skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Challenges and Opportunities in Biological Funneling of Heterogeneous and Toxic Substrates Beyond Lignin

Journal Article · · Current Opinion in Biotechnology

Significant developments in the understanding and manipulation of microbial metabolism have enabled the use of engineered biological systems toward a more sustainable energy and materials economy. While developments in metabolic engineering have primarily focused on the conversion of carbohydrates, substantial opportunities exist for using these same principles to extract value from more heterogeneous and toxic waste streams, such as those derived from lignin, biomass pyrolysis, or industrial waste. Funneling heterogeneous substrates from these streams toward valuable products, termed biological funneling, presents new challenges in balancing multiple catabolic pathways competing for shared cellular resources and engineering against perturbation from toxic substrates. Solutions to many of these challenges have been explored within the field of lignin valorization. This perspective aims to extend beyond lignin to highlight the challenges and discuss opportunities for use of biological systems to upgrade previously inaccessible waste streams.

Research Organization:
National Renewable Energy Lab. (NREL), Golden, CO (United States)
Sponsoring Organization:
USDOE Office of Energy Efficiency and Renewable Energy (EERE), Transportation Office. Bioenergy Technologies Office
DOE Contract Number:
DE-AC36-08GO28308
OSTI ID:
1808495
Report Number(s):
NREL/JA-2A00-80221; MainId:42424; UUID:66e685ae-ca4a-4992-8c14-c493793e6789; MainAdminID:25797
Journal Information:
Current Opinion in Biotechnology, Vol. 73
Country of Publication:
United States
Language:
English

References (127)

