1
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Jordan EN, Shirali Hossein Zade R, Pillay S, van Lent P, Abeel T, Kayser O. Integrated omics of Saccharomyces cerevisiae CENPK2-1C reveals pleiotropic drug resistance and lipidomic adaptations to cannabidiol. NPJ Syst Biol Appl 2024; 10:63. [PMID: 38821949 PMCID: PMC11143246 DOI: 10.1038/s41540-024-00382-0] [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: 08/24/2023] [Accepted: 05/13/2024] [Indexed: 06/02/2024] Open
Abstract
Yeast metabolism can be engineered to produce xenobiotic compounds, such as cannabinoids, the principal isoprenoids of the plant Cannabis sativa, through heterologous metabolic pathways. However, yeast cell factories continue to have low cannabinoid production. This study employed an integrated omics approach to investigate the physiological effects of cannabidiol on S. cerevisiae CENPK2-1C yeast cultures. We treated the experimental group with 0.5 mM CBD and monitored CENPK2-1C cultures. We observed a latent-stationary phase post-diauxic shift in the experimental group and harvested samples in the inflection point of this growth phase for transcriptomic and metabolomic analysis. We compared the transcriptomes of the CBD-treated yeast and the positive control, identifying eight significantly overexpressed genes with a log fold change of at least 1.5 and a significant adjusted p-value. Three notable genes were PDR5 (an ABC-steroid and cation transporter), CIS1, and YGR035C. These genes are all regulated by pleiotropic drug resistance linked promoters. Knockout and rescue of PDR5 showed that it is a causal factor in the post-diauxic shift phenotype. Metabolomic analysis revealed 48 significant spectra associated with CBD-fed cell pellets, 20 of which were identifiable as non-CBD compounds, including fatty acids, glycerophospholipids, and phosphate-salvage indicators. Our results suggest that mitochondrial regulation and lipidomic remodeling play a role in yeast's response to CBD, which are employed in tandem with pleiotropic drug resistance (PDR). We conclude that bioengineers should account for off-target product C-flux, energy use from ABC-transport, and post-stationary phase cell growth when developing cannabinoid-biosynthetic yeast strains.
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Affiliation(s)
- Erin Noel Jordan
- Technical Biochemistry, TU Dortmund University, Emil-Figge-Straße 66, 44227, Dortmund, Germany.
| | - Ramin Shirali Hossein Zade
- Delft Bioinformatics Lab, Delft University of Technology Van Mourik, Broekmanweg 6, 2628 XE, Delft, The Netherlands
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
- Leiden Center for Computational Oncology, Leiden University Medical Center, Leiden, The Netherlands
| | - Stephanie Pillay
- Delft Bioinformatics Lab, Delft University of Technology Van Mourik, Broekmanweg 6, 2628 XE, Delft, The Netherlands
| | - Paul van Lent
- Delft Bioinformatics Lab, Delft University of Technology Van Mourik, Broekmanweg 6, 2628 XE, Delft, The Netherlands
| | - Thomas Abeel
- Delft Bioinformatics Lab, Delft University of Technology Van Mourik, Broekmanweg 6, 2628 XE, Delft, The Netherlands
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
| | - Oliver Kayser
- Technical Biochemistry, TU Dortmund University, Emil-Figge-Straße 66, 44227, Dortmund, Germany.
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2
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Williams TC, Kroukamp H, Xu X, Wightman EL, Llorente B, Borneman AR, Carpenter AC, Van Wyk N, Meier F, Collier TR, Espinosa MI, Daniel EL, Walker RS, Cai Y, Nevalainen HK, Curach NC, Deveson IW, Mercer TR, Johnson DL, Mitchell LA, Bader JS, Stracquadanio G, Boeke JD, Goold HD, Pretorius IS, Paulsen IT. Parallel laboratory evolution and rational debugging reveal genomic plasticity to S. cerevisiae synthetic chromosome XIV defects. CELL GENOMICS 2023; 3:100379. [PMID: 38020977 PMCID: PMC10667330 DOI: 10.1016/j.xgen.2023.100379] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 12/01/2023]
Abstract
Synthetic chromosome engineering is a complex process due to the need to identify and repair growth defects and deal with combinatorial gene essentiality when rearranging chromosomes. To alleviate these issues, we have demonstrated novel approaches for repairing and rearranging synthetic Saccharomyces cerevisiae genomes. We have designed, constructed, and restored wild-type fitness to a synthetic 753,096-bp version of S. cerevisiae chromosome XIV as part of the Synthetic Yeast Genome project. In parallel to the use of rational engineering approaches to restore wild-type fitness, we used adaptive laboratory evolution to generate a general growth-defect-suppressor rearrangement in the form of increased TAR1 copy number. We also extended the utility of the synthetic chromosome recombination and modification by loxPsym-mediated evolution (SCRaMbLE) system by engineering synthetic-wild-type tetraploid hybrid strains that buffer against essential gene loss, highlighting the plasticity of the S. cerevisiae genome in the presence of rational and non-rational modifications.
