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Tierney JAS, Świrski M, Tjeldnes H, Mudge JM, Kufel J, Whiffin N, Valen E, Baranov PV. Ribosome Decision Graphs for the Representation of Eukaryotic RNA Translation Complexity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.10.566564. [PMID: 37986835 PMCID: PMC10659439 DOI: 10.1101/2023.11.10.566564] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
The application of ribosome profiling has revealed an unexpected abundance of translation in addition to that responsible for the synthesis of previously annotated protein-coding regions. Multiple short sequences have been found to be translated within single RNA molecules, both within annotated protein-coding and non-coding regions. The biological significance of this translation is a matter of intensive investigation. However, current schematic or annotation-based representations of mRNA translation generally do not account for the apparent multitude of translated regions within the same molecules. They also do not take into account the stochasticity of the process that allows alternative translations of the same RNA molecules by different ribosomes. There is a need for formal representations of mRNA complexity that would enable the analysis of quantitative information on translation and more accurate models for predicting the phenotypic effects of genetic variants affecting translation. To address this, we developed a conceptually novel abstraction that we term Ribosome Decision Graphs (RDGs). RDGs represent translation as multiple ribosome paths through untranslated and translated mRNA segments. We termed the later 'translons'. Non-deterministic events, such as initiation, re-initiation, selenocysteine insertion or ribosomal frameshifting are then represented as branching points. This representation allows for an adequate representation of eukaryotic translation complexity and focuses on locations critical for translation regulation. We show how RDGs can be used for depicting translated regions, analysis of genetic variation and quantitative genome-wide data on translation for characterisation of regulatory modulators of translation.
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Affiliation(s)
- Jack A S Tierney
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
- SFI Centre for Research Training in Genomics Data Science, University College Cork, Cork, Ireland
| | - Michał Świrski
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Håkon Tjeldnes
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Joanna Kufel
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Nicola Whiffin
- The Big Data Institute and Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Eivind Valen
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
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2
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Antonov IV, O’Loughlin S, Gorohovski AN, O’Connor PB, Baranov PV, Atkins JF. Streptomyces rare codon UUA: from features associated with 2 adpA related locations to candidate phage regulatory translational bypassing. RNA Biol 2023; 20:926-942. [PMID: 37968863 PMCID: PMC10732093 DOI: 10.1080/15476286.2023.2270812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 10/02/2023] [Indexed: 11/17/2023] Open
Abstract
In Streptomyces species, the cell cycle involves a switch from an early and vegetative state to a later phase where secondary products including antibiotics are synthesized, aerial hyphae form and sporulation occurs. AdpA, which has two domains, activates the expression of numerous genes involved in the switch from the vegetative growth phase. The adpA mRNA of many Streptomyces species has a UUA codon in a linker region between 5' sequence encoding one domain and 3' sequence encoding its other and C-terminal domain. UUA codons are exceptionally rare in Streptomyces, and its functional cognate tRNA is not present in a fully modified and acylated form, in the early and vegetative phase of the cell cycle though it is aminoacylated later. Here, we report candidate recoding signals that may influence decoding of the linker region UUA. Additionally, a short ORF 5' of the main ORF has been identified with a GUG at, or near, its 5' end and an in-frame UUA near its 3' end. The latter is commonly 5 nucleotides 5' of the main ORF start. Ribosome profiling data show translation of that 5' region. Ten years ago, UUA-mediated translational bypassing was proposed as a sensor by a Streptomyces phage of its host's cell cycle stage and an effector of its lytic/lysogeny switch. We provide the first experimental evidence supportive of this proposal.