Engineering Cellular Metabolism journal March 2016
Engineering microbial pathways for production of bio-based chemicals from lignocellulosic sugars: current status and perspectives journal July 2020
Mutant phenotypes for thousands of bacterial genes of unknown function journal May 2018
Bioremediation 3 . 0 : Engineering pollutant-removing bacteria in the times of systemic biology journal November 2017
Removing environmental organic pollutants with bioremediation and phytoremediation journal February 2014
Distillery Stillage: Characteristics, Treatment, and Valorization journal June 2020
Valorizing a hydrothermal liquefaction aqueous phase through co-production of chemicals and lipids using the oleaginous yeast Yarrowia lipolytica journal October 2020
Valorization of Food and Agricultural Waste: A Step towards Greener Future journal December 2018
Lignin valorization through integrated biological funneling and chemical catalysis journal August 2014
Valorization of pyrolysis water: a biorefinery side stream, for 1,2-propanediol production with engineered Corynebacterium glutamicum journal November 2017
Evaluation of small organic acids present in fast pyrolysis bio‐oil from lignocellulose as feedstocks for bacterial bioconversion journal May 2019
Characterization of lignin monomers in low rank coal humic acids using the derivatization/reductive cleavage method journal September 2010
Biological approaches for treatment of distillery wastewater: A review journal September 2007
Opportunities and challenges in biological lignin valorization journal December 2016
Chemicals from lignin: an interplay of lignocellulose fractionation, depolymerisation, and upgrading journal January 2018
Recent advances in lignin valorization with bacterial cultures: microorganisms, metabolic pathways, and bio-products journal February 2019
Biotechnological Perspectives of Pyrolysis Oil for a Bio-Based Economy journal October 2017
Catalytic Fast Pyrolysis: A Review journal January 2013
Valorization of aqueous waste streams from thermochemical biorefineries journal January 2019
Aqueous Stream Characterization from Biomass Fast Pyrolysis and Catalytic Fast Pyrolysis journal September 2016
Characterization and Catalytic Upgrading of Aqueous Stream Carbon from Catalytic Fast Pyrolysis of Biomass journal November 2017
Drying and depolymerization technologies of Zhaotong lignite: A review journal April 2019
Analysis of chemical characteristics of lignite upgrading wastewater and its agricultural utilization journal April 2020
Plastic waste as a novel substrate for industrial biotechnology: Plastic waste as substrate for biotechnology journal August 2015
An engineered PET depolymerase to break down and recycle plastic bottles journal April 2020
Characterization and engineering of a two-enzyme system for plastics depolymerization journal September 2020
Defined Microbial Mixed Culture for Utilization of Polyurethane Monomers journal November 2020
Conversion of post consumer polyethylene to the biodegradable polymer polyhydroxyalkanoate journal January 2014
Development of a bioprocess to convert PET derived terephthalic acid and biodiesel derived glycerol to medium chain length polyhydroxyalkanoate journal May 2012
Waste paper for recycling: Overview and identification of potentially critical substances journal November 2015
A critical review on textile wastewater treatments: Possible approaches journal November 2016
Textile dye wastewater characteristics and constituents of synthetic effluents: a critical review journal November 2018
The effect of phenolic acids and molasses spent wash concentration on distillery wastewater remediation by fungi journal November 1998
Product based evaluation of pyrolysis of food waste and its digestate journal December 2015
Adipic acid production from lignin journal January 2015
Chasing bacterial chassis for metabolic engineering: a perspective review from classical to non-traditional microorganisms journal June 2018
Innovative Chemicals and Materials from Bacterial Aromatic Catabolic Pathways journal June 2019
From lignin to nylon: Cascaded chemical and biochemical conversion using metabolically engineered Pseudomonas putida journal May 2018
Fatty Acid and Alcohol Metabolism in Pseudomonas putida: Functional Analysis Using Random Barcode Transposon Sequencing journal October 2020
Complete Genome Sequence of Sphingobium sp. Strain SYK-6, a Degrader of Lignin-Derived Biaryls and Monoaryls journal December 2011
Metabolic engineering of Corynebacterium glutamicum for the production of cis, cis-muconic acid from lignin journal July 2018
Multi-omic elucidation of aromatic catabolism in adaptively evolved Rhodococcus opacus journal September 2018
Towards lignin consolidated bioprocessing: simultaneous lignin depolymerization and product generation by bacteria journal January 2015
Base-Catalyzed Depolymerization of Solid Lignin-Rich Streams Enables Microbial Conversion journal August 2017
Thermochemical wastewater valorization via enhanced microbial toxicity tolerance journal January 2018
Bacterial contributions to delignification and lignocellulose degradation in forest soils with metagenomic and quantitative stable isotope probing journal September 2018
Removal of aromatic inhibitors produced from lignocellulosic hydrolysates by Acinetobacter baylyi ADP1 with formation of ethanol by Kluyveromyces marxianus journal April 2019
Better together: engineering and application of microbial symbioses journal December 2015
Synthetic microbial communities of heterotrophs and phototrophs facilitate sustainable growth journal July 2020
Modeling microbial communities from atrazine contaminated soils promotes the development of biostimulation solutions journal October 2018
Microbial mutualism dynamics governed by dose-dependent toxicity of cross-fed nutrients journal November 2016
SEVA 3.0: an update of the Standard European Vector Architecture for enabling portability of genetic constructs among diverse bacterial hosts journal November 2019
Bacterial Genetic Engineering by Means of Recombineering for Reverse Genetics journal September 2020
Improved bacterial recombineering by parallelized protein discovery journal May 2020
Development of a high efficiency integration system and promoter library for rapid modification of Pseudomonas putida KT2440 journal December 2017
Genome editing with CRISPR–Cas nucleases, base editors, transposases and prime editors journal June 2020
Enabling genetic analysis of diverse bacteria with Mobile-CRISPRi journal January 2019
A decade of advances in transposon-insertion sequencing journal June 2020
Multifunctional SEVA shuttle vectors for actinomycetes and Gram‐negative bacteria journal March 2020
The future of metabolic engineering and synthetic biology: Towards a systematic practice journal May 2012
Development of a Method for Markerless Gene Deletion in Pseudomonas putida journal June 2011
Extending the Host Range of Bacteriophage Particles for DNA Transduction journal June 2017
Programming Bacteriophages by Swapping Their Specificity Determinants journal December 2015