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Affiliation(s)
- Thomas C. Williams
- School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
- CSIRO Synthetic Biology Future Science Platform, Canberra, ACT 2601, Australia
| | - Heinrich Kroukamp
- School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
| | - Xin Xu
- School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
| | - Elizabeth L.I. Wightman
- School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
| | - Briardo Llorente
- School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
- CSIRO Synthetic Biology Future Science Platform, Canberra, ACT 2601, Australia
- The Australian Genome Foundry, Sydney, NSW, Australia
| | - Anthony R. Borneman
- The Australian Wine Research Institute, Adelaide, SA 5064, Australia
- School of Agriculture, Food & Wine, Faculty of Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Alexander C. Carpenter
- School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
- CSIRO Synthetic Biology Future Science Platform, Canberra, ACT 2601, Australia
| | - Niel Van Wyk
- School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
- Department of Microbiology and Biochemistry, Hochschule Geisenheim University, Geisenheim, Germany
| | - Felix Meier
- School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
| | - Thomas R.V. Collier
- School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
| | - Monica I. Espinosa
- School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
| | - Elizabeth L. Daniel
- School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
| | - Roy S.K. Walker
- School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, Scotland, UK
- School of Engineering, Institute for Bioengineering, The University of Edinburgh, Edinburgh EH9 3BF, Scotland, UK
| | - Yizhi Cai
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, Scotland, UK
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Helena K.M. Nevalainen
- School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
| | - Natalie C. Curach
- School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
- Bioplatforms Australia, Research Park Drive, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Ira W. Deveson
- St Vincent’s Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
- The Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Timothy R. Mercer
- St Vincent’s Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
- The Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia
| | - Daniel L. Johnson
- School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
- The Australian Wine Research Institute, Adelaide, SA 5064, Australia
| | - Leslie A. Mitchell
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Joel S. Bader
- Department of Biomedical Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Giovanni Stracquadanio
- Institute of Quantitative Biology, Biochemistry, and Biotechnology, SynthSys, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Jef D. Boeke
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
| | - Hugh D. Goold
- School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
- New South Wales Department of Primary Industries, Orange, NSW 2800, Australia
| | - Isak S. Pretorius
- School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
| | - Ian T. Paulsen
- School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
- The Australian Genome Foundry, Sydney, NSW, Australia
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3
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Feng S, Desotell A, Ross A, Jovanovic M, Manley JL. A nucleolar long "non-coding" RNA encodes a novel protein that functions in response to stress. Proc Natl Acad Sci U S A 2023; 120:e2221109120. [PMID: 36812203 PMCID: PMC9992852 DOI: 10.1073/pnas.2221109120] [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: 12/12/2022] [Accepted: 01/14/2023] [Indexed: 02/24/2023] Open
Abstract
Certain long non-coding RNAs (lncRNAs) are known to contain small open reading frames that can be translated. Here we describe a much larger 25 kDa human protein, "Ribosomal IGS Encoded Protein" (RIEP), that remarkably is encoded by the well-characterized RNA polymerase (RNAP) II-transcribed nucleolar "promoter and pre-rRNA antisense" lncRNA (PAPAS). Strikingly, RIEP, which is conserved throughout primates but not found in other species, predominantly localizes to the nucleolus as well as mitochondria, but both exogenously expressed and endogenous RIEP increase in the nuclear and perinuclear regions upon heat shock (HS). RIEP associates specifically with the rDNA locus, increases levels of the RNA:DNA helicase Senataxin, and functions to sharply reduce DNA damage induced by heat shock. Proteomics analysis identified two mitochondrial proteins, C1QBP and CHCHD2, both known to have mitochondrial and nuclear functions, that we show interact directly, and relocalize following heat shock, with RIEP. Finally, it is especially notable that the rDNA sequences encoding RIEP are multifunctional, giving rise to an RNA that functions both as RIEP messenger RNA (mRNA) and as PAPAS lncRNA, as well as containing the promoter sequences responsible for rRNA synthesis by RNAP I. Our work has thus not only shown that a nucleolar "non-coding" RNA in fact encodes a protein, but also established a novel link between mitochondria and nucleoli that contributes to the cellular stress response.
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Affiliation(s)
- Shuang Feng
- Department of Biological Sciences, Columbia University, New York, NY10027
| | - Anthony Desotell
- Department of Biological Sciences, Columbia University, New York, NY10027
| | - Alison Ross
- Department of Biological Sciences, Columbia University, New York, NY10027
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, NY10027
| | - James L. Manley
- Department of Biological Sciences, Columbia University, New York, NY10027
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4
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Miotelo L, Ferro M, Maloni G, Otero IVR, Nocelli RCF, Bacci M, Malaspina O. Transcriptomic analysis of Malpighian tubules from the stingless bee Melipona scutellaris reveals thiamethoxam-induced damages. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 850:158086. [PMID: 35985603 DOI: 10.1016/j.scitotenv.2022.158086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/21/2022] [Accepted: 08/13/2022] [Indexed: 06/15/2023]
Abstract
The concern about pesticide exposure to neotropical bees has been increasing in the last few years, and knowledge gaps have been identified. Although stingless bees, (e.g.: Melipona scutellaris), are more diverse than honeybees and they stand out in the pollination of several valuable economical crops, toxicity assessments with stingless bees are still scarce. Nowadays new approaches in ecotoxicological studies, such as omic analysis, were pointed out as a strategy to reveal mechanisms of how bees deal with these stressors. To date, no molecular techniques have been applied for the evaluation of target and/or non-target organs in stingless bees, such as the Malpighian tubules (Mt). Therefore, in the present study, we evaluated the differentially expressed genes (DEGs) in the Mt of M. scutellaris after one and eight days of exposure to LC50/100 (0.000543 ng a.i./μL) of thiamethoxam (TMX). Through functional annotation analysis of four transcriptome libraries, the time course line approach revealed 237 DEGs (nine clusters) associated with carbon/energy metabolism and cellular processes (lysosomes, autophagy, and glycan degradation). The expression profiles of Mt were altered by TMX in processes, such as detoxification, excretion, tissue regeneration, oxidative stress, apoptosis, and DNA repair. Transcriptome analysis showed that cell metabolism in Mt was mainly affected after 8 days of exposure. Nine genes were selected from different clusters and validated by RT-qPCR. According to our findings, TMX promotes several types of damage in Mt cells at the molecular level. Therefore, interference of different cellular processes directly affects the health of M. scutellaris by compromising the function of Mt.
