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Chen PK, Chang YJ, Chou YW, Chen MY. Dysfunction of Avo3, an essential component of target of rapamycin complex 2, induces ubiquitin-proteasome-dependent downregulation of Avo2 in Saccharomyces cerevisiae. Biochem Biophys Res Commun 2024; 717:150045. [PMID: 38718572 DOI: 10.1016/j.bbrc.2024.150045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 04/24/2024] [Accepted: 05/01/2024] [Indexed: 05/21/2024]
Abstract
The ubiquitin-proteasome system (UPS) plays a key role in maintaining cellular protein homeostasis and participates in modulating various cellular functions. Target of rapamycin (TOR), a highly conserved Ser/Thr kinase found across species from yeasts to humans, forms two multi-protein complexes, TORC1 and TORC2, to orchestrate cellular processes crucial for optimal growth, survival, and stress responses. While UPS-mediated regulation of mammalian TOR complexes has been documented, the ubiquitination of yeast TOR complexes remains largely unexplored. Here we report a functional interplay between the UPS and TORC2 in Saccharomyces cerevisiae. Using avo3-2ts, a temperature-sensitive mutant of the essential TORC2 component Avo3 exhibiting TORC2 defects at restrictive temperatures, we obtained evidence for UPS-dependent protein degradation and downregulation of the TORC2 component Avo2. Our results established the involvement of the E3 ubiquitin ligase Ubr1 and its catalytic activity in mediating Avo2 degradation in cells with defective Avo3. Coimmunoprecipitation revealed the interaction between Avo2 and Ubr1, indicating Avo2 as a potential substrate of Ubr1. Furthermore, depleting Ubr1 rescued the growth of avo3-2ts cells at restrictive temperatures, suggesting an essential role of Avo2 in sustaining cell viability under heat stress and/or TORC2 dysfunction. This study uncovers a role of UPS in yeast TORC2 regulation, highlighting the impact of protein degradation control on cellular signaling.
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Affiliation(s)
- Pao-Kuang Chen
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei, 112304, Taiwan
| | - Yu-Jung Chang
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei, 112304, Taiwan
| | - Yu-Wen Chou
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei, 112304, Taiwan
| | - Mei-Yu Chen
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei, 112304, Taiwan; Faculty of Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei, 112304, Taiwan; Cancer and Immunology Research Center, National Yang Ming Chiao Tung University, Taipei, 112304, Taiwan.
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2
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Latifah E, Ivanesthi IR, Tseng Y, Pan H, Wang C. Adaptive evolution: Eukaryotic enzyme's specificity shift to a bacterial substrate. Protein Sci 2024; 33:e5028. [PMID: 38757396 PMCID: PMC11099734 DOI: 10.1002/pro.5028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/18/2024] [Accepted: 05/04/2024] [Indexed: 05/18/2024]
Abstract
Prolyl-tRNA synthetase (ProRS), belonging to the family of aminoacyl-tRNA synthetases responsible for pairing specific amino acids with their respective tRNAs, is categorized into two distinct types: the eukaryote/archaeon-like type (E-type) and the prokaryote-like type (P-type). Notably, these types are specific to their corresponding cognate tRNAs. In an intriguing paradox, Thermus thermophilus ProRS (TtProRS) aligns with the E-type ProRS but selectively charges the P-type tRNAPro, featuring the bacterium-specific acceptor-stem elements G72 and A73. This investigation reveals TtProRS's notable resilience to the inhibitor halofuginone, a synthetic derivative of febrifugine emulating Pro-A76, resembling the characteristics of the P-type ProRS. Furthermore, akin to the P-type ProRS, TtProRS identifies its cognate tRNA through recognition of the acceptor-stem elements G72/A73, along with the anticodon elements G35/G36. However, in contrast to the P-type ProRS, which relies on a strictly conserved R residue within the bacterium-like motif 2 loop for recognizing G72/A73, TtProRS achieves this through a non-conserved sequence, RTR, within the otherwise non-interacting eukaryote-like motif 2 loop. This investigation sheds light on the adaptive capacity of a typically conserved housekeeping enzyme to accommodate a novel substrate.
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Affiliation(s)
- Emi Latifah
- Department of Life SciencesNational Central UniversityTaoyuanTaiwan
| | | | - Yi‐Kuan Tseng
- Graduate Institute of StatisticsNational Central UniversityTaoyuanTaiwan
| | - Hung‐Chuan Pan
- Department of NeurosurgeryTaichung Veterans General HospitalTaichungTaiwan
| | - Chien‐Chia Wang
- Department of Life SciencesNational Central UniversityTaoyuanTaiwan
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3
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Orleneva AP, Teslya PN, Serebrianyi VA. In vivo assembly of genetic constructs in filamentous fungus Talaromyces cellulolyticus. J Microbiol Methods 2024; 219:106893. [PMID: 38320738 DOI: 10.1016/j.mimet.2024.106893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/30/2024] [Accepted: 01/30/2024] [Indexed: 02/10/2024]
Abstract
In the filamentous fungus Talaromyces cellulolyticus, similar to other filamentous fungi, non-homologous recombination predominates over homologous recombination. For instance, to achieve an acceptable integration frequency of a genetic construct into a target site on the intact chromosome, the flanking sequences directing this integration should be approximately 2.5 kb in length. However, despite the requirement of long flanks for integration into the intact chromosome, we found that homologous recombination between linear DNA fragments in T. cellulolyticus effectively occurs when these fragments overlap by just 50 bp. This allows for the assembly of full-sized genetic constructs in vivo from relatively small blocks, eliminating the need for in vitro assembly, similar to the approach previously developed for the yeast Saccharomyces cerevisiae. To validate this possibility, we replaced the native promoter of the target gene by transforming the recipient strain with five DNA fragments: two flanks for recombination with the target locus, two parts of the marker gene, and a donor promoter. This discovery significantly expedites the genetic engineering of T. cellulolyticus and potentially other fungi.
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Affiliation(s)
- Alexandra P Orleneva
- Ajinomoto-Genetika Research Institute, 1st Dorozhny proezd, 1-1, Moscow 117545, Russia
| | - Petr N Teslya
- Ajinomoto-Genetika Research Institute, 1st Dorozhny proezd, 1-1, Moscow 117545, Russia
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4
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Zheng Y, Li Y, Zhou K, Li T, VanDusen NJ, Hua Y. Precise genome-editing in human diseases: mechanisms, strategies and applications. Signal Transduct Target Ther 2024; 9:47. [PMID: 38409199 PMCID: PMC10897424 DOI: 10.1038/s41392-024-01750-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 02/28/2024] Open
Abstract
Precise genome-editing platforms are versatile tools for generating specific, site-directed DNA insertions, deletions, and substitutions. The continuous enhancement of these tools has led to a revolution in the life sciences, which promises to deliver novel therapies for genetic disease. Precise genome-editing can be traced back to the 1950s with the discovery of DNA's double-helix and, after 70 years of development, has evolved from crude in vitro applications to a wide range of sophisticated capabilities, including in vivo applications. Nonetheless, precise genome-editing faces constraints such as modest efficiency, delivery challenges, and off-target effects. In this review, we explore precise genome-editing, with a focus on introduction of the landmark events in its history, various platforms, delivery systems, and applications. First, we discuss the landmark events in the history of precise genome-editing. Second, we describe the current state of precise genome-editing strategies and explain how these techniques offer unprecedented precision and versatility for modifying the human genome. Third, we introduce the current delivery systems used to deploy precise genome-editing components through DNA, RNA, and RNPs. Finally, we summarize the current applications of precise genome-editing in labeling endogenous genes, screening genetic variants, molecular recording, generating disease models, and gene therapy, including ex vivo therapy and in vivo therapy, and discuss potential future advances.
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Affiliation(s)
- Yanjiang Zheng
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yifei Li
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Kaiyu Zhou
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Tiange Li
- Department of Cardiovascular Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Nathan J VanDusen
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
| | - Yimin Hua
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
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Mannino PJ, Perun A, Surovstev I, Ader NR, Shao L, Melia TJ, King MC, Lusk CP. A quantitative ultrastructural timeline of nuclear autophagy reveals a role for dynamin-like protein 1 at the nuclear envelope. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.14.580336. [PMID: 38405892 PMCID: PMC10888867 DOI: 10.1101/2024.02.14.580336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Autophagic mechanisms that maintain nuclear envelope homeostasis are bulwarks to aging and disease. By leveraging 4D lattice light sheet microscopy and correlative light and electron tomography, we define a quantitative and ultrastructural timeline of a nuclear macroautophagy (nucleophagy) pathway in yeast. Nucleophagy initiates with a rapid local accumulation of the nuclear cargo adaptor Atg39 at the nuclear envelope adjacent to the nucleus-vacuole junction and is delivered to the vacuole in ~300 seconds through an autophagosome intermediate. Mechanistically, nucleophagy incorporates two consecutive and genetically defined membrane fission steps: inner nuclear membrane (INM) fission generates a lumenal vesicle in the perinuclear space followed by outer nuclear membrane (ONM) fission to liberate a double membraned vesicle to the cytosol. ONM fission occurs independently of phagophore engagement and instead relies surprisingly on dynamin-like protein1 (Dnm1), which is recruited to sites of Atg39 accumulation at the nuclear envelope. Loss of Dnm1 compromises nucleophagic flux by stalling nucleophagy after INM fission. Our findings reveal how nuclear and INM cargo are removed from an intact nucleus without compromising its integrity, achieved in part by a non-canonical role for Dnm1 in nuclear envelope remodeling.
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Affiliation(s)
- Philip J. Mannino
- Department of Cell Biology, Yale School of Medicine, 295 Congress Ave, New Haven, CT, 06520
| | - Andrew Perun
- Department of Cell Biology, Yale School of Medicine, 295 Congress Ave, New Haven, CT, 06520
| | - Ivan Surovstev
- Department of Cell Biology, Yale School of Medicine, 295 Congress Ave, New Haven, CT, 06520
- Department of Physics, Yale University, New Haven, CT, 06511
| | - Nicholas R. Ader
- Department of Cell Biology, Yale School of Medicine, 295 Congress Ave, New Haven, CT, 06520
| | - Lin Shao
- Department of Cell Biology, Yale School of Medicine, 295 Congress Ave, New Haven, CT, 06520
| | - Thomas J. Melia
- Department of Cell Biology, Yale School of Medicine, 295 Congress Ave, New Haven, CT, 06520
| | - Megan C. King
- Department of Cell Biology, Yale School of Medicine, 295 Congress Ave, New Haven, CT, 06520
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT, 06511
| | - C. Patrick Lusk
- Department of Cell Biology, Yale School of Medicine, 295 Congress Ave, New Haven, CT, 06520
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Cui H, Cui X, Yang X, Cui X, Sun Y, Yuan D, Cui Q, Deng Y, Sun E, Chen YQ, Guo H, Deng Z, Wang J, Xu S, Sun X, Wei Z, Liu X. Effect of ATG8 or SAC1 deficiency on the cell proliferation and lifespan of the long-lived PMT1 deficiency yeast cells. FEMS Microbiol Lett 2024; 371:fnad121. [PMID: 38258560 DOI: 10.1093/femsle/fnad121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 10/22/2023] [Accepted: 11/20/2023] [Indexed: 01/24/2024] Open
Abstract
Autophagy is pivotal in maintaining intracellular homeostasis, which involves various biological processes, including cellular senescence and lifespan modulation. Being an important member of the protein O-mannosyltransferase (PMT) family of enzymes, Pmt1p deficiency can significantly extend the replicative lifespan (RLS) of yeast cells through an endoplasmic reticulum (ER) unfolded protein response (UPR) pathway, which is participated in protein homeostasis. Nevertheless, the mechanisms that Pmt1p regulates the lifespan of yeast cells still need to be explored. In this study, we found that the long-lived PMT1 deficiency strain (pmt1Δ) elevated the expression levels of most autophagy-related genes, the expression levels of total GFP-Atg8 fusion protein and free GFP protein compared with wild-type yeast strain (BY4742). Moreover, the long-lived pmt1Δ strain showed the greater dot-signal accumulation from GFP-Atg8 fusion protein in the vacuole lumen through a confocal microscope. However, deficiency of SAC1 or ATG8, two essential components of the autophagy process, decreased the cell proliferation ability of the long-lived pmt1Δ yeast cells, and prevented the lifespan extension. In addition, our findings demonstrated that overexpression of ATG8 had no potential effect on the RLS of the pmt1Δ yeast cells, and the maintained incubation of minimal synthetic medium lacking nitrogen (SD-N medium as starvation-induced autophagy) inhibited the cell proliferation ability of the pmt1Δ yeast cells with the culture time, and blocked the lifespan extension, especially in the SD-N medium cultured for 15 days. Our results suggest that the long-lived pmt1Δ strain enhances the basal autophagy activity, while deficiency of SAC1 or ATG8 decreases the cell proliferation ability and shortens the RLS of the long-lived pmt1Δ yeast cells. Moreover, the maintained starvation-induced autophagy impairs extension of the long-lived pmt1Δ yeast cells, and even leads to the cell death.
