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Gupta A, Pal SK, Nema V. High frequency of silent mutations in gyrA gene of Mycobacterium tuberculosis in Indian isolates. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2024. [PMID: 39262280 DOI: 10.1002/em.22629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2024] [Revised: 08/26/2024] [Accepted: 08/27/2024] [Indexed: 09/13/2024]
Abstract
Reporting any uncommon or untapped changes in bacterial genetics or physiology would be of great importance to support the drug development process. We studied 120 Mycobacterium tuberculosis clinical isolates with different geographical origin within India and their resistance profile and found a significant number of isolates (109) harboring the polymorphism at nucleotide positions 61 and 284 of the gyrA gene. Bioinformatics analysis of these changes for drug binding suggested no significant change in the binding of the drug but have lower binding energies as compared with the wild-type proteins. Although functionally silent for the gyrA gene, these changes are indicating a silent geographical and evolutionary change that needs to be further studied for drug discovery and bacterial fitness.
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Affiliation(s)
- Anamika Gupta
- Division of Molecular Biology, ICMR-National Institute of Translational Virology and AIDS Research (formerly: National AIDS Research Institute), Pune, Maharashtra, India
| | - Sudhir K Pal
- Division of Molecular Biology, ICMR-National Institute of Translational Virology and AIDS Research (formerly: National AIDS Research Institute), Pune, Maharashtra, India
| | - Vijay Nema
- Division of Molecular Biology, ICMR-National Institute of Translational Virology and AIDS Research (formerly: National AIDS Research Institute), Pune, Maharashtra, India
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2
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Zhong T, Wu H, Hu J, Liu Y, Zheng Y, Li N, Sun Z, Yin XF, He QY, Sun X. Two synonymous single-nucleotide polymorphisms promoting fluoroquinolone resistance of Escherichia coli in the environment. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:133849. [PMID: 38432089 DOI: 10.1016/j.jhazmat.2024.133849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 02/05/2024] [Accepted: 02/19/2024] [Indexed: 03/05/2024]
Abstract
Single-nucleotide polymorphism (SNP) is one of the core mechanisms that respond to antibiotic resistance of Escherichia coli (E. coli), which is a major issue in environmental pollution. A specific type of SNPs, synonymous SNPs, have been generally considered as the "silent" SNPs since they do not change the encoded amino acid. However, the impact of synonymous SNPs on mRNA splicing, nucleo-cytoplasmic export, stability, and translation was gradually discovered in the last decades. Figuring out the mechanism of synonymous SNPs in regulating antibiotic resistance is critical to improve antimicrobial therapy strategies in clinics and biological treatment strategies of antibiotic-resistant E. coli-polluted materials. With our newly designed antibiotic resistant SNPs prediction algorithm, Multilocus Sequence Type based Identification for Phenotype-single nucleotide polymorphism Analysis (MIPHA), and in vivo validation, we identified 2 important synonymous SNPs 522 G>A and 972 C>T, located at hisD gene, which was previously predicted as a fluoroquinolone resistance-related gene without a detailed mechanism in the E. coli samples with environmental backgrounds. We first discovered that hisD causes gyrA mutation via the upregulation of sbmC and its downstream gene umuD. Moreover, those 2 synonymous SNPs of hisD cause its own translational slowdown and further reduce the expression levels of sbmC and its downstream gene umuD, making the fluoroquinolone resistance determining region of gyrA remains unmutated, ultimately causing the bacteria to lose their ability to resist drugs. This study provided valuable insight into the role of synonymous SNPs in mediating antibiotic resistance of bacteria and a new perspective for the treatment of environmental pollution caused by drug-resistant bacteria.
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Affiliation(s)
- Tairan Zhong
- MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Haiming Wu
- MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Jiehua Hu
- MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Yun Liu
- MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Yundan Zheng
- MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Nan Li
- MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Zhenghua Sun
- MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Xing-Feng Yin
- MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Qing-Yu He
- MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China.
| | - Xuesong Sun
- MOE Key Laboratory of Tumor Molecular Biology and State Key Laboratory of Bioactive Molecules and Druggability Assessment, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China.
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3
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Nkurikiyimfura O, Waheed A, Fang H, Yuan X, Chen L, Wang YP, Lu G, Zhan J, Yang L. Fitness difference between two synonymous mutations of Phytophthora infestans ATP6 gene. BMC Ecol Evol 2024; 24:36. [PMID: 38494489 PMCID: PMC10946160 DOI: 10.1186/s12862-024-02223-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 03/11/2024] [Indexed: 03/19/2024] Open
Abstract
BACKGROUND Sequence variation produced by mutation provides the ultimate source of natural selection for species adaptation. Unlike nonsynonymous mutation, synonymous mutations are generally considered to be selectively neutral but accumulating evidence suggests they also contribute to species adaptation by regulating the flow of genetic information and the development of functional traits. In this study, we analysed sequence characteristics of ATP6, a housekeeping gene from 139 Phytophthora infestans isolates, and compared the fitness components including metabolic rate, temperature sensitivity, aggressiveness, and fungicide tolerance among synonymous mutations. RESULTS We found that the housekeeping gene exhibited low genetic variation and was represented by two major synonymous mutants at similar frequency (0.496 and 0.468, respectively). The two synonymous mutants were generated by a single nucleotide substitution but differed significantly in fitness as well as temperature-mediated spatial distribution and expression. The synonymous mutant ending in AT was more common in cold regions and was more expressed at lower experimental temperature than the synonymous mutant ending in GC and vice versa. CONCLUSION Our results are consistent with the argument that synonymous mutations can modulate the adaptive evolution of species including pathogens and have important implications for sustainable disease management, especially under climate change.
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Affiliation(s)
- Oswald Nkurikiyimfura
- Institute of Plant Virology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Abdul Waheed
- Institute of Plant Virology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Hanmei Fang
- Institute of Plant Virology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Xiaoxian Yuan
- Institute of Plant Virology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Lixia Chen
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, 350108, China
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Yan-Ping Wang
- College of Chemistry and Life Sciences, Sichuan Provincial Key Laboratory for Development and Utilization of Characteristic Horticultural Biological Resources, Chengdu Normal University, Chengdu, Sichuan, 611130, China
| | - Guodong Lu
- Department of Plant Pathology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Jiasui Zhan
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, 75007, Sweden.
| | - Lina Yang
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, 350108, China.
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McGrath KM, Russell SJ, Fer E, Garmendia E, Hosgel A, Baltrus DA, Kaçar B. Fitness benefits of a synonymous substitution in an ancient EF-Tu gene depend on the genetic background. J Bacteriol 2024; 206:e0032923. [PMID: 38289064 PMCID: PMC10882980 DOI: 10.1128/jb.00329-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 01/05/2024] [Indexed: 02/13/2024] Open
Abstract
Synonymous mutations are changes to DNA sequence, which occur within translated genes but which do not affect the protein sequence. Although often referred to as silent mutations, evidence suggests that synonymous mutations can affect gene expression, mRNA stability, and even translation efficiency. A collection of both experimental and bioinformatic data has shown that synonymous mutations can impact cell phenotype, yet less is known about the molecular mechanisms and potential of beneficial or adaptive effects of such changes within evolved populations. Here, we report a beneficial synonymous mutation acquired via experimental evolution in an essential gene variant encoding the translation elongation factor protein EF-Tu. We demonstrate that this particular synonymous mutation increases EF-Tu mRNA and protein levels as well as global polysome abundance on RNA transcripts. Although presence of the synonymous mutation is clearly causative of such changes, we also demonstrate that fitness benefits are highly contingent on other potentiating mutations present within the genetic background in which the mutation arose. Our results underscore the importance of beneficial synonymous mutations, especially those that affect levels of proteins that are key for cellular processes.IMPORTANCEThis study explores the degree to which synonymous mutations in essential genes can influence adaptation in bacteria. An experimental system whereby an Escherichia coli strain harboring an engineered translation protein elongation factor-Tu (EF-Tu) was subjected to laboratory evolution. We find that a synonymous mutation acquired on the gene encoding for EF-Tu is conditionally beneficial for bacterial fitness. Our findings provide insight into the importance of the genetic background when a synonymous substitution is favored by natural selection and how such changes have the potential to impact evolution when critical cellular processes are involved.
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Affiliation(s)
- Kaitlyn M. McGrath
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
- School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Steven J. Russell
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Evrim Fer
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Microbial Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Eva Garmendia
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Ali Hosgel
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - David A. Baltrus
- School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Betül Kaçar
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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Bajaj P, Bhasin M, Varadarajan R. Molecular bases for strong phenotypic effects of single synonymous codon substitutions in the E. coli ccdB toxin gene. BMC Genomics 2023; 24:732. [PMID: 38049728 PMCID: PMC10694988 DOI: 10.1186/s12864-023-09817-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 11/18/2023] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND Single synonymous codon mutations typically have only minor or no effects on gene function. Here, we estimate the effects on cell growth of ~ 200 single synonymous codon mutations in an operonic context by mutating almost all positions of ccdB, the 101-residue long cytotoxin of the ccdAB Toxin-Antitoxin (TA) operon to most degenerate codons. Phenotypes were assayed by transforming the mutant library into CcdB sensitive and resistant E. coli strains, isolating plasmid pools, and subjecting them to deep sequencing. Since autoregulation is a hallmark of TA operons, phenotypes obtained for ccdB synonymous mutants after transformation in a RelE toxin reporter strain followed by deep sequencing provided information on the amount of CcdAB complex formed. RESULTS Synonymous mutations in the N-terminal region involved in translation initiation showed the strongest non-neutral phenotypic effects. We observe an interplay of numerous factors, namely, location of the codon, codon usage, t-RNA abundance, formation of anti-Shine Dalgarno sequences, predicted transcript secondary structure, and evolutionary conservation in determining phenotypic effects of ccdB synonymous mutations. Incorporation of an N-terminal, hyperactive synonymous mutation, in the background of the single synonymous codon mutant library sufficiently increased translation initiation, such that mutational effects on either folding or termination of translation became more apparent. Introduction of putative pause sites not only affects the translational rate, but might also alter the folding kinetics of the protein in vivo. CONCLUSION In summary, the study provides novel insights into diverse mechanisms by which synonymous mutations modulate gene function. This information is useful in optimizing heterologous gene expression in E. coli and understanding the molecular bases for alteration in gene expression that arise due to synonymous mutations.
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Affiliation(s)
- Priyanka Bajaj
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
- Present address: Department of Bioengineering and Therapeutic Sciences, University of CA - San Francisco, San Francisco, CA, 94158, USA
| | - Munmun Bhasin
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
| | - Raghavan Varadarajan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India.