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Affiliation(s)
- Lucas Miotelo
- Department of General and Applied Biology, Institute of Biosciences, São Paulo State University (UNESP), Rio Claro, SP, Brazil.
| | - Milene Ferro
- Department of General and Applied Biology, Institute of Biosciences, São Paulo State University (UNESP), Rio Claro, SP, Brazil
| | - Geovana Maloni
- Department of General and Applied Biology, Institute of Biosciences, São Paulo State University (UNESP), Rio Claro, SP, Brazil
| | - Igor Vinicius Ramos Otero
- Department of General and Applied Biology, Institute of Biosciences, São Paulo State University (UNESP), Rio Claro, SP, Brazil
| | | | - Mauricio Bacci
- Department of General and Applied Biology, Institute of Biosciences, São Paulo State University (UNESP), Rio Claro, SP, Brazil
| | - Osmar Malaspina
- Department of General and Applied Biology, Institute of Biosciences, São Paulo State University (UNESP), Rio Claro, SP, Brazil
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5
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Feng S, Manley JL. Beyond rRNA: nucleolar transcription generates a complex network of RNAs with multiple roles in maintaining cellular homeostasis. Genes Dev 2022; 36:876-886. [PMID: 36207140 PMCID: PMC9575697 DOI: 10.1101/gad.349969.122] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Nucleoli are the major cellular compartments for the synthesis of rRNA and assembly of ribosomes, the macromolecular complexes responsible for protein synthesis. Given the abundance of ribosomes, there is a huge demand for rRNA, which indeed constitutes ∼80% of the mass of RNA in the cell. Thus, nucleoli are characterized by extensive transcription of multiple rDNA loci by the dedicated polymerase, RNA polymerase (Pol) I. However, in addition to producing rRNAs, there is considerable additional transcription in nucleoli by RNA Pol II as well as Pol I, producing multiple noncoding (nc) and, in one instance, coding RNAs. In this review, we discuss important features of these transcripts, which often appear species-specific and reflect transcription antisense to pre-rRNA by Pol II and within the intergenic spacer regions on both strands by both Pol I and Pol II. We discuss how expression of these RNAs is regulated, their propensity to form cotranscriptional R loops, and how they modulate rRNA transcription, nucleolar structure, and cellular homeostasis more generally.
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6
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Vallabhaneni AR, Kabashi M, Haymowicz M, Bhatt K, Wayman V, Ahmed S, Conrad-Webb H. HSF1 induces RNA polymerase II synthesis of ribosomal RNA in S. cerevisiae during nitrogen deprivation. Curr Genet 2021; 67:937-951. [PMID: 34363098 PMCID: PMC8594204 DOI: 10.1007/s00294-021-01197-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 11/29/2022]
Abstract
The resource intensive process of accurate ribosome synthesis is essential for cell viability in all organisms. Ribosome synthesis regulation centers on RNA polymerase I (pol I) transcription of a 35S rRNA precursor that is processed into the mature 18S, 5.8S and 25S rRNAs. During nutrient deprivation or stress, pol I synthesis of rRNA is dramatically reduced. Conversely, chronic stress such as mitochondrial dysfunction induces RNA polymerase II (pol II) to transcribe functional rRNA using an evolutionarily conserved cryptic pol II rDNA promoter suggesting a universal phenomenon. However, this polymerase switches and its role in regulation of rRNA synthesis remain unclear. In this paper, we demonstrate that extended nitrogen deprivation induces the polymerase switch via components of the environmental stress response. We further show that the switch is repressed by Sch9 and activated by the stress kinase Rim15. Like stress-induced genes, the switch requires not only pol II transcription machinery, including the mediator, but also requires the HDAC, Rpd3 and stress transcription factor Hsf1. The current work shows that the constitutive allele, Hsf1PO4* displays elevated levels of induction in non-stress conditions while binding to a conserved site in the pol II rDNA promoter upstream of the pol I promoter. Whether the polymerase switch serves to provide rRNA when pol I transcription is inhibited or fine-tunes pol I initiation via RNA interactions is yet to be determined. Identifying the underlying mechanism for this evolutionary conserved phenomenon will help understand the mechanism of pol II rRNA synthesis and its role in stress adaptation.
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Affiliation(s)
- Arjuna Rao Vallabhaneni
- Department of Biology, Texas Woman's University, 304 Administration Dr., Denton, TX, 76204, USA
| | - Merita Kabashi
- Department of Biology, Texas Woman's University, 304 Administration Dr., Denton, TX, 76204, USA
| | - Matt Haymowicz
- Department of Biology, Texas Woman's University, 304 Administration Dr., Denton, TX, 76204, USA
| | - Kushal Bhatt
- Department of Biology, Texas Woman's University, 304 Administration Dr., Denton, TX, 76204, USA.,Department of Bioinformatics, University of Texas Southwestern, 5323 Harry Hines Blvd., Dallas, Texas, 75390, USA
| | - Violet Wayman
- Department of Biology, Texas Woman's University, 304 Administration Dr., Denton, TX, 76204, USA
| | - Shazia Ahmed
- Department of Biology, Texas Woman's University, 304 Administration Dr., Denton, TX, 76204, USA
| | - Heather Conrad-Webb
- Department of Biology, Texas Woman's University, 304 Administration Dr., Denton, TX, 76204, USA.