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Affiliation(s)
- Hongjing Cui
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, No. 1 Xincheng Avenue, Songshan Lake, Dongguan City 523808, Guangdong Province, China
- School of Medical Technology, Guangdong Medical University, No. 1 Xincheng Avenue, Songshan Lake, Dongguan 523808, China
- School of Basic Medicine, Guangdong Medical University, No. 1 Xincheng Avenue, Songshan Lake, Dongguan 523808, China
| | - Xiaojing Cui
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, No. 1 Xincheng Avenue, Songshan Lake, Dongguan City 523808, Guangdong Province, China
- School of Medical Technology, Guangdong Medical University, No. 1 Xincheng Avenue, Songshan Lake, Dongguan 523808, China
- The First Dongguan Affiliated Hospital,Guangdong Medical University, No. 42 Jiaoping Road, Tangxia Town, Dongguan 523808, China
| | - Xiaodi Yang
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, No. 1 Xincheng Avenue, Songshan Lake, Dongguan City 523808, Guangdong Province, China
- School of Medical Technology, Guangdong Medical University, No. 1 Xincheng Avenue, Songshan Lake, Dongguan 523808, China
| | - Xingang Cui
- Mudanjiang Medical College, No. 3 Tongxiang Street, Aimin District, Mudanjiang City 157011, Hei Longjiang Proviince, China
| | - Yaxin Sun
- Mudanjiang Medical College, No. 3 Tongxiang Street, Aimin District, Mudanjiang City 157011, Hei Longjiang Proviince, China
| | - Di Yuan
- School of the Second Clinical, Guangdong Medical University, No. 1 Xincheng Avenue, Songshan Lake, Dongguan 523808, China
| | - Qiong Cui
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, No. 1 Xincheng Avenue, Songshan Lake, Dongguan City 523808, Guangdong Province, China
- School of Medical Technology, Guangdong Medical University, No. 1 Xincheng Avenue, Songshan Lake, Dongguan 523808, China
| | - Yanwen Deng
- School of the Second Clinical, Guangdong Medical University, No. 1 Xincheng Avenue, Songshan Lake, Dongguan 523808, China
| | - Enhao Sun
- School of the Second Clinical, Guangdong Medical University, No. 1 Xincheng Avenue, Songshan Lake, Dongguan 523808, China
| | - Ya-Qin Chen
- School of Medical Technology, Guangdong Medical University, No. 1 Xincheng Avenue, Songshan Lake, Dongguan 523808, China
| | - Hongsheng Guo
- School of Basic Medicine, Guangdong Medical University, No. 1 Xincheng Avenue, Songshan Lake, Dongguan 523808, China
| | - Ziliang Deng
- School of Basic Medicine, Guangdong Medical University, No. 1 Xincheng Avenue, Songshan Lake, Dongguan 523808, China
| | - Junfang Wang
- School of Basic Medicine, Guangdong Medical University, No. 1 Xincheng Avenue, Songshan Lake, Dongguan 523808, China
| | - Shun Xu
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, No. 1 Xincheng Avenue, Songshan Lake, Dongguan City 523808, Guangdong Province, China
- School of Medical Technology, Guangdong Medical University, No. 1 Xincheng Avenue, Songshan Lake, Dongguan 523808, China
| | - Xuerong Sun
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, No. 1 Xincheng Avenue, Songshan Lake, Dongguan City 523808, Guangdong Province, China
- School of Medical Technology, Guangdong Medical University, No. 1 Xincheng Avenue, Songshan Lake, Dongguan 523808, China
| | - Zhao Wei
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, No. 1 Xincheng Avenue, Songshan Lake, Dongguan City 523808, Guangdong Province, China
- School of Medical Technology, Guangdong Medical University, No. 1 Xincheng Avenue, Songshan Lake, Dongguan 523808, China
| | - Xinguang Liu
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, No. 1 Xincheng Avenue, Songshan Lake, Dongguan City 523808, Guangdong Province, China
- School of Medical Technology, Guangdong Medical University, No. 1 Xincheng Avenue, Songshan Lake, Dongguan 523808, China
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Kobashi Y, Nakayama E, Fukumori N, Shimojima A, Tabira M, Nishimura Y, Mukae M, Muto A, Nakashima N, Okutsu K, Yoshizaki Y, Futagami T, Takamine K, Tamaki H. Homozygous gene disruption in diploid yeast through a single transformation. J Biosci Bioeng 2024; 137:31-37. [PMID: 37981488 DOI: 10.1016/j.jbiosc.2023.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 10/13/2023] [Accepted: 11/05/2023] [Indexed: 11/21/2023]
Abstract
As industrial shochu yeast is a diploid strain, obtaining a strain with mutations in both allelic genes was considered difficult. We investigated a method for disrupting two copies of a homozygous gene with a single transformation. We designed a disruption cassette containing an intact LYS5 flanked by nonfunctional ura3 gene fragments divided into the 5'- and 3'-regions. These fragments had overlapping sequences that enabled LYS5 removal as well as URA3 regeneration through loop-out. Furthermore, both ends of the disruption cassette had an additional repeat sequence that allowed the cassette to be removed from the chromosome through loop-out. First, 45 bases of 5'- and 3'-regions of target gene sequences were added on both ends of this cassette using polymerase chain reaction; the resultant disruption cassette was introduced into a shochu yeast strain (ura3/ura3 lys5/lys5); then, single allele disrupted strains were selected on Lys drop-out plates; and after cultivation in YPD medium, double-disrupted strains, in which replacement of another allelic gene with disruption cassette by loss of heterozygosity and regeneration of URA3 in one of the cassettes by loop-out, were obtained by selection on Ura and Lys drop-out plates. The disruption cassettes were removed from the double-disrupted strain via loop-out between repeat sequences in the disruption cassette. The strains that lost either URA3 or LYS5 were counter-selected on 5-fluoroorotic acid or α-amino adipic acid plates, respectively. Using this method, we obtained leu2/leu2 and leu2/leu2 his3/his3 strains in shochu yeast, demonstrating the effectiveness and repeatability of this gene disruption technique in diploid yeast Saccharomyces cerevisiae.
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Affiliation(s)
- Yuki Kobashi
- United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Eri Nakayama
- Graduate School of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Naoki Fukumori
- Graduate School of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Ayane Shimojima
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Manami Tabira
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Yuki Nishimura
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Manami Mukae
- Graduate School of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Ai Muto
- Graduate School of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Naoto Nakashima
- Graduate School of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Kayu Okutsu
- Education and Research Center for Fermentation Studies, Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Yumiko Yoshizaki
- United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan; Education and Research Center for Fermentation Studies, Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Taiki Futagami
- United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan; Education and Research Center for Fermentation Studies, Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Kazunori Takamine
- United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan; Education and Research Center for Fermentation Studies, Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Hisanori Tamaki
- United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan; Education and Research Center for Fermentation Studies, Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan.
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Miao Z, Wang H, Tu X, Huang Z, Huang S, Zhang X, Wang F, Huang Z, Li H, Jiao Y, Gao S, Zhou Z, Shan CM, Li J, Yue JX. GetPrimers: A generalized PCR-based genetic targeting primer designer enabling easy and standardized targeted gene modification across multiple systems. Yeast 2024; 41:19-34. [PMID: 38041528 DOI: 10.1002/yea.3916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/02/2023] [Accepted: 11/17/2023] [Indexed: 12/03/2023] Open
Abstract
Genetic targeting (e.g., gene knockout and tagging) based on polymerase chain reaction (PCR) is a simple yet powerful approach for studying gene functions. Although originally developed in classic budding and fission yeast models, the same principle applies to other eukaryotic systems with efficient homologous recombination. One-step PCR-based genetic targeting is conventionally used but the sizes of the homologous arms that it generates for recombination-mediated genetic targeting are usually limited. Alternatively, gene targeting can also be performed via fusion PCR, which can create homologous arms that are orders of magnitude larger, therefore substantially increasing the efficiency of recombination-mediated genetic targeting. Here, we present GetPrimers (https://www.evomicslab.org/app/getprimers/), a generalized computational framework and web tool to assist automatic targeting and verification primer design for both one-step PCR-based and fusion PCR-based genetic targeting experiments. Moreover, GetPrimers by design runs for any given genetic background of any species with full genome scalability. Therefore, GetPrimers is capable of empowering high-throughput functional genomic assays at multipopulation and multispecies levels. Comprehensive experimental validations have been performed for targeting and verification primers designed by GetPrimers across multiple organism systems and experimental setups. We anticipate GetPrimers to become a highly useful and popular tool to facilitate easy and standardized gene modification across multiple systems.
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Affiliation(s)
- Zepu Miao
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Haiting Wang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xinyu Tu
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Zhengshen Huang
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shujing Huang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xinxin Zhang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Fan Wang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Zhishen Huang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Huihui Li
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yue Jiao
- Development Center of Science and Technology, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Song Gao
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Zhipeng Zhou
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chun-Min Shan
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jing Li
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jia-Xing Yue
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
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9
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Tai J, Guerra RM, Rogers SW, Fang Z, Muehlbauer LK, Shishkova E, Overmyer KA, Coon JJ, Pagliarini DJ. Hem25p is required for mitochondrial IPP transport in fungi. Nat Cell Biol 2023; 25:1616-1624. [PMID: 37813972 PMCID: PMC10759932 DOI: 10.1038/s41556-023-01250-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 09/05/2023] [Indexed: 10/11/2023]
Abstract
Coenzyme Q (CoQ, ubiquinone) is an essential cellular cofactor composed of a redox-active quinone head group and a long hydrophobic polyisoprene tail. How mitochondria access cytosolic isoprenoids for CoQ biosynthesis is a longstanding mystery. Here, via a combination of genetic screening, metabolic tracing and targeted uptake assays, we reveal that Hem25p-a mitochondrial glycine transporter required for haem biosynthesis-doubles as an isopentenyl pyrophosphate (IPP) transporter in Saccharomyces cerevisiae. Mitochondria lacking Hem25p failed to efficiently incorporate IPP into early CoQ precursors, leading to loss of CoQ and turnover of CoQ biosynthetic proteins. Expression of Hem25p in Escherichia coli enabled robust IPP uptake and incorporation into the CoQ biosynthetic pathway. HEM25 orthologues from diverse fungi, but not from metazoans, were able to rescue hem25∆ CoQ deficiency. Collectively, our work reveals that Hem25p drives the bulk of mitochondrial isoprenoid transport for CoQ biosynthesis in fungi.
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Affiliation(s)
- Jonathan Tai
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
- Morgridge Institute for Research, Madison, WI, USA
- Department of Cell Biology and Physiology, Washington University School of Medicine, St Louis, MO, USA
| | - Rachel M Guerra
- Department of Cell Biology and Physiology, Washington University School of Medicine, St Louis, MO, USA
| | - Sean W Rogers
- Department of Cell Biology and Physiology, Washington University School of Medicine, St Louis, MO, USA
| | - Zixiang Fang
- Department of Cell Biology and Physiology, Washington University School of Medicine, St Louis, MO, USA
| | - Laura K Muehlbauer
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Evgenia Shishkova
- National Center for Quantitative Biology of Complex Systems, Madison, WI, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Katherine A Overmyer
- Morgridge Institute for Research, Madison, WI, USA
- National Center for Quantitative Biology of Complex Systems, Madison, WI, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Joshua J Coon
- Morgridge Institute for Research, Madison, WI, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- National Center for Quantitative Biology of Complex Systems, Madison, WI, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - David J Pagliarini
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
- Morgridge Institute for Research, Madison, WI, USA.
- Department of Cell Biology and Physiology, Washington University School of Medicine, St Louis, MO, USA.
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA.
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA.
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10
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Alhajouj S, Turkolmez S, Abalkhail T, Alwan ZHO, James Gilmour D, Mitchell PJ, Hettema EH. Efficient PCR-based gene targeting in isolates of the nonconventional yeast Debaryomyces hansenii. Yeast 2023; 40:550-564. [PMID: 37870109 DOI: 10.1002/yea.3902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/29/2023] [Accepted: 09/30/2023] [Indexed: 10/24/2023] Open
Abstract
Debaryomyces hansenii is a yeast with considerable biotechnological potential as an osmotolerant, stress-tolerant oleaginous microbe. However, targeted genome modification tools are limited and require a strain with auxotrophic markers. Gene targeting by homologous recombination has been reported to be inefficient, but here we describe a set of reagents and a method that allows gene targeting at high efficiency in wild-type isolates. It uses a simple polymerase chain reaction (PCR)-based amplification that extends a completely heterologous selectable marker with 50 bp flanks identical to the target site in the genome. Transformants integrate the PCR product through homologous recombination at high frequency (>75%). We illustrate the potential of this method by disrupting genes at high efficiency and by expressing a heterologous protein from a safe chromosomal harbour site. These methods should stimulate and facilitate further analysis of D. hansenii strains and open the way to engineer strains for biotechnology.
