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Ruan S, Bourne CR. Escherichia coli cells evade inducible parE toxin expression by reducing plasmid copy number. Microbiol Spectr 2024; 12:e0397323. [PMID: 38700352 DOI: 10.1128/spectrum.03973-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 04/15/2024] [Indexed: 05/05/2024] Open
Abstract
Plasmids play important roles in microbial ecosystems, serving as carriers of antibiotic resistance and virulence. In the laboratory, they are essential tools for genetic manipulation and recombinant protein expression. We uncovered an intriguing survival phenotype in a fraction of the bacterial population while using plasmid-mediated arabinose-inducible gene expression to monitor the production of toxic ParE proteins. This phenotype was not correlated with changes to the plasmid sequence and could not be rescued by increasing arabinose uptake. Instead, survival correlates with a marked reduction in plasmid copy number (PCN). Reduced PCN is reproducible, not a function of the pre-existing population, and can be sequentially enriched by continual passage with induction. The reduction in PCN appears to allow mitigation of toxicity from the expression of ParE proteins while balancing the need to maintain a threshold PCN to withstand selection conditions. This indicates an adaptive cellular response to stressful conditions, likely by altering the regulation of plasmid replication. Furthermore, this survival mechanism appears to not be limited to a specific bacterial strain of Escherichia coli or ParE toxin family member, suggesting a generalized response. Finally, bacterial whole genome sequencing indicated an N845S residue substitution in DNA polymerase I, which correlates with the observed reduction in PCN and has been previously reported to impact plasmid replication. Further understanding this molecular mechanism has broader implications for this adaptive response of the dynamics of plasmid-mediated gene expression, microbial adaptation, and genetic engineering methodologies. IMPORTANCE This research has increased our understanding of how bacteria respond to the pressure from plasmid-borne toxic genes, such as those found in toxin-antitoxin systems. Surprisingly, we found that bacteria survived toxic ParE protein expression by reducing the number of these plasmids in the cells. This discovery reveals another way in which bacteria can balance toxin expression with antibiotic selection to attenuate the effects of deleterious genes. This insight is not only valuable for understanding bacterial survival strategies but may also influence the development of better tools in biotechnology, where plasmids are often used to study the functional roles of genes.
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Affiliation(s)
- Shengfeng Ruan
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Christina R Bourne
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
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2
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Grosse C, Sigoillot M, Megalizzi V, Tanina A, Willand N, Baulard AR, Wintjens R. Crystal structure of the Mycobacterium tuberculosis VirS regulator reveals its interaction with the lead compound SMARt751. J Struct Biol 2024; 216:108090. [PMID: 38548139 DOI: 10.1016/j.jsb.2024.108090] [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: 01/23/2024] [Revised: 03/25/2024] [Accepted: 03/25/2024] [Indexed: 04/02/2024]
Abstract
Ethionamide (ETO) is a prodrug that is primarily used as a second-line agent in the treatment of tuberculosis. Among the bacterial ETO activators, the monooxygenase MymA has been recently identified, and its expression is regulated by the mycobacterial regulator VirS. The discovery of VirS ligands that can enhance mymA expression and thereby increase the antimycobacterial efficacy of ETO, has led to the development of a novel therapeutic strategy against tuberculosis. This strategy involves the selection of preclinical candidates, including SMARt751. We report the first crystal structure of the AraC-like regulator VirS, in complex with SMARt751, refined at 1.69 Å resolution. Crystals were obtained via an in situ proteolysis method in the requisite presence of SMARt751. The elucidated structure corresponds to the ligand-binding domain of VirS, adopting an α/β fold with structural similarities to H-NOX domains. Within the VirS structure, SMARt751 is situated in a completely enclosed hydrophobic cavity, where it forms hydrogen bonds with Asn11 and Asn149 as well as van der Waals contacts with various hydrophobic amino acids. Comprehensive structural comparisons within the AraC family of transcriptional regulators are conducted and analyzed to figure out the effects of the SMARt751 binding on the regulatory activity of VirS.
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Affiliation(s)
- Camille Grosse
- Unit of Microbiology, Bioorganic and Macromolecular Chemistry, Department of Research in Drug Development, Faculty of Pharmacy, Université Libre de Bruxelles, Belgium; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Maud Sigoillot
- Unit of Microbiology, Bioorganic and Macromolecular Chemistry, Department of Research in Drug Development, Faculty of Pharmacy, Université Libre de Bruxelles, Belgium
| | - Véronique Megalizzi
- Unit of Microbiology, Bioorganic and Macromolecular Chemistry, Department of Research in Drug Development, Faculty of Pharmacy, Université Libre de Bruxelles, Belgium
| | - Abdalkarim Tanina
- Unit of Microbiology, Bioorganic and Macromolecular Chemistry, Department of Research in Drug Development, Faculty of Pharmacy, Université Libre de Bruxelles, Belgium
| | - Nicolas Willand
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Alain R Baulard
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - René Wintjens
- Unit of Microbiology, Bioorganic and Macromolecular Chemistry, Department of Research in Drug Development, Faculty of Pharmacy, Université Libre de Bruxelles, Belgium.
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Wang J, Wang H, Zhang D, Liu F, Li X, Gao M, Cheng M, Bao H, Zhan J, Zeng Y, Wang C, Cao X. Lactiplantibacillus plantarum surface-displayed VP6 (PoRV) protein can prevent PoRV infection in piglets. Int Immunopharmacol 2024; 133:112079. [PMID: 38615376 DOI: 10.1016/j.intimp.2024.112079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/09/2024] [Accepted: 04/09/2024] [Indexed: 04/16/2024]
Abstract
Porcine rotavirus (PoRV) poses a threat to the development of animal husbandry and human health, leading to substantial economic losses. VP6 protein is the most abundant component in virus particles and also the core structural protein of the virus. Firstly, this study developed an antibiotic-resistance-free, environmentally friendly expression vector, named asd-araC-PBAD-alr (AAPA). Then Recombinant Lactiplantibacillus plantarum (L. plantarum) strains induced by arabinose to express VP6 and VP6-pFc fusion proteins was constructed. Subsequently, This paper discovered that NC8/Δalr-pCXa-VP6-S and NC8/Δalr-pCXa-VP6-pFc-S could enhance host immunity and prevent rotavirus infection in neonatal mice and piglets. The novel recombinant L. plantarum strains constructed in this study can serve as oral vaccines to boost host immunity, offering a new strategy to prevent PoRV infection.
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Affiliation(s)
- Junhong Wang
- College of Veterinary Medicine, Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Engineering Research Center of Microecological Vaccines (Drugs) for Major Animal Diseases, Ministry of Education, Jilin Agricultural University, Changchun, 130118, China
| | - Haixu Wang
- College of Veterinary Medicine, Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Engineering Research Center of Microecological Vaccines (Drugs) for Major Animal Diseases, Ministry of Education, Jilin Agricultural University, Changchun, 130118, China
| | - Dongliang Zhang
- College of Veterinary Medicine, Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Engineering Research Center of Microecological Vaccines (Drugs) for Major Animal Diseases, Ministry of Education, Jilin Agricultural University, Changchun, 130118, China
| | - Fangyuan Liu
- College of Veterinary Medicine, Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Engineering Research Center of Microecological Vaccines (Drugs) for Major Animal Diseases, Ministry of Education, Jilin Agricultural University, Changchun, 130118, China
| | - Xiaoxu Li
- College of Veterinary Medicine, Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Engineering Research Center of Microecological Vaccines (Drugs) for Major Animal Diseases, Ministry of Education, Jilin Agricultural University, Changchun, 130118, China
| | - Ming Gao
- College of Veterinary Medicine, Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Engineering Research Center of Microecological Vaccines (Drugs) for Major Animal Diseases, Ministry of Education, Jilin Agricultural University, Changchun, 130118, China
| | - Mingyang Cheng
- College of Veterinary Medicine, Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Engineering Research Center of Microecological Vaccines (Drugs) for Major Animal Diseases, Ministry of Education, Jilin Agricultural University, Changchun, 130118, China
| | - Hongyu Bao
- College of Veterinary Medicine, Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Engineering Research Center of Microecological Vaccines (Drugs) for Major Animal Diseases, Ministry of Education, Jilin Agricultural University, Changchun, 130118, China
| | - Jiaxing Zhan
- College of Veterinary Medicine, Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Engineering Research Center of Microecological Vaccines (Drugs) for Major Animal Diseases, Ministry of Education, Jilin Agricultural University, Changchun, 130118, China
| | - Yan Zeng
- College of Veterinary Medicine, Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Engineering Research Center of Microecological Vaccines (Drugs) for Major Animal Diseases, Ministry of Education, Jilin Agricultural University, Changchun, 130118, China.
| | - Chunfeng Wang
- College of Veterinary Medicine, Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Engineering Research Center of Microecological Vaccines (Drugs) for Major Animal Diseases, Ministry of Education, Jilin Agricultural University, Changchun, 130118, China.
| | - Xin Cao
- College of Veterinary Medicine, Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Engineering Research Center of Microecological Vaccines (Drugs) for Major Animal Diseases, Ministry of Education, Jilin Agricultural University, Changchun, 130118, China.
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Cottam C, White RT, Beck LC, Stewart CJ, Beatson SA, Lowe EC, Grinter R, Connolly JPR. Metabolism of L-arabinose converges with virulence regulation to promote enteric pathogen fitness. Nat Commun 2024; 15:4462. [PMID: 38796512 PMCID: PMC11127945 DOI: 10.1038/s41467-024-48933-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 05/16/2024] [Indexed: 05/28/2024] Open
Abstract
Virulence and metabolism are often interlinked to control the expression of essential colonisation factors in response to host-associated signals. Here, we identified an uncharacterised transporter of the dietary monosaccharide ʟ-arabinose that is widely encoded by the zoonotic pathogen enterohaemorrhagic Escherichia coli (EHEC), required for full competitive fitness in the mouse gut and highly expressed during human infection. Discovery of this transporter suggested that EHEC strains have an enhanced ability to scavenge ʟ-arabinose and therefore prompted us to investigate the impact of this nutrient on pathogenesis. Accordingly, we discovered that ʟ-arabinose enhances expression of the EHEC type 3 secretion system, increasing its ability to colonise host cells, and that the underlying mechanism is dependent on products of its catabolism rather than the sensing of ʟ-arabinose as a signal. Furthermore, using the murine pathogen Citrobacter rodentium, we show that ʟ-arabinose metabolism provides a fitness benefit during infection via virulence factor regulation, as opposed to supporting pathogen growth. Finally, we show that this mechanism is not restricted to ʟ-arabinose and extends to other pentose sugars with a similar metabolic fate. This work highlights the importance integrating central metabolism with virulence regulation in order to maximise competitive fitness of enteric pathogens within the host-niche.
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Affiliation(s)
- Curtis Cottam
- Newcastle University Biosciences Institute, Newcastle University, NE2 4HH, Newcastle-upon-Tyne, UK
| | - Rhys T White
- Institute of Environmental Science and Research, Wellington, New Zealand
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Lauren C Beck
- Newcastle University Translation and Clinical Research Institute, Newcastle University, NE2 4HH, Newcastle-upon-Tyne, UK
| | - Christopher J Stewart
- Newcastle University Translation and Clinical Research Institute, Newcastle University, NE2 4HH, Newcastle-upon-Tyne, UK
| | - Scott A Beatson
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Elisabeth C Lowe
- Newcastle University Biosciences Institute, Newcastle University, NE2 4HH, Newcastle-upon-Tyne, UK
| | - Rhys Grinter
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - James P R Connolly
- Newcastle University Biosciences Institute, Newcastle University, NE2 4HH, Newcastle-upon-Tyne, UK.
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Zhu Y, Mou X, Song Y, Zhang Q, Sun B, Liu H, Tang H, Bao R. Molecular mechanism of the one-component regulator RccR on bacterial metabolism and virulence. Nucleic Acids Res 2024; 52:3433-3449. [PMID: 38477394 PMCID: PMC11014249 DOI: 10.1093/nar/gkae171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 02/22/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
The regulation of carbon metabolism and virulence is critical for the rapid adaptation of pathogenic bacteria to host conditions. In Pseudomonas aeruginosa, RccR is a transcriptional regulator of genes involved in primary carbon metabolism and is associated with bacterial resistance and virulence, although the exact mechanism is unclear. Our study demonstrates that PaRccR is a direct repressor of the transcriptional regulator genes mvaU and algU. Biochemical and structural analyses reveal that PaRccR can switch its DNA recognition mode through conformational changes triggered by KDPG binding or release. Mutagenesis and functional analysis underscore the significance of allosteric communication between the SIS domain and the DBD domain. Our findings suggest that, despite its overall structural similarity to other bacterial RpiR-type regulators, RccR displays a more complex regulatory element binding mode induced by ligands and a unique regulatory mechanism.
