waiting further characterization. In this study, Trypanosoma brucei ribose 5-phosphate isomerase B showed in vitro isomerase activity. RNAi against this enzyme reduced parasites' in vitro growth, and more importantly, bloodstream forms infectivity. Mice infected with induced RNAi clones exhibited lower parasitaemia and a prolonged survival compared to control mice. Phenotypic reversion was achieved by complementing induced RNAi clones with an ectopic copy of Trypanosoma cruzi gene. Our results present the first functional characterization of Trypanosoma brucei ribose 5-phosphate isomerase B, and show the relevance of an enzyme belonging to the non-oxidative branch of the pentose phosphate pathway in the context of Trypanosoma brucei infection. Within the non-oxidative branch of the pentose phosphate pathway, ribose 5-phosphate isomerase catalyzes the inter-conversion of ribose 5-phosphate and ribulose 5-phosphate. There are two types of ribose 5-phosphate isomerase, namely A and B. The presence of type B in Trypanosoma brucei, and its absence in humans, make this protein a promising drug target. African sleeping sickness is a serious parasitic disease that relies on limited chemotherapeutic options for control. In our study, a functional characterization of Trypanosoma brucei ribose 5-phosphate isomerase B is reported. Biochemical studies confirmed enzyme isomerase activity and its downregulation by RNAi affected mainly parasites infectivity in vivo. Overall this study shows that ribose 5-phosphate isomerase depletion is detrimental for parasites infectivity under host pressure.
Collapse
Affiliation(s)
- Inês Loureiro
- Parasite Disease Group, Instituto de Biologia Molecular e Celular da Universidade do Porto, Porto, Portugal
| | - Joana Faria
- Parasite Disease Group, Instituto de Biologia Molecular e Celular da Universidade do Porto, Porto, Portugal
| | - Christine Clayton
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH cv Alliance, Heidelberg, Germany
| | - Sandra Macedo-Ribeiro
- Protein Crystallography Group, Instituto de Biologia Molecular e Celular da Universidade do Porto, Porto, Portugal
| | - Nuno Santarém
- Parasite Disease Group, Instituto de Biologia Molecular e Celular da Universidade do Porto, Porto, Portugal
| | - Nilanjan Roy
- Ashok & Rita Patel Institute of Integrated Study & Research in Biotechnology & Allied Sciences, New Vallabh Vidyanagar, Dist-Anand, Gujarat, India
| | - Anabela Cordeiro-da-Siva
- Parasite Disease Group, Instituto de Biologia Molecular e Celular da Universidade do Porto, Porto, Portugal
- Departamento de Ciências Biológicas, Faculdade de Farmácia da Universidade do Porto, Porto, Portugal
- * E-mail: (ACdS); (JT)
| | - Joana Tavares
- Parasite Disease Group, Instituto de Biologia Molecular e Celular da Universidade do Porto, Porto, Portugal
- * E-mail: (ACdS); (JT)
| |
Collapse
|
11
|
Ermolova N, Kramerova I, Spencer MJ. Autolytic activation of calpain 3 proteinase is facilitated by calmodulin protein. J Biol Chem 2014; 290:996-1004. [PMID: 25389288 DOI: 10.1074/jbc.m114.588780] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Calpains are broadly distributed, calcium-dependent enzymes that induce limited proteolysis in a wide range of substrates. Mutations in the gene encoding the muscle-specific family member calpain 3 (CAPN3) underlie limb-girdle muscular dystrophy 2A. We have shown previously that CAPN3 knockout muscles exhibit attenuated calcium release, reduced calmodulin kinase (CaMKII) signaling, and impaired muscle adaptation to exercise. However, neither the precise role of CAPN3 in these processes nor the mechanisms of CAPN3 activation in vivo have been fully elucidated. In this study, we identify calmodulin (CaM), a known transducer of the calcium signal, as the first positive regulator of CAPN3 autolytic activity. CaM was shown to bind CAPN3 at two sites located in the C2L domain. Biochemical studies using muscle extracts from transgenic mice overexpressing CAPN3 or its inactive mutant revealed that CaM binding enhanced CAPN3 autolytic activation. Furthermore, CaM facilitated CAPN3-mediated cleavage of its in vivo substrate titin in tissue extracts. Therefore, these studies reveal a novel interaction between CAPN3 and CaM and identify CaM as the first positive regulator of CAPN3 activity.
Collapse
Affiliation(s)
- Natalia Ermolova
- From the Department of Neurology, Geffen School of Medicine, and Center for Duchenne Muscular Dystrophy, UCLA, Los Angeles, CA 90095
| | - Irina Kramerova
- From the Department of Neurology, Geffen School of Medicine, and Center for Duchenne Muscular Dystrophy, UCLA, Los Angeles, CA 90095
| | - Melissa J Spencer
- From the Department of Neurology, Geffen School of Medicine, and Center for Duchenne Muscular Dystrophy, UCLA, Los Angeles, CA 90095
| |
Collapse
|
12
|
Smith JL, Izumi T, Borbet TC, Hagedorn AN, Pathak VK. HIV-1 and HIV-2 Vif interact with human APOBEC3 proteins using completely different determinants. J Virol 2014; 88:9893-908. [PMID: 24942576 PMCID: PMC4136346 DOI: 10.1128/jvi.01318-14] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 06/09/2014] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Human APOBEC3 (A3) restriction factors provide intrinsic immunity against zoonotic transmission of pathogenic viruses. A3D, A3F, A3G, and A3H haplotype II (A3H-hapII) can be packaged into virion infectivity factor (Vif)-deficient HIVs to inhibit viral replication. To overcome these restriction factors, Vif binds to the A3 proteins in viral producer cells to target them for ubiquitination and proteasomal degradation, thus preventing their packaging into assembling virions. Therefore, the Vif-A3 interactions are attractive targets for novel drug development. HIV-1 and HIV-2 arose via distinct zoonotic transmission events of simian immunodeficiency viruses from chimpanzees and sooty mangabeys, respectively, and Vifs from these viruses have limited homology. To gain insights into the evolution of virus-host interactions that led to successful cross-species transmission of lentiviruses, we characterized the determinants of the interaction between HIV-2 Vif (Vif2) with human A3 proteins and compared them to the previously identified HIV-1 Vif (Vif1) interactions with the A3 proteins. We found that A3G, A3F, and A3H-hapII, but not A3D, were susceptible to Vif2-induced degradation. Alanine-scanning mutational analysis of the first 62 amino acids of Vif2 indicated that Vif2 determinants important for degradation of A3G and A3F are completely distinct from these regions in Vif1, as are the determinants in A3G and A3F that are critical for Vif2-induced degradation. These observations suggest that distinct Vif-A3 interactions evolved independently in different SIVs and their nonhuman primate hosts and conservation of the A3 determinants targeted by the SIV Vif proteins resulted in successful zoonotic transmission into humans. IMPORTANCE Primate APOBEC3 proteins provide innate immunity against invading pathogens, and Vif proteins of primate lentiviruses have evolved to overcome these host defenses by interacting with them and inducing their proteasomal degradation. HIV-1 and HIV-2 are two human pathogens that induce AIDS, and elucidating interactions between their Vif proteins and human A3 proteins could facilitate the development of novel antiviral drugs. Furthermore, understanding Vif-A3 interactions can provide novel insights into the cross-species transmission events that led to the HIV-1 and HIV-2 pandemics and evolution of host-virus interactions. We carried out mutational analysis of the N-terminal 62 amino acids of HIV-2 Vif (Vif2) and analyzed A3G/A3F chimeras that retained antiviral activity to identify the determinants of the Vif2 and A3 interaction. Our results show that the Vif2-A3 interactions are completely different from the Vif1-A3 interactions, suggesting that these interactions evolved independently and that conservation of the A3 determinants resulted in successful zoonotic transmission into humans.
Collapse
Affiliation(s)
- Jessica L Smith
- Viral Mutation Section, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Taisuke Izumi
- Viral Mutation Section, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Timothy C Borbet
- Viral Mutation Section, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Ariel N Hagedorn
- Viral Mutation Section, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Vinay K Pathak
- Viral Mutation Section, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| |
Collapse
|
13
|
Ginter T, Fahrer J, Kröhnert U, Fetz V, Garrone A, Stauber RH, Reichardt W, Müller-Newen G, Kosan C, Heinzel T, Krämer OH. Arginine residues within the DNA binding domain of STAT3 promote intracellular shuttling and phosphorylation of STAT3. Cell Signal 2014; 26:1698-706. [PMID: 24721162 DOI: 10.1016/j.cellsig.2014.03.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 03/20/2014] [Accepted: 03/31/2014] [Indexed: 01/10/2023]
Abstract
Acetylation-dependent inactivation of STAT1 can be mimicked by the exchange of its lysine residues K410 and K413 to glutamine residues. STAT3 harbors non-acetylatable arginine moieties at the corresponding sites R414 and R417. It is unclear whether the mutation of these sites to glutamine residues antagonizes STAT3 activation. Here, we show that an arginine-glutamine-exchange at the STAT3 moieties R414 and R417 (R414Q and R417Q) reduces cytokine-dependent tyrosine phosphorylation of STAT3. This inhibitory effect can be partially rescued by phosphatase inhibition. In addition, the R414Q and R417Q mutations enhance the nuclear accumulation of unphosphorylated STAT3. STAT3 R414Q and STAT3 R417Q show a reduced response to cytokine stimulation emanating from the plasma membrane. Moreover, these STAT3 mutants have no direct inhibitory effect on the cytokine-induced activation of STAT1/STAT3-mediated gene expression. Since the mutations R414Q and R417Q reside within the STAT3 DNA binding domain (DBD), the STAT3 R414Q and R417Q mutants also lack intrinsic activity as transcription factors. Furthermore, in contrast to wild-type STAT3 they cannot compensate for a loss of STAT1 and they cannot promote STAT1/STAT3-dependent transcriptional activation. We further analyzed a STAT3 arginine-lysine-exchange mutant (R414K/R417K). This molecule mimics corresponding lysine residues found within the DBD of STAT1. Compared to wild-type STAT3, the STAT3 R414K/R417K mutant shows attenuated tyrosine phosphorylation and it is a less active transcription factor. In addition, STAT3 R414K/R417K is not activated by deacetylase inhibition. On the other hand, C-terminal acetylation of STAT3 is intact in STAT3 R414K/R417K. Our results suggest that the exchange of amino acid residues within the DBDs of STAT1/STAT3 affects their phosphorylation as well as their intracellular shuttling.