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Affiliation(s)
- Sondos Alhajouj
- School of Bioscience, University of Sheffield, Sheffield, UK
| | - Selva Turkolmez
- School of Bioscience, University of Sheffield, Sheffield, UK
| | - Tarad Abalkhail
- School of Bioscience, University of Sheffield, Sheffield, UK
- Future address: Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | | | | | - Phil J Mitchell
- School of Bioscience, University of Sheffield, Sheffield, UK
| | - Ewald H Hettema
- School of Bioscience, University of Sheffield, Sheffield, UK
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11
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Zhai B, Zhang S, Li B, Zhang J, Yang X, Tan Y, Wang Y, Tan T, Yang X, Chen B, Tian Z, Cao Y, Huang Q, Gao J, Wang S, Zhang L. Dna2 removes toxic ssDNA-RPA filaments generated from meiotic recombination-associated DNA synthesis. Nucleic Acids Res 2023; 51:7914-7935. [PMID: 37351599 PMCID: PMC10450173 DOI: 10.1093/nar/gkad537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 06/01/2023] [Accepted: 06/09/2023] [Indexed: 06/24/2023] Open
Abstract
During the repair of DNA double-strand breaks (DSBs), de novo synthesized DNA strands can displace the parental strand to generate single-strand DNAs (ssDNAs). Many programmed DSBs and thus many ssDNAs occur during meiosis. However, it is unclear how these ssDNAs are removed for the complete repair of meiotic DSBs. Here, we show that meiosis-specific depletion of Dna2 (dna2-md) results in an abundant accumulation of RPA and an expansion of RPA from DSBs to broader regions in Saccharomyces cerevisiae. As a result, DSB repair is defective and spores are inviable, although the levels of crossovers/non-crossovers seem to be unaffected. Furthermore, Dna2 induction at pachytene is highly effective in removing accumulated RPA and restoring spore viability. Moreover, the depletion of Pif1, an activator of polymerase δ required for meiotic recombination-associated DNA synthesis, and Pif1 inhibitor Mlh2 decreases and increases RPA accumulation in dna2-md, respectively. In addition, blocking DNA synthesis during meiotic recombination dramatically decreases RPA accumulation in dna2-md. Together, our findings show that meiotic DSB repair requires Dna2 to remove ssDNA-RPA filaments generated from meiotic recombination-associated DNA synthesis. Additionally, we showed that Dna2 also regulates DSB-independent RPA distribution.
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Affiliation(s)
- Binyuan Zhai
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, Shandong 250014, China
| | - Shuxian Zhang
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Bo Li
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, China
| | - Jiaming Zhang
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Xuan Yang
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Yingjin Tan
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Ying Wang
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, Shandong 250014, China
| | - Taicong Tan
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Xiao Yang
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong 250012, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Jinan, Shandong 250001, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong 250012, China
| | - Beiyi Chen
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
- Advanced Medical Research Institute, Shandong University, Jinan, Shandong 250012, China
| | - Zhongyu Tian
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
- Advanced Medical Research Institute, Shandong University, Jinan, Shandong 250012, China
| | - Yanding Cao
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Qilai Huang
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, China
| | - Jinmin Gao
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, Shandong 250014, China
| | - Shunxin Wang
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong 250012, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Jinan, Shandong 250001, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong 250012, China
| | - Liangran Zhang
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, Shandong 250014, China
- Advanced Medical Research Institute, Shandong University, Jinan, Shandong 250012, China
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12
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Stepchenkova EI, Zadorsky SP, Shumega AR, Aksenova AY. Practical Approaches for the Yeast Saccharomyces cerevisiae Genome Modification. Int J Mol Sci 2023; 24:11960. [PMID: 37569333 PMCID: PMC10419131 DOI: 10.3390/ijms241511960] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/21/2023] [Accepted: 07/22/2023] [Indexed: 08/13/2023] Open
Abstract
The yeast S. cerevisiae is a unique genetic object for which a wide range of relatively simple, inexpensive, and non-time-consuming methods have been developed that allow the performing of a wide variety of genome modifications. Among the latter, one can mention point mutations, disruptions and deletions of particular genes and regions of chromosomes, insertion of cassettes for the expression of heterologous genes, targeted chromosomal rearrangements such as translocations and inversions, directed changes in the karyotype (loss or duplication of particular chromosomes, changes in the level of ploidy), mating-type changes, etc. Classical yeast genome manipulations have been advanced with CRISPR/Cas9 technology in recent years that allow for the generation of multiple simultaneous changes in the yeast genome. In this review we discuss practical applications of both the classical yeast genome modification methods as well as CRISPR/Cas9 technology. In addition, we review methods for ploidy changes, including aneuploid generation, methods for mating type switching and directed DSB. Combined with a description of useful selective markers and transformation techniques, this work represents a nearly complete guide to yeast genome modification.
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Affiliation(s)
- Elena I. Stepchenkova
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (E.I.S.); (S.P.Z.); (A.R.S.)
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Sergey P. Zadorsky
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (E.I.S.); (S.P.Z.); (A.R.S.)
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Andrey R. Shumega
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (E.I.S.); (S.P.Z.); (A.R.S.)
| | - Anna Y. Aksenova
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
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13
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Zhao W, Kong L, Guan W, Liu J, Cui H, Cai M, Fang B, Liu X. Yeast UPS1 deficiency leads to UVC radiation sensitivity and shortened lifespan. Antonie Van Leeuwenhoek 2023:10.1007/s10482-023-01847-8. [PMID: 37222845 DOI: 10.1007/s10482-023-01847-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 05/16/2023] [Indexed: 05/25/2023]
Abstract
UPS1/YLR193C of Saccharomyces cerevisiae (S. cerevisiae) encodes a mitochondrial intermembrane space protein. A previous study found that Ups1p is needed for normal mitochondrial morphology and that UPS1 deficiency disrupts the intramitochondrial transport of phosphatidic acid in yeast cells and leads to an altered unfolded protein response and mTORC1 signaling activation. In this paper, we first provide evidence showing that the UPS1 gene is involved in the UVC-induced DNA damage response and aging. We show that UPS1 deficiency leads to sensitivity to ultraviolet C (UVC) radiation and that this effect is accompanied by elevated DNA damage, increased intracellular ROS levels, abnormal mitochondrial respiratory function, an increased early apoptosis rate, and shortened replicative lifespan and chronological lifespan. Moreover, we show that overexpression of the DNA damage-induced checkpoint gene RAD9 effectively eliminates the senescence-related defects observed in the UPS1-deficient strain. Collectively, these results suggest a novel role for UPS1 in the UVC-induced DNA damage response and aging.
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Affiliation(s)
- Wei Zhao
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, Dongguan, 523808, China
- School of Medical Technology, Guangdong Medical University, Dongguan, China
| | - Lingyue Kong
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, Dongguan, 523808, China
- School of Medical Technology, Guangdong Medical University, Dongguan, China
| | - Wenbin Guan
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, Dongguan, 523808, China
- School of Medical Technology, Guangdong Medical University, Dongguan, China
| | - Jiaxin Liu
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, Dongguan, 523808, China
- School of Medical Technology, Guangdong Medical University, Dongguan, China
| | - Hongjing Cui
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, Dongguan, 523808, China
- School of Medical Technology, Guangdong Medical University, Dongguan, China
| | - Mianshan Cai
- Precision Medicine Centre, Department of Pediatrics, Puning People's Hospital, Puning, 515300, Guangdong, China
| | - Bingxiong Fang
- Precision Medicine Centre, Department of Pediatrics, Puning People's Hospital, Puning, 515300, Guangdong, China.
| | - Xinguang Liu
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, Dongguan, 523808, China.
- School of Medical Technology, Guangdong Medical University, Dongguan, China.
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14
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Tapia SM, Macías LG, Pérez-Torrado R, Daroqui N, Manzanares P, Querol A, Barrio E. A novel aminotransferase gene and its regulator acquired in Saccharomyces by a horizontal gene transfer event. BMC Biol 2023; 21:102. [PMID: 37158891 PMCID: PMC10169451 DOI: 10.1186/s12915-023-01566-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 03/16/2023] [Indexed: 05/10/2023] Open
Abstract
BACKGROUND Horizontal gene transfer (HGT) is an evolutionary mechanism of adaptive importance, which has been deeply studied in wine S. cerevisiae strains, where those acquired genes conferred improved traits related to both transport and metabolism of the nutrients present in the grape must. However, little is known about HGT events that occurred in wild Saccharomyces yeasts and how they determine their phenotypes. RESULTS Through a comparative genomic approach among Saccharomyces species, we detected a subtelomeric segment present in the S. uvarum, S. kudriavzevii, and S. eubayanus species, belonging to the first species to diverge in the Saccharomyces genus, but absent in the other Saccharomyces species. The segment contains three genes, two of which were characterized, named DGD1 and DGD2. DGD1 encodes dialkylglicine decarboxylase, whose specific substrate is the non-proteinogenic amino acid 2-aminoisobutyric acid (AIB), a rare amino acid present in some antimicrobial peptides of fungal origin. DGD2 encodes putative zinc finger transcription factor, which is essential to induce the AIB-dependent expression of DGD1. Phylogenetic analysis showed that DGD1 and DGD2 are closely related to two adjacent genes present in Zygosaccharomyces. CONCLUSIONS The presented results show evidence of an early HGT event conferring new traits to the ancestor of the Saccharomyces genus that could be lost in the evolutionary more recent Saccharomyces species, perhaps due to loss of function during the colonization of new habitats.
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Affiliation(s)
- Sebastián M Tapia
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, Spain
| | - Laura G Macías
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, Spain
| | | | - Noemi Daroqui
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, Spain
| | - Paloma Manzanares
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, Spain
| | - Amparo Querol
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, Spain
| | - Eladio Barrio
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, Spain.
- Departament de Genètica, Universitat de València, Valencia, Spain.
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15
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Sato G, Kuroda K. Overcoming the Limitations of CRISPR-Cas9 Systems in Saccharomyces cerevisiae: Off-Target Effects, Epigenome, and Mitochondrial Editing. Microorganisms 2023; 11:microorganisms11041040. [PMID: 37110464 PMCID: PMC10145089 DOI: 10.3390/microorganisms11041040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Modification of the genome of the yeast Saccharomyces cerevisiae has great potential for application in biological research and biotechnological advancements, and the CRISPR-Cas9 system has been increasingly employed for these purposes. The CRISPR-Cas9 system enables the precise and simultaneous modification of any genomic region of the yeast to a desired sequence by altering only a 20-nucleotide sequence within the guide RNA expression constructs. However, the conventional CRISPR-Cas9 system has several limitations. In this review, we describe the methods that were developed to overcome these limitations using yeast cells. We focus on three types of developments: reducing the frequency of unintended editing to both non-target and target sequences in the genome, inducing desired changes in the epigenetic state of the target region, and challenging the expansion of the CRISPR-Cas9 system to edit genomes within intracellular organelles such as mitochondria. These developments using yeast cells to overcome the limitations of the CRISPR-Cas9 system are a key factor driving the advancement of the field of genome editing.
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Affiliation(s)
- Genki Sato
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kouichi Kuroda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
- Department of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Sakyo-ku, Kyoto 606-8585, Japan
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16
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Karpukhin AD, Sabirzyanov FA, Serebrianyi VA. Acceleration of CRISPR/Cas9-Mediated Editing at Multiple Sites in the Saccharomyces cerevisiae Genome. Methods Protoc 2023; 6:mps6020039. [PMID: 37104021 PMCID: PMC10141985 DOI: 10.3390/mps6020039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/28/2023] [Accepted: 04/02/2023] [Indexed: 04/08/2023] Open
Abstract
The application of the CRISPR/Cas9-based genome editing technique to the yeast Saccharomyces cerevisiae has made it possible to simultaneously modify several sites, particularly to integrate several expression cassettes. The existing methods provide high efficiency for such modifications; however, common protocols include several preparatory steps, namely, the construction of an intermediate Cas9-expressing strain, the assembly of a plasmid bearing several single guide RNA (sgRNA) expression cassettes, and the surrounding integrated DNA fragments with long flanks for recombination with target loci. Since these preparatory steps are time consuming and may not be desirable in some types of experiments, we explored the possibility of multiple integration without these steps. We have demonstrated that it is possible to skip them simultaneously and integrate up to three expression cassettes into separate sites by transforming the recipient strain with the Cas9 expression plasmid, three differently marked sgRNA plasmids, and three donor DNAs flanked with short (70 bp) arms for recombination. This finding increases the flexibility of choosing the optimal experimental design for multiple editing of the genome of S. cerevisiae and can significantly accelerate such experiments.
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Affiliation(s)
- Alexey D. Karpukhin
- Ajinomoto-Genetika Research Institute, 1st Dorozhny Proezd, b.1-1, Moscow 117545, Russia
| | - Fanis A. Sabirzyanov
- Ajinomoto-Genetika Research Institute, 1st Dorozhny Proezd, b.1-1, Moscow 117545, Russia
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17
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Bennis NX, Kostanjšek M, van den Broek M, Daran JMG. Improving CRISPR-Cas9 mediated genome integration in interspecific hybrid yeasts. N Biotechnol 2023; 76:49-62. [PMID: 37028644 DOI: 10.1016/j.nbt.2023.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/03/2023] [Accepted: 04/04/2023] [Indexed: 04/08/2023]
Abstract
Saccharomyces pastorianus is not a classical taxon, it is an interspecific hybrid resulting from the cross of Saccharomyces cerevisiae and Saccharomyces eubayanus. Exhibiting heterosis for phenotypic traits such as wort α-oligosaccharide consumption and fermentation at low temperature, it has been domesticated to become the main workhorse of the brewing industry. Although CRISPR-Cas9 has been shown to be functional in S. pastorianus, repair of CRISPR- induced double strand break is unpredictable and preferentially uses the homoeologous chromosome as template, preventing targeted introduction of the desired repair construct. Here, we demonstrate that lager hybrids can be edited with near 100% efficiency at carefully selected landing sites on the chimeric SeScCHRIII. The landing sites were systematically selected and evaluated for (i) absence of loss of heterozygosity upon CRISPR-editing, (ii) efficiency of the gRNA, and (iii) absence of effect on strain physiology. Successful examples of highly efficient single and double gene integration illustrated that genome editing can be applied in interspecies hybrids, paving the way to a new impulse to lager yeast strain development. DATA AVAILABILITY: Data underlying graphs and figures found in this manuscript are deposited at the 4TU research dat center (https://data.4tu.nl/info/en/) and available through the doi: 10.4121/21648329.
