1
|
Türkyılmaz O, Darcan C. Resistance mechanism of Escherichia coli strains with different ampicillin resistance levels. Appl Microbiol Biotechnol 2024; 108:5. [PMID: 38165477 DOI: 10.1007/s00253-023-12929-y] [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: 08/01/2023] [Revised: 10/06/2023] [Accepted: 10/19/2023] [Indexed: 01/03/2024]
Abstract
Antibiotic resistance is an important problem that threatens medical treatment. Differences in the resistance levels of microorganisms cause great difficulties in understanding the mechanisms of antibiotic resistance. Therefore, the molecular reasons underlying the differences in the level of antibiotic resistance need to be clarified. For this purpose, genomic and transcriptomic analyses were performed on three Escherichia coli strains with varying degrees of adaptive resistance to ampicillin. Whole-genome sequencing of strains with different levels of resistance detected five mutations in strains with 10-fold resistance and two additional mutations in strains with 95-fold resistance. Overall, three of the seven mutations occurred as a single base change, while the other four occurred as insertions or deletions. While it was thought that 10-fold resistance was achieved by the effect of mutations in the ftsI, marAR, and rpoC genes, it was found that 95-fold resistance was achieved by the synergistic effect of five mutations and the ampC mutation. In addition, when the general transcriptomic profiles were examined, it was found that similar transcriptomic responses were elicited in strains with different levels of resistance. This study will improve our view of resistance mechanisms in bacteria with different levels of resistance and provide the basis for our understanding of the molecular mechanism of antibiotic resistance in ampicillin-resistant E. coli strains. KEY POINTS: •The mutation of the ampC promoter may act synergistically with other mutations and lead to higher resistance. •Similar transcriptomic responses to ampicillin are induced in strains with different levels of resistance. •Low antibiotic concentrations are the steps that allow rapid achievement of high antibiotic resistance.
Collapse
Affiliation(s)
- Osman Türkyılmaz
- Biotechnology Application & Research Centre, Bilecik Seyh Edebali University, Bilecik, Turkey.
| | - Cihan Darcan
- Department of Molecular Biology and Genetics, Bilecik Seyh Edebali University, Bilecik, Turkey
| |
Collapse
|
2
|
Pan RW, Röschinger T, Faizi K, Garcia H, Phillips R. Deciphering regulatory architectures from synthetic single-cell expression patterns. ARXIV 2024:arXiv:2401.15880v2. [PMID: 38351929 PMCID: PMC10862939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/19/2024]
Abstract
For the vast majority of genes in sequenced genomes, there is limited understanding of how they are regulated. Without such knowledge, it is not possible to perform a quantitative theory-experiment dialogue on how such genes give rise to physiological and evolutionary adaptation. One category of high-throughput experiments used to understand the sequence-phenotype relationship of the transcriptome is massively parallel reporter assays (MPRAs). However, to improve the versatility and scalability of MPRA pipelines, we need a "theory of the experiment" to help us better understand the impact of various biological and experimental parameters on the interpretation of experimental data. These parameters include binding site copy number, where a large number of specific binding sites may titrate away transcription factors, as well as the presence of overlapping binding sites, which may affect analysis of the degree of mutual dependence between mutations in the regulatory region and expression levels. To that end, in this paper we create tens of thousands of synthetic single-cell gene expression outputs using both equilibrium and out-of-equilibrium models. These models make it possible to imitate the summary statistics (information footprints and expression shift matrices) used to characterize the output of MPRAs and from this summary statistic to infer the underlying regulatory architecture. Specifically, we use a more refined implementation of the so-called thermodynamic models in which the binding energies of each sequence variant are derived from energy matrices. Our simulations reveal important effects of the parameters on MPRA data and we demonstrate our ability to optimize MPRA experimental designs with the goal of generating thermodynamic models of the transcriptome with base-pair specificity. Further, this approach makes it possible to carefully examine the mapping between mutations in binding sites and their corresponding expression profiles, a tool useful not only for better designing MPRAs, but also for exploring regulatory evolution.
Collapse
Affiliation(s)
- Rosalind Wenshan Pan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA
| | - Tom Röschinger
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA
| | - Kian Faizi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA
| | - Hernan Garcia
- Biophysics Graduate Group, University of California, Berkeley, CA
- Department of Physics, University of California, Berkeley, CA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA
- Institute for Quantitative Biosciences-QB3, University of California, Berkeley, CA
| | - Rob Phillips
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA
- Department of Physics, California Institute of Technology, Pasadena, CA
| |
Collapse
|
3
|
Pan RW, Röschinger T, Faizi K, Garcia H, Phillips R. Deciphering regulatory architectures from synthetic single-cell expression patterns. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.28.577658. [PMID: 38352569 PMCID: PMC10862715 DOI: 10.1101/2024.01.28.577658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
For the vast majority of genes in sequenced genomes, there is limited understanding of how they are regulated. Without such knowledge, it is not possible to perform a quantitative theory-experiment dialogue on how such genes give rise to physiological and evolutionary adaptation. One category of high-throughput experiments used to understand the sequence-phenotype relationship of the transcriptome is massively parallel reporter assays (MPRAs). However, to improve the versatility and scalability of MPRA pipelines, we need a "theory of the experiment" to help us better understand the impact of various biological and experimental parameters on the interpretation of experimental data. These parameters include binding site copy number, where a large number of specific binding sites may titrate away transcription factors, as well as the presence of overlapping binding sites, which may affect analysis of the degree of mutual dependence between mutations in the regulatory region and expression levels. To that end, in this paper we create tens of thousands of synthetic single-cell gene expression outputs using both equilibrium and out-of-equilibrium models. These models make it possible to imitate the summary statistics (information footprints and expression shift matrices) used to characterize the output of MPRAs and from this summary statistic to infer the underlying regulatory architecture. Specifically, we use a more refined implementation of the so-called thermodynamic models in which the binding energies of each sequence variant are derived from energy matrices. Our simulations reveal important effects of the parameters on MPRA data and we demonstrate our ability to optimize MPRA experimental designs with the goal of generating thermodynamic models of the transcriptome with base-pair specificity. Further, this approach makes it possible to carefully examine the mapping between mutations in binding sites and their corresponding expression profiles, a tool useful not only for better designing MPRAs, but also for exploring regulatory evolution.
Collapse
Affiliation(s)
- Rosalind Wenshan Pan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA
| | - Tom Röschinger
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA
| | - Kian Faizi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA
| | - Hernan Garcia
- Biophysics Graduate Group, University of California, Berkeley, CA
- Department of Physics, University of California, Berkeley, CA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA
- Institute for Quantitative Biosciences-QB3, University of California, Berkeley, CA
| | - Rob Phillips
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA
- Department of Physics, California Institute of Technology, Pasadena, CA
| |
Collapse
|
4
|
Raghunandanan S, Priya R, Alanazi F, Lybecker MC, Schlax P, Yang X. A Fur family protein BosR is a novel RNA-binding protein that controls rpoS RNA stability in the Lyme disease pathogen. Nucleic Acids Res 2024; 52:5320-5335. [PMID: 38366569 PMCID: PMC11109971 DOI: 10.1093/nar/gkae114] [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: 10/13/2023] [Revised: 02/01/2024] [Accepted: 02/06/2024] [Indexed: 02/18/2024] Open
Abstract
The σ54-σS sigma factor cascade plays a central role in regulating differential gene expression during the enzootic cycle of Borreliella burgdorferi, the Lyme disease pathogen. In this pathway, the primary transcription of rpoS (which encodes σS) is under the control of σ54 which is activated by a bacterial enhancer-binding protein (EBP), Rrp2. The σ54-dependent activation in B. burgdorferi has long been thought to be unique, requiring an additional factor, BosR, a homologue of classical Fur/PerR repressor/activator. However, how BosR is involved in this σ54-dependent activation remains unclear and perplexing. In this study, we demonstrate that BosR does not function as a regulator for rpoS transcriptional activation. Instead, it functions as a novel RNA-binding protein that governs the turnover rate of rpoS mRNA. We further show that BosR directly binds to the 5' untranslated region (UTR) of rpoS mRNA, and the binding region overlaps with a region required for rpoS mRNA degradation. Mutations within this 5'UTR region result in BosR-independent RpoS production. Collectively, these results uncover a novel role of Fur/PerR family regulators as RNA-binding proteins and redefine the paradigm of the σ54-σS pathway in B. burgdorferi.
Collapse
Affiliation(s)
- Sajith Raghunandanan
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Raj Priya
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Fuad Alanazi
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh 12372, Saudi Arabia
| | - Meghan C Lybecker
- Bacterial Diseases Branch, Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Center for Disease Control and Prevention, Fort Collins, CO, USA
| | - Paula Jean Schlax
- Department of Chemistry and Biochemistry, Bates College, Lewiston, ME, USA
| | - X Frank Yang
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| |
Collapse
|
5
|
Bajić D. Information Theory, Living Systems, and Communication Engineering. ENTROPY (BASEL, SWITZERLAND) 2024; 26:430. [PMID: 38785679 PMCID: PMC11120474 DOI: 10.3390/e26050430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/08/2024] [Accepted: 05/17/2024] [Indexed: 05/25/2024]
Abstract
Mainstream research on information theory within the field of living systems involves the application of analytical tools to understand a broad range of life processes. This paper is dedicated to an opposite problem: it explores the information theory and communication engineering methods that have counterparts in the data transmission process by way of DNA structures and neural fibers. Considering the requirements of modern multimedia, transmission methods chosen by nature may be different, suboptimal, or even far from optimal. However, nature is known for rational resource usage, so its methods have a significant advantage: they are proven to be sustainable. Perhaps understanding the engineering aspects of methods of nature can inspire a design of alternative green, stable, and low-cost transmission.
Collapse
Affiliation(s)
- Dragana Bajić
- Department of Communications and Signal Processing, Faculty of Technical Sciences, University of Novi Sad, Trg Dositeja Obradovica 6, 21000 Novi Sad, Serbia
| |
Collapse
|
6
|
Hu Q, Wang J, Liu C, Feng Y, Chen H. Determinants of mer Promoter Activity from Pseudomonas aeruginosa. Genes (Basel) 2024; 15:490. [PMID: 38674424 PMCID: PMC11049809 DOI: 10.3390/genes15040490] [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: 03/18/2024] [Revised: 04/11/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
Since the MerR family is known for its special regulatory mechanism, we aimed to explore which factors determine the expression activity of the mer promoter. The Tn501/Tn21 mer promoter contains an abnormally long spacer (19 bp) between the -35 and -10 elements, which is essential for the unique DNA distortion mechanism. To further understand the role of base sequences in the mer promoter spacer, this study systematically engineered a series of mutant derivatives and used luminescent and fluorescent reporter genes to investigate the expression activity of these derivatives. The results reveal that the expression activity of the mer promoter is synergistically modulated by the spacer length (17 bp is optimal) and the region upstream of -10 (especially -13G). The spacing is regulated by MerR transcription factors through symmetrical sequences, and -13G presumably functions through interaction with the RNA polymerase sigma-70 subunit.
Collapse
Affiliation(s)
| | | | | | | | - Hao Chen
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China; (Q.H.); (J.W.); (C.L.); (Y.F.)
| |
Collapse
|
7
|
Zheng X, Sun X, Xiang W, Ni H, Zou L, Long ZE. Expression of Staphylococcus aureus translation elongation factor P is regulated by a stress-inducible promotor. Antonie Van Leeuwenhoek 2024; 117:54. [PMID: 38489110 DOI: 10.1007/s10482-024-01954-0] [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: 09/04/2023] [Accepted: 02/20/2024] [Indexed: 03/17/2024]
Abstract
Translation elongation factor P, expressed by the efp gene, is a conserved protein closely related to bacterial virulence and environmental stress regulation responses, however, little is known about the efp gene expression regulations. Here, the strain of Staphylococcus aureus subsp. aureus NCTC 8325 was taken as the research object and cultured under different conditions, including different culture temperatures, pH, and antibiotics, to study the expression of the efp gene in S. aureus by qRT-PCR, the results showed that the expression of the efp gene is upregulated under high temperature (40 °C), acidic (pH 5.4) or alkaline (pH 9.4) culture conditions, but upregulated early and downregulated later under the conditions of 0.5 MIC antibiotics (chloramphenicol at the final concentration of 2 μg/mL and vancomycin at the final concentration of 0.25 μg/mL), indicating that the efp promoter in S. aureus is inducible. The efp promoter sequence and structure in S. aureus were predicted by bioinformatics methods, and the predicted promoter was validated by constructing a promoter-probe vector and a series of promoter mutants, the results showed that the efp promoter sequence in S. aureus, named Pro, located in 1,548,179-1,548,250 of the S. aureus genome (NC_007795.1), and the sequence of - 10 element is CCTTATAGT, - 35 element is TTTACT. The results above could lay a foundation for screening transcription factors involved in the expression of the efp gene and then exploring the transcriptional regulation mechanism of EF-P in S. aureus.
