1
|
Guo M, Chen S, Su H, Chen X, Liu H, Sun B. High-throughput visualization mutation screening technology to enhance the specificity of CadR based whole-cell cadmium biosensor. Biosens Bioelectron 2024; 256:116266. [PMID: 38636122 DOI: 10.1016/j.bios.2024.116266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 03/27/2024] [Accepted: 04/01/2024] [Indexed: 04/20/2024]
Abstract
As a heavy metal pollutant, Cd2+ often enters the human body through the food chain causing great harm to human health. Whole-cell biosensor is an emerging technology for rapid on-site detection of heavy metals with the advantages of inexpensive, fast to mass-produce, and strong in anti-interference resistance, but suffering from insatisfactory specificity. In this study, a strategy of Adjacent Site Saturation Mutation (ASSM) was designed to improve the specificity of transcription factor CadR, which acted as the recognition element and determined the specificity of whole cell Cd2+ biosensors. A specific saturated library was constructed using the strategy of adjacent mutation. After two rounds of high-throughput visual screening, a whole-cell biosensor with good response to Cd2+, and with significant weakened Hg2+ interference was obtained. The optimized whole-cell biosensor showed a linear dynamic concentration range from 500 nM to 100 μM, a detection limit of 0.079 μM, and has satisfactory specificity and anti-interference. The ASSM strategy proposed in this study can provide a new method for the application of synthetic biology in food safety detection, indicating the importance of whole-cell biosensors for the detection of heavy metals.
Collapse
Affiliation(s)
- Mingzhang Guo
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, Beijing, 100048, China.
| | - Shijing Chen
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, Beijing, 100048, China
| | - Hongfei Su
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, Beijing, 100048, China
| | - Xiaolin Chen
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, Beijing, 100048, China
| | - Huilin Liu
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, Beijing, 100048, China.
| | - Baoguo Sun
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, Beijing, 100048, China
| |
Collapse
|
2
|
Kang H, Park D, Kim J. Logical regulation of endogenous gene expression using programmable, multi-input processing CRISPR guide RNAs. Nucleic Acids Res 2024:gkae549. [PMID: 38943344 DOI: 10.1093/nar/gkae549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 06/07/2024] [Accepted: 06/13/2024] [Indexed: 07/01/2024] Open
Abstract
The CRISPR-Cas system provides a versatile RNA-guided approach for a broad range of applications. Thanks to advances in RNA synthetic biology, the engineering of guide RNAs (gRNAs) has enabled the conditional control of the CRISPR-Cas system. However, achieving precise regulation of the CRISPR-Cas system for efficient modulation of internal metabolic processes remains challenging. In this work, we developed a robust dCas9 regulator with engineered conditional gRNAs to enable tight control of endogenous genes. Our conditional gRNAs in Escherichia coli can control gene expression upon specific interaction with trigger RNAs with a dynamic range as high as 130-fold, evaluating up to a three-input logic A OR (B AND C). The conditional gRNA-mediated targeting of endogenous metabolic genes, lacZ, malT and poxB, caused differential regulation of growth in Escherichia coli via metabolic flux control. Further, conditional gRNAs could regulate essential cytoskeleton genes, ftsZ and mreB, to control cell filamentation and division. Finally, three types of two-input logic gates could be applied for the conditional control of ftsZ regulation, resulting in morphological changes. The successful operation and application of conditional gRNAs based on programmable RNA interactions suggests that our system could be compatible with other Cas-effectors and implemented in other host organisms.
Collapse
Affiliation(s)
- Hansol Kang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Dongwon Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Jongmin Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| |
Collapse
|
3
|
Shin J, Zielinski DC, Palsson BO. Deciphering nutritional stress responses via knowledge-enriched transcriptomics for microbial engineering. Metab Eng 2024; 84:34-47. [PMID: 38825177 DOI: 10.1016/j.ymben.2024.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/27/2024] [Accepted: 05/28/2024] [Indexed: 06/04/2024]
Abstract
Understanding diverse bacterial nutritional requirements and responses is foundational in microbial research and biotechnology. In this study, we employed knowledge-enriched transcriptomic analytics to decipher complex stress responses of Vibrio natriegens to supplied nutrients, aiming to enhance microbial engineering efforts. We computed 64 independently modulated gene sets that comprise a quantitative basis for transcriptome dynamics across a comprehensive transcriptomics dataset containing a broad array of nutrient conditions. Our approach led to the i) identification of novel transporter systems for diverse substrates, ii) a detailed understanding of how trace elements affect metabolism and growth, and iii) extensive characterization of nutrient-induced stress responses, including osmotic stress, low glycolytic flux, proteostasis, and altered protein expression. By clarifying the relationship between the acetate-associated regulon and glycolytic flux status of various nutrients, we have showcased its vital role in directing optimal carbon source selection. Our findings offer deep insights into the transcriptional landscape of bacterial nutrition and underscore its significance in tailoring strain engineering strategies, thereby facilitating the development of more efficient and robust microbial systems for biotechnological applications.
Collapse
Affiliation(s)
- Jongoh Shin
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Daniel C Zielinski
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, 2800, Denmark; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
| |
Collapse
|
4
|
Vo TM, Park JY, Kim D, Park S. Use of acetate as substrate for sustainable production of homoserine and threonine by Escherichia coli W3110: A modular metabolic engineering approach. Metab Eng 2024; 84:13-22. [PMID: 38796054 DOI: 10.1016/j.ymben.2024.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 04/29/2024] [Accepted: 05/22/2024] [Indexed: 05/28/2024]
Abstract
Acetate, a promising yet underutilized carbon source for biological production, was explored for the efficient production of homoserine and threonine in Escherichia coli W. A modular metabolic engineering approach revealed the crucial roles of both acetate assimilation pathways (AckA/Pta and Acs), optimized TCA cycle flux and glyoxylate shunt activity, and enhanced CoA availability, mediated by increased pantothenate kinase activity, for efficient homoserine production. The engineered strain W-H22/pM2/pR1P exhibited a high acetate assimilation rate (5.47 mmol/g cell/h) and produced 44.1 g/L homoserine in 52 h with a 53% theoretical yield (0.18 mol/mol) in fed-batch fermentation. Similarly, strain W-H31/pM2/pR1P achieved 45.8 g/L threonine in 52 h with a 65% yield (0.22 mol/mol). These results represent the highest reported levels of amino acid production using acetate, highlighting its potential as a valuable and sustainable feedstock for biomanufacturing.
Collapse
Affiliation(s)
- Toan Minh Vo
- School of Energy and Chemical Engineering, UNIST, Ulsan, 44919, Republic of Korea
| | - Joon Young Park
- School of Energy and Chemical Engineering, UNIST, Ulsan, 44919, Republic of Korea
| | - Donghyuk Kim
- School of Energy and Chemical Engineering, UNIST, Ulsan, 44919, Republic of Korea
| | - Sunghoon Park
- School of Energy and Chemical Engineering, UNIST, Ulsan, 44919, Republic of Korea.
| |
Collapse
|
5
|
Wang X, Qiu C, Chen C, Gao C, Wei W, Song W, Wu J, Liu L, Chen X. Metabolic Engineering of Escherichia coli for High-Level Production of l-Phenylalanine. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:11029-11040. [PMID: 38699920 DOI: 10.1021/acs.jafc.4c01563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
l-Phenylalanine (l-Phe) is widely used in the food and pharmaceutical industries. However, the biosynthesis of l-Phe using Escherichia coli remains challenging due to its lower tolerance to high concentration of l-Phe. In this study, to efficiently synthesize l-Phe, the l-Phe biosynthetic pathway was reconstructed by expressing the heterologous genes aroK1, aroL1, and pheA1, along with the native genes aroA, aroC, and tyrB in the shikimate-producing strain E. coli SA09, resulting in the engineered strain E. coli PHE03. Subsequently, adaptive evolution was conducted on E. coli PHE03 to enhance its tolerance to high concentrations of l-Phe, resulting in the strain E. coli PHE04, which reduced the cell mortality to 36.2% after 48 h of fermentation. To elucidate the potential mechanisms, transcriptional profiling was conducted, revealing MarA, a DNA-binding transcriptional dual regulator, as playing a crucial role in enhancing cell membrane integrity and fluidity for improving cell tolerance to high concentrations of l-Phe. Finally, the titer, yield, and productivity of l-Phe with E. coli PHE05 overexpressing marA were increased to 80.48 g/L, 0.27 g/g glucose, and 1.68 g/L/h in a 5-L fed-batch fermentation, respectively.
Collapse
Affiliation(s)
- Xiaoge Wang
- School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Chong Qiu
- School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Chenghu Chen
- School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Cong Gao
- School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Wanqing Wei
- School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Wei Song
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
| | - Jing Wu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
| | - Liming Liu
- School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Xiulai Chen
- School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| |
Collapse
|
6
|
Rothkranz B, Rieb M, Unrau EL, Frindi-Wosch I, Hemmerich J, Sehl T, Rother D. High Cell Density Cultivation Combined with high Specific Enzyme Activity: Cultivation Protocol for the Production of an Amine Transaminase from Bacillus megaterium in E. coli. Chembiochem 2024; 25:e202400006. [PMID: 38457364 DOI: 10.1002/cbic.202400006] [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: 01/10/2024] [Revised: 03/06/2024] [Accepted: 03/08/2024] [Indexed: 03/10/2024]
Abstract
High cell density cultivation is an established method for the production of various industrially important products such as recombinant proteins. However, these protocols are not always suitable for biocatalytic processes as the focus often lies on biomass production rather than high specific activities of the enzyme inside the cells. In contrast, a range of shake flask protocols are well known with high specific activities but rather low cell densities. To overcome this gap, we established a tailor-made fed-batch protocol combining both aspects: high cell density and high specific activities of heterologously produced enzyme. Using the example of an industrially relevant amine transaminase from Bacillus megaterium, we describe a strategy to optimize the cultivation yield based on the feed rate, IPTG concentration, and post-induction temperature. By adjusting these key parameters, we were able to increase the specific activity by 2.6-fold and the wet cell weight by even 17-fold compared to shake flasks. Finally, we were able to verify our established protocol by transferring it to another experimenter. With that, our optimization strategy can serve as a template for the production of high titers of heterologously produced, active enzymes and might enable the availability of these catalysts for upscaling biocatalytic processes.
Collapse
Affiliation(s)
- Berit Rothkranz
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geo Science 1 (IBG-1): Biotechnology, Wilhelm-Johnen-Straße, 52425, Jülich, Germany
- RWTH Aachen University, Aachen Biology and Biotechnology (ABBt), Worringer Weg 1, 52074, Aachen, Germany
| | - Matthias Rieb
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geo Science 1 (IBG-1): Biotechnology, Wilhelm-Johnen-Straße, 52425, Jülich, Germany
| | - Evelin Lisa Unrau
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geo Science 1 (IBG-1): Biotechnology, Wilhelm-Johnen-Straße, 52425, Jülich, Germany
| | - Ilona Frindi-Wosch
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geo Science 1 (IBG-1): Biotechnology, Wilhelm-Johnen-Straße, 52425, Jülich, Germany
| | - Johannes Hemmerich
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geo Science 1 (IBG-1): Biotechnology, Wilhelm-Johnen-Straße, 52425, Jülich, Germany
- dsm-firmenich, Alexander Fleminglaan 1, 2613 AX, Delft, The Netherlands
| | - Torsten Sehl
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geo Science 1 (IBG-1): Biotechnology, Wilhelm-Johnen-Straße, 52425, Jülich, Germany
| | - Dörte Rother
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geo Science 1 (IBG-1): Biotechnology, Wilhelm-Johnen-Straße, 52425, Jülich, Germany
- RWTH Aachen University, Aachen Biology and Biotechnology (ABBt), Worringer Weg 1, 52074, Aachen, Germany
| |
Collapse
|
7
|
Labourel FJF, Daubin V, Menu F, Rajon E. Proteome allocation and the evolution of metabolic cross-feeding. Evolution 2024; 78:849-859. [PMID: 38376478 DOI: 10.1093/evolut/qpae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 02/21/2024]
Abstract
In a common instance of metabolic cross-feeding (MCF), an organism incompletely metabolizes nutrients and releases metabolites that are used by another to produce energy or building blocks. Why would the former waste edible food, and why does this preferentially occur at specific locations in a metabolic pathway have challenged evolutionary theory for decades. To address these questions, we combine adaptive dynamics with an explicit model of cell metabolism, including enzyme-driven catalysis of metabolic reactions and the cellular constraints acting on the proteome that may incur a cost to expressing all enzymes along a pathway. After pointing out that cells should in principle prioritize upstream reactions when metabolites are restrained inside the cell, we show that the occurrence of permeability-driven MCF is rare and requires that an intermediate metabolite be extremely diffusive. Indeed, only at very high levels of membrane permeability (consistent with those of acetate and glycerol, for instance) and under distinctive sets of parameters should the population diversify and MCF evolve. These results help understand the origins of simple microbial communities, such as those that readily evolve in short-term evolutionary experiments, and may later be extended to investigate how evolution has progressively built up today's extremely diverse ecosystems.
Collapse
Affiliation(s)
- Florian J F Labourel
- Univ Lyon, Universite Lyon 1, CNRS, Laboratoire de Biometrie et Biologie Evolutive UMR5558, Villeurbanne, France
- Milner Centre for Evolution, University of Bath, Bath, United Kingdom
- Department of Life Sciences, University of Bath, Bath, United Kingdom
| | - Vincent Daubin
- Univ Lyon, Universite Lyon 1, CNRS, Laboratoire de Biometrie et Biologie Evolutive UMR5558, Villeurbanne, France
| | - Frédéric Menu
- Univ Lyon, Universite Lyon 1, CNRS, Laboratoire de Biometrie et Biologie Evolutive UMR5558, Villeurbanne, France
| | - Etienne Rajon
- Univ Lyon, Universite Lyon 1, CNRS, Laboratoire de Biometrie et Biologie Evolutive UMR5558, Villeurbanne, France
| |
Collapse
|
8
|
Jana M, Sahoo S, Kottekad S, Usharani D, Rath H. Rational and controllable syntheses of variants of modified N-confused N-fused porphodimethenes and a porphotrimethene with adaptive properties. Dalton Trans 2024; 53:7397-7405. [PMID: 38587541 DOI: 10.1039/d4dt00770k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Retrosynthetic design and synthesis with structural isolation of two unprecedented core modified N-confused N-fused porphodimethene-like porphyrinoids possessing a [5.5.5.5] tetracyclic ring with tunable photophysical properties is reported. The solid-state X-ray crystal structure reveals the expected cis geometry for the meso-sp3 carbons. Controlled chemical oxidation of the porphodimethene analogue 11 bearing the N-confused pyrrole moiety to the corresponding porphotrimethene 12 has been achieved in quantitative yield, while 10 bearing the N-methyl N-confused pyrrole moiety remained unsusceptible to chemical oxidation. All three S2N3 hybrid N-confused N-fused porphodi(tri)methene-like porphyrinoids 10-12 could recognize the fluoride anion with high selectivity; however, porphodimethene 10 and porphotrimethene 12 do so via deprotonation rather than an anion recognition based mechanism as has been anticipated in the case of porphodimethene 11.