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18
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Tai J, Guerra RM, Rogers SW, Fang Z, Muehlbauer LK, Shishkova E, Overmyer KA, Coon JJ, Pagliarini DJ. Hem25p is a mitochondrial IPP transporter. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.14.532620. [PMID: 36993473 PMCID: PMC10055127 DOI: 10.1101/2023.03.14.532620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Coenzyme Q (CoQ, ubiquinone) is an essential cellular cofactor comprised of a redox-active quinone head group and a long hydrophobic polyisoprene tail. How mitochondria access cytosolic isoprenoids for CoQ biosynthesis is a longstanding mystery. Here, via a combination of genetic screening, metabolic tracing, and targeted uptake assays, we reveal that Hem25p-a mitochondrial glycine transporter required for heme biosynthesis-doubles as an isopentenyl pyrophosphate (IPP) transporter in Saccharomyces cerevisiae. Mitochondria lacking Hem25p fail to efficiently incorporate IPP into early CoQ precursors, leading to loss of CoQ and turnover of CoQ biosynthetic proteins. Expression of Hem25p in Escherichia coli enables robust IPP uptake demonstrating that Hem25p is sufficient for IPP transport. Collectively, our work reveals that Hem25p drives the bulk of mitochondrial isoprenoid transport for CoQ biosynthesis in yeast.
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Affiliation(s)
- Jonathan Tai
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53715, USA
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Rachel M. Guerra
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Sean W. Rogers
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Zixiang Fang
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Laura K. Muehlbauer
- Department of Chemistry, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Evgenia Shishkova
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA
- Department of Biomolecular Chemistry, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Katherine A. Overmyer
- Morgridge Institute for Research, Madison, WI 53715, USA
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA
- Department of Biomolecular Chemistry, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Joshua J. Coon
- Morgridge Institute for Research, Madison, WI 53715, USA
- Department of Chemistry, University of Wisconsin–Madison, Madison, WI 53706, USA
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA
- Department of Biomolecular Chemistry, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - David J. Pagliarini
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53715, USA
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
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19
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Kim GB, Choi SY, Cho IJ, Ahn DH, Lee SY. Metabolic engineering for sustainability and health. Trends Biotechnol 2023; 41:425-451. [PMID: 36635195 DOI: 10.1016/j.tibtech.2022.12.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/17/2022] [Accepted: 12/21/2022] [Indexed: 01/12/2023]
Abstract
Bio-based production of chemicals and materials has attracted much attention due to the urgent need to establish sustainability and enhance human health. Metabolic engineering (ME) allows purposeful modification of cellular metabolic, regulatory, and signaling networks to achieve enhanced production of desired chemicals and degradation of environmentally harmful chemicals. ME has significantly progressed over the past 30 years through further integration of the strategies of synthetic biology, systems biology, evolutionary engineering, and data science aided by artificial intelligence. Here we review the field of ME from its emergence to the current state-of-the-art, highlighting its contribution to sustainable production of chemicals, health, and the environment through representative examples. Future challenges of ME and perspectives are also discussed.
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Affiliation(s)
- Gi Bae Kim
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - So Young Choi
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - In Jin Cho
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Da-Hee Ahn
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
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20
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Schmitz JM, Wolters JF, Murray NH, Guerra RM, Bingman CA, Hittinger CT, Pagliarini DJ. Aim18p and Aim46p are chalcone isomerase domain-containing mitochondrial hemoproteins in Saccharomyces cerevisiae. J Biol Chem 2023; 299:102981. [PMID: 36739946 PMCID: PMC9996372 DOI: 10.1016/j.jbc.2023.102981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/26/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023] Open
Abstract
Chalcone isomerases (CHIs) have well-established roles in the biosynthesis of plant flavonoid metabolites. Saccharomyces cerevisiae possesses two predicted CHI-like proteins, Aim18p (encoded by YHR198C) and Aim46p (YHR199C), but it lacks other enzymes of the flavonoid pathway, suggesting that Aim18p and Aim46p employ the CHI fold for distinct purposes. Here, we demonstrate using proteinase K protection assays, sodium carbonate extractions, and crystallography that Aim18p and Aim46p reside on the mitochondrial inner membrane and adopt CHI folds, but they lack select active site residues and possess an extra fungal-specific loop. Consistent with these differences, Aim18p and Aim46p lack CHI activity and also the fatty acid-binding capabilities of other CHI-like proteins, but instead bind heme. We further show that diverse fungal homologs also bind heme and that Aim18p and Aim46p possess structural homology to a bacterial hemoprotein. Collectively, our work reveals a distinct function and cellular localization for two CHI-like proteins, introduces a new variation of a hemoprotein fold, and suggests that ancestral CHI-like proteins were hemoproteins.
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Affiliation(s)
- Jonathan M Schmitz
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; Morgridge Institute for Research, Madison, Wisconsin, USA
| | - John F Wolters
- Laboratory of Genetics, Center for Genomic Science Innovation, Wisconsin Energy Institute, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Nathan H Murray
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; Morgridge Institute for Research, Madison, Wisconsin, USA; Department of Cell Biology and Physiology, Washington University School of Medicine, St Louis, Missouri, USA
| | - Rachel M Guerra
- Morgridge Institute for Research, Madison, Wisconsin, USA; Department of Cell Biology and Physiology, Washington University School of Medicine, St Louis, Missouri, USA
| | - Craig A Bingman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Chris Todd Hittinger
- Laboratory of Genetics, Center for Genomic Science Innovation, Wisconsin Energy Institute, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - David J Pagliarini
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; Morgridge Institute for Research, Madison, Wisconsin, USA; Department of Cell Biology and Physiology, Washington University School of Medicine, St Louis, Missouri, USA; Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, Missouri, USA; Department of Genetics, Washington University School of Medicine, St Louis, Missouri, USA.
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21
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Qiu Y, Kenana R, Beharry A, Wilhelm SDP, Hsu SY, Siu VM, Duennwald M, Heinemann IU. Histidine supplementation can escalate or rescue HARS deficiency in a Charcot-Marie-Tooth disease model. Hum Mol Genet 2023; 32:810-824. [PMID: 36164730 PMCID: PMC9941834 DOI: 10.1093/hmg/ddac239] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 08/30/2022] [Accepted: 09/15/2022] [Indexed: 11/13/2022] Open
Abstract
Aminoacyl-tRNA synthetases are essential enzymes responsible for charging amino acids onto cognate tRNAs during protein synthesis. In histidyl-tRNA synthetase (HARS), autosomal dominant mutations V133F, V155G, Y330C and S356N in the HARS catalytic domain cause Charcot-Marie-Tooth disease type 2 W (CMT2W), while tRNA-binding domain mutation Y454S causes recessive Usher syndrome type IIIB. In a yeast model, all human HARS variants complemented a genomic deletion of the yeast ortholog HTS1 at high expression levels. CMT2W associated mutations, but not Y454S, resulted in reduced growth. We show mistranslation of histidine to glutamine and threonine in V155G and S356N but not Y330C mutants in yeast. Mistranslating V155G and S356N mutants lead to accumulation of insoluble proteins, which was rescued by histidine. Mutants V133F and Y330C showed the most significant growth defect and decreased HARS abundance in cells. Here, histidine supplementation led to insoluble protein aggregation and further reduced viability, indicating histidine toxicity associated with these mutants. V133F proteins displayed reduced thermal stability in vitro, which was rescued by tRNA. Our data will inform future treatment options for HARS patients, where histidine supplementation may either have a toxic or compensating effect depending on the nature of the causative HARS variant.
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Affiliation(s)
- Yi Qiu
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Rosan Kenana
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Aruun Beharry
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Sarah D P Wilhelm
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Sung Yuan Hsu
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Victoria M Siu
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Martin Duennwald
- Department of Anatomy and Cell Biology, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Ilka U Heinemann
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
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22
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Maloisel L, Ma E, Phipps J, Deshayes A, Mattarocci S, Marcand S, Dubrana K, Coïc E. Rad51 filaments assembled in the absence of the complex formed by the Rad51 paralogs Rad55 and Rad57 are outcompeted by translesion DNA polymerases on UV-induced ssDNA gaps. PLoS Genet 2023; 19:e1010639. [PMID: 36749784 PMCID: PMC9937489 DOI: 10.1371/journal.pgen.1010639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 02/17/2023] [Accepted: 01/26/2023] [Indexed: 02/08/2023] Open
Abstract
The bypass of DNA lesions that block replicative polymerases during DNA replication relies on DNA damage tolerance pathways. The error-prone translesion synthesis (TLS) pathway depends on specialized DNA polymerases that incorporate nucleotides in front of base lesions, potentially inducing mutagenesis. Two error-free pathways can bypass the lesions: the template switching pathway, which uses the sister chromatid as a template, and the homologous recombination pathway (HR), which also can use the homologous chromosome as template. The balance between error-prone and error-free pathways controls the mutagenesis level. Therefore, it is crucial to precisely characterize factors that influence the pathway choice to better understand genetic stability at replication forks. In yeast, the complex formed by the Rad51 paralogs Rad55 and Rad57 promotes HR and template-switching at stalled replication forks. At DNA double-strand breaks (DSBs), this complex promotes Rad51 filament formation and stability, notably by counteracting the Srs2 anti-recombinase. To explore the role of the Rad55-Rad57 complex in error-free pathways, we monitored the genetic interactions between Rad55-Rad57, the translesion polymerases Polζ or Polη, and Srs2 following UV radiation that induces mostly single-strand DNA gaps. We found that the Rad55-Rad57 complex was involved in three ways. First, it protects Rad51 filaments from Srs2, as it does at DSBs. Second, it promotes Rad51 filament stability independently of Srs2. Finally, we observed that UV-induced HR is almost abolished in Rad55-Rad57 deficient cells, and is partially restored upon Polζ or Polη depletion. Hence, we propose that the Rad55-Rad57 complex is essential to promote Rad51 filament stability on single-strand DNA gaps, notably to counteract the error-prone TLS polymerases and mutagenesis.
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Affiliation(s)
- Laurent Maloisel
- Université de Paris and Université Paris-Saclay, INSERM, CEA, Institut de Biologie François Jacob, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
- * E-mail: (LM); (EC)
| | - Emilie Ma
- Université de Paris and Université Paris-Saclay, INSERM, CEA, Institut de Biologie François Jacob, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
| | - Jamie Phipps
- Université de Paris and Université Paris-Saclay, INSERM, CEA, Institut de Biologie François Jacob, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
| | - Alice Deshayes
- Université de Paris and Université Paris-Saclay, INSERM, CEA, Institut de Biologie François Jacob, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
| | - Stefano Mattarocci
- Université de Paris and Université Paris-Saclay, INSERM, CEA, Institut de Biologie François Jacob, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
| | - Stéphane Marcand
- Université de Paris and Université Paris-Saclay, INSERM, CEA, Institut de Biologie François Jacob, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
| | - Karine Dubrana
- Université de Paris and Université Paris-Saclay, INSERM, CEA, Institut de Biologie François Jacob, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
| | - Eric Coïc
- Université de Paris and Université Paris-Saclay, INSERM, CEA, Institut de Biologie François Jacob, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
- * E-mail: (LM); (EC)
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23
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Badura J, van Wyk N, Zimmer K, Pretorius IS, von Wallbrunn C, Wendland J. PCR-based gene targeting in Hanseniaspora uvarum. FEMS Yeast Res 2023; 23:foad034. [PMID: 37500280 DOI: 10.1093/femsyr/foad034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 06/09/2023] [Accepted: 07/26/2023] [Indexed: 07/29/2023] Open
Abstract
Lack of gene-function analyses tools limits studying the biology of Hanseniaspora uvarum, one of the most abundant yeasts on grapes and in must. We investigated a rapid PCR-based gene targeting approach for one-step gene replacement in this diploid yeast. To this end, we generated and validated two synthetic antibiotic resistance genes, pFA-hygXL and pFA-clnXL, providing resistance against hygromycin and nourseothricin, respectively, for use with H. uvarum. Addition of short flanking-homology regions of 56-80 bp to these selection markers via PCR was sufficient to promote gene targeting. We report here the deletion of the H. uvarum LEU2 and LYS2 genes with these marker genes via two rounds of consecutive transformations, each resulting in the generation of auxotrophic strains (leu2/leu2; lys2/lys2). The hereby constructed leucine auxotrophic leu2/leu2 strain was subsequently complemented in a targeted manner, thereby further validating this approach. PCR-based gene targeting in H. uvarum was less efficient than in Saccharomyces cerevisiae. However, this approach, combined with the availability of two marker genes, provides essential tools for directed gene manipulations in H. uvarum.
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Affiliation(s)
- Jennifer Badura
- Department of Microbiology and Biochemistry, Hochschule Geisenheim University, Von-Lade-Strasse 1, 65366 Geisenheim, Germany
| | - Niël van Wyk
- Department of Microbiology and Biochemistry, Hochschule Geisenheim University, Von-Lade-Strasse 1, 65366 Geisenheim, Germany
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
| | - Kerstin Zimmer
- Department of Microbiology and Biochemistry, Hochschule Geisenheim University, Von-Lade-Strasse 1, 65366 Geisenheim, Germany
| | - Isak S Pretorius
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
| | - Christian von Wallbrunn
- Department of Microbiology and Biochemistry, Hochschule Geisenheim University, Von-Lade-Strasse 1, 65366 Geisenheim, Germany
| | - Jürgen Wendland
- Department of Microbiology and Biochemistry, Hochschule Geisenheim University, Von-Lade-Strasse 1, 65366 Geisenheim, Germany
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24
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Ekal L, Hettema E. Targeted Modifications of the Yeast Genome to Study Peroxisomes. Methods Mol Biol 2023; 2643:217-232. [PMID: 36952189 DOI: 10.1007/978-1-0716-3048-8_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
PCR-based gene targeting enables rapid alteration of the Saccharomyces cerevisiae genome. Here we describe how this method can be applied for directed gene deletions, epitope and fluorescence protein tagging, and conditional gene expression, with a specific focus on peroxisomal proteins.
