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Cherrak Y, Salazar MA, Näpflin N, Malfertheiner L, Herzog MKM, Schubert C, von Mering C, Hardt WD. Non-canonical start codons confer context-dependent advantages in carbohydrate utilization for commensal E. coli in the murine gut. Nat Microbiol 2024:10.1038/s41564-024-01775-x. [PMID: 39160293 DOI: 10.1038/s41564-024-01775-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 07/04/2024] [Indexed: 08/21/2024]
Abstract
Resource competition is a driver of gut microbiota composition. Bacteria can outcompete metabolically similar rivals through the limitation of shared growth-fuelling nutrients. The mechanisms underlying this remain unclear for bacteria with identical sets of metabolic genes. Here we analysed the lactose utilization operon in the murine commensal Escherichia coli 8178. Using in vitro and in vivo approaches, we showed that translation of the lactose utilization repressor gene lacI from its native non-canonical GTG start codon increases the basal expression of the lactose utilization cluster, enhancing adaptation to lactose consumption. Consequently, a strain carrying the wild type lacI GTG start codon outperformed the lacI ATG start codon mutant in the mouse intestine. This advantage was attenuated upon limiting host lactose intake through diet shift or altering the mutant frequency, emphasizing the context-dependent effect of a single nucleotide change on the bacterial fitness of a common member of the gut microbiota. Coupled with a genomic analysis highlighting the selection of non-ATG start codons in sugar utilization regulator genes across the Enterobacteriaceae family, our data exposed an unsuspected function of non-canonical start codons in metabolic competition.
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Affiliation(s)
- Yassine Cherrak
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland.
| | - Miguel Angel Salazar
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Nicolas Näpflin
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Lukas Malfertheiner
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Mathias K-M Herzog
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Christopher Schubert
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Christian von Mering
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Wolf-Dietrich Hardt
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland.
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2
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Brand JA, Garcia-Gonzalez F, Dowling DK, Wong BBM. Mitochondrial genetic variation as a potential mediator of intraspecific behavioural diversity. Trends Ecol Evol 2024; 39:199-212. [PMID: 37839905 DOI: 10.1016/j.tree.2023.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/11/2023] [Accepted: 09/11/2023] [Indexed: 10/17/2023]
Abstract
Mitochondrial genes play an essential role in energy metabolism. Variation in the mitochondrial DNA (mtDNA) sequence often exists within species, and this variation can have consequences for energy production and organismal life history. Yet, despite potential links between energy metabolism and the expression of animal behaviour, mtDNA variation has been largely neglected to date in studies investigating intraspecific behavioural diversity. We outline how mtDNA variation and interactions between mitochondrial and nuclear genotypes may contribute to the expression of individual-to-individual behavioural differences within populations, and why such effects may lead to sex differences in behaviour. We contend that integration of the mitochondrial genome into behavioural ecology research may be key to fully understanding the evolutionary genetics of animal behaviour.
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Affiliation(s)
- Jack A Brand
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia; Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden.
| | - Francisco Garcia-Gonzalez
- Doñana Biological Station-CSIC, Seville, Spain; Centre for Evolutionary Biology, School of Biological Sciences, University of Western Australia, Crawley, Western Australia, Australia
| | - Damian K Dowling
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
| | - Bob B M Wong
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
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3
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Arnqvist G, Rowe L. Ecology, the pace-of-life, epistatic selection and the maintenance of genetic variation in life-history genes. Mol Ecol 2023; 32:4713-4724. [PMID: 37386734 DOI: 10.1111/mec.17062] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 06/09/2023] [Accepted: 06/19/2023] [Indexed: 07/01/2023]
Abstract
Evolutionary genetics has long struggled with understanding how functional genes under selection remain polymorphic in natural populations. Taking as a starting point that natural selection is ultimately a manifestation of ecological processes, we spotlight an underemphasized and potentially ubiquitous ecological effect that may have fundamental effects on the maintenance of genetic variation. Negative frequency dependency is a well-established emergent property of density dependence in ecology, because the relative profitability of different modes of exploiting or utilizing limiting resources tends to be inversely proportional to their frequency in a population. We suggest that this may often generate negative frequency-dependent selection (NFDS) on major effect loci that affect rate-dependent physiological processes, such as metabolic rate, that are phenotypically manifested as polymorphism in pace-of-life syndromes. When such a locus under NFDS shows stable intermediate frequency polymorphism, this should generate epistatic selection potentially involving large numbers of loci with more minor effects on life-history (LH) traits. When alternative alleles at such loci show sign epistasis with a major effect locus, this associative NFDS will promote the maintenance of polygenic variation in LH genes. We provide examples of the kind of major effect loci that could be involved and suggest empirical avenues that may better inform us on the importance and reach of this process.
