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Dong Z, Li L, Du G, Zhang Y, Wang X, Li S, Xiang W. A previously unidentified sugar transporter for engineering of high-yield Streptomyces. Appl Microbiol Biotechnol 2024; 108:72. [PMID: 38194147 DOI: 10.1007/s00253-023-12964-9] [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: 08/28/2023] [Revised: 11/04/2023] [Accepted: 11/07/2023] [Indexed: 01/10/2024]
Abstract
Sugar transporters have significant contributions to regulate metabolic flux towards products and they are general potential targets for engineering of high-yield microbial cell factories. Streptomyces, well-known producers of natural product pharmaceuticals, contain an abundance of sugar transporters, while few of them are well characterized and applied. Here, we report a previously unidentified ATP-binding cassette (ABC) sugar transporter TP6568 found within a Streptomyces avermitilis transposon library, along with its key regulator GM006564. Subsequent in silico molecular docking and genetic experiments demonstrated that TP6568 possessed a broad substrate specificity. It could not only promote uptake of diverse monosaccharides and disaccharides, but also enhance the utilization of industrial carbon sources such as starch, sucrose, and dextrin. Constitutive overexpression of TP6568 resulted in decrease of residual total sugar by 36.16%, 39.04%, 38.40%, and 30.21% in engineered S. avermitilis S0, Streptomyces caniferus NEAU6, Streptomyces bingchenggensis BC-101-4, and Streptomyces roseosporus NRRL 11379 than their individual parent strain, respectively. Production of avermectin B1a, guvermectin, and milbemycin A3/A4 increased by 75.61%, 56.89%, and 41.13%, respectively. We then overexpressed TP6568 in combination with the regulator GM006564 in a high-yield strain S. avermitilis S45, and further fine-tuning of their overexpression levels boosted production of avermectin B1a by 50.97% to 7.02 g/L in the engineering strain. Our work demonstrates that TP6568 as a promising sugar transporter may have broad applications in construction of high-yield Streptomyces microbial cell factories for desirable natural product pharmaceuticals. KEY POINTS: • TP6568 from Streptomyces avermitilis was identified as a sugar transporter • TP6568 enhanced utilization of diverse industrially used sugars in Streptomyces • TP6568 is a useful transporter to construct high-yield Streptomyces cell factories.
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Affiliation(s)
- Zhuoxu Dong
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Lei Li
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Guozhong Du
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yanyan Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiangjing Wang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, China
| | - Shanshan Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Wensheng Xiang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, China.
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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2
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Møller-Hansen I, Sáez-Sáez J, van der Hoek SA, Dyekjær JD, Christensen HB, Wright Muelas M, O’Hagan S, Kell DB, Borodina I. Deorphanizing solute carriers in Saccharomyces cerevisiae for secondary uptake of xenobiotic compounds. Front Microbiol 2024; 15:1376653. [PMID: 38680917 PMCID: PMC11045925 DOI: 10.3389/fmicb.2024.1376653] [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: 01/25/2024] [Accepted: 03/25/2024] [Indexed: 05/01/2024] Open
Abstract
The exchange of small molecules between the cell and the environment happens through transporter proteins. Besides nutrients and native metabolic products, xenobiotic molecules are also transported, however it is not well understood which transporters are involved. In this study, by combining exo-metabolome screening in yeast with transporter characterization in Xenopus oocytes, we mapped the activity of 30 yeast transporters toward six small non-toxic substrates. Firstly, using LC-MS, we determined 385 compounds from a chemical library that were imported and exported by S. cerevisiae. Of the 385 compounds transported by yeast, we selected six compounds (viz. sn-glycero-3-phosphocholine, 2,5-furandicarboxylic acid, 2-methylpyrazine, cefadroxil, acrylic acid, 2-benzoxazolol) for characterization against 30 S. cerevisiae xenobiotic transport proteins expressed in Xenopus oocytes. The compounds were selected to represent a diverse set of chemicals with a broad interest in applied microbiology. Twenty transporters showed activity toward one or more of the compounds. The tested transporter proteins were mostly promiscuous in equilibrative transport (i.e., facilitated diffusion). The compounds 2,5-furandicarboxylic acid, 2-methylpyrazine, cefadroxil, and sn-glycero-3-phosphocholine were transported equilibratively by transporters that could transport up to three of the compounds. In contrast, the compounds acrylic acid and 2-benzoxazolol, were strictly transported by dedicated transporters. The prevalence of promiscuous equilibrative transporters of non-native substrates has significant implications for strain development in biotechnology and offers an explanation as to why transporter engineering has been a challenge in metabolic engineering. The method described here can be generally applied to study the transport of other small non-toxic molecules. The yeast transporter library is available at AddGene (ID 79999).