Collapse
Affiliation(s)
- Xingxing Zheng
- Nanchang Key Laboratory of Microbial Resources Exploitation and Utilization From Poyang Lake Wetland, College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Xiuhui Sun
- Chongren County Center for Disease Prevention and Control, Chongren, 344203, China
| | - Weiwei Xiang
- Nanchang Key Laboratory of Microbial Resources Exploitation and Utilization From Poyang Lake Wetland, College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Haiyan Ni
- Nanchang Key Laboratory of Microbial Resources Exploitation and Utilization From Poyang Lake Wetland, College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Long Zou
- Nanchang Key Laboratory of Microbial Resources Exploitation and Utilization From Poyang Lake Wetland, College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Zhong-Er Long
- Nanchang Key Laboratory of Microbial Resources Exploitation and Utilization From Poyang Lake Wetland, College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China.
| |
Collapse
|
8
|
Lee SM, Le HT, Taizhanova A, Nong LK, Park JY, Lee EJ, Palsson BO, Kim D. Experimental promoter identification of a foodborne pathogen Salmonella enterica subsp. enterica serovar Typhimurium with near single base-pair resolution. Front Microbiol 2024; 14:1271121. [PMID: 38239730 PMCID: PMC10794520 DOI: 10.3389/fmicb.2023.1271121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 12/01/2023] [Indexed: 01/22/2024] Open
Abstract
Salmonella enterica serovar Typhimurium (S. Typhimurium) is a common foodborne pathogen which is frequently used as the reference strain for Salmonella. Investigating the sigma factor network and protomers is crucial to understand the genomic and transcriptomic properties of the bacterium. Its promoters were identified using various methods such as dRNA-seq, ChIP-chip, or ChIP-Seq. However, validation using ChIP-exo, which exhibits higher-resolution performance compared to conventional ChIP, has not been conducted to date. In this study, using the representative strain S. Typhimurium LT2 (LT2), the ChIP-exo experiment was conducted to accurately determine the binding sites of catalytic RNA polymerase subunit RpoB and major sigma factors (RpoD, RpoN, RpoS, and RpoE) during exponential phase. Integrated with the results of RNA-Seq, promoters and sigmulons for the sigma factors and their association with RpoB have been discovered. Notably, the overlapping regions among binding sites of each alternative sigma factor were found. Furthermore, comparative analysis with Escherichia coli str. K-12 substr. MG1655 (MG1655) revealed conserved binding sites of RpoD and RpoN across different species. In the case of small RNAs (sRNAs), 50 sRNAs observed their expression during the exponential growth of LT2. Collectively, the integration of ChIP-exo and RNA-Seq enables genome-scale promoter mapping with high resolution and facilitates the characterization of binding events of alternative sigma factors, enabling a comprehensive understanding of the bacterial sigma factor network and condition-specific active promoters.
Collapse
Affiliation(s)
- Sang-Mok Lee
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Hoa Thi Le
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Assiya Taizhanova
- Department of Genetic Engineering and Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin, Republic of Korea
| | - Linh Khanh Nong
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Joon Young Park
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Eun-Jin Lee
- Department of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA, United States
| | - Donghyuk Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| |
Collapse
|
9
|
Ogunlana L, Kaur D, Shaw LP, Jangir P, Walsh T, Uphoff S, MacLean RC. Regulatory fine-tuning of mcr-1 increases bacterial fitness and stabilises antibiotic resistance in agricultural settings. THE ISME JOURNAL 2023; 17:2058-2069. [PMID: 37723338 PMCID: PMC10579358 DOI: 10.1038/s41396-023-01509-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 08/18/2023] [Accepted: 09/01/2023] [Indexed: 09/20/2023]
Abstract
Antibiotic resistance tends to carry fitness costs, making it difficult to understand how resistance can be maintained in the absence of continual antibiotic exposure. Here we investigate this problem in the context of mcr-1, a globally disseminated gene that confers resistance to colistin, an agricultural antibiotic that is used as a last resort for the treatment of multi-drug resistant infections. Here we show that regulatory evolution has fine-tuned the expression of mcr-1, allowing E. coli to reduce the fitness cost of mcr-1 while simultaneously increasing colistin resistance. Conjugative plasmids have transferred low-cost/high-resistance mcr-1 alleles across an incredible diversity of E. coli strains, further stabilising mcr-1 at the species level. Regulatory mutations were associated with increased mcr-1 stability in pig farms following a ban on the use of colistin as a growth promoter that decreased colistin consumption by 90%. Our study shows how regulatory evolution and plasmid transfer can combine to stabilise resistance and limit the impact of reducing antibiotic consumption.
Collapse
Affiliation(s)
- Lois Ogunlana
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Divjot Kaur
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Liam P Shaw
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
- Department of Biosciences, Durham University, Stockton Road, Durham, DH1 3LE, UK
| | - Pramod Jangir
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Timothy Walsh
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
- Ineos Oxford Institute for Antimicrobial Research, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Stephan Uphoff
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - R C MacLean
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK.
| |
Collapse
|
10
|
Hwang Y, Na JG, Lee SJ. Transcriptional regulation of soluble methane monooxygenase via enhancer-binding protein derived from Methylosinus sporium 5. Appl Environ Microbiol 2023; 89:e0210422. [PMID: 37668365 PMCID: PMC10537576 DOI: 10.1128/aem.02104-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 07/07/2023] [Indexed: 09/06/2023] Open
Abstract
Methane is a major greenhouse gas, and methanotrophs regulate the methane level in the carbon cycle. Soluble methane monooxygenase (sMMO) is expressed in various methanotroph genera, including Alphaproteobacteria and Gammaproteobacteria, and catalyzes the hydroxylation of methane to methanol. It has been proposed that MmoR regulates the expression of sMMO as an enhancer-binding protein under copper-limited conditions; however, details on this transcriptional regulation remain limited. Herein, we elucidate the transcriptional pathway of sMMO depending on copper ion concentration, which affects the interaction of MmoR and sigma factor. MmoR and sigma-54 (σ54) from Methylosinus sporium 5 were successfully overexpressed in Escherichia coli and purified to investigate sMMO transcription in methanotrophs. The results indicated that σ54 binds to a promoter positioned -24 (GG) and -12 (TGC) upstream between mmoG and mmoX1. The binding affinity and selectivity are lower (Kd = 184.6 ± 6.2 nM) than those of MmoR. MmoR interacts with the upstream activator sequence (UAS) with a strong binding affinity (Kd = 12.5 ± 0.5 nM). Mutational studies demonstrated that MmoR has high selectivity to its binding partner (ACA-xx-TGT). Titration assays have demonstrated that MmoR does not coordinate with copper ions directly; however, its binding affinity to UAS decreases in a low-copper-containing medium. MmoR strongly interacts with adenosine triphosphate (Kd = 62.8 ± 0.5 nM) to generate RNA polymerase complex. This study demonstrated that the binding events of both MmoR and σ54 that regulate transcription in M. sporium 5 depend on the copper ion concentration. IMPORTANCE This study provides biochemical evidence of transcriptional regulation of soluble methane monooxygenase (sMMO) in methanotrophs that control methane levels in ecological systems. Previous studies have proposed transcriptional regulation of MMOs, including sMMO and pMMO, while we provide further evidence to elucidate its mechanism using a purified enhancer-binding protein (MmoR) and transcription factor (σ54). The characterization studies of σ54 and MmoR identified the promoter binding sites and enhancer-binding sequences essential for sMMO expression. Our findings also demonstrate that MmoR functions as a trigger for sMMO expression due to the high specificity and selectivity for enhancer-binding sequences. The UV-visible spectrum of purified MmoR suggested an iron coordination like other GAF domain, and that ATP is essential for the initiation of enhancer elements. Binding assays indicated that these interactions are blocked by the copper ion. These results provide novel insights into gene regulation of methanotrophs.
Collapse
Affiliation(s)
- Yunha Hwang
- Department of Chemistry, Jeonbuk National University , Jeonju, South Korea
| | - Jeong-Geol Na
- Department of Chemical Engineering, Sogang University , Seoul, South Korea
| | - Seung Jae Lee
- Department of Chemistry, Jeonbuk National University , Jeonju, South Korea
- Institute of Molecular Biology and Genetics, Jeonbuk National University , Jeonju, South Korea
| |
Collapse
|
11
|
Lilic M, Holmes NA, Bush MJ, Marti AK, Widdick DA, Findlay KC, Choi YJ, Froom R, Koh S, Buttner MJ, Campbell EA. Structural basis of dual activation of cell division by the actinobacterial transcription factors WhiA and WhiB. Proc Natl Acad Sci U S A 2023; 120:e2220785120. [PMID: 36888660 PMCID: PMC10243135 DOI: 10.1073/pnas.2220785120] [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: 12/06/2022] [Accepted: 01/26/2023] [Indexed: 03/09/2023] Open
Abstract
Studies of transcriptional initiation in different bacterial clades reveal diverse molecular mechanisms regulating this first step in gene expression. The WhiA and WhiB factors are both required to express cell division genes in Actinobacteria and are essential in notable pathogens such as Mycobacterium tuberculosis. The WhiA/B regulons and binding sites have been elucidated in Streptomyces venezuelae (Sven), where they coordinate to activate sporulation septation. However, how these factors cooperate at the molecular level is not understood. Here we present cryoelectron microscopy structures of Sven transcriptional regulatory complexes comprising RNA polymerase (RNAP) σA-holoenzyme and WhiA and WhiB, in complex with the WhiA/B target promoter sepX. These structures reveal that WhiB binds to domain 4 of σA (σA4) of the σA-holoenzyme, bridging an interaction with WhiA while making non-specific contacts with the DNA upstream of the -35 core promoter element. The N-terminal homing endonuclease-like domain of WhiA interacts with WhiB, while the WhiA C-terminal domain (WhiA-CTD) makes base-specific contacts with the conserved WhiA GACAC motif. Notably, the structure of the WhiA-CTD and its interactions with the WhiA motif are strikingly similar to those observed between σA4 housekeeping σ-factors and the -35 promoter element, suggesting an evolutionary relationship. Structure-guided mutagenesis designed to disrupt these protein-DNA interactions reduces or abolishes developmental cell division in Sven, confirming their significance. Finally, we compare the architecture of the WhiA/B σA-holoenzyme promoter complex with the unrelated but model CAP Class I and Class II complexes, showing that WhiA/WhiB represent a new mechanism in bacterial transcriptional activation.
