99951
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Abstract
Background Target-primed (non-LTR) retrotransposons, such as the human L1 element, are mobile genetic elements found in many eukaryotic genomes. They are often present in large numbers and their retrotransposition can cause mutations and genomic rearrangements. Despite their importance, many aspects of their replication are not well understood. Results We have developed a yeast model system for studying target-primed retrotransposons. This system uses the Zorro3 element from Candida albicans. A cloned copy of Zorro3, tagged with a retrotransposition indicator gene, retrotransposes at a high frequency when introduced into an appropriate C. albicans host strain. Retrotransposed copies of the tagged element exhibit similar features to the native copies, indicating that the natural retrotransposition pathway is being used. Retrotransposition is dependent on the products of the tagged element's own genes and is highly temperature-regulated. The new assay permits the analysis of the effects of specific mutations introduced into the cloned element. Conclusion This Zorro3 retrotransposition assay system complements previously available target-primed retrotransposition assays. Due to the relative simplicity of the growth, manipulation and analysis of yeast cells, the system should advance our understanding of target-primed retrotransposition.
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Affiliation(s)
| | - Jason N Busby
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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99952
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Zheng D, Frankish A, Baertsch R, Kapranov P, Reymond A, Choo SW, Lu Y, Denoeud F, Antonarakis SE, Snyder M, Ruan Y, Wei CL, Gingeras TR, Guigó R, Harrow J, Gerstein MB. Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Res 2007; 17:839-51. [PMID: 17568002 PMCID: PMC1891343 DOI: 10.1101/gr.5586307] [Citation(s) in RCA: 131] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Arising from either retrotransposition or genomic duplication of functional genes, pseudogenes are "genomic fossils" valuable for exploring the dynamics and evolution of genes and genomes. Pseudogene identification is an important problem in computational genomics, and is also critical for obtaining an accurate picture of a genome's structure and function. However, no consensus computational scheme for defining and detecting pseudogenes has been developed thus far. As part of the ENCyclopedia Of DNA Elements (ENCODE) project, we have compared several distinct pseudogene annotation strategies and found that different approaches and parameters often resulted in rather distinct sets of pseudogenes. We subsequently developed a consensus approach for annotating pseudogenes (derived from protein coding genes) in the ENCODE regions, resulting in 201 pseudogenes, two-thirds of which originated from retrotransposition. A survey of orthologs for these pseudogenes in 28 vertebrate genomes showed that a significant fraction ( approximately 80%) of the processed pseudogenes are primate-specific sequences, highlighting the increasing retrotransposition activity in primates. Analysis of sequence conservation and variation also demonstrated that most pseudogenes evolve neutrally, and processed pseudogenes appear to have lost their coding potential immediately or soon after their emergence. In order to explore the functional implication of pseudogene prevalence, we have extensively examined the transcriptional activity of the ENCODE pseudogenes. We performed systematic series of pseudogene-specific RACE analyses. These, together with complementary evidence derived from tiling microarrays and high throughput sequencing, demonstrated that at least a fifth of the 201 pseudogenes are transcribed in one or more cell lines or tissues.
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Affiliation(s)
- Deyou Zheng
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
- Corresponding authors.E-mail ; fax (360) 838-7861.E-mail ; fax (360) 838-7861
| | - Adam Frankish
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1HH, United Kingdom
| | - Robert Baertsch
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, California 95064, USA
| | | | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
| | - Siew Woh Choo
- Genome Institute of Singapore, Singapore 138672, Singapore
| | - Yontao Lu
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, California 95064, USA
| | - France Denoeud
- Grup de Recerca en Informática Biomèdica, Institut Municipal d’Investigació Mèdica/Universitat Pompeu Fabra, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Catalonia, Spain
| | - Stylianos E. Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
| | - Michael Snyder
- Molecular, Cellular & Developmental Biology Department, Yale University, New Haven, Connecticut 06520, USA
| | - Yijun Ruan
- Genome Institute of Singapore, Singapore 138672, Singapore
| | - Chia-Lin Wei
- Genome Institute of Singapore, Singapore 138672, Singapore
| | | | - Roderic Guigó
- Grup de Recerca en Informática Biomèdica, Institut Municipal d’Investigació Mèdica/Universitat Pompeu Fabra, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Catalonia, Spain
- Center for Genomic Regulation, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Catalonia, Spain
| | - Jennifer Harrow
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1HH, United Kingdom
| | - Mark B. Gerstein
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
- Department of Computer Science, Yale University, New Haven, Connecticut 06520, USA
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA
- Corresponding authors.E-mail ; fax (360) 838-7861.E-mail ; fax (360) 838-7861
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99953
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Lee JA, Beigneux A, Ahmad ST, Young SG, Gao FB. ESCRT-III dysfunction causes autophagosome accumulation and neurodegeneration. Curr Biol 2007; 17:1561-7. [PMID: 17683935 DOI: 10.1016/j.cub.2007.07.029] [Citation(s) in RCA: 365] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2007] [Revised: 07/13/2007] [Accepted: 07/16/2007] [Indexed: 12/12/2022]
Abstract
Defects in the endosomal-lysosomal pathway have been implicated in a number of neurodegenerative disorders. A key step in the endocytic regulation of transmembrane proteins occurs in a subset of late-endosomal compartments known as multivesicular bodies (MVBs), whose formation is controlled by endosomal sorting complex required for transport (ESCRT). The roles of ESCRT in dendritic maintenance and neurodegeneration remain unknown. Here, we show that mSnf7-2, a key component of ESCRT-III, is highly expressed in most mammalian neurons. Loss of mSnf7-2 in mature cortical neurons caused retraction of dendrites and neuronal cell loss. mSnf7-2 binds to CHMP2B, another ESCRT-III subunit, in which a rare dominant mutation is associated with frontotemporal dementia linked to chromosome 3 (FTD3). Ectopic expression of the mutant protein CHMP2B(Intron5) also caused dendritic retraction prior to neurodegeneration. CHMP2B(Intron5) was associated more avidly than CHMP2B(WT) with mSnf7-2, resulting in sequestration of mSnf7-2 in ubiquitin-positive late-endosomal vesicles in cortical neurons. Moreover, loss of mSnf7-2 or CHMP2B(Intron5) expression caused the accumulation of autophagosomes in cortical neurons and flies. These findings indicate that ESCRT-III dysfunction is associated with the autophagy pathway, suggesting a novel neurodegeneration mechanism that may have important implications for understanding FTD and other age-dependent neurodegenerative diseases.
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Affiliation(s)
- Jin-A Lee
- Gladstone Institute of Neurological Disease and Department of Neurology, University of California, San Francisco, California 94158, USA
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99954
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Abstract
The biogenesis of mitochondria depends on the coordinated expression of nuclear and mitochondrial genomes. Consequently, the control of mitochondrial biogenesis and function depends on extremely complex processes requiring a variety of well orchestrated regulatory mechanisms. It is clear that the interplay of transcription factors and coactivators contributes to the expression of both nuclear and mitochondrial respiratory genes. In addition, the regulation of mitochondria biogenesis depends on proteins that, interacting with messenger RNAs for mitochondrial proteins, influence their metabolism and expression. Moreover, a tight regulation of the import and final assembly of mitochondrial protein is essential to endow mitochondria with functional complexes. These studies represent the basis for understanding the mechanisms involved in the nucleus-mitochondrion communication, a cross-talk essential for the cell.
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Affiliation(s)
- G Cannino
- Dipartimento di Biologia Cellulare e dello Sviluppo A.Monroy, University of Palermo, Italy
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99955
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Rensing SA, Ick J, Fawcett JA, Lang D, Zimmer A, Van de Peer Y, Reski R. An ancient genome duplication contributed to the abundance of metabolic genes in the moss Physcomitrella patens. BMC Evol Biol 2007; 7:130. [PMID: 17683536 PMCID: PMC1952061 DOI: 10.1186/1471-2148-7-130] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2007] [Accepted: 08/02/2007] [Indexed: 11/13/2022] Open
Abstract
Background: Analyses of complete genomes and large collections of gene transcripts have shown that most, if not all seed plants have undergone one or more genome duplications in their evolutionary past. Results: In this study, based on a large collection of EST sequences, we provide evidence that the haploid moss Physcomitrella patens is a paleopolyploid as well. Based on the construction of linearized phylogenetic trees we infer the genome duplication to have occurred between 30 and 60 million years ago. Gene Ontology and pathway association of the duplicated genes in P. patens reveal different biases of gene retention compared with seed plants. Conclusion: Metabolic genes seem to have been retained in excess following the genome duplication in P. patens. This might, at least partly, explain the versatility of metabolism, as described for P. patens and other mosses, in comparison to other land plants.