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Affiliation(s)
- Iben Møller-Hansen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
| | - Javier Sáez-Sáez
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
| | - Steven A. van der Hoek
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
| | - Jane D. Dyekjær
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
| | - Hanne B. Christensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
| | - Marina Wright Muelas
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Steve O’Hagan
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| | - Douglas B. Kell
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
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3
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Ruffinatti FA, Scarpellino G, Chinigò G, Visentin L, Munaron L. The Emerging Concept of Transportome: State of the Art. Physiology (Bethesda) 2023; 38:0. [PMID: 37668550 DOI: 10.1152/physiol.00010.2023] [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: 04/12/2023] [Revised: 09/01/2023] [Accepted: 09/01/2023] [Indexed: 09/06/2023] Open
Abstract
The array of ion channels and transporters expressed in cell membranes, collectively referred to as the transportome, is a complex and multifunctional molecular machinery; in particular, at the plasma membrane level it finely tunes the exchange of biomolecules and ions, acting as a functionally adaptive interface that accounts for dynamic plasticity in the response to environmental fluctuations and stressors. The transportome is responsible for the definition of membrane potential and its variations, participates in the transduction of extracellular signals, and acts as a filter for most of the substances entering and leaving the cell, thus enabling the homeostasis of many cellular parameters. For all these reasons, physiologists have long been interested in the expression and functionality of ion channels and transporters, in both physiological and pathological settings and across the different domains of life. Today, thanks to the high-throughput technologies of the postgenomic era, the omics approach to the study of the transportome is becoming increasingly popular in different areas of biomedical research, allowing for a more comprehensive, integrated, and functional perspective of this complex cellular apparatus. This article represents a first effort for a systematic review of the scientific literature on this topic. Here we provide a brief overview of all those studies, both primary and meta-analyses, that looked at the transportome as a whole, regardless of the biological problem or the models they used. A subsequent section is devoted to the methodological aspect by reviewing the most important public databases annotating ion channels and transporters, along with the tools they provide to retrieve such information. Before conclusions, limitations and future perspectives are also discussed.
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Affiliation(s)
- Federico Alessandro Ruffinatti
- Turin Cell Physiology Laboratory (TCP-Lab), Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Giorgia Scarpellino
- Turin Cell Physiology Laboratory (TCP-Lab), Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Giorgia Chinigò
- Turin Cell Physiology Laboratory (TCP-Lab), Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Luca Visentin
- Turin Cell Physiology Laboratory (TCP-Lab), Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Luca Munaron
- Turin Cell Physiology Laboratory (TCP-Lab), Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
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4
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Deng S, Kim J, Pomraning KR, Gao Y, Evans JE, Hofstad BA, Dai Z, Webb-Robertson BJ, Powell SM, Novikova IV, Munoz N, Kim YM, Swita M, Robles AL, Lemmon T, Duong RD, Nicora C, Burnum-Johnson KE, Magnuson J. Identification of a specific exporter that enables high production of aconitic acid in Aspergillus pseudoterreus. Metab Eng 2023; 80:163-172. [PMID: 37778408 DOI: 10.1016/j.ymben.2023.09.011] [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: 01/31/2023] [Revised: 07/25/2023] [Accepted: 09/18/2023] [Indexed: 10/03/2023]
Abstract
Aconitic acid is an unsaturated tricarboxylic acid that is attractive for its potential use in manufacturing biodegradable and biocompatible polymers, plasticizers, and surfactants. Previously Aspergillus pseudoterreus was engineered as a platform to produce aconitic acid by deleting the cadA (cis-aconitic acid decarboxylase) gene in the itaconic acid biosynthetic pathway. In this study, the aconitic acid transporter gene (aexA) was identified using comparative global discovery proteomics analysis between the wild-type and cadA deletion strains. The protein AexA belongs to the Major Facilitator Superfamily (MFS). Deletion of aexA almost abolished aconitic acid secretion, while its overexpression led to a significant increase in aconitic acid production. Transportation of aconitic acid across the plasma membrane is a key limiting step in its production. In vitro, proteoliposome transport assay further validated AexA's function and substrate specificity. This research provides new approaches to efficiently pinpoint and characterize exporters of fungal organic acids and accelerate metabolic engineering to improve secretion capability and lower the cost of bioproduction.