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Affiliation(s)
- Ivan V. Antonov
- Russian Academy of Science, Institute of Bioengineering, Research Center of Biotechnology, Moscow, Russia
- Laboratory of Bioinformatics, Faculty of Computer Science, National Research University Higher School of Economics, Moscow, Russia
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Sinéad O’Loughlin
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Alessandro N. Gorohovski
- Russian Academy of Science, Institute of Bioengineering, Research Center of Biotechnology, Moscow, Russia
- Structural Biology and BioComputing Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | | | - Pavel V. Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - John F. Atkins
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
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3
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De Lise F, Strazzulli A, Iacono R, Curci N, Di Fenza M, Maurelli L, Moracci M, Cobucci-Ponzano B. Programmed Deviations of Ribosomes From Standard Decoding in Archaea. Front Microbiol 2021; 12:688061. [PMID: 34149676 PMCID: PMC8211752 DOI: 10.3389/fmicb.2021.688061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/04/2021] [Indexed: 11/13/2022] Open
Abstract
Genetic code decoding, initially considered to be universal and immutable, is now known to be flexible. In fact, in specific genes, ribosomes deviate from the standard translational rules in a programmed way, a phenomenon globally termed recoding. Translational recoding, which has been found in all domains of life, includes a group of events occurring during gene translation, namely stop codon readthrough, programmed ± 1 frameshifting, and ribosome bypassing. These events regulate protein expression at translational level and their mechanisms are well known and characterized in viruses, bacteria and eukaryotes. In this review we summarize the current state-of-the-art of recoding in the third domain of life. In Archaea, it was demonstrated and extensively studied that translational recoding regulates the decoding of the 21st and the 22nd amino acids selenocysteine and pyrrolysine, respectively, and only one case of programmed -1 frameshifting has been reported so far in Saccharolobus solfataricus P2. However, further putative events of translational recoding have been hypothesized in other archaeal species, but not extensively studied and confirmed yet. Although this phenomenon could have some implication for the physiology and adaptation of life in extreme environments, this field is still underexplored and genes whose expression could be regulated by recoding are still poorly characterized. The study of these recoding episodes in Archaea is urgently needed.
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Affiliation(s)
- Federica De Lise
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy
| | - Andrea Strazzulli
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Naples, Italy.,Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Roberta Iacono
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy.,Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Naples, Italy
| | - Nicola Curci
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy.,Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Naples, Italy
| | - Mauro Di Fenza
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy
| | - Luisa Maurelli
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy
| | - Marco Moracci
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy.,Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Naples, Italy.,Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
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4
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O'Loughlin S, Capece MC, Klimova M, Wills NM, Coakley A, Samatova E, O'Connor PBF, Loughran G, Weissman JS, Baranov PV, Rodnina MV, Puglisi JD, Atkins JF. Polysomes Bypass a 50-Nucleotide Coding Gap Less Efficiently Than Monosomes Due to Attenuation of a 5' mRNA Stem-Loop and Enhanced Drop-off. J Mol Biol 2020; 432:4369-4387. [PMID: 32454154 PMCID: PMC7245268 DOI: 10.1016/j.jmb.2020.05.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/08/2020] [Accepted: 05/11/2020] [Indexed: 01/03/2023]
Abstract
Efficient translational bypassing of a 50-nt non-coding gap in a phage T4 topoisomerase subunit gene (gp60) requires several recoding signals. Here we investigate the function of the mRNA stem–loop 5′ of the take-off codon, as well as the importance of ribosome loading density on the mRNA for efficient bypassing. We show that polysomes are less efficient at mediating bypassing than monosomes, both in vitro and in vivo, due to their preventing formation of a stem–loop 5′ of the take-off codon and allowing greater peptidyl-tRNA drop off. A ribosome profiling analysis of phage T4-infected Escherichia coli yielded protected mRNA fragments within the normal size range derived from ribosomes stalled at the take-off codon. However, ribosomes at this position also yielded some 53-nucleotide fragments, 16 longer. These were due to protection of the nucleotides that form the 5′ stem–loop. NMR shows that the 5′ stem–loop is highly dynamic. The importance of different nucleotides in the 5′ stem–loop is revealed by mutagenesis studies. These data highlight the significance of the 5′ stem–loop for the 50-nt bypassing and further enhance appreciation of relevance of the extent of ribosome loading for recoding. Monosomes are more efficient than polysome in mediating 50-nt translational bypassing. A 5′ mRNA stem–loop facilitates translational bypassing by monosomes. Ribosome profiling yields an extra-long, 53-nt, protected fragment of mRNA.
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Affiliation(s)
- Sinéad O'Loughlin
- School of Biochemistry, University College Cork, Western Gateway Building, Western Road, Cork, T12 XF62, Ireland; School of Microbiology, University College Cork, Western Gateway Building, Western Road, Cork, T12 YT57, Ireland
| | - Mark C Capece
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-4090, USA
| | - Mariia Klimova
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Norma M Wills
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112-5330, USA
| | - Arthur Coakley
- School of Biochemistry, University College Cork, Western Gateway Building, Western Road, Cork, T12 XF62, Ireland
| | - Ekaterina Samatova
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Patrick B F O'Connor
- School of Biochemistry, University College Cork, Western Gateway Building, Western Road, Cork, T12 XF62, Ireland
| | - Gary Loughran
- School of Biochemistry, University College Cork, Western Gateway Building, Western Road, Cork, T12 XF62, Ireland
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Pavel V Baranov
- School of Biochemistry, University College Cork, Western Gateway Building, Western Road, Cork, T12 XF62, Ireland; Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow 117997, Russia
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-4090, USA
| | - John F Atkins
- School of Biochemistry, University College Cork, Western Gateway Building, Western Road, Cork, T12 XF62, Ireland; School of Microbiology, University College Cork, Western Gateway Building, Western Road, Cork, T12 YT57, Ireland; Department of Human Genetics, University of Utah, Salt Lake City, UT 84112-5330, USA.
