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Punzo P, Ruggiero A, Possenti M, Perrella G, Nurcato R, Costa A, Morelli G, Grillo S, Batelli G. DRT111/SFPS Splicing Factor Controls Abscisic Acid Sensitivity during Seed Development and Germination. PLANT PHYSIOLOGY 2020; 183:793-807. [PMID: 32123040 PMCID: PMC7271812 DOI: 10.1104/pp.20.00037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 02/12/2020] [Indexed: 05/22/2023]
Abstract
RNA splicing is a fundamental mechanism contributing to the definition of the cellular protein population in any given environmental condition. DNA-DAMAGE REPAIR/TOLERATION PROTEIN111 (DRT111)/SPLICING FACTOR FOR PHYTOCHROME SIGNALING is a splicing factor previously shown to interact with phytochrome B and characterized for its role in splicing of pre-mRNAs involved in photomorphogenesis. Here, we show that DRT111 interacts with Arabidopsis (Arabidopsis thaliana) Splicing Factor1, involved in 3' splicing site recognition. Double- and triple-mutant analysis shows that DRT111 controls splicing of ABI3 and acts upstream of the splicing factor SUPPRESSOR OF ABI3-ABI5. DRT111 is highly expressed in seeds and stomata of Arabidopsis and is induced by long-term treatments of polyethylene glycol and abscisic acid (ABA). DRT111 knock-out mutants are defective in ABA-induced stomatal closure and are hypersensitive to ABA during seed germination. Conversely, DRT111 overexpressing plants show ABA-hyposensitive seed germination. RNA-sequencing experiments show that in dry seeds, DRT111 controls expression and splicing of genes involved in osmotic-stress and ABA responses, light signaling, and mRNA splicing, including targets of ABSCISIC ACID INSENSITIVE3 (ABI3) and PHYTOCHROME INTERACTING FACTORs (PIFs). Consistently, expression of the germination inhibitor SOMNUS, induced by ABI3 and PIF1, is upregulated in imbibed seeds of drt111-2 mutants. Together, these results indicate that DRT111 controls sensitivity to ABA during seed development, germination, and stomatal movements, and integrates ABA- and light-regulated pathways to control seed germination.
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Affiliation(s)
- Paola Punzo
- National Research Council of Italy, Institute of Biosciences and Bioresources, 80055 Portici, Naples, Italy
| | - Alessandra Ruggiero
- National Research Council of Italy, Institute of Biosciences and Bioresources, 80055 Portici, Naples, Italy
| | - Marco Possenti
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, 00178 Rome, Italy
| | - Giorgio Perrella
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development, 75026 Rotondella, Matera, Italy
| | - Roberta Nurcato
- National Research Council of Italy, Institute of Biosciences and Bioresources, 80055 Portici, Naples, Italy
| | - Antonello Costa
- National Research Council of Italy, Institute of Biosciences and Bioresources, 80055 Portici, Naples, Italy
| | - Giorgio Morelli
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, 00178 Rome, Italy
| | - Stefania Grillo
- National Research Council of Italy, Institute of Biosciences and Bioresources, 80055 Portici, Naples, Italy
| | - Giorgia Batelli
- National Research Council of Italy, Institute of Biosciences and Bioresources, 80055 Portici, Naples, Italy
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2
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Xin R, Zhu L, Salomé PA, Mancini E, Marshall CM, Harmon FG, Yanovsky MJ, Weigel D, Huq E. SPF45-related splicing factor for phytochrome signaling promotes photomorphogenesis by regulating pre-mRNA splicing in Arabidopsis. Proc Natl Acad Sci U S A 2017; 114:E7018-E7027. [PMID: 28760995 PMCID: PMC5565451 DOI: 10.1073/pnas.1706379114] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Light signals regulate plant growth and development by controlling a plethora of gene expression changes. Posttranscriptional regulation, especially pre-mRNA processing, is a key modulator of gene expression; however, the molecular mechanisms linking pre-mRNA processing and light signaling are not well understood. Here we report a protein related to the human splicing factor 45 (SPF45) named splicing factor for phytochrome signaling (SFPS), which directly interacts with the photoreceptor phytochrome B (phyB). In response to light, SFPS-RFP (red fluorescent protein) colocalizes with phyB-GFP in photobodies. sfps loss-of-function plants are hyposensitive to red, far-red, and blue light, and flower precociously. SFPS colocalizes with U2 small nuclear ribonucleoprotein-associated factors including U2AF65B, U2A', and U2AF35A in nuclear speckles, suggesting SFPS might be involved in the 3' splice site determination. SFPS regulates pre-mRNA splicing of a large number of genes, of which many are involved in regulating light signaling, photosynthesis, and the circadian clock under both dark and light conditions. In vivo RNA immunoprecipitation (RIP) assays revealed that SFPS associates with EARLY FLOWERING 3 (ELF3) mRNA, a critical link between light signaling and the circadian clock. Moreover, PHYTOCHROME INTERACTING FACTORS (PIFs) transcription factor genes act downstream of SFPS, as the quadruple pif mutant pifq suppresses defects of sfps mutants. Taken together, these data strongly suggest SFPS modulates light-regulated developmental processes by controlling pre-mRNA splicing of light signaling and circadian clock genes.