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7
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Park SM, Kim DA, Jo JK, Jun SK, Jang TS, Kim HW, Lee JH, Lee HH. Ceria-Incorporated Biopolymer for Preventing Fungal Adhesion. ACS Biomater Sci Eng 2020; 7:1808-1816. [PMID: 33966380 DOI: 10.1021/acsbiomaterials.0c01039] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Although biopolymers are widely used in biomedical fields, the issue of poor antimicrobial properties remains unsolved, leading to a potential increase in infections. Here, ceria nanoparticles (CNPs) were incorporated into a representative biopolymer, poly(methyl methacrylate) (PMMA), for drug-free antimicrobial properties. After characterizing the CNPs and surface/mechanical properties of the CNP-PMMA nanocomposite, antiadhesive effects against Candida albicans, the most common fungal species responsible for fungal infections, were determined using metabolic activity assays, and the underlying microbial antiadhesive mechanism was revealed. Hydrothermally fabricated CNPs showed a size of ∼20 nm with a zeta potential of 12 ± 2.3 mV and showed catalytic properties as a ROS modulator. Successful incorporation of CNPs into PMMA up to 2 wt % was confirmed by EDS analysis. The surface roughness and mechanical properties such as flexural strength and modulus were relatively unchanged up to 2 wt %. In contrast, the surface energy increased, and the Vickers hardness decreased in the 2 wt % PMMA compared with the control. A drop of up to 90% of adherent Candida albicans was observed in CNP-incorporated PMMA, which was confirmed and quantified via fungus staining images. The antiadhesive mechanism was revealed from the direct antimicrobial effects of CNP via the upregulation of the intracellular ROS level. Taken together, the antimicrobial-adhesive properties of the CNP-PMMA nanocomposite suggest the potential usefulness of CNP as a promising drug-free antimicrobial ingredient for biopolymers, which could lead to the prevention of microbial-induced complications in clinical settings.
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Affiliation(s)
- Sung-Min Park
- Institute of Tissue Regeneration Engineering (ITREN), Dankook University, Cheonan 31116, South Korea.,Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine Research Center, Dankook University, Cheonan 31116, South Korea
| | - Dong-Ae Kim
- Department of Dental Hygiene, Yeoju College, Yeoju 12652, South Korea.,Department of Biomaterials Science, School of Dentistry, Dankook University, Cheonan 31116, South Korea
| | - Jeong-Ki Jo
- Department of Biomaterials Science, School of Dentistry, Dankook University, Cheonan 31116, South Korea
| | - Soo-Kyung Jun
- Institute of Tissue Regeneration Engineering (ITREN), Dankook University, Cheonan 31116, South Korea.,Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine Research Center, Dankook University, Cheonan 31116, South Korea.,Department of Dental Hygiene, Hanseo University, Seosan 31962, South Korea
| | - Tae-Su Jang
- Department of Pre-medi, College of Medicine, Dankook University, Cheonan 31116, Republic of Korea
| | - Hae-Won Kim
- Institute of Tissue Regeneration Engineering (ITREN), Dankook University, Cheonan 31116, South Korea.,Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine Research Center, Dankook University, Cheonan 31116, South Korea.,Department of Biomaterials Science, School of Dentistry, Dankook University, Cheonan 31116, South Korea.,UCL Eastman-Korea Dental Medicine Innovation Centre, Dankook University, Cheonan 31116, Republic of Korea
| | - Jung-Hwan Lee
- Institute of Tissue Regeneration Engineering (ITREN), Dankook University, Cheonan 31116, South Korea.,Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine Research Center, Dankook University, Cheonan 31116, South Korea.,Department of Biomaterials Science, School of Dentistry, Dankook University, Cheonan 31116, South Korea.,UCL Eastman-Korea Dental Medicine Innovation Centre, Dankook University, Cheonan 31116, Republic of Korea
| | - Hae-Hyoung Lee
- Institute of Tissue Regeneration Engineering (ITREN), Dankook University, Cheonan 31116, South Korea.,Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine Research Center, Dankook University, Cheonan 31116, South Korea.,Department of Biomaterials Science, School of Dentistry, Dankook University, Cheonan 31116, South Korea.,UCL Eastman-Korea Dental Medicine Innovation Centre, Dankook University, Cheonan 31116, Republic of Korea
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8
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English J, Son JM, Cardamone MD, Lee C, Perissi V. Decoding the rosetta stone of mitonuclear communication. Pharmacol Res 2020; 161:105161. [PMID: 32846213 PMCID: PMC7755734 DOI: 10.1016/j.phrs.2020.105161] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/04/2020] [Accepted: 08/14/2020] [Indexed: 12/12/2022]
Abstract
Cellular homeostasis in eukaryotic cells requires synchronized coordination of multiple organelles. A key role in this stage is played by mitochondria, which have recently emerged as highly interconnected and multifunctional hubs that process and coordinate diverse cellular functions. Beyond producing ATP, mitochondria generate key metabolites and are central to apoptotic and metabolic signaling pathways. Because most mitochondrial proteins are encoded in the nuclear genome, the biogenesis of new mitochondria and the maintenance of mitochondrial functions and flexibility critically depend upon effective mitonuclear communication. This review addresses the complex network of signaling molecules and pathways allowing mitochondria-nuclear communication and coordinated regulation of their independent but interconnected genomes, and discusses the extent to which dynamic communication between the two organelles has evolved for mutual benefit and for the overall maintenance of cellular and organismal fitness.
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Affiliation(s)
- Justin English
- Department of Biochemistry, Boston University, Boston, MA, 02115, USA; Graduate Program in Biomolecular Pharmacology, Department of Pharmacology and Experimental Therapeutics, Boston University, Boston, MA, 02115, USA
| | - Jyung Mean Son
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | | | - Changhan Lee
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA; USC Norris Comprehensive Cancer Center, Los Angeles, CA, 90089, USA; Biomedical Sciences, Graduate School, Ajou University, Suwon, 16499, South Korea
| | - Valentina Perissi
- Department of Biochemistry, Boston University, Boston, MA, 02115, USA.