Collapse
Affiliation(s)
- Mirjana Lilic
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY10065
| | - Neil A. Holmes
- Department of Molecular Microbiology, John Innes Centre, NorwichNR4 7UH, UK
| | - Matthew J. Bush
- Department of Molecular Microbiology, John Innes Centre, NorwichNR4 7UH, UK
| | - Alexandra K. Marti
- Department of Molecular Microbiology, John Innes Centre, NorwichNR4 7UH, UK
| | - David A. Widdick
- Department of Molecular Microbiology, John Innes Centre, NorwichNR4 7UH, UK
| | - Kim C. Findlay
- Department of Cell and Developmental Biology, John Innes Centre, NorwichNR4 7UH, UK
| | - Young Joo Choi
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY10065
| | - Ruby Froom
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY10065
| | - Steven Koh
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY10065
| | - Mark J. Buttner
- Department of Molecular Microbiology, John Innes Centre, NorwichNR4 7UH, UK
| | | |
Collapse
|
12
|
Deng S. The origin of genetic and metabolic systems: Evolutionary structuralinsights. Heliyon 2023; 9:e14466. [PMID: 36967965 PMCID: PMC10036676 DOI: 10.1016/j.heliyon.2023.e14466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 02/27/2023] [Accepted: 03/06/2023] [Indexed: 03/16/2023] Open
Abstract
DNA is derived from reverse transcription and its origin is related to reverse transcriptase, DNA polymerase and integrase. The gene structure originated from the evolution of the first RNA polymerase. Thus, an explanation of the origin of the genetic system must also explain the evolution of these enzymes. This paper proposes a polymer structure model, termed the stable complex evolution model, which explains the evolution of enzymes and functional molecules. Enzymes evolved their functions by forming locally tightly packed complexes with specific substrates. A metabolic reaction can therefore be considered to be the result of adaptive evolution in this way when a certain essential molecule is lacking in a cell. The evolution of the primitive genetic and metabolic systems was thus coordinated and synchronized. According to the stable complex model, almost all functional molecules establish binding affinity and specific recognition through complementary interactions, and functional molecules therefore have the nature of being auto-reactive. This is thermodynamically favorable and leads to functional duplication and self-organization. Therefore, it can be speculated that biological systems have a certain tendency to maintain functional stability or are influenced by an inherent selective power. The evolution of dormant bacteria may support this hypothesis, and inherent selectivity can be unified with natural selection at the molecular level.
Collapse
|
13
|
Carrillo Rincón AF, Farny NG. Unlocking the strength of inducible promoters in Gram-negative bacteria. Microb Biotechnol 2023; 16:961-976. [PMID: 36738130 PMCID: PMC10128130 DOI: 10.1111/1751-7915.14219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 01/02/2023] [Accepted: 01/07/2023] [Indexed: 02/05/2023] Open
Abstract
Inducible bacterial promoters are ubiquitous biotechnology tools that have a consistent architecture including two key elements: the operator region recognized by the transcriptional regulatory proteins, and the -10 and -35 consensus sequences required to recruit the sigma (σ) 70 subunits of RNA polymerase to initiate transcription. Despite their widespread use, leaky transcription in the OFF state remains a challenge. We have updated the architecture of the lac and tet promoters to improve their strength, control and portability by the adaptation of the consensus -10 and -35 sequence boxes strongly targeted by σ70 , incorporation of a strong ribosome binding site recognized broadly by Gram-negative bacteria, and independent control of the transcriptional regulators by constitutive promoters. To test the promoters, we use the far-red fluorescent protein mCardinal, which significantly improves the signal-to-background ratio of promoter measurements over widely utilized green fluorescent proteins. We validate the improvement in OFF state control and inducibility by demonstrating production of the toxic and aggregate-prone cocaine esterase enzyme CocE. We further demonstrate portability of the promoters to additional Gram-negative species Pseudomonas putida and Vibrio natriegens. Our results represent a significant improvement over existing protein expression systems that will enable advances in protein production for various biotechnology applications.
Collapse
Affiliation(s)
| | - Natalie G Farny
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts, USA
| |
Collapse
|
14
|
Barman A, Shaw R, Bhawsinghka N, Das Gupta SK. A CRISPRi-based investigation reveals that multiple promoter elements drive gene expression from the genome of mycobacteriophage D29. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36748635 DOI: 10.1099/mic.0.001276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
A unique feature found in the genomes of mycobacteriophages such as L5 belonging to the A cluster is the presence of multiple dispersed repeated elements known as stoperators. The phage repressor binds these repeat elements, shutting off transcription globally and thereby promoting lysogeny. Interestingly, the sequence of these stoperators closely matches that of the consensus -35 region of prokaryotic promoters, leading us to propose that they may have a role to play in the initiation of transcription by serving as RNA polymerase binding sites. Mycobacteriophage D29 is closely related to phage L5, and their genome organizations are very similar. As in L5, there are multiple stoperators in the genome of D29. The positions occupied by the stoperators in the two genomes are almost identical. The significant difference between the two phages is that D29 lacks the gene encoding the equivalent of the L5 repressor. Since phage D29 does not produce a repressor, we considered it to be a suitable model for testing our hypothesis that the stoperators function as promoters in the absence of the repressor. To prove our point, we targeted CRISPR guide RNAs against six stoperators. In the case of five out of the six, we found a significant reduction in downstream gene expression and phage growth. Based on this observation and primer extension assays, we conclude that promoting gene expression is likely to be the primary function of stoperators.
Collapse
Affiliation(s)
- Anik Barman
- Department of Microbiology, Bose Institute, P-1/12 C.I.T. Scheme VIIM, Kolkata-700054, India
| | - Rahul Shaw
- Department of Microbiology, Bose Institute, P-1/12 C.I.T. Scheme VIIM, Kolkata-700054, India
| | - Niketa Bhawsinghka
- Department of Microbiology, Bose Institute, P-1/12 C.I.T. Scheme VIIM, Kolkata-700054, India.,Present address: Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Sujoy K Das Gupta
- Department of Microbiology, Bose Institute, P-1/12 C.I.T. Scheme VIIM, Kolkata-700054, India
| |
Collapse
|
15
|
Gene regulation in Escherichia coli is commonly selected for both high plasticity and low noise. Nat Ecol Evol 2022; 6:1165-1179. [PMID: 35726087 DOI: 10.1038/s41559-022-01783-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 05/03/2022] [Indexed: 11/08/2022]
Abstract
Bacteria often respond to dynamically changing environments by regulating gene expression. Despite this regulation being critically important for growth and survival, little is known about how selection shapes gene regulation in natural populations. To better understand the role natural selection plays in shaping bacterial gene regulation, here we compare differences in the regulatory behaviour of naturally segregating promoter variants from Escherichia coli (which have been subject to natural selection) to randomly mutated promoter variants (which have never been exposed to natural selection). We quantify gene expression phenotypes (expression level, plasticity and noise) for hundreds of promoter variants across multiple environments and show that segregating promoter variants are enriched for mutations with minimal effects on expression level. In many promoters, we infer that there is strong selection to maintain high levels of plasticity, and direct selection to decrease or increase cell-to-cell variability in expression. Taken together, these results expand our knowledge of how gene regulation is affected by natural selection and highlight the power of comparing naturally segregating polymorphisms to de novo random mutations to quantify the action of selection.
Collapse
|
16
|
|
17
|
Foe VE. Does the Pachytene Checkpoint, a Feature of Meiosis, Filter Out Mistakes in Double-Strand DNA Break Repair and as a side-Effect Strongly Promote Adaptive Speciation? Integr Org Biol 2022; 4:obac008. [PMID: 36827645 PMCID: PMC8998493 DOI: 10.1093/iob/obac008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
This essay aims to explain two biological puzzles: why eukaryotic transcription units are composed of short segments of coding DNA interspersed with long stretches of non-coding (intron) DNA, and the near ubiquity of sexual reproduction. As is well known, alternative splicing of its coding sequences enables one transcription unit to produce multiple variants of each encoded protein. Additionally, padding transcription units with non-coding DNA (often many thousands of base pairs long) provides a readily evolvable way to set how soon in a cell cycle the various mRNAs will begin being expressed and the total amount of mRNA that each transcription unit can make during a cell cycle. This regulation complements control via the transcriptional promoter and facilitates the creation of complex eukaryotic cell types, tissues, and organisms. However, it also makes eukaryotes exceedingly vulnerable to double-strand DNA breaks, which end-joining break repair pathways can repair incorrectly. Transcription units cover such a large fraction of the genome that any mis-repair producing a reorganized chromosome has a high probability of destroying a gene. During meiosis, the synaptonemal complex aligns homologous chromosome pairs and the pachytene checkpoint detects, selectively arrests, and in many organisms actively destroys gamete-producing cells with chromosomes that cannot adequately synapse; this creates a filter favoring transmission to the next generation of chromosomes that retain the parental organization, while selectively culling those with interrupted transcription units. This same meiotic checkpoint, reacting to accidental chromosomal reorganizations inflicted by error-prone break repair, can, as a side effect, provide a mechanism for the formation of new species in sympatry. It has been a long-standing puzzle how something as seemingly maladaptive as hybrid sterility between such new species can arise. I suggest that this paradox is resolved by understanding the adaptive importance of the pachytene checkpoint, as outlined above.
Collapse
|
18
|
Tietze L, Mangold A, Hoff MW, Lale R. Identification and Cross-Characterisation of Artificial Promoters and 5′ Untranslated Regions in Vibrio natriegens. Front Bioeng Biotechnol 2022; 10:826142. [PMID: 35155395 PMCID: PMC8830501 DOI: 10.3389/fbioe.2022.826142] [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: 11/30/2021] [Accepted: 01/07/2022] [Indexed: 11/13/2022] Open
Abstract
Vibrio natriegens has recently gained attention as a novel fast-growing bacterium in synthetic biology applications. Currently, a limited set of genetic elements optimised for Escherichia coli are used in V. natriegens due to the lack of DNA parts characterised in this novel host. In this study, we report the identification and cross-characterisation of artificial promoters and 5′ untranslated regions (artificial regulatory sequence, ARES) that lead to production of fluorescent proteins with a wide-range of expression levels. We identify and cross-characterise 52 constructs in V. natriegens and E. coli. Furthermore, we report the DNA sequence and motif analysis of the ARESs using various algorithms. With this study, we expand the pool of characterised genetic DNA parts that can be used for different biotechnological applications using V. natriegens as a host microorganism.
Collapse
|
19
|
Genome-scale analysis of genetic regulatory elements in Streptomyces avermitilis MA-4680 using transcript boundary information. BMC Genomics 2022; 23:68. [PMID: 35062881 PMCID: PMC8780764 DOI: 10.1186/s12864-022-08314-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 01/12/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
The gram-positive bacterium, Streptomyces avermitilis, holds industrial importance as the producer of avermectin, a widely used anthelmintic agent, and a heterologous expression host of secondary metabolite-biosynthetic gene clusters. Despite its industrial importance, S. avermitilis’ genome organization and regulation of gene expression remain poorly understood. In this study, four different types of Next-Generation Sequencing techniques, including dRNA-Seq, Term-Seq, RNA-Seq and ribosome profiling, were applied to S. avermitilis to determine transcription units of S. avermitilis at a genome-wide level and elucidate regulatory elements for transcriptional and translational control of individual transcription units.
Result
By applying dRNA-Seq and Term-Seq to S. avermitilis MA-4680, a total of 2361 transcription start sites and 2017 transcript 3′-end positions were identified, respectively, leading to determination of 1601 transcription units encoded in S. avermitilis’ genome. Cataloguing the transcription units and integrated analysis of multiple high-throughput data types revealed the presence of diverse regulatory elements for gene expression, such as promoters, 5′-UTRs, terminators, 3′-UTRs and riboswitches. The conserved promoter motifs were identified from 2361 transcription start sites as 5′-TANNNT and 5′-BTGACN for the − 10 and − 35 elements, respectively. The − 35 element and spacer lengths between − 10 and − 35 elements were critical for transcriptional regulation of functionally distinct genes, suggesting the involvement of unique sigma factors. In addition, regulatory sequences recognized by antibiotic regulatory proteins were identified from the transcription start site information. Analysis of the 3′-end of RNA transcript revealed that stem structure formation is a major determinant for transcription termination of most transcription units.
Conclusions
The transcription unit architecture elucidated from the transcripts’ boundary information provides insights for unique genetic regulatory mechanisms of S. avermitilis. Our findings will elevate S. avermitilis’ potential as a production host for a diverse set of secondary metabolites.