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Affiliation(s)
- Ruijiao Xin
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
- The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712
| | - Ling Zhu
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
- The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712
| | - Patrice A Salomé
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany
| | - Estefania Mancini
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina, C1405BWE Buenos Aires, Argentina
| | - Carine M Marshall
- Plant Gene Expression Center, U.S. Department of Agriculture Agricultural Research Service, Albany, CA 94710
- Department of Plant & Microbial Biology, University of California, Berkeley, CA 94720
| | - Frank G Harmon
- Plant Gene Expression Center, U.S. Department of Agriculture Agricultural Research Service, Albany, CA 94710
- Department of Plant & Microbial Biology, University of California, Berkeley, CA 94720
| | - Marcelo J Yanovsky
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina, C1405BWE Buenos Aires, Argentina
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany
| | - Enamul Huq
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712;
- The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712
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3
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Zhang Z, Liu Y, Ding P, Li Y, Kong Q, Zhang Y. Splicing of receptor-like kinase-encoding SNC4 and CERK1 is regulated by two conserved splicing factors that are required for plant immunity. MOLECULAR PLANT 2014; 7:1766-75. [PMID: 25267732 PMCID: PMC4261838 DOI: 10.1093/mp/ssu103] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 09/09/2014] [Indexed: 05/20/2023]
Abstract
Plant immune receptors belonging to the receptor-like kinase (RLK) family play important roles in the recognition of microbial pathogens and activation of downstream defense responses. The Arabidopsis mutant snc4-1D contains a gain-of-function mutation in the RLK SNC4 (SUPPRESSOR OF NPR1-1, CONSTITUTIVE4), which leads to constitutive activation of defense responses. Analysis of suppressor mutants of snc4-1D identified two conserved splicing factors, SUA (SUPPRESSOR OF ABI3-5) and RSN2 (REQUIRED FOR SNC4-1D 2), that are required for the constitutive defense responses in snc4-1D. In sua and rsn2 mutants, SNC4 splicing is altered and the amount of SNC4 transcripts is reduced. Further analysis showed that SUA and RSN2 are also required for the proper splicing of CERK1 (CHITIN ELICITOR RECEPTOR KINASE1), which encodes another RLK that functions as a receptor for chitin. In sua and rsn2 mutants, induction of reactive oxygen species by chitin is reduced and the non-pathogenic bacteria Pseudomonas syringae pv. tomato DC3000hrcC grows to higher titers than in wild-type plants. Our study suggests that pre-mRNA splicing plays important roles in the regulation of plant immunity mediated by the RLKs SNC4 and CERK1.
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Affiliation(s)
- Zhibin Zhang
- Department of Botany, University of British Columbia, Vancouver, Canada V6T 1Z4
| | - Yanan Liu
- Department of Botany, University of British Columbia, Vancouver, Canada V6T 1Z4
| | - Pingtao Ding
- Department of Botany, University of British Columbia, Vancouver, Canada V6T 1Z4
| | - Yan Li
- National Institute of Biological Sciences, Zhongguancun Life Science Park, Beijing, People's Republic of China, 102206
| | - Qing Kong
- Department of Botany, University of British Columbia, Vancouver, Canada V6T 1Z4
| | - Yuelin Zhang
- Department of Botany, University of British Columbia, Vancouver, Canada V6T 1Z4
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Chen M, Mishra S, Heckathorn SA, Frantz JM, Krause C. Proteomic analysis of Arabidopsis thaliana leaves in response to acute boron deficiency and toxicity reveals effects on photosynthesis, carbohydrate metabolism, and protein synthesis. JOURNAL OF PLANT PHYSIOLOGY 2014; 171:235-42. [PMID: 23988561 DOI: 10.1016/j.jplph.2013.07.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 07/25/2013] [Accepted: 07/25/2013] [Indexed: 05/10/2023]
Abstract
Boron (B) stress (deficiency and toxicity) is common in plants, but as the functions of this essential micronutrient are incompletely understood, so too are the effects of B stress. To investigate mechanisms underlying B stress, we examined protein profiles in leaves of Arabidopsis thaliana plants grown under normal B (30 μM), compared to plants transferred for 60 and 84 h (i.e., before and after initial visible symptoms) in deficient (0 μM) or toxic (3 mM) levels of B. B-responsive polypeptides were sequenced by mass spectrometry, following 2D gel electrophoresis, and 1D gels and immunoblotting were used to confirm the B-responsiveness of some of these proteins. Fourteen B-responsive proteins were identified, including: 9 chloroplast proteins, 6 proteins of photosynthetic/carbohydrate metabolism (rubisco activase, OEC23, photosystem I reaction center subunit II-1, ATPase δ-subunit, glycolate oxidase, fructose bisphosphate aldolase), 6 stress proteins, and 3 proteins involved in protein synthesis (note that the 14 proteins may fall into multiple categories). Most (8) of the B-responsive proteins decreased under both B deficiency and toxicity; only 3 increased with B stress. Boron stress decreased, or had no effect on, 3 of 4 oxidative stress proteins examined, and did not affect total protein. Hence, our results indicate relatively early specific effects of B stress on chloroplasts and protein synthesis.
