scholarly journals Systematic investigation of the link between enzyme catalysis and cold adaptation

2021 ◽  
Author(s):  
Catherine Stark ◽  
Teanna Bautista-Leung ◽  
Joanna Siegfried ◽  
Daniel Herschlag
Keyword(s):  
Enzyme Catalysis ◽  
Cold Adaptation ◽  
Optimal Growth ◽  
Systematic Investigation ◽  
Physical Models ◽  
Temperature Adaptation ◽  
Rate Variation ◽  
Adaptive Trait ◽  
Evolutionary Forces ◽  
Reduced Temperature

Cold temperature is prevalent across the biosphere and slows the rates of chemical reactions. Increased catalysis has been predicted to be a general adaptive trait of enzymes to reduced temperature, and this expectation has informed physical models for enzyme catalysis and influenced bioprospecting strategies. To broadly test rate as an adaptive trait to cold, we paired kinetic constants of 2223 enzyme reactions with their organism’s optimal growth temperature (TGrowth) and analyzed trends of rate as a function of TGrowth. These data do not support a prevalent increase in rate in cold adaptation. In the model enzyme ketosteroid isomerase (KSI), there was prior evidence for temperature adaptation from a change in an active site residue that results in a tradeoff between activity and stability. Here, we found that little of the overall rate variation for 20 KSI variants was accounted for by TGrowth. In contrast, and consistent with prior expectations, we observed a correlation between stability and TGrowth across 433 proteins. These results suggest that temperature exerts a weaker selection pressure on enzyme rate than stability and that evolutionary forces other than temperature are responsible for the majority of enzymatic rate variation.

scholarly journals Systematic investigation of the link between enzyme catalysis and cold adaptation

eLife ◽  
2022 ◽  
Vol 11 ◽  
Author(s):  
Catherine Stark ◽  
Teanna Bautista-Leung ◽  
Joanna Siegfried ◽  
Daniel Herschlag
Keyword(s):  
Rate Constant ◽  
Rate Constants ◽  
Enzyme Catalysis ◽  
Cold Adaptation ◽  
Optimal Growth ◽  
Physical Models ◽  
Temperature Adaptation ◽  
Rate Enhancement ◽  
Adaptive Trait ◽  
Evolutionary Forces

Cold temperature is prevalent across the biosphere and slows the rates of chemical reactions. Increased catalysis has been predicted to be a dominant adaptive trait of enzymes to reduced temperature, and this expectation has informed physical models for enzyme catalysis and influenced bioprospecting strategies. To systematically test rate enhancement as an adaptive trait to cold, we paired kinetic constants of 2223 enzyme reactions with their organism’s optimal growth temperature (TGrowth) and analyzed trends of rate constants as a function of TGrowth. These data do not support a general increase in rate enhancement in cold adaptation. In the model enzyme ketosteroid isomerase (KSI), there is prior evidence for temperature adaptation from a change in an active site residue that results in a tradeoff between activity and stability. Nevertheless, we found that little of the rate constant variation for 20 KSI variants was accounted for by TGrowth. In contrast, and consistent with prior expectations, we observed a correlation between stability and TGrowth across 433 proteins. These results suggest that temperature exerts a weaker selection pressure on enzyme rate constants than stability and that evolutionary forces other than temperature are responsible for the majority of enzymatic rate constant variation.

scholarly journals Coevolution between transposable elements and recombination

2017 ◽  
Vol 372 (1736) ◽  
pp. 20160458 ◽  
Author(s):  
Tyler V. Kent ◽  
Jasmina Uzunović ◽  
Stephen I. Wright
Keyword(s):  
Transposable Elements ◽  
Genome Structure ◽  
Rate Variation ◽  
Species Variation ◽  
Insertion Polymorphism ◽  
Recombination Rates ◽  
Recombination Suppression ◽  
Evolutionary Forces ◽  
Genomic Regions ◽  
Recombination Rate Variation