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Affiliation(s)
- Lakhan Ekal
- European Molecular Biology Laboratory, Hamburg, Germany.
| | - Ewald Hettema
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, UK
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25
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Yu JSL, Heineike BM, Hartl J, Aulakh SK, Correia-Melo C, Lehmann A, Lemke O, Agostini F, Lee CT, Demichev V, Messner CB, Mülleder M, Ralser M. Inorganic sulfur fixation via a new homocysteine synthase allows yeast cells to cooperatively compensate for methionine auxotrophy. PLoS Biol 2022; 20:e3001912. [PMID: 36455053 PMCID: PMC9757880 DOI: 10.1371/journal.pbio.3001912] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 12/16/2022] [Accepted: 11/14/2022] [Indexed: 12/03/2022] Open
Abstract
The assimilation, incorporation, and metabolism of sulfur is a fundamental process across all domains of life, yet how cells deal with varying sulfur availability is not well understood. We studied an unresolved conundrum of sulfur fixation in yeast, in which organosulfur auxotrophy caused by deletion of the homocysteine synthase Met17p is overcome when cells are inoculated at high cell density. In combining the use of self-establishing metabolically cooperating (SeMeCo) communities with proteomic, genetic, and biochemical approaches, we discovered an uncharacterized gene product YLL058Wp, herein named Hydrogen Sulfide Utilizing-1 (HSU1). Hsu1p acts as a homocysteine synthase and allows the cells to substitute for Met17p by reassimilating hydrosulfide ions leaked from met17Δ cells into O-acetyl-homoserine and forming homocysteine. Our results show that cells can cooperate to achieve sulfur fixation, indicating that the collective properties of microbial communities facilitate their basic metabolic capacity to overcome sulfur limitation.
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Affiliation(s)
- Jason S. L. Yu
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Benjamin M. Heineike
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Johannes Hartl
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany
| | - Simran K. Aulakh
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Clara Correia-Melo
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Andrea Lehmann
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany
| | - Oliver Lemke
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany
| | - Federica Agostini
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany
| | - Cory T. Lee
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany
| | - Vadim Demichev
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany
| | - Christoph B. Messner
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Michael Mülleder
- Core Facility—High Throughput Mass Spectrometry, Charité Universitätsmedizin, Berlin, Germany
| | - Markus Ralser
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany
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26
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Cao Y, Zhang C, Fang Y, Liu Y, Lyu K, Ding J, Wang X. Investigation the global effect of rare earth gadolinium on the budding Saccharomyces cerevisiae by genome-scale screening. Front Microbiol 2022; 13:1022054. [DOI: 10.3389/fmicb.2022.1022054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 11/11/2022] [Indexed: 11/29/2022] Open
Abstract
IntroductionThe rare earth gadolinium (Gd) is widely used in industry and medicine, which has been treated as an emerging pollutant in environment. The increasing pollution of Gd has potential hazards to living organisms. Thus it is essential to investigate the toxicity and action mechanism of Gd in biological system.MethodsIn this study, the global effect and activation mechanism of Gd on yeast were investigated by genome-scale screening.Results and discussionOur results show that 45 gene deletion strains are sensitive to Gd and 10 gene deletion strains are Gd resistant from the diploid gene deletion strain library of Saccharomyces cerevisiae. The result of localization analysis shows that most of these genes are involved in cell metabolism, cell cycle, transcription, translation, protein synthesis, protein folding, and cell transport. The result of functional analysis shows that four genes (CNB1, CRZ1, VCX1, and GDT1) are involved in the calcium signaling pathway, and four genes (PHO84, PHO86, PHO2, and PHO4) are involved in phosphorus metabolism. For Gd3+ has the similar ion radius with Ca2+ and easily binds to the phosphate radical, it affects Ca2+ signaling pathway and phosphorus metabolism. The genes ARF1, ARL1, ARL3, SYS1, COG5, COG6, YPT6, VPS9, SSO2, MRL1, AKL1, and TRS85 participate in vesicle transport and protein sorting. Thus, Gd accumulation affects the function of proteins related to vesicle transport, which may result in the failure of Gd transport out of cells. In addition, the intracellular Gd content in the 45 sensitive deletion strains is higher than that in the wild type yeast under Gd stress. It suggests that the sensitivity of yeast deletion strains is related to the excessive intracellular Gd accumulation.
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27
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Khatape AB, Dastager SG, Rangaswamy V. An overview of erythritol production by yeast strains. FEMS Microbiol Lett 2022; 369:6819949. [PMID: 36354105 DOI: 10.1093/femsle/fnac107] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/26/2022] [Accepted: 11/07/2022] [Indexed: 11/11/2022] Open
Abstract
Erythritol is a 4-carbon polyol produced with the aid of microbes in presence of hyper-osmotic stress. It is the most effective sugar alcohol that is produced predominantly by fermentation. In comparison to various polyols, it has many precise functions and is used as a flavor enhancer, sequestrant, humectant, nutritive sweetener, stabilizer, formulation aid, thickener, and a texturizer. Erythritol production is a common trait in a number of the yeast genera viz., Trigonopsis, Candida, Pichia, Moniliella, Yarrowia, Pseudozyma, Trichosporonoides, Aureobasidium, and Trichoderma. Extensive work has been carried out on the biological production of erythritol through Yarrowia, Moniliella, Candida, and other yeast strains, and numerous strategies used to improve erythritol productivity through mutagenesis and genetic engineering are discussed in this review.
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Affiliation(s)
- Anil B Khatape
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India.,NCIM-Resource Center, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune-411008, India.,High Value Chemicals group, Reliance Industries Limited, Ghansoli, Navi Mumbai 400701, India
| | - Syed G Dastager
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India.,NCIM-Resource Center, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune-411008, India
| | - Vidhya Rangaswamy
- High Value Chemicals group, Reliance Industries Limited, Ghansoli, Navi Mumbai 400701, India
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28
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Tapia SM, Pérez‐Torrado R, Adam AC, Macías LG, Barrio E, Querol A. Adaptive evolution in the Saccharomyces kudriavzevii Aro4p promoted a reduced production of higher alcohols. Microb Biotechnol 2022; 15:2958-2969. [PMID: 36307988 PMCID: PMC9733642 DOI: 10.1111/1751-7915.14154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 12/30/2022] Open
Abstract
The use of unconventional yeast species in human-driven fermentations has attracted a lot of attention in the last few years. This tool allows the alcoholic beverage industries to solve problems related to climate change or the consumer demand for newer high-quality products. In this sense, one of the most attractive species is Saccharomyces kudriavzevii, which shows interesting fermentative traits such as the increased and diverse aroma compound production in wines. Specifically, it has been observed that different isolates of this species can produce higher amounts of higher alcohols such as phenylethanol compared with Saccharomyces cerevisiae. In this work, we have shed light on this feature relating it to the S. kudriavzevii aromatic amino acid anabolic pathway in which the enzyme Aro4p plays an essential role. Unexpectedly, we observed that the presence of the S. kudriavzevii ARO4 variant reduces phenylethanol production compared with the S. cerevisiae ARO4 allele. Our experiments suggest that this can be explained by increased feedback inhibition, which might be a consequence of the changes detected in the Aro4p amino end such as L26 Q24 that have been under positive selection in the S. kudriavzevii specie.
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Affiliation(s)
- Sebastián M. Tapia
- Departamento de Biotecnología de los AlimentosInstituto de Agroquímica y Tecnología de Los Alimentos (IATA)‐CSICValenciaSpain
| | - Roberto Pérez‐Torrado
- Departamento de Biotecnología de los AlimentosInstituto de Agroquímica y Tecnología de Los Alimentos (IATA)‐CSICValenciaSpain
| | - Ana Cristina Adam
- Departamento de Biotecnología de los AlimentosInstituto de Agroquímica y Tecnología de Los Alimentos (IATA)‐CSICValenciaSpain
| | - Laura G. Macías
- Departamento de Biotecnología de los AlimentosInstituto de Agroquímica y Tecnología de Los Alimentos (IATA)‐CSICValenciaSpain,Departament de GenèticaUniversitat de ValènciaValenciaSpain
| | - Eladio Barrio
- Departamento de Biotecnología de los AlimentosInstituto de Agroquímica y Tecnología de Los Alimentos (IATA)‐CSICValenciaSpain,Departament de GenèticaUniversitat de ValènciaValenciaSpain
| | - Amparo Querol
- Departamento de Biotecnología de los AlimentosInstituto de Agroquímica y Tecnología de Los Alimentos (IATA)‐CSICValenciaSpain
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29
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Jacobs KC, Gorman O, Lew DJ. Mechanism of commitment to a mating partner in Saccharomyces cerevisiae. Mol Biol Cell 2022; 33:ar112. [PMID: 35947501 DOI: 10.1091/mbc.e22-02-0043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Many cells detect and follow gradients of chemical signals to perform their functions. Yeast cells use gradients of extracellular pheromones to locate mating partners, providing a tractable model to understand how cells decode the spatial information in gradients. To mate, yeast cells must orient polarity toward the mating partner. Polarity sites are mobile, exploring the cell cortex until they reach the proper position, where they stop moving and "commit" to the partner. A simple model to explain commitment posits that a high concentration of pheromone is only detected upon alignment of partner cells' polarity sites, and causes polarity site movement to stop. Here we explore how yeast cells respond to partners that make different amounts of pheromone. Commitment was surprisingly robust to varying pheromone levels, ruling out the simple model. We also tested whether adaptive pathways were responsible for the robustness of commitment, but our results show that cells lacking those pathways were still able to accommodate changes in pheromone. To explain this robustness, we suggest that the steep pheromone gradients near each mating partner's polarity site trap the polarity site in place.
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Affiliation(s)
- Katherine C Jacobs
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27708
| | - Olivia Gorman
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27708
| | - Daniel J Lew
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27708
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Sato M, Irie K, Suda Y, Mizuno T, Irie K. The RNA-binding protein Puf5 and the HMGB protein Ixr1 contribute to cell cycle progression through the regulation of cell cycle-specific expression of CLB1 in Saccharomyces cerevisiae. PLoS Genet 2022; 18:e1010340. [PMID: 35905103 PMCID: PMC9365169 DOI: 10.1371/journal.pgen.1010340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 08/10/2022] [Accepted: 07/14/2022] [Indexed: 11/18/2022] Open
Abstract
Puf5, a Puf-family RNA-binding protein, binds to 3´ untranslated region of target mRNAs and negatively regulates their expression in Saccharomyces cerevisiae. The puf5Δ mutant shows pleiotropic phenotypes including a weakened cell wall, a temperature-sensitive growth, and a shorter lifespan. To further analyze a role of Puf5 in cell growth, we searched for a multicopy suppressor of the temperature-sensitive growth of the puf5Δ mutant in this study. We found that overexpression of CLB2 encoding B-type cyclin suppressed the temperature-sensitive growth of the puf5Δ mutant. The puf5Δ clb2Δ double mutant displayed a severe growth defect, suggesting that Puf5 positively regulates the expression of a redundant factor with Clb2 in cell cycle progression. We found that expression of CLB1 encoding a redundant B-type cyclin was decreased in the puf5Δ mutant, and that this decrease of the CLB1 expression contributed to the growth defect of the puf5Δ clb2Δ double mutant. Since Puf5 is a negative regulator of the gene expression, we hypothesized that Puf5 negatively regulates the expression of a factor that represses CLB1 expression. We found such a repressor, Ixr1, which is an HMGB (High Mobility Group box B) protein. Deletion of IXR1 restored the decreased expression of CLB1 caused by the puf5Δ mutation and suppressed the growth defect of the puf5Δ clb2Δ double mutant. The expression of IXR1 was negatively regulated by Puf5 in an IXR1 3´ UTR-dependent manner. Our results suggest that IXR1 mRNA is a physiologically important target of Puf5, and that Puf5 and Ixr1 contribute to the cell cycle progression through the regulation of the cell cycle-specific expression of CLB1.