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9
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Ballesteros GI, Torres-Díaz C, Bravo LA, Balboa K, Caruso C, Bertini L, Proietti S, Molina-Montenegro MA. In silico analysis of metatranscriptomic data from the Antarctic vascular plant Colobanthus quitensis: Responses to a global warming scenario through changes in fungal gene expression levels. FUNGAL ECOL 2020. [DOI: 10.1016/j.funeco.2019.100873] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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10
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Peruzza L, Shekhar MS, Kumar KV, Swathi A, Karthic K, Hauton C, Vijayan KK. Temporal changes in transcriptome profile provide insights of White Spot Syndrome Virus infection in Litopenaeus vannamei. Sci Rep 2019; 9:13509. [PMID: 31534145 PMCID: PMC6751192 DOI: 10.1038/s41598-019-49836-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 08/30/2019] [Indexed: 02/08/2023] Open
Abstract
Shrimp aquaculture is severely affected by WSSV. Despite an increasing effort to understand host/virus interaction by characterizing changes in gene expression (GE) following WSSV infection, the majority of published studies have focussed on a single time-point, providing limited insight on the development of host-pathogen interaction over the infection cycle. Using RNA-seq, we contrasted GE in gills of Litopenaeus vannamei at 1.5, 18 and 56 hours-post-infection (hpi), between WSSV-challenged and control shrimps. Time course analysis revealed 5097 differentially expressed genes: 63 DEGs were viral genes and their expression in WSSV group either peaked at 18 hpi (and decreased at 56 hpi) or increased linearly up to 56 hpi, suggesting a different role played by these genes during the course of infection. The remaining DEGs showed that WSSV altered the expression of metabolic, immune, apoptotic and cytoskeletal genes and was able to inhibit NF-κB and JAK/STAT pathways. Interestingly, GE changes were not consistent through the course of infection but were dynamic with time, suggesting the complexity of host-pathogen interaction. These data offer novel insights into the cellular functions that are affected during the course of infection and ultimately provide a valuable resource towards our understanding of the host-pathogen dynamics and its variation with time.
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Affiliation(s)
- Luca Peruzza
- School of Ocean and Earth Science, University of Southampton, Hampshire, SO14 3ZH, United Kingdom.
| | - M S Shekhar
- Genetics and Biotechnology Unit, Central Institute of Brackishwater Aquaculture, 75 Santhome High Road, R.A. Puram, Chennai, 600004, Tamil Nadu, India
| | - K Vinaya Kumar
- Genetics and Biotechnology Unit, Central Institute of Brackishwater Aquaculture, 75 Santhome High Road, R.A. Puram, Chennai, 600004, Tamil Nadu, India
| | - A Swathi
- Genetics and Biotechnology Unit, Central Institute of Brackishwater Aquaculture, 75 Santhome High Road, R.A. Puram, Chennai, 600004, Tamil Nadu, India
| | - K Karthic
- Genetics and Biotechnology Unit, Central Institute of Brackishwater Aquaculture, 75 Santhome High Road, R.A. Puram, Chennai, 600004, Tamil Nadu, India
| | - Chris Hauton
- School of Ocean and Earth Science, University of Southampton, Hampshire, SO14 3ZH, United Kingdom
| | - K K Vijayan
- Genetics and Biotechnology Unit, Central Institute of Brackishwater Aquaculture, 75 Santhome High Road, R.A. Puram, Chennai, 600004, Tamil Nadu, India
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11
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Benayoun BA, Lee C. MOTS-c: A Mitochondrial-Encoded Regulator of the Nucleus. Bioessays 2019; 41:e1900046. [PMID: 31378979 PMCID: PMC8224472 DOI: 10.1002/bies.201900046] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 06/28/2019] [Indexed: 12/25/2022]
Abstract
Mitochondria are increasingly being recognized as information hubs that sense cellular changes and transmit messages to other cellular components, such as the nucleus, the endoplasmic reticulum (ER), the Golgi apparatus, and lysosomes. Nonetheless, the interaction between mitochondria and the nucleus is of special interest because they both host part of the cellular genome. Thus, the communication between genome-bearing organelles would likely include gene expression regulation. Multiple nuclear-encoded proteins have been known to regulate mitochondrial gene expression. On the contrary, no mitochondrial-encoded factors are known to actively regulate nuclear gene expression. MOTS-c (mitochondrial open reading frame of the 12S ribosomal RNA type-c) is a recently identified peptide encoded within the mitochondrial 12S ribosomal RNA gene that has metabolic functions. Notably, MOTS-c can translocate to the nucleus upon metabolic stress (e.g., glucose restriction and oxidative stress) and directly regulate adaptive nuclear gene expression to promote cellular homeostasis. It is hypothesized that cellular fitness requires the coevolved mitonuclear genomes to coordinate adaptive responses using gene-encoded factors that cross-regulate the opposite genome. This suggests that cellular gene expression requires the bipartite split genomes to operate as a unified system, rather than the nucleus being the sole master regulator.
