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Shi Z, Long X, Zhang C, Chen Z, Usman M, Zhang Y, Zhang S, Luo G. Viral and Bacterial Community Dynamics in Food Waste and Digestate from Full-Scale Biogas Plants. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:13010-13022. [PMID: 38989650 DOI: 10.1021/acs.est.4c04109] [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: 07/12/2024]
Abstract
Anaerobic digestion (AD) is commonly used in food waste treatment. Prokaryotic microbial communities in AD of food waste have been comprehensively studied. The role of viruses, known to affect microbial dynamics and metabolism, remains largely unexplored. This study employed metagenomic analysis and recovered 967 high-quality viral bins within food waste and digestate derived from 8 full-scale biogas plants. The diversity of viral communities was higher in digestate. In silico predictions linked 20.8% of viruses to microbial host populations, highlighting possible virus predators of key functional microbes. Lineage-specific virus-host ratio varied, indicating that viral infection dynamics might differentially affect microbial responses to the varying process parameters. Evidence for virus-mediated gene transfer was identified, emphasizing the potential role of viruses in controlling the microbiome. AD altered the specific process parameters, potentially promoting a shift in viral lifestyle from lysogenic to lytic. Viruses encoding auxiliary metabolic genes (AMGs) were involved in microbial carbon and nutrient cycling, and most AMGs were transcriptionally expressed in digestate, meaning that viruses with active functional states were likely actively involved in AD. These findings provided a comprehensive profile of viral and bacterial communities and expanded knowledge of the interactions between viruses and hosts in food waste and digestate.
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Affiliation(s)
- Zhijian Shi
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200438, China
| | - Xinyi Long
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200438, China
| | - Chao Zhang
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200438, China
| | - Zheng Chen
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200438, China
| | - Muhammad Usman
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Yalei Zhang
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Shicheng Zhang
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200438, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
- Shanghai Technical Service Platform for Pollution Control and Resource Utilization of Organic Wastes, Shanghai 200438, China
| | - Gang Luo
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200438, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
- Shanghai Technical Service Platform for Pollution Control and Resource Utilization of Organic Wastes, Shanghai 200438, China
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Lee J, Kim H, Park JS. Beyond the Bile: Exploring the Microbiome and Metabolites in Cholangiocarcinoma. Life (Basel) 2024; 14:698. [PMID: 38929681 PMCID: PMC11204422 DOI: 10.3390/life14060698] [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: 05/03/2024] [Revised: 05/25/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024] Open
Abstract
INTRODUCTION Cholangiocarcinoma (CCC) still has a high mortality rate despite improvements in diagnostic and therapeutic techniques. The role of the human microbiome in CCC is poorly understood, and a recent metagenomic analysis demonstrated a significant correlation between microbiome-associated carcinogenesis and CCC. This study aimed to investigate changes in microbiome composition associated with CCC and its metabolic signature by integrating taxonomic and functional information with metabolomics data and in vitro experimental results. METHODS From February 2019 to January 2021, this study included patients who underwent endoscopic retrograde cholangiopancreatography (ERCP), both with and without a diagnosis of CCC. Bile samples were collected via endoscopic nasobiliary drainages (ENBD) and subjected to DNA extraction, PCR amplification of the bacterial 16S rRNA gene V3-V4 region, and data analysis using QIIME2. In vitro Carboxyfluorescein succinimidyl ester (CFSE) proliferation and Annexin V/PI apoptosis assays were performed to investigate the effects of metabolites on CCC cells. RESULTS A total of 24 patients were included in the study. Bile fluid analysis revealed a significantly higher abundance of Escherichia coli in the CCC group. Alpha diversity analyses exhibited significant differences between the CCC and non-CCC groups, and Nuclear Magnetic Resonance (NMR) spectroscopy metabolic profiling identified 15 metabolites with significant concentration differences; isoleucine showed the most notable difference. In vitro experiments demonstrated that isoleucine suppressed CCC cell proliferation but did not induce apoptosis. CONCLUSIONS This research underlines the significance of biliary dysbiosis and specific bile metabolites, such as isoleucine, in influencing the development and progression of CCC.
