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Christinaki AC, Kanellopoulos SG, Kortsinoglou AM, Andrikopoulos MΑ, Theelen B, Boekhout T, Kouvelis VN. Mitogenomics and mitochondrial gene phylogeny decipher the evolution of Saccharomycotina yeasts. Genome Biol Evol 2022; 14:6586520. [PMID: 35576568 PMCID: PMC9154068 DOI: 10.1093/gbe/evac073] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/12/2022] [Indexed: 11/17/2022] Open
Abstract
Saccharomycotina yeasts belong to diverse clades within the kingdom of fungi and are important to human everyday life. This work investigates the evolutionary relationships among these yeasts from a mitochondrial (mt) genomic perspective. A comparative study of 155 yeast mt genomes representing all major phylogenetic lineages of Saccharomycotina was performed, including genome size and content variability, intron and intergenic regions’ diversity, genetic code alterations, and syntenic variation. Findings from this study suggest that mt genome size diversity is the result of a ceaseless random process, mainly based on genetic recombination and intron mobility. Gene order analysis revealed conserved syntenic units and many occurring rearrangements, which can be correlated with major evolutionary events as shown by the phylogenetic analysis of the concatenated mt protein matrix. For the first time, molecular dating indicated a slower mt genome divergence rate in the early stages of yeast evolution, in contrast with a faster rate in the late evolutionary stages, compared to their nuclear time divergence. Genetic code reassignments of mt genomes are a perpetual process happening in many different parallel evolutionary steps throughout the evolution of Saccharomycotina. Overall, this work shows that phylogenetic studies based on the mt genome of yeasts highlight major evolutionary events.
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Affiliation(s)
- Anastasia C Christinaki
- National and Kapodistrian University of Athens, Faculty of Biology, Department of Genetics and Biotechnology, Athens, Greece
| | - Spyros G Kanellopoulos
- National and Kapodistrian University of Athens, Faculty of Biology, Department of Genetics and Biotechnology, Athens, Greece
| | - Alexandra M Kortsinoglou
- National and Kapodistrian University of Athens, Faculty of Biology, Department of Genetics and Biotechnology, Athens, Greece
| | - Marios Α Andrikopoulos
- National and Kapodistrian University of Athens, Faculty of Biology, Department of Genetics and Biotechnology, Athens, Greece
| | - Bart Theelen
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,University of Amsterdam, Institute of Biodiversity and Ecosystem Dynamics (IBED), Amsterdam, The Netherlands
| | - Vassili N Kouvelis
- National and Kapodistrian University of Athens, Faculty of Biology, Department of Genetics and Biotechnology, Athens, Greece
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2
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Bezerra AR, Oliveira C, Correia I, Guimarães AR, Sousa G, Carvalho MJ, Moura G, Santos MAS. The role of non-standard translation in Candida albicans pathogenesis. FEMS Yeast Res 2021; 21:6280978. [PMID: 34021562 PMCID: PMC8178436 DOI: 10.1093/femsyr/foab032] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/20/2021] [Indexed: 12/22/2022] Open
Abstract
Candida albicans typically resides in the human gastrointestinal tract and mucosal membranes as a commensal organism. To adapt and cope with the host immune system, it has evolved a variety of mechanisms of adaptation such as stress-induced mutagenesis and epigenetic regulation. Niche-specific patterns of gene expression also allow the fungus to fine-tune its response to specific microenvironments in the host and switch from harmless commensal to invasive pathogen. Proteome plasticity produced by CUG ambiguity, on the other hand is emerging as a new layer of complexity in C. albicans adaptation, pathogenesis, and drug resistance. Such proteome plasticity is the result of a genetic code alteration where the leucine CUG codon is translated mainly as serine (97%), but maintains some level of leucine (3%) assignment. In this review, we dissect the link between C. albicans non-standard CUG translation, proteome plasticity, host adaptation and pathogenesis. We discuss published work showing how this pathogen uses the fidelity of protein synthesis to spawn novel virulence traits.
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Affiliation(s)
- Ana Rita Bezerra
- Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Carla Oliveira
- Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Inês Correia
- Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Ana Rita Guimarães
- Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Gonçalo Sousa
- Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Maria João Carvalho
- Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Gabriela Moura
- Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Manuel A S Santos
- Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
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3
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Dantuluri S, Schwer B, Abdullahu L, Damha MJ, Shuman S. Activity and substrate specificity of Candida, Aspergillus, and Coccidioides Tpt1: essential tRNA splicing enzymes and potential anti-fungal targets. RNA (NEW YORK, N.Y.) 2021; 27:rna.078660.120. [PMID: 33509912 PMCID: PMC8051265 DOI: 10.1261/rna.078660.120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 01/22/2021] [Indexed: 06/12/2023]
Abstract
The enzyme Tpt1 is an essential agent of fungal tRNA splicing that removes an internal RNA 2'-PO4 generated by fungal tRNA ligase. Tpt1 performs a two-step reaction in which: (i) the 2'-PO4 attacks NAD+ to form an RNA-2'-phospho-(ADP-ribose) intermediate; and (ii) transesterification of the ADP-ribose O2'' to the RNA 2'-phosphodiester yields 2'-OH RNA and ADP-ribose-1'',2''-cyclic phosphate. Because Tpt1 does not participate in metazoan tRNA splicing, and Tpt1 knockout has no apparent impact on mammalian physiology, Tpt1 is considered a potential anti-fungal drug target. Here we characterize Tpt1 enzymes from four human fungal pathogens: Coccidioides immitis, the agent of Valley Fever; Aspergillus fumigatus and Candida albicans, which cause invasive, often fatal, infections in immunocompromised hosts; and Candida auris, an emerging pathogen that is resistant to current therapies. All four pathogen Tpt1s were active in vivo in complementing a lethal Saccharomyces cerevisiae tpt1∆ mutation and in vitro in NAD+-dependent conversion of a 2'-PO4 to a 2'-OH. The fungal Tpt1s utilized nicotinamide hypoxanthine dinucleotide as a substrate in lieu of NAD+, albeit with much lower affinity, whereas nicotinic acid adenine dinucleotide was ineffective. Fungal Tpt1s efficiently removed an internal ribonucleotide 2'-phosphate from an otherwise all-DNA substrate. Replacement of an RNA ribose-2'-PO4 nucleotide with arabinose-2'-PO4 diminished enzyme specific activity by ≥2000-fold and selectively slowed step 2 of the reaction pathway, resulting in transient accumulation of an ara-2'-phospho-ADP-ribosylated intermediate. Our results implicate the 2'-PO4 ribonucleotide as the principal determinant of fungal Tpt1 nucleic acid substrate specificity.
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4
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Singh T, Yadav SK, Vainstein A, Kumar V. Genome recoding strategies to improve cellular properties: mechanisms and advances. ABIOTECH 2021; 2:79-95. [PMID: 34377578 PMCID: PMC7675020 DOI: 10.1007/s42994-020-00030-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 10/07/2020] [Indexed: 11/10/2022]
Abstract
The genetic code, once believed to be universal and immutable, is now known to contain many variations and is not quite universal. The basis for genome recoding strategy is genetic code variation that can be harnessed to improve cellular properties. Thus, genome recoding is a promising strategy for the enhancement of genome flexibility, allowing for novel functions that are not commonly documented in the organism in its natural environment. Here, the basic concept of genetic code and associated mechanisms for the generation of genetic codon variants, including biased codon usage, codon reassignment, and ambiguous decoding, are extensively discussed. Knowledge of the concept of natural genetic code expansion is also detailed. The generation of recoded organisms and associated mechanisms with basic targeting components, including aminoacyl-tRNA synthetase-tRNA pairs, elongation factor EF-Tu and ribosomes, are highlighted for a comprehensive understanding of this concept. The research associated with the generation of diverse recoded organisms is also discussed. The success of genome recoding in diverse multicellular organisms offers a platform for expanding protein chemistry at the biochemical level with non-canonical amino acids, genetically isolating the synthetic organisms from the natural ones, and fighting viruses, including SARS-CoV2, through the creation of attenuated viruses. In conclusion, genome recoding can offer diverse applications for improving cellular properties in the genome-recoded organisms.
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Affiliation(s)
- Tanya Singh
- Department of Botany, School of Basic Sciences, Central University of Punjab, Bathinda, 151001 India
| | | | - Alexander Vainstein
- Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Vinay Kumar
- Department of Botany, School of Basic Sciences, Central University of Punjab, Bathinda, 151001 India
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5
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LaBella AL, Opulente DA, Steenwyk JL, Hittinger CT, Rokas A. Variation and selection on codon usage bias across an entire subphylum. PLoS Genet 2019; 15:e1008304. [PMID: 31365533 PMCID: PMC6701816 DOI: 10.1371/journal.pgen.1008304] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/20/2019] [Accepted: 07/11/2019] [Indexed: 01/04/2023] Open
Abstract
Variation in synonymous codon usage is abundant across multiple levels of organization: between codons of an amino acid, between genes in a genome, and between genomes of different species. It is now well understood that variation in synonymous codon usage is influenced by mutational bias coupled with both natural selection for translational efficiency and genetic drift, but how these processes shape patterns of codon usage bias across entire lineages remains unexplored. To address this question, we used a rich genomic data set of 327 species that covers nearly one third of the known biodiversity of the budding yeast subphylum Saccharomycotina. We found that, while genome-wide relative synonymous codon usage (RSCU) for all codons was highly correlated with the GC content of the third codon position (GC3), the usage of codons for the amino acids proline, arginine, and glycine was inconsistent with the neutral expectation where mutational bias coupled with genetic drift drive codon usage. Examination between genes' effective numbers of codons and their GC3 contents in individual genomes revealed that nearly a quarter of genes (381,174/1,683,203; 23%), as well as most genomes (308/327; 94%), significantly deviate from the neutral expectation. Finally, by evaluating the imprint of translational selection on codon usage, measured as the degree to which genes' adaptiveness to the tRNA pool were correlated with selective pressure, we show that translational selection is widespread in budding yeast genomes (264/327; 81%). These results suggest that the contribution of translational selection and drift to patterns of synonymous codon usage across budding yeasts varies across codons, genes, and genomes; whereas drift is the primary driver of global codon usage across the subphylum, the codon bias of large numbers of genes in the majority of genomes is influenced by translational selection.