Collapse
Affiliation(s)
- Torsten Ginter
- Center for Molecular Biomedicine (CMB), Dept. of Biochemistry, University of Jena, Germany
| | - Jörg Fahrer
- Department of Toxicology, University Medical Center, Obere Zahlbacher Str. 67, 55131 Mainz, Germany
| | - Ulrike Kröhnert
- Center for Molecular Biomedicine (CMB), Dept. of Biochemistry, University of Jena, Germany
| | - Verena Fetz
- Department of Molecular and Cellular Oncology, University Hospital, Mainz, Germany
| | - Alessio Garrone
- Center for Molecular Biomedicine (CMB), Dept. of Biochemistry, University of Jena, Germany
| | - Roland H Stauber
- Department of Molecular and Cellular Oncology, University Hospital, Mainz, Germany
| | - Werner Reichardt
- University of Applied Sciences Jena, Department of Medical Engineering and Biotechnology, 07745 Jena, Germany
| | - Gerhard Müller-Newen
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, 52074 Aachen, Germany
| | - Christian Kosan
- Center for Molecular Biomedicine (CMB), Dept. of Biochemistry, University of Jena, Germany
| | - Thorsten Heinzel
- Center for Molecular Biomedicine (CMB), Dept. of Biochemistry, University of Jena, Germany
| | - Oliver H Krämer
- Department of Toxicology, University Medical Center, Obere Zahlbacher Str. 67, 55131 Mainz, Germany.
| |
Collapse
|
14
|
Molecular models of the Mojave rattlesnake (Crotalus scutulatus scutulatus) venom metalloproteinases reveal a structural basis for differences in hemorrhagic activities. J Biol Phys 2014; 40:193-216. [PMID: 24522289 DOI: 10.1007/s10867-013-9339-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 12/23/2013] [Indexed: 01/22/2023] Open
Abstract
Rattlesnake venom can differ in composition and in metalloproteinase-associated activities. The molecular basis for this intra-species variation in Crotalus scutulatus scutulatus (Mojave rattlesnake) remains an enigma. To understand the molecular basis for intra-species variation of metalloproteinase-associated activities, we modeled the three-dimensional structures of four metalloproteinases based on the amino acid sequence of four variations of the proteinase domain of the C. s. scutulatus metalloproteinase gene (GP1, GP2, GP3, and GP4). For comparative purposes, we modeled the atrolysin metalloproteinases of C. atrox as well. All molecular models shared the same topology. While the atrolysin metalloproteinase molecular models contained highly conserved substrate binding sites, the Mojave rattlesnake metalloproteinases showed higher structural divergence when superimposed onto each other. The highest structural divergence among the four C. s. scutulatus molecular models was located at the northern cleft wall and the S'1-pocket of the substrate binding site, molecular regions that modulate substrate selectivity. Molecular dynamics and field potential maps for each C. s. scutulatus metalloproteinase model demonstrated that the non-hemorrhagic metalloproteinases (GP2 and GP3) contain highly basic molecular and field potential surfaces while the hemorrhagic metalloproteinases GP1 and atrolysin C showed extensive acidic field potential maps and shallow but less dynamic active site pockets. Hence, differences in the spatial arrangement of the northern cleft wall, the S'1-pocket, and the physico-chemical environment surrounding the catalytic site contribute to differences in metalloproteinase activities in the Mojave rattlesnake. Our results provide a structural basis for variation of metalloproteinase-associated activities in the rattlesnake venom of the Mojave rattlesnake.
Collapse
|
15
|
Loureiro I, Faria J, Clayton C, Ribeiro SM, Roy N, Santarém N, Tavares J, Cordeiro-da-Silva A. Knockdown of asparagine synthetase A renders Trypanosoma brucei auxotrophic to asparagine. PLoS Negl Trop Dis 2013; 7:e2578. [PMID: 24340117 PMCID: PMC3854871 DOI: 10.1371/journal.pntd.0002578] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 10/25/2013] [Indexed: 11/29/2022] Open
Abstract
Asparagine synthetase (AS) catalyzes the ATP-dependent conversion of aspartate into asparagine using ammonia or glutamine as nitrogen source. There are two distinct types of AS, asparagine synthetase A (AS-A), known as strictly ammonia-dependent, and asparagine synthetase B (AS-B), which can use either ammonia or glutamine. The absence of AS-A in humans, and its presence in trypanosomes, suggested AS-A as a potential drug target that deserved further investigation. We report the presence of functional AS-A in Trypanosoma cruzi (TcAS-A) and Trypanosoma brucei (TbAS-A): the purified enzymes convert L-aspartate into L-asparagine in the presence of ATP, ammonia and Mg2+. TcAS-A and TbAS-A use preferentially ammonia as a nitrogen donor, but surprisingly, can also use glutamine, a characteristic so far never described for any AS-A. TbAS-A knockdown by RNAi didn't affect in vitro growth of bloodstream forms of the parasite. However, growth was significantly impaired when TbAS-A knockdown parasites were cultured in medium with reduced levels of asparagine. As expected, mice infections with induced and non-induced T. brucei RNAi clones were similar to those from wild-type parasites. However, when induced T. brucei RNAi clones were injected in mice undergoing asparaginase treatment, which depletes blood asparagine, the mice exhibited lower parasitemia and a prolonged survival in comparison to similarly-treated mice infected with control parasites. Our results show that TbAS-A can be important under in vivo conditions when asparagine is limiting, but is unlikely to be suitable as a drug target. The amino acid asparagine is important not only for protein biosynthesis, but also for nitrogen homeostasis. Asparagine synthetase catalyzes the synthesis of this amino acid. There are two forms of asparagine synthetase, A and B. The presence of type A in trypanosomes, and its absence in humans, makes this protein a potential drug target. Trypanosomes are responsible for serious parasitic diseases that rely on limited drug therapeutic options for control. In our study we present a functional characterization of trypanosomes asparagine synthetase A. We describe that Trypanosoma brucei and Trypanosoma cruzi type A enzymes are able to use either ammonia or glutamine as a nitrogen donor, within the conversion of aspartate into asparagine. Furthermore, we show that asparagine synthetase A knockdown renders Trypanosoma brucei auxotrophic to asparagine. Overall, this study demonstrates that interfering with asparagine metabolism represents a way to control parasite growth and infectivity.
Collapse
Affiliation(s)
- Inês Loureiro
- Parasite Disease Group, Instituto de Biologia Molecular e Celular da Universidade do Porto, Porto, Portugal
| | - Joana Faria
- Parasite Disease Group, Instituto de Biologia Molecular e Celular da Universidade do Porto, Porto, Portugal
| | - Christine Clayton
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Sandra Macedo Ribeiro
- Protein Crystallography Group, Instituto de Biologia Molecular e Celular da Universidade do Porto, Porto, Portugal
| | - Nilanjan Roy
- Ashok and Rita Patel Institute of Integrated Study and Research in Biotechnology and Allied Sciences, New Vallabh Vidyanagar, Gujarat, India
| | - Nuno Santarém
- Parasite Disease Group, Instituto de Biologia Molecular e Celular da Universidade do Porto, Porto, Portugal
| | - Joana Tavares
- Parasite Disease Group, Instituto de Biologia Molecular e Celular da Universidade do Porto, Porto, Portugal
- * E-mail: (JT); (ACdS)
| | - Anabela Cordeiro-da-Silva
- Parasite Disease Group, Instituto de Biologia Molecular e Celular da Universidade do Porto, Porto, Portugal
- Departamento de Ciências Biológicas, Faculdade de Farmácia da Universidade do Porto, Porto, Portugal
- * E-mail: (JT); (ACdS)
| |
Collapse
|
16
|
Partial deletion of beta9 loop in pancreatic lipase-related protein 2 reduces enzyme activity with a larger effect on long acyl chain substrates. Biochim Biophys Acta Mol Cell Biol Lipids 2013; 1831:1293-301. [PMID: 24046870 DOI: 10.1016/j.bbalip.2013.04.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Structural studies on pancreatic lipase have revealed a complex architecture of surface loops surrounding the enzyme active site and potentially involved in interactions with lipids. Two of them, the lid and beta loop, expose a large hydrophobic surface and are considered as acyl chain binding sites based on their interaction with an alkyl phosphonate inhibitor. While the role of the lid in substrate recognition and selectivity has been extensively studied, the implication of beta9 loop in acyl chain stabilization remained hypothetical. The characterization of an enzyme with a natural deletion of the lid, guinea pig pancreatic lipase-related protein 2 (GPLRP2), suggests however an essential contribution of the beta9 loop in the stabilization of the acyl enzyme intermediate formed during the lipolysis reaction. A GPLRP2 mutant with a seven-residue deletion of beta9 loop (GPLRP2-deltabeta9) was produced and its enzyme activity was measured using various substrates (triglycerides, monoglycerides, galactolipids, phospholipids, vinyl esters) with short, medium and long acyl chains. Whatever the substrate tested, GPLRP2-deltabeta9 activity is drastically reduced compared to that of wild-type GPLRP2 and this effect is more pronounced as the length of substrate acyl chain increases. Changes in relative substrate selectivity and stereoselectivity remained however weak. The deletion within beta9 loop has also a negative effect on the rate of enzyme inhibition by alkyl phosphonates. All these findings indicate that the reduced enzyme turnover observed with GPLRP2-deltabeta9 results from a weaker stabilization of the acyl enzyme intermediate due to a loss of hydrophobic interactions.