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Affiliation(s)
- Megumi Sato
- Colledge of Medicine, School of Medicine and Health Sciences, University of Tsukuba, Tsukuba, Japan
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kaoru Irie
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Yasuyuki Suda
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
- Live Cell Super-resolution Imaging Research Team, RIKEN Center for Advanced Photonics, Wako, Saitama, Japan
| | - Tomoaki Mizuno
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kenji Irie
- Colledge of Medicine, School of Medicine and Health Sciences, University of Tsukuba, Tsukuba, Japan
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
- * E-mail:
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31
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Insertion orientation within the cassette affects gene-targeting success during ends-out recombination in the yeast Saccharomyces cerevisiae. Curr Genet 2022; 68:551-564. [DOI: 10.1007/s00294-022-01246-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 06/08/2022] [Accepted: 06/09/2022] [Indexed: 11/03/2022]
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32
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Uribe-Calvillo T, Maestroni L, Marsolier MC, Khadaroo B, Arbiol C, Schott J, Llorente B. Comprehensive analysis of cis- and trans-acting factors affecting ectopic Break-Induced Replication. PLoS Genet 2022; 18:e1010124. [PMID: 35727827 PMCID: PMC9249352 DOI: 10.1371/journal.pgen.1010124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 07/01/2022] [Accepted: 05/19/2022] [Indexed: 11/24/2022] Open
Abstract
Break-induced replication (BIR) is a highly mutagenic eukaryotic homologous DNA recombination pathway that repairs one-ended DNA double strand breaks such as broken DNA replication forks and eroded telomeres. While searching for cis-acting factors regulating ectopic BIR efficiency, we found that ectopic BIR efficiency is the highest close to chromosome ends. The variations of ectopic BIR efficiency as a function of the length of DNA to replicate can be described as a combination of two decreasing exponential functions, a property in line with repeated cycles of strand invasion, elongation and dissociation that characterize BIR. Interestingly, the apparent processivity of ectopic BIR depends on the length of DNA already synthesized. Ectopic BIR is more susceptible to disruption during the synthesis of the first ~35–40 kb of DNA than later, notably when the template chromatid is being transcribed or heterochromatic. Finally, we show that the Srs2 helicase promotes ectopic BIR from both telomere proximal and telomere distal regions in diploid cells but only from telomere proximal sites in haploid cells. Altogether, we bring new light on the factors impacting a last resort DNA repair pathway. DNA is a long molecule composed of two anti-parallel strands that can undergo breaks that need to be efficiently repaired to ensure genomic stability, hence preventing genetic diseases such as cancer. Homologous recombination is a major DNA repair pathway that copies DNA from intact homologous templates to seal DNA double strand breaks. Short DNA repair tracts are favored when homologous sequences for the two extremities of the broken molecule are present. However, when homologous sequences are present for only one extremity of the broken molecule, DNA repair synthesis can proceed up to the end of the chromosome, the telomere. This notably occurs at eroded telomeres when telomerase, the enzyme normally responsible for telomere elongation, is inactive, and at broken DNA replication intermediates. However, this Break-Induced Replication or BIR pathway is highly mutagenic. By initiating BIR at various distances from the telomere, we found that the length of DNA to synthesize significantly reduces BIR efficiency. Interestingly, our findings support two DNA synthesis phases, the first one being much less processive than the second one. Ultimately, this tends to restrain the use of this last resort DNA repair pathway to chromosome extremities notably when it takes place between non-allelic homologous sequences.
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Affiliation(s)
- Tannia Uribe-Calvillo
- Cancer Research Center of Marseille, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille Université UM105, Marseille, France
| | - Laetitia Maestroni
- Cancer Research Center of Marseille, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille Université UM105, Marseille, France
| | - Marie-Claude Marsolier
- Institute for Integrative Biology of the Cell (I2BC), Institut des sciences du vivant Frédéric Joliot, CNRS UMR 9198, CEA Saclay, Gif-sur-Yvette, France
- Eco-anthropologie (EA), Muséum national d’Histoire naturelle, CNRS, Université de Paris, Musée de l’Homme, Paris, France
| | - Basheer Khadaroo
- Cancer Research Center of Marseille, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille Université UM105, Marseille, France
| | - Christine Arbiol
- Cancer Research Center of Marseille, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille Université UM105, Marseille, France
| | - Jonathan Schott
- Cancer Research Center of Marseille, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille Université UM105, Marseille, France
| | - Bertrand Llorente
- Cancer Research Center of Marseille, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille Université UM105, Marseille, France
- * E-mail:
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Tapia SM, Pérez-Torrado R, Adam AC, Macías LG, Barrio E, Querol A. Functional divergence in the proteins encoded by ARO80 from S. uvarum, S. kudriavzevii and S. cerevisiae explain differences in the aroma production during wine fermentation. Microb Biotechnol 2022; 15:2281-2291. [PMID: 35536034 PMCID: PMC9328738 DOI: 10.1111/1751-7915.14071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 04/19/2022] [Accepted: 04/24/2022] [Indexed: 11/27/2022] Open
Abstract
Phenylethanol (PE) and phenylethyl acetate (PEA) are commonly desired compounds in wine because of their rose‐like aroma. The yeast S. cerevisiae produces the PE either through de novo biosynthesis by shikimate pathway followed by the Ehrlich pathway or the direct phenylalanine catabolism via Ehrlich pathway, and then converted into PEA. Previous work demonstrated that, compared to S. cerevisiae, other Saccharomyces species, such as S. kudriavzevii and S. uvarum, produce higher concentrations of PE and PEA from the precursor phenylalanine, which indicates differential activities of the biosynthetic‐involved enzymes. A previous in‐silico analysis suggested that the transcriptional activator Aro80p is one of the best candidates to explain these differences. An improved functional analysis identified significant radical amino acid changes in the S. uvarum and S. kudriavzevii Aro80p that could impact the expression of the catabolic genes ARO9 and ARO10, and hence, the production of PE from phenylalanine. Indeed, wine S. cerevisiae strains carrying the S. uvarum and S. kudriavzevii ARO80 alleles increased the production of both compounds in the presence of phenylalanine by increasing the expression of ARO9 and ARO10. This study provides novel insights of the unidentified Aro80p regulatory region and the potential usage of alternatives ARO80 alleles to enhance the PE and PEA concentration in wine.
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Affiliation(s)
- Sebastián M Tapia
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de Los Alimentos (IATA)-CSIC, 46980, Valencia, Spain
| | - Roberto Pérez-Torrado
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de Los Alimentos (IATA)-CSIC, 46980, Valencia, Spain
| | - Ana Cristina Adam
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de Los Alimentos (IATA)-CSIC, 46980, Valencia, Spain
| | - Laura G Macías
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de Los Alimentos (IATA)-CSIC, 46980, Valencia, Spain.,Departament de Genètica, Universitat de València, Valencia, Spain
| | - Eladio Barrio
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de Los Alimentos (IATA)-CSIC, 46980, Valencia, Spain.,Departament de Genètica, Universitat de València, Valencia, Spain
| | - Amparo Querol
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de Los Alimentos (IATA)-CSIC, 46980, Valencia, Spain
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Saguez C, Viterbo D, Descorps-Declère S, Cormack BP, Dujon B, Richard GF. Functional variability in adhesion and flocculation of yeast megasatellite genes. Genetics 2022; 221:iyac042. [PMID: 35274698 PMCID: PMC9071537 DOI: 10.1093/genetics/iyac042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/07/2022] [Indexed: 11/14/2022] Open
Abstract
Megasatellites are large tandem repeats found in all fungal genomes but especially abundant in the opportunistic pathogen Candida glabrata. They are encoded in genes involved in cell-cell interactions, either between yeasts or between yeast and human cells. In the present work, we have been using an iterative genetic system to delete several Candida glabrata megasatellite-containing genes and found that 2 of them were positively involved in adhesion to epithelial cells, whereas 3 genes negatively controlled adhesion. Two of the latter, CAGL0B05061g or CAGL0A04851g, were also negative regulators of yeast-to-yeast adhesion, making them central players in controlling Candida glabrata adherence properties. Using a series of synthetic Saccharomyces cerevisiae strains in which the FLO1 megasatellite was replaced by other tandem repeats of similar length but different sequences, we showed that the capacity of a strain to flocculate in liquid culture was unrelated to its capacity to adhere to epithelial cells or to invade agar. Finally, to understand how megasatellites were initially created and subsequently expanded, an experimental evolution system was set up, in which modified yeast strains containing different megasatellite seeds were grown in bioreactors for more than 200 generations and selected for their ability to sediment at the bottom of the culture tube. Several flocculation-positive mutants were isolated. Functionally relevant mutations included general transcription factors as well as a 230-kbp segmental duplication.
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Affiliation(s)
- Cyril Saguez
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Genétique des Génomes, Paris F-75015, France
- Present address: Abolis Biotechnologies, 5 Rue Henri Desbruères, Evry 91030, France
| | - David Viterbo
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Genétique des Génomes, Paris F-75015, France
| | - Stéphane Descorps-Declère
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Genétique des Génomes, Paris F-75015, France
- Institut Pasteur, Bioinformatics and Biostatistics Hub, Department of Computational Biology, Paris F-75015, France
| | - Brendan P Cormack
- Department of Molecular Biology & Genetics, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Bernard Dujon
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Genétique des Génomes, Paris F-75015, France
| | - Guy-Franck Richard
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Genétique des Génomes, Paris F-75015, France
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35
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Snf1p/Hxk2p/Mig1p pathway regulates hexose transporters transcript levels, affecting the exponential growth and mitochondrial respiration of Saccharomyces cerevisiae. Fungal Genet Biol 2022; 161:103701. [DOI: 10.1016/j.fgb.2022.103701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 04/12/2022] [Accepted: 04/30/2022] [Indexed: 11/19/2022]
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Huang H, Ayaz A, Zheng M, Yang X, Zaman W, Zhao H, Lü S. ArabidopsisKCS5 and KCS6 Play Redundant Roles in Wax Synthesis. Int J Mol Sci 2022; 23:ijms23084450. [PMID: 35457268 PMCID: PMC9027390 DOI: 10.3390/ijms23084450] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/11/2022] [Accepted: 04/14/2022] [Indexed: 01/09/2023] Open
Abstract
3-ketoacyl-CoA synthases (KCSs), as components of a fatty acid elongase (FAE) complex, play key roles in determining the chain length of very-long-chain fatty acids (VLCFAs). KCS6, taking a predominate role during the elongation from C26 to C28, is well known to play an important role in wax synthesis. KCS5 is one paralog of KCS6 and its role in wax synthesis remains unknown. Wax phenotype analysis showed that in kcs5 mutants, the total amounts of wax components derived from carbon 32 (C32) and C34 were apparently decreased in leaves, and those of C26 to C32 derivatives were obviously decreased in flowers. Heterologous yeast expression analysis showed that KCS5 alone displayed specificity towards C24 to C28 acids, and its coordination with CER2 and CER26 catalyzed the elongation of acids exceeding C28, especially displaying higher activity towards C28 acids than KCS6. BiLC experiments identified that KCS5 physically interacts with CER2 and CER26. Wax phenotype analysis of different organs in kcs5 and kcs6 single or double mutants showed that KCS6 mutation causes greater effects on the wax synthesis than KCS5 mutation in the tested organs, and simultaneous repression of both protein activities caused additive effects, suggesting that during the wax biosynthesis process, KCS5 and KCS6 play redundant roles, among which KCS6 plays a major role. In addition, simultaneous mutations of two genes nearly block drought-induced wax production, indicating that the reactions catalyzed by KCS5 and KCS6 play a critical role in the wax biosynthesis in response to drought.
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Affiliation(s)
- Haodong Huang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China; (H.H.); (A.A.); (M.Z.)
| | - Asma Ayaz
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China; (H.H.); (A.A.); (M.Z.)
| | - Minglü Zheng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China; (H.H.); (A.A.); (M.Z.)
| | - Xianpeng Yang
- College of Life Sciences, Shandong Normal University, Jinan 250014, China;
| | - Wajid Zaman
- Department of Life Sciences, Yeungnam University, Gyeongsan 38541, Korea;
| | - Huayan Zhao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China; (H.H.); (A.A.); (M.Z.)
- Correspondence: (H.Z.); (S.L.); Tel.: +86-27-88663882 (S.L.)
| | - Shiyou Lü
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China; (H.H.); (A.A.); (M.Z.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Correspondence: (H.Z.); (S.L.); Tel.: +86-27-88663882 (S.L.)
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Pheromone Guidance of Polarity Site Movement in Yeast. Biomolecules 2022; 12:biom12040502. [PMID: 35454091 PMCID: PMC9027094 DOI: 10.3390/biom12040502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 03/21/2022] [Accepted: 03/25/2022] [Indexed: 01/11/2023] Open
Abstract
Cells’ ability to track chemical gradients is integral to many biological phenomena, including fertilization, development, accessing nutrients, and combating infection. Mating of the yeast Saccharomyces cerevisiae provides a tractable model to understand how cells interpret the spatial information in chemical gradients. Mating yeast of the two different mating types secrete distinct peptide pheromones, called a-factor and α-factor, to communicate with potential partners. Spatial gradients of pheromones are decoded to guide mobile polarity sites so that polarity sites in mating partners align towards each other, as a prerequisite for cell-cell fusion and zygote formation. In ascomycetes including S. cerevisiae, one pheromone is prenylated (a-factor) while the other is not (α-factor). The difference in physical properties between the pheromones, combined with associated differences in mechanisms of secretion and extracellular pheromone metabolism, suggested that the pheromones might differ in the spatial information that they convey to potential mating partners. However, as mating appears to be isogamous in this species, it is not clear why any such signaling difference would be advantageous. Here we report assays that directly track movement of the polarity site in each partner as a way to understand the spatial information conveyed by each pheromone. Our findings suggest that both pheromones convey very similar information. We speculate that the different pheromones were advantageous in ancestral species with asymmetric mating systems and may represent an evolutionary vestige in yeasts that mate isogamously.