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Affiliation(s)
- Abigail L. LaBella
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Dana A. Opulente
- Laboratory of Genetics, Genome Center of Wisconsin, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin–Madison, Wisconsin, United States of America
| | - Jacob L. Steenwyk
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Chris Todd Hittinger
- Laboratory of Genetics, Genome Center of Wisconsin, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin–Madison, Wisconsin, United States of America
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
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6
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Noutahi E, Calderon V, Blanchette M, Lang FB, El-Mabrouk N. CoreTracker: accurate codon reassignment prediction, applied to mitochondrial genomes. Bioinformatics 2018; 33:3331-3339. [PMID: 28655158 DOI: 10.1093/bioinformatics/btx421] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/23/2017] [Indexed: 11/13/2022] Open
Abstract
Motivation Codon reassignments have been reported across all domains of life. With the increasing number of sequenced genomes, the development of systematic approaches for genetic code detection is essential for accurate downstream analyses. Three automated prediction tools exist so far: FACIL, GenDecoder and Bagheera; the last two respectively restricted to metazoan mitochondrial genomes and CUG reassignments in yeast nuclear genomes. These tools can only analyze a single genome at a time and are often not followed by a validation procedure, resulting in a high rate of false positives. Results We present CoreTracker, a new algorithm for the inference of sense-to-sense codon reassignments. CoreTracker identifies potential codon reassignments in a set of related genomes, then uses statistical evaluations and a random forest classifier to predict those that are the most likely to be correct. Predicted reassignments are then validated through a phylogeny-aware step that evaluates the impact of the new genetic code on the protein alignment. Handling simultaneously a set of genomes in a phylogenetic framework, allows tracing back the evolution of each reassignment, which provides information on its underlying mechanism. Applied to metazoan and yeast genomes, CoreTracker significantly outperforms existing methods on both precision and sensitivity. Availability and implementation CoreTracker is written in Python and available at https://github.com/UdeM-LBIT/CoreTracker. Contact mabrouk@iro.umontreal.ca. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Emmanuel Noutahi
- Département d'Informatique et de Recherche Opérationnelle (DIRO), Université de Montréal, Montréal, QC CP 6128, Canada
| | - Virginie Calderon
- Département d'Informatique et de Recherche Opérationnelle (DIRO), Université de Montréal, Montréal, QC CP 6128, Canada
| | - Mathieu Blanchette
- School of Computer Science, McGill University, McConnell Engineering Bldg., Montréal, QC H3A 0E9, Canada
| | - Franz B Lang
- Département de Biochimie, Centre Robert Cedergren, Université de Montréal, Montréal, QC CP 6128, Canada
| | - Nadia El-Mabrouk
- Département d'Informatique et de Recherche Opérationnelle (DIRO), Université de Montréal, Montréal, QC CP 6128, Canada
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7
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Mühlhausen S, Schmitt HD, Pan KT, Plessmann U, Urlaub H, Hurst LD, Kollmar M. Endogenous Stochastic Decoding of the CUG Codon by Competing Ser- and Leu-tRNAs in Ascoidea asiatica. Curr Biol 2018; 28:2046-2057.e5. [PMID: 29910077 PMCID: PMC6041473 DOI: 10.1016/j.cub.2018.04.085] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 04/22/2018] [Accepted: 04/24/2018] [Indexed: 12/24/2022]
Abstract
Although the “universal” genetic code is now known not to be universal, and stop codons can have multiple meanings, one regularity remains, namely that for a given sense codon there is a unique translation. Examining CUG usage in yeasts that have transferred CUG away from leucine, we here report the first example of dual coding: Ascoidea asiatica stochastically encodes CUG as both serine and leucine in approximately equal proportions. This is deleterious, as evidenced by CUG codons being rare, never at conserved serine or leucine residues, and predominantly in lowly expressed genes. Related yeasts solve the problem by loss of function of one of the two tRNAs. This dual coding is consistent with the tRNA-loss-driven codon reassignment hypothesis, and provides a unique example of a proteome that cannot be deterministically predicted. Video Abstract
Ascoidea asiatica stochastically encodes CUG as leucine and serine It is the only known example of a proteome with non-deterministic features Stochastic encoding is caused by competing tRNALeu(CAG) and tRNASer(CAG) A. asiatica copes with stochastic encoding by avoiding CUG at key positions
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Affiliation(s)
- Stefanie Mühlhausen
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Hans Dieter Schmitt
- Department of Neurobiology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Kuan-Ting Pan
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Uwe Plessmann
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany; Bioanalytics Group, Department of Clinical Chemistry, University Medical Center Göttingen, Robert Koch Strasse 40, 37075 Göttingen, Germany
| | - Laurence D Hurst
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Martin Kollmar
- Group Systems Biology of Motor Proteins, Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
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8
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Grosjean H, Westhof E. An integrated, structure- and energy-based view of the genetic code. Nucleic Acids Res 2016; 44:8020-40. [PMID: 27448410 PMCID: PMC5041475 DOI: 10.1093/nar/gkw608] [Citation(s) in RCA: 177] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Revised: 06/11/2016] [Accepted: 06/17/2016] [Indexed: 12/25/2022] Open
Abstract
The principles of mRNA decoding are conserved among all extant life forms. We present an integrative view of all the interaction networks between mRNA, tRNA and rRNA: the intrinsic stability of codon-anticodon duplex, the conformation of the anticodon hairpin, the presence of modified nucleotides, the occurrence of non-Watson-Crick pairs in the codon-anticodon helix and the interactions with bases of rRNA at the A-site decoding site. We derive a more information-rich, alternative representation of the genetic code, that is circular with an unsymmetrical distribution of codons leading to a clear segregation between GC-rich 4-codon boxes and AU-rich 2:2-codon and 3:1-codon boxes. All tRNA sequence variations can be visualized, within an internal structural and energy framework, for each organism, and each anticodon of the sense codons. The multiplicity and complexity of nucleotide modifications at positions 34 and 37 of the anticodon loop segregate meaningfully, and correlate well with the necessity to stabilize AU-rich codon-anticodon pairs and to avoid miscoding in split codon boxes. The evolution and expansion of the genetic code is viewed as being originally based on GC content with progressive introduction of A/U together with tRNA modifications. The representation we present should help the engineering of the genetic code to include non-natural amino acids.
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Affiliation(s)
- Henri Grosjean
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Eric Westhof
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, 15 rue René Descartes, 67084 Strasbourg, France
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9
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Prista C, Michán C, Miranda IM, Ramos J. The halotolerant Debaryomyces hansenii, the Cinderella of non-conventional yeasts. Yeast 2016; 33:523-533. [PMID: 27279567 DOI: 10.1002/yea.3177] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 05/10/2016] [Accepted: 05/10/2016] [Indexed: 11/10/2022] Open
Abstract
Debaryomyces hansenii is a halotolerant yeast with a high biotechnological potential, particularly in the food industry. However, research in this yeast is limited by its molecular peculiarities. In this review we summarize the state of the art of research in this microorganisms, describing both pros and cons. We discuss (i) its halotolerance, (ii) the molecular factors involved in saline and osmotic stress, (iii) its high gene density and ambiguous CUG decoding, and (iv) its biotechnological and medical interests. We trust that all the bottlenecks in its study will soon be overcome and D. hansenii will become a fundamental organism for food biotechnological processes. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Catarina Prista
- LEAF - Research Centre Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, 1649-003, Portugal
| | - Carmen Michán
- Departamento de Bioquímica y Biología Molecular, Campus de Rabanales, Universidad de Córdoba, 14071, Córdoba, Spain
| | - Isabel M Miranda
- Department of Microbiology, Faculty of Medicine, University of Porto, Porto, Portugal.,CINTESIS - Centre for Health Technology and Services Research, Faculty of Medicine of the University of Porto, Portugal
| | - José Ramos
- Departamento de Microbiología, Campus de Rabanales, Universidad de Córdoba, 14071, Córdoba, Spain.
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10
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Mühlhausen S, Findeisen P, Plessmann U, Urlaub H, Kollmar M. A novel nuclear genetic code alteration in yeasts and the evolution of codon reassignment in eukaryotes. Genome Res 2016; 26:945-55. [PMID: 27197221 PMCID: PMC4937558 DOI: 10.1101/gr.200931.115] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 04/28/2016] [Indexed: 01/12/2023]
Abstract
The genetic code is the cellular translation table for the conversion of nucleotide sequences into amino acid sequences. Changes to the meaning of sense codons would introduce errors into almost every translated message and are expected to be highly detrimental. However, reassignment of single or multiple codons in mitochondria and nuclear genomes, although extremely rare, demonstrates that the code can evolve. Several models for the mechanism of alteration of nuclear genetic codes have been proposed (including “codon capture,” “genome streamlining,” and “ambiguous intermediate” theories), but with little resolution. Here, we report a novel sense codon reassignment in Pachysolen tannophilus, a yeast related to the Pichiaceae. By generating proteomics data and using tRNA sequence comparisons, we show that Pachysolen translates CUG codons as alanine and not as the more usual leucine. The Pachysolen tRNACAG is an anticodon-mutated tRNAAla containing all major alanine tRNA recognition sites. The polyphyly of the CUG-decoding tRNAs in yeasts is best explained by a tRNA loss driven codon reassignment mechanism. Loss of the CUG-tRNA in the ancient yeast is followed by gradual decrease of respective codons and subsequent codon capture by tRNAs whose anticodon is not part of the aminoacyl-tRNA synthetase recognition region. Our hypothesis applies to all nuclear genetic code alterations and provides several testable predictions. We anticipate more codon reassignments to be uncovered in existing and upcoming genome projects.