Collapse
|
20
|
The bacterial promoter spacer modulates promoter strength and timing by length, TG-motifs and DNA supercoiling sensitivity. Sci Rep 2021; 11:24399. [PMID: 34937877 PMCID: PMC8695583 DOI: 10.1038/s41598-021-03817-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 12/09/2021] [Indexed: 01/25/2023] Open
Abstract
Transcription, the first step to gene expression, is a central coordination process in all living matter. Besides a plethora of regulatory mechanisms, the promoter architecture sets the foundation of expression strength, timing and the potential for further regulatory modulation. In this study, we investigate the effects of promoter spacer length and sequence composition on strength and supercoiling sensitivity in bacteria. Combining transcriptomics data analysis and standardized synthetic promoter libraries, we exclude effects of specific promoter sequence contexts. Analysis of promoter activity shows a strong variance with spacer length and spacer sequence composition. A detailed study of the spacer sequence composition under selective conditions reveals an extension to the -10 region that enhances RNAP binding but damps promoter activity. Using physiological changes in DNA supercoiling levels, we link promoter supercoiling sensitivity to overall spacer GC-content. Time-resolved promoter activity screens, only possible with a novel mild treatment approach, reveal strong promoter timing potentials solely based on DNA supercoiling sensitivity in the absence of regulatory sites or alternative sigma factors.
Collapse
|
21
|
Minor Alterations in Core Promoter Element Positioning Reveal Functional Plasticity of a Bacterial Transcription Factor. mBio 2021; 12:e0275321. [PMID: 34724814 PMCID: PMC8561392 DOI: 10.1128/mbio.02753-21] [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] [Indexed: 12/17/2022] Open
Abstract
IscR is a global transcription factor that regulates Fe-S cluster homeostasis and other functions in Escherichia coli by either activating or repressing transcription. While the interaction of IscR with its DNA sites has been studied, less is known about the mechanism of IscR regulation of transcription. Here, we show that IscR recruits RNA polymerase to an activated promoter and that IscR binding compensates for the lack of an optimal RNA polymerase σ70 −35 promoter element. We also find that the position of the −35 promoter element within the IscR DNA site impacts whether IscR activates or represses transcription. RNA polymerase binding at a distally positioned −35 element within the IscR site results in IscR activation. Molecular modeling suggests that this position of the −35 element allows IscR and RNA polymerase to bind to the promoter from opposite faces of the helix. Shifting the −35 element 1 nucleotide upstream within the IscR binding site results in IscR repression and a steric clash of IscR and RNA polymerase binding in the models. We propose that the sequence similarity of the IscR binding site with the −35 element is an important feature in allowing plasticity in the mechanism of IscR regulation.
Collapse
|
22
|
Jia H, Cao S, Wu Y, Zhu W, Luo J, Shen Y, Wang M. Genomewide Transcriptome Responses of Arthrobacter simplex to Cortisone Acetate and its Mutants with Enhanced Δ 1-Dehydrogenation Efficiency. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:12773-12784. [PMID: 34694802 DOI: 10.1021/acs.jafc.1c04934] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Due to its superior Δ1-dehydrogenation ability, Arthrobacter simplex has been widely used for the biotransformation of cortisone acetate (CA) into prednisone acetate (PA) in the steroid industry. However, its molecular fundamentals are still unclear. Herein, the genome organization, gene regulation, and previously unreported genes involved in Δ1-dehydrogenation are revealed through genome and transcriptome analysis. A comparative study of transcriptomes of an industrial strain induced by CA or at different biotransformation periods was performed. By overexpression, the roles of six genes in CA conversion were confirmed, among which sufC and hsaA behaved better by reinforcing catalytic enzyme activity and substrate transmembrane transport. Additionally, GroEL endowed cells with the strongest stress tolerance by alleviating oxidative damage and enhancing energy levels. Finally, an optimal strain was created by coexpressing three genes, achieving 46.8 and 70.6% increase in PA amount and productivity compared to the initial values, respectively. Our study expanded the understanding of the Δ1-dehydrogenation mechanism and offered an effective approach for excellent steroid-transforming strains.
Collapse
Affiliation(s)
- Hongchen Jia
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science &Technology), Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| | - Shuting Cao
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science &Technology), Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| | - Yan Wu
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science &Technology), Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| | - Wencheng Zhu
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science &Technology), Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| | - Jianmei Luo
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science &Technology), Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| | - Yanbing Shen
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science &Technology), Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| | - Min Wang
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science &Technology), Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| |
Collapse
|
23
|
Vu HN, Downs DM. Loss of YggS (COG0325) impacts aspartate metabolism in Salmonella enterica. Mol Microbiol 2021; 116:1232-1240. [PMID: 34498310 DOI: 10.1111/mmi.14810] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/24/2021] [Accepted: 09/07/2021] [Indexed: 12/01/2022]
Abstract
YggS is a pyridoxal 5'-phosphate (PLP)-binding protein of the conserved COG0325 family. Despite a connection with vitamin B6 homeostasis in many species, neither a precise biochemical activity nor the molecular mechanism of how YggS contributes to cellular function has been described. In a transposon mutagenesis screen, we found that insertions in aspC (encoding a PLP-dependent aspartate aminotransferase, EC 2.6.1.1) in a Salmonella enterica strain lacking yggS caused a synthetic growth defect, which could be rescued by the addition of exogenous aspartate. Characterization of spontaneous suppressors which improved the growth of the yggS aspC double mutant suggested that this synthetic aspartate limitation was dependent on TyrB, a PLP-dependent aromatic amino acid aminotransferase (EC 2.6.1.57). Genetic and biochemical data were consistent with the hypothesis that TyrB activity was inhibited by accumulated pyridoxine 5'-phosphate and α-keto acids caused by a yggS mutation. This study provides data consistent with a working model implicating YggS in modulating concentrations of B6 vitamers via transamination.
Collapse
Affiliation(s)
- Huong N Vu
- Department of Microbiology, The University of Georgia, Athens, Georgia, USA
| | - Diana M Downs
- Department of Microbiology, The University of Georgia, Athens, Georgia, USA
| |
Collapse
|
24
|
Cazier AP, Blazeck J. Advances in promoter engineering: novel applications and predefined transcriptional control. Biotechnol J 2021; 16:e2100239. [PMID: 34351706 DOI: 10.1002/biot.202100239] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 11/08/2022]
Abstract
Synthetic biology continues to progress by relying on more robust tools for transcriptional control, of which promoters are the most fundamental component. Numerous studies have sought to characterize promoter function, determine principles to guide their engineering, and create promoters with stronger expression or tailored inducible control. In this review, we will summarize promoter architecture and highlight recent advances in the field, focusing on the novel applications of inducible promoter design and engineering towards metabolic engineering and cellular therapeutic development. Additionally, we will highlight how the expansion of new, machine learning techniques for modeling and engineering promoter sequences are enabling more accurate prediction of promoter characteristics. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Andrew P Cazier
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst St. NW, Atlanta, Georgia, 30332, USA
| | - John Blazeck
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst St. NW, Atlanta, Georgia, 30332, USA
| |
Collapse
|
25
|
Wu Q, Fu J, Sun J, Wang X, Tang X, Lu W, Tan C, Li L, Deng X, Xu Q. A plant CitPITP1 protein-coding exon sequence serves as a promoter in bacteria. J Biotechnol 2021; 339:1-13. [PMID: 34298024 DOI: 10.1016/j.jbiotec.2021.07.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/17/2021] [Accepted: 07/18/2021] [Indexed: 11/19/2022]
Abstract
Genetic manipulation of plant genes in prokaryotes has been widely used in molecular biology, but the function of a DNA sequence is far from being fully known. Here, we discovered that a plant protein-coding gene containing the CRAL_TRIO domain serves as a promoter in bacteria. We firstly characterized CitPITP1 from Citrus, which contains the CRAL_TRIO domain, and identified a 64-bp sequence (key64) that is critical for prokaryotic promoter activity. In vitro experiments indicated that the bacterial RNA polymerase subunit RpoD specifically binds to key64. We then expanded our research to fungi, plant and animal species to identify key64-like sequences. Five such prokaryotic promoters were isolated from Amborella, Rice, Arabidopsis and Citrus. Two conserved motifs were identified, and mutation analysis indicated that the nucleotides at positions 7, 29 and 30 are crucial for key64-like transcription activity. We detected full-length recombinant CitPITP1 from E. coli, and visualized a CitPITP1-GFP fusion protein in plant cells, supporting the idea that CitPITP1 encodes a protein. However, although exon 4 of CitPITP1 contained key64, it did not demonstrate promoter activity in plants. Our study describes a new basal promoter, provides evidence for neofunction of gene elements across different kingdoms, and provides new knowledge for the modular design of promoters.
Collapse
Affiliation(s)
- Qingjiang Wu
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430000, China
| | - Jialing Fu
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430000, China
| | - Juan Sun
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430000, China
| | - Xia Wang
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430000, China
| | - Xiaomei Tang
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430000, China
| | - Wenjia Lu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430000, China
| | - Chen Tan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430000, China
| | - Li Li
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA; Robert W. Holley Center for Agriculture and Health, USDA-Agricultural Research Service, Cornell University, Ithaca, NY, 14853, USA
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430000, China
| | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430000, China.
| |
Collapse
|
26
|
Duang-Nkern J, Nontaleerak B, Udomkanarat T, Saninjuk K, Sukchawalit R, Mongkolsuk S. NieR is the repressor of a NaOCl-inducible efflux system in Agrobacterium tumefaciens C58. Microbiol Res 2021; 251:126816. [PMID: 34273784 DOI: 10.1016/j.micres.2021.126816] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 05/15/2021] [Accepted: 07/08/2021] [Indexed: 11/24/2022]
Abstract
The Agrobacterium tumefaciens atu4217 gene, which encodes a TetR family transcription regulator, is a repressor of the atu4218-atu4219-atu4220 operon. The Atu4218 and Atu4219 proteins belong to the HlyD family (membrane fusion protein) and the AcrB/AcrD/AcrF family (inner membrane transporter), respectively, and may form an efflux pump. The atu4220 gene encodes a short-chain dehydrogenase. Quantitative real-time PCR analysis showed induction of atu4217 and atu4218 by NaOCl but not by N-ethylmaleimide or reactive oxygen species (ROS) including H2O2, menadione and cumene hydroperoxide; therefore, the atu4218 and atu4219 were named NaOCl-inducible efflux genes nieA and nieB, respectively. The atu4217 gene, which was named nieR, serves as a repressor of nieA and nieB. DNase I footprinting assays identified 20-bp imperfect inverted repeat (IR, underlined) motifs 5'-TAGATTTAGGATGCAATCTA-3' (box A) and 5'-TAGATTTCACTTGACATCTA-3' (box R) in the intergenic region of the divergent nieA and nieR genes; these motifs were recognized by the NieR protein. Electrophoretic mobility shift assays demonstrated that NieR specifically binds to the 20-bp IR motifs and that NaOCl prevents this NieR-DNA interaction. Promoter-lacZ fusions and mutagenesis of the NieR boxes (A and R) showed a more dominant role for box A than for box R in the repression of the nieA and nieR promoters. However, full repression of either promoter required both operators. The nieR mutant strain exhibited a small colony phenotype and was more sensitive than the wild-type to NaOCl and antibiotics, including ciprofloxacin, nalidixic acid, novobiocin, and tetracycline. By contrast, the nieAB mutant strain showed no phenotype changes under the tested conditions.
