Evolutionary Approaches for Engineering Industrially Relevant Phenotypes in Bacterial Cell Factories

Abstract

The bio‐based production of added‐value compounds (with applications as pharmaceuticals, biofuels, food ingredients, and building blocks) using bacterial platforms is a well‐established industrial activity. The design and construction of microbial cell factories (MCFs) with robust and stable industrially relevant phenotypes, however, remains one of the biggest challenges of contemporary biotechnology. In this review, traditional and cutting‐edge approaches for optimizing the performance of MCFs for industrial bioprocesses, rooted on the engineering principle of natural evolution (i.e., genetic variation and selection), are discussed. State‐of‐the‐art techniques to manipulate and increase genetic variation in bacterial populations and to construct combinatorial libraries of strains, both globally (i.e., genome level) and locally (i.e., individual genes or pathways, and entire sections and gene clusters of the bacterial genome) are presented. Cutting‐edge screening and selection technologies applied to isolate MCFs displaying enhanced phenotypes are likewise discussed. The review article is closed by presenting future trends in the design and construction of a new generation of MCFs that will contribute to the long‐sought‐after transformation from a petrochemical industry to a veritable sustainable bio‐based industry.

Non‐invasive, ratiometric determination of intracellular pH in Pseudomonas species using a novel genetically encoded indicator

“…Simple approaches for the online assessment of intracellular properties such as pH i will thus enable both fundamental and applied studies, e.g. biosensor‐based evolution of phenotypic traits (Fernández‐Cabezón et al ., ).…”

The emergence of adaptive laboratory evolution as an efficient tool for biological discovery and industrial biotechnology

“…The review will also touch on the emergence of automation and bioinformatics in the field and the impact this has had. Previous reviews relating to ALE have addressed the underlying genetic and metabolic basis for adaptive evolution experiments (Conrad et al, 2011;Gresham and Dunham, 2014;Long et al, 2015;Remigi et al, 2019), the role of systems biology and in silico evolution (Hansen et al, 2017;Hindré et al, 2012;Papp et al, 2011), overall strategies to improve metabolic performance (Rabbers et al, 2015;Shepelin et al, 2018;Williams et al, 2016) and tolerance (Peabody et al, 2014), as well as other industrially relevant strain properties (Bachmann et al, 2015;Dragosits and Mattanovich, 2013;Portnoy et 5 al., 2011/8;Stella et al, 2019;Fernández-Cabezón et al, 2019). This work provides an updated review and categorization of studies useful for metabolic engineering, as well as other selected foundational studies using laboratory evolution that are relevant to industrial biotechnology.…”

A fluoride-responsive genetic circuit enables in vivo biofluorination in engineered Pseudomonas putida

“…Efficient bioproduction of chemicals demands significant efforts to reduce costs derived, among other factors, from the additives needed for protein expression (e.g., inducers or antibiotics) 25 . Riboswitches are regulatory elements found in the 5′-UTR of bacterial mRNAs, exerting post-transcriptional control of gene expression upon binding to a specific metabolite 26 .…”