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5
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Discordant evolution of mitochondrial and nuclear yeast genomes at population level. BMC Biol 2020; 18:49. [PMID: 32393264 PMCID: PMC7216626 DOI: 10.1186/s12915-020-00786-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 04/22/2020] [Indexed: 12/31/2022] Open
Abstract
Background Mitochondria are essential organelles partially regulated by their own genomes. The mitochondrial genome maintenance and inheritance differ from the nuclear genome, potentially uncoupling their evolutionary trajectories. Here, we analysed mitochondrial sequences obtained from the 1011 Saccharomyces cerevisiae strain collection and identified pronounced differences with their nuclear genome counterparts. Results In contrast with pre-whole genome duplication fungal species, S. cerevisiae mitochondrial genomes show higher genetic diversity compared to the nuclear genomes. Strikingly, mitochondrial genomes appear to be highly admixed, resulting in a complex interconnected phylogeny with a weak grouping of isolates, whereas interspecies introgressions are very rare. Complete genome assemblies revealed that structural rearrangements are nearly absent with rare inversions detected. We tracked intron variation in COX1 and COB to infer gain and loss events throughout the species evolutionary history. Mitochondrial genome copy number is connected with the nuclear genome and linearly scale up with ploidy. We observed rare cases of naturally occurring mitochondrial DNA loss, petite, with a subset of them that do not suffer the expected growth defect in fermentable rich media. Conclusions Overall, our results illustrate how differences in the biology of two genomes coexisting in the same cells can lead to discordant evolutionary histories.
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6
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Tomáška Ľ, Nosek J. Co-evolution in the Jungle: From Leafcutter Ant Colonies to Chromosomal Ends. J Mol Evol 2020; 88:293-318. [PMID: 32157325 DOI: 10.1007/s00239-020-09935-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 02/25/2020] [Indexed: 02/06/2023]
Abstract
Biological entities are multicomponent systems where each part is directly or indirectly dependent on the others. In effect, a change in a single component might have a consequence on the functioning of its partners, thus affecting the fitness of the entire system. In this article, we provide a few examples of such complex biological systems, ranging from ant colonies to a population of amino acids within a single-polypeptide chain. Based on these examples, we discuss one of the central and still challenging questions in biology: how do such multicomponent consortia co-evolve? More specifically, we ask how telomeres, nucleo-protein complexes protecting the integrity of linear DNA chromosomes, originated from the ancestral organisms having circular genomes and thus not dealing with end-replication and end-protection problems. Using the examples of rapidly evolving topologies of mitochondrial genomes in eukaryotic microorganisms, we show what means of co-evolution were employed to accommodate various types of telomere-maintenance mechanisms in mitochondria. We also describe an unprecedented runaway evolution of telomeric repeats in nuclei of ascomycetous yeasts accompanied by co-evolution of telomere-associated proteins. We propose several scenarios derived from research on telomeres and supported by other studies from various fields of biology, while emphasizing that the relevant answers are still not in sight. It is this uncertainty and a lack of a detailed roadmap that makes the journey through the jungle of biological systems still exciting and worth undertaking.
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Affiliation(s)
- Ľubomír Tomáška
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15, Bratislava, Slovakia.
