99901
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Abstract
The papillomavirus life cycle is intimately coupled to the differentiation state of the infected epithelium. Since papillomaviruses lack most of the rate-limiting enzymes required for genome synthesis, they need to uncouple keratinocyte differentiation from cell cycle arrest and maintain or reestablish a replication-competent state within terminally differentiated keratinocytes. The human papillomavirus (HPV) E7 protein appears to be a major determinant for this activity and induces aberrant S-phase entry through the inactivation of the retinoblastoma tumor suppressor and related pocket proteins. In addition, E7 can abrogate p21 and p27. Together, this leads to the activation of E2F1 to E2F5, enhanced expression of E2F-responsive genes, and increased cdk2 activity. E2F6 is a pRB-independent, noncanonical member of the E2F transcription factor family that acts as a transcriptional repressor. E2F6 expression is activated in S phase through an E2F-dependent mechanism and thus may provide a negative-feedback mechanism that slows down S-phase progression and/or exit in response to the activation of the other E2F transcription factors. Here, we show that low- and high-risk HPV E7 proteins, as well as simian virus 40 T antigen and adenovirus E1A, can associate with and inactivate the transcriptional repression activity of E2F6, thereby subverting a critical cellular defense mechanism. This may result in the extended S-phase competence of HPV-infected cells. E2F6 is a component of polycomb group complexes, which bind to silenced chromatin and are critical for the maintenance of cell fate. We show that E7-expressing cells show decreased staining for E2F6/polycomb complexes and that this is at least in part dependent on the association with E2F6.
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99902
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Excess MCM proteins protect human cells from replicative stress by licensing backup origins of replication. Proc Natl Acad Sci U S A 2008; 105:8956-61. [PMID: 18579778 DOI: 10.1073/pnas.0803978105] [Citation(s) in RCA: 364] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The six main minichromosome maintenance proteins (Mcm2-7), which presumably constitute the core of the replicative DNA helicase, are present in chromatin in large excess relative to the number of active replication forks. To evaluate the relevance of this apparent surplus of Mcm2-7 complexes in human cells, their levels were down-regulated by using RNA interference. Interestingly, cells continued to proliferate for several days after the acute (>90%) reduction of Mcm2-7 concentration. However, they became hypersensitive to DNA replication stress, accumulated DNA lesions, and eventually activated a checkpoint response that prevented mitotic division. When this checkpoint was abrogated by the addition of caffeine, cells quickly lost viability, and their karyotypes revealed striking chromosomal aberrations. Single-molecule analyses revealed that cells with a reduced concentration of Mcm2-7 complexes display normal fork progression but have lost the potential to activate "dormant" origins that serve a backup function during DNA replication. Our data show that the chromatin-bound "excess" Mcm2-7 complexes play an important role in maintaining genomic integrity under conditions of replicative stress.
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99903
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Buchholz K, Rahlfs S, Schirmer RH, Becker K, Matuschewski K. Depletion of Plasmodium berghei plasmoredoxin reveals a non-essential role for life cycle progression of the malaria parasite. PLoS One 2008; 3:e2474. [PMID: 18575607 PMCID: PMC2429964 DOI: 10.1371/journal.pone.0002474] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2008] [Accepted: 04/30/2008] [Indexed: 11/18/2022] Open
Abstract
Proliferation of the pathogenic Plasmodium asexual blood stages in host erythrocytes requires an exquisite capacity to protect the malaria parasite against oxidative stress. This function is achieved by a complex antioxidant defence system composed of redox-active proteins and low MW antioxidants. Here, we disrupted the P. berghei plasmoredoxin gene that encodes a parasite-specific 22 kDa member of the thioredoxin superfamily. The successful generation of plasmoredoxin knockout mutants in the rodent model malaria parasite and phenotypic analysis during life cycle progression revealed a non-vital role in vivo. Our findings suggest that plasmoredoxin fulfils a specialized and dispensable role for Plasmodium and highlights the need for target validation to inform drug development strategies.
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Affiliation(s)
- Kathrin Buchholz
- Interdisciplinary Research Centre, Justus-Liebig University, Giessen, Germany
- Biochemistry Centre, Ruprecht-Karls University, Heidelberg, Germany
- Department of Parasitology, School of Medicine, Heidelberg University, Heidelberg, Germany
| | - Stefan Rahlfs
- Interdisciplinary Research Centre, Justus-Liebig University, Giessen, Germany
| | | | - Katja Becker
- Interdisciplinary Research Centre, Justus-Liebig University, Giessen, Germany
- * E-mail: (KB); (KM)
| | - Kai Matuschewski
- Department of Parasitology, School of Medicine, Heidelberg University, Heidelberg, Germany
- * E-mail: (KB); (KM)
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99904
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Stordal B, Davey R. ERCC1 expression and RAD51B activity correlate with cell cycle response to platinum drug treatment not DNA repair. Cancer Chemother Pharmacol 2008; 63:661-72. [PMID: 18575867 DOI: 10.1007/s00280-008-0783-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2008] [Accepted: 06/02/2008] [Indexed: 11/29/2022]
Abstract
BACKGROUND The H69CIS200 and H69OX400 cell lines are novel models of low-level platinum-drug resistance. Resistance was not associated with increased cellular glutathione or decreased accumulation of platinum, rather the resistant cell lines have a cell cycle alteration allowing them to rapidly proliferate post drug treatment. RESULTS A decrease in ERCC1 protein expression and an increase in RAD51B foci activity was observed in association with the platinum induced cell cycle arrest but these changes did not correlate with resistance or altered DNA repair capacity. The H69 cells and resistant cell lines have a p53 mutation and consequently decrease expression of p21 in response to platinum drug treatment, promoting progression of the cell cycle instead of increasing p21 to maintain the arrest. CONCLUSION Decreased ERCC1 protein and increased RAD51B foci may in part be mediating the maintenance of the cell cycle arrest in the sensitive cells. Resistance in the H69CIS200 and H69OX400 cells may therefore involve the regulation of ERCC1 and RAD51B independent of their roles in DNA repair. The novel mechanism of platinum resistance in the H69CIS200 and H69OX400 cells demonstrates the multifactorial nature of platinum resistance which can occur independently of alterations in DNA repair capacity and changes in ERCC1.
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Affiliation(s)
- Britta Stordal
- Bill Walsh Cancer Research Laboratories, Royal North Shore Hospital and The University of Sydney, St Leonards, NSW, Australia
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99905
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Zeglis BM, Barton JK. Binding of Ru(bpy)2(eilatin)2+ to matched and mismatched DNA. Inorg Chem 2008; 47:6452-7. [PMID: 18576614 DOI: 10.1021/ic8006537] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The DNA-binding properties of Ru(bpy)2(eilatin)(2+) have been investigated to determine if the sterically expansive eilatin ligand confers specificity for destabilized single-base mismatches in DNA. Competitive DNA photocleavage experiments employing a sequence-neutral metallointercalator, Rh(bpy)2(phi)(3+) (phi = 9,10-phenanthrenequinonediimine), and a mismatch-specific metalloinsertor, Rh(bpy)2(chrysi)(3+) (chrysi = chrysene-5,6-quinonediimine), reveal that the eilatin complex binds to a CC mismatched site with an apparent binding constant of 2.2(2) x 10(6) M(-1). Nonetheless, the selectivity in binding mismatched DNA is not high: competitive titrations with Rh(bpy)2(phi)(3+) show that the complex binds also to well-matched B-form sites. Thus, Ru(bpy)2(eilatin)(2+), despite containing the extremely expansive eilatin ligand, displays lower selectivity for the mismatch than does Rh(bpy)2(chrysi)(3+), a metalloinsertor containing the smaller, though still bulky, chrysene-5,6-quinonediimine ligand. In summary, the size and shape of the eilatin ligand allow stacking with both well-matched and mismatched DNA.