Collapse
|
17
|
Hofmeister-Brix A, Kollmann K, Langer S, Schultz J, Lenzen S, Baltrusch S. Identification of the ubiquitin-like domain of midnolin as a new glucokinase interaction partner. J Biol Chem 2013; 288:35824-39. [PMID: 24187134 DOI: 10.1074/jbc.m113.526632] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Glucokinase acts as a glucose sensor in pancreatic beta cells. Its posttranslational regulation is important but not yet fully understood. Therefore, a pancreatic islet yeast two-hybrid library was produced and searched for glucokinase-binding proteins. A protein sequence containing a full-length ubiquitin-like domain was identified to interact with glucokinase. Mammalian two-hybrid and fluorescence resonance energy transfer analyses confirmed the interaction between glucokinase and the ubiquitin-like domain in insulin-secreting MIN6 cells and revealed the highest binding affinity at low glucose. Overexpression of parkin, an ubiquitin E3 ligase exhibiting an ubiquitin-like domain with high homology to the identified, diminished insulin secretion in MIN6 cells but had only some effect on glucokinase activity. Overexpression of the elucidated ubiquitin-like domain or midnolin, containing exactly this ubiquitin-like domain, significantly reduced both intrinsic glucokinase activity and glucose-induced insulin secretion. Midnolin has been to date classified as a nucleolar protein regulating mouse development. However, we could not confirm localization of midnolin in nucleoli. Fluorescence microscopy analyses revealed localization of midnolin in nucleus and cytoplasm and co-localization with glucokinase in pancreatic beta cells. In addition we could show that midnolin gene expression in pancreatic islets is up-regulated at low glucose and that the midnolin protein is highly expressed in pancreatic beta cells and also in liver, muscle, and brain of the adult mouse and cell lines of human and rat origin. Thus, the results of our study suggest that midnolin plays a role in cellular signaling of adult tissues and regulates glucokinase enzyme activity in pancreatic beta cells.
Collapse
Affiliation(s)
- Anke Hofmeister-Brix
- From the Institute of Clinical Biochemistry, Hannover Medical School, 30625 Hannover, Germany and
| | | | | | | | | | | |
Collapse
|
18
|
Schmidt HF, Sakowski EG, Williamson SJ, Polson SW, Wommack KE. Shotgun metagenomics indicates novel family A DNA polymerases predominate within marine virioplankton. ISME JOURNAL 2013; 8:103-14. [PMID: 23985748 DOI: 10.1038/ismej.2013.124] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 06/07/2013] [Accepted: 06/18/2013] [Indexed: 02/07/2023]
Abstract
Virioplankton have a significant role in marine ecosystems, yet we know little of the predominant biological characteristics of aquatic viruses that influence the flow of nutrients and energy through microbial communities. Family A DNA polymerases, critical to DNA replication and repair in prokaryotes, are found in many tailed bacteriophages. The essential role of DNA polymerase in viral replication makes it a useful target for connecting viral diversity with an important biological feature of viruses. Capturing the full diversity of this polymorphic gene by targeted approaches has been difficult; thus, full-length DNA polymerase genes were assembled out of virioplankton shotgun metagenomic sequence libraries (viromes). Within the viromes novel DNA polymerases were common and found in both double-stranded (ds) DNA and single-stranded (ss) DNA libraries. Finding DNA polymerase genes in ssDNA viral libraries was unexpected, as no such genes have been previously reported from ssDNA phage. Surprisingly, the most common virioplankton DNA polymerases were related to a siphovirus infecting an α-proteobacterial symbiont of a marine sponge and not the podoviral T7-like polymerases seen in many other studies. Amino acids predictive of catalytic efficiency and fidelity linked perfectly to the environmental clades, indicating that most DNA polymerase-carrying virioplankton utilize a lower efficiency, higher fidelity enzyme. Comparisons with previously reported, PCR-amplified DNA polymerase sequences indicated that the most common virioplankton metagenomic DNA polymerases formed a new group that included siphoviruses. These data indicate that slower-replicating, lytic or lysogenic phage populations rather than fast-replicating, highly lytic phages may predominate within the virioplankton.
Collapse
Affiliation(s)
- Helen F Schmidt
- Department of Plant & Soil Science, College of Marine Studies, Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
| | - Eric G Sakowski
- Department of Plant & Soil Science, College of Marine Studies, Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
| | | | - Shawn W Polson
- Department of Plant & Soil Science, College of Marine Studies, Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
| | - K Eric Wommack
- Department of Plant & Soil Science, College of Marine Studies, Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
| |
Collapse
|
19
|
Rhipicephalus microplus lipocalins (LRMs): Genomic identification and analysis of the bovine immune response using in silico predicted B and T cell epitopes. Int J Parasitol 2013; 43:739-52. [DOI: 10.1016/j.ijpara.2013.04.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 04/23/2013] [Accepted: 04/25/2013] [Indexed: 11/17/2022]
|
20
|
Mason PA, Boubriak I, Robbins T, Lasala R, Saunders R, Cox LS. The Drosophila orthologue of progeroid human WRN exonuclease, DmWRNexo, cleaves replication substrates but is inhibited by uracil or abasic sites : analysis of DmWRNexo activity in vitro. AGE (DORDRECHT, NETHERLANDS) 2013; 35:793-806. [PMID: 22562358 PMCID: PMC3636389 DOI: 10.1007/s11357-012-9411-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Accepted: 04/17/2012] [Indexed: 05/31/2023]
Abstract
Werner syndrome (WS) is a rare late-onset premature ageing disease showing many of the phenotypes associated with normal ageing, and provides one of the best models for investigating cellular pathways that lead to normal ageing. WS is caused by mutation of WRN, which encodes a multifunctional DNA replication and repair helicase/exonuclease. To investigate the role of WRN protein's unique exonuclease domain, we have recently identified DmWRNexo, the fly orthologue of the exonuclease domain of human WRN. Here, we fully characterise DmWRNexo exonuclease activity in vitro, confirming 3'-5' polarity, demonstrating a requirement for Mg(2+), inhibition by ATP, and an ability to degrade both single-stranded DNA and duplex DNA substrates with 3' or 5' overhangs, or bubble structures, but with no activity on blunt ended DNA duplexes. We report a novel active site mutation that ablates enzyme activity. Lesional substrates containing uracil are partially cleaved by DmWRNexo, but the enzyme pauses on such substrates and is inhibited by abasic sites. These strong biochemical similarities to human WRN suggest that Drosophila can provide a valuable experimental system for analysing the importance of WRN exonuclease in cell and organismal ageing.
Collapse
Affiliation(s)
- Penelope A. Mason
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU UK
| | - Ivan Boubriak
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU UK
| | - Timothy Robbins
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU UK
| | - Ralph Lasala
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU UK
- Department of Life Sciences, The Open University, Milton Keynes, MK7 6AA UK
| | - Robert Saunders
- Department of Life Sciences, The Open University, Milton Keynes, MK7 6AA UK
| | - Lynne S. Cox
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU UK
| |
Collapse
|
21
|
Lozada-Ramírez JD, Sánchez-Ferrer A, García-Carmona F. Recombinant S-adenosylhomocysteine hydrolase from Thermotoga maritima: cloning, overexpression, characterization, and thermal purification studies. Appl Biochem Biotechnol 2013; 170:639-53. [PMID: 23588970 DOI: 10.1007/s12010-013-0218-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2013] [Accepted: 04/01/2013] [Indexed: 01/24/2023]
Abstract
S-Adenosylhomocysteine hydrolase (SAHase) encoded by sahase gene is a determinant when catalyzing the reversible conversion of adenosine and homocysteine to S-adenosylhomocysteine in most living organisms. The sahase gene was isolated from the genome of the highly thermostable anaerobic bacteria Thermotoga maritima, and then it was cloned, characterized, overexpressed using Escherichia coli, and partially purified by thermal precipitation. The thermal purification of the recombinant SAHase resulted in changes in the circular dichroism spectra. As a result of this analysis, it was possible to determine the structural changes in the composition of the α-helix and β-sheet content of the recombinant enzyme after purification. Moreover, a predicted secondary structure and 3D structural model was rendered by comparative molecular modeling to further understand the molecular function of this protein including its attractive biotechnological use.