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Affiliation(s)
- Yibo Zhu
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xingyu Mou
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yingjie Song
- College of Life Science, Sichuan Normal University, Chengdu, China
| | - Qianqian Zhang
- Centre for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao 999078, China
| | - Bo Sun
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
| | - Huanxiang Liu
- Centre for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao 999078, China
| | - Hong Tang
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Rui Bao
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
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Yetiman A, Horzum M, Bahar D, Akbulut M. Assessment of Genomic and Metabolic Characteristics of Cholesterol-Reducing and GABA Producer Limosilactobacillus fermentum AGA52 Isolated from Lactic Acid Fermented Shalgam Based on "In Silico" and "In Vitro" Approaches. Probiotics Antimicrob Proteins 2024; 16:334-351. [PMID: 36735220 DOI: 10.1007/s12602-022-10038-2] [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] [Accepted: 12/19/2022] [Indexed: 02/04/2023]
Abstract
This study aimed to characterize the genomic and metabolic properties of a novel Lb. fermentum strain AGA52 which was isolated from a lactic acid fermented beverage called "shalgam." The genome size of AGA52 was 2,001,184 bp, which is predicted to carry 2024 genes, including 50 tRNAs, 3 rRNAs, 3 ncRNAs, 15 CRISPR repeats, 14 CRISPR spacers, and 1 CRISPR array. The genome has a GC content of 51.82% including 95 predicted pseudogenes, 56 complete or partial transposases, and 2 intact prophages. The similarity of the clusters of orthologous groups (COG) was analyzed by comparison with the other Lb. fermentum strains. The detected resistome on the genome of AGA52 was found to be intrinsic originated. Besides, it has been determined that AGA52 has an obligate heterofermentative carbohydrate metabolism due to the absence of the 1-phosphofructokinase (pfK) enzyme. Furthermore, the strain is found to have a better antioxidant capacity and to be tolerant to gastrointestinal simulated conditions. It was also observed that the AGA52 has antimicrobial activity against Yersinia enterocolitica ATCC9610, Bacillus cereus ATCC33019, Salmonella enterica sv. Typhimurium, Escherichia coli O157:h7 ATCC43897, Listeria monocytogenes ATCC7644, Klebsiella pneumoniae ATCC13883, and Proteus vulgaris ATCC8427. Additionally, AGA52 exhibited 42.74 ± 4.82% adherence to HT29 cells. Cholesterol assimilation (33.9 ± 0.005%) and GABA production capacities were also confirmed by "in silico" and "in vitro." Overall, the investigation of genomic and metabolic features of the AGA52 revealed that is a potential psychobiotic and probiotic dietary supplement candidate and can bring functional benefits to the host.
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Affiliation(s)
- Ahmet Yetiman
- Food Engineering Department, Faculty of Engineering, Erciyes University, 38030, Kayseri, Turkey.
| | - Mehmet Horzum
- Food Engineering Department, Graduate School of Natural and Applied Sciences, Erciyes University, 38030, Kayseri, Turkey
| | - Dilek Bahar
- Genkök Genome and Stem Cell Center, Erciyes University, 38030, Kayseri, Turkey
| | - Mikail Akbulut
- Department of Biology, Faculty of Science, Erciyes University, 38030, Kayseri, Turkey
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Lages MA, do Vale A, Lemos ML, Balado M. Remodulation of bacterial transcriptome after acquisition of foreign DNA: the case of irp-HPI high-pathogenicity island in Vibrio anguillarum. mSphere 2024; 9:e0059623. [PMID: 38078732 PMCID: PMC10826351 DOI: 10.1128/msphere.00596-23] [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: 10/11/2023] [Accepted: 10/27/2023] [Indexed: 01/31/2024] Open
Abstract
The high-pathogenicity island irp-HPI is widespread in Vibrionaceae and encodes the siderophore piscibactin, as well as the regulator PbtA that is essential for its expression. In this work, we aim to study whether PbtA directly interacts with irp-HPI promoters. Furthermore, we hypothesize that PbtA, and thereby the acquisition of irp-HPI island, may also influence the expression of other genes elsewhere in the bacterial genome. To address this question, an RNAseq analysis was conducted to identify differentially expressed genes after pbtA deletion in Vibrio anguillarum RV22 genetic background. The results showed that PbtA not only modulates the irp-HPI genes but also modulates the expression of a plethora of V. anguillarum core genome genes, inducing nitrate, arginine, and sulfate metabolism, T6SS1, and quorum sensing, while repressing lipopolysaccharide (LPS) production, MARTX toxin, and major porins such as OmpV and ChiP. The direct binding of the C-terminal domain of PbtA to piscibactin promoters (PfrpA and PfrpC), quorum sensing (vanT), LPS transporter wza, and T6SS structure- and effector-encoding genes was demonstrated by electrophoretic mobility shift assay (EMSA). The results provide valuable insights into the regulatory mechanisms underlying the expression of irp-HPI island and its impact on Vibrios transcriptome, with implications in pathogenesis.IMPORTANCEHorizontal gene transfer enables bacteria to acquire traits, such as virulence factors, thereby increasing the risk of the emergence of new pathogens. irp-HPI genomic island has a broad dissemination in Vibrionaceae and is present in numerous potentially pathogenic marine bacteria, some of which can infect humans. Previous works showed that certain V. anguillarum strains exhibit an expanded host range plasticity and heightened virulence, a phenomenon linked to the acquisition of the irp-HPI genomic island. The present work shows that this adaptive capability is likely achieved through comprehensive changes in the transcriptome of the bacteria and that these changes are mediated by the master regulator PbtA encoded within the irp-HPI element. Our results shed light on the broad implications of horizontal gene transfer in bacterial evolution, showing that the acquired DNA can directly mediate changes in the expression of the core genome, with profounds implications in pathogenesis.
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Affiliation(s)
- Marta A. Lages
- Department of Microbiology and Parasitology, Institute of Aquaculture, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Ana do Vale
- Fish Immunology and Vaccinology Group, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Manuel L. Lemos
- Department of Microbiology and Parasitology, Institute of Aquaculture, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Miguel Balado
- Department of Microbiology and Parasitology, Institute of Aquaculture, University of Santiago de Compostela, Santiago de Compostela, Spain
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Clausen U, Vital ST, Lambertus P, Gehler M, Scheve S, Wöhlbrand L, Rabus R. Catabolic Network of the Fermentative Gut Bacterium Phocaeicola vulgatus (Phylum Bacteroidota) from a Physiologic-Proteomic Perspective. Microb Physiol 2024; 34:88-107. [PMID: 38262373 DOI: 10.1159/000536327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 01/10/2024] [Indexed: 01/25/2024]
Abstract
INTRODUCTION Phocaeicola vulgatus (formerly Bacteroides vulgatus) is a prevalent member of human and animal guts, where it influences by its dietary-fiber-fueled, fermentative metabolism the microbial community as well as the host health. Moreover, the fermentative metabolism of P. vulgatus bears potential for a sustainable production of bulk chemicals. The aim of the present study was to refine the current understanding of the P. vulgatus physiology. METHODS P. vulgatus was adapted to anaerobic growth with 14 different carbohydrates, ranging from hexoses, pentoses, hemicellulose, via an uronic acid to deoxy sugars. These substrate-adapted cells formed the basis to define the growth stoichiometries by quantifying growth/fermentation parameters and to reconstruct the catabolic network by applying differential proteomics. RESULTS The determination of growth performance revealed, e.g., doubling times (h) from 1.39 (arabinose) to 14.26 (glucuronate), biomass yields (gCDW/mmolS) from 0.01 (fucose) to 0.27 (α-cyclodextrin), and ATP yields (mMATP/mMC) from 0.21 (rhamnose) to 0.60 (glucuronate/xylan). Furthermore, fermentation product spectra were determined, ranging from broad and balanced (with xylan: acetate, succinate, formate, and propanoate) to rather one sided (with rhamnose or fucose: mainly propane-1,2-diol). The fermentation network serving all tested compounds is composed of 56 proteins (all identified), with several peripheral reaction sequences formed with high substrate specificity (e.g., conversion of arabinose to d-xylulose-3-phosphate) implicating a fine-tuned regulation. By contrast, central modules (e.g., glycolysis or the reaction sequence from PEP to succinate) were constitutively formed. Extensive formation of propane-1,2-diol from rhamnose and fucose involves rhamnulokinase (RhaB), rhamnulose-1-phosphate kinase (RhaD), and lactaldehyde reductase (FucO). Furthermore, Sus-like systems are apparently the most relevant uptake systems and a complex array of transmembrane electron-transfer systems (e.g., Na+-pumping Rnf and Nqr complexes, fumarate reductase) as well as F- and V-type ATP-synthases were detected. CONCLUSIONS The present study provides insights into the potential contribution of P. vulgatus to the gut metabolome and into the strain's biotechnological potential for sustainable production of short-chain fatty acids and alcohols.
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Affiliation(s)
- Urte Clausen
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Sören-Tobias Vital
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Pia Lambertus
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Martina Gehler
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Sabine Scheve
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Lars Wöhlbrand
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Ralf Rabus
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
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Pearson AN, Incha MR, Ho CN, Schmidt M, Roberts JB, Nava AA, Keasling JD. Characterization and Diversification of AraC/XylS Family Regulators Guided by Transposon Sequencing. ACS Synth Biol 2024; 13:206-219. [PMID: 38113125 DOI: 10.1021/acssynbio.3c00441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
In this study, we explored the development of engineered inducible systems. Publicly available data from previous transposon sequencing assays were used to identify regulators of metabolism in Pseudomonas putida KT2440. For AraC family regulators (AFRs) represented in these data, we posited AFR/promoter/inducer groupings. Twelve promoters were characterized for a response to their proposed inducers in P. putida, and the resultant data were used to create and test nine two-plasmid sensor systems in Escherichia coli. Several of these were further developed into a palette of single-plasmid inducible systems. From these experiments, we observed an unreported inducer response from a previously characterized AFR, demonstrated that the addition of a P. putida transporter improved the sensor dynamics of an AFR in E. coli, and identified an uncharacterized AFR with a novel potential inducer specificity. Finally, targeted mutations in an AFR, informed by structural predictions, enabled the further diversification of these inducible plasmids.
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Affiliation(s)
- Allison N Pearson
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, United States
| | - Matthew R Incha
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, United States
| | - Cindy N Ho
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Matthias Schmidt
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Institute of Applied Microbiology-iAMB, Aachen Biology and Biotechnology-ABBt, RWTH Aachen University, Aachen 52062, Germany
| | - Jacob B Roberts
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Joint Program in Bioengineering, University of California, Berkeley/San Francisco, California 94720, United States
| | - Alberto A Nava
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Jay D Keasling
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Joint Program in Bioengineering, University of California, Berkeley/San Francisco, California 94720, United States
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, United States
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen 518055, China
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10
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McGregor NS, de Boer C, Foucart QPO, Beenakker T, Offen WA, Codée JDC, Willems LI, Overkleeft HS, Davies GJ. A Multiplexing Activity-Based Protein-Profiling Platform for Dissection of a Native Bacterial Xyloglucan-Degrading System. ACS CENTRAL SCIENCE 2023; 9:2306-2314. [PMID: 38161374 PMCID: PMC10755729 DOI: 10.1021/acscentsci.3c00831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/26/2023] [Accepted: 11/06/2023] [Indexed: 01/03/2024]
Abstract
Bacteria and yeasts grow on biomass polysaccharides by expressing and excreting a complex array of glycoside hydrolase (GH) enzymes. Identification and annotation of such GH pools, which are valuable commodities for sustainable energy and chemistries, by conventional means (genomics, proteomics) are complicated, as primary sequence or secondary structure alignment with known active enzymes is not always predictive for new ones. Here we report a "low-tech", easy-to-use, and sensitive multiplexing activity-based protein-profiling platform to characterize the xyloglucan-degrading GH system excreted by the soil saprophyte, Cellvibrio japonicus, when grown on xyloglucan. A suite of activity-based probes bearing orthogonal fluorophores allows for the visualization of accessory exo-acting glycosidases, which are then identified using biotin-bearing probes. Substrate specificity of xyloglucanases is directly revealed by imbuing xyloglucan structural elements into bespoke activity-based probes. Our ABPP platform provides a highly useful tool to dissect xyloglucan-degrading systems from various sources and to rapidly select potentially useful ones. The observed specificity of the probes moreover bodes well for the study of other biomass polysaccharide-degrading systems, by modeling probe structures to those of desired substrates.
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Affiliation(s)
| | - Casper de Boer
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA, Leiden, The Netherlands
| | - Quentin P. O. Foucart
- Department
of Chemistry, The University of York, Heslington, York YO10 5DD, United
Kingdom
| | - Thomas Beenakker
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA, Leiden, The Netherlands
| | - Wendy A. Offen
- Department
of Chemistry, The University of York, Heslington, York YO10 5DD, United
Kingdom
| | - Jeroen D. C. Codée
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA, Leiden, The Netherlands
| | - Lianne I. Willems
- York
Structural Biology Laboratory and York Biomedical Research Institute,
Department of Chemistry, University of York, Heslington, York YO10 5DD, United
Kingdom
| | - Herman S. Overkleeft
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA, Leiden, The Netherlands
| | - Gideon J. Davies
- Department
of Chemistry, The University of York, Heslington, York YO10 5DD, United
Kingdom
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11
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Frumkin I, Laub MT. Selection of a de novo gene that can promote survival of Escherichia coli by modulating protein homeostasis pathways. Nat Ecol Evol 2023; 7:2067-2079. [PMID: 37945946 PMCID: PMC10697842 DOI: 10.1038/s41559-023-02224-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 09/12/2023] [Indexed: 11/12/2023]
Abstract
Cellular novelty can emerge when non-functional loci become functional genes in a process termed de novo gene birth. But how proteins with random amino acid sequences beneficially integrate into existing cellular pathways remains poorly understood. We screened ~108 genes, generated from random nucleotide sequences and devoid of homology to natural genes, for their ability to rescue growth arrest of Escherichia coli cells producing the ribonuclease toxin MazF. We identified ~2,000 genes that could promote growth, probably by reducing transcription from the promoter driving toxin expression. Additionally, one random protein, named Random antitoxin of MazF (RamF), modulated protein homeostasis by interacting with chaperones, leading to MazF proteolysis and a consequent loss of its toxicity. Finally, we demonstrate that random proteins can improve during evolution by identifying beneficial mutations that turned RamF into a more efficient inhibitor. Our work provides a mechanistic basis for how de novo gene birth can produce functional proteins that effectively benefit cells evolving under stress.
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Affiliation(s)
- Idan Frumkin
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Michael T Laub
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Cambridge, MA, USA.