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Cho NH, Cheveralls KC, Brunner AD, Kim K, Michaelis AC, Raghavan P, Kobayashi H, Savy L, Li JY, Canaj H, Kim JYS, Stewart EM, Gnann C, McCarthy F, Cabrera JP, Brunetti RM, Chhun BB, Dingle G, Hein MY, Huang B, Mehta SB, Weissman JS, Gómez-Sjöberg R, Itzhak DN, Royer LA, Mann M, Leonetti MD. OpenCell: Endogenous tagging for the cartography of human cellular organization. Science 2022; 375:eabi6983. [PMID: 35271311 DOI: 10.1126/science.abi6983] [Citation(s) in RCA: 127] [Impact Index Per Article: 63.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Elucidating the wiring diagram of the human cell is a central goal of the postgenomic era. We combined genome engineering, confocal live-cell imaging, mass spectrometry, and data science to systematically map the localization and interactions of human proteins. Our approach provides a data-driven description of the molecular and spatial networks that organize the proteome. Unsupervised clustering of these networks delineates functional communities that facilitate biological discovery. We found that remarkably precise functional information can be derived from protein localization patterns, which often contain enough information to identify molecular interactions, and that RNA binding proteins form a specific subgroup defined by unique interaction and localization properties. Paired with a fully interactive website (opencell.czbiohub.org), our work constitutes a resource for the quantitative cartography of human cellular organization.
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Affiliation(s)
| | | | - Andreas-David Brunner
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Kibeom Kim
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - André C Michaelis
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | | | | | - Laura Savy
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Jason Y Li
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Hera Canaj
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | | | - Christian Gnann
- Chan Zuckerberg Biohub, San Francisco, CA, USA.,Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, Stockholm, Sweden
| | | | | | - Rachel M Brunetti
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | | | - Greg Dingle
- Chan Zuckerberg Initiative, Redwood City, CA, USA
| | | | - Bo Huang
- Chan Zuckerberg Biohub, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | | | - Jonathan S Weissman
- Whitehead Institute, Koch Institute, Howard Hughes Medical Institute, and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | | | | | | | - Matthias Mann
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.,NNF Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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39
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Bravo Ruiz G, Lorenz A. Genetic Transformation of Candida auris via Homology-Directed Repair Using a Standard Lithium Acetate Protocol. Methods Mol Biol 2022; 2517:95-110. [PMID: 35674948 DOI: 10.1007/978-1-0716-2417-3_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Reverse genetics is a particularly powerful tool in non-model organisms with known whole-genome sequences enabling the characterization of gene and, thus, protein function via a mutant phenotype. Reverse genetic approaches require genetic manipulation techniques which often need to be specifically developed for non-model organisms; this can be fraught with difficulties. Here, we describe a genetic transformation protocol for the recently emerged human pathogen Candida auris to target the integration of DNA constructs into genomic locations via homology-directed repair using long flanking homologous sequences (>1 kb). We detail the generation of DNA constructs for gene deletion with dominant drug resistance markers via fusion PCR, the transformation of these constructs into chemically competent C. auris cells, and the confirmation of correct integration by PCR. This strategy can be adapted to deliver DNA constructs other than deletion cassettes, including promoter exchanges and protein tags.
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Affiliation(s)
- Gustavo Bravo Ruiz
- Institute of Medical Sciences (IMS), University of Aberdeen, Aberdeen, UK
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, UK
| | - Alexander Lorenz
- Institute of Medical Sciences (IMS), University of Aberdeen, Aberdeen, UK.
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40
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Shenoy A, Barb AW. Recent Advances Toward Engineering Glycoproteins Using Modified Yeast Display Platforms. Methods Mol Biol 2022; 2370:185-205. [PMID: 34611870 DOI: 10.1007/978-1-0716-1685-7_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Yeast are capable recombinant protein expression hosts that provide eukaryotic posttranslational modifications such as disulfide bond formation and N-glycosylation. This property has been used to create surface display libraries for protein engineering; however, yeast surface display (YSD) with common laboratory strains has limitations in terms of diversifying glycoproteins due to the incorporation of high levels of mannose residues which often obscure important epitopes and are immunogenic in humans. Developing new strains for efficient and appropriate display will require combining existing technologies to permit efficient glycoprotein engineering. Foundational efforts generating knockout strains lacking characteristic hypermannosylation reactions exhibited morphological defects and poor growth. Later strains with "humanized" N-glycosylation machinery surmounted these limitations by targeting a small suite of glycosylhydrolase and glycosyltransferase enzymes from other taxa to the endoplasmic reticulum and Golgi. Advanced yeast strains also provide key modifications at the glycan termini that are essential for the full function of many glycoproteins. Here we review progress toward glycoprotein engineering when glycosylation is required for full function using advanced yeast expression platforms and the suitability of each for YSD of glycoproteins.
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Affiliation(s)
- Anjali Shenoy
- Biochemistry and Molecular Biology Department, University of Georgia, Athens, GA, USA
| | - Adam W Barb
- Biochemistry and Molecular Biology Department, University of Georgia, Athens, GA, USA.
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Vázquez-Franco N, Gutiérrez-Escobedo G, Juárez-Reyes A, Orta-Zavalza E, Castaño I, De Las Peñas A. Candida glabrata Hst1-Rfm1-Sum1 complex evolved to control virulence-related genes. Fungal Genet Biol 2021; 159:103656. [PMID: 34974188 DOI: 10.1016/j.fgb.2021.103656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 12/25/2021] [Accepted: 12/27/2021] [Indexed: 11/15/2022]
Abstract
C. glabrata is an opportunistic fungal pathogen and the second most common cause of opportunistic fungal infections in humans, that has evolved virulence factors to become a successful pathogen: strong resistance to oxidative stress, capable to adhere and form biofilms in human epithelial cells as well as to abiotic surfaces and high resistance to xenobiotics. Hst1 (a NAD+-dependent histone deacetylase), Sum1 (putative DNA binding protein) and Rfm1 (connector protein) form a complex (HRS-C) and control the resistance to oxidative stress, to xenobiotics (the antifungal fluconazole), and adherence to epithelial cells. Hst1 is functionally conserved within the Saccharomycetaceae family, Rfm1 shows a close phylogenetic relation within the Saccharomycetaceae family while Sum1 displays a distant phylogenetic relation with members of the family and is not conserved functionally. CDR1 encodes for an ABC transporter (resistance to fluconazole) negatively controlled by HRS-C, for which its binding site is located within 223 bp upstream from the ATG of CDR1. The absence of Hst1 and Sum1 renders the cells hyper-adherent, possibly due to the overexpression of AED1, EPA1, EPA22 and EPA6, all encoding for adhesins. Finally, in a neutrophil survival assay, HST1 and SUM1, are not required for survival. We propose that Sum1 in the HRS-C diverged functionally to control a set of genes implicated in virulence: adherence, resistance to xenobiotics and oxidative stress.
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Affiliation(s)
- Norma Vázquez-Franco
- IPICYT, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José, #2055, Col. Lomas 4ª Sección, San Luis Potosí, San Luis Potosí 78216, Mexico
| | - Guadalupe Gutiérrez-Escobedo
- IPICYT, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José, #2055, Col. Lomas 4ª Sección, San Luis Potosí, San Luis Potosí 78216, Mexico
| | - Alejandro Juárez-Reyes
- IPICYT, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José, #2055, Col. Lomas 4ª Sección, San Luis Potosí, San Luis Potosí 78216, Mexico
| | - Emmanuel Orta-Zavalza
- Departamento de Ciencias Químico-Biológicas, Universidad Autónoma de Ciudad Juárez, Chihuahua, Mexico
| | - Irene Castaño
- IPICYT, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José, #2055, Col. Lomas 4ª Sección, San Luis Potosí, San Luis Potosí 78216, Mexico
| | - Alejandro De Las Peñas
- IPICYT, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José, #2055, Col. Lomas 4ª Sección, San Luis Potosí, San Luis Potosí 78216, Mexico.
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Hayashi H, Kishi T. A Set of Plasmid-Based Modules for Easy Switching of C-Terminal Epitope Tags in Saccharomyces cerevisiae. Microorganisms 2021; 9:2505. [PMID: 34946108 PMCID: PMC8707574 DOI: 10.3390/microorganisms9122505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 11/24/2022] Open
Abstract
Epitope tagging is a powerful strategy for analyzing the functions of targeted proteins. The use of this strategy has become more convenient with the development of the epitope switch, which is another type of epitope tagging designed to convert the previously tagged epitopes on the chromosome to other epitopes of interest. Various modules for C-terminal epitope switching have been developed and amplified using the one-step polymerase chain reaction (PCR) method before transformation. However, PCR amplification occasionally generates mutations that affect the fidelity of epitope switching. Here, we constructed several plasmids to isolate modules for epitope switching through digestion by restriction enzymes. The isolated modules contained DNA sequences for homologous recombination, various epitopes (13×Myc, 6×HA, GFP, Venus, YFP, mCherry, and CFP), and a transformation marker (Candida glabrata LEU2). The restriction enzyme-digested plasmids were used to directly transform the cells for epitope switching. We demonstrate the efficient and accurate switching of the MX6 module-based C-terminal tandem affinity purification tags to each aforementioned epitope. We believe that our plasmids can serve as powerful tools for the functional analysis of yeast proteins.
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Affiliation(s)
| | - Tsutomu Kishi
- College of Engineering, Nihon University, Koriyama, Fukushima 963-8642, Japan;
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43
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Zeng F, Li X, Pires-Alves M, Chen X, Hawk CW, Jin H. Conserved heterodimeric GTPase Rbg1/Tma46 promotes efficient translation in eukaryotic cells. Cell Rep 2021; 37:109877. [PMID: 34706231 DOI: 10.1016/j.celrep.2021.109877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/21/2021] [Accepted: 09/30/2021] [Indexed: 11/19/2022] Open
Abstract
Conserved developmentally regulated guanosine triphosphate (GTP)-binding proteins (Drgs) and their binding partner Drg family regulatory proteins (Dfrps) are important for embryonic development, cellular growth control, differentiation, and proliferation. Here, we report that the yeast Drg1/Dfrp1 ortholog Rbg1/Tma46 facilitates translational initiation, elongation, and termination by suppressing prolonged ribosome pausing. Consistent with the genome-wide observations, deletion of Rbg1 exacerbates the growth defect resulting from translation stalling, and Rbg1 stabilizes mRNAs against no-go decay. Furthermore, we provide a cryoelectron microscopy (cryo-EM) structure of the 80S ribosome bound with Rbg1/Tma46 that reveals the molecular interactions responsible for Rbg1/Tma46 function. The Rbg1 subunit binds to the GTPase association center of the ribosome and the A-tRNA, and the N-terminal zinc finger domain of the Tma46 subunit binds to the 40S, establishing an interaction critical for the ribosomal association. Our results answer the fundamental question of how a paused ribosome resumes translation and show that Drg1/Dfrp1 play a critical role in ensuring orderly translation.
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Affiliation(s)
- Fuxing Zeng
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA; Department of Biology, School of Life Sciences, Southern University of Science and Technology, No. 1088 Xueyuan Blvd., Shenzhen 518055, People's Republic of China
| | - Xin Li
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, No. 1088 Xueyuan Blvd., Shenzhen 518055, People's Republic of China
| | - Melissa Pires-Alves
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA
| | - Xin Chen
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA
| | - Christopher W Hawk
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA
| | - Hong Jin
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, 1206 West Gregory Drive, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA.
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44
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Huang MY, Joshi MB, Boucher MJ, Lee S, Loza LC, Gaylord EA, Doering TL, Madhani HD. Short homology-directed repair using optimized Cas9 in the pathogen Cryptococcus neoformans enables rapid gene deletion and tagging. Genetics 2021; 220:6409193. [PMID: 34791226 PMCID: PMC8733451 DOI: 10.1093/genetics/iyab180] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 10/08/2021] [Indexed: 01/07/2023] Open
Abstract
Cryptococcus neoformans, the most common cause of fungal meningitis, is a basidiomycete haploid budding yeast with a complete sexual cycle. Genome modification by homologous recombination is feasible using biolistic transformation and long homology arms, but the method is arduous and unreliable. Recently, multiple groups have reported the use of CRISPR-Cas9 as an alternative to biolistics, but long homology arms are still necessary, limiting the utility of this method. Since the S. pyogenes Cas9 derivatives used in prior studies were not optimized for expression in C. neoformans, we designed, synthesized, and tested a fully C. neoformans-optimized (Cno) Cas9. We found that a Cas9 harboring only common C. neoformans codons and a consensus C. neoformans intron together with a TEF1 promoter and terminator and a nuclear localization signal (Cno CAS9 or "CnoCAS9") reliably enabled genome editing in the widely used KN99α C. neoformans strain. Furthermore, editing was accomplished using donors harboring short (50 bp) homology arms attached to marker DNAs produced with synthetic oligonucleotides and PCR amplification. We also demonstrated that prior stable integration of CnoCAS9 further enhances both transformation and homologous recombination efficiency; importantly, this manipulation does not impact virulence in animals. We also implemented a universal tagging module harboring a codon-optimized fluorescent protein (mNeonGreen) and a tandem Calmodulin Binding Peptide-2X FLAG Tag that allows for both localization and purification studies of proteins for which the corresponding genes are modified by short homology-directed recombination. These tools enable short-homology genome engineering in C. neoformans.
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Affiliation(s)
- Manning Y Huang
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Meenakshi B Joshi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Michael J Boucher
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Sujin Lee
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Liza C Loza
- Department of Molecular Microbiology, Washington University School of Medicine, Washington University, St. Louis, MO 63110, USA
| | - Elizabeth A Gaylord
- Department of Molecular Microbiology, Washington University School of Medicine, Washington University, St. Louis, MO 63110, USA
| | - Tamara L Doering
- Department of Molecular Microbiology, Washington University School of Medicine, Washington University, St. Louis, MO 63110, USA
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA,Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA,Corresponding author: 600 16th Street, Genentech Hall, Rm. N374, San Francisco, CA 94158, USA.
