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Bradley CC, Wang C, Gordon AJE, Wen AX, Luna PN, Cooke MB, Kohrn BF, Kennedy SR, Avadhanula V, Piedra PA, Lichtarge O, Shaw CA, Ronca SE, Herman C. Targeted accurate RNA consensus sequencing (tARC-seq) reveals mechanisms of replication error affecting SARS-CoV-2 divergence. Nat Microbiol 2024; 9:1382-1392. [PMID: 38649410 DOI: 10.1038/s41564-024-01655-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/28/2024] [Indexed: 04/25/2024]
Abstract
RNA viruses, like SARS-CoV-2, depend on their RNA-dependent RNA polymerases (RdRp) for replication, which is error prone. Monitoring replication errors is crucial for understanding the virus's evolution. Current methods lack the precision to detect rare de novo RNA mutations, particularly in low-input samples such as those from patients. Here we introduce a targeted accurate RNA consensus sequencing method (tARC-seq) to accurately determine the mutation frequency and types in SARS-CoV-2, both in cell culture and clinical samples. Our findings show an average of 2.68 × 10-5 de novo errors per cycle with a C > T bias that cannot be solely attributed to APOBEC editing. We identified hotspots and cold spots throughout the genome, correlating with high or low GC content, and pinpointed transcription regulatory sites as regions more susceptible to errors. tARC-seq captured template switching events including insertions, deletions and complex mutations. These insights shed light on the genetic diversity generation and evolutionary dynamics of SARS-CoV-2.
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Affiliation(s)
- Catherine C Bradley
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor College of Medicine Medical Scientist Training Program, Houston, TX, USA
- Robert and Janice McNair Foundation/ McNair Medical Institute M.D./Ph.D. Scholars program, Houston, TX, USA
| | - Chen Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Alasdair J E Gordon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Alice X Wen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor College of Medicine Medical Scientist Training Program, Houston, TX, USA
- Robert and Janice McNair Foundation/ McNair Medical Institute M.D./Ph.D. Scholars program, Houston, TX, USA
| | - Pamela N Luna
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Matthew B Cooke
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Brendan F Kohrn
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Scott R Kennedy
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Pedro A Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Shannon E Ronca
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Feigin Biosafety Level 3 Facility, Texas Children's Hospital, Houston, TX, USA
- National School of Tropical Medicine, Department of Pediatrics Tropical Medicine, Texas Children's Hospital and Baylor College of Medicine, Houston, TX, USA
| | - Christophe Herman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA.
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Szekely O, Rangadurai AK, Gu S, Manghrani A, Guseva S, Al-Hashimi HM. NMR measurements of transient low-populated tautomeric and anionic Watson-Crick-like G·T/U in RNA:DNA hybrids: implications for the fidelity of transcription and CRISPR/Cas9 gene editing. Nucleic Acids Res 2024; 52:2672-2685. [PMID: 38281263 PMCID: PMC10954477 DOI: 10.1093/nar/gkae027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 01/02/2024] [Accepted: 01/17/2024] [Indexed: 01/30/2024] Open
Abstract
Many biochemical processes use the Watson-Crick geometry to distinguish correct from incorrect base pairing. However, on rare occasions, mismatches such as G·T/U can transiently adopt Watson-Crick-like conformations through tautomerization or ionization of the bases, giving rise to replicative and translational errors. The propensities to form Watson-Crick-like mismatches in RNA:DNA hybrids remain unknown, making it unclear whether they can also contribute to errors during processes such as transcription and CRISPR/Cas editing. Here, using NMR R1ρ experiments, we show that dG·rU and dT·rG mismatches in two RNA:DNA hybrids transiently form tautomeric (Genol·T/U $ \mathbin{\lower.3ex\hbox{$\buildrel\textstyle\rightarrow\over {\smash{\leftarrow}\vphantom{_{\vbox to.5ex{\vss}}}}$}}$ G·Tenol/Uenol) and anionic (G·T-/U-) Watson-Crick-like conformations. The tautomerization dynamics were like those measured in A-RNA and B-DNA duplexes. However, anionic dG·rU- formed with a ten-fold higher propensity relative to dT-·rG and dG·dT- and this could be attributed to the lower pKa (ΔpKa ∼0.4-0.9) of U versus T. Our findings suggest plausible roles for Watson-Crick-like G·T/U mismatches in transcriptional errors and CRISPR/Cas9 off-target gene editing, uncover a crucial difference between the chemical dynamics of G·U versus G·T, and indicate that anionic Watson-Crick-like G·U- could play a significant role evading Watson-Crick fidelity checkpoints in RNA:DNA hybrids and RNA duplexes.
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Affiliation(s)
- Or Szekely
- Department of Biology, Duke University, Durham, NC 27710, USA
- Howard Hughes Medical Institute, Duke University, Durham, NC 27710, USA
| | | | - Stephanie Gu
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, NY, NY 10032, USA
| | - Akanksha Manghrani
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, NY, NY 10032, USA
| | - Serafima Guseva
- Department of Biochemistry and Molecular Biophysics, Columbia University, NY, NY 10032, USA
| | - Hashim M Al-Hashimi
- Department of Biochemistry and Molecular Biophysics, Columbia University, NY, NY 10032, USA
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Bénitière F, Necsulea A, Duret L. Random genetic drift sets an upper limit on mRNA splicing accuracy in metazoans. eLife 2024; 13:RP93629. [PMID: 38470242 DOI: 10.7554/elife.93629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024] Open
Abstract
Most eukaryotic genes undergo alternative splicing (AS), but the overall functional significance of this process remains a controversial issue. It has been noticed that the complexity of organisms (assayed by the number of distinct cell types) correlates positively with their genome-wide AS rate. This has been interpreted as evidence that AS plays an important role in adaptive evolution by increasing the functional repertoires of genomes. However, this observation also fits with a totally opposite interpretation: given that 'complex' organisms tend to have small effective population sizes (Ne), they are expected to be more affected by genetic drift, and hence more prone to accumulate deleterious mutations that decrease splicing accuracy. Thus, according to this 'drift barrier' theory, the elevated AS rate in complex organisms might simply result from a higher splicing error rate. To test this hypothesis, we analyzed 3496 transcriptome sequencing samples to quantify AS in 53 metazoan species spanning a wide range of Ne values. Our results show a negative correlation between Ne proxies and the genome-wide AS rates among species, consistent with the drift barrier hypothesis. This pattern is dominated by low abundance isoforms, which represent the vast majority of the splice variant repertoire. We show that these low abundance isoforms are depleted in functional AS events, and most likely correspond to errors. Conversely, the AS rate of abundant isoforms, which are relatively enriched in functional AS events, tends to be lower in more complex species. All these observations are consistent with the hypothesis that variation in AS rates across metazoans reflects the limits set by drift on the capacity of selection to prevent gene expression errors.
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Affiliation(s)
- Florian Bénitière
- Laboratoire de Biometrie et Biologie Evolutive, CNRS, Universite Lyon 1, Villeurbanne, France
| | - Anamaria Necsulea
- Laboratoire de Biometrie et Biologie Evolutive, CNRS, Universite Lyon 1, Villeurbanne, France
| | - Laurent Duret
- Laboratoire de Biometrie et Biologie Evolutive, CNRS, Universite Lyon 1, Villeurbanne, France
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Szekely O, Rangadurai AK, Gu S, Manghrani A, Guseva S, Al-Hashimi HM. NMR measurements of transient low-populated tautomeric and anionic Watson-Crick-like G·T/U in RNA:DNA hybrids: Implications for the fidelity of transcription and CRISPR/Cas9 gene editing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.24.554670. [PMID: 37662220 PMCID: PMC10473728 DOI: 10.1101/2023.08.24.554670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Many biochemical processes use the Watson-Crick geometry to distinguish correct from incorrect base pairing. However, on rare occasions, mismatches such as G•T/U can transiently adopt Watson-Crick-like conformations through tautomerization or ionization of the bases, giving rise to replicative and translational errors. The propensities to form Watson-Crick-like mismatches in RNA:DNA hybrids remain unknown, making it unclear whether they can also contribute to errors during processes such as transcription and CRISPR/Cas editing. Here, using NMR R 1ρ experiments, we show that dG•rU and dT•rG mismatches in two RNA:DNA hybrids transiently form tautomeric (G enol •T/U ⇄G•T enol /U enol ) and anionic (G•T - /U - ) Watson-Crick-like conformations. The tautomerization dynamics were like those measured in A-RNA and B-DNA duplexes. However, anionic dG•rU - formed with a ten-fold higher propensity relative to dT - •rG and dG•dT - and this could be attributed to the lower pK a (Δ pK a ∼0.4-0.9) of U versus T. Our findings suggest plausible roles for Watson-Crick-like G•T/U mismatches in transcriptional errors and CRISPR/Cas9 off-target gene editing, uncover a crucial difference between the chemical dynamics of G•U versus G•T, and indicate that anionic Watson-Crick-like G•U - could play a significant role evading Watson-Crick fidelity checkpoints in RNA:DNA hybrids and RNA duplexes.
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Zhang M, Bouland GA, Holstege H, Reinders MJT. Identifying Aging and Alzheimer Disease-Associated Somatic Variations in Excitatory Neurons From the Human Frontal Cortex. Neurol Genet 2023; 9:e200066. [PMID: 37123987 PMCID: PMC10136684 DOI: 10.1212/nxg.0000000000200066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 02/03/2023] [Indexed: 05/02/2023]
Abstract
Background and Objectives With age, somatic mutations accumulated in human brain cells can lead to various neurologic disorders and brain tumors. Because the incidence rate of Alzheimer disease (AD) increases exponentially with age, investigating the association between AD and the accumulation of somatic mutation can help understand the etiology of AD. Methods We designed a somatic mutation detection workflow by contrasting genotypes derived from whole-genome sequencing (WGS) data with genotypes derived from scRNA-seq data and applied this workflow to 76 participants from the Religious Order Study and the Rush Memory and Aging Project (ROSMAP) cohort. We focused only on excitatory neurons, the dominant cell type in the scRNA-seq data. Results We identified 196 sites that harbored at least 1 individual with an excitatory neuron-specific somatic mutation (ENSM), and these 196 sites were mapped to 127 genes. The single base substitution (SBS) pattern of the putative ENSMs was best explained by signature SBS5 from the Catalogue of Somatic Mutations in Cancer (COSMIC) mutational signatures, a clock-like pattern correlating with the age of the individual. The count of ENSMs per individual also showed an increasing trend with age. Among the mutated sites, we found 2 sites tend to have more mutations in older individuals (16:6899517 [RBFOX1], p = 0.04; 4:21788463 [KCNIP4], p < 0.05). In addition, 2 sites were found to have a higher odds ratio to detect a somatic mutation in AD samples (6:73374221 [KCNQ5], p = 0.01 and 13:36667102 [DCLK1], p = 0.02). Thirty-two genes that harbor somatic mutations unique to AD and the KCNQ5 and DCLK1 genes were used for gene ontology (GO)-term enrichment analysis. We found the AD-specific ENSMs enriched in the GO-term "vocalization behavior" and "intraspecies interaction between organisms." Of interest we observed both age-specific and AD-specific ENSMs enriched in the K+ channel-associated genes. Discussion Our results show that combining scRNA-seq and WGS data can successfully detect putative somatic mutations. The putative somatic mutations detected from ROSMAP data set have provided new insights into the association of AD and aging with brain somatic mutagenesis.