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12
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Trasanidou D, Potocnik A, Barendse P, Mohanraju P, Bouzetos E, Karpouzis E, Desmet A, van Kranenburg R, van der Oost J, Staals RHJ, Mougiakos I. Characterization of the AcrIIC1 anti‒CRISPR protein for Cas9‒based genome engineering in E. coli. Commun Biol 2023; 6:1042. [PMID: 37833505 PMCID: PMC10576004 DOI: 10.1038/s42003-023-05418-5] [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: 05/25/2023] [Accepted: 10/04/2023] [Indexed: 10/15/2023] Open
Abstract
Anti-CRISPR proteins (Acrs) block the activity of CRISPR-associated (Cas) proteins, either by inhibiting DNA interference or by preventing crRNA loading and complex formation. Although the main use of Acrs in genome engineering applications is to lower the cleavage activity of Cas proteins, they can also be instrumental for various other CRISPR-based applications. Here, we explore the genome editing potential of the thermoactive type II-C Cas9 variants from Geobacillus thermodenitrificans T12 (ThermoCas9) and Geobacillus stearothermophilus (GeoCas9) in Escherichia coli. We then demonstrate that the AcrIIC1 protein from Neisseria meningitidis robustly inhibits their DNA cleavage activity, but not their DNA binding capacity. Finally, we exploit these AcrIIC1:Cas9 complexes for gene silencing and base-editing, developing Acr base-editing tools. With these tools we pave the way for future engineering applications in mesophilic and thermophilic bacteria combining the activities of Acr and CRISPR-Cas proteins.
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Affiliation(s)
- Despoina Trasanidou
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Ana Potocnik
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Patrick Barendse
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Prarthana Mohanraju
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Evgenios Bouzetos
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Efthymios Karpouzis
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Amber Desmet
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Richard van Kranenburg
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
- Corbion, Gorinchem, The Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Raymond H J Staals
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands.
| | - Ioannis Mougiakos
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands.
- SNIPR Biome, Copenhagen, Denmark.
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13
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Naseri G, Raasch H, Charpentier E, Erhardt M. A versatile regulatory toolkit of arabinose-inducible artificial transcription factors for Enterobacteriaceae. Commun Biol 2023; 6:1005. [PMID: 37789111 PMCID: PMC10547716 DOI: 10.1038/s42003-023-05363-3] [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: 05/31/2023] [Accepted: 09/15/2023] [Indexed: 10/05/2023] Open
Abstract
The Gram-negative bacteria Salmonella enterica and Escherichia coli are important model organisms, powerful prokaryotic expression platforms for biotechnological applications, and pathogenic strains constitute major public health threats. To facilitate new approaches for research and biotechnological applications, we here develop a set of arabinose-inducible artificial transcription factors (ATFs) using CRISPR/dCas9 and Arabidopsis-derived DNA-binding proteins to control gene expression in E. coli and Salmonella over a wide inducer concentration range. The transcriptional output of the different ATFs, in particular when expressed in Salmonella rewired for arabinose catabolism, varies over a wide spectrum (up to 35-fold gene activation). As a proof-of-concept, we use the developed ATFs to engineer a Salmonella two-input biosensor strain, SALSOR 0.2 (SALmonella biosenSOR 0.2), which detects and quantifies alkaloid drugs through a measurable fluorescent output. Moreover, we use plant-derived ATFs to regulate β-carotene biosynthesis in E. coli, resulting in ~2.1-fold higher β-carotene production compared to expression of the biosynthesis pathway using a strong constitutive promoter.
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Affiliation(s)
- Gita Naseri
- Max Planck Unit for the Science of Pathogens, Charitéplatz 1, 10117, Berlin, Germany.
- Institut für Biologie, Humboldt-Universität zu Berlin, Philippstrasse 13, 10115, Berlin, Germany.
| | - Hannah Raasch
- Institut für Biologie, Humboldt-Universität zu Berlin, Philippstrasse 13, 10115, Berlin, Germany
| | - Emmanuelle Charpentier
- Max Planck Unit for the Science of Pathogens, Charitéplatz 1, 10117, Berlin, Germany
- Institut für Biologie, Humboldt-Universität zu Berlin, Philippstrasse 13, 10115, Berlin, Germany
| | - Marc Erhardt
- Max Planck Unit for the Science of Pathogens, Charitéplatz 1, 10117, Berlin, Germany.
- Institut für Biologie, Humboldt-Universität zu Berlin, Philippstrasse 13, 10115, Berlin, Germany.
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14
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Mathony J, Aschenbrenner S, Becker P, Niopek D. Dissecting the Determinants of Domain Insertion Tolerance and Allostery in Proteins. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303496. [PMID: 37562980 PMCID: PMC10558690 DOI: 10.1002/advs.202303496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/21/2023] [Indexed: 08/12/2023]
Abstract
Domain insertion engineering is a promising approach to recombine the functions of evolutionarily unrelated proteins. Insertion of light-switchable receptor domains into a selected effector protein, for instance, can yield allosteric effectors with light-dependent activity. However, the parameters that determine domain insertion tolerance and allostery are poorly understood. Here, an unbiased screen is used to systematically assess the domain insertion permissibility of several evolutionary unrelated proteins. Training machine learning models on the resulting data allow to dissect features informative for domain insertion tolerance and revealed sequence conservation statistics as the strongest indicators of suitable insertion sites. Finally, extending the experimental pipeline toward the identification of switchable hybrids results in opto-chemogenetic derivatives of the transcription factor AraC that function as single-protein Boolean logic gates. The study reveals determinants of domain insertion tolerance and yielded multimodally switchable proteins with unique functional properties.
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Affiliation(s)
- Jan Mathony
- Center for Synthetic BiologyTechnical University of Darmstadt64287DarmstadtGermany
- Department of BiologyTechnical University of Darmstadt64287DarmstadtGermany
- Institute of Pharmacy and Molecular Biotechnology (IPMB)Faculty of Engineering SciencesHeidelberg University69120HeidelbergGermany
| | - Sabine Aschenbrenner
- Institute of Pharmacy and Molecular Biotechnology (IPMB)Faculty of Engineering SciencesHeidelberg University69120HeidelbergGermany
| | - Philipp Becker
- Center for Synthetic BiologyTechnical University of Darmstadt64287DarmstadtGermany
- Department of BiologyTechnical University of Darmstadt64287DarmstadtGermany
- Department of Biotechnology and BiomedicineTechnical University of DenmarkKongens Lyngby2800Denmark
| | - Dominik Niopek
- Institute of Pharmacy and Molecular Biotechnology (IPMB)Faculty of Engineering SciencesHeidelberg University69120HeidelbergGermany
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15
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Bhat S, Banerjee A, Alagesan S. AraC-Based Biosensor for the Detection of Isoprene in E. coli. ACS OMEGA 2023; 8:26806-26815. [PMID: 37546622 PMCID: PMC10399174 DOI: 10.1021/acsomega.3c01164] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 06/27/2023] [Indexed: 08/08/2023]
Abstract
Isoprene is a valuable platform chemical, which is produced by engineered microorganisms, albeit in low quantities. The amount of isoprene produced is usually measured by gas chromatography, which can be time-consuming and expensive. Alternatively, biosensors have evolved as a powerful tool for real-time high-throughput screening and monitoring of product synthesis. The AraC-pBAD-inducible system has been widely studied, evolved, and engineered to develop biosensors for small molecules. In our preliminary studies, the AraC-pBAD system was mildly induced at higher isoprene concentrations when arabinose was also available. Hence, in the present study, we designed and constructed a synthetic biosensor based on the AraC-pBAD system, wherein the ligand-binding domain of AraC was replaced with IsoA. On introducing this chimeric AraC-IsoA (AcIa) transcription factor with the native PBAD promoter system regulating rfp gene expression, fluorescence output was observed only when wild-type Escherichia coli cells were induced with both isoprene and arabinose. The biosensor sensitivity and dynamic range were further enhanced by removing operator sequences and by substituting the native promoter (PAraC) with the strong tac promoter (Ptac). The chimeric sensor did not work in AraC knockout strains; however, functionality was restored by reintroducing AraC. Hence, AraC is essential for the functioning of our biosensor, while AcIa provides enhanced sensitivity and specificity for isoprene. However, insights into how AraC-AcIa interacts and the possible working mechanism remain to be explored. This study provides a prototype for developing chimeric AraC-based biosensors with proteins devoid of known dimerizing domains and opens a new avenue for further study and exploration.
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16
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Zhang L, Sun L, Srinivasan R, Lin M, Gong L, Lin X. Unveiling a Virulence-Regulating Mechanism in Aeromonas hydrophila: a Quantitative Exoproteomic Analysis of an AraC-Like Protein. Front Immunol 2023; 14:1191209. [PMID: 37228602 PMCID: PMC10203433 DOI: 10.3389/fimmu.2023.1191209] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 04/17/2023] [Indexed: 05/27/2023] Open
Abstract
Bacterial AraC is a transcription factor family that initiates transcription by recruiting RNA polymerase to the promoter and directly regulating various bacterial phenotypes. It also directly regulates various bacterial phenotypes. However, how this transcription factor regulates bacterial virulence and affects host immunity is still largely unknown. In this study, deleting the orf02889 (AraC-like transcription factor) gene in virulent Aeromonas hydrophila LP-2 affected several important phenotypes, such as increasing biofilm formation and siderophore production abilities. Moreover, Δorf02889 also significantly decreased the virulence of A. hydrophila and has promising attenuated vaccine potential. To better understand the effects of orf02889 on biological functions, a data independent acquisition (DIA)-based quantitative proteomics method was performed to compare the differentially expressed proteins between Δorf02889 and the wild-type strain in extracellular fractions. The following bioinformatics analysis suggested that ORF02889 may regulate various metabolic pathways, such as quorum sensing and ATP binding cassette (ABC) transporter metabolism. Moreover, 10 selected genes from the top 10 decreasing abundances in proteomics data were deleted, and their virulence to zebrafish was evaluated, respectively. The results showed that ΔcorC, Δorf00906, and Δorf04042 significantly reduced bacterial virulence. Finally, the following chromatin immunoprecipitation and polymerase chain reaction (ChIP-PCR) assay validated that the promoter of corC was directly regulated by ORF02889. Overall, these results provide insight into the biological function of ORF02889 and demonstrate its inherent regulatory mechanism for the virulence of A. hydrophila.
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Affiliation(s)
- Lishan Zhang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring (School of Life Sciences, Fujian Agriculture and Forestry University), Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
| | - Lina Sun
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring (School of Life Sciences, Fujian Agriculture and Forestry University), Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Ramanathan Srinivasan
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring (School of Life Sciences, Fujian Agriculture and Forestry University), Fuzhou, China
- Centre for Research, Centre for Materials Engineering and Regenerative Medicine, Bharath Institute of Higher Education and Research, Selaiyur, Chennai, Tamil Nadu, India
| | - Meizhen Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring (School of Life Sciences, Fujian Agriculture and Forestry University), Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
| | - Lanqing Gong
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring (School of Life Sciences, Fujian Agriculture and Forestry University), Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
| | - Xiangmin Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring (School of Life Sciences, Fujian Agriculture and Forestry University), Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
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17
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Yu H, Yang H, Haridas S, Hayes RD, Lynch H, Andersen S, Newman M, Li G, Martínez-Soto D, Milo-Cochavi S, Hazal Ayhan D, Zhang Y, Grigoriev IV, Ma LJ. Conservation and Expansion of Transcriptional Factor Repertoire in the Fusarium oxysporum Species Complex. J Fungi (Basel) 2023; 9:359. [PMID: 36983527 PMCID: PMC10056406 DOI: 10.3390/jof9030359] [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: 02/07/2023] [Revised: 03/11/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023] Open
Abstract
The Fusarium oxysporum species complex (FOSC) includes both plant and human pathogens that cause devastating plant vascular wilt diseases and threaten public health. Each F. oxysporum genome comprises core chromosomes (CCs) for housekeeping functions and accessory chromosomes (ACs) that contribute to host-specific adaptation. This study inspects global transcription factor profiles (TFomes) and their potential roles in coordinating CC and AC functions to accomplish host-specific interactions. Remarkably, we found a clear positive correlation between the sizes of TFomes and the proteomes of an organism. With the acquisition of ACs, the FOSC TFomes were larger than the other fungal genomes included in this study. Among a total of 48 classified TF families, 14 families involved in transcription/translation regulations and cell cycle controls were highly conserved. Among the 30 FOSC expanded families, Zn2-C6 and Znf_C2H2 were most significantly expanded to 671 and 167 genes per family including well-characterized homologs of Ftf1 (Zn2-C6) and PacC (Znf_C2H2) that are involved in host-specific interactions. Manual curation of characterized TFs increased the TFome repertoires by 3% including a disordered protein Ren1. RNA-Seq revealed a steady pattern of expression for conserved TF families and specific activation for AC TFs. Functional characterization of these TFs could enhance our understanding of transcriptional regulation involved in FOSC cross-kingdom interactions, disentangle species-specific adaptation, and identify targets to combat diverse diseases caused by this group of fungal pathogens.