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45
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Wang Y, Zhai B, Tan T, Yang X, Zhang J, Song M, Tan Y, Yang X, Chu T, Zhang S, Wang S, Zhang L. ESA1 regulates meiotic chromosome axis and crossover frequency via acetylating histone H4. Nucleic Acids Res 2021; 49:9353-9373. [PMID: 34417612 PMCID: PMC8450111 DOI: 10.1093/nar/gkab722] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 08/05/2021] [Accepted: 08/11/2021] [Indexed: 01/02/2023] Open
Abstract
Meiotic recombination is integrated into and regulated by meiotic chromosomes, which is organized as loop/axis architecture. However, the regulation of chromosome organization is poorly understood. Here, we show Esa1, the NuA4 complex catalytic subunit, is constitutively expressed and localizes on chromatin loops during meiosis. Esa1 plays multiple roles including homolog synapsis, sporulation efficiency, spore viability, and chromosome segregation in meiosis. Detailed analyses show the meiosis-specific depletion of Esa1 results in decreased chromosome axis length independent of another axis length regulator Pds5, which further leads to a decreased number of Mer2 foci, and consequently a decreased number of DNA double-strand breaks, recombination intermediates, and crossover frequency. However, Esa1 depletion does not impair the occurrence of the obligatory crossover required for faithful chromosome segregation, or the strength of crossover interference. Further investigations demonstrate Esa1 regulates chromosome axis length via acetylating the N-terminal tail of histone H4 but not altering transcription program. Therefore, we firstly show a non-chromosome axis component, Esa1, acetylates histone H4 on chromatin loops to regulate chromosome axis length and consequently recombination frequency but does not affect the basic meiotic recombination process. Additionally, Esa1 depletion downregulates middle induced meiotic genes, which probably causing defects in sporulation and chromosome segregation.
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Affiliation(s)
- Ying Wang
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University, China
| | - Binyuan Zhai
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University, China
| | - Taicong Tan
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University, China
| | - Xiao Yang
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University, China
| | - Jiaming Zhang
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University, China
| | - Meihui Song
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University, China
| | - Yingjin Tan
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University, China
| | - Xuan Yang
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University, China
| | - Tingting Chu
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University, China
| | - Shuxian Zhang
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University, China
| | - Shunxin Wang
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong 250012, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Jinan, Shandong250001, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong 250012, China
| | - Liangran Zhang
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University, China.,Advanced Medical Research Institute, Shandong University, Jinan, Shandong250012, China.,Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan250014, Shandong, China
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46
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Zhao W, Guo F, Kong L, Liu J, Hong X, Jiang Z, Song H, Cui X, Ruan J, Liu X. Yeast YPK9 deficiency results in shortened replicative lifespan and sensitivity to hydrogen peroxide. Biogerontology 2021; 22:547-563. [PMID: 34524607 DOI: 10.1007/s10522-021-09935-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 08/26/2021] [Indexed: 11/26/2022]
Abstract
YPK9/YOR291W of Saccharomyces cerevisiae encodes a vacuolar membrane protein. Previous research has suggested that Ypk9p is similar to the yeast P5-type ATPase Spf1p and that it plays a role in the sequestration of heavy metals. In addition, bioinformatics analysis has suggested that Ypk9p is a homolog of human ATP13A2, which encodes a protein of the subfamily of P5 ATPases. However, no specific function of Ypk9p has been described to date. In this study, we found, for the first time, that YPK9 is involved in the oxidative stress response and modulation of the replicative lifespan (RLS). We found that YPK9 deficiency confers sensitivity to the oxidative stress inducer hydrogen peroxide accompanied by increased intracellular ROS levels, decreased mitochondrial membrane potential, abnormal mitochondrial function, and increased incidence of early apoptosis in budding yeast. More importantly, YPK9 deficiency can lead to a shortened RLS. In addition, we found that overexpression of the catalase-encoding gene CTA1 can reverse the phenotypic abnormalities of the ypk9Δ yeast strain. Collectively, these findings highlight the involvement of Ypk9p in the oxidative stress response and modulation of RLS.
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Affiliation(s)
- Wei Zhao
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, Dongguan, 523808, China
- Institute of Biochemistry and Molecular Biology, Guangdong Medical University, Dongguan, 523808, China
| | - Fang Guo
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, Dongguan, 523808, China
- Institute of Biochemistry and Molecular Biology, Guangdong Medical University, Dongguan, 523808, China
| | - Lingyue Kong
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, Dongguan, 523808, China
- Institute of Biochemistry and Molecular Biology, Guangdong Medical University, Dongguan, 523808, China
| | - Jiaxin Liu
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, Dongguan, 523808, China
- Institute of Biochemistry and Molecular Biology, Guangdong Medical University, Dongguan, 523808, China
| | - Xiaoshan Hong
- Institute of Gynecology, Women and Children's Hospital of Guangdong Province, Guangzhou, 511442, China
| | - Zhiwen Jiang
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, Dongguan, 523808, China
- Institute of Biochemistry and Molecular Biology, Guangdong Medical University, Dongguan, 523808, China
| | - Haochang Song
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, Dongguan, 523808, China
- Institute of Biochemistry and Molecular Biology, Guangdong Medical University, Dongguan, 523808, China
| | - Xiaojing Cui
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, Dongguan, 523808, China
- Institute of Biochemistry and Molecular Biology, Guangdong Medical University, Dongguan, 523808, China
| | - Jie Ruan
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, Dongguan, 523808, China.
- Institute of Biochemistry and Molecular Biology, Guangdong Medical University, Dongguan, 523808, China.
| | - Xinguang Liu
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, Dongguan, 523808, China.
- Institute of Biochemistry and Molecular Biology, Guangdong Medical University, Dongguan, 523808, China.
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47
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Campos TL, Korhonen PK, Hofmann A, Gasser RB, Young ND. Harnessing model organism genomics to underpin the machine learning-based prediction of essential genes in eukaryotes - Biotechnological implications. Biotechnol Adv 2021; 54:107822. [PMID: 34461202 DOI: 10.1016/j.biotechadv.2021.107822] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 08/17/2021] [Accepted: 08/24/2021] [Indexed: 12/17/2022]
Abstract
The availability of high-quality genomes and advances in functional genomics have enabled large-scale studies of essential genes in model eukaryotes, including the 'elegant worm' (Caenorhabditis elegans; Nematoda) and the 'vinegar fly' (Drosophila melanogaster; Arthropoda). However, this is not the case for other, much less-studied organisms, such as socioeconomically important parasites, for which functional genomic platforms usually do not exist. Thus, there is a need to develop innovative techniques or approaches for the prediction, identification and investigation of essential genes. A key approach that could enable the prediction of such genes is machine learning (ML). Here, we undertake an historical review of experimental and computational approaches employed for the characterisation of essential genes in eukaryotes, with a particular focus on model ecdysozoans (C. elegans and D. melanogaster), and discuss the possible applicability of ML-approaches to organisms such as socioeconomically important parasites. We highlight some recent results showing that high-performance ML, combined with feature engineering, allows a reliable prediction of essential genes from extensive, publicly available 'omic data sets, with major potential to prioritise such genes (with statistical confidence) for subsequent functional genomic validation. These findings could 'open the door' to fundamental and applied research areas. Evidence of some commonality in the essential gene-complement between these two organisms indicates that an ML-engineering approach could find broader applicability to ecdysozoans such as parasitic nematodes or arthropods, provided that suitably large and informative data sets become/are available for proper feature engineering, and for the robust training and validation of algorithms. This area warrants detailed exploration to, for example, facilitate the identification and characterisation of essential molecules as novel targets for drugs and vaccines against parasitic diseases. This focus is particularly important, given the substantial impact that such diseases have worldwide, and the current challenges associated with their prevention and control and with drug resistance in parasite populations.
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Affiliation(s)
- Tulio L Campos
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia; Bioinformatics Core Facility, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz (IAM-Fiocruz), Recife, Pernambuco, Brazil
| | - Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Andreas Hofmann
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
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48
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UbiB proteins regulate cellular CoQ distribution in Saccharomyces cerevisiae. Nat Commun 2021; 12:4769. [PMID: 34362905 PMCID: PMC8346625 DOI: 10.1038/s41467-021-25084-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 07/22/2021] [Indexed: 11/08/2022] Open
Abstract
Beyond its role in mitochondrial bioenergetics, Coenzyme Q (CoQ, ubiquinone) serves as a key membrane-embedded antioxidant throughout the cell. However, how CoQ is mobilized from its site of synthesis on the inner mitochondrial membrane to other sites of action remains a longstanding mystery. Here, using a combination of Saccharomyces cerevisiae genetics, biochemical fractionation, and lipid profiling, we identify two highly conserved but poorly characterized mitochondrial proteins, Ypl109c (Cqd1) and Ylr253w (Cqd2), that reciprocally affect this process. Loss of Cqd1 skews cellular CoQ distribution away from mitochondria, resulting in markedly enhanced resistance to oxidative stress caused by exogenous polyunsaturated fatty acids, whereas loss of Cqd2 promotes the opposite effects. The activities of both proteins rely on their atypical kinase/ATPase domains, which they share with Coq8-an essential auxiliary protein for CoQ biosynthesis. Overall, our results reveal protein machinery central to CoQ trafficking in yeast and lend insights into the broader interplay between mitochondria and the rest of the cell.
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49
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Fujii S, Duy DL, Valderrama AL, Takeuchi R, Matsuura E, Ito A, Irie K, Suda Y, Mizuno T, Irie K. Pan2-Pan3 complex, together with Ccr4-Not complex, has a role in the cell growth on non-fermentable carbon sources. Biochem Biophys Res Commun 2021; 570:125-130. [PMID: 34280615 DOI: 10.1016/j.bbrc.2021.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 07/04/2021] [Indexed: 11/29/2022]
Abstract
There are two major deadenylase complexes, Ccr4-Not and Pan2-Pan3, which shorten the 3' poly(A) tail of mRNA and are conserved from yeast to human. We have previously shown that the Ccr4-mediated deadenylation plays the important role in gene expression regulation in the yeast stationary phase cell. In order to further understand the role of deadenylases in different growth condition, in this study we investigated the effect of deletion of both deadenylases on the cell in non-fermentable carbon containing media. We found that both ccr4Δ and ccr4Δ pan2Δ mutants showed similar growth defect in YPD media: when switched to media containing non-fermentable source (Glycerol-Lactate) only the ccr4Δ grew while the ccr4Δ pan2Δ did not. Ccr4, Pan2, and Pan3 were phosphorylated in GlyLac medium, suggesting that the activities of Ccr4, Pan2, and Pan3 may be regulated by phosphorylation in response to change of carbon sources. To get insights how Ccr4 and Pan2 function in the cell growth in media containing non-fermentable source only, we isolated multicopy suppressors for the growth defect on YPGlyLac media of the ccr4Δ pan2Δ mutant and identified two genes, STM1 and REX2, which encode a ribosome-associated protein and a 3'-5' RNA exonuclease, respectively. Our results suggest that the Pan2-Pan3 complex, together with the Ccr4-Not complex, has important roles in the growth on non-fermentable carbon sources.
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Affiliation(s)
- Shiori Fujii
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Duong Long Duy
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Arvin Lapiz Valderrama
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan; Ph.D. Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Japan
| | - Risa Takeuchi
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Eri Matsuura
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Ayaka Ito
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kaoru Irie
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Yasuyuki Suda
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan; Live Cell Super-resolution Imaging Research Team, RIKEN Center for Advanced Photonics, Wako, Saitama, Japan
| | - Tomoaki Mizuno
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kenji Irie
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan; Ph.D. Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Japan.
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50
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Higuchi Y, Fujii S, Valderrama AL, Irie K, Suda Y, Mizuno T, Irie K. The eIF4E-binding protein Eap1 has similar but independent roles in cell growth and gene expression with the cytoplasmic deadenylase Ccr4. Biosci Biotechnol Biochem 2021; 85:1452-1459. [PMID: 33784392 DOI: 10.1093/bbb/zbab056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 03/24/2021] [Indexed: 11/12/2022]
Abstract
eIF4E-binding proteins (4E-BPs) are translational repressors that compete with eIF4G for binding to eIF4E. Here we investigated the roles of yeast 4E-BPs, Eap1, and Caf20 in cell wall integrity pathway and gene expression. We found that eap1∆ mutation, but not caf20∆ mutation, showed synthetic growth defect with mutation in ROM2 gene encoding Rho1 GEF. The eap1∆ mutation also showed synthetic lethality with mutation in CCR4 gene encoding cytoplasmic deadenylase. Ccr4 functions in the degradation of LRG1 mRNA encoding Rho1 GAP. Eap1-Y109A L114A, which could not bind to eIF4E, did not suppress the synthetic lethality of eap1∆ ccr4∆ mutant, suggesting that 4E-binding of Eap1 is important for its function. We also found that eap1∆ mutant showed the derepression of stress response gene HSP12. 4E-binding of Eap1 was also required for the repression of HSP12 expression. Our results indicate that Eap1 has similar but independent roles in cell growth and gene expression with Ccr4.
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Affiliation(s)
- Yudai Higuchi
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Shiori Fujii
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Arvin Lapiz Valderrama
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan.,Ph.D. Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Japan
| | - Kaoru Irie
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Yasuyuki Suda
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan.,Live Cell Super-resolution Imaging Research Team, RIKEN Center for Advanced Photonics, Wako, Saitama, Japan
| | - Tomoaki Mizuno
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kenji Irie
- Department of Molecular Cell Biology, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of Tsukuba, Tsukuba, Japan.,Ph.D. Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Japan
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