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Affiliation(s)
- Jungnam Lee
- Department of Internal Medicine, Inha University Hospital, Inha University School of Medicine, Incheon 22332, Republic of Korea; (J.L.); (H.K.)
| | - Hanul Kim
- Department of Internal Medicine, Inha University Hospital, Inha University School of Medicine, Incheon 22332, Republic of Korea; (J.L.); (H.K.)
| | - Jin-Seok Park
- Department of Internal Medicine, Shihwa Medical Center, Siheung 15034, Republic of Korea
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Schulz-Mirbach H, Dronsella B, He H, Erb TJ. Creating new-to-nature carbon fixation: A guide. Metab Eng 2024; 82:12-28. [PMID: 38160747 DOI: 10.1016/j.ymben.2023.12.012] [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: 10/10/2023] [Revised: 12/23/2023] [Accepted: 12/27/2023] [Indexed: 01/03/2024]
Abstract
Synthetic biology aims at designing new biological functions from first principles. These new designs allow to expand the natural solution space and overcome the limitations of naturally evolved systems. One example is synthetic CO2-fixation pathways that promise to provide more efficient ways for the capture and conversion of CO2 than natural pathways, such as the Calvin Benson Bassham (CBB) cycle of photosynthesis. In this review, we provide a practical guideline for the design and realization of such new-to-nature CO2-fixation pathways. We introduce the concept of "synthetic CO2-fixation", and give a general overview over the enzymology and topology of synthetic pathways, before we derive general principles for their design from their eight naturally evolved analogs. We provide a comprehensive summary of synthetic carbon-assimilation pathways and derive a step-by-step, practical guide from the theoretical design to their practical implementation, before ending with an outlook on new developments in the field.
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Affiliation(s)
- Helena Schulz-Mirbach
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Beau Dronsella
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany; Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Hai He
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Tobias J Erb
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany; Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch-Str. 16, D-35043, Marburg, Germany.
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4
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Qiao W, Dong G, Xu S, Li L, Shi S. Engineering propionyl-CoA pools for de novo biosynthesis of odd-chain fatty acids in microbial cell factories. Crit Rev Biotechnol 2023; 43:1063-1072. [PMID: 35994297 DOI: 10.1080/07388551.2022.2100736] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 06/28/2022] [Indexed: 11/03/2022]
Abstract
Odd-chain fatty acids (OcFAs) and their derivatives have attracted great interest due to their wide applications in the food, pharmaceutical and petrochemical industries. Microorganisms can naturally de novo produce fatty acids (FAs), where mainly, even-chain with acetyl-CoA instead of odd-chain with propionyl-CoA is used as the primer. Usually, the absence of the precursor propionyl-CoA is considered the main reason that limits the efficient production of OcFAs. It is thus crucial to explore/evaluate/identify promising propionyl-CoA biosynthetic pathways to achieve large-scale biosynthesis of OcFAs. This review discusses the latest advances in microbial metabolism engineering toward producing propionyl-CoA and considers future research directions and challenges toward optimized production of OcFAs.
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Affiliation(s)
- Weibo Qiao
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, PR China
| | - Genlai Dong
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, PR China
| | - Shijie Xu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, PR China
| | - Lingyun Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, PR China
| | - Shuobo Shi
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, PR China
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5
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Chlebek JL, Leonard SP, Kang-Yun C, Yung MC, Ricci DP, Jiao Y, Park DM. Prolonging genetic circuit stability through adaptive evolution of overlapping genes. Nucleic Acids Res 2023; 51:7094-7108. [PMID: 37260076 PMCID: PMC10359631 DOI: 10.1093/nar/gkad484] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/12/2023] [Accepted: 05/23/2023] [Indexed: 06/02/2023] Open
Abstract
The development of synthetic biological circuits that maintain functionality over application-relevant time scales remains a significant challenge. Here, we employed synthetic overlapping sequences in which one gene is encoded or 'entangled' entirely within an alternative reading frame of another gene. In this design, the toxin-encoding relE was entangled within ilvA, which encodes threonine deaminase, an enzyme essential for isoleucine biosynthesis. A functional entanglement construct was obtained upon modification of the ribosome-binding site of the internal relE gene. Using this optimized design, we found that the selection pressure to maintain functional IlvA stabilized the production of burdensome RelE for >130 generations, which compares favorably with the most stable kill-switch circuits developed to date. This stabilizing effect was achieved through a complete alteration of the allowable landscape of mutations such that mutations inactivating the entangled genes were disfavored. Instead, the majority of lineages accumulated mutations within the regulatory region of ilvA. By reducing baseline relE expression, these more 'benign' mutations lowered circuit burden, which suppressed the accumulation of relE-inactivating mutations, thereby prolonging kill-switch function. Overall, this work demonstrates the utility of sequence entanglement paired with an adaptive laboratory evolution campaign to increase the evolutionary stability of burdensome synthetic circuits.