One of the most striking patterns of genome structure is the tight, typically negative, association between transposable elements (TEs) and meiotic recombination rates. While this is a highly recurring feature of eukaryotic genomes, the mechanisms driving correlations between TEs and recombination remain poorly understood, and distinguishing cause versus effect is challenging. Here, we review the evidence for a relation between TEs and recombination, and discuss the underlying evolutionary forces. Evidence to date suggests that overall TE densities correlate negatively with recombination, but the strength of this correlation varies across element types, and the pattern can be reversed. Results suggest that heterogeneity in the strength of selection against ectopic recombination and gene disruption can drive TE accumulation in regions of low recombination, but there is also strong evidence that the regulation of TEs can influence local recombination rates. We hypothesize that TE insertion polymorphism may be important in driving within-species variation in recombination rates in surrounding genomic regions. Furthermore, the interaction between TEs and recombination may create positive feedback, whereby TE accumulation in non-recombining regions contributes to the spread of recombination suppression. Further investigation of the coevolution between recombination and TEs has important implications for our understanding of the evolution of recombination rates and genome structure. This article is part of the themed issue ‘Evolutionary causes and consequences of recombination rate variation in sexual organisms’.

scholarly journals Predicting protein domain temperature adaptation across the prokaryote-eukaryote divide

2021 ◽  
Author(s):  
Sarah E Jensen ◽  
Lynn C Johnson ◽  
Terry Casstevens ◽  
Edward S. Buckler
Keyword(s):  
Amino Acid ◽  
Temperature Sensitivity ◽  
Prediction Models ◽  
Pfam Domain ◽  
Optimal Growth ◽  
Temperature Adaptation ◽  
Amino Acid Residues ◽  
Protein Thermostability ◽  
Site Specific ◽  
Change Models

Protein thermostability is important for fitness but difficult to measure across the proteome. Fortunately, protein thermostability is correlated with prokaryote optimal growth temperatures (OGTs), which can be predicted from genome features. Models that can predict temperature sensitivity across the prokaryote-eukaryote divide would help inform how eukaryotes adapt to elevated temperatures, such as those predicted by climate change models. In this study we test whether prediction models can cross the prokaryote-eukaryote divide to predict protein stability in both prokaryotes and eukaryotes. We compare models built using a) the whole proteome, b) Pfam domains, and c) individual amino acid residues. Proteome-wide models accurately predict prokaryote optimal growth temperatures (r2 up to 0.93), while site-specific models demonstrate that nearly half of the proteome is associated with optimal growth temperature in both Archaea and Bacteria. Comparisons with the small number of eukaryotes with temperature sensitivity data suggest that site-specific models are the most transferable across the prokaryote-eukaryote divide. Using the site-specific models, we evaluated temperature sensitivity for 323,850 amino acid residues in 2,088 Pfam domain clusters in Archaea and Bacteria species separately. 59.0% of tested residues are significantly associated with OGT in Archaea and 75.2% of tested residues are significantly associated with OGT in Bacteria species at a 5% false discovery rate. These models make it possible to identify which Pfam domains and amino acid residues are involved in temperature adaptation and facilitate future research questions about how species will fare in the face of increasing environmental temperatures.

scholarly journals Natural selection and recombination rate variation shape nucleotide polymorphism across the genomes of three relatedPopulusspecies

2015 ◽  
Author(s):  
Jing Wang ◽  
Nathaniel R Street ◽  
Douglas G Scofield ◽  
Pär K Ingvarsson
Keyword(s):  
Natural Selection ◽  
Rate Variation ◽  
Sequencing Data ◽  
Nucleotide Polymorphism ◽  
Effective Population ◽  
Recombination Rates ◽  
Evolutionary Forces ◽  
Genome Wide ◽  
Population Sizes ◽  
Wide Scale

AbstractA central aim of evolutionary genomics is to identify the relative roles that various evolutionary forces have played in generating and shaping genetic variation within and among species. Here we use whole-genome re-sequencing data to characterize and compare genome-wide patterns of nucleotide polymorphism, site frequency spectrum and population-scaled recombination rates in three species ofPopulus:P. tremula, P. tremuloidesandP. trichocarpa. We find thatP. tremuloideshas the highest level of genome-wide variation, skewed allele frequencies and population-scaled recombination rates, whereasP. trichocarpaharbors the lowest. Our findings highlight multiple lines of evidence suggesting that natural selection, both due to purifying and positive selection, has widely shaped patterns of nucleotide polymorphism at linked neutral sites in all three species. Differences in effective population sizes and rates of recombination are largely explaining the disparate magnitudes and signatures of linked selection we observe among species. The present work provides the first phylogenetic comparative study at genome-wide scale in forest trees. This information will also improve our ability to understand how various evolutionary forces have interacted to influence genome evolution among related species.

