1
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Wacholder A, Parikh SB, Coelho NC, Acar O, Houghton C, Chou L, Carvunis AR. A vast evolutionarily transient translatome contributes to phenotype and fitness. Cell Syst 2023; 14:363-381.e8. [PMID: 37164009 PMCID: PMC10348077 DOI: 10.1016/j.cels.2023.04.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 01/30/2023] [Accepted: 04/06/2023] [Indexed: 05/12/2023]
Abstract
Translation is the process by which ribosomes synthesize proteins. Ribosome profiling recently revealed that many short sequences previously thought to be noncoding are pervasively translated. To identify protein-coding genes in this noncanonical translatome, we combine an integrative framework for extremely sensitive ribosome profiling analysis, iRibo, with high-powered selection inferences tailored for short sequences. We construct a reference translatome for Saccharomyces cerevisiae comprising 5,400 canonical and almost 19,000 noncanonical translated elements. Only 14 noncanonical elements were evolving under detectable purifying selection. A representative subset of translated elements lacking signatures of selection demonstrated involvement in processes including DNA repair, stress response, and post-transcriptional regulation. Our results suggest that most translated elements are not conserved protein-coding genes and contribute to genotype-phenotype relationships through fast-evolving molecular mechanisms.
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Affiliation(s)
- Aaron Wacholder
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Saurin Bipin Parikh
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Integrative Systems Biology Program, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Nelson Castilho Coelho
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Omer Acar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Joint CMU-Pitt PhD Program in Computational Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Carly Houghton
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Joint CMU-Pitt PhD Program in Computational Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Lin Chou
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Integrative Systems Biology Program, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Anne-Ruxandra Carvunis
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA.
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2
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Sing TL, Brar GA, Ünal E. Gametogenesis: Exploring an Endogenous Rejuvenation Program to Understand Cellular Aging and Quality Control. Annu Rev Genet 2022; 56:89-112. [PMID: 35878627 PMCID: PMC9712276 DOI: 10.1146/annurev-genet-080320-025104] [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: 01/07/2023]
Abstract
Gametogenesis is a conserved developmental program whereby a diploid progenitor cell differentiates into haploid gametes, the precursors for sexually reproducing organisms. In addition to ploidy reduction and extensive organelle remodeling, gametogenesis naturally rejuvenates the ensuing gametes, leading to resetting of life span. Excitingly, ectopic expression of the gametogenesis-specific transcription factor Ndt80 is sufficient to extend life span in mitotically dividing budding yeast, suggesting that meiotic rejuvenation pathways can be repurposed outside of their natural context. In this review, we highlight recent studies of gametogenesis that provide emerging insight into natural quality control, organelle remodeling, and rejuvenation strategies that exist within a cell. These include selective inheritance, programmed degradation, and de novo synthesis, all of which are governed by the meiotic gene expression program entailing many forms of noncanonical gene regulation. Finally, we highlight critical questions that remain in the field and provide perspective on the implications of gametogenesis research on human health span.
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Affiliation(s)
- Tina L Sing
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA;
| | - Gloria A Brar
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA;
| | - Elçin Ünal
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA;
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3
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Oliver SG. From Petri Plates to Petri Nets, a revolution in yeast biology. FEMS Yeast Res 2022; 22:6526310. [PMID: 35142857 PMCID: PMC8862034 DOI: 10.1093/femsyr/foac008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 01/26/2022] [Accepted: 02/07/2022] [Indexed: 11/22/2022] Open
Affiliation(s)
- Stephen G Oliver
- Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK
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4
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Weidenbach K, Gutt M, Cassidy L, Chibani C, Schmitz RA. Small Proteins in Archaea, a Mainly Unexplored World. J Bacteriol 2022; 204:e0031321. [PMID: 34543104 PMCID: PMC8765429 DOI: 10.1128/jb.00313-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
In recent years, increasing numbers of small proteins have moved into the focus of science. Small proteins have been identified and characterized in all three domains of life, but the majority remains functionally uncharacterized, lack secondary structure, and exhibit limited evolutionary conservation. While quite a few have already been described for bacteria and eukaryotic organisms, the amount of known and functionally analyzed archaeal small proteins is still very limited. In this review, we compile the current state of research, show strategies for systematic approaches for global identification of small archaeal proteins, and address selected functionally characterized examples. Besides, we document exemplarily for one archaeon the tool development and optimization to identify small proteins using genome-wide approaches.
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Affiliation(s)
- Katrin Weidenbach
- Institute for General Microbiology, Christian Albrechts University, Kiel, Germany
| | - Miriam Gutt
- Institute for General Microbiology, Christian Albrechts University, Kiel, Germany
| | - Liam Cassidy
- AG Proteomics & Bioanalytics, Institute for Experimental Medicine, Christian Albrechts University, Kiel, Germany
| | - Cynthia Chibani
- Institute for General Microbiology, Christian Albrechts University, Kiel, Germany
| | - Ruth A. Schmitz
- Institute for General Microbiology, Christian Albrechts University, Kiel, Germany
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5
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Bouwknegt J, Koster CC, Vos AM, Ortiz-Merino RA, Wassink M, Luttik MAH, van den Broek M, Hagedoorn PL, Pronk JT. Class-II dihydroorotate dehydrogenases from three phylogenetically distant fungi support anaerobic pyrimidine biosynthesis. Fungal Biol Biotechnol 2021; 8:10. [PMID: 34656184 PMCID: PMC8520639 DOI: 10.1186/s40694-021-00117-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 10/02/2021] [Indexed: 11/10/2022] Open
Abstract
Background In most fungi, quinone-dependent Class-II dihydroorotate dehydrogenases (DHODs) are essential for pyrimidine biosynthesis. Coupling of these Class-II DHODHs to mitochondrial respiration makes their in vivo activity dependent on oxygen availability. Saccharomyces cerevisiae and closely related yeast species harbor a cytosolic Class-I DHOD (Ura1) that uses fumarate as electron acceptor and thereby enables anaerobic pyrimidine synthesis. Here, we investigate DHODs from three fungi (the Neocallimastigomycete Anaeromyces robustus and the yeasts Schizosaccharomyces japonicus and Dekkera bruxellensis) that can grow anaerobically but, based on genome analysis, only harbor a Class-II DHOD. Results Heterologous expression of putative Class-II DHOD-encoding genes from fungi capable of anaerobic, pyrimidine-prototrophic growth (Arura9, SjURA9, DbURA9) in an S. cerevisiae ura1Δ strain supported aerobic as well as anaerobic pyrimidine prototrophy. A strain expressing DbURA9 showed delayed anaerobic growth without pyrimidine supplementation. Adapted faster growing DbURA9-expressing strains showed mutations in FUM1, which encodes fumarase. GFP-tagged SjUra9 and DbUra9 were localized to S. cerevisiae mitochondria, while ArUra9, whose sequence lacked a mitochondrial targeting sequence, was localized to the yeast cytosol. Experiments with cell extracts showed that ArUra9 used free FAD and FMN as electron acceptors. Expression of SjURA9 in S. cerevisiae reproducibly led to loss of respiratory competence and mitochondrial DNA. A cysteine residue (C265 in SjUra9) in the active sites of all three anaerobically active Ura9 orthologs was shown to be essential for anaerobic activity of SjUra9 but not of ArUra9. Conclusions Activity of fungal Class-II DHODs was long thought to be dependent on an active respiratory chain, which in most fungi requires the presence of oxygen. By heterologous expression experiments in S. cerevisiae, this study shows that phylogenetically distant fungi independently evolved Class-II dihydroorotate dehydrogenases that enable anaerobic pyrimidine biosynthesis. Further structure–function studies are required to understand the mechanistic basis for the anaerobic activity of Class-II DHODs and an observed loss of respiratory competence in S. cerevisiae strains expressing an anaerobically active DHOD from Sch. japonicus. Supplementary Information The online version contains supplementary material available at 10.1186/s40694-021-00117-4.