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Affiliation(s)
- Mei Chen
- Department of Environmental Sciences, University of Toledo, Toledo, OH 43606, USA
| | - Sasmita Mishra
- Department of Environmental Sciences, University of Toledo, Toledo, OH 43606, USA.
| | - Scott A Heckathorn
- Department of Environmental Sciences, University of Toledo, Toledo, OH 43606, USA
| | - Jonathan M Frantz
- United States Department of Agriculture-Agricultural Research Service, University of Toledo, Toledo, OH 43606, USA
| | - Charles Krause
- United States Department of Agriculture-Agricultural Research Service, University of Toledo, Toledo, OH 43606, USA
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Batelli G, Massarelli I, Van Oosten M, Nurcato R, Vannini C, Raimondi G, Leone A, Zhu JK, Maggio A, Grillo S. Asg1 is a stress-inducible gene which increases stomatal resistance in salt stressed potato. JOURNAL OF PLANT PHYSIOLOGY 2012; 169:1849-57. [PMID: 22854180 PMCID: PMC3586823 DOI: 10.1016/j.jplph.2012.07.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 07/06/2012] [Accepted: 07/07/2012] [Indexed: 05/08/2023]
Abstract
The identification of critical components in plant salt stress adaptation has greatly benefitted, in the last two decades, from fundamental discoveries in Arabidopsis and close model systems. Nevertheless, this approach has also highlighted a non-complete overlap between stress tolerance mechanisms in Arabidopsis and agricultural crops. Within a long-running research program aimed at identifying salt stress genetic determinants in potato by functional screening in Escherichia coli, we isolated Asg1, a stress-related gene with an unknown function. Asg1 is induced by salt stress in both potato and Arabidopsis and by abscisic acid in Arabidopsis. Asg1 is actively transcribed in all plant tissues. Furthermore, Asg1 promoter analysis confirmed its ubiquitous expression, which was remarkable in pollen, a plant tissue that undergoes drastic dehydration/hydration processes. Fusion of Asg1 with green fluorescent protein showed that the encoded protein is localized close to the plasma membrane with a non-continuous pattern of distribution. In addition, Arabidopsis knockout asg1 mutants were insensitive to both NaCl and sugar hyperosmotic environments during seed germination. Transgenic potato plants over-expressing the Asg1 gene revealed a stomatal hypersensitivity to NaCl stress which, however, did not result in a significantly improved tuber yield in stress conditions. Altogether, these data suggest that Asg1 might interfere with components of the stress signaling pathway by promoting stomatal closure and participating in stress adaptation.
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Affiliation(s)
- Giorgia Batelli
- CNR Institute of Plant Genetics (CNR-IGV), Via Universita’, 133 80055 Portici, Italy
| | - Immacolata Massarelli
- CNR Institute of Plant Genetics (CNR-IGV), Via Universita’, 133 80055 Portici, Italy
| | - Michael Van Oosten
- Department of Agricultural Engineering and Agronomy, University of Naples Federico II, Via Università 100, 80055 Portici, Italy
| | - Roberta Nurcato
- CNR Institute of Plant Genetics (CNR-IGV), Via Universita’, 133 80055 Portici, Italy
| | - Candida Vannini
- Department of Environment, Health and Safety, University of Insubria, Via J. H. Dunant, 3, 21100 Varese, Italy
| | - Giampaolo Raimondi
- Department of Agricultural Engineering and Agronomy, University of Naples Federico II, Via Università 100, 80055 Portici, Italy
| | - Antonella Leone
- Department of Pharmaceutical and Biomedical Sciences, University of Salerno, Via Ponte Don Melillo, 84084 Fisciano, Italy
| | - Jian-Kang Zhu
- Department of Horticulture and Landscape Architecture, Purdue University, 47907 West Lafayette, IN, USA
| | - Albino Maggio
- Department of Agricultural Engineering and Agronomy, University of Naples Federico II, Via Università 100, 80055 Portici, Italy
| | - Stefania Grillo
- CNR Institute of Plant Genetics (CNR-IGV), Via Universita’, 133 80055 Portici, Italy
- Corresponding author at: National Research Council, Institute of Plant Genetics (CNR-IGV), Via Universita’, 133 80055 Portici (NA), Italy. Tel.: +39 081 2539213/2539205; fax: +39 081 7753579., (S. Grillo)
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6
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Eblen ST. Regulation of chemoresistance via alternative messenger RNA splicing. Biochem Pharmacol 2012; 83:1063-72. [PMID: 22248731 DOI: 10.1016/j.bcp.2011.12.041] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Revised: 12/29/2011] [Accepted: 12/29/2011] [Indexed: 12/17/2022]
Abstract
The acquisition of resistance to chemotherapy is a significant problem in the treatment of cancer, greatly increasing patient morbidity and mortality. Tumors are often sensitive to chemotherapy upon initial treatment, but repeated treatments can select for those cells that were able to survive initial therapy and have acquired cellular mechanisms to enhance their resistance to subsequent chemotherapy treatment. Many cellular mechanisms of drug resistance have been identified, most of which result from changes in gene and protein expression. While changes at the transcriptional level have been duly noted, it is primarily the post-transcriptional processing of pre-mRNA into mature mRNA that regulates the composition of the proteome and it is the proteome that actually regulates the cell's response to chemotherapeutic insult, inducing cell survival or death. During pre-mRNA processing, intronic non-protein-coding sequences are removed and protein-coding exons are spliced to form a continuous template for protein translation. Alternative splicing involves the differential inclusion or exclusion of exonic sequences into the mature transcript, generating different mRNA templates for protein production. This regulatory mechanism enables the potential to produce many different protein isoforms from the same gene. In this review I will explain the mechanism of alternative pre-mRNA splicing and look at some specific examples of how splicing factors, splicing factor kinases and alternative splicing of specific pre-mRNAs from genes have been shown to contribute to acquisition of the drug resistant phenotype.