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Affiliation(s)
- Stefan A Rensing
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, D-79104 Freiburg, Germany
| | - Julia Ick
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, D-79104 Freiburg, Germany
| | - Jeffrey A Fawcett
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium
- Bioinformatics and Evolutionary Genomics, Department of Molecular Genetics, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium
| | - Daniel Lang
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, D-79104 Freiburg, Germany
| | - Andreas Zimmer
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, D-79104 Freiburg, Germany
| | - Yves Van de Peer
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium
- Bioinformatics and Evolutionary Genomics, Department of Molecular Genetics, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, D-79104 Freiburg, Germany
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99956
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Richardson MK, Crooijmans RPMA, Groenen MAM. Sequencing and genomic annotation of the chicken (Gallus gallus) Hox clusters, and mapping of evolutionarily conserved regions. Cytogenet Genome Res 2007; 117:110-9. [PMID: 17675851 DOI: 10.1159/000103171] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2006] [Accepted: 09/29/2006] [Indexed: 11/19/2022] Open
Abstract
Hox genes encode transcription factors that are involved in the regulation of normal development and are mutated in some diseases and malformations. Chicken HOX genes have been extensively studied in the chick limb and other developmental models. To date while the chicken HOXA cluster has been completely sequenced many other chicken HOX genes are known only from partial mRNAs or unfinished genome assemblies. Furthermore, although a finished sequence of the HOXA cluster is available, the sequence has not yet been annotated. We have therefore manually annotated the available HOX sequences and improved the sequences by sequencing PCR fragments that bridge existing gaps in the genome sequences. These sequences complement the published sequences, including the currently incomplete WashUC Gallus_gallus-2.1 build, to give an improved coverage of the cluster. We used phylogenetic footprinting to map the genomic location of 398 Ultra Conserved Regions in the HOX complex 248 of which do not overlap with any known annotated coding exon. These included the hox-related microRNAs miR-10 and miR-196. The chicken HOX clusters appear to be broadly comparable to their human counterparts. A few human orthologues were not recovered from the chicken, presumably because of incomplete sequence.
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Affiliation(s)
- M K Richardson
- Department of Integrative Zoology, Institute of Biology, Leiden University, Leiden, The Netherlands
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99957
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Abstract
In mammals, dosage compensation is achieved by transcriptional silencing of one of the two female X chromosomes. X inactivation is dynamically regulated in development. The non-coding Xist RNA localizes to the inactive X, initiates gene repression in the early embryo, and later stabilizes the inactive state. Different functions of Xist are observed depending on which epigenetic regulatory pathways are active in a given cell. Because Xist has evolved recently, with the origin of placental mammals, the underlying pathways are also important in regulating developmental control genes. This review emphasizes the opportunity that Xist provides to functionally define epigenetic transitions in development, to understand cell identity, pluripotency and stem cell differentiation.
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Affiliation(s)
- Anton Wutz
- Research Institute of Molecular Pathology, Dr. Bohr-Gasse 7, 1030 Vienna, Austria.
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99958
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Abstract
Three protease mutants--7 (tap-), 12 (tap-, ssp-), and 17 (multiple mutations)--of Streptomyces lividans were tested for their influence on protein secretion. Streptomyces lividans grown in xylan secretes 3 xylanases (A, B, and C). Xylanases A (XlnA) and B (XlnB) are secreted by the Sec pathway, whereas xylanase C (XlnC) is secreted by the Tat pathway. The production of XlnA and XlnC was affected in the mutants, suggesting that the mutations interfered with both Sec- and Tat-secretion systems. However, the processing rate for the Sec and Tat precursor was similar to the wild-type strain, indicating that the mutations had no direct effect on secretion. Streptomyces lividans naturally produced 2 forms of XlnB: XlnB1, which contains the catalytic and the xylan-binding domains, and XlnB2, which contains the catalytic domain only. There was no change from the wild-type strain in the ratio of XlnB1/XlnB2 produced by the mutants, indicating that these proteases are not involved in this process. Although XlnA1, partially truncated in its xylan-binding domain, was rapidly degraded to its catalytic domain (XlnA2) in the wild-type strain, the rate of conversion was reduced in the 3 mutants, indicating that the proteases participated to some extent in this proteolytic process.
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Affiliation(s)
- Eliana Arias
- INRS - Institut Armand-Frappier, Université du Québec, 531 boulevard des Prairies, Laval, QC H7V 1B7, Canada
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99959
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Grueber CE, Jamieson IG. Quantifying and managing the loss of genetic variation in a free-ranging population of takahe through the use of pedigrees. CONSERV GENET 2008; 9:645-51. [DOI: 10.1007/s10592-007-9390-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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99960
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Pérez C, Muñoz-Garay C, Portugal LC, Sánchez J, Gill SS, Soberón M, Bravo A. Bacillus thuringiensis ssp. israelensis Cyt1Aa enhances activity of Cry11Aa toxin by facilitating the formation of a pre-pore oligomeric structure. Cell Microbiol 2007; 9:2931-7. [PMID: 17672866 PMCID: PMC3700374 DOI: 10.1111/j.1462-5822.2007.01007.x] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bacillus thuringiensis ssp. israelensis (Bti) has been used worldwide for the control of dipteran insect pests. This bacterium produces several Cry and Cyt toxins that individually show activity against mosquitoes but together show synergistic effect. Previous work demonstrated that Cyt1Aa synergizes the toxic activity of Cry11Aa by functioning as a membrane-bound receptor. In the case of Cry toxins active against lepidopteran insects, receptor interaction triggers the formation of a pre-pore oligomer that is responsible for pore formation and toxicity. In this work we report that binding of Cry11Aa to Cyt1Aa facilitates the formation of a Cry11Aa pre-pore oligomeric structure that is capable of forming pores in membrane vesicles. Cry11Aa and Cyt1A point mutants affected in binding and in synergism had a correlative effect on the formation of Cry11Aa pre-pore oligomer and on pore-formation activity of Cry11Aa. These data further support that Cyt1Aa interacts with Cry11Aa and demonstrate the molecular mechanism by which Cyt1Aa synergizes or suppresses resistance to Cry11Aa, by providing a binding site for Cry11Aa that will result in an efficient formation of Cry11Aa pre-pore that inserts into membranes and forms ionic pores.
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Affiliation(s)
- Claudia Pérez
- Instituto de Biotecnología, Universidad Nacional Autónoma de México. Apdo. postal 510-3, Cuernavaca 62250, Morelos, Mexico
| | - Carlos Muñoz-Garay
- Instituto de Biotecnología, Universidad Nacional Autónoma de México. Apdo. postal 510-3, Cuernavaca 62250, Morelos, Mexico
| | - Leivi C. Portugal
- Instituto de Biotecnología, Universidad Nacional Autónoma de México. Apdo. postal 510-3, Cuernavaca 62250, Morelos, Mexico
| | - Jorge Sánchez
- Instituto de Biotecnología, Universidad Nacional Autónoma de México. Apdo. postal 510-3, Cuernavaca 62250, Morelos, Mexico
| | - Sarjeet S. Gill
- Department of Cell Biology and Neuroscience, University of California, Riverside, CA 92506, USA
| | - Mario Soberón
- Instituto de Biotecnología, Universidad Nacional Autónoma de México. Apdo. postal 510-3, Cuernavaca 62250, Morelos, Mexico
| | - Alejandra Bravo
- Instituto de Biotecnología, Universidad Nacional Autónoma de México. Apdo. postal 510-3, Cuernavaca 62250, Morelos, Mexico
- For correspondence. ; Tel. (+52) 777 3291635; Fax (+52) 777 3291624
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99961
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Shimada K, Valdez MB, Mizutani M, Namikawa T. Potential application of sperm bearing female-specific chromosome in chickens. Cytogenet Genome Res 2007; 117:240-7. [PMID: 17675865 DOI: 10.1159/000103185] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2006] [Accepted: 09/10/2006] [Indexed: 11/19/2022] Open
Abstract
This paper reviews studies on sex reversal experiments in chickens, production of sperm bearing a female-specific chromosome, its application for poultry resources and finally a mechanism of sex differentiation of gonads in the chicken.
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Affiliation(s)
- K Shimada
- Division of Applied Genetics and Physiology, Graduate School of Bioagricultural Science, Nagoya University Chikusa, Nagoya, Japan.
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99962
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Dobeš C, Sharbel TF, Koch M. Towards understanding the dynamics of hybridization and apomixis in the evolution of the genus Boechera (Brassicaceae). SYST BIODIVERS 2007; 5:321-31. [DOI: 10.1017/s1477200007002423] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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99963
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Stevanin TM, Read RC, Poole RK. The hmp gene encoding the NO-inducible flavohaemoglobin in Escherichia coli confers a protective advantage in resisting killing within macrophages, but not in vitro: Links with swarming motility. Gene 2007; 398:62-8. [PMID: 17611046 DOI: 10.1016/j.gene.2007.03.021] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2006] [Revised: 02/25/2007] [Accepted: 03/01/2007] [Indexed: 11/30/2022]
Abstract
Escherichia coli flavohaemoglobin (Hmp) is the best-understood nitric oxide (NO) detoxifying protein and exhibits a robust dioxygenase activity, converting NO to nitrate ion with oxygen as co-substrate. Synthesis of Hmp via transcriptional regulation of hmp gene expression is an adaptive response to NO and related nitrosative stresses since Hmp levels are greatly elevated on exposure in vitro to these agents. Here we show that expression of hmp is greatly enhanced by NO but not by other haem ligands (azide, cyanide and carbon monoxide). Flavohaemoglobins of other pathogenic bacteria have been implicated in conferring resistance to NO in vitro and in macrophage-like cells but the role of the E. coli flavohaemoglobin has not been studied in macrophages. We therefore compared survival of wild-type K-12 E. coli cells and an isogenic hmp mutant after internalisation by human macrophages. Wild-type bacteria survived significantly better than the hmp mutant after incubation with macrophages, despite binding and internalisation rates being similar for both strains. Unexpectedly, however, when grown in MOPS minimal medium, in mixed cultures, more hmp mutant cells were recovered than wild-type. Significantly, an hmp mutant failed to exhibit swarming motility on soft agar and this phenotype was rescued by a plasmid-borne copy of the wild-type hmp(+) gene. Thus, although Hmp constitutes an important mechanism of protection from NO-mediated killing by human macrophages in the model E. coli strain K-12, and probably contributes to the survival of enteropathogenic E. coli during the intestinal inflammatory response, synthesis of Hmp in vitro may represent a selective disadvantage. The lack of swarming motility of the hmp mutant and its aflagellate state suggest that Hmp synthesis is a metabolic burden in the absence of NO-related stresses.
