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Zhang Z, Zhu N, Yang G, Leng F, Wang Y. Bioinformatics analysis of gene bhsA and its role in Ca 2+ -treated Escherichia coli. J Basic Microbiol 2024; 64:e2300222. [PMID: 37919047 DOI: 10.1002/jobm.202300222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 09/06/2023] [Accepted: 09/23/2023] [Indexed: 11/04/2023]
Abstract
One of the commonly employed methods in molecular biology is to utilize calcium chloride to treat Escherichia coli for the preparation of competent cells to facilitate foreign gene expression. However, the molecular mechanisms underlying Ca2+ mediation of competent cell formation and identification of the key genes involved in the process remain unclear. In previous studies, the combined analysis of transcriptomics and proteomics revealed bhsA as one of the crucial genes. The gene ontology functional annotation of bhsA identified it as a member of the YhcN family encoding an outer membrane protein that confers resistance to various stresses. The IPR0108542 domain found within the protein plays a significant role in stress response and biofilm formation in E. coli. Analysis of the STRING database showed that the proteins interacting with bhsA are primarily involved in biofilm formation and stress resistance. Using the RED homologous recombination method, a bhsA deletion strain was constructed to verify its role in E. coli genetic transformation. Although the mutant strain showed no significant differences in morphology or growth trend when compared to the wild-type strain, its transformation efficiency decreased by 1.14- and 1.64-fold with plasmids pUC19 and pET-32a. Furthermore, the 1-N-phenylnaphthylamine assay indicated a 1.71-fold reduction in cell membrane permeability in the mutant strain.
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Affiliation(s)
- Zefang Zhang
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, China
| | - Ning Zhu
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, China
- School of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, China
| | - Guangrui Yang
- Gansu Zhongshang Food Quality Test and Detection Co., Ltd., Lanzhou, China
- Gansu Business Science and Technology Institute Co., Ltd., Lanzhou, China
| | - Feifan Leng
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, China
| | - Yonggang Wang
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, China
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2
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Fang L, Han Z, Feng X, Hao X, Liu M, Song H, Cao Y. Identification of crucial roles of transcription factor IhfA on high production of free fatty acids in Escherichia coli. Synth Syst Biotechnol 2024; 9:144-151. [PMID: 38322110 PMCID: PMC10844884 DOI: 10.1016/j.synbio.2024.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 01/07/2024] [Accepted: 01/18/2024] [Indexed: 02/08/2024] Open
Abstract
Transcription factor engineering has unique advantages in improving the performance of microbial cell factories due to the global regulation of gene transcription. Omics analyses and reverse engineering enable learning and subsequent incorporation of novel design strategies for further engineering. Here, we identify the role of the global regulator IhfA for overproduction of free fatty acids (FFAs) using CRISPRi-facilitated reverse engineering and cellular physiological characterization. From the differentially expressed genes in the ihfAL- strain, a total of 14 beneficial targets that enhance FFAs production by above 20 % are identified, which involve membrane function, oxidative stress, and others. For membrane-related genes, the engineered strains obtain lower cell surface hydrophobicity and increased average length of membrane lipid tails. For oxidative stress-related genes, the engineered strains present decreased reactive oxygen species (ROS) levels. These gene modulations enhance cellular robustness and save cellular resources, contributing to FFAs production. This study provides novel targets and strategies for engineering microbial cell factories with improved FFAs bioproduction.
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Affiliation(s)
- Lixia Fang
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, China
| | - Ziyi Han
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, China
| | - Xueru Feng
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, China
| | - Xueyan Hao
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, China
| | - Mengxiao Liu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, China
| | - Hao Song
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, China
| | - Yingxiu Cao
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, China
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3
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Su Y, Mangus AM, Cordell WT, Pfleger BF. Overcoming barriers to medium-chain fatty alcohol production. Curr Opin Biotechnol 2024; 85:103063. [PMID: 38219523 PMCID: PMC10922944 DOI: 10.1016/j.copbio.2023.103063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/16/2024]
Abstract
Medium-chain fatty alcohols (mcFaOHs) are aliphatic primary alcohols containing six to twelve carbons that are widely used in materials, pharmaceuticals, and cosmetics. Microbial biosynthesis has been touted as a route to less-abundant chain-length molecules and as a sustainable alternative to current petrochemical processes. Several metabolic engineering strategies for producing mcFaOHs have been demonstrated in the literature, yet processes continue to suffer from poor selectivity and mcFaOH toxicity, leading to reduced titers, rates, and yields of the desired compounds. This opinion examines the current state of microbial mcFaOH biosynthesis, summarizing engineering efforts to tailor selectivity and improve product tolerance by implementing engineering strategies that circumvent or overcome mcFaOH toxicity.