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Affiliation(s)
- Brian M Zeglis
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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99906
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Simmons LW, Beveridge M, Evans JP. Molecular evidence for multiple paternity in a feral population of green swordtails. J Hered 2008; 99:610-5. [PMID: 18579557 DOI: 10.1093/jhered/esn053] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Genetic parentage analyses provide insights into mating systems and have revealed widespread evidence for polyandry in natural populations. Here, we use 5 microsatellite markers to estimate female mating rates in a feral population of green swordtails, Xiphophorus helleri, a live-bearing poeciliid fish that has become a model system in the study of precopulatory mate choice and mating competition. Although heralded as a potential model for investigating sperm competition as early as 1950, there has been no attempt to explore postcopulatory sexual selection in its mating system. We thus obtained information on the prevalence, and therefore biological relevance, of polyandry from a wild population. We genotyped the offspring from 14 wild-caught gravid females and determined the number of fathers in each brood using allele counting methods and the programs GERUD and PARENTAGE. Our analyses revealed that 57% (allele counts and GERUD) and 71% (PARENTAGE) of the sampled broods had at least 2 sires, with a global mean 1.74 fathers per brood. Paternity skew was generally high in mixed paternity broods so that our analyses almost certainly underestimate actual mating frequencies in the wild. Our data provide a solid underpinning for future studies of postcopulatory sexual selection in this species.
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Affiliation(s)
- Leigh W Simmons
- Centre for Evolutionary Biology, School of Animal Biology, The University of Western Australia, Crawley, 6009, Australia.
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99907
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Zhang S, Wei T, Hou G, Zhang C, Liang P, Ni J, Sheng D, Shen Y. Archaeal DNA helicase HerA interacts with Mre11 homologue and unwinds blunt-ended double-stranded DNA and recombination intermediates. DNA Repair (Amst) 2008; 7:380-91. [PMID: 18243819 DOI: 10.1016/j.dnarep.2007.10.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2007] [Revised: 10/19/2007] [Accepted: 10/20/2007] [Indexed: 01/26/2023]
Abstract
HerA is a novel family DNA helicases that exist ubiquitously in thermophilic archaea. The genes are linked to homologues of eukaryotic recombination and repair proteins Mre11 and Rad50 in some of the genomes. However, the relationship between HerA and the related proteins is unclear. In this study, a homologue from the hyperthermophilic archaeon Sulfolobus tokodaii (StoHerA) was characterized and physical and functional interactions between StoHerA and StoMre11 (Mre11 from S. tokodaii) were studied. It was found that StoHerA was able to unwind blunt-ended double-stranded DNA (dsDNA), although with lower efficiency. StoHerA was also able to unwind Holliday junction, splayed-arm DNA, as well as 5'- or 3'-overhang with high efficiency. Pull-down and yeast two-hybrid analyses revealed that StoHerA interacted with StoMre11 physically. The helicase activity of StoHerA was stimulated by StoMre11, indicating a functional role of this interaction. In addition, site-directed mutagenesis of StoHerA was performed to analyze functions of conserved residues of StoHerA. Interestingly, mutation of E355 to alanine in Walker B resulted in not only loss of ATPase and DNA helicase activities, but also dsDNA-binding ability, indicating that this residue is involved in the coupling of ATP hydrolysis, dsDNA-binding, and helicase activities.
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Affiliation(s)
- Songtao Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, People's Republic of China
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99908
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Shin W, Lee B, Hong S, Ryou C, Kwon M. Cloning and expression of a prion protein (PrP) gene from Korean bovine (Bos taurus coreanae) and production of rabbit anti-bovine PrP antibody. Biotechnol Lett 2008; 30:1705-11. [PMID: 18574558 DOI: 10.1007/s10529-008-9768-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2008] [Accepted: 05/30/2008] [Indexed: 10/21/2022]
Abstract
A PrP gene, from a Korean bovine, exhibiting a nonsense and a missense polymorphism respectively at nucleotides 576 and 652 has been cloned. The latter resulted in Glu to Lys substitution at amino acid residue 218. After expression and purification of the recombinant bovine PrP (recBoPrP) with Glu218Lys substitution, a polyclonal antibody against this protein was raised. ELISA and Western blot analysis suggested that the recBoPrP obtained in this study had a unique conformation not presented in native PrP(C), and the polyclonal antibody recognized PrP in a conformation dependent manner. These reagents will be valuable tools for studying PrP conformation.
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Affiliation(s)
- Wooseok Shin
- Department of Genetic Engineering, Sungkyunkwan University, 300 Chunchun-Dong, Changan-Ku, Suwon 440-746, Republic of Korea
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99909
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Guzmán E, Romeu A, Garcia-Vallve S. Completely sequenced genomes of pathogenic bacteria: a review. Enferm Infecc Microbiol Clin 2008; 26:88-98. [PMID: 18341921 DOI: 10.1157/13115544] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Six out of ten completely sequenced bacterial genomes are pathogenic or opportunistic bacteria. The genome sequence of at least one strain of all the principal pathogenic bacteria will soon be available. This information should enable us to identify genes that encode virulence factors. As these genes are potential targets for drugs and vaccines, their identification should have considerable repercussions on prevention, diagnosis, and treatment of the main bacterial infectious diseases. Comparison of genome sequences of several strains of the same species should allow identification of the genetic clues responsible for the differing behavior of related bacterial pathogens. This article reviews the genomes from pathogenic bacteria that have been or are currently being sequenced, describes the main tasks to be accomplished after a genome sequence becomes available, and discusses the benefits of having the genome sequence of bacterial pathogens.
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Affiliation(s)
- Eduard Guzmán
- Institut Català de la Salut, Area Bàsica de Salut, Tarragona, Spain.
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99910
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Mutants defective in Rad1-Rad10-Slx4 exhibit a unique pattern of viability during mating-type switching in Saccharomyces cerevisiae. Genetics 2008; 179:1807-21. [PMID: 18579504 DOI: 10.1534/genetics.108.090654] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Efficient repair of DNA double-strand breaks (DSBs) requires the coordination of checkpoint signaling and enzymatic repair functions. To study these processes during gene conversion at a single chromosomal break, we monitored mating-type switching in Saccharomyces cerevisiae strains defective in the Rad1-Rad10-Slx4 complex. Rad1-Rad10 is a structure-specific endonuclease that removes 3' nonhomologous single-stranded ends that are generated during many recombination events. Slx4 is a known target of the DNA damage response that forms a complex with Rad1-Rad10 and is critical for 3'-end processing during repair of DSBs by single-strand annealing. We found that mutants lacking an intact Rad1-Rad10-Slx4 complex displayed RAD9- and MAD2-dependent cell cycle delays and decreased viability during mating-type switching. In particular, these mutants exhibited a unique pattern of dead and switched daughter cells arising from the same DSB-containing cell. Furthermore, we observed that mutations in post-replicative lesion bypass factors (mms2Delta, mph1Delta) resulted in decreased viability during mating-type switching and conferred shorter cell cycle delays in rad1Delta mutants. We conclude that Rad1-Rad10-Slx4 promotes efficient repair during gene conversion events involving a single 3' nonhomologous tail and propose that the rad1Delta and slx4Delta mutant phenotypes result from inefficient repair of a lesion at the MAT locus that is bypassed by replication-mediated repair.
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99911
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Sousa SF, Fernandes PA, Ramos MJ. Enzyme Flexibility and the Catalytic Mechanism of Farnesyltransferase: Targeting the Relation. J Phys Chem B 2008; 112:8681-91. [DOI: 10.1021/jp711214j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sérgio F. Sousa
- REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
| | - Pedro A. Fernandes
- REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
| | - Maria João Ramos
- REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
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99912
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Interplay of DNA repair pathways controls methylation damage toxicity in Saccharomyces cerevisiae. Genetics 2008; 179:1835-44. [PMID: 18579505 DOI: 10.1534/genetics.108.089979] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Methylating agents of S(N)1 type are widely used in cancer chemotherapy, but their mode of action is poorly understood. In particular, it is unclear how the primary cytotoxic lesion, O(6)-methylguanine ((Me)G), causes cell death. One hypothesis stipulates that binding of mismatch repair (MMR) proteins to (Me)G/T mispairs arising during DNA replication triggers cell-cycle arrest and cell death. An alternative hypothesis posits that (Me)G cytotoxicity is linked to futile processing of (Me)G-containing base pairs by the MMR system. In this study, we provide compelling genetic evidence in support of the latter hypothesis. Treatment of 4644 deletion mutants of Saccharomyces cerevisiae with the prototypic S(N)1-type methylating agent N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) identified MMR as the only pathway that sensitizes cells to MNNG. In contrast, homologous recombination (HR), postreplicative repair, DNA helicases, and chromatin maintenance factors protect yeast cells against the cytotoxicity of this chemical. Notably, DNA damage signaling proteins played a protective rather than sensitizing role in the MNNG response. Taken together, this evidence demonstrates that (Me)G-containing lesions in yeast must be processed to be cytotoxic.