Collapse
Affiliation(s)
- Manik Jana
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A/2B Raja S.C Mullick Road, Jadavpur, Kolkata, West Bengal 700 032, India.
| | - Sumit Sahoo
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A/2B Raja S.C Mullick Road, Jadavpur, Kolkata, West Bengal 700 032, India.
| | - Sanjay Kottekad
- Department of Food Safety and Quality Control Laboratory, CSIR-Central Food Technology Research Institute, Mysuru, Karnataka, 700020, India.
| | - Dandamudi Usharani
- Department of Food Safety and Quality Control Laboratory, CSIR-Central Food Technology Research Institute, Mysuru, Karnataka, 700020, India.
- Academy of Scientific and Innovative Research (ACSIR), CSIR-HRDC, Ghaziabad, Uttar Pradesh, India
| | - Harapriya Rath
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A/2B Raja S.C Mullick Road, Jadavpur, Kolkata, West Bengal 700 032, India.
| |
Collapse
|
9
|
Ao W, Qin L, Wu N, Ge P, Hu C, Hu J, Peng Y, Zhu Y. Intensification of rice flour gel structure by fermenting corresponding rice with Lactobacillus plantarum. Curr Res Food Sci 2024; 8:100743. [PMID: 38681524 PMCID: PMC11053268 DOI: 10.1016/j.crfs.2024.100743] [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: 01/09/2024] [Revised: 03/10/2024] [Accepted: 04/17/2024] [Indexed: 05/01/2024] Open
Abstract
In starch gel foods processing, lactic acid fermentation is an effective strategy to improve the quality of the gel. This study revealed the effects of Lactobacillus plantarum fermentation for rice on the textural and rheological properties of the corresponding gels. The hardness, adhesiveness and chewiness of the gel showed ascending trends with the forwarding of fermentation. The role of Lactobacillus plantarum on rheological properties of gel depended on fermentation time. As the time was within 3 days, the process reduced the viscoelastic of the gel, while as the time was for 5 days, the process enhanced the viscoelastic of the gel. During fermentation, amylose content increased from 21.56 ± 1.17% to 27.39 ± 0.63%, and crude protein content descended from 12.60 ± 0.44 g/100 g DW to 4.8 ± 0.49 g/100 g DW. Total organic acids were ascending in the whole process, and lactic acid (LA), acetic acid (AA) and citric acid (CA) made the dominant contribution. The enthalpy change (ΔH) of the rice flour fermented for 5 days was significantly (p < 0.05) increased to 9.90 ± 0.24 J/g, indicating the formation of more double helix structures. These organic acids may contribute to the formation of the pores on the surface of granules by hydrolyzing the components, which provides a channel for enzymes to enter the interior of granules. These results provide the basis for the development of fermented rice-based foods.
Collapse
Affiliation(s)
- Wenmin Ao
- School of Liquor and Food Engineering, Guizhou University, Guiyang, 550025, PR China
| | - Likang Qin
- School of Liquor and Food Engineering, Guizhou University, Guiyang, 550025, PR China
| | - Ning Wu
- Zunyi Jinziyang Foods Co., Ltd, Zunyi, 563000, PR China
| | - Pingzhen Ge
- Bijie Institute of Agricultural Sciences, Bijie, 551700, PR China
| | - Chengmei Hu
- School of Liquor and Food Engineering, Guizhou University, Guiyang, 550025, PR China
| | - Jinlan Hu
- School of Liquor and Food Engineering, Guizhou University, Guiyang, 550025, PR China
| | - Yujie Peng
- School of Liquor and Food Engineering, Guizhou University, Guiyang, 550025, PR China
| | - Yong Zhu
- School of Liquor and Food Engineering, Guizhou University, Guiyang, 550025, PR China
| |
Collapse
|
10
|
Rodrigues T, Torres CAV, Marques S, Gírio F, Freitas F, Reis MAM. Polyhydroxyalkanoate Production from Eucalyptus Bark's Enzymatic Hydrolysate. MATERIALS (BASEL, SWITZERLAND) 2024; 17:1773. [PMID: 38673131 PMCID: PMC11050922 DOI: 10.3390/ma17081773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 04/06/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024]
Abstract
In recent years, polyhydroxyalkanoates (PHAs) have gained notoriety because of their desirable properties that include proven biodegradability, biocompatibility, and thermal stability, which make them suitable alternatives to fossil-based polymers. However, the widespread use of PHAs is still challenging because of their production costs, which are greatly associated with the cultivation medium used for bacterial cultivation. In Portugal, one-quarter of the forest area is covered by Eucalyptus globulus wood, making its residues a cheap, abundant, and sustainable potential carbon source for biotechnological uses. In this work, eucalyptus bark was used as the sole feedstock for PHA production in a circular bioeconomic approach. Eucalyptus bark hydrolysate was obtained after enzymatic saccharification using Cellic® CTec3, resulting in a sugar-rich solution containing glucose and xylose. Although with differing performances, several bacteria were able to grow and produce PHA with distinct compositions, using the enzymatic hydrolysate as the sole carbon source. Pseudomonas citronellolis NRRL B-2504 achieved a high cellular growth rate in bioreactor assays (24.4 ± 0.15 g/L) but presented a low accumulation of a medium-chain-length PHA (mcl-PHA) comprising the monomers hydroxydecanoate (HD, 65%), hydroxydodecanoate (HDd, 25%), and hydroxytetradecanoate (HTd, 14%). Burkholderia thailandensis E264, on the other hand, reached a lower cellular growth rate (8.87 ± 0.34 g/L) but showed a higher biopolymer accumulation, with a polyhydroxybutyrate (PHB) content in the cells of 12.3 wt.%. The new isolate, Pseudomonas sp., revealed that under nitrogen availability, it was able to reach a higher accumulation of the homopolymer PHB (31 wt.%). These results, although preliminary, demonstrate the suitability of eucalyptus bark's enzymatic hydrolysate as a feedstock for PHA production, thus offering an exciting avenue for achieving sustainable and environmentally responsible plastic products from an undervalued forestry waste.
Collapse
Affiliation(s)
- Thomas Rodrigues
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal; (T.R.); (C.A.V.T.); (M.A.M.R.)
- UCIBIO—Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal
| | - Cristiana A. V. Torres
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal; (T.R.); (C.A.V.T.); (M.A.M.R.)
- UCIBIO—Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal
| | - Susana Marques
- Unidade de Bioenergia e Biorrefinarias, Laboratório Nacional de Energia e Geologia I.P., 2610-999 Lisboa, Portugal; (S.M.); (F.G.)
| | - Francisco Gírio
- Unidade de Bioenergia e Biorrefinarias, Laboratório Nacional de Energia e Geologia I.P., 2610-999 Lisboa, Portugal; (S.M.); (F.G.)
| | - Filomena Freitas
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal; (T.R.); (C.A.V.T.); (M.A.M.R.)
- UCIBIO—Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal
| | - Maria A. M. Reis
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal; (T.R.); (C.A.V.T.); (M.A.M.R.)
- UCIBIO—Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal
| |
Collapse
|
11
|
Jiang J, Luo Y, Fei P, Zhu Z, Peng J, Lu J, Zhu D, Wu H. Effect of adaptive laboratory evolution of engineered Escherichia coli in acetate on the biosynthesis of succinic acid from glucose in two-stage cultivation. BIORESOUR BIOPROCESS 2024; 11:34. [PMID: 38647614 PMCID: PMC10997558 DOI: 10.1186/s40643-024-00749-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 03/14/2024] [Indexed: 04/25/2024] Open
Abstract
Escherichia coli MLB (MG1655 ΔpflB ΔldhA), which can hardly grow on glucose with little succinate accumulation under anaerobic conditions. Two-stage fermentation is a fermentation in which the first stage is used for cell growth and the second stage is used for product production. The ability of glucose consumption and succinate production of MLB under anaerobic conditions can be improved significantly by using acetate as the solo carbon source under aerobic condition during the two-stage fermentation. Then, the adaptive laboratory evolution (ALE) of growing on acetate was applied here. We assumed that the activities of succinate production related enzymes might be further improved in this study. E. coli MLB46-05 evolved from MLB and it had an improved growth phenotype on acetate. Interestingly, in MLB46-05, the yield and tolerance of succinic acid in the anaerobic condition of two-stage fermentation were improved significantly. According to transcriptome analysis, upregulation of the glyoxylate cycle and the activity of stress regulatory factors are the possible reasons for the elevated yield. And the increased tolerance to acetate made it more tolerant to high concentrations of glucose and succinate. Finally, strain MLB46-05 produced 111 g/L of succinic acid with a product yield of 0.74 g/g glucose. SYNOPSIS.
Collapse
Affiliation(s)
- Jiaping Jiang
- State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Yuanchan Luo
- State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Peng Fei
- State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Zhengtong Zhu
- State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Jing Peng
- State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Juefeng Lu
- State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Du Zhu
- Key Lab of Bioprocess Engineering of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, 330013, China
| | - Hui Wu
- State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian, China.
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 130 Meilong Road, Shanghai, 200237, China.
| |
Collapse
|
12
|
Wang S, Han J, Ge Z, Su X, Chen Y, Meng J. Biotransformation characteristics of tetracycline by strain Serratia marcescens MSM2304 and its mechanism evaluation based on products analysis and genomics. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 356:120684. [PMID: 38531133 DOI: 10.1016/j.jenvman.2024.120684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/22/2024] [Accepted: 03/15/2024] [Indexed: 03/28/2024]
Abstract
Microbial biotransformation is a recommended and reliable method in face of formidable tetracycline (TC) with broad-spectrum antibacterial activity. Herein, comprehensive characteristics of a newfound strain and its molecular mechanism in process of TC bioremediation were involved in this study. Specifically, Serratia marcescens MSM2304 isolated from pig manure sludge grew well in presence of TC and achieved optimal removal efficiency of 61% under conditions of initial TC concentration of 10 mg/L, pH of 7.0, cell inoculation amount of 5%, and tryptone of 10 g/L as additional carbon. The pathways of biotransformation include EPS biosorption, cell surface biosorption and biodegradation, which enzymatic processes of biodegradation were occurred through TC adsorbed by biofilms was firstly broken down by extracellular enzymes and part of TC migrated towards biofilm interior and degraded by intracellular enzymes. Wherein extracellular polysaccharides in extracellular polymeric substances (EPS) from biofilm of strain MSM2304 mainly performed extracellular adsorption, and changes in position and intensity of CO, =CH and C-O-C/C-O of EPS possible further implied TC adsorption by it. Biodegradation accounting for 79.07% played a key role in TC biotransformation and could be fitted well by first-order model that manifesting rapid and thorough removal. Potential biodegradation pathway including demethylation, dihydroxylation, oxygenation, and ring opening possibly involved in TC disposal process of MSM2304, TC-degrading metabolites exhibited lower toxicity to indicator bacteria relative to parent TC. Whole genome sequencing as underlying molecular evidence revealed that TC resistance genes, dehydrogenases-encoding genes, monooxygenase-encoding genes, and methyltransferase-encoding genes of strain MSM2304 were positively related to TC biodegradation. Collectively, these results favored a theoretical evaluation for Serratia marcescens MSM2304 as a promising TC-control agent in environmental bioremediation processes.
Collapse
Affiliation(s)
- Siyu Wang
- National Biochar Institute of Shenyang Agricultural University, Key Laboratory of Biochar and Soil Improvement, Ministry of Agriculture and Rural Afairs, 120 # Dongling Road, Shenyang 110866, China
| | - Jie Han
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang,110866, China.
| | - Ziyi Ge
- National Biochar Institute of Shenyang Agricultural University, Key Laboratory of Biochar and Soil Improvement, Ministry of Agriculture and Rural Afairs, 120 # Dongling Road, Shenyang 110866, China
| | - Xu Su
- National Biochar Institute of Shenyang Agricultural University, Key Laboratory of Biochar and Soil Improvement, Ministry of Agriculture and Rural Afairs, 120 # Dongling Road, Shenyang 110866, China
| | - Yixuan Chen
- National Biochar Institute of Shenyang Agricultural University, Key Laboratory of Biochar and Soil Improvement, Ministry of Agriculture and Rural Afairs, 120 # Dongling Road, Shenyang 110866, China
| | - Jun Meng
- National Biochar Institute of Shenyang Agricultural University, Key Laboratory of Biochar and Soil Improvement, Ministry of Agriculture and Rural Afairs, 120 # Dongling Road, Shenyang 110866, China.
| |
Collapse
|
13
|
Snoeck S, Guidi C, De Mey M. "Metabolic burden" explained: stress symptoms and its related responses induced by (over)expression of (heterologous) proteins in Escherichia coli. Microb Cell Fact 2024; 23:96. [PMID: 38555441 PMCID: PMC10981312 DOI: 10.1186/s12934-024-02370-9] [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: 12/01/2023] [Accepted: 03/18/2024] [Indexed: 04/02/2024] Open
Abstract
BACKGROUND Engineering bacterial strains to redirect the metabolism towards the production of a specific product has enabled the development of industrial biotechnology. However, rewiring the metabolism can have severe implications for a microorganism, rendering cells with stress symptoms such as a decreased growth rate, impaired protein synthesis, genetic instability and an aberrant cell size. On an industrial scale, this is reflected in processes that are not economically viable. MAIN TEXT In literature, most stress symptoms are attributed to "metabolic burden", however the actual triggers and stress mechanisms involved are poorly understood. Therefore, in this literature review, we aimed to get a better insight in how metabolic engineering affects Escherichia coli and link the observed stress symptoms to its cause. Understanding the possible implications that chosen engineering strategies have, will help to guide the reader towards optimising the envisioned process more efficiently. CONCLUSION This review addresses the gap in literature and discusses the triggers and effects of stress mechanisms that can be activated when (over)expressing (heterologous) proteins in Escherichia coli. It uncovers that the activation of the different stress mechanisms is complex and that many are interconnected. The reader is shown that care has to be taken when (over)expressing (heterologous) proteins as the cell's metabolism is tightly regulated.