| | - Jozef Nosek
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15, Bratislava, Slovakia
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7
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Dujon B. Mitochondrial genetics revisited. Yeast 2020; 37:191-205. [DOI: 10.1002/yea.3445] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 10/05/2019] [Accepted: 10/08/2019] [Indexed: 12/17/2022] Open
Affiliation(s)
- Bernard Dujon
- Department Genomes and GeneticsInstitut Pasteur Paris France
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8
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Talotta R, Sarzi-Puttini P, Laska MJ, Atzeni F. Retrotransposons shuttling genetic and epigenetic information from the nuclear to the mitochondrial compartment: Do they play a pathogenetic role in scleroderma? Cytokine Growth Factor Rev 2019; 49:42-58. [PMID: 31677967 DOI: 10.1016/j.cytogfr.2019.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 10/09/2019] [Accepted: 10/10/2019] [Indexed: 10/25/2022]
Abstract
Endogenous retroelements are a class of ancient defective viral insertions contained in the genome of host cells, where they account for up to 40% of all DNA. Centuries of co-existence in host genome have led to the development of immunotolerance to endogenous retroelements, most of which are defective and unable to replicate or transcribe functional proteins. However, given their capacity to move across the nuclear and mitochondrial genome and recombine, they could mix phenotypes and give rise to infections that may trigger innate and adaptive immune responses by sensing receptors capable of recognising foreign nucleic acids and proteins. It has recently been suggested that they play a role in the pathogenesis of autoimmune diseases on the grounds of their partial reactivation or the epigenetic control of host gene transcription. A number of studies have confirmed their contribution to the development of rheumatoid arthritis, multiple sclerosis and systemic lupus erythematosus, but there is still a lack of data concerning systemic sclerosis (SSc). Their role in the pathogenesis of SSc can be hypothesised on the basis of mitochondrial and nuclear chromatinic damage, and hyper-activation of the immune pathway involved in antiviral defense. SSc is characterised by genetic and immunological evidence of a viral infection but, as no viral agent has yet been isolated from SSc patients, the hypothesis that partial reactivation of endogenous retroviruses may trigger the disease cannot be excluded and deserves further investigation.
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Affiliation(s)
- Rossella Talotta
- Rheumatology Unit, University of Messina, Azienda Ospedaliera Gaetano Martino, Via Consolare Valeria 1, 98100 Messina, Italy.
| | - Piercarlo Sarzi-Puttini
- Rheumatology Unit, University Hospital ASST-Fatebenefratelli-Sacco, Via G.B Grassi 74, 20157 Milan, Italy.
| | | | - Fabiola Atzeni
- Rheumatology Unit, University of Messina, Azienda Ospedaliera Gaetano Martino, Via Consolare Valeria 1, 98100 Messina, Italy.
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9
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Brejová B, Lichancová H, Brázdovič F, Hegedűsová E, Forgáčová Jakúbková M, Hodorová V, Džugasová V, Baláž A, Zeiselová L, Cillingová A, Neboháčová M, Raclavský V, Tomáška Ľ, Lang BF, Vinař T, Nosek J. Genome sequence of the opportunistic human pathogen Magnusiomyces capitatus. Curr Genet 2018; 65:539-560. [PMID: 30456648 DOI: 10.1007/s00294-018-0904-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 11/12/2018] [Accepted: 11/13/2018] [Indexed: 01/12/2023]
Abstract
The yeast Magnusiomyces capitatus is an opportunistic human pathogen causing rare yet severe infections, especially in patients with hematological malignancies. Here, we report the 20.2 megabase genome sequence of an environmental strain of this species as well as the genome sequences of eight additional isolates from human and animal sources providing an insight into intraspecies variation. The distribution of single-nucleotide variants is indicative of genetic recombination events, supporting evidence for sexual reproduction in this heterothallic yeast. Using RNAseq-aided annotation, we identified genes for 6518 proteins including several expanded families such as kexin proteases and Hsp70 molecular chaperones. Several of these families are potentially associated with the ability of M. capitatus to infect and colonize humans. For the purpose of comparative analysis, we also determined the genome sequence of a closely related yeast, Magnusiomyces ingens. The genome sequences of M. capitatus and M. ingens exhibit many distinct features and represent a basis for further comparative and functional studies.
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Affiliation(s)
- Bronislava Brejová
- Faculty of Mathematics, Physics, and Informatics, Comenius University in Bratislava, Bratislava, Slovakia.
| | - Hana Lichancová
- Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Filip Brázdovič
- Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Eva Hegedűsová
- Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia.,Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | | | - Viktória Hodorová
- Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Vladimíra Džugasová
- Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Andrej Baláž
- Faculty of Mathematics, Physics, and Informatics, Comenius University in Bratislava, Bratislava, Slovakia
| | - Lucia Zeiselová
- Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Andrea Cillingová
- Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Martina Neboháčová
- Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Vladislav Raclavský
- Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Ľubomír Tomáška
- Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - B Franz Lang
- Robert Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montréal, QC, Canada
| | - Tomáš Vinař
- Faculty of Mathematics, Physics, and Informatics, Comenius University in Bratislava, Bratislava, Slovakia
| | - Jozef Nosek
- Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia.