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McGuire BE, Nano FE. Whole-genome sequencing analysis of two heat-evolved Escherichia coli strains. BMC Genomics 2023; 24:154. [PMID: 36973666 PMCID: PMC10044804 DOI: 10.1186/s12864-023-09266-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 03/21/2023] [Indexed: 03/29/2023] Open
Abstract
BACKGROUND High temperatures cause a suite of problems for cells, including protein unfolding and aggregation; increased membrane fluidity; and changes in DNA supercoiling, RNA stability, transcription and translation. Consequently, enhanced thermotolerance can evolve through an unknown number of genetic mechanisms even in the simple model bacterium Escherichia coli. To date, each E. coli study exploring this question resulted in a different set of mutations. To understand the changes that can arise when an organism evolves to grow at higher temperatures, we sequenced and analyzed two previously described E. coli strains, BM28 and BM28 ΔlysU, that have been laboratory adapted to the highest E. coli growth temperature reported to date. RESULTS We found three large deletions in the BM28 and BM28 ΔlysU strains of 123, 15 and 8.5 kb in length and an expansion of IS10 elements. We found that BM28 and BM28 ΔlysU have considerably different genomes, suggesting that the BM28 culture that gave rise to BM28 and BM28 ΔlysU was a mixed population of genetically different cells. Consistent with published findings of high GroESL expression in BM28, we found that BM28 inexplicitly carries the groESL bearing plasmid pOF39 that was maintained simply by high-temperature selection pressure. We identified over 200 smaller insertions, deletions, single nucleotide polymorphisms and other mutations, including changes in master regulators such as the RNA polymerase and the transcriptional termination factor Rho. Importantly, this genome analysis demonstrates that the commonly cited findings that LysU plays a crucial role in thermotolerance and that GroESL hyper-expression is brought about by chromosomal mutations are based on a previous misinterpretation of the genotype of BM28. CONCLUSIONS This whole-genome sequencing study describes genetically distinct mechanisms of thermotolerance evolution from those found in other heat-evolved E. coli strains. Studying adaptive laboratory evolution to heat in simple model organisms is important in the context of climate change. It is important to better understand genetic mechanisms of enhancing thermotolerance in bacteria and other organisms, both in terms of optimizing laboratory evolution methods for various organisms and in terms of potential genetic engineering of organisms most at risk or most important to our societies and ecosystems.
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Affiliation(s)
- Bailey E McGuire
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, B.C, Canada.
| | - Francis E Nano
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, B.C, Canada
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7
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Most synonymous allelic variants in HIV tat are not silent. Genomics 2023; 115:110603. [PMID: 36893872 DOI: 10.1016/j.ygeno.2023.110603] [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: 11/19/2022] [Revised: 02/12/2023] [Accepted: 03/03/2023] [Indexed: 03/09/2023]
Abstract
The genetic code has degenerate codons that produce no change in the translated protein sequence and are generally thought to be silent. However, some synonymous variants are clearly not silent. Herein, we questioned the frequency of non-silent synonymous variants. We tested how random synonymous variants in the HIV Tat transcription factor effect transcription of an LTR-GFP reporter. Our model system has the advantage of directly measuring the function of the gene in human cells. Approximately, 67% of synonymous variants in Tat were non-silent, either having reduced activity or were full loss-of-function alleles. Eight mutant codons had higher codon usage than wild type, accompanied by reduced transcriptional activity. These were clustered on a loop in the Tat structure. We conclude that most synonymous Tat variants are not silent in human cells, and 25% are associated with changes in codon usage, likely effecting protein folding.
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Conversion of Escherichia coli into Mixotrophic CO 2 Assimilation with Malate and Hydrogen Based on Recombinant Expression of 2-Oxoglutarate:Ferredoxin Oxidoreductase Using Adaptive Laboratory Evolution. Microorganisms 2023; 11:microorganisms11020253. [PMID: 36838218 PMCID: PMC9967407 DOI: 10.3390/microorganisms11020253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/04/2023] [Accepted: 01/13/2023] [Indexed: 01/21/2023] Open
Abstract
We report the mixotrophic growth of Escherichia coli based on recombinant 2-oxoglutarate:ferredoxin oxidoreductase (OGOR) to assimilate CO2 using malate as an auxiliary carbon source and hydrogen as an energy source. We employ a long-term (~184 days) two-stage adaptive evolution to convert heterotrophic E. coli into mixotrophic E. coli. In the first stage of evolution with serine, diauxic growth emerges as a prominent feature. At the end of the second stage of evolution with malate, the strain exhibits mixotrophy with CO2 as an essential substrate for growth. We expect this work will open new possibilities in the utilization of OGOR for microbial CO2 assimilation and future hydrogen-based electro-microbial conversion.
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Genome-wide sequencing identifies a thermal-tolerance related synonymous mutation in the mussel, Mytilisepta virgata. Commun Biol 2023; 6:5. [PMID: 36596992 PMCID: PMC9810668 DOI: 10.1038/s42003-022-04407-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 12/23/2022] [Indexed: 01/05/2023] Open
Abstract
The roles of synonymous mutations for adapting to stressful thermal environments are of fundamental biological and ecological interests but poorly understood. To study whether synonymous mutations influence thermal adaptation at specific microhabitats, a genome-wide genotype-phenotype association analysis is carried out in the black mussels Mytilisepta virgata. A synonymous mutation of Ubiquitin-specific Peptidase 15 (MvUSP15) is significantly associated with the physiological upper thermal limit. The individuals carrying GG genotype (the G-type) at the mutant locus possess significantly lower heat tolerance compared to the individuals carrying GA and AA genotypes (the A-type). When heated to sublethal temperature, the G-type exhibit higher inter-individual variations in MvUSP15 expression, especially for the mussels on the sun-exposed microhabitats. Taken together, a synonymous mutation in MvUSP15 can affect the gene expression profile and interact with microhabitat heterogeneity to influence thermal resistance. This integrative study sheds light on the ecological importance of adaptive synonymous mutations as an underappreciated genetic buffer against heat stress and emphasizes the importance of integrative studies at a microhabitat scale for evaluating and predicting the impacts of climate change.
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Chandra S, Gupta K, Khare S, Kohli P, Asok A, Mohan SV, Gowda H, Varadarajan R. The High Mutational Sensitivity of ccdA Antitoxin Is Linked to Codon Optimality. Mol Biol Evol 2022; 39:msac187. [PMID: 36069948 PMCID: PMC9555053 DOI: 10.1093/molbev/msac187] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Deep mutational scanning studies suggest that synonymous mutations are typically silent and that most exposed, nonactive-site residues are tolerant to mutations. Here, we show that the ccdA antitoxin component of the Escherichia coli ccdAB toxin-antitoxin system is unusually sensitive to mutations when studied in the operonic context. A large fraction (∼80%) of single-codon mutations, including many synonymous mutations in the ccdA gene shows inactive phenotype, but they retain native-like binding affinity towards cognate toxin, CcdB. Therefore, the observed phenotypic effects are largely not due to alterations in protein structure/stability, consistent with a large region of CcdA being intrinsically disordered. E. coli codon preference and strength of ribosome-binding associated with translation of downstream ccdB gene are found to be major contributors of the observed ccdA mutant phenotypes. In select cases, proteomics studies reveal altered ratios of CcdA:CcdB protein levels in vivo, suggesting that the ccdA mutations likely alter relative translation efficiencies of the two genes in the operon. We extend these results by studying single-site synonymous mutations that lead to loss of function phenotypes in the relBE operon upon introduction of rarer codons. Thus, in their operonic context, genes are likely to be more sensitive to both synonymous and nonsynonymous point mutations than inferred previously.
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Affiliation(s)
- Soumyanetra Chandra
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Kritika Gupta
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Shruti Khare
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Pehu Kohli
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Aparna Asok
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | | | - Harsha Gowda
- Institute of Bioinformatics, Bangalore 560100, India
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The Roles of Mutation and Selection Acting on Mitochondrial Genomes Inferred from Intraspecific Variation in Seed Plants. Genes (Basel) 2022; 13:genes13061036. [PMID: 35741799 PMCID: PMC9222611 DOI: 10.3390/genes13061036] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/20/2022] [Accepted: 06/07/2022] [Indexed: 12/03/2022] Open
Abstract
There is a paradox in the plant mitochondrial genome, that is, the genic region evolves slowly while the intergenic region evolves rapidly. Thus, the intergenic regions of the plant mitochondrial genome are difficult to align across different species, even in closely related species. Here, to character the mechanism of this paradox, we identified interspecific variations in the Ginkgo biloba, Oryza sativa, and Arabidopsis thaliana mitochondrial and plastid genome at a genome-wide level. The substitution rate of synonymous sites in genic regions was similar to the substitution rate of intergenic regions, while the substitution rate of nonsynonymous sites in genic regions was lower than that in intergenic regions, suggesting the mutation inputs were the same among different categories within the organelle genome, but the selection pressure varied. The substitution rate of single-copy regions was higher than that of IR (inverted repeats) in the plastid genome at an intraspecific level. The substitution rate of single-copy regions was higher than that of repeats in the G. biloba and A. thaliana mitochondrial genomes, but lower in that of O. sativa. This difference may be related to the length and distribution of repeats. Copy number variations that existed in the G. biloba and O. sativa mitochondrial genomes were confirmed. This study reveals the intraspecific variation pattern of organelle genomes at a genome-wide level, and that copy number variations were common in plant mitochondrial genomes.
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12
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Schick A, Shewaramani S, Kassen R. Genomics of diversification of Pseudomonas aeruginosa in cystic fibrosis lung-like conditions. Genome Biol Evol 2022; 14:6602282. [PMID: 35660861 PMCID: PMC9168666 DOI: 10.1093/gbe/evac074] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 04/22/2022] [Accepted: 05/12/2022] [Indexed: 12/03/2022] Open
Abstract
Pseudomonas aeruginosa is among the most problematic opportunistic pathogens for adults with cystic fibrosis (CF), causing repeated and resilient infections in the lung and surrounding airways. Evidence suggests that long-term infections are associated with diversification into specialized types but the underlying cause of that diversification and the effect it has on the persistence of infections remains poorly understood. Here, we use evolve-and-resequence experiments to investigate the genetic changes accompanying rapid, de novo phenotypic diversification in lab environments designed to mimic two aspects of human lung ecology: spatial structure and complex nutritional content. After ∼220 generations of evolution, we find extensive genetic variation present in all environments, including those that most closely resemble the CF lung. We use the abundance and frequency of nonsynonymous and synonymous mutations to estimate the ratio of mutations that are selectively neutral (hitchhikers) to those that are under positive selection (drivers). A significantly lower proportion of driver mutations in spatially structured populations suggests that reduced dispersal generates subpopulations with reduced effective population size, decreasing the supply of beneficial mutations and causing more divergent evolutionary trajectories. In addition, we find mutations in a handful of genes typically associated with chronic infection in the CF lung, including one gene associated with antibiotic resistance. This demonstrates that many of the genetic changes considered to be hallmarks of CF lung adaptation can arise as a result of adaptation to a novel environment and do not necessarily require antimicrobial treatment, immune system suppression, or competition from other microbial species to occur.