Collapse
Affiliation(s)
- Sofie Snoeck
- Department of Biotechnology, Centre for Synthetic Biology, Coupure Links 653, Gent, 9000, Belgium
| | - Chiara Guidi
- Department of Biotechnology, Centre for Synthetic Biology, Coupure Links 653, Gent, 9000, Belgium
| | - Marjan De Mey
- Department of Biotechnology, Centre for Synthetic Biology, Coupure Links 653, Gent, 9000, Belgium.
| |
Collapse
|
14
|
Zhang Y, Boyanov MI, O'Loughlin EJ, Kemner KM, Sanford RA, Kim HS, Park SC, Kwon MJ. Reaction pathways and Sb(III) minerals formation during the reduction of Sb(V) by Rhodoferax ferrireducens strain YZ-1. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133240. [PMID: 38134691 DOI: 10.1016/j.jhazmat.2023.133240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/30/2023] [Accepted: 12/10/2023] [Indexed: 12/24/2023]
Abstract
Antimony (Sb), a non-essential metalloid, can be released into the environment through various industrial activities. Sb(III) is considered more toxic than Sb(V), but Sb(III) can be immobilized through the precipitation of insoluble Sb2S3 or Sb2O3. In the subsurface, Sb redox chemistry is largely controlled by microorganisms; however, the exact mechanisms of Sb(V) reduction to Sb(III) are still unclear. In this study, a new strain of Sb(V)-reducing bacterium, designated as strain YZ-1, that can respire Sb(V) as a terminal electron acceptor was isolated from Sb-contaminated soils. 16S-rRNA gene sequencing of YZ-1 revealed high similarity to a known Fe(III)-reducer, Rhodoferax ferrireducens. XRD and XAFS analyses revealed that bioreduction of Sb(V) to Sb(III) proceed through a transition from amorphous valentinite to crystalline senarmontite (allotropes of Sb2O3). Genomic DNA sequencing found that YZ-1 possesses arsenic (As) metabolism genes, including As(V) reductase arsC. The qPCR analysis showed that arsC was highly expressed during Sb(V)-reduction by YZ-1, and thus is proposed as the potential Sb(V) reductase in YZ-1. This study provides new insight into the pathways and products of microbial Sb(V) reduction and demonstrates the potential of a newly isolated bacterium for Sb bioremediation.
Collapse
Affiliation(s)
- Yidan Zhang
- Department of Earth and Environmental Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Maxim I Boyanov
- Biosciences Division, Argonne National Laboratory, Lemont, IL 60439, USA; Bulgarian Academy of Sciences, Institute of Chemical Engineering, Sofia 1113, Bulgaria
| | | | - Kenneth M Kemner
- Biosciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Robert A Sanford
- Department of Earth Science & Environmental Change, University of Illinois Urbana-Champaign, Champaign, IL 61801, USA
| | - Han-Suk Kim
- Department of Earth and Environmental Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Soo-Chan Park
- Department of Earth and Environmental Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Man Jae Kwon
- Department of Earth and Environmental Sciences, Korea University, Seoul 02841, Republic of Korea.
| |
Collapse
|
15
|
Hosmer J, McEwan AG, Kappler U. Bacterial acetate metabolism and its influence on human epithelia. Emerg Top Life Sci 2024; 8:1-13. [PMID: 36945843 PMCID: PMC10903459 DOI: 10.1042/etls20220092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/16/2023] [Accepted: 03/02/2023] [Indexed: 03/23/2023]
Abstract
Short-chain fatty acids are known modulators of host-microbe interactions and can affect human health, inflammation, and outcomes of microbial infections. Acetate is the most abundant but least well-studied of these modulators, with most studies focusing on propionate and butyrate, which are considered to be more potent. In this mini-review, we summarize current knowledge of acetate as an important anti-inflammatory modulator of interactions between hosts and microorganisms. This includes a summary of the pathways by which acetate is metabolized by bacteria and human cells, the functions of acetate in bacterial cells, and the impact that microbially derived acetate has on human immune function.
Collapse
Affiliation(s)
- Jennifer Hosmer
- School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, Australia
| | - Alastair G. McEwan
- School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, Australia
| | - Ulrike Kappler
- School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, Australia
| |
Collapse
|
16
|
Gecse G, Labunskaite R, Pedersen M, Kilstrup M, Johanson T. Minimizing acetate formation from overflow metabolism in Escherichia coli: comparison of genetic engineering strategies to improve robustness toward sugar gradients in large-scale fermentation processes. Front Bioeng Biotechnol 2024; 12:1339054. [PMID: 38419731 PMCID: PMC10899681 DOI: 10.3389/fbioe.2024.1339054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 01/15/2024] [Indexed: 03/02/2024] Open
Abstract
Introduction: Escherichia coli, a well characterized workhorse in biotechnology, has been used to produce many recombinant proteins and metabolites, but have a major drawback in its tendency to revert to overflow metabolism. This phenomenon occurs when excess sugar triggers the production of mainly acetate under aerobic conditions, a detrimental by-product that reduces carbon efficiency, increases cell maintenance, and ultimately inhibits growth. Although this can be prevented by controlled feeding of the sugar carbon source to limit its availability, gradients in commercial-scale bioreactors can still induce it in otherwise carbon-limited cells. While the underlying mechanisms have been extensively studied, these have mostly used non-limited cultures. In contrast, industrial production typically employs carbon-limited processes, which results in a substantially different cell physiology. Objective: The objective of this study was to evaluate and compare the efficiency of different metabolic engineering strategies with the aim to reduce overflow metabolism and increase the robustness of an industrial 2'-O-fucosyllactose producing strain under industrially relevant conditions. Methods: Three distinct metabolic engineering strategies were compared: i) alterations to pathways leading to and from acetate, ii) increased flux towards the tricarboxylic acid (TCA) cycle, and iii) reduced glucose uptake rate. The engineered strains were evaluated for growth, acetate formation, and product yield under non-limiting batch conditions, carbon limited fed-batch conditions, and after a glucose pulse in fed-batch mode. Results and Discussion: The findings demonstrated that blockage of the major acetate production pathways by deletion of the pta and poxB genes or increased carbon flux into the TCA cycle by overexpression of the gltA and deletion of the iclR genes, were efficient ways to reduce acetate accumulation. Surprisingly, a reduced glucose uptake rate did not reduce acetate formation despite it having previously been shown as a very effective strategy. Interestingly, overexpression of gltA was the most efficient way to reduce acetate accumulation in non-limited cultures, whereas disruption of the poxB and pta genes was more effective for carbon-limited cultures exposed to a sudden glucose shock. Strains from both strategies showed increased tolerance towards a glucose pulse during carbon-limited growth indicating feasible ways to engineer industrial E. coli strains with enhanced robustness.
Collapse
Affiliation(s)
| | | | | | - Mogens Kilstrup
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | |
Collapse
|
17
|
Egas RA, Sahonero-Canavesi DX, Bale NJ, Koenen M, Yildiz Ç, Villanueva L, Sousa DZ, Sánchez-Andrea I. Acetic acid stress response of the acidophilic sulfate reducer Acididesulfobacillus acetoxydans. Environ Microbiol 2024; 26:e16565. [PMID: 38356112 DOI: 10.1111/1462-2920.16565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 12/12/2023] [Indexed: 02/16/2024]
Abstract
Acid mine drainage (AMD) waters are a severe environmental threat, due to their high metal content and low pH (pH <3). Current technologies treating AMD utilize neutrophilic sulfate-reducing microorganisms (SRMs), but acidophilic SRM could offer advantages. As AMDs are low in organics these processes require electron donor addition, which is often incompletely oxidized into organic acids (e.g., acetic acid). At low pH, acetic acid is undissociated and toxic to microorganisms. We investigated the stress response of the acetotrophic Acididesulfobacillus acetoxydans to acetic acid. A. acetoxydans was cultivated in bioreactors at pH 5.0 (optimum). For stress experiments, triplicate reactors were spiked until 7.5 mM of acetic acid and compared with (non-spiked) triplicate reactors for physiological, transcriptomic, and membrane lipid changes. After acetic acid spiking, the optical density initially dropped, followed by an adaptation phase during which growth resumed at a lower growth rate. Transcriptome analysis revealed a downregulation of genes involved in glutamate and aspartate synthesis following spiking. Membrane lipid analysis revealed a decrease in iso and anteiso fatty acid relative abundance; and an increase of acetyl-CoA as a fatty acid precursor. These adaptations allow A. acetoxydans to detoxify acetic acid, creating milder conditions for other microorganisms in AMD environments.
Collapse
Affiliation(s)
- Reinier A Egas
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Diana X Sahonero-Canavesi
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Texel, Den Burg, The Netherlands
| | - Nicole J Bale
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Texel, Den Burg, The Netherlands
| | - Michel Koenen
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Texel, Den Burg, The Netherlands
| | - Çağlar Yildiz
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Texel, Den Burg, The Netherlands
- Department of Earth Sciences, Utrecht University, Utrecht, The Netherlands
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, Utrecht, The Netherlands
| | - Irene Sánchez-Andrea
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Environmental Sciences and Sustainability Department, Science & Technology School, IE University, Segovia, Spain
| |
Collapse
|
18
|
Gu P, Li F, Huang Z, Gao J. Application of Acetate as a Substrate for the Production of Value-Added Chemicals in Escherichia coli. Microorganisms 2024; 12:309. [PMID: 38399713 PMCID: PMC10891810 DOI: 10.3390/microorganisms12020309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 01/24/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
At present, the production of the majority of valuable chemicals is dependent on the microbial fermentation of carbohydrate substrates. However, direct competition is a potential problem for microbial feedstocks that are also used within the food/feed industries. The use of alternative carbon sources, such as acetate, has therefore become a research focus. As a common organic acid, acetate can be generated from lignocellulosic biomass and C1 gases, as well as being a major byproduct in microbial fermentation, especially in the presence of an excess carbon source. As a model microorganism, Escherichia coli has been widely applied in the production of valuable chemicals using different carbon sources. Recently, several valuable chemicals (e.g., succinic acid, itaconic acid, isobutanol, and mevalonic acid) have been investigated for synthesis in E. coli using acetate as the sole carbon source. In this review, we summarize the acetate metabolic pathway in E. coli and recent research into the microbial production of chemical compounds in E. coli using acetate as the carbon source. Although microbial synthetic pathways for different compounds have been developed in E. coli, the production titer and yield are insufficient for commercial applications. Finally, we discuss the development prospects and challenges of using acetate for microbial fermentation.
Collapse
Affiliation(s)
- Pengfei Gu
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China;
| | - Fangfang Li
- Yantai Food and Drug Control and Test Center, Yantai 264003, China;
| | - Zhaosong Huang
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China;
| | - Juan Gao
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China;
| |
Collapse
|
19
|
Fusco F, Pires MC, Lopes APY, Alves VDS, Gonçalves VM. Influence of the mRNA initial region on protein production: a case study using recombinant detoxified pneumolysin as a model. Front Bioeng Biotechnol 2024; 11:1304965. [PMID: 38260740 PMCID: PMC10800503 DOI: 10.3389/fbioe.2023.1304965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 12/12/2023] [Indexed: 01/24/2024] Open
Abstract
Recombinant proteins are of great importance in modern society, mostly as biopharmaceutical products. However, challenging and complex processes with low production yield are major drawbacks. Normally, the optimization to overcome these obstacles is focused on bioreactor and purification processes, and the biomolecular aspects are neglected, seen as less important. In this work, we present how the 5' mRNA secondary structure region can be relevant for translation and, therefore, protein production. For this, Escherichia coli BL21(DE3) clones, producing recombinant detoxified pneumolysin (PdT) with and without the N-terminal His-tag, were cultivated in 10-L bioreactors. Another version of the pdt gene (version 2) with synonymous changes in the 5'-end nucleotide sequence was also obtained. Protein production, plasmid stability, carbon sources, and acetic acid were quantified during the cultures. Furthermore, in silico mRNA analyses were performed using TIsigner and RNAfold. The results showed that the His-tag presence at the N-terminus generated a minimum 1.5-fold increase in target protein synthesis, which was explained by the in silico mRNA analyses that returned an mRNA secondary structure easier to translate and, therefore, higher protein production than without the His-tag. The pdt gene version 2 showed lower 5' mRNA opening energy than version 1, allowing higher PdT production even without a tag. This work reveals that simple mRNA analyses during heterologous gene design and production steps can help reach high-recombinant protein titers in a shorter time than using only traditional bioprocess optimization strategies.