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10
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Burger G, Moreira S, Valach M. Genes in Hiding. Trends Genet 2016; 32:553-565. [PMID: 27460648 DOI: 10.1016/j.tig.2016.06.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 06/23/2016] [Accepted: 06/24/2016] [Indexed: 12/25/2022]
Abstract
Unrecognizable genes are an unsettling problem in genomics. Here, we survey the various types of cryptic genes and the corresponding deciphering strategies employed by cells. Encryption that renders genes substantially different from homologs in other species includes sequence substitution, insertion, deletion, fragmentation plus scrambling, and invasion by mobile genetic elements. Cells decode cryptic genes at the DNA, RNA or protein level. We will focus on a recently discovered case of unparalleled encryption involving massive gene fragmentation and nucleotide deletions and substitutions, occurring in the mitochondrial genome of a poorly understood protist group, the diplonemids. This example illustrates that comprehensive gene detection requires not only auxiliary sequence information - transcriptome and proteome data - but also knowledge about a cell's deciphering arsenal.
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Affiliation(s)
- Gertraud Burger
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Canada.
| | - Sandrine Moreira
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Canada
| | - Matus Valach
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Canada
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11
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Atkins JF, Loughran G, Bhatt PR, Firth AE, Baranov PV. Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use. Nucleic Acids Res 2016; 44:7007-78. [PMID: 27436286 PMCID: PMC5009743 DOI: 10.1093/nar/gkw530] [Citation(s) in RCA: 161] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/26/2016] [Indexed: 12/15/2022] Open
Abstract
Genetic decoding is not ‘frozen’ as was earlier thought, but dynamic. One facet of this is frameshifting that often results in synthesis of a C-terminal region encoded by a new frame. Ribosomal frameshifting is utilized for the synthesis of additional products, for regulatory purposes and for translational ‘correction’ of problem or ‘savior’ indels. Utilization for synthesis of additional products occurs prominently in the decoding of mobile chromosomal element and viral genomes. One class of regulatory frameshifting of stable chromosomal genes governs cellular polyamine levels from yeasts to humans. In many cases of productively utilized frameshifting, the proportion of ribosomes that frameshift at a shift-prone site is enhanced by specific nascent peptide or mRNA context features. Such mRNA signals, which can be 5′ or 3′ of the shift site or both, can act by pairing with ribosomal RNA or as stem loops or pseudoknots even with one component being 4 kb 3′ from the shift site. Transcriptional realignment at slippage-prone sequences also generates productively utilized products encoded trans-frame with respect to the genomic sequence. This too can be enhanced by nucleic acid structure. Together with dynamic codon redefinition, frameshifting is one of the forms of recoding that enriches gene expression.
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Affiliation(s)
- John F Atkins
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland School of Microbiology, University College Cork, Cork, Ireland Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Gary Loughran
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Pramod R Bhatt
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Andrew E Firth
- Division of Virology, Department of Pathology, University of Cambridge, Hills Road, Cambridge CB2 0QQ, UK
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
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12
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The molecular choreography of protein synthesis: translational control, regulation, and pathways. Q Rev Biophys 2016; 49:e11. [PMID: 27658712 DOI: 10.1017/s0033583516000056] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Translation of proteins by the ribosome regulates gene expression, with recent results underscoring the importance of translational control. Misregulation of translation underlies many diseases, including cancer and many genetic diseases. Decades of biochemical and structural studies have delineated many of the mechanistic details in prokaryotic translation, and sketched the outlines of eukaryotic translation. However, translation may not proceed linearly through a single mechanistic pathway, but likely involves multiple pathways and branchpoints. The stochastic nature of biological processes would allow different pathways to occur during translation that are biased by the interaction of the ribosome with other translation factors, with many of the steps kinetically controlled. These multiple pathways and branchpoints are potential regulatory nexus, allowing gene expression to be tuned at the translational level. As research focus shifts toward eukaryotic translation, certain themes will be echoed from studies on prokaryotic translation. This review provides a general overview of the dynamic data related to prokaryotic and eukaryotic translation, in particular recent findings with single-molecule methods, complemented by biochemical, kinetic, and structural findings. We will underscore the importance of viewing the process through the viewpoints of regulation, translational control, and heterogeneous pathways.