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Affiliation(s)
- Shuang Deng
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA; Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Joonhoon Kim
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA; Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Kyle R Pomraning
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA; Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Yuqian Gao
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA; Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - James E Evans
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Beth A Hofstad
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA; Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Ziyu Dai
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA; Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Bobbie-Jo Webb-Robertson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Samantha M Powell
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Irina V Novikova
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Nathalie Munoz
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA; Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Young-Mo Kim
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA; Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Marie Swita
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Ana L Robles
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA; Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Teresa Lemmon
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Rylan D Duong
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Carrie Nicora
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Kristin E Burnum-Johnson
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA; Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Jon Magnuson
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA; Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
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Benyamin MS, Perisin MP, Hellman CA, Schwalm ND, Jahnke JP, Sund CJ. Modeling control and transduction of electrochemical gradients in acid-stressed bacteria. iScience 2023; 26:107140. [PMID: 37404371 PMCID: PMC10316662 DOI: 10.1016/j.isci.2023.107140] [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: 09/15/2022] [Revised: 03/05/2023] [Accepted: 06/12/2023] [Indexed: 07/06/2023] Open
Abstract
Transmembrane electrochemical gradients drive solute uptake and constitute a substantial fraction of the cellular energy pool in bacteria. These gradients act not only as "homeostatic contributors," but also play a dynamic and keystone role in several bacterial functions, including sensing, stress response, and metabolism. At the system level, multiple gradients interact with ion transporters and bacterial behavior in a complex, rapid, and emergent manner; consequently, experiments alone cannot untangle their interdependencies. Electrochemical gradient modeling provides a general framework to understand these interactions and their underlying mechanisms. We quantify the generation, maintenance, and interactions of electrical, proton, and potassium potential gradients under lactic acid-stress and lactic acid fermentation. Further, we elucidate a gradient-mediated mechanism for intracellular pH sensing and stress response. We demonstrate that this gradient model can yield insights on the energetic limitations of membrane transport, and can predict bacterial behavior across changing environments.
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Affiliation(s)
- Marcus S. Benyamin
- Biological and Biotechnology Sciences Division, DEVCOM Army Research Laboratory, Adelphi, MD, USA
| | - Matthew P. Perisin
- Biological and Biotechnology Sciences Division, DEVCOM Army Research Laboratory, Adelphi, MD, USA
| | - Caleb A. Hellman
- Biological and Biotechnology Sciences Division, DEVCOM Army Research Laboratory, Adelphi, MD, USA
| | - Nathan D. Schwalm
- Biological and Biotechnology Sciences Division, DEVCOM Army Research Laboratory, Adelphi, MD, USA
| | - Justin P. Jahnke
- Biological and Biotechnology Sciences Division, DEVCOM Army Research Laboratory, Adelphi, MD, USA
| | - Christian J. Sund
- Biological and Biotechnology Sciences Division, DEVCOM Army Research Laboratory, Adelphi, MD, USA
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Malla S, van der Helm E, Darbani B, Wieschalka S, Förster J, Borodina I, Sommer MOA. A Novel Efficient L-Lysine Exporter Identified by Functional Metagenomics. Front Microbiol 2022; 13:855736. [PMID: 35495724 PMCID: PMC9048822 DOI: 10.3389/fmicb.2022.855736] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 03/23/2022] [Indexed: 12/14/2022] Open
Abstract
Lack of active export system often limits the industrial bio-based production processes accumulating the intracellular product and hence complexing the purification steps. L-lysine, an essential amino acid, is produced biologically in quantities exceeding two million tons per year; yet, L-lysine production is challenged by efficient export system at high titers during fermentation. To address this issue, new exporter candidates for efficient efflux of L-lysine are needed. Using metagenomic functional selection, we identified 58 genes encoded on 28 unique metagenomic fragments from cow gut microbiome library that improved L-lysine tolerance. These genes include a novel L-lysine transporter, belonging to a previously uncharacterized EamA superfamily, which is further in vivo characterized as L-lysine exporter using Xenopus oocyte expression system as well as Escherichia coli host. This novel exporter improved L-lysine tolerance in E. coli by 40% and enhanced yield, titer, and the specific production of L-lysine in an industrial Corynebacterium glutamicum strain by 7.8%, 9.5%, and 12%, respectively. Our approach allows the sequence-independent discovery of novel exporters and can be deployed to increase titers and productivity of toxicity-limited bioprocesses.