Collapse
Affiliation(s)
- J D Lozada-Ramírez
- Department of Chemical and Biological Sciences, School of Sciences, Universidad de las Américas Puebla, Santa Catarina Mártir Cholula 72820, Puebla, México.
| | | | | |
Collapse
|
22
|
Resistance to antibody neutralization in HIV-2 infection occurs in late stage disease and is associated with X4 tropism. AIDS 2012; 26:2275-84. [PMID: 23151495 DOI: 10.1097/qad.0b013e328359a89d] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
OBJECTIVES To characterize the nature and dynamics of the neutralizing antibody (NAb) response and escape in chronically HIV-2 infected patients. METHODS Twenty-eight chronically infected adults were studied over a period of 1-4 years. The neutralizing activity of plasma immunoglobulin G (IgG) antibodies against autologous and heterologous primary isolates was analyzed using a standard assay in TZM-bl cells. Coreceptor usage was determined in ghost cells. The sequence and predicted three-dimensional structure of the C2V3C3 Env region were determined for all isolates. RESULTS Only 50% of the patients consistently produced IgG NAbs to autologous and contemporaneous virus isolates. In contrast, 96% of the patients produced IgG antibodies that neutralized at least two isolates of a panel of six heterologous R5 isolates. Breadth and potency of the neutralizing antibodies were positively associated with the number of CD4(+) T cells and with the titer and avidity of C2V3C3-specific binding IgG antibodies. X4 isolates were obtained only from late stage disease patients and were fully resistant to neutralization. The V3 loop of X4 viruses was longer, had a higher net charge, and differed markedly in secondary structure compared to R5 viruses. CONCLUSION Most HIV-2 patients infected with R5 isolates produce C2V3C3-specific neutralizing antibodies whose potency and breadth decreases as the disease progresses. Resistance to antibody neutralization occurs in late stage disease and is usually associated with X4 viral tropism and major changes in V3 sequence and conformation. Our studies support a model of HIV-2 pathogenesis in which the neutralizing antibodies play a central role and have clear implications for the vaccine field.
Collapse
|
23
|
Haglund E, Sułkowska JI, He Z, Feng GS, Jennings PA, Onuchic JN. The unique cysteine knot regulates the pleotropic hormone leptin. PLoS One 2012; 7:e45654. [PMID: 23029163 PMCID: PMC3454405 DOI: 10.1371/journal.pone.0045654] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Accepted: 08/20/2012] [Indexed: 11/30/2022] Open
Abstract
Leptin plays a key role in regulating energy intake/expenditure, metabolism and hypertension. It folds into a four-helix bundle that binds to the extracellular receptor to initiate signaling. Our work on leptin revealed a hidden complexity in the formation of a previously un-described, cysteine-knotted topology in leptin. We hypothesized that this unique topology could offer new mechanisms in regulating the protein activity. A combination of in silico simulation and in vitro experiments was used to probe the role of the knotted topology introduced by the disulphide-bridge on leptin folding and function. Our results surprisingly show that the free energy landscape is conserved between knotted and unknotted protein, however the additional complexity added by the knot formation is structurally important. Native state analyses led to the discovery that the disulphide-bond plays an important role in receptor binding and thus mediate biological activity by local motions on distal receptor-binding sites, far removed from the disulphide-bridge. Thus, the disulphide-bridge appears to function as a point of tension that allows dissipation of stress at a distance in leptin.
Collapse
Affiliation(s)
- Ellinor Haglund
- Department of Chemistry and Biochemistry and Center for theoretical Biological Physics (CTBP), University of California San Diego, La Jolla, California, United States of America
| | - Joanna I. Sułkowska
- Department of Chemistry and Biochemistry and Center for theoretical Biological Physics (CTBP), University of California San Diego, La Jolla, California, United States of America
| | - Zhao He
- Department of Pathology; School of Medicine and Molecular Biology Section, Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Gen-Sheng Feng
- Department of Pathology; School of Medicine and Molecular Biology Section, Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Patricia A. Jennings
- Department of Chemistry and Biochemistry and Center for theoretical Biological Physics (CTBP), University of California San Diego, La Jolla, California, United States of America
| | - José N. Onuchic
- Center for Theoretical Biological physics and Department of Physics and Astronomy, Chemistry, and Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America
| |
Collapse
|
24
|
Liu Y, Hu B, Xu Y, Bo J, Fan S, Wang J, Lu F. Improvement of the acid stability of Bacillus licheniformis alpha amylase by error-prone PCR. J Appl Microbiol 2012; 113:541-9. [DOI: 10.1111/j.1365-2672.2012.05359.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2012] [Revised: 05/25/2012] [Accepted: 05/28/2012] [Indexed: 11/27/2022]
Affiliation(s)
| | | | | | | | | | - J.L. Wang
- College of Biotechnology; Tianjin University of Science & Technology; Tianjin; China
| | | |
Collapse
|
25
|
Tokmakov AA, Kurotani A, Takagi T, Toyama M, Shirouzu M, Fukami Y, Yokoyama S. Multiple post-translational modifications affect heterologous protein synthesis. J Biol Chem 2012; 287:27106-16. [PMID: 22674579 DOI: 10.1074/jbc.m112.366351] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Post-translational modifications (PTMs) are required for proper folding of many proteins. The low capacity for PTMs hinders the production of heterologous proteins in the widely used prokaryotic systems of protein synthesis. Until now, a systematic and comprehensive study concerning the specific effects of individual PTMs on heterologous protein synthesis has not been presented. To address this issue, we expressed 1488 human proteins and their domains in a bacterial cell-free system, and we examined the correlation of the expression yields with the presence of multiple PTM sites bioinformatically predicted in these proteins. This approach revealed a number of previously unknown statistically significant correlations. Prediction of some PTMs, such as myristoylation, glycosylation, palmitoylation, and disulfide bond formation, was found to significantly worsen protein amenability to soluble expression. The presence of other PTMs, such as aspartyl hydroxylation, C-terminal amidation, and Tyr sulfation, did not correlate with the yield of heterologous protein expression. Surprisingly, the predicted presence of several PTMs, such as phosphorylation, ubiquitination, SUMOylation, and prenylation, was associated with the increased production of properly folded soluble proteins. The plausible rationales for the existence of the observed correlations are presented. Our findings suggest that identification of potential PTMs in polypeptide sequences can be of practical use for predicting expression success and optimizing heterologous protein synthesis. In sum, this study provides the most compelling evidence so far for the role of multiple PTMs in the stability and solubility of heterologously expressed recombinant proteins.
Collapse
Affiliation(s)
- Alexander A Tokmakov
- RIKEN Systems and Structural Biology Center, University of Tokyo, Bunkyo, Tokyo 113-0033, Japan.
| | | | | | | | | | | | | |
Collapse
|
26
|
Tokmakov AA. Comparative homology modeling of pyruvate dehydrogenase kinase isozymes from Xenopus tropicalis reveals structural basis for their subfunctionalization. J Mol Model 2011; 18:2567-76. [PMID: 22069030 DOI: 10.1007/s00894-011-1281-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Accepted: 10/13/2011] [Indexed: 10/15/2022]
Abstract
Structural-functional divergence is responsible for the preservation of highly homologous genes. Protein functions affected by mutagenesis in divergent sequences require investigation on an individual basis. In the present study, comparative homology modeling and predictive bioinformatics analysis were used to reveal for the first time the subfunctionalization of two pyruvate dehydrogenase kinase (PDK) isozymes in the western clawed frog Xenopus tropicalis. Three-dimensional structures of the two proteins were built by homology modeling based on the crystal structures of mammalian PDKs. A detailed comparison of them revealed important structural differences that modify the accessibility of the nucleotide binding site in the two isozymes. Based on the generated models and bioinformatics data analysis, the differences between the two proteins in terms of kinetic parameters, metabolic regulation, and tissue distribution are predicted. The results obtained are consistent with the idea that one of the xtPDKs is the major isozyme responsible for metabolic control of PDC activity in X. tropicalis, whereas the other one has more specialized functions. Hence, this study provides a rationale for the existence of two closely related PDK isozymes in X. tropicalis, thereby enhancing our understanding of the functional evolution of PDK family genes.
Collapse
Affiliation(s)
- Alexander A Tokmakov
- Research Center for Environmental Genomics and Graduate School of Science, Kobe University, Nada, Kobe, Japan.
| |
Collapse
|
27
|
Ermolova N, Kudryashova E, DiFranco M, Vergara J, Kramerova I, Spencer MJ. Pathogenity of some limb girdle muscular dystrophy mutations can result from reduced anchorage to myofibrils and altered stability of calpain 3. Hum Mol Genet 2011; 20:3331-45. [PMID: 21624972 DOI: 10.1093/hmg/ddr239] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Calpain 3 (CAPN3) is a muscle-specific, calcium-dependent proteinase that is mutated in Limb Girdle Muscle Dystrophy type 2A. Most pathogenic missense mutations in LGMD2A affect CAPN3's proteolytic activity; however, two mutations, D705G and R448H, retain activity but nevertheless cause muscular dystrophy. Previously, we showed that D705G and R448H mutations reduce CAPN3s ability to bind to titin in vitro. In this investigation, we tested the consequence of loss of titin binding in vivo and examined whether this loss can be an underlying pathogenic mechanism in LGMD2A. To address this question, we created transgenic mice that express R448H or D705G in muscles, on wild-type (WT) CAPN3 or knock-out background. Both mutants were readily expressed in insect cells, but when D705G was expressed in skeletal muscle, it was not stable enough to study. Moreover, the D705G mutation had a dominant negative effect on endogenous CAPN3 when expressed on a WT background. The R448H protein was stably expressed in muscles; however, it was more rapidly degraded in muscle extracts compared with WT CAPN3. Increased degradation of R448H was due to non-cysteine, cellular proteases acting on the autolytic sites of CAPN3, rather than autolysis. Fractionation experiments revealed a significant decrease of R448H from the myofibrillar fraction, likely due to the mutant's inability to bind titin. Our data suggest that R448H and D705G mutations affect both CAPN3s anchorage to titin and its stability. These studies reveal a novel mechanism by which mutations that spare enzymatic activity can still lead to calpainopathy.