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Affiliation(s)
- Tânia M Stevanin
- The University of Sheffield, Division of Genomic Medicine, Beech Hill Road, Sheffield, S10 2RX, UK
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99964
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Watkins KP, Kroeger TS, Cooke AM, Williams-Carrier RE, Friso G, Belcher SE, van Wijk KJ, Barkan A. A ribonuclease III domain protein functions in group II intron splicing in maize chloroplasts. Plant Cell 2007; 19:2606-23. [PMID: 17693527 PMCID: PMC2002627 DOI: 10.1105/tpc.107.053736] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Chloroplast genomes in land plants harbor approximately 20 group II introns. Genetic approaches have identified proteins involved in the splicing of many of these introns, but the proteins identified to date cannot account for the large size of intron ribonucleoprotein complexes and are not sufficient to reconstitute splicing in vitro. Here, we describe an additional protein that promotes chloroplast group II intron splicing in vivo. This protein, RNC1, was identified by mass spectrometry analysis of maize (Zea mays) proteins that coimmunoprecipitate with two previously identified chloroplast splicing factors, CAF1 and CAF2. RNC1 is a plant-specific protein that contains two ribonuclease III (RNase III) domains, the domain that harbors the active site of RNase III and Dicer enzymes. However, several amino acids that are essential for catalysis by RNase III and Dicer are missing from the RNase III domains in RNC1. RNC1 is found in complexes with a subset of chloroplast group II introns that includes but is not limited to CAF1- and CAF2-dependent introns. The splicing of many of the introns with which it associates is disrupted in maize rnc1 insertion mutants, indicating that RNC1 facilitates splicing in vivo. Recombinant RNC1 binds both single-stranded and double-stranded RNA with no discernible sequence specificity and lacks endonuclease activity. These results suggest that RNC1 is recruited to specific introns via protein-protein interactions and that its role in splicing involves RNA binding but not RNA cleavage activity.
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Affiliation(s)
- Kenneth P Watkins
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
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99965
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99966
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Takasu M, Hayashi R, Maruya E, Ota M, Imura K, Kougo K, Kobayashi C, Saji H, Ishikawa Y, Asai T, Tokunaga K. Deletion of entire HLA-A gene accompanied by an insertion of a retrotransposon. ACTA ACUST UNITED AC 2007; 70:144-50. [PMID: 17610419 DOI: 10.1111/j.1399-0039.2007.00870.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Unusual HLA-A'null' alleles because of an entire gene deletion were found in three apparently unrelated Japanese families with leukemia patients. Inclusion of the entire HLA-A gene in the deletion was confirmed by polymerase chain reaction direct sequencing of the surrounding regions of HLA-A. Further localization of the breakpoints of the HLA-A deletion at the centromeric and telomeric sides was performed, and these families were shown to possess the identical deletion. We then determined the genomic sequence of the HLA-A-deleted haplotype. Surprisingly, the haplotype turned out to carry an insertion of an SVA (SINE-VNTR-Alu) retrotransposon of 2 kb as well as the 14 kb deletion that included the entire HLA-A gene.
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Affiliation(s)
- M Takasu
- Department of Human Genetics, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
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99967
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Abstract
An increased DNA-repair activity in tumour cells has been associated with resistance to treatment to DNA-directed drugs, while defects in DNA repair pathways result in hypersensitivity to these agents. In the past years the unravelling of the molecular basis of these DNA pathways, with a better understanding of the DNA damage caused by different anticancer agents, has provided the rationale for the use of some DNA repair inhibitors to optimise the therapeutic use of DNA-damaging agents currently used in the treatment of tumours. In addition, the possibility to specifically target the differences in DNA repair capacity between normal and tumour cells has recently emerged as an exciting possibility. The present review will mainly cover those approaches that are currently under clinical investigation.
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Affiliation(s)
- Giovanna Damia
- Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri, Via Eritrea 62, 20157 Milan, Italy
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99968
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Yuan Z, Zhang X, Sengupta N, Lane WS, Seto E. SIRT1 regulates the function of the Nijmegen breakage syndrome protein. Mol Cell 2007; 27:149-62. [PMID: 17612497 PMCID: PMC2679807 DOI: 10.1016/j.molcel.2007.05.029] [Citation(s) in RCA: 222] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2006] [Revised: 03/22/2007] [Accepted: 05/25/2007] [Indexed: 01/21/2023]
Abstract
MRE11-RAD50-NBS1 (MRN) is a conserved nuclease complex that exhibits properties of a DNA damage sensor and is critical in regulating cellular responses to DNA double-strand breaks. NBS1, which is mutated in the human genetic disease Nijmegen breakage syndrome, serves as the regulatory subunit of MRN. Phosphorylation of NBS1 by the ATM kinase is necessary for both activation of the S phase checkpoint and for efficient DNA damage repair response. Here, we report that NBS1 is an acetylated protein and that the acetylation level is tightly regulated by the SIRT1 deacetylase. SIRT1 associates with the MRN complex and, importantly, maintains NBS1 in a hypoacetylated state, which is required for ionizing radiation-induced NBS1 Ser343 phosphorylation. Our results demonstrate the presence of crosstalk between two different posttranslational modifications in NBS1 and strongly suggest that deacetylation of NBS1 by SIRT1 plays a key role in the dynamic regulation of the DNA damage response and in the maintenance of genomic stability.
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Affiliation(s)
- Zhigang Yuan
- H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612, USA
| | - Xiaohong Zhang
- H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612, USA
| | - Nilanjan Sengupta
- H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612, USA
| | - William S. Lane
- Microchemistry and Proteomics Analysis Facility, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Edward Seto
- H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612, USA
- Correspondence:
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99969
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Dermyer M, Wise SC, Braden T, Holler TP. Simultaneous Screening of Multiple Bacterial tRNA Synthetases Using an Escherichia coli S30-Based Transcription and Translation Assay. Assay Drug Dev Technol 2007; 5:515-21. [PMID: 17767419 DOI: 10.1089/adt.2007.061] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The search for novel antibiotics to combat the growing threat of resistance has led researchers to screen libraries with coupled transcription and translation systems. In these systems, a bacterial cell lysate supplies the proteins necessary for transcription and translation, a plasmid encoding a reporter protein is added as a template, and a complex mixture of amino acids and cofactors is added to supply building blocks and energy to the assay. Firefly luciferase is typically used as the reporter protein in high-throughput screens because the luminescent signal is strong and, since bacterial lysates contain no luciferase, the background is negligible. The typical coupled transcription and translation assay is sensitive to inhibitors of RNA polymerase and to compounds that bind tightly to the ribosome. We have found a way to increase the information content of the screen by making the assay more sensitive to inhibitors of tRNA synthetases. Restricting the concentration of amino acids added to the reaction mixture allows the simultaneous screening of multiple tRNA synthetase enzymes along with the classic transcription and translation targets. In addition, this assay can be used as a convenient way to determine if an antibacterial compound of unknown mechanism inhibits translation through inhibition of a tRNA synthetase, and to identify which synthetase is the target.
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Affiliation(s)
- Michael Dermyer
- Pfizer Global Research and Development, Michigan Laboratories, Arbor, MI 48105, USA
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99970
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Yevdakova NA, von Schwartzenberg K. Characterisation of a prokaryote-type tRNA-isopentenyltransferase gene from the moss Physcomitrella patens. Planta 2007; 226:683-95. [PMID: 17450376 DOI: 10.1007/s00425-007-0516-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2006] [Accepted: 03/16/2007] [Indexed: 05/15/2023]
Abstract
Cytokinins are of critical importance to numerous developmental processes in plants. Two cytokinin biosynthetic pathways have been described; each one uses a different type of isopentenyltransferases (IPTs) as the key enzyme. In the first pathway, adenylate-IPTs (EC 2.5.1.27) prenylate adenylic nucleotides to cytokinin nucleotides, thus catalysing the direct de novo biosynthesis of free cytokinins. In the second pathway, tRNA-IPTs (EC 2.5.1.8) catalyse cytokinin formation by isopentenylation of tRNA, the degradation of which liberates cytokinin nucleotides. Seed plants have been shown to possess both forms of IPTs. Here, we report on the in-silico based identification and on the functional characterisation of an IPT encoding gene (PpIPT1) from the bryophyte Physcomitrella patens. Analysis of the PpIPT1 amino acid sequence revealed high similarities to tRNA-IPTs of other plants. No adenylate-IPT genes were found in the Physcomitrella sequenced transcriptome/genome. PpIPT1 functionally complemented a defective tRNA-IPT gene of Saccharomyces cerevisiae (ScMOD5) in the strain MT-8. Dephosphorylated tRNA hydrolysates from PpIPT1-transformed MT-8 showed cytokinin activity in a moss bioassay and the presence of isopentenyladenosine in HPLC analysis, in contrast to those prepared from untransformed MT-8. A comparison of pro- and eukaryotic homologues revealed two classes of tRNA-IPTs; PpIPT1 belongs to a prokaryotic type with predicted chloroplast targeting. RT-PCR experiments revealed a stronger expression in the cytokinin overproducing mutant oveST25, thus indicating the potential role of PpIPT1 for cytokinin biosynthesis in the evolutionary old land plant Physcomitrella.