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Affiliation(s)
- Göran Arnqvist
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Locke Rowe
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
- Swedish Collegium of Advanced Study, Uppsala, Sweden
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4
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Dowling DK, Wolff JN. Evolutionary genetics of the mitochondrial genome: insights from Drosophila. Genetics 2023; 224:iyad036. [PMID: 37171259 PMCID: PMC10324950 DOI: 10.1093/genetics/iyad036] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 02/05/2023] [Indexed: 05/13/2023] Open
Abstract
Mitochondria are key to energy conversion in virtually all eukaryotes. Intriguingly, despite billions of years of evolution inside the eukaryote, mitochondria have retained their own small set of genes involved in the regulation of oxidative phosphorylation (OXPHOS) and protein translation. Although there was a long-standing assumption that the genetic variation found within the mitochondria would be selectively neutral, research over the past 3 decades has challenged this assumption. This research has provided novel insight into the genetic and evolutionary forces that shape mitochondrial evolution and broader implications for evolutionary ecological processes. Many of the seminal studies in this field, from the inception of the research field to current studies, have been conducted using Drosophila flies, thus establishing the species as a model system for studies in mitochondrial evolutionary biology. In this review, we comprehensively review these studies, from those focusing on genetic processes shaping evolution within the mitochondrial genome, to those examining the evolutionary implications of interactions between genes spanning mitochondrial and nuclear genomes, and to those investigating the dynamics of mitochondrial heteroplasmy. We synthesize the contribution of these studies to shaping our understanding of the evolutionary and ecological implications of mitochondrial genetic variation.
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Affiliation(s)
- Damian K Dowling
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
| | - Jonci N Wolff
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
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5
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Wang T, Li TC, Miao YH, Wu LN, Chen YQ, Huang DW, Xiao JH. The gender-specific impact of starvation on mitotypes diversity in adults of Drosophila melanogaster. Open Biol 2022; 12:220108. [PMID: 36167086 PMCID: PMC9514890 DOI: 10.1098/rsob.220108] [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] [Indexed: 11/12/2022] Open
Abstract
In animals, starvation can increase the level of reactive oxygen species (ROS) in some tissues. Mitochondrial DNA (mtDNA) is more vulnerable to being attacked by ROS due to the lack of histone protection, leading to oxidative damage. However, whether starvation is associated with the genetic diversity of mtDNA remains unclear. Here, by using adult individuals of Drosophila melanogaster under three different feeding treatments (starvation, with the provision of only water, and normal feeding), based on the high-throughput sequencing results of the PCR amplicons of the partial sequences of the mitochondrial gene cytochrome c oxidase subunit I (mt-cox1), no significant difference in the mean number of mitochondrial haplotypes and the mean genetic distance of haplotypes within individuals were identified between the three treatment groups. Coupled with the low proportion of heterogeneous mt-cox1 sequences within each individual, it suggested that starvation had a limited impact on mitotype genetic diversity and mitochondrial function. Nevertheless, starvation could significantly increase the sequence number of haplotypes containing specific mutations, and for males with higher levels of mitochondrial heteroplasmy than females in the normal feeding group, starvation could further increase their mitochondrial heteroplasmy.
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Affiliation(s)
- Tao Wang
- College of Life Sciences, Nankai University, Tianjin 300071, People's Republic of China
| | - Tian-Chu Li
- College of Life Sciences, Nankai University, Tianjin 300071, People's Republic of China
| | - Yun-Heng Miao
- College of Life Sciences, Nankai University, Tianjin 300071, People's Republic of China
| | - Luo-Nan Wu
- College of Life Sciences, Nankai University, Tianjin 300071, People's Republic of China
| | - Yu-Qiao Chen
- College of Life Sciences, Nankai University, Tianjin 300071, People's Republic of China
| | - Da-Wei Huang
- College of Life Sciences, Nankai University, Tianjin 300071, People's Republic of China
| | - Jin-Hua Xiao
- College of Life Sciences, Nankai University, Tianjin 300071, People's Republic of China
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6
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Immonen E, Berger D, Sayadi A, Liljestrand‐Rönn J, Arnqvist G. An experimental test of temperature-dependent selection on mitochondrial haplotypes in Callosobruchus maculatus seed beetles. Ecol Evol 2020; 10:11387-11398. [PMID: 33144972 PMCID: PMC7593184 DOI: 10.1002/ece3.6775] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/11/2020] [Accepted: 08/12/2020] [Indexed: 01/05/2023] Open
Abstract
Mitochondrial DNA (mtDNA) consists of few but vital maternally inherited genes that interact closely with nuclear genes to produce cellular energy. How important mtDNA polymorphism is for adaptation is still unclear. The assumption in population genetic studies is often that segregating mtDNA variation is selectively neutral. This contrasts with empirical observations of mtDNA haplotypes affecting fitness-related traits and thermal sensitivity, and latitudinal clines in mtDNA haplotype frequencies. Here, we experimentally test whether ambient temperature affects selection on mtDNA variation, and whether such thermal effects are influenced by intergenomic epistasis due to interactions between mitochondrial and nuclear genes, using replicated experimental evolution in Callosobruchus maculatus seed beetle populations seeded with a mixture of different mtDNA haplotypes. We also test for sex-specific consequences of mtDNA evolution on reproductive success, given that mtDNA mutations can have sexually antagonistic fitness effects. Our results demonstrate natural selection on mtDNA haplotypes, with some support for thermal environment influencing mtDNA evolution through mitonuclear epistasis. The changes in male and female reproductive fitness were both aligned with changes in mtDNA haplotype frequencies, suggesting that natural selection on mtDNA is sexually concordant in stressful thermal environments. We discuss the implications of our findings for the evolution of mtDNA.