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Affiliation(s)
- Houlin Yu
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - He Yang
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Sajeet Haridas
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, University of California Berkeley, Berkeley, CA 94720, USA
| | - Richard D. Hayes
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, University of California Berkeley, Berkeley, CA 94720, USA
| | - Hunter Lynch
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Sawyer Andersen
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Madison Newman
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Gengtan Li
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Domingo Martínez-Soto
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Shira Milo-Cochavi
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Dilay Hazal Ayhan
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Yong Zhang
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Igor V. Grigoriev
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94598, USA
| | - Li-Jun Ma
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
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18
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Xu SQ, Wang X, Xu L, Wang KX, Jiang YH, Zhang FY, Hong Q, He J, Liu SJ, Qiu JG. The MocR family transcriptional regulator DnfR has multiple binding sites and regulates Dirammox gene transcription in Alcaligenes faecalis JQ135. Environ Microbiol 2023; 25:675-688. [PMID: 36527381 DOI: 10.1111/1462-2920.16318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
Microbial ammonia oxidation is vital to the nitrogen cycle. A biological process, called Dirammox (direct ammonia oxidation, NH3 →NH2 OH→N2 ), has been recently identified in Alcaligenes ammonioxydans and Alcaligenes faecalis. However, its transcriptional regulatory mechanism has not yet been fully elucidated. The present study characterized a new MocR-like transcription factor DnfR that is involved in the Dirammox process in A. faecalis strain JQ135. The entire dnf cluster was composed of 10 genes and transcribed as five transcriptional units, that is, dnfIH, dnfR, dnfG, dnfABCDE and dnfF. DnfR activates the transcription of dnfIH, dnfG and dnfABCDE genes, and represses its own transcription. The intact 1506-bp dnfR gene was required for activation of Dirammox. Electrophoretic mobility shift assays and DNase I footprinting analyses showed that DnfR has one binding site in the dnfH-dnfR intergenic region and two binding sites in the dnfG-dnfA intergenic region. Three binding sites of DnfR shared a 6-bp repeated conserved sequence 5'-GGTCTG-N17 -GGTCTG-3' which was essential for the transcription of downstream target genes. Cysteine and glutamate act as possible effectors of DnfR to activate the transcription of transcriptional units of dnfG and dnfABCDE, respectively. This study provided new insights in the transcriptional regulation mechanism of Dirammox by DnfR in A. faecalis JQ135.
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Affiliation(s)
- Si-Qiong Xu
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Xiao Wang
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Lu Xu
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Ke-Xin Wang
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yin-Hu Jiang
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Fu-Yin Zhang
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Qing Hong
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Jian He
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Ji-Guo Qiu
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
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19
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Yu H, Yang H, Haridas S, Hayes RD, Lynch H, Andersen S, Li G, Mart Nez-Soto D, Milo-Cochavi S, Hazal Ayhan D, Zhang Y, Grigoriev IV, Ma LJ. Conservation and Expansion of Transcriptional Factor Repertoire in the Fusarium oxysporum Species Complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.09.527873. [PMID: 36798233 PMCID: PMC9934661 DOI: 10.1101/2023.02.09.527873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
The Fusarium oxysporum species complex (FOSC) includes both plant and human pathogens that cause devastating plant vascular wilt diseases and threaten public health. Each F. oxysporum genome comprises core chromosomes (CCs) for housekeeping functions and accessory chromosomes (ACs) that contribute to host-specific adaptation. This study inspected global transcription factor profiles (TFomes) and their potential roles in coordinating CCs and ACs functions to accomplish host-specific pathogenicity. Remarkably, we found a clear positive correlation between the sizes of TFome and proteome of an organism, and FOSC TFomes are larger due to the acquisition of ACs. Among a total of 48 classified TF families, 14 families involved in transcription/translation regulations and cell cycle controls are highly conserved. Among 30 FOSC expanded families, Zn2-C6 and Znf_C2H2 are most significantly expanded to 671 and 167 genes per family, including well-characterized homologs of Ftf1 (Zn2-C6) and PacC (Znf_C2H2) involved in host-specific interactions. Manual curation of characterized TFs increased the TFome repertoires by 3%, including a disordered protein Ren1. Expression profiles revealed a steady expression of conserved TF families and specific activation of AC TFs. Functional characterization of these TFs could enhance our understanding of transcriptional regulation involved in FOSC cross-kingdom interactions, disentangle species-specific adaptation, and identify targets to combat diverse diseases caused by this group of fungal pathogens.
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Gahlot DK, Taheri N, MacIntyre S. Diversity in Genetic Regulation of Bacterial Fimbriae Assembled by the Chaperone Usher Pathway. Int J Mol Sci 2022; 24:ijms24010161. [PMID: 36613605 PMCID: PMC9820224 DOI: 10.3390/ijms24010161] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 12/24/2022] Open
Abstract
Bacteria express different types of hair-like proteinaceous appendages on their cell surface known as pili or fimbriae. These filamentous structures are primarily involved in the adherence of bacteria to both abiotic and biotic surfaces for biofilm formation and/or virulence of non-pathogenic and pathogenic bacteria. In pathogenic bacteria, especially Gram-negative bacteria, fimbriae play a key role in bacteria-host interactions which are critical for bacterial invasion and infection. Fimbriae assembled by the Chaperone Usher pathway (CUP) are widespread within the Enterobacteriaceae, and their expression is tightly regulated by specific environmental stimuli. Genes essential for expression of CUP fimbriae are organised in small blocks/clusters, which are often located in proximity to other virulence genes on a pathogenicity island. Since these surface appendages play a crucial role in bacterial virulence, they have potential to be harnessed in vaccine development. This review covers the regulation of expression of CUP-assembled fimbriae in Gram-negative bacteria and uses selected examples to demonstrate both dedicated and global regulatory mechanisms.
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Affiliation(s)
- Dharmender K. Gahlot
- School of Biological Sciences, University of Reading, Reading RG6 6EX, UK
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå University, 901 87 Umeå, Sweden
- Correspondence: (D.K.G.); (S.M.)
| | - Nayyer Taheri
- APC Microbiome Institute, University College Cork, T12 K8AF Cork, Ireland
| | - Sheila MacIntyre
- School of Biological Sciences, University of Reading, Reading RG6 6EX, UK
- Correspondence: (D.K.G.); (S.M.)
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21
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Schleif R. A Career's Work, the l-Arabinose Operon: How It Functions and How We Learned It. EcoSal Plus 2022; 10:eESP00122021. [PMID: 36519894 PMCID: PMC10729937 DOI: 10.1128/ecosalplus.esp-0012-2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 07/20/2021] [Indexed: 06/17/2023]
Abstract
Very few labs have had the good fortune to have been able to focus for more than 50 years on a relatively narrow research topic and to be in a field in which both basic knowledge and the research technology and methods have progressed as rapidly as they have in molecular biology. My research group, first at Brandeis University and then at Johns Hopkins University, has had this opportunity. In this review, therefore, I will describe largely the work from my laboratory that has spanned this period and which was carried out by 40 plus graduate students, several postdoctoral associates, my technician, and me. In addition to presenting the scientific findings or results, I will place many of the topics in scientific context and, because we needed to develop a good many of the experimental methods behind our findings, I will also describe some of these methods and their importance. Also included will be occasional comments on how the research community or my research group functioned. Because a wide variety of approaches were used throughout our work, no ideal organization of this review is apparent. Therefore, I have chosen to use a hybrid structure in which there are six sections. Within each of the sections, experiments and findings will be described roughly in chronological order. Frequent cross references between parts and sections will be made because some findings and experimental approaches could logically have been described in more than one place.
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Zhao D, Li H, Cui Y, Tang S, Wang C, Du B, Ding Y. MsmR1, a global transcription factor, regulates polymyxin synthesis and carbohydrate metabolism in Paenibacillus polymyxa SC2. Front Microbiol 2022; 13:1039806. [PMID: 36483206 PMCID: PMC9722767 DOI: 10.3389/fmicb.2022.1039806] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/26/2022] [Indexed: 10/19/2023] Open
Abstract
The multiple-sugar metabolism regulator (MsmR), a transcription factor belonging to the AraC/XylS family, participates in polysaccharide metabolism and virulence. However, the transcriptional regulatory mechanisms of MsmR1 in Paenibacillus polymyxa remain unclear. In this study, knocking out msmR1 was found to reduce polymyxin synthesis by the SC2-M1 strain. Chromatin immunoprecipitation assay with sequencing (ChIP-seq) revealed that most enriched pathway was that of carbohydrate metabolism. Additionally, electromobility shift assays (EMSA) confirmed the direct interaction between MsmR1 and the promoter regions of oppC3, sucA, sdr3, pepF, yycN, PPSC2_23180, pppL, and ydfp. MsmR1 stimulates polymyxin biosynthesis by directly binding to the promoter regions of oppC3 and sdr3, while also directly regulating sucA and influencing the citrate cycle (TCA cycle). In addition, MsmR1 directly activates pepF and was beneficial for spore and biofilm formation. These results indicated that MsmR1 could regulate carbohydrate and amino acid metabolism, and indirectly affect biological processes such as polymyxin synthesis, biofilm formation, and motility. Moreover, MsmR1 could be autoregulated. Hence, this study expand the current knowledge of MsmR1 and will be beneficial for the application of P. polymyxa SC2 in the biological control against the certain pathogens in pepper.
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Affiliation(s)
| | | | | | | | | | - Binghai Du
- College of Life Sciences and Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-alkali Land and Shandong Key Laboratory of Agricultural Microbiology and National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Tai’an, China
| | - Yanqin Ding
- College of Life Sciences and Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-alkali Land and Shandong Key Laboratory of Agricultural Microbiology and National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Tai’an, China
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23
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Fernandez-Lopez R, Ruiz R, del Campo I, Gonzalez-Montes L, Boer D, de la Cruz F, Moncalian G. Structural basis of direct and inverted DNA sequence repeat recognition by helix-turn-helix transcription factors. Nucleic Acids Res 2022; 50:11938-11947. [PMID: 36370103 PMCID: PMC9723621 DOI: 10.1093/nar/gkac1024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 10/13/2022] [Accepted: 10/25/2022] [Indexed: 11/13/2022] Open
Abstract
Some transcription factors bind DNA motifs containing direct or inverted sequence repeats. Preference for each of these DNA topologies is dictated by structural constraints. Most prokaryotic regulators form symmetric oligomers, which require operators with a dyad structure. Binding to direct repeats requires breaking the internal symmetry, a property restricted to a few regulators, most of them from the AraC family. The KorA family of transcriptional repressors, involved in plasmid propagation and stability, includes members that form symmetric dimers and recognize inverted repeats. Our structural analyses show that ArdK, a member of this family, can form a symmetric dimer similar to that observed for KorA, yet it binds direct sequence repeats as a non-symmetric dimer. This is possible by the 180° rotation of one of the helix-turn-helix domains. We then probed and confirmed that ArdK shows affinity for an inverted repeat, which, surprisingly, is also recognized by a non-symmetrical dimer. Our results indicate that structural flexibility at different positions in the dimerization interface constrains transcription factors to bind DNA sequences with one of these two alternative DNA topologies.
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Affiliation(s)
- Raul Fernandez-Lopez
- Departamento de Biología Molecular, Universidad de Cantabria and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), CSIC-Universidad de Cantabria, 39011, Santander, Spain
| | - Raul Ruiz
- Departamento de Biología Molecular, Universidad de Cantabria and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), CSIC-Universidad de Cantabria, 39011, Santander, Spain
| | - Irene del Campo
- Departamento de Biología Molecular, Universidad de Cantabria and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), CSIC-Universidad de Cantabria, 39011, Santander, Spain
| | - Lorena Gonzalez-Montes
- Departamento de Biología Molecular, Universidad de Cantabria and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), CSIC-Universidad de Cantabria, 39011, Santander, Spain
| | - D Roeland Boer
- Alba Synchrotron, Cerdanyola del Vallès, 08290, Barcelona, Spain
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Hou Y, Kumar P, Aggarwal M, Sarkari F, Wolcott KM, Chattoraj DK, Crooke E, Saxena R. The linker domain of the initiator DnaA contributes to its ATP binding and membrane association in E. coli chromosomal replication. SCIENCE ADVANCES 2022; 8:eabq6657. [PMID: 36197974 PMCID: PMC9534497 DOI: 10.1126/sciadv.abq6657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 08/18/2022] [Indexed: 06/16/2023]
Abstract
DnaA, the initiator of Escherichia coli chromosomal replication, has in its adenosine triphosphatase (ATPase) domain residues required for adenosine 5'-triphosphate (ATP) binding and membrane attachment. Here, we show that D118Q substitution in the DnaA linker domain, a domain known to be without major regulatory functions, influences ATP binding of DnaA and replication initiation in vivo. Although initiation defective by itself, overexpression of DnaA(D118Q) caused overinitiation of replication in dnaA46ts cells and prevented cell growth. The growth defect was rescued by overexpressing the initiation inhibitor, SeqA, indicating that the growth inhibition resulted from overinitiation. Small deletions within the linker showed another unexpected phenotype: cellular growth without requiring normal levels of anionic membrane lipids, a property found in DnaA mutated in its ATPase domain. The deleted proteins were defective in association with anionic membrane vesicles. These results show that changes in the linker domain can alter DnaA functions similarly to the previously shown changes in the ATPase domain.
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Affiliation(s)
- Yanqi Hou
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Pankaj Kumar
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Monika Aggarwal
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Farzad Sarkari
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Karen M. Wolcott
- Laboratory of Genome Integrity, Flow Cytometry Core Facility, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dhruba K. Chattoraj
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Elliott Crooke
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC 20007, USA
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Rahul Saxena
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC 20007, USA
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25
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Saldaña-Ahuactzi Z, Knodler LA. FoxR is an AraC-like transcriptional regulator of ferrioxamine uptake in Salmonella enterica. Mol Microbiol 2022; 118:369-386. [PMID: 35970762 DOI: 10.1111/mmi.14970] [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: 03/23/2022] [Revised: 07/30/2022] [Accepted: 08/02/2022] [Indexed: 01/07/2023]
Abstract
Salmonella enterica spp. produce siderophores to bind iron with high affinity and can also use three xenosiderophores secreted by other microorganisms, ferrichrome, coprogen, and ferrioxamine. Here we focused on FoxA, a TonB-dependent transporter of ferrioxamines. Adjacent to foxA is a gene annotated as a helix-turn-helix (HTH) domain-containing protein, SL0358 (foxR), in the Salmonella enterica serovar Typhimurium SL1344 genome. FoxR shares homology with transcriptional regulators belonging to the AraC/XylS family. foxR is syntenic with foxA in the Enterobacteriaceae family, suggesting their functional relatedness. Both foxA and foxR are repressed by the ferric uptake regulator (Fur) under iron-rich growth conditions. When iron is scarce, FoxR acts as a transcriptional activator of foxA by directly binding to its upstream regulatory region. A point mutation in the HTH domain of FoxR abolished this binding, as did mutation of a direct repeat motif in the foxA upstream regulatory region. Desferrioxamine (DFOE) enhanced FoxR protein stability and foxA transcription but did not affect the affinity of FoxR binding to the foxA regulatory region. In summary, we have identified FoxR as a new member of the AraC/XylS family that regulates xenosiderophore-mediated iron uptake by S. Typhimurium and likely other Enterobacteriaceae members.