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Affiliation(s)
- Stefanie Mühlhausen
- Group Systems Biology of Motor Proteins, Department of NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Peggy Findeisen
- Group Systems Biology of Motor Proteins, Department of NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Uwe Plessmann
- Bioanalytical Mass Spectrometry, Max-Planck-Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max-Planck-Institute for Biophysical Chemistry, 37077 Göttingen, Germany; Bioanalytics Group, Department of Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Martin Kollmar
- Group Systems Biology of Motor Proteins, Department of NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, 37077 Göttingen, Germany
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11
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Bezerra AR, Guimarães AR, Santos MAS. Non-Standard Genetic Codes Define New Concepts for Protein Engineering. Life (Basel) 2015; 5:1610-28. [PMID: 26569314 PMCID: PMC4695839 DOI: 10.3390/life5041610] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 10/12/2015] [Accepted: 10/21/2015] [Indexed: 11/16/2022] Open
Abstract
The essential feature of the genetic code is the strict one-to-one correspondence between codons and amino acids. The canonical code consists of three stop codons and 61 sense codons that encode 20% of the amino acid repertoire observed in nature. It was originally designated as immutable and universal due to its conservation in most organisms, but sequencing of genes from the human mitochondrial genomes revealed deviations in codon assignments. Since then, alternative codes have been reported in both nuclear and mitochondrial genomes and genetic code engineering has become an important research field. Here, we review the most recent concepts arising from the study of natural non-standard genetic codes with special emphasis on codon re-assignment strategies that are relevant to engineering genetic code in the laboratory. Recent tools for synthetic biology and current attempts to engineer new codes for incorporation of non-standard amino acids are also reviewed in this article.
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Affiliation(s)
- Ana R Bezerra
- Health Sciences Department, Institute for Biomedicine-iBiMED, University of Aveiro, Campus de Santiago, Aveiro 3810-193, Portugal.
| | - Ana R Guimarães
- Health Sciences Department, Institute for Biomedicine-iBiMED, University of Aveiro, Campus de Santiago, Aveiro 3810-193, Portugal.
| | - Manuel A S Santos
- Health Sciences Department, Institute for Biomedicine-iBiMED, University of Aveiro, Campus de Santiago, Aveiro 3810-193, Portugal.
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12
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Evolution of Robustness to Protein Mistranslation by Accelerated Protein Turnover. PLoS Biol 2015; 13:e1002291. [PMID: 26544557 PMCID: PMC4636289 DOI: 10.1371/journal.pbio.1002291] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 09/30/2015] [Indexed: 11/19/2022] Open
Abstract
Translational errors occur at high rates, and they influence organism viability and the onset of genetic diseases. To investigate how organisms mitigate the deleterious effects of protein synthesis errors during evolution, a mutant yeast strain was engineered to translate a codon ambiguously (mistranslation). It thereby overloads the protein quality-control pathways and disrupts cellular protein homeostasis. This strain was used to study the capacity of the yeast genome to compensate the deleterious effects of protein mistranslation. Laboratory evolutionary experiments revealed that fitness loss due to mistranslation can rapidly be mitigated. Genomic analysis demonstrated that adaptation was primarily mediated by large-scale chromosomal duplication and deletion events, suggesting that errors during protein synthesis promote the evolution of genome architecture. By altering the dosages of numerous, functionally related proteins simultaneously, these genetic changes introduced large phenotypic leaps that enabled rapid adaptation to mistranslation. Evolution increased the level of tolerance to mistranslation through acceleration of ubiquitin-proteasome–mediated protein degradation and protein synthesis. As a consequence of rapid elimination of erroneous protein products, evolution reduced the extent of toxic protein aggregation in mistranslating cells. However, there was a strong evolutionary trade-off between adaptation to mistranslation and survival upon starvation: the evolved lines showed fitness defects and impaired capacity to degrade mature ribosomes upon nutrient limitation. Moreover, as a response to an enhanced energy demand of accelerated protein turnover, the evolved lines exhibited increased glucose uptake by selective duplication of hexose transporter genes. We conclude that adjustment of proteome homeostasis to mistranslation evolves rapidly, but this adaptation has several side effects on cellular physiology. Our work also indicates that translational fidelity and the ubiquitin-proteasome system are functionally linked to each other and may, therefore, co-evolve in nature. Tolerance to errors during protein synthesis evolves rapidly through acceleration of protein turnover—a process determined by the combined rates of protein synthesis and degradation. However, this adaptation has deleterious side effects due to its energy costs. Although fidelity of information transfer has a substantial impact on cellular survival, many steps in protein production are strikingly error-prone. Such errors during protein synthesis can have a substantial influence on viability and the onset of genetic diseases. These considerations raise the question as to how organisms can tolerate errors during protein synthesis. In this paper, for the first time, we study organisms’ capacity to evolve robustness against mistranslation and explore the underlying cellular mechanisms. A mutant yeast strain was engineered to translate a codon ambiguously (mistranslation). This thereby overloads the protein quality-control pathways and disrupts cellular protein homeostasis. This strain was used to study the capacity of the yeast genome to compensate for the deleterious effects of protein mistranslation. We found that mistranslation led to rapid evolution of genomic rearrangements, including chromosomal duplications and deletions. By altering the dosages of numerous, functionally related proteins simultaneously, these genetic changes introduce large phenotypic leaps that enable adaptation to mistranslation. Robustness against mistranslation during laboratory evolution was achieved through acceleration of protein turnover—a process that was determined by the combined rates of protein synthesis and ubiquitin-proteasome system-mediated degradation. However, as both translation and active degradation of proteins are exceptionally energy-consuming cellular processes, accelerated proteome turnover has substantial energy costs.
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Mukai T, Yamaguchi A, Ohtake K, Takahashi M, Hayashi A, Iraha F, Kira S, Yanagisawa T, Yokoyama S, Hoshi H, Kobayashi T, Sakamoto K. Reassignment of a rare sense codon to a non-canonical amino acid in Escherichia coli. Nucleic Acids Res 2015; 43:8111-22. [PMID: 26240376 PMCID: PMC4652775 DOI: 10.1093/nar/gkv787] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 07/22/2015] [Indexed: 11/13/2022] Open
Abstract
The immutability of the genetic code has been challenged with the successful reassignment of the UAG stop codon to non-natural amino acids in Escherichia coli. In the present study, we demonstrated the in vivo reassignment of the AGG sense codon from arginine to L-homoarginine. As the first step, we engineered a novel variant of the archaeal pyrrolysyl-tRNA synthetase (PylRS) able to recognize L-homoarginine and L-N(6)-(1-iminoethyl)lysine (L-NIL). When this PylRS variant or HarRS was expressed in E. coli, together with the AGG-reading tRNA(Pyl) CCU molecule, these arginine analogs were efficiently incorporated into proteins in response to AGG. Next, some or all of the AGG codons in the essential genes were eliminated by their synonymous replacements with other arginine codons, whereas the majority of the AGG codons remained in the genome. The bacterial host's ability to translate AGG into arginine was then restricted in a temperature-dependent manner. The temperature sensitivity caused by this restriction was rescued by the translation of AGG to L-homoarginine or L-NIL. The assignment of AGG to L-homoarginine in the cells was confirmed by mass spectrometric analyses. The results showed the feasibility of breaking the degeneracy of sense codons to enhance the amino-acid diversity in the genetic code.
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Affiliation(s)
- Takahito Mukai
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Atsushi Yamaguchi
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Kazumasa Ohtake
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Mihoko Takahashi
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Akiko Hayashi
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Fumie Iraha
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Satoshi Kira
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Tatsuo Yanagisawa
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Shigeyuki Yokoyama
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Hiroko Hoshi
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Takatsugu Kobayashi
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Kensaku Sakamoto
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
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Wu B, Buljic A, Hao W. Extensive Horizontal Transfer and Homologous Recombination Generate Highly Chimeric Mitochondrial Genomes in Yeast. Mol Biol Evol 2015; 32:2559-70. [PMID: 26018571 DOI: 10.1093/molbev/msv127] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The frequency of horizontal gene transfer (HGT) in mitochondrial DNA varies substantially. In plants, HGT is relatively common, whereas in animals it appears to be quite rare. It is of considerable importance to understand mitochondrial HGT across the major groups of eukaryotes at a genome-wide level, but so far this has been well studied only in plants. In this study, we generated ten new mitochondrial genome sequences and analyzed 40 mitochondrial genomes from the Saccharomycetaceae to assess the magnitude and nature of mitochondrial HGT in yeasts. We provide evidence for extensive, homologous-recombination-mediated, mitochondrial-to-mitochondrial HGT occurring throughout yeast mitochondrial genomes, leading to genomes that are highly chimeric evolutionarily. This HGT has led to substantial intraspecific polymorphism in both sequence content and sequence divergence, which to our knowledge has not been previously documented in any mitochondrial genome. The unexpectedly high frequency of mitochondrial HGT in yeast may be driven by frequent mitochondrial fusion, relatively low mitochondrial substitution rates and pseudohyphal fusion to produce heterokaryons. These findings suggest that mitochondrial HGT may play an important role in genome evolution of a much broader spectrum of eukaryotes than previously appreciated and that there is a critical need to systematically study the frequency, extent, and importance of mitochondrial HGT across eukaryotes.
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Affiliation(s)
- Baojun Wu
- Department of Biological Sciences, Wayne State University
| | - Adnan Buljic
- Department of Biological Sciences, Wayne State University
| | - Weilong Hao
- Department of Biological Sciences, Wayne State University
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Sárkány Z, Silva A, Pereira PJB, Macedo-Ribeiro S. Ser or Leu: structural snapshots of mistranslation in Candida albicans. Front Mol Biosci 2014; 1:27. [PMID: 25988168 PMCID: PMC4428446 DOI: 10.3389/fmolb.2014.00027] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 12/04/2014] [Indexed: 11/29/2022] Open
Abstract
Candida albicans is a polymorphic opportunistic fungal pathogen normally residing as commensal on mucosal surfaces, skin and gastrointestinal and genitourinary tracts. However, in immunocompromised patients C. albicans can cause superficial mucosal infections or life-threatening disseminated candidemia. A change in physiological conditions triggers a cascade of molecular events leading to morphogenetic alterations and increased resistance to damage induced by host defenses. The complex biology of this human pathogen is reflected in its morphological plasticity and reinforced by the ability to ambiguously translate the universal leucine CUG codon predominantly as serine, but also as leucine. Mistranslation affects more than half of C. albicans proteome and it is widespread across many biological processes. A previous analysis of CTG-codon containing gene products in C. albicans suggested that codon ambiguity subtly shapes protein function and might have a pivotal role in signaling cascades associated with morphological changes and pathogenesis. In this review we further explore this hypothesis by highlighting the role of ambiguous decoding in macromolecular recognition of key effector proteins associated with the regulation of signal transduction cascades and the cell cycle, which are critical processes for C. albicans morphogenic plasticity under a variety of environmental conditions.