scholarly journals The molecular signal for the adaptation to cold temperature during early life on Earth

2013 ◽  
Vol 9 (5) ◽  
pp. 20130608 ◽  
Author(s):  
Mathieu Groussin ◽  
Bastien Boussau ◽  
Sandrine Charles ◽  
Samuel Blanquart ◽  
Manolo Gouy
Keyword(s):  
Phylogenetic Trees ◽  
Large Scale ◽  
Common Ancestor ◽  
Phylogenetic Signal ◽  
Optimal Growth ◽  
Ancestral Sequence ◽  
Rate Variation ◽  
Last Common Ancestor ◽  
Ancestral Sequence Reconstruction ◽  
Sequence Reconstruction

Several lines of evidence such as the basal location of thermophilic lineages in large-scale phylogenetic trees and the ancestral sequence reconstruction of single enzymes or large protein concatenations support the conclusion that the ancestors of the bacterial and archaeal domains were thermophilic organisms which were adapted to hot environments during the early stages of the Earth. A parsimonious reasoning would therefore suggest that the last universal common ancestor (LUCA) was also thermophilic. Various authors have used branch-wise non-homogeneous evolutionary models that better capture the variation of molecular compositions among lineages to accurately reconstruct the ancestral G + C contents of ribosomal RNAs and the ancestral amino acid composition of highly conserved proteins. They confirmed the thermophilic nature of the ancestors of Bacteria and Archaea but concluded that LUCA, their last common ancestor, was a mesophilic organism having a moderate optimal growth temperature. In this letter, we investigate the unknown nature of the phylogenetic signal that informs ancestral sequence reconstruction to support this non-parsimonious scenario. We find that rate variation across sites of molecular sequences provides information at different time scales by recording the oldest adaptation to temperature in slow-evolving regions and subsequent adaptations in fast-evolving ones.

scholarly journals Estimation of the Genome-Wide Mutation Rate and Spectrum in the Archaeal Species Haloferax volcanii

Genetics ◽  
2020 ◽  
Vol 215 (4) ◽  
pp. 1107-1116 ◽  
Author(s):  
Sibel Kucukyildirim ◽  
Megan Behringer ◽  
Emily M. Williams ◽  
Thomas G. Doak ◽  
Michael Lynch
Keyword(s):  
Molecular Mechanisms ◽  
Model Organism ◽  
Optimal Growth ◽  
Haloferax Volcanii ◽  
Base Substitution ◽  
Spontaneous Mutations ◽  
Evolutionary Forces ◽  
Genome Wide ◽  
Archaeal Species ◽  
A Genome

Organisms adapted to life in extreme habitats (extremophiles) can further our understanding of the mechanisms of genetic stability, particularly replication and repair. Despite the harsh environmental conditions they endure, these extremophiles represent a great deal of the Earth’s biodiversity. Here, for the first time in a member of the archaeal domain, we report a genome-wide assay of spontaneous mutations in the halophilic species Haloferax volcanii using a direct and unbiased method: mutation accumulation experiments combined with deep whole-genome sequencing. H. volcanii is a key model organism not only for the study of halophilicity, but also for archaeal biology in general. Our methods measure the genome-wide rate, spectrum, and spatial distribution of spontaneous mutations. The estimated base substitution rate of 3.15 × 10−10 per site per generation, or 0.0012 per genome per generation, is similar to the value found in mesophilic prokaryotes (optimal growth at ∼20–45°). This study contributes to a comprehensive phylogenetic view of how evolutionary forces and molecular mechanisms shape the rate and molecular spectrum of mutations across the tree of life.

scholarly journals Mutation rate variation shapes genome-wide diversity in Drosophila melanogaster

2021 ◽  
Author(s):  
Gustavo Valadares Barroso ◽  
Julien Y Dutheil
Keyword(s):  
Drosophila Melanogaster ◽  
Molecular Evolution ◽  
Mutation Rate ◽  
Nucleotide Diversity ◽  
Population Genomics ◽  
Genomic Variation ◽  
Mutation Rates ◽  
Rate Variation ◽  
Evolutionary Forces ◽  
Mutation Rate Variation