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Affiliation(s)
- Natalya A Yevdakova
- Biocenter Klein Flottbek and Botanical Garden, University of Hamburg, Ohnhorst street 18, 22609 Hamburg, Germany
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99971
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Sutherland A, Davies J, Owen CJ, Vaikkakara S, Walker C, Cheetham TD, James RA, Perros P, Donaldson PT, Cordell HJ, Quinton R, Pearce SHS. Genomic polymorphism at the interferon-induced helicase (IFIH1) locus contributes to Graves' disease susceptibility. J Clin Endocrinol Metab 2007; 92:3338-41. [PMID: 17535987 PMCID: PMC6952273 DOI: 10.1210/jc.2007-0173] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
CONTEXT A recent large-scale analysis of nonsynonymous coding polymorphisms showed strong evidence that an alanine to threonine amino acid change at codon 946 of the interferon-induced helicase (IFIH1) gene (SNP ID rs1990760) was associated with type 1 diabetes. Previous investigations have also demonstrated that an intronic polymorphism (termed PD1.3; SNP ID rs11568821) in the programmed cell death (PDCD1) gene was associated with systemic lupus erythematosus and rheumatoid arthritis. OBJECTIVE We sought to replicate these genetic associations in Graves' disease and autoimmune Addison's disease patient cohorts. PATIENTS AND METHODS A total of 602 Graves' disease subjects, 214 Addison's disease subjects, and 446 healthy controls were genotyped for the IFIH1 and PDCD1 single-nucleotide polymorphisms using mass spectrometer analysis of primer extension products (Sequenom). RESULTS The alanine-carrying allele at the IFIH1 codon 946 polymorphism was present in 796 of 1204 (66%) Graves' disease patient alleles compared with 508 of 892 (57%) control subject alleles [odds ratio 1.47 (5-95% confidence interval, 1.23-1.76); P = 1.9 x 10(-5)]. In contrast, there was no association of alleles at this marker in autoimmune Addison's disease. Neither was there evidence for association in either patient cohort at the PD1.3 polymorphism. CONCLUSIONS We confirm a significant contribution of the Ala946Thr IFIH1 polymorphism to organ-specific autoimmune diseases, extending the range of conditions associated with this variant to include Graves' disease. This polymorphism may also contribute to several other autoimmune disorders.
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Affiliation(s)
- Alison Sutherland
- Institute of Human Genetics, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom
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99972
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Gómez-Arroyo S, Cortés-Eslava J, Villalobos-Pietrini R, Calderón-Segura ME, Flores-Márquez AR, Espinosa-Aguirre JJ. Differential mutagenic response of Salmonella typhimurium to the plant-metabolized organophosphorus insecticides, phoxim and azinphos methyl. Toxicol In Vitro 2007; 21:950-5. [PMID: 17383850 DOI: 10.1016/j.tiv.2007.01.027] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2006] [Revised: 01/29/2007] [Accepted: 01/31/2007] [Indexed: 11/29/2022]
Abstract
The plant cell/microbe coincubation assay was used to analyze organophosphorus insecticide activation. Salmonella typhimurium strains TA98 and TA100 were exposed to several concentrations of the pesticides phoxim and azinphos methyl with and without TX1 cell line of Nicotiana tabacum activation. When the bacterial strains were treated directly with phoxim, mutagenic activity increased significantly. In contrast, no mutagenic activity was detected with plant activation. Azinphos methyl inhibited the growth of Salmonella strains without plant activation. The coincubation with N. tabacum increased mutagenic activity significantly. These findings and those obtained in animals demonstrated that azinphos-methyl was an indirect mutagen or pro-mutagen activated by the plant metabolism.
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Affiliation(s)
- Sandra Gómez-Arroyo
- Laboratorio de Citogenética Ambiental, Centro de Ciencias de la Atmósfera, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán 04510 D.F., México.
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99973
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Crawford TQ, Roelink H. The notch response inhibitor DAPT enhances neuronal differentiation in embryonic stem cell-derived embryoid bodies independently of sonic hedgehog signaling. Dev Dyn 2007; 236:886-92. [PMID: 17295317 DOI: 10.1002/dvdy.21083] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
During development of the neural tube, inhibition of the Notch response as well as the activation of the Sonic Hedgehog (Shh) response results in the formation of neuronal cell types. To determine whether Shh and Notch act independently, we tested the effects of the Notch inhibitor DAPT (N-[N-(3,5-difluorophenacetyl)-l-alanyl]-S-phenylglycine t-butyl ester) on neuralized, embryonic stem (ES) cell-derived embryoid bodies (EBs), while varying the levels of Shh pathway activation. Shh-resistant EBs were derived from Smo null ES cells, while EBs with constitutive high level of Shh pathway activation were derived from Ptc1 null ES cells. Intermediate levels of Shh pathway activation was achieved by the addition of ShhN to the EB culture medium. It was found that DAPT-mediated inhibition of the Notch response resulted in enhanced neuronal differentiation. In the absence of Shh, more interneurons were detected, while the main effect of DAPT on EBs with an activated Shh response was the precocious loss of ventral neuronal precursor-specific markers.
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Affiliation(s)
- T Quinn Crawford
- Department of Biological Structure, University of Washington School of Medicine, Seattle, WA 98195-7420, USA
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99974
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Abstract
We explore patterns of diversification in the plant clades Adoxaceae and Valerianaceae (within Dipsacales), evaluating correlations between biogeographic change (i.e., movements into new areas), morphological change (e.g., the origin of putative key innovations associated with vegetative and reproductive characters), and shifts in rates of diversification. Our findings indicate that rates of diversification in these plants tend to be less tightly correlated with the evolution of morphological innovations but instead exhibit a pronounced correlation with movement into new geographic areas, particularly the dispersal of lineages into new mountainous regions. The interdependence among apparent novelties (arising from their nested phylogenetic distribution) and the correlation between morphological and biogeographic change suggests a complex history of diversification in Dipsacales. Overall, these findings highlight the importance of incorporating biogeographic history in studies of diversification rates and in the study of geographic gradients in species richness. Furthermore, these results argue against a simple deterministic relationship between dispersal and diversification: like other factors that may influence the probability of speciation and/or extinction, the impact of dispersal on diversification rates depends on being in the right place at the right time.
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Affiliation(s)
- Brian R Moore
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA.
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99975
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Karpathy SE, Qin X, Gioia J, Jiang H, Liu Y, Petrosino JF, Yerrapragada S, Fox GE, Haake SK, Weinstock GM, Highlander SK. Genome sequence of Fusobacterium nucleatum subspecies polymorphum - a genetically tractable fusobacterium. PLoS One 2007; 2:e659. [PMID: 17668047 PMCID: PMC1924603 DOI: 10.1371/journal.pone.0000659] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2007] [Accepted: 06/26/2007] [Indexed: 11/19/2022] Open
Abstract
Fusobacterium nucleatum is a prominent member of the oral microbiota and is a common cause of human infection. F. nucleatum includes five subspecies: polymorphum, nucleatum, vincentii, fusiforme, and animalis. F. nucleatum subsp. polymorphum ATCC 10953 has been well characterized phenotypically and, in contrast to previously sequenced strains, is amenable to gene transfer. We sequenced and annotated the 2,429,698 bp genome of F. nucleatum subsp. polymorphum ATCC 10953. Plasmid pFN3 from the strain was also sequenced and analyzed. When compared to the other two available fusobacterial genomes (F. nucleatum subsp. nucleatum, and F. nucleatum subsp. vincentii) 627 open reading frames unique to F. nucleatum subsp. polymorphum ATCC 10953 were identified. A large percentage of these mapped within one of 28 regions or islands containing five or more genes. Seventeen percent of the clustered proteins that demonstrated similarity were most similar to proteins from the clostridia, with others being most similar to proteins from other gram-positive organisms such as Bacillus and Streptococcus. A ten kilobase region homologous to the Salmonella typhimurium propanediol utilization locus was identified, as was a prophage and integrated conjugal plasmid. The genome contains five composite ribozyme/transposons, similar to the CdISt IStrons described in Clostridium difficile. IStrons are not present in the other fusobacterial genomes. These findings indicate that F. nucleatum subsp. polymorphum is proficient at horizontal gene transfer and that exchange with the Firmicutes, particularly the Clostridia, is common.