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Affiliation(s)
- Alana Schick
- Biology Department and Centre for Advanced Research in Environmental Genomics, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Sonal Shewaramani
- Biology Department and Centre for Advanced Research in Environmental Genomics, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Rees Kassen
- Biology Department and Centre for Advanced Research in Environmental Genomics, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
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13
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Xiong W, Cai J, Li R, Wen C, Tan H. Rare Variant Analysis and Molecular Dynamics Simulation in Alzheimer’s Disease Identifies Exonic Variants in FLG. Genes (Basel) 2022; 13. [PMID: 35627223 PMCID: PMC9141140 DOI: 10.3390/genes13050838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/03/2022] [Accepted: 05/04/2022] [Indexed: 02/05/2023] Open
Abstract
Background: Although an increasing number of common variants contributing to Alzheimer’s disease (AD) are uncovered by genome-wide association studies, they can only explain less than half of the heritability of AD. Rare variant association studies (RVAS) has become an increasingly important area to explain the risk or trait variability of AD. Method: To investigate the potential rare variants that cause AD, we screened 70,209 rare variants from two cohorts of a 175 AD cohort and a 214 cognitively normal cohort from the Alzheimer’s Disease Neuroimaging Initiative database. MIRARE, a novel RVAS method, was performed on 232 non-synonymous variants selected by ANNOVAR annotation. Molecular docking and molecular dynamics (MD) simulation were adopted to verify the interaction between the chosen functional variants and BACE1. Results: MIRAGE analysis revealed significant associations between AD and six potential pathogenic genes, including PREX2, FLG, DHX16, NID2, ZnF585B and ZnF875. Only interactions between FLG (including wild type and rs3120654(SER742TYR)) and BACE1 were verified by molecular docking and MD simulation. The interaction of FLG(SER742TYR) with BACE1 was greater than that of wildtype FLG with BACE1. Conclusions: According to the literature search, bio-informatics analysis, and molecular docking and MD simulation, we find non-synonymous rare variants in six genes, especially FLG(rs3120654), that may play key roles in AD.
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Affiliation(s)
- Weixue Xiong
- Department of Preventive Medicine, Shantou University Medical College, Shantou 515000, China
| | - Jiahui Cai
- Department of Preventive Medicine, Shantou University Medical College, Shantou 515000, China
| | - Ruijia Li
- Department of Statistics and Finance, School of Management, University of Science and Technology of China, Hefei 230000, China;
| | - Canhong Wen
- Department of Statistics and Finance, School of Management, University of Science and Technology of China, Hefei 230000, China
| | - Haizhu Tan
- Department of Preventive Medicine, Shantou University Medical College, Shantou 515000, China
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14
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Ramdass AC, Rampersad SN. Molecular signatures of Janthinobacterium lividum from Trinidad support high potential for crude oil metabolism. BMC Microbiol 2021; 21:287. [PMID: 34670489 PMCID: PMC8527658 DOI: 10.1186/s12866-021-02346-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 10/06/2021] [Indexed: 11/30/2022] Open
Abstract
Background Janthinobacterium lividum is considered to be a psychrotrophic bacterial species. For the first time in the literature, J. lividum strains were isolated from Trinidad presenting with atypical features - hydrocarbonoclastic and able to survive in a tropical environment. Methods Identification of the Trinidad strains was carried out through 16S rRNA phylogenetic analysis. Gene-specific primers were designed to target the VioA which encodes violacein pigment and the EstA/B gene which encodes secreted extracellular lipase. Bioinformatics analyses were carried out on the nucleotide and amino acid sequences of VioA and EstA/B genes of the Trinidad Janthinobacterium strains to assess functionality and phylogenetic relatedness to other Janthinobacterium sequences specifically and more broadly, to other members of the Oxalobacteraceae family of betaproteobacteria. Results 16S rRNA confirmed the identity of the Trinidad strains as J. lividum and resolved three of the Trinidad strains at the intra-specific level. Typical motility patterns of this species were recorded. VioAp sequences were highly conserved, however, synonymous substitutions located outside of the critical sites for enzyme function were detected for the Trinidad strains. Comparisons with PDB 6g2p model from aa231 to aa406 further indicated no functional disruption of the VioA gene of the Trinidad strains. Phylogeny of the VioA protein sequences inferred placement of all J. lividum taxa into a highly supported species-specific clade (bs = 98%). EstA/Bp sequences were highly conserved, however, synonymous substitutions were detected that were unique to the Trinidad strains. Phylogenetic inference positioned the Trinidad consensus VioA and EstA protein sequences in a clearly distinct branch. Conclusions The findings showed that the primary sequence of VioAp and EstA/Bp were unique to the Trinidad strains and these molecular signatures were reflected in phylogenetic inference. Our results supported chemotaxis, possible elective inactivation of VioA gene expression and secreted lipase activity as survival mechanisms of the Trinidad strains in petrogenic conditions. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02346-4.
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Affiliation(s)
- Amanda C Ramdass
- Biochemistry Research Lab (Rm216), Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Sephra N Rampersad
- Biochemistry Research Lab (Rm216), Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago.
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15
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Bailey SF, Alonso Morales LA, Kassen R. Effects of synonymous mutations beyond codon bias: The evidence for adaptive synonymous substitutions from microbial evolution experiments. Genome Biol Evol 2021; 13:6300525. [PMID: 34132772 PMCID: PMC8410137 DOI: 10.1093/gbe/evab141] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2021] [Indexed: 12/22/2022] Open
Abstract
Synonymous mutations are often assumed to be neutral with respect to fitness because they do not alter the encoded amino acid and so cannot be 'seen' by natural selection. Yet a growing body of evidence suggests that synonymous mutations can have fitness effects that drive adaptive evolution through their impacts on gene expression and protein folding. Here, we review what microbial experiments have taught us about the contribution of synonymous mutations to adaptation. A survey of site-directed mutagenesis experiments reveals the distributions of fitness effects for nonsynonymous and synonymous mutations are more similar, especially for beneficial mutations, than expected if all synonymous mutations were neutral, suggesting they should drive adaptive evolution more often than is typically observed. A review of experimental evolution studies where synonymous mutations have contributed to adaptation shows they can impact fitness through a range of mechanisms including the creation of illicit RNA polymerase binding sites impacting transcription and changes to mRNA folding stability that modulate translation. We suggest that clonal interference in evolving microbial populations may be the reason synonymous mutations play a smaller role in adaptive evolution than expected based on their observed fitness effects. We finish by discussing the impacts of falsely assuming synonymous mutations are neutral and discuss directions for future work exploring the role of synonymous mutations in adaptive evolution.
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Affiliation(s)
- Susan F Bailey
- Department of Biology, Clarkson University, Potsdam, NY 13699, USA
| | | | - Rees Kassen
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
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16
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Van Leuven JT, Ederer MM, Burleigh K, Scott L, Hughes RA, Codrea V, Ellington AD, Wichman HA, Miller CR. ΦX174 Attenuation by Whole-Genome Codon Deoptimization. Genome Biol Evol 2020; 13:5921183. [PMID: 33045052 PMCID: PMC7881332 DOI: 10.1093/gbe/evaa214] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2020] [Indexed: 12/11/2022] Open
Abstract
Natural selection acting on synonymous mutations in protein-coding genes influences genome composition and evolution. In viruses, introducing synonymous mutations in genes encoding structural proteins can drastically reduce viral growth, providing a means to generate potent, live-attenuated vaccine candidates. However, an improved understanding of what compositional features are under selection and how combinations of synonymous mutations affect viral growth is needed to predictably attenuate viruses and make them resistant to reversion. We systematically recoded all nonoverlapping genes of the bacteriophage ΦX174 with codons rarely used in its Escherichia coli host. The fitness of recombinant viruses decreases as additional deoptimizing mutations are made to the genome, although not always linearly, and not consistently across genes. Combining deoptimizing mutations may reduce viral fitness more or less than expected from the effect size of the constituent mutations and we point out difficulties in untangling correlated compositional features. We test our model by optimizing the same genes and find that the relationship between codon usage and fitness does not hold for optimization, suggesting that wild-type ΦX174 is at a fitness optimum. This work highlights the need to better understand how selection acts on patterns of synonymous codon usage across the genome and provides a convenient system to investigate the genetic determinants of virulence.
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Affiliation(s)
- James T Van Leuven
- Department of Biological Science, University of Idaho.,Institute for Modeling Collaboration and Innovation, University of Idaho
| | | | - Katelyn Burleigh
- Department of Biological Science, University of Idaho.,Present address: Seattle Children's Research Institute, Seattle, WA
| | - LuAnn Scott
- Department of Biological Science, University of Idaho
| | - Randall A Hughes
- Applied Research Laboratories, University of Texas, Austin.,Present address: Biotechnology Branch, CCDC US Army Research Laboratory, Adelphi, MD
| | - Vlad Codrea
- Institute for Cellular and Molecular Biology, University of Texas, Austin
| | - Andrew D Ellington
- Applied Research Laboratories, University of Texas, Austin.,Institute for Cellular and Molecular Biology, University of Texas, Austin
| | - Holly A Wichman
- Department of Biological Science, University of Idaho.,Institute for Modeling Collaboration and Innovation, University of Idaho
| | - Craig R Miller
- Department of Biological Science, University of Idaho.,Institute for Modeling Collaboration and Innovation, University of Idaho
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17
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Demographic history and adaptive synonymous and nonsynonymous variants of nuclear genes in Rhododendron oldhamii (Ericaceae). Sci Rep 2020; 10:16658. [PMID: 33028947 PMCID: PMC7542430 DOI: 10.1038/s41598-020-73748-z] [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: 01/20/2020] [Accepted: 09/22/2020] [Indexed: 11/23/2022] Open
Abstract
Demographic events are important in shaping the population genetic structure and exon variation can play roles in adaptive divergence. Twelve nuclear genes were used to investigate the species-level phylogeography of Rhododendron oldhamii, test the difference in the average GC content of coding sites and of third codon positions with that of surrounding non-coding regions, and test exon variants associated with environmental variables. Spatial expansion was suggested by R2 index of the aligned intron sequences of all genes of the regional samples and sum of squared deviations statistic of the aligned intron sequences of all genes individually and of all genes of the regional and pooled samples. The level of genetic differentiation was significantly different between regional samples. Significantly lower and higher average GC contents across 94 sequences of the 12 genes at third codon positions of coding sequences than that of surrounding non-coding regions were found. We found seven exon variants associated strongly with environmental variables. Our results demonstrated spatial expansion of R. oldhamii in the late Pleistocene and the optimal third codon position could end in A or T rather than G or C as frequent alleles and could have been important for adaptive divergence in R. oldhamii.