Collapse
Affiliation(s)
- Filipe Fusco
- Laboratory of Vaccine Development, Butantan Institute, Sao Paulo, Brazil
- Interunits Graduate Program in Biotechnology, University of Sao Paulo, Sao Paulo, Brazil
| | - Manuella Cazelato Pires
- Laboratory of Vaccine Development, Butantan Institute, Sao Paulo, Brazil
- Interunits Graduate Program in Biotechnology, University of Sao Paulo, Sao Paulo, Brazil
| | | | - Vítor dos Santos Alves
- Laboratory of Vaccine Development, Butantan Institute, Sao Paulo, Brazil
- Interunits Graduate Program in Biotechnology, University of Sao Paulo, Sao Paulo, Brazil
| | | |
Collapse
|
20
|
Jang YS, Yang J, Kim JK, Kim TI, Park YC, Kim IJ, Kim KH. Adaptive laboratory evolution and transcriptomics-guided engineering of Escherichia coli for increased isobutanol tolerance. Biotechnol J 2024; 19:e2300270. [PMID: 37799109 DOI: 10.1002/biot.202300270] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 09/08/2023] [Accepted: 09/26/2023] [Indexed: 10/07/2023]
Abstract
As a renewable energy from biomass, isobutanol is considered as a promising alternative to fossil fuels. To biotechnologically produce isobutanol, strain development using industrial microbial hosts, such as Escherichia coli, has been conducted by introducing a heterologous isobutanol synthetic pathway. However, the toxicity of produced isobutanol inhibits cell growth, thereby restricting improvements in isobutanol titer, yield, and productivity. Therefore, the development of robust microbial strains tolerant to isobutanol is required. In this study, isobutanol-tolerant mutants were isolated from two E. coli parental strains, E. coli BL21(DE3) and MG1655(DE3), through adaptive laboratory evolution (ALE) under high isobutanol concentrations. Subsequently, 16 putative genes responsible for isobutanol tolerance were identified by transcriptomic analysis. When overexpressed in E. coli, four genes (fadB, dppC, acs, and csiD) conferred isobutanol tolerance. A fermentation study with a reverse engineered isobutanol-producing E. coli JK209 strain showed that fadB or dppC overexpression improved isobutanol titers by 1.5 times, compared to the control strain. Through coupling adaptive evolution with transcriptomic analysis, new genetic targets utilizable were identified as the basis for the development of an isobutanol-tolerant strain. Thus, these new findings will be helpful not only for a fundamental understanding of microbial isobutanol tolerance but also for facilitating industrially feasible isobutanol production.
Collapse
Affiliation(s)
- Young Seo Jang
- Department of Biotechnology, Graduate School, Korea University, Seoul, Republic of Korea
| | - Jungwoo Yang
- Department of Biotechnology, Graduate School, Korea University, Seoul, Republic of Korea
| | - Jae Kyun Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul, Republic of Korea
| | - Tae In Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul, Republic of Korea
| | - Yong-Cheol Park
- Department of Bio and Fermentation Convergence Technology, Kookmin University, Seoul, Republic of Korea
| | - In Jung Kim
- Department of Food Science and Technology, Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Kyoung Heon Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul, Republic of Korea
| |
Collapse
|
21
|
Zünd JN, Plüss S, Mujezinovic D, Menzi C, von Bieberstein PR, de Wouters T, Lacroix C, Leventhal GE, Pugin B. A flexible high-throughput cultivation protocol to assess the response of individuals' gut microbiota to diet-, drug-, and host-related factors. ISME COMMUNICATIONS 2024; 4:ycae035. [PMID: 38562261 PMCID: PMC10982853 DOI: 10.1093/ismeco/ycae035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/13/2023] [Accepted: 03/08/2024] [Indexed: 04/04/2024]
Abstract
The anaerobic cultivation of fecal microbiota is a promising approach to investigating how gut microbial communities respond to specific intestinal conditions and perturbations. Here, we describe a flexible protocol using 96-deepwell plates to cultivate stool-derived gut microbiota. Our protocol aims to address gaps in high-throughput culturing in an anaerobic chamber. We characterized the influence of the gas phase on the medium chemistry and microbial physiology and introduced a modular medium preparation process to enable the testing of several conditions simultaneously. Furthermore, we identified a medium formulation that maximized the compositional similarity of ex vivo cultures and donor microbiota while limiting the bloom of Enterobacteriaceae. Lastly, we validated the protocol by demonstrating that cultivated fecal microbiota responded similarly to dietary fibers (resistant dextrin, soluble starch) and drugs (ciprofloxacin, 5-fluorouracil) as reported in vivo. This high-throughput cultivation protocol has the potential to facilitate culture-dependent studies, accelerate the discovery of gut microbiota-diet-drug-host interactions, and pave the way to personalized microbiota-centered interventions.
Collapse
Affiliation(s)
- Janina N Zünd
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zürich, 8092 Zürich, Switzerland
| | - Serafina Plüss
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zürich, 8092 Zürich, Switzerland
| | - Denisa Mujezinovic
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zürich, 8092 Zürich, Switzerland
| | - Carmen Menzi
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zürich, 8092 Zürich, Switzerland
- PharmaBiome AG, 8952 Schlieren, Switzerland
| | - Philipp R von Bieberstein
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zürich, 8092 Zürich, Switzerland
- PharmaBiome AG, 8952 Schlieren, Switzerland
| | | | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zürich, 8092 Zürich, Switzerland
| | | | - Benoit Pugin
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zürich, 8092 Zürich, Switzerland
| |
Collapse
|
22
|
Lai D, Hedlund BP, Mau RL, Jiao JY, Li J, Hayer M, Dijkstra P, Schwartz E, Li WJ, Dong H, Palmer M, Dodsworth JA, Zhou EM, Hungate BA. Resource partitioning and amino acid assimilation in a terrestrial geothermal spring. THE ISME JOURNAL 2023; 17:2112-2122. [PMID: 37741957 PMCID: PMC10579274 DOI: 10.1038/s41396-023-01517-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 08/31/2023] [Accepted: 09/13/2023] [Indexed: 09/25/2023]
Abstract
High-temperature geothermal springs host simplified microbial communities; however, the activities of individual microorganisms and their roles in the carbon cycle in nature are not well understood. Here, quantitative stable isotope probing (qSIP) was used to track the assimilation of 13C-acetate and 13C-aspartate into DNA in 74 °C sediments in Gongxiaoshe Hot Spring, Tengchong, China. This revealed a community-wide preference for aspartate and a tight coupling between aspartate incorporation into DNA and the proliferation of aspartate utilizers during labeling. Both 13C incorporation into DNA and changes in the abundance of taxa during incubations indicated strong resource partitioning and a significant phylogenetic signal for aspartate incorporation. Of the active amplicon sequence variants (ASVs) identified by qSIP, most could be matched with genomes from Gongxiaoshe Hot Spring or nearby springs with an average nucleotide similarity of 99.4%. Genomes corresponding to aspartate primary utilizers were smaller, near-universally encoded polar amino acid ABC transporters, and had codon preferences indicative of faster growth rates. The most active ASVs assimilating both substrates were not abundant, suggesting an important role for the rare biosphere in the community response to organic carbon addition. The broad incorporation of aspartate into DNA over acetate by the hot spring community may reflect dynamic cycling of cell lysis products in situ or substrates delivered during monsoon rains and may reflect N limitation.
Collapse
Affiliation(s)
- Dengxun Lai
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA.
- Nevada Institute for Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, USA.
| | - Rebecca L Mau
- Center for Ecosystem Science and Society, Northern Arizona University and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Junhui Li
- Center for Ecosystem Science and Society, Northern Arizona University and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Michaela Hayer
- Center for Ecosystem Science and Society, Northern Arizona University and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Paul Dijkstra
- Center for Ecosystem Science and Society, Northern Arizona University and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Egbert Schwartz
- Center for Ecosystem Science and Society, Northern Arizona University and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Hailiang Dong
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, China and Department of Geology and Environmental Earth Science, Miami University, Oxford, OH, USA
| | - Marike Palmer
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA
| | - Jeremy A Dodsworth
- Department of Biology, California State University, San Bernardino, CA, USA
| | - En-Min Zhou
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
- School of Resource Environment and Earth Science, Yunnan University, Kunming, China
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.
| |
Collapse
|
23
|
Wang S, Chen X, Jin X, Gu F, Jiang W, Qi Q, Liang Q. Creating Polyploid Escherichia Coli and Its Application in Efficient L-Threonine Production. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2302417. [PMID: 37749873 PMCID: PMC10625114 DOI: 10.1002/advs.202302417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 07/31/2023] [Indexed: 09/27/2023]
Abstract
Prokaryotic genomes are generally organized in haploid. In synthetic biological research, efficient chassis cells must be constructed to produce bio-based products. Here, the essential division of the ftsZ gene to create functional polyploid E. coli is regulated. The artificial polyploid E. coli containing 2-4 chromosomes is confirmed through PCR amplification, terminator localization, and flow cytometry. The polyploid E. coli exhibits a larger cell size, and its low pH tolerance and acetate resistance are stronger than those of haploid E. coli. Transcriptome analysis shows that the genes of the cell's main functional pathways are significantly upregulated in the polyploid E. coli. These advantages of the polyploid E. coli results in the highest reported L-threonine yield (160.3 g L-1 ) in fed-batch fermentation to date. In summary, an easy and convenient method for constructing polyploid E. coli and demonstrated its application in L-threonine production is developed. This work provides a new approach for creating an excellent host strain for biochemical production and studying the evolution of prokaryotes and their chromosome functions.
Collapse
Affiliation(s)
- Sumeng Wang
- State Key Laboratory of Microbial TechnologyShandong UniversityQingdao266237P. R. China
| | - Xuanmu Chen
- State Key Laboratory of Microbial TechnologyShandong UniversityQingdao266237P. R. China
| | - Xin Jin
- State Key Laboratory of Microbial TechnologyShandong UniversityQingdao266237P. R. China
| | - Fei Gu
- State Key Laboratory of Microbial TechnologyShandong UniversityQingdao266237P. R. China
| | - Wei Jiang
- Research Center of Basic MedicineCentral Hospital Affiliated to Shandong First Medical UniversityJinan250013P. R. China
| | - Qingsheng Qi
- State Key Laboratory of Microbial TechnologyShandong UniversityQingdao266237P. R. China
| | - Quanfeng Liang
- State Key Laboratory of Microbial TechnologyShandong UniversityQingdao266237P. R. China
| |
Collapse
|
24
|
Boecker S, Schulze P, Klamt S. Growth-coupled anaerobic production of isobutanol from glucose in minimal medium with Escherichia coli. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:148. [PMID: 37789464 PMCID: PMC10548627 DOI: 10.1186/s13068-023-02395-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 09/18/2023] [Indexed: 10/05/2023]
Abstract
BACKGROUND The microbial production of isobutanol holds promise to become a sustainable alternative to fossil-based synthesis routes for this important chemical. Escherichia coli has been considered as one production host, however, due to redox imbalance, growth-coupled anaerobic production of isobutanol from glucose in E. coli is only possible if complex media additives or small amounts of oxygen are provided. These strategies have a negative impact on product yield, productivity, reproducibility, and production costs. RESULTS In this study, we propose a strategy based on acetate as co-substrate for resolving the redox imbalance. We constructed the E. coli background strain SB001 (ΔldhA ΔfrdA ΔpflB) with blocked pathways from glucose to alternative fermentation products but with an enabled pathway for acetate uptake and subsequent conversion to ethanol via acetyl-CoA. This strain, if equipped with the isobutanol production plasmid pIBA4, showed robust exponential growth (µ = 0.05 h-1) under anaerobic conditions in minimal glucose medium supplemented with small amounts of acetate. In small-scale batch cultivations, the strain reached a glucose uptake rate of 4.8 mmol gDW-1 h-1, a titer of 74 mM and 89% of the theoretical maximal isobutanol/glucose yield, while secreting only small amounts of ethanol synthesized from acetate. Furthermore, we show that the strain keeps a high metabolic activity also in a pulsed fed-batch bioreactor cultivation, even if cell growth is impaired by the accumulation of isobutanol in the medium. CONCLUSIONS This study showcases the beneficial utilization of acetate as a co-substrate and redox sink to facilitate growth-coupled production of isobutanol under anaerobic conditions. This approach holds potential for other applications with different production hosts and/or substrate-product combinations.
Collapse
Affiliation(s)
- Simon Boecker
- Analysis and Redesign of Biological Networks, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, 39106, Magdeburg, Germany
- University of Applied Sciences Berlin, Seestr. 64, 13347, Berlin, Germany
| | - Peter Schulze
- Physical and Chemical Foundations of Process Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, 39106, Magdeburg, Germany
| | - Steffen Klamt
- Analysis and Redesign of Biological Networks, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, 39106, Magdeburg, Germany.
| |
Collapse
|
25
|
Dekevic G, Tertel T, Tasto L, Schmidt D, Giebel B, Czermak P, Salzig D. A Bioreactor-Based Yellow Fever Virus-like Particle Production Process with Integrated Process Analytical Technology Based on Transient Transfection. Viruses 2023; 15:2013. [PMID: 37896790 PMCID: PMC10612092 DOI: 10.3390/v15102013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
Yellow Fever (YF) is a severe disease that, while preventable through vaccination, lacks rapid intervention options for those already infected. There is an urgent need for passive immunization techniques using YF-virus-like particles (YF-VLPs). To address this, we successfully established a bioreactor-based production process for YF-VLPs, leveraging transient transfection and integrating Process Analytical Technology. A cornerstone of this approach was the optimization of plasmid DNA (pDNA) production to a yield of 11 mg/L using design of experiments. Glucose, NaCl, yeast extract, and a phosphate buffer showed significant influence on specific pDNA yield. The preliminary work for VLP-production in bioreactor showed adjustments to the HEK cell density, the polyplex formation duration, and medium exchanges effectively elevated transfection efficiencies. The additive Pluronic F-68 was neutral in its effects, and anti-clumping agents (ACA) adversely affected the transfection process. Finally, we established the stirred-tank bioreactor process with integrated dielectric spectroscopy, which gave real-time insight in relevant process steps, e.g., cell growth, polyplex uptake, and harvest time. We confirmed the presence and integrity of YF-VLP via Western blot, imaging flow cytometry measurement, and transmission electron microscopy. The YF-VLP production process can serve as a platform to produce VLPs as passive immunizing agents against other neglected tropical diseases.
Collapse
Affiliation(s)
- Gregor Dekevic
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Wiesenstrasse 14, 35390 Giessen, Germany; (G.D.); (L.T.); (D.S.); (P.C.)
| | - Tobias Tertel
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Virchowstrasse 179, 45147 Essen, Germany; (T.T.); (B.G.)
| | - Lars Tasto
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Wiesenstrasse 14, 35390 Giessen, Germany; (G.D.); (L.T.); (D.S.); (P.C.)
| | - Deborah Schmidt
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Wiesenstrasse 14, 35390 Giessen, Germany; (G.D.); (L.T.); (D.S.); (P.C.)
| | - Bernd Giebel
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Virchowstrasse 179, 45147 Essen, Germany; (T.T.); (B.G.)
| | - Peter Czermak
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Wiesenstrasse 14, 35390 Giessen, Germany; (G.D.); (L.T.); (D.S.); (P.C.)
