Current status and applications of genome-scale metabolic models
Genome-scale metabolic models (GEMs) computationally describe gene-protein-reaction
associations for entire metabolic genes in an organism, and can be simulated to predict …
associations for entire metabolic genes in an organism, and can be simulated to predict …
The limits of enzyme specificity and the evolution of metabolism
A Peracchi - Trends in biochemical sciences, 2018 - cell.com
The substrate specificity of enzymes is bound to be imperfect, because of unavoidable
physicochemical limits. In extant metabolic enzymes, furthermore, such limits are seldom …
physicochemical limits. In extant metabolic enzymes, furthermore, such limits are seldom …
Vitamin B6 metabolism in microbes and approaches for fermentative production
J Rosenberg, T Ischebeck, FM Commichau - Biotechnology advances, 2017 - Elsevier
Vitamin B6 is a designation for the six vitamers pyridoxal, pyridoxine, pyridoxamine,
pyridoxal 5′-phosphate (PLP), pyridoxine 5′-phosphate, and pyridoxamine. PLP, being …
pyridoxal 5′-phosphate (PLP), pyridoxine 5′-phosphate, and pyridoxamine. PLP, being …
Advances in gap-filling genome-scale metabolic models and model-driven experiments lead to novel metabolic discoveries
S Pan, JL Reed - Current opinion in biotechnology, 2018 - Elsevier
Highlights•Gap-filling is an important tool for making model-driven metabolic
discoveries.•Recent gap-filling algorithms are more efficient and/or show superior …
discoveries.•Recent gap-filling algorithms are more efficient and/or show superior …
Evolution of enzyme superfamilies: comprehensive exploration of sequence–function relationships
The sequence and functional diversity of enzyme superfamilies have expanded through
billions of years of evolution from a common ancestor. Understanding how protein sequence …
billions of years of evolution from a common ancestor. Understanding how protein sequence …
Systems biology based metabolic engineering for non-natural chemicals
Production of chemicals in microorganisms is no longer restricted to products arising from
native metabolic potential. In this review, we highlight the evolution of metabolic engineering …
native metabolic potential. In this review, we highlight the evolution of metabolic engineering …
Underground metabolism: network-level perspective and biotechnological potential
Highlights•High-throughput technologies drive the discovery of underground enzyme
activities.•Novel computational approaches complement the high-throughput technologies.• …
activities.•Novel computational approaches complement the high-throughput technologies.• …
A Survey of Pyridoxal 5′-Phosphate-Dependent Proteins in the Gram-Positive Model Bacterium Bacillus subtilis
B Richts, J Rosenberg, FM Commichau - Frontiers in molecular …, 2019 - frontiersin.org
The B6 vitamer pyridoxal 5′-phosphate (PLP) is a co-factor for proteins and enzymes that
are involved in diverse cellular processes. Therefore, PLP is essential for organisms from all …
are involved in diverse cellular processes. Therefore, PLP is essential for organisms from all …
Underground isoleucine biosynthesis pathways in E. coli
The promiscuous activities of enzymes provide fertile ground for the evolution of new
metabolic pathways. Here, we systematically explore the ability of E. coli to harness …
metabolic pathways. Here, we systematically explore the ability of E. coli to harness …
Underground metabolism facilitates the evolution of novel pathways for vitamin B6 biosynthesis
B Richts, FM Commichau - Applied Microbiology and Biotechnology, 2021 - Springer
The term vitamin B6 is a designation for the vitamers pyridoxal, pyridoxamine, pyridoxine
and the respective phosphate esters pyridoxal-5′-phosphate (PLP), pyridoxamine-5 …
and the respective phosphate esters pyridoxal-5′-phosphate (PLP), pyridoxamine-5 …