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Claus S, Jezierska S, Elbourne LDH, Van Bogaert I. Exploring the transportome of the biosurfactant producing yeast Starmerella bombicola. BMC Genomics 2022; 23:22. [PMID: 34998388 PMCID: PMC8742932 DOI: 10.1186/s12864-021-08177-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 11/16/2021] [Indexed: 12/13/2022] Open
Abstract
Starmerella bombicola is a non-conventional yeast mainly known for its capacity to produce high amounts of the glycolipids 'sophorolipids'. Although its product has been used as biological detergent for a couple of decades, the genetics of S. bombicola are still largely unknown. Computational analysis of the yeast's genome enabled us to identify 254 putative transporter genes that make up the entire transportome. For each of them, a potential substrate was predicted using homology analysis, subcellular localization prediction and RNA sequencing in different stages of growth. One transporter family is of exceptional importance to this yeast: the ATP Binding Cassette (ABC) transporter Superfamily, because it harbors the main driver behind the highly efficient sophorolipid export. Furthermore, members of this superfamily translocate a variety of compounds ranging from antibiotics to hydrophobic molecules. We conducted an analysis of this family by creating deletion mutants to understand their role in the export of hydrophobic compounds, antibiotics and sophorolipids. Doing this, we could experimentally confirm the transporters participating in the efflux of medium chain fatty alcohols, particularly decanol and undecanol, and identify a second sophorolipid transporter that is located outside the sophorolipid biosynthetic gene cluster.
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Affiliation(s)
- Silke Claus
- Centre for Synthetic Biology, Department of Biotechnology, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Sylwia Jezierska
- Centre for Synthetic Biology, Department of Biotechnology, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Liam D H Elbourne
- Department of Molecular Sciences, Macquarie University, Macquarie Park, NSW, 2109, Australia
| | - Inge Van Bogaert
- Centre for Synthetic Biology, Department of Biotechnology, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
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Kell DB. The Transporter-Mediated Cellular Uptake and Efflux of Pharmaceutical Drugs and Biotechnology Products: How and Why Phospholipid Bilayer Transport Is Negligible in Real Biomembranes. Molecules 2021; 26:5629. [PMID: 34577099 PMCID: PMC8470029 DOI: 10.3390/molecules26185629] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/03/2021] [Accepted: 09/14/2021] [Indexed: 12/12/2022] Open
Abstract
Over the years, my colleagues and I have come to realise that the likelihood of pharmaceutical drugs being able to diffuse through whatever unhindered phospholipid bilayer may exist in intact biological membranes in vivo is vanishingly low. This is because (i) most real biomembranes are mostly protein, not lipid, (ii) unlike purely lipid bilayers that can form transient aqueous channels, the high concentrations of proteins serve to stop such activity, (iii) natural evolution long ago selected against transport methods that just let any undesirable products enter a cell, (iv) transporters have now been identified for all kinds of molecules (even water) that were once thought not to require them, (v) many experiments show a massive variation in the uptake of drugs between different cells, tissues, and organisms, that cannot be explained if lipid bilayer transport is significant or if efflux were the only differentiator, and (vi) many experiments that manipulate the expression level of individual transporters as an independent variable demonstrate their role in drug and nutrient uptake (including in cytotoxicity or adverse drug reactions). This makes such transporters valuable both as a means of targeting drugs (not least anti-infectives) to selected cells or tissues and also as drug targets. The same considerations apply to the exploitation of substrate uptake and product efflux transporters in biotechnology. We are also beginning to recognise that transporters are more promiscuous, and antiporter activity is much more widespread, than had been realised, and that such processes are adaptive (i.e., were selected by natural evolution). The purpose of the present review is to summarise the above, and to rehearse and update readers on recent developments. These developments lead us to retain and indeed to strengthen our contention that for transmembrane pharmaceutical drug transport "phospholipid bilayer transport is negligible".
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Affiliation(s)
- Douglas B. Kell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown St, Liverpool L69 7ZB, UK;
- Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs Lyngby, Denmark
- Mellizyme Biotechnology Ltd., IC1, Liverpool Science Park, Mount Pleasant, Liverpool L3 5TF, UK
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9
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Darbani B. Genome Evolutionary Dynamics Meets Functional Genomics: A Case Story on the Identification of SLC25A44. Int J Mol Sci 2021; 22:ijms22115669. [PMID: 34073512 PMCID: PMC8199184 DOI: 10.3390/ijms22115669] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/09/2021] [Accepted: 05/23/2021] [Indexed: 12/14/2022] Open
Abstract
Gene clusters are becoming promising tools for gene identification. The study reveals the purposive genomic distribution of genes toward higher inheritance rates of intact metabolic pathways/phenotypes and, thereby, higher fitness. The co-localization of co-expressed, co-interacting, and functionally related genes was found as genome-wide trends in humans, mouse, golden eagle, rice fish, Drosophila, peanut, and Arabidopsis. As anticipated, the analyses verified the co-segregation of co-localized events. A negative correlation was notable between the likelihood of co-localization events and the inter-loci distances. The evolution of genomic blocks was also found convergent and uniform along the chromosomal arms. Calling a genomic block responsible for adjacent metabolic reactions is therefore recommended for identification of candidate genes and interpretation of cellular functions. As a case story, a function in the metabolism of energy and secondary metabolites was proposed for Slc25A44, based on its genomic local information. Slc25A44 was further characterized as an essential housekeeping gene which has been under evolutionary purifying pressure and belongs to the phylogenetic ETC-clade of SLC25s. Pathway enrichment mapped the Slc25A44s to the energy metabolism. The expression of peanut and human Slc25A44s in oocytes and Saccharomyces cerevisiae strains confirmed the transport of common precursors for secondary metabolites and ubiquinone. These results suggest that SLC25A44 is a mitochondrion-ER-nucleus zone transporter with biotechnological applications. Finally, a conserved three-amino acid signature on the cytosolic face of transport cavity was found important for rational engineering of SLC25s.