- Faculty of Biology and Chemistry, University of Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Denise Salzig
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Wiesenstrasse 14, 35390 Giessen, Germany; (G.D.); (L.T.); (D.S.); (P.C.)
| |
Collapse
|
26
|
Mutyala S, Li S, Khandelwal H, Kong DS, Kim JR. Citrate Synthase Overexpression of Pseudomonas putida Increases Succinate Production from Acetate in Microaerobic Cultivation. ACS OMEGA 2023; 8:26231-26242. [PMID: 37521642 PMCID: PMC10373214 DOI: 10.1021/acsomega.3c02520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 06/28/2023] [Indexed: 08/01/2023]
Abstract
Acetate is an end-product of anaerobic biodegradation and one of the major metabolites of microbial fermentation and lingo-cellulosic hydrolysate. Recently, acetate has been highlighted as a feedstock to produce value-added chemicals. This study examined acetate conversion to succinate by citrate synthase (gltA)-overexpressed Pseudomonas putida under microaerobic conditions. The acetate metabolism is initiated with the gltA enzyme, which converts acetyl-CoA to citrate. gltA-overexpressing P. putida (gltA-KT) showed an ∼50% improvement in succinate production compared to the wild type. Under the optimal pH of 7.5, the accumulation of succinate (4.73 ± 0.6 mM in 36 h) was ∼400% higher than that of the wild type. Overall, gltA overexpression alone resulted in 9.5% of the maximum theoretical yield in a minimal medium with acetate as the sole carbon source. This result shows that citrate synthase is important in acetate conversion to succinate by P. putida under microaerobic conditions.
Collapse
|
27
|
Navarro S, Abla H, Delgado B, Colmer-Hamood JA, Ventolini G, Hamood AN. Glycogen availability and pH variation in a medium simulating vaginal fluid influence the growth of vaginal Lactobacillus species and Gardnerella vaginalis. BMC Microbiol 2023; 23:186. [PMID: 37442975 PMCID: PMC10339506 DOI: 10.1186/s12866-023-02916-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND Glycogen metabolism by Lactobacillus spp. that dominate the healthy vaginal microbiome contributes to a low vaginal pH (3.5-4.5). During bacterial vaginosis (BV), strict and facultative anaerobes including Gardnerella vaginalis become predominant, leading to an increase in the vaginal pH (> 4.5). BV enhances the risk of obstetrical complications, acquisition of sexually transmitted infections, and cervical cancer. Factors critical for the maintenance of the healthy vaginal microbiome or the transition to the BV microbiome are not well defined. Vaginal pH may affect glycogen metabolism by the vaginal microflora, thus influencing the shift in the vaginal microbiome. RESULTS The medium simulating vaginal fluid (MSVF) supported growth of L. jensenii 62G, L. gasseri 63 AM, and L. crispatus JV-V01, and G. vaginalis JCP8151A at specific initial pH conditions for 30 d. L. jensenii at all three starting pH levels (pH 4.0, 4.5, and 5.0), G. vaginalis at pH 4.5 and 5.0, and L. gasseri at pH 5.0 exhibited the long-term stationary phase when grown in MSVF. L. gasseri at pH 4.5 and L. crispatus at pH 5.0 displayed an extended lag phase over 30 d suggesting inefficient glycogen metabolism. Glycogen was essential for the growth of L. jensenii, L. crispatus, and G. vaginalis; only L. gasseri was able to survive in MSVF without glycogen, and only at pH 5.0, where it used glucose. All four species were able to survive for 15 d in MSVF with half the glycogen content but only at specific starting pH levels - pH 4.5 and 5.0 for L. jensenii, L. gasseri, and G. vaginalis and pH 5.0 for L. crispatus. CONCLUSIONS These results suggest that variations in the vaginal pH critically influence the colonization of the vaginal tract by lactobacilli and G. vaginalis JCP8151A by affecting their ability to metabolize glycogen. Further, we found that L. jensenii 62G is capable of glycogen metabolism over a broader pH range (4.0-5.0) while L. crispatus JV-V01 glycogen utilization is pH sensitive (only functional at pH 5.0). Finally, our results showed that G. vaginalis JCP8151A can colonize the vaginal tract for an extended period as long as the pH remains at 4.5 or above.
Collapse
Affiliation(s)
- Stephany Navarro
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX USA
| | - Habib Abla
- School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX USA
| | - Betsaida Delgado
- Honors College, Texas Tech University, Lubbock, TX USA
- Woody L. Hunt School of Dental Medicine, Texas Tech University Health Sciences Center, Lubbock, TX USA
| | - Jane A. Colmer-Hamood
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX USA
- Department of Medical Education, Texas Tech University Health Sciences Center, Lubbock, TX USA
| | - Gary Ventolini
- Department of Obstetrics and Gynecology, Texas Tech University Health Sciences Center Permian Basin, Odessa, TX USA
| | - Abdul N. Hamood
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX USA
- Department of Surgery, Texas Tech University Health Sciences Center, Lubbock, TX USA
| |
Collapse
|
28
|
Mishra NN, de Paula Baptista R, Tran TT, Lapitan CK, Garcia-de-la-Maria C, Miró JM, Proctor RA, Bayer AS. Membrane Phenotypic, Metabolic and Genotypic Adaptations of Streptococcus oralis Strains Destined to Rapidly Develop Stable, High-Level Daptomycin Resistance during Daptomycin Exposures. Antibiotics (Basel) 2023; 12:1083. [PMID: 37508179 PMCID: PMC10376253 DOI: 10.3390/antibiotics12071083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/15/2023] [Accepted: 06/16/2023] [Indexed: 07/30/2023] Open
Abstract
The Streptococcus mitis-oralis subgroup of viridans group streptococci are important human pathogens. We previously showed that a substantial portion of S. mitis-oralis strains (>25%) are 'destined' to develop rapid, high-level, and stable daptomycin (DAP) resistance (DAP-R) during DAP exposures in vitro. Such DAP-R is often accompanied by perturbations in distinct membrane phenotypes and metabolic pathways. The current study evaluated two S. oralis bloodstream isolates, 73 and 205. Strain 73 developed stable, high-level DAP-R (minimum inhibitory concentration [MIC] > 256 µg/mL) within 2 days of in vitro DAP passage ("high level" DAP-R [HLDR]). In contrast, strain 205 evolved low-level and unstable DAP-R (MIC = 8 µg/mL) under the same exposure conditions in vitro ("non-HLDR"). Comparing the parental 73 vs. 73-D2 (HLDR) strain-pair, we observed the 73-D2 had the following major differences: (i) altered cell membrane (CM) phospholipid profiles, featuring the disappearance of phosphatidylglycerol (PG) and cardiolipin (CL), with accumulation of the PG-CL pathway precursor, phosphatidic acid (PA); (ii) enhanced CM fluidity; (iii) increased DAP surface binding; (iv) reduced growth rates; (v) decreased glucose utilization and lactate accumulation; and (vi) increased enzymatic activity within the glycolytic (i.e., lactate dehydrogenase [LDH]) and lipid biosynthetic (glycerol-3-phosphate dehydrogenase [GPDH]) pathways. In contrast, the 205 (non-HLDR) strain-pair did not show these same phenotypic or metabolic changes over the 2-day DAP exposure. WGS analyses confirmed the presence of mutations in genes involved in the above glycolytic and phospholipid biosynthetic pathways in the 73-D2 passage variant. These data suggest that S. oralis strains which are 'destined' to rapidly develop HLDR do so via a conserved cadre of genotypic, membrane phenotypic, and metabolic adaptations.
Collapse
Affiliation(s)
- Nagendra N Mishra
- Division of Infectious Diseases, The Lundquist Institute at Harbor-UCLA Medical Center, 1124 West Carson St. MRL Bldg. Room 224, Torrance, CA 90502, USA
- The David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Rodrigo de Paula Baptista
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, TX 77030, USA
- Division of Infectious Diseases, Department of Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
- Department of Medicine, Weill-Cornell Medical College, New York, NY 10065, USA
| | - Truc T Tran
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, TX 77030, USA
- Division of Infectious Diseases, Department of Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
- Department of Medicine, Weill-Cornell Medical College, New York, NY 10065, USA
| | - Christian K Lapitan
- Division of Infectious Diseases, The Lundquist Institute at Harbor-UCLA Medical Center, 1124 West Carson St. MRL Bldg. Room 224, Torrance, CA 90502, USA
| | - Cristina Garcia-de-la-Maria
- Infectious Diseases Service, Hospital Clinic-IDIBAPS, University of Barcelona, 08036 Barcelona, Spain
- CIBERINFEC, Instituto de Salud Carlos III, 28220 Madrid, Spain
| | - Jose M Miró
- CIBERINFEC, Instituto de Salud Carlos III, 28220 Madrid, Spain
| | - Richard A Proctor
- The Department of Medicine, University of Wisconsin School of Medicine, Madison, WI 53705, USA
| | - Arnold S Bayer
- Division of Infectious Diseases, The Lundquist Institute at Harbor-UCLA Medical Center, 1124 West Carson St. MRL Bldg. Room 224, Torrance, CA 90502, USA
- The David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| |
Collapse
|
29
|
Diankristanti PA, Ng IS. Microbial itaconic acid bioproduction towards sustainable development: Insights, challenges, and prospects. BIORESOURCE TECHNOLOGY 2023:129280. [PMID: 37290713 DOI: 10.1016/j.biortech.2023.129280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 06/10/2023]
Abstract
Microbial biomanufacturing is a promising approach to produce high-value compounds with low-carbon footprint and significant economic benefits. Among twelve "Top Value-Added Chemicals from Biomass", itaconic acid (IA) stands out as a versatile platform chemical with numerous applications. IA is naturally produced by Aspergillus and Ustilago species through a cascade enzymatic reaction between aconitase (EC 4.2.1.3) and cis-aconitic acid decarboxylase (EC 4.1.1.6). Recently, non-native hosts such as Escherichia coli, Corynebacterium glutamicum, Saccharomyces cerevisiae, and Yarrowia lipolytica have been genetically engineered to produce IA through the introduction of key enzymes. This review provides an up-to-date summary of the progress made in IA bioproduction, from native to engineered hosts, covers in vivo and in vitro approaches, and highlights the prospects of combination tactics. Current challenges and recent endeavors are also addressed to envision comprehensive strategies for renewable IA production in the future towards sustainable development goals (SDGs).
Collapse
Affiliation(s)
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan.
| |
Collapse
|
30
|
Amarnath K, Narla AV, Pontrelli S, Dong J, Reddan J, Taylor BR, Caglar T, Schwartzman J, Sauer U, Cordero OX, Hwa T. Stress-induced metabolic exchanges between complementary bacterial types underly a dynamic mechanism of inter-species stress resistance. Nat Commun 2023; 14:3165. [PMID: 37258505 DOI: 10.1038/s41467-023-38913-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 05/19/2023] [Indexed: 06/02/2023] Open
Abstract
Metabolic cross-feeding plays vital roles in promoting ecological diversity. While some microbes depend on exchanges of essential nutrients for growth, the forces driving the extensive cross-feeding needed to support the coexistence of free-living microbes are poorly understood. Here we characterize bacterial physiology under self-acidification and establish that extensive excretion of key metabolites following growth arrest provides a collaborative, inter-species mechanism of stress resistance. This collaboration occurs not only between species isolated from the same community, but also between unrelated species with complementary (glycolytic vs. gluconeogenic) modes of metabolism. Cultures of such communities progress through distinct phases of growth-dilution cycles, comprising of exponential growth, acidification-triggered growth arrest, collaborative deacidification, and growth recovery, with each phase involving different combinations of physiological states of individual species. Our findings challenge the steady-state view of ecosystems commonly portrayed in ecological models, offering an alternative dynamical view based on growth advantages of complementary species in different phases.
Collapse
Affiliation(s)
- Kapil Amarnath
- Department of Physics, U.C. San Diego, La Jolla, CA, 92093-0319, USA
| | - Avaneesh V Narla
- Department of Physics, U.C. San Diego, La Jolla, CA, 92093-0319, USA
| | - Sammy Pontrelli
- Institute of Molecular and Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Jiajia Dong
- Department of Physics, U.C. San Diego, La Jolla, CA, 92093-0319, USA
- Department of Physics and Astronomy, Bucknell University, Lewisburg, PA, 17837, USA
| | - Jack Reddan
- Division of Biological Sciences, U.C. San Diego, La Jolla, CA, 92093, USA
| | - Brian R Taylor
- Department of Physics, U.C. San Diego, La Jolla, CA, 92093-0319, USA
| | - Tolga Caglar
- Department of Physics, U.C. San Diego, La Jolla, CA, 92093-0319, USA
| | - Julia Schwartzman
- Department of Civil and Environmental Engineering, MIT, Cambridge, MA, 02139, USA
| | - Uwe Sauer
- Institute of Molecular and Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Otto X Cordero
- Department of Civil and Environmental Engineering, MIT, Cambridge, MA, 02139, USA
| | - Terence Hwa
- Department of Physics, U.C. San Diego, La Jolla, CA, 92093-0319, USA.