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18
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Sandberg TE, Szubin R, Phaneuf PV, Palsson BO. Synthetic cross-phyla gene replacement and evolutionary assimilation of major enzymes. Nat Ecol Evol 2020; 4:1402-1409. [PMID: 32778753 PMCID: PMC7529951 DOI: 10.1038/s41559-020-1271-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 07/10/2020] [Indexed: 01/06/2023]
Abstract
The ability of DNA to produce a functional protein even after transfer to a foreign host is of fundamental importance in both evolutionary biology and biotechnology, enabling horizontal gene transfer in the wild and heterologous expression in the lab. However, the influence of genetic particulars on DNA functionality in a new host is poorly understood, as are the evolutionary mechanisms of assimilation and refinement. Here, we describe an automation-enabled large-scale experiment wherein Escherichia coli strains were evolved in parallel after replacement of the genes pgi or tpiA with orthologous DNA from donor species spanning all domains of life, from humans to hyperthermophilic archaea. Via analysis of hundreds of clones evolved for 50,000+ cumulative generations across dozens of independent lineages, we show that orthogene-upregulating mutations can completely mitigate fitness defects that result from initial non-functionality, with coding sequence changes unnecessary. Gene target, donor species and genomic location of the swap all influenced outcomes-both the nature of adaptive mutations (often synonymous) and the frequency with which strains successfully evolved to assimilate the foreign DNA. Additionally, time series DNA sequencing and replay evolution experiments revealed transient copy number expansions, the contingency of lineage outcome on first-step mutations and the ability for strains to escape from suboptimal local fitness maxima. Overall, this study establishes the influence of various DNA and protein features on cross-species genetic interchangeability and evolutionary outcomes, with implications for both horizontal gene transfer and rational strain design.
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Affiliation(s)
- Troy E Sandberg
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Richard Szubin
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Patrick V Phaneuf
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA. .,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
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19
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Wisotsky SR, Kosakovsky Pond SL, Shank SD, Muse SV. Synonymous Site-to-Site Substitution Rate Variation Dramatically Inflates False Positive Rates of Selection Analyses: Ignore at Your Own Peril. Mol Biol Evol 2020; 37:2430-2439. [PMID: 32068869 PMCID: PMC7403620 DOI: 10.1093/molbev/msaa037] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Most molecular evolutionary studies of natural selection maintain the decades-old assumption that synonymous substitution rate variation (SRV) across sites within genes occurs at levels that are either nonexistent or negligible. However, numerous studies challenge this assumption from a biological perspective and show that SRV is comparable in magnitude to that of nonsynonymous substitution rate variation. We evaluated the impact of this assumption on methods for inferring selection at the molecular level by incorporating SRV into an existing method (BUSTED) for detecting signatures of episodic diversifying selection in genes. Using simulated data we found that failing to account for even moderate levels of SRV in selection testing is likely to produce intolerably high false positive rates. To evaluate the effect of the SRV assumption on actual inferences we compared results of tests with and without the assumption in an empirical analysis of over 13,000 Euteleostomi (bony vertebrate) gene alignments from the Selectome database. This exercise reveals that close to 50% of positive results (i.e., evidence for selection) in empirical analyses disappear when SRV is modeled as part of the statistical analysis and are thus candidates for being false positives. The results from this work add to a growing literature establishing that tests of selection are much more sensitive to certain model assumptions than previously believed.
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Affiliation(s)
- Sadie R Wisotsky
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
| | | | - Stephen D Shank
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
| | - Spencer V Muse
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC
- Department of Statistics, North Carolina State University, Raleigh, NC
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20
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Dench J, Hinz A, Aris‐Brosou S, Kassen R. Identifying the drivers of computationally detected correlated evolution among sites under antibiotic selection. Evol Appl 2020; 13:781-793. [PMID: 32211067 PMCID: PMC7086105 DOI: 10.1111/eva.12900] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/02/2019] [Accepted: 11/14/2019] [Indexed: 11/29/2022] Open
Abstract
The ultimate causes of correlated evolution among sites in a genome remain difficult to tease apart. To address this problem directly, we performed a high-throughput search for correlated evolution among sites associated with resistance to a fluoroquinolone antibiotic using whole-genome data from clinical strains of Pseudomonas aeruginosa, before validating our computational predictions experimentally. We show that for at least two sites, this correlation is underlain by epistasis. Our analysis also revealed eight additional pairs of synonymous substitutions displaying correlated evolution underlain by physical linkage, rather than selection associated with antibiotic resistance. Our results provide direct evidence that both epistasis and physical linkage among sites can drive the correlated evolution identified by high-throughput computational tools. In other words, the observation of correlated evolution is not by itself sufficient evidence to guarantee that the sites in question are epistatic; such a claim requires additional evidence, ideally coming from direct estimates of epistasis, based on experimental evidence.
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Affiliation(s)
- Jonathan Dench
- Department of BiologyUniversity of OttawaOttawaOntarioCanada
| | - Aaron Hinz
- Department of BiologyUniversity of OttawaOttawaOntarioCanada
| | - Stéphane Aris‐Brosou
- Department of BiologyUniversity of OttawaOttawaOntarioCanada
- Department of Mathematics and StatisticsUniversity of OttawaOttawaOntarioCanada
| | - Rees Kassen
- Department of BiologyUniversity of OttawaOttawaOntarioCanada
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21
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Penesyan A, Nagy SS, Kjelleberg S, Gillings MR, Paulsen IT. Rapid microevolution of biofilm cells in response to antibiotics. NPJ Biofilms Microbiomes 2019; 5:34. [PMID: 31728201 PMCID: PMC6834608 DOI: 10.1038/s41522-019-0108-3] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 10/03/2019] [Indexed: 02/08/2023] Open
Abstract
Infections caused by Acinetobacter baumannii are increasingly antibiotic resistant, generating a significant public health problem. Like many bacteria, A. baumannii adopts a biofilm lifestyle that enhances its antibiotic resistance and environmental resilience. Biofilms represent the predominant mode of microbial life, but research into antibiotic resistance has mainly focused on planktonic cells. We investigated the dynamics of A. baumannii biofilms in the presence of antibiotics. A 3-day exposure of A. baumannii biofilms to sub-inhibitory concentrations of antibiotics had a profound effect, increasing biofilm formation and antibiotic resistance in the majority of biofilm dispersal isolates. Cells dispersing from biofilms were genome sequenced to identify mutations accumulating in their genomes, and network analysis linked these mutations to their phenotypes. Transcriptomics of biofilms confirmed the network analysis results, revealing novel gene functions of relevance to both resistance and biofilm formation. This approach is a rapid and objective tool for investigating resistance dynamics of biofilms.
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Affiliation(s)
- Anahit Penesyan
- 1Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW 2109 Australia.,2School of Chemical Engineering, University of New South Wales, Sydney, NSW 2052 Australia
| | - Stephanie S Nagy
- 1Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW 2109 Australia
| | - Staffan Kjelleberg
- 3Singapore Centre for Environmental Life Sciences Engineering, 60 Nanyang Drive, SBS-01N-27, Singapore, 637551 Singapore.,4School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551 Singapore.,5School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052 Australia
| | - Michael R Gillings
- 6Department of Biological Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW 2109 Australia
| | - Ian T Paulsen
- 1Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW 2109 Australia
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22
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Kemble H, Nghe P, Tenaillon O. Recent insights into the genotype-phenotype relationship from massively parallel genetic assays. Evol Appl 2019; 12:1721-1742. [PMID: 31548853 PMCID: PMC6752143 DOI: 10.1111/eva.12846] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 06/21/2019] [Accepted: 07/02/2019] [Indexed: 12/20/2022] Open
Abstract
With the molecular revolution in Biology, a mechanistic understanding of the genotype-phenotype relationship became possible. Recently, advances in DNA synthesis and sequencing have enabled the development of deep mutational scanning assays, capable of scoring comprehensive libraries of genotypes for fitness and a variety of phenotypes in massively parallel fashion. The resulting empirical genotype-fitness maps pave the way to predictive models, potentially accelerating our ability to anticipate the behaviour of pathogen and cancerous cell populations from sequencing data. Besides from cellular fitness, phenotypes of direct application in industry (e.g. enzyme activity) and medicine (e.g. antibody binding) can be quantified and even selected directly by these assays. This review discusses the technological basis of and recent developments in massively parallel genetics, along with the trends it is uncovering in the genotype-phenotype relationship (distribution of mutation effects, epistasis), their possible mechanistic bases and future directions for advancing towards the goal of predictive genetics.
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Affiliation(s)
- Harry Kemble
- Infection, Antimicrobials, Modelling, Evolution, INSERM, Unité Mixte de Recherche 1137Université Paris Diderot, Université Paris NordParisFrance
- École Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), UMR CNRS‐ESPCI CBI 8231PSL Research UniversityParis Cedex 05France
| | - Philippe Nghe
- École Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), UMR CNRS‐ESPCI CBI 8231PSL Research UniversityParis Cedex 05France
| | - Olivier Tenaillon
- Infection, Antimicrobials, Modelling, Evolution, INSERM, Unité Mixte de Recherche 1137Université Paris Diderot, Université Paris NordParisFrance
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23
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Lebeuf-Taylor E, McCloskey N, Bailey SF, Hinz A, Kassen R. The distribution of fitness effects among synonymous mutations in a gene under directional selection. eLife 2019; 8:45952. [PMID: 31322500 PMCID: PMC6692132 DOI: 10.7554/elife.45952] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 07/18/2019] [Indexed: 12/21/2022] Open
Abstract
The fitness effects of synonymous mutations, nucleotide changes that do not alter the encoded amino acid, have often been assumed to be neutral, but a growing body of evidence suggests otherwise. We used site-directed mutagenesis coupled with direct measures of competitive fitness to estimate the distribution of fitness effects among synonymous mutations for a gene under directional selection and capable of adapting via synonymous nucleotide changes. Synonymous mutations had highly variable fitness effects, both deleterious and beneficial, resembling those of nonsynonymous mutations in the same gene. This variation in fitness was underlain by changes in transcription linked to the creation of internal promoter sites. A positive correlation between fitness and the presence of synonymous substitutions across a phylogeny of related Pseudomonads suggests these mutations may be common in nature. Taken together, our results provide the most compelling evidence to date that synonymous mutations with non-neutral fitness effects may in fact be commonplace.