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Affiliation(s)
- Zsuzsa Sárkány
- Protein Crystallography Group, IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto Porto, Portugal
| | - Alexandra Silva
- Protein Crystallography Group, IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto Porto, Portugal
| | - Pedro J B Pereira
- Biomolecular Structure Group, IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto Porto, Portugal
| | - Sandra Macedo-Ribeiro
- Protein Crystallography Group, IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto Porto, Portugal
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16
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Su Z, Wang Z, López-Giráldez F, Townsend JP. The impact of incorporating molecular evolutionary model into predictions of phylogenetic signal and noise. Front Ecol Evol 2014. [DOI: 10.3389/fevo.2014.00011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Abstract
Candida species exhibit a variety of ploidy states and modes of sexual reproduction. Most species possess the requisite genes for sexual reproduction, recombination, and meiosis, yet only a few have been reported to undergo a complete sexual cycle including mating and sporulation. Candida albicans, the most studied Candida species and a prevalent human fungal pathogen, completes its sexual cycle via a parasexual process of concerted chromosome loss rather than a conventional meiosis. In this study, we examine ploidy changes in Candida tropicalis, a closely related species to C. albicans that was recently revealed to undergo sexual mating. C. tropicalis diploid cells mate to form tetraploid cells, and we show that these can be induced to undergo chromosome loss to regenerate diploid forms by growth on sorbose medium. The diploid products are themselves mating competent, thereby establishing a parasexual cycle in this species for the first time. Extended incubation (>120 generations) of C. tropicalis tetraploid cells under rich culture conditions also resulted in instability of the tetraploid form and a gradual reduction in ploidy back to the diploid state. The fitness levels of C. tropicalis diploid and tetraploid cells were compared, and diploid cells exhibited increased fitness relative to tetraploid cells in vitro, despite diploid and tetraploid cells having similar doubling times. Collectively, these experiments demonstrate distinct pathways by which a parasexual cycle can occur in C. tropicalis and indicate that nonmeiotic mechanisms drive ploidy changes in this prevalent human pathogen.
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18
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Ling J, Daoud R, Lajoie MJ, Church GM, Söll D, Lang BF. Natural reassignment of CUU and CUA sense codons to alanine in Ashbya mitochondria. Nucleic Acids Res 2013; 42:499-508. [PMID: 24049072 PMCID: PMC3874161 DOI: 10.1093/nar/gkt842] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The discovery of diverse codon reassignment events has demonstrated that the canonical genetic code is not universal. Studying coding reassignment at the molecular level is critical for understanding genetic code evolution, and provides clues to genetic code manipulation in synthetic biology. Here we report a novel reassignment event in the mitochondria of Ashbya (Eremothecium) gossypii, a filamentous-growing plant pathogen related to yeast (Saccharomycetaceae). Bioinformatics studies of conserved positions in mitochondrial DNA-encoded proteins suggest that CUU and CUA codons correspond to alanine in A. gossypii, instead of leucine in the standard code or threonine in yeast mitochondria. Reassignment of CUA to Ala was confirmed at the protein level by mass spectrometry. We further demonstrate that a predicted tRNA(Ala)UAG is transcribed and accurately processed in vivo, and is responsible for Ala reassignment. Enzymatic studies reveal that tRNA(Ala)UAG is efficiently recognized by A. gossypii mitochondrial alanyl-tRNA synthetase (AgAlaRS). AlaRS typically recognizes the G3:U70 base pair of tRNA(Ala); a G3A change in Ashbya tRNA(Ala)UAG abolishes its recognition by AgAlaRS. Conversely, an A3G mutation in Saccharomyces cerevisiae tRNA(Thr)UAG confers tRNA recognition by AgAlaRS. Our work highlights the dynamic feature of natural genetic codes in mitochondria, and the relative simplicity by which tRNA identity may be switched.
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Affiliation(s)
- Jiqiang Ling
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA, Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, 2900 Boulevard Edouard Montpetit, Montréal, Québec, H3C 3J7, Canada, Program in Chemical Biology, Harvard University, Cambridge, MA 02138, USA, Department of Genetics, Harvard Medical School, Boston, MA 02115, USA and Department of Chemistry, Yale University, New Haven, CT 06520-8114, USA
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19
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López-Giráldez F, Moeller AH, Townsend JP. Evaluating phylogenetic informativeness as a predictor of phylogenetic signal for metazoan, fungal, and mammalian phylogenomic data sets. BIOMED RESEARCH INTERNATIONAL 2013; 2013:621604. [PMID: 23878813 PMCID: PMC3708382 DOI: 10.1155/2013/621604] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 06/03/2013] [Indexed: 11/17/2022]
Abstract
Phylogenetic research is often stymied by selection of a marker that leads to poor phylogenetic resolution despite considerable cost and effort. Profiles of phylogenetic informativeness provide a quantitative measure for prioritizing gene sampling to resolve branching order in a particular epoch. To evaluate the utility of these profiles, we analyzed phylogenomic data sets from metazoans, fungi, and mammals, thus encompassing diverse time scales and taxonomic groups. We also evaluated the utility of profiles created based on simulated data sets. We found that genes selected via their informativeness dramatically outperformed haphazard sampling of markers. Furthermore, our analyses demonstrate that the original phylogenetic informativeness method can be extended to trees with more than four taxa. Thus, although the method currently predicts phylogenetic signal without specifically accounting for the misleading effects of stochastic noise, it is robust to the effects of homoplasy. The phylogenetic informativeness rankings obtained will allow other researchers to select advantageous genes for future studies within these clades, maximizing return on effort and investment. Genes identified might also yield efficient experimental designs for phylogenetic inference for many sister clades and outgroup taxa that are closely related to the diverse groups of organisms analyzed.
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Affiliation(s)
- Francesc López-Giráldez
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06520, USA
| | - Andrew H. Moeller
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06520, USA
| | - Jeffrey P. Townsend
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06520, USA
- Department of Biostatistics, Yale University, 135 College Street, New Haven, CT 06520, USA
- Program in Computational Biology and Bioinformatics, 300 George Street, Yale University, New Haven, CT 06520, USA
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20
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Mateus DD, Paredes JA, Español Y, Ribas de Pouplana L, Moura GR, Santos MAS. Molecular reconstruction of a fungal genetic code alteration. RNA Biol 2013; 10:969-80. [PMID: 23619021 DOI: 10.4161/rna.24683] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Fungi of the CTG clade translate the Leu CUG codon as Ser. This genetic code alteration is the only eukaryotic sense-to-sense codon reassignment known to date, is mediated by an ambiguous serine tRNA (tRNACAG(Ser)), exposes unanticipated flexibility of the genetic code and raises major questions about its selection and fixation in this fungal lineage. In particular, the origin of the tRNACAG(Ser) and the evolutionary mechanism of CUG reassignment from Leu to Ser remain poorly understood. In this study, we have traced the origin of the tDNACAG(Ser) gene and studied critical mutations in the tRNACAG(Ser) anticodon-loop that modulated CUG reassignment. Our data show that the tRNACAG(Ser) emerged from insertion of an adenosine in the middle position of the 5'-CGA-3'anticodon of a tRNACGA(Ser) ancestor, producing the 5'-CAG-3' anticodon of the tRNACAG(Ser), without altering its aminoacylation properties. This mutation initiated CUG reassignment while two additional mutations in the anticodon-loop resolved a structural conflict produced by incorporation of the Leu 5'-CAG-3'anticodon in the anticodon-arm of a tRNA(Ser). Expression of the mutant tRNACAG(Ser) in yeast showed that it cannot be expressed at physiological levels and we postulate that such downregulation was essential to maintain Ser misincorporation at sub-lethal levels during the initial stages of CUG reassignment. We demonstrate here that such low level CUG ambiguity is advantageous in specific ecological niches and we propose that misreading tRNAs are targeted for degradation by an unidentified tRNA quality control pathway.
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Affiliation(s)
- Denisa D Mateus
- RNA Biology Laboratory, Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal
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21
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Yadavalli SS, Ibba M. Selection of tRNA charging quality control mechanisms that increase mistranslation of the genetic code. Nucleic Acids Res 2012; 41:1104-12. [PMID: 23222133 PMCID: PMC3553970 DOI: 10.1093/nar/gks1240] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Mistranslation can follow two events during protein synthesis: production of non-cognate amino acid:transfer RNA (tRNA) pairs by aminoacyl-tRNA synthetases (aaRSs) and inaccurate selection of aminoacyl-tRNAs by the ribosome. Many aaRSs actively edit non-cognate amino acids, but editing mechanisms are not evolutionarily conserved, and their physiological significance remains unclear. To address the connection between aaRSs and mistranslation, the evolutionary divergence of tyrosine editing by phenylalanyl-tRNA synthetase (PheRS) was used as a model. Certain PheRSs are naturally error prone, most notably a Mycoplasma example that displayed a low level of specificity consistent with elevated mistranslation of the proteome. Mycoplasma PheRS was found to lack canonical editing activity, relying instead on discrimination against the non-cognate amino acid by kinetic proofreading. This mechanism of discrimination is inadequate for organisms where translation is more accurate, as Mycoplasma PheRS failed to support Escherichia coli growth. However, minor changes in the defunct editing domain of the Mycoplasma enzyme were sufficient to restore E. coli growth, indicating that translational accuracy is an evolutionarily selectable trait.