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Affiliation(s)
- Zeus Saldaña-Ahuactzi
- Paul G. Allen School for Global Health, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
| | - Leigh A Knodler
- Paul G. Allen School for Global Health, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
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26
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Abstract
DNA looping has emerged as a central paradigm of transcriptional regulation, as it is shared across many living systems. One core property of DNA looping-based regulation is its ability to greatly enhance repression or activation of genes with only a few copies of transcriptional regulators. However, this property based on a small number of proteins raises the question of the robustness of such a mechanism with respect to the large intracellular perturbations taking place during growth and division of the cell. Here we address the issue of sensitivity to variations of intracellular parameters of gene regulation by DNA looping. We use the lac system as a prototype to experimentally identify the key features of the robustness of DNA looping in growing Escherichia coli cells. Surprisingly, we observe time intervals of tight repression spanning across division events, which can sometimes exceed 10 generations. Remarkably, the distribution of such long time intervals exhibits memoryless statistics that is mostly insensitive to repressor concentration, cell division events, and the number of distinct loops accessible to the system. By contrast, gene regulation becomes highly sensitive to these perturbations when DNA looping is absent. Using stochastic simulations, we propose that the observed robustness to division emerges from the competition between fast, multiple rebinding events of repressors and slow initiation rate of the RNA polymerase. We argue that fast rebinding events are a direct consequence of DNA looping that ensures robust gene repression across a range of intracellular perturbations.
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Tomioka S, Seki N, Sugiura Y, Akiyama M, Uchiyama J, Yamaguchi G, Yakabe K, Ejima R, Hattori K, Kimizuka T, Fujimura Y, Sato H, Gondo M, Ozaki S, Honme Y, Suematsu M, Kimura I, Inohara N, Núñez G, Hase K, Kim YG. Cooperative action of gut-microbiota-accessible carbohydrates improves host metabolic function. Cell Rep 2022; 40:111087. [PMID: 35858544 DOI: 10.1016/j.celrep.2022.111087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 03/17/2022] [Accepted: 06/22/2022] [Indexed: 12/31/2022] Open
Abstract
Microbiota-accessible carbohydrates (MACs) exert health-promoting effects, but how each MAC impacts gut microbiota and regulates host physiology remains unclear. Here, we show that l-arabinose and sucrose cooperatively act on gut microbiota and exert anti-obesogenic effects. Specifically, l-arabinose, a monosaccharide that is poorly absorbed in the gut and inhibits intestinal sucrase, suppresses diet-induced obesity in mice in the presence of sucrose. Additionally, the suppressive effect of l-arabinose on adiposity is abrogated in mice lacking the short-chain fatty acid (SCFA) receptors GPR43 and GPR41. Mechanistically, l-arabinose increases the relative abundance of acetate and propionate producers (e.g., Bacteroides), while sucrose enhances SCFA production. Furthermore, l-arabinose and sucrose activate the glycolytic and pentose phosphate pathways of Bacteroides, respectively, indicating that they synergistically promote acetate production through distinct pathways. These findings suggest that each MAC has a unique property and thus may serve as a precision gut-microbiota modulator to promote host homeostasis.
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Affiliation(s)
- Sawako Tomioka
- Research Center for Drug Discovery and Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan; Division of Biochemistry, Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan
| | - Natsumi Seki
- Research Center for Drug Discovery and Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan; Division of Biochemistry, Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan
| | - Yuki Sugiura
- Department of Biochemistry, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Masahiro Akiyama
- Research Center for Drug Discovery and Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan
| | - Jun Uchiyama
- Research Center for Drug Discovery and Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan; Division of Biochemistry, Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan
| | - Genki Yamaguchi
- Research Center for Drug Discovery and Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan; Division of Biochemistry, Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan
| | - Kyosuke Yakabe
- Research Center for Drug Discovery and Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan; Division of Biochemistry, Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan
| | - Ryuta Ejima
- Research Center for Drug Discovery and Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan; Division of Biochemistry, Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan
| | - Kouya Hattori
- Research Center for Drug Discovery and Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan; Division of Biochemistry, Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan
| | - Tatsuki Kimizuka
- Research Center for Drug Discovery and Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan; Division of Biochemistry, Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan
| | - Yumiko Fujimura
- Division of Biochemistry, Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan
| | - Hiroki Sato
- Research Center for Drug Discovery and Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan
| | - Monica Gondo
- Research Center for Drug Discovery and Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan; Division of Biochemistry, Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan
| | - Satoru Ozaki
- Co-Creation Center, Meiji Holdings Co., Ltd., Tokyo 192-0919, Japan
| | - Yoshiko Honme
- Co-Creation Center, Meiji Holdings Co., Ltd., Tokyo 192-0919, Japan
| | - Makoto Suematsu
- Department of Biochemistry, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Ikuo Kimura
- Laboratory of Molecular Neurobiology, Graduate School of Biostudies, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Naohiro Inohara
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Gabriel Núñez
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Koji Hase
- Division of Biochemistry, Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan
| | - Yun-Gi Kim
- Research Center for Drug Discovery and Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan.
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Shilling PJ, Khananisho D, Cumming J, Söderström B, Daley DO. Signal Amplification of araC pBAD Using a Standardised Translation Initiation Region. Synth Biol (Oxf) 2022; 7:ysac009. [PMID: 35903559 PMCID: PMC9316229 DOI: 10.1093/synbio/ysac009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 05/11/2022] [Accepted: 07/04/2022] [Indexed: 11/16/2022] Open
Abstract
araC pBAD is a genetic fragment that regulates the expression of the araBAD operon in bacteria, which is required for the metabolism of L-arabinose. It is widely used in bioengineering applications because it can drive regulatable and titratable expression of genes and genetic pathways in microbial cell factories. A notable limitation of araC pBAD is that it generates a low signal when induced with high concentrations of L-arabinose (the maximum ON state). Herein we have amplified the maximum ON state of araC pBAD by coupling it to a synthetically evolved translation initiation region (TIREVOL). The coupling maintains regulatable and titratable expression from araC pBAD and yet increases the maximal ON state by >5-fold. The general principle demonstrated in the study can be applied to amplify the signal from similar genetic modules.
Graphical Abstract
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Affiliation(s)
- Patrick J Shilling
- Department of Biochemistry and Biophysics, Stockholm University , Stockholm, Sweden
| | - Diana Khananisho
- Department of Biochemistry and Biophysics, Stockholm University , Stockholm, Sweden
| | - James Cumming
- Department of Biochemistry and Biophysics, Stockholm University , Stockholm, Sweden
| | - Bill Söderström
- Australian Institute for Microbiology and Infection, University of Technology Sydney , Sydney, New South Wales, Australia
| | - Daniel O Daley
- Department of Biochemistry and Biophysics, Stockholm University , Stockholm, Sweden
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Salvail H, Choi J, Groisman EA. Differential synthesis of novel small protein times Salmonella virulence program. PLoS Genet 2022; 18:e1010074. [PMID: 35245279 PMCID: PMC8896665 DOI: 10.1371/journal.pgen.1010074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 02/03/2022] [Indexed: 11/18/2022] Open
Abstract
Gene organization in operons enables concerted transcription of functionally related genes and efficient control of cellular processes. Typically, an operon is transcribed as a polycistronic mRNA that is translated into corresponding proteins. Here, we identify a bicistronic operon transcribed as two mRNAs, yet only one allows translation of both genes. We establish that the novel gene ugtS forms an operon with virulence gene ugtL, an activator of the master virulence regulatory system PhoP/PhoQ in Salmonella enterica serovar Typhimurium. Only the longer ugtSugtL mRNA carries the ugtS ribosome binding site and therefore allows ugtS translation. Inside macrophages, the ugtSugtL mRNA species allowing translation of both genes is produced hours before that allowing translation solely of ugtL. The small protein UgtS controls the kinetics of PhoP phosphorylation by antagonizing UgtL activity, preventing premature activation of a critical virulence program. Moreover, S. enterica serovars that infect cold-blooded animals lack ugtS. Our results establish how foreign gene control of ancestral regulators enables pathogens to time their virulence programs. Pathogens must express their virulence genes at precisely the right time to cause disease. Here, we identify a novel small protein that governs a critical virulence program in the pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium). We establish that the novel small protein UgtS prevents the virulence protein UgtL from activating the master virulence regulator PhoP inside macrophages. S. Typhimurium produces two ugtSugtL mRNAs, but only one of them allows ugtS translation. The absence of ugtS from S. enterica serovars that infect cold-blooded animals raises the possibility of UgtS playing a regulatory role during infection of warm-blooded animals. Our findings establish how a horizontally acquired bicistron enables pathogens to time their virulence programs by controlling ancestral regulators.
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Affiliation(s)
- Hubert Salvail
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
| | - Jeongjoon Choi
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Eduardo A. Groisman
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, United States of America
- Yale Microbial Sciences Institute, West Haven, Connecticut, United States of America
- * E-mail:
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30
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Femerling G, Gama-Castro S, Lara P, Ledezma-Tejeida D, Tierrafría VH, Muñiz-Rascado L, Bonavides-Martínez C, Collado-Vides J. Sensory Systems and Transcriptional Regulation in Escherichia coli. Front Bioeng Biotechnol 2022; 10:823240. [PMID: 35237580 PMCID: PMC8882922 DOI: 10.3389/fbioe.2022.823240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 01/18/2022] [Indexed: 11/13/2022] Open
Abstract
In free-living bacteria, the ability to regulate gene expression is at the core of adapting and interacting with the environment. For these systems to have a logic, a signal must trigger a genetic change that helps the cell to deal with what implies its presence in the environment; briefly, the response is expected to include a feedback to the signal. Thus, it makes sense to think of genetic sensory mechanisms of gene regulation. Escherichia coli K-12 is the bacterium model for which the largest number of regulatory systems and its sensing capabilities have been studied in detail at the molecular level. In this special issue focused on biomolecular sensing systems, we offer an overview of the transcriptional regulatory corpus of knowledge for E. coli that has been gathered in our database, RegulonDB, from the perspective of sensing regulatory systems. Thus, we start with the beginning of the information flux, which is the signal’s chemical or physical elements detected by the cell as changes in the environment; these signals are internally transduced to transcription factors and alter their conformation. Signals transduced to effectors bind allosterically to transcription factors, and this defines the dominant sensing mechanism in E. coli. We offer an updated list of the repertoire of known allosteric effectors, as well as a list of the currently known different mechanisms of this sensing capability. Our previous definition of elementary genetic sensory-response units, GENSOR units for short, that integrate signals, transport, gene regulation, and the biochemical response of the regulated gene products of a given transcriptional factor fit perfectly with the purpose of this overview. We summarize the functional heterogeneity of their response, based on our updated collection of GENSORs, and we use them to identify the expected feedback as part of their response. Finally, we address the question of multiple sensing in the regulatory network of E. coli. This overview introduces the architecture of sensing and regulation of native components in E.coli K-12, which might be a source of inspiration to bioengineering applications.
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Affiliation(s)
- Georgette Femerling
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Socorro Gama-Castro
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Paloma Lara
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México
| | | | - Víctor H. Tierrafría
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México
- Department of Biomedical Engineering, Boston University, Boston, MA, United States
| | - Luis Muñiz-Rascado
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México
| | | | - Julio Collado-Vides
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México
- Department of Biomedical Engineering, Boston University, Boston, MA, United States
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Universitat Pompeu Fabra (UPF), Barcelona, Spain
- *Correspondence: Julio Collado-Vides,
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Co-evolution of drug resistance and broadened substrate recognition in HIV protease variants isolated from an Escherichia coli genetic selection system. Biochem J 2022; 479:479-501. [PMID: 35089310 DOI: 10.1042/bcj20210767] [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: 11/02/2021] [Revised: 01/07/2022] [Accepted: 01/28/2022] [Indexed: 11/17/2022]
Abstract
A genetic selection system for activity of HIV protease is described that is based on a synthetic substrate constructed as a modified AraC regulatory protein that when cleaved stimulate L-arabinose metabolism in an Escherichia coli araC strain. Growth stimulation on selective plates was shown to depend on active HIV protease and the scissile bond in the substrate. In addition, the growth of cells correlated well with the established cleavage efficiency of the sites in the viral polyprotein, Gag, when these sites were individually introduced into the synthetic substate of the selection system. Plasmids encoding protease variants selected based on stimulation of cell growth in the presence of saquinavir or cleavage of a site not cleaved by wild-type protease, were indistinguishable with respect to both phenotypes. Also, both groups of selected plasmids encoded side chain substitutions known from clinical isolates or displayed different side chain substitutions but at identical positions. One highly frequent side chain substitution, E34V, not regarded as a major drug resistance substitution was found in variants obtained under both selective conditions and is suggested to improve protease processing of the synthetic substrate. This substitution is away from the substrate-binding cavity and together with other substitutions in the selected reading frames supports the previous suggestion of a substrate-binding site extended from the active site binding pocket itself.