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Affiliation(s)
- Yun Su
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Anna M Mangus
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - William T Cordell
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Brian F Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA.
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4
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Liao C, Santoscoy MC, Craft J, Anderson C, Soupir ML, Jarboe LR. Allelic variation of Escherichia coli outer membrane protein A: Impact on cell surface properties, stress tolerance and allele distribution. PLoS One 2022; 17:e0276046. [PMID: 36227900 PMCID: PMC9560509 DOI: 10.1371/journal.pone.0276046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 09/27/2022] [Indexed: 12/02/2022] Open
Abstract
Outer membrane protein A (OmpA) is one of the most abundant outer membrane proteins of Gram-negative bacteria and is known to have patterns of sequence variations at certain amino acids-allelic variation-in Escherichia coli. Here we subjected seven exemplar OmpA alleles expressed in a K-12 (MG1655) ΔompA background to further characterization. These alleles were observed to significantly impact cell surface charge (zeta potential), cell surface hydrophobicity, biofilm formation, sensitivity to killing by neutrophil elastase, and specific growth rate at 42°C and in the presence of acetate, demonstrating that OmpA is an attractive target for engineering cell surface properties and industrial phenotypes. It was also observed that cell surface charge and biofilm formation both significantly correlate with cell surface hydrophobicity, a cell property that is increasingly intriguing for bioproduction. While there was poor alignment between the observed experimental values relative to the known sequence variation, differences in hydrophobicity and biofilm formation did correspond to the identity of residue 203 (N vs T), located within the proposed dimerization domain. The relative abundance of the (I, δ) allele was increased in extraintestinal pathogenic E. coli (ExPEC) isolates relative to environmental isolates, with a corresponding decrease in (I, α) alleles in ExPEC relative to environmental isolates. The (I, α) and (I, δ) alleles differ at positions 203 and 251. Variations in distribution were also observed among ExPEC types and phylotypes. Thus, OmpA allelic variation and its influence on OmpA function warrant further investigation.
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Affiliation(s)
- Chunyu Liao
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, Iowa, United States of America
| | - Miguel C. Santoscoy
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa United States of America
| | - Julia Craft
- Department of Chemical and Biological Engineering, Biological Materials and Processes (BioMAP) NSF REU Program, Iowa State University, Ames, Iowa, United States of America
| | - Chiron Anderson
- Department of Chemical and Biological Engineering, Biological Materials and Processes (BioMAP) NSF REU Program, Iowa State University, Ames, Iowa, United States of America
| | - Michelle L. Soupir
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, Iowa, United States of America
| | - Laura R. Jarboe
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, Iowa, United States of America
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa United States of America
- * E-mail:
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5
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Fang L, Feng X, Liu D, Han Z, Liu M, Hao X, Cao Y. 大肠杆菌合成中链脂肪酸研究进展. CHINESE SCIENCE BULLETIN-CHINESE 2022. [DOI: 10.1360/tb-2022-0290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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6
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Moon S, Yoon BK, Jackman JA. Effect of Membrane Curvature Nanoarchitectonics on Membrane-Disruptive Interactions of Antimicrobial Lipids and Surfactants. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:4606-4616. [PMID: 35389653 DOI: 10.1021/acs.langmuir.1c03384] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Single-chain lipid amphiphiles such as fatty acids and monoglycerides along with structurally related surfactants have received significant attention as membrane-disrupting antimicrobials to inhibit bacteria and viruses. Such promise has motivated deeper exploration of how these compounds disrupt phospholipid membranes, and the membrane-mimicking, supported lipid bilayer (SLB) platform has provided a useful model system to evaluate corresponding mechanisms of action and potency levels. Even so, it remains largely unknown how biologically relevant membrane properties, such as sub-100 nm membrane curvature, might affect these membrane-disruptive interactions, especially from a nanoarchitectonics perspective. Herein, using the quartz crystal microbalance-dissipation (QCM-D) technique, we fabricated intact vesicle adlayers composed of different-size vesicles (70 or 120 nm diameter) with varying degrees of membrane curvature on a titanium oxide surface and tracked changes in vesicle adlayer properties upon adding lauric acid (LA), glycerol monolaurate (GML), or sodium dodecyl sulfate (SDS). Above their critical micelle concentration (CMC) values, LA and GML caused QCM-D measurement shifts associated with tubule- and bud-like formation, respectively, and both compounds interacted similarly with small (high curvature) and large (low curvature) vesicles. In marked contrast, SDS exhibited distinct interactions with small and large vesicles. For large vesicles, SDS caused nearly complete membrane solubilization in a CMC-independent manner, whereas SDS was largely ineffective at solubilizing small vesicles at all tested concentrations. We rationalize these experimental observations by taking into account the interplay of the headgroup properties of LA, GML, and SDS and curvature-induced membrane geometry, and our findings demonstrate that membrane curvature nanoarchitectonics can strongly influence the membrane interaction profiles of antimicrobial lipids and surfactants.