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Affiliation(s)
- Srujana S Yadavalli
- Department of Microbiology, Ohio State University, 484 West 12th Avenue, Columbus, OH 43210-1292, USA
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Procházka E, Franko F, Poláková S, Sulo P. A complete sequence of Saccharomyces paradoxus mitochondrial genome that restores the respiration in S. cerevisiae. FEMS Yeast Res 2012; 12:819-30. [PMID: 22830625 DOI: 10.1111/j.1567-1364.2012.00833.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Revised: 06/19/2012] [Accepted: 07/21/2012] [Indexed: 12/01/2022] Open
Abstract
We determined the complete sequence of 71 355-bp-long mitochondrial genome from Saccharomyces paradoxus entirely by direct sequencing of purified mitochondrial DNA (mtDNA). This mtDNA possesses the same features as its close relative Saccharomyces cerevisiae - A + T content 85.9%, set of genes coding for the three components of cytochrome oxidase, cytochrome b, three subunits of ATPase, both ribosomal subunits, gene for ribosomal protein, rnpB gene, tRNA package (24) and yeast genetic code. Genes are interrupted by nine group I and group II introns, two of which are in positions unknown in S. cerevisiae, but recognized in Saccharomyces pastorianus. The gene products are related to S. cerevisiae, and the identity of amino acid residues varies from 100% for cox2 to 83% for rps3. The remarkable differences from S. cerevisiae are (1) different gene order (translocation of trnF-trnT1-trnV-cox3-trnfM-rnpb-trnP and transposition of trnW-rns), (2) occurrence of two unusual GI introns, (3) eight active ori elements, and (4) reduced number of GC clusters and divergent intergenic spacers. Despite these facts, the sequenced S. paradoxus mtDNA introduced to S. cerevisiae was able to support the respiratory function to the same extent as the original mtDNAs.
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Affiliation(s)
- Emanuel Procházka
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Mlynská Dolina, Bratislava, Slovakia
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Eldarov MA, Mardanov AV, Beletsky AV, Dzhavakhiya VV, Ravin NV, Skryabin KG. Complete mitochondrial genome of compactin-producing fungus Penicillium solitum and comparative analysis of Trichocomaceae mitochondrial genomes. FEMS Microbiol Lett 2012; 329:9-17. [PMID: 22239643 DOI: 10.1111/j.1574-6968.2012.02497.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2011] [Revised: 12/08/2011] [Accepted: 01/01/2012] [Indexed: 11/30/2022] Open
Abstract
We determined the complete mitochondrial genome sequence of the compactin-producing fungus Penicillium solitum strain 20-01. The 28 601-base pair circular-mapping DNA molecule encodes a characteristic set of mitochondrial proteins and RNA genes and is intron-free. All 46 protein- and RNA-encoding genes are located on one strand and apparently transcribed in one direction. Comparative analysis of this mtDNA and previously sequenced but unannotated mitochondrial genomes of several medically and industrially important species of the Aspergillus/Penicillium group revealed their extensive similarity in terms of size, gene content and sequence, which is also reflected in the almost perfect conservation of mitochondrial gene order in Penicillium and Aspergillus. Phylogenetic analysis based on concatenated mitochondrial protein sequences confirmed the monophyletic origin of Eurotiomycetes.
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Affiliation(s)
- Michael A Eldarov
- Centre 'Bioengineering,' Russian Academy of Sciences, Moscow, Russia.
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24
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Unveiling the structural basis for translational ambiguity tolerance in a human fungal pathogen. Proc Natl Acad Sci U S A 2011; 108:14091-6. [PMID: 21825144 DOI: 10.1073/pnas.1102835108] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In a restricted group of opportunistic fungal pathogens the universal leucine CUG codon is translated both as serine (97%) and leucine (3%), challenging the concept that translational ambiguity has a negative impact in living organisms. To elucidate the molecular mechanisms underlying the in vivo tolerance to a nonconserved genetic code alteration, we have undertaken an extensive structural analysis of proteins containing CUG-encoded residues and solved the crystal structures of the two natural isoforms of Candida albicans seryl-tRNA synthetase. We show that codon reassignment resulted in a nonrandom genome-wide CUG redistribution tailored to minimize protein misfolding events induced by the large-scale leucine-to-serine replacement within the CTG clade. Leucine or serine incorporation at the CUG position in C. albicans seryl-tRNA synthetase induces only local structural changes and, although both isoforms display tRNA serylation activity, the leucine-containing isoform is more active. Similarly, codon ambiguity is predicted to shape the function of C. albicans proteins containing CUG-encoded residues in functionally relevant positions, some of which have a key role in signaling cascades associated with morphological changes and pathogenesis. This study provides a first detailed analysis on natural reassignment of codon identity, unveiling a highly dynamic evolutionary pattern of thousands of fungal CUG codons to confer an optimized balance between protein structural robustness and functional plasticity.
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Eldarov MA, Mardanov AV, Beletsky AV, Ravin NV, Skryabin KG. Complete sequence and analysis of the mitochondrial genome of the methylotrophic yeast Hansenula polymorpha DL-1. FEMS Yeast Res 2011; 11:464-72. [PMID: 21545683 DOI: 10.1111/j.1567-1364.2011.00736.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
We determined the complete nucleotide sequence of the 41 719 bp mitochondrial genome of the methylotrophic yeast Hansenula polymorpha strain DL-1. It contains genes for three subunits of cytochrome oxidase (cox1, cox2 and cox3), three subunits of ATP synthase (atp6, atp8 and atp9), seven subunits of NADH dehydrogenase (nad1-6 and nad4L), apocytochrome b (cob), four endonuclease/maturase homologs, a ribosomal protein (rps3), large and small rRNAs and a complete set of tRNAs. The structural genes are organized in two major transcriptional units. Phylogenetic, gene content and gene order analyses revealed the close phylogenetic relationship between H. polymorpha and Brettanomyces custersianus, and support the assignment of strain DL-1 to a separate genus rather than including it in the polyphyletic genus Pichia.
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Affiliation(s)
- Mikhail A Eldarov
- Laboratory of Genetic Engineering, Centre 'Bioengineering' of RAS, Moscow, Russia.
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26
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Su D, Lieberman A, Lang BF, Simonovic M, Söll D, Ling J. An unusual tRNAThr derived from tRNAHis reassigns in yeast mitochondria the CUN codons to threonine. Nucleic Acids Res 2011; 39:4866-74. [PMID: 21321019 PMCID: PMC3113583 DOI: 10.1093/nar/gkr073] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The standard genetic code is used by most living organisms, yet deviations have been observed in many genomes, suggesting that the genetic code has been evolving. In certain yeast mitochondria, CUN codons are reassigned from leucine to threonine, which requires an unusual tRNA(Thr) with an enlarged 8-nt anticodon loop ( ). To trace its evolutionary origin we performed a comprehensive phylogenetic analysis which revealed that evolved from yeast mitochondrial tRNA(His). To understand this tRNA identity change, we performed mutational and biochemical experiments. We show that Saccharomyces cerevisiae mitochondrial threonyl-tRNA synthetase (MST1) could attach threonine to both and the regular , but not to the wild-type tRNA(His). A loss of the first nucleotide (G(-1)) in tRNA(His) converts it to a substrate for MST1 with a K(m) value (0.7 μM) comparable to that of (0.3 μM), and addition of G(-1) to allows efficient histidylation by histidyl-tRNA synthetase. We also show that MST1 from Candida albicans, a yeast in which CUN codons remain assigned to leucine, could not threonylate , suggesting that MST1 has coevolved with . Our work provides the first clear example of a recent recoding event caused by alloacceptor tRNA gene recruitment.
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Affiliation(s)
- Dan Su
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
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27
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Reynolds NM, Lazazzera BA, Ibba M. Cellular mechanisms that control mistranslation. Nat Rev Microbiol 2010; 8:849-56. [PMID: 21079633 DOI: 10.1038/nrmicro2472] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Mistranslation broadly encompasses the introduction of errors during any step of protein synthesis, leading to the incorporation of an amino acid that is different from the one encoded by the gene. Recent research has vastly enhanced our understanding of the mechanisms that control mistranslation at the molecular level and has led to the discovery that the rates of mistranslation in vivo are not fixed but instead are variable. In this Review we describe the different steps in translation quality control and their variations under different growth conditions and between species though a comparison of in vitro and in vivo findings. This provides new insights as to why mistranslation can have both positive and negative effects on growth and viability.
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Affiliation(s)
- Noah M Reynolds
- Department of Microbiology, Ohio State University, Columbus, Ohio 43210, USA
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28
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New insights into the fructosyltransferase activity of Schwanniomyces occidentalis ß-fructofuranosidase, emerging from nonconventional codon usage and directed mutation. Appl Environ Microbiol 2010; 76:7491-9. [PMID: 20851958 DOI: 10.1128/aem.01614-10] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Schwanniomyces occidentalis β-fructofuranosidase (Ffase) releases β-fructose from the nonreducing ends of β-fructans and synthesizes 6-kestose and 1-kestose, both considered prebiotic fructooligosaccharides. Analyzing the amino acid sequence of this protein revealed that it includes a serine instead of a leucine at position 196, caused by a nonuniversal decoding of the unique mRNA leucine codon CUG. Substitution of leucine for Ser196 dramatically lowers the apparent catalytic efficiency (k(cat)/K(m)) of the enzyme (approximately 1,000-fold), but surprisingly, its transferase activity is enhanced by almost 3-fold, as is the enzymes' specificity for 6-kestose synthesis. The influence of 6 Ffase residues on enzyme activity was analyzed on both the Leu196/Ser196 backgrounds (Trp47, Asn49, Asn52, Ser111, Lys181, and Pro232). Only N52S and P232V mutations improved the transferase activity of the wild-type enzyme (about 1.6-fold). Modeling the transfructosylation products into the active site, in combination with an analysis of the kinetics and transfructosylation reactions, defined a new region responsible for the transferase specificity of the enzyme.
