Tatsinine

19966064

In an attempt to understand whether it should be expected that some genes tend to be used disproportionately often by natural selection, we investigated two related phenomena: the evolution of flux control among enzymes in a metabolic pathway and properties of adaptive substitutions in pathway enzymes. These two phenomena are related by the principle that adaptive substitutions should occur more frequently in enzymes with greater flux control. Predicting which enzymes will be preferentially involved in adaptive evolution thus requires an evolutionary theory of flux control. We investigated the evolution of enzyme control in metabolic pathways with two models of enzyme kinetics: metabolic control theory (MCT) and Michaelis-Menten saturation kinetics (SK). Our models generate two main predictions for pathways in which reactions are moderately to highly irreversible: (1) flux control will evolve to be highly unequal among enzymes in a pathway and (2) upstream enzymes evolve a greater control coefficient then those downstream. This results in upstream enzymes fixing the majority of beneficial mutations during adaptive evolution. Once the population has reached high fitness, the trend is reversed, with the majority of neutral/slightly deleterious mutations occurring in downstream enzymes. These patterns are the result of three factors (the first of these is unique to the MCT simulations while the other two seem to be general properties of the metabolic pathways): (1) the majority of randomly selected, starting combinations of enzyme kinetic rates generate pathways that possess greater control for the upstream enzymes compared to downstream enzymes; (2) selection against large pools of intermediate substrates tends to prevent majority control by downstream enzymes; and (3) equivalent mutations in enzyme kinetic rates have the greatest effect on flux for enzymes with high levels of flux control, and these enzymes will accumulate adaptive substitutions, strengthening their control. Prediction 1 is well supported by available data on control coefficients. Data for evaluating prediction 2 are sparse but not inconsistent with this prediction

The Evolution of Control and Distribution of Adaptive Mutations in a Metabolic Pathway

Kevin M. Wright1 and Mark D. Rausher

2010 Feb;

26864432

The genus Trichoderma contains fungi with high relevance for humans, with applications in enzyme production for plant cell wall degradation and use in biocontrol. Here, we provide a broad, comprehensive overview of the genomic content of these species for “hot topic” research aspects, including CAZymes, transport, transcription factors, and development, along with a detailed analysis and annotation of less-studied topics, such as signal transduction, genome integrity, chromatin, photobiology, or lipid, sulfur, and nitrogen metabolism in T. reesei, T. atroviride, and T. virens, and we open up new perspectives to those topics discussed previously. In total, we covered more than 2,000 of the predicted 9,000 to 11,000 genes of each Trichoderma species discussed, which is >20% of the respective gene content. Additionally, we considered available transcriptome data for the annotated genes. Highlights of our analyses include overall carbohydrate cleavage preferences due to the different genomic contents and regulation of the respective genes. We found light regulation of many sulfur metabolic genes. Additionally, a new Golgi 1,2-mannosidase likely involved in N-linked glycosylation was detected, as were indications for the ability of Trichoderma spp. to generate hybrid galactose-containing N-linked glycans. The genomic inventory of effector proteins revealed numerous compounds unique to Trichoderma, and these warrant further investigation. We found interesting expansions in the Trichoderma genus in several signaling pathways, such as G-protein-coupled receptors, RAS GTPases, and casein kinases. A particularly interesting feature absolutely unique to T. atroviride is the duplication of the alternative sulfur amino acid synthesis pathway.

The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species

Monika Schmoll,corresponding authora,*Christoph Dattenbock,a Nohemi Carreras-VillaseNor,b Artemio Mendoza-Mendoza,c Doris Tisch,d Mario Ivan Aleman,e Scott E. Baker,f Christopher Brown,g Mayte Guadalupe Cervantes-Badillo,h Jose Cetz-Chel,b Gema Rosa Cristobal-Mondragon,h Luis Delaye,e Edgardo Ulises Esquivel-Naranjo,b,* Alexa Frischmann,d Jose de Jesus Gallardo-Negrete,h Monica Garcia-Esquivel,b Elida Yazmin Gomez-Rodriguez,h David R. Greenwood,i Miguel Hernandez-ONate,b,* Joanna S. Kruszewska,j Robert Lawry,c Hector M. Mora-Montes,k Tania MuNoz-Centeno,h Maria Fernanda Nieto-Jacobo,c Guillermo Nogueira Lopez,c Vianey Olmedo-Monfil,k Macario Osorio-Concepcion,h Sebastian Piłsyk,j Kyle R. Pomraning,f Aroa Rodriguez-Iglesias,a Maria Teresa Rosales-Saavedra,h J. Alejandro Sanchez-Arreguin,b Verena Seidl-Seiboth,d Alison Stewart,l Edith Elena Uresti-Rivera,h Chih-Li Wang,m Ting-Fang Wang,n Susanne Zeilinger,d,o Sergio Casas-Flores,h and Alfredo Herrera-Estrellacorresponding authorb,*

2016 Mar;