Collapse
Affiliation(s)
- Jintana Duang-Nkern
- Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok, 10210, Thailand
| | - Benya Nontaleerak
- Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok, 10210, Thailand
| | - Tham Udomkanarat
- Environmental Toxicology, Chulabhorn Graduate Institute, Lak Si, Bangkok, 10210, Thailand
| | - Kritsakorn Saninjuk
- Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok, 10210, Thailand
| | - Rojana Sukchawalit
- Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok, 10210, Thailand; Applied Biological Sciences, Chulabhorn Graduate Institute, Lak Si, Bangkok, 10210, Thailand; Center of Excellence on Environmental Health and Toxicology (EHT), Ministry of Education, Bangkok, Thailand.
| | - Skorn Mongkolsuk
- Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok, 10210, Thailand; Center of Excellence on Environmental Health and Toxicology (EHT), Ministry of Education, Bangkok, Thailand
| |
Collapse
|
27
|
Wilson EH, Groom JD, Sarfatis MC, Ford SM, Lidstrom ME, Beck DAC. A Computational Framework for Identifying Promoter Sequences in Nonmodel Organisms Using RNA-seq Data Sets. ACS Synth Biol 2021; 10:1394-1405. [PMID: 33988977 DOI: 10.1021/acssynbio.1c00017] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Engineering microorganisms into biological factories that convert renewable feedstocks into valuable materials is a major goal of synthetic biology; however, for many nonmodel organisms, we do not yet have the genetic tools, such as suites of strong promoters, necessary to effectively engineer them. In this work, we developed a computational framework that can leverage standard RNA-seq data sets to identify sets of constitutive, strongly expressed genes and predict strong promoter signals within their upstream regions. The framework was applied to a diverse collection of RNA-seq data measured for the methanotroph Methylotuvimicrobium buryatense 5GB1 and identified 25 genes that were constitutively, strongly expressed across 12 experimental conditions. For each gene, the framework predicted short (27-30 nucleotide) sequences as candidate promoters and derived -35 and -10 consensus promoter motifs (TTGACA and TATAAT, respectively) for strong expression in M. buryatense. This consensus closely matches the canonical E. coli sigma-70 motif and was found to be enriched in promoter regions of the genome. A subset of promoter predictions was experimentally validated in a XylE reporter assay, including the consensus promoter, which showed high expression. The pmoC, pqqA, and ssrA promoter predictions were additionally screened in an experiment that scrambled the -35 and -10 signal sequences, confirming that transcription initiation was disrupted when these specific regions of the predicted sequence were altered. These results indicate that the computational framework can make biologically meaningful promoter predictions and identify key pieces of regulatory systems that can serve as foundational tools for engineering diverse microorganisms for biomolecule production.
Collapse
Affiliation(s)
- Erin H. Wilson
- The Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Joseph D. Groom
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - M. Claire Sarfatis
- Department of Microbiology, University of Washington, Seattle, Washington 98195, United States
| | - Stephanie M. Ford
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Mary E. Lidstrom
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
- Department of Microbiology, University of Washington, Seattle, Washington 98195, United States
| | - David A. C. Beck
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
- eScience Institute, University of Washington, Seattle, Washington 98195, United States
| |
Collapse
|
28
|
He S, Guo F, Zou Q, HuiDing. MRMD2.0: A Python Tool for Machine Learning with Feature Ranking and Reduction. Curr Bioinform 2021. [DOI: 10.2174/1574893615999200503030350] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Aims:
The study aims to find a way to reduce the dimensionality of the dataset.
Background:
Dimensionality reduction is the key issue of the machine learning process. It does
not only improve the prediction performance but also could recommend the intrinsic features and
help to explore the biological expression of the machine learning “black box”.
Objective:
A variety of feature selection algorithms are used to select data features to achieve
dimensionality reduction.
Methods:
First, MRMD2.0 integrated 7 different popular feature ranking algorithms with
PageRank strategy. Second, optimized dimensionality was detected with forward adding strategy.
Result:
We have achieved good results in our experiments.
Conclusion:
Several works have been tested with MRMD2.0. It showed well performance.
Otherwise, it also can draw the performance curves according to the feature dimensionality. If
users want to sacrifice accuracy for fewer features, they can select the dimensionality from the
performance curves.
Other:
We developed friendly python tools together with the web server. The users could upload
their csv, arff or libsvm format files. Then the webserver would help to rank features and find the
optimized dimensionality.
Collapse
Affiliation(s)
- Shida He
- College of Intelligence and Computing, Tianjin University, Tianjin, China
| | - Fei Guo
- College of Intelligence and Computing, Tianjin University, Tianjin, China
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
| | - HuiDing
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| |
Collapse
|
29
|
Kozakai T, Shimofusa Y, Nomura I, Suzuki T. Construction of a reporter system for bifidobacteria using chloramphenicol acetyltransferase and its application for evaluation of promoters and terminators. BIOSCIENCE OF MICROBIOTA FOOD AND HEALTH 2021; 40:115-122. [PMID: 33996368 PMCID: PMC8099631 DOI: 10.12938/bmfh.2020-070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 11/30/2020] [Indexed: 11/23/2022]
Abstract
A reporter assay system is an essential tool for investigating gene expression
mechanisms. In the case of bifidobacteria, several convenient and sensitive reporter
systems have been developed. Here, we developed a new reporter system for bifidobacteria
using the chloramphenicol acetyltransferase gene (cat) from
Staphylococcus aureus. This enzyme stoichiometrically produced free
CoA-SH, which was analyzed quantitatively with Ellman’s test using 2-nitrobenzoic acid
(DTNB). The 2-nitro-5-thiobenzoate (TNB2-) produced showed a strong yellowish
color with maximum absorbance at 412 nm. We also constructed a new pBCMAT plasmid series
for CAT assays in bifidobacteria to evaluate promoters and terminators. Analyses using
promoters from Bifidobacterium longum NCC2705 indicated that the CAT
assay using these promoters is quantitative, has a wide measurement range, and is stable.
In addition, this assay was useful for several bifidobacterial species, including
B. longum, Bifidobacterium breve, and
Bifidobacterium adolescentis. Compared with evoglow-Bs2, a fluorescent
protein used under anaerobic conditions, the CAT assay showed about 0.25% background
activity. In analyses using this CAT assay, we identified 11 promoters and 12 terminators
of B. longum NCC2705. The genes encoding ribosomal proteins, elongation
factors, and transfer RNAs possessed strong promoters, and terminators that include strong
stem-loops and poly-U tails structures tended to show high activities. Although the
abovementioned promoters made stronger contributions to expression activities than the
terminators, the maximum fold difference in the activities among the tested terminators
was approximately 17-fold. Modification of the -10 box and 5’-UTR in the
promoters and the structure around the stem-loop in the terminators affected expression
levels. These results suggest that the CAT assay is useful for various analyses of
bifidobacterial gene expression.
Collapse
Affiliation(s)
- Tomoya Kozakai
- United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan
| | - Yoko Shimofusa
- Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan
| | - Izumi Nomura
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan
| | - Tohru Suzuki
- United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan.,Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan.,Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan
| |
Collapse
|
30
|
Soft Computing in Bioinformatics. Adv Bioinformatics 2021. [DOI: 10.1007/978-981-33-6191-1_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
|
31
|
Écija-Conesa A, Gallego-Jara J, Lozano Terol G, Browning DF, Busby SJW, Wolfe AJ, Cánovas Díaz M, de Diego Puente T. An ideal spacing is required for the control of Class II CRP-dependent promoters by the status of CRP K100. FEMS Microbiol Lett 2020; 367:5936555. [PMID: 33095239 DOI: 10.1093/femsle/fnaa164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/07/2020] [Indexed: 11/14/2022] Open
Abstract
Transcription activation by the Escherichia coli CRP at Class II promoters is dependent on direct interactions between RNA polymerase and CRP, therefore the spatial proximity between both proteins plays a significant role in the ability of CRP to activate transcription. Using both in vivo and in vitro techniques, here we demonstrate that the CRP K100 positive charge, adjacent to AR2, is required for full promoter activity when CRP is optimally positioned. Accordingly, K100 mediated activation is very position-dependent and our data confirm that the largest impact of the K100 status on transcription activation occurs when the spacing between the CRP binding site and the A2 of the -10 element is 22 bp. From the results of this study and the progress in the understanding about open complex DNA scrunching, we propose that CRP-dependent promoters should now be numbered by the distance from the center of the DNA site for CRP and the most highly conserved base at position 2 of the -10 hexamer in bacterial promoters.
Collapse
Affiliation(s)
- Ana Écija-Conesa
- 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", P.O. Box 4021, Murcia E-30100, 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", P.O. Box 4021, Murcia E-30100, Spain
| | - 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", P.O. Box 4021, Murcia E-30100, Spain
| | - Douglas F Browning
- Institute of Microbiology and Infection and School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Steve J W Busby
- Institute of Microbiology and Infection and School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Alan J Wolfe
- Department of Microbiology and Immunology, Loyola University Chicago, Health Sciences Division, Stritch School of Medicine, Maywood, IL, 60153, USA
| | - 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", P.O. Box 4021, Murcia E-30100, 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", P.O. Box 4021, Murcia E-30100, Spain
| |
Collapse
|
32
|
Discovery of small-molecule inhibitors of multidrug-resistance plasmid maintenance using a high-throughput screening approach. Proc Natl Acad Sci U S A 2020; 117:29839-29850. [PMID: 33168749 DOI: 10.1073/pnas.2005948117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Carbapenem-resistant Enterobacteriaceae (CRE) are multidrug-resistant pathogens for which new treatments are desperately needed. Carbapenemases and other types of antibiotic resistance genes are carried almost exclusively on large, low-copy-number plasmids (pCRE). Accordingly, small molecules that efficiently evict pCRE plasmids should restore much-needed treatment options. We therefore designed a high-throughput screen to identify such compounds. A synthetic plasmid was constructed containing the plasmid replication machinery from a representative Escherichia coli CRE isolate as well as a fluorescent reporter gene to easily monitor plasmid maintenance. The synthetic plasmid was then introduced into an E. coli K12 tolC host. We used this screening strain to test a library of over 12,000 known bioactive agents for molecules that selectively reduce plasmid levels relative to effects on bacterial growth. From 366 screen hits we further validated the antiplasmid activity of kasugamycin, an aminoglycoside; CGS 15943, a nucleoside analog; and Ro 90-7501, a bibenzimidazole. All three compounds exhibited significant antiplasmid activity including up to complete suppression of plasmid replication and/or plasmid eviction in multiple orthogonal readouts and potentiated activity of the carbapenem, meropenem, against a strain carrying the large, pCRE plasmid from which we constructed the synthetic screening plasmid. Additionally, we found kasugamycin and CGS 15943 blocked plasmid replication, respectively, by inhibiting expression or function of the plasmid replication initiation protein, RepE. In summary, we validated our approach to identify compounds that alter plasmid maintenance, confer resensitization to antimicrobials, and have specific mechanisms of action.
Collapse
|
33
|
Wu F, Chen W, Peng Y, Tu R, Lin Y, Xing J, Wang Q. Design and Reconstruction of Regulatory Parts for Fast-frowing Vibrio natriegens Synthetic Biology. ACS Synth Biol 2020; 9:2399-2409. [PMID: 32786358 DOI: 10.1021/acssynbio.0c00158] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The fast-growing Vibrio natriegens is an attractive robust chassis for diverse synthetic biology applications. However, V. natriegens lacks the suitable constitutive regulatory parts for precisely tuning the gene expression and, thus, recapitulating physiologically relevant changes in gene expression levels. In this study, we designed, constructed, and screened the synthetic regulatory parts by varying the promoter region and ribosome binding site element for V. natriegens with different transcriptional or translational strengths, respectively. The fluorescence intensities of the cells with different synthetic regulatory parts could distribute evenly over a wide range of 5 orders of magnitude. The selected synthetic regulatory parts had good stability in both nutrient-rich and minimal media. The precise combinatorial modulation of galP (GalP = galactose permease) and glk (Glk = glucokinase) from Escherichia coli by using three synthetic regulatory parts with different strengths was confirmed in a phosphoenolpyruvate:carbohydrate phosphotransferase system with inactive V. natriegens strain to alter the glucose transport. This work provides the simple, efficient, and standardized constitutive regulatory parts for V. natriegens synthetic biology.
Collapse
Affiliation(s)
- Fengli Wu
- CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Wujiu Chen
- CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Yanfeng Peng
- CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Ran Tu
- CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Yuping Lin
- CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Jianmin Xing
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Qinhong Wang
- CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| |
Collapse
|
34
|
Wang Y, Wang H, Wei L, Li S, Liu L, Wang X. Synthetic promoter design in Escherichia coli based on a deep generative network. Nucleic Acids Res 2020; 48:6403-6412. [PMID: 32424410 PMCID: PMC7337522 DOI: 10.1093/nar/gkaa325] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 04/05/2020] [Accepted: 04/22/2020] [Indexed: 01/11/2023] Open
Abstract
Promoter design remains one of the most important considerations in metabolic engineering and synthetic biology applications. Theoretically, there are 450 possible sequences for a 50-nt promoter, of which naturally occurring promoters make up only a small subset. To explore the vast number of potential sequences, we report a novel AI-based framework for de novo promoter design in Escherichia coli. The model, which was guided by sequence features learned from natural promoters, could capture interactions between nucleotides at different positions and design novel synthetic promoters in silico. We combined a deep generative model that guides the search for artificial sequences with a predictive model to preselect the most promising promoters. The AI-designed promoters were optimized based on the promoter activity in E. coli and the predictive model. After two rounds of optimization, up to 70.8% of the AI-designed promoters were experimentally demonstrated to be functional, and few of them shared significant sequence similarity with the E. coli genome. Our work provided an end-to-end approach to the de novo design of novel promoter elements, indicating the potential to apply deep learning methods to de novo genetic element design.