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Affiliation(s)
- Jennifer L Chlebek
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Sean P Leonard
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Christina Kang-Yun
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Mimi C Yung
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Dante P Ricci
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Yongqin Jiao
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Dan M Park
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
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Li Z, Liu Q, Sun J, Sun J, Li M, Zhang Y, Deng A, Liu S, Wen T. Multivariate modular metabolic engineering for enhanced L-methionine biosynthesis in Escherichia coli. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:101. [PMID: 37312226 DOI: 10.1186/s13068-023-02347-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/23/2023] [Indexed: 06/15/2023]
Abstract
BACKGROUND L-Methionine is the only bulk amino acid that has not been industrially produced by the fermentation method. Due to highly complex and strictly regulated biosynthesis, the development of microbial strains for high-level L-methionine production has remained challenging in recent years. RESULTS By strengthening the L-methionine terminal synthetic module via site-directed mutation of L-homoserine O-succinyltransferase (MetA) and overexpression of metAfbr, metC, and yjeH, L-methionine production was increased to 1.93 g/L in shake flask fermentation. Deletion of the pykA and pykF genes further improved L-methionine production to 2.51 g/L in shake flask fermentation. Computer simulation and auxotrophic experiments verified that during the synthesis of L-methionine, equimolar amounts of L-isoleucine were accumulated via the elimination reaction of cystathionine γ-synthetase MetB due to the insufficient supply of L-cysteine. To increase the supply of L-cysteine, the L-cysteine synthetic module was strengthened by overexpression of cysEfbr, serAfbr, and cysDN, which further increased the production of L-methionine by 52.9% and significantly reduced the accumulation of the byproduct L-isoleucine by 29.1%. After optimizing the addition of ammonium thiosulfate, the final metabolically engineered strain MET17 produced 21.28 g/L L-methionine in 64 h with glucose as the carbon source in a 5 L fermenter, representing the highest L-methionine titer reported to date. CONCLUSIONS In this study, a high-efficiency strain for L-methionine production was derived from wild-type Escherichia coli W3110 by rational metabolic engineering strategies, providing an efficient platform for the industrial production of L-methionine.
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Affiliation(s)
- Zhongcai Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qian Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jiahui Sun
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, Hebei University, Baoding, 071002, China
| | - Jianjian Sun
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Mingjie Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yun Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Aihua Deng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shuwen Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Tingyi Wen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China.
- China Innovation Academy for Green Manufacture, Chinese Academy of Sciences, Beijing, 100049, China.