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Affiliation(s)
- Meng Zhang
- Delft Bioinformatics Lab (M.Z., G.A.B., H.H., M.J.T.R.), Delft University of Technology; Department of Human Genetics (M.Z., H.H.), Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC; and Department of Human Genetics (G.A.B., M.J.T.R.), Leiden University Medical Center, the Netherlands
| | - Gerard A Bouland
- Delft Bioinformatics Lab (M.Z., G.A.B., H.H., M.J.T.R.), Delft University of Technology; Department of Human Genetics (M.Z., H.H.), Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC; and Department of Human Genetics (G.A.B., M.J.T.R.), Leiden University Medical Center, the Netherlands
| | - Henne Holstege
- Delft Bioinformatics Lab (M.Z., G.A.B., H.H., M.J.T.R.), Delft University of Technology; Department of Human Genetics (M.Z., H.H.), Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC; and Department of Human Genetics (G.A.B., M.J.T.R.), Leiden University Medical Center, the Netherlands
| | - Marcel J T Reinders
- Delft Bioinformatics Lab (M.Z., G.A.B., H.H., M.J.T.R.), Delft University of Technology; Department of Human Genetics (M.Z., H.H.), Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC; and Department of Human Genetics (G.A.B., M.J.T.R.), Leiden University Medical Center, the Netherlands
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6
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Rodnina MV. Decoding and Recoding of mRNA Sequences by the Ribosome. Annu Rev Biophys 2023; 52:161-182. [PMID: 37159300 DOI: 10.1146/annurev-biophys-101922-072452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Faithful translation of messenger RNA (mRNA) into protein is essential to maintain protein homeostasis in the cell. Spontaneous translation errors are very rare due to stringent selection of cognate aminoacyl transfer RNAs (tRNAs) and the tight control of the mRNA reading frame by the ribosome. Recoding events, such as stop codon readthrough, frameshifting, and translational bypassing, reprogram the ribosome to make intentional mistakes and produce alternative proteins from the same mRNA. The hallmark of recoding is the change of ribosome dynamics. The signals for recoding are built into the mRNA, but their reading depends on the genetic makeup of the cell, resulting in cell-specific changes in expression programs. In this review, I discuss the mechanisms of canonical decoding and tRNA-mRNA translocation; describe alternative pathways leading to recoding; and identify the links among mRNA signals, ribosome dynamics, and recoding.
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Affiliation(s)
- Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany;
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7
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Romero Romero ML, Landerer C, Poehls J, Toth‐Petroczy A. Phenotypic mutations contribute to protein diversity and shape protein evolution. Protein Sci 2022; 31:e4397. [PMID: 36040266 PMCID: PMC9375231 DOI: 10.1002/pro.4397] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/14/2022] [Accepted: 07/04/2022] [Indexed: 11/16/2022]
Abstract
Errors in DNA replication generate genetic mutations, while errors in transcription and translation lead to phenotypic mutations. Phenotypic mutations are orders of magnitude more frequent than genetic ones, yet they are less understood. Here, we review the types of phenotypic mutations, their quantifications, and their role in protein evolution and disease. The diversity generated by phenotypic mutation can facilitate adaptive evolution. Indeed, phenotypic mutations, such as ribosomal frameshift and stop codon readthrough, sometimes serve to regulate protein expression and function. Phenotypic mutations have often been linked to fitness decrease and diseases. Thus, understanding the protein heterogeneity and phenotypic diversity caused by phenotypic mutations will advance our understanding of protein evolution and have implications on human health and diseases.
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Affiliation(s)
- Maria Luisa Romero Romero
- Max Planck Institute of Molecular Cell Biology and Genetics Dresden Germany
- Center for Systems Biology Dresden Dresden Germany
| | - Cedric Landerer
- Max Planck Institute of Molecular Cell Biology and Genetics Dresden Germany
- Center for Systems Biology Dresden Dresden Germany
| | - Jonas Poehls
- Max Planck Institute of Molecular Cell Biology and Genetics Dresden Germany
- Center for Systems Biology Dresden Dresden Germany
| | - Agnes Toth‐Petroczy
- Max Planck Institute of Molecular Cell Biology and Genetics Dresden Germany
- Center for Systems Biology Dresden Dresden Germany
- Cluster of Excellence Physics of Life TU Dresden Dresden Germany
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8
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Ho AT, Hurst LD. Stop codon usage as a window into genome evolution: mutation, selection, biased gene conversion and the TAG paradox. Genome Biol Evol 2022; 14:6648529. [PMID: 35867377 PMCID: PMC9348620 DOI: 10.1093/gbe/evac115] [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] [Accepted: 07/17/2022] [Indexed: 11/16/2022] Open
Abstract
Protein coding genes terminate with one of three stop codons (TAA, TGA, or TAG) that, like synonymous codons, are not employed equally. With TGA and TAG having identical nucleotide content, analysis of their differential usage provides an unusual window into the forces operating on what are ostensibly functionally identical residues. Across genomes and between isochores within the human genome, TGA usage increases with G + C content but, with a common G + C → A + T mutation bias, this cannot be explained by mutation bias-drift equilibrium. Increased usage of TGA in G + C-rich genomes or genomic regions is also unlikely to reflect selection for the optimal stop codon, as TAA appears to be universally optimal, probably because it has the lowest read-through rate. Despite TAA being favored by selection and mutation bias, as with codon usage bias G + C pressure is the prime determinant of between-species TGA usage trends. In species with strong G + C-biased gene conversion (gBGC), such as mammals and birds, the high usage and conservation of TGA is best explained by an A + T → G + C repair bias. How to explain TGA enrichment in other G + C-rich genomes is less clear. Enigmatically, across bacterial and archaeal species and between human isochores TAG usage is mostly unresponsive to G + C pressure. This unresponsiveness we dub the TAG paradox as currently no mutational, selective, or gBGC model provides a well-supported explanation. That TAG does increase with G + C usage across eukaryotes makes the usage elsewhere yet more enigmatic. We suggest resolution of the TAG paradox may provide insights into either an unknown but common selective preference (probably at the DNA/RNA level) or an unrecognized complexity to the action of gBGC.
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Affiliation(s)
- Alexander T Ho
- Milner Centre for Evolution, University of Bath, Bath, UK
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9
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Dave B, Kanyal A, Mamatharani DV, Karmodiya K. Pervasive sequence-level variation in the transcriptome of Plasmodium falciparum. NAR Genom Bioinform 2022; 4:lqac036. [PMID: 35591889 PMCID: PMC9112769 DOI: 10.1093/nargab/lqac036] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 03/09/2022] [Accepted: 05/14/2022] [Indexed: 12/05/2022] Open
Abstract
Single-nucleotide variations (SNVs) in RNA, arising from co- and post-transcriptional phenomena including transcription errors and RNA-editing, are well studied in a range of organisms. In the malaria parasite Plasmodium falciparum, stage-specific and non-specific gene-expression variations accompany the parasite's array of developmental and morphological phenotypes over the course of its complex life cycle. However, the extent, rate and effect of sequence-level variation in the parasite's transcriptome are unknown. Here, we report the presence of pervasive, non-specific SNVs in the P. falciparum transcriptome. SNV rates for a gene were correlated to gene length (r[Formula: see text]0.65-0.7) but not to the AT-content of that gene. Global SNV rates for the P. falciparum lines we used, and for publicly available P. vivax and P. falciparum clinical isolate datasets, were of the order of 10-3 per base, ∼10× higher than rates we calculated for bacterial datasets. These variations may reflect an intrinsic transcriptional error rate in the parasite, and RNA editing may be responsible for a subset of them. This seemingly characteristic property of the parasite may have implications for clinical outcomes and the basic biology and evolution of P. falciparum and parasite biology more broadly. We anticipate that our study will prompt further investigations into the exact sources, consequences and possible adaptive roles of these SNVs.
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Affiliation(s)
- Bruhad Dave
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, Maharashtra, India
| | - Abhishek Kanyal
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, Maharashtra, India
| | - D V Mamatharani
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, Maharashtra, India
| | - Krishanpal Karmodiya
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, Maharashtra, India
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Pan J, Li W, Ni J, Wu K, Konigsberg I, Rivera CE, Tincher C, Gregory C, Zhou X, Doak TG, Lee H, Wang Y, Gao X, Lynch M, Long H. Rates of Mutations and Transcript Errors in the Foodborne Pathogen Salmonella enterica subsp. enterica. Mol Biol Evol 2022; 39:msac081. [PMID: 35446958 PMCID: PMC9040049 DOI: 10.1093/molbev/msac081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Because errors at the DNA level power pathogen evolution, a systematic understanding of the rate and molecular spectra of mutations could guide the avoidance and treatment of infectious diseases. We thus accumulated tens of thousands of spontaneous mutations in 768 repeatedly bottlenecked lineages of 18 strains from various geographical sites, temporal spread, and genetic backgrounds. Entailing over ∼1.36 million generations, the resultant data yield an average mutation rate of ∼0.0005 per genome per generation, with a significant within-species variation. This is one of the lowest bacterial mutation rates reported, giving direct support for a high genome stability in this pathogen resulting from high DNA-mismatch-repair efficiency and replication-machinery fidelity. Pathogenicity genes do not exhibit an accelerated mutation rate, and thus, elevated mutation rates may not be the major determinant for the diversification of toxin and secretion systems. Intriguingly, a low error rate at the transcript level is not observed, suggesting distinct fidelity of the replication and transcription machinery. This study urges more attention on the most basic evolutionary processes of even the best-known human pathogens and deepens the understanding of their genome evolution.
