Since the first half of the twentieth century, evolutionary theory has been dominated by the idea that mutations occur randomly with respect to their consequences
. Here we test this assumption with ...large surveys of de novo mutations in the plant Arabidopsis thaliana. In contrast to expectations, we find that mutations occur less often in functionally constrained regions of the genome-mutation frequency is reduced by half inside gene bodies and by two-thirds in essential genes. With independent genomic mutation datasets, including from the largest Arabidopsis mutation accumulation experiment conducted to date, we demonstrate that epigenomic and physical features explain over 90% of variance in the genome-wide pattern of mutation bias surrounding genes. Observed mutation frequencies around genes in turn accurately predict patterns of genetic polymorphisms in natural Arabidopsis accessions (r = 0.96). That mutation bias is the primary force behind patterns of sequence evolution around genes in natural accessions is supported by analyses of allele frequencies. Finally, we find that genes subject to stronger purifying selection have a lower mutation rate. We conclude that epigenome-associated mutation bias
reduces the occurrence of deleterious mutations in Arabidopsis, challenging the prevailing paradigm that mutation is a directionless force in evolution.
Mutations are the ultimate source of all genetic variation. However, few direct estimates of the contribution of mutation to molecular genetic variation are available. To address this issue, we first ...analyzed the rate and spectrum of mutations in the
reference accession after 25 generations of single-seed descent. We then compared the mutation profile in these mutation accumulation (MA) lines against genetic variation observed in the 1001 Genomes Project. The estimated haploid single nucleotide mutation (SNM) rate for
is 6.95 × 10
(SE ± 2.68 × 10
) per site per generation, with SNMs having higher frequency in transposable elements (TEs) and centromeric regions. The estimated indel mutation rate is 1.30 × 10
(±1.07 × 10
) per site per generation, with deletions being more frequent and larger than insertions. Among the 1694 unique SNMs identified in the MA lines, the positions of 389 SNMs (23%) coincide with biallelic SNPs from the 1001 Genomes population, and in 289 (17%) cases the changes are identical. Of the 329 unique indels identified in the MA lines, 96 (29%) overlap with indels from the 1001 Genomes dataset, and 16 indels (5% of the total) are identical. These overlap frequencies are significantly higher than expected, suggesting that
mutations are not uniformly distributed and arise at polymorphic sites more frequently than assumed. These results suggest that high mutation rate potentially contributes to high polymorphism and low mutation rate to reduced polymorphism in natural populations providing insights of mutational inputs in generating natural genetic diversity.
Aims/hypothesis
Mitochondrial oxidative metabolism is central to glucose-stimulated insulin secretion (GSIS). Whether Ca
2+
uptake into pancreatic beta cell mitochondria potentiates or antagonises ...this process is still a matter of debate. Although the mitochondrial Ca
2+
importer (MCU) complex is thought to represent the main route for Ca
2+
transport across the inner mitochondrial membrane, its role in beta cells has not previously been examined in vivo.
Methods
Here, we inactivated the pore-forming subunit of the MCU, encoded by
Mcu
, selectively in mouse beta cells using
Ins1
Cre
-mediated recombination. Whole or dissociated pancreatic islets were isolated and used for live beta cell fluorescence imaging of cytosolic or mitochondrial Ca
2+
concentration and ATP production in response to increasing glucose concentrations. Electrophysiological recordings were also performed on whole islets. Serum and blood samples were collected to examine oral and i.p. glucose tolerance.
Results
Glucose-stimulated mitochondrial Ca
2+
accumulation (
p
< 0.05), ATP production (
p
< 0.05) and insulin secretion (
p
< 0.01) were strongly inhibited in beta cell-specific
Mcu
-null (β
Mcu
-KO) animals, in vitro, as compared with wild-type (WT) mice. Interestingly, cytosolic Ca
2+
concentrations increased (
p
< 0.001), whereas mitochondrial membrane depolarisation improved in β
Mcu
-KO animals. β
Mcu
-KO mice displayed impaired in vivo insulin secretion at 5 min (
p
< 0.001) but not 15 min post-i.p. injection of glucose, whilst the opposite phenomenon was observed following an oral gavage at 5 min. Unexpectedly, glucose tolerance was improved (
p
< 0.05) in young β
Mcu
-KO (<12 weeks), but not in older animals vs WT mice.
Conclusions/interpretation
MCU is crucial for mitochondrial Ca
2+
uptake in pancreatic beta cells and is required for normal GSIS. The apparent compensatory mechanisms that maintain glucose tolerance in β
Mcu
-KO mice remain to be established.
Using a mechanistic spatially explicit trait-based neighborhood-model, we quantify the impact of mutations on intraspecific spatial interactions to better understand mechanisms underlying the ...maintenance of genetic variation and the potential effects of these evolved interactions on the population dynamics of
Arabidopsis thaliana
. We use 100 twenty-fifth generation mutation accumulation (MA) lines (genotypes) derived from one founder genotype to study mutational effects on neighbor responses in a field experiment. We created individual-based maps (15,000 individuals), including phenotypic variation, to quantify mutational effects within genotypes versus between genotypes on reproduction and survival. At small-scale (within 80 cm of the focal plant), survival is enhanced but seed-set is decreased when a genotype is surrounded by different genotypes. At large-scale (within 200 cm of the focal plant), seed set is facilitated by different genotypes while the same genotype has either no effect or negative effects. The direction of the interactions among MA lines suggests that at small scale these interactions may contribute to the maintenance of genetic variation and at large scale contribute to the survival of the population. This may suggest, that, mutations potentially have immediate effects on population and community dynamics by influencing the outcome of competitive and faciliatory interactions among conspecifics.