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Affiliation(s)
- Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation Program, Los Angeles, CA, 90089, USA
- USC Stem Cell Initiative, Los Angeles, CA, 90089, USA
| | - Changhan Lee
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation Program, Los Angeles, CA, 90089, USA
- Biomedical Sciences, Graduate School, Ajou University, Suwon, 16499, Republic of Korea
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12
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The Ribosome as a Missing Link in Prebiotic Evolution III: Over-Representation of tRNA- and rRNA-Like Sequences and Plieofunctionality of Ribosome-Related Molecules Argues for the Evolution of Primitive Genomes from Ribosomal RNA Modules. Int J Mol Sci 2019; 20:ijms20010140. [PMID: 30609737 PMCID: PMC6337102 DOI: 10.3390/ijms20010140] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 12/21/2018] [Accepted: 12/23/2018] [Indexed: 12/18/2022] Open
Abstract
We propose that ribosomal RNA (rRNA) formed the basis of the first cellular genomes, and provide evidence from a review of relevant literature and proteonomic tests. We have proposed previously that the ribosome may represent the vestige of the first self-replicating entity in which rRNAs also functioned as genes that were transcribed into functional messenger RNAs (mRNAs) encoding ribosomal proteins. rRNAs also encoded polymerases to replicate itself and a full complement of the transfer RNAs (tRNAs) required to translate its genes. We explore here a further prediction of our “ribosome-first” theory: the ribosomal genome provided the basis for the first cellular genomes. Modern genomes should therefore contain an unexpectedly large percentage of tRNA- and rRNA-like modules derived from both sense and antisense reading frames, and these should encode non-ribosomal proteins, as well as ribosomal ones with key cell functions. Ribosomal proteins should also have been co-opted by cellular evolution to play extra-ribosomal functions. We review existing literature supporting these predictions. We provide additional, new data demonstrating that rRNA-like sequences occur at significantly higher frequencies than predicted on the basis of mRNA duplications or randomized RNA sequences. These data support our “ribosome-first” theory of cellular evolution.
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13
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Abstract
The vast majority of mitochondrial proteins are encoded by nuclear genes, giving the nucleus ultimate control of mitochondrial biogenesis, dynamics, and function. However, in this issue Kim et al. (2018) demonstrate a reversal of fortune, whereby an mtDNA-encoded peptide, MOTS-c, is targeted to the nucleus to signal changes in gene expression.
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14
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Wang L, Sun Y, Xia XL, Jiang TB. Screening of proteins interacting with ERF transcriptional factor from Populus simonii × P.nigra by yeast two-hybrid method. BIOTECHNOL BIOTEC EQ 2018. [DOI: 10.1080/13102818.2018.1453309] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Affiliation(s)
- Lei Wang
- Department of Plant Science, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, PR China
- Department of Biotechnology, Institute of Advanced Technology, Heilongjiang Academy of Sciences, Harbin, Heilongjiang, PR China
| | - Yao Sun
- Department of Biotechnology, Institute of Advanced Technology, Heilongjiang Academy of Sciences, Harbin, Heilongjiang, PR China
| | - Xin-Li Xia
- Department of Plant Science, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, PR China
| | - Ting-Bo Jiang
- State Key Laboratory of Tree Genetics and Breeding, College of Forestry, Northeast Forestry University, Harbin, Heilongjiang, PR China
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15
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de Ruijter JC, Jurgens G, Frey AD. Screening for novel genes of Saccharomyces cerevisiae involved in recombinant antibody production. FEMS Yeast Res 2016; 17:fow104. [PMID: 27956492 DOI: 10.1093/femsyr/fow104] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 12/05/2016] [Indexed: 01/17/2023] Open
Abstract
Cost-effective manufacturing of biopharmaceuticals in non-mammalian hosts still requires tremendous efforts in strain development. In order to expedite identification of novel leads for strain engineering, we used a transposon-mutagenized yeast genomic DNA library to create a collection of Saccharomyces cerevisiae deletion strains expressing a full-length IgG antibody. Using a high-throughput screening, transformants with either significantly higher or lower IgG expression were selected. The integration site of the transposon in three of the selected strains was located by DNA sequencing. The inserted DNA lay within the VPS30 and TAR1 open reading frame, and upstream of the HEM13 open reading frame. The complete coding sequence of these genes was deleted in the wild-type strain background to confirm the IgG expression phenotypes. Production of recombinant antibody was increased 2-fold in the Δvps30 strain, but only mildly affected secretion levels in the Δtar1 strain. Remarkably, expression of endogenous yeast acid phosphatase was increased 1.7- and 2.4-fold in Δvps30 and Δtar1 strains. The study confirmed the power of genome-wide high-throughput screens for strain development and highlights the importance of using the target molecule during the screening process.
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Affiliation(s)
- Jorg C de Ruijter
- Department of Biotechnology and Chemical Technology, Aalto University, 02150 Espoo, Finland
| | | | - Alexander D Frey
- Department of Biotechnology and Chemical Technology, Aalto University, 02150 Espoo, Finland
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16
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Jin XL, Ma CL, Yang LT, Chen LS. Alterations of physiology and gene expression due to long-term magnesium-deficiency differ between leaves and roots of Citrus reticulata. JOURNAL OF PLANT PHYSIOLOGY 2016; 198:103-15. [PMID: 27163764 DOI: 10.1016/j.jplph.2016.04.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 04/08/2016] [Accepted: 04/17/2016] [Indexed: 05/03/2023]
Abstract
Seedlings of Ponkan (Citrus reticulata) were irrigated with nutrient solution containing 0 (Mg-deficiency) or 1mM MgSO4 (control) every two day for 16 weeks. Thereafter, we examined magnesium (Mg)-deficiency-induced changes in leaf and root gas exchange, total soluble proteins and gene expression. Mg-deficiency lowered leaf CO2 assimilation, and increased leaf dark respiration. However, Mg-deficient roots had lower respiration. Total soluble protein level was not significantly altered by Mg-deficiency in roots, but was lower in Mg-deficient leaves than in controls. Using cDNA-AFLP, we obtained 70 and 71 differentially expressed genes from leaves and roots. These genes mainly functioned in signal transduction, stress response, carbohydrate and energy metabolism, cell transport, cell wall and cytoskeleton metabolism, nucleic acid, and protein metabolisms. Lipid metabolism (Ca(2+) signals)-related Mg-deficiency-responsive genes were isolated only from roots (leaves). Although little difference existed in the number of Mg-deficiency-responsive genes between them both, most of these genes only presented in Mg-deficient leaves or roots, and only four genes were shared by them both. Our data clearly demonstrated that Mg-deficiency-induced alterations of physiology and gene expression greatly differed between leaves and roots. In addition, we focused our discussion on the causes for photosynthetic decline in Mg-deficient leaves and the responses of roots to Mg-deficiency.