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Affiliation(s)
- Jiao Pan
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, 5 Yushan Road, Qingdao, Shandong Province 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Weiyi Li
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Jiahao Ni
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, 5 Yushan Road, Qingdao, Shandong Province 266003, China
| | - Kun Wu
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, 5 Yushan Road, Qingdao, Shandong Province 266003, China
| | - Iain Konigsberg
- Division of Biomedical Informatics & Personalized Medicine, Department of Medicine, University of Colorado, Aurora, CO 80045, USA
| | - Caitlyn E. Rivera
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Clayton Tincher
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Colin Gregory
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Xia Zhou
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, 5 Yushan Road, Qingdao, Shandong Province 266003, China
| | - Thomas G. Doak
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
- National Center for Genome Analysis Support, Indiana University, Bloomington, IN 47405, USA
| | - Heewook Lee
- School of Computing and Augmented Intelligence, Arizona State University, Tempe, AZ 85281, USA
| | - Yan Wang
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, 5 Yushan Road, Qingdao, Shandong Province 266003, China
| | - Xiang Gao
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, School of Life Science, Shandong University, No. 72 Binhai Road, Qingdao, Shandong Province 266237, China
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85281, USA
| | - Hongan Long
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, 5 Yushan Road, Qingdao, Shandong Province 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
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11
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Lyu Z, Ling J. Increase in Ribosomal Fidelity Benefits Salmonella upon Bile Salt Exposure. Genes (Basel) 2022; 13:184. [PMID: 35205229 PMCID: PMC8872077 DOI: 10.3390/genes13020184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 02/04/2023] Open
Abstract
Translational fidelity is maintained by multiple quality control steps in all three domains of life. Increased translational errors (mistranslation) occur due to genetic mutations and external stresses. Severe mistranslation is generally harmful, but moderate levels of mistranslation may be favored under certain conditions. To date, little is known about the link between translational fidelity and host-pathogen interactions. Salmonella enterica can survive in the gall bladder during systemic or chronic infections due to bile resistance. Here we show that increased translational fidelity contributes to the fitness of Salmonella upon bile salt exposure, and the improved fitness depends on an increased level of intracellular adenosine triphosphate (ATP). Our work thus reveals a previously unknown linkage between translational fidelity and bacterial fitness under bile stress.
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Affiliation(s)
- Zhihui Lyu
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
| | - Jiqiang Ling
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
- Molecular and Cellular Biology, Bilogical Sciences Graduate Program, The University of Maryland, College Park, MD 20742, USA
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12
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Zuo X, Chou T. Density- and elongation speed-dependent error correction in RNA polymerization. Phys Biol 2021; 19. [PMID: 34937012 DOI: 10.1088/1478-3975/ac45e2] [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: 03/08/2021] [Accepted: 12/22/2021] [Indexed: 11/11/2022]
Abstract
Backtracking of RNA polymerase (RNAP) is an important pausing mechanism during DNA transcription that is part of the error correction process that enhances transcription fidelity. We model the backtracking mechanism of RNA polymerase, which usually happens when the polymerase tries to incorporate a noncognate or "mismatched" nucleotide triphosphate. Previous models have made simplifying assumptions such as neglecting the trailing polymerase behind the backtracking polymerase or assuming that the trailing polymerase is stationary. We derive exact analytic solutions of a stochastic model that includes locally interacting RNAPs by explicitly showing how a trailing RNAP influences the probability that an error is corrected or incorporated by the leading backtracking RNAP. We also provide two related methods for computing the mean times for error correction and incorporation given an initial local RNAP configuration. Using these results, we propose an effective interacting-RNAP lattice that can be readily simulated.
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Affiliation(s)
- Xinzhe Zuo
- Department of Mathematics, University of California - Los Angeles, Los Angeles, CA 90095-1555, USA, Los Angeles, California, 90095, UNITED STATES
| | - Tom Chou
- Department of Mathematics, University of California - Los Angeles, Los Angeles, CA 90095-1555, USA, Los Angeles, California, 90095, UNITED STATES
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13
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Buchumenski I, Roth SH, Kopel E, Katsman E, Feiglin A, Levanon EY, Eisenberg E. Global quantification exposes abundant low-level off-target activity by base editors. Genome Res 2021; 31:2354-2361. [PMID: 34667118 PMCID: PMC8647836 DOI: 10.1101/gr.275770.121] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 10/14/2021] [Indexed: 12/26/2022]
Abstract
Base editors are dedicated engineered deaminases that enable directed conversion of specific bases in the genome or transcriptome in a precise and efficient manner, and hold promise for correcting pathogenic mutations. A major concern limiting application of this powerful approach is the issue of off-target edits. Several recent studies have shown substantial off-target RNA activity induced by base editors and demonstrated that off-target mutations may be suppressed by improved deaminases versions or optimized guide RNAs. Here, we describe a new class of off-target events that are invisible to the established methods for detection of genomic variations and were thus far overlooked. We show that nonspecific, seemingly stochastic, off-target events affect a large number of sites throughout the genome or the transcriptome, and account for the majority of off-target activity. We develop and employ a different, complementary approach that is sensitive to the stochastic off-target activity and use it to quantify the abundant off-target RNA mutations due to current, optimized deaminase editors. We provide a computational tool to quantify global off-target activity, which can be used to optimize future base editors. Engineered base editors enable directed manipulation of the genome or transcriptome at single-base resolution. We believe that implementation of this computational approach would facilitate design of more specific base editors.
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Affiliation(s)
- Ilana Buchumenski
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Shalom Hillel Roth
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Eli Kopel
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Efrat Katsman
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Ariel Feiglin
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
- The Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 69978, Israel
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14
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Luzon-Hidalgo R, Risso VA, Delgado A, Andrés-León E, Ibarra-Molero B, Sanchez-Ruiz JM. Evidence for a role of phenotypic mutations in virus adaptation. iScience 2021; 24:102257. [PMID: 33817569 PMCID: PMC8010470 DOI: 10.1016/j.isci.2021.102257] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 01/22/2021] [Accepted: 02/26/2021] [Indexed: 12/12/2022] Open
Abstract
Viruses interact extensively with the host molecular machinery, but the underlying mechanisms are poorly understood. Bacteriophage T7 recruits the small protein thioredoxin of the Escherichia coli host as an essential processivity factor for the viral DNA polymerase. We challenged the phage to propagate in a host in which thioredoxin had been extensively modified to hamper its recruitment. The virus adapted to the engineered host without losing the capability to propagate in the original host, but no genetic mutations were fixed in the thioredoxin binding domain of the viral DNA polymerase. Virus adaptation correlated with mutations in the viral RNA polymerase, supporting that promiscuous thioredoxin recruitment was enabled by phenotypic mutations caused by transcription errors. These results point to a mechanism of virus adaptation that may play a role in cross-species transmission. We propose that phenotypic mutations may generally contribute to the capability of viruses to evade antiviral strategies. Phage adapts to a host modified to hinder the essential recruitment of a host protein No genetic mutations are fixed at the engineered virus-host interaction interface Adaptation is likely linked to phenotypic mutations caused by transcription errors Sub-genomic RNAs may enable this kind of adaptation mechanism in coronaviruses
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Affiliation(s)
- Raquel Luzon-Hidalgo
- Departamento de Quimica Fisica. Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, Granada 18071, Spain
| | - Valeria A Risso
- Departamento de Quimica Fisica. Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, Granada 18071, Spain
| | - Asuncion Delgado
- Departamento de Quimica Fisica. Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, Granada 18071, Spain
| | - Eduardo Andrés-León
- Unidad de Bioinformática. Instituto de Parasitología y Biomedicina "López Neyra", CSIC, Armilla, Granada 18016, Spain
| | - Beatriz Ibarra-Molero
- Departamento de Quimica Fisica. Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, Granada 18071, Spain
| | - Jose M Sanchez-Ruiz
- Departamento de Quimica Fisica. Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, Granada 18071, Spain
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15
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Nieuwkoop T, Finger-Bou M, van der Oost J, Claassens NJ. The Ongoing Quest to Crack the Genetic Code for Protein Production. Mol Cell 2020; 80:193-209. [PMID: 33010203 DOI: 10.1016/j.molcel.2020.09.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 08/10/2020] [Accepted: 09/10/2020] [Indexed: 01/05/2023]
Abstract
Understanding the genetic design principles that determine protein production remains a major challenge. Although the key principles of gene expression were discovered 50 years ago, additional factors are still being uncovered. Both protein-coding and non-coding sequences harbor elements that collectively influence the efficiency of protein production by modulating transcription, mRNA decay, and translation. The influences of many contributing elements are intertwined, which complicates a full understanding of the individual factors. In natural genes, a functional balance between these factors has been obtained in the course of evolution, whereas for genetic-engineering projects, our incomplete understanding still limits optimal design of synthetic genes. However, notable advances have recently been made, supported by high-throughput analysis of synthetic gene libraries as well as by state-of-the-art biomolecular techniques. We discuss here how these advances further strengthen understanding of the gene expression process and how they can be harnessed to optimize protein production.
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Affiliation(s)
- Thijs Nieuwkoop
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, the Netherlands
| | - Max Finger-Bou
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, the Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, the Netherlands
| | - Nico J Claassens
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, the Netherlands.
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16
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Abstract
The genomes of bacteria contain fewer genes and substantially less noncoding DNA than those of eukaryotes, and as a result, they have much less raw material to invent new traits. Yet, bacteria are vastly more taxonomically diverse, numerically abundant, and globally successful in colonizing new habitats compared to eukaryotes. Although bacterial genomes are generally considered to be optimized for efficient growth and rapid adaptation, nonadaptive processes have played a major role in shaping the size, contents, and compact organization of bacterial genomes and have allowed the establishment of deleterious traits that serve as the raw materials for genetic innovation.
