scholarly journals Enzyme promiscuity shapes evolutionary innovation and optimization

2018 ◽  
Author(s):  
Gabriela I. Guzmán ◽  
Troy E. Sandberg ◽  
Ryan A. LaCroix ◽  
Akos Nyerges ◽  
Henrietta Papp ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
High Efficiency ◽  
Scale Model ◽  
Turnover Rates ◽  
Enzyme Promiscuity ◽  
Evolutionary Innovation ◽  
K 12 ◽  
Enzyme Functions ◽  
Genome Scale

AbstractEvidence suggests that novel enzyme functions evolved from low-level promiscuous activities in ancestral enzymes. Yet, the evolutionary dynamics and physiological mechanisms of how such side activities contribute to systems-level adaptations are poorly understood. Furthermore, it remains untested whether knowledge of an organism’s promiscuous reaction set (‘underground metabolism’) can aid in forecasting the genetic basis of metabolic adaptations. Here, we employ a computational model of underground metabolism and laboratory evolution experiments to examine the role of enzyme promiscuity in the acquisition and optimization of growth on predicted non-native substrates inE. coliK-12 MG1655. After as few as 20 generations, the evolving populations repeatedly acquired the capacity to grow on five predicted novel substrates–D-lyxose, D-2-deoxyribose, D-arabinose, m-tartrate, and monomethyl succinate–none of which could support growth in wild-type cells. Promiscuous enzyme activities played key roles in multiple phases of adaptation. Altered promiscuous activities not only established novel high-efficiency pathways, but also suppressed undesirable metabolic routes. Further, structural mutations shifted enzyme substrate turnover rates towards the new substrate while retaining a preference for the primary substrate. Finally, genes underlying the phenotypic innovations were accurately predicted by genome-scale model simulations of metabolism with enzyme promiscuity. Computational approaches will be essential to synthesize the complex role of promiscuous activities in applied biotechnology and in models of evolutionary adaptation.

scholarly journals Uncovering Novel Pathways for Enhancing Hyaluronan Synthesis in Recombinant Lactococcus lactis: Genome-Scale Metabolic Modeling and Experimental Validation

Processes ◽  
2019 ◽  
Vol 7 (6) ◽  
pp. 343 ◽  
Author(s):  
Abinaya Badri ◽  
Karthik Raman ◽  
Guhan Jayaraman
Keyword(s):  
Metabolic Network ◽  
Lactococcus Lactis ◽  
Experimental Validation ◽  
Fold Increase ◽  
Scale Model ◽  
A Genome ◽  
Recombinant Lactococcus Lactis ◽  
Genome Scale ◽  
Genome Scale Model

Hyaluronan (HA), a glycosaminoglycan with important medical applications, is commercially produced from pathogenic microbial sources. The metabolism of HA-producing recombinant generally regarded as safe (GRAS) systems needs to be more strategically engineered to achieve yields higher than native producers. Here, we use a genome-scale model (GEM) to account for the entire metabolic network of the cell while predicting strategies to improve HA production. We analyze the metabolic network of Lactococcus lactis adapted to produce HA and identify non-conventional strategies to enhance HA flux. We also show experimental verification of one of the predicted strategies. We thus identified an alternate route for enhancement of HA synthesis, originating from the nucleoside inosine, that can function in parallel with the traditionally known route from glucose. Adopting this strategy resulted in a 2.8-fold increase in HA yield. The strategies identified and the experimental results show that the cell is capable of involving a larger subset of metabolic pathways in HA production. Apart from being the first report to use a nucleoside to improve HA production, we demonstrate the role of experimental validation in model refinement and strategy improvisation. Overall, we point out that well-constructed GEMs could be used to derive efficient strategies to improve the biosynthesis of high-value products.

scholarly journals Megaevolutionary dynamics in reptiles and the role of adaptive radiations in evolutionary innovation

2020 ◽  
Author(s):  
Tiago R. Simões ◽  
Oksana Vernygora ◽  
Michael W. Caldwell ◽  
Stephanie E. Pierce
Keyword(s):  
Evolutionary Dynamics ◽  
Phenotypic Diversity ◽  
Total Evidence ◽  
Phenotypic Evolution ◽  
Data Set ◽  
Evolutionary Innovation ◽  
Rates Of Evolution ◽  
Adaptive Radiations ◽  
Rates Of Molecular Evolution

AbstractAdaptive radiations are long believed to be responsible for the origin of phenotypic diversity and new body plans among higher clades in the fossil record. However, few studies have assessed rates of phenotypic evolution and disparity across broad scales of time to understand the evolutionary dynamics behind the origin of major clades, or how they relate to rates of molecular evolution. Here, we provide a total evidence approach to this problem using the largest available data set on diapsid reptiles. We find a strong decoupling between phenotypic and molecular rates of evolution, with many periods of accelerated phenotypic evolution or expansion of phenotypic disparity at the origin of major reptile clades and body plans that do not correspond to periods of adaptive radiation. We find heterogeneous rates of evolution during the acquisition of similarly adapted functional types, and that the origin of snakes is marked by exceptionally high evolutionary rates.

scholarly journals A Cretaceous bug with exaggerated antennae might be a double-edged sword in evolution

2020 ◽  
Author(s):  
Bao-Jie Du ◽  
Rui Chen ◽  
Wen-Tao Tao ◽  
Hong-Liang Shi ◽  
Wen-Jun Bu ◽  
...  
Keyword(s):  
Sexual Selection ◽  
High Efficiency ◽  
Sensory System ◽  
Sensory Organs ◽  
Evolutionary Innovation ◽  
Key Factor ◽  
Opposite Sex ◽  
New Type ◽  
Species Evolution