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Affiliation(s)
- Xiao-Lin Jin
- Institute of Plant Nutritional Physiology and Molecular Biology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China; College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Cui-Lan Ma
- Institute of Plant Nutritional Physiology and Molecular Biology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China; College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Lin-Tong Yang
- Institute of Plant Nutritional Physiology and Molecular Biology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, Fuzhou 350002, China.
| | - Li-Song Chen
- Institute of Plant Nutritional Physiology and Molecular Biology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, Fuzhou 350002, China.
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17
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The ribosome as a missing link in prebiotic evolution II: Ribosomes encode ribosomal proteins that bind to common regions of their own mRNAs and rRNAs. J Theor Biol 2016; 397:115-27. [DOI: 10.1016/j.jtbi.2016.02.030] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Revised: 02/16/2016] [Accepted: 02/19/2016] [Indexed: 11/18/2022]
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18
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Wang D, Mansisidor A, Prabhakar G, Hochwagen A. Condensin and Hmo1 Mediate a Starvation-Induced Transcriptional Position Effect within the Ribosomal DNA Array. Cell Rep 2016; 14:1010-1017. [PMID: 26832415 DOI: 10.1016/j.celrep.2016.01.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 10/30/2015] [Accepted: 12/28/2015] [Indexed: 02/06/2023] Open
Abstract
Repetitive DNA arrays are important structural features of eukaryotic genomes that are often heterochromatinized to suppress repeat instability. It is unclear, however, whether all repeats within an array are equally subject to heterochromatin formation and gene silencing. Here, we show that in starving Saccharomyces cerevisiae, silencing of reporter genes within the ribosomal DNA (rDNA) array is less pronounced in outer repeats compared with inner repeats. This position effect is linked to the starvation-induced contraction of the nucleolus. We show that the chromatin regulators condensin and Hmo1 redistribute within the rDNA upon starvation; that Hmo1, like condensin, is required for nucleolar contraction; and that the position effect partially depends on both proteins. Starvation-induced nucleolar contraction and differential desilencing of the outer rDNA repeats may provide a mechanism to activate rDNA-encoded RNAPII transcription units without causing general rDNA instability.
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Affiliation(s)
- Danni Wang
- Department of Biology, New York University, New York, NY 10003, USA
| | | | | | - Andreas Hochwagen
- Department of Biology, New York University, New York, NY 10003, USA.
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19
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From Compositional Chemical Ecologies to Self-replicating Ribosomes and on to Functional Trait Ecological Networks. Evol Biol 2016. [DOI: 10.1007/978-3-319-41324-2_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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20
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Wang LQ, Yang LT, Guo P, Zhou XX, Ye X, Chen EJ, Chen LS. Leaf cDNA-AFLP analysis reveals novel mechanisms for boron-induced alleviation of aluminum-toxicity in Citrus grandis seedlings. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2015; 120:349-59. [PMID: 26099466 DOI: 10.1016/j.ecoenv.2015.06.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 05/24/2015] [Accepted: 06/05/2015] [Indexed: 05/18/2023]
Abstract
Little information is available on the molecular mechanisms of boron (B)-induced alleviation of aluminum (Al)-toxicity. 'Sour pummelo' (Citrus grandis) seedlings were irrigated for 18 weeks with nutrient solution containing different concentrations of B (2.5 or 20μM H3BO3) and Al (0 or 1.2mM AlCl3·6H2O). B alleviated Al-induced inhibition in plant growth accompanied by lower leaf Al. We used cDNA-AFLP to isolate 127 differentially expressed genes from leaves subjected to B and Al interactions. These genes were related to signal transduction, transport, cell wall modification, carbohydrate and energy metabolism, nucleic acid metabolism, amino acid and protein metabolism, lipid metabolism and stress responses. The ameliorative mechanisms of B on Al-toxicity might be related to: (a) triggering multiple signal transduction pathways; (b) improving the expression levels of genes related to transport; (c) activating genes involved in energy production; and (d) increasing amino acid accumulation and protein degradation. Also, genes involved in nucleic acid metabolism, cell wall modification and stress responses might play a role in B-induced alleviation of Al-toxicity. To conclude, our findings reveal some novel mechanisms on B-induced alleviation of Al-toxicity at the transcriptional level in C. grandis leaves.