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Affiliation(s)
- Paul C Kirchberger
- Department of Integrative Biology, University of Texas at Austin, Texas 78712, USA; ; ;
| | - Marian L Schmidt
- Department of Integrative Biology, University of Texas at Austin, Texas 78712, USA; ; ;
| | - Howard Ochman
- Department of Integrative Biology, University of Texas at Austin, Texas 78712, USA; ; ;
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17
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Martín-Alonso S, Frutos-Beltrán E, Menéndez-Arias L. Reverse Transcriptase: From Transcriptomics to Genome Editing. Trends Biotechnol 2020; 39:194-210. [PMID: 32653101 DOI: 10.1016/j.tibtech.2020.06.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/10/2020] [Accepted: 06/15/2020] [Indexed: 01/01/2023]
Abstract
Reverse transcriptases (RTs) are enzymes that can generate a complementary strand of DNA (cDNA) from RNA. Coupled with PCR, RTs have been widely used to detect RNAs and to clone expressed genes. Classical retroviral RTs have been improved by protein engineering. These enzymes and newly characterized RTs are key elements in the development of next-generation sequencing techniques that are now being applied to the study of transcriptomics. In addition, engineered RTs fused to a CRISPR/Cas9 nickase have recently shown great potential as tools to manipulate eukaryotic genomes. In this review, we discuss the properties and uses of wild type and engineered RTs in biotechnological applications, from conventional RT-PCR to recently introduced prime editing.
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Affiliation(s)
- Samara Martín-Alonso
- Centro de Biología Molecular 'Severo Ochoa' (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), c/ Nicolás Cabrera 1, Campus de Cantoblanco-UAM, 28049 Madrid, Spain
| | - Estrella Frutos-Beltrán
- Centro de Biología Molecular 'Severo Ochoa' (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), c/ Nicolás Cabrera 1, Campus de Cantoblanco-UAM, 28049 Madrid, Spain
| | - Luis Menéndez-Arias
- Centro de Biología Molecular 'Severo Ochoa' (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), c/ Nicolás Cabrera 1, Campus de Cantoblanco-UAM, 28049 Madrid, Spain. @cbm.csic.es
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18
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Meer KM, Nelson PG, Xiong K, Masel J. High Transcriptional Error Rates Vary as a Function of Gene Expression Level. Genome Biol Evol 2020; 12:3754-3761. [PMID: 31841128 PMCID: PMC6988749 DOI: 10.1093/gbe/evz275] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2019] [Indexed: 02/06/2023] Open
Abstract
Errors in gene transcription can be costly, and organisms have evolved to prevent their occurrence or mitigate their costs. The simplest interpretation of the drift barrier hypothesis suggests that species with larger population sizes would have lower transcriptional error rates. However, Escherichia coli seems to have a higher transcriptional error rate than species with lower effective population sizes, for example Saccharomyces cerevisiae. This could be explained if selection in E. coli were strong enough to maintain adaptations that mitigate the consequences of transcriptional errors through robustness, on a gene by gene basis, obviating the need for low transcriptional error rates and associated costs of global proofreading. Here, we note that if selection is powerful enough to evolve local robustness, selection should also be powerful enough to locally reduce error rates. We therefore predict that transcriptional error rates will be lower in highly abundant proteins on which selection is strongest. However, we only expect this result when error rates are high enough to significantly impact fitness. As expected, we find such a relationship between expression and transcriptional error rate for non-C→U errors in E. coli (especially G→A), but not in S. cerevisiae. We do not find this pattern for C→U changes in E. coli, presumably because most deamination events occurred during sample preparation, but do for C→U changes in S. cerevisiae, supporting the interpretation that C→U error rates estimated with an improved protocol, and which occur at rates comparable with E. coli non-C→U errors, are biological.
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Affiliation(s)
- Kendra M Meer
- Department of Ecology & Evolutionary Biology, University of Arizona.,Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Paul G Nelson
- Department of Ecology & Evolutionary Biology, University of Arizona
| | - Kun Xiong
- Department of Molecular & Cellular Biology, University of Arizona.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT
| | - Joanna Masel
- Department of Ecology & Evolutionary Biology, University of Arizona
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19
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Vecchi D. DNA is not an ontologically distinctive developmental cause. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2020; 81:101245. [PMID: 31899119 DOI: 10.1016/j.shpsc.2019.101245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 12/14/2019] [Accepted: 12/27/2019] [Indexed: 06/10/2023]
Abstract
In this article I critically evaluate the thesis that DNA is an ontologically distinctive developmental cause. I shall critically analyse different versions of the latter thesis by taking into consideration concrete developmental cases. I shall argue that DNA is neither a developmental determinant nor an ontologically distinctive developmental cause. Instead, I shall argue that mechanistic analysis shows that DNA's causal role in development depends on the higher robustness of the developmental processes in which it exerts its causal capacities. The focus on process and developmental system implies a metaphysical shift: rather than attributing to DNA molecules biochemically unique properties, I suggest that it might be better to think about DNA's causal role in development in terms of the causal capacities that DNA molecules manifest in a rich developmental milieu. I shall also suggest that my position is distinct both from the view advocating the instrumental primacy of DNA-centric biology and developmental constructionism. It is different from the former because it provides a substantial answer to the question of what makes DNA causally central in developmental processes. Finally, I argue that evolutionary considerations pose an important challenge to developmental constructionism.
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Affiliation(s)
- Davide Vecchi
- Centro de Filosofia das Ciências, Departamento de História e Filosofia das Ciências, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal.
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20
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Li W, Lynch M. Universally high transcript error rates in bacteria. eLife 2020; 9:54898. [PMID: 32469307 PMCID: PMC7259958 DOI: 10.7554/elife.54898] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 04/28/2020] [Indexed: 12/22/2022] Open
Abstract
Errors can occur at any level during the replication and transcription of genetic information. Genetic mutations derived mainly from replication errors have been extensively studied. However, fundamental details of transcript errors, such as their rate, molecular spectrum, and functional effects, remain largely unknown. To globally identify transcript errors, we applied an adapted rolling-circle sequencing approach to Escherichia coli, Bacillus subtilis, Agrobacterium tumefaciens, and Mesoplasma florum, revealing transcript-error rates 3 to 4 orders of magnitude higher than the corresponding genetic mutation rates. The majority of detected errors would result in amino-acid changes, if translated. With errors identified from 9929 loci, the molecular spectrum and distribution of errors were uncovered in great detail. A G→A substitution bias was observed in M. florum, which apparently has an error-prone RNA polymerase. Surprisingly, an increased frequency of nonsense errors towards the 3' end of mRNAs was observed, suggesting a Nonsense-Mediated Decay-like quality-control mechanism in prokaryotes.
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Affiliation(s)
- Weiyi Li
- Department of Biology, Indiana University, Bloomington, United States
| | - Michael Lynch
- Department of Biology, Indiana University, Bloomington, United States.,Center for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, United States
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21
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Miropolskaya N, Kulbachinskiy A, Esyunina D. Factor-specific effects of mutations in the active site of RNA polymerase on RNA cleavage. Biochem Biophys Res Commun 2020; 523:165-170. [PMID: 31837805 DOI: 10.1016/j.bbrc.2019.12.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 12/07/2019] [Indexed: 10/25/2022]
Abstract
Bacterial RNA polymerase (RNAP) relies on the same active site for RNA synthesis and co-transcriptional RNA proofreading. The intrinsic RNA proofreading activity of RNAP can be greatly stimulated by Gre factors, which bind within the secondary channel and directly participate in the RNA cleavage reaction in the active site of RNAP. Here, we characterize mutations in Escherichia coli RNAP that differentially affect intrinsic and Gre-stimulated RNA cleavage. Substitution of a highly conserved arginine residue that contacts nascent RNA upstream of the active site strongly impairs intrinsic and GreA-dependent cleavage, without reducing GreA affinity or catalytic Mg2+ binding. In contrast, substitutions of several nonconserved residues at the Gre-interacting interface in the secondary channel primarily affect GreB-dependent cleavage, by decreasing both the catalytic rate and GreB affinity. The results suggest that RNAP residues not directly involved in contacts with the reacting RNA groups or catalytic ions play essential roles in RNA cleavage and can modulate its regulation by transcription factors.
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Affiliation(s)
- Nataliya Miropolskaya
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia
| | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia.
| | - Daria Esyunina
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia.
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22
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Piñeros WD, Tlusty T. Kinetic proofreading and the limits of thermodynamic uncertainty. Phys Rev E 2020; 101:022415. [PMID: 32168722 DOI: 10.1103/physreve.101.022415] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 01/24/2020] [Indexed: 06/10/2023]
Abstract
To mitigate errors induced by the cell's heterogeneous noisy environment, its main information channels and production networks utilize the kinetic proofreading (KPR) mechanism. Here, we examine two extensively studied KPR circuits, DNA replication by the T7 DNA polymerase and translation by the E. coli ribosome. Using experimental data, we analyze the performance of these two vital systems in light of the fundamental bounds set by the recently discovered thermodynamic uncertainty relation (TUR), which places an inherent trade-off between the precision of a desirable output and the amount of energy dissipation required. We show that the DNA polymerase operates close to the TUR lower bound, while the ribosome operates ∼5 times farther from this bound. This difference originates from the enhanced binding discrimination of the polymerase which allows it to operate effectively as a reduced reaction cycle prioritizing correct product formation. We show that approaching this limit also decouples the thermodynamic uncertainty factor from speed and error, thereby relaxing the accuracy-speed trade-off of the system. Altogether, our results show that operating near this reduced cycle limit not only minimizes thermodynamic uncertainty, but also results in global performance enhancement of KPR circuits.