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Affiliation(s)
- Behrooz Darbani
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark; or ; Tel.: +45-(53)-578055
- Research Center Flakkebjerg, Department of Agroecology, Aarhus University, 4200 Slagelse, Denmark
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10
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Kell DB. A protet-based, protonic charge transfer model of energy coupling in oxidative and photosynthetic phosphorylation. Adv Microb Physiol 2021; 78:1-177. [PMID: 34147184 DOI: 10.1016/bs.ampbs.2021.01.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Textbooks of biochemistry will explain that the otherwise endergonic reactions of ATP synthesis can be driven by the exergonic reactions of respiratory electron transport, and that these two half-reactions are catalyzed by protein complexes embedded in the same, closed membrane. These views are correct. The textbooks also state that, according to the chemiosmotic coupling hypothesis, a (or the) kinetically and thermodynamically competent intermediate linking the two half-reactions is the electrochemical difference of protons that is in equilibrium with that between the two bulk phases that the coupling membrane serves to separate. This gradient consists of a membrane potential term Δψ and a pH gradient term ΔpH, and is known colloquially as the protonmotive force or pmf. Artificial imposition of a pmf can drive phosphorylation, but only if the pmf exceeds some 150-170mV; to achieve in vivo rates the imposed pmf must reach 200mV. The key question then is 'does the pmf generated by electron transport exceed 200mV, or even 170mV?' The possibly surprising answer, from a great many kinds of experiment and sources of evidence, including direct measurements with microelectrodes, indicates it that it does not. Observable pH changes driven by electron transport are real, and they control various processes; however, compensating ion movements restrict the Δψ component to low values. A protet-based model, that I outline here, can account for all the necessary observations, including all of those inconsistent with chemiosmotic coupling, and provides for a variety of testable hypotheses by which it might be refined.
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Affiliation(s)
- Douglas B Kell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative, Biology, University of Liverpool, Liverpool, United Kingdom; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
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11
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Wang G, Møller-Hansen I, Babaei M, D'Ambrosio V, Christensen HB, Darbani B, Jensen MK, Borodina I. Transportome-wide engineering of Saccharomyces cerevisiae. Metab Eng 2021; 64:52-63. [PMID: 33465478 PMCID: PMC7970624 DOI: 10.1016/j.ymben.2021.01.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/16/2020] [Accepted: 01/10/2021] [Indexed: 12/17/2022]
Abstract
Synthetic biology enables the production of small molecules by recombinant microbes for pharma, food, and materials applications. The secretion of products reduces the cost of separation and purification, but it is challenging to engineer due to the limited understanding of the transporter proteins' functions. Here we describe a method for genome-wide transporter disruption that, in combination with a metabolite biosensor, enables the identification of transporters impacting the production of a given target metabolite in yeast Saccharomyces cerevisiae. We applied the method to study the transport of xenobiotic compounds, cis,cis-muconic acid (CCM), protocatechuic acid (PCA), and betaxanthins. We found 22 transporters that influenced the production of CCM or PCA. The transporter of the 12-spanner drug:H(+) antiporter (DHA1) family Tpo2p was further confirmed to import CCM and PCA in Xenopus expression assays. We also identified three transporter proteins (Qdr1p, Qdr2p, and Apl1p) involved in betaxanthins transport. In summary, the described method enables high-throughput transporter identification for small molecules in cell factories.
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Affiliation(s)
- Guokun Wang
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Iben Møller-Hansen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Mahsa Babaei
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Vasil D'Ambrosio
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Hanne Bjerre Christensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Behrooz Darbani
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Michael Krogh Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark.