Collapse
Affiliation(s)
- Natalia Ermolova
- Department of Neurology, David Geffen School of Medicine at University of California, Los Angeles, CA 90095, USA
| | | | | | | | | | | |
Collapse
|
28
|
Schlesinger SR, Kim SG, Lee JS, Kim SK. Purification development and characterization of the zinc-dependent metallo-β-lactamase from Bacillus anthracis. Biotechnol Lett 2011; 33:1417-22. [PMID: 21369909 DOI: 10.1007/s10529-011-0569-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Accepted: 02/14/2011] [Indexed: 11/29/2022]
Abstract
Metallo-β-lactamase from Bacillus anthracis (Bla2) catalyzes the hydrolysis of β-lactam antibiotics which are commonly prescribed to combat bacterial infections. Bla2 contributes to the antibiotic resistance of this bacterium. An understanding of it is necessary to design potential inhibitors that can be introduced with current antibiotics for effective eradication of anthrax infections. We have purified Bla2 using Ni(2+)-affinity chromatography with over 140-fold increase in activity with a yield of 3.5%. The final specific activity was 19,000 units/mg. Purified Bla2 displays different K ( m ), V ( max ), and (k ( cat ) /K (M)) with penicillin G and cephalexin as substrates and is also sensitive to pH, with maximum activity between pH 7.0-9.0. The IC(50) (50% inhibition concentration) value of EDTA against Bla2 is 630 nM, which can be understood by observing its three-dimensional interaction with the enzyme.
Collapse
Affiliation(s)
- Sara R Schlesinger
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76798-7348, USA.
| | | | | | | |
Collapse
|
29
|
O’Connell LA, Matthews BJ, Patel SB, O’Connell JD, Crews D. Molecular characterization and brain distribution of the progesterone receptor in whiptail lizards. Gen Comp Endocrinol 2011; 171:64-74. [PMID: 21185292 PMCID: PMC3041865 DOI: 10.1016/j.ygcen.2010.12.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2010] [Revised: 12/06/2010] [Accepted: 12/16/2010] [Indexed: 11/21/2022]
Abstract
Progesterone and its nuclear receptor are critical in modulating reproductive physiology and behavior in female and male vertebrates. Whiptail lizards (genus Cnemidophorus) are an excellent model system in which to study the evolution of sexual behavior, as both the ancestral and descendent species exist. Male-typical sexual behavior is mediated by progesterone in both the ancestral species and the descendant all-female species, although the molecular characterization and distribution of the progesterone receptor protein throughout the reptilian brain is not well understood. To better understand the gene targets and ligand binding properties of the progesterone receptor in whiptails, we cloned the promoter and coding sequence of the progesterone receptor and analyzed the predicted protein structure. We next determined the distribution of the progesterone receptor protein and mRNA throughout the brain of Cnemidophorus inornatus and Cnemidophorus uniparens by immunohistochemistry and in situ hybridization. We found the progesterone receptor to be present in many brain regions known to regulate social behavior and processing of stimulus salience across many vertebrates, including the ventral tegmental area, amygdala, nucleus accumbens and several hypothalamic nuclei. Additionally, we quantified immunoreactive cells in the preoptic area and ventromedial hypothalamus in females of both species and males of the ancestral species. We found differences between both species and across ovarian states. Our results significantly extend our understanding of progesterone modulation in the reptilian brain and support the important role of the nuclear progesterone receptor in modulating sexual behavior in reptiles and across vertebrates.
Collapse
Affiliation(s)
- Lauren A. O’Connell
- Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, Texas 78712
- Section of Integrative Biology, University of Texas at Austin, Austin, Texas 78712
| | - Bryan J. Matthews
- Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, Texas 78712
| | - Sagar B. Patel
- Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, Texas 78712
| | - Jeremy D. O’Connell
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712
| | - David Crews
- Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, Texas 78712
- Section of Integrative Biology, University of Texas at Austin, Austin, Texas 78712
- All correspondence and requests for reprints should to addressed to: David Crews, Section of Integrative Biology, University of Texas at Austin, Austin, TX 78712, Phone: 512-471-1113,
| |
Collapse
|
30
|
Tsaousis AD, Gaston D, Stechmann A, Walker PB, Lithgow T, Roger AJ. A functional Tom70 in the human parasite Blastocystis sp.: implications for the evolution of the mitochondrial import apparatus. Mol Biol Evol 2010; 28:781-91. [PMID: 20871025 DOI: 10.1093/molbev/msq252] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Core proteins of mitochondrial protein import are found in all mitochondria, suggesting a common origin of this import machinery. Despite the presence of a universal core import mechanism, there are specific proteins found only in a few groups of organisms. One of these proteins is the translocase of outer membrane 70 (Tom70), a protein that is essential for the import of preproteins with internal targeting sequences into the mitochondrion. Until now, Tom70 has only been found in animals and Fungi. We have identified a tom70 gene in the human parasitic anaerobic stramenopile Blastocystis sp. that is neither an animal nor a fungus. Using a combination of bioinformatics, genetic complementation, and immunofluorescence microscopy analyses, we demonstrate that this protein functions as a typical Tom70 in Blastocystis mitochondrion-related organelles. Additionally, we identified putative tom70 genes in the genomes of other stramenopiles and a haptophyte, that, in phylogenies, form a monophyletic group distinct from the animal and the fungal homologues. The presence of Tom70 in these lineages significantly expands the evolutionary spectrum of eukaryotes that contain this protein and suggests that it may have been part of the core mitochondrial protein import apparatus of the last common ancestral eukaryote.
Collapse
Affiliation(s)
- Anastasios D Tsaousis
- Department of Biochemistry and Molecular Biology, Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Canada.
| | | | | | | | | | | |
Collapse
|
31
|
Comparison of human and guinea pig acetylcholinesterase sequences and rates of oxime-assisted reactivation. Chem Biol Interact 2010; 187:229-33. [DOI: 10.1016/j.cbi.2010.04.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Revised: 04/16/2010] [Accepted: 04/19/2010] [Indexed: 11/22/2022]
|
32
|
Liu X, Tang Z, Li C, Yang K, Gan G, Zhang Z, Liu J, Jiang F, Wang Q, Liu M. Novel USH2A compound heterozygous mutations cause RP/USH2 in a Chinese family. Mol Vis 2010; 16:454-61. [PMID: 20309401 PMCID: PMC2842093 DOI: 10.1167/3.9.454] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2009] [Accepted: 03/09/2010] [Indexed: 11/24/2022] Open
Abstract
PURPOSE To identify the disease-causing gene in a four-generation Chinese family affected with retinitis pigmentosa (RP). METHODS Linkage analysis was performed with a panel of microsatellite markers flanking the candidate genetic loci of RP. These loci included 38 known RP genes. The complete coding region and exon-intron boundaries of Usher syndrome 2A (USH2A) were sequenced with the proband DNA to screen the disease-causing gene mutation. Restriction fragment length polymorphism (RFLP) analysis and direct DNA sequence analysis were done to demonstrate co-segregation of the USH2A mutations with the family disease. One hundred normal controls were used without the mutations. RESULTS The disease-causing gene in this Chinese family was linked to the USH2A locus on chromosome 1q41. Direct DNA sequence analysis of USH2A identified two novel mutations in the patients: one missense mutation p.G1734R in exon 26 and a splice site mutation, IVS32+1G>A, which was found in the donor site of intron 32 of USH2A. Neither the p.G1734R nor the IVS32+1G>A mutation was found in the unaffected family members or the 100 normal controls. One patient with a homozygous mutation displayed only RP symptoms until now, while three patients with compound heterozygous mutations in the family of study showed both RP and hearing impairment. CONCLUSIONS This study identified two novel mutations: p.G1734R and IVS32+1G>A of USH2A in a four-generation Chinese RP family. In this study, the heterozygous mutation and the homozygous mutation in USH2A may cause Usher syndrome Type II or RP, respectively. These two mutations expand the mutant spectrum of USH2A.
Collapse
Affiliation(s)
- Xiaowen Liu
- The Union Hospital, Huazhong University of Science and Technology, Wuhan, Hubei, P.R. China
| | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Bailly M, de Crécy-Lagard V. Predicting the pathway involved in post-translational modification of elongation factor P in a subset of bacterial species. Biol Direct 2010; 5:3. [PMID: 20070887 PMCID: PMC2821294 DOI: 10.1186/1745-6150-5-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Accepted: 01/13/2010] [Indexed: 11/10/2022] Open
Abstract
Background The bacterial elongation factor P (EF-P) is strictly conserved in bacteria and essential for protein synthesis. It is homologous to the eukaryotic translation initiation factor 5A (eIF5A). A highly conserved eIF5A lysine is modified into an unusual amino acid derived from spermidine, hypusine. Hypusine is absolutely required for eIF5A's role in translation in Saccharomyces cerevisiae. The homologous lysine of EF-P is also modified to a spermidine derivative in Escherichia coli. However, the biosynthesis pathway of this modification in the bacterial EF-P is yet to be elucidated. Presentation of the Hypothesis Here we propose a potential mechanism for the post-translational modification of EF-P. By using comparative genomic methods based on physical clustering and phylogenetic pattern analysis, we identified two protein families of unknown function, encoded by yjeA and yjeK genes in E. coli, as candidates for this missing pathway. Based on the analysis of the structural and biochemical properties of both protein families, we propose two potential mechanisms for the modification of EF-P. Testing the hypothesis This hypothesis could be tested genetically by constructing a bacterial strain with a tagged efp gene. The tag would allow the purification of EF-P by affinity chromatography and the analysis of the purified protein by mass spectrometry. yjeA or yjeK could then be deleted in the efp tagged strain and the EF-P protein purified from each mutant analyzed by mass spectrometry for the presence or the absence of the modification. This hypothesis can also be tested by purifying the different components (YjeK, YjeA and EF-P) and reconstituting the pathway in vitro. Implication of the hypothesis The requirement for a fully modified EF-P for protein synthesis in certain bacteria implies the presence of specific post-translational modification mechanism in these organisms. All of the 725 bacterial genomes analyzed, possess an efp gene but only 200 (28%) possess both yjeA and yjeK genes. In the other organisms, EF-P may be modified by another pathway or the translation machinery must have adapted to the lack of EF-P modification. Our hypotheses, if confirmed, will lead to the discovery of a new post-translational modification pathway. Reviewers This article was reviewed by Céline Brochier-Armanet, Igor B. Zhulin and Mikhail Gelfand. For the full reviews, please go to the Reviewers' reports section.