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Affiliation(s)
- William D Piñeros
- Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan 44919, Korea
| | - Tsvi Tlusty
- Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan 44919, Korea
- Department of Physics, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
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23
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Abstract
Bacteria participate in a wide diversity of symbiotic associations with eukaryotic hosts that require precise interactions for bacterial recognition and persistence. Most commonly, host-associated bacteria interfere with host gene expression to modulate the immune response to the infection. However, many of these bacteria also interfere with host cellular differentiation pathways to create a hospitable niche, resulting in the formation of novel cell types, tissues, and organs. In both of these situations, bacterial symbionts must interact with eukaryotic regulatory pathways. Here, we detail what is known about how bacterial symbionts, from pathogens to mutualists, control host cellular differentiation across the central dogma, from epigenetic chromatin modifications, to transcription and mRNA processing, to translation and protein modifications. We identify four main trends from this survey. First, mechanisms for controlling host gene expression appear to evolve from symbionts co-opting cross-talk between host signaling pathways. Second, symbiont regulatory capacity is constrained by the processes that drive reductive genome evolution in host-associated bacteria. Third, the regulatory mechanisms symbionts exhibit correlate with the cost/benefit nature of the association. And, fourth, symbiont mechanisms for interacting with host genetic regulatory elements are not bound by native bacterial capabilities. Using this knowledge, we explore how the ubiquitous intracellular Wolbachia symbiont of arthropods and nematodes may modulate host cellular differentiation to manipulate host reproduction. Our survey of the literature on how infection alters gene expression in Wolbachia and its hosts revealed that, despite their intermediate-sized genomes, different strains appear capable of a wide diversity of regulatory manipulations. Given this and Wolbachia's diversity of phenotypes and eukaryotic-like proteins, we expect that many symbiont-induced host differentiation mechanisms will be discovered in this system.
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Affiliation(s)
- Shelbi L Russell
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA.
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24
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Garofalo R, Wohlgemuth I, Pearson M, Lenz C, Urlaub H, Rodnina MV. Broad range of missense error frequencies in cellular proteins. Nucleic Acids Res 2019; 47:2932-2945. [PMID: 30649420 PMCID: PMC6451103 DOI: 10.1093/nar/gky1319] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 12/21/2018] [Accepted: 12/30/2018] [Indexed: 12/25/2022] Open
Abstract
Assessment of the fidelity of gene expression is crucial to understand cell homeostasis. Here we present a highly sensitive method for the systematic Quantification of Rare Amino acid Substitutions (QRAS) using absolute quantification by targeted mass spectrometry after chromatographic enrichment of peptides with missense amino acid substitutions. By analyzing incorporation of near- and non-cognate amino acids in a model protein EF-Tu, we show that most of missense errors are too rare to detect by conventional methods, such as DDA, and are estimated to be between <10−7–10-5 by QRAS. We also observe error hotspots of up to 10−3 for some types of mismatches, including the G-U mismatch. The error frequency depends on the expression level of EF-Tu and, surprisingly, the amino acid position in the protein. QRAS is not restricted to any particular miscoding event, organism, strain or model protein and is a reliable tool to analyze very rare proteogenomic events.
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Affiliation(s)
- Raffaella Garofalo
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Goettingen, Germany
| | - Ingo Wohlgemuth
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Goettingen, Germany
| | - Michael Pearson
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Goettingen, Germany
| | - Christof Lenz
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Goettingen, Germany.,Department of Clinical Chemistry, Bioanalytics, University Medical Center Goettingen, Robert-Koch-Straße 40, 37075 Goettingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Goettingen, Germany.,Department of Clinical Chemistry, Bioanalytics, University Medical Center Goettingen, Robert-Koch-Straße 40, 37075 Goettingen, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Goettingen, Germany
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25
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Mordret E, Dahan O, Asraf O, Rak R, Yehonadav A, Barnabas GD, Cox J, Geiger T, Lindner AB, Pilpel Y. Systematic Detection of Amino Acid Substitutions in Proteomes Reveals Mechanistic Basis of Ribosome Errors and Selection for Translation Fidelity. Mol Cell 2019; 75:427-441.e5. [DOI: 10.1016/j.molcel.2019.06.041] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 03/05/2019] [Accepted: 06/26/2019] [Indexed: 11/26/2022]
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26
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Bradley CC, Gordon AJE, Halliday JA, Herman C. Transcription fidelity: New paradigms in epigenetic inheritance, genome instability and disease. DNA Repair (Amst) 2019; 81:102652. [PMID: 31326363 DOI: 10.1016/j.dnarep.2019.102652] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
RNA transcription errors are transient, yet frequent, events that do have consequences for the cell. However, until recently we lacked the tools to empirically measure and study these errors. Advances in RNA library preparation and next generation sequencing (NGS) have allowed the spectrum of transcription errors to be empirically measured over the entire transcriptome and in nascent transcripts. Combining these powerful methods with forward and reverse genetic strategies has refined our understanding of transcription factors known to enhance RNA accuracy and will enable the discovery of new candidates. Furthermore, these approaches will shed additional light on the complex interplay between transcription fidelity and other DNA transactions, such as replication and repair, and explore a role for transcription errors in cellular evolution and disease.
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Affiliation(s)
- Catherine C Bradley
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, 77030, USA; Robert and Janice McNair Foundation/ McNair Medical Institute M.D./Ph.D. Scholars Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Alasdair J E Gordon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jennifer A Halliday
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Christophe Herman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA.
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27
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Aeschlimann SH, Graf C, Mayilo D, Lindecker H, Urda L, Kappes N, Burr AL, Simonis M, Splinter E, Min M, Laux H. Enhanced CHO Clone Screening: Application of Targeted Locus Amplification and Next‐Generation Sequencing Technologies for Cell Line Development. Biotechnol J 2019; 14:e1800371. [DOI: 10.1002/biot.201800371] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 12/20/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Samuel H. Aeschlimann
- Novartis Institutes for BioMedical Research, Integrated Biologics Profiling UnitCH‐4002 Basel Switzerland
| | - Christian Graf
- Novartis Technical R&D, Technical Development BiosimilarsHexal AG, Keltenring 1+3 82041 Oberhaching Germany
| | - Dmytro Mayilo
- Novartis Institutes for BioMedical Research, Integrated Biologics Profiling UnitCH‐4002 Basel Switzerland
| | - Hélène Lindecker
- Novartis Institutes for BioMedical Research, Integrated Biologics Profiling UnitCH‐4002 Basel Switzerland
| | - Lorena Urda
- Novartis Institutes for BioMedical Research, Integrated Biologics Profiling UnitCH‐4002 Basel Switzerland
| | - Nora Kappes
- Novartis Institutes for BioMedical Research, Integrated Biologics Profiling UnitCH‐4002 Basel Switzerland
| | - Alicia Leone Burr
- Novartis Institutes for BioMedical Research, Integrated Biologics Profiling UnitCH‐4002 Basel Switzerland
| | | | - Erik Splinter
- Cergentis B.VYalelaan 62 3584 CM Utrecht The Netherlands
| | - Max Min
- Cergentis B.VYalelaan 62 3584 CM Utrecht The Netherlands
| | - Holger Laux
- Novartis Institutes for BioMedical Research, Integrated Biologics Profiling UnitCH‐4002 Basel Switzerland
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28
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Long C, E. C, Da LT, Yu J. A Viral T7 RNA Polymerase Ratcheting Along DNA With Fidelity Control. Comput Struct Biotechnol J 2019; 17:638-644. [PMID: 31193497 PMCID: PMC6535458 DOI: 10.1016/j.csbj.2019.05.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/25/2019] [Accepted: 05/04/2019] [Indexed: 12/02/2022] Open
Abstract
RNA polymerase (RNAP) from bacteriophage T7 is a representative single-subunit viral RNAP that can transcribe with high promoter activities without assistances from transcription factors. We accordingly studied this small transcription machine computationally as a model system to understand underlying mechanisms of mechano-chemical coupling and fidelity control in the RNAP transcription elongation. Here we summarize our computational work from several recent publications to demonstrate first how T7 RNAP translocates via Brownian alike motions along DNA right after the catalytic product release. Then we show how the backward translocation motions are prevented at post-translocation upon successful nucleotide incorporation, which is also subject to stepwise nucleotide selection and acts as a pawl for "selective ratcheting". The structural dynamics and energetics features revealed from our atomistic molecular dynamics (MD) simulations and related analyses on the single-subunit T7 RNAP thus provided detailed and quantitative characterizations on the Brownian-ratchet working scenario of a prototypical transcription machine with sophisticated nucleotide selectivity for fidelity control. The presented mechanisms can be more or less general for structurally similar viral or mitochondrial RNAPs and some of DNA polymerases, or even for the RNAP engine of the more complicated transcription machinery in higher organisms.
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Affiliation(s)
- Chunhong Long
- Beijing Computational Science Research Center, Beijing, 100193, China
| | - Chao E.
- Beijing Computational Science Research Center, Beijing, 100193, China
| | - Lin-Tai Da
- Shanghai Center for Systems Biomedicine, Shanghai JiaoTong University, Shanghai 200240, China
| | - Jin Yu
- Beijing Computational Science Research Center, Beijing, 100193, China
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29
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Cui J, Gizzi A, Stivers JT. Deoxyuridine in DNA has an inhibitory and promutagenic effect on RNA transcription by diverse RNA polymerases. Nucleic Acids Res 2019; 47:4153-4168. [PMID: 30892639 PMCID: PMC6486633 DOI: 10.1093/nar/gkz183] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/04/2019] [Accepted: 03/09/2019] [Indexed: 12/16/2022] Open
Abstract
dUTP is a close structural congener of dTTP and can be readily incorporated into DNA opposite to adenine during DNA replication leading to non-mutagenic dU/A base pairs ('uracilation'). We find that dU/A pairs located within DNA transcriptional templates optimized for either T7 RNA polymerase (T7 RNAP) or human RNA polymerase II (pol II) have inhibitory and mutagenic effects on transcription. The data for T7 RNAP establishes that even a single dU/A pair can inhibit promoter binding and transcription initiation up to 30-fold, and that inhibitory effects on transcription elongation are also possible. Sequencing of the mRNA transcribed from uniformly uracilated DNA templates by T7 RNAP indicated an increased frequency of transversion and insertion mutations compared to all T/A templates. Strong effects of dU/A pairs on cellular transcription activity and fidelity were also observed with RNA pol II using uracil base excision repair (UBER)-deficient human cells. At the highest levels of template uracilation, transcription by RNA pol II was completely blocked. We propose that these effects arise from the decreased thermodynamic stability and increased dynamics of dU/A pairs in DNA. The potential implications of these findings on gene regulation and disease are discussed.