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Guharajan S, Chhabra S, Parisutham V, Brewster RC. Quantifying the regulatory role of individual transcription factors in Escherichia coli. Cell Rep 2021; 37:109952. [PMID: 34758318 PMCID: PMC8667592 DOI: 10.1016/j.celrep.2021.109952] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 08/02/2021] [Accepted: 10/13/2021] [Indexed: 11/30/2022] Open
Abstract
Gene regulation often results from the action of multiple transcription factors (TFs) acting at a promoter, obscuring the individual regulatory effect of each TF on RNA polymerase (RNAP). Here we measure the fundamental regulatory interactions of TFs in E. coli by designing synthetic target genes that isolate individual TFs' regulatory effects. Using a thermodynamic model, each TF's regulatory interactions are decoupled from TF occupancy and interpreted as acting through (de)stabilization of RNAP and (de)acceleration of transcription initiation. We find that the contribution of each mechanism depends on TF identity and binding location; regulation immediately downstream of the promoter is insensitive to TF identity, but the same TFs regulate by distinct mechanisms upstream of the promoter. These two mechanisms are uncoupled and can act coherently, to reinforce the observed regulatory role (activation/repression), or incoherently, wherein the TF regulates two distinct steps with opposing effects.
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Affiliation(s)
- Sunil Guharajan
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Shivani Chhabra
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Vinuselvi Parisutham
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Robert C Brewster
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.
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Burgess RR. What is in the black box? The discovery of the sigma factor and the subunit structure of E. coli RNA polymerase. J Biol Chem 2021; 297:101310. [PMID: 34673029 PMCID: PMC8569590 DOI: 10.1016/j.jbc.2021.101310] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/13/2021] [Indexed: 11/24/2022] Open
Abstract
This Reflections article is focused on the 5 years while I was a graduate student (1964-1969). During this period, I made some of the most significant discoveries of my career. I have written this article primarily for a protein biochemistry audience, my colleagues who shared this exciting time in science, and the many scientists over the last 50 years who have contributed to our knowledge of transcriptional machinery and their regulation. It is also written for today's graduate students, postdocs, and scientists who may not know much about the discoveries and technical advances that are now taken for granted, to show that even with methods primitive by today's standards, we were still able to make foundational advances. I also hope to provide a glimpse into how fortunate I was to be a graduate student over 50 years ago in the golden age of molecular biology.
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Affiliation(s)
- Richard R Burgess
- James D. Watson Professor Emeritus of Oncology, McArdle Laboratory for Cancer Research, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA.
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Optimised Heterologous Expression and Functional Analysis of the Yersinia pestis F1-Capsular Antigen Regulator Caf1R. Int J Mol Sci 2021; 22:ijms22189805. [PMID: 34575967 PMCID: PMC8470410 DOI: 10.3390/ijms22189805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/02/2021] [Accepted: 09/06/2021] [Indexed: 12/14/2022] Open
Abstract
The bacterial pathogen, Yersinia pestis, has caused three historic pandemics and continues to cause small outbreaks worldwide. During infection, Y. pestis assembles a capsule-like protective coat of thin fibres of Caf1 subunits. This F1 capsular antigen has attracted much attention due to its clinical value in plague diagnostics and anti-plague vaccine development. Expression of F1 is tightly regulated by a transcriptional activator, Caf1R, of the AraC/XylS family, proteins notoriously prone to aggregation. Here, we have optimised the recombinant expression of soluble Caf1R. Expression from the native and synthetic codon-optimised caf1R cloned in three different expression plasmids was examined in a library of E. coli host strains. The functionality of His-tagged Caf1R was demonstrated in vivo, but insolubility was a problem with overproduction. High levels of soluble MBP-Caf1R were produced from codon optimised caf1R. Transcriptional-lacZ reporter fusions defined the PM promoter and Caf1R binding site responsible for transcription of the cafMA1 operon. Use of the identified Caf1R binding caf DNA sequence in an electrophoretic mobility shift assay (EMSA) confirmed correct folding and functionality of the Caf1R DNA-binding domain in recombinant MBP-Caf1R. Availability of functional recombinant Caf1R will be a valuable tool to elucidate control of expression of F1 and Caf1R-regulated pathophysiology of Y. pestis.
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Fricke PM, Lürkens M, Hünnefeld M, Sonntag CK, Bott M, Davari MD, Polen T. Highly tunable TetR-dependent target gene expression in the acetic acid bacterium Gluconobacter oxydans. Appl Microbiol Biotechnol 2021; 105:6835-6852. [PMID: 34448898 PMCID: PMC8426231 DOI: 10.1007/s00253-021-11473-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 11/27/2022]
Abstract
Abstract For the acetic acid bacterium (AAB) Gluconobacter oxydans only recently the first tight system for regulatable target gene expression became available based on the heterologous repressor-activator protein AraC from Escherichia coli and the target promoter ParaBAD. In this study, we tested pure repressor-based TetR- and LacI-dependent target gene expression in G. oxydans by applying the same plasmid backbone and construction principles that we have used successfully for the araC-ParaBAD system. When using a pBBR1MCS-5-based plasmid, the non-induced basal expression of the Tn10-based TetR-dependent expression system was extremely low. This allowed calculated induction ratios of up to more than 3500-fold with the fluorescence reporter protein mNeonGreen (mNG). The induction was highly homogeneous and tunable by varying the anhydrotetracycline concentration from 10 to 200 ng/mL. The already strong reporter gene expression could be doubled by inserting the ribosome binding site AGGAGA into the 3’ region of the Ptet sequence upstream from mNG. Alternative plasmid constructs used as controls revealed a strong influence of transcription terminators and antibiotics resistance gene of the plasmid backbone on the resulting expression performance. In contrast to the TetR-Ptet-system, pBBR1MCS-5-based LacI-dependent expression from PlacUV5 always exhibited some non-induced basal reporter expression and was therefore tunable only up to 40-fold induction by IPTG. The leakiness of PlacUV5 when not induced was independent of potential read-through from the lacI promoter. Protein-DNA binding simulations for pH 7, 6, 5, and 4 by computational modeling of LacI, TetR, and AraC with DNA suggested a decreased DNA binding of LacI when pH is below 6, the latter possibly causing the leakiness of LacI-dependent systems hitherto tested in AAB. In summary, the expression performance of the pBBR1MCS-5-based TetR-Ptet system makes this system highly suitable for applications in G. oxydans and possibly in other AAB. Key Points • A pBBR1MCS-5-based TetR-Ptet system was tunable up to more than 3500-fold induction. • A pBBR1MCS-5-based LacI-PlacUV5 system was leaky and tunable only up to 40-fold. • Modeling of protein-DNA binding suggested decreased DNA binding of LacI at pH < 6. Supplementary Information The online version contains supplementary material available at 10.1007/s00253-021-11473-x.
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Affiliation(s)
- Philipp Moritz Fricke
- Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, Institute of Bio- and Geosciences, 52425 Jülich, Germany
| | - Martha Lürkens
- RWTH Aachen University, Institute of Biotechnology, Worringerweg 3, 52074 Aachen, Germany
| | - Max Hünnefeld
- Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, Institute of Bio- and Geosciences, 52425 Jülich, Germany
| | - Christiane K. Sonntag
- Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, Institute of Bio- and Geosciences, 52425 Jülich, Germany
| | - Michael Bott
- Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, Institute of Bio- and Geosciences, 52425 Jülich, Germany
| | - Mehdi D. Davari
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
| | - Tino Polen
- Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, Institute of Bio- and Geosciences, 52425 Jülich, Germany
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Ranade S, He Q. Escherichia coli AraJ boosts utilization of arabinose in metabolically engineered cyanobacterium Synechocystis sp. PCC 6803. AMB Express 2021; 11:115. [PMID: 34387784 PMCID: PMC8363721 DOI: 10.1186/s13568-021-01277-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 08/06/2021] [Indexed: 12/02/2022] Open
Abstract
Lignocellulosic biomass can serve as an inexpensive and renewable source of carbon for the biosynthesis of commercially important compounds. L-arabinose is the second most abundant pentose sugar present in the plant materials. Model cyanobacterium Synechocystis sp. PCC 6803 is incapable of catabolism of L-arabinose as a source of carbon and energy. In this study, all the heterologous genes expressed in Synechocystis were derived from Escherichia coli K-12. Initially we constructed four Synechocystis strains that expressed AraBAD enzymes involved in L-arabinose catabolism, either in combination with or without one of the three arabinose transporters, AraE, AraFGH or AraJ. Among the recombinants, the strain possessing AraJ transporter was observed to be the most efficient in terms of dry biomass production and L-arabinose consumption. Later, an additional strain was generated by the expression of AraJ in the AraE-possessing strain. The resultant strain was shown to be advantageous over its parent. This study demonstrates that AraJ, a protein with hitherto unknown function plays a role in the uptake of L-arabinose to boost its catabolism in the transgenic Synechocystis strains. The work also contributes to the current knowledge regarding metabolic engineering of cyanobacteria for the utilization of pentose sugars.
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37
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Cautionary Notes on the Use of Arabinose- and Rhamnose-Inducible Expression Vectors in Pseudomonas aeruginosa. J Bacteriol 2021; 203:e0022421. [PMID: 34096777 DOI: 10.1128/jb.00224-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The Pseudomonas aeruginosa virulence factor regulator (Vfr) is a cyclic AMP (cAMP)-responsive transcription factor homologous to the Escherichia coli cAMP receptor protein (CRP). Unlike CRP, which plays a central role in E. coli energy metabolism and catabolite repression, Vfr is primarily involved in the control of P. aeruginosa virulence factor expression. Expression of the Vfr regulon is controlled at the level of vfr transcription, Vfr translation, cAMP synthesis, and cAMP degradation. While investigating mechanisms that regulate Vfr translation, we placed vfr transcription under the control of the rhaBp rhamnose-inducible promoter system (designated PRha) and found that PRha promoter activity was highly dependent upon vfr. Vfr dependence was also observed for the araBp arabinose-inducible promoter (designated PBAD). The observation of Vfr dependence was not entirely unexpected. Both promoters are derived from E. coli, where maximal promoter activity is dependent upon CRP. Like CRP, we found that Vfr directly binds to promoter probes derived from the PRha and PBAD promoters in vitro. Because Vfr-cAMP activity is highly integrated into numerous global regulatory systems, including c-di-GMP signaling, the Gac/Rsm system, MucA/AlgU/AlgZR signaling, and Hfq/sRNAs, the potential exists for significant variability in PRha and PBAD promoter activity in a variety of genetic backgrounds, and use of these promoter systems in P. aeruginosa should be employed with caution. IMPORTANCE Heterologous gene expression and complementation constitute a valuable and widely utilized tool in bacterial genetics. The arabinose-inducible ParaBAD (PBAD) and rhamnose-inducible PrhaBAD (PRha) promoter systems are commonly used in P. aeruginosa genetics and prized for the tight control and dynamic expression ranges that can be achieved. In this study, we demonstrate that the activity of both promoters is dependent upon the cAMP-dependent transcription factor Vfr. While this poses an obvious problem for use in a vfr mutant background, the issue is more pervasive, considering that vfr transcription/synthesis and cAMP homeostasis are highly integrated into the cellular physiology of the organism and influenced by numerous global regulatory systems. Fortunately, the synthetic PTac promoter is not subject to Vfr regulatory control.
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38
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Vasicek EM, O'Neal L, Parsek MR, Fitch J, White P, Gunn JS. L-Arabinose Transport and Metabolism in Salmonella Influences Biofilm Formation. Front Cell Infect Microbiol 2021; 11:698146. [PMID: 34368016 PMCID: PMC8341724 DOI: 10.3389/fcimb.2021.698146] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/21/2021] [Indexed: 11/28/2022] Open
Abstract
L-arabinose inducible promoters are commonly used in gene expression analysis. However, nutrient source and availability also play a role in biofilm formation; therefore, L-arabinose metabolism could impact biofilm development. In this study we examined the impact of L-arabinose on Salmonella enterica serovar Typhimurium (S. Typhimurium) biofilm formation. Using mutants impaired for the transport and metabolism of L-arabinose, we showed that L-arabinose metabolism negatively impacts S. Typhimurium biofilm formation in vitro. When L-arabinose metabolism is abrogated, biofilm formation returned to baseline levels. However, without the ability to import extracellular L-arabinose, biofilm formation significantly increased. Using RNA-Seq we identified several gene families involved in these different phenotypes including curli expression, amino acid synthesis, and L-arabinose metabolism. Several individual candidate genes were tested for their involvement in the L-arabinose-mediated biofilm phenotypes, but most played no significant role. Interestingly, in the presence of L-arabinose the diguanylate cyclase gene adrA was downregulated in wild type S. Typhimurium. Meanwhile cyaA, encoding an adenylate cyclase, was downregulated in an L-arabinose transport mutant. Using an IPTG-inducible plasmid to deplete c-di-GMP via vieA expression, we were able to abolish the increased biofilm phenotype seen in the transport mutant. However, the mechanism by which the L-arabinose import mutant forms significantly larger biofilms remains to be determined. Regardless, these data suggest that L-arabinose metabolism influences intracellular c-di-GMP levels and therefore biofilm formation. These findings are important when considering the use of an L-arabinose inducible promoter in biofilm conditions.