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Affiliation(s)
- Scott T Eblen
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, Charleston, 29425, USA.
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7
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Horikoshi N, Morozumi Y, Takaku M, Takizawa Y, Kurumizaka H. Holliday junction-binding activity of human SPF45. Genes Cells 2010; 15:373-83. [PMID: 20236180 DOI: 10.1111/j.1365-2443.2010.01383.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
SPF45 is considered to be a bifunctional protein that functions in splicing and DNA repair. A previous genetic study reported that Drosophila SPF45 participates in the DNA-repair pathway with a RAD51-family protein, RAD201, suggesting that SPF45 may function in DNA repair by the homologous-recombination pathway. To study the function of SPF45 in homologous recombination, we purified human SPF45 and found that it preferentially binds to the Holliday junction, which is a key DNA intermediate in the homologous-recombination pathway. Deletion analyses revealed that the RNA recognition motif, which is located in the C-terminal region of human SPF45, is not involved in DNA binding. On the other hand, alanine-scanning mutagenesis identified the N-terminal lysine residues, which may be involved in Holliday junction binding by human SPF45. We also found that human SPF45 significantly binds to a RAD51 paralog, RAD51B, although it also binds to RAD51 and DMC1 with lower affinity. These biochemical results support the idea that human SPF45 functions in DNA repair by homologous recombination.
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Affiliation(s)
- Naoki Horikoshi
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
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Chaouki AS, Salz HK. Drosophila SPF45: a bifunctional protein with roles in both splicing and DNA repair. PLoS Genet 2007; 2:e178. [PMID: 17154718 PMCID: PMC1687153 DOI: 10.1371/journal.pgen.0020178] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2006] [Accepted: 09/01/2006] [Indexed: 11/18/2022] Open
Abstract
The sequence of the SPF45 protein is significantly conserved, yet functional studies have identified it as a splicing factor in animal cells and as a DNA-repair protein in plants. Using a combined genetic and biochemical approach to investigate this apparent functional discrepancy, we unify and validate both of these studies by demonstrating that the Drosophila melanogaster protein is bifunctional, with independent functions in DNA repair and splicing. We find that SPF45 associates with the U2 snRNP and that mutations that remove the C-terminal end of the protein disrupt this interaction. Although animals carrying this mutation are viable, they are nevertheless compromised in their ability to regulate Sex-lethal splicing, demonstrating that Sex-lethal is an important physiological target of SPF45. Furthermore, these mutant animals exhibit phenotypes diagnostic of difficulties in recovering from exogenously induced DNA damage. The conclusion that SPF45 functions in the DNA-repair pathway is strengthened by finding both genetic and physical interactions between SPF45 and RAD201, a previously uncharacterized member of the RecA/Rad51 protein family. Together with our finding that the fly SPF45 protein increases the survival rate of mutagen-treated bacteria lacking the RecG helicase, these studies provide the tantalizing suggestion that SPF45 has an ancient and evolutionarily conserved role in DNA repair. Assigning function to a protein relies on information about similar proteins in different species, and is based on the view that conservation of sequence generally parallels conservation of function. In this article, Chaouki and Salz focus on SPF45, a protein that, at first glance, appears to break this rule. Although the sequence of SPF45 is highly conserved, in animals cells SPF45 functions as a splicing factor, but in plant cells it functions as a DNA repair protein. This functional discrepancy is resolved here through the demonstration that, in D. melanogaster, SPF45 is a bifunctional protein with independent functions in DNA repair and splicing. Support for this conclusion includes the observation that mutant animals lacking SPF45 function display defects in both splicing and DNA repair. In addition, the authors show that SPF45 associates with two distinct groups of proteins; those that participate in RNA splicing and those that participate in DNA repair. The finding that the D. melanogaster protein is bifunctional suggests that the human protein may also have more than one function. This has important clinical implications because elevated SPF45 levels have been correlated with resistance to chemotherapy.
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Affiliation(s)
- Ahmad Sami Chaouki
- Department of Genetics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Helen K Salz
- Department of Genetics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
- * To whom correspondence should be addressed. E-mail:
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9
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Herrmann G, Kais S, Hoffbauer J, Shah-Hosseini K, Brüggenolte N, Schober H, Fäsi M, Schär P. Conserved interactions of the splicing factor Ntr1/Spp382 with proteins involved in DNA double-strand break repair and telomere metabolism. Nucleic Acids Res 2007; 35:2321-32. [PMID: 17389648 PMCID: PMC1874655 DOI: 10.1093/nar/gkm127] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2006] [Revised: 02/14/2007] [Accepted: 02/15/2007] [Indexed: 11/25/2022] Open
Abstract
The ligation of DNA double-strand breaks in the process of non-homologous end-joining (NHEJ) is accomplished by a heterodimeric enzyme complex consisting of DNA ligase IV and an associated non-catalytic factor. This DNA ligase also accounts for the fatal joining of unprotected telomere ends. Hence, its activity must be tightly controlled. Here, we describe interactions of the DNA ligase IV-associated proteins Lif1p and XRCC4 of yeast and human with the putatively orthologous G-patch proteins Ntr1p/Spp382p and NTR1/TFIP11 that have recently been implicated in mRNA splicing. These conserved interactions occupy the DNA ligase IV-binding sites of Lif1p and XRCC4, thus preventing the formation of an active enzyme complex. Consistently, an excess of Ntr1p in yeast reduces NHEJ efficiency in a plasmid ligation assay as well as in a chromosomal double-strand break repair (DSBR) assay. Both yeast and human NTR1 also interact with PinX1, another G-patch protein that has dual functions in the regulation of telomerase activity and telomere stability, and in RNA processing. Like PinX1, NTR1 localizes to telomeres and associates with nucleoli in yeast and human cells, suggesting a function in localized control of DSBR.