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Affiliation(s)
- Junru Cui
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205-2185, USA
| | - Anthony Gizzi
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205-2185, USA
| | - James T Stivers
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205-2185, USA
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30
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Williams AM, Friso G, van Wijk KJ, Sloan DB. Extreme variation in rates of evolution in the plastid Clp protease complex. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:243-259. [PMID: 30570818 DOI: 10.1111/tpj.14208] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 11/29/2018] [Accepted: 12/10/2018] [Indexed: 05/08/2023]
Abstract
Eukaryotic cells represent an intricate collaboration between multiple genomes, even down to the level of multi-subunit complexes in mitochondria and plastids. One such complex in plants is the caseinolytic protease (Clp), which plays an essential role in plastid protein turnover. The proteolytic core of Clp comprises subunits from one plastid-encoded gene (clpP1) and multiple nuclear genes. TheclpP1 gene is highly conserved across most green plants, but it is by far the fastest evolving plastid-encoded gene in some angiosperms. To better understand these extreme and mysterious patterns of divergence, we investigated the history ofclpP1 molecular evolution across green plants by extracting sequences from 988 published plastid genomes. We find thatclpP1 has undergone remarkably frequent bouts of accelerated sequence evolution and architectural changes (e.g. a loss of introns andRNA-editing sites) within seed plants. AlthoughclpP1 is often assumed to be a pseudogene in such cases, multiple lines of evidence suggest that this is rarely true. We applied comparative native gel electrophoresis of chloroplast protein complexes followed by protein mass spectrometry in two species within the angiosperm genusSilene, which has highly elevated and heterogeneous rates ofclpP1 evolution. We confirmed thatclpP1 is expressed as a stable protein and forms oligomeric complexes with the nuclear-encoded Clp subunits, even in one of the most divergentSilene species. Additionally, there is a tight correlation between amino acid substitution rates inclpP1 and the nuclear-encoded Clp subunits across a broad sampling of angiosperms, suggesting continuing selection on interactions within this complex.
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Affiliation(s)
- Alissa M Williams
- Department of Biology, Graduate Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Giulia Friso
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, NY, 14853, USA
| | - Klaas J van Wijk
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, NY, 14853, USA
| | - Daniel B Sloan
- Department of Biology, Graduate Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
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31
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Sivaramakrishnan P, Gordon AJE, Halliday JA, Herman C. How Acts of Infidelity Promote DNA Break Repair: Collision and Collusion Between DNA Repair and Transcription. Bioessays 2018; 40:e1800045. [PMID: 30091472 PMCID: PMC6334755 DOI: 10.1002/bies.201800045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 07/07/2018] [Indexed: 12/20/2022]
Abstract
Transcription is a fundamental cellular process and the first step in gene regulation. Although RNA polymerase (RNAP) is highly processive, in growing cells the progression of transcription can be hindered by obstacles on the DNA template, such as damaged DNA. The authors recent findings highlight a trade-off between transcription fidelity and DNA break repair. While a lot of work has focused on the interaction between transcription and nucleotide excision repair, less is known about how transcription influences the repair of DNA breaks. The authors suggest that when the cell experiences stress from DNA breaks, the control of RNAP processivity affects the balance between preserving transcription integrity and DNA repair. Here, how the conflict between transcription and DNA double-strand break (DSB) repair threatens the integrity of both RNA and DNA are discussed. In reviewing this field, the authors speculate on cellular paradigms where this equilibrium is well sustained, and instances where the maintenance of transcription fidelity is favored over genome stability.
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Affiliation(s)
- Priya Sivaramakrishnan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alasdair J E Gordon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jennifer A Halliday
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christophe Herman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Baylor College of Medicine, Dan L. Duncan Comprehensive Cancer Center, Houston, TX 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA
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32
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Errors during Gene Expression: Single-Cell Heterogeneity, Stress Resistance, and Microbe-Host Interactions. mBio 2018; 9:mBio.01018-18. [PMID: 29970467 PMCID: PMC6030554 DOI: 10.1128/mbio.01018-18] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Gene expression has been considered a highly accurate process, and deviation from such fidelity has been shown previously to be detrimental for the cell. More recently, increasing evidence has supported the notion that the accuracy of gene expression is indeed flexibly variable. The levels of errors during gene expression differ from condition to condition and even from cell to cell within genetically identical populations grown under the same conditions. The different levels of errors resulting from inaccurate gene expression are now known to play key roles in regulating microbial stress responses and host interactions. This minireview summarizes the recent development in understanding the level, regulation, and physiological impact of errors during gene expression. Gene expression has been considered a highly accurate process, and deviation from such fidelity has been shown previously to be detrimental for the cell. More recently, increasing evidence has supported the notion that the accuracy of gene expression is indeed flexibly variable.
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33
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Traverse CC, Ochman H. A Genome-Wide Assay Specifies Only GreA as a Transcription Fidelity Factor in Escherichia coli. G3 (BETHESDA, MD.) 2018; 8:2257-2264. [PMID: 29769292 PMCID: PMC6027873 DOI: 10.1534/g3.118.200209] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 04/28/2018] [Indexed: 02/07/2023]
Abstract
Although mutations are the basis for adaptation and heritable genetic change, transient errors occur during transcription at rates that are orders of magnitude higher than the mutation rate. High rates of transcription errors can be detrimental by causing the production of erroneous proteins that need to be degraded. Two transcription fidelity factors, GreA and GreB, have previously been reported to stimulate the removal of errors that occur during transcription, and a third fidelity factor, DksA, is thought to decrease the error rate through an unknown mechanism. Because the majority of transcription-error assays of these fidelity factors were performed in vitro and on individual genes, we measured the in vivo transcriptome-wide error rates in all possible combinations of mutants of the three fidelity factors. This method expands measurements of these fidelity factors to the full spectrum of errors across the entire genome. Our assay shows that GreB and DksA have no significant effect on transcription error rates, and that GreA only influences the transcription error rate by reducing G-to-A errors.
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Affiliation(s)
- Charles C Traverse
- Department of Integrative Biology, University of Texas, Austin, Texas 78712
| | - Howard Ochman
- Department of Integrative Biology, University of Texas, Austin, Texas 78712
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34
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Sloan DB, Broz AK, Sharbrough J, Wu Z. Detecting Rare Mutations and DNA Damage with Sequencing-Based Methods. Trends Biotechnol 2018; 36:729-740. [PMID: 29550161 PMCID: PMC6004327 DOI: 10.1016/j.tibtech.2018.02.009] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 02/16/2018] [Accepted: 02/20/2018] [Indexed: 12/18/2022]
Abstract
There is a great need in biomedical and genetic research to detect DNA damage and de novo mutations, but doing so is inherently challenging because of the rarity of these events. The enormous capacity of current DNA sequencing technologies has opened the door for quantifying sequence variants present at low frequencies in vivo, such as within cancerous tissues. However, these sequencing technologies are error prone, resulting in high noise thresholds. Most DNA sequencing methods are also generally incapable of identifying chemically modified bases arising from DNA damage. In recent years, numerous specialized modifications to sequencing methods have been developed to address these shortcomings. Here, we review this landscape of emerging techniques, highlighting their respective strengths, weaknesses, and target applications.
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Affiliation(s)
- Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO, USA.
| | - Amanda K Broz
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Joel Sharbrough
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Zhiqiang Wu
- Department of Biology, Colorado State University, Fort Collins, CO, USA
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35
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Sebastián-Martín A, Barrioluengo V, Menéndez-Arias L. Transcriptional inaccuracy threshold attenuates differences in RNA-dependent DNA synthesis fidelity between retroviral reverse transcriptases. Sci Rep 2018; 8:627. [PMID: 29330371 PMCID: PMC5766491 DOI: 10.1038/s41598-017-18974-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 12/18/2017] [Indexed: 01/01/2023] Open
Abstract
In M13mp2 lacZα forward mutation assays measuring intrinsic fidelity of DNA-dependent DNA synthesis, wild-type human immunodeficiency virus type 1 (HIV-1) RTs of group M/subtype B previously showed >10-fold higher error rates than murine leukaemia virus (MLV) and avian myeloblastosis virus (AMV) RTs. An adapted version of the assay was used to obtain error rates of RNA-dependent DNA synthesis for several RTs, including wild-type HIV-1BH10, HIV-1ESP49, AMV and MLV RTs, and the high-fidelity mutants of HIV-1ESP49 RT K65R and K65R/V75I. Our results showed that there were less than two-fold differences in fidelity between the studied RTs with error rates ranging within 2.5 × 10-5 and 3.5 × 10-5. These results were consistent with the existence of a transcriptional inaccuracy threshold, generated by the RNA polymerase while synthesizing the RNA template used in the assay. A modest but consistent reduction of the inaccuracy threshold was achieved by lowering the pH and Mg2+ concentration of the transcription reaction. Despite assay limitations, we conclude that HIV-1BH10 and HIV-1ESP49 RTs are less accurate when copying DNA templates than RNA templates. Analysis of the RNA-dependent mutational spectra revealed a higher tendency to introduce large deletions at the initiation of reverse transcription by all HIV-1 RTs except the double-mutant K65R/V75I.
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Affiliation(s)
- Alba Sebastián-Martín
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas & Universidad Autónoma de Madrid), c/Nicolás Cabrera, 1, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Verónica Barrioluengo
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas & Universidad Autónoma de Madrid), c/Nicolás Cabrera, 1, Campus de Cantoblanco, 28049, Madrid, Spain.,DiaSorin Iberia S.A., Avenida de la Vega 1, 28108, Alcobendas (Madrid), Spain
| | - Luis Menéndez-Arias
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas & Universidad Autónoma de Madrid), c/Nicolás Cabrera, 1, Campus de Cantoblanco, 28049, Madrid, Spain.
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36
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Marasco M, Li W, Lynch M, Pikaard CS. Catalytic properties of RNA polymerases IV and V: accuracy, nucleotide incorporation and rNTP/dNTP discrimination. Nucleic Acids Res 2017; 45:11315-11326. [PMID: 28977461 PMCID: PMC5737373 DOI: 10.1093/nar/gkx794] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 08/29/2017] [Indexed: 02/05/2023] Open
Abstract
All eukaryotes have three essential nuclear multisubunit RNA polymerases, abbreviated as Pol I, Pol II and Pol III. Plants are remarkable in having two additional multisubunit RNA polymerases, Pol IV and Pol V, which synthesize noncoding RNAs that coordinate RNA-directed DNA methylation for silencing of transposons and a subset of genes. Based on their subunit compositions, Pols IV and V clearly evolved as specialized forms of Pol II, but their catalytic properties remain undefined. Here, we show that Pols IV and V differ from one another, and Pol II, in nucleotide incorporation rate, transcriptional accuracy and the ability to discriminate between ribonucleotides and deoxyribonucleotides. Pol IV transcription is considerably more error-prone than Pols II or V, which may be tolerable in its synthesis of short RNAs that serve as precursors for siRNAs targeting non-identical members of transposon families. By contrast, Pol V exhibits high fidelity transcription, similar to Pol II, suggesting a need for Pol V transcripts to faithfully reflect the DNA sequence of target loci to which siRNA–Argonaute silencing complexes are recruited.