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Affiliation(s)
- Jonna Bouwknegt
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Charlotte C Koster
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Aurin M Vos
- Wageningen Plant Research, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Raúl A Ortiz-Merino
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Mats Wassink
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Marijke A H Luttik
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Marcel van den Broek
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Peter L Hagedoorn
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands.
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6
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Tharakan R, Sawa A. Minireview: Novel Micropeptide Discovery by Proteomics and Deep Sequencing Methods. Front Genet 2021; 12:651485. [PMID: 34025718 PMCID: PMC8136307 DOI: 10.3389/fgene.2021.651485] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 03/22/2021] [Indexed: 12/12/2022] Open
Abstract
A novel class of small proteins, called micropeptides, has recently been discovered in the genome. These proteins, which have been found to play important roles in many physiological and cellular systems, are shorter than 100 amino acids and were overlooked during previous genome annotations. Discovery and characterization of more micropeptides has been ongoing, often using -omics methods such as proteomics, RNA sequencing, and ribosome profiling. In this review, we survey the recent advances in the micropeptides field and describe the methodological and conceptual challenges facing future micropeptide endeavors.
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Affiliation(s)
- Ravi Tharakan
- National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Akira Sawa
- Departments of Psychiatry, Neuroscience, Biomedical Engineering, and Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States.,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
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7
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Petruschke H, Anders J, Stadler PF, Jehmlich N, von Bergen M. Enrichment and identification of small proteins in a simplified human gut microbiome. J Proteomics 2020; 213:103604. [DOI: 10.1016/j.jprot.2019.103604] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/22/2019] [Accepted: 12/07/2019] [Indexed: 02/06/2023]
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8
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Martinez TF, Chu Q, Donaldson C, Tan D, Shokhirev MN, Saghatelian A. Accurate annotation of human protein-coding small open reading frames. Nat Chem Biol 2019; 16:458-468. [PMID: 31819274 PMCID: PMC7085969 DOI: 10.1038/s41589-019-0425-0] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 11/01/2019] [Indexed: 12/13/2022]
Abstract
Functional protein-coding small open reading frames (smORFs) are emerging as an important class of genes. However, the number of translated smORFs in the human genome is unclear because proteogenomic methods are not sensitive enough, and, as we show, Ribo-Seq strategies require additional measures to ensure comprehensive and accurate smORF annotation. Here, we integrate de novo transcriptome assembly and Ribo-Seq into an improved workflow that overcomes obstacles with previous methods to more confidently annotate thousands of smORFs. Evolutionary conservation analyses suggest that hundreds of smORF-encoded microproteins are likely functional. Additionally, many smORFs are regulated during fundamental biological processes, such as cell stress. Peptides derived from smORFs are also detectable on human leukocyte antigen complexes, revealing smORFs as a source of antigens. Thus, by including additional validation into our smORF annotation workflow, we accurately identify thousands of unannotated translated smORFs that will provide a rich pool of unexplored, functional human genes.
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Affiliation(s)
- Thomas F Martinez
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA.
| | - Qian Chu
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Cynthia Donaldson
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Dan Tan
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Maxim N Shokhirev
- Razavi Newman Integrative Genomics Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA.
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9
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Dujon B. My route to the intimacy of genomes. FEMS Yeast Res 2019; 19:5371124. [PMID: 30844063 DOI: 10.1093/femsyr/foz023] [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: 03/04/2019] [Accepted: 03/06/2019] [Indexed: 11/12/2022] Open
Abstract
Being invited by a prestigious journal to write the retrospective of one's life is first a great honor, and then a chore when starting to do it. These feelings did not spare me. But trying to recall my past to the best of my memory, I learned how lucky I was to have been born to a generation that witnessed so many scientific discoveries. There is little in common between the genetic courses I taught recently and those that I received more than 50 years ago. Thinking that a tiny bit of this fantastic evolution might come from my accidental encountering with yeasts is a stunning experience. I wish the same for the new generation.
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Affiliation(s)
- Bernard Dujon
- Department Genomes and Genetics, Institut Pasteur, CNRS (UMR3525) and Sorbonne Université (UFR927), 25 rue du Docteur Roux, Paris F-78724 , France
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10
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Mat-Sharani S, Firdaus-Raih M. Computational discovery and annotation of conserved small open reading frames in fungal genomes. BMC Bioinformatics 2019; 19:551. [PMID: 30717662 PMCID: PMC7394265 DOI: 10.1186/s12859-018-2550-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 11/30/2018] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Small open reading frames (smORF/sORFs) that encode short protein sequences are often overlooked during the standard gene prediction process thus leading to many sORFs being left undiscovered and/or misannotated. For many genomes, a second round of sORF targeted gene prediction can complement the existing annotation. In this study, we specifically targeted the identification of ORFs encoding for 80 amino acid residues or less from 31 fungal genomes. We then compared the predicted sORFs and analysed those that are highly conserved among the genomes. RESULTS A first set of sORFs was identified from existing annotations that fitted the maximum of 80 residues criterion. A second set was predicted using parameters that specifically searched for ORF candidates of 80 codons or less in the exonic, intronic and intergenic sequences of the subject genomes. A total of 1986 conserved sORFs were predicted and characterized. CONCLUSIONS It is evident that numerous open reading frames that could potentially encode for polypeptides consisting of 80 amino acid residues or less are overlooked during standard gene prediction and annotation. From our results, additional targeted reannotation of genomes is clearly able to complement standard genome annotation to identify sORFs. Due to the lack of, and limitations with experimental validation, we propose that a simple conservation analysis can provide an acceptable means of ensuring that the predicted sORFs are sufficiently clear of gene prediction artefacts.
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Affiliation(s)
- Shuhaila Mat-Sharani
- Centre for Frontier Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM, 43600, Bangi, Selangor, Malaysia.,Malaysia Genome Institute, Ministry of Science, Technology & Innovation, Jalan Bangi, 43000, Kajang, Selangor, Malaysia
| | - Mohd Firdaus-Raih
- Centre for Frontier Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM, 43600, Bangi, Selangor, Malaysia. .,Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM, 43600, Bangi, Selangor, Malaysia.
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11
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Erpf PE, Fraser JA. The Long History of the Diverse Roles of Short ORFs: sPEPs in Fungi. Proteomics 2018; 18:e1700219. [PMID: 29465163 DOI: 10.1002/pmic.201700219] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 01/30/2018] [Indexed: 12/30/2022]
Abstract
Since the completion of the genome sequence of the model eukaryote Saccharomyces cerevisiae, there have been significant advancements in the field of genome annotation, in no small part due to the availability of datasets that make large-scale comparative analyses possible. As a result, since its completion there has been a significant change in annotated ORF size distribution in this first eukaryotic genome, especially in short ORFs (sORFs) predicted to encode polypeptides less than 150 amino acids in length. Due to their small size and the difficulties associated with their study, it is only relatively recently that these genomic features and the sORF-encoded peptides (sPEPs) they encode have become a focus of many researchers. Yet while this class of peptides may seem new and exciting, the study of this part of the proteome is nothing new in S. cerevisiae, a species where the biological importance of sPEPs has been elegantly illustrated over the past 30 years. Here the authors showcase a range of different sORFs found in S. cerevisiae and the diverse biological roles of their encoded sPEPs, and provide an insight into the sORFs found in other fungal species, particularly those pathogenic to humans.
