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Lama-Diaz T, Blanco MG. Alternative translation initiation by ribosomal leaky scanning produces multiple isoforms of the Pif1 helicase. Nucleic Acids Res 2024:gkae400. [PMID: 38783074 DOI: 10.1093/nar/gkae400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 04/24/2024] [Accepted: 05/01/2024] [Indexed: 05/25/2024] Open
Abstract
In budding yeast, the integrity of both the nuclear and mitochondrial genomes relies on dual-targeted isoforms of the conserved Pif1 helicase, generated by alternative translation initiation (ATI) of PIF1 mRNA from two consecutive AUG codons flanking a mitochondrial targeting signal. Here, we demonstrate that ribosomal leaky scanning is the specific ATI mechanism that produces not only these, but also novel, previously uncharacterized Pif1 isoforms. Both in-frame, downstream AUGs as well as near-cognate start codons contribute to the generation of these alternative isoforms. This has crucial implications for the rational design of genuine separation-of-function alleles and provides an explanation for the suboptimal behaviour of the widely employed mitochondrial- (pif1-m1) and nuclear-deficient (pif1-m2) alleles, with mutations in the first or second AUG codon, respectively. We have taken advantage of this refined model to develop improved versions of these alleles, which will serve as valuable tools to elucidate novel functions of this helicase and to disambiguate previously described genetic interactions of PIF1 in the context of nuclear and mitochondrial genome stability.
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Affiliation(s)
- Tomas Lama-Diaz
- Department of Biochemistry and Molecular Biology, CIMUS, Universidade de Santiago de Compostela-Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, A Coruña 15782, Spain
| | - Miguel G Blanco
- Department of Biochemistry and Molecular Biology, CIMUS, Universidade de Santiago de Compostela-Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, A Coruña 15782, Spain
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Terzioğlu E, Alkım C, Arslan M, Balaban BG, Holyavkin C, Kısakesen Hİ, Topaloğlu A, Yılmaz Şahin Ü, Gündüz Işık S, Akman S, Çakar ZP. Genomic, transcriptomic and physiological analyses of silver-resistant Saccharomyces cerevisiae obtained by evolutionary engineering. Yeast 2020; 37:413-426. [PMID: 33464648 DOI: 10.1002/yea.3514] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 06/12/2020] [Accepted: 07/15/2020] [Indexed: 12/24/2022] Open
Abstract
Silver is a non-essential metal used in medical applications as an antimicrobial agent, but it is also toxic for biological systems. To investigate the molecular basis of silver resistance in yeast, we employed evolutionary engineering using successive batch cultures at gradually increased silver stress levels up to 0.25-mM AgNO3 in 29 populations and obtained highly silver-resistant and genetically stable Saccharomyces cerevisiae strains. Cross-resistance analysis results indicated that the silver-resistant mutants also gained resistance against copper and oxidative stress. Growth physiological analysis results revealed that the highly silver-resistant evolved strain 2E was not significantly inhibited by silver stress, unlike the reference strain. Genomic and transcriptomic analysis results revealed that there were mutations and/or significant changes in the expression levels of the genes involved in cell wall integrity, cellular respiration, oxidative metabolism, copper homeostasis, endocytosis and vesicular transport activities. Particularly the missense mutation in the RLM1 gene encoding a transcription factor involved in the maintenance of cell wall integrity and with 707 potential gene targets might have a key role in the high silver resistance of 2E, along with its improved cell wall integrity, as confirmed by the lyticase sensitivity assay results. In conclusion, the comparative physiological, transcriptomic and genomic analysis results of the silver-resistant S. cerevisiae strain revealed potential key factors that will help understand the complex molecular mechanisms of silver resistance in yeast.
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Affiliation(s)
- Ergi Terzioğlu
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, Istanbul, Turkey.,Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Ceren Alkım
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, Istanbul, Turkey.,Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Mevlüt Arslan
- Department of Genetics, Faculty of Veterinary Medicine, Van Yüzüncü Yıl University, Van, Turkey
| | - Berrak Gülçin Balaban
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, Istanbul, Turkey.,Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Can Holyavkin
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, Istanbul, Turkey.,Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Halil İbrahim Kısakesen
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, Istanbul, Turkey.,Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Alican Topaloğlu
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, Istanbul, Turkey.,Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Ülkü Yılmaz Şahin
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, Istanbul, Turkey.,Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Sema Gündüz Işık
- Department of Chemistry, Faculty of Science and Letters, Istanbul Technical University, Istanbul, Turkey
| | - Süleyman Akman
- Department of Chemistry, Faculty of Science and Letters, Istanbul Technical University, Istanbul, Turkey
| | - Zeynep Petek Çakar
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, Istanbul, Turkey.,Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
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3
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Zhou J, Wang Y, Liang X, Xie C, Liu W, Miao W, Kang Z, Zheng L. Molecular Characterization of a Novel Ourmia-Like Virus Infecting Phoma matteucciicola. Viruses 2020; 12:v12020231. [PMID: 32093074 PMCID: PMC7077192 DOI: 10.3390/v12020231] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 02/03/2020] [Accepted: 02/16/2020] [Indexed: 12/18/2022] Open
Abstract
Here, we report a novel (+) ssRNA mycovirus, Phoma matteucciicola ourmia-like virus 1 (PmOLV1), isolated from Phoma matteucciicola strain LG915-1. The genome of PmOLV1 was 2603 nucleotides long and contained a single open reading frame (ORF), which could be translated into a product of RNA-dependent RNA polymerase (RdRp) by both standard and mitochondrial genetic codons. Cellular fractionation assay indicated that PmOLV1 RNAs are likely more enriched in mitochondria than in cytoplasm. Phylogenetic analysis indicated that PmOLV1 is a new member of the genus Penoulivirus (recently proposed) within the family Botourmiaviridae.