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13
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Burger G. Non-functional genes repaired at the RNA level. C R Biol 2016; 339:289-95. [PMID: 27180109 DOI: 10.1016/j.crvi.2016.04.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 04/12/2016] [Indexed: 11/29/2022]
Abstract
Genomes and genes continuously evolve. Gene sequences undergo substitutions, deletions or nucleotide insertions; mobile genetic elements invade genomes and interleave in genes; chromosomes break, even within genes, and pieces reseal in reshuffled order. To maintain functional gene products and assure an organism's survival, two principal strategies are used - either repair of the gene itself or of its product. I will introduce common types of gene aberrations and how gene function is restored secondarily, and then focus on systematically fragmented genes found in a poorly studied protist group, the diplonemids. Expression of their broken genes involves restitching of pieces at the RNA-level, and substantial RNA editing, to compensate for point mutations. I will conclude with thoughts on how such a grotesquely unorthodox system may have evolved, and why this group of organisms persists and thrives since tens of millions of years.
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Affiliation(s)
- Gertraud Burger
- Department of Biochemistry, Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montréal, Canada.
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14
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Coupling of mRNA Structure Rearrangement to Ribosome Movement during Bypassing of Non-coding Regions. Cell 2016; 163:1267-1280. [PMID: 26590426 DOI: 10.1016/j.cell.2015.10.064] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 09/07/2015] [Accepted: 10/21/2015] [Indexed: 01/13/2023]
Abstract
Nearly half of the ribosomes translating a particular bacteriophage T4 mRNA bypass a region of 50 nt, resuming translation 3' of this gap. How this large-scale, specific hop occurs and what determines whether a ribosome bypasses remain unclear. We apply single-molecule fluorescence with zero-mode waveguides to track individual Escherichia coli ribosomes during translation of T4's gene 60 mRNA. Ribosomes that bypass are characterized by a 10- to 20-fold longer pause in a non-canonical rotated state at the take-off codon. During the pause, mRNA secondary structure rearrangements are coupled to ribosome forward movement, facilitated by nascent peptide interactions that disengage the ribosome anticodon-codon interactions for slippage. Close to the landing site, the ribosome then scans mRNA in search of optimal base-pairing interactions. Our results provide a mechanistic and conformational framework for bypassing, highlighting a non-canonical ribosomal state to allow for mRNA structure refolding to drive large-scale ribosome movements.
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15
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Wolters JF, Chiu K, Fiumera HL. Population structure of mitochondrial genomes in Saccharomyces cerevisiae. BMC Genomics 2015; 16:451. [PMID: 26062918 PMCID: PMC4464245 DOI: 10.1186/s12864-015-1664-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 05/29/2015] [Indexed: 12/13/2022] Open
Abstract
Background Rigorous study of mitochondrial functions and cell biology in the budding yeast, Saccharomyces cerevisiae has advanced our understanding of mitochondrial genetics. This yeast is now a powerful model for population genetics, owing to large genetic diversity and highly structured populations among wild isolates. Comparative mitochondrial genomic analyses between yeast species have revealed broad evolutionary changes in genome organization and architecture. A fine-scale view of recent evolutionary changes within S. cerevisiae has not been possible due to low numbers of complete mitochondrial sequences. Results To address challenges of sequencing AT-rich and repetitive mitochondrial DNAs (mtDNAs), we sequenced two divergent S. cerevisiae mtDNAs using a single-molecule sequencing platform (PacBio RS). Using de novo assemblies, we generated highly accurate complete mtDNA sequences. These mtDNA sequences were compared with 98 additional mtDNA sequences gathered from various published collections. Phylogenies based on mitochondrial coding sequences and intron profiles revealed that intraspecific diversity in mitochondrial genomes generally recapitulated the population structure of nuclear genomes. Analysis of intergenic sequence indicated a recent expansion of mobile elements in certain populations. Additionally, our analyses revealed that certain populations lacked introns previously believed conserved throughout the species, as well as the presence of introns never before reported in S. cerevisiae. Conclusions Our results revealed that the extensive variation in S. cerevisiae mtDNAs is often population specific, thus offering a window into the recent evolutionary processes shaping these genomes. In addition, we offer an effective strategy for sequencing these challenging AT-rich mitochondrial genomes for small scale projects. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1664-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- John F Wolters
- Department of Biological Sciences, Binghamton University, Binghamton, NY, USA.
| | - Kenneth Chiu
- Computer Science Department, Binghamton University, Binghamton, NY, USA.
| | - Heather L Fiumera
- Department of Biological Sciences, Binghamton University, Binghamton, NY, USA.
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