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29
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Solieri L. Mitochondrial inheritance in budding yeasts: towards an integrated understanding. Trends Microbiol 2010; 18:521-30. [PMID: 20832322 DOI: 10.1016/j.tim.2010.08.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Revised: 07/23/2010] [Accepted: 08/04/2010] [Indexed: 01/08/2023]
Abstract
Recent advances in yeast mitogenomics have significantly contributed to our understanding of the diversity of organization, structure and topology in the mitochondrial genome of budding yeasts. In parallel, new insights on mitochondrial DNA (mtDNA) inheritance in the model organism Saccharomyces cerevisiae highlighted an integrated scenario where recombination, replication and segregation of mtDNA are intricately linked to mitochondrial nucleoid (mt-nucleoid) structure and organelle sorting. In addition to this, recent discoveries of bifunctional roles of some mitochondrial proteins have interesting implications on mito-nuclear genome interactions and the relationship between mtDNA inheritance, yeast fitness and speciation. This review summarizes the current knowledge on yeast mitogenomics, mtDNA inheritance with regard to mt-nucleoid structure and organelle dynamics, and mito-nuclear genome interactions.
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Affiliation(s)
- Lisa Solieri
- Department of Agricultural and Food Sciences, University of Modena and Reggio Emilia, via Amendola 2, Padiglione Besta, 42100 Reggio Emilia, Italy.
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30
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Seaborg DM. Was Wright right? The canonical genetic code is an empirical example of an adaptive peak in nature; deviant genetic codes evolved using adaptive bridges. J Mol Evol 2010; 71:87-99. [PMID: 20711776 PMCID: PMC2924497 DOI: 10.1007/s00239-010-9373-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Accepted: 07/02/2010] [Indexed: 11/30/2022]
Abstract
The canonical genetic code is on a sub-optimal adaptive peak with respect to its ability to minimize errors, and is close to, but not quite, optimal. This is demonstrated by the near-total adjacency of synonymous codons, the similarity of adjacent codons, and comparisons of frequency of amino acid usage with number of codons in the code for each amino acid. As a rare empirical example of an adaptive peak in nature, it shows adaptive peaks are real, not merely theoretical. The evolution of deviant genetic codes illustrates how populations move from a lower to a higher adaptive peak. This is done by the use of "adaptive bridges," neutral pathways that cross over maladaptive valleys by virtue of masking of the phenotypic expression of some maladaptive aspects in the genotype. This appears to be the general mechanism by which populations travel from one adaptive peak to another. There are multiple routes a population can follow to cross from one adaptive peak to another. These routes vary in the probability that they will be used, and this probability is determined by the number and nature of the mutations that happen along each of the routes. A modification of the depiction of adaptive landscapes showing genetic distances and probabilities of travel along their multiple possible routes would throw light on this important concept.
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Affiliation(s)
- David M Seaborg
- Foundation for Biological Conservation and Research, 1888 Pomar Way, Walnut Creek, CA 94598-1424, USA.
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31
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Townsend JP, Lopez-Giraldez F. Optimal Selection of Gene and Ingroup Taxon Sampling for Resolving Phylogenetic Relationships. Syst Biol 2010; 59:446-57. [DOI: 10.1093/sysbio/syq025] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Jeffrey P. Townsend
- Department of Ecology and Evolutionary Biology
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
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32
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Procházka E, Poláková S, Piskur J, Sulo P. Mitochondrial genome from the facultative anaerobe and petite-positive yeast Dekkera bruxellensis contains the NADH dehydrogenase subunit genes. FEMS Yeast Res 2010; 10:545-57. [PMID: 20528950 DOI: 10.1111/j.1567-1364.2010.00644.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The progenitor of the Dekkera/Brettanomyces clade separated from the Saccharomyces/Kluyveromyces clade over 200 million years ago. However, within both clades, several lineages developed similar physiological traits. Both Saccharomyces cerevisiae and Dekkera bruxellensis are facultative anaerobes; in the presence of excess oxygen and sugars, they accumulate ethanol (Crabtree effect) and they both spontaneously generate respiratory-deficient mutants (petites). In order to understand the role of respiratory metabolism, the mitochondrial DNA (mtDNA) molecules of two Dekkera/Brettanomyces species were analysed. Dekkera bruxellensis mtDNA shares several properties with S. cerevisiae, such as the large genome size (76 453 bp), and the organization of the intergenic sequences consisting of spacious AT-rich regions containing a number of hairpin GC-rich cluster-like elements. In addition to a basic set of the mitochondrial genes coding for the components of cytochrome oxidase, cytochrome b, subunits of ATPase, two rRNA subunits and 25 tRNAs, D. bruxellensis also carries genes for the NADH dehydrogenase complex. Apparently, in yeast, the loss of this complex is not a precondition to develop a petite-positive, Crabtree-positive and anaerobic nature. On the other hand, mtDNA from a petite-negative Brettanomyces custersianus is much smaller (30 058 bp); it contains a similar gene set and has only short intergenic sequences.
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Affiliation(s)
- Emanuel Procházka
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
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33
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Feketová Z, Masek T, Vopálenský V, Pospísek M. Ambiguous decoding of the CUG codon alters the functionality of the Candida albicans translation initiation factor 4E. FEMS Yeast Res 2010; 10:558-69. [PMID: 20491942 DOI: 10.1111/j.1567-1364.2010.00629.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The eukaryotic translation initiation factor 4E is an essential and highly conserved protein. As a part of the translational machinery, it plays a key role in the recruitment of mRNA via binding to its m(7)GpppN 5' terminal cap structure. The opportunistic human pathogen Candida albicans is the only known eukaryotic organism with the ability to survive defects in mRNA capping, which suggests unique features of its eIF4E protein. Here, we provide the first experimental evidence of the function of the C. albicans putative gene orf19.7626 as an eIF4E protein. We also show that Ca4E(Leu116) and Ca4E(Ser116) protein variants, both of which occur naturally in C. albicans due to the ambiguous decoding of the CUG(116) codon, display different sensitivities to elevated temperature. Our results clearly point to the importance of the S4-H4 loop for the function of the Ca4E translation initiation factor, and suggest the possible regulatory role of the codon-reading ambiguity within this loop in C. albicans. We proved Saccharomyces cerevisiae as a useful tool organism for studies of C. albicans translation initiation apparatus.
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Affiliation(s)
- Zuzana Feketová
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
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34
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35
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Innate immune and chemically triggered oxidative stress modifies translational fidelity. Nature 2010; 462:522-6. [PMID: 19940929 PMCID: PMC2785853 DOI: 10.1038/nature08576] [Citation(s) in RCA: 250] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2009] [Accepted: 10/09/2009] [Indexed: 12/12/2022]
Abstract
Translational fidelity, essential for protein and cell function, requires accurate tRNA aminoacylation. Purified aminoacyl-tRNA synthetases exhibit a fidelity of 1 error per 10,000 to 100,000 couplings 1, 2. The accuracy of tRNA aminoacylation in vivo is uncertain, however, and might be considerably lower 3–6. Here, we show that in mammalian cells, approximately 1% of methionine (Met) residues used in protein synthesis are aminoacylated to non-methionyl-tRNAs. Remarkably, Met-misacylation increases up to 10-fold upon exposing cells to live or non-infectious viruses, toll-like receptor ligands, or chemically induced oxidative stress. Met is misacylated to specific non-methionyl-tRNA families, and these Met-misacylated tRNAs are used in translation. Met-misacylation is blocked by an inhibitor of cellular oxidases, implicating reactive oxygen species (ROS) as the misacylation trigger. Among six amino acids tested, tRNA misacylation occurs exclusively with Met. As Met residues are known to protect proteins against ROS-mediated damage 7, we propose that Met-misacylation functions adaptively to increase Met incorporation into proteins to protect cells against oxidative stress. In demonstrating an unexpected conditional aspect of decoding mRNA, our findings illustrate the importance of considering alternative iterations of the genetic code.
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36
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Moura GR, Paredes JA, Santos MA. Development of the genetic code: Insights from a fungal codon reassignment. FEBS Lett 2009; 584:334-41. [DOI: 10.1016/j.febslet.2009.11.066] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Revised: 11/17/2009] [Accepted: 11/18/2009] [Indexed: 01/03/2023]
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37
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Abstract
Translating the 4-letter code of RNA into the 22-letter alphabet of proteins is a central feature of cellular life. The fidelity with which mRNA is translated during protein synthesis is determined by two factors: the availability of aminoacyl-tRNAs composed of cognate amino acid:tRNA pairs and the accurate selection of aminoacyl-tRNAs on the ribosome. The role of aminoacyl-tRNA synthetases in translation is to define the genetic code by accurately pairing cognate tRNAs with their corresponding amino acids. Synthetases achieve the amino acid substrate specificity necessary to keep errors in translation to an acceptable level in two ways: preferential binding of the cognate amino acid and selective editing of near-cognate amino acids. Editing significantly decreases the frequency of errors and is important for translational quality control, and many details of the various editing mechanisms and their effect on different cellular systems are now starting to emerge.
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Affiliation(s)
- Jiqiang Ling
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, USA
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38
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Jung PP, Schacherer J, Souciet JL, Potier S, Wincker P, de Montigny J. The complete mitochondrial genome of the yeastPichia sorbitophila. FEMS Yeast Res 2009; 9:903-10. [DOI: 10.1111/j.1567-1364.2009.00540.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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39
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Jiménez-Montaño MA. The fourfold way of the genetic code. Biosystems 2009; 98:105-14. [PMID: 19643160 DOI: 10.1016/j.biosystems.2009.07.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2009] [Revised: 07/14/2009] [Accepted: 07/16/2009] [Indexed: 11/29/2022]
Abstract
We describe a compact representation of the genetic code that factorizes the table in quartets. It represents a "least grammar" for the genetic language. It is justified by the Klein-4 group structure of RNA bases and codon doublets. The matrix of the outer product between the column-vector of bases and the corresponding row-vector V(T)=(C G U A), considered as signal vectors, has a block structure consisting of the four cosets of the KxK group of base transformations acting on doublet AA. This matrix, translated into weak/strong (W/S) and purine/pyrimidine (R/Y) nucleotide classes, leads to a code table with mixed and unmixed families in separate regions. A basic difference between them is the non-commuting (R/Y) doublets: AC/CA, GU/UG. We describe the degeneracy in the canonical code and the systematic changes in deviant codes in terms of the divisors of 24, employing modulo multiplication groups. We illustrate binary sub-codes characterizing mutations in the quartets. We introduce a decision-tree to predict the mode of tRNA recognition corresponding to each codon, and compare our result with related findings by Jestin and Soulé [Jestin, J.-L., Soulé, C., 2007. Symmetries by base substitutions in the genetic code predict 2' or 3' aminoacylation of tRNAs. J. Theor. Biol. 247, 391-394], and the rearrangements of the table by Delarue [Delarue, M., 2007. An asymmetric underlying rule in the assignment of codons: possible clue to a quick early evolution of the genetic code via successive binary choices. RNA 13, 161-169] and Rodin and Rodin [Rodin, S.N., Rodin, A.S., 2008. On the origin of the genetic code: signatures of its primordial complementarity in tRNAs and aminoacyl-tRNA synthetases. Heredity 100, 341-355], respectively.
