Evolutionary dynamics of natural product biosynthesis in bacteria

MG Chevrette, K Gutiérrez-García… - Natural product …, 2020 - pubs.rsc.org
Covering: 2008 up to 2019 The forces of biochemical adaptive evolution operate at the level
of genes, manifesting in complex phenotypes and the global biodiversity of proteins and …

A bird's-eye view of enzyme evolution: chemical, physicochemical, and physiological considerations

D Davidi, LM Longo, J Jabłońska, R Milo… - Chemical …, 2018 - ACS Publications
Enzymes catalyze a vast range of reactions. Their catalytic performances, mechanisms,
global folds, and active-site architectures are also highly diverse, suggesting that enzymes …

[HTML][HTML] Enzyme evolution: innovation is easy, optimization is complicated

MS Newton, VL Arcus, ML Gerth, WM Patrick - Current Opinion in Structural …, 2018 - Elsevier
Highlights•Enzyme 'promiscuity space'is vast.•Functional innovation by divergent evolution
is easy.•Gene loss is also an important driver of enzyme evolution.•Evolutionary trajectories …

Social network analysis methods for exploring SARS-CoV-2 contact tracing data

K Nagarajan, M Muniyandi, B Palani… - BMC medical research …, 2020 - Springer
Background Contact tracing data of severe acute respiratory syndrome coronavirus 2 (SARS-
CoV-2) pandemic is used to estimate basic epidemiological parameters. Contact tracing …

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 …

How enzyme promiscuity and horizontal gene transfer contribute to metabolic innovation

ME Glasner, DP Truong, BC Morse - The FEBS journal, 2020 - Wiley Online Library
Promiscuity is the coincidental ability of an enzyme to catalyze its native reaction and
additional reactions that are not biological functions in the same active site. Promiscuity …

The sphingolipid anteome: implications for evolution of the sphingolipid metabolic pathway

TCB Santos, T Dingjan, AH Futerman - FEBS letters, 2022 - Wiley Online Library
Modern cell membranes contain a bewildering complexity of lipids, among them
sphingolipids (SLs). Advances in mass spectrometry have led to the realization that the …

Complex Loop Dynamics Underpin Activity, Specificity, and Evolvability in the (βα)8 Barrel Enzymes of Histidine and Tryptophan Biosynthesis

A Romero-Rivera, M Corbella, A Parracino, WM Patrick… - JACS Au, 2022 - ACS Publications
Enzymes are conformationally dynamic, and their dynamical properties play an important
role in regulating their specificity and evolvability. In this context, substantial attention has …

Distal mutations in the β-clamp of DNA polymerase III* disrupt DNA orientation and affect exonuclease activity

MB Berger, GA Cisneros - Journal of the American Chemical …, 2023 - ACS Publications
DNA polymerases are responsible for the replication and repair of DNA found in all DNA-
based organisms. DNA Polymerase III is the main replicative polymerase of E. coli and is …

Rhodococcus comparative genomics reveals a phylogenomic-dependent non-ribosomal peptide synthetase distribution: insights into biosynthetic gene cluster …

A Undabarrena, R Valencia, A Cumsille… - Microbial …, 2021 - microbiologyresearch.org
Natural products (NPs) are synthesized by biosynthetic gene clusters (BGCs), whose genes
are involved in producing one or a family of chemically related metabolites. Advances in …