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Affiliation(s)
- Suji Moon
- School of Chemical Engineering and Translational Nanobioscience Research Center, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Bo Kyeong Yoon
- School of Healthcare and Biomedical Engineering, Chonnam National University, Yeosu 59626, Republic of Korea
| | - Joshua A Jackman
- School of Chemical Engineering and Translational Nanobioscience Research Center, Sungkyunkwan University, Suwon 16419, Republic of Korea
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7
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Liu H, Zhou P, Qi M, Guo L, Gao C, Hu G, Song W, Wu J, Chen X, Chen J, Chen W, Liu L. Enhancing biofuels production by engineering the actin cytoskeleton in Saccharomyces cerevisiae. Nat Commun 2022; 13:1886. [PMID: 35393407 PMCID: PMC8991263 DOI: 10.1038/s41467-022-29560-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 03/23/2022] [Indexed: 01/03/2023] Open
Abstract
Saccharomyces cerevisiae is widely employed as a cell factory for the production of biofuels. However, product toxicity has hindered improvements in biofuel production. Here, we engineer the actin cytoskeleton in S. cerevisiae to increase both the cell growth and production of n-butanol and medium-chain fatty acids. Actin cable tortuosity is regulated using an n-butanol responsive promoter-based autonomous bidirectional signal conditioner in S. cerevisiae. The budding index is increased by 14.0%, resulting in the highest n-butanol titer of 1674.3 mg L−1. Moreover, actin patch density is fine-tuned using a medium-chain fatty acid responsive promoter-based autonomous bidirectional signal conditioner. The intracellular pH is stabilized at 6.4, yielding the highest medium-chain fatty acids titer of 692.3 mg L−1 in yeast extract peptone dextrose medium. Engineering the actin cytoskeleton in S. cerevisiae can efficiently alleviate biofuels toxicity and enhance biofuels production. Product toxicity is one of the factors that hinder biofuel production. Here, the authors engineer the actin cytoskeleton to increase cell growth and production of n-butanol and medium-chain fatty acids in Saccharomyces cerevisiae.
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Affiliation(s)
- Hui Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Pei Zhou
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Mengya Qi
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Liang Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Guipeng Hu
- School of Pharmaceutical Science, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
| | - Wei Song
- School of Pharmaceutical Science, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
| | - Jing Wu
- School of Pharmaceutical Science, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jian Chen
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China. .,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.
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8
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The Rcs System Contributes to the Motility Defects of the Twin-Arginine Translocation System Mutant of Extraintestinal Pathogenic Escherichia coli. J Bacteriol 2022; 204:e0061221. [PMID: 35311558 DOI: 10.1128/jb.00612-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Flagellum-mediated bacterial motility is important for bacteria to take up nutrients, adapt to environmental changes, and establish infection. The twin-arginine translocation system (Tat) is an important protein export system, playing a critical role in bacterial physiology and pathogenesis. It has been observed for a long time that the Tat system is critical for bacterial motility. However, the underlying mechanism remains unrevealed. In this study, a comparative transcriptomics analysis was performed with extraintestinal pathogenic Escherichia coli (ExPEC), which identified a considerable number of genes differentially expressed when the Tat system was disrupted. Among them, a large proportion of flagellar biosynthesis genes showed downregulation, indicating that transcription regulation plays an important role in mediating the motility defects. We further identified three Tat substrate proteins, MdoD, AmiA, and AmiC, that were responsible for the nonmotile phenotype. The Rcs system was deleted in the Δtat, the ΔmdoD, and the ΔamiAΔamiC strains, which restored the motility of ΔmdoD and partially restored the motility of Δtat and ΔamiAΔamiC. The flagella were also observed in all of the ΔtatΔrcsDB, ΔmdoDΔrcsDB, and ΔamiAΔamiCΔrcsDB strains, but not in the Δtat, ΔmdoD, and ΔamiAΔamiC strains, by using transmission electron microscopy. Quantitative reverse transcription-PCR data revealed that the regulons of the Rcs system displayed differential expression in the tat mutant, indicating that the Rcs signaling was activated. Our results suggest that the Rcs system plays an important role in mediating the motility defects of the tat mutant of ExPEC. IMPORTANCE The Tat system is an important protein export system critical for bacterial physiology and pathogenesis. It has been observed for a long time that the Tat system is critical for bacterial motility. However, the underlying mechanism remains unrevealed. In this study, we combine transcriptomics analysis and bacterial genetics, which reveal that transcription regulation plays an important role in mediating the motility defects of the tat mutant of extraintestinal pathogenic Escherichia coli. The Tat substrate proteins responsible for the motility defects are identified. We further show that the Rcs system contributes to the motility suppression. We for the first time reveal the link between the Tat system and bacterial motility, which is important for understanding the physiological functions of the Tat system.