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Affiliation(s)
- Jia Zhou
- Key Laboratory of Green Prevention and Control of Tropical Plant Disease and Pests, Ministry of Education and College of Plant Protection, Hainan University, Haikou 570228, China
| | - Yuhua Wang
- Key Laboratory of Green Prevention and Control of Tropical Plant Disease and Pests, Ministry of Education and College of Plant Protection, Hainan University, Haikou 570228, China
| | - Xiaofei Liang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling 712100, China
| | - Changping Xie
- Key Laboratory of Green Prevention and Control of Tropical Plant Disease and Pests, Ministry of Education and College of Plant Protection, Hainan University, Haikou 570228, China
| | - Wenbo Liu
- Key Laboratory of Green Prevention and Control of Tropical Plant Disease and Pests, Ministry of Education and College of Plant Protection, Hainan University, Haikou 570228, China
| | - Weiguo Miao
- Key Laboratory of Green Prevention and Control of Tropical Plant Disease and Pests, Ministry of Education and College of Plant Protection, Hainan University, Haikou 570228, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling 712100, China
| | - Li Zheng
- Key Laboratory of Green Prevention and Control of Tropical Plant Disease and Pests, Ministry of Education and College of Plant Protection, Hainan University, Haikou 570228, China
- Correspondence:
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García-Rodríguez N, Wong RP, Ulrich HD. The helicase Pif1 functions in the template switching pathway of DNA damage bypass. Nucleic Acids Res 2019; 46:8347-8356. [PMID: 30107417 PMCID: PMC6144865 DOI: 10.1093/nar/gky648] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 08/08/2018] [Indexed: 11/13/2022] Open
Abstract
Replication of damaged DNA is challenging because lesions in the replication template frequently interfere with an orderly progression of the replisome. In this situation, complete duplication of the genome is ensured by the action of DNA damage bypass pathways effecting either translesion synthesis by specialized, damage-tolerant DNA polymerases or a recombination-like mechanism called template switching (TS). Here we report that budding yeast Pif1, a helicase known to be involved in the resolution of complex DNA structures as well as the maturation of Okazaki fragments during replication, contributes to DNA damage bypass. We show that Pif1 expands regions of single-stranded DNA, so-called daughter-strand gaps, left behind the replication fork as a consequence of replisome re-priming. This function requires interaction with the replication clamp, proliferating cell nuclear antigen, facilitating its recruitment to damage sites, and complements the activity of an exonuclease, Exo1, in the processing of post-replicative daughter-strand gaps in preparation for TS. Our results thus reveal a novel function of a conserved DNA helicase that is known as a key player in genome maintenance.
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Affiliation(s)
| | - Ronald P Wong
- Institute of Molecular Biology (IMB), Ackermannweg 4, D-55128 Mainz, Germany
| | - Helle D Ulrich
- Institute of Molecular Biology (IMB), Ackermannweg 4, D-55128 Mainz, Germany
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Guirola M, Jiménez-Martí E, Atrian S. On the molecular relationships between high-zinc tolerance and aconitase (Aco1) in Saccharomyces cerevisiae. Metallomics 2014; 6:634-45. [DOI: 10.1039/c3mt00360d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In yeast, the lack of mitochondrial aconitase activity determines high-zinc tolerance, which is accompanied by the alteration of several low-iron sensor signals.
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Affiliation(s)
- Maria Guirola
- Dept. de Genètica
- Fac. de Biologia
- Universitat de Barcelona
- 08028-Barcelona, Spain
| | - Elena Jiménez-Martí
- Dept. de Genètica
- Fac. de Biologia
- Universitat de Barcelona
- 08028-Barcelona, Spain
| | - Silvia Atrian
- Dept. de Genètica
- Fac. de Biologia
- Universitat de Barcelona
- 08028-Barcelona, Spain
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