scholarly journals The Recruitment Model of Metabolic Evolution: Jasmonate-Responsive Transcription Factors and a Conceptual Model for the Evolution of Metabolic Pathways

2019 ◽  
Vol 10 ◽  
Author(s):  
Tsubasa Shoji
Keyword(s):  
Transcription Factors ◽  
Conceptual Model ◽  
Metabolic Pathways ◽  
Metabolic Evolution ◽  
Evolution Of Metabolic Pathways ◽  
Recruitment Model

scholarly journals In Silico Evolution of Early Metabolism

2011 ◽  
Vol 17 (2) ◽  
pp. 87-108 ◽  
Author(s):  
Alexander Ullrich ◽  
Markus Rohrschneider ◽  
Gerik Scheuermann ◽  
Peter F. Stadler ◽  
Christoph Flamm
Keyword(s):  
Metabolic Pathways ◽  
Genetic System ◽  
Simulation Tool ◽  
Metabolic Evolution ◽  
Metabolic System ◽  
Evolution Of Metabolic Pathways ◽  
Core Set ◽  
Catalytically Active ◽  
Almost Open ◽  
In Silico Evolution

We developed a simulation tool for investigating the evolution of early metabolism, allowing us to speculate on the formation of metabolic pathways from catalyzed chemical reactions and on the development of their characteristic properties. Our model consists of a protocellular entity with a simple RNA-based genetic system and an evolving metabolism of catalytically active ribozymes that manipulate a rich underlying chemistry. Ensuring an almost open-ended and fairly realistic simulation is crucial for understanding the first steps in metabolic evolution. We show here how our simulation tool can be helpful in arguing for or against hypotheses on the evolution of metabolic pathways. We demonstrate that seemingly mutually exclusive hypotheses may well be compatible when we take into account that different processes dominate different phases in the evolution of a metabolic system. Our results suggest that forward evolution shapes metabolic network in the very early steps of evolution. In later and more complex stages, enzyme recruitment supersedes forward evolution, keeping a core set of pathways from the early phase.

scholarly journals DIRECTED EVOLUTION OF METABOLIC PATHWAYS IN MICROBIAL POPULATIONS. I. MODIFICATION OF THE ACID PHOSPHATASE pH OPTIMUM IN S. CEREVISIAE

Genetics ◽  
1972 ◽  
Vol 70 (1) ◽  
pp. 59-73 ◽  
Author(s):  
J C Francis ◽  
P E Hansche
Keyword(s):  
Acid Phosphatase ◽  
Metabolic Pathways ◽  
Experimental System ◽  
Microbial Populations ◽  
Kinetic Properties ◽  
Mutational Event ◽  
Ph Optimum ◽  
Functional Changes ◽  
Evolution Of Metabolic Pathways ◽  
Wide Range

ABSTRACT An experimental system for directing the evolution of enzymes and metabolic pathways in microbial populations is proposed and an initial test of its power is provided.—The test involved an attempt to genetically enhance certain functional properties of the enzyme acid phosphatase in S. cerevisiae by constructing an environment in which the functional changes desired would be "adaptive". Naturally occurring mutations in a population of 109 cells were automatically and continuously screened, over 1,000 generations, for their effect on the efficiency (Km) and activity of acid phosphatase at pH 6, and for their effect on the efficiency of orthophosphate metabolism.—The first adaptation observed, M1, was due to a single mutational event that effected a 30% increase in the efficiency of orthophosphate metabolism. The second, M2, effected an adaptive shift in the pH optimum of acid phosphatase and an increase in its activity over a wide range of pH values (an increment of 60% at pH 6). M2 was shown to result from a single mutational event in the region of the acid phosphatase structural gene. The third, M3, effected cell clumping, an adaptation to the culture apparatus that had no effect on phosphate metabolism.—The power of this system for directing the evolution of enzymes and of metabolic pathways is discussed in terms of the kinetic properties of the experimental system and in terms of the results obtained.

Directed evolution of metabolic pathways

2006 ◽  
Vol 24 (1) ◽  
pp. 28-38 ◽  
Author(s):  
Ranjini Chatterjee ◽  
Ling Yuan
Keyword(s):  
Directed Evolution ◽  
Metabolic Pathways ◽  
Evolution Of Metabolic Pathways

scholarly journals Deep Proteomics of Mouse Skeletal Muscle Enables Quantitation of Protein Isoforms, Metabolic Pathways, and Transcription Factors

2015 ◽  
Vol 14 (4) ◽  
pp. 841-853 ◽  
Author(s):  
Atul S. Deshmukh ◽  
Marta Murgia ◽  
Nagarjuna Nagaraj ◽  
Jonas T. Treebak ◽  
Jürgen Cox ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Transcription Factors ◽  
Metabolic Pathways ◽  
Protein Isoforms ◽  
Mouse Skeletal Muscle

scholarly journals Adaptive Evolution of Metabolic Pathways in Drosophila

2007 ◽  
Vol 24 (6) ◽  
pp. 1347-1354 ◽  
Author(s):  
J. Flowers ◽  
E Sezgin ◽  
S Kumagai ◽  
D. Duvernell ◽  
L. Matzkin ◽  
...  
Keyword(s):  
Adaptive Evolution ◽  
Metabolic Pathways ◽  
Evolution Of Metabolic Pathways

scholarly journals Adaptive Evolution of Metabolic Pathways in Drosophila

2007 ◽  
Vol 24 (7) ◽  
pp. 1575-1575 ◽  
Author(s):  
J. Flowers ◽  
E Sezgin ◽  
S Kumagai ◽  
D. Duvernell ◽  
L. Matzkin ◽  
...  
Keyword(s):  
Adaptive Evolution ◽  
Metabolic Pathways ◽  
Evolution Of Metabolic Pathways

ASSESSING OPTIMAL DESIGNS IN METABOLIC PATHWAYS

1995 ◽  
Vol 03 (01) ◽  
pp. 197-206 ◽  
Author(s):  
J. PUIGJANER ◽  
M. CASCANTE ◽  
A. SORRIBAS
Keyword(s):  
Metabolic Pathways ◽  
Reaction Network ◽  
Metabolic Control Analysis ◽  
Optimal Designs ◽  
Control Analysis ◽  
Chemical Transformations ◽  
Evolution Of Metabolic Pathways ◽  
Biochemical Systems ◽  
Optimum Reaction ◽  
Alternative Designs

The evolution of metabolic pathways is characterized by the search of the optimum reaction network, both as for chemical transformations and for the associated pattern of regulation. Understanding this process requires the evaluation of alternative designs for a given function. After this evaluation, we would be in a good situation for drawing general conclusions on the evolution of the considered system. This goal can be undertaken by means of different complementary approaches. The method of Control Comparisons, first developed within Biochemical Systems Analysis, has produced some valuable insights on this kind of problems. In this contribution, we present this method within the context of Metabolic Control Analysis.

In vivo evolution of metabolic pathways by homeologous recombination in mitotic cells

2014 ◽  
Vol 23 ◽  
pp. 123-135 ◽  
Author(s):  
Alejandro Luque ◽  
Sarra C. Sebai ◽  
Beatrix Santiago-Schübel ◽  
Yann Le Coz ◽  
Delphine Jenot ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Evolution Of Metabolic Pathways ◽  
Homeologous Recombination ◽  
Mitotic Cells
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