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Affiliation(s)
- Paige E Erpf
- Australian Infectious Diseases Research Centre, St Lucia, Queensland, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - James A Fraser
- Australian Infectious Diseases Research Centre, St Lucia, Queensland, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
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12
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New Peptides Under the s(ORF)ace of the Genome. Trends Biochem Sci 2016; 41:665-678. [DOI: 10.1016/j.tibs.2016.05.003] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 04/28/2016] [Accepted: 05/03/2016] [Indexed: 01/30/2023]
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13
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Emmanouilidis L, Gopalswamy M, Passon DM, Wilmanns M, Sattler M. Structural biology of the import pathways of peroxisomal matrix proteins. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:804-13. [DOI: 10.1016/j.bbamcr.2015.09.034] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 09/29/2015] [Accepted: 09/30/2015] [Indexed: 11/28/2022]
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14
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Dujon B. Basic principles of yeast genomics, a personal recollection: Graphical Abstract Figure. FEMS Yeast Res 2015; 15:fov047. [DOI: 10.1093/femsyr/fov047] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2015] [Indexed: 12/12/2022] Open
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15
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Engel SR, Dietrich FS, Fisk DG, Binkley G, Balakrishnan R, Costanzo MC, Dwight SS, Hitz BC, Karra K, Nash RS, Weng S, Wong ED, Lloyd P, Skrzypek MS, Miyasato SR, Simison M, Cherry JM. The reference genome sequence of Saccharomyces cerevisiae: then and now. G3 (BETHESDA, MD.) 2014; 4:389-98. [PMID: 24374639 PMCID: PMC3962479 DOI: 10.1534/g3.113.008995] [Citation(s) in RCA: 247] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 12/21/2013] [Indexed: 11/18/2022]
Abstract
The genome of the budding yeast Saccharomyces cerevisiae was the first completely sequenced from a eukaryote. It was released in 1996 as the work of a worldwide effort of hundreds of researchers. In the time since, the yeast genome has been intensively studied by geneticists, molecular biologists, and computational scientists all over the world. Maintenance and annotation of the genome sequence have long been provided by the Saccharomyces Genome Database, one of the original model organism databases. To deepen our understanding of the eukaryotic genome, the S. cerevisiae strain S288C reference genome sequence was updated recently in its first major update since 1996. The new version, called "S288C 2010," was determined from a single yeast colony using modern sequencing technologies and serves as the anchor for further innovations in yeast genomic science.
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Affiliation(s)
- Stacia R. Engel
- Department of Genetics, Stanford University, Stanford, California 94305
| | - Fred S. Dietrich
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina 27710
| | - Dianna G. Fisk
- Department of Genetics, Stanford University, Stanford, California 94305
| | - Gail Binkley
- Department of Genetics, Stanford University, Stanford, California 94305
| | - Rama Balakrishnan
- Department of Genetics, Stanford University, Stanford, California 94305
| | - Maria C. Costanzo
- Department of Genetics, Stanford University, Stanford, California 94305
| | - Selina S. Dwight
- Department of Genetics, Stanford University, Stanford, California 94305
| | - Benjamin C. Hitz
- Department of Genetics, Stanford University, Stanford, California 94305
| | - Kalpana Karra
- Department of Genetics, Stanford University, Stanford, California 94305
| | - Robert S. Nash
- Department of Genetics, Stanford University, Stanford, California 94305
| | - Shuai Weng
- Department of Genetics, Stanford University, Stanford, California 94305
| | - Edith D. Wong
- Department of Genetics, Stanford University, Stanford, California 94305
| | - Paul Lloyd
- Department of Genetics, Stanford University, Stanford, California 94305
| | - Marek S. Skrzypek
- Department of Genetics, Stanford University, Stanford, California 94305
| | | | - Matt Simison
- Department of Genetics, Stanford University, Stanford, California 94305
| | - J. Michael Cherry
- Department of Genetics, Stanford University, Stanford, California 94305
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16
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Su M, Ling Y, Yu J, Wu J, Xiao J. Small proteins: untapped area of potential biological importance. Front Genet 2013; 4:286. [PMID: 24379829 PMCID: PMC3864261 DOI: 10.3389/fgene.2013.00286] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 11/27/2013] [Indexed: 01/13/2023] Open
Abstract
Polypeptides containing ≤100 amino acid residues (AAs) are generally considered to be small proteins (SPs). Many studies have shown that some SPs are involved in important biological processes, including cell signaling, metabolism, and growth. SP generally has a simple domain and has an advantage to be used as model system to overcome folding speed limits in protein folding simulation and drug design. But SPs were once thought to be trivial molecules in biological processes compared to large proteins. Because of the constraints of experimental methods and bioinformatics analysis, many genome projects have used a length threshold of 100 amino acid residues to minimize erroneous predictions and SPs are relatively under-represented in earlier studies. The general protein discovery methods have potential problems to predict and validate SPs, and very few effective tools and algorithms were developed specially for SPs identification. In this review, we mainly consider the diverse strategies applied to SPs prediction and discuss the challenge for differentiate SP coding genes from artifacts. We also summarize current large-scale discovery of SPs in species at the genome level. In addition, we present an overview of SPs with regard to biological significance, structural application, and evolution characterization in an effort to gain insight into the significance of SPs.
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Affiliation(s)
- Mingming Su
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences Beijing, China ; Graduate University of Chinese Academy of Sciences Beijing, China
| | - Yunchao Ling
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences Beijing, China ; Graduate University of Chinese Academy of Sciences Beijing, China
| | - Jun Yu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences Beijing, China
| | - Jiayan Wu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences Beijing, China
| | - Jingfa Xiao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences Beijing, China
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17
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Mandrioli M, Manicardi GC. Unlocking holocentric chromosomes: new perspectives from comparative and functional genomics? Curr Genomics 2013; 13:343-9. [PMID: 23372420 PMCID: PMC3401891 DOI: 10.2174/138920212801619250] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 05/11/2012] [Accepted: 05/17/2012] [Indexed: 12/30/2022] Open
Abstract
The presence of chromosomes with diffuse centromeres (holocentric chromosomes) has been reported in several taxa since more than fifty years, but a full understanding of their origin is still lacking. Comparative and functional genomics are nowadays furnishing new data to better understand holocentric chromosome evolution thus opening new perspectives to analyse karyotype rearrangements in species with holocentric chromosomes in particular evidencing unusual common features, such as the uniform GC content and gene distribution along chromosomes.
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Affiliation(s)
- Mauro Mandrioli
- Dipartimento di Biologia, Università di Modena e Reggio Emilia, Via Campi 213/D, Modena, Italy
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Agier N, Fischer G. The Mutational Profile of the Yeast Genome Is Shaped by Replication. Mol Biol Evol 2011; 29:905-13. [DOI: 10.1093/molbev/msr280] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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Luo L, Li H, Zhang L. ORF organization and gene recognition in the yeast genome. Comp Funct Genomics 2010; 4:318-28. [PMID: 18629282 PMCID: PMC2448446 DOI: 10.1002/cfg.292] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2002] [Revised: 03/03/2003] [Accepted: 03/10/2003] [Indexed: 11/10/2022] Open
Abstract
Some rules on gene recognition and ORF organization in the Saccharomyces cerevisiae genome are demonstrated by statistical analyses of sequence data. This study includes: (a) The random frame rule-that the six reading frames W1, W2, W3, C1, C2 and C3 in the double-stranded genome are randomly occupied by ORFs (related phenomena on ORF overlapping are also discussed). (b) The inhomogeneity rule-coding and non-coding ORFs differ in inhomogeneity of base composition in the three codon positions. By use of the inhomogeneity index (IHI), one can make a distinction between coding (IHI > 14) and non-coding (IHI < or = 14) ORFs at 95% accuracy. We find that 'spurious' ORFs (with IHI < or = 14) are distributed mainly in three classes of ORFs, namely, those with 'similarity to unknown proteins', those with 'no similarity', or 'questionable ORFs'. The total number of spurious ORFs (which are unlikely to be regarded as coding ORFs) is estimated to be 470. (c) The evaluation of ORF length distribution shows that below 200 amino acids the occurrence of ATG initiator ORFs is close to random.