AbstractIn the competition for the opposite sex, sexual selection can favor production of exaggerated features, but the high cost of such features in terms of energy consumption and enemy avoidance makes them go to extinction under the influence of natural selection. However, to our knowledge, fossil on exaggerated traits that are conducive to attracting opposite sex are very rare. Here, we report the exaggerated leaf-like expansion antennae of Magnusantenna wuae Du & Chen gen. et sp. nov. (Hemiptera: Coreidae) with more abundant sensory hairs from a new nymph coreid preserved in a Cretaceous Myanmar amber. The antennae are the largest among species of coreid and one of the largest known insects. Such bizarre antennae indicate that sensitive and delicate sensory system and magnificent appearance in Hemiptera have been already well established in mid-Cretaceous. Our findings provide evidence for Darwin’s view that sensory organs play an important role in sexual selection. This nymph with the leaf-like antennae may also represents a new camouflage pattern for defense. However, the oversized antennae are costly to develop and maintain, increasing the risks from predators. Such unparalleled expanded antennae might be the key factor for the evolutionary fate of this Myanmar amber coreid species.SignificanceDarwin proposed the importance of sensory organs in sexual selection, but it was greatly ignored compared with weapons and other common ornaments. Here, we report a new type of insect antennae, the multiple segments leaf-like expansion antennae from a new nymph coreid preserved in a Cretaceous Myanmar amber. Our finding provides evidence for the prominent role of sensory organs in sexual selection and thus supports Darwin’s viewpoint. This discovery demonstrates that high-efficiency antennae were present in Coreidae 99 million years ago. In addition, the exaggerated antennae might represent a new evolutionary innovation for defensive behavior. This is a case in which the high benefits and high costs brought by the exaggerated antennae jointly determine the direction of species evolution.

Clustering-Triggered Efficient Room Temperature Phosphorescence from Nonconventional Luminophores

2019 ◽  
Author(s):  
Shuyuan Zheng ◽  
Taiping Hu ◽  
Xin Bin ◽  
Yunzhong Wang ◽  
Yuanping Yi ◽  
...  
Keyword(s):  
Room Temperature ◽  
High Efficiency ◽  
Spin Orbit Coupling ◽  
Design Rationale ◽  
Emission Mechanism ◽  
Room Temperature Phosphorescence ◽  
Electronic Interactions ◽  
Energy Gaps ◽  
Theoretical Results

Pure organic room temperature phosphorescence (RTP) and luminescence from nonconventional luminophores have gained increasing attention. However, it remains challenging to achieve efficient RTP from unorthodox luminophores, on account of the unsophisticated understanding of the emission mechanism. Here we propose a strategy to realize efficient RTP in nonconventional luminophores through incorporation of lone pairs together with clustering and effective electronic interactions. The former promotes spin-orbit coupling and boost the consequent intersystem crossing, whereas the latter narrows energy gaps and stabilizes the triplets, thus synergistically affording remarkable RTP. Experimental and theoretical results of urea and its derivatives verify the design rationale. Remarkably, RTP from thiourea solids with unprecedentedly high efficiency of up to 24.5% is obtained. Further control experiments testify the crucial role of through-space delocalization on the emission. These results would spur the future fabrication of nonconventional phosphors, and moreover should advance understanding of the underlying emission mechanism.<br>

scholarly journals Landscape resistance constrains hybridization across contact zones in a reproductively and morphologically polymorphic salamander

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Guillermo Velo-Antón ◽  
André Lourenço ◽  
Pedro Galán ◽  
Alfredo Nicieza ◽  
Pedro Tarroso
Keyword(s):  
Contact Zone ◽  
Environmental Heterogeneity ◽  
Evolutionary Dynamics ◽  
Morphological Differentiation ◽  
Phenotypic Traits ◽  
Hybrid Zones ◽  
Landscape Resistance ◽  
Phenotypic Differentiation ◽  
Contact Zones

AbstractExplicitly accounting for phenotypic differentiation together with environmental heterogeneity is crucial to understand the evolutionary dynamics in hybrid zones. Species showing intra-specific variation in phenotypic traits that meet across environmentally heterogeneous regions constitute excellent natural settings to study the role of phenotypic differentiation and environmental factors in shaping the spatial extent and patterns of admixture in hybrid zones. We studied three environmentally distinct contact zones where morphologically and reproductively divergent subspecies of Salamandra salamandra co-occur: the pueriparous S. s. bernardezi that is mostly parapatric to its three larviparous subspecies neighbours. We used a landscape genetics framework to: (i) characterise the spatial location and extent of each contact zone; (ii) assess patterns of introgression and hybridization between subspecies pairs; and (iii) examine the role of environmental heterogeneity in the evolutionary dynamics of hybrid zones. We found high levels of introgression between parity modes, and between distinct phenotypes, thus demonstrating the evolution to pueriparity alone or morphological differentiation do not lead to reproductive isolation between these highly divergent S. salamandra morphotypes. However, we detected substantial variation in patterns of hybridization across contact zones, being lower in the contact zone located on a topographically complex area. We highlight the importance of accounting for spatial environmental heterogeneity when studying evolutionary dynamics of hybrid zones.

The critical role of the coordination sphere in the high-efficiency blue-light emission from aminopyrazine metal-organic polymers

2021 ◽  
Vol 186 ◽  
pp. 109025
Author(s):  
João Humberto Dias Campos ◽  
Meiry Edivirges Alvarenga ◽  
Maykon Alves Lemes ◽  
José Antônio do Nascimento Neto ◽  
Freddy Fernandes Guimarães ◽  
...  
Keyword(s):  
Blue Light ◽  
Coordination Sphere ◽  
High Efficiency ◽  
Light Emission ◽  
Critical Role ◽  
Organic Polymers ◽  
Blue Light Emission ◽  
Metal Organic
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