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9
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Hidajat MJ, Yun GN, Hwang DW. Highly selective and stable ZnO-supported bimetallic RuSn catalyst for the hydrogenation of octanoic acid to octanol. MOLECULAR CATALYSIS 2021. [DOI: 10.1016/j.mcat.2021.111770] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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10
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Santoscoy MC, Jarboe LR. A systematic framework for using membrane metrics for strain engineering. Metab Eng 2021; 66:98-113. [PMID: 33813035 DOI: 10.1016/j.ymben.2021.03.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 03/14/2021] [Accepted: 03/15/2021] [Indexed: 11/20/2022]
Abstract
The cell membrane plays a central role in the fitness and performance of microbial cell factories and therefore it is an attractive engineering target. The goal of this work is to develop a systematic framework for identifying membrane features for use as engineering targets. The metrics that describe the composition of the membrane can be visualized as "knobs" that modulate various "outcomes", such as physical properties of the membrane and metabolic activity in the form of growth and productivity, with these relationships varying depending on the condition. We generated a set of strains with altered membrane lipid composition via expression of des, fabA and fabB and performed a rigorous characterization of these knobs and outcomes across several individual inhibitory conditions. Here, the knobs are the relative abundance of unsaturated lipids and lipids containing cyclic rings; the average lipid length, and the ratio of linear and non-linear lipids (L/nL ratio). The outcomes are membrane permeability, hydrophobicity, fluidity, and specific growth rate. This characterization identified significant correlations between knobs and outcomes that were specific to individual inhibitors, but also were significant across all tested conditions. For example, across all conditions, the L/nL ratio is positively correlated with the cell surface hydrophobicity, and the average lipid length is positively correlated with specific growth rate. A subsequent analysis of the data with the individual inhibitors identified pairs of lipid metrics and membrane properties that were predicted to impact cell growth in seven modeled scenarios with two or more inhibitors. The L/nL ratio and the membrane hydrophobicity were predicted to impact cell growth with the highest frequency. We experimentally validated this prediction in the combined condition of 42 °C, 2.5 mM furfural and 2% v/v ethanol in minimal media. Membrane hydrophobicity was confirmed to be a significant predictor of ethanol production. This work demonstrates that membrane physical properties can be used to predict the performance of biocatalysts in single and multiple inhibitory conditions, and possibly as an engineering target. In this manner, membrane properties can possibly be used as screening or selection metrics for library- or evolution-based strain engineering.
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Affiliation(s)
- Miguel C Santoscoy
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, 50011, USA
| | - Laura R Jarboe
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, 50011, USA.
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11
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Chen Y, Boggess EE, Ocasio ER, Warner A, Kerns L, Drapal V, Gossling C, Ross W, Gourse RL, Shao Z, Dickerson J, Mansell TJ, Jarboe LR. Reverse engineering of fatty acid-tolerant Escherichia coli identifies design strategies for robust microbial cell factories. Metab Eng 2020; 61:120-130. [PMID: 32474056 DOI: 10.1016/j.ymben.2020.05.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 02/05/2020] [Accepted: 05/02/2020] [Indexed: 10/24/2022]
Abstract
Adaptive laboratory evolution is often used to improve the performance of microbial cell factories. Reverse engineering of evolved strains enables learning and subsequent incorporation of novel design strategies via the design-build-test-learn cycle. Here, we reverse engineer a strain of Escherichia coli previously evolved for increased tolerance of octanoic acid (C8), an attractive biorenewable chemical, resulting in increased C8 production, increased butanol tolerance, and altered membrane properties. Here, evolution was determined to have occurred first through the restoration of WaaG activity, involved in the production of lipopolysaccharides, then an amino acid change in RpoC, a subunit of RNA polymerase, and finally mutation of the BasS-BasR two component system. All three mutations were required in order to reproduce the increased growth rate in the presence of 20 mM C8 and increased cell surface hydrophobicity; the WaaG and RpoC mutations both contributed to increased C8 titers, with the RpoC mutation appearing to be the major driver of this effect. Each of these mutations contributed to changes in the cell membrane. Increased membrane integrity and rigidity and decreased abundance of extracellular polymeric substances can be attributed to the restoration of WaaG. The increase in average lipid tail length can be attributed to the RpoCH419P mutation, which also confers tolerance to other industrially-relevant inhibitors, such as furfural, vanillin and n-butanol. The RpoCH419P mutation may impact binding or function of the stringent response alarmone ppGpp to RpoC site 1. Each of these mutations provides novel strategies for engineering microbial robustness, particularly at the level of the microbial cell membrane.