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99913
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Gerr HD, Nassin ML, Davis EM, Jayathilaka N, Neilly ME, Schlegelberger B, Zhang Y, Rowley JD. Cytogenetic and molecular study of the PRDX4 gene in a t(X;18)(p22;q23): a cautionary tale. ACTA ACUST UNITED AC 2008; 176:131-6. [PMID: 17656256 PMCID: PMC2083648 DOI: 10.1016/j.cancergencyto.2007.03.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2006] [Revised: 02/23/2007] [Accepted: 03/29/2007] [Indexed: 11/19/2022]
Abstract
The PRDX4 gene located at Xp22 encodes for a member of the peroxiredoxin gene family. Genes within this family exhibit thioredoxin-dependent peroxidase activity and have been implicated in cellular functioning, including proliferation and differentiation. Recently, PRDX4 has been identified as a partner gene in a t(X;21) translocation in a patient with acute myeloid leukemia. To determine whether PRDX4 was involved in other translocations, leukemia cells from 15 patients with Xp22 abnormalities were screened for involvement of the gene using fluorescence in situ hybridization (FISH). One sample from a 41-year-old woman with acute lymphoblastic leukemia showed three signals when hybridized with the PRDX4 probe. Cytogenetic analysis of the sample had identified a t(X;18)(p22;q23). Assuming that the three signals indicated a break within the PRDX4 gene, we performed FISH experiments and successfully narrowed the breakpoint on chromosome 18 to a 50-kb region. Subsequent analysis using spectral karyotyping showed that the leukemic cells had undergone multiple rearrangements and that a third X chromosome was present, albeit rearranged. Additional FISH experiments revealed that the third PRDX4 signal was the result of a third copy of the gene. Analysis of the other rearrangements has helped to characterize the multiple abnormalities within the leukemic cells. The findings underscore the importance of using multiple techniques when analyzing complex chromosomal rearrangements in malignant cells.
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Affiliation(s)
- Heidrun D. Gerr
- Institute for Cell and Molecular Pathology, Medizinische Hochschule Hannover, Hannover Germany
| | - Michele L. Nassin
- Department of Medicine, Section Hematology/Oncology, University of Chicago, Chicago, Illinois, USA
| | - Elizabeth M. Davis
- Department of Medicine, Section Hematology/Oncology, University of Chicago, Chicago, Illinois, USA
| | - Nimanthi Jayathilaka
- Department of Medicine, Section Hematology/Oncology, University of Chicago, Chicago, Illinois, USA
| | - Mary E. Neilly
- Department of Medicine, Section Hematology/Oncology, University of Chicago, Chicago, Illinois, USA
| | - Brigitte Schlegelberger
- Institute for Cell and Molecular Pathology, Medizinische Hochschule Hannover, Hannover Germany
| | - Yanming Zhang
- Department of Medicine, Section Hematology/Oncology, University of Chicago, Chicago, Illinois, USA
| | - Janet D. Rowley
- Department of Medicine, Section Hematology/Oncology, University of Chicago, Chicago, Illinois, USA
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99914
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Two subunits specific to the PBAP chromatin remodeling complex have distinct and redundant functions during drosophila development. Mol Cell Biol 2008; 28:5238-50. [PMID: 18573871 DOI: 10.1128/mcb.00747-08] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Chromatin remodeling complexes control the availability of DNA binding sites to transcriptional regulators. Two distinct conserved forms of the SWI/SNF class of complexes are characterized by the presence of specific accessory subunits. In Drosophila, the core Brahma complex associates either with Osa to form the BAP complex or with Bap170 and Bap180 to form the PBAP complex. osa mutations reproduce only a subset of the developmental phenotypes caused by mutations in subunits of the core complex. To test whether the PBAP complex performs the remaining functions, we generated mutations in bap170 and bap180. Surprisingly, we found that Bap180 is not essential for viability, although it is required in ovarian follicle cells for normal eggshell development. Bap170 is necessary to stabilize the Bap180 protein, but a mutant form that retains this function is sufficient for both survival and fertility. The two subunits act redundantly to allow metamorphosis; using gene expression profiling of bap170 bap180 double mutants, we found that the PBAP complex regulates genes involved in tissue remodeling and immune system function. Finally, we generated mutants lacking Bap170, Bap180, and Osa in the germ line to demonstrate that the core Brahma complex can function in oogenesis without any of these accessory subunits.
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99915
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Repression of prespliceosome complex formation at two distinct steps by Fox-1/Fox-2 proteins. Mol Cell Biol 2008; 28:5507-16. [PMID: 18573872 DOI: 10.1128/mcb.00530-08] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Precise and robust regulation of alternative splicing provides cells with an essential means of gene expression control. However, the mechanisms that ensure the tight control of tissue-specific alternative splicing are not well understood. It has been demonstrated that robust regulation often results from the contributions of multiple factors to one particular splicing pathway. We report here a novel strategy used by a single splicing regulator that blocks the formation of two distinct prespliceosome complexes to achieve efficient regulation. Fox-1/Fox-2 proteins, potent regulators of alternative splicing in the heart, skeletal muscle, and brain, repress calcitonin-specific splicing of the calcitonin/CGRP pre-mRNA. Using biochemical analysis, we found that Fox-1/Fox-2 proteins block prespliceosome complex formation at two distinct steps through binding to two functionally important UGCAUG elements. First, Fox-1/Fox-2 proteins bind to the intronic site to inhibit SF1-dependent E' complex formation. Second, these proteins bind to the exonic site to block the transition of E' complex that escaped the control of the intronic site to E complex. These studies provide evidence for the first example of regulated E' complex formation. The two-step repression of presplicing complexes by a single regulator provides a powerful and accurate regulatory strategy.
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99916
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99917
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Gupta R, Brosh RM. Helicases as prospective targets for anti-cancer therapy. Anticancer Agents Med Chem 2008; 8:390-401. [PMID: 18473724 DOI: 10.2174/187152008784220339] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
It has been proposed that selective inactivation of a DNA repair pathway may enhance anti-cancer therapies that eliminate cancerous cells through the cytotoxic effects of DNA damaging agents or radiation. Given the unique and critically important roles of DNA helicases in the DNA damage response, DNA repair, and maintenance of genomic stability, a number of strategies currently being explored or in use to combat cancer may be either mediated or enhanced through the modulation of helicase function. The focus of this review will be to examine the roles of helicases in DNA repair that might be suitably targeted by cancer therapeutic approaches. Treatment of cancers with anti-cancer drugs such as small molecule compounds that modulate helicase expression or function is a viable approach to selectively kill cancer cells through the inactivation of helicase-dependent DNA repair pathways, particularly those associated with DNA recombination, replication restart, and cell cycle checkpoint.
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Affiliation(s)
- Rigu Gupta
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, 5600 Nathan Shock Drive, Baltimore, MD 21224, USA
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99918
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Enhancer-promoter communication is regulated by insulator pairing in a Drosophila model bigenic locus. Mol Cell Biol 2008; 28:5469-77. [PMID: 18573869 DOI: 10.1128/mcb.00461-08] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The complexity of regulatory systems in higher eukaryotes, featuring many distantly located enhancers that nonetheless properly activate the target promoters, has prompted the hypothesis that the action of enhancers should be restricted by insulators. Continuing our research on the functional role of insulators and the consequences of their interaction in Drosophila, we studied the interplay of different Su(Hw)-dependent Drosophila insulators. The set of transgenic constructs comprised two consecutive genes (yellow and white) with their enhancers and insulator elements differently arranged in between and/or around the gene(s). All insulators were found to interact in twin or mixed tandems, demonstrating the bypass phenomenon. However, insulator pairing around a gene did not always improve its isolation from an outside enhancer. On the other hand, merely two insulator elements (identical or different) in appropriate positions can permit the expression of one gene but not the gene next to it or, conversely, largely block the transcription of the first gene, while allowing full enhancement of the second, or make them behave similarly. Thus, the results of this study support the model that loop formation by insulators is an essential component of insulator action on a positive and negative regulation of an enhancer-promoter communication.