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Affiliation(s)
- Michelle Marasco
- Department of Biology, Indiana University, 915 E. Third Street, Bloomington, IN 47405, USA
| | - Weiyi Li
- Department of Biology, Indiana University, 915 E. Third Street, Bloomington, IN 47405, USA
| | - Michael Lynch
- Department of Biology, Indiana University, 915 E. Third Street, Bloomington, IN 47405, USA
| | - Craig S Pikaard
- Department of Biology, Indiana University, 915 E. Third Street, Bloomington, IN 47405, USA.,Department of Molecular and Cellular Biochemistry, Indiana University, 915 E. Third Street, Bloomington, IN 47405, USA.,Howard Hughes Medical Institute, Indiana University, Bloomington, IN 47405, USA
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37
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Wong HE, Huang CJ, Zhang Z. Amino acid misincorporation in recombinant proteins. Biotechnol Adv 2017; 36:168-181. [PMID: 29107148 DOI: 10.1016/j.biotechadv.2017.10.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 09/12/2017] [Accepted: 10/24/2017] [Indexed: 11/26/2022]
Abstract
Proteins provide the molecular basis for cellular structure, catalytic activity, signal transduction, and molecular transport in biological systems. Recombinant protein expression is widely used to prepare and manufacture novel proteins that serve as the foundation of many biopharmaceutical products. However, protein translation bioprocesses are inherently prone to low-level errors. These sequence variants caused by amino acid misincorporation have been observed in both native and recombinant proteins. Protein sequence variants impact product quality, and their presence can be exacerbated through cellular stress, overexpression, and nutrient starvation. Therefore, the cell line selection process, which is used in the biopharmaceutical industry, is not only directed towards maximizing productivity, but also focuses on selecting clones which yield low sequence variant levels, thereby proactively avoiding potentially inauspicious patient safety and efficacy outcomes. Here, we summarize a number of hallmark studies aimed at understanding the mechanisms of amino acid misincorporation, as well as exacerbating factors, and mitigation strategies. We also describe key advances in analytical technologies in the identification and quantification of sequence variants, and some practical considerations when using LC-MS/MS for detecting sequence variants.
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Affiliation(s)
- H Edward Wong
- Process Development, Amgen Inc., 1 Amgen Center Drive, Thousand Oaks, CA 91320, United States
| | - Chung-Jr Huang
- Process Development, Amgen Inc., 1 Amgen Center Drive, Thousand Oaks, CA 91320, United States
| | - Zhongqi Zhang
- Process Development, Amgen Inc., 1 Amgen Center Drive, Thousand Oaks, CA 91320, United States.
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38
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Gout JF, Li W, Fritsch C, Li A, Haroon S, Singh L, Hua D, Fazelinia H, Smith Z, Seeholzer S, Thomas K, Lynch M, Vermulst M. The landscape of transcription errors in eukaryotic cells. SCIENCE ADVANCES 2017; 3:e1701484. [PMID: 29062891 PMCID: PMC5650487 DOI: 10.1126/sciadv.1701484] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 09/21/2017] [Indexed: 05/09/2023]
Abstract
Accurate transcription is required for the faithful expression of genetic information. To understand the molecular mechanisms that control the fidelity of transcription, we used novel sequencing technology to provide the first comprehensive analysis of the fidelity of transcription in eukaryotic cells. Our results demonstrate that transcription errors can occur in any gene, at any location, and affect every aspect of protein structure and function. In addition, we show that multiple proteins safeguard the fidelity of transcription and provide evidence suggesting that errors that evade these layers of RNA quality control profoundly affect the physiology of living cells. Together, these observations demonstrate that there is an inherent limit to the faithful expression of the genome and suggest that the impact of mutagenesis on cellular health and fitness is substantially greater than currently appreciated.
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Affiliation(s)
| | - Weiyi Li
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Clark Fritsch
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19102, USA
- Department of Cellular and Molecular Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Annie Li
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19102, USA
| | - Suraiya Haroon
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19102, USA
| | - Larry Singh
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19102, USA
| | - Ding Hua
- Protein and Proteomics Core, Children’s Hospital of Philadelphia, Philadelphia, PA 19102, USA
| | - Hossein Fazelinia
- Protein and Proteomics Core, Children’s Hospital of Philadelphia, Philadelphia, PA 19102, USA
| | - Zach Smith
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA
| | - Steven Seeholzer
- Protein and Proteomics Core, Children’s Hospital of Philadelphia, Philadelphia, PA 19102, USA
| | - Kelley Thomas
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Michael Lynch
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
- Corresponding author. (M.V.); (M.L.)
| | - Marc Vermulst
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19102, USA
- Corresponding author. (M.V.); (M.L.)
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39
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Sultana S, Solotchi M, Ramachandran A, Patel SS. Transcriptional fidelities of human mitochondrial POLRMT, yeast mitochondrial Rpo41, and phage T7 single-subunit RNA polymerases. J Biol Chem 2017; 292:18145-18160. [PMID: 28882896 DOI: 10.1074/jbc.m117.797480] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 08/23/2017] [Indexed: 12/31/2022] Open
Abstract
Single-subunit RNA polymerases (RNAPs) are present in phage T7 and in mitochondria of all eukaryotes. This RNAP class plays important roles in biotechnology and cellular energy production, but we know little about its fidelity and error rates. Herein, we report the error rates of three single-subunit RNAPs measured from the catalytic efficiencies of correct and all possible incorrect nucleotides. The average error rates of T7 RNAP (2 × 10-6), yeast mitochondrial Rpo41 (6 × 10-6), and human mitochondrial POLRMT (RNA polymerase mitochondrial) (2 × 10-5) indicate high accuracy/fidelity of RNA synthesis resembling those of replicative DNA polymerases. All three RNAPs exhibit a distinctly high propensity for GTP misincorporation opposite dT, predicting frequent A→G errors in RNA with rates of ∼10-4 The A→C, G→A, A→U, C→U, G→U, U→C, and U→G errors mostly due to pyrimidine-purine mismatches were relatively frequent (10-5-10-6), whereas C→G, U→A, G→C, and C→A errors from purine-purine and pyrimidine-pyrimidine mismatches were rare (10-7-10-10). POLRMT also shows a high C→A error rate on 8-oxo-dG templates (∼10-4). Strikingly, POLRMT shows a high mutagenic bypass rate, which is exacerbated by TEFM (transcription elongation factor mitochondrial). The lifetime of POLRMT on terminally mismatched elongation substrate is increased in the presence of TEFM, which allows POLRMT to efficiently bypass the error and continue with transcription. This investigation of nucleotide selectivity on normal and oxidatively damaged DNA by three single-subunit RNAPs provides the basic information to understand the error rates in mitochondria and, in the case of T7 RNAP, to assess the quality of in vitro transcribed RNAs.
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Affiliation(s)
- Shemaila Sultana
- From the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School and
| | - Mihai Solotchi
- School of Arts and Sciences, Rutgers University, Piscataway, New Jersey 08854
| | - Aparna Ramachandran
- From the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School and
| | - Smita S Patel
- From the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School and
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40
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Reid-Bayliss KS, Loeb LA. Accurate RNA consensus sequencing for high-fidelity detection of transcriptional mutagenesis-induced epimutations. Proc Natl Acad Sci U S A 2017; 114:9415-9420. [PMID: 28798064 PMCID: PMC5584456 DOI: 10.1073/pnas.1709166114] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Transcriptional mutagenesis (TM) due to misincorporation during RNA transcription can result in mutant RNAs, or epimutations, that generate proteins with altered properties. TM has long been hypothesized to play a role in aging, cancer, and viral and bacterial evolution. However, inadequate methodologies have limited progress in elucidating a causal association. We present a high-throughput, highly accurate RNA sequencing method to measure epimutations with single-molecule sensitivity. Accurate RNA consensus sequencing (ARC-seq) uniquely combines RNA barcoding and generation of multiple cDNA copies per RNA molecule to eliminate errors introduced during cDNA synthesis, PCR, and sequencing. The stringency of ARC-seq can be scaled to accommodate the quality of input RNAs. We apply ARC-seq to directly assess transcriptome-wide epimutations resulting from RNA polymerase mutants and oxidative stress.
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Affiliation(s)
- Kate S Reid-Bayliss
- Department of Pathology, University of Washington School of Medicine, Seattle, WA 98195
| | - Lawrence A Loeb
- Department of Pathology, University of Washington School of Medicine, Seattle, WA 98195;
- Department of Biochemistry, University of Washington School of Medicine, Seattle, WA 98195
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41
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Genome-Wide Spectra of Transcription Insertions and Deletions Reveal That Slippage Depends on RNA:DNA Hybrid Complementarity. mBio 2017; 8:mBio.01230-17. [PMID: 28851848 PMCID: PMC5574713 DOI: 10.1128/mbio.01230-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Advances in sequencing technologies have enabled direct quantification of genome-wide errors that occur during RNA transcription. These errors occur at rates that are orders of magnitude higher than rates during DNA replication, but due to technical difficulties such measurements have been limited to single-base substitutions and have not yet quantified the scope of transcription insertions and deletions. Previous reporter gene assay findings suggested that transcription indels are produced exclusively by elongation complex slippage at homopolymeric runs, so we enumerated indels across the protein-coding transcriptomes of Escherichia coli and Buchnera aphidicola, which differ widely in their genomic base compositions and incidence of repeat regions. As anticipated from prior assays, transcription insertions prevailed in homopolymeric runs of A and T; however, transcription deletions arose in much more complex sequences and were rarely associated with homopolymeric runs. By reconstructing the relocated positions of the elongation complex as inferred from the sequences inserted or deleted during transcription, we show that continuation of transcription after slippage hinges on the degree of nucleotide complementarity within the RNA:DNA hybrid at the new DNA template location. The high level of mistakes generated during transcription can result in the accumulation of malfunctioning and misfolded proteins which can alter global gene regulation and in the expenditure of energy to degrade these nonfunctional proteins. The transcriptome-wide occurrence of base substitutions has been elucidated in bacteria, but information on transcription insertions and deletions—errors that potentially have more dire effects on protein function—is limited to reporter gene constructs. Here, we capture the transcriptome-wide spectrum of insertions and deletions in Escherichia coli and Buchnera aphidicola and show that they occur at rates approaching those of base substitutions. Knowledge of the full extent of sequences subject to transcription indels supports a new model of bacterial transcription slippage, one that relies on the number of complementary bases between the transcript and the DNA template to which it slipped.