Collapse
Affiliation(s)
- Marc Bailly
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
| | | |
Collapse
|
34
|
VIM-19, a metallo-beta-lactamase with increased carbapenemase activity from Escherichia coli and Klebsiella pneumoniae. Antimicrob Agents Chemother 2009; 54:471-6. [PMID: 19917750 DOI: 10.1128/aac.00458-09] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Two carbapenem-resistant isolates, one Escherichia coli isolate and one Klebsiella pneumoniae isolate, recovered from an Algerian patient expressed a novel VIM-type metallo-beta-lactamase (MBL). The identified bla(VIM-19) gene was located on a ca. 160-kb plasmid and located inside a class 1 integron in both isolates. VIM-19 differed from VIM-1 by the Asn215Lys and Ser228Arg substitutions, increasing its hydrolytic activity toward carbapenems. Site-directed mutagenesis experiments showed that both substitutions were necessary for the increased carbapenemase activity of VIM-19. This study indicates that MBLs with enhanced activity toward carbapenems may be obtained as a result of very few amino acid substitutions.
Collapse
|
35
|
Lai TP, Stauffer KA, Murthi A, Shaheen HH, Peng G, Martin NC, Hopper AK. Mechanism and a peptide motif for targeting peripheral proteins to the yeast inner nuclear membrane. Traffic 2009; 10:1243-56. [PMID: 19602197 DOI: 10.1111/j.1600-0854.2009.00956.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Trm1 is a tRNA specific m(2)(2)G methyltransferase shared by nuclei and mitochondria in Saccharomyces cerevisiae. In nuclei, Trm1 is peripherally associated with the inner nuclear membrane (INM). We investigated the mechanism delivering/tethering Trm1 to the INM. Analyses of mutations of the Ran pathway and nuclear pore components showed that Trm1 accesses the nucleoplasm via the classical nuclear import pathway. We identified a Trm1 cis-acting sequence sufficient to target passenger proteins to the INM. Detailed mutagenesis of this region uncovered specific amino acids necessary for authentic Trm1 to locate at the INM. The INM information is contained within a sequence of less than 20 amino acids, defining the first motif for addressing a peripheral protein to this important subnuclear location. The combined studies provide a multi-step process to direct Trm1 to the INM: (i) translation in the cytoplasm; (ii) Ran-dependent import into the nucleoplasm; and (iii) redistribution from the nucleoplasm to the INM via the INM motif. Furthermore, we demonstrate that the Trm1 mitochondrial targeting and nuclear localization signals are in competition with each other, as Trm1 becomes mitochondrial if prevented from entering the nucleus.
Collapse
Affiliation(s)
- Tsung-Po Lai
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | | | | | | | | | | | | |
Collapse
|
36
|
Janzon J, Yuan Q, Malatesta F, Hellwig P, Ludwig B, Durham B, Millett F. Probing the Paracoccus denitrificans cytochrome c(1)-cytochrome c(552) interaction by mutagenesis and fast kinetics. Biochemistry 2009; 47:12974-84. [PMID: 19006325 DOI: 10.1021/bi800932c] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Electron transfer (ET) between Paracoccus denitrificans cytochrome (cyt) c(1) and cytochrome c(552) was studied using the soluble redox fragments cyt c(1CF) and cyt c(552F). A new ruthenium cyt c(552F) derivative labeled at C23 (Ru(z)-23-c(552F)) was designed to measure rapid electron transfer with cyt c(1CF) in the physiological direction using flash photolysis. The bimolecular rate constant k(12) decreased rapidly with ionic strength above 40 mM, consistent with a diffusional process guided by long-range electrostatic interactions between the two proteins. However, a new kinetic phase was detected at an ionic strength of <35 mM with the ruthenium photoexcitation technique in which k(12) became very rapid (3 x 10(9) M(-1) s(-1)) and nearly independent of ionic strength, suggesting that the reaction became so fast that it was controlled by short-range diffusion along the protein surfaces guided by hydrophobic interactions. These results are consistent with a two-step model for formation of the final encounter complex. No intracomplex electron transfer between Ru(z)-23-c(552F) and c(1CF) was observed even at the lowest ionic strength, indicating that the dissociation constant of the complex was >30 microM. On the other hand, the ruthenium-labeled yeast cytochrome c derivative Ru(z)-39-Cc formed a tight 1:1 complex with cyt c(1CF) at ionic strengths of <60 mM with an intracomplex electron transfer rate constant of 50000 s(-1). A group of cyt c(1CF) variants in the presumed docking site were generated on the basis of information from the yeast cyt bc(1)-cyt c cocrystal structure. Kinetic analysis of cyt c(1CF) mutants located near the heme crevice provided preliminary identification of the interaction site for cyt c(552F) and suggested that formation of the encounter complex is guided primarily by the overall electrostatic surface potential rather than by defined ions.
Collapse
Affiliation(s)
- Julia Janzon
- Molecular Genetics, Institute of Biochemistry, Biocentre Goethe-University, 60438 Frankfurt/Main, Germany.
| | | | | | | | | | | | | |
Collapse
|
37
|
Xiao Q, Prussia A, Yu K, Cui YY, Hartzell HC. Regulation of bestrophin Cl channels by calcium: role of the C terminus. ACTA ACUST UNITED AC 2009; 132:681-92. [PMID: 19029375 PMCID: PMC2585866 DOI: 10.1085/jgp.200810056] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Human bestrophin-1 (hBest1), which is genetically linked to several kinds of retinopathy and macular degeneration in both humans and dogs, is the founding member of a family of Cl− ion channels that are activated by intracellular Ca2+. At present, the structures and mechanisms responsible for Ca2+ sensing remain unknown. Here, we have used a combination of molecular modeling, density functional–binding energy calculations, mutagenesis, and patch clamp to identify the regions of hBest1 involved in Ca2+ sensing. We identified a cluster of a five contiguous acidic amino acids in the C terminus immediately after the last transmembrane domain, followed by an EF hand and another regulatory domain that are essential for Ca2+ sensing by hBest1. The cluster of five amino acids (293–308) is crucial for normal channel gating by Ca2+ because all but two of the 35 mutations we made in this region rendered the channel incapable of being activated by Ca2+. Using homology models built on the crystal structure of calmodulin (CaM), an EF hand (EF1) was identified in hBest1. EF1 was predicted to bind Ca2+ with a slightly higher affinity than the third EF hand of CaM and lower affinity than the second EF hand of troponin C. As predicted by the model, the D312G mutation in the putative Ca2+-binding loop (312–323) reduced the apparent Ca2+ affinity by 20-fold. In addition, the D312G and D323N mutations abolished Ca2+-dependent rundown of the current. Furthermore, analysis of truncation mutants of hBest1 identified a domain adjacent to EF1 that is rich in acidic amino acids (350–390) that is required for Ca2+ activation and plays a role in current rundown. These experiments identify a region of hBest1 (312–323) that is involved in the gating of hBest1 by Ca2+ and suggest a model in which Ca2+ binding to EF1 activates the channel in a process that requires the acidic domain (293–308) and another regulatory domain (350–390). Many of the ∼100 disease-causing mutations in hBest1 are located in this region that we have implicated in Ca2+ sensing, suggesting that these mutations disrupt hBest1 channel gating by Ca2+.
Collapse
Affiliation(s)
- Qinghuan Xiao
- Department of Cell Biology and Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA 30322, USA
| | | | | | | | | |
Collapse
|
38
|
Structure–Function Relationships in Fungal Large-Subunit Catalases. J Mol Biol 2009; 386:218-32. [DOI: 10.1016/j.jmb.2008.12.019] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2008] [Revised: 12/03/2008] [Accepted: 12/07/2008] [Indexed: 11/23/2022]
|
39
|
Klassen TL, O'Mara ML, Redstone M, Spencer AN, Gallin WJ. Non-linear intramolecular interactions and voltage sensitivity of a KV1 family potassium channel from Polyorchis penicillatus (Eschscholtz 1829). ACTA ACUST UNITED AC 2008; 211:3442-53. [PMID: 18931317 DOI: 10.1242/jeb.022608] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Voltage sensitivity of voltage-gated potassium channels (VKCs) is a primary factor in shaping action potentials in excitable cells. Variation in the amino acid sequence of the channel proteins is responsible for differences in the voltage range over which the channel opens. Thus, understanding how changes in voltage sensitivity are effected by changes in channel protein sequence illuminates the functional evolution of excitability. The K(V)1-family channel jShak1, from the jellyfish Polyorchis penicillatus, differs from most other K(V)1 channels in ways that are useful for studying the problem of how voltage sensitivity is related to channel sequence. We assessed the contributions of changes in sequence of the S4, voltage sensing, helix and changes in one asparagine residue in the S2 helix, to the relative stability of the open and closed states of the channel. Mutation of the neutral S2 residue (Asn227) to glutamate stabilized the open conformation of the channel. Different modifications of charge and length in S4 favoured either the closed conformation or the open conformation. The interactions between pairs of mutations revealed that some of the S4 mutations alter the conformation of the voltage-sensing domain such that the S4 helix is constrained to be closer to the S2 helix than in the wild-type conformation. These results, taken in conjunction with three-dimensional models of the channel, identify intra-molecular interactions that control the balance between open and closed states. These interactions are likely to be relevant to understanding the functional characteristics of members of this channel family from other organisms.