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Affiliation(s)
| | - Nick McCloskey
- Department of Biology, University of Ottawa, Ottawa, Canada
| | - Susan F Bailey
- Department of Biology, Clarkson University, Potsdam, United States
| | - Aaron Hinz
- Department of Biology, University of Ottawa, Ottawa, Canada
| | - Rees Kassen
- Department of Biology, University of Ottawa, Ottawa, Canada
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24
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Hockenberry AJ, Jewett MC, Amaral LAN, Wilke CO. Within-Gene Shine-Dalgarno Sequences Are Not Selected for Function. Mol Biol Evol 2019; 35:2487-2498. [PMID: 30085185 DOI: 10.1093/molbev/msy150] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The Shine-Dalgarno (SD) sequence motif facilitates translation initiation and is frequently found upstream of bacterial start codons. However, thousands of instances of this motif occur throughout the middle of protein coding genes in a typical bacterial genome. Here, we use comparative evolutionary analysis to test whether SD sequences located within genes are functionally constrained. We measure the conservation of SD sequences across Enterobacteriales, and find that they are significantly less conserved than expected. Further, the strongest SD sequences are the least conserved whereas we find evidence of conservation for the weakest possible SD sequences given amino acid constraints. Our findings indicate that most SD sequences within genes are likely to be deleterious and removed via selection. To illustrate the origin of these deleterious costs, we show that ATG start codons are significantly depleted downstream of SD sequences within genes, highlighting the constraint that these sequences impose on the surrounding nucleotides to minimize the potential for erroneous translation initiation.
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Affiliation(s)
- Adam J Hockenberry
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL.,Chemistry of Life Processes Institute, Northwestern University, Evanston, IL.,Center for Synthetic Biology, Northwestern University, Evanston, IL.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL.,Simpson Querrey Institute, Northwestern University, Evanston, IL
| | - Luís A N Amaral
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL.,Northwestern Institute on Complex Systems, Northwestern University, Evanston, IL
| | - Claus O Wilke
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX
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25
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Guzmán GI, Olson CA, Hefner Y, Phaneuf PV, Catoiu E, Crepaldi LB, Micas LG, Palsson BO, Feist AM. Reframing gene essentiality in terms of adaptive flexibility. BMC SYSTEMS BIOLOGY 2018; 12:143. [PMID: 30558585 PMCID: PMC6296033 DOI: 10.1186/s12918-018-0653-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Accepted: 11/13/2018] [Indexed: 12/17/2022]
Abstract
BACKGROUND Essentiality assays are important tools commonly utilized for the discovery of gene functions. Growth/no growth screens of single gene knockout strain collections are also often utilized to test the predictive power of genome-scale models. False positive predictions occur when computational analysis predicts a gene to be non-essential, however experimental screens deem the gene to be essential. One explanation for this inconsistency is that the model contains the wrong information, possibly an incorrectly annotated alternative pathway or isozyme reaction. Inconsistencies could also be attributed to experimental limitations, such as growth tests with arbitrary time cut-offs. The focus of this study was to resolve such inconsistencies to better understand isozyme activities and gene essentiality. RESULTS In this study, we explored the definition of conditional essentiality from a phenotypic and genomic perspective. Gene-deletion strains associated with false positive predictions of gene essentiality on defined minimal medium for Escherichia coli were targeted for extended growth tests followed by population sequencing and transcriptome analysis. Of the twenty false positive strains available and confirmed from the Keio single gene knock-out collection, 11 strains were shown to grow with longer incubation periods making these actual true positives. These strains grew reproducibly with a diverse range of growth phenotypes. The lag phase observed for these strains ranged from less than one day to more than 7 days. It was found that 9 out of 11 of the false positive strains that grew acquired mutations in at least one replicate experiment and the types of mutations ranged from SNPs and small indels associated with regulatory or metabolic elements to large regions of genome duplication. Comparison of the detected adaptive mutations, modeling predictions of alternate pathways and isozymes, and transcriptome analysis of KO strains suggested agreement for the observed growth phenotype for 6 out of the 9 cases where mutations were observed. CONCLUSIONS Longer-term growth experiments followed by whole genome sequencing and transcriptome analysis can provide a better understanding of conditional gene essentiality and mechanisms of adaptation to such perturbations. Compensatory mutations are largely reproducible mechanisms and are in agreement with genome-scale modeling predictions to loss of function gene deletion events.
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Affiliation(s)
- Gabriela I Guzmán
- Department of Bioengineering, University of California, San Diego, La Jolla, 92093, CA, USA
| | - Connor A Olson
- Department of Bioengineering, University of California, San Diego, La Jolla, 92093, CA, USA
| | - Ying Hefner
- Department of Bioengineering, University of California, San Diego, La Jolla, 92093, CA, USA
| | - Patrick V Phaneuf
- Department of Bioinformatics and Systems Biology, University of California, San Diego, 92093, La Jolla, CA, USA
| | - Edward Catoiu
- Department of Bioengineering, University of California, San Diego, La Jolla, 92093, CA, USA
| | - Lais B Crepaldi
- Department of Bioengineering, University of California, San Diego, La Jolla, 92093, CA, USA.,Department of Chemical Engineering, University of Ribeirão Preto, São Paulo, Brazil
| | - Lucas Goldschmidt Micas
- Department of Bioengineering, University of California, San Diego, La Jolla, 92093, CA, USA.,Department of Chemical and Petroleum Engineering, Fluminense Federal University, Niterói, Rio de Janeiro, Brazil
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, 92093, CA, USA.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.,Department of Pediatrics, University of California, San Diego, La Jolla, 92093, CA, USA
| | - Adam M Feist
- Department of Bioengineering, University of California, San Diego, La Jolla, 92093, CA, USA. .,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
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26
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Van den Bergh B, Swings T, Fauvart M, Michiels J. Experimental Design, Population Dynamics, and Diversity in Microbial Experimental Evolution. Microbiol Mol Biol Rev 2018; 82:e00008-18. [PMID: 30045954 PMCID: PMC6094045 DOI: 10.1128/mmbr.00008-18] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In experimental evolution, laboratory-controlled conditions select for the adaptation of species, which can be monitored in real time. Despite the current popularity of such experiments, nature's most pervasive biological force was long believed to be observable only on time scales that transcend a researcher's life-span, and studying evolution by natural selection was therefore carried out solely by comparative means. Eventually, microorganisms' propensity for fast evolutionary changes proved us wrong, displaying strong evolutionary adaptations over a limited time, nowadays massively exploited in laboratory evolution experiments. Here, we formulate a guide to experimental evolution with microorganisms, explaining experimental design and discussing evolutionary dynamics and outcomes and how it is used to assess ecoevolutionary theories, improve industrially important traits, and untangle complex phenotypes. Specifically, we give a comprehensive overview of the setups used in experimental evolution. Additionally, we address population dynamics and genetic or phenotypic diversity during evolution experiments and expand upon contributing factors, such as epistasis and the consequences of (a)sexual reproduction. Dynamics and outcomes of evolution are most profoundly affected by the spatiotemporal nature of the selective environment, where changing environments might lead to generalists and structured environments could foster diversity, aided by, for example, clonal interference and negative frequency-dependent selection. We conclude with future perspectives, with an emphasis on possibilities offered by fast-paced technological progress. This work is meant to serve as an introduction to those new to the field of experimental evolution, as a guide to the budding experimentalist, and as a reference work to the seasoned expert.
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Affiliation(s)
- Bram Van den Bergh
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
- Douglas Lab, Department of Entomology, Cornell University, Ithaca, New York, USA
| | - Toon Swings
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
| | - Maarten Fauvart
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
- imec, Leuven, Belgium
| | - Jan Michiels
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
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27
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Kristofich J, Morgenthaler AB, Kinney WR, Ebmeier CC, Snyder DJ, Old WM, Cooper VS, Copley SD. Synonymous mutations make dramatic contributions to fitness when growth is limited by a weak-link enzyme. PLoS Genet 2018; 14:e1007615. [PMID: 30148850 PMCID: PMC6128649 DOI: 10.1371/journal.pgen.1007615] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 09/07/2018] [Accepted: 08/07/2018] [Indexed: 01/26/2023] Open
Abstract
Synonymous mutations do not alter the specified amino acid but may alter the structure or function of an mRNA in ways that impact fitness. There are few examples in the literature, however, in which the effects of synonymous mutations on microbial growth rates have been measured, and even fewer for which the underlying mechanism is understood. We evolved four populations of a strain of Salmonella enterica in which a promiscuous enzyme has been recruited to replace an essential enzyme. A previously identified point mutation increases the enzyme’s ability to catalyze the newly needed reaction (required for arginine biosynthesis) but decreases its ability to catalyze its native reaction (required for proline biosynthesis). The poor performance of this enzyme limits growth rate on glucose. After 260 generations, we identified two synonymous mutations in the first six codons of the gene encoding the weak-link enzyme that increase growth rate by 41 and 67%. We introduced all possible synonymous mutations into the first six codons and found substantial effects on growth rate; one doubles growth rate, and another completely abolishes growth. Computational analyses suggest that these mutations affect either the stability of a stem-loop structure that sequesters the start codon or the accessibility of the region between the Shine-Dalgarno sequence and the start codon. Thus, these mutations would be predicted to affect translational efficiency and thereby indirectly affect mRNA stability because translating ribosomes protect mRNA from degradation. Experimental data support these hypotheses. We conclude that the effects of the synonymous mutations are due to a combination of effects on mRNA stability and translation efficiency that alter levels of the weak-link enzyme. These findings suggest that synonymous mutations can have profound effects on fitness under strong selection and that their importance in evolution may be under-appreciated. When a new enzyme is needed, microbes often recruit a pre-existing enzyme with a promiscuous activity corresponding to the newly needed activity. Such enzymes are often the “weak-link” in metabolism because they have not evolved to efficiently catalyze the new reaction. Under these circumstances, increasing the level of the weak-link enzyme can improve fitness. We evolved a strain of S. enterica in which a weak-link enzyme–E383A ProA–serves essential functions in synthesis of proline and arginine for 260 generations and then sequenced the genomes of several evolved strains. A mutation in the promoter of the operon encoding E383A ProA increased growth rate 9-fold. More surprisingly, a mutation upstream of the start codon and two synonymous mutations within the first six codons also increased growth rate by up to 68%. Introduction of all possible synonymous mutations in the first six codons showed that some doubled growth rate, while others slowed or even prevented growth. Computational and experimental data suggest that these effects were due to enhanced translational efficiency of the weak-link enzyme. These results show that synonymous mutations, once assumed to be selectively neutral, can have strong impacts on fitness when growth rate is limited by a weak-link enzyme.