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Affiliation(s)
- Erin M Vasicek
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, OH, United States.,Infectious Diseases Institute, The Ohio State University, Columbus, OH, United States.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, United States
| | - Lindsey O'Neal
- Department of Microbiology, University of Washington, Seattle, WA, United States
| | - Matthew R Parsek
- Department of Microbiology, University of Washington, Seattle, WA, United States
| | - James Fitch
- The Institute for Genomic Medicine, The Research Institute at Nationwide Children's Hospital, Columbus, OH, United States
| | - Peter White
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, United States.,The Institute for Genomic Medicine, The Research Institute at Nationwide Children's Hospital, Columbus, OH, United States
| | - John S Gunn
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, OH, United States.,Infectious Diseases Institute, The Ohio State University, Columbus, OH, United States.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, United States
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Engineering AraC to make it responsive to light instead of arabinose. Nat Chem Biol 2021; 17:817-827. [PMID: 33903769 DOI: 10.1038/s41589-021-00787-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 03/19/2021] [Indexed: 02/02/2023]
Abstract
The L-arabinose-responsive AraC and its cognate PBAD promoter underlie one of the most often used chemically inducible prokaryotic gene expression systems in microbiology and synthetic biology. Here, we change the sensing capability of AraC from L-arabinose to blue light, making its dimerization and the resulting PBAD activation light-inducible. We engineer an entire family of blue light-inducible AraC dimers in Escherichia coli (BLADE) to control gene expression in space and time. We show that BLADE can be used with pre-existing L-arabinose-responsive plasmids and strains, enabling optogenetic experiments without the need to clone. Furthermore, we apply BLADE to control, with light, the catabolism of L-arabinose, thus externally steering bacterial growth with a simple transformation step. Our work establishes BLADE as a highly practical and effective optogenetic tool with plug-and-play functionality-features that we hope will accelerate the broader adoption of optogenetics and the realization of its vast potential in microbiology, synthetic biology and biotechnology.
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40
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Lozano Terol G, Gallego-Jara J, Sola Martínez RA, Martínez Vivancos A, Cánovas Díaz M, de Diego Puente T. Impact of the Expression System on Recombinant Protein Production in Escherichia coli BL21. Front Microbiol 2021; 12:682001. [PMID: 34234760 PMCID: PMC8257044 DOI: 10.3389/fmicb.2021.682001] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/18/2021] [Indexed: 12/13/2022] Open
Abstract
Recombinant protein production for medical, academic, or industrial applications is essential for our current life. Recombinant proteins are obtained mainly through microbial fermentation, with Escherichia coli being the host most used. In spite of that, some problems are associated with the production of recombinant proteins in E. coli, such as the formation of inclusion bodies, the metabolic burden, or the inefficient translocation/transport system of expressed proteins. Optimizing transcription of heterologous genes is essential to avoid these drawbacks and develop competitive biotechnological processes. Here, expression of YFP reporter protein is evaluated under the control of four promoters of different strength (PT7lac, Ptrc, Ptac, and PBAD) and two different replication origins (high copy number pMB1′ and low copy number p15A). In addition, the study has been carried out with the E. coli BL21 wt and the ackA mutant strain growing in a rich medium with glucose or glycerol as carbon sources. Results showed that metabolic burden associated with transcription and translation of foreign genes involves a decrease in recombinant protein expression. It is necessary to find a balance between plasmid copy number and promoter strength to maximize soluble recombinant protein expression. The results obtained represent an important advance on the most suitable expression system to improve both the quantity and quality of recombinant proteins in bioproduction engineering.
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Affiliation(s)
- Gema Lozano Terol
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
| | - Julia Gallego-Jara
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
| | - Rosa Alba Sola Martínez
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
| | - Adrián Martínez Vivancos
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
| | - Manuel Cánovas Díaz
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
| | - Teresa de Diego Puente
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
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Norris N, Levine NM, Fernandez VI, Stocker R. Mechanistic model of nutrient uptake explains dichotomy between marine oligotrophic and copiotrophic bacteria. PLoS Comput Biol 2021; 17:e1009023. [PMID: 34010286 PMCID: PMC8168909 DOI: 10.1371/journal.pcbi.1009023] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 06/01/2021] [Accepted: 04/28/2021] [Indexed: 11/24/2022] Open
Abstract
Marine bacterial diversity is immense and believed to be driven in part by trade-offs in metabolic strategies. Here we consider heterotrophs that rely on organic carbon as an energy source and present a molecular-level model of cell metabolism that explains the dichotomy between copiotrophs—which dominate in carbon-rich environments—and oligotrophs—which dominate in carbon-poor environments—as the consequence of trade-offs between nutrient transport systems. While prototypical copiotrophs, like Vibrios, possess numerous phosphotransferase systems (PTS), prototypical oligotrophs, such as SAR11, lack PTS and rely on ATP-binding cassette (ABC) transporters, which use binding proteins. We develop models of both transport systems and use them in proteome allocation problems to predict the optimal nutrient uptake and metabolic strategy as a function of carbon availability. We derive a Michaelis–Menten approximation of ABC transport, analytically demonstrating how the half-saturation concentration is a function of binding protein abundance. We predict that oligotrophs can attain nanomolar half-saturation concentrations using binding proteins with only micromolar dissociation constants and while closely matching transport and metabolic capacities. However, our model predicts that this requires large periplasms and that the slow diffusion of the binding proteins limits uptake. Thus, binding proteins are critical for oligotrophic survival yet severely constrain growth rates. We propose that this trade-off fundamentally shaped the divergent evolution of oligotrophs and copiotrophs. Marine bacteria utilize carbon as a building block and an energy source and thus exert an important control on the amount of carbon that is sequestered in the ocean versus respired into the atmosphere. They use a spectrum of strategies to consume carbon: while copiotrophic bacteria dominate in nutrient-rich environments, oligotrophic bacteria dominate in nutrient-poor environments and are typically smaller, nonmotile, and slower growing. Yet the paragon oligotroph SAR11 is the planet’s most abundant organism. Despite this, most of our understanding of bacteria derives from research on copiotrophs. Here we use molecular-level models to understand how an oligotroph’s physiology enables it to outperform copiotrophs in nutrient-poor but not in nutrient-rich environments. We contrast copiotrophs’ prevalent method of sugar transport with oligotrophs’ reliance on binding proteins, which trap nutrients in the periplasm. Binding proteins allow cells to attain affinities that are much higher than the transport proteins’ intrinsic affinities. However, our model predicts that attaining such high affinities requires large periplasms with high abundances of the slowly diffusing binding proteins, which precludes high growth rates. By quantifying the benefits and costs of binding proteins, we provide a mechanistic explanation for the divergent evolution of oligotrophs and copiotrophs.
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Affiliation(s)
- Noele Norris
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, United States of America
- Department of Biological Sciences, University of Southern California, Los Angeles, United States of America
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zürich, Zürich, Switzerland
- * E-mail: (NN); (RS)
| | - Naomi M. Levine
- Department of Biological Sciences, University of Southern California, Los Angeles, United States of America
| | - Vicente I. Fernandez
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zürich, Zürich, Switzerland
| | - Roman Stocker
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zürich, Zürich, Switzerland
- * E-mail: (NN); (RS)
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Kotecka K, Kawalek A, Kobylecki K, Bartosik AA. The AraC-Type Transcriptional Regulator GliR (PA3027) Activates Genes of Glycerolipid Metabolism in Pseudomonas aeruginosa. Int J Mol Sci 2021; 22:5066. [PMID: 34064685 PMCID: PMC8151288 DOI: 10.3390/ijms22105066] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 05/04/2021] [Accepted: 05/06/2021] [Indexed: 12/13/2022] Open
Abstract
Pseudomonas aeruginosa encodes a large set of transcriptional regulators (TRs) that modulate and manage cellular metabolism to survive in variable environmental conditions including that of the human body. The AraC family regulators are an abundant group of TRs in bacteria, mostly acting as gene expression activators, controlling diverse cellular functions (e.g., carbon metabolism, stress response, and virulence). The PA3027 protein from P. aeruginosa has been classified in silico as a putative AraC-type TR. Transcriptional profiling of P. aeruginosa PAO1161 overexpressing PA3027 revealed a spectacular increase in the mRNA levels of PA3026-PA3024 (divergent to PA3027), PA3464, and PA3342 genes encoding proteins potentially involved in glycerolipid metabolism. Concomitantly, chromatin immunoprecipitation-sequencing (ChIP-seq) analysis revealed that at least 22 regions are bound by PA3027 in the PAO1161 genome. These encompass promoter regions of PA3026, PA3464, and PA3342, showing the major increase in expression in response to PA3027 excess. In Vitro DNA binding assay confirmed interactions of PA3027 with these regions. Furthermore, promoter-reporter assays in a heterologous host showed the PA3027-dependent activation of the promoter of the PA3026-PA3024 operon. Two motifs representing the preferred binding sites for PA3027, one localized upstream and one overlapping with the -35 promoter sequence, were identified in PA3026p and our data indicate that both motifs are required for full activation of this promoter by PA3027. Overall, the presented data show that PA3027 acts as a transcriptional regulator in P. aeruginosa, activating genes likely engaged in glycerolipid metabolism. The GliR name, from a glycerolipid metabolism regulator, is proposed for PA3027 of P. aeruginosa.
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Affiliation(s)
| | | | | | - Aneta Agnieszka Bartosik
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland; (K.K.); (A.K.); (K.K.)
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43
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Fricke PM, Klemm A, Bott M, Polen T. On the way toward regulatable expression systems in acetic acid bacteria: target gene expression and use cases. Appl Microbiol Biotechnol 2021; 105:3423-3456. [PMID: 33856535 PMCID: PMC8102297 DOI: 10.1007/s00253-021-11269-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/24/2021] [Accepted: 04/04/2021] [Indexed: 01/06/2023]
Abstract
Acetic acid bacteria (AAB) are valuable biocatalysts for which there is growing interest in understanding their basics including physiology and biochemistry. This is accompanied by growing demands for metabolic engineering of AAB to take advantage of their properties and to improve their biomanufacturing efficiencies. Controlled expression of target genes is key to fundamental and applied microbiological research. In order to get an overview of expression systems and their applications in AAB, we carried out a comprehensive literature search using the Web of Science Core Collection database. The Acetobacteraceae family currently comprises 49 genera. We found overall 6097 publications related to one or more AAB genera since 1973, when the first successful recombinant DNA experiments in Escherichia coli have been published. The use of plasmids in AAB began in 1985 and till today was reported for only nine out of the 49 AAB genera currently described. We found at least five major expression plasmid lineages and a multitude of further expression plasmids, almost all enabling only constitutive target gene expression. Only recently, two regulatable expression systems became available for AAB, an N-acyl homoserine lactone (AHL)-inducible system for Komagataeibacter rhaeticus and an L-arabinose-inducible system for Gluconobacter oxydans. Thus, after 35 years of constitutive target gene expression in AAB, we now have the first regulatable expression systems for AAB in hand and further regulatable expression systems for AAB can be expected. KEY POINTS: • Literature search revealed developments and usage of expression systems in AAB. • Only recently 2 regulatable plasmid systems became available for only 2 AAB genera. • Further regulatable expression systems for AAB are in sight.
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Affiliation(s)
- Philipp Moritz Fricke
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Angelika Klemm
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Michael Bott
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Tino Polen
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
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44
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Pilkiewicz KR, Mayo ML. Magnetic induction inspires a schematic theory for crosstalk-driven relaxation dynamics in cells. Phys Rev E 2021; 103:042417. [PMID: 34005977 DOI: 10.1103/physreve.103.042417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/19/2021] [Indexed: 11/07/2022]
Abstract
Establishing formal mathematical analogies between disparate physical systems can be a powerful tool, allowing for the well studied behavior of one system to be directly translated into predictions about the behavior of another that may be harder to probe. In this paper we lay the foundation for such an analogy between the macroscale electrodynamics of simple magnetic circuits and the microscale chemical kinetics of transcriptional regulation in cells. By artificially allowing the inductor coils of the former to elastically expand under the action of their Lorentz pressure, we introduce nonlinearities into the system that we interpret through the lens of our analogy as a schematic model for the impact of crosstalk on the rates of gene expression near steady state. Synthetic plasmids introduced into a cell must compete for a finite pool of metabolic and enzymatic resources against a maelstrom of crisscrossing biological processes, and our theory makes sensible predictions about how this noisy background might impact the expression profiles of synthetic constructs without explicitly modeling the kinetics of numerous interconnected regulatory interactions. We conclude the paper with a discussion of how our theory might be expanded to a broader class of plasmid circuits and how our predictions might be tested experimentally.
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Affiliation(s)
- Kevin R Pilkiewicz
- U.S. Army Engineer Research and Development Center, Vicksburg, Mississippi 39180, USA
| | - Michael L Mayo
- U.S. Army Engineer Research and Development Center, Vicksburg, Mississippi 39180, USA
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45
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Horne CR, Venugopal H, Panjikar S, Wood DM, Henrickson A, Brookes E, North RA, Murphy JM, Friemann R, Griffin MDW, Ramm G, Demeler B, Dobson RCJ. Mechanism of NanR gene repression and allosteric induction of bacterial sialic acid metabolism. Nat Commun 2021; 12:1988. [PMID: 33790291 PMCID: PMC8012715 DOI: 10.1038/s41467-021-22253-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 03/03/2021] [Indexed: 12/20/2022] Open
Abstract
Bacteria respond to environmental changes by inducing transcription of some genes and repressing others. Sialic acids, which coat human cell surfaces, are a nutrient source for pathogenic and commensal bacteria. The Escherichia coli GntR-type transcriptional repressor, NanR, regulates sialic acid metabolism, but the mechanism is unclear. Here, we demonstrate that three NanR dimers bind a (GGTATA)3-repeat operator cooperatively and with high affinity. Single-particle cryo-electron microscopy structures reveal the DNA-binding domain is reorganized to engage DNA, while three dimers assemble in close proximity across the (GGTATA)3-repeat operator. Such an interaction allows cooperative protein-protein interactions between NanR dimers via their N-terminal extensions. The effector, N-acetylneuraminate, binds NanR and attenuates the NanR-DNA interaction. The crystal structure of NanR in complex with N-acetylneuraminate reveals a domain rearrangement upon N-acetylneuraminate binding to lock NanR in a conformation that weakens DNA binding. Our data provide a molecular basis for the regulation of bacterial sialic acid metabolism. The GntR superfamily is one of the largest families of transcription factors in prokaryotes. Here the authors combine biophysical analysis and structural biology to dissect the mechanism by which NanR — a GntR-family regulator — binds to its promoter to repress the transcription of genes necessary for sialic acid metabolism.