- Division of Biological Sciences, U.C. San Diego, La Jolla, CA, 92093, USA.
| |
Collapse
|
31
|
Carruthers DN, Kim J, Mendez-Perez D, Monroe E, Myllenbeck N, Liu Y, Davis RW, Sundstrom E, Lee TS. Microbial production of high octane and high sensitivity olefinic ester biofuels. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:60. [PMID: 37016410 PMCID: PMC10071710 DOI: 10.1186/s13068-023-02301-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/08/2023] [Indexed: 04/06/2023]
Abstract
BACKGROUND Advanced spark ignition engines require high performance fuels with improved resistance to autoignition. Biologically derived olefinic alcohols have arisen as promising blendstock candidates due to favorable octane numbers and synergistic blending characteristics. However, production and downstream separation of these alcohols are limited by their intrinsic toxicity and high aqueous solubility, respectively. Bioproduction of carboxylate esters of alcohols can improve partitioning and reduce toxicity, but in practice has been limited to saturated esters with characteristically low octane sensitivity. If olefinic esters retain the synergistic blending characteristics of their alcohol counterparts, they could improve the bioblendstock combustion performance while also retaining the production advantages of the ester moiety. RESULTS Optimization of Escherichia coli isoprenoid pathways has led to high titers of isoprenol and prenol, which are not only excellent standalone biofuel and blend candidates, but also novel targets for esterification. Here, a selection of olefinic esters enhanced blendstock performance according to their degree of unsaturation and branching. E. coli strains harboring optimized mevalonate pathways, thioester pathways, and heterologous alcohol acyltransferases (ATF1, ATF2, and SAAT) were engineered for the bioproduction of four novel olefinic esters. Although prenyl and isoprenyl lactate titers were limited to 1.48 ± 0.41 mg/L and 5.57 ± 1.36 mg/L, strains engineered for prenyl and isoprenyl acetate attained titers of 176.3 ± 16.0 mg/L and 3.08 ± 0.27 g/L, respectively. Furthermore, prenyl acetate (20% bRON = 125.8) and isoprenyl acetate (20% bRON = 108.4) exhibited blend properties comparable to ethanol and significantly better than any saturated ester. By further scaling cultures to a 2-L bioreactor under fed-batch conditions, 15.0 ± 0.9 g/L isoprenyl acetate was achieved on minimal medium. Metabolic engineering of acetate pathway flux further improved titer to attain an unprecedented 28.0 ± 1.0 g/L isoprenyl acetate, accounting for 75.7% theoretical yield from glucose. CONCLUSION Our study demonstrated novel bioproduction of four isoprenoid oxygenates for fuel blending. Our optimized E. coli production strain generated an unprecedented titer of isoprenyl acetate and when paired with its favorable blend properties, may enable rapid scale-up of olefinic alcohol esters for use as a fuel blend additive or as a precursor for longer-chain biofuels and biochemicals.
Collapse
Affiliation(s)
- David N Carruthers
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
| | - Jinho Kim
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
| | - Daniel Mendez-Perez
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
| | - Eric Monroe
- Sandia National Laboratories, Livermore, CA, 94551, USA
| | | | - Yuzhong Liu
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
| | - Ryan W Davis
- Sandia National Laboratories, Livermore, CA, 94551, USA
| | - Eric Sundstrom
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Advanced Biofuels and Bioproducts Process Development Unit, Emeryville, CA, 94608, USA
| | - Taek Soon Lee
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA.
| |
Collapse
|
32
|
Long BHD, Matsubara K, Tanaka T, Ohara H, Aso Y. Production of glycerate from glucose using engineered Escherichiacoli. J Biosci Bioeng 2023; 135:375-381. [PMID: 36841726 DOI: 10.1016/j.jbiosc.2023.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 02/07/2023] [Accepted: 02/08/2023] [Indexed: 02/27/2023]
Abstract
In this study, glycerate was produced from glucose using engineered Escherichia coli BW25113. Plasmid pSR3 carrying gpd1 and gpp2 encoding two isoforms of glycerol-3-phosphate dehydrogenase from Saccharomyces cerevisiae and plasmid pLB2 carrying aldO encoding alditol oxidase from Streptomyces violaceoruber were introduced into E. coli to enable the production of glycerate from glucose via glycerol. Disruptions of garK and glxK genes in the E. coli genome were performed to minimize the consumption of glycerate produced. As a result, E. coli carrying these plasmids could produce nearly three times higher concentration of glycerate (0.50 ± 0.01 g/L) from 10 g/L glucose compared to E. coli EG_2 (0.14 ± 0.02 g/L). In M9 medium, disruption of garK and glxK resulted in an impaired growth rate with low production of glycerate, while supplementation of 0.5 g/L casamino acids and 0.5 g/L manganese sulfate to the medium replenished the growth rate and elevated the glycerate titer. Further disruption of glpF, encoding a glycerol transporter, increased the glycerate production to 0.80 ± 0.00 g/L. MR2 medium improved the glycerate production titers and specific productivities of E. coli EG_4, EG_5, and EG_6. Upscale production of glycerate was carried out in a jar fermentor with MR2 medium using E. coli EG_6, resulting in an improvement in glycerate production up to 2.37 ± 0.46 g/L with specific productivity at 0.34 ± 0.11 g-glycerate/g-cells. These results indicate that E. coli is an appropriate host for glycerate production from glucose.
Collapse
Affiliation(s)
- Bui Hoang Dang Long
- Department of Biobased Materials Science, Kyoto Institute of Technology, 1 Hashigami-cho, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Kotaro Matsubara
- Department of Biobased Materials Science, Kyoto Institute of Technology, 1 Hashigami-cho, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Tomonari Tanaka
- Department of Biobased Materials Science, Kyoto Institute of Technology, 1 Hashigami-cho, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Hitomi Ohara
- Department of Biobased Materials Science, Kyoto Institute of Technology, 1 Hashigami-cho, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Yuji Aso
- Department of Biobased Materials Science, Kyoto Institute of Technology, 1 Hashigami-cho, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan.
| |
Collapse
|
33
|
Ting WW, Ng IS. Effective 5-aminolevulinic acid production via T7 RNA polymerase and RuBisCO equipped Escherichia coli W3110. Biotechnol Bioeng 2023; 120:583-592. [PMID: 36302745 DOI: 10.1002/bit.28273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/25/2022] [Accepted: 10/25/2022] [Indexed: 01/13/2023]
Abstract
Chromosome-based engineering is a superior approach for gene integration generating a stable and robust chassis. Therefore, an effective amplifier, T7 RNA polymerase (T7RNAP) from bacteriophage, has been incorporated into Escherichia coli W3110 by site-specific integration. Herein, we performed the 5-aminolevulinic acid (5-ALA) production in four T7RNAP-equipped W3110 strains using recombinant 5-aminolevulinic synthase and further explored the metabolic difference in best strain. The fastest glucose consumption resulted in the highest biomass and the 5-ALA production reached to 5.5 g/L; thus, the least by-product of acetate was shown in RH strain in which T7RNAP was inserted at HK022 phage attack site. Overexpression of phosphoenolpyruvate (PEP) carboxylase would pull PEP to oxaloacetic acid in tricarboxylic acid cycle, leading to energy conservation and even no acetate production, thus, 6.53 g/L of 5-ALA was achieved. Amino acid utilization in RH deciphered the major metabolic flux in α-ketoglutaric acid dominating 5-ALA production. Finally, the ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and phosphoribulokinase were expressed for carbon dioxide recycling; a robust and efficient chassis toward low-carbon assimilation and high-level of 5-ALA production up to 11.2 g/L in fed-batch fermentation was established.
Collapse
Affiliation(s)
- Wan-Wen Ting
- Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan
| |
Collapse
|
34
|
Karlsen E, Gylseth M, Schulz C, Almaas E. A study of a diauxic growth experiment using an expanded dynamic flux balance framework. PLoS One 2023; 18:e0280077. [PMID: 36607958 PMCID: PMC9821518 DOI: 10.1371/journal.pone.0280077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 12/20/2022] [Indexed: 01/07/2023] Open
Abstract
Flux balance analysis (FBA) remains one of the most used methods for modeling the entirety of cellular metabolism, and a range of applications and extensions based on the FBA framework have been generated. Dynamic flux balance analysis (dFBA), the expansion of FBA into the time domain, still has issues regarding accessibility limiting its widespread adoption and application, such as a lack of a consistently rigid formalism and tools that can be applied without expert knowledge. Recent work has combined dFBA with enzyme-constrained flux balance analysis (decFBA), which has been shown to greatly improve accuracy in the comparison of computational simulations and experimental data, but such approaches generally do not take into account the fact that altering the enzyme composition of a cell is not an instantaneous process. Here, we have developed a decFBA method that explicitly takes enzyme change constraints (ecc) into account, decFBAecc. The resulting software is a simple yet flexible framework for using genome-scale metabolic modeling for simulations in the time domain that has full interoperability with the COBRA Toolbox 3.0. To assess the quality of the computational predictions of decFBAecc, we conducted a diauxic growth fermentation experiment with Escherichia coli BW25113 in glucose minimal M9 medium. The comparison of experimental data with dFBA, decFBA and decFBAecc predictions demonstrates how systematic analyses within a fixed constraint-based framework can aid the study of model parameters. Finally, in explaining experimentally observed phenotypes, our computational analysis demonstrates the importance of non-linear dependence of exchange fluxes on medium metabolite concentrations and the non-instantaneous change in enzyme composition, effects of which have not previously been accounted for in constraint-based analysis.
Collapse
Affiliation(s)
- Emil Karlsen
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Marianne Gylseth
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Christian Schulz
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Eivind Almaas
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
- K. G. Jebsen Center for Genetic Epidemiology Department of Public Health and General Practice, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
- * E-mail:
| |
Collapse
|
35
|
Wang J, Kong K, Guo C, Yin G, Meng S, Lan L, Luo L, Song Y. Cultureless enumeration of live bacteria in urinary tract infection by single-cell Raman spectroscopy. Front Microbiol 2023; 14:1144607. [PMID: 37032883 PMCID: PMC10076591 DOI: 10.3389/fmicb.2023.1144607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 03/06/2023] [Indexed: 04/11/2023] Open
Abstract
Urinary tract infections (UTIs) are the most common outpatient infections. Obtaining the concentration of live pathogens in the sample is crucial for the treatment. Still, the enumeration depends on urine culture and plate counting, which requires days of turn-around time (TAT). Single-cell Raman spectra combined with deuterium isotope probing (Raman-DIP) has been proven to identify the metabolic-active bacteria with high accuracy but is not able to reveal the number of live pathogens due to bacteria replication during the Raman-DIP process. In this study, we established a new approach of using sodium acetate to inhibit the replication of the pathogen and applying Raman-DIP to identify the active single cells. By combining microscopic image stitching and recognition, we could further improve the efficiency of the new method. Validation of the new method on nine artificial urine samples indicated that the exact number of live pathogens obtained with Raman-DIP is consistent with plate-counting while shortening the TAT from 18 h to within 3 h, and the potential of applying Raman-DIP for pathogen enumeration in clinics is promising.
Collapse
Affiliation(s)
- Jingkai Wang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Kang Kong
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai, China
| | - Chen Guo
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
- Division of Life Sciences and Medicine, School of Biomedical Engineering (Suzhou), University of Science and Technology of China, Suzhou, China
| | - Guangyao Yin
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Siyu Meng
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Lu Lan
- VibroniX, Inc., Suzhou, China
| | - Liqiang Luo
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai, China
| | - Yizhi Song
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
- Division of Life Sciences and Medicine, School of Biomedical Engineering (Suzhou), University of Science and Technology of China, Suzhou, China
- Chongqing Guoke Medical Technology Development Co., Ltd., Chongqing, China
- *Correspondence: Yizhi Song,
| |
Collapse
|
36
|
Sheng L, Madika A, Lau MSH, Zhang Y, Minton NP. Metabolic engineering for the production of acetoin and 2,3-butanediol at elevated temperature in Parageobacillus thermoglucosidasius NCIMB 11955. Front Bioeng Biotechnol 2023; 11:1191079. [PMID: 37200846 PMCID: PMC10185769 DOI: 10.3389/fbioe.2023.1191079] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 04/20/2023] [Indexed: 05/20/2023] Open
Abstract
The current climate crisis has emphasised the need to achieve global net-zero by 2050, with countries being urged to set considerable emission reduction targets by 2030. Exploitation of a fermentative process that uses a thermophilic chassis can represent a way to manufacture chemicals and fuels through more environmentally friendly routes with a net reduction in greenhouse gas emissions. In this study, the industrially relevant thermophile Parageobacillus thermoglucosidasius NCIMB 11955 was engineered to produce 3-hydroxybutanone (acetoin) and 2,3-butanediol (2,3-BDO), organic compounds with commercial applications. Using heterologous acetolactate synthase (ALS) and acetolactate decarboxylase (ALD) enzymes, a functional 2,3-BDO biosynthetic pathway was constructed. The formation of by-products was minimized by the deletion of competing pathways surrounding the pyruvate node. Redox imbalance was addressed through autonomous overexpression of the butanediol dehydrogenase and by investigating appropriate aeration levels. Through this, we were able to produce 2,3-BDO as the predominant fermentation metabolite, with up to 6.6 g/L 2,3-BDO (0.33 g/g glucose) representing 66% of the theoretical maximum at 50°C. In addition, the identification and subsequent deletion of a previously unreported thermophilic acetoin degradation gene (acoB1) resulted in enhanced acetoin production under aerobic conditions, producing 7.6 g/L (0.38 g/g glucose) representing 78% of the theoretical maximum. Furthermore, through the generation of a ΔacoB1 mutant and by testing the effect of glucose concentration on 2,3-BDO production, we were able to produce 15.6 g/L of 2,3-BDO in media supplemented with 5% glucose, the highest titre of 2,3-BDO produced in Parageobacillus and Geobacillus species to date.
Collapse
Affiliation(s)
- Lili Sheng
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, Biodiscovery Institute, The University of Nottingham, Nottingham, United Kingdom
| | - Abubakar Madika
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, Biodiscovery Institute, The University of Nottingham, Nottingham, United Kingdom
- Department of Microbiology, Faculty of Life Sciences, Ahmadu Bello University, Zaria, Nigeria
| | - Matthew S. H. Lau
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, Biodiscovery Institute, The University of Nottingham, Nottingham, United Kingdom
| | - Ying Zhang
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, Biodiscovery Institute, The University of Nottingham, Nottingham, United Kingdom
| | - Nigel P. Minton
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, Biodiscovery Institute, The University of Nottingham, Nottingham, United Kingdom
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, The University of Nottingham, Nottingham, United Kingdom
- *Correspondence: Nigel P. Minton,
| |
Collapse
|
37
|
Im J, Lee D, Park OJ, Natarajan S, Park J, Yun CH, Han SH. RNA-Seq-based transcriptome analysis of methicillin-resistant Staphylococcus aureus growth inhibition by propionate. Front Microbiol 2022; 13:1063650. [PMID: 36620009 PMCID: PMC9814166 DOI: 10.3389/fmicb.2022.1063650] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
Staphylococcus aureus is a pathogen that causes a variety of infectious diseases such as pneumonia, endocarditis, and septic shock. Methicillin-resistant S. aureus (MRSA) evades virtually all available treatments, creating the need for an alternative control strategy. Although we previously demonstrated the inhibitory effect of sodium propionate (NaP) on MRSA, the regulatory mechanism of this effect remains unclear. In this study, we investigated the regulatory mechanism responsible for the inhibitory effect of NaP on MRSA using RNA-Seq analysis. Total RNAs were isolated from non-treated and 50 mM NaP-treated S. aureus USA300 for 3 h and transcriptional profiling was conducted by RNA-Seq analysis. A total of 171 differentially expressed genes (DEGs) with log2 fold change ≥2 and p < 0.05 was identified in the NaP treatment group compared with the control group. Among the 171 genes, 131 were up-regulated and 40 were down-regulated. Upon gene ontology (GO) annotation analysis, total 26 specific GO terms in "Biological process," "Molecular function," and "Cellular component" were identified in MRSA treated with NaP for 3 h. "Purine metabolism"; "riboflavin metabolism"; and "glycine, serine, and threonine metabolism" were identified as major altered metabolic pathways among the eight significantly enriched KEGG pathways in MRSA treated with NaP. Furthermore, the MRSA strains deficient in purF, ilvA, ribE, or ribA, which were the up-regulated DEGs in the metabolic pathways, were more susceptible to NaP than wild-type MRSA. Collectively, these results demonstrate that NaP attenuates MRSA growth by altering its metabolic pathways, suggesting that NaP can be used as a potential bacteriostatic agent for prevention of MRSA infection.