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Affiliation(s)
- Gernot Herrmann
- Department of Dermatology, University of Cologne, Cologne, Germany.
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10
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DNA replication, recombination, and repair in plastids. CELL AND MOLECULAR BIOLOGY OF PLASTIDS 2007. [DOI: 10.1007/4735_2007_0231] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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11
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Abstract
Recent structures of the heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) have revealed two unexpected examples of RNA recognition motif (RRM)-like domains with specialized features for protein recognition. These unusual RRMs, called U2AF homology motifs (UHMs), represent a novel class of protein recognition motifs. Defining a set of rules to distinguish traditional RRMs from UHMs is key to identifying novel UHM family members. Here we review the critical sequence features necessary to mediate protein-UHM interactions, and perform comprehensive database searches to identify new members of the UHM family. The resulting implications for the functional and evolutionary relationships among candidate UHM family members are discussed.
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Affiliation(s)
- Clara L. Kielkopf
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
- Corresponding author. E-MAIL ; FAX (410) 955-2926
| | - Stephan Lücke
- Howard Hughes Medical Institute, Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Michael R. Green
- Howard Hughes Medical Institute, Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
- Corresponding author. E-MAIL ; FAX (508) 856-5473
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12
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Affiliation(s)
- Aram M Nersissian
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, USA
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13
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Reiss B. Homologous recombination and gene targeting in plant cells. INTERNATIONAL REVIEW OF CYTOLOGY 2003; 228:85-139. [PMID: 14667043 DOI: 10.1016/s0074-7696(03)28003-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Gene targeting has become an indispensable tool for functional genomics in yeast and mouse; however, this tool is still missing in plants. This review discusses the gene targeting problem in plants in the context of general knowledge on recombination and gene targeting. An overview on the history of gene targeting is followed by a general introduction to genetic recombination of bacteria, yeast, and vertebrates. This abridged discussion serves as a guide to the following sections, which cover plant-specific aspects of recombination assay systems, the mechanism of recombination, plant recombination genes, the relationship of recombination to the environment, approaches to stimulate homologous recombination and gene targeting, and a description of two plant systems, the moss Physcomitrella patens and the chloroplast, that naturally have high efficiencies of gene targeting. The review concludes with a discussion of alternatives to gene targeting.
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Affiliation(s)
- Bernd Reiss
- Max-Planck-Institut für Zuechtungsforschung, Carl-von-Linne-Weg 10, D-50829 Köln, Germany
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14
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Dendouga N, Callebaut I, Tomavo S. A novel DNA repair enzyme containing RNA recognition, G-patch and specific splicing factor 45-like motifs in the protozoan parasite Toxoplasma gondii. EUROPEAN JOURNAL OF BIOCHEMISTRY 2002; 269:3393-401. [PMID: 12135477 DOI: 10.1046/j.1432-1033.2002.02993.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We report the cloning and functional characterization of the full-length cDNA and gene encoding a Toxoplasma gondii DNA repair enzyme designated TgDRE. The gene is composed of three exons separated by two introns of 780 and 630 bp, and encodes a protein with a predicted molecular mass of 49.6 kDa. The native TgDRE protein, with a molecular mass of 60 kDa, is only detected in the virulent tachyzoite stage of T. gondii. However, the transcript is present in both asexual parasite stages, virulent tachyzoite and avirulent encysted bradyzoite. When an Escherichia coli mutant lacking ruvC endonuclease and recG helicase was transformed with TgDRE cDNA, a significant increase in resistance to DNA-damaging agents, such as UV light and mitomycin C, was observed. Moreover, database searches revealed that TgDRE orthologues were present in the genome sequences of the related apicomplexa parasites Plasmodium falciparum and Plasmodium yoelii, as well as in those of Arabidopsis thaliana, Drosophila melanogaster, Caenorhabditis elegans and Homo sapiens. This novel family of proteins is characterized by the presence of human splicing factor SF45-like, RNA recognition (RRM) and glycine-rich (G-patch) motifs. The presence of these motifs suggests that T. gondii TgDRE might also be involved in other biological functions such as RNA metabolism in addition to DNA-repair.
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Affiliation(s)
- Najoua Dendouga
- Equipe de Parasitologie Moléculaire, Laboratoire de Chimie Biologique, CNRS UMR 8576, Université des Sciences et Technologies de Lille, France
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15
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Kmiec EB, Johnson C, May GD. Chloroplast lysates support directed mutagenesis via modified DNA and chimeric RNA/DNA oligonucleotides. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2001; 27:267-274. [PMID: 11532172 DOI: 10.1046/j.1365-313x.2001.01083.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Chimeric RNA/DNA and modified DNA oligonucleotides have been shown to direct gene-conversion events in vitro through a process involving proteins from several DNA-repair pathways. Recent experiments have extended the utility of these molecules to plants, and we previously demonstrated that plant cell-free extracts are competent to support oligonucleotide-directed genetic repair. Using this system, we are studying Arabidopsis DNA-repair mutants and the role of plant proteins in the DNA-repair process. Here we describe a method for investigating mechanisms of plastid DNA-repair pathways. Using a genetic readout system in bacteria and chimeric or modified DNA oligonucleotides designed to direct the conversion of mutations in antibiotic resistance genes, we have developed an assay for genetic repair of mutations in a spinach chloroplast lysate system. We report genetic repair of point and frameshift mutations directed by both types of modified oligonucleotides. This system enables the mechanistic study of plastid gene repair and facilitates the direct comparison between plant nuclear and organelle DNA-repair pathways.