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99919
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Sirtuins: novel targets for metabolic disease in drug development. Biochem Biophys Res Commun 2008; 373:341-4. [PMID: 18577374 DOI: 10.1016/j.bbrc.2008.06.048] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2008] [Accepted: 06/16/2008] [Indexed: 01/22/2023]
Abstract
Calorie restriction extends lifespan and produces a metabolic profile desirable for treating diseases such as type 2 diabetes. SIRT1, an NAD(+)-dependent deacetylase, is a principal modulator of pathways downstream of calorie restriction that produces beneficial effects on glucose homeostasis and insulin sensitivity. Activation of SIRT1 leads to enhanced activity of multiple proteins, including peroxisome proliferator-activated receptor coactivator-1alpha (PGC-1alpha) and FOXO which helps to mediate some of the in vitro and in vivo effects of sirtuins. Resveratrol, a polyphenolic SIRT1 activator, mimics the effects of calorie restriction in lower organisms and in mice fed a high-fat diet ameliorates insulin resistance. In this review, we summarize recent research advances in unveiling the molecular mechanisms that underpin sirtuin as therapeutic candidates and discuss the possibility of using resveratrol as potential drug for treatment of diabetes.
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99920
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Viens A, Harper F, Pichard E, Comisso M, Pierron G, Ogryzko V. Use of protein biotinylation in vivo for immunoelectron microscopic localization of a specific protein isoform. J Histochem Cytochem 2008; 56:911-9. [PMID: 18574249 DOI: 10.1369/jhc.2008.951624] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Tagging of proteins in vivo by covalent attachment of a biotin moiety has emerged as a new prospective tool for protein detection and purification. Previously, we established a strategy for expression of in vivo biotinylated proteins in mammalian cells. It is based on coexpression of the protein of interest fused to a short biotin acceptor peptide and biotin ligase BirA cloned in the same vector. We show here that the in vivo biotinylation can be used for immunogold postembedding labeling in immunoelectron microscopy experiments. We show that immunoelectron microscopy with biotinylated nuclear proteins is compatible with a wide range of postembedding methods, facilitating combination of morphological and localization studies in a single experiment. We also show that the method works in both transient transfection and stable cell line expression protocols and can be used for colocalization studies. This manuscript contains online supplemental material at http://www.jhc.org. Please visit this article online to view these materials.
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Affiliation(s)
- Antoine Viens
- Université Paris-Sud 11, CNRS, Interactions Moléculaires et Cancer UMR 8126, Institut de Cancérologie Gustave-Roussy, Villejuif, France
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99921
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Litman R, Gupta R, Brosh RM, Cantor SB. BRCA-FA pathway as a target for anti-tumor drugs. Anticancer Agents Med Chem 2008; 8:426-30. [PMID: 18473727 DOI: 10.2174/187152008784220285] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Promising research on DNA repair signaling pathways predicts a new age of anti-tumor drugs. This research was initiated through the discovery and characterization of proteins that functioned together in signaling pathways to sense, respond, and repair DNA damage. It was realized that tumor cells often lacked distinct DNA repair pathways, but simultaneously relied heavily on compensating pathways. More recently, researchers have begun to manipulate these compensating pathways to reign in and kill tumor cells. In a striking example it was shown that tumors derived from mutations in the DNA repair genes, of BRCA-FA pathway, were selectively sensitive to inhibition of the base excision repair pathway. These findings suggest that tumors derived from defects in DNA repair genes will be easier to treat clinically, providing a streamlined and targeted therapy that spares healthy cells. In the future, identifying patients with susceptible tumors and discovering additional DNA repair targets amenable to anti-tumor drugs will have a major impact on the course of cancer treatment.
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Affiliation(s)
- Rachel Litman
- Department of Cancer Biology, University of Massachusetts Medical School, 364 Plantation St., Worcester, MA 01605, USA
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99922
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Cooper A, Tait A, Sweeney L, Tweedie A, Morrison L, Turner CMR, MacLeod A. Genetic analysis of the human infective trypanosome Trypanosoma brucei gambiense: chromosomal segregation, crossing over, and the construction of a genetic map. Genome Biol 2008; 9:R103. [PMID: 18570680 PMCID: PMC2481433 DOI: 10.1186/gb-2008-9-6-r103] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2008] [Revised: 05/20/2008] [Accepted: 06/22/2008] [Indexed: 11/29/2022] Open
Abstract
A high-resolution genetic linkage map of the STIB 386 strain of Trypanosoma brucei gambiense is presented. Background Trypanosoma brucei is the causative agent of human sleeping sickness and animal trypanosomiasis in sub-Saharan Africa, and it has been subdivided into three subspecies: Trypanosoma brucei gambiense and Trypanosoma brucei rhodesiense, which cause sleeping sickness in humans, and the nonhuman infective Trypanosoma brucei brucei. T. b. gambiense is the most clinically relevant subspecies, being responsible for more than 90% of all trypanosomal disease in humans. The genome sequence is now available, and a Mendelian genetic system has been demonstrated in T. brucei, facilitating genetic analysis in this diploid protozoan parasite. As an essential step toward identifying loci that determine important traits in the human-infective subspecies, we report the construction of a high-resolution genetic map of the STIB 386 strain of T. b. gambiense. Results The genetic map was determined using 119 microsatellite markers assigned to the 11 megabase chromosomes. The total genetic map length of the linkage groups was 733.1 cM, covering a physical distance of 17.9 megabases with an average map unit size of 24 kilobases/cM. Forty-seven markers in this map were also used in a genetic map of the nonhuman infective T. b. brucei subspecies, permitting comparison of the two maps and showing that synteny is conserved between the two subspecies. Conclusion The genetic linkage map presented here is the first available for the human-infective trypanosome T. b. gambiense. In combination with the genome sequence, this opens up the possibility of using genetic analysis to identify the loci responsible for T. b. gambiense specific traits such as human infectivity as well as comparative studies of parasite field populations.
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Affiliation(s)
- Anneli Cooper
- Wellcome Centre for Molecular Parasitology, Glasgow Biomedical Research Centre, University Place, Glasgow G12 8TA, UK.
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99923
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99924
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Teng H, Parker MI, Prince S. Functional characterization of cis-acting elements involved in basal transcription of the human Tbx2 gene: a new insight into the role of Sp1 in transcriptional regulation. Gene 2008; 423:8-13. [PMID: 18640248 DOI: 10.1016/j.gene.2008.06.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2008] [Revised: 06/06/2008] [Accepted: 06/16/2008] [Indexed: 11/25/2022]
Abstract
Tbx2, a member of the T-box family of genes that encode developmentally important transcription factors, plays a critical role in development and has been linked to cancer. Here a 5'-flanking region of the human Tbx2 gene was cloned and characterized. While we identify a Sp1 element and a reverse CCAAT box to be essential for basal Tbx2 promoter activity, a physical interaction between Sp1 and NF-Y does not seem to be required for mediating their effect. Furthermore, our data reveal a downstream promoter element (DPE) in the Tbx2 promoter which significantly influences basal activity.
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Affiliation(s)
- Huajian Teng
- Division of Cell Biology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, 7925, Cape Town, South Africa
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99925
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Yu BJ, Kang KH, Lee JH, Sung BH, Kim MS, Kim SC. Rapid and efficient construction of markerless deletions in the Escherichia coli genome. Nucleic Acids Res 2008; 36:e84. [PMID: 18567910 PMCID: PMC2504295 DOI: 10.1093/nar/gkn359] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
We have developed an improved and rapid genomic engineering procedure for the construction of custom-designed microorganisms. This method, which can be performed in 2 days, permits restructuring of the Escherichia coli genome via markerless deletion of selected genomic regions. The deletion process was mediated by a special plasmid, pREDI, which carries two independent inducible promoters: (i) an arabinose-inducible promoter that drives expression of lambda-Red recombination proteins, which carry out the replacement of a target genomic region with a marker-containing linear DNA cassette, and (ii) a rhamnose-inducible promoter that drives expression of I-SceI endonuclease, which stimulates deletion of the introduced marker by double-strand breakage-mediated intramolecular recombination. This genomic deletion was performed successively with only one plasmid, pREDI, simply by changing the carbon source in the bacterial growth medium from arabinose to rhamnose. The efficiencies of targeted region replacement and deletion of the inserted linear DNA cassette were nearly 70 and 100%, respectively. This rapid and efficient procedure can be adapted for use in generating a variety of genome modifications.