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7
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Stecker D, Hoffmann T, Link H, Commichau FM, Bremer E. L-Proline Synthesis Mutants of Bacillus subtilis Overcome Osmotic Sensitivity by Genetically Adapting L-Arginine Metabolism. Front Microbiol 2022; 13:908304. [PMID: 35783388 PMCID: PMC9245794 DOI: 10.3389/fmicb.2022.908304] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/17/2022] [Indexed: 11/30/2022] Open
Abstract
The accumulation of the compatible solute L-proline by Bacillus subtilis via synthesis is a cornerstone in the cell’s defense against high salinity as the genetic disruption of this biosynthetic process causes osmotic sensitivity. To understand how B. subtilis could potentially cope with high osmolarity surroundings without the functioning of its natural osmostress adaptive L-proline biosynthetic route (ProJ-ProA-ProH), we isolated suppressor strains of proA mutants under high-salinity growth conditions. These osmostress-tolerant strains carried mutations affecting either the AhrC transcriptional regulator or its operator positioned in front of the argCJBD-carAB-argF L-ornithine/L-citrulline/L-arginine biosynthetic operon. Osmostress protection assays, molecular analysis and targeted metabolomics showed that these mutations, in conjunction with regulatory mutations affecting rocR-rocDEF expression, connect and re-purpose three different physiological processes: (i) the biosynthetic pathway for L-arginine, (ii) the RocD-dependent degradation route for L-ornithine, and (iii) the last step in L-proline biosynthesis. Hence, osmostress adaptation without a functional ProJ-ProA-ProH route is made possible through a naturally existing, but inefficient, metabolic shunt that allows to substitute the enzyme activity of ProA by feeding the RocD-formed metabolite γ-glutamate-semialdehyde/Δ1-pyrroline-5-carboxylate into the biosynthetic route for the compatible solute L-proline. Notably, in one class of mutants, not only substantial L-proline pools but also large pools of L-citrulline were accumulated, a rather uncommon compatible solute in microorganisms. Collectively, our data provide an example of the considerable genetic plasticity and metabolic resourcefulness of B. subtilis to cope with everchanging environmental conditions.
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Affiliation(s)
- Daniela Stecker
- Faculty of Biology, Philipps-University Marburg, Marburg, Germany
| | - Tamara Hoffmann
- Faculty of Biology, Philipps-University Marburg, Marburg, Germany
- SYNMIKRO Research Center, Philipps-University Marburg, Marburg, Germany
| | - Hannes Link
- SYNMIKRO Research Center, Philipps-University Marburg, Marburg, Germany
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Fabian M. Commichau
- Insitute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
- Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, Germany
| | - Erhard Bremer
- Faculty of Biology, Philipps-University Marburg, Marburg, Germany
- SYNMIKRO Research Center, Philipps-University Marburg, Marburg, Germany
- *Correspondence: Erhard Bremer,
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Perchat N, Dubois C, Mor-Gautier R, Duquesne S, Lechaplais C, Roche D, Fouteau S, Darii E, Perret A. Characterization of a novel β-alanine biosynthetic pathway consisting of promiscuous metabolic enzymes. J Biol Chem 2022; 298:102067. [PMID: 35623386 PMCID: PMC9213253 DOI: 10.1016/j.jbc.2022.102067] [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: 12/16/2021] [Revised: 05/19/2022] [Accepted: 05/22/2022] [Indexed: 10/28/2022] Open
Abstract
Bacteria adapt to utilize the nutrients available in their environment through a sophisticated metabolic system composed of highly specialized enzymes. Although these enzymes can metabolize molecules other than those for which they evolved, their efficiency toward promiscuous substrates is considered too low to be of physiological relevance. Herein, we investigated the possibility that these promiscuous enzymes are actually efficient enough at metabolizing secondary substrates to modify the phenotype of the cell. For example, in the bacterium Acinetobacter baylyi ADP1 (ADP1), panD (coding for l-aspartate decarboxylase) encodes the only protein known to catalyze the synthesis of β-alanine, an obligate intermediate in CoA synthesis. However, we show that the ADP1 ΔpanD mutant could also form this molecule through an unknown metabolic pathway arising from promiscuous enzymes and grow as efficiently as the wildtype strain. Using metabolomic analyses, we identified 1,3-diaminopropane and 3-aminopropanal as intermediates in this novel pathway. We also conducted activity screening and enzyme kinetics to elucidate candidate enzymes involved in this pathway, including 2,4-diaminobutyrate aminotransferase (Dat) and 2,4-diaminobutyrate decarboxylase (Ddc) and validated this pathway in vivo by analyzing the phenotype of mutant bacterial strains. Finally, we experimentally demonstrate that this novel metabolic route is not restricted to ADP1. We propose that the occurrence of conserved genes in hundreds of genomes across many phyla suggests that this previously undescribed pathway is widespread in prokaryotes.