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Affiliation(s)
- Sandor E. Karpathy
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Microbiology and Molecular Genetics, University of Texas Medical School, Houston, Texas, United States of America
| | - Xiang Qin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Jason Gioia
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Huaiyang Jiang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Yamei Liu
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Joseph F. Petrosino
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Shailaja Yerrapragada
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - George E. Fox
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Susan Kinder Haake
- Associated Clinical Specialties, University of California at Los Angeles School of Dentistry, Los Angeles, California, United States of America
| | - George M. Weinstock
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Microbiology and Molecular Genetics, University of Texas Medical School, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Sarah K. Highlander
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- * To whom correspondence should be addressed. E-mail:
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99976
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Shell SS, Putnam CD, Kolodner RD. The N terminus of Saccharomyces cerevisiae Msh6 is an unstructured tether to PCNA. Mol Cell 2007; 26:565-78. [PMID: 17531814 PMCID: PMC2001284 DOI: 10.1016/j.molcel.2007.04.024] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2006] [Revised: 03/27/2007] [Accepted: 04/18/2007] [Indexed: 11/22/2022]
Abstract
The eukaryotic MutS homolog complexes, Msh2-Msh6 and Msh2-Msh3, recognize mismatched bases in DNA during mismatch repair (MMR). The eukaryote-specific N-terminal regions (NTRs) of Msh6 and Msh3 have not been characterized other than by demonstrating that they contain an N-terminal PCNA-interacting motif. Here we have demonstrated genetically that the NTR of Msh6 has an important role in MMR that is partially redundant with PCNA binding. Small-angle X-ray scattering (SAXS) was used to determine the solution structure of the complex of PCNA with Msh2-Msh6 and with the isolated Msh6 NTR, revealing that the Msh6 NTR is a natively disordered domain that forms an extended tether between Msh6 and PCNA. Moreover, computational analysis of PCNA-interacting motifs in the S. cerevisiae proteome indicated that flexible linkers are a common theme for PCNA-interacting proteins that may serve to localize these binding partners without tightly restraining them to the immediate vicinity of PCNA.
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Affiliation(s)
- Scarlet S. Shell
- Ludwig Institute for Cancer Research
- Departments of Medicine and Cellular and Molecular Medicine and Cancer Center, University of California, San Diego, School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093-0669, USA
| | - Christopher D. Putnam
- Ludwig Institute for Cancer Research
- Departments of Medicine and Cellular and Molecular Medicine and Cancer Center, University of California, San Diego, School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093-0669, USA
| | - Richard D. Kolodner
- Ludwig Institute for Cancer Research
- Departments of Medicine and Cellular and Molecular Medicine and Cancer Center, University of California, San Diego, School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093-0669, USA
- Correspondence:
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99977
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Simmons MJ, Niemi JB, Ryzek DF, Lamour C, Goodman JW, Kraszkiewicz W, Wolff R. Cytotype regulation by telomeric P elements in Drosophila melanogaster: interactions with P elements from M' strains. Genetics 2007; 176:1957-66. [PMID: 17565961 PMCID: PMC1950605 DOI: 10.1534/genetics.106.066670] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2006] [Accepted: 05/21/2007] [Indexed: 11/18/2022] Open
Abstract
P strains of Drosophila are distinguished from M strains by having P elements in their genomes and also by having the P cytotype, a maternally inherited condition that strongly represses P-element-induced hybrid dysgenesis. The P cytotype is associated with P elements inserted near the left telomere of the X chromosome. Repression by the telomeric P elements TP5 and TP6 is significantly enhanced when these elements are crossed into M' strains, which, like P strains, carry P elements, but have little or no ability to repress dysgenesis. The telomeric and M' P elements must coexist in females for this enhanced repression ability to develop. However, once established, it is transmitted maternally to the immediate offspring independently of the telomeric P elements themselves. Females that carry a telomeric P element but that do not carry M' P elements may also transmit an ability to repress dysgenesis to their offspring independently of the telomeric P element. Cytotype regulation therefore involves a maternally transmissible product of telomeric P elements that can interact synergistically with products from paternally inherited M' P elements. This synergism between TP and M' P elements also appears to persist for at least one generation after the TP has been removed from the genotype.
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Affiliation(s)
- Michael J Simmons
- Department of Genetics, Cell Biology, and Development, 250 BioScience Center, University of Minnesota, 1445 Gortner Avenue, St. Paul, MN 55108-1095, USA.
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99978
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Mummenhoff K, Franzke A. Gone with the bird: Late tertiary and quaternary intercontinental long‐distance dispersal and allopolyploidization in plants. SYST BIODIVERS 2007; 5:255-60. [DOI: 10.1017/s1477200007002393] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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99979
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Prozorov AA. Regularities of the location of genes having different functions and of some other nucleotide sequences in the bacterial chromosome. Microbiology (Reading) 2007. [DOI: 10.1134/s0026261707040017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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99980
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Baryshnikova EN, Balobanov VA, Katina NS, Melnik BS, Dolgikh DA, Semisotnov GV, Bychkova VE. Equilibrium unfolding of mutant apomyoglobins carrying substitutions of conserved nonfunctional residues with alanine. Mol Biol 2007. [DOI: 10.1134/s0026893307040139] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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99981
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Boyer FE, Vara Prasad JVN, Choy AL, Chupak L, Dermyer MR, Ding Q, Huband MD, Jiao W, Kaneko T, Khlebnikov V, Kim JY, Lall MS, Maiti SN, Romero K, Wu X. Synthesis and SAR of novel conformationally-restricted oxazolidinones possessing Gram-positive and fastidious Gram-negative antibacterial activity. Part 1: Substituted pyrazoles. Bioorg Med Chem Lett 2007; 17:4694-8. [PMID: 17590334 DOI: 10.1016/j.bmcl.2007.05.056] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2007] [Revised: 05/15/2007] [Accepted: 05/18/2007] [Indexed: 11/18/2022]
Abstract
A novel series of conformationally-restricted oxazolidinones was synthesized which possess a fused pyrazole ring substituted with various alkyl, aryl and heteroaryl substituents. A number of analogs exhibited potent activity against both gram-positive and fastidious gram-negative organisms.
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Affiliation(s)
- Frederick E Boyer
- Pfizer Global Research and Development, 2800 Plymouth Road, Ann Arbor, MI 48105, USA.
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99982
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Abstract
1. Cerebral vessels express oestrogen receptors (ER) in both the smooth muscle and endothelial cell layers of cerebral blood vessels. Levels of ERalpha are higher in female rats chronically exposed to oestrogen, either endogenous or exogenous. 2. Chronic exposure to oestrogen, either endogenous (normally cycling females) or exogenous (ovariectomized with oestrogen replacement), results in cerebral arteries that are more dilated than arteries from ovariectomized counterparts when studied in vitro. This effect is primarily mediated by an increase in the production of vasodilator factors, including nitric oxide (NO) and prostacylin. In contrast, oestrogen appears to suppress the production of endothelial-derived hyperpolarizing factor. Oestrogen treatment increases cerebrovascular levels of endothelial nitric oxide synthase (eNOS), cyclo-oxygenase (COX)-1 and prostacyclin synthase. In addition, via activation of the phosphatidylinositol 3-kinase/Akt pathway, both acute and chronic oestrogen exposure increases eNOS phosphorylation, increasing NO production. 3. Oestrogen receptors have also been localized to cerebrovascular mitochondria and exposure to oestrogen increases the efficiency of energy production while simultaneously reducing mitochondrial production of reactive oxygen species. Oestrogen increases the production of mitochondrial proteins encoded by both mitochondrial and nuclear DNA, including cytochrome c, subunits I and IV of complex IV and Mn-superoxide dismutase. Oestrogen treatment increases the activity of citrate synthase and complex IV and decreases mitochondrial production of H(2)O(2). 4. Oestrogen also has potent anti-inflammatory effects in the cerebral circulation that may have important implications for the incidence and severity of cerebrovascular disease. Administration of lipopolysaccharide or interleukin-1beta to ovariectomized female rats induces cerebrovascular COX-2 and inducible nitric oxide synthase (iNOS) protein expression and increases prostaglandin E(2) expression. Levels of COX-2 and iNOS expression vary with the stage of the oestrous cycle, and the cerebrovascular inflammatory response is suppressed in ovariectomized animals treated with oestrogen. Interleukin-1beta induction of COX-2 protein is prevented by treatment with a nuclear factor (NF)-kappaB inhibitor, and oestrogen treatment reduces cerebrovascular NF-kappaB activity. 5. Cerebrovascular dysfunction and pathology contribute to the pathogenesis of stroke, brain trauma, oedema and dementias, such as Alzheimer's disease. A better understanding of the action of oestrogen on cerebrovascular function holds promise for the development of new therapeutic entities that could be useful in preventing or treating a wide variety of cerebrovascular diseases.
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Affiliation(s)
- Sue P Duckles
- Department of Pharmacology, School of Medicine, University of California, Irvine, California 92697, USA.
