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Chauhan V, Baptista ISC, Arsh AM, Jagadeesan R, Dash S, Ribeiro AS. Transcription Attenuation in Synthetic Promoters in Nonoverlapping Tandem Formation. Biochemistry 2024. [PMID: 38997112 DOI: 10.1021/acs.biochem.4c00012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2024]
Abstract
Closely spaced promoters are ubiquitous in prokaryotic and eukaryotic genomes. How their structure and dynamics relate remains unclear, particularly for tandem formations. To study their transcriptional interference, we engineered two pairs and one trio of synthetic promoters in nonoverlapping, tandem formation, in single-copy plasmids transformed into Escherichia coli cells. From in vivo measurements, we found that these promoters in tandem formation can have attenuated transcription rates. The attenuation strength can be widely fine-tuned by the promoters' positioning, natural regulatory mechanisms, and other factors, including the antibiotic rifampicin, which is known to hamper RNAP promoter escape. From this, and supported by in silico models, we concluded that the attenuation in these constructs emerges from premature terminations generated by collisions between RNAPs elongating from upstream promoters and RNAPs occupying downstream promoters. Moreover, we found that these collisions can cause one or both RNAPs to falloff. Finally, the broad spectrum of possible, externally regulated, attenuation strengths observed in our synthetic tandem promoters suggests that they could become useful as externally controllable regulators of future synthetic circuits.
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Affiliation(s)
- Vatsala Chauhan
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland
- Department of Cell and Molecular Biology (ICM), Uppsala University, 751 24 Uppsala, Sweden
| | - Ines S C Baptista
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland
| | - Amir M Arsh
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland
| | - Rahul Jagadeesan
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland
| | - Suchintak Dash
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland
| | - Andre S Ribeiro
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland
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Dash S, Jagadeesan R, Baptista ISC, Chauhan V, Kandavalli V, Oliveira SMD, Ribeiro AS. A library of reporters of the global regulators of gene expression in Escherichia coli. mSystems 2024; 9:e0006524. [PMID: 38687030 PMCID: PMC11237500 DOI: 10.1128/msystems.00065-24] [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: 01/11/2024] [Accepted: 04/01/2024] [Indexed: 05/02/2024] Open
Abstract
The topology of the transcription factor network (TFN) of Escherichia coli is far from uniform, with 22 global regulator (GR) proteins controlling one-third of all genes. So far, their production rates cannot be tracked by comparable fluorescent proteins. We developed a library of fluorescent reporters for 16 GRs for this purpose. Each consists of a single-copy plasmid coding for green fluorescent protein (GFP) fused to the full-length copy of the native promoter. We tracked their activity in exponential and stationary growth, as well as under weak and strong stresses. We show that the reporters have high sensitivity and specificity to all stresses tested and detect single-cell variability in transcription rates. Given the influence of GRs on the TFN, we expect that the new library will contribute to dissecting global transcriptional stress-response programs of E. coli. Moreover, the library can be invaluable in bioindustrial applications that tune those programs to, instead of cell growth, favor productivity while reducing energy consumption.IMPORTANCECells contain thousands of genes. Many genes are involved in the control of cellular activities. Some activities require a few hundred genes to run largely synchronous transcriptional programs. To achieve this, cells have evolved global regulator (GR) proteins that can influence hundreds of genes simultaneously. We have engineered a library of Escherichia coli strains to track the levels over time of these, phenotypically critical, GRs. Each strain has a single-copy plasmid coding for a fast-maturing green fluorescent protein whose transcription is controlled by a copy of the natural GR promoter. By allowing the tracking of GR levels, with sensitivity and specificity, this library should become of wide use in scientific research on bacterial gene expression (from molecular to synthetic biology) and, later, be used in applications in therapeutics and bioindustries.
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Affiliation(s)
- Suchintak Dash
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Rahul Jagadeesan
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Ines S. C. Baptista
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Vatsala Chauhan
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Vinodh Kandavalli
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Samuel M. D. Oliveira
- Joint School of Nanoscience and Nanoengineering, North Carolina A&T State University, Greensboro, North Carolina, USA
| | - Andre S. Ribeiro
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
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Feng H, Li F, Wang T, Xing XH, Zeng AP, Zhang C. Deep-learning-assisted Sort-Seq enables high-throughput profiling of gene expression characteristics with high precision. SCIENCE ADVANCES 2023; 9:eadg5296. [PMID: 37939173 PMCID: PMC10631719 DOI: 10.1126/sciadv.adg5296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 10/06/2023] [Indexed: 11/10/2023]
Abstract
Owing to the nondeterministic and nonlinear nature of gene expression, the steady-state intracellular protein abundance of a clonal population forms a distribution. The characteristics of this distribution, including expression strength and noise, are closely related to cellular behavior. However, quantitative description of these characteristics has so far relied on arrayed methods, which are time-consuming and labor-intensive. To address this issue, we propose a deep-learning-assisted Sort-Seq approach (dSort-Seq) in this work, enabling high-throughput profiling of expression properties with high precision. We demonstrated the validity of dSort-Seq for large-scale assaying of the dose-response relationships of biosensors. In addition, we comprehensively investigated the contribution of transcription and translation to noise production in Escherichia coli, from which we found that the expression noise is strongly coupled with the mean expression level. We also found that the transcriptional interference caused by overlapping RpoD-binding sites contributes to noise production, which suggested the existence of a simple and feasible noise control strategy in E. coli.