Collapse
Affiliation(s)
- Tara L Klassen
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada T6G 2E9
| | | | | | | | | |
Collapse
|
40
|
Liu YH, Lu FP, Li Y, Wang JL, Gao C. Acid stabilization of Bacillus licheniformis alpha amylase through introduction of mutations. Appl Microbiol Biotechnol 2008; 80:795-803. [DOI: 10.1007/s00253-008-1580-5] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2008] [Revised: 06/13/2008] [Accepted: 06/16/2008] [Indexed: 10/21/2022]
|
41
|
Contreras-Vergara CA, Valenzuela-Soto EM, Arvizu-Flores AA, Sotelo-Mundo RR, Yepiz-Plascencia G. Role of invariant tyrosines in a crustacean mu-class glutathione S-transferase from shrimp Litopenaeus vannamei: site-directed mutagenesis of Y7 and Y116. Biochimie 2008; 90:968-71. [PMID: 18314012 DOI: 10.1016/j.biochi.2008.02.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2007] [Accepted: 02/05/2008] [Indexed: 11/25/2022]
Abstract
Y6 and Y115 are key amino acids involved in enzyme-substrate interactions in mu-class glutathione S-transferase (GST). They provide electrophilic assistance and stabilize substrates through their hydroxyl groups. Two site-directed mutants (Y7F and Y116F) and the wild-type shrimp GSTs were expressed in Escherichia coli, and the steady-state kinetic parameters were determined using CDNB as the second substrate. The mutants were modeled based on a crystal structure of a mu-class GST to obtain further insights about the changes at the active site. The Y116F mutant had an increase in kcat contrary to Y7F compared to the wild type. Molecular modeling showed that the shrimp GST has a H108 residue that may contribute to compensate and lead to a less deleterious change when conserved tyrosine residues are mutated. This work indicates that shrimp GST is a useful model to understand the catalysis mechanisms in this critical enzyme.
Collapse
Affiliation(s)
- Carmen A Contreras-Vergara
- Aquatic Molecular Biology, Centro de Investigación en Alimentación y Desarrollo, Carretera a la Victoria Km 0.6, PO Box 1735, Hermosillo, Sonora 83000, México
| | | | | | | | | |
Collapse
|
42
|
Characterisation of mutagenised acid-resistant alpha-amylase expressed in Bacillus subtilis WB600. Appl Microbiol Biotechnol 2008; 78:85-94. [DOI: 10.1007/s00253-007-1287-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2007] [Revised: 11/11/2007] [Accepted: 11/14/2007] [Indexed: 10/22/2022]
|
43
|
Alyamani EJ, Brandt P, Pena JA, Major AM, Fox JG, Suerbaum S, Versalovic J. Helicobacter hepaticus catalase shares surface-predicted epitopes with mammalian catalases. MICROBIOLOGY-SGM 2007; 153:1006-1016. [PMID: 17379710 DOI: 10.1099/mic.0.29184-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Helicobacter hepaticus colonizes the murine intestine and has been associated with hepatic inflammation and neoplasia in susceptible mouse strains. In this study, the catalase of an enterohepatic Helicobacter was characterized for the first time. H. hepaticus catalase is a highly conserved enzyme that may be important for bacterial survival in the mammalian intestine. Recombinant H. hepaticus catalase was expressed in Escherichia coli in order to verify its enzymic activity in vitro. H. hepaticus catalase comprises 478 amino acids with a highly conserved haem-ligand domain. Three conserved motifs (R-F-Y-D, RERIPER and VVHAKG) in the haem-ligand domain and three surface-predicted motifs were identified in H. hepaticus catalase and are shared among bacterial and mammalian catalases. H. hepaticus catalase is present in the cytoplasmic and periplasmic compartments. Mice infected with H. hepaticus demonstrated immune responses to murine and H. hepaticus catalase, suggesting that Helicobacter catalase contains conserved structural motifs and may contribute to autoimmune responses. Antibodies to H. hepaticus catalase recognized murine hepatocyte catalase in hepatic tissue from infected mice. Antibodies from sera of H. hepaticus-infected mice reacted with peptides comprising two conserved surface-predicted motifs in H. hepaticus catalase. Catalases are highly conserved enzymes in bacteria and mammals that may contribute to autoimmune responses in animals infected with catalase-producing pathogens.
Collapse
Affiliation(s)
- Essam J Alyamani
- Department of Pathology, Texas Children's Hospital, Houston, TX 77030, USA
- Department of Pharmaceutical Sciences, Northeastern University, Boston, MA 01225, USA
| | | | - Jeremy A Pena
- Department of Pathology, Texas Children's Hospital, Houston, TX 77030, USA
| | - Angela M Major
- Department of Pathology, Texas Children's Hospital, Houston, TX 77030, USA
| | - James G Fox
- Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sebastian Suerbaum
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
| | - James Versalovic
- Department of Pathology, Texas Children's Hospital, Houston, TX 77030, USA
- Departments of Pathology, Molecular Virology & Microbiology, and Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| |
Collapse
|
44
|
Jacquot G, Le Rouzic E, David A, Mazzolini J, Bouchet J, Bouaziz S, Niedergang F, Pancino G, Benichou S. Localization of HIV-1 Vpr to the nuclear envelope: impact on Vpr functions and virus replication in macrophages. Retrovirology 2007; 4:84. [PMID: 18039376 PMCID: PMC2211753 DOI: 10.1186/1742-4690-4-84] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2007] [Accepted: 11/26/2007] [Indexed: 12/23/2022] Open
Abstract
Background HIV-1 Vpr is a dynamic protein that primarily localizes in the nucleus, but a significant fraction is concentrated at the nuclear envelope (NE), supporting an interaction between Vpr and components of the nuclear pore complex, including the nucleoporin hCG1. In the present study, we have explored the contribution of Vpr accumulation at the NE to the Vpr functions, including G2-arrest and pro-apoptotic activities, and virus replication in primary macrophages. Results In order to define the functional role of Vpr localization at the NE, we have characterized a set of single-point Vpr mutants, and selected two new mutants with substitutions within the first α-helix of the protein, Vpr-L23F and Vpr-K27M, that failed to associate with hCG1, but were still able to interact with other known relevant host partners of Vpr. In mammalian cells, these mutants failed to localize at the NE resulting in a diffuse nucleocytoplasmic distribution both in HeLa cells and in primary human monocyte-derived macrophages. Other mutants with substitutions in the first α-helix (Vpr-A30L and Vpr-F34I) were similarly distributed between the nucleus and cytoplasm, demonstrating that this helix contains the determinants required for localization of Vpr at the NE. All these mutations also impaired the Vpr-mediated G2-arrest of the cell cycle and the subsequent cell death induction, indicating a functional link between these activities and the Vpr accumulation at the NE. However, this localization is not sufficient, since mutations within the C-terminal basic region of Vpr (Vpr-R80A and Vpr-R90K), disrupted the G2-arrest and apoptotic activities without altering NE localization. Finally, the replication of the Vpr-L23F and Vpr-K27M hCG1-binding deficient mutant viruses was also affected in primary macrophages from some but not all donors. Conclusion These results indicate that the targeting of Vpr to the nuclear pore complex may constitute an early step toward Vpr-induced G2-arrest and subsequent apoptosis; they also suggest that Vpr targeting to the nuclear pore complex is not absolutely required, but can improve HIV-1 replication in macrophages.
Collapse
Affiliation(s)
- Guillaume Jacquot
- Institut Cochin, Université Paris Descartes, CNRS (UMR 8104), Paris, France.
| | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Yoder DW, Kadirjan-Kalbach D, Olson BJSC, Miyagishima SY, Deblasio SL, Hangarter RP, Osteryoung KW. Effects of mutations in Arabidopsis FtsZ1 on plastid division, FtsZ ring formation and positioning, and FtsZ filament morphology in vivo. PLANT & CELL PHYSIOLOGY 2007; 48:775-91. [PMID: 17468127 DOI: 10.1093/pcp/pcm049] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
In plants, chloroplast division FtsZ proteins have diverged into two families, FtsZ1 and FtsZ2. FtsZ1 is more divergent from its bacterial counterparts and lacks a C-terminal motif conserved in most other FtsZs. To begin investigating FtsZ1 structure-function relationships, we first identified a T-DNA insertion mutation in the single FtsZ1 gene in Arabidopsis thaliana, AtFtsZ1-1. Homozygotes null for FtsZ1, though impaired in chloroplast division, could be isolated and set seed normally, indicating that FtsZ1 is not essential for viability. We then mapped five additional atftsZ1-1 alleles onto an FtsZ1 structural model and characterized chloroplast morphologies, FtsZ protein levels and FtsZ filament morphologies in young and mature leaves of the corresponding mutants. atftsZ1-1(G267R), atftsZ1-1(R298Q) and atftsZ1-1(Delta404-433) exhibit reduced FtsZ1 accumulation but wild-type FtsZ2 levels. The semi-dominant atftsZ1-1(G267R) mutation caused the most severe phenotype, altering a conserved residue in the predicted T7 loop. atftsZ1-1(G267R) protein accumulates normally in young leaves but is not detected in rings or filaments. atftsZ1-1(R298Q) has midplastid FtsZ1-containing rings in young leaves, indicating that R298 is not critical for ring formation or positioning despite its conservation. atftsZ1-1(D159N) and atftsZ1-1(G366A) both have overly long, sometimes spiral-like FtsZ filaments, suggesting that FtsZ dynamics are altered in these mutants. However, atftsZ1-1(D159N) exhibits loss of proper midplastid FtsZ positioning while atftsZ1-1(G366A) does not. Finally, truncation of the FtsZ1 C-terminus in atftsZ1-1(Delta404-433) impairs chloroplast division somewhat but does not prevent midplastid Z ring formation. These alleles will facilitate understanding of how the in vitro biochemical properties of FtsZ1 are related to its in vivo function.