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Affiliation(s)
- Liaofu Luo
- Laboratory of Theoretical Biophysics, Faculty of Science and Technology, Inner Mongolia University, Hohhot 010021, China
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Richard GF, Kerrest A, Dujon B. Comparative genomics and molecular dynamics of DNA repeats in eukaryotes. Microbiol Mol Biol Rev 2008; 72:686-727. [PMID: 19052325 PMCID: PMC2593564 DOI: 10.1128/mmbr.00011-08] [Citation(s) in RCA: 323] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Repeated elements can be widely abundant in eukaryotic genomes, composing more than 50% of the human genome, for example. It is possible to classify repeated sequences into two large families, "tandem repeats" and "dispersed repeats." Each of these two families can be itself divided into subfamilies. Dispersed repeats contain transposons, tRNA genes, and gene paralogues, whereas tandem repeats contain gene tandems, ribosomal DNA repeat arrays, and satellite DNA, itself subdivided into satellites, minisatellites, and microsatellites. Remarkably, the molecular mechanisms that create and propagate dispersed and tandem repeats are specific to each class and usually do not overlap. In the present review, we have chosen in the first section to describe the nature and distribution of dispersed and tandem repeats in eukaryotic genomes in the light of complete (or nearly complete) available genome sequences. In the second part, we focus on the molecular mechanisms responsible for the fast evolution of two specific classes of tandem repeats: minisatellites and microsatellites. Given that a growing number of human neurological disorders involve the expansion of a particular class of microsatellites, called trinucleotide repeats, a large part of the recent experimental work on microsatellites has focused on these particular repeats, and thus we also review the current knowledge in this area. Finally, we propose a unified definition for mini- and microsatellites that takes into account their biological properties and try to point out new directions that should be explored in a near future on our road to understanding the genetics of repeated sequences.
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Affiliation(s)
- Guy-Franck Richard
- Institut Pasteur, Unité de Génétique Moléculaire des Levures, CNRS, URA2171, Université Pierre et Marie Curie, UFR927, 25 rue du Dr. Roux, F-75015, Paris, France.
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21
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Biochemistry and molecular biology in Portugal: An overview of past and current contributions. IUBMB Life 2008; 60:265-9. [DOI: 10.1002/iub.65] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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22
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Thireos G, Panayotou G, Thanos D. Biochemistry and molecular biology research achievements in Greece. IUBMB Life 2008; 60:254-7. [DOI: 10.1002/iub.64] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Guarraia C, Norris L, Raman A, Farabaugh PJ. Saturation mutagenesis of a +1 programmed frameshift-inducing mRNA sequence derived from a yeast retrotransposon. RNA (NEW YORK, N.Y.) 2007; 13:1940-7. [PMID: 17881742 PMCID: PMC2040094 DOI: 10.1261/rna.735107] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Errors during the process of translating mRNA information into protein products occur infrequently. Frameshift errors occur less frequently than other types of errors, suggesting that the translational machinery has more robust mechanisms for precluding that kind of error. Despite these mechanisms, mRNA sequences have evolved that increase the frequency up to 10,000-fold. These sequences, termed programmed frameshift sites, usually consist of a heptameric nucleotide sequence, at which the change in frames occurs along with additional sequences that stimulate the efficiency of frameshifting. One such stimulatory site derived from the Ty3 retrotransposon of the yeast Saccharomyces cerevisiae (the Ty3 stimulator) comprises a 14 nucleotide sequence with partial complementarity to a Helix 18 of the 18S rRNA, a component of the ribosome's accuracy center. A model for the function of the Ty3 stimulator predicts that it base pairs with Helix 18, reducing the efficiency with which the ribosome rejects erroneous out of frame decoding. We have tested this model by making a saturating set of single-base mutations of the Ty3 stimulator. The phenotypes of these mutations are inconsistent with the Helix 18 base-pairing model. We discuss the phenotypes of these mutations in light of structural data on the path of the mRNA on the ribosome, suggesting that the true target of the Ty3 stimulator may be rRNA and ribosomal protein elements of the ribosomal entry tunnel, as well as unknown constituents of the solvent face of the 40S subunit.
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Affiliation(s)
- Carla Guarraia
- Department of Biological Sciences and Chemistry/Biology Interface Program, University of Maryland Baltimore County, Baltimore, MD 21250, USA
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24
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Díaz-Castillo C, Golic KG. Evolution of gene sequence in response to chromosomal location. Genetics 2007; 177:359-74. [PMID: 17890366 PMCID: PMC2013720 DOI: 10.1534/genetics.107.077081] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2007] [Accepted: 06/06/2007] [Indexed: 12/26/2022] Open
Abstract
Evolutionary forces acting on the repetitive DNA of heterochromatin are not constrained by the same considerations that apply to protein-coding genes. Consequently, such sequences are subject to rapid evolutionary change. By examining the Troponin C gene family of Drosophila melanogaster, which has euchromatic and heterochromatic members, we find that protein-coding genes also evolve in response to their chromosomal location. The heterochromatic members of the family show a reduced CG content and increased variation in DNA sequence. We show that the CG reduction applies broadly to the protein-coding sequences of genes located at the heterochromatin:euchromatin interface, with a very strong correlation between CG content and the distance from centric heterochromatin. We also observe a similar trend in the transition from telomeric heterochromatin to euchromatin. We propose that the methylation of DNA is one of the forces driving this sequence evolution.
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Gaziova I, Bhat KM. Generating asymmetry: with and without self-renewal. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2007; 45:143-78. [PMID: 17585500 DOI: 10.1007/978-3-540-69161-7_7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
At some point during the history of organismal evolution, unicellular, unipotent and mitotically active cells acquired an ability to undergo a special type of cell division called asymmetric division. By this special type of cell division, these cells could divide to generate two different progeny or to self-renew and at the same time generate a progeny that is committed to become a cell different from the mother cell. This type of cell division, which forms the basis for the functioning of totipotent or multipotent stem cells, underlies the fundamental basis for the developmental evolution of organisms. It is not clear if the asymmetric division without self-renewal preceded the asymmetric division with self-renewal. It is reasonable to assume that the asymmetric division without self-renewal preceded the asymmetric division with self-renewal. In this review we explore the genetic regulation of these two types of asymmetric divisions using the Drosophila central nervous system (CNS) as a model system. The results from recent studies argue that for cells to undergo a self-renewing asymmetric division, certain "stem cell" proteins must be maintained or up-regulated, while genes encoding proteins responsible for differentiation must be repressed or down-regulated. As long as a balance between these two classes of proteins is maintained via asymmetric segregation and activation/repression, the progeny that receives stem cell proteins/maintains stem cell competence will have the potential to undergo self-renewing asymmetric division. The other progeny will commit to differentiate. In non-self-renewing asymmetric division, down-regulation of stem cell proteins/competence combined with asymmetric segregation of cell identity specifying factors (either cell-autonomous or a combination of cell autonomous and non-cell autonomous signals) cause the two progeny to assume different differentiated identities. Identification of mutations that confer a stem cell type of division to nonstem cell precursors, or mutations that eliminate asymmetric division, has led the way in elucidating the molecular basis for these divisions. Given that there is a considerable degree of conservation of genes and their function, these studies should provide clear insight into how the self-renewing asymmetric division of stem cells in neural and other lineages is regulated not only in Drosophila but also in vertebrates including humans.
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Affiliation(s)
- Ivana Gaziova
- Department of Neuroscience and Cell Biology, University of Texas Medical Branch School of Medicine, Galveston, Texas 77555, USA
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Qian J, Lin J, Zack DJ. Characterization of binding sites of eukaryotic transcription factors. GENOMICS PROTEOMICS & BIOINFORMATICS 2006; 4:67-79. [PMID: 16970547 PMCID: PMC5054036 DOI: 10.1016/s1672-0229(06)60019-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
To explore the nature of eukaryotic transcription factor (TF) binding sites and determine how they differ from surrounding DNA sequences, we examined four features associated with DNA binding sites: G+C content, pattern complexity, palindromic structure, and Markov sequence ordering. Our analysis of the regulatory motifs obtained from the TRANSFAC database, using yeast intergenic sequences as background, revealed that these four features show variable enrichment in motif sequences. For example, motif sequences were more likely to have palindromic structure than were background sequences. In addition, these features were tightly localized to the regulatory motifs, indicating that they are a property of the motif sequences themselves and are not shared by the general promoter “environment” in which the regulatory motifs reside. By breaking down the motif sequences according to the TF classes to which they bind, more specific associations were identified. Finally, we found that some correlations, such as G+C content enrichment, were species-specific, while others, such as complexity enrichment, were universal across the species examined. The quantitative analysis provided here should increase our understanding of protein-DNA interactions and also help facilitate the discovery of regulatory motifs through bioinformatics.