Collapse
Affiliation(s)
- Jintaek Im
- Department of Oral Microbiology and Immunology, and Dental Research Institute, School of Dentistry, Seoul National University, Seoul, South Korea
| | - Dongwook Lee
- Department of Oral Microbiology and Immunology, and Dental Research Institute, School of Dentistry, Seoul National University, Seoul, South Korea
| | - Ok-Jin Park
- Department of Oral Microbiology and Immunology, and Dental Research Institute, School of Dentistry, Seoul National University, Seoul, South Korea
| | | | | | - Cheol-Heui Yun
- Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea,Institutes of Green Bio Science and Technology, Seoul National University, Pyeongchang, South Korea
| | - Seung Hyun Han
- Department of Oral Microbiology and Immunology, and Dental Research Institute, School of Dentistry, Seoul National University, Seoul, South Korea,*Correspondence: Seung Hyun Han,
| |
Collapse
|
38
|
Diaz-Tang G, Meneses EM, Patel K, Mirkin S, García-Diéguez L, Pajon C, Barraza I, Patel V, Ghali H, Tracey AP, Blanar CA, Lopatkin AJ, Smith RP. Growth productivity as a determinant of the inoculum effect for bactericidal antibiotics. SCIENCE ADVANCES 2022; 8:eadd0924. [PMID: 36516248 PMCID: PMC9750144 DOI: 10.1126/sciadv.add0924] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 11/11/2022] [Indexed: 06/10/2023]
Abstract
Understanding the mechanisms by which populations of bacteria resist antibiotics has implications in evolution, microbial ecology, and public health. The inoculum effect (IE), where antibiotic efficacy declines as the density of a bacterial population increases, has been observed for multiple bacterial species and antibiotics. Several mechanisms to account for IE have been proposed, but most lack experimental evidence or cannot explain IE for multiple antibiotics. We show that growth productivity, the combined effect of growth and metabolism, can account for IE for multiple bactericidal antibiotics and bacterial species. Guided by flux balance analysis and whole-genome modeling, we show that the carbon source supplied in the growth medium determines growth productivity. If growth productivity is sufficiently high, IE is eliminated. Our results may lead to approaches to reduce IE in the clinic, help standardize the analysis of antibiotics, and further our understanding of how bacteria evolve resistance.
Collapse
Affiliation(s)
- Gabriela Diaz-Tang
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL 33314, USA
| | - Estefania Marin Meneses
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL 33314, USA
| | - Kavish Patel
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL 33314, USA
| | - Sophia Mirkin
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL 33314, USA
| | - Laura García-Diéguez
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL 33314, USA
| | - Camryn Pajon
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL 33314, USA
| | - Ivana Barraza
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL 33314, USA
| | - Vijay Patel
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL 33314, USA
| | - Helana Ghali
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL 33314, USA
| | - Angelica P. Tracey
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL 33314, USA
| | - Christopher A. Blanar
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL 33314, USA
| | - Allison J. Lopatkin
- Department of Biology, Barnard College, Columbia University, New York, NY10025, USA
- Data Science Institute, Columbia University, New York, NY10025, USA
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY10025, USA
| | - Robert P. Smith
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL 33314, USA
- Cell Therapy Institute, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL 33314, USA
| |
Collapse
|
39
|
Growth of Coniochaeta Species on Acetate in Biomass Sugars. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8120721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Degradation products from sugars and lignin are commonly generated as byproducts during pretreatment of biomass being processed for production of renewable fuels and chemicals. Many of the degradation products act as microbial inhibitors, including furanic and phenolic compounds and acetate, which is solubilized from hemicellulose. We previously identified a group of fungi, Coniochaeta species, that are intrinsically tolerant to and capable of mineralizing furans present in biomass hydrolysates. Here, we challenged 20 C. ligniaria and phylogenetically related isolates with acetate to test if the robustness phenotype extended to this important inhibitor as well, and all strains grew at concentrations up to 2.5% (w/v) sodium acetate. At the highest concentrations tested (5.0–7.5% w/v), some variation in growth on solid medium containing glucose plus acetate was apparent among the strains. The hardiness of four promising strains was further evaluated by challenging them (0.5% w/v sodium acetate) in mineral medium containing 10 or 15 mM furfural. The strains grew and consumed all of the acetate and furfural. At a higher (2.5% w/v) concentration, consumption of acetate varied among the strains: only one consumed any acetate in the presence of furfural, but all four strains consumed acetate provided that a small amount (0.2% w/v) of glucose was added. Finally, the four strains were evaluated for biological abatement of rice hull hydrolysates having elevated acetate content. The hardiest strains were also able to consume furfural and 5-hydroxymethylfurfural (HMF) within 24 h, followed by acetate within 40 h when grown in dilute acid pretreated rice hulls containing 0.55% acetate, 15 mM furfural, and 1.7 mM HMF. As such, these strains are expected to be helpful for abating non-desirable compounds from unrefined hydrolysates so as to enable their conversion to bioproducts.
Collapse
|
40
|
Seekatz AM, Safdar N, Khanna S. The role of the gut microbiome in colonization resistance and recurrent Clostridioides difficile infection. Therap Adv Gastroenterol 2022; 15:17562848221134396. [PMID: 36425405 PMCID: PMC9679343 DOI: 10.1177/17562848221134396] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 10/04/2022] [Indexed: 11/21/2022] Open
Abstract
The species composition of the human gut microbiota is related to overall health, and a healthy gut microbiome is crucial in maintaining colonization resistance against pathogens. Disruption of gut microbiome composition and functionality reduces colonization resistance and has been associated with several gastrointestinal and non-gastrointestinal diseases. One prime example is Clostridioides difficile infection (CDI) and subsequent recurrent infections that occur after the development of systemic antibiotic-related dysbiosis. Standard-of-care antibiotics used for both acute and recurrent infections do not address dysbiosis and often worsen the condition. Moreover, monoclonal antibodies, recommended in conjunction with standard-of-care antibiotics for the prevention of recurrent CDI in patients at high risk of recurrence, reduce recurrences but do not address the underlying dysbiosis. Fecal microbiota transplantation (FMT) is an evolving therapeutic strategy in which microbes are harvested from healthy donor stool and transplanted into the gut of a recipient to restore the gut microbiome. Although effective in the prevention of recurrent CDI, some existing challenges include screening and the standardization of stool acquisition and processing. Recent safety alerts by the US Food and Drug Administration raised concern about the possibility of transmission of multidrug-resistant organisms or severe acute respiratory syndrome coronavirus 2 via FMT. Increased knowledge that microbes are beneficial in restoring the gut microbiome has led to the clinical development of several newer biotherapeutic formulations that are more regulated than FMT, which may allow for improved restoration of the gut microbiome and prevention of CDI recurrence. This review focuses on mechanisms by which gut microbiome restoration could influence colonization resistance against the pathogen C. difficile. Plain language summary The Role of the Gut Microbiome in Clostridioides difficile Infection Introduction: A rich and diverse gut microbiome is key to immune system regulation and colonization resistance against pathogens.A disruption in the gut microbiome composition can make the gut more vulnerable to diseases such as Clostridioides difficile infection (CDI), caused by the bacterium C. difficile.CDI management presents a therapeutic dilemma, as it is usually treated with antibiotics that can treat the infection but also can damage the microbiome.Treatment of CDI using antibiotics can further reduce microbial diversity and deplete beneficial bacteria from the gut leading to a condition called dysbiosis.Antibiotic treatment can be followed by therapies that restore the gut microbiota, boost colonization resistance, and prevent the development of antimicrobial resistance.It is important to evaluate treatment options to determine their safety and effectiveness. Methods: The researchers provided an overview of the mechanisms that the gut microbiome uses to prevent colonization of the gut by pathogens.They subsequently reviewed the efficacy and shortcomings of the following treatments for CDI: - Antibiotics- Monoclonal antibodies- Fecal microbiota transplantation (FMT) Results: Commensal intestinal bacteria prevent colonization of the gut by pathogens using mechanisms such as: - Competition for key nutrients- Production of inhibitory bile acids- Short-chain fatty acid production- Lowering the luminal pH- Production of bacteriocinsAntibiotic therapy is recommended as a standard treatment for CDI. However, patients are vulnerable to recurrent CDI after discontinuation of the therapy.Monoclonal antibodies that inactivate C. difficile toxins may be recommended along with antibiotics to prevent recurrent CDI. However, this approach does not restore the microbiome.FMT is one method of microbial restoration, where stool is harvested from a healthy donor and transplanted into a patient's colon.Although FMT has shown some efficacy in the treatment of recurrent CDI, the procedure is not standardized.Safety concerns have been raised about the possibility of transmission of multidrug-resistant pathogens via FMT. Conclusion: Treatment methods that can efficiently restore the diversity of the gut microbiome are crucial in preventing recurrence of CDI.
Collapse
Affiliation(s)
| | - Nasia Safdar
- University of Wisconsin, Madison, WI, USA
- William S. Middleton Memorial VA Hospital, Madison, WI, USA
| | - Sahil Khanna
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
| |
Collapse
|
41
|
Falyouna O, Maamoun I, Ghosh S, Malloum A, Othmani A, Eljamal O, Amen TW, Oroke A, Bornman C, Ahmadi S, Hadi Dehghani M, Hossein Mahvi A, Nasseri S, Tyagi I, Suhas, Reddy Koduru J. Sustainable Technologies for the Removal of Chloramphenicol from Pharmaceutical Industries Effluent: A critical review. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
42
|
Jung M, Ahn YJ. Growth-enhancing effect of bacterial and plant heat shock proteins in Escherichia coli. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2022.102545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
43
|
Dank A, Biel G, Abee T, Smid EJ. Microaerobic metabolism of lactate and propionate enhances vitamin B 12 production in Propionibacterium freudenreichii. Microb Cell Fact 2022; 21:225. [PMID: 36307780 DOI: 10.1186/s12934-022-01945-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 10/02/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Propionibacterium freudenreichii is used in biotechnological applications to produce vitamin B12. Although cultured mainly in anaerobic conditions, microaerobic conditions can greatly enhance biomass formation in P. freudenreichii. Since B12 yields may be coupled to biomass formation, microaerobic conditions show great potential for increasing B12 yields in P. freudenreichii. RESULTS Here we show biomass formation increases 2.7 times for P. freudenreichii grown in microaerobic conditions on lactate versus anaerobic conditions (1.87 g/L vs 0.70 g/L). Consumption of lactate in microaerobic conditions resulted first in production of pyruvate, propionate and acetate. When lactate was depleted, pyruvate and propionate were oxidised with a concomitant sixfold increase in the B12 titer compared to anaerobic conditions, showing potential for propionate and pyruvate as carbon sources for B12 production. Consequently, a fed-batch reactor with anaerobically precultured lactate-grown cells was fed propionate in microaerobic conditions resulting in biomass increase and production of B12. Vitamin yields increased from 0.3 [Formula: see text] B12 per mmol lactate in anaerobic conditions to 2.4 [Formula: see text] B12 per mmol lactate and 8.4 [Formula: see text] B12 per mmol propionate in microaerobic conditions. Yield per cell dry weight (CDW) increased from 41 [Formula: see text] per g CDW in anaerobic conditions on lactate to 92 [Formula: see text] per g CDW on lactate and 184 [Formula: see text] per g CDW on propionate in microaerobic conditions. CONCLUSIONS Here we have shown both B12 yield per substrate and per CDW were highest on cells oxidising propionate in microaerobic conditions, showing the potential of propionate for biotechnological production of vitamin B12 by P. freudenreichii.
Collapse
Affiliation(s)
- Alexander Dank
- Food Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Gabriela Biel
- Food Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Tjakko Abee
- Food Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Eddy J Smid
- Food Microbiology, Wageningen University and Research, Wageningen, The Netherlands.
| |
Collapse
|
44
|
Park T, Im J, Kim AR, Lee D, Jeong S, Yun CH, Han SH. Propionate Attenuates Growth of Oral Streptococci through Enhancing Methionine Biosynthesis. J Microbiol Biotechnol 2022; 32:1234-1244. [PMID: 36198670 PMCID: PMC9668084 DOI: 10.4014/jmb.2205.05037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 08/26/2022] [Accepted: 08/30/2022] [Indexed: 12/15/2022]
Abstract
Oral streptococci are considered as an opportunistic pathogen associated with initiation and progression of various oral diseases. However, since the currently-available treatments often accompany adverse effects, alternative strategy is demanded to control streptococci. In the current study, we investigated whether short-chain fatty acids (SCFAs), including sodium acetate (NaA), sodium propionate (NaP), and sodium butyrate (NaB), can inhibit the growth of oral streptococci. Among the tested SCFAs, NaP most potently inhibited the growth of laboratory and clinically isolated strains of Streptococcus gordonii under anaerobic culture conditions. However, the growth inhibitory effect of NaP on six different species of other oral streptococci was different depending on their culture conditions. Metabolic changes such as alteration of methionine biosynthesis can affect bacterial growth. Indeed, NaP enhanced intracellular methionine levels of oral streptococci as well as the mRNA expression level of methionine biosynthesis-related genes. Collectively, these results suggest that NaP has an inhibitory effect on the growth of oral streptococci, which might be due to alteration of methionine biosynthesis. Thus, NaP can be used an effective bacteriostatic agent for the prevention of oral infectious diseases caused by oral streptococci.