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Affiliation(s)
- Liu-Qing Wang
- College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lin-Tong Yang
- College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Peng Guo
- College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xin-Xing Zhou
- College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xin Ye
- College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - En-Jun Chen
- College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Li-Song Chen
- College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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21
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Schroeder EA, Shadel GS. Crosstalk between mitochondrial stress signals regulates yeast chronological lifespan. Mech Ageing Dev 2013; 135:41-9. [PMID: 24373996 DOI: 10.1016/j.mad.2013.12.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 12/04/2013] [Accepted: 12/16/2013] [Indexed: 01/09/2023]
Abstract
Mitochondrial DNA (mtDNA) exists in multiple copies per cell and is essential for oxidative phosphorylation. Depleted or mutated mtDNA promotes numerous human diseases and may contribute to aging. Reduced TORC1 signaling in the budding yeast, Saccharomyces cerevisiae, extends chronological lifespan (CLS) in part by generating a mitochondrial ROS (mtROS) signal that epigenetically alters nuclear gene expression. To address the potential requirement for mtDNA maintenance in this response, we analyzed strains lacking the mitochondrial base-excision repair enzyme Ntg1p. Extension of CLS by mtROS signaling and reduced TORC1 activity, but not caloric restriction, was abrogated in ntg1Δ strains that exhibited mtDNA depletion without defects in respiration. The DNA damage response (DDR) kinase Rad53p, which transduces pro-longevity mtROS signals, is also activated in ntg1Δ strains. Restoring mtDNA copy number alleviated Rad53p activation and re-established CLS extension following mtROS signaling, indicating that Rad53p senses mtDNA depletion directly. Finally, DDR kinases regulate nucleus-mitochondria localization dynamics of Ntg1p. From these results, we conclude that the DDR pathway senses and may regulate Ntg1p-dependent mtDNA stability. Furthermore, Rad53p senses multiple mitochondrial stresses in a hierarchical manner to elicit specific physiological outcomes, exemplified by mtDNA depletion overriding the ability of Rad53p to transduce an adaptive mtROS longevity signal.
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Affiliation(s)
- Elizabeth A Schroeder
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, United States; Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, United States
| | - Gerald S Shadel
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, United States; Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, United States.
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22
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Schroeder EA, Raimundo N, Shadel GS. Epigenetic silencing mediates mitochondria stress-induced longevity. Cell Metab 2013; 17:954-964. [PMID: 23747251 PMCID: PMC3694503 DOI: 10.1016/j.cmet.2013.04.003] [Citation(s) in RCA: 152] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Revised: 02/27/2013] [Accepted: 04/01/2013] [Indexed: 11/30/2022]
Abstract
Reactive oxygen species (ROS) play complex roles in aging, having both damaging effects and signaling functions. Transiently elevating mitochondrial stress, including mitochondrial ROS (mtROS), elicits beneficial responses that extend lifespan. However, these adaptive, longevity-signaling pathways remain poorly understood. We show here that Tel1p and Rad53p, homologs of the mammalian DNA damage response kinases ATM and Chk2, mediate a hormetic mtROS longevity signal that extends yeast chronological lifespan. This pathway senses mtROS in a manner distinct from the nuclear DNA damage response and ultimately imparts longevity by inactivating the histone demethylase Rph1p specifically at subtelomeric heterochromatin, enhancing binding of the silencing protein Sir3p, and repressing subtelomeric transcription. These results demonstrate the existence of conserved mitochondria-to-nucleus stress-signaling pathways that regulate aging through epigenetic modulation of nuclear gene expression.
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Affiliation(s)
- Elizabeth A Schroeder
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Nuno Raimundo
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Gerald S Shadel
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA.
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23
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Poole AM, Kobayashi T, Ganley ARD. A positive role for yeast extrachromosomal rDNA circles? Extrachromosomal ribosomal DNA circle accumulation during the retrograde response may suppress mitochondrial cheats in yeast through the action of TAR1. Bioessays 2012; 34:725-9. [PMID: 22706794 PMCID: PMC3563013 DOI: 10.1002/bies.201200037] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Anthony M Poole
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
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24
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Galopier A, Hermann-Le Denmat S. Mitochondria of the yeasts Saccharomyces cerevisiae and Kluyveromyces lactis contain nuclear rDNA-encoded proteins. PLoS One 2011; 6:e16325. [PMID: 21283537 PMCID: PMC3026818 DOI: 10.1371/journal.pone.0016325] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Accepted: 12/10/2010] [Indexed: 12/03/2022] Open
Abstract
In eukaryotes, the nuclear ribosomal DNA (rDNA) is the source of the structural 18S, 5.8S and 25S rRNAs. In hemiascomycetous yeasts, the 25S rDNA sequence was described to lodge an antisense open reading frame (ORF) named TAR1 for Transcript Antisense to Ribosomal RNA. Here, we present the first immuno-detection and sub-cellular localization of the authentic product of this atypical yeast gene. Using specific antibodies against the predicted amino-acid sequence of the Saccharomyces cerevisiae TAR1 product, we detected the endogenous Tar1p polypeptides in S. cerevisiae (Sc) and Kluyveromyces lactis (Kl) species and found that both proteins localize to mitochondria. Protease and carbonate treatments of purified mitochondria further revealed that endogenous Sc Tar1p protein sub-localizes in the inner membrane in a Nin-Cout topology. Plasmid-versions of 5′ end or 3′ end truncated TAR1 ORF were used to demonstrate that neither the N-terminus nor the C-terminus of Sc Tar1p were required for its localization. Also, Tar1p is a presequence-less protein. Endogenous Sc Tar1p was found to be a low abundant protein, which is expressed in fermentable and non-fermentable growth conditions. Endogenous Sc TAR1 transcripts were also found low abundant and consistently 5′ flanking regions of TAR1 ORF exhibit modest promoter activity when assayed in a luciferase-reporter system. Using rapid amplification of cDNA ends (RACE) PCR, we also determined that endogenous Sc TAR1 transcripts possess heterogeneous 5′ and 3′ ends probably reflecting the complex expression of a gene embedded in actively transcribed rDNA sequence. Altogether, our results definitively ascertain that the antisense yeast gene TAR1 constitutes a functional transcription unit within the nuclear rDNA repeats.
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25
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Current awareness on yeast. Yeast 2009. [DOI: 10.1002/yea.1618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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