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Affiliation(s)
- Nadia Perchat
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Christelle Dubois
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Rémi Mor-Gautier
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Sophie Duquesne
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Christophe Lechaplais
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - David Roche
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Stéphanie Fouteau
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Ekaterina Darii
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Alain Perret
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France.
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Bhayani J, Iglesias MJ, Minen RI, Cereijo AE, Ballicora MA, Iglesias AA, Asencion Diez MD. Carbohydrate Metabolism in Bacteria: Alternative Specificities in ADP-Glucose Pyrophosphorylases Open Novel Metabolic Scenarios and Biotechnological Tools. Front Microbiol 2022; 13:867384. [PMID: 35572620 PMCID: PMC9093745 DOI: 10.3389/fmicb.2022.867384] [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: 02/01/2022] [Accepted: 03/22/2022] [Indexed: 11/13/2022] Open
Abstract
We explored the ability of ADP-glucose pyrophosphorylase (ADP-Glc PPase) from different bacteria to use glucosamine (GlcN) metabolites as a substrate or allosteric effectors. The enzyme from the actinobacteria Kocuria rhizophila exhibited marked and distinctive sensitivity to allosteric activation by GlcN-6P when producing ADP-Glc from glucose-1-phosphate (Glc-1P) and ATP. This behavior is also seen in the enzyme from Rhodococcus spp., the only one known so far to portray this activation. GlcN-6P had a more modest effect on the enzyme from other Actinobacteria (Streptomyces coelicolor), Firmicutes (Ruminococcus albus), and Proteobacteria (Agrobacterium tumefaciens) groups. In addition, we studied the catalytic capacity of ADP-Glc PPases from the different sources using GlcN-1P as a substrate when assayed in the presence of their respective allosteric activators. In all cases, the catalytic efficiency of Glc-1P was 1-2 orders of magnitude higher than GlcN-1P, except for the unregulated heterotetrameric protein (GlgC/GgD) from Geobacillus stearothermophilus. The Glc-1P substrate preference is explained using a model of ADP-Glc PPase from A. tumefaciens based on the crystallographic structure of the enzyme from potato tuber. The substrate-binding domain localizes near the N-terminal of an α-helix, which has a partial positive charge, thus favoring the interaction with a hydroxyl rather than a charged primary amine group. Results support the scenario where the ability of ADP-Glc PPases to use GlcN-1P as an alternative occurred during evolution despite the enzyme being selected to use Glc-1P and ATP for α-glucans synthesis. As an associated consequence in such a process, certain bacteria could have improved their ability to metabolize GlcN. The work also provides insights in designing molecular tools for producing oligo and polysaccharides with amino moieties.
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Affiliation(s)
- Jaina Bhayani
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Maria Josefina Iglesias
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Santa Fe, Argentina
| | - Romina I Minen
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Santa Fe, Argentina
| | - Antonela E Cereijo
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Santa Fe, Argentina
| | - Miguel A Ballicora
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Alberto A Iglesias
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Santa Fe, Argentina
| | - Matias D Asencion Diez
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Santa Fe, Argentina
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10
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Iacometti C, Marx K, Hönick M, Biletskaia V, Schulz-Mirbach H, Dronsella B, Satanowski A, Delmas VA, Berger A, Dubois I, Bouzon M, Döring V, Noor E, Bar-Even A, Lindner SN. Activating Silent Glycolysis Bypasses in Escherichia coli. BIODESIGN RESEARCH 2022; 2022:9859643. [PMID: 37850128 PMCID: PMC10521649 DOI: 10.34133/2022/9859643] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 04/08/2022] [Indexed: 10/19/2023] Open
Abstract
All living organisms share similar reactions within their central metabolism to provide precursors for all essential building blocks and reducing power. To identify whether alternative metabolic routes of glycolysis can operate in E. coli, we complementarily employed in silico design, rational engineering, and adaptive laboratory evolution. First, we used a genome-scale model and identified two potential pathways within the metabolic network of this organism replacing canonical Embden-Meyerhof-Parnas (EMP) glycolysis to convert phosphosugars into organic acids. One of these glycolytic routes proceeds via methylglyoxal and the other via serine biosynthesis and degradation. Then, we implemented both pathways in E. coli strains harboring defective EMP glycolysis. Surprisingly, the pathway via methylglyoxal seemed to immediately operate in a triosephosphate isomerase deletion strain cultivated on glycerol. By contrast, in a phosphoglycerate kinase deletion strain, the overexpression of methylglyoxal synthase was necessary to restore growth of the strain. Furthermore, we engineered the "serine shunt" which converts 3-phosphoglycerate via serine biosynthesis and degradation to pyruvate, bypassing an enolase deletion. Finally, to explore which of these alternatives would emerge by natural selection, we performed an adaptive laboratory evolution study using an enolase deletion strain. Our experiments suggest that the evolved mutants use the serine shunt. Our study reveals the flexible repurposing of metabolic pathways to create new metabolite links and rewire central metabolism.