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Affiliation(s)
- Miguel Angel Jiménez-Montaño
- Division of Mathematics, Science, and Technology, Parker Building, Nova Southeastern University, Fort Lauderdale, FL 33314-7796, USA.
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40
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Souciet JL, Dujon B, Gaillardin C, Johnston M, Baret PV, Cliften P, Sherman DJ, Weissenbach J, Westhof E, Wincker P, Jubin C, Poulain J, Barbe V, Ségurens B, Artiguenave F, Anthouard V, Vacherie B, Val ME, Fulton RS, Minx P, Wilson R, Durrens P, Jean G, Marck C, Martin T, Nikolski M, Rolland T, Seret ML, Casarégola S, Despons L, Fairhead C, Fischer G, Lafontaine I, Leh V, Lemaire M, de Montigny J, Neuvéglise C, Thierry A, Blanc-Lenfle I, Bleykasten C, Diffels J, Fritsch E, Frangeul L, Goëffon A, Jauniaux N, Kachouri-Lafond R, Payen C, Potier S, Pribylova L, Ozanne C, Richard GF, Sacerdot C, Straub ML, Talla E. Comparative genomics of protoploid Saccharomycetaceae. Genome Res 2009; 19:1696-709. [PMID: 19525356 DOI: 10.1101/gr.091546.109] [Citation(s) in RCA: 180] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Our knowledge of yeast genomes remains largely dominated by the extensive studies on Saccharomyces cerevisiae and the consequences of its ancestral duplication, leaving the evolution of the entire class of hemiascomycetes only partly explored. We concentrate here on five species of Saccharomycetaceae, a large subdivision of hemiascomycetes, that we call "protoploid" because they diverged from the S. cerevisiae lineage prior to its genome duplication. We determined the complete genome sequences of three of these species: Kluyveromyces (Lachancea) thermotolerans and Saccharomyces (Lachancea) kluyveri (two members of the newly described Lachancea clade), and Zygosaccharomyces rouxii. We included in our comparisons the previously available sequences of Kluyveromyces lactis and Ashbya (Eremothecium) gossypii. Despite their broad evolutionary range and significant individual variations in each lineage, the five protoploid Saccharomycetaceae share a core repertoire of approximately 3300 protein families and a high degree of conserved synteny. Synteny blocks were used to define gene orthology and to infer ancestors. Far from representing minimal genomes without redundancy, the five protoploid yeasts contain numerous copies of paralogous genes, either dispersed or in tandem arrays, that, altogether, constitute a third of each genome. Ancient, conserved paralogs as well as novel, lineage-specific paralogs were identified.
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Affiliation(s)
-
- Université de Strasbourg, CNRS UMR, France.
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41
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Otto W, Stadler PF, López-Giraldéz F, Townsend JP, Lynch VJ, Wagner GP. Measuring transcription factor-binding site turnover: a maximum likelihood approach using phylogenies. Genome Biol Evol 2009; 1:85-98. [PMID: 20333180 PMCID: PMC2817405 DOI: 10.1093/gbe/evp010] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2009] [Indexed: 12/30/2022] Open
Abstract
A major mode of gene expression evolution is based on changes in cis-regulatory elements (CREs) whose function critically depends on the presence of transcription factor-binding sites (TFBS). Because CREs experience extensive TFBS turnover even with conserved function, alignment-based studies of CRE sequence evolution are limited to very closely related species. Here, we propose an alternative approach based on a stochastic model of TFBS turnover. We implemented a maximum likelihood model that permits variable turnover rates in different parts of the species tree. This model can be used to detect changes in turnover rate as a proxy for differences in the selective pressures acting on TFBS in different clades. We applied this method to five TFBS in the fungi methionine biosynthesis pathway and three TFBS in the HoxA clusters of vertebrates. We find that the estimated turnover rate is generally high, with half-life ranging between approximately 5 and 150 My and a mode around tens of millions of years. This rate is consistent with the finding that even functionally conserved enhancers can show very low sequence similarity. We also detect statistically significant differences in the equilibrium densities of estrogen- and progesterone-response elements in the HoxA clusters between mammal and nonmammal vertebrates. Even more extreme clade-specific differences were found in the fungal data. We conclude that stochastic models of TFBS turnover enable the detection of shifts in the selective pressures acting on CREs in different organisms. The analysis tool, called CRETO (Cis-Regulatory Element Turn-Over) can be downloaded from http://www.bioinf.uni-leipzig.de/Software/creto/.
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Affiliation(s)
- Wolfgang Otto
- Lehrstuhl für Bioinformatik, Institut für Informatik, Universität Leipzig, Leipzig, Germany
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42
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Dostál J, Brynda J, Hrusková-Heidingsfeldová O, Sieglová I, Pichová I, Rezácová P. The crystal structure of the secreted aspartic protease 1 from Candida parapsilosis in complex with pepstatin A. J Struct Biol 2009; 167:145-52. [PMID: 19401235 DOI: 10.1016/j.jsb.2009.04.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Revised: 03/18/2009] [Accepted: 04/17/2009] [Indexed: 01/12/2023]
Abstract
Opportunistic pathogens of the genus Candida cause infections representing a major threat to long-term survival of immunocompromised patients. Virulence of the Candida pathogens is enhanced by production of extracellular proteolytic enzymes and secreted aspartic proteases (Saps) are therefore studied as potential virulence factors and possible targets for therapeutic drug design. Candida parapsilosis is less invasive than C. albicans, however, it is one of the leading causative agents of yeast infections. We report three-dimensional crystal structure of Sapp1p from C. parapsilosis in complex with pepstatin A, the classical inhibitor of aspartic proteases. The structure of Sapp1p was determined from protein isolated from its natural source and represents the first structure of Sap from C. parapsilosis. Overall fold and topology of Sapp1p is very similar to the archetypic fold of monomeric aspartic protease family and known structures of Sap isoenzymes from C. albicans and Sapt1p from C. tropicalis. Structural comparison revealed noticeable differences in the structure of loops surrounding the active site. This resulted in differential character, shape, and size of the substrate binding site explaining divergent substrate specificities and inhibitor affinities. Determination of structures of Sap isoenzymes from various species might contribute to the development of new Sap-specific inhibitors.
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Affiliation(s)
- Jirí Dostál
- Gilead Sciences and IOCB Research Centre, Prague, Czech Republic
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43
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Silva RM, Duarte ICN, Paredes JA, Lima-Costa T, Perrot M, Boucherie H, Goodfellow BJ, Gomes AC, Mateus DD, Moura GR, Santos MAS. The yeast PNC1 longevity gene is up-regulated by mRNA mistranslation. PLoS One 2009; 4:e5212. [PMID: 19381334 PMCID: PMC2667667 DOI: 10.1371/journal.pone.0005212] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2008] [Accepted: 03/16/2009] [Indexed: 11/18/2022] Open
Abstract
Translation fidelity is critical for protein synthesis and to ensure correct cell functioning. Mutations in the protein synthesis machinery or environmental factors that increase synthesis of mistranslated proteins result in cell death and degeneration and are associated with neurodegenerative diseases, cancer and with an increasing number of mitochondrial disorders. Remarkably, mRNA mistranslation plays critical roles in the evolution of the genetic code, can be beneficial under stress conditions in yeast and in Escherichia coli and is an important source of peptides for MHC class I complex in dendritic cells. Despite this, its biology has been overlooked over the years due to technical difficulties in its detection and quantification. In order to shed new light on the biological relevance of mistranslation we have generated codon misreading in Saccharomyces cerevisiae using drugs and tRNA engineering methodologies. Surprisingly, such mistranslation up-regulated the longevity gene PNC1. Similar results were also obtained in cells grown in the presence of amino acid analogues that promote protein misfolding. The overall data showed that PNC1 is a biomarker of mRNA mistranslation and protein misfolding and that PNC1-GFP fusions can be used to monitor these two important biological phenomena in vivo in an easy manner, thus opening new avenues to understand their biological relevance.
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Affiliation(s)
- Raquel M Silva
- Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal
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44
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Atkins JF, Björk GR. A gripping tale of ribosomal frameshifting: extragenic suppressors of frameshift mutations spotlight P-site realignment. Microbiol Mol Biol Rev 2009; 73:178-210. [PMID: 19258537 PMCID: PMC2650885 DOI: 10.1128/mmbr.00010-08] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mutants of translation components which compensate for both -1 and +1 frameshift mutations showed the first evidence for framing malleability. Those compensatory mutants isolated in bacteria and yeast with altered tRNA or protein factors are reviewed here and are considered to primarily cause altered P-site realignment and not altered translocation. Though the first sequenced tRNA mutant which suppressed a +1 frameshift mutation had an extra base in its anticodon loop and led to a textbook "yardstick" model in which the number of anticodon bases determines codon size, this model has long been discounted, although not by all. Accordingly, the reviewed data suggest that reading frame maintenance and translocation are two distinct features of the ribosome. None of the -1 tRNA suppressors have anticodon loops with fewer than the standard seven nucleotides. Many of the tRNA mutants potentially affect tRNA bending and/or stability and can be used for functional assays, and one has the conserved C74 of the 3' CCA substituted. The effect of tRNA modification deficiencies on framing has been particularly informative. The properties of some mutants suggest the use of alternative tRNA anticodon loop stack conformations by individual tRNAs in one translation cycle. The mutant proteins range from defective release factors with delayed decoding of A-site stop codons facilitating P-site frameshifting to altered EF-Tu/EF1alpha to mutant ribosomal large- and small-subunit proteins L9 and S9. Their study is revealing how mRNA slippage is restrained except where it is programmed to occur and be utilized.