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Affiliation(s)
- E B Kmiec
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
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16
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Affiliation(s)
- T J Oh
- Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73402, USA
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17
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Kieselbach T, Bystedt M, Hynds P, Robinson C, Schröder WP. A peroxidase homologue and novel plastocyanin located by proteomics to the Arabidopsis chloroplast thylakoid lumen. FEBS Lett 2000; 480:271-6. [PMID: 11034343 DOI: 10.1016/s0014-5793(00)01890-1] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A study by two-dimensional electrophoresis showed that the soluble, lumenal fraction of Arabidopsis thaliana thylakoids can be resolved into 300 protein spots. After subtraction of low-intensity spots and accounting for low-level stromal contamination, the number of more abundant, lumenal proteins was estimated to be between 30 and 60. Two of these proteins have been identified: a novel plastocyanin that also was the predominant component of the total plastocyanin pool, and a putative ascorbate peroxidase. Import studies showed that these proteins are routed to the thylakoid lumen by the Sec- and delta pH-dependent translocation pathways, respectively. In addition, novel isoforms of PsbO and PsbQ were identified.
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Affiliation(s)
- T Kieselbach
- Karolinska Institute, Department of Medical Nutrition, Huddinge, Sweden
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18
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Doerig C, Chakrabarti D, Kappes B, Matthews K. The cell cycle in protozoan parasites. PROGRESS IN CELL CYCLE RESEARCH 2000; 4:163-83. [PMID: 10740824 DOI: 10.1007/978-1-4615-4253-7_15] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Research into cell cycle control in protozoan parasites, which are responsible for major public health problems in the developing world, has been hampered by the difficulties in performing classical genetic analysis with these organisms. Nevertheless, in a large part thanks to the data gathered in other eukaryotic systems and to the acquisition of the sequences of parasite genes homologous to cell cycle regulators, many molecular tools required for an in-depth study of the cell cycle in protozoan parasites have been collected over the past few years. Despite the considerable phylogenetic divergence between these organisms and other eukaryotes, and notwithstanding important specificities such as the apparent lack of checkpoints during cell cycle progression, available data indicate that the major families of cell cycle regulators appear to operate in protozoan parasites. Functional studies are now needed to define the precise role of these regulators in the life cycle of the parasites, and to possibly validate cell cycle control elements as potential targets for chemotherapy.
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Affiliation(s)
- C Doerig
- INSERM U313, Immunobiologie moléculaire et cellulaire des maladies parasitaires, Paris, France
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19
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Abstract
Hydrogen peroxide (H(2)O(2)) is generated in plants after exposure to a variety of biotic and abiotic stresses, and has been shown to induce a number of cellular responses. Previously, we showed that H(2)O(2) generated during plant-elicitor interactions acts as a signaling molecule to induce the expression of defense genes and initiate programmed cell death in Arabidopsis thaliana suspension cultures. Here, we report for the first time the identification by RNA differential display of four genes whose expression is induced by H(2)O(2). These include genes that have sequence homology to previously identified Arabidopsis genes encoding a late embryogenesis-abundant protein, a DNA-damage repair protein, and a serine/threonine kinase. Their putative roles in H(2)O(2)-induced defense responses are discussed.
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Affiliation(s)
- R Desikan
- Department of Biological and Biomedical Sciences, University of the West of England, Bristol, UK
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20
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Kuno N, Muramatsu T, Hamazato F, Furuya M. Identification by large-scale screening of phytochrome-regulated genes in etiolated seedlings of Arabidopsis using a fluorescent differential display technique. PLANT PHYSIOLOGY 2000; 122:15-24. [PMID: 10631245 PMCID: PMC1539239 DOI: 10.1104/pp.122.1.15] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Phytochrome A (PhyA)-regulated genes in 6-d-old etiolated seedlings of Arabidopsis Landsberg erecta were identified by fluorescent differential display. To screen for PhyA-regulated genes, mRNA fingerprints of the wild type and the phyA-201 mutant were compared from samples prepared 4 h after far-red light irradiation. Approximately 30,000 bands of cDNA were displayed by fluorescent differential display, and 24 differentially expressed bands were observed. Sequence analysis revealed that they represent 20 distinct genes. Among them, 15 genes were confirmed as PhyA regulated by northern-blot (or reverse transcription-polymerase chain reaction) analysis. Thirteen up-regulated genes included 12 known genes that encode nine photosynthetic proteins, two enzymes involved in the biosynthesis of chlorophyll, one DNA damage repair/toleration-related protein, and one unknown gene. Two down-regulated genes were identified as encoding a xyloglucan endotransglycosylase-related protein and a novel member of the ASK protein kinase family. In the phyA-201 mutant and the phyA-201phyB-1 double mutant, expression of all of these genes was photoreversibly up- or down-regulated by type II phytochromes. The results indicate that modes of photoperception differ between PhyA and PhyB, but that both types of phytochromes have overlapping effects on the photoregulation of gene expression.