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Affiliation(s)
- Camillo Iacometti
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Katharina Marx
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Maria Hönick
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Viktoria Biletskaia
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Helena Schulz-Mirbach
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Beau Dronsella
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Ari Satanowski
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Valérie A. Delmas
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry-Courcouronne, France
| | - Anne Berger
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry-Courcouronne, France
| | - Ivan Dubois
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry-Courcouronne, France
| | - Madeleine Bouzon
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry-Courcouronne, France
| | - Volker Döring
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry-Courcouronne, France
| | - Elad Noor
- Institute of Molecular Systems Biology, ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Arren Bar-Even
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Steffen N. Lindner
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Department of Biochemistry, Charité Universitätsmedizin, Virchowweg 6, 10117 Berlin, Germany
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11
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Wan C, Gao L, Wang J, Lei X, Wu Y, Gao J. Proteomics characterization nitrogen fertilizer promotes the starch synthesis and metabolism and amino acid biosynthesis in common buckwheat. Int J Biol Macromol 2021; 192:342-349. [PMID: 34599992 DOI: 10.1016/j.ijbiomac.2021.09.170] [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: 08/03/2021] [Revised: 09/21/2021] [Accepted: 09/24/2021] [Indexed: 11/16/2022]
Abstract
Nitrogen (N) affects common buckwheat quality by affecting starch and amino acids (AAs) content, but its molecular mechanism is still unclear. We selected two common buckwheat varieties with high and low starch content, and designed two treatments with 180 and 0 kg N/ha. Application of high-N led to significant increases in starch, amylose and amylopectin content. Of 1337 differentially expressed proteins (DEPs) induced by high-N conditions. 472DEPs were significantly upregulated and 176DEPs downregulated for Xinong9976. 239DEPs were significantly upregulated and 126DEPs downregulated for Beizaosheng. The six alpha-glucan phosphorylases, three alpha-amylases, one granule-bound starch synthase 1 and one sucrose synthase exhibited higher expression at the 180 kg N/ha than at the 0 kg N/ha. In addition, high-N application promoted arginine, leucine, isoleucine and valine biosynthesis. This study revealed the effect of N on the starch and AA content of common buckwheat and its mechanism. The crucial proteins identified may develop the quality of common buckwheat.
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Affiliation(s)
- Chenxi Wan
- Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Licheng Gao
- Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Jiale Wang
- Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Xinhui Lei
- Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Yixin Wu
- Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Jinfeng Gao
- Northwest A&F University, Yangling, Shaanxi Province 712100, China.