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Affiliation(s)
- Jiang Qian
- The Wilmer Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
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Panda SP, Gao YT, Roman LJ, Martásek P, Salerno JC, Masters BSS. The role of a conserved serine residue within hydrogen bonding distance of FAD in redox properties and the modulation of catalysis by Ca2+/calmodulin of constitutive nitric-oxide synthases. J Biol Chem 2006; 281:34246-57. [PMID: 16966328 DOI: 10.1074/jbc.m601041200] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The crystal structure of the neuronal nitric-oxide synthase (nNOS) NADPH/FAD binding domain indicated that Ser-1176 is within hydrogen bonding distance of Asp-1393 and the O4 atom of FAD and is also near the N5 atom of FAD (3.7 A). This serine residue is conserved in most of the ferredoxin-NADP+ reductase family of proteins and is important in electron transfer. In the present study, the homologous serines of both nNOS (Ser-1176) and endothelial nitric-oxide synthase (eNOS) (Ser-942) were mutated to threonine and alanine. Both substitutions yielded proteins that exhibited decreased rates of electron transfer through the flavin domains, in the presence and absence of Ca2+/CaM, as measured by reduction of potassium ferricyanide and cytochrome c. Rapid kinetics measurements of flavin reduction of all the mutants also showed a decrease in the rate of flavin reduction, in the absence and presence of Ca2+/CaM, as compared with the wild type proteins. The serine to alanine substitution caused both nNOS and eNOS to synthesize NO more slowly; however, the threonine mutants gave equal or slightly higher rates of NO production compared with the wild type enzymes. The midpoint redox potential measurements of all the redox centers revealed that wild type and threonine mutants of both nNOS and eNOS are very similar. However, the redox potentials of the FMN/FMNH* couple for alanine substitutions of both nNOS and eNOS are >100 mV higher than those of wild type proteins and are positive. These data presented here suggest that hydrogen bonding of the hydroxyl group of serine or threonine with the isoalloxazine ring of FAD and with the amino acids in its immediate milieu, particularly nNOS Asp-1393, affects the redox potentials of various flavin states, influencing the rate of electron transfer.
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Affiliation(s)
- Satya Prakash Panda
- Department of Biochemistry, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229-3900, USA
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Raman A, Guarraia C, Taliaferro D, Stahl G, Farabaugh PJ. An mRNA sequence derived from a programmed frameshifting signal decreases codon discrimination during translation initiation. RNA (NEW YORK, N.Y.) 2006; 12:1154-60. [PMID: 16682566 PMCID: PMC1484443 DOI: 10.1261/rna.13306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Sequences and structures in the mRNA can alter the accuracy of translation. In some cases, mRNA secondary structures like hairpin loops or pseudoknots can cause frequent errors of translational reading frame (programmed frameshifting) or misreading of termination codons as sense (nonsense readthrough). In other cases, the primary mRNA sequence stimulates the error probably by interacting with an element of the ribosome to interfere with error correction. One such primary mRNA sequence, the Ty3 stimulator, increases programmed +1 frameshifting 7.5 times in the yeast Saccharomyces cerevisiae. Here we show that this stimulator also increases the usage of non-AUG initiation codons in the bacterium Escherichia coli but not in S. cerevisiae. These data suggest that in E. coli, though not in yeast, an element of the ribosome's elongation accuracy mechanism ensures initiation accuracy.
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Baranov PV, Hammer AW, Zhou J, Gesteland RF, Atkins JF. Transcriptional slippage in bacteria: distribution in sequenced genomes and utilization in IS element gene expression. Genome Biol 2005; 6:R25. [PMID: 15774026 PMCID: PMC1088944 DOI: 10.1186/gb-2005-6-3-r25] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2004] [Revised: 12/16/2004] [Accepted: 01/25/2005] [Indexed: 11/13/2022] Open
Abstract
To find a length of slippage-prone sequences at which selection against transcriptional slippage is evident, the transcription of repetitive runs of A and T of different lengths in 108 bacterial genomes was analyzed. IS element genes were found to exploit transcriptional slippage for regulation of gene expression. Background Transcription slippage occurs on certain patterns of repeat mononucleotides, resulting in synthesis of a heterogeneous population of mRNAs. Individual mRNA molecules within this population differ in the number of nucleotides they contain that are not specified by the template. When transcriptional slippage occurs in a coding sequence, translation of the resulting mRNAs yields more than one protein product. Except where the products of the resulting mRNAs have distinct functions, transcription slippage occurring in a coding region is expected to be disadvantageous. This probably leads to selection against most slippage-prone sequences in coding regions. Results To find a length at which such selection is evident, we analyzed the distribution of repetitive runs of A and T of different lengths in 108 bacterial genomes. This length varies significantly among different bacteria, but in a large proportion of available genomes corresponds to nine nucleotides. Comparative sequence analysis of these genomes was used to identify occurrences of 9A and 9T transcriptional slippage-prone sequences used for gene expression. Conclusions IS element genes are the largest group found to exploit this phenomenon. A number of genes with disrupted open reading frames (ORFs) have slippage-prone sequences at which transcriptional slippage would result in uninterrupted ORF restoration at the mRNA level. The ability of such genes to encode functional full-length protein products brings into question their annotation as pseudogenes and in these cases is pertinent to the significance of the term 'authentic frameshift' frequently assigned to such genes.
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Affiliation(s)
- Pavel V Baranov
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112-5330, USA
- Bioscience Institute, University College Cork, Cork, Ireland
| | - Andrew W Hammer
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112-5330, USA
| | - Jiadong Zhou
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112-5330, USA
- Current address: Gene Technology Division, Nitto Denko Technical Corporation, 401 Jones Road, Oceanside, CA 92054, USA
| | - Raymond F Gesteland
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112-5330, USA
| | - John F Atkins
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112-5330, USA
- Bioscience Institute, University College Cork, Cork, Ireland
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Hanzálek P, Kypr J. DNA in phosphorus atom representation: the heteronomous double helices of poly(dA).poly(dT) and poly(dG).poly(dC) and simulation of the yeast genome and of a human chromosome DNA. J Theor Biol 2004; 232:83-91. [PMID: 15498595 DOI: 10.1016/j.jtbi.2004.07.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2003] [Revised: 07/23/2004] [Accepted: 07/26/2004] [Indexed: 10/26/2022]
Abstract
We extracted phosphorus atom coordinates from the database of DNA crystal structures and calculated geometrical parameters needed to reproduce the crystal structures in the phosphorus atom representation. Using the geometrical parameters we wrote a piece of software assigning the phosphorus atom coordinates to the DNA of any nucleotide sequence. The software demonstrates non-negligible influence of the primary structure on DNA helicity, which may stand behind the heteromonous double helices of poly(dA).poly(dT) and poly(dG).poly(dC). In addition, the software is so simple that it makes possible to simulate the "crystal" structures of not only viral DNAs, but also the whole genome of Saccharomyces cerevisiae as well as the DNA human chromosome 22 having dozens of megabases in length.