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Affiliation(s)
- Byung Jo Yu
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Korea
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99926
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Moriarty TJ, Norman MU, Colarusso P, Bankhead T, Kubes P, Chaconas G. Real-time high resolution 3D imaging of the lyme disease spirochete adhering to and escaping from the vasculature of a living host. PLoS Pathog 2008; 4:e1000090. [PMID: 18566656 PMCID: PMC2408724 DOI: 10.1371/journal.ppat.1000090] [Citation(s) in RCA: 138] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2008] [Accepted: 05/14/2008] [Indexed: 02/05/2023] Open
Abstract
Pathogenic spirochetes are bacteria that cause a number of emerging and re-emerging diseases worldwide, including syphilis, leptospirosis, relapsing fever, and Lyme borreliosis. They navigate efficiently through dense extracellular matrix and cross the blood–brain barrier by unknown mechanisms. Due to their slender morphology, spirochetes are difficult to visualize by standard light microscopy, impeding studies of their behavior in situ. We engineered a fluorescent infectious strain of Borrelia burgdorferi, the Lyme disease pathogen, which expressed green fluorescent protein (GFP). Real-time 3D and 4D quantitative analysis of fluorescent spirochete dissemination from the microvasculature of living mice at high resolution revealed that dissemination was a multi-stage process that included transient tethering-type associations, short-term dragging interactions, and stationary adhesion. Stationary adhesions and extravasating spirochetes were most commonly observed at endothelial junctions, and translational motility of spirochetes appeared to play an integral role in transendothelial migration. To our knowledge, this is the first report of high resolution 3D and 4D visualization of dissemination of a bacterial pathogen in a living mammalian host, and provides the first direct insight into spirochete dissemination in vivo. Pathogenic spirochetes are bacteria that cause a number of emerging and re-emerging diseases worldwide, including syphilis, leptospirosis, relapsing fever, and Lyme disease. They exhibit an unusual form of motility and can infect many different tissues; however, the mechanism by which they disseminate from the blood to target sites is unknown. Direct visualization of bacterial pathogens at the single cell level in living hosts is an important goal of microbiology, since this approach is likely to yield critical insight into disease processes. We engineered a fluorescent strain of Borrelia burgdorferi, a Lyme disease pathogen, and used conventional and spinning disk confocal intravital microscopy to directly visualize these bacteria in real time and 3D in living mice. We found that spirochete interaction with and dissemination out of the vasculature was a multi-stage process of unexpected complexity and that spirochete movement appeared to play an integral role in dissemination. To our knowledge, this is the first report of high resolution 3D visualization of dissemination of a bacterial pathogen in a living mammalian host, and provides the first direct insight into spirochete dissemination in vivo.
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Affiliation(s)
- Tara J. Moriarty
- Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, Alberta, Canada
- Department of Microbiology & Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - M. Ursula Norman
- Department of Physiology & Biophysics, University of Calgary, Calgary, Alberta, Canada
| | - Pina Colarusso
- Department of Physiology & Biophysics, University of Calgary, Calgary, Alberta, Canada
| | - Troy Bankhead
- Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, Alberta, Canada
- Department of Microbiology & Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Paul Kubes
- Department of Physiology & Biophysics, University of Calgary, Calgary, Alberta, Canada
| | - George Chaconas
- Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, Alberta, Canada
- Department of Microbiology & Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
- * E-mail:
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99927
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Abstract
For many bacterial viruses, the choice of whether to kill host cells or enter a latent state depends on the multiplicity of coinfection. Here, we present a mathematical theory of how bacterial viruses can make collective decisions concerning the fate of infected cells. We base our theory on mechanistic models of gene regulatory dynamics. Unlike most previous work, we treat the copy number of viral genes as variable. Increasing the viral copy number increases the rate of transcription of viral mRNAs. When viral regulation of cell fate includes nonlinear feedback loops, very small changes in transcriptional rates can lead to dramatic changes in steady-state gene expression. Hence, we prove that deterministic decisions can be reached, e.g., lysis or latency, depending on the cellular multiplicity of infection within a broad class of gene regulatory models of viral decision-making. Comparisons of a parameterized version of the model with molecular studies of the decision structure in the temperate bacteriophage lambda are consistent with our conclusions. Because the model is general, it suggests that bacterial viruses can respond adaptively to changes in population dynamics, and that features of collective decision-making in viruses are evolvable life history traits.
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99928
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Cortese MS, Uversky VN, Dunker AK. Intrinsic disorder in scaffold proteins: getting more from less. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2008; 98:85-106. [PMID: 18619997 DOI: 10.1016/j.pbiomolbio.2008.05.007] [Citation(s) in RCA: 224] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Regulation, recognition and cell signaling involve the coordinated actions of many players. Signaling scaffolds, with their ability to bring together proteins belonging to common and/or interlinked pathways, play crucial roles in orchestrating numerous events by coordinating specific interactions among signaling proteins. This review examines the roles of intrinsic disorder (ID) in signaling scaffold protein function. Several well-characterized scaffold proteins with structurally and functionally characterized ID regions are used here to illustrate the importance of ID for scaffolding function. These examples include scaffolds that are mostly disordered, only partially disordered or those in which the ID resides in a scaffold partner. Specific scaffolds discussed include RNase, voltage-activated potassium channels, axin, BRCA1, GSK-3beta, p53, Ste5, titin, Fus3, BRCA1, MAP2, D-AKAP2 and AKAP250. Among the mechanisms discussed are: molecular recognition features, fly-casting, ease of encounter complex formation, structural isolation of partners, modulation of interactions between bound partners, masking of intramolecular interaction sites, maximized interaction surface per residue, toleration of high evolutionary rates, binding site overlap, allosteric modification, palindromic binding, reduced constraints for alternative splicing, efficient regulation via posttranslational modification, efficient regulation via rapid degradation, protection of normally solvent-exposed sites, enhancing the plasticity of interaction and molecular crowding. We conclude that ID can enhance scaffold function by a diverse array of mechanisms. In other words, scaffold proteins utilize several ID-facilitated mechanisms to enhance function, and by doing so, get more functionality from less structure.
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Affiliation(s)
- Marc S Cortese
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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99929
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Mitochondrial medicine for aging and neurodegenerative diseases. Neuromolecular Med 2008; 10:291-315. [PMID: 18566920 DOI: 10.1007/s12017-008-8044-z] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2008] [Accepted: 05/22/2008] [Indexed: 12/22/2022]
Abstract
Mitochondria are key cytoplasmic organelles, responsible for generating cellular energy, regulating intracellular calcium levels, altering the reduction-oxidation potential of cells, and regulating cell death. Increasing evidence suggests that mitochondria play a central role in aging and in neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, Huntington's disease, amyotrophic lateral sclerosis, and Freidriech ataxia. Further, several lines of evidence suggest that mitochondrial dysfunction is an early event in most late-onset neurodegenerative diseases. Biochemical and animal model studies of inherited neurodegenerative diseases have revealed that mutant proteins of these diseases are associated with mitochondria. Mutant proteins are reported to block the transport of nuclear-encoded mitochondrial proteins to mitochondria, interact with mitochondrial proteins and disrupt the electron transport chain, induce free radicals, cause mitochondrial dysfunction, and, ultimately, damage neurons. This article discusses critical issues of mitochondria causing dysfunction in aging and neurodegenerative diseases, and discusses the potential of developing mitochondrial medicine, particularly mitochondrially targeted antioxidants, to treat aging and neurodegenerative diseases.
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99930
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Casals F, Ferrer-Admetlla A, Chillarón J, Torrents D, Palacín M, Bertranpetit J. Is There Selection for the Pace of Successive Inactivation of the arpAT Gene in Primates? J Mol Evol 2008; 67:23-8. [DOI: 10.1007/s00239-008-9120-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2007] [Revised: 03/27/2008] [Accepted: 05/06/2008] [Indexed: 11/29/2022]
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99931
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Calisto V, Fuzinatto VA, Message HJ, Mendes-Bonato AB, Boldrini KR, Pagliarini MS, do Valle CB. Desynapsis and precocious cytokinesis in Brachiaria humidicola (Poaceae) compromise meiotic division. J Genet 2008; 87:27-31. [PMID: 18560171 DOI: 10.1007/s12041-008-0004-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The forage grass species Brachiaria humidicola is native to African savannas. Owing to its good adaptation to poorly drained and infertile acid soils, it has achieved wide utilization for pastures in Brazilian farms. Among the 55 accessions of B. humidicola analysed from the Embrapa Beef Cattle collection, one (H022), presented desynapsis and an abnormal pattern of cytokinesis in the first meiotic division. Among 28 inflorescences analysed in this accession, 12 were affected by the anomaly. In affected meiocytes, the first cytokinesis occurred in metaphase I and was generally perpendicular to a wide-metaphase plate, dividing the genome into two parts with an equal or unequal number of chromosomes. The normal cytokinesis after telophase I did not occur, and the meiocytes entered metaphase II, progressing to the end of meiosis with the occurrence of the second cytokinesis. As the first cytokinesis occurred precociously, whereas the second was normal, tetrads were formed but with unbalanced chromosome numbers in microspores. Abnormal cytokinesis occurred only in those meiocytes that underwent desynapsis after diakinesis. The implications of this abnormality in the Brachiaria breeding programme are discussed.