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Affiliation(s)
- Huibao Feng
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Fan Li
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Tianmin Wang
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xin-hui Xing
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
- Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - An-ping Zeng
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Hamburg 21073, Germany
- Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, Hangzhou 310024, China
| | - Chong Zhang
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
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Su C, Gong JS, Wu ZX, Liu YL, Li H, Shi JS, Xu ZH. Development of a Growth-Dependent System to Regulate Cell Growth and Keratinase Production in B. subtilis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:2421-2429. [PMID: 36629862 DOI: 10.1021/acs.jafc.2c07624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Keratinases specifically degrade insoluble keratin waste, thus contributing to environmental protection and sustainable biomass development. However, their industrial application is hindered by inefficient enzyme production and poor biomass generation. In this study, the heterologous expression of keratinase was found to have cytotoxicity and might block host cell growth due to its proteolytic property. To address this problem, an autoregulatory expression system based on quorum sensing was developed to synergistically regulate cell growth and keratinase production in Bacillus subtilis. The growth-dependent promoter PaprE was chosen and shown to be effective in delaying keratinase production while promoting host cell proliferation. Copy number screening and core region mutations further balanced the two states. Carbon supplement optimization indicated that addition of 2% glucose facilitated biomass accumulation during the early stage of fermentation. Cell density increased to 15.6 (OD600 nm) from 8 with keratinase activity raised to 4200 U·mL-1 from 1162 U·mL-1. Keratinase was then utilized in the bioconversion of feather waste to prepare soluble keratins, polypeptides, and amino acids. This study provides a powerful system for efficient production of keratinase and paves the way for keratin waste recycling.
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Affiliation(s)
- Chang Su
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Jin-Song Gong
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Ze-Xi Wu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Yan-Ling Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Heng Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Jin-Song Shi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Zheng-Hong Xu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
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Dash S, Palma CSD, Baptista ISC, Almeida BLB, Bahrudeen MNM, Chauhan V, Jagadeesan R, Ribeiro AS. Alteration of DNA supercoiling serves as a trigger of short-term cold shock repressed genes of E. coli. Nucleic Acids Res 2022; 50:8512-8528. [PMID: 35920318 PMCID: PMC9410904 DOI: 10.1093/nar/gkac643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 07/07/2022] [Accepted: 07/20/2022] [Indexed: 11/14/2022] Open
Abstract
Cold shock adaptability is a key survival skill of gut bacteria of warm-blooded animals. Escherichia coli cold shock responses are controlled by a complex multi-gene, timely-ordered transcriptional program. We investigated its underlying mechanisms. Having identified short-term, cold shock repressed genes, we show that their responsiveness is unrelated to their transcription factors or global regulators, while their single-cell protein numbers' variability increases after cold shock. We hypothesized that some cold shock repressed genes could be triggered by high propensity for transcription locking due to changes in DNA supercoiling (likely due to DNA relaxation caused by an overall reduction in negative supercoiling). Concomitantly, we found that nearly half of cold shock repressed genes are also highly responsive to gyrase inhibition (albeit most genes responsive to gyrase inhibition are not cold shock responsive). Further, their response strengths to cold shock and gyrase inhibition correlate. Meanwhile, under cold shock, nucleoid density increases, and gyrases and nucleoid become more colocalized. Moreover, the cellular energy decreases, which may hinder positive supercoils resolution. Overall, we conclude that sensitivity to diminished negative supercoiling is a core feature of E. coli's short-term, cold shock transcriptional program, and could be used to regulate the temperature sensitivity of synthetic circuits.
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Affiliation(s)
- Suchintak Dash
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Cristina S D Palma
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Ines S C Baptista
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Bilena L B Almeida
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Mohamed N M Bahrudeen
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Vatsala Chauhan
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Rahul Jagadeesan
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Andre S Ribeiro
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland.,Center of Technology and Systems (CTS-Uninova), NOVA University of Lisbon 2829-516, Monte de Caparica, Portugal
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L.B. Almeida B, M. Bahrudeen MN, Chauhan V, Dash S, Kandavalli V, Häkkinen A, Lloyd-Price J, S.D. Cristina P, Baptista ISC, Gupta A, Kesseli J, Dufour E, Smolander OP, Nykter M, Auvinen P, Jacobs HT, M.D. Oliveira S, S. Ribeiro A. The transcription factor network of E. coli steers global responses to shifts in RNAP concentration. Nucleic Acids Res 2022; 50:6801-6819. [PMID: 35748858 PMCID: PMC9262627 DOI: 10.1093/nar/gkac540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/02/2022] [Accepted: 06/14/2022] [Indexed: 12/24/2022] Open
Abstract
The robustness and sensitivity of gene networks to environmental changes is critical for cell survival. How gene networks produce specific, chronologically ordered responses to genome-wide perturbations, while robustly maintaining homeostasis, remains an open question. We analysed if short- and mid-term genome-wide responses to shifts in RNA polymerase (RNAP) concentration are influenced by the known topology and logic of the transcription factor network (TFN) of Escherichia coli. We found that, at the gene cohort level, the magnitude of the single-gene, mid-term transcriptional responses to changes in RNAP concentration can be explained by the absolute difference between the gene's numbers of activating and repressing input transcription factors (TFs). Interestingly, this difference is strongly positively correlated with the number of input TFs of the gene. Meanwhile, short-term responses showed only weak influence from the TFN. Our results suggest that the global topological traits of the TFN of E. coli shape which gene cohorts respond to genome-wide stresses.