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Affiliation(s)
- Elina Immonen
- Department of Ecology and Evolution/Evolutionary BiologyUppsala UniversityUppsalaSweden
| | - David Berger
- Department of Ecology and Evolution/Animal EcologyUppsala UniversityUppsalaSweden
| | - Ahmed Sayadi
- Department of Ecology and Evolution/Animal EcologyUppsala UniversityUppsalaSweden
| | | | - Göran Arnqvist
- Department of Ecology and Evolution/Animal EcologyUppsala UniversityUppsalaSweden
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7
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Global allele polymorphism indicates a high rate of allele genesis at a locus under balancing selection. Heredity (Edinb) 2020; 126:163-177. [PMID: 32855546 DOI: 10.1038/s41437-020-00358-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 08/13/2020] [Accepted: 08/16/2020] [Indexed: 11/08/2022] Open
Abstract
When selection favours rare alleles over common ones (balancing selection in the form of negative frequency-dependent selection), a locus may maintain a large number of alleles, each at similar frequency. To better understand how allelic richness is generated and maintained at such loci, we assessed 201 sequences of the complementary sex determiner (csd) of the Asian honeybee (Apis cerana), sampled from across its range. Honeybees are haplodiploid; hemizygotes at csd develop as males and heterozygotes as females, while homozygosity is lethal. Thus, csd is under strong negative frequency-dependent selection because rare alleles are less likely to end up in the lethal homozygous form. We find that in A. cerana, as in other Apis, just a few amino acid differences between csd alleles in the hypervariable region are sufficient to trigger female development. We then show that while allelic lineages are spread across geographical regions, allelic differentiation is high between populations, with most csd alleles (86.3%) detected in only one sample location. Furthermore, nucleotide diversity in the hypervariable region indicates an excess of recently arisen alleles, possibly associated with population expansion across Asia since the last glacial maximum. Only the newly invasive populations of the Austral-Pacific share most of their csd alleles. In all, the geographic patterns of csd diversity in A. cerana indicate that high mutation rates and balancing selection act together to produce high rates of allele genesis and turnover at the honeybee sex locus, which in turn leads to its exceptionally high local and global polymorphism.
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8
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Kurbalija Novičić Z, Bodén R, Kozarski K, Jelić M, Jovanović VM, Cunningham JL. Lithium influences whole-organism metabolic rate in Drosophila subobscura. J Neurosci Res 2020; 99:407-418. [PMID: 32729199 DOI: 10.1002/jnr.24678] [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: 10/26/2019] [Revised: 05/25/2020] [Accepted: 05/28/2020] [Indexed: 11/09/2022]
Abstract
Lithium is widely used to treat bipolar disorder. However, the efficacy and vulnerability as to its side effects are known to differ. Although the specific biochemical mechanism of action is still elusive, lithium may influence mitochondrial function, and consequently, metabolism. Lithium exposure in this study was conducted on a unique set of mito-nuclear introgression lines of Drosophila subobscura to disentangle the independent effects of mitochondrial DNA (mtDNA) against a common nuclear DNA background. The study addressed three issues: (a) whether lithium has a dose-dependent effect on whole-organism metabolic rate, (b) whether mtDNA haplotypes show divergent metabolic efficiency measured by metabolic rate to lithium exposure and (c) whether lithium influences the whole-organism metabolic rate across sexes. The results confirm that lithium influenced the whole-organism metabolic rate, showing a subtle balance between efficacy and adverse effects within a narrow dose range. In addition, lithium exposure was found to influence metabolism differently based on mtDNA haplotypes and sex. This preliminary research may have a range of biological implications for the role of mitochondrial variability in psychiatric disease and treatment by contributing to the understanding and predicting of the lithium treatment response and risk for toxic side effects.
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Affiliation(s)
- Zorana Kurbalija Novičić
- Department of Neuroscience, Psychiatry, Uppsala University Hospital, Uppsala, Sweden.,Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Center, Uppsala University, Uppsala, Sweden
| | - Robert Bodén
- Department of Neuroscience, Psychiatry, Uppsala University Hospital, Uppsala, Sweden
| | - Ksenija Kozarski
- Department of Neuroscience, Psychiatry, Uppsala University Hospital, Uppsala, Sweden
| | - Mihailo Jelić
- Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Vladimir M Jovanović
- Bioinformatics Solution Center, Freie Universität Berlin, Berlin, Germany.,Human Biology Group, Freie Universität Berlin, Berlin, Germany.,Institute for Zoology, Freie Universität Berlin, Berlin, Germany.,Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Janet L Cunningham
- Department of Neuroscience, Psychiatry, Uppsala University Hospital, Uppsala, Sweden
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