Light-Controlled Fermentations for Microbial Chemical and Protein Production

Summary

Optogenetic control of microbial metabolism offers flexible dynamic control over fermentation processes. The protocol here shows how to set up blue light-regulated fermentations for chemical and protein production at different volumetric scales.

Abstract

Microbial cell factories offer a sustainable alternative for producing chemicals and recombinant proteins from renewable feedstocks. However, overburdening a microorganism with genetic modifications can reduce host fitness and productivity. This problem can be overcome by using dynamic control: inducible expression of enzymes and pathways, typically using chemical- or nutrient-based additives, to balance cellular growth and production. Optogenetics offers a non-invasive, highly tunable, and reversible method of dynamically regulating gene expression. Here, we describe how to set up light-controlled fermentations of engineered Escherichia coli and Saccharomyces cerevisiae for the production of chemicals or recombinant proteins. We discuss how to apply light at selected times and dosages to decouple microbial growth and production for improved fermentation control and productivity, as well as the key optimization considerations for best results. Additionally, we describe how to implement light controls for lab-scale bioreactor experiments. These protocols facilitate the adoption of optogenetic controls in engineered microorganisms for improved fermentation performance.

Introduction

Optogenetics, the control of biological processes with light-responsive proteins, offers a new strategy to dynamically control microbial fermentations for chemical and protein production^1,2. The burden of engineered metabolic pathways and the toxicity of some intermediates and products often impairs cell growth³. Such stresses can lead to poor biomass accumulation and reduced productivity³. This challenge can be addressed by temporally dividing fermentations into a growth and production phase, which devote metabolic resources to biomass accumulation or product sy....

Protocol

1. Light-controlled chemical production using the S. cerevisiae OptoINVRT7 circuit

1. Strain construction
   1. Obtain a strain with his3 auxotrophy, as this marker is necessary for most existing OptoINVRT plasmids⁵. If seeking optogenetic regulation of a gene that is native to S. cerevisiae, construct a strain in which any endogenous copy of the gene is deleted.
   2. Linearize the plasmid containing the OptoINVRT7 circuit, such as EZ-L439⁵, and integrate it into the his3-locus of the auxotrophic strain using standard lithium-acetate transfor....

Results

Optogenetic regulation of microbial metabolism has been successfully implemented to produce a variety of products, including biofuels, bulk chemicals, proteins, and natural products^5,6,7,12,13. Most of these processes are designed for cell growth to occur in the light (when low cell density poses minimal challenges with light penetration), and for production t.......

Discussion

Dynamic control has long been applied to improve yields for metabolic engineering and recombinant protein production⁴. Shifts in enzymatic expression are most typically implemented using chemical inducers such as IPTG²¹, galactose²², and tetracycline²³, but have also been mediated using process conditions such as temperature and pH. Optogenetic control of gene expression eliminates the need for changes to fermentation paramete.......

Materials

Name	Company	Catalog Number	Comments
Light-controlled chemical production using S. cerevisiae
24-well culture plate	USA Scientific	CC7672-7524
Agar powder	Thermo Fisher Scientific	303991049
Aluminum foil	Reynolds	B004NG90YO
BioSpectrometer with μcuvette	Eppendorf	6135000923
Blue LED panel	HQRP	884667106091218
EZ-L439 OptoINVRT7 Plasmid	N/A	N/A	See Reference 1
Glucose	Thermo Fisher Scientific	501879892 (G8270-5KG)
Microcentrifuge	Thermo Fisher Scientific	75002403
Microcentrifuge tubes	USA Scientific	1615-5510
Orbital Shaker	Yamato Scientific America	SOU-300
Petri dish	Celltreat	229656
PmeI	New England Biolabs	R0560L
Quantum meter	Apogee Instruments	MQ-510
Replica-plating device	Thomas Scientific	F37848-0000
Replica-plating pads	Sunrise Science Products	3005-012
SC-His powder	Sunrise Science Products	1303-030
SC Complete powder	Sunrise Science Products	1459-100
Sterile sealing film	Excel Scientific	STR-SEAL-PLT
YPD agar plates	VWR	100217-054
Zeocin	Thermo Fisher Scientific	R25005
Light-controlled protein production using E. coli
6X SDS Sample Buffer	Cepham Life Sciences	10502
12% Acrylamide protein gels	Thermo Fisher Scientific	NP0341BOX
24-well culture plate	USA Scientific	CC7672-7524
Aluminum foil	Reynolds	B004NG90YO
BioSpectrometer with μcuvette	Eppendorf	6135000923
Blue LED panel	HQRP	884667106091218
Coomassie Brilliant Blue G-250	Thermo Fisher Scientific	20279
Electrophoresis cell	Bio-Rad	1658004
Electrophoresis power supply	Bio-Rad	1645050
LB broth (Miller)	Fisher Scientific	BP97235
Microcentrifuge	Thermo Fisher Scientific	75002403
Microcentrifuge tubes	USA Scientific	1615-5510
NaCl	Thomas Scientific	SX0425-1
OptoLAC plasmids	N/A	N/A	See Reference 2
Orbital Shaker	Yamato Scientific America	SOU-300
Petri dish	Celltreat	229656
Quantum meter	Apogee Instruments	MQ-510
SOC medium	Thermo Fisher Scientific	15544034
Thermomixer	Eppendorf	5382000015
Tris base	Fisher Scientific	BP1521
Three-phase fermentation using S. cerevisiae
Same materials as "Light-controlled chemical production using S. cerevisiae" protocol plus the following:
EZ-L580 OptoAMP4 Plasmid	N/A	N/A	See Reference 10
Chemical production in a light-controlled bioreactor
Aluminum foil	Reynolds	B004NG90YO
Antifoam	Sigma-Aldrich	A8311
Bioreactor with control station	Eppendorf	B120110001
BioSpectrometer with μcuvette	Eppendorf	6135000923
Bleach	VWR Scientific	89501-620 (CS)
Blue LED panel	HQRP	884667106091218
BPT tubing	Fisher Scientific	14-170-15
Glucose	Thermo Fisher Scientific	501879892 (G8270-5KG)
Hydrochloric acid (HCl)	Fisher Scientific	7647-01-0
M9 Minimal Salts	Thermo Fisher Scientific	A1374401
Microcentrifuge	Thermo Fisher Scientific	75002403
Microcentrifuge tubes	USA Scientific	1615-5510
NH4OH Solution	Sigma-Aldrich	I0503-1VL
Orbital Shaker	Yamato Scientific America	SOU-300
Quantum meter	Apogee Instruments	MQ-510
SC Complete powder	Sunrise Science Products	1459-100