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Affiliation(s)
- Petr Hanzálek
- Institute of Biophysics of the Academy of Sciences, of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic
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Stahl G, Salem SNB, Chen L, Zhao B, Farabaugh PJ. Translational accuracy during exponential, postdiauxic, and stationary growth phases in Saccharomyces cerevisiae. EUKARYOTIC CELL 2004; 3:331-8. [PMID: 15075263 PMCID: PMC387642 DOI: 10.1128/ec.3.2.331-338.2004] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
When the yeast Saccharomyces cerevisiae shifts from rapid growth on glucose to slow growth on ethanol, it undergoes profound changes in cellular metabolism, including the destruction of most of the translational machinery. We have examined the effect of this metabolic change, termed the diauxic shift, on the frequency of translational errors. Recoding sites are mRNA sequences that increase the frequency of translational errors, providing a convenient reporter of translational accuracy. We found that the diauxic shift causes no overall change in translational accuracy but does cause a strong reduction in the frequency of one type of programmed error: Ty +1 frameshifting. Genetic data suggest that this effect may be due to changes in the relative amounts of tRNA participating in translation elongation. We discuss possible implications for expression strategies that use recoding.
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Affiliation(s)
- Guillaume Stahl
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland 21250, USA.
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Mougel F, Manichanh C, Duchateau N'guyen G, Termier M. Genomic Choice of Codons in 16 Microbial Species. J Biomol Struct Dyn 2004; 22:315-29. [PMID: 15473705 DOI: 10.1080/07391102.2004.10507003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
We study the codon usage over whole set of ORFs of 16 unicellular microbial species: eight archaebacteria, seven eubacteria, and one eukarya. We first try to define, for each species, the neutral expected codon usage to better approach subsequently the influence of selection. Overlapping triplets counted from the complete DNA genomic sequence and mean amino acid composition of ORFs allow us to build satisfying expected codon usage for each species. Within species deviation from this neutral model is then studied through Correspondence Analysis and characterization with bias index, N(C)' (effective number of codons reported to neutral model). Our results are compared to previously published ones for three species and let appear good agreement in spite of very different methods. We thus propose set of codons probably preferred by selection for nine other species. In the four last species, no clear preference can be evidenced. Finally, we characterize variation of codon usage over functional categories. We propose that the high degree of bias of proteins involved in translation, ribosomal structure and biogenesis has a positive influence on overexpression of the corresponding genes under optimum growth conditions and is a negative regulator of the same genes when amino acids become limited resources.
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Affiliation(s)
- F Mougel
- Bioinformatique des Genomes, IGM, bat. 400, 91405 Orsay CEDEX, France
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Kellis M, Patterson N, Birren B, Berger B, Lander ES. Methods in comparative genomics: genome correspondence, gene identification and regulatory motif discovery. J Comput Biol 2004; 11:319-55. [PMID: 15285895 DOI: 10.1089/1066527041410319] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In Kellis et al. (2003), we reported the genome sequences of S. paradoxus, S. mikatae, and S. bayanus and compared these three yeast species to their close relative, S. cerevisiae. Genomewide comparative analysis allowed the identification of functionally important sequences, both coding and noncoding. In this companion paper we describe the mathematical and algorithmic results underpinning the analysis of these genomes. (1) We present methods for the automatic determination of genome correspondence. The algorithms enabled the automatic identification of orthologs for more than 90% of genes and intergenic regions across the four species despite the large number of duplicated genes in the yeast genome. The remaining ambiguities in the gene correspondence revealed recent gene family expansions in regions of rapid genomic change. (2) We present methods for the identification of protein-coding genes based on their patterns of nucleotide conservation across related species. We observed the pressure to conserve the reading frame of functional proteins and developed a test for gene identification with high sensitivity and specificity. We used this test to revisit the genome of S. cerevisiae, reducing the overall gene count by 500 genes (10% of previously annotated genes) and refining the gene structure of hundreds of genes. (3) We present novel methods for the systematic de novo identification of regulatory motifs. The methods do not rely on previous knowledge of gene function and in that way differ from the current literature on computational motif discovery. Based on genomewide conservation patterns of known motifs, we developed three conservation criteria that we used to discover novel motifs. We used an enumeration approach to select strongly conserved motif cores, which we extended and collapsed into a small number of candidate regulatory motifs. These include most previously known regulatory motifs as well as several noteworthy novel motifs. The majority of discovered motifs are enriched in functionally related genes, allowing us to infer a candidate function for novel motifs. Our results demonstrate the power of comparative genomics to further our understanding of any species. Our methods are validated by the extensive experimental knowledge in yeast and will be invaluable in the study of complex genomes like that of the human.
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Affiliation(s)
- Manolis Kellis
- Whitehead Institute Center for Genome Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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Yeast transport-ATPases and the genome-sequencing project. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/s0069-8032(04)43024-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Sorimachi K, Okayasu T. Gene assembly consisting of small units with similar amino acid composition in the Saccharomyces cerevisiae genome. MYCOSCIENCE 2003. [DOI: 10.1007/s10267-003-0131-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Talla E, Tekaia F, Brino L, Dujon B. A novel design of whole-genome microarray probes for Saccharomyces cerevisiae which minimizes cross-hybridization. BMC Genomics 2003; 4:38. [PMID: 14499002 PMCID: PMC239980 DOI: 10.1186/1471-2164-4-38] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2003] [Accepted: 09/22/2003] [Indexed: 12/19/2022] Open
Abstract
Background Numerous DNA microarray hybridization experiments have been performed in yeast over the last years using either synthetic oligonucleotides or PCR-amplified coding sequences as probes. The design and quality of the microarray probes are of critical importance for hybridization experiments as well as subsequent analysis of the data. Results We present here a novel design of Saccharomyces cerevisiae microarrays based on a refined annotation of the genome and with the aim of reducing cross-hybridization between related sequences. An effort was made to design probes of similar lengths, preferably located in the 3'-end of reading frames. The sequence of each gene was compared against the entire yeast genome and optimal sub-segments giving no predicted cross-hybridization were selected. A total of 5660 novel probes (more than 97% of the yeast genes) were designed. For the remaining 143 genes, cross-hybridization was unavoidable. Using a set of 18 deletant strains, we have experimentally validated our cross-hybridization procedure. Sensitivity, reproducibility and dynamic range of these new microarrays have been measured. Based on this experience, we have written a novel program to design long oligonucleotides for microarray hybridizations of complete genome sequences. Conclusions A validated procedure to predict cross-hybridization in microarray probe design was defined in this work. Subsequently, a novel Saccharomyces cerevisiae microarray (which minimizes cross-hybridization) was designed and constructed. Arrays are available at Eurogentec S. A. Finally, we propose a novel design program, OliD, which allows automatic oligonucleotide design for microarrays. The OliD program is available from authors.
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Affiliation(s)
- Emmanuel Talla
- Institut Pasteur, Unité de Génétique Moléculaire des Levures (URA 2171 CNRS, UFR 927 Université PM Curie), 25 rue du Docteur Roux, F-75724 Paris cedex 15, France
| | - Fredj Tekaia
- Institut Pasteur, Unité de Génétique Moléculaire des Levures (URA 2171 CNRS, UFR 927 Université PM Curie), 25 rue du Docteur Roux, F-75724 Paris cedex 15, France
| | - Laurent Brino
- Eurogentec s.a., Parc Scientifique du Sart Tilman, B-4102 Seraing, Belgium
| | - Bernard Dujon
- Institut Pasteur, Unité de Génétique Moléculaire des Levures (URA 2171 CNRS, UFR 927 Université PM Curie), 25 rue du Docteur Roux, F-75724 Paris cedex 15, France
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37
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Abstract
The notion of transmembrane electron transport is usually associated with mitochondria and chloroplasts. However, since the early 1970s, it has been known that this phenomenon also occurs at the level of the plasma membrane. Ever since, evidence has accumulated for the existence of a plethora of transplasma membrane electron transport enzymes. In this review, we discuss the various enzymes known, their molecular characteristics and their biological functions.