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Affiliation(s)
- N Kuno
- Hitachi Advanced Research Laboratory, Hatoyama, Saitama 350-0395, Japan
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21
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22
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Abstract
Numerous studies have demonstrated a requirement in plants for repair of DNA damage arising from either intrinsic or extrinsic sources. Investigations also have revealed a capacity for repair of certain types of DNA damage, and conversely, identified mutants apparently defective in such repair. This article provides a concise overview of nuclear DNA repair mechanisms in higher plants, particularly those processes concerned with the repair of UV-induced lesions, and includes surveys of UV-sensitive mutants and genes implicated in DNA repair.
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Affiliation(s)
- E J Vonarx
- School of Biological and Chemical Sciences, Deakin University, Geelong, Victoria 3217, Australia
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23
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Dürrenberger F, Thompson AJ, Herrin DL, Rochaix JD. Double strand break-induced recombination in Chlamydomonas reinhardtii chloroplasts. Nucleic Acids Res 1996; 24:3323-31. [PMID: 8811085 PMCID: PMC146090 DOI: 10.1093/nar/24.17.3323] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The mechanisms of chloroplast recombination are largely unknown. Using the chloroplast-encoded homing endonuclease I-CreI from Chlamydomonas reinhardtii, an experimental system is described that allows the study of double strand break (DSB)-induced recombination in chloroplasts. The I-CreI endonuclease is encoded by the chloroplast ribosomal group I intron of C.reinhardtii and cleaves specifically intronless copies of the large ribosomal RNA (23S) gene. To study DSB-induced recombination in chloroplast DNA, the genes encoding the I-CreI endonuclease were deleted and a target site for I-CreI, embedded in a cDNA of the 23S gene, was integrated at an ectopic location. Endonuclease function was transiently provided by mating the strains containing the recombination substrate to a wild-type strain. The outcome of DSB repair was analyzed in haploid progeny of these crosses. Interestingly, resolution of DSB repair strictly depended upon the relative orientation of the ectopic ribosomal cDNA and the adjacent copy of the 23S gene. Gene conversion was observed when the 23S cDNA and the neighbouring copy of the 23S gene were in opposite orientation, leading to mobilization of the intron to the 23S cDNA. In contrast, arrangement of the 23S cDNA in direct repeat orientation relative to the proximal 23S gene resulted in a deletion between the 23S cDNA and the 23S gene. These results demonstrate that C.reinhardtii chloroplasts have an efficient system for DSB repair and that homologous recombination is strongly stimulated by DSBs in chloroplast DNA.
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MESH Headings
- Animals
- Blotting, Southern
- Chlamydomonas reinhardtii/genetics
- Chloroplasts/genetics
- Crosses, Genetic
- DNA Damage
- DNA Repair
- DNA Restriction Enzymes
- DNA, Complementary/genetics
- DNA, Ribosomal/metabolism
- Deoxyribonucleases, Type II Site-Specific/metabolism
- Introns/genetics
- Models, Genetic
- Polymerase Chain Reaction
- RNA, Ribosomal, 23S/genetics
- Recombination, Genetic
- Repetitive Sequences, Nucleic Acid
- Sequence Deletion
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Affiliation(s)
- F Dürrenberger
- Department of Molecular Biology, University of Geneva, Switzerland
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24
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Goulding SE, Olmstead RG, Morden CW, Wolfe KH. Ebb and flow of the chloroplast inverted repeat. MOLECULAR & GENERAL GENETICS : MGG 1996; 252:195-206. [PMID: 8804393 DOI: 10.1007/bf02173220] [Citation(s) in RCA: 222] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The endpoints of the large inverted repeat (IR) of chloroplast DNA in flowering plants differ by small amounts between species. To quantify the extent of this movement and define a possible mechanism for IR expansion, DNA sequences across the IR-large single-copy (IR-LSC) junctions were compared among 13 Nicotiana species and other dicots. In most Nicotiana species the IR terminates just upstream of, or somewhere within, the 5' portion of the rps19 gene. The truncated copy of this gene, rps19', varies in length even between closely related species but is of constant size within a single species. In Nicotiana, six different rps19' structures were found. A phylogenetic tree of Nicotiana species based on restriction site data shows that the IR has both expanded and contracted during the evolution of this genus. Gene conversion is proposed to account for these small and apparently random IR expansions. A large IR expansion of over 12 kb has occurred in Nicotiana acuminata. The new IR-LSC junction in this species lies within intron 1 of the clpP gene. This rearrangement occurred via a double-strand DNA break and recombination between poly (A) tracts in clpP intron 1 and upstream of rps19. Nicotiana acuminata chloroplast DNA contains a "molecular fossil' of the IR-LSC junction that existed prior to this dramatic rearrangement.
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Affiliation(s)
- S E Goulding
- Department of Genetics, University of Dublin, Trinity College, Ireland
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25
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Abstract
The biological impact of any DNA damaging agent is a combined function of the chemical nature of the induced lesions and the efficiency and accuracy of their repair. Although much has been learned from microbes and mammals about both the repair of DNA damage and the biological effects of the persistence of these lesions, much remains to be learned about the mechanism and tissue-specificity of repair in plants. This review focuses on recent work on the induction and repair of DNA damage in higher plants, with special emphasis on UV-induced DNA damage products.