Little is empirically known about the contribution of mutations to fitness in natural environments. However, Fisher’s Geometric Model (FGM) provides a conceptual foundation to consider the influence ...of the environment on mutational effects. To quantify mutational properties in the field, we established eight sets of MA lines (7-10 generations) derived from eight founders collected from natural populations of Arabidopsis thaliana from French and Swedish sites, representing the range margins of the species in Europe. We reciprocally planted the MA lines and their founders at French and Swedish sites, allowing us to test predictions of FGM under naturally occurring environmental conditions. The performance of the MA lines relative to each other and to their respective founders confirmed some and contradicted other predictions of the FGM: the contribution of mutation to fitness variance increased when the genotype was in an environment where its fitness was low, that is, in the away environment, but mutations were more likely to be beneficial when the genotype was in its home environment. Consequently, environmental context plays a large role in the contribution of mutations to the evolutionary process and local adaptation does not guarantee that a genotype is at or close to its optimum.
Impaired pancreatic β-cell function and insulin secretion are hallmarks of type 2 diabetes. miRNAs are short, noncoding RNAs that silence gene expression vital for the development and function of β ...cells. We have previously shown that β cell-specific deletion of the important energy sensor AMP-activated protein kinase (AMPK) results in increased miR-125b-5p levels. Nevertheless, the function of this miRNA in β cells is unclear. We hypothesized that miR-125b-5p expression is regulated by glucose and that this miRNA mediates some of the deleterious effects of hyperglycemia in β cells. Here, we show that islet miR-125b-5p expression is upregulated by glucose in an AMPK-dependent manner and that short-term miR-125b-5p overexpression impairs glucose-stimulated insulin secretion (GSIS) in the mouse insulinoma MIN6 cells and in human islets. An unbiased, high-throughput screen in MIN6 cells identified multiple miR-125b-5p targets, including the transporter of lysosomal hydrolases M6pr and the mitochondrial fission regulator Mtfp1. Inactivation of miR-125b-5p in the human β-cell line EndoCβ-H1 shortened mitochondria and enhanced GSIS, whereas mice overexpressing miR-125b-5p selectively in β cells (MIR125B-Tg) were hyperglycemic and glucose intolerant. MIR125B-Tg β cells contained enlarged lysosomal structures and had reduced insulin content and secretion. Collectively, we identify miR-125b as a glucose-controlled regulator of organelle dynamics that modulates insulin secretion.
Plant populations may vary substantially in their tolerance for and accumulation of heavy metals, and assessment of this variability is important when selecting species to use in restoration or ...phytoremediation projects. We examined the population variation in cadmium tolerance and accumulation in a leguminous pioneer species native to the eastern United States, the partridge pea (Chamaecrista fasciculata). We assayed growth, reproduction and patterns of cadmium accumulation in six populations of C. fasciculata grown on a range of cadmium-contaminated soils. In general, C. fasciculata exhibited tolerance in low to moderate soil cadmium concentrations. Both tolerance and accumulation patterns varied across populations. C. fasciculata exhibited many characteristics of a hyperaccumulator species, with high cadmium uptake in shoots and roots. However, cadmium was excluded from extrafloral nectar. As a legume with tolerance for moderate cadmium contamination, C. fasciculata has potential for phytoremediation. However, our findings also indicate the importance of considering the effects of genetic variation on plant performance when screening plant populations for utilization in remediation and restoration activities. Also, there is potential for cadmium contamination to affect other species through contamination of leaves, fruits, flowers, pollen and root nodules.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Nature https://doi.org/10.1038/s41586-021-04269-6 Published online 12 January 2022 Open access Check for updates J. Grey Monroe, Thanvi Srikant, Pablo Carbonell-Bejerano, Claude Becker, Mariele ...Lensink, Moises Exposito-Alonso, Marie Klein, Julia Hildebrandt, Manuela Neumann, Daniel Kliebenstein, Mao-Lun Weng, Eric Imbert, Jon Ågren, Matthew T. Rutter, Charles B. Fenster & Detlef Weigel The second sentence in the Methods section "Identification of de novo somatic mutations in a resequencing dataset of A. thaliana leaves" has been corrected from "Raw fastq files were downloaded from NCBI and mapped to the TAIR10 reference genome using bwa-mem..." to "Raw fastq files were downloaded from NCBI and forward reads were mapped twice to the TAIR10 reference genome using bwa-mem (bwa mem ${sample}_R1.fastq.gz ${sample}_R1.fastq.gz)..." In our study1, we tested whether trends of lower mutation rates in gene bodies and in essential genes observed in our initial set of sequence data were also observable in other datasets. The architecture of intra-organism mutation rate variation in plants.
As the ultimate source of genetic diversity, spontaneous mutation is critical to the evolutionary process. The fitness effects of spontaneous mutations are almost always studied under controlled ...laboratory conditions rather than under the evolutionarily relevant conditions of the field. Of particular interest is the conditionality of new mutations—that is, is a new mutation harmful regardless of the environment in which it is found? In other words, what is the extent of genotype–environment interaction for spontaneous mutations? We studied the fitness effects of 25 generations of accumulated spontaneous mutations in Arabidopsis thaliana in two geographically widely separated field environments, in Michigan and Virginia. At both sites, mean total fitness of mutation accumulation lines exceeded that of the ancestors, contrary to the expected decrease in the mean due to new mutations but in accord with prior work on these MA lines. We observed genotype–environment interactions in the fitness effects of new mutations, such that the effects of mutations in Michigan were a poor predictor of their effects in Virginia and vice versa. In particular, mutational variance for fitness was much larger in Virginia compared to Michigan. This strong genotype–environment interaction would increase the amount of genetic variation maintained by mutation-selection balance.
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