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12
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Salcedo-Sora JE, Jindal S, O'Hagan S, Kell DB. A palette of fluorophores that are differentially accumulated by wild-type and mutant strains of Escherichia coli: surrogate ligands for profiling bacterial membrane transporters. MICROBIOLOGY (READING, ENGLAND) 2021; 167:001016. [PMID: 33406033 PMCID: PMC8131027 DOI: 10.1099/mic.0.001016] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 12/15/2020] [Indexed: 12/12/2022]
Abstract
Our previous work demonstrated that two commonly used fluorescent dyes that were accumulated by wild-type Escherichia coli MG1655 were differentially transported in single-gene knockout strains, and also that they might be used as surrogates in flow cytometric transporter assays. We summarize the desirable properties of such stains, and here survey 143 candidate dyes. We eventually triage them (on the basis of signal, accumulation levels and cost) to a palette of 39 commercially available and affordable fluorophores that are accumulated significantly by wild-type cells of the 'Keio' strain BW25113, as measured flow cytometrically. Cheminformatic analyses indicate both their similarities and their (much more considerable) structural differences. We describe the effects of pH and of the efflux pump inhibitor chlorpromazine on the accumulation of the dyes. Even the 'wild-type' MG1655 and BW25113 strains can differ significantly in their ability to take up such dyes. We illustrate the highly differential uptake of our dyes into strains with particular lesions in, or overexpressed levels of, three particular transporters or transporter components (yhjV, yihN and tolC). The relatively small collection of dyes described offers a rapid, inexpensive, convenient and informative approach to the assessment of microbial physiology and phenotyping of membrane transporter function.
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Affiliation(s)
- Jesus Enrique Salcedo-Sora
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Crown St, Liverpool L69 7ZB, UK
| | - Srijan Jindal
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Crown St, Liverpool L69 7ZB, UK
| | - Steve O'Hagan
- Department of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess St, Manchester M1 7DN, UK
| | - Douglas B. Kell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Crown St, Liverpool L69 7ZB, UK
- Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs Lyngby, Denmark
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13
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O’Hagan S, Kell DB. Structural Similarities between Some Common Fluorophores Used in Biology, Marketed Drugs, Endogenous Metabolites, and Natural Products. Mar Drugs 2020; 18:E582. [PMID: 33238416 PMCID: PMC7700180 DOI: 10.3390/md18110582] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 11/16/2020] [Accepted: 11/20/2020] [Indexed: 12/12/2022] Open
Abstract
It is known that at least some fluorophores can act as 'surrogate' substrates for solute carriers (SLCs) involved in pharmaceutical drug uptake, and this promiscuity is taken to reflect at least a certain structural similarity. As part of a comprehensive study seeking the 'natural' substrates of 'orphan' transporters that also serve to take up pharmaceutical drugs into cells, we have noted that many drugs bear structural similarities to natural products. A cursory inspection of common fluorophores indicates that they too are surprisingly 'drug-like', and they also enter at least some cells. Some are also known to be substrates of efflux transporters. Consequently, we sought to assess the structural similarity of common fluorophores to marketed drugs, endogenous mammalian metabolites, and natural products. We used a set of some 150 fluorophores along with standard fingerprinting methods and the Tanimoto similarity metric. Results: The great majority of fluorophores tested exhibited significant similarity (Tanimoto similarity > 0.75) to at least one drug, as judged via descriptor properties (especially their aromaticity, for identifiable reasons that we explain), by molecular fingerprints, by visual inspection, and via the "quantitative estimate of drug likeness" technique. It is concluded that this set of fluorophores does overlap with a significant part of both the drug space and natural products space. Consequently, fluorophores do indeed offer a much wider opportunity than had possibly been realised to be used as surrogate uptake molecules in the competitive or trans-stimulation assay of membrane transporter activities.
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Affiliation(s)
- Steve O’Hagan
- Department of Chemistry, The University of Manchester, Manchester M13 9PT, UK;
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess St, Manchester M1 7DN, UK
| | - Douglas B. Kell
- Department of Biochemistry and Systems Biology, Institute of Molecular, Integrative and Systems Biology, Biosciences Building, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
- Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kongens Lyngby, Denmark
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14
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Tiukova IA, Møller-Hansen I, Belew ZM, Darbani B, Boles E, Nour-Eldin HH, Linder T, Nielsen J, Borodina I. Identification and characterisation of two high-affinity glucose transporters from the spoilage yeast Brettanomyces bruxellensis. FEMS Microbiol Lett 2020; 366:5610216. [PMID: 31665273 PMCID: PMC6847091 DOI: 10.1093/femsle/fnz222] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 10/25/2019] [Indexed: 12/17/2022] Open
Abstract
The yeast Brettanomyces bruxellensis (syn. Dekkera bruxellensis) is an emerging and undesirable contaminant in industrial low-sugar ethanol fermentations that employ the yeast Saccharomyces cerevisiae. High-affinity glucose import in B. bruxellensis has been proposed to be the mechanism by which this yeast can outcompete S. cerevisiae. The present study describes the characterization of two B. bruxellensis genes (BHT1 and BHT3) believed to encode putative high-affinity glucose transporters. In vitro-generated transcripts of both genes as well as the S. cerevisiae HXT7 high-affinity glucose transporter were injected into Xenopus laevis oocytes and subsequent glucose uptake rates were assayed using 14C-labelled glucose. At 0.1 mM glucose, Bht1p was shown to transport glucose five times faster than Hxt7p. pH affected the rate of glucose transport by Bht1p and Bht3p, indicating an active glucose transport mechanism that involves proton symport. These results suggest a possible role for BHT1 and BHT3 in the competitive ability of B. bruxellensis.
