1
|
Rodríguez-Robles E, Müller D, Künzl T, Nemat SJ, Edelmann MP, Srivastava P, Louis D, Groaz E, Tiefenbacher K, Roberts TM, Herdewijn P, Marlière P, Panke S. Rational design of a bacterial import system for new-to-nature molecules. Metab Eng 2024:S1096-7176(24)00071-5. [PMID: 38802041 DOI: 10.1016/j.ymben.2024.05.005] [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: 01/14/2024] [Revised: 04/27/2024] [Accepted: 05/23/2024] [Indexed: 05/29/2024]
Abstract
Integration of novel compounds into biological processes holds significant potential for modifying or expanding existing cellular functions. However, the cellular uptake of these compounds is often hindered by selectively permeable membranes. We present a novel bacterial transport system that has been rationally designed to address this challenge. Our approach utilizes a highly promiscuous sulfonate membrane transporter, which allows the passage of cargo molecules attached as amides to a sulfobutanoate transport vector molecule into the cytoplasm of the cell. These cargoes can then be unloaded from the sulfobutanoyl amides using an engineered variant of the enzyme γ-glutamyl transferase, which hydrolyzes the amide bond and releases the cargo molecule within the cell. Here, we provide evidence for the broad substrate specificity of both components of the system by evaluating a panel of structurally diverse sulfobutanoyl amides. Furthermore, we successfully implement the synthetic uptake system in vivo and showcase its functionality by importing an impermeant non-canonical amino acid.
Collapse
Affiliation(s)
- Emilio Rodríguez-Robles
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - David Müller
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Tilmann Künzl
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Suren J Nemat
- Department of Chemistry, University of Basel, Basel, Switzerland
| | - Martin Peter Edelmann
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Puneet Srivastava
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | | | - Elisabetta Groaz
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | | | - Tania Michelle Roberts
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Piet Herdewijn
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | | | - Sven Panke
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
| |
Collapse
|
2
|
Live Cell Imaging of Peptide Uptake Using a Microfluidic Platform. Int J Pept Res Ther 2021. [DOI: 10.1007/s10989-021-10228-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
3
|
Chen W, Wang Z, Xu W, Tian R, Zeng J. Dibutyl phthalate contamination accelerates the uptake and metabolism of sugars by microbes in black soil. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 262:114332. [PMID: 32182534 DOI: 10.1016/j.envpol.2020.114332] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 02/21/2020] [Accepted: 03/04/2020] [Indexed: 06/10/2023]
Abstract
Dibutyl phthalate (DBP) is widely used as plasticizer and has been detected in the environment, posing a threat to animal health. However, the effects of DBP on agricultural microbiomes are not known. In this study, DBP levels in black soil were evaluated, and the impact of DBP contamination on the uptake and metabolism of sugars in microbes was assessed by glucose absorption tests, metaproteomics, metabolomics, enzyme activity assays and computational simulation analysis. The results indicated that DBP contamination accelerated glucose consumption and upregulated the expression of porins and periplasmic monosaccharide ATP-binding cassette (ABC) transporter solute-binding proteins (SBPs). DBP and its metabolic intermediates (carboxymuconate and butanol) may form a stable complex with sugar transporters and enhance the rigidity and stability of these proteins. Sugar metabolism resulting in the generation of ATP and reducing agent (NADPH), as well as the expression of some key enzymes (dehydrogenases) were also upregulated by DBP treatment. Moreover, a diverse bacterial community appears to utilize sugar, suggesting that there are widespread effects of DBP contamination on soil microbial ecosystems. The results of this study provide a theoretical basis for investigating the toxicological effects of DBP on microbes in black soil.
Collapse
Affiliation(s)
- Wenjing Chen
- Center for Ecological Research, Northeast Forestry University, Heilongjiang Province, Harbin, 150040, China; Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar, 161006, China; College of Life Sciences, Agriculture and Forestry, Qiqihar University, Heilongjiang Province, Qiqihar, 161006, China.
| | - Zhigang Wang
- Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar, 161006, China; College of Life Sciences, Agriculture and Forestry, Qiqihar University, Heilongjiang Province, Qiqihar, 161006, China.
| | - Weihui Xu
- Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar, 161006, China; College of Life Sciences, Agriculture and Forestry, Qiqihar University, Heilongjiang Province, Qiqihar, 161006, China.
| | - Renmao Tian
- Institute for Food Safety and Health, Illinois Institute of Technology, Chicago, IL, 60501, USA.
| | - Jin Zeng
- Nanjing Institute of Geography & Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.
| |
Collapse
|
4
|
Defining the Environmental Adaptations of Genus Devosia: Insights into its Expansive Short Peptide Transport System and Positively Selected Genes. Sci Rep 2020; 10:1151. [PMID: 31980727 PMCID: PMC6981132 DOI: 10.1038/s41598-020-58163-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 12/19/2019] [Indexed: 12/21/2022] Open
Abstract
Devosia are well known for their dominance in soil habitats contaminated with various toxins and are best characterized for their bioremediation potential. In this study, we compared the genomes of 27 strains of Devosia with aim to understand their metabolic abilities. The analysis revealed their adaptive gene repertoire which was bared from 52% unique pan-gene content. A striking feature of all genomes was the abundance of oligo- and di-peptide permeases (oppABCDF and dppABCDF) with each genome harboring an average of 60.7 ± 19.1 and 36.5 ± 10.6 operon associated genes respectively. Apart from their primary role in nutrition, these permeases may help Devosia to sense environmental signals and in chemotaxis at stressed habitats. Through sequence similarity network analyses, we identified 29 Opp and 19 Dpp sequences that shared very little homology with any other sequence suggesting an expansive short peptidic transport system within Devosia. The substrate determining components of these permeases viz. OppA and DppA further displayed a large diversity that separated into 12 and 9 homologous clusters respectively in addition to large number of isolated nodes. We also dissected the genome scale positive evolution and found genes associated with growth (exopolyphosphatase, HesB_IscA_SufA family protein), detoxification (moeB, nifU-like domain protein, alpha/beta hydrolase), chemotaxis (cheB, luxR) and stress response (phoQ, uspA, luxR, sufE) were positively selected. The study highlights the genomic plasticity of the Devosia spp. for conferring adaptation, bioremediation and the potential to utilize a wide range of substrates. The widespread toxin-antitoxin loci and ‘open’ state of the pangenome provided evidence of plastic genomes and a much larger genetic repertoire of the genus which is yet uncovered.
Collapse
|