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Affiliation(s)
- Jennifer D Ly
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Melbourne, Victoria, Australia
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38
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Gueldry O, Lazard M, Delort F, Dauplais M, Grigoras I, Blanquet S, Plateau P. Ycf1p-dependent Hg(II) detoxification in Saccharomyces cerevisiae. EUROPEAN JOURNAL OF BIOCHEMISTRY 2003; 270:2486-96. [PMID: 12755704 DOI: 10.1046/j.1432-1033.2003.03620.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In Saccharomyces cerevisiae, disruption of the YCF1 gene increases the sensitivity of cell growth to mercury. Transformation of the resulting ycf1 null mutant with a plasmid harbouring YCF1 under the control of the GAL promoter largely restores the wild-type resistance to the metal ion. The protective effect of Ycf1p against the toxicity of mercury is especially pronounced when yeast cells are grown in rich medium or in minimal medium supplemented with glutathione. Secretory vesicles from S. cerevisiae cells overproducing Ycf1p are shown to exhibit ATP-dependent transport of bis(glutathionato)mercury. Moreover, using beta-galactosidase as a reporter protein, a relationship between mercury addition and the activity of the YCF1 promoter can be shown. Altogether, these observations indicate a defence mechanism involving an induction of the expression of Ycf1p and transport by this protein of mercury-glutathione adducts into the vacuole. Finally, possible coparticipation in mercury tolerance of other ABC proteins sharing close homology with Ycf1p was investigated. Gene disruption experiments enable us to conclude that neither Bpt1p, Yor1p, Ybt1p nor YHL035p plays a major role in the detoxification of mercury.
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Affiliation(s)
- Olivier Gueldry
- Laboratoire de Biochimie, Unité Mixte de Recherche CNRS-Ecole Polytechnique, Palaiseau, France
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39
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Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 2003; 423:241-54. [PMID: 12748633 DOI: 10.1038/nature01644] [Citation(s) in RCA: 1305] [Impact Index Per Article: 62.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2003] [Accepted: 04/01/2003] [Indexed: 11/09/2022]
Abstract
Identifying the functional elements encoded in a genome is one of the principal challenges in modern biology. Comparative genomics should offer a powerful, general approach. Here, we present a comparative analysis of the yeast Saccharomyces cerevisiae based on high-quality draft sequences of three related species (S. paradoxus, S. mikatae and S. bayanus). We first aligned the genomes and characterized their evolution, defining the regions and mechanisms of change. We then developed methods for direct identification of genes and regulatory motifs. The gene analysis yielded a major revision to the yeast gene catalogue, affecting approximately 15% of all genes and reducing the total count by about 500 genes. The motif analysis automatically identified 72 genome-wide elements, including most known regulatory motifs and numerous new motifs. We inferred a putative function for most of these motifs, and provided insights into their combinatorial interactions. The results have implications for genome analysis of diverse organisms, including the human.
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Affiliation(s)
- Manolis Kellis
- Whitehead/MIT Center for Genome Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA.
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40
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Ricchetti M, Dujon B, Fairhead C. Distance from the chromosome end determines the efficiency of double strand break repair in subtelomeres of haploid yeast. J Mol Biol 2003; 328:847-62. [PMID: 12729759 DOI: 10.1016/s0022-2836(03)00315-2] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Double strand break (DSB) repair plays an important role in chromosome evolution. We have investigated the fate of DSBs as a function of their location along the yeast chromosome XI, in a system where no conventional homologous recombination can occur. We report that the relative frequency of non-homologous endjoining (NHEJ), which is the exclusive mode of DSB repair in the internal chromosomal portion, decreases gradually towards the telomere, keeping the absolute frequency nearly constant, and that other repair mechanisms, which generally involve the loss of the distal chromosomal fragment, appear in subtelomeric regions. Distance of the DSB from chromosome ends plays a critical role in the global frequency of these repair mechanisms. Direct telomere additions are rare, and other events such as break-induced replication, plasmid incorporation, and gene conversion, involve acquisition of heterologous sequences. Therefore, in subtelomeric regions, cell survival to DSBs is higher and alternative modes of repair allow new genomic combinations to be generated. Furthermore, subtelomeric rearrangements depend on the recombination process, which, unexpectedly, also promotes the joining of heterologous sequences. Finally, we report that the Rad52 protein increases the efficiency of NHEJ.
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Affiliation(s)
- Miria Ricchetti
- Unité de Génétique Moléculaire des Levures, (UFR 927 Univ. P. et M. Curie and URA 2171 CNRS), Structure and Dynamics of Genomes Departement, Institut Pasteur, Paris, France.
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41
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Abstract
The genomes of most newly sequenced organisms contain a significant fraction of ORFs (open reading frames) that match no other sequence in the databases. We refer to these singleton ORFs as sequence ORFans. Because little can be learned about ORFans by homology, the origin and functions of ORFans remain a mystery. However, in this era of full genome sequencing, it seems that ORFans have been underemphasized. In this minireview, we draw attention to the increasing number of ORFans and to the consequences of this growth to biological research in the postgenomic era.
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Affiliation(s)
- Naomi Siew
- Department of Chemistry, Department of Computer Science, Ben Gurion University, Beer-Sheva 84105, Israel
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42
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O'Brian MR, Thöny-Meyer L. Biochemistry, regulation and genomics of haem biosynthesis in prokaryotes. Adv Microb Physiol 2002; 46:257-318. [PMID: 12073655 DOI: 10.1016/s0065-2911(02)46006-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Haems are involved in many cellular processes in prokaryotes and eukaryotes. The biosynthetic pathway leading to haem formation is, with few exceptions, well-conserved, and is controlled in accordance with cellular function. Here, we review the biosynthesis of haem and its regulation in prokaryotes. In addition, we focus on a modification of haem for cytochrome c biogenesis, a complex process that entails both transport between cellular compartments and a specific thioether linkage between the haem moiety and the apoprotein. Finally, a whole genome analysis from 63 prokaryotes indicates intriguing exceptions to the universality of the haem biosynthetic pathway and helps define new frontiers for future study.
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Affiliation(s)
- Mark R O'Brian
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY 14214, USA
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43
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Abstract
Recent localization of cohesin association regions along the yeast chromatin fibre suggests that compositional variability of DNA in yeast is related to the function and organization of the chromosomal loops. The bases of the loops, where the chromatin fibre is attached to the chromosomal axis, are AT-rich, bind cohesin, and are flanked by genes transcribed convergently. The hotspots of meiotic recombination are mainly found in the GC-rich parts of the loops, 'external' with respect to the chromosomal axis, frequently in the vicinity of the promoters of divergently transcribed genes. There are two possible reasons why the regions of the hotspots of recombination were enriched in GC content during evolution. One is a biased repair of recombination intermediates, and the second is a selective advantage due to an increased chromatin accessibility, which may have the carriers of GC-enriched alleles over the carriers of AT-rich alleles.
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Affiliation(s)
- Jan Filipski
- Institut J. Monod, Laboratoire de: Biochimie de la Chromatine, 2, place Jussieu, Tour 43, 75251, Paris, France.
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44
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Basrai MA, Hieter P. Transcriptome analysis of Saccharomyces cerevisiae using serial analysis of gene expression. Methods Enzymol 2002; 350:414-44. [PMID: 12073327 DOI: 10.1016/s0076-6879(02)50977-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Affiliation(s)
- Munira A Basrai
- Genetics Branch, National Cancer Institute, Bethesda, Maryland 20889, USA
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45
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Mackiewicz P, Kowalczuk M, Mackiewicz D, Nowicka A, Dudkiewicz M, Laszkiewicz A, Dudek MR, Cebrat S. How many protein-coding genes are there in the Saccharomyces cerevisiae genome? Yeast 2002; 19:619-29. [PMID: 11967832 DOI: 10.1002/yea.865] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
We have compared the results of estimations of the total number of protein-coding genes in the Saccharomyces cerevisiae genome, which have been obtained by many laboratories since the yeast genome sequence was published in 1996. We propose that there are 5300-5400 genes in the genome. This makes the first estimation of the number of intronless ORFs longer than 100 codons, based on the features of the set of genes with phenotypes known in 1997 to be correct. This estimation assumed that the set of the first 2300 genes with known phenotypes was representative for the whole set of protein-coding genes in the genome. The same method used in this paper for the approximation of the total number of protein-coding sequences among more than 40 000 ORFs longer than 20 codons gives a result that is only slightly higher. This suggests that there are still some non-coding ORFs in the databases and a few dozen small ORFs, not yet annotated, which probably code for proteins.