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Affiliation(s)
- Yingxi Chen
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, 50011, USA
| | - Erin E Boggess
- Department of Electrical and Computer Engineering, Iowa State University, Ames, IA, 50011, USA; Bioinformatics & Computational Biology Graduate Program, Iowa State University, Ames, IA, 50011, USA
| | - Efrain Rodriguez Ocasio
- NSF Center for Biorenewable Chemicals (CBiRC) Research Experience for Undergraduates, Ames, IA, 50011, USA; Industrial Biotechnology Program, University of Puerto Rico Mayagüez, 00681, Puerto Rico
| | - Aric Warner
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, 50011, USA
| | - Lucas Kerns
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, 50011, USA
| | - Victoria Drapal
- NSF Center for Biorenewable Chemicals (CBiRC) Research Experience for Undergraduates, Ames, IA, 50011, USA; Department of Biological Systems Engineering, University of Nebraska-Lincoln, Lincoln, NE, 68508, USA
| | - Chloe Gossling
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, 50011, USA
| | - Wilma Ross
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Richard L Gourse
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Zengyi Shao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, 50011, USA; Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, 50011, USA
| | - Julie Dickerson
- Department of Electrical and Computer Engineering, Iowa State University, Ames, IA, 50011, USA; Bioinformatics & Computational Biology Graduate Program, Iowa State University, Ames, IA, 50011, USA
| | - Thomas J Mansell
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, 50011, USA; Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, 50011, USA.
| | - Laura R Jarboe
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, 50011, USA; Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, 50011, USA.
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12
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Huo J, Shanks BH. Bioprivileged Molecules: Integrating Biological and Chemical Catalysis for Biomass Conversion. Annu Rev Chem Biomol Eng 2020; 11:63-85. [PMID: 32155351 DOI: 10.1146/annurev-chembioeng-101519-121127] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Further development of biomass conversions to viable chemicals and fuels will require improved atom utilization, process efficiency, and synergistic allocation of carbon feedstock into diverse products, as is the case in the well-developed petroleum industry. The integration of biological and chemical processes, which harnesses the strength of each type of process, can lead to advantaged processes over processes limited to one or the other. This synergy can be achieved through bioprivileged molecules that can be leveraged to produce a diversity of products, including both replacement molecules and novel molecules with enhanced performance properties. However, important challenges arise in the development of bioprivileged molecules. This review discusses the integration of biological and chemical processes and its use in the development of bioprivileged molecules, with a further focus on key hurdles that must be overcome for successful implementation.
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Affiliation(s)
- Jiajie Huo
- Center for Biorenewable Chemicals and Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, USA;
| | - Brent H Shanks
- Center for Biorenewable Chemicals and Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, USA;
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13
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Streamlined assessment of membrane permeability and its application to membrane engineering of Escherichia coli for octanoic acid tolerance. ACTA ACUST UNITED AC 2019; 46:843-853. [DOI: 10.1007/s10295-019-02158-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 02/17/2019] [Indexed: 10/27/2022]
Abstract
Abstract
The economic viability of bio-production processes is often limited by damage to the microbial cell membrane and thus there is a demand for strategies to increase the robustness of the cell membrane. Damage to the microbial membrane is also a common mode of action by antibiotics. Membrane-impermeable DNA-binding dyes are often used to assess membrane integrity in conjunction with flow cytometry. We demonstrate that in situ assessment of the membrane permeability of E. coli to SYTOX Green is consistent with flow cytometry, with the benefit of lower experimental intensity, lower cost, and no need for a priori selection of sampling times. This method is demonstrated by the characterization of four membrane engineering strategies (deletion of aas, deletion of cfa, increased expression of cfa, and deletion of bhsA) for their effect on octanoic acid tolerance, with the finding that deletion of bhsA increased tolerance and substantially decreased membrane leakage.
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