CRISPR-Enabled Tools for Engineering Microbial Genomes and Phenotypes journal July 2018
Accelerated genome engineering of Pseudomonas putida by I‐ Sce I―mediated recombination and CRISPR ‐Cas9 counterselection journal March 2019
Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants journal March 2020
Recent Advances of CRISPR/Cas9-Based Genetic Engineering and Transcriptional Regulation in Industrial Biology journal January 2020
Rapid Quantification of Mutant Fitness in Diverse Bacteria by Sequencing Randomly Bar-Coded Transposons journal May 2015
Rapid, Parallel Identification of Catabolism Pathways of Lignin-Derived Aromatic Compounds in Novosphingobium aromaticivorans journal September 2018
Perturbation of the metabolic network in Salmonella enterica reveals cross-talk between coenzyme A and thiamine pathways journal May 2018
Eliminating a global regulator of carbon catabolite repression enhances the conversion of aromatic lignin monomers to muconate in Pseudomonas putida KT2440 journal December 2017
Mixed carbon substrates: a necessary nuisance or a missed opportunity? journal April 2020
Metabolic pathway balancing and its role in the production of biofuels and chemicals journal June 2015
Carbon catabolite repression in bacteria: many ways to make the most out of nutrients journal August 2008
Engineering E. coli for simultaneous glucose–xylose utilization during methyl ketone production journal January 2018
Protein post-translational modifications in bacteria journal September 2019
Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow journal October 2018
Cofactor Engineering for Enhancing the Flux of Metabolic Pathways journal August 2014
Enhancing muconic acid production from glucose and lignin-derived aromatic compounds via increased protocatechuate decarboxylase activity journal December 2016
Cofactor engineering for more efficient production of chemicals and biofuels journal December 2017
Cofactor engineering to regulate NAD+/NADH ratio with its application to phytosterols biotransformation journal October 2017
The Metabolic Redox Regime of Pseudomonas putida Tunes Its Evolvability toward Novel Xenobiotic Substrates journal August 2018
Genome reduction boosts heterologous gene expression in Pseudomonas putida journal January 2015
Pseudomonas 2.0: genetic upgrading of P. putida KT2440 as an enhanced host for heterologous gene expression journal November 2014
The metabolic cost of flagellar motion in P seudomonas putida  KT2440 : Cost vs. benefit of journal November 2013
Deletion of genomic islands in the Pseudomonas putida KT2440 genome can create an optimal chassis for synthetic biology applications journal March 2020
Dynamic allocation of orthogonal ribosomes facilitates uncoupling of co-expressed genes journal February 2018
Dynamic metabolic control: towards precision engineering of metabolism journal January 2018
Programming mRNA decay to modulate synthetic circuit resource allocation journal April 2017
Horizontal transfer of a pathway for coumarate catabolism unexpectedly inhibits purine nucleotide biosynthesis journal October 2019
Reactive Enamines and Imines In Vivo: Lessons from the RidA Paradigm journal October 2019
How formaldehyde reacts with amino acids journal November 2019
Metabolite Damage and Metabolite Damage Control in Plants journal April 2016
A comparative view of metabolite and substrate stress and tolerance in microbial bioprocessing: From biofuels and chemicals, to biocatalysis and bioremediation journal July 2010
RND efflux pumps in Gram-negative bacteria; regulation, structure and role in antibiotic resistance journal January 2020
Multidrug efflux pumps of Gram-positive bacteria journal July 2016
Adaptive laboratory evolution of tolerance to dicarboxylic acids in Saccharomyces cerevisiae journal December 2019
Mechanisms of solvent resistance mediated by interplay of cellular factors in Pseudomonas putida journal April 2015
Solvent tolerance in Gram-negative bacteria journal June 2012
Addressing the role of the extrusion pump-bearing pGRT1 plasmid in toluene biodegradation by Pseudomonas putida DOT-T1E under real case scenarios journal November 2009
Engineering of Pseudomonas taiwanensis VLB120 for Constitutive Solvent Tolerance and Increased Specific Styrene Epoxidation Activity journal August 2014
Minimal Functions and Physiological Conditions Required for Growth of Salmonella enterica on Ethanolamine in the Absence of the Metabolosome journal November 2005
Bacterial microcompartments: widespread prokaryotic organelles for isolation and optimization of metabolic pathways: Bacterial microcompartments journal August 2015
Bacterial microcompartments: catalysis-enhancing metabolic modules for next generation metabolic and biomedical engineering journal October 2019
Outer membrane vesicles catabolize lignin-derived aromatic compounds in Pseudomonas putida KT2440 journal April 2020
Metabolic engineering of Escherichia coli for the utilization of ethanol journal January 2020
Comparative transcriptomics elucidates adaptive phenol tolerance and utilization in lipid-accumulating Rhodococcus opacus PD630 journal February 2016
Physiological responses of Pseudomonas putida to formaldehyde during detoxification: Microarrays revealed P. putida responses to toxins journal December 2007
Lipid metabolism of phenol-tolerant Rhodococcus opacus strains for lignin bioconversion journal December 2018
Engineering membrane and cell-wall programs for tolerance to toxic chemicals: Beyond solo genes journal October 2016
Engineering Escherichia coli membrane phospholipid head distribution improves tolerance and production of biorenewables journal November 2017
Reverse engineering of fatty acid-tolerant Escherichia coli identifies design strategies for robust microbial cell factories journal September 2020
Engineering alcohol tolerance in yeast journal October 2014
Hidden resources in the Escherichia coli genome restore PLP synthesis and robust growth after deletion of the essential gene pdxB journal November 2019
Shining a light on enzyme promiscuity journal December 2017
Metabolite Repair Enzymes Control Metabolic Damage in Glycolysis journal March 2020
Metabolite damage and its repair or pre-emption journal January 2013
Recent advances in the reconstruction of metabolic models and integration of omics data journal October 2014
Multiple High-Throughput Analyses Monitor the Response of E. coli to Perturbations journal April 2007
Current status and applications of genome-scale metabolic models journal June 2019
Using Genome-scale Models to Predict Biological Capabilities journal May 2015
A machine learning approach to predict metabolic pathway dynamics from time-series multiomics data journal May 2018
Machine and deep learning meet genome-scale metabolic modeling journal July 2019
The Escherichia coli transcriptome mostly consists of independently regulated modules journal December 2019
Machine learning for metabolic engineering: A review journal January 2021
Machine Learning for High-Throughput Stress Phenotyping in Plants journal February 2016
A White-Box Machine Learning Approach for Revealing Antibiotic Mechanisms of Action journal May 2019