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Affiliation(s)
- JohnCarlo Kristofich
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, United States of America
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO, United States of America
| | - Andrew B. Morgenthaler
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, United States of America
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO, United States of America
| | - Wallis R. Kinney
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, United States of America
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO, United States of America
| | - Christopher C. Ebmeier
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, United States of America
| | - Daniel J. Snyder
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States of America
| | - William M. Old
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, United States of America
| | - Vaughn S. Cooper
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States of America
| | - Shelley D. Copley
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, United States of America
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO, United States of America
- * E-mail:
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28
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Mittal P, Brindle J, Stephen J, Plotkin JB, Kudla G. Codon usage influences fitness through RNA toxicity. Proc Natl Acad Sci U S A 2018; 115:8639-8644. [PMID: 30082392 PMCID: PMC6112741 DOI: 10.1073/pnas.1810022115] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Many organisms are subject to selective pressure that gives rise to unequal usage of synonymous codons, known as codon bias. To experimentally dissect the mechanisms of selection on synonymous sites, we expressed several hundred synonymous variants of the GFP gene in Escherichia coli, and used quantitative growth and viability assays to estimate bacterial fitness. Unexpectedly, we found many synonymous variants whose expression was toxic to E. coli Unlike previously studied effects of synonymous mutations, the effect that we discovered is independent of translation, but it depends on the production of toxic mRNA molecules. We identified RNA sequence determinants of toxicity and evolved suppressor strains that can tolerate the expression of toxic GFP variants. Genome sequencing of these suppressor strains revealed a cluster of promoter mutations that prevented toxicity by reducing mRNA levels. We conclude that translation-independent RNA toxicity is a previously unrecognized obstacle in bacterial gene expression.
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Affiliation(s)
- Pragya Mittal
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, EH4 2XU Edinburgh, United Kingdom
| | - James Brindle
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, EH4 2XU Edinburgh, United Kingdom
| | - Julie Stephen
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, EH4 2XU Edinburgh, United Kingdom
| | - Joshua B Plotkin
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Grzegorz Kudla
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, EH4 2XU Edinburgh, United Kingdom;
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29
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The fitness landscape of the codon space across environments. Heredity (Edinb) 2018; 121:422-437. [PMID: 30127529 DOI: 10.1038/s41437-018-0125-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 06/16/2018] [Accepted: 06/18/2018] [Indexed: 12/24/2022] Open
Abstract
Fitness landscapes map the relationship between genotypes and fitness. However, most fitness landscape studies ignore the genetic architecture imposed by the codon table and thereby neglect the potential role of synonymous mutations. To quantify the fitness effects of synonymous mutations and their potential impact on adaptation on a fitness landscape, we use a new software based on Bayesian Monte Carlo Markov Chain methods and re-estimate selection coefficients of all possible codon mutations across 9 amino acid positions in Saccharomyces cerevisiae Hsp90 across 6 environments. We quantify the distribution of fitness effects of synonymous mutations and show that it is dominated by many mutations of small or no effect and few mutations of larger effect. We then compare the shape of the codon fitness landscape across amino acid positions and environments, and quantify how the consideration of synonymous fitness effects changes the evolutionary dynamics on these fitness landscapes. Together these results highlight a possible role of synonymous mutations in adaptation and indicate the potential mis-inference when they are neglected in fitness landscape studies.
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30
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Bilska K, Jurczak S, Kulik T, Ropelewska E, Olszewski J, Żelechowski M, Zapotoczny P. Species Composition and Trichothecene Genotype Profiling of Fusarium Field Isolates Recovered from Wheat in Poland. Toxins (Basel) 2018; 10:E325. [PMID: 30103473 PMCID: PMC6115980 DOI: 10.3390/toxins10080325] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 07/29/2018] [Accepted: 08/07/2018] [Indexed: 12/20/2022] Open
Abstract
Fusarium head blight (FHB) of cereals is the major head disease negatively affecting grain production worldwide. In 2016 and 2017, serious outbreaks of FHB occurred in wheat crops in Poland. In this study, we characterized the diversity of Fusaria responsible for these epidemics using TaqMan assays. From a panel of 463 field isolates collected from wheat, four Fusarium species were identified. The predominant species were F. graminearum s.s. (81%) and, to a lesser extent, F. avenaceum (15%). The emergence of the 15ADON genotype was found ranging from 83% to 87% of the total trichothecene genotypes isolated in 2016 and 2017, respectively. Our results indicate two dramatic shifts within fungal field populations in Poland. The first shift is associated with the displacement of F. culmorum by F. graminearum s.s. The second shift resulted from a loss of nivalenol genotypes. We suggest that an emerging prevalence of F. graminearum s.s. may be linked to boosted maize production, which has increased substantially over the last decade in Poland. To detect variation within Tri core clusters, we compared sequence data from randomly selected field isolates with a panel of strains from geographically diverse origins. We found that the newly emerged 15ADON genotypes do not exhibit a specific pattern of polymorphism enabling their clear differentiation from the other European strains.
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Affiliation(s)
- Katarzyna Bilska
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland.
| | - Sebastian Jurczak
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland.
| | - Tomasz Kulik
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland.
| | - Ewa Ropelewska
- Department of Systems Engineering, Faculty of Engineering, University of Warmia and Mazury in Olsztyn, Heweliusza 14, 10-718 Olsztyn, Poland.
| | - Jacek Olszewski
- Experimental Education Unit, Oczapowskiego 8, 10-719 Olsztyn, Poland.
| | - Maciej Żelechowski
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland.
| | - Piotr Zapotoczny
- Department of Systems Engineering, Faculty of Engineering, University of Warmia and Mazury in Olsztyn, Heweliusza 14, 10-718 Olsztyn, Poland.
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31
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Timing during translation matters: synonymous mutations in human pathologies influence protein folding and function. Biochem Soc Trans 2018; 46:937-944. [PMID: 30065107 DOI: 10.1042/bst20170422] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 05/18/2018] [Accepted: 06/25/2018] [Indexed: 12/11/2022]
Abstract
Ribosomes translate mRNAs with non-uniform speed. Translation velocity patterns are a conserved feature of mRNA and have evolved to fine-tune protein folding, expression and function. Synonymous single-nucleotide polymorphisms (sSNPs) that alter programmed translational speed affect expression and function of the encoded protein. Synergistic advances in next-generation sequencing have led to the identification of sSNPs associated with disease penetrance. Here, we draw on studies with disease-related proteins to enhance our understanding of mechanistic contributions of sSNPs to functional alterations of the encoded protein. We emphasize the importance of identification of sSNPs along with disease-causing mutations to understand genotype-phenotype relationships.
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32
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The genetic background of antibiotic resistance among clinical uropathogenic Escherichia coli strains. Mol Biol Rep 2018; 45:1055-1065. [PMID: 30008141 PMCID: PMC6156760 DOI: 10.1007/s11033-018-4254-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 07/10/2018] [Indexed: 01/07/2023]
Abstract
The spreading mechanisms of antibiotic resistance are related to many bacterial and environment factors. The overuse of antibiotics is leading to an unceasing emergence of new multidrug resistant strains. This problem also concerns uropathogenic Escherichia coli strains, which is the most common pathogen causing urinary tract infections. The aim of this study was the genetic analysis of antibiotic resistance in comparison to the phenotypic background of E. coli strains. The characterized collection of E. coli strains isolated 10 years ago from the urine samples of patients with urinary tract infections was used for antimicrobial susceptibility testing (the disc diffusion method) and analysis of antibiotic resistance genes (PCR reaction, sequencing). Additionally, the presence of ESBL strains was analyzed. Fourteen genes were associated with resistance to beta-lactams, aminoglycosides, sulfonamides and quinolones. The genetic analysis revealed that blaTEM-1 and sul2 were present in almost all of the studied strains. Other drug-resistance genes were very rare or non-existent. Otherwise, the phenotypic resistance to fluoroquinolones was well correlated with the genotypic background of the studied bacteria. The presence of particular genes and specific mutations indicate a high bacterial potential to multidrug resistance. On the other hand, it needs to be emphasized that the standard disk diffusion test for the routine antimicrobial susceptibility analysis is still the best way to estimate the current situation of bacterial drug-resistance.
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33
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Zwart MP, Schenk MF, Hwang S, Koopmanschap B, de Lange N, van de Pol L, Nga TTT, Szendro IG, Krug J, de Visser JAGM. Unraveling the causes of adaptive benefits of synonymous mutations in TEM-1 β-lactamase. Heredity (Edinb) 2018; 121:406-421. [PMID: 29967397 PMCID: PMC6180035 DOI: 10.1038/s41437-018-0104-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 05/19/2018] [Indexed: 11/23/2022] Open
Abstract
While synonymous mutations were long thought to be without phenotypic consequences, there is growing evidence they can affect gene expression, protein folding, and ultimately the fitness of an organism. In only a few cases have the mechanisms by which synonymous mutations affect the phenotype been elucidated. We previously identified 48 mutations in TEM-1 β-lactamase that increased resistance of Escherichia coli to cefotaxime, 10 of which were synonymous. To better understand the molecular mechanisms underlying the beneficial effect of these synonymous mutations, we made a series of measurements for a panel containing the 10 synonymous together with 10 non-synonymous mutations as a reference. Whereas messenger levels were unaffected, we found that total and functional TEM protein levels were higher for 5 out of 10 synonymous mutations. These observations suggest that some of these mutations act on translation or a downstream process. Similar effects were observed for some small-benefit non-synonymous mutations, suggesting a similar causal mechanism. For the synonymous mutations, we found that the cost of resistance scales with TEM protein levels. A resistance landscape for four synonymous mutations revealed strong epistasis: none of the combinations of mutations exceeded the resistance of the largest-effect mutation and there were synthetically neutral combinations. By considering combined effects of these mutations, we could infer that functional TEM protein level is a multi-dimensional phenotype. These results suggest that synonymous mutations may have beneficial effects by increasing the expression of an enzyme with low substrate activity, which may be realized via multiple, yet unknown, post-transcriptional mechanisms.