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99983
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Kirk EP, Sunde M, Costa MW, Rankin SA, Wolstein O, Castro ML, Butler TL, Hyun C, Guo G, Otway R, Mackay JP, Waddell LB, Cole AD, Hayward C, Keogh A, Macdonald P, Griffiths L, Fatkin D, Sholler GF, Zorn AM, Feneley MP, Winlaw DS, Harvey RP. Mutations in cardiac T-box factor gene TBX20 are associated with diverse cardiac pathologies, including defects of septation and valvulogenesis and cardiomyopathy. Am J Hum Genet 2007; 81:280-91. [PMID: 17668378 PMCID: PMC1950799 DOI: 10.1086/519530] [Citation(s) in RCA: 267] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2007] [Accepted: 05/01/2007] [Indexed: 12/12/2022] Open
Abstract
The T-box family transcription factor gene TBX20 acts in a conserved regulatory network, guiding heart formation and patterning in diverse species. Mouse Tbx20 is expressed in cardiac progenitor cells, differentiating cardiomyocytes, and developing valvular tissue, and its deletion or RNA interference-mediated knockdown is catastrophic for heart development. TBX20 interacts physically, functionally, and genetically with other cardiac transcription factors, including NKX2-5, GATA4, and TBX5, mutations of which cause congenital heart disease (CHD). Here, we report nonsense (Q195X) and missense (I152M) germline mutations within the T-box DNA-binding domain of human TBX20 that were associated with a family history of CHD and a complex spectrum of developmental anomalies, including defects in septation, chamber growth, and valvulogenesis. Biophysical characterization of wild-type and mutant proteins indicated how the missense mutation disrupts the structure and function of the TBX20 T-box. Dilated cardiomyopathy was a feature of the TBX20 mutant phenotype in humans and mice, suggesting that mutations in developmental transcription factors can provide a sensitized template for adult-onset heart disease. Our findings are the first to link TBX20 mutations to human pathology. They provide insights into how mutation of different genes in an interactive regulatory circuit lead to diverse clinical phenotypes, with implications for diagnosis, genetic screening, and patient follow-up.
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Affiliation(s)
- Edwin P Kirk
- Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, 2010, Australia
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99984
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Burgess KS, Etterson JR, Galloway LF. Artificial selection shifts flowering phenology and other correlated traits in an autotetraploid herb. Heredity (Edinb) 2007; 99:641-8. [PMID: 17687248 DOI: 10.1038/sj.hdy.6801043] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
There is mounting evidence that plants are responding to anthropogenic climate change with shifts in flowering phenologies. We conducted a three-generation artificial selection experiment on flowering time in Campanulastrum americanum, an autotetraploid herb, to determine the potential for adaptive evolution of this trait as well as possible costs associated with enhanced or delayed flowering. Divergent selection for earlier and later flowering resulted in a 25-day difference in flowering time. Experiment-wide heritability was 0.31 and 0.23 for the initiation of flowering in early and late lines, respectively. Selection for earlier flowering resulted in significant correlated responses in other traits including smaller size, fewer branches, smaller floral displays, longer fruit maturation times, fewer seeds per fruit and slower seed germination. Results suggest that although flowering time shows the potential to adapt to a changing climate, phenological shifts may be associated with reduced plant fitness possibly hindering evolutionary change.
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Affiliation(s)
- K S Burgess
- Department of Biology, University of Virginia, Charlottesville, VA, USA.
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99985
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Springer NM, Stupar RM. Allele-specific expression patterns reveal biases and embryo-specific parent-of-origin effects in hybrid maize. Plant Cell 2007; 19:2391-402. [PMID: 17693532 PMCID: PMC2002603 DOI: 10.1105/tpc.107.052258] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
We employed allele-specific expression (ASE) analyses to document biased allelic expression in maize (Zea mays). A set of 316 quantitative ASE assays were used to profile the relative allelic expression in seedling tissue derived from five maize hybrids. The different hybrids included in this study exhibit a range of heterosis levels; however, we did not observe differences in the frequencies of allelic bias. Allelic biases in gene expression were consistently observed for approximately 50% of the genes assayed in hybrid seedlings. The relative proportion of genes that exhibit cis- or trans-acting regulatory variation was very similar among the different genotypes. The cis-acting regulatory variation was more prevalent and resulted in greater expression differences than trans-acting regulatory variation for these genes. The ASE assays were further used to compare the relative expression of the B73 and Mo17 alleles in three tissue types (seedling, immature ear, and embryo) derived from reciprocal hybrids. These comparisons provided evidence for tissue-specific cis-acting variation and for a slight maternal expression bias in approximately 20% of genes in embryo tissue. Collectively, these data provide evidence for prevalent cis-acting regulatory variation that contributes to biased allelic expression between genotypes and between tissues.
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Affiliation(s)
- Nathan M Springer
- Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minesota, St. Paul, Minnesota 55108, USA.
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99986
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Mankouri HW, Ngo HP, Hickson ID. Shu proteins promote the formation of homologous recombination intermediates that are processed by Sgs1-Rmi1-Top3. Mol Biol Cell 2007; 18:4062-73. [PMID: 17671161 PMCID: PMC1995734 DOI: 10.1091/mbc.e07-05-0490] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
CSM2, PSY3, SHU1, and SHU2 (collectively referred to as the SHU genes) were identified in Saccharomyces cerevisiae as four genes in the same epistasis group that suppress various sgs1 and top3 mutant phenotypes when mutated. Although the SHU genes have been implicated in homologous recombination repair (HRR), their precise role(s) within this pathway remains poorly understood. Here, we have identified a specific role for the Shu proteins in a Rad51/Rad54-dependent HRR pathway(s) to repair MMS-induced lesions during S-phase. We show that, although mutation of RAD51 or RAD54 prevented the formation of MMS-induced HRR intermediates (X-molecules) arising during replication in sgs1 cells, mutation of SHU genes attenuated the level of these structures. Similar findings were also observed in shu1 cells in which Rmi1 or Top3 function was impaired. We propose a model in which the Shu proteins act in HRR to promote the formation of HRR intermediates that are processed by the Sgs1-Rmi1-Top3 complex.
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Affiliation(s)
- Hocine W. Mankouri
- Cancer Research UK Laboratories, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, United Kingdom
| | - Hien-Ping Ngo
- Cancer Research UK Laboratories, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, United Kingdom
| | - Ian D. Hickson
- Cancer Research UK Laboratories, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, United Kingdom
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99987
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de Leeuw M, Roiz L, Smirnoff P, Schwartz B, Shoseyov O, Almog O. Binding assay and preliminary X-ray crystallographic analysis of ACTIBIND, a protein with anticarcinogenic and antiangiogenic activities. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:716-9. [PMID: 17671376 PMCID: PMC2335156 DOI: 10.1107/s1744309107034483] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2007] [Accepted: 07/14/2007] [Indexed: 11/10/2022]
Abstract
ACTIBIND is a T2 RNase extracellular glycoprotein produced by the mould Aspergillus niger B1 (CMI CC 324626) that possesses anticarcinogenic and antiangiogenic activities. ACTIBIND was found to be an actin-binding protein that interacts with rabbit muscle actin in a 1:2 molar ratio (ACTIBIND:actin) with a binding constant of 16.17 x 10(4) M(-1). Autoclave-treated ACTIBIND (EI-ACTIBIND) lost its RNase activity, but its actin-binding ability was conserved. ACTIBIND crystals were grown using 20% PEG 3350, 0.2 M ammonium dihydrogen phosphate solution at room temperature (293 K). One to four single crystals appeared in each droplet within a few days and grew to approximate dimensions of 0.5 x 0.5 x 0.5 mm after about two weeks. Diffraction studies of these crystals at low temperature (100 K) indicated that they belong to the P3(1)21 space group, with unit-cell parameters a = 78, b = 78, c = 104 A.
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Affiliation(s)
- Marina de Leeuw
- Department of Clinical Biochemistry, Faculty of Health Sciences, Ben-Gurion University, Beer-Sheva 84105, Israel
| | - Levava Roiz
- The Institute of Plant Sciences and Genetics in Agriculture, The Faculty of Agricultural, Food and Environmental Quality Sciences, The Hebrew University of Jerusalem, PO Box 12, Rehovot 76100, Israel
| | - Patricia Smirnoff
- The Institute of Biochemistry, Food Science and Nutrition, Faculty of Agricultural, Food and Environmental Quality Sciences, The Hebrew University of Jerusalem, Israel
| | - Betty Schwartz
- The Institute of Biochemistry, Food Science and Nutrition, Faculty of Agricultural, Food and Environmental Quality Sciences, The Hebrew University of Jerusalem, Israel
| | - Oded Shoseyov
- The Institute of Plant Sciences and Genetics in Agriculture, The Faculty of Agricultural, Food and Environmental Quality Sciences, The Hebrew University of Jerusalem, PO Box 12, Rehovot 76100, Israel
| | - Orna Almog
- Department of Clinical Biochemistry, Faculty of Health Sciences, Ben-Gurion University, Beer-Sheva 84105, Israel
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99988
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Whitmarsh AJ. Regulation of gene transcription by mitogen-activated protein kinase signaling pathways. Biochimica et Biophysica Acta (BBA) - Molecular Cell Research 2007; 1773:1285-98. [PMID: 17196680 DOI: 10.1016/j.bbamcr.2006.11.011] [Citation(s) in RCA: 194] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2006] [Revised: 11/14/2006] [Accepted: 11/15/2006] [Indexed: 11/22/2022]
Abstract
Mitogen-activated protein kinase (MAPK) signaling pathways are key mediators of eukaryotic transcriptional responses to extracellular signals. These pathways control gene expression in a number of ways including the phosphorylation and regulation of transcription factors, co-regulatory proteins and chromatin proteins. MAPK pathways therefore target multiple components of transcriptional complexes at gene promoters and can regulate DNA binding, protein stability, cellular localization, transactivation or repression, and nucleosome structure. Recent work has uncovered further complexities in the mechanisms by which MAPKs control gene expression including their roles as integral components of transcription factor complexes and their interplay with other post-translational modification pathways. In this review I discuss these advances with particular focus on how MAPK signals are integrated by transcription factor complexes to provide specific transcriptional responses and how this relates to cellular function.