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Affiliation(s)
- Vergílio Calisto
- Department of Cell Biology and Genetics, State University of Maringá, 87020-900 Maringá, Paraná, Brazil
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99932
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Abstract
The idea of subfertile or altogether infertile sperm seems an evolutionary paradox, so why have they evolved in a diverse set of species, from molluscs to mice? Understanding sperm sociality may provide the answer.
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Affiliation(s)
- Tommaso Pizzari
- Edward Grey Institute in Department of Zoology of University of Oxford, Oxford, United Kingdom.
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99933
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Strbo N, Podack ER. Secreted heat shock protein gp96-Ig: an innovative vaccine approach. Am J Reprod Immunol 2008; 59:407-16. [PMID: 18405311 DOI: 10.1111/j.1600-0897.2008.00594.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Heat shock proteins (HSPs) are a large family of proteins with different molecular weights and different intracellular localizations. These proteins undertake crucial functions in maintaining cell homeostasis, and therefore they have been conserved during evolution. HSP gp96 also known as glucose-regulated protein grp94, is the primary chaperone of the endoplasmatic reticulum. Gp96/grp94, because of its peptide chaperone capacity and its ability to interact actively with professional antigen-presenting cells (APCs), is also endowed with crucial immunological functions such as natural adjuvant for priming innate and adaptive immunity. To make gp96 accessible to the immune system without biochemical purification and without cell lysis, we generated a secreted form of gp96. The immunological properties of secreted gp96 and its implications for vaccine in human cancer and infectious diseases will be discussed.
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Affiliation(s)
- Natasa Strbo
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, USA
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99934
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Saccone SF, Saccone NL, Swan GE, Madden PAF, Goate AM, Rice JP, Bierut LJ. Systematic biological prioritization after a genome-wide association study: an application to nicotine dependence. ACTA ACUST UNITED AC 2008; 24:1805-11. [PMID: 18565990 DOI: 10.1093/bioinformatics/btn315] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MOTIVATION A challenging problem after a genome-wide association study (GWAS) is to balance the statistical evidence of genotype-phenotype correlation with a priori evidence of biological relevance. RESULTS We introduce a method for systematically prioritizing single nucleotide polymorphisms (SNPs) for further study after a GWAS. The method combines evidence across multiple domains including statistical evidence of genotype-phenotype correlation, known pathways in the pathologic development of disease, SNP/gene functional properties, comparative genomics, prior evidence of genetic linkage, and linkage disequilibrium. We apply this method to a GWAS of nicotine dependence, and use simulated data to test it on several commercial SNP microarrays. AVAILABILITY A comprehensive database of biological prioritization scores for all known SNPs is available at http://zork.wustl.edu/gin. This can be used to prioritize nicotine dependence association studies through a straightforward mathematical formula-no special software is necessary. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Scott F Saccone
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, Missouri 63110, USA.
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99935
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Li F, Dong J, Pan X, Oum JH, Boeke JD, Lee SE. Microarray-based genetic screen defines SAW1, a gene required for Rad1/Rad10-dependent processing of recombination intermediates. Mol Cell 2008; 30:325-35. [PMID: 18471978 DOI: 10.1016/j.molcel.2008.02.028] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2007] [Revised: 01/29/2008] [Accepted: 02/27/2008] [Indexed: 11/18/2022]
Abstract
Elimination of a double-strand break (DSB) flanked by direct repeat sequences is mediated by single-strand annealing (SSA), which relies on a distinct set of gene products involving recombination, mismatch repair, and nucleotide excision repair. Here, we screened for yeast mutants defective in SSA with a plasmid-based SSA assay coupled to a barcode microarray readout. The screen identified Yal027Wp/Saw1 (single-strand annealing weakened 1) and Slx4 besides other known SSA proteins. Saw1 interacts physically with Rad1/Rad10, Msh2/Msh3, and Rad52 proteins, and cells lacking SLX4 or SAW1 accumulate recombination intermediates blocked at the Rad1/Rad10-dependent 3' flap cleavage step. Slx4 and Saw1 also contribute to the integrity of ribosomal DNA arrays. Saw1 mutants that fail to interact with Rad1, but retain interaction with Rad52 and Msh2, are defective in 3' flap removal and SSA repair. Deletion of SAW1 abolished association of Rad1 at SSA intermediates in vivo. We propose that Saw1 targets Rad1/Rad10 to Rad52-coated recombination intermediates.
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Affiliation(s)
- Fuyang Li
- Department of Molecular Medicine and Institute of Biotechnology, University of Texas Health Science Center at San Antonio, 15355 Lambda Drive, San Antonio, TX 78245, USA
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99936
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Moon S, Cho S, Kim H. Organization and evolution of mitochondrial gene clusters in human. Genomics 2008; 92:85-93. [PMID: 18559289 DOI: 10.1016/j.ygeno.2008.01.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2007] [Revised: 01/07/2008] [Accepted: 01/08/2008] [Indexed: 11/29/2022]
Abstract
Currently, the spatial patterns of mitochondrial genes and how the genomic localization of (pseudo)genes originated from mitochondrial DNA remain largely unexplained. The aim of this study was to elucidate the organization of mitochondrial (pseudo)genes given their evolutionary origin. We used a keyword finding method and a bootstrapping method to estimate parameter values that represent the distribution pattern of mitochondrial genes in the nuclear genome. Almost half of mitochondrial genes showing physical clusters were located in the pericentromeric and subtelomeric regions of the chromosome. Most interestingly, the size of these clusters ranged from 0.085 to 3.2 Mb (average+/-SD 1.3+/-0.73 Mb), which coincides with the size of the evolutionary pocket, or the average size of evolutionary breakpoint regions. Our findings imply that the localization of mitochondrial genes in the human genome is determined independent of adaptation.
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Affiliation(s)
- Sunjin Moon
- Laboratory of Bioinformatics and Population Genetics, Department of Agricultural Biotechnology, Seoul National University, Seoul 151-742, Korea
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99937
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Shahid M, Han S, Yoell H, Xu J. Fitness distribution and transgressive segregation across 40 environments in a hybrid progeny population of the human-pathogenic yeast Cryptococcus neoformans. Genome 2008; 51:272-81. [PMID: 18356963 DOI: 10.1139/g08-004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The opportunistic human fungal pathogen Cryptococcus neoformans includes two varieties, C. neoformans var. grubii and C. neoformans var. neoformans, which correspond to serotypes A and D, respectively. Recent population genetic studies revealed that multiple natural hybridizations have occurred recently between these two divergent lineages. However, the biological effects of such hybridizations are little understood. In this study, we used colony size as a proxy for vegetative fitness to examine the phenotypic effects of hybridization between these two lineages in a laboratory cross. Two genetically diverged parental strains that differed in their growth at different temperatures and on different media as well as in their susceptibility to the common antifungal drug fluconazole were chosen. A total of 269 progeny were obtained and their vegetative growth was determined in 40 environments that differed in nutrients, temperature, and fluconazole concentration. Our analyses indicated little evidence for outbreeding depression or heterosis in the average vegetative fitness of the hybrid progeny population. The progeny, each of the three environmental variables, and their two-way, three-way, and four-way interactions all contributed significantly to the overall vegetative fitness variation. Interestingly, a variable number of progeny displayed evidence of transgressive segregation in vegetative fitness among the tested environments. Our study suggests that hybridization could play a significant role in the phenotypic evolution of this important human-pathogenic fungus.