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Affiliation(s)
- Mark P Zwart
- Institute for Theoretical Physics, University of Cologne, Cologne, Germany. .,Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands. .,Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.
| | - Martijn F Schenk
- Institute for Theoretical Physics, University of Cologne, Cologne, Germany.,Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands.,The Netherlands Food and Consumer Product Safety Authority, Utrecht, The Netherlands
| | - Sungmin Hwang
- Institute for Theoretical Physics, University of Cologne, Cologne, Germany.,LPTMS, Université Paris-Sud 11, UMR 8626 CNRS, Orsay Cedex, France
| | | | - Niek de Lange
- Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands.,Physical Chemistry and Soft Matter, Wageningen University, Wageningen, The Netherlands
| | - Lion van de Pol
- Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands.,Veluws College, Twello, The Netherlands
| | - Tran Thi Thuy Nga
- Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands.,Biomedic JSC, Hanoi, Vietnam
| | - Ivan G Szendro
- Institute for Theoretical Physics, University of Cologne, Cologne, Germany
| | - Joachim Krug
- Institute for Theoretical Physics, University of Cologne, Cologne, Germany
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34
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Swings T, Marciano DC, Atri B, Bosserman RE, Wang C, Leysen M, Bonte C, Schalck T, Furey I, Van den Bergh B, Verstraeten N, Christie PJ, Herman C, Lichtarge O, Michiels J. CRISPR-FRT targets shared sites in a knock-out collection for off-the-shelf genome editing. Nat Commun 2018; 9:2231. [PMID: 29884781 PMCID: PMC5993718 DOI: 10.1038/s41467-018-04651-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 05/11/2018] [Indexed: 01/12/2023] Open
Abstract
CRISPR advances genome engineering by directing endonuclease sequence specificity with a guide RNA molecule (gRNA). For precisely targeting a gene for modification, each genetic construct requires a unique gRNA. By generating a gRNA against the flippase recognition target (FRT) site, a common genetic element shared by multiple genetic collections, CRISPR-FRT circumvents this design constraint to provide a broad platform for fast, scarless, off-the-shelf genome engineering.
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Affiliation(s)
- Toon Swings
- Centre of Microbial and Plant Genetics, KU Leuven - University of Leuven, Kasteelpark Arenberg 20, 3001, Leuven, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 20, 3001, Leuven, Belgium
| | - David C Marciano
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Benu Atri
- Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Rachel E Bosserman
- Department of Microbiology and Molecular Genetics, McGovern Medical School, Houston, TX, 77030, USA
| | - Chen Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Marlies Leysen
- Centre of Microbial and Plant Genetics, KU Leuven - University of Leuven, Kasteelpark Arenberg 20, 3001, Leuven, Belgium
| | - Camille Bonte
- Centre of Microbial and Plant Genetics, KU Leuven - University of Leuven, Kasteelpark Arenberg 20, 3001, Leuven, Belgium
| | - Thomas Schalck
- Centre of Microbial and Plant Genetics, KU Leuven - University of Leuven, Kasteelpark Arenberg 20, 3001, Leuven, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 20, 3001, Leuven, Belgium
| | - Ian Furey
- Department of Pharmacology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Bram Van den Bergh
- Centre of Microbial and Plant Genetics, KU Leuven - University of Leuven, Kasteelpark Arenberg 20, 3001, Leuven, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 20, 3001, Leuven, Belgium
| | - Natalie Verstraeten
- Centre of Microbial and Plant Genetics, KU Leuven - University of Leuven, Kasteelpark Arenberg 20, 3001, Leuven, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 20, 3001, Leuven, Belgium
| | - Peter J Christie
- Department of Microbiology and Molecular Genetics, McGovern Medical School, Houston, TX, 77030, USA
| | - Christophe Herman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
- Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Pharmacology, Baylor College of Medicine, Houston, TX, 77030, USA.
- Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, KU Leuven - University of Leuven, Kasteelpark Arenberg 20, 3001, Leuven, Belgium.
- Center for Microbiology, VIB, Kasteelpark Arenberg 20, 3001, Leuven, Belgium.
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35
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Kula A, Saelens J, Cox J, Schubert AM, Travisano M, Putonti C. The Evolution of Molecular Compatibility between Bacteriophage ΦX174 and its Host. Sci Rep 2018; 8:8350. [PMID: 29844443 PMCID: PMC5974221 DOI: 10.1038/s41598-018-25914-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 05/01/2018] [Indexed: 12/05/2022] Open
Abstract
Viruses rely upon their hosts for biosynthesis of viral RNA, DNA and protein. This dependency frequently engenders strong selection for virus genome compatibility with potential hosts, appropriate gene regulation and expression necessary for a successful infection. While bioinformatic studies have shown strong correlations between codon usage in viral and host genomes, the selective factors by which this compatibility evolves remain a matter of conjecture. Engineered to include codons with a lesser usage and/or tRNA abundance within the host, three different attenuated strains of the bacterial virus ФX174 were created and propagated via serial transfers. Molecular sequence data indicate that biosynthetic compatibility was recovered rapidly. Extensive computational simulations were performed to assess the role of mutational biases as well as selection for translational efficiency in the engineered phage. Using bacteriophage as a model system, we can begin to unravel the evolutionary processes shaping codon compatibility between viruses and their host.
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Affiliation(s)
- Alexander Kula
- Department of Biology, Loyola University Chicago, Chicago, IL, USA.,Department of Biology, University of Miami, Coral Gables, FL, USA
| | - Joseph Saelens
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, USA.,Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | - Jennifer Cox
- Department of Biology, Loyola University Chicago, Chicago, IL, USA
| | - Alyxandria M Schubert
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, USA.,Division of Bacterial, Parasitic, and Allergenic Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Michael Travisano
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN, USA.,BioTechnology Institute, University of Minnesota, Saint Paul, MN, USA
| | - Catherine Putonti
- Department of Biology, Loyola University Chicago, Chicago, IL, USA. .,Bioinformatics Program, Loyola University Chicago, Chicago, IL, USA. .,Department of Computer Science, Loyola University Chicago, Chicago, IL, USA.
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36
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Population size changes and selection drive patterns of parallel evolution in a host-virus system. Nat Commun 2018; 9:1706. [PMID: 29703896 PMCID: PMC5923231 DOI: 10.1038/s41467-018-03990-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 03/26/2018] [Indexed: 11/09/2022] Open
Abstract
Predicting the repeatability of evolution remains elusive. Theory and empirical studies suggest that strong selection and large population sizes increase the probability for parallel evolution at the phenotypic and genotypic levels. However, selection and population sizes are not constant, but rather change continuously and directly affect each other even on short time scales. Here, we examine the degree of parallel evolution shaped through eco-evolutionary dynamics in an algal host population coevolving with a virus. We find high degrees of parallelism at the level of population size changes (ecology) and at the phenotypic level between replicated populations. At the genomic level, we find evidence for parallelism, as the same large genomic region was duplicated in all replicated populations, but also substantial novel sequence divergence between replicates. These patterns of genome evolution can be explained by considering population size changes as an important driver of rapid evolution.
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37
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Triplet-Based Codon Organization Optimizes the Impact of Synonymous Mutation on Nucleic Acid Molecular Dynamics. J Mol Evol 2018; 86:91-102. [PMID: 29344693 PMCID: PMC5846835 DOI: 10.1007/s00239-018-9828-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 01/06/2018] [Indexed: 11/22/2022]
Abstract
Since the elucidation of the genetic code almost 50 years ago, many nonrandom aspects of its codon organization remain only partly resolved. Here, we investigate the recent hypothesis of ‘dual-use’ codons which proposes that in addition to allowing adjustment of codon optimization to tRNA abundance, the degeneracy in the triplet-based genetic code also multiplexes information regarding DNA’s helical shape and protein-binding dynamics while avoiding interference with other protein-level characteristics determined by amino acid properties. How such structural optimization of the code within eukaryotic chromatin could have arisen from an RNA world is a mystery, but would imply some preadaptation in an RNA context. We analyzed synonymous (protein-silent) and nonsynonymous (protein-altering) mutational impacts on molecular dynamics in 13823 identically degenerate alternative codon reorganizations, defined by codon transitions in 7680 GPU-accelerated molecular dynamic simulations of implicitly and explicitly solvated double-stranded aRNA and bDNA structures. When compared to all possible alternative codon assignments, the standard genetic code minimized the impact of synonymous mutations on the random atomic fluctuations and correlations of carbon backbone vector trajectories while facilitating the specific movements that contribute to DNA polymer flexibility. This trend was notably stronger in the context of RNA supporting the idea that dual-use codon optimization and informational multiplexing in DNA resulted from the preadaptation of the RNA duplex to resist changes to thermostability. The nonrandom and divergent molecular dynamics of synonymous mutations also imply that the triplet-based code may have resulted from adaptive functional expansion enabling a primordial doublet code to multiplex gene regulatory information via the shape and charge of the minor groove.
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38
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Schmitt C, Garant D, Bélisle M, Pelletier F. Linking innate immunogenetic variation with phenotypic traits in a wild population of tree swallows, Tachycineta bicolor. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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39
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Abstract
Lateral gene transfer (LGT) profoundly shapes the evolution of bacterial lineages. LGT across disparate phylogenetic groups and genome content diversity between related organisms suggest a model of bacterial evolution that views LGT as rampant and promiscuous. It has even driven the argument that species concepts and tree-based phylogenetics cannot be applied to bacteria. Here, we show that acquisition and retention of genes through LGT are surprisingly rare in the ubiquitous and biomedically important bacterial genus Streptomyces Using a molecular clock, we estimate that the Streptomyces bacteria are ~380 million years old, indicating that this bacterial genus is as ancient as land vertebrates. Calibrating LGT rate to this geologic time span, we find that on average only 10 genes per million years were acquired and subsequently maintained. Over that same time span, Streptomyces accumulated thousands of point mutations. By explicitly incorporating evolutionary timescale into our analyses, we provide a dramatically different view on the dynamics of LGT and its impact on bacterial evolution.IMPORTANCE Tree-based phylogenetics and the use of species as units of diversity lie at the foundation of modern biology. In bacteria, these pillars of evolutionary theory have been called into question due to the observation of thousands of lateral gene transfer (LGT) events within and between lineages. Here, we show that acquisition and retention of genes through LGT are exceedingly rare in the bacterial genus Streptomyces, with merely one gene acquired in Streptomyces lineages every 100,000 years. These findings stand in contrast to the current assumption of rampant genetic exchange, which has become the dominant hypothesis used to explain bacterial diversity. Our results support a more nuanced understanding of genetic exchange, with LGT impacting evolution over short timescales but playing a significant role over long timescales. Deeper understanding of LGT provides new insight into the evolutionary history of life on Earth, as the vast majority of this history is microbial.