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Affiliation(s)
- Bilena L.B. Almeida
- Correspondence may also be addressed to Bilena L.B. Almeida. Tel: +358 2945211;
| | | | | | | | - Vinodh Kandavalli
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Antti Häkkinen
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, FI-00014 Helsinki, Finland
| | | | - Palma S.D. Cristina
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Ines S C Baptista
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Abhishekh Gupta
- Center for Quantitative Medicine and Department of Cell Biology, University of Connecticut School of Medicine, 263 Farmington Av., Farmington, CT 06030-6033, USA
| | - Juha Kesseli
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Eric Dufour
- Mitochondrial bioenergetics and metabolism, BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Olli-Pekka Smolander
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
- Institute of Biotechnology, University of Helsinki, Viikinkaari 5D, 00790 Helsinki, Finland
| | - Matti Nykter
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Petri Auvinen
- Institute of Biotechnology, University of Helsinki, Viikinkaari 5D, 00790 Helsinki, Finland
| | - Howard T Jacobs
- Faculty of Medicine and Health Technology, FI-33014 Tampere University, Finland; Department of Environment and Genetics, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Samuel M.D. Oliveira
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
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Chauhan V, Bahrudeen MNM, Palma CSD, Baptista ISC, Almeida BLB, Dash S, Kandavalli V, Ribeiro AS. Analytical kinetic model of native tandem promoters in E. coli. PLoS Comput Biol 2022; 18:e1009824. [PMID: 35100257 PMCID: PMC8830795 DOI: 10.1371/journal.pcbi.1009824] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 02/10/2022] [Accepted: 01/11/2022] [Indexed: 02/04/2023] Open
Abstract
Closely spaced promoters in tandem formation are abundant in bacteria. We investigated the evolutionary conservation, biological functions, and the RNA and single-cell protein expression of genes regulated by tandem promoters in E. coli. We also studied the sequence (distance between transcription start sites ‘dTSS’, pause sequences, and distances from oriC) and potential influence of the input transcription factors of these promoters. From this, we propose an analytical model of gene expression based on measured expression dynamics, where RNAP-promoter occupancy times and dTSS are the key regulators of transcription interference due to TSS occlusion by RNAP at one of the promoters (when dTSS ≤ 35 bp) and RNAP occupancy of the downstream promoter (when dTSS > 35 bp). Occlusion and downstream promoter occupancy are modeled as linear functions of occupancy time, while the influence of dTSS is implemented by a continuous step function, fit to in vivo data on mean single-cell protein numbers of 30 natural genes controlled by tandem promoters. The best-fitting step is at 35 bp, matching the length of DNA occupied by RNAP in the open complex formation. This model accurately predicts the squared coefficient of variation and skewness of the natural single-cell protein numbers as a function of dTSS. Additional predictions suggest that promoters in tandem formation can cover a wide range of transcription dynamics within realistic intervals of parameter values. By accurately capturing the dynamics of these promoters, this model can be helpful to predict the dynamics of new promoters and contribute to the expansion of the repertoire of expression dynamics available to synthetic genetic constructs. Tandem promoters are common in nature, but investigations on their dynamics have so far largely relied on synthetic constructs. Thus, their regulation and potentially unique dynamics remain unexplored. We first performed a comprehensive exploration of the conservation of genes regulated by these promoters in E. coli and the properties of their input transcription factors. We then measured protein and RNA levels expressed by 30 Escherichia coli tandem promoters, to establish an analytical model of the expression dynamics of genes controlled by such promoters. We show that start site occlusion and downstream RNAP occupancy can be realistically captured by a model with RNAP binding affinity, the time length of open complex formation, and the nucleotide distance between transcription start sites. This study contributes to a better understanding of the unique dynamics tandem promoters can bring to the dynamics of gene networks and will assist in their use in synthetic genetic circuits.
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Affiliation(s)
- Vatsala Chauhan
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Finland
| | - Mohamed N. M. Bahrudeen
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Finland
| | - Cristina S. D. Palma
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Finland
| | - Ines S. C. Baptista
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Finland
| | - Bilena L. B. Almeida
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Finland
| | - Suchintak Dash
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Finland
| | - Vinodh Kandavalli
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Andre S. Ribeiro
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Finland
- * E-mail:
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