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Affiliation(s)
- Morvarid Shahid
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
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99938
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Guo JY, Yamada A, Kajino T, Wu JQ, Tang W, Freel CD, Feng J, Chau BN, Wang MZ, Margolis SS, Yoo HY, Wang XF, Dunphy WG, Irusta PM, Hardwick JM, Kornbluth S. Aven-dependent activation of ATM following DNA damage. Curr Biol 2008; 18:933-42. [PMID: 18571408 DOI: 10.1016/j.cub.2008.05.045] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2007] [Revised: 05/23/2008] [Accepted: 05/23/2008] [Indexed: 01/22/2023]
Abstract
BACKGROUND In response to DNA damage, cells undergo either cell-cycle arrest or apoptosis, depending on the extent of damage and the cell's capacity for DNA repair. Cell-cycle arrest induced by double-stranded DNA breaks depends on activation of the ataxia-telangiectasia (ATM) protein kinase, which phosphorylates cell-cycle effectors such as Chk2 and p53 to inhibit cell-cycle progression. ATM is recruited to double-stranded DNA breaks by a complex of sensor proteins, including Mre11/Rad50/Nbs1, resulting in autophosphorylation, monomerization, and activation of ATM kinase. RESULTS In characterizing Aven protein, a previously reported apoptotic inhibitor, we have found that Aven can function as an ATM activator to inhibit G2/M progression. Aven bound to ATM and Aven overexpressed in cycling Xenopus egg extracts prevented mitotic entry and induced phosphorylation of ATM and its substrates. Immunodepletion of endogenous Aven allowed mitotic entry even in the presence of damaged DNA, and RNAi-mediated knockdown of Aven in human cells prevented autophosphorylation of ATM at an activating site (S1981) in response to DNA damage. Interestingly, Aven is also a substrate of the ATM kinase. Mutation of ATM-mediated phosphorylation sites on Aven reduced its ability to activate ATM, suggesting that Aven activation of ATM after DNA damage is enhanced by ATM-mediated Aven phosphorylation. CONCLUSIONS These results identify Aven as a new ATM activator and describe a positive feedback loop operating between Aven and ATM. In aggregate, these findings place Aven, a known apoptotic inhibitor, as a critical transducer of the DNA-damage signal.
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Affiliation(s)
- Jessie Yanxiang Guo
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
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99939
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Desai S, Heffelfinger AK, Orcutt TM, Litman GW, Yoder JA. The medaka novel immune-type receptor (NITR) gene clusters reveal an extraordinary degree of divergence in variable domains. BMC Evol Biol 2008; 8:177. [PMID: 18565225 PMCID: PMC2442602 DOI: 10.1186/1471-2148-8-177] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2008] [Accepted: 06/19/2008] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Novel immune-type receptor (NITR) genes are members of diversified multigene families that are found in bony fish and encode type I transmembrane proteins containing one or two extracellular immunoglobulin (Ig) domains. The majority of NITRs can be classified as inhibitory receptors that possess cytoplasmic immunoreceptor tyrosine-based inhibition motifs (ITIMs). A much smaller number of NITRs can be classified as activating receptors by the lack of cytoplasmic ITIMs and presence of a positively charged residue within their transmembrane domain, which permits partnering with an activating adaptor protein. RESULTS Forty-four NITR genes in medaka (Oryzias latipes) are located in three gene clusters on chromosomes 10, 18 and 21 and can be organized into 24 families including inhibitory and activating forms. The particularly large dataset acquired in medaka makes direct comparison possible to another complete dataset acquired in zebrafish in which NITRs are localized in two clusters on different chromosomes. The two largest medaka NITR gene clusters share conserved synteny with the two zebrafish NITR gene clusters. Shared synteny between NITRs and CD8A/CD8B is limited but consistent with a potential common ancestry. CONCLUSION Comprehensive phylogenetic analyses between the complete datasets of NITRs from medaka and zebrafish indicate multiple species-specific expansions of different families of NITRs. The patterns of sequence variation among gene family members are consistent with recent birth-and-death events. Similar effects have been observed with mammalian immunoglobulin (Ig), T cell antigen receptor (TCR) and killer cell immunoglobulin-like receptor (KIR) genes. NITRs likely diverged along an independent pathway from that of the somatically rearranging antigen binding receptors but have undergone parallel evolution of V family diversity.
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Affiliation(s)
- Salil Desai
- Department of Molecular Biomedical Sciences and Center for Comparative Medicine and Translational Research, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough Street, Raleigh, NC 27606, USA.
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99940
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Abstract
Mitochondria are semi-autonomously reproductive organelles within eukaryotic cells carrying their own genetic material, called the mitochondrial genome (mtDNA). Until some years ago, mtDNA had primarily been used as a tool in population genetics. As scientists began associating mtDNA mutations with dozens of mysterious disorders, as well as the aging process and a variety of chronic degenerative diseases, it became increasingly evident that the information contained in this genome had substantial potential applications to improve human health. Today, mitochondria research covers a wide range of disciplines, including clinical medicine, biochemistry, genetics, molecular cell biology, bioinformatics, plant sciences and physiology. The present review intends to present a summary of the most exiting fields of the mitochondrial research bringing together several contributes in terms of original prospective and future applications.
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Affiliation(s)
- Marco Crimi
- National Institute of Molecular Genetics (INGM), Functional Genomics Unit, Milan, Italy.
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99941
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Kunkel TA. Oligonucleotide-directed mutagenesis without phenotypic selection. ACTA ACUST UNITED AC 2008; Chapter 4:Unit 4.10. [PMID: 18428474 DOI: 10.1002/0471142301.ns0410s03] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A DNA sequence can be specifically altered by synthesizing the desired sequence change within an oligonucleotide, and then converting this into a biologically active circular DNA strand by using the oligonucleotide to prime in vitro synthesis on a single-stranded circular template. This unit presents a protocol which uses a DNA template containing a small number of uracil residues in place of thymine. Use of the uracil-containing template allows rapid and efficient recovery of mutants; in principle this same template can be applied to most of the other mutagenesis protocols in use. The length of the oligonucleotide primer is highly variable and depends on the nature of the change being made.
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Affiliation(s)
- T A Kunkel
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
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99942
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Juhász A, Pfeiffer I, Keszthelyi A, Kucsera J, Vágvölgyi C, Hamari Z. Comparative analysis of the complete mitochondrial genomes of Aspergillus niger mtDNA type 1a and Aspergillus tubingensis mtDNA type 2b. FEMS Microbiol Lett 2008; 281:51-7. [PMID: 18318841 DOI: 10.1111/j.1574-6968.2008.01077.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
To understand the differences in the organization of mitochondrial genomes of the very closely related Aspergillus niger and Aspergillus tubingensis species, we determined the complete genome sequence of the 1a mtDNA type of A. niger and 2b mtDNA type of A. tubingensis and now we provide a comparative analysis of the two mtDNAs. We found that (1) the organization (gene content and order) of the two genomes is almost identical and (2) the size difference between them is principally attributed to the different intron content of their cox1, atp9 and ndh4L genes.
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Affiliation(s)
- Akos Juhász
- Department of Microbiology, Faculty of Sciences, University of Szeged, Szeged, Hungary
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99943
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Bajaj R, Mohanty S, Dash AP, Das A. Fine-scale genetic characterization of Plasmodium falciparum chromosome 7 encompassing the antigenic var and the drug-resistant pfcrt genes. J Genet 2008; 87:59-64. [PMID: 18560175 DOI: 10.1007/s12041-008-0008-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The fact that malaria is still an uncontrolled disease is reflected by the genetic organization of the parasite genome. Efforts to curb malaria should begin with proper understanding of the mechanism by which the parasites evade human immune system and evolve resistance to different antimalarial drugs. We have initiated such a study and presented herewith the results from the in silico understanding of a seventh chromosomal region of the malarial parasite Plasmodium falciparum encompassing the antigenic var genes (coding pfemp1) and the drug-resistant gene pfcrt located at a specified region of the chromosome 7. We found 60 genes of various functions and lengths, majority (61.67%) of them were performing known functions. Almost all the genes have orthologs in other four species of Plasmodium, of which P. chabaudi seems to be the closest to P. falciparum. However, only two genes were found to be paralogous. Interestingly, the drug-resistant gene, pfcrt was found to be surrounded by seven genes coding for several CG proteins out of which six were reported to be responsible for providing drug resistance to P. vivax. The intergenic regions, in this specified region were generally large in size, majority (73%) of them were of more than 500 nucleotide bp length. We also designed primers for amplification of 21 noncoding DNA fragments in the whole region for estimating genetic diversity and inferring the evolutionary history of this region of P. falciparum genome.