Collapse
Affiliation(s)
- David W Yoder
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | | | | | | | | | | | | |
Collapse
|
46
|
Nord D, Torrents E, Sjöberg BM. A functional homing endonuclease in the Bacillus anthracis nrdE group I intron. J Bacteriol 2007; 189:5293-301. [PMID: 17496101 PMCID: PMC1951841 DOI: 10.1128/jb.00234-07] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The essential Bacillus anthracis nrdE gene carries a self-splicing group I intron with a putative homing endonuclease belonging to the GIY-YIG family. Here, we show that the nrdE pre-mRNA is spliced and that the homing endonuclease cleaves an intronless nrdE gene 5 nucleotides (nt) upstream of the intron insertion site, producing 2-nt 3' extensions. We also show that the sequence required for efficient cleavage spans at least 4 bp upstream and 31 bp downstream of the cleaved coding strand. The position of the recognition sequence in relation to the cleavage position is as expected for a GIY-YIG homing endonuclease. Interestingly, nrdE genes from several other Bacillaceae were also susceptible to cleavage, with those of Bacillus cereus, Staphylococcus epidermidis (nrdE1), B. anthracis, and Bacillus thuringiensis serovar konkukian being better substrates than those of Bacillus subtilis, Bacillus lichenformis, and S. epidermidis (nrdE2). On the other hand, nrdE genes from Lactococcus lactis, Escherichia coli, Salmonella enterica serovar Typhimurium, and Corynebacterium ammoniagenes were not cleaved. Intervening sequences (IVSs) residing in protein-coding genes are often found in enzymes involved in DNA metabolism, and the ribonucleotide reductase nrdE gene is a frequent target for self-splicing IVSs. A comparison of nrdE genes from seven gram-positive low-G+C bacteria, two bacteriophages, and Nocardia farcinica showed five different insertion sites for self-splicing IVSs within the coding region of the nrdE gene.
Collapse
Affiliation(s)
- David Nord
- Department of Molecular Biology and Functional Genomics, Stockholm University, SE-10691 Stockholm, Sweden
| | | | | |
Collapse
|
47
|
Hodis E, Schreiber G, Rother K, Sussman JL. eMovie: a storyboard-based tool for making molecular movies. Trends Biochem Sci 2007; 32:199-204. [PMID: 17448663 DOI: 10.1016/j.tibs.2007.03.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2007] [Revised: 03/02/2007] [Accepted: 03/27/2007] [Indexed: 11/20/2022]
Abstract
The 3D structures of macromolecules are difficult to grasp and also to communicate. By their nature, movies or animations are particularly useful for highlighting key features by offering a 'guided tour' of structures and conformation changes. However, high-quality movies are rarely seen because they are currently difficult and time consuming to make. By adopting the traditional movie 'storyboard' concept, which gives guidance and direction to filming, eMovie makes the creation of lengthy molecular animations much easier. This tool is a plug-in for the open-source molecular graphics program PyMOL, and enables experts and novices alike to produce informative and high-quality molecular animations.
Collapse
Affiliation(s)
- Eran Hodis
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 76100, Israel
| | | | | | | |
Collapse
|
48
|
Ruike T, Takeuchi R, Takata KI, Oshige M, Kasai N, Shimanouchi K, Kanai Y, Nakamura R, Sugawara F, Sakaguchi K. Characterization of a second proliferating cell nuclear antigen (PCNA2) from Drosophila melanogaster. FEBS J 2007; 273:5062-73. [PMID: 17087725 DOI: 10.1111/j.1742-4658.2006.05504.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The eukaryotic DNA polymerase processivity factor, proliferating cell nuclear antigen, is an essential component in the DNA replication and repair machinery. In Drosophila melanogaster, we cloned a second PCNA cDNA that differs from that encoded by the gene mus209 (for convenience called DmPCNA1 in this article). The second PCNA cDNA (DmPCNA2) encoded a 255 amino acid protein with 51.7% identity to DmPCNA1, and was ubiquitously expressed during Drosophila development. DmPCNA2 was localized in nuclei as a homotrimeric complex and associated with Drosophila DNA polymerase delta and epsilonin vivo. Treatment of cells with methyl methanesulfonate or hydrogen peroxide increased the amount of both DmPCNA2 and DmPCNA1 associating with chromatin, whereas exposure to UV light increased the level of association of only DmPCNA1. Our observations suggest that DmPCNA2 may function as an independent sliding clamp of DmPCNA1 when DNA repair occurs.
Collapse
Affiliation(s)
- Tatsushi Ruike
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Japan
| | | | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Ranjbar S, Rajsbaum R, Goldfeld AE. Transactivator of transcription from HIV type 1 subtype E selectively inhibits TNF gene expression via interference with chromatin remodeling of the TNF locus. THE JOURNAL OF IMMUNOLOGY 2006; 176:4182-90. [PMID: 16547255 DOI: 10.4049/jimmunol.176.7.4182] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The transactivator of transcription (Tat) protein is essential for efficient HIV type 1 (HIV-1) replication and is involved in the transcriptional regulation of the host immune response gene, TNF. In this study, we demonstrate that Tat proteins from representative HIV-1 subtype E isolates, but not from subtypes B or C, selectively inhibit TNF gene transcription and protein production in CD4(+) Jurkat T cells. Strikingly, we show that this repression is due to a tryptophan at residue 32 of Tat E and is secondary to interference with recruitment of the histone acetyltransferase P/CAF to the TNF promoter and with chromatin remodeling of the TNF locus. This study presents a novel mechanism by which HIV-1 manipulates a host immune response gene that is important in its own replication. Moreover, these results demonstrate a new mechanism by which the TNF gene is regulated via chromatin remodeling secondary to viral infection.
Collapse
Affiliation(s)
- Shahin Ranjbar
- CBR Institute for Biomedical Research, Harvard Medical School, Boston, MA 02115, USA
| | | | | |
Collapse
|
50
|
Liao WQ, Liang XF, Wang L, Lei LM, Han BP. Molecular cloning and characterization of alpha-class glutathioneS-transferase gene from the liver of silver carp, bighead carp, and other major chinese freshwater fishes. J Biochem Mol Toxicol 2006; 20:114-26. [PMID: 16788955 DOI: 10.1002/jbt.20125] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Two full-length cDNAs encoding glutathione S-transferase (GST) were cloned and sequenced from the hepatopancreas of planktivorous silver carp (Hypophthalmichthys molitrix) and bighead carp (Aristichthys nobilis). The silver carp and bighead carp GST cDNA were 920 and 978 bp in length, respectively, and both contained an open reading frame that encoding 223 amino acids. Partial GST cDNA sequences were also obtained from the liver of grass carp (Ctenopharyngodon idellus), crucian carp (Carassius auratu), mud carp (Cirrhinus molitorella), and tilapia (Oreochromis nilotica). All these GSTs could be classified as alpha-class GSTs on the basis of their amino acid sequence identity with other species. The three-dimensional structure of the silver carp GST was predicted using a computer program, and was found to fit the classical two-domain GST structure. Using the genome walker method, a 875-bp 5'-flanking region of the silver carp GST gene was obtained, and several lipopolysaccharide (LPS) response elements were identified in the promoter region of the phytoplanktivorous fish GST gene, indicating that the GST gene expression of this fish might be regulated by LPS, released from the toxic blue-green algae producing microcystins. To compare the constitutive expression level of the liver GST gene among the six freshwater fishes with completely different tolerance to microcystins, beta-actin was used as control and the ratio GST/beta-actin mRNA (%) was determined as 130.7 +/- 6.6 (grass carp), 103.1 +/- 8.9 (bighead carp), 92.6 +/- 15.0 (crucian carp), 72.3 +/- 7.8 (mud carp), 58.8 +/- 11.5 (silver carp), and 33.6 +/- 13.7 (tilapia). The constitutive expression level of the liver GST gene clearly shows that all the six freshwater fishes had a negative relationship with their tolerance to microcystins: high-resistant fishes (phytoplanktivorous silver carp and tilapia) had the lowest tolerance to microcystins and the high-sensitive fish (herbivorous grass carp) had the highest tolerance to microcystins. Taken together with the reciprocal relationship of constitutive and inducible liver GST expression level in some of the tested fish species to microcystin exposure, a molecular mechanism for different microcystin detoxification abilities of the warm freshwater fishes was discussed.
Collapse
Affiliation(s)
- Wan-Qin Liao
- College of Life Science and Technology, Jinan University, Shipai, Guangzhou 510632, People's Republic of China
| | | | | | | | | |
Collapse
|