Collapse
Affiliation(s)
- Ye Wang
- Ministry of Education Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Bioinformatics Division, Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University, Beijing 100084, China
| | - Haochen Wang
- Ministry of Education Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Bioinformatics Division, Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University, Beijing 100084, China
| | - Lei Wei
- Ministry of Education Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Bioinformatics Division, Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University, Beijing 100084, China
| | - Shuailin Li
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Liyang Liu
- Ministry of Education Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Bioinformatics Division, Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University, Beijing 100084, China
| | - Xiaowo Wang
- Ministry of Education Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Bioinformatics Division, Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University, Beijing 100084, China
| |
Collapse
|
35
|
Luo JM, Cui HL, Jia HC, Li F, Cheng HJ, Shen YB, Wang M. Identification, Biological Characteristics, and Active Site Residues of 3-Ketosteroid Δ 1-Dehydrogenase Homologues from Arthrobacter simplex. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:9496-9512. [PMID: 32786835 DOI: 10.1021/acs.jafc.0c03360] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
3-Ketosteroid Δ1-dehydrogenase (KsdD) is the key enzyme responsible for Δ1-dehydrogenation, which is one of the most valuable reactions for steroid catabolism. Arthrobacter simplex has been widely used in the industry due to its superior bioconversion efficiency, but KsdD information is not yet fully clear. Here, five KsdD homologues were identified in A. simplex CGMCC 14539. Bioinformatic analysis indicated their distinct properties and structures. Each KsdD was functionally confirmed by transcriptional response, overexpression, and heterologous expression. The substantial difference in substrate profiles might be related to the enzyme loop structure. Two promising enzymes (KsdD3 and KsdD5) were purified and characterized, exhibiting strong organic solvent tolerance and clear preference for 4-ene-3-oxosteroids. KsdD5 seemed to be more versatile due to good activity on substrates with or without a substituent at C11 and high optimal temperature and also possessed unique residues. It is the first time that KsdDs have been comprehensively disclosed in the A. simplex industrial strain.
Collapse
Affiliation(s)
- Jian-Mei Luo
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science & Technology), Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, College of Biotechnology, Tianjin University of Science and Technology, 89 P.O. Box, No. 29, Street No. 13, Tianjin Economic-Technological Development Area (TEDA), Tianjin 30057, P. R. China
- Ministry of Education Key Laboratory of Molecular Microbiology and Technology, Nankai University, Tianjin 300071, P. R. China
| | - Hui-Lin Cui
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science & Technology), Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, College of Biotechnology, Tianjin University of Science and Technology, 89 P.O. Box, No. 29, Street No. 13, Tianjin Economic-Technological Development Area (TEDA), Tianjin 30057, P. R. China
| | - Hong-Chen Jia
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science & Technology), Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, College of Biotechnology, Tianjin University of Science and Technology, 89 P.O. Box, No. 29, Street No. 13, Tianjin Economic-Technological Development Area (TEDA), Tianjin 30057, P. R. China
| | - Fang Li
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science & Technology), Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, College of Biotechnology, Tianjin University of Science and Technology, 89 P.O. Box, No. 29, Street No. 13, Tianjin Economic-Technological Development Area (TEDA), Tianjin 30057, P. R. China
| | - Hong-Jin Cheng
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science & Technology), Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, College of Biotechnology, Tianjin University of Science and Technology, 89 P.O. Box, No. 29, Street No. 13, Tianjin Economic-Technological Development Area (TEDA), Tianjin 30057, P. R. China
| | - Yan-Bing Shen
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science & Technology), Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, College of Biotechnology, Tianjin University of Science and Technology, 89 P.O. Box, No. 29, Street No. 13, Tianjin Economic-Technological Development Area (TEDA), Tianjin 30057, P. R. China
| | - Min Wang
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science & Technology), Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, College of Biotechnology, Tianjin University of Science and Technology, 89 P.O. Box, No. 29, Street No. 13, Tianjin Economic-Technological Development Area (TEDA), Tianjin 30057, P. R. China
| |
Collapse
|
36
|
Piccolo SR, Lee TJ, Suh E, Hill K. ShinyLearner: A containerized benchmarking tool for machine-learning classification of tabular data. Gigascience 2020; 9:giaa026. [PMID: 32249316 PMCID: PMC7131989 DOI: 10.1093/gigascience/giaa026] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 12/05/2019] [Accepted: 02/28/2020] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Classification algorithms assign observations to groups based on patterns in data. The machine-learning community have developed myriad classification algorithms, which are used in diverse life science research domains. Algorithm choice can affect classification accuracy dramatically, so it is crucial that researchers optimize the choice of which algorithm(s) to apply in a given research domain on the basis of empirical evidence. In benchmark studies, multiple algorithms are applied to multiple datasets, and the researcher examines overall trends. In addition, the researcher may evaluate multiple hyperparameter combinations for each algorithm and use feature selection to reduce data dimensionality. Although software implementations of classification algorithms are widely available, robust benchmark comparisons are difficult to perform when researchers wish to compare algorithms that span multiple software packages. Programming interfaces, data formats, and evaluation procedures differ across software packages; and dependency conflicts may arise during installation. FINDINGS To address these challenges, we created ShinyLearner, an open-source project for integrating machine-learning packages into software containers. ShinyLearner provides a uniform interface for performing classification, irrespective of the library that implements each algorithm, thus facilitating benchmark comparisons. In addition, ShinyLearner enables researchers to optimize hyperparameters and select features via nested cross-validation; it tracks all nested operations and generates output files that make these steps transparent. ShinyLearner includes a Web interface to help users more easily construct the commands necessary to perform benchmark comparisons. ShinyLearner is freely available at https://github.com/srp33/ShinyLearner. CONCLUSIONS This software is a resource to researchers who wish to benchmark multiple classification or feature-selection algorithms on a given dataset. We hope it will serve as example of combining the benefits of software containerization with a user-friendly approach.
Collapse
Affiliation(s)
- Stephen R Piccolo
- Department of Biology, Brigham Young University, 4102 Life Sciences Building, Provo, UT, 84602, USA
| | - Terry J Lee
- Department of Biology, Brigham Young University, 4102 Life Sciences Building, Provo, UT, 84602, USA
| | - Erica Suh
- Department of Biology, Brigham Young University, 4102 Life Sciences Building, Provo, UT, 84602, USA
| | - Kimball Hill
- Department of Biology, Brigham Young University, 4102 Life Sciences Building, Provo, UT, 84602, USA
| |
Collapse
|
37
|
Structure of a Core Promoter in Bifidobacterium longum NCC2705. J Bacteriol 2020; 202:JB.00540-19. [PMID: 31964699 DOI: 10.1128/jb.00540-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 01/14/2020] [Indexed: 01/04/2023] Open
Abstract
Bacterial promoters consist of core sequence motifs termed -35 and -10 boxes. The consensus motifs are TTGACA and TATAAT, respectively, which were identified from leading investigations on Escherichia coli However, the consensus sequences are not likely to fit genetically divergent bacteria. The sigma factor of the genus Bifidobacterium has a characteristic polar domain in the N terminus, suggesting the possibility of specific promoter recognition. We reevaluated the structure of Bifidobacterium longum NCC2705 promoters and compared them to other bacteria. Transcriptional start sites (TSSs) of the B. longum NCC2705 strain were identified using transcriptome sequencing (RNA-Seq) analysis to extract promoter regions. Conserved motifs of a bifidobacterial promoter were determined using regions upstream of TSSs and a hidden Markov model. As a result, consensus motifs of the -35 and -10 boxes were TTGTGC and TACAAT, respectively. To assess each base of both motifs, we constructed 37 plasmids based on pKO403-TPCTcon, including the hup promoter connected with a chloramphenicol acetyltransferase as a reporter gene. This reporter assay showed two optimal motifs of the -35 and -10 boxes, namely, TTGNNN and TANNNT, respectively. We further analyzed spacer lengths between the -35 and -10 boxes via a bioinformatics approach. The spacer lengths predominant in bacteria have been generally reported to be approximately 17 bp. In contrast, the predominant spacer lengths in the genus Bifidobacterium and related species were 11 bp, in addition to 17 bp. A reporter assay to assess the spacer lengths indicated that the 11-bp spacer length produced unusually high activity.IMPORTANCE The structures of sigma factors vary among bacterial strains, indicating that recognition rules may also vary. Therefore, we investigated the promoter structure of Bifidobacterium longum NCC2705 using a bioinformatics approach and wet analyses. The most frequent and optimal motifs were similar to other bacterial consensus motifs. The optimal spacer length between the two boxes was reported to be 17 bp. It is widely applied to a bioinformatics approach for other bacteria. Unexpectedly, conserved spacer lengths were 11 bp as well as 17 bp in the genus Bifidobacterium Moreover, the sigma factor of the genus Bifidobacterium has a characteristic domain in the N terminus which may contribute to the additional functions. Hence, it would be valuable to reevaluate the promoter in other organisms.
Collapse
|
38
|
Rihtar E, Žgur Bertok D, Podlesek Z. The Uropathogenic Specific Protein Gene usp from Escherichia coli and Salmonella bongori is a Novel Member of the TyrR and H-NS Regulons. Microorganisms 2020; 8:E330. [PMID: 32111072 PMCID: PMC7142922 DOI: 10.3390/microorganisms8030330] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 02/25/2020] [Indexed: 12/16/2022] Open
Abstract
The Escherichia coli PAIusp is a small pathogenicity island encoding usp, for the uropathogenic specific protein (Usp), a genotoxin and three associated downstream imu1-3 genes that protect the producer against its own toxin. Bioinformatic analysis revealed the presence of the PAIusp also in publically available Salmonella bongori and Salmonella enterica subps. salamae genome sequences. PAIusp is in all examined sequences integrated within the aroP-pdhR chromosomal intergenic region. The focus of this work was identification of the usp promoter and regulatory elements controlling its activity. We show that, in both E. coli and S. bongori, the divergent TyrR regulated P3 promoter of the aroP gene, encoding an aromatic amino acid membrane transporter, drives usp transcription while H-NS acts antagonistically repressing expression. Our results show that the horizontally acquired PAIusp has integrated into the TyrR regulatory network and that environmental factors such as aromatic amino acids, temperature and urea induce usp expression.
Collapse
Affiliation(s)
- Erik Rihtar
- Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (E.R.); (Z.P.)