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Affiliation(s)
- Ievgeniia A Tiukova
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemigården 4, 412 96 Gothenburg, Sweden
| | - Iben Møller-Hansen
- The Novo Nordisk Foundation for Biosustainability, Technical University of Denmark, Building 220, 2800 Kongens Lyngby, Denmark
| | - Zeinu M Belew
- Department of Plant and Environmental Sciences, DynaMo Center, Copenhagen Plant Science Center, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Behrooz Darbani
- The Novo Nordisk Foundation for Biosustainability, Technical University of Denmark, Building 220, 2800 Kongens Lyngby, Denmark
| | - Eckhard Boles
- Institute of Molecular Biosciences, Faculty of Biological Sciences, Goethe University Frankfurt, Max-von-Laue Straße 9, 60438, Frankfurt am Main, Germany
| | - Hussam H Nour-Eldin
- Department of Plant and Environmental Sciences, DynaMo Center, Copenhagen Plant Science Center, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Tomas Linder
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Almas allé 5, 750 07 Uppsala, Sweden
| | - Jens Nielsen
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemigården 4, 412 96 Gothenburg, Sweden
| | - Irina Borodina
- The Novo Nordisk Foundation for Biosustainability, Technical University of Denmark, Building 220, 2800 Kongens Lyngby, Denmark
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15
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Engineering energetically efficient transport of dicarboxylic acids in yeast Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 2019; 116:19415-19420. [PMID: 31467169 PMCID: PMC6765260 DOI: 10.1073/pnas.1900287116] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The export of organic acids is typically proton or sodium coupled and requires energetic expenditure. Consequently, the cell factories producing organic acids must use part of the carbon feedstock on generating the energy for export, which decreases the overall process yield. Here, we show that organic acids can be exported from yeast cells by voltage-gated anion channels without the use of proton, sodium, or ATP motive force, resulting in more efficient fermentation processes. Biobased C4-dicarboxylic acids are attractive sustainable precursors for polymers and other materials. Commercial scale production of these acids at high titers requires efficient secretion by cell factories. In this study, we characterized 7 dicarboxylic acid transporters in Xenopus oocytes and in Saccharomyces cerevisiae engineered for dicarboxylic acid production. Among the tested transporters, the Mae1(p) from Schizosaccharomyces pombe had the highest activity toward succinic, malic, and fumaric acids and resulted in 3-, 8-, and 5-fold titer increases, respectively, in S. cerevisiae, while not affecting growth, which was in contrast to the tested transporters from the tellurite-resistance/dicarboxylate transporter (TDT) family or the Na+ coupled divalent anion–sodium symporter family. Similar to SpMae1(p), its homolog in Aspergillus carbonarius, AcDct(p), increased the malate titer 12-fold without affecting the growth. Phylogenetic and protein motif analyses mapped SpMae1(p) and AcDct(p) into the voltage-dependent slow-anion channel transporter (SLAC1) clade of transporters, which also include plant Slac1(p) transporters involved in stomata closure. The conserved phenylalanine residue F329 closing the transport pore of SpMae1(p) is essential for the transporter activity. The voltage-dependent SLAC1 transporters do not use proton or Na+ motive force and are, thus, less energetically expensive than the majority of other dicarboxylic acid transporters. Such transporters present a tremendous advantage for organic acid production via fermentation allowing a higher overall product yield.