What shapes the distribution of nucleotide diversity along the genome? Attempts to answer this question have sparked debate about the roles of neutral stochastic processes and natural selection in molecular evolution. However, the mechanisms of evolution do not act in isolation, and integrative models that simultaneously consider the influence of multiple factors on diversity are lacking; without them, confounding factors lurk in the estimates. Here we present a new statistical method that jointly infers the genomic landscapes of genealogies, recombination rates and mutation rates. In doing so, our model captures the effects of genetic drift, linked selection and local mutation rates on patterns of genomic variation. Guided by our causal model, we use linear regression to estimate the individual contributions of these micro-evolutionary forces to levels of nucleotide diversity. Our analyses reveal the signature of selection in Drosophila melanogaster, but we estimate that the mutation landscape is the major driver of the distribution of diversity in this species. Furthermore, our simulation study suggests that in many evolutionary scenarios the mutation landscape will be a crucial force shaping diversity, depending notably on the genomic window size used in the analysis. We argue that incorporating mutation rate variation into the null model of molecular evolution will lead to more realistic inference in population genomics.

Recent Radiative and Collisional Atomic Data of Astrophysical Interest

1988 ◽  
Vol 102 ◽  
pp. 129-132
Author(s):  
K.L. Baluja ◽  
K. Butler ◽  
J. Le Bourlot ◽  
C.J. Zeippen
Keyword(s):  
Mass Production ◽  
Bound States ◽  
Physical Models ◽  
Impact Excitation ◽  
Electron Impact Excitation ◽  
Atomic Data ◽  
Isoelectronic Sequence ◽  
Astrophysical Interest ◽  
Radiative Transitions ◽  
Forbidden Transitions

SummaryUsing sophisticated computer programs and elaborate physical models, accurate radiative and collisional atomic data of astrophysical interest have been or are being calculated. The cases treated include radiative transitions between bound states in the 2p4and 2s2p5configurations of many ions in the oxygen isoelectronic sequence, the photoionisation of the ground state of neutral iron, the electron impact excitation of the fine-structure forbidden transitions within the 3p3ground configuration of CℓIII, Ar IV and K V, and the mass-production of radiative data for ions in the oxygen and fluorine isoelectronic sequences, as part of the international Opacity Project.

Grain Refinement in Titanium-Erbium Alloys

1974 ◽  
Vol 32 ◽  
pp. 522-523
Author(s):  
B. B. Rath ◽  
J. E. O'Neal ◽  
R. J. Lederich
Keyword(s):  
Electron Microscopy ◽  
Size Distribution ◽  
Grain Refinement ◽  
Grain Growth ◽  
Volume Fraction ◽  
Pure Titanium ◽  
Systematic Investigation ◽  
Second Phase ◽  
Titanium Matrix ◽  
Average Size

Addition of small amounts of erbium has a profound effect on recrystallization and grain growth in titanium. Erbium, because of its negligible solubility in titanium, precipitates in the titanium matrix as a finely dispersed second phase. The presence of this phase, depending on its average size, distribution, and volume fraction in titanium, strongly inhibits the migration of grain boundaries during recrystallization and grain growth, and thus produces ultimate grains of sub-micrometer dimensions. A systematic investigation has been conducted to study the isothermal grain growth in electrolytically pure titanium and titanium-erbium alloys (Er concentration ranging from 0-0.3 at.%) over the temperature range of 450 to 850°C by electron microscopy.

Optical Properties of HVEM Accelerators

1975 ◽  
Vol 33 ◽  
pp. 180-181
Author(s):  
A. Strojnik ◽  
J.W. Scholl ◽  
V. Bevc
Keyword(s):  
Optical Properties ◽  
Electron Accelerator ◽  
Systematic Investigation ◽  
Electron Source ◽  
High Brightness ◽  
The Past ◽  
Wide Range ◽  
Optical Behavior

The electron accelerator, as inserted between the electron source (injector) and the imaging column of the HVEM, is usually a strong lens and should be optimized in order to ensure high brightness over a wide range of accelerating voltages and illuminating conditions. This is especially true in the case of the STEM where the brightness directly determines the highest resolution attainable. In the past, the optical behavior of accelerators was usually determined for a particular configuration. During the development of the accelerator for the Arizona 1 MEV STEM, systematic investigation was made of the major optical properties for a variety of electrode configurations, number of stages N, accelerating voltages, 1 and 10 MEV, and a range of injection voltages ϕ0 = 1, 3, 10, 30, 100, 300 kV).

Sign in / Sign up

Export Citation Format

Share Document