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Affiliation(s)
- John F Atkins
- BioSciences Institute, University College, Cork, Ireland.
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45
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Krauke Y, Sychrova H. Functional comparison of plasma-membrane Na+/H+ antiporters from two pathogenic Candida species. BMC Microbiol 2008; 8:80. [PMID: 18492255 PMCID: PMC2424070 DOI: 10.1186/1471-2180-8-80] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2007] [Accepted: 05/20/2008] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The virulence of Candida species depends on many environmental conditions. Extracellular pH and concentration of alkali metal cations belong among important factors. Nevertheless, the contribution of transporters mediating the exchange of alkali metal cations for protons across the plasma membrane to the cell salt tolerance and other physiological properties of various Candida species has not been studied so far. RESULTS The tolerance/sensitivity of four pathogenic Candida species to alkali metal cations was tested and the role of one of the cation transporters in that tolerance (presumed to be the plasma-membrane Na+/H+ antiporter) was studied. The genes encoding these antiporters in the most and least salt sensitive species, C. dubliniensis and C. parapsilosis respectively, were identified, cloned and functionally expressed in the plasma membranes of Saccharomyces cerevisiae cells lacking their own cation exporters. Both CpCnh1 and CdCnh1 antiporters had broad substrate specificity and transported Na+, K+, Li+, and Rb+. Their activity in S. cerevisiae cells differed; CpCnh1p provided cells with a much higher salt tolerance than the CdCnh1 antiporter. The observed difference in activity was confirmed by direct measurements of sodium and potassium efflux mediated by these antiporters. CONCLUSION We have cloned two genes encoding putative Na+/H+ antiporters in C. parapsilosis and C. dubliniensis, and characterized the transport properties of encoded proteins. Our results show that the activity of plasma-membrane Na+/H+ antiporters is one of the factors determining the tolerance of pathogenic Candida species to high external concentrations of alkali metal cations.
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Affiliation(s)
- Yannick Krauke
- Department of Membrane Transport, Institute of Physiology AS CR, v,v,i,, Videnska 1083, 14220 Prague 4, Czech Republic.
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Pelletier B, Mercier A, Durand M, Peter C, Jbel M, Beaudoin J, Labbé S. Expression of Candida albicans Sfu1 in fission yeast complements the loss of the iron-regulatory transcription factor Fep1 and requires Tup co-repressors. Yeast 2007; 24:883-900. [PMID: 17724773 DOI: 10.1002/yea.1539] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The opportunistic pathogenic yeast Candida albicans contains a gene which encodes a putative member of the iron-regulatory GATA factor protein family. This protein, referred to as suppressor of ferric uptake (Sfu1), has two Cys(2)/Cys(2)-type zinc finger domains separated by a conserved Cys-rich region. In Schizosaccharomyces pombe, the GATA-type transcription factor Fe protein 1 (Fep1) represses target gene expression when iron levels exceed those needed by the cell. To ascertain the functional similarity between Sfu1 and Fep1, the C. albicans Sfu1 was expressed in Sz. pombe cells lacking the endogenous fep1(+) gene. We determined that Sfu1 is capable of suppressing iron-related phenotypes of fep1Delta mutant cells. Using a functional SFU1-GFP fusion allele, the Sfu1 protein was localized to the nucleus under both iron-replete and iron-starved conditions. Sfu1 effectively regulated the expression of genes encoding components of the reductive and non-reductive iron transport systems. Furthermore, the iron-responsive regulation mediated by Sfu1 was GATA-dependent. The N-terminal 250 amino acid segment of Sfu1 expressed in and purified from Escherichia coli specifically associated with the hexanucleotide sequence AGATAA in an iron-dependent manner. On the other hand, expression of the full-length C. albicans Sfu1 in Sz. pombe fep1Delta tup11Delta tup12Delta triple mutant cells failed to repress target gene expression under conditions of high iron concentration. Using two-hybrid analysis, we demonstrated that Tup11 and Tup12 physically interacted with Sfu1. Taken together, these results reveal a remarkable functional conservation between Sfu1 from C. albicans and Fep1 from Sz. pombe in their ability to sense excess iron and respond by repressing target gene transcription.
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Affiliation(s)
- Benoit Pelletier
- Département de Biochimie, Faculté de Médecine, Université de Sherbrooke, 3001 12e Ave Nord, Sherbrooke, QC J1H 5N4, Canada
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Silva RM, Paredes JA, Moura GR, Manadas B, Lima-Costa T, Rocha R, Miranda I, Gomes AC, Koerkamp MJG, Perrot M, Holstege FCP, Boucherie H, Santos MAS. Critical roles for a genetic code alteration in the evolution of the genus Candida. EMBO J 2007; 26:4555-65. [PMID: 17932489 PMCID: PMC2063480 DOI: 10.1038/sj.emboj.7601876] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2007] [Accepted: 09/10/2007] [Indexed: 11/09/2022] Open
Abstract
During the last 30 years, several alterations to the standard genetic code have been discovered in various bacterial and eukaryotic species. Sense and nonsense codons have been reassigned or reprogrammed to expand the genetic code to selenocysteine and pyrrolysine. These discoveries highlight unexpected flexibility in the genetic code, but do not elucidate how the organisms survived the proteome chaos generated by codon identity redefinition. In order to shed new light on this question, we have reconstructed a Candida genetic code alteration in Saccharomyces cerevisiae and used a combination of DNA microarrays, proteomics and genetics approaches to evaluate its impact on gene expression, adaptation and sexual reproduction. This genetic manipulation blocked mating, locked yeast in a diploid state, remodelled gene expression and created stress cross-protection that generated adaptive advantages under environmental challenging conditions. This study highlights unanticipated roles for codon identity redefinition during the evolution of the genus Candida, and strongly suggests that genetic code alterations create genetic barriers that speed up speciation.
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Affiliation(s)
- Raquel M Silva
- Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal
| | - João A Paredes
- Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal
| | - Gabriela R Moura
- Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal
| | - Bruno Manadas
- Centre for Neurosciences and Cell Biology, University of Coimbra, Coimbra, Portugal
| | | | - Rita Rocha
- Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal
| | - Isabel Miranda
- Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal
| | - Ana C Gomes
- Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal
| | - Marian J G Koerkamp
- Department of Physiological Chemistry, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Michel Perrot
- Institut de Biochimie et Génétique Cellulaires, CNRS, Bordeaux, France
| | - Frank C P Holstege
- Department of Physiological Chemistry, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Hélian Boucherie
- Institut de Biochimie et Génétique Cellulaires, CNRS, Bordeaux, France
| | - Manuel A S Santos
- Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal
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Miranda I, Rocha R, Santos MC, Mateus DD, Moura GR, Carreto L, Santos MAS. A genetic code alteration is a phenotype diversity generator in the human pathogen Candida albicans. PLoS One 2007; 2:e996. [PMID: 17912373 PMCID: PMC1991585 DOI: 10.1371/journal.pone.0000996] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2007] [Accepted: 09/18/2007] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The discovery of genetic code alterations and expansions in both prokaryotes and eukaryotes abolished the hypothesis of a frozen and universal genetic code and exposed unanticipated flexibility in codon and amino acid assignments. It is now clear that codon identity alterations involve sense and non-sense codons and can occur in organisms with complex genomes and proteomes. However, the biological functions, the molecular mechanisms of evolution and the diversity of genetic code alterations remain largely unknown. In various species of the genus Candida, the leucine CUG codon is decoded as serine by a unique serine tRNA that contains a leucine 5'-CAG-3'anticodon (tRNA(CAG)(Ser)). We are using this codon identity redefinition as a model system to elucidate the evolution of genetic code alterations. METHODOLOGY/PRINCIPAL FINDINGS We have reconstructed the early stages of the Candida genetic code alteration by engineering tRNAs that partially reverted the identity of serine CUG codons back to their standard leucine meaning. Such genetic code manipulation had profound cellular consequences as it exposed important morphological variation, altered gene expression, re-arranged the karyotype, increased cell-cell adhesion and secretion of hydrolytic enzymes. CONCLUSION/SIGNIFICANCE Our study provides the first experimental evidence for an important role of genetic code alterations as generators of phenotypic diversity of high selective potential and supports the hypothesis that they speed up evolution of new phenotypes.
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Affiliation(s)
- Isabel Miranda
- Department of Biology, Centro de Estudos do Ambiente e do Mar (CESAM), University of Aveiro, Aveiro, Portugal
| | - Rita Rocha
- Department of Biology, Centro de Estudos do Ambiente e do Mar (CESAM), University of Aveiro, Aveiro, Portugal
| | - Maria C. Santos
- Department of Biology, Centro de Estudos do Ambiente e do Mar (CESAM), University of Aveiro, Aveiro, Portugal
| | - Denisa D. Mateus
- Department of Biology, Centro de Estudos do Ambiente e do Mar (CESAM), University of Aveiro, Aveiro, Portugal
| | - Gabriela R. Moura
- Department of Biology, Centro de Estudos do Ambiente e do Mar (CESAM), University of Aveiro, Aveiro, Portugal
| | - Laura Carreto
- Department of Biology, Centro de Estudos do Ambiente e do Mar (CESAM), University of Aveiro, Aveiro, Portugal
| | - Manuel A. S. Santos
- Department of Biology, Centro de Estudos do Ambiente e do Mar (CESAM), University of Aveiro, Aveiro, Portugal
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Bacher JM, Waas WF, Metzgar D, de Crécy-Lagard V, Schimmel P. Genetic code ambiguity confers a selective advantage on Acinetobacter baylyi. J Bacteriol 2007; 189:6494-6. [PMID: 17616603 PMCID: PMC1951902 DOI: 10.1128/jb.00622-07] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A primitive genetic code, composed of a smaller set of amino acids, may have expanded via recursive periods of genetic code ambiguity that were followed by specificity. Here we model a step in this process by showing how genetic code ambiguity could result in an enhanced growth rate in Acinetobacter baylyi.
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Affiliation(s)
- Jamie M Bacher
- The Scripps Research Institute, 10550 N. Torrey Pines Rd., BCC-379, La Jolla, CA 92037, USA
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