Collapse
Affiliation(s)
- Taehwan Park
- Department of Oral Microbiology and Immunology, and Dental Research Institute, School of Dentistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Jintaek Im
- Department of Oral Microbiology and Immunology, and Dental Research Institute, School of Dentistry, Seoul National University, Seoul 08826, Republic of Korea
| | - A Reum Kim
- Department of Oral Microbiology and Immunology, and Dental Research Institute, School of Dentistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Dongwook Lee
- Department of Oral Microbiology and Immunology, and Dental Research Institute, School of Dentistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Sungho Jeong
- Department of Oral Microbiology and Immunology, and Dental Research Institute, School of Dentistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Cheol-Heui Yun
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea,Institute of Green Bio Science and Technology, Seoul National University, Pyeongchang 25354, Republic of Korea
| | - Seung Hyun Han
- Department of Oral Microbiology and Immunology, and Dental Research Institute, School of Dentistry, Seoul National University, Seoul 08826, Republic of Korea,Corresponding author Phone +82-2-880-2310 Fax: +82-2-743-0311 E-mail:
| |
Collapse
|
45
|
Scale-Up of Capsular Polysaccharide Production Process by Haemophilus influenzae Type b Using kLa Criterion. Bioengineering (Basel) 2022; 9:bioengineering9090415. [PMID: 36134961 PMCID: PMC9495314 DOI: 10.3390/bioengineering9090415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 11/26/2022] Open
Abstract
Polyribosyl-ribitol-phosphate (PRP) from Haemophilus influenzae type b (Hib) is an active immunizing molecule used in the production of the vaccine against H. influenzae, and industrial production could contribute to satisfying a world demand especially in developing countries. In this sense, the aim of this study was to establish a scale-up process using the constant oxygen mass transfer coefficient (kLa) such as the criterion for production of PRP in three different sizes of bioreactor systems. Three different kLa values (24, 52 and 80 h−1) were evaluated in which the biological influence in a 1.5 L bioreactor and 52 h−1 was selected to scale-up the production process until a 75 L pilot-scale bioreactor was achieved. Finally, the fed-batch phase was started under a dissolved oxygen concentration (pO2) at 30% of the saturation in the 75 L bioreactor to avoid oxygen limitation; the performance of production presented high efficiency (9.0 g/L DCW-dry cell weight and 1.4 g/L PRP) in comparison with previous scale-up studies. The yields, productivity and kinetic behavior were similar in the three-size bioreactor systems in the batch mode indicating that kLa is possible to use for PRP production at large scales. This process operated under two stages and successfully produced DCW and PRP in the pilot scale and could be beneficial for future bioprocess operations that may lead to higher production and less operative cost.
Collapse
|
46
|
Li S, Liu G, Xu Y, Liu J, Chen Z, Zheng A, Cai H, Chang W. Comparison of the effects of applying xylooligosaccharides alone or in combination with calcium acetate in broiler chickens. Anim Feed Sci Technol 2022. [DOI: 10.1016/j.anifeedsci.2022.115360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
47
|
Metabolic Phenotyping of Marine Heterotrophs on Refactored Media Reveals Diverse Metabolic Adaptations and Lifestyle Strategies. mSystems 2022; 7:e0007022. [PMID: 35856685 PMCID: PMC9426600 DOI: 10.1128/msystems.00070-22] [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] [Indexed: 11/20/2022] Open
Abstract
Microbial communities, through their metabolism, drive carbon cycling in marine environments. These complex communities are composed of many different microorganisms including heterotrophic bacteria, each with its own nutritional needs and metabolic capabilities. Yet, models of ecosystem processes typically treat heterotrophic bacteria as a “black box,” which does not resolve metabolic heterogeneity nor address ecologically important processes such as the successive modification of different types of organic matter. Here we directly address the heterogeneity of metabolism by characterizing the carbon source utilization preferences of 63 heterotrophic bacteria representative of several major marine clades. By systematically growing these bacteria on 10 media containing specific subsets of carbon sources found in marine biomass, we obtained a phenotypic fingerprint that we used to explore the relationship between metabolic preferences and phylogenetic or genomic features. At the class level, these bacteria display broadly conserved patterns of preference for different carbon sources. Despite these broad taxonomic trends, growth profiles correlate poorly with phylogenetic distance or genome-wide gene content. However, metabolic preferences are strongly predicted by a handful of key enzymes that preferentially belong to a few enriched metabolic pathways, such as those involved in glyoxylate metabolism and biofilm formation. We find that enriched pathways point to enzymes directly involved in the metabolism of the corresponding carbon source and suggest potential associations between metabolic preferences and other ecologically relevant traits. The availability of systematic phenotypes across multiple synthetic media constitutes a valuable resource for future quantitative modeling efforts and systematic studies of interspecies interactions. IMPORTANCE Half of the Earth’s annual primary production is carried out by phytoplankton in the surface ocean. However, this metabolic activity is heavily impacted by heterotrophic bacteria, which dominate the transformation of organic matter released from phytoplankton. Here, we characterize the diversity of metabolic preferences across many representative heterotrophs by systematically growing them on different fractions of dissolved organic carbon. Our analysis suggests that different clades of bacteria have substantially distinct preferences for specific carbon sources, in a way that cannot be simply mapped onto phylogeny. These preferences are associated with the presence of specific genes and pathways, reflecting an association between metabolic capabilities and ecological lifestyles. In addition to helping understand the importance of heterotrophs under different conditions, the phenotypic fingerprint we obtained can help build higher resolution quantitative models of global microbial activity and biogeochemical cycles in the oceans.
Collapse
|
48
|
Kim M, Im E, Jin Ahn Y. Enhanced Acetate Tolerance and Recombinant Protein Accumulation in Escherichia coli by Transgenic Expression of a Heat Shock Protein from Carrot ( Daucus carota L.). IRANIAN JOURNAL OF BIOTECHNOLOGY 2022; 20:e3177. [PMID: 36381282 PMCID: PMC9618011 DOI: 10.30498/ijb.2022.309657.3177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND In Escherichia coli (E. coli) culture, acetate accumulates as an undesirable by-product of aerobic fermentation on glucose and inhibits cell growth and recombinant protein production. OBJECTIVES We examined whether the heterologous expression of a eukaryotic heat shock protein (Hsp) can confer tolerance to acetate in E. coli. MATERIALS AND METHODS Transgenic cell lines (TCLs) heterologously expressing a small heat shock protein (sHsp) from carrot (Daucus carota L.), DcHsp17.7, were exposed to heat, sodium acetate, and alkaline conditions. The cell growth and cell viability were examined by measuring O.D.600 and colony-forming units (CFU), respectively. The His-tagged recombinant alcohol dehydrogenase (ADH) gene cloned in a pET11a expression vector was introduced into TCL1 and expressed by isopropyl β-D-1-thiogalactopyranoside treatment. After purifying using Ni-NTA affinity chromatography, its accumulation levels were examined using SDS-PAGE in the presence of acetate. RESULTS TCLs constitutively expressing DcHsp17.7 showed improved growth, cell density, and cell viability under the stress conditions of heat, acetate, and alkaline compared to an empty vector control line. In acetate stress conditions, TCL1 accumulated more cellular proteins (approximately 130%) than the control. The recombinant ADH accumulated to a higher level in TCL1 (2.2-fold at 16 °C) than the control. The addition of acetate reduced the recombinant ADH level by 70% in the control when compared with the absence of acetate. In contrast, recombinant ADH accumulation was not affected by acetate in TCL1. In the presence of acetate, TCL1 accumulated 6.4-fold more recombinant ADH than did the control. Furthermore, recombinant ADH produced in TCL1 showed 1.5-fold higher enzyme activity than that produced in the control in the presence or absence of acetate. CONCLUSION Our study showed that heterologously expressed DcHsp17.7 from carrot can alleviate the negative effects of acetate on E. coli.
Collapse
Affiliation(s)
- Minhye Kim
- Department of Biotechnology, Sangmyung University, 20 Hongjimun 2-gil, Jongno-gu, Seoul 03016, Korea
| | - Eunju Im
- Department of Biotechnology, Sangmyung University, 20 Hongjimun 2-gil, Jongno-gu, Seoul 03016, Korea
| | - Yeh Jin Ahn
- Department of Biotechnology, Sangmyung University, 20 Hongjimun 2-gil, Jongno-gu, Seoul 03016, Korea
| |
Collapse
|
49
|
Kang JW, Tang X, Walton CJ, Brown MJ, Brewer RA, Maddela RL, Zheng JJ, Agus JK, Zivkovic AM. Multi-Omic Analyses Reveal Bifidogenic Effect and Metabolomic Shifts in Healthy Human Cohort Supplemented With a Prebiotic Dietary Fiber Blend. Front Nutr 2022; 9:908534. [PMID: 35782954 PMCID: PMC9248813 DOI: 10.3389/fnut.2022.908534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/20/2022] [Indexed: 12/14/2022] Open
Abstract
Dietary fiber, a nutrient derived mainly from whole grains, vegetables, fruits, and legumes, is known to confer a number of health benefits, yet most Americans consume less than half of the daily recommended amount. Convenience and affordability are key factors determining the ability of individuals to incorporate fiber-rich foods into their diet, and many Americans struggle to access, afford, and prepare foods rich in fiber. The objective of this clinical study was to test the changes in microbial community composition, human metabolomics, and general health markers of a convenient, easy to use prebiotic supplement in generally healthy young participants consuming a diet low in fiber. Twenty healthy adults participated in this randomized, placebo-controlled, double-blind, crossover study which was registered at clinicaltrials.gov as NCT03785860. During the study participants consumed 12 g of a prebiotic fiber supplement and 12 g of placebo daily as a powder mixed with water as part of their habitual diet in randomized order for 4 weeks, with a 4-week washout between treatment arms. Fecal microbial DNA was extracted and sequenced by shallow shotgun sequencing on an Illumina NovaSeq. Plasma metabolites were detected using liquid chromatography–mass spectrometry with untargeted analysis. The phylum Actinobacteria, genus Bifidobacterium, and several Bifidobacterium species (B. bifidum, B. adolescentis, B. breve, B. catenulatum, and B. longum) significantly increased after prebiotic supplementation when compared to the placebo. The abundance of genes associated with the utilization of the prebiotic fiber ingredients (sacA, xfp, xpk) and the production of acetate (poxB, ackA) significantly changed with prebiotic supplementation. Additionally, the abundance of genes associated with the prebiotic utilization (xfp, xpk), acetate production (ackA), and choline to betaine oxidation (gbsB) were significantly correlated with changes in the abundance of the genus Bifidobacterium in the prebiotic group. Plasma concentrations of the bacterially produced metabolite indolepropionate significantly increased. The results of this study demonstrate that an easy to consume, low dose (12 g) of a prebiotic powder taken daily increases the abundance of beneficial bifidobacteria and the production of health-promoting bacteria-derived metabolites in healthy individuals with a habitual low-fiber diet.
Collapse
Affiliation(s)
- Jea Woo Kang
- Department of Nutrition, University of California, Davis, Davis, CA, United States
| | - Xinyu Tang
- Department of Nutrition, University of California, Davis, Davis, CA, United States
| | | | - Mark J. Brown
- USANA Health Sciences, Inc., Salt Lake City, UT, United States
| | | | | | - Jack Jingyuan Zheng
- Department of Nutrition, University of California, Davis, Davis, CA, United States
| | - Joanne K. Agus
- Department of Nutrition, University of California, Davis, Davis, CA, United States
| | - Angela M. Zivkovic
- Department of Nutrition, University of California, Davis, Davis, CA, United States
- *Correspondence: Angela M. Zivkovic
| |
Collapse
|
50
|
Stark C, Münßinger S, Rosenau F, Eikmanns BJ, Schwentner A. The Potential of Sequential Fermentations in Converting C1 Substrates to Higher-Value Products. Front Microbiol 2022; 13:907577. [PMID: 35722332 PMCID: PMC9204031 DOI: 10.3389/fmicb.2022.907577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 05/18/2022] [Indexed: 11/13/2022] Open
Abstract
Today production of (bulk) chemicals and fuels almost exclusively relies on petroleum-based sources, which are connected to greenhouse gas release, fueling climate change. This increases the urgence to develop alternative bio-based technologies and processes. Gaseous and liquid C1 compounds are available at low cost and often occur as waste streams. Acetogenic bacteria can directly use C1 compounds like CO, CO2, formate or methanol anaerobically, converting them into acetate and ethanol for higher-value biotechnological products. However, these microorganisms possess strict energetic limitations, which in turn pose limitations to their potential for biotechnological applications. Moreover, efficient genetic tools for strain improvement are often missing. However, focusing on the metabolic abilities acetogens provide, they can prodigiously ease these technological disadvantages. Producing acetate and ethanol from C1 compounds can fuel via bio-based intermediates conversion into more energy-demanding, higher-value products, by deploying aerobic organisms that are able to grow with acetate/ethanol as carbon and energy source. Promising new approaches have become available combining these two fermentation steps in sequential approaches, either as separate fermentations or as integrated two-stage fermentation processes. This review aims at introducing, comparing, and evaluating the published approaches of sequential C1 fermentations, delivering a list of promising organisms for the individual fermentation steps and giving an overview of the existing broad spectrum of products based on acetate and ethanol. Understanding of these pioneering approaches allows collecting ideas for new products and may open avenues toward making full use of the technological potential of these concepts for establishment of a sustainable biotechnology.
Collapse
Affiliation(s)
- Christina Stark
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
| | - Sini Münßinger
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
| | - Frank Rosenau
- Institute of Pharmaceutical Biotechnology, University of Ulm, Ulm, Germany
| | - Bernhard J. Eikmanns
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
- *Correspondence: Bernhard J. Eikmanns,
| | - Andreas Schwentner
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
| |
Collapse
|