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16
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Jindal S, Yang L, Day PJ, Kell DB. Involvement of multiple influx and efflux transporters in the accumulation of cationic fluorescent dyes by Escherichia coli. BMC Microbiol 2019; 19:195. [PMID: 31438868 PMCID: PMC6704527 DOI: 10.1186/s12866-019-1561-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 07/31/2019] [Indexed: 12/11/2022] Open
Abstract
Background It is widely believed that most xenobiotics cross biomembranes by diffusing through the phospholipid bilayer, and that the use of protein transporters is an occasional adjunct. According to an alternative view, phospholipid bilayer transport is negligible, and several different transporters may be involved in the uptake of an individual molecular type. We recognise here that the availability of gene knockout collections allows one to assess the contributions of all potential transporters, and flow cytometry based on fluorescence provides a convenient high-throughput assay for xenobiotic uptake in individual cells. Results We used high-throughput flow cytometry to assess the ability of individual gene knockout strains of E coli to take up two membrane-permeable, cationic fluorescent dyes, namely the carbocyanine diS-C3(5) and the DNA dye SYBR Green. Individual strains showed a large range of distributions of uptake. The range of modal steady-state uptakes for the carbocyanine between the different strains was 36-fold. Knockouts of the ATP synthase α- and β-subunits greatly inhibited uptake, implying that most uptake was ATP-driven rather than being driven by a membrane potential. Dozens of transporters changed the steady-state uptake of the dye by more than 50% with respect to that of the wild type, in either direction (increased or decreased); knockouts of known influx and efflux transporters behaved as expected, giving credence to the general strategy. Many of the knockouts with the most reduced uptake were transporter genes of unknown function (‘y-genes’). Similarly, several overexpression variants in the ‘ASKA’ collection had the anticipated, opposite effects. Similar results were obtained with SYBR Green (the range being approximately 69-fold). Although it too contains a benzothiazole motif there was negligible correlation between its uptake and that of the carbocyanine when compared across the various strains (although the membrane potential is presumably the same in each case). Conclusions Overall, we conclude that the uptake of these dyes may be catalysed by a great many transporters of putatively broad and presently unknown specificity, and that the very large range between the ‘lowest’ and the ‘highest’ levels of uptake, even in knockouts of just single genes, implies strongly that phospholipid bilayer transport is indeed negligible. This work also casts serious doubt upon the use of such dyes as quantitative stains for representing either bioenergetic parameters or the amount of cellular DNA in unfixed cells (in vivo). By contrast, it opens up their potential use as transporter assay substrates in high-throughput screening. Electronic supplementary material The online version of this article (10.1186/s12866-019-1561-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Srijan Jindal
- Department of Chemistry, The University of Manchester, 131 Princess St, Manchester, M1 7DN, UK.,Manchester Institute of Biotechnology, The University of Manchester, 131 Princess St, Manchester, M1 7DN, UK.,Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PT, UK
| | - Lei Yang
- Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs, Lyngby, Denmark
| | - Philip J Day
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess St, Manchester, M1 7DN, UK.,Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PT, UK
| | - Douglas B Kell
- Department of Chemistry, The University of Manchester, 131 Princess St, Manchester, M1 7DN, UK. .,Manchester Institute of Biotechnology, The University of Manchester, 131 Princess St, Manchester, M1 7DN, UK. .,Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs, Lyngby, Denmark. .,Department of Biochemistry, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Crown St, Liverpool, L69 7ZB, UK.
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17
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Diep P, Mahadevan R, Yakunin AF. Heavy Metal Removal by Bioaccumulation Using Genetically Engineered Microorganisms. Front Bioeng Biotechnol 2018; 6:157. [PMID: 30420950 PMCID: PMC6215804 DOI: 10.3389/fbioe.2018.00157] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 10/09/2018] [Indexed: 11/25/2022] Open
Abstract
Wastewater effluents from mines and metal refineries are often contaminated with heavy metal ions, so they pose hazards to human and environmental health. Conventional technologies to remove heavy metal ions are well-established, but the most popular methods have drawbacks: chemical precipitation generates sludge waste, and activated carbon and ion exchange resins are made from unsustainable non-renewable resources. Using microbial biomass as the platform for heavy metal ion removal is an alternative method. Specifically, bioaccumulation is a natural biological phenomenon where microorganisms use proteins to uptake and sequester metal ions in the intracellular space to utilize in cellular processes (e.g., enzyme catalysis, signaling, stabilizing charges on biomolecules). Recombinant expression of these import-storage systems in genetically engineered microorganisms allows for enhanced uptake and sequestration of heavy metal ions. This has been studied for over two decades for bioremediative applications, but successful translation to industrial-scale processes is virtually non-existent. Meanwhile, demands for metal resources are increasing while discovery rates to supply primary grade ores are not. This review re-thinks how bioaccumulation can be used and proposes that it can be developed for bioextractive applications-the removal and recovery of heavy metal ions for downstream purification and refining, rather than disposal. This review consolidates previously tested import-storage systems into a biochemical framework and highlights efforts to overcome obstacles that limit industrial feasibility, thereby identifying gaps in knowledge and potential avenues of research in bioaccumulation.
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Affiliation(s)
| | | | - Alexander F. Yakunin
- BioZone - Centre for Applied Biosciences and Bioengineering, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
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