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Affiliation(s)
- Christopher R Horne
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Hariprasad Venugopal
- Clive and Vera Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, VIC, Australia
| | - Santosh Panjikar
- Australian Synchrotron, ANSTO, Clayton, VIC, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - David M Wood
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Amy Henrickson
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada
| | - Emre Brookes
- Department of Chemistry, University of Montana, Missoula, MT, USA
| | - Rachel A North
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - James M Murphy
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Rosmarie Friemann
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Michael D W Griffin
- Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, Australia
| | - Georg Ramm
- Clive and Vera Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, VIC, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Borries Demeler
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada.,Department of Chemistry, University of Montana, Missoula, MT, USA
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand. .,Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, Australia.
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46
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Stargardt P, Striedner G, Mairhofer J. Tunable expression rate control of a growth-decoupled T7 expression system by L-arabinose only. Microb Cell Fact 2021; 20:27. [PMID: 33522916 PMCID: PMC7852362 DOI: 10.1186/s12934-021-01512-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 01/07/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Precise regulation of gene expression is of utmost importance for the production of complex membrane proteins (MP), enzymes or other proteins toxic to the host cell. In this article we show that genes under control of a normally Isopropyl β-D-1-thiogalactopyranoside (IPTG)-inducible PT7-lacO promoter can be induced solely with L-arabinose in a newly constructed Escherichia coli expression host BL21-AI<gp2>, a strain based on the recently published approach of bacteriophage inspired growth-decoupled recombinant protein production. RESULTS Here, we show that BL21-AI<gp2> is able to precisely regulate protein production rates on a cellular level in an L-arabinose concentration-dependent manner and simultaneously allows for reallocation of metabolic resources due to L-arabinose induced growth decoupling by the phage derived inhibitor peptide Gp2. We have successfully characterized the system under relevant fed-batch like conditions in microscale cultivation (800 µL) and generated data proofing a relevant increase in specific yields for 6 different Escherichia coli derived MP-GFP fusion proteins by using online-GFP signals, FACS analysis, SDS-PAGE and western blotting. CONCLUSIONS In all cases tested, BL21-AI<gp2> outperformed the parental strain BL21-AI, operated in growth-associated production mode. Specific MP-GFP fusion proteins yields have been improved up to 2.7-fold. Therefore, this approach allows for fine tuning of MP production or expression of multi-enzyme pathways where e.g. particular stoichiometries have to be met to optimize product flux.
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Affiliation(s)
| | - Gerald Striedner
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria
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Kravchenko U, Gogoleva N, Kalubaka N, Kruk A, Diubo Y, Gogolev Y, Nikolaichik Y. The PhoPQ Two-Component System Is the Major Regulator of Cell Surface Properties, Stress Responses and Plant-Derived Substrate Utilisation During Development of Pectobacterium versatile-Host Plant Pathosystems. Front Microbiol 2021; 11:621391. [PMID: 33519782 PMCID: PMC7843439 DOI: 10.3389/fmicb.2020.621391] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 12/24/2020] [Indexed: 11/19/2022] Open
Abstract
Pectobacterium versatile (formerly P. carotovorum) is a recently defined species of soft rot enterobacteria capable of infecting many plant hosts and damaging different tissues. Complex transcriptional regulation of virulence properties can be expected for such a versatile pathogen. However, the relevant information is available only for related species and is rather limited. The PhoPQ two-component system, originally described in pectobacteria as PehRS, was previously shown to regulate a single gene, pehA. Using an insertional phoP mutant of Pectobacterium versatile (earlier-P. carotovorum), we demonstrate that PhoP regulates at least 115 genes with a majority of them specific for pectobacteria. The functions performed by PhoP-controlled genes include degradation, transport and metabolism of plant-derived carbon sources (polygalacturonate, arabinose-containing polysaccharides and citrate), modification of bacterial cell envelope and stress resistance. We also demonstrated PhoP involvement in establishing the order of plant cell wall decomposition and utilisation of the corresponding breakdown products. Based on experimental data and in silico analysis, we defined a PhoP binding site motif and provided proof for its universality in enteric bacteria. Scanning P. versatile genome for the locations of this motif suggested a much larger PhoP regulon enriched with the genes important for a plant pathogen, which makes PhoP a global virulence regulator. Potential PhoP targets include many regulatory genes and PhoP control over one of them, expI, was confirmed experimentally, highlighting the link between the PhoPQ two-component and quorum sensing systems. High concentrations of calcium and magnesium ions were found to abolish the PhoPQ-dependent transcription activation but did not relieve repression. Reduced PhoP expression and minimisation of PhoP dependence of regulon members' expression in P. versatile cells isolated from potato tuber tissues suggest that PhoPQ system is a key switch of expression levels of multiple virulence-related genes fine-tuned to control the development of P. versatile-host plant pathosystem.
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Affiliation(s)
- Uljana Kravchenko
- Department of Molecular Biology, Belarusian State University, Minsk, Belarus
| | - Natalia Gogoleva
- Federal Research Center “Kazan Scientific Center of RAS”, Kazan Institute of Biochemistry and Biophysics, Kazan, Russia
- Laboratory of Extreme Biology, Kazan Federal University Institute of Fundamental Medicine and Biology, Kazan, Russia
| | - Nastassia Kalubaka
- Department of Molecular Biology, Belarusian State University, Minsk, Belarus
| | - Alla Kruk
- Department of Molecular Biology, Belarusian State University, Minsk, Belarus
| | - Yuliya Diubo
- Department of Molecular Biology, Belarusian State University, Minsk, Belarus
| | - Yuri Gogolev
- Federal Research Center “Kazan Scientific Center of RAS”, Kazan Institute of Biochemistry and Biophysics, Kazan, Russia
- Department of Biochemistry, Biotechnology and Pharmacology, Kazan Federal University Institute of Fundamental Medicine and Biology, Kazan, Russia
| | - Yevgeny Nikolaichik
- Department of Molecular Biology, Belarusian State University, Minsk, Belarus
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Flores-Sánchez A, Rathinasabapathy A, López-Cuellar MDR, Vergara-Porras B, Pérez-Guevara F. Biosynthesis of polyhydroxyalkanoates from vegetable oil under the co-expression of fadE and phaJ genes in Cupriavidus necator. Int J Biol Macromol 2020; 164:1600-1607. [PMID: 32768477 DOI: 10.1016/j.ijbiomac.2020.07.275] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 07/15/2020] [Accepted: 07/19/2020] [Indexed: 11/17/2022]
Abstract
The acyl-CoA dehydrogenase (FadE) and (R)-specific enoyl-CoA hydratase (PhaJ) are functionally related to the degradation of fatty acids and the synthesis of polyhydroxyalkanoates (PHAs). To verify this, a recombinant Cupriavidus necator H16 harboring the plasmid -pMPJAS03- with fadE from Escherichia coli strain K12 and phaJ1 from Pseudomonas putida strain KT2440 under the arabinose promoter (araC-PBAD) was constructed. The impact of co-expressing fadE and phaJ genes on C. necator H16/pMPJAS03 maintaining the wild-type synthase on short-chain-length/medium-chain-length PHA formation from canola or avocado oil at different arabinose concentrations was investigated. The functional activity of fadEE.c led to obtaining higher biomass and PHA concentrations compared to the cultures without expressing the gene. While high transcriptional levels of phaJ1P.p, at 0.1% of arabinose, aid the wild-type synthase to polymerize larger-side chain monomers, such as 3-Hydroxyoctanoate (3HO) and 3-Hydroxydecanoate (3HD). The presence of even small amounts of 3HO and 3HD in the co-polymers significantly depresses the melting temperature of the polymers, compared to those composed of pure 3-hydroxybutyrate (3HB). Our data presents supporting evidence that the synthesis of larger-side chain monomers by the recombinant strain relies not only upon the affinity of the wild-type synthase but also on the functionality of the intermediate supplying enzymes.
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Affiliation(s)
- Araceli Flores-Sánchez
- Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, ITESM, Atizapán de Zaragoza, México 52926, Mexico
| | - Arthi Rathinasabapathy
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y Estudios Avanzados (CINVESTAV), Ciudad de México 07360, Mexico
| | - Ma Del Rocío López-Cuellar
- Cuerpo Académico de Biotecnología Agroalimentaria, Instituto de Ciencias Agropecuarias, Universidad Autónoma del Estado de Hidalgo, Hidalgo 43600, Mexico
| | - Berenice Vergara-Porras
- Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, ITESM, Atizapán de Zaragoza, México 52926, Mexico; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Fermín Pérez-Guevara
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y Estudios Avanzados (CINVESTAV), Ciudad de México 07360, Mexico.
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Lau YY, How KY, Yin WF, Chan KG. Functional characterization of quorum sensing LuxR-type transcriptional regulator, EasR in Enterobacter asburiae strain L1. PeerJ 2020; 8:e10068. [PMID: 33150063 PMCID: PMC7585371 DOI: 10.7717/peerj.10068] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 09/08/2020] [Indexed: 01/17/2023] Open
Abstract
Over the past decades, Enterobacter spp. have been identified as challenging and important pathogens. The emergence of multidrug-resistant Enterobacteria especially those that produce Klebsiella pneumoniae carbapenemase has been a very worrying health crisis. Although efforts have been made to unravel the complex mechanisms that contribute to the pathogenicity of different Enterobacter spp., there is very little information associated with AHL-type QS mechanism in Enterobacter spp. Signaling via N-acyl homoserine lactone (AHL) is the most common quorum sensing (QS) mechanism utilized by Proteobacteria. A typical AHL-based QS system involves two key players: a luxI gene homolog to synthesize AHLs and a luxR gene homolog, an AHL-dependent transcriptional regulator. These signaling molecules enable inter-species and intra-species interaction in response to external stimuli according to population density. In our recent study, we reported the genome of AHL-producing bacterium, Enterobacter asburiae strain L1. Whole genome sequencing and in silico analysis revealed the presence of a pair of luxI/R genes responsible for AHL-type QS, designated as easI/R, in strain L1. In a QS system, a LuxR transcriptional protein detects and responds to the concentration of a specific AHL controlling gene expression. In E. asburiae strain L1, EasR protein binds to its cognate AHLs, N-butanoyl homoserine lactone (C4-HSL) and N–hexanoyl homoserine lactone (C6-HSL), modulating the expression of targeted genes. In this current work, we have cloned the 693 bp luxR homolog of strain L1 for further characterization. The functionality and specificity of EasR protein in response to different AHL signaling molecules to activate gene transcription were tested and validated with β-galactosidase assays. Higher β-galactosidase activities were detected for cells harboring EasR, indicating EasR is a functional transcriptional regulator. This is the first report documenting the cloning and characterization of transcriptional regulator, luxR homolog of E. asburiae.
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Affiliation(s)
- Yin Yin Lau
- International Genome Centre, Jiangsu University, Zhenjiang, China.,Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Malaysia
| | - Kah Yan How
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Malaysia
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Malaysia
| | - Kok-Gan Chan
- International Genome Centre, Jiangsu University, Zhenjiang, China.,Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Malaysia
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50
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Fricke PM, Link T, Gätgens J, Sonntag C, Otto M, Bott M, Polen T. A tunable L-arabinose-inducible expression plasmid for the acetic acid bacterium Gluconobacter oxydans. Appl Microbiol Biotechnol 2020; 104:9267-9282. [PMID: 32974745 PMCID: PMC7567684 DOI: 10.1007/s00253-020-10905-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 09/04/2020] [Accepted: 09/10/2020] [Indexed: 01/21/2023]
Abstract
Abstract The acetic acid bacterium (AAB) Gluconobacter oxydans incompletely oxidizes a wide variety of carbohydrates and is therefore used industrially for oxidative biotransformations. For G. oxydans, no system was available that allows regulatable plasmid-based expression. We found that the l-arabinose-inducible PBAD promoter and the transcriptional regulator AraC from Escherichia coli MC4100 performed very well in G. oxydans. The respective pBBR1-based plasmids showed very low basal expression of the reporters β-glucuronidase and mNeonGreen, up to 480-fold induction with 1% l-arabinose, and tunability from 0.1 to 1% l-arabinose. In G. oxydans 621H, l-arabinose was oxidized by the membrane-bound glucose dehydrogenase, which is absent in the multi-deletion strain BP.6. Nevertheless, AraC-PBAD performed similar in both strains in the exponential phase, indicating that a gene knockout is not required for application of AraC-PBAD in wild-type G. oxydans strains. However, the oxidation product arabinonic acid strongly contributed to the acidification of the growth medium in 621H cultures during the stationary phase, which resulted in drastically decreased reporter activities in 621H (pH 3.3) but not in BP.6 cultures (pH 4.4). These activities could be strongly increased quickly solely by incubating stationary cells in d-mannitol-free medium adjusted to pH 6, indicating that the reporters were hardly degraded yet rather became inactive. In a pH-controlled bioreactor, these reporter activities remained high in the stationary phase (pH 6). Finally, we created a multiple cloning vector with araC-PBAD based on pBBR1MCS-5. Together, we demonstrated superior functionality and good tunability of an AraC-PBAD system in G. oxydans that could possibly also be used in other AAB. Key points • We found the AraC-PBADsystem from E. coli MC4100 was well tunable in G. oxydans. • In the absence of AraC orl-arabinose, expression from PBADwas extremely low. • This araC-PBADsystem could also be fully functional in other acetic acid bacteria. Electronic supplementary material The online version of this article (10.1007/s00253-020-10905-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Philipp Moritz Fricke
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Tobias Link
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Jochem Gätgens
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Christiane Sonntag
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Maike Otto
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Michael Bott
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Tino Polen
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.
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