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Affiliation(s)
- Pawel Mackiewicz
- Institute of Microbiology, Wroclaw University, ul. Przybyszewskiego 63/77, 51-148 Wroclaw, Poland
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46
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Harrison PM, Kumar A, Lang N, Snyder M, Gerstein M. A question of size: the eukaryotic proteome and the problems in defining it. Nucleic Acids Res 2002; 30:1083-90. [PMID: 11861898 PMCID: PMC101239 DOI: 10.1093/nar/30.5.1083] [Citation(s) in RCA: 148] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2001] [Revised: 12/20/2001] [Accepted: 01/02/2002] [Indexed: 11/14/2022] Open
Abstract
We discuss the problems in defining the extent of the proteomes for completely sequenced eukaryotic organisms (i.e. the total number of protein-coding sequences), focusing on yeast, worm, fly and human. (i) Six years after completion of its genome sequence, the true size of the yeast proteome is still not defined. New small genes are still being discovered, and a large number of existing annotations are being called into question, with these questionable ORFs (qORFs) comprising up to one-fifth of the 'current' proteome. We discuss these in the context of an ideal genome-annotation strategy that considers the proteome as a rigorously defined subset of all possible coding sequences ('the orfome'). (ii) Despite the greater apparent complexity of the fly (more cells, more complex physiology, longer lifespan), the nematode worm appears to have more genes. To explain this, we compare the annotated proteomes of worm and fly, relating to both genome-annotation and genome evolution issues. (iii) The unexpectedly small size of the gene complement estimated for the complete human genome provoked much public debate about the nature of biological complexity. However, in the first instance, for the human genome, the relationship between gene number and proteome size is far from simple. We survey the current estimates for the numbers of human genes and, from this, we estimate a range for the size of the human proteome. The determination of this is substantially hampered by the unknown extent of the cohort of pseudogenes ('dead' genes), in combination with the prevalence of alternative splicing. (Further information relating to yeast is available at http://genecensus.org/yeast/orfome)
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Affiliation(s)
- Paul M Harrison
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, PO Box 208114, New Haven, CT 06520-8114, USA
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47
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Zhang CT, Wang J, Zhang R. Using a Euclid distance discriminant method to find protein coding genes in the yeast genome. COMPUTERS & CHEMISTRY 2002; 26:195-206. [PMID: 11868909 DOI: 10.1016/s0097-8485(01)00107-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The Euclid distance discriminant method is used to find protein coding genes in the yeast genome, based on the single nucleotide frequencies at three codon positions in the ORFs. The method is extremely simple and may be extended to find genes in prokaryotic genomes or eukaryotic genomes with less introns. Six-fold cross-validation tests have demonstrated that the accuracy of the algorithm is better than 93%. Based on this, it is found that the total number of protein coding genes in the yeast genome is less than or equal to 5579 only, about 3.8-7.0% less than 5800-6000, which is currently widely accepted. The base compositions at three codon positions are analyzed in details using a graphic method. The result shows that the preference codons adopted by yeast genes are of the RGW type, where R, G and W indicate the bases of purine, non-G and A/T, whereas the 'codons' in the intergenic sequences are of the form NNN, where N denotes any base. This fact constitutes the basis of the algorithm to distinguish between coding and non-coding ORFs in the yeast genome. The names of putative non-coding ORFs are listed here in detail.
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48
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Higgins VJ, Alic N, Thorpe GW, Breitenbach M, Larsson V, Dawes IW. Phenotypic analysis of gene deletant strains for sensitivity to oxidative stress. Yeast 2002; 19:203-14. [PMID: 11816028 DOI: 10.1002/yea.811] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Ascertaining the impact of inhibitors on the growth phenotype of yeast mutants can be useful in elucidating the function of genes within the cell. Microtitre plates and robotics have been used to screen over 600 deletions from EUROSCARF, constructed in an FY1679 strain background, for sensitivity to various oxidants. These included the inorganic hydroperoxide, H(2)O(2), an organic peroxide (cumene hydroperoxide) and a lipid hydroperoxide (linoleic acid hydroperoxide). These produce within the cell several different reactive oxygen species that can cause damage to DNA, proteins and lipids. Approximately 14% of deletants displayed sensitivity to at least one of the oxidants and there was also a distribution of deletants that showed sensitivity to all or different combinations of the oxidants. Deletants included genes encoding proteins involved in stress responses, heavy metal homeostasis and putative cell wall proteins. Although global mechanisms have been identified that provide general stress responses, these results imply that there are also distinct mechanisms involved in the protection of the cell against specific damage caused by different oxidants. Further analysis of these genes may reveal unknown mechanisms protecting the cell against reactive oxygen species.
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Affiliation(s)
- Vincent J Higgins
- Clive and Vera Ramaciotti Centre for Gene Function Analysis, School of Biochemistry and Molecular Genetics, University of New South Wales, Sydney, NSW 2052, Australia.
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49
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Abstract
Exposure of cells to a variety of external signals causes rapid changes in plasma membrane morphology. Plasma membrane dynamics, including membrane ruffle and microspike formation, fusion or fission of intracellular vesicles, and the spatial organization of transmembrane proteins, is directly controlled by the dynamic reorganization of the underlying actin cytoskeleton. Two members of the Rho family of small GTPases, Cdc42 and Rac, have been well established as mediators of extracellular signaling events that impact cortical actin organization. Actin-based signaling through Cdc42 and Rac ultimately results in activation of the actin-related protein (Arp) 2/3 complex, which promotes the formation of branched actin networks. In addition, the activity of both receptor and non-receptor protein tyrosine kinases along with numerous actin binding proteins works in concert with Arp2/3-mediated actin polymerization in regulating the formation of dynamic cortical actin-associated structures. In this review we discuss the structure and role of the cortical actin binding protein cortactin in Rho GTPase and tyrosine kinase signaling events, with the emphasis on the roles cortactin plays in tyrosine phosphorylation-based signal transduction, regulating cortical actin assembly, transmembrane receptor organization and membrane dynamics. We also consider how aberrant regulation of cortactin levels contributes to tumor cell invasion and metastasis.
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Affiliation(s)
- S A Weed
- Department of Craniofacial Biology, University of Colorado Health Sciences Center, Denver, Colorado, CO 80262, USA.
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50
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Chong SS, Hu P, Hernandez N. Reconstitution of transcription from the human U6 small nuclear RNA promoter with eight recombinant polypeptides and a partially purified RNA polymerase III complex. J Biol Chem 2001; 276:20727-34. [PMID: 11279001 DOI: 10.1074/jbc.m100088200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The human U6 small nuclear (sn) RNA core promoter consists of a proximal sequence element, which recruits the multisubunit factor SNAP(c), and a TATA box, which recruits the TATA box-binding protein, TBP. In addition to SNAP(c) and TBP, transcription from the human U6 promoter requires two well defined factors. The first is hB", a human homologue of the B" subunit of yeast TFIIIB generally required for transcription of RNA polymerase III genes, and the second is hBRFU, one of two human homologues of the yeast TFIIIB subunit BRF specifically required for transcription of U6-type RNA polymerase III promoters. Here, we have partially purified and characterized a RNA polymerase III complex that can direct transcription from the human U6 promoter when combined with recombinant SNAP(c), recombinant TBP, recombinant hB", and recombinant hBRFU. These results open the way to reconstitution of U6 transcription from entirely defined components.
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Affiliation(s)
- S S Chong
- Department of Microbiology and Graduate Program of Molecular and Cellular Biology, State University of New York at Stony Brook, Stony Brook, New York 11794, USA
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