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Affiliation(s)
- Ruchi Bajaj
- Evolutionary Genomics and Bioinformatics Laboratory, National Institute of Malaria Research, 22 Sham Nath Marg, New Delhi 110 054, India
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99944
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Abstract
Insulators define interactions between transcriptional control elements in eukaryotic genomes. The gypsy insulator found in the gypsy retrovirus binds the zinc-finger Suppressor of Hairy-wing [Su(Hw)] protein that associates with hundreds of non-gypsy regions throughout the Drosophila genome. Models of insulator function predict that the gypsy insulator forms chromatin loop domains through interactions with endogenous Su(Hw) insulators (SIs) to limit the action of transcriptional control elements. Here we study SI 62D and show that interactions occur between two SI 62D elements, but not between SI 62D and the gypsy insulator, limiting the scope of genomic gypsy insulator interactions. Enhancer blocking by SI 62D requires fewer Su(Hw)-binding sites than needed for gypsy insulator function, with these target regions having distinct zinc-finger requirements for in vivo Su(Hw) association. These observations led to an investigation of the role of the Su(Hw) zinc-finger domain in insulator function. Using a combination of in vitro and in vivo studies, we find that this domain makes sequence-dependent and -independent contributions to in vivo chromosome association, but is not essential for enhancer or silencer blocking. These studies extend our understanding of the properties of Su(Hw) and the endogenous genomic regions to which this protein localizes.
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99945
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Griffith KL, Grossman AD. A degenerate tripartite DNA-binding site required for activation of ComA-dependent quorum response gene expression in Bacillus subtilis. J Mol Biol 2008; 381:261-75. [PMID: 18585392 DOI: 10.1016/j.jmb.2008.06.035] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2008] [Revised: 06/09/2008] [Accepted: 06/11/2008] [Indexed: 11/20/2022]
Abstract
In Bacillus subtilis, the transcription factor ComA activates several biological processes in response to increasing population density. Extracellular peptide signaling is used to coordinate the activity of ComA with population density. At low culture densities, when the concentration of signaling peptides is lowest, ComA is largely inactive. At higher densities, when the concentration of signaling peptides is higher, ComA is active and activates the transcription of at least nine operons involved in the development of competence and in the production of degradative enzymes and antibiotics. We found that ComA binds a degenerate tripartite sequence consisting of three DNA-binding determinants or "recognition elements." Mutational analyses showed that all three recognition elements are required for transcription activation in vivo and for specific DNA binding by ComA in vitro. Degeneracy of the recognition elements in the ComA-binding site is an important regulatory feature for coordinating transcription with population density (i.e., promoters containing an optimized binding site have high activity at low culture density and are no longer regulated in the normal-density-dependent manner). We found that purified ComA forms a dimer in solution, and we propose a model for how two dimers of ComA bind to an odd number of DNA-binding determinants to activate transcription of target genes. This DNA-protein architecture for transcription activation appears to be conserved for ComA homologs in other Bacillus species.
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Affiliation(s)
- Kevin L Griffith
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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99946
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99947
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Sequence divergence impedes crossover more than noncrossover events during mitotic gap repair in yeast. Genetics 2008; 179:1251-62. [PMID: 18562664 DOI: 10.1534/genetics.108.090233] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Homologous recombination between dispersed repeated sequences is important in shaping eukaryotic genome structure, and such ectopic interactions are affected by repeat size and sequence identity. A transformation-based, gap-repair assay was used to examine the effect of 2% sequence divergence on the efficiency of mitotic double-strand break repair templated by chromosomal sequences in yeast. Because the repaired plasmid could either remain autonomous or integrate into the genome, the effect of sequence divergence on the crossover-noncrossover (CO-NCO) outcome was also examined. Finally, proteins important for regulating the CO-NCO outcome and for enforcing identity requirements during recombination were examined by transforming appropriate mutant strains. Results demonstrate that the basic CO-NCO outcome is regulated by the Rad1-Rad10 endonuclease and the Sgs1 and Srs2 helicases, that sequence divergence impedes CO to a much greater extent than NCO events, that an intact mismatch repair system is required for the discriminating identical and nonidentical repair templates, and that the Sgs1 and Srs2 helicases play additional, antirecombination roles when the interacting sequences are not identical.
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99948
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Abstract
Meiotic reciprocal recombination (crossing over) was examined in the outermost 60-80 kb of almost all Saccharomyces cerevisiae chromosomes. These sequences included both repetitive gene-poor subtelomeric heterochromatin-like regions and their adjacent unique gene-rich euchromatin-like regions. Subtelomeric sequences underwent very little crossing over, exhibiting approximately two- to threefold fewer crossovers per kilobase of DNA than the genomic average. Surprisingly, the adjacent euchromatic regions underwent crossing over at twice the average genomic rate and contained at least nine new recombination "hot spots." These results prompted an analysis of existing genetic mapping data, which showed that meiotic reciprocal recombination rates were on average greater near chromosome ends exclusive of the subtelomeres. Thus, the distribution of crossovers in S. cerevisiae appears to resemble that found in several higher eukaryotes where the outermost chromosomal regions show increased crossing over.
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99949
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Hasegawa K, Yoshiyama K, Maki H. Spontaneous mutagenesis associated with nucleotide excision repair in Escherichia coli. Genes Cells 2008; 13:459-69. [PMID: 18429818 DOI: 10.1111/j.1365-2443.2008.01185.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The vast majority of spontaneous mutations occurring in Escherichia coli are thought to be derived from spontaneous DNA lesions, which include oxidative base damage. Systems for removing intrinsic mutagens and repairing DNA lesions contribute to the suppression of spontaneous mutations. Nucleotide excision repair (NER) is a general DNA repair system that eliminates various kinds of lesions from DNA. We therefore predicted that NER might be involved in suppression of spontaneous mutations, and analyzed base substitutions occurring spontaneously within the rpoB gene in NER-proficient (wild-type), -deficient and -overproducing E. coli strains. Surprisingly, the mutation frequency was lower in NER-deficient strains, and higher in NER-overproducing strains, than in the NER-proficient strain. These results suggest, paradoxically, that NER contributes to the generation of spontaneous mutation rather than to its suppression under normal growth conditions, and that transcription-coupled repair also participates in this process. Using E. coli strains that carried an editing exonuclease-deficient polA mutation, we further obtained data suggesting that unnecessary NER might account for these findings, so that errors introduced during repair DNA synthesis by DNA polymerase I would result in unwanted base substitutions. The repair system itself may thus be an important generator of spontaneous mutation.
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Affiliation(s)
- Kimiko Hasegawa
- Department of Molecular Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
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99950
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Attempts to establish RNA interference in the parasitic nematode Heligmosomoides polygyrus. Mol Biochem Parasitol 2008; 161:21-31. [PMID: 18606194 DOI: 10.1016/j.molbiopara.2008.06.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2008] [Revised: 05/30/2008] [Accepted: 06/03/2008] [Indexed: 01/29/2023]
Abstract
To analyze the potential of RNA interference (RNAi) in the intestinal nematode Heligmosomoides polygyrus, we delivered double-stranded RNA (dsRNA) of tropomyosin to various life stages of the parasite. Three different methods were examined for their potential use. First, feeding of recombinant bacteria that expressed dsRNA did neither result in phenotypical changes of H. polygyrus nor in a significant reduction of tropomyosin mRNA levels. In contrast, feeding of such bacteria to Caenorhabditis elegans elicited the expected phenotypes. Quantification of bacteria ingested by C. elegans and H. polygyrus larvae (L1) revealed that the parasitic worms took up only a fraction of the bacteria ingested by C. elegans. Second, electroporation of L1 failed to transport siRNA through the cuticle and was lethal to the larvae. However, the cuticle of adult worms was penetrated by dye-labeled RNA, but no systemic spreading was observed. Third, soaking of adult H. polygyrus in tropomyosin dsRNA led to a higher proportion of worms showing symptoms of ageing, such as a disintegrated gut and ovaries, but did not induce reduction of tropomyosin mRNA levels. Database analysis revealed that orthologous proteins involved in dsRNA-uptake and -systemic spread in C. elegans are missing in the parasitic nematodes Brugia malayi and Haemonchus contortus, whereas proteins responsible for dsRNA-processing, -amplification and mRNA-regulation are present. Thus, our data indicate that the study of gene function by RNAi in H. polygyrus is limited, possibly due to deficiencies of genes involved in RNA-uptake and spread.
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