- National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Darja Žgur Bertok
- Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (E.R.); (Z.P.)
| | - Zdravko Podlesek
- Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (E.R.); (Z.P.)
| |
Collapse
|
39
|
Nuonming P, Khemthong S, Sukchawalit R, Mongkolsuk S. Identification of Zur boxes and determination of their roles in the differential regulation of the Zur regulon in Agrobacterium tumefaciens C58. Appl Microbiol Biotechnol 2020; 104:2109-2123. [PMID: 31927759 DOI: 10.1007/s00253-020-10346-z] [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: 10/01/2019] [Revised: 12/19/2019] [Accepted: 01/03/2020] [Indexed: 11/29/2022]
Abstract
Zinc uptake regulator (Zur) is a transcriptional regulator that represses zinc acquisition genes under high zinc conditions. The aim of this study was to identify and investigate the role of Zur-binding motifs (Zur boxes) in the differential regulation of Zur target genes, including the zinT, znuA, znuCB-zur operon, the troCBA operon, and yciC, in Agrobacterium tumefaciens. DNase I footprinting and gel shift assays were performed, confirming that Zur directly binds to 18-bp inverted repeat motifs found in the promoter of these Zur-regulated genes. Furthermore, promoter-lacZ fusions and mutagenesis of the identified Zur boxes were performed to assess the role of each Zur box. A Zur box found in the zinT promoter was required for zinc-dependent repression by Zur. The intergenic region between the znuA gene and the znuCB-zur operon contains two Zur boxes, named A and C, which immediately precede the genes znuA and znuC, respectively. Zur box A, but not Zur box C, was essential for the repression of the znuA promoter. Both Zur boxes A and C were implicated in the repression of the znuC promoter, in which mutation of either box alone was sufficient for full derepression of the znuC promoter. Three Zur boxes named T, M, and Y were identified in the intergenic region between the troCBA operon and the yciC gene. Zur box Y, which immediately precedes yciC, was shown to be responsible for Zur repression of the yciC promoter. In contrast, two Zur boxes, T and M, were essential for the complete repression of the troCBA operon, and full derepression of the troC promoter was exhibited when both Zur boxes were mutated simultaneously. Sequence analysis of the identified Zur boxes revealed a correlation between deviation from the core recognition sequence of the Zur box and the requirement of two Zur boxes for Zur regulation of distinctive promoters.
Collapse
Affiliation(s)
- Puttamas Nuonming
- Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok, 10210, Thailand
| | - Sasimaporn Khemthong
- Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok, 10210, Thailand
| | - Rojana Sukchawalit
- Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok, 10210, Thailand. .,Applied Biological Sciences, Chulabhorn Graduate Institute, Lak Si, Bangkok, 10210, Thailand. .,Center of Excellence on Environmental Health and Toxicology (EHT), Ministry of Education, Bangkok, Thailand.
| | - Skorn Mongkolsuk
- Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok, 10210, Thailand.,Center of Excellence on Environmental Health and Toxicology (EHT), Ministry of Education, Bangkok, Thailand
| |
Collapse
|
40
|
Brandi A, Giangrossi M, Paoloni S, Spurio R, Giuliodori AM, Pon CL, Gualerzi CO. Transcriptional and post-transcriptional events trigger de novo infB expression in cold stressed Escherichia coli. Nucleic Acids Res 2019; 47:4638-4651. [PMID: 30916329 PMCID: PMC6511841 DOI: 10.1093/nar/gkz187] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 03/07/2019] [Accepted: 03/22/2019] [Indexed: 11/13/2022] Open
Abstract
After a 37 to 10°C temperature downshift the level of translation initiation factor IF2, like that of IF1 and IF3, increases at least 3-fold with respect to the ribosomes. To clarify the mechanisms and conditions leading to cold-stress induction of infB expression, the consequences of this temperature shift on infB (IF2) transcription, infB mRNA stability and translation were analysed. The Escherichia coli gene encoding IF2 is part of the metY-nusA-infB operon that contains three known promoters (P-1, P0 and P2) in addition to two promoters P3 and P4 identified in this study, the latter committed to the synthesis of a monocistronic mRNA encoding exclusively IF2. The results obtained indicate that the increased level of IF2 following cold stress depends on three mechanisms: (i) activation of all the promoters of the operon, P-1 being the most cold-responsive, as a likely consequence of the reduction of the ppGpp level that follows cold stress; (ii) a large increase in infB mRNA half-life and (iii) the cold-shock induced translational bias that ensures efficient translation of infB mRNA by the translational apparatus of cold shocked cells. A comparison of the mechanisms responsible for the cold shock induction of the three initiation factors is also presented.
Collapse
Affiliation(s)
- Anna Brandi
- Laboratory of Genetics, Department of Biosciences and Biotechnology University of Camerino, 62032 Camerino (MC), Italy
| | - Mara Giangrossi
- Laboratory of Genetics, Department of Biosciences and Biotechnology University of Camerino, 62032 Camerino (MC), Italy
| | - Silvia Paoloni
- Laboratory of Genetics, Department of Biosciences and Biotechnology University of Camerino, 62032 Camerino (MC), Italy
| | - Roberto Spurio
- Laboratory of Genetics, Department of Biosciences and Biotechnology University of Camerino, 62032 Camerino (MC), Italy
| | - Anna M Giuliodori
- Laboratory of Genetics, Department of Biosciences and Biotechnology University of Camerino, 62032 Camerino (MC), Italy
| | - Cynthia L Pon
- Laboratory of Genetics, Department of Biosciences and Biotechnology University of Camerino, 62032 Camerino (MC), Italy
| | - Claudio O Gualerzi
- Laboratory of Genetics, Department of Biosciences and Biotechnology University of Camerino, 62032 Camerino (MC), Italy
| |
Collapse
|
41
|
Singh DK, Lingaswamy B, Koduru TN, Nagu PP, Jogadhenu PSS. A putative merR family transcription factor Slr0701 regulates mercury inducible expression of MerA in the cyanobacterium Synechocystis sp. PCC6803. Microbiologyopen 2019; 8:e00838. [PMID: 31094100 PMCID: PMC6741143 DOI: 10.1002/mbo3.838] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 02/24/2019] [Accepted: 02/26/2019] [Indexed: 11/23/2022] Open
Abstract
In cyanobacteria, genes conferring mercury resistance are not organized as mer‐operon, unlike in other bacterial phyla. Synechocystis contains only a putative MerR regulator, Slr0701, and a mercury reductase, MerA, located aside from each other in the genome. The slr0701‐mutant showed reduction in photosynthetic activity and reduced tolerance to mercury compared to the wild‐type. The incubation of wild‐type cells with HgCl2 resulted in the upregulation of slr0701 and slr1849 genes whereas mercury‐induced expression was not observed in the slr0701‐mutant. Slr0701 binds to a conserved cis‐regulatory element located in the upstream of slr1849 and slr0701 ORFs. The same element was also identified in the upstream of other cyanobacterial homologs. Slr0701 binds to cis‐regulatory element with faster association and slower dissociation rates in the presence of HgCl2. Although these genes were constitutively expressed, the addition of HgCl2 enhanced their promoter activity suggesting that mercury‐bound Slr0701 triggers induced expression of these genes. The enhanced promoter activity could be attributed to the observed secondary structural changes in Slr0701 in the presence of HgCl2. For the first time, we demonstrated the mechanism of merA regulation in a cyanobacterium, Synechocystis. Although merA and merR genes are distantly located on the cyanobacterial genome and distinct from other bacterial mer‐operons, the transcriptional regulatory mechanism is conserved.
Collapse
Affiliation(s)
- Deepak Kumar Singh
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Bantu Lingaswamy
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Tejaswi Naidu Koduru
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Prakash Prabhu Nagu
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | | |
Collapse
|
42
|
Khemthong S, Nuonming P, Nookabkaewb S, Sukchawalit R, Mongkolsuk S. The Agrobacterium tumefaciens atu3184 gene, a member of the COG0523 family of GTPases, is regulated by the transcriptional repressor Zur. Microbiol Res 2019; 222:14-24. [PMID: 30928026 DOI: 10.1016/j.micres.2019.02.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 02/11/2019] [Accepted: 02/23/2019] [Indexed: 02/06/2023]
Abstract
Analysis of the Agrobacterium tumefaciens C58 genome revealed a potential Zur (zinc uptake regulator) binding site (5'-GATATGTTATTACATTAC-3', the underlined letters are the center of symmetry of the inverted palindrome) located in the upstream region of atu3184, whose gene product is a member of the COG0523 subfamily of G3E GTPases. The specific interaction of the Zur protein with the 18-bp inverted repeat operator motif in the presence of zinc was demonstrated in vitro by a DNA band shift assay and a DNase I footprinting assay. A LacZ reporter fusion assay further confirmed that Zur negatively regulates atu3184 promoter activity in vivo. The expression of atu3184 was upregulated in response to zinc limitation in the wild-type strain, but the zur mutant strain exhibited high-level constitutive expression of atu3184 under all conditions, irrespective of the zinc levels. It is likely that A. tumefaciens Zur senses zinc and directly regulates the atu3184 promoter by a molecular mechanism similar to that of Escherichia coli Zur, where the operator DNA is surrounded by four Zur monomers forming two dimers bound on the opposite sides of the DNA duplex. Disruption of atu3184 did not affect cell growth under metal-limited conditions and had no effect on the total cellular zinc content. Furthermore, an A. tumefaciens strain lacking atu3184 caused a tumor disease in a host plant.
Collapse
Affiliation(s)
- Sasimaporn Khemthong
- Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok, 10210, Thailand
| | - Puttamas Nuonming
- Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok, 10210, Thailand
| | - Sumontha Nookabkaewb
- Laboratory of Pharmacology, Chulabhorn Research Institute, Lak Si, Bangkok, 10210, Thailand
| | - Rojana Sukchawalit
- Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok, 10210, Thailand; Applied Biological Sciences, Chulabhorn Graduate Institute, Lak Si, Bangkok, 10210, Thailand; Center of Excellence on Environmental Health and Toxicology (EHT), Ministry of Education, Bangkok, Thailand.
| | - Skorn Mongkolsuk
- Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok, 10210, Thailand; Center of Excellence on Environmental Health and Toxicology (EHT), Ministry of Education, Bangkok, Thailand
| |
Collapse
|
43
|
Allala F, Bouacem K, Boucherba N, Azzouz Z, Mechri S, Sahnoun M, Benallaoua S, Hacene H, Jaouadi B, Bouanane-Darenfed A. Purification, biochemical, and molecular characterization of a novel extracellular thermostable and alkaline α-amylase from Tepidimonas fonticaldi strain HB23. Int J Biol Macromol 2019; 132:558-574. [PMID: 30928371 DOI: 10.1016/j.ijbiomac.2019.03.201] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 01/16/2019] [Accepted: 03/26/2019] [Indexed: 11/25/2022]
Abstract
The present study investigated the purification, biochemical, and molecular characterization of a novel thermostable α-amylase (TfAmy48) from Tepidimonas fonticaldi strain HB23. MALDI-TOF/MS analysis indicated that the purified enzyme is a monomer with a molecular mass of 48,138.10 Da. The results from amino-acid sequence analysis revealed high homology between the 25 NH2-terminal residues of TfAmy48 and those of Gammaproteobacteria α-amylases. The optimum pH and temperature values for α-amylase activity were pH 8 and 80 °C, respectively. Thin-layer chromatography (TLC) analysis showed that the final hydrolyzed products of the enzyme from soluble potato starch were maltopentaose, maltose, and maltotriose, which indicate that TfAmy48 possessed an endo-acting pattern. Compared to Termamyl®300 L, TfAmy48 showed extreme stability and tolerance towards organic solvents and excellent compatibility with some commercial laundry detergents. These proprieties make TfAmy48 enzyme a potential candidate as a cleaning bioadditive in detergent composition. The Tfamy48 gene encoding TfAmy48 was cloned, sequenced, and heterologously-expressed in the extracellular fraction of Escherichia coli strain BL21(DE3)pLysS. The biochemical properties of the extracellular purified recombinant enzyme (rTfAmy48) were similar to those of native one. The highest sequence identity value (97%) was obtained with PsAmy1 α-amylase from Pseudomonas sp. strain KFCC10818, with only 16 amino-acid (aa) residues of difference.