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Affiliation(s)
- Anne B. Britt
- Section of Plant Biology, University of California, Davis, California 95616
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26
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Machado CR, de Oliveira RL, Boiteux S, Praekelt UM, Meacock PA, Menck CF. Thi1, a thiamine biosynthetic gene in Arabidopsis thaliana, complements bacterial defects in DNA repair. PLANT MOLECULAR BIOLOGY 1996; 31:585-93. [PMID: 8790291 DOI: 10.1007/bf00042231] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
An Arabidopsis thaliana cDNA was isolated by complementation of the Escherichia coli mutant strain BW535 (xth, nfo, nth), which is defective in DNA base excision repair pathways. This cDNA partially complements the methyl methane sulfonate (MMS) sensitive phenotype of BW535. It also partially corrects the UV-sensitive phenotype of E. coli AB1886 (uvrA) and restores its ability to reactivate UV-irradiated lambda phage. It has an insert of ca. 1.3 kb with an open reading frame of 1047 bp (predicting a protein with a molecular mass of 36 kDa). This cDNA presents a high homology to a stress related gene from two species of Fusarium (sti35) and to genes whose products participate in the thiamine biosynthesis pathway, THI4, from Saccharomyces cerevisiae and nmt2 from Schizosaccharomyces pombe. The Arabidopsis predicted polypeptide has homology to several protein motifs: amino-terminal chloroplast transit peptide, dinucleotide binding site, DNA binding and bacterial DNA polymerases. The auxotrophy for thiamine in the yeast thi4::URA3 disruption strain is complemented by the Arabidopsis gene. Thus, the cloned gene, named thi1, is likely to function in the biosynthesis of thiamine in plants. The data presented in this work indicate that thi1 may also be involved in DNA damage tolerance in plant cells.
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Affiliation(s)
- C R Machado
- Depto. de Biologia, Universidade de São Paulo, Brazil
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27
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Cerutti H, Johnson AM, Boynton JE, Gillham NW. Inhibition of chloroplast DNA recombination and repair by dominant negative mutants of Escherichia coli RecA. Mol Cell Biol 1995; 15:3003-11. [PMID: 7760798 PMCID: PMC230531 DOI: 10.1128/mcb.15.6.3003] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The occurrence of homologous DNA recombination in chloroplasts is well documented, but little is known about the molecular mechanisms involved or their biological significance. The endosymbiotic origin of plastids and the recent finding of an Arabidopsis nuclear gene, encoding a chloroplast-localized protein homologous to Escherichia coli RecA, suggest that the plastid recombination system is related to its eubacterial counterpart. Therefore, we examined whether dominant negative mutants of the E. coli RecA protein can interfere with the activity of their putative homolog in the chloroplast of the unicellular green alga Chlamydomonas reinhardtii. Transformants expressing these mutant RecA proteins showed reduced survival rates when exposed to DNA-damaging agents, deficient repair of chloroplast DNA, and diminished plastid DNA recombination. These results strongly support the existence of a RecA-mediated recombination system in chloroplasts. We also found that the wild-type E. coli RecA protein enhances the frequency of plastid DNA recombination over 15-fold, although it has no effect on DNA repair or cell survival. Thus, chloroplast DNA recombination appears to be limited by the availability of enzymes involved in strand exchange rather than by the level of initiating DNA substrates. Our observations suggest that a primary biological role of the recombination system in plastids is in the repair of their DNA, most likely needed to cope with damage due to photooxidation and other environmental stresses. This hypothesis could explain the evolutionary conservation of DNA recombination in chloroplasts despite the predominantly uniparental inheritance of their genomes.
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Affiliation(s)
- H Cerutti
- Department of Botany, Duke University, Durham, North Carolina 27708, USA
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28
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Huang H, Tudor M, Weiss CA, Hu Y, Ma H. The Arabidopsis MADS-box gene AGL3 is widely expressed and encodes a sequence-specific DNA-binding protein. PLANT MOLECULAR BIOLOGY 1995; 28:549-67. [PMID: 7632923 DOI: 10.1007/bf00020401] [Citation(s) in RCA: 76] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The Arabidopsis AGL3 gene was previously identified on the basis of sequence similarity to the floral homeotic gene AGAMOUS (AG), which encodes a protein with a conserved MADS domain that is also found in human and yeast transcription factors (SRF and MCM1, respectively). Analysis of newly isolated full-length cDNA clones as well as genomic clones indicates that AGL3 is indeed a MADS-box gene with a general intron-exon structure similar to other plant MADS-box genes. However, unlike the others, which are expressed specifically in flowers, AGL3 is expressed in all above-ground vegetative organs, as well as in flowers, but not in roots. Furthermore, since AGL3 is MADS-domain protein, it is likely that it is also a DNA-binding protein regulating transcription. To characterize AGL3 as a DNA-binding protein in vitro, we expressed the AGL3 protein in Escherichia coli, and characterized its DNA-binding properties. We show that AGL3 binds to sequences which resemble the target sequences of SRF and MCM1, and have determined the consensus sequence to which AGL3 binds using random oligonucleotides. These results suggest that AGL3 is a widely distributed DNA-binding protein, which may be involved the transcriptional regulation of genes in many cells.
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Affiliation(s)
- H Huang
- Cold Spring Harbor Laboratory, NY 11724, USA
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