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De novo evolved interference competition promotes the spread of biofilm defectors. Nat Commun 2017; 8:15127. [PMID: 28462927 PMCID: PMC5418572 DOI: 10.1038/ncomms15127] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 03/02/2017] [Indexed: 11/16/2022] Open
Abstract
Biofilms are social entities where bacteria live in tightly packed agglomerations, surrounded by self-secreted exopolymers. Since production of exopolymers is costly and potentially exploitable by non-producers, mechanisms that prevent invasion of non-producing mutants are hypothesized. Here we study long-term dynamics and evolution in Bacillus subtilis biofilm populations consisting of wild-type (WT) matrix producers and mutant non-producers. We show that non-producers initially fail to incorporate into biofilms formed by the WT cells, resulting in 100-fold lower final frequency compared to the WT. However, this is modulated in a long-term scenario, as non-producers evolve the ability to better incorporate into biofilms, thereby slightly decreasing the productivity of the whole population. Detailed molecular analysis reveals that the unexpected shift in the initially stable biofilm is coupled with newly evolved phage-mediated interference competition. Our work therefore demonstrates how collective behaviour can be disrupted as a result of rapid adaptation through mobile genetic elements. The production of secreted polymers in bacterial biofilms is costly, and therefore mechanisms preventing invasion of non-producing mutants are hypothesized. Here, the authors show that non-producers can evolve the ability to better incorporate into biofilms via phage-mediated interference.
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Bradley AS, Swanson PK, Muller EEL, Bringel F, Caroll SM, Pearson A, Vuilleumier S, Marx CJ. Hopanoid-free Methylobacterium extorquens DM4 overproduces carotenoids and has widespread growth impairment. PLoS One 2017; 12:e0173323. [PMID: 28319163 PMCID: PMC5358736 DOI: 10.1371/journal.pone.0173323] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 02/17/2017] [Indexed: 01/27/2023] Open
Abstract
Hopanoids are sterol-like membrane lipids widely used as geochemical proxies for bacteria. Currently, the physiological role of hopanoids is not well understood, and this represents one of the major limitations in interpreting the significance of their presence in ancient or contemporary sediments. Previous analyses of mutants lacking hopanoids in a range of bacteria have revealed a range of phenotypes under normal growth conditions, but with most having at least an increased sensitivity to toxins and osmotic stress. We employed hopanoid-free strains of Methylobacterium extorquens DM4, uncovering severe growth defects relative to the wild-type under many tested conditions, including normal growth conditions without additional stressors. Mutants overproduce carotenoids-the other major isoprenoid product of this strain-and show an altered fatty acid profile, pronounced flocculation in liquid media, and lower growth yields than for the wild-type strain. The flocculation phenotype can be mitigated by addition of cellulase to the medium, suggesting a link between the function of hopanoids and the secretion of cellulose in M. extorquens DM4. On solid media, colonies of the hopanoid-free mutant strain were smaller than wild-type, and were more sensitive to osmotic or pH stress, as well as to a variety of toxins. The results for M. extorquens DM4 are consistent with the hypothesis that hopanoids are important for membrane fluidity and lipid packing, but also indicate that the specific physiological processes that require hopanoids vary across bacterial lineages. Our work provides further support to emerging observations that the role of hopanoids in membrane robustness and barrier function may be important across lineages, possibly mediated through an interaction with lipid A in the outer membrane.
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Affiliation(s)
- Alexander S. Bradley
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States of America
- Department of Earth and Planetary Sciences, Washington University in St Louis, St Louis, MO, United States of America
| | - Paige K. Swanson
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States of America
| | - Emilie E. L. Muller
- Equipe Adaptations et interactions microbiennes, Université de Strasbourg, UMR 7156 UNISTRA–CNRS Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
| | - Françoise Bringel
- Equipe Adaptations et interactions microbiennes, Université de Strasbourg, UMR 7156 UNISTRA–CNRS Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
| | - Sean M. Caroll
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States of America
| | - Ann Pearson
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, United States of America
| | - Stéphane Vuilleumier
- Equipe Adaptations et interactions microbiennes, Université de Strasbourg, UMR 7156 UNISTRA–CNRS Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
| | - Christopher J. Marx
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States of America
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, United States of America
- Center for Modeling Complex Interactions, University of Idaho, Moscow, ID, United States of America
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RNA Structural Determinants of Optimal Codons Revealed by MAGE-Seq. Cell Syst 2016; 3:563-571.e6. [PMID: 28009265 DOI: 10.1016/j.cels.2016.11.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Revised: 05/25/2016] [Accepted: 11/08/2016] [Indexed: 01/30/2023]
Abstract
Synonymous codon choices at the beginning of genes optimize 5' RNA structures for enhanced translation initiation, but less is known about mechanisms that drive codon optimization downstream within the gene. To understand what determines codon choices across a gene, we generated 12,726 in situ codon mutants in the Escherichia coli essential gene infA and measured their fitness by combining multiplex automated genome engineering mutagenesis with amplicon deep sequencing (MAGE-seq). Correlating predicted 5' RNA structure with fitness revealed that codons even far from the start of the gene are deleterious if they disrupt the native 5' RNA conformation. These long-range structural interactions generate context-dependent rules that constrain codon choices beyond intrinsic codon preferences. Genome-wide RNA folding predictions confirm that natural codon choices far from the start codon are optimized in part to prevent disruption of native structures near the 5' UTR. Our results shed light on natural codon distributions and should improve engineering of gene expression for synthetic biology applications.
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Abstract
In prokaryotes, translation initiation typically depends on complementary binding between a G-rich Shine–Dalgarno (SD) motif in the 5′ untranslated region of mRNAs, and the 3′ tail of the 16S ribosomal RNA (the anti-SD sequence). In some cases, internal SD-like motifs in the coding region generate “programmed” ribosomal pauses that are beneficial for protein folding or accurate targeting. On the other hand, such pauses can also reduce protein production, generating purifying selection against internal SD-like motifs. This selection should be stronger in GC-rich genomes that are more likely to harbor the G-rich SD motif. However, the nature and consequences of selection acting on internal SD-like motifs within genomes and across species remains unclear. We analyzed the frequency of SD-like hexamers in the coding regions of 284 prokaryotes (277 with known anti-SD sequences and 7 without a typical SD mechanism). After accounting for GC content, we found that internal SD-like hexamers are avoided in 230 species, including three without a typical SD mechanism. The degree of avoidance was higher in GC-rich genomes, mesophiles, and N-terminal regions of genes. In contrast, 54 species either showed no signature of avoidance or were enriched in internal SD-like motifs. C-terminal gene regions were relatively enriched in SD-like hexamers, particularly for genes in operons or those followed closely by downstream genes. Together, our results suggest that the frequency of internal SD-like hexamers is governed by multiple factors including GC content and genome organization, and further empirical work is necessary to understand the evolution and functional roles of these motifs.
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Affiliation(s)
- Gaurav D Diwan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India SASTRA University, Thanjavur, India
| | - Deepa Agashe
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
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Nayak DD, Agashe D, Lee MC, Marx CJ. Selection Maintains Apparently Degenerate Metabolic Pathways due to Tradeoffs in Using Methylamine for Carbon versus Nitrogen. Curr Biol 2016; 26:1416-26. [PMID: 27212407 DOI: 10.1016/j.cub.2016.04.029] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 02/17/2016] [Accepted: 04/11/2016] [Indexed: 01/12/2023]
Abstract
Microorganisms often encode multiple non-orthologous metabolic modules that catalyze the same reaction. However, little experimental evidence actually demonstrates a selective basis for metabolic degeneracy. Many methylotrophs-microorganisms that grow on reduced single-carbon compounds-like Methylobacterium extorquens AM1 encode two routes for methylamine oxidation: the periplasmic methylamine dehydrogenase (MaDH) and the cytoplasmic N-methylglutamate (NMG) pathway. In Methylobacterium extorquens AM1, MaDH is essential for methylamine growth, but the NMG pathway has no known physiological role. Here, we use experimental evolution of two isolates lacking (or incapable of using) MaDH to uncover the physiological challenges that need to be overcome in order to use the NMG pathway for growth on methylamine as a carbon and energy source. Physiological characterization of the evolved isolates revealed regulatory rewiring to increase expression of the NMG pathway and novel mechanisms to mitigate cytoplasmic ammonia buildup. These adaptations led us to infer and validate environmental conditions under which the NMG pathway is advantageous compared to MaDH. The highly expressed MaDH enables rapid growth on high concentrations of methylamine as the primary carbon and energy substrate, whereas the energetically expensive NMG pathway plays a pivotal role during growth with methylamine as the sole nitrogen source, which we demonstrate is especially true under limiting concentrations (<1 mM). Tradeoffs between cellular localization and ammonium toxicity lead to selection for this apparent degeneracy as it is beneficial to facultative methylotrophs that have to switch between using methylamine as a carbon and energy source or just a nitrogen source.
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Affiliation(s)
- Dipti D Nayak
- Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Deepa Agashe
- Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Ming-Chun Lee
- Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Christopher J Marx
- Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA; Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844, USA; Center for Modeling Complex Interactions, University of Idaho, Moscow, ID 83844, USA.
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Carroll SM, Chubiz LM, Agashe D, Marx CJ. Parallel and Divergent Evolutionary Solutions for the Optimization of an Engineered Central Metabolism in Methylobacterium extorquens AM1. Microorganisms 2015; 3:152-74. [PMID: 27682084 PMCID: PMC5023240 DOI: 10.3390/microorganisms3020152] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 03/30/2015] [Accepted: 04/01/2015] [Indexed: 11/16/2022] Open
Abstract
Bioengineering holds great promise to provide fast and efficient biocatalysts for methanol-based biotechnology, but necessitates proven methods to optimize physiology in engineered strains. Here, we highlight experimental evolution as an effective means for optimizing an engineered Methylobacterium extorquens AM1. Replacement of the native formaldehyde oxidation pathway with a functional analog substantially decreased growth in an engineered Methylobacterium, but growth rapidly recovered after six hundred generations of evolution on methanol. We used whole-genome sequencing to identify the basis of adaptation in eight replicate evolved strains, and examined genomic changes in light of other growth and physiological data. We observed great variety in the numbers and types of mutations that occurred, including instances of parallel mutations at targets that may have been "rationalized" by the bioengineer, plus other "illogical" mutations that demonstrate the ability of evolution to expose unforeseen optimization solutions. Notably, we investigated mutations to RNA polymerase, which provided a massive growth benefit but are linked to highly aberrant transcriptional profiles. Overall, we highlight the power of experimental evolution to present genetic and physiological solutions for strain optimization, particularly in systems where the challenges of engineering are too many or too difficult to overcome via traditional engineering methods.
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Affiliation(s)
- Sean Michael Carroll
- Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Lon M Chubiz
- Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
- Department of Biology, University of Missouri-St. Louis, St. Louis, MO 63103, USA.
| | - Deepa Agashe
- Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
- National Centre for Biological Sciences, Bangalore 560065, India.
| | - Christopher J Marx
- Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
- Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83843, USA.
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