Collapse
Affiliation(s)
- Fawzi Allala
- Laboratory of Cellular and Molecular Biology (LCMB), Microbiology Team, Faculty of Biological Sciences, University of Sciences and Technology Houari Boumediene (USTHB), P.O. Box 32, El Alia, Bab Ezzouar, 16111, Algiers, Algeria; Laboratory of Applied Microbiology (LAM), Faculty of Nature and Life Sciences, University of Bejaïa, Targa Ouzemmour, 06000 Bejaïa, Algeria
| | - Khelifa Bouacem
- Laboratory of Cellular and Molecular Biology (LCMB), Microbiology Team, Faculty of Biological Sciences, University of Sciences and Technology Houari Boumediene (USTHB), P.O. Box 32, El Alia, Bab Ezzouar, 16111, Algiers, Algeria; Laboratory of Microbial Biotechnology and Engineering Enzymes (LMBEE), Centre of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, P.O. Box 1177, Sfax 3018, Tunisia
| | - Nawel Boucherba
- Laboratory of Applied Microbiology (LAM), Faculty of Nature and Life Sciences, University of Bejaïa, Targa Ouzemmour, 06000 Bejaïa, Algeria.
| | - Zahra Azzouz
- Laboratory of Applied Microbiology (LAM), Faculty of Nature and Life Sciences, University of Bejaïa, Targa Ouzemmour, 06000 Bejaïa, Algeria
| | - Sondes Mechri
- Laboratory of Microbial Biotechnology and Engineering Enzymes (LMBEE), Centre of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, P.O. Box 1177, Sfax 3018, Tunisia
| | - Mouna Sahnoun
- Laboratory of Microbial Biotechnology and Engineering Enzymes (LMBEE), Centre of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, P.O. Box 1177, Sfax 3018, Tunisia
| | - Said Benallaoua
- Laboratory of Applied Microbiology (LAM), Faculty of Nature and Life Sciences, University of Bejaïa, Targa Ouzemmour, 06000 Bejaïa, Algeria
| | - Hocine Hacene
- Laboratory of Cellular and Molecular Biology (LCMB), Microbiology Team, Faculty of Biological Sciences, University of Sciences and Technology Houari Boumediene (USTHB), P.O. Box 32, El Alia, Bab Ezzouar, 16111, Algiers, Algeria
| | - Bassem Jaouadi
- Laboratory of Microbial Biotechnology and Engineering Enzymes (LMBEE), Centre of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, P.O. Box 1177, Sfax 3018, Tunisia; Biotech ECOZYM Start-up, Business Incubator, Centre of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, P.O. Box 1177, Sfax 3018, Tunisia
| | - Amel Bouanane-Darenfed
- Laboratory of Cellular and Molecular Biology (LCMB), Microbiology Team, Faculty of Biological Sciences, University of Sciences and Technology Houari Boumediene (USTHB), P.O. Box 32, El Alia, Bab Ezzouar, 16111, Algiers, Algeria.
| |
Collapse
|
44
|
Contribution of Active Iron Uptake to Acinetobacter baumannii Pathogenicity. Infect Immun 2019; 87:IAI.00755-18. [PMID: 30718286 DOI: 10.1128/iai.00755-18] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 01/25/2019] [Indexed: 11/20/2022] Open
Abstract
Acinetobacter baumannii is an important nosocomial pathogen. Mechanisms that allow A. baumannii to cause human infection are still poorly understood. Iron is an essential nutrient for bacterial growth in vivo, and the multiplicity of iron uptake systems in A. baumannii suggests that iron acquisition contributes to the ability of A. baumannii to cause infection. In Gram-negative bacteria, active transport of ferrisiderophores and heme relies on the conserved TonB-ExbB-ExbD energy-transducing complex, while active uptake of ferrous iron is mediated by the Feo system. The A. baumannii genome invariably contains three tonB genes (tonB1, tonB2, and tonB3), whose role in iron uptake is poorly understood. Here, we generated A. baumannii mutants with knockout mutations in the feo and/or tonB gene. We report that tonB3 is essential for A. baumannii growth under iron-limiting conditions, whereas tonB1, tonB2, and feoB appear to be dispensable for ferric iron uptake. tonB3 deletion resulted in reduced intracellular iron content despite siderophore overproduction, supporting a key role of TonB3 in iron uptake. In contrast to the case for tonB1 and tonB2, the promoters of tonB3 and feo contain functional Fur boxes and are upregulated in iron-poor media. Both TonB3 and Feo systems are required for growth in complement-free human serum and contribute to resistance to the bactericidal activity of normal human serum, but only TonB3 appears to be essential for virulence in insect and mouse models of infection. Our findings highlight a central role of the TonB3 system for A. baumannii pathogenicity. Hence, TonB3 represents a promising target for novel antibacterial therapies and for the generation of attenuated vaccine strains.
Collapse
|
45
|
Transcription in cyanobacteria: a distinctive machinery and putative mechanisms. Biochem Soc Trans 2019; 47:679-689. [DOI: 10.1042/bst20180508] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 01/11/2019] [Accepted: 02/04/2019] [Indexed: 02/03/2023]
Abstract
Abstract
Transcription in cyanobacteria involves several fascinating features. Cyanobacteria comprise one of the very few groups in which no proofreading factors (Gre homologues) have been identified. Gre factors increase the efficiency of RNA cleavage, therefore helping to maintain the fidelity of the RNA transcript and assist in the resolution of stalled RNAPs to prevent genome damage. The vast majority of bacterial species encode at least one of these highly conserved factors and so their absence in cyanobacteria is intriguing. Additionally, the largest subunit of bacterial RNAP has undergone a split in cyanobacteria to form two subunits and the SI3 insertion within the integral trigger loop element is roughly 3.5 times larger than in Escherichia coli. The Rho termination factor also appears to be absent, leaving cyanobacteria to rely solely on an intrinsic termination mechanism. Furthermore, cyanobacteria must be able to respond to environment signals such as light intensity and tightly synchronise gene expression and other cell activities to a circadian rhythm.
Collapse
|
46
|
Expanding the promoter toolbox of Bacillus megaterium. J Biotechnol 2019; 294:38-48. [DOI: 10.1016/j.jbiotec.2019.01.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 01/18/2019] [Accepted: 01/22/2019] [Indexed: 02/02/2023]
|
47
|
Zhao S, Engelhardt BE, Mukherjee S, Dunson DB. Fast Moment Estimation for Generalized Latent Dirichlet Models. J Am Stat Assoc 2018; 113:1528-1540. [DOI: 10.1080/01621459.2017.1341839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Shiwen Zhao
- Department of Statistical Science, Duke University, Durham, NC
| | - Barbara E. Engelhardt
- Department of Computer Science and Center for Statistics and Machine Learning, Princeton University, Princeton, NJ
| | - Sayan Mukherjee
- Department of Statistical Science, Duke University, Durham, NC
| | - David B. Dunson
- Department of Statistical Science, Duke University, Durham, NC
| |
Collapse
|
48
|
Core element characterization of Rhodococcus promoters and development of a promoter-RBS mini-pool with different activity levels for efficient gene expression. N Biotechnol 2018; 44:41-49. [DOI: 10.1016/j.nbt.2018.04.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 04/19/2018] [Accepted: 04/19/2018] [Indexed: 11/15/2022]
|
49
|
Mishra A, Siwach P, Misra P, Jayaram B, Bansal M, Olson WK, Thayer KM, Beveridge DL. Toward a Universal Structural and Energetic Model for Prokaryotic Promoters. Biophys J 2018; 115:1180-1189. [PMID: 30172386 DOI: 10.1016/j.bpj.2018.08.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 07/28/2018] [Accepted: 08/02/2018] [Indexed: 01/04/2023] Open
Abstract
With almost no consensus promoter sequence in prokaryotes, recruitment of RNA polymerase (RNAP) to precise transcriptional start sites (TSSs) has remained an unsolved puzzle. Uncovering the underlying mechanism is critical for understanding the principle of gene regulation. We attempted to search the hidden code in ∼16,500 promoters of 12 prokaryotes representing two kingdoms in their structure and energetics. Twenty-eight fundamental parameters of DNA structure including backbone angles, basepair axis, and interbasepair and intrabasepair parameters were used, and information was extracted from x-ray crystallography data. Three parameters (solvation energy, hydrogen-bond energy, and stacking energy) were selected for creating energetics profiles using in-house programs. DNA of promoter regions was found to be inherently designed to undergo a change in every parameter undertaken for the study, in all prokaryotes. The change starts from some distance upstream of TSSs and continues past some distance from TSS, hence giving a signature state to promoter regions. These signature states might be the universal hidden codes recognized by RNAP. This observation was reiterated when randomly selected promoter sequences (with little sequence conservation) were subjected to structure generation; all developed into very similar three-dimensional structures quite distinct from those of conventional B-DNA and coding sequences. Fine structural details at important motifs (viz. -11, -35, and -75 positions relative to TSS) of promoters reveal novel to our knowledge and pointed insights for RNAP interaction at these locations; it could be correlated with how some particular structural changes at the -11 region may allow insertion of RNAP amino acids in interbasepair space as well as facilitate the flipping out of bases from the DNA duplex.
Collapse
Affiliation(s)
- Akhilesh Mishra
- Supercomputing Facility for Bioinformatics & Computational Biology; Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, India
| | - Priyanka Siwach
- Supercomputing Facility for Bioinformatics & Computational Biology; Department of Biotechnology, Chaudhary Devi Lal University, Sirsa, Haryana, India
| | - Pallavi Misra
- Supercomputing Facility for Bioinformatics & Computational Biology
| | - Bhyravabhotla Jayaram
- Supercomputing Facility for Bioinformatics & Computational Biology; Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, India; Department of Chemistry, Indian Institute of Technology, Delhi, India.
| | - Manju Bansal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
| | - Wilma K Olson
- Department of Chemistry & Chemical Biology and BioMaPS Institute for Quantitative Biology, Rutgers, Piscataway, New Jersey
| | - Kelly M Thayer
- Department of Chemistry, Vassar College, Poughkeepsie, New York
| | - David L Beveridge
- Departments of Chemistry, Molecular Biology, and Biochemistry and Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut
| |
Collapse
|
50
|
Nuonming P, Khemthong S, Dokpikul T, Sukchawalit R, Mongkolsuk S. Characterization and regulation of AcrABR, a RND-type multidrug efflux system, in Agrobacterium tumefaciens C58. Microbiol Res 2018; 214:146-155. [PMID: 30031477 DOI: 10.1016/j.micres.2018.06.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 06/11/2018] [Accepted: 06/30/2018] [Indexed: 10/28/2022]
Abstract
Agrobacterium tumefaciens AcrR is the transcriptional repressor of the acrABR operon. The AcrAB efflux pump confers resistance to various toxic compounds, including antibiotics [ciprofloxacin (CIP), nalidixic acid (NAL), novobiocin (NOV) and tetracycline (TET)], a detergent [sodium dodecyl sulfate (SDS)] and a biocide [triclosan (TRI)]. The sequence to which AcrR specifically binds in the acrA promoter region was determined by EMSA and DNase I footprinting. The AcrR-DNA interaction was abolished by adding NAL, SDS and TRI. Quantitative real time-PCR analysis showed that induction of the acrA transcript occurred when wild-type cells were exposed to NAL, SDS and TRI. Indole is a signaling molecule that increases the antibiotic resistance of bacteria, at least in part, through activation of efflux pumps. Expression of the A. tumefaciens acrA transcript was also inducible by indole in a dose-dependent manner. Indole induced protection against CIP, NAL and SDS but enhanced susceptibility to NOV and TRI. Additionally, the TET resistance of A. tumefaciens was not apparently modulated by indole. A. tumefaciens AcrAB played a dominant role and was required for tolerance to high levels of the toxic compounds. Understanding the regulation of multidrug efflux pumps and bacterial adaptive responses to intracellular and extracellular signaling molecules for antibiotic resistance is essential. This information will be useful for the rational design of effective treatments for bacterial infection to overcome possible multidrug-resistant pathogens.
Collapse
Affiliation(s)
- Puttamas Nuonming
- Applied Biological Sciences, Chulabhorn Graduate Institute, Lak Si, Bangkok 10210, Thailand
| | - Sasimaporn Khemthong
- Applied Biological Sciences, Chulabhorn Graduate Institute, Lak Si, Bangkok 10210, Thailand
| | - Thanittra Dokpikul
- Environmental Toxicology, Chulabhorn Graduate Institute, Lak Si, Bangkok 10210, Thailand
| | - Rojana Sukchawalit
- Applied Biological Sciences, Chulabhorn Graduate Institute, Lak Si, Bangkok 10210, Thailand; Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok 10210, Thailand; Center of Excellence on Environmental Health and Toxicology (EHT), Ministry of Education, Bangkok, Thailand.
| | - Skorn Mongkolsuk
- Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok 10210, Thailand; Center of Excellence on Environmental Health and Toxicology (EHT), Ministry of Education, Bangkok, Thailand; Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| |
Collapse
|