Exploring the past and the future of protein evolution with ancestral sequence reconstruction: the 'retro'approach to protein engineering

Y Gumulya, EMJ Gillam - Biochemical Journal, 2017 - portlandpress.com
A central goal in molecular evolution is to understand the ways in which genes and proteins
evolve in response to changing environments. In the absence of intact DNA from fossils …

How to resurrect ancestral proteins as proxies for ancient biogeochemistry

AK Garcia, B Kaçar - Free Radical Biology and Medicine, 2019 - Elsevier
Throughout the history of life, enzymes have served as the primary molecular mediators of
biogeochemical cycles by catalyzing the metabolic pathways that interact with geochemical …

Evolution of chalcone isomerase from a noncatalytic ancestor

M Kaltenbach, JR Burke, M Dindo, A Pabis… - Nature chemical …, 2018 - nature.com
The emergence of catalysis in a noncatalytic protein scaffold is a rare, unexplored event.
Chalcone isomerase (CHI), a key enzyme in plant flavonoid biosynthesis, is presumed to …

Evolution of bacterial steroid biosynthesis and its impact on eukaryogenesis

Y Hoshino, EA Gaucher - Proceedings of the National …, 2021 - National Acad Sciences
Steroids are components of the eukaryotic cellular membrane and have indispensable roles
in the process of eukaryotic endocytosis by regulating membrane fluidity and permeability. In …

High performance crystalline nanocellulose using an ancestral endoglucanase

B Alonso-Lerma, L Barandiaran, L Ugarte… - Communications …, 2020 - nature.com
Improving the efficiency of enzymes towards decomposing substrates has been one of the
central goals in the biotechnology industry. However, the modification of enzymes for …

Structure, mechanism, and evolution of the last step in vitamin C biosynthesis

A Boverio, N Jamil, B Mannucci, ML Mascotti… - Nature …, 2024 - nature.com
Photosynthetic organisms, fungi, and animals comprise distinct pathways for vitamin C
biosynthesis. Besides this diversity, the final biosynthetic step consistently involves an …

Manipulating conformational dynamics to repurpose ancient proteins for modern catalytic functions

JM Gardner, M Biler, VA Risso, JM Sanchez-Ruiz… - ACS …, 2020 - ACS Publications
Conformational flexibility plays a critical role in enzyme function and regulation.
Conformational changes, which can occur on multiple length and time scales, facilitate, for …

Alignment modulates ancestral sequence reconstruction accuracy

RA Vialle, AU Tamuri, N Goldman - Molecular biology and …, 2018 - academic.oup.com
Accurate reconstruction of ancestral states is a critical evolutionary analysis when studying
ancient proteins and comparing biochemical properties between parental or extinct species …

Evolutionary gain and loss of a plant pattern-recognition receptor for HAMP recognition

S Snoeck, BW Abramson, AGK Garcia, AN Egan… - Elife, 2022 - elifesciences.org
As a first step in innate immunity, pattern recognition receptors (PRRs) recognize the distinct
pathogen and herbivore-associated molecular patterns and mediate activation of immune …

Highly thermostable carboxylic acid reductases generated by ancestral sequence reconstruction

A Thomas, R Cutlan, W Finnigan… - Communications …, 2019 - nature.com
Carboxylic acid reductases (CARs) are biocatalysts of industrial importance. Their
properties, especially their poor stability, render them sub-optimal for use in a bioindustrial …