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Mistranslation can enhance fitness through purging of deleterious mutations. Nat Commun 2017; 8:15410. [PMID: 28524864 PMCID: PMC5454534 DOI: 10.1038/ncomms15410] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 03/20/2017] [Indexed: 01/01/2023] Open
Abstract
Phenotypic mutations are amino acid changes caused by mistranslation. How phenotypic mutations affect the adaptive evolution of new protein functions is unknown. Here we evolve the antibiotic resistance protein TEM-1 towards resistance on the antibiotic cefotaxime in an Escherichia coli strain with a high mistranslation rate. TEM-1 populations evolved in such strains endow host cells with a general growth advantage, not only on cefotaxime but also on several other antibiotics that ancestral TEM-1 had been unable to deactivate. High-throughput sequencing of TEM-1 populations shows that this advantage is associated with a lower incidence of weakly deleterious genotypic mutations. Our observations show that mistranslation is not just a source of noise that delays adaptive evolution. It could even facilitate adaptive evolution by exacerbating the effects of deleterious mutations and leading to their more efficient purging. The ubiquity of mistranslation and its effects render mistranslation an important factor in adaptive protein evolution. Mistranslation results in amino acid changes in proteins known as phenotypic mutations and these occur at a much higher rate than DNA mutations. Here, the authors show that mistranslation can increase the response to directional selection by exacerbating the fitness effects of deleterious DNA mutations.
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Menéndez-Arias L, Sebastián-Martín A, Álvarez M. Viral reverse transcriptases. Virus Res 2016; 234:153-176. [PMID: 28043823 DOI: 10.1016/j.virusres.2016.12.019] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 12/19/2016] [Accepted: 12/24/2016] [Indexed: 12/11/2022]
Abstract
Reverse transcriptases (RTs) play a major role in the replication of Retroviridae, Metaviridae, Pseudoviridae, Hepadnaviridae and Caulimoviridae. RTs are enzymes that are able to synthesize DNA using RNA or DNA as templates (DNA polymerase activity), and degrade RNA when forming RNA/DNA hybrids (ribonuclease H activity). In retroviruses and LTR retrotransposons (Metaviridae and Pseudoviridae), the coordinated action of both enzymatic activities converts single-stranded RNA into a double-stranded DNA that is flanked by identical sequences known as long terminal repeats (LTRs). RTs of retroviruses and LTR retrotransposons are active as monomers (e.g. murine leukemia virus RT), homodimers (e.g. Ty3 RT) or heterodimers (e.g. human immunodeficiency virus type 1 (HIV-1) RT). RTs lack proofreading activity and display high intrinsic error rates. Besides, high recombination rates observed in retroviruses are promoted by poor processivity that causes template switching, a hallmark of reverse transcription. HIV-1 RT inhibitors acting on its polymerase activity constitute the backbone of current antiretroviral therapies, although novel drugs, including ribonuclease H inhibitors, are still necessary to fight HIV infections. In Hepadnaviridae and Caulimoviridae, reverse transcription leads to the formation of nicked circular DNAs that will be converted into episomal DNA in the host cell nucleus. Structural and biochemical information on their polymerases is limited, although several drugs inhibiting HIV-1 RT are known to be effective against the human hepatitis B virus polymerase. In this review, we summarize current knowledge on reverse transcription in the five virus families and discuss available biochemical and structural information on RTs, including their biosynthesis, enzymatic activities, and potential inhibition.
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Affiliation(s)
- Luis Menéndez-Arias
- Centro de Biología Molecular "Severo Ochoa", Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, c/Nicolás Cabrera, 1, Campus de Cantoblanco, 28049 Madrid, Spain.
| | - Alba Sebastián-Martín
- Centro de Biología Molecular "Severo Ochoa", Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, c/Nicolás Cabrera, 1, Campus de Cantoblanco, 28049 Madrid, Spain
| | - Mar Álvarez
- Centro de Biología Molecular "Severo Ochoa", Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, c/Nicolás Cabrera, 1, Campus de Cantoblanco, 28049 Madrid, Spain
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Drift Barriers to Quality Control When Genes Are Expressed at Different Levels. Genetics 2016; 205:397-407. [PMID: 27838629 DOI: 10.1534/genetics.116.192567] [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: 06/11/2016] [Accepted: 11/02/2016] [Indexed: 11/18/2022] Open
Abstract
Gene expression is imperfect, sometimes leading to toxic products. Solutions take two forms: globally reducing error rates, or ensuring that the consequences of erroneous expression are relatively harmless. The latter is optimal, but because it must evolve independently at so many loci, it is subject to a stringent "drift barrier"-a limit to how weak the effects of a deleterious mutation s can be, while still being effectively purged by selection, expressed in terms of the population size N of an idealized population such that purging requires s < -1/N In previous work, only large populations evolved the optimal local solution, small populations instead evolved globally low error rates, and intermediate populations were bistable, with either solution possible. Here, we take into consideration the fact that the effectiveness of purging varies among loci, because of variation in gene expression level, and variation in the intrinsic vulnerabilities of different gene products to error. The previously found dichotomy between the two kinds of solution breaks down, replaced by a gradual transition as a function of population size. In the extreme case of a small enough population, selection fails to maintain even the global solution against deleterious mutations, explaining the nonmonotonic relationship between effective population size and transcriptional error rate that was recently observed in experiments on Escherichia coli, Caenorhabditis elegans, and Buchnera aphidicola.
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Fan Y, Evans CR, Ling J. Reduced Protein Synthesis Fidelity Inhibits Flagellar Biosynthesis and Motility. Sci Rep 2016; 6:30960. [PMID: 27468805 PMCID: PMC4965754 DOI: 10.1038/srep30960] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 07/12/2016] [Indexed: 01/02/2023] Open
Abstract
Accurate translation of the genetic information from DNA to protein is maintained by multiple quality control steps from bacteria to mammals. Genetic and environmental alterations have been shown to compromise translational quality control and reduce fidelity during protein synthesis. The physiological impact of increased translational errors is not fully understood. While generally considered harmful, translational errors have recently been shown to benefit cells under certain stress conditions. In this work, we describe a novel regulatory pathway in which reduced translational fidelity downregulates expression of flagellar genes and suppresses bacterial motility. Electron microscopy imaging shows that the error-prone Escherichia coli strain lacks mature flagella. Further genetic analyses reveal that translational errors upregulate expression of a small RNA DsrA through enhancing its transcription, and deleting DsrA from the error-prone strain restores motility. DsrA regulates expression of H-NS and RpoS, both of which regulate flagellar genes. We demonstrate that an increased level of DsrA in the error-prone strain suppresses motility through the H-NS pathway. Our work suggests that bacteria are capable of switching on and off the flagellar system by altering translational fidelity, which may serve as a previously unknown mechanism to improve fitness in response to environmental cues.
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Affiliation(s)
- Yongqiang Fan
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Christopher R Evans
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Jiqiang Ling
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA.,Graduate School of Biomedical Sciences, Houston, TX 77030, USA
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Fungtammasan A, Tomaszkiewicz M, Campos-Sánchez R, Eckert KA, DeGiorgio M, Makova KD. Reverse Transcription Errors and RNA-DNA Differences at Short Tandem Repeats. Mol Biol Evol 2016; 33:2744-58. [PMID: 27413049 PMCID: PMC5026258 DOI: 10.1093/molbev/msw139] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Transcript variation has important implications for organismal function in health and disease. Most transcriptome studies focus on assessing variation in gene expression levels and isoform representation. Variation at the level of transcript sequence is caused by RNA editing and transcription errors, and leads to nongenetically encoded transcript variants, or RNA–DNA differences (RDDs). Such variation has been understudied, in part because its detection is obscured by reverse transcription (RT) and sequencing errors. It has only been evaluated for intertranscript base substitution differences. Here, we investigated transcript sequence variation for short tandem repeats (STRs). We developed the first maximum-likelihood estimator (MLE) to infer RT error and RDD rates, taking next generation sequencing error rates into account. Using the MLE, we empirically evaluated RT error and RDD rates for STRs in a large-scale DNA and RNA replicated sequencing experiment conducted in a primate species. The RT error rates increased exponentially with STR length and were biased toward expansions. The RDD rates were approximately 1 order of magnitude lower than the RT error rates. The RT error rates estimated with the MLE from a primate data set were concordant with those estimated with an independent method, barcoded RNA sequencing, from a Caenorhabditis elegans data set. Our results have important implications for medical genomics, as STR allelic variation is associated with >40 diseases. STR nonallelic transcript variation can also contribute to disease phenotype. The MLE and empirical rates presented here can be used to evaluate the probability of disease-associated transcripts arising due to RDD.
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Affiliation(s)
- Arkarachai Fungtammasan
- Integrative Biosciences, Bioinformatics and Genomics Option, Pennsylvania State University Department of Biology, Pennsylvania State University Center for Medical Genomics, Pennsylvania State University Huck Institute of Genome Sciences, Pennsylvania State University
| | - Marta Tomaszkiewicz
- Department of Biology, Pennsylvania State University Center for Medical Genomics, Pennsylvania State University
| | - Rebeca Campos-Sánchez
- Department of Biology, Pennsylvania State University Center for Medical Genomics, Pennsylvania State University
| | - Kristin A Eckert
- Center for Medical Genomics, Pennsylvania State University Department of Pathology, The Jake Gittlen Laboratories for Cancer Research, The Pennsylvania State University College of Medicine
| | - Michael DeGiorgio
- Department of Biology, Pennsylvania State University Center for Medical Genomics, Pennsylvania State University Institute for CyberScience, Pennsylvania State University
| | - Kateryna D Makova
- Department of Biology, Pennsylvania State University Center for Medical Genomics, Pennsylvania State University Huck Institute of Genome Sciences, Pennsylvania State University
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