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12
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Griffith CM, Walvekar AS, Linster CL. Approaches for completing metabolic networks through metabolite damage and repair discovery. CURRENT OPINION IN SYSTEMS BIOLOGY 2021; 28:None. [PMID: 34957344 PMCID: PMC8669784 DOI: 10.1016/j.coisb.2021.100379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Metabolites are prone to damage, either via enzymatic side reactions, which collectively form the underground metabolism, or via spontaneous chemical reactions. The resulting non-canonical metabolites that can be toxic, are mended by dedicated "metabolite repair enzymes." Deficiencies in the latter can cause severe disease in humans, whereas inclusion of repair enzymes in metabolically engineered systems can improve the production yield of value-added chemicals. The metabolite damage and repair loops are typically not yet included in metabolic reconstructions and it is likely that many remain to be discovered. Here, we review strategies and associated challenges for unveiling non-canonical metabolites and metabolite repair enzymes, including systematic approaches based on high-resolution mass spectrometry, metabolome-wide side-activity prediction, as well as high-throughput substrate and phenotypic screens.
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Affiliation(s)
| | | | - Carole L. Linster
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
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13
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Jahn M, Crang N, Janasch M, Hober A, Forsström B, Kimler K, Mattausch A, Chen Q, Asplund-Samuelsson J, Hudson EP. Protein allocation and utilization in the versatile chemolithoautotroph Cupriavidus necator. eLife 2021; 10:69019. [PMID: 34723797 PMCID: PMC8591527 DOI: 10.7554/elife.69019] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 10/30/2021] [Indexed: 12/12/2022] Open
Abstract
Bacteria must balance the different needs for substrate assimilation, growth
functions, and resilience in order to thrive in their environment. Of all
cellular macromolecules, the bacterial proteome is by far the most important
resource and its size is limited. Here, we investigated how the highly versatile
'knallgas' bacterium Cupriavidus necator reallocates protein
resources when grown on different limiting substrates and with different growth
rates. We determined protein quantity by mass spectrometry and estimated enzyme
utilization by resource balance analysis modeling. We found that C.
necator invests a large fraction of its proteome in functions that
are hardly utilized. Of the enzymes that are utilized, many are present in
excess abundance. One prominent example is the strong expression of CBB cycle
genes such as Rubisco during growth on fructose. Modeling and mutant competition
experiments suggest that CO2-reassimilation through Rubisco does not
provide a fitness benefit for heterotrophic growth, but is rather an investment
in readiness for autotrophy.
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Affiliation(s)
- Michael Jahn
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Nick Crang
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Markus Janasch
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Andreas Hober
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Björn Forsström
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Kyle Kimler
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Alexander Mattausch
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Qi Chen
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Johannes Asplund-Samuelsson
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Elton Paul Hudson
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
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14
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Orsi E, Claassens NJ, Nikel PI, Lindner SN. Growth-coupled selection of synthetic modules to accelerate cell factory development. Nat Commun 2021; 12:5295. [PMID: 34489458 PMCID: PMC8421431 DOI: 10.1038/s41467-021-25665-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 08/23/2021] [Indexed: 11/18/2022] Open
Abstract
Synthetic biology has brought about a conceptual shift in our ability to redesign microbial metabolic networks. Combining metabolic pathway-modularization with growth-coupled selection schemes is a powerful tool that enables deep rewiring of the cell factories’ biochemistry for rational bioproduction.
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Affiliation(s)
- Enrico Orsi
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Nico J Claassens
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Steffen N Lindner
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.
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15
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Copley SD. Setting the stage for evolution of a new enzyme. Curr Opin Struct Biol 2021; 69:41-49. [PMID: 33865035 DOI: 10.1016/j.sbi.2021.03.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 02/19/2021] [Accepted: 03/03/2021] [Indexed: 12/18/2022]
Abstract
The evolution of novel enzymes has fueled the diversification of life on earth for billions of years. Insights into events that set the stage for the evolution of a new enzyme can be obtained from ancestral reconstruction and laboratory evolution. Ancestral reconstruction can reveal the emergence of a promiscuous activity in a pre-existing protein and the impact of subsequent mutations that enhance a new activity. Laboratory evolution provides a more holistic view by revealing mutations elsewhere in the genome that indirectly enhance the level of a newly important enzymatic activity. This review will highlight recent studies that probe the early stages of the evolution of a new enzyme from these complementary points of view.
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Affiliation(s)
- Shelley D Copley
- Department of Molecular, Cellular and Developmental Biology, The Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO, 80309, USA.
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