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Affiliation(s)
- Alan J Whitmarsh
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK.
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99989
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Abstract
The absence of Bacillus subtilis RecG branch migration translocase causes a defect in cell proliferation, renders cells very sensitive to DNA-damaging agents and increases approximately 150-fold the amount of non-partitioned chromosomes. Inactivation of recF, addA, recH, recV or recU increases both the sensitivity to DNA-damaging agents and the chromosomal segregation defect of recG mutants. Deletion of recS or recN gene partially suppresses cell proliferation, DNA repair and segregation defects of DeltarecG cells, whereas deletion of recA only partially suppresses the segregation defect of DeltarecG cells. Deletion of recG and ripX render cells with very poor viability, extremely sensitive to DNA-damaging agents, and with a drastic segregation defect. After exposure to mitomycin C recG or ripX cells show a drastic defect in chromosome partitioning (approximately 40% of the cells), and this defect is even larger (approximately 60% of the cells) in recG ripX cells. Taken together, these data indicate that: (i) RecG defines a new epistatic group (eta), (ii) RecG is required for proper chromosomal segregation even in the presence of other proteins that process and resolve Holliday junctions, and (iii) different avenues could process Holliday junctions.
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Affiliation(s)
- Humberto Sanchez
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Madrid, E-28049 Spain
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99990
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Rodríguez-Ezpeleta N, Brinkmann H, Burger G, Roger AJ, Gray MW, Philippe H, Lang BF. Toward Resolving the Eukaryotic Tree: The Phylogenetic Positions of Jakobids and Cercozoans. Curr Biol 2007; 17:1420-5. [PMID: 17689961 DOI: 10.1016/j.cub.2007.07.036] [Citation(s) in RCA: 157] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2006] [Revised: 07/10/2007] [Accepted: 07/17/2007] [Indexed: 11/18/2022]
Abstract
Resolving the global phylogeny of eukaryotes has proven to be challenging. Among the eukaryotic groups of uncertain phylogenetic position are jakobids, a group of bacterivorous flagellates that possess the most bacteria-like mitochondrial genomes known. Jakobids share several ultrastructural features with malawimonads and an assemblage of anaerobic protists (e.g., diplomonads and oxymonads). These lineages together with Euglenozoa and Heterolobosea have collectively been designated "excavates". However, published molecular phylogenies based on the sequences of nuclear rRNAs and up to six nucleus-encoded proteins do not provide convincing support for the monophyly of excavates, nor do they uncover their relationship to other major eukaryotic groups. Here, we report the first large-scale eukaryotic phylogeny, inferred from 143 nucleus-encoded proteins comprising 31,604 amino acid positions, that includes jakobids, malawimonads and cercozoans. We obtain compelling support for the monophyly of jakobids, Euglenozoa plus Heterolobosea (JEH group), and for the association of cercozoans with stramenopiles plus alveolates. Furthermore, we observe a sister-group relationship between the JEH group and malawimonads after removing fast-evolving species from the dataset. We discuss the implications of these results for the concept of "excavates" and for the elucidation of eukaryotic phylogeny in general.
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Affiliation(s)
- Naiara Rodríguez-Ezpeleta
- Centre Robert Cedergren, Département de Biochimie, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, Québec H3T 1J4, Canada
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99991
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Browman DT, Hoegg MB, Robbins SM. The SPFH domain-containing proteins: more than lipid raft markers. Trends Cell Biol 2007; 17:394-402. [PMID: 17766116 DOI: 10.1016/j.tcb.2007.06.005] [Citation(s) in RCA: 259] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2007] [Revised: 06/06/2007] [Accepted: 06/06/2007] [Indexed: 01/03/2023]
Abstract
Membrane microdomains with distinct lipid compositions, called lipid rafts, represent a potential mechanism for compartmentalizing cellular functions within the plane of biological membranes. SPFH domain-containing proteins are found in lipid raft microdomains in diverse cellular membranes. The functions of these proteins are just beginning to be elucidated. Recent advances in the understanding of structural features and their roles within lipid rafts include a potential function for SPFH proteins in the formation of membrane microdomains and lipid raft-associated processes, such as endocytosis and mechanosensation.
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Affiliation(s)
- Duncan T Browman
- Southern Alberta Cancer Research Institute, Department of Oncology, University of Calgary, Calgary, AB, T2N 4N1, Canada
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99992
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Wu J, Kang JH, Hettenhausen C, Baldwin IT. Nonsense-mediated mRNA decay (NMD) silences the accumulation of aberrant trypsin proteinase inhibitor mRNA in Nicotiana attenuata. Plant J 2007; 51:693-706. [PMID: 17587303 DOI: 10.1111/j.1365-313x.2007.03173.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
In eukaryotes, genes carrying premature termination codons (PTCs) are often associated with decreased mRNA levels compared with their counterparts without PTCs. PTC-harboring mRNA is rapidly degraded through the nonsense-mediated mRNA decay (NMD) pathway to prevent the accumulation of potentially detrimental truncated proteins. In a native ecotype of Nicotiana attenuata collected from Arizona (AZ), the mRNA levels of a trypsin proteinase inhibitor (TPI) gene are substantially lower than in plants collected from Utah (UT). Cloning the AZ TPI gene revealed a 6 bp deletion mutation in exon 2 resulting in a PTC and decreased mRNA levels through NMD. Silencing UPF1, 2 and 3 in N. attenuata AZ plants by virus-induced gene silencing (VIGS) enhanced the levels of PTC-harboring TPI mRNA, demonstrating a conserved role for UPF genes in plants. Furthermore, using cell suspension cultures that express variants of the TPI construct, we demonstrate that both intron-containing and intronless genes are subject to NMD in plants; unlike PTCs in mammals, PTCs downstream of introns activate NMD in plants. However, when a PTC is only 4 bp upstream of an intron, the NMD surveillance mechanism is abrogated. We also demonstrate that, in an intronless TPI gene, a PTC located at the beginning or the end of the coding sequence triggers NMD less efficiently than do PTCs located at the middle of the coding sequence. Taken together, these results highlight the complexity of the NMD activation mechanisms in plants.
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Affiliation(s)
- Jianqiang Wu
- Department of Molecular Ecology, Max-Planck-Institute for Chemical Ecology, Beutenberg Campus, Hans-Knöll Strasse 8, D-07745 Jena, Germany
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99993
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Gingerich DJ, Hanada K, Shiu SH, Vierstra RD. Large-scale, lineage-specific expansion of a bric-a-brac/tramtrack/broad complex ubiquitin-ligase gene family in rice. Plant Cell 2007; 19:2329-48. [PMID: 17720868 PMCID: PMC2002615 DOI: 10.1105/tpc.107.051300] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Selective ubiquitination of proteins is directed by diverse families of ubiquitin-protein ligases (or E3s) in plants. One important type uses Cullin-3 as a scaffold to assemble multisubunit E3 complexes containing one of a multitude of bric-a-brac/tramtrack/broad complex (BTB) proteins that function as substrate recognition factors. We previously described the 80-member BTB gene superfamily in Arabidopsis thaliana. Here, we describe the complete BTB superfamily in rice (Oryza sativa spp japonica cv Nipponbare) that contains 149 BTB domain-encoding genes and 43 putative pseudogenes. Amino acid sequence comparisons of the rice and Arabidopsis superfamilies revealed a near equal repertoire of putative substrate recognition module types. However, phylogenetic comparisons detected numerous gene duplication and/or loss events since the rice and Arabidopsis BTB lineages split, suggesting possible functional specialization within individual BTB families. In particular, a major expansion and diversification of a subset of BTB proteins containing Meprin and TRAF homology (MATH) substrate recognition sites was evident in rice and other monocots that likely occurred following the monocot/dicot split. The MATH domain of a subset appears to have evolved significantly faster than those in a smaller core subset that predates flowering plants, suggesting that the substrate recognition module in many monocot MATH-BTB E3s are diversifying to ubiquitinate a set of substrates that are themselves rapidly changing. Intriguing possibilities include pathogen proteins attempting to avoid inactivation by the monocot host.
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Affiliation(s)
- Derek J Gingerich
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706, USA
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99994
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Itoi-Babaya M, Ikegami H, Fujisawa T, Ueda H, Nojima K, Babaya N, Kobayashi M, Noso S, Kawaguchi Y, Yamaji K, Shibata M, Ogihara T. Fatty liver and obesity: phenotypically correlated but genetically distinct traits in a mouse model of type 2 diabetes. Diabetologia 2007; 50:1641-8. [PMID: 17549450 DOI: 10.1007/s00125-007-0700-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2007] [Accepted: 03/29/2007] [Indexed: 01/14/2023]
Abstract
AIMS/HYPOTHESIS Obesity and fatty liver are commonly associated with type 2 diabetes, but the genetic and functional bases linking fatty liver with obesity and diabetes are largely unknown. Our aim was to investigate the association of fatty liver with obesity and other diabetes-related phenotypes and to define the genetic control of obesity and fatty liver. MATERIALS AND METHODS We established 306 F2 mice by crossing Nagoya-Shibata-Yasuda (NSY) mice, an animal model of type 2 diabetes, with control C3H mice, and analysed their phenotypes. Whole-genome screening of F2 mice was performed to identify the loci responsible for fatty liver and obesity. RESULTS A strong association of fatty liver with obesity, hyperinsulinaemia and hyperglycaemia was observed in F2 mice. Using whole-genome screening in 306 F2 mice, we mapped a new locus for fatty liver (Fl1n) on chromosome 6 (maximum logarithm of odds score [MLS] 10.0) and one for body weight (Bw1n) on chromosome 7 (MLS 5.1). Fl1n was linked to epididymal fat weight as well as fatty liver, but its effects were opposite in the two tissues in that the NSY allele increased liver fat but decreased epididymal fat, suggesting a role of Fl1n in partitioning of fat mass. The sequence of peroxisome proliferator-activated receptor gamma (Pparg), a candidate for Fl1n, showed allelic variation between NSY and C3H mice. CONCLUSIONS/INTERPRETATION These data suggest that fatty liver and obesity are phenotypically related but genetically independent. Loci homologous to Fl1n and Bw1n are good candidate genes for susceptibility to fatty liver and obesity in humans.
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Affiliation(s)
- M Itoi-Babaya
- Department of Geriatric Medicine, Osaka University Graduate School of Medicine, Suita, Japan
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99995
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Simmons MJ, Ryzek DF, Lamour C, Goodman JW, Kummer NE, Merriman PJ. Cytotype regulation by telomeric P elements in Drosophila melanogaster: evidence for involvement of an RNA interference gene. Genetics 2007; 176:1945-55. [PMID: 17603126 PMCID: PMC1950604 DOI: 10.1534/genetics.106.066746] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2006] [Accepted: 04/23/2007] [Indexed: 11/18/2022] Open
Abstract
P elements inserted at the left telomere of the X chromosome evoke the P cytotype, a maternally inherited condition that regulates the P-element family in the Drosophila germline. This regulation is completely disrupted in stocks heterozygous for mutations in aubergine, a gene whose protein product is involved in RNA interference. However, cytotype is not disrupted in stocks heterozygous for mutations in two other RNAi genes, piwi and homeless (spindle-E), or in a stock heterozygous for a mutation in the chromatin protein gene Enhancer of zeste. aubergine mutations exert their effects in the female germline, where the P cytotype is normally established and through which it is maintained. These effects are transmitted maternally to offspring of both sexes independently of the mutations themselves. Lines derived from mutant aubergine stocks reestablish the P cytotype quickly, unlike lines derived from stocks heterozygous for a mutation in Suppressor of variegation 205, the gene that encodes the telomere-capping protein HP1. Cytotype regulation by telomeric P elements may be tied to a system that uses RNAi to regulate the activities of telomeric retrotransposons in Drosophila.
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Affiliation(s)
- Michael J Simmons
- Department of Genetics, Cell Biology, and Development, 250 BioScience Center, University of Minnesota, 1445 Gortner Avenue, St. Paul, MN 55108-1095, USA.
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99996
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Causse M, Chaïb J, Lecomte L, Buret M, Hospital F. Both additivity and epistasis control the genetic variation for fruit quality traits in tomato. Theor Appl Genet 2007; 115:429-42. [PMID: 17571252 DOI: 10.1007/s00122-007-0578-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2006] [Accepted: 05/14/2007] [Indexed: 05/15/2023]
Abstract
The effect of a gene involved in the variation of a quantitative trait may change due to epistatic interactions with the overall genetic background or with other genes through digenic interactions. The classical populations used to map quantitative trait loci (QTL) are poorly efficient to detect epistasis. To assess the importance of epistasis in the genetic control of fruit quality traits, we compared 13 tomato lines having the same genetic background except for one to five chromosome fragments introgressed from a distant line. Six traits were assessed: fruit soluble solid content, sugar content and titratable acidity, fruit weight, locule number and fruit firmness. Except for firmness, a large part of the variation of the six traits was under additive control, but interactions between QTL leading to epistasis effects were common. In the lines cumulating several QTL regions, all the significant epistatic interactions had a sign opposite to the additive effects, suggesting less than additive epistasis. Finally the re-examination of the segregating population initially used to map the QTL confirmed the extent of epistasis, which frequently involved a region where main effect QTL have been detected in this progeny or in other studies.
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Affiliation(s)
- Mathilde Causse
- UR 1052, Unité de Génétique et Amélioration des Fruits et Légumes, Institut National de la Recherche Agronomique, Domaine Saint-Maurice, 84143 Montfavet, France.
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99997
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99998
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Vernarecci S, Colotti G, Ornaghi P, Schiebel E, Chiancone E, Filetici P. The yeast penta-EF protein Pef1p is involved in cation-dependent budding and cell polarization. Mol Microbiol 2007; 65:1122-38. [PMID: 17640275 DOI: 10.1111/j.1365-2958.2007.05852.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Penta-EF-hand (PEF) proteins bind calcium and participate in a variety of calcium-dependent processes in vertebrates. In yeast, intracellular cations regulate processes like cell division and polarized growth. This study reports the identification of a unique PEF protein in Saccharomyces cerevisiae encoded by the uncharacterized open reading frame YGR058w. Pef1p has a long and unstructured N-terminal domain conserved in ascomycetes, and a highly conserved C-terminal calcium binding domain homologous to human ALG-2 and sorcin. Pef1p binds calcium and zinc and homodimerizes in vitro and in vivo like vertebrate homologues. Disruption of PEF1 induces defective growth in SDS and cation depletion conditions. Significantly, a critical substitution in the second EF hand (E218A) lowers the in vitro affinity for zinc and phenocopies growth defects. The dissection of protein-protein interactions and the cellular localization of Pef1p analogous to that of RAM pathway components controlling daughter-specific gene expression at the site of bud emergence bring out the importance of this novel protein. Our data suggest that cation homeostasis is involved in the control of polarized growth and in stress response in budding yeast.
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Affiliation(s)
- Stefano Vernarecci
- Istituto di Biologia e Patologia Molecolari, CNR, and Dipartemento di Genetica e Biologia Molecolare, Sapienza Università di Roma, P. le A. Moro 5, 00185 Rome, Italy
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99999
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Abstract
Genotype x environment interactions can facilitate coexistence of locally adapted specialists. Interactions evolve if adaptation to one environment trades off with performance in others. We investigated whether evolution on one host genotype traded off with performance on others in long-term experimental populations of different genotypes of the protozoan Paramecium caudatum, infected with the bacterial parasite Holospora undulata. A total of nine parasite selection lines evolving on three host genotypes and the ancestral parasite were tested in a cross-infection experiment. We found that evolved parasites produced more infections than did the ancestral parasites, both on host genotypes they had evolved on (positive direct response to selection) and on genotypes they had not evolved on (positive correlated response to selection). On two host genotypes, a negative relationship between direct and correlated responses indicated pleiotropic costs of adaptation. On the third, a positive relationship suggested cost-free adaptation. Nonetheless, on all three hosts, resident parasites tended to be superior to the average nonresident parasite. Thus genotype specificity (i.e., patterns of local adaptation) may evolve without costs of adaptation, as long as direct responses to selection exceed correlated responses.
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Affiliation(s)
- Thibault Nidelet
- Laboratoire de Parasitologie Evolutive (CC 237), CNRS-UMR 7103, Université Pierre et Marie Curie, 7 quai St. Bernard, 75252 Paris Cedex 05, France.
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100000
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Zhang J, Wang C, Ke N, Bliesath J, Chionis J, He QS, Li QX, Chatterton JE, Wong-Staal F, Zhou D. A more efficient RNAi inducible system for tight regulation of gene expression in mammalian cells and xenograft animals. RNA 2007; 13:1375-83. [PMID: 17616554 PMCID: PMC1924899 DOI: 10.1261/rna.520707] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Two types of tetracycline-controlled inducible RNAi expression systems have been developed that generally utilize multiple tetracycline operators (TetOs) or repressor fusion proteins to overcome the siRNA leakiness. Here, we report a novel system that overexpresses the tetracycline repressor (TetR) via a bicistronic construct to control siRNA expression. The high level of TetR expression ensures that the inducible promoter is tightly bound, with minimal basal transcription, allowing for regulation solely dependent on TetR rather than a TetR fusion protein via a more complicated mechanism. At the same time, this system contains only a single TetO, thus minimizing the promoter impairment occurring in existing systems due to the incorporation of multiple TetOs, and maximizing the siRNA expression upon induction. In addition, this system combines all the components required for regulation of siRNA expression into a single lentiviral vector, so that stable cell lines can be generated by a single transduction and selection, with significant reduction in time and cost. Taken together, this all-in-one lentiviral vector with the feature of TetR overexpression provides a unique and more efficient tool for conditional gene knockdown that has wide applications. We have demonstrated the high degree of robustness and versatility of this system as applied to several mammalian cells and xenograft animals.
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