1
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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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2
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Jiao F, Li J, Liu T, Zhu Y, Che W, Bleris L, Jia C. What can we learn when fitting a simple telegraph model to a complex gene expression model? PLoS Comput Biol 2024; 20:e1012118. [PMID: 38743803 PMCID: PMC11125521 DOI: 10.1371/journal.pcbi.1012118] [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: 02/06/2024] [Revised: 05/24/2024] [Accepted: 04/27/2024] [Indexed: 05/16/2024] Open
Abstract
In experiments, the distributions of mRNA or protein numbers in single cells are often fitted to the random telegraph model which includes synthesis and decay of mRNA or protein, and switching of the gene between active and inactive states. While commonly used, this model does not describe how fluctuations are influenced by crucial biological mechanisms such as feedback regulation, non-exponential gene inactivation durations, and multiple gene activation pathways. Here we investigate the dynamical properties of four relatively complex gene expression models by fitting their steady-state mRNA or protein number distributions to the simple telegraph model. We show that despite the underlying complex biological mechanisms, the telegraph model with three effective parameters can accurately capture the steady-state gene product distributions, as well as the conditional distributions in the active gene state, of the complex models. Some effective parameters are reliable and can reflect realistic dynamic behaviors of the complex models, while others may deviate significantly from their real values in the complex models. The effective parameters can also be applied to characterize the capability for a complex model to exhibit multimodality. Using additional information such as single-cell data at multiple time points, we provide an effective method of distinguishing the complex models from the telegraph model. Furthermore, using measurements under varying experimental conditions, we show that fitting the mRNA or protein number distributions to the telegraph model may even reveal the underlying gene regulation mechanisms of the complex models. The effectiveness of these methods is confirmed by analysis of single-cell data for E. coli and mammalian cells. All these results are robust with respect to cooperative transcriptional regulation and extrinsic noise. In particular, we find that faster relaxation speed to the steady state results in more precise parameter inference under large extrinsic noise.
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Affiliation(s)
- Feng Jiao
- Guangzhou Center for Applied Mathematics, Guangzhou University, Guangzhou, China
| | - Jing Li
- Guangzhou Center for Applied Mathematics, Guangzhou University, Guangzhou, China
| | - Ting Liu
- Guangzhou Center for Applied Mathematics, Guangzhou University, Guangzhou, China
| | - Yifeng Zhu
- Guangzhou Center for Applied Mathematics, Guangzhou University, Guangzhou, China
| | - Wenhao Che
- Guangzhou Center for Applied Mathematics, Guangzhou University, Guangzhou, China
| | - Leonidas Bleris
- Bioengineering Department, The University of Texas at Dallas, Richardson, Texas, United States of America
- Center for Systems Biology, The University of Texas at Dallas, Richardson, Texas, United States of America
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, United States of America
| | - Chen Jia
- Applied and Computational Mathematics Division, Beijing Computational Science Research Center, Beijing, China
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3
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Lopez MLD, Lin YY, Schneider SQ, Hsieh CH, Shiah FK, Machida RJ. Allometric scaling of interspecific RNA transcript abundance to extend the use of metatranscriptomics in characterizing complex communities. Mol Ecol Resour 2022; 23:52-63. [PMID: 36062315 PMCID: PMC10087904 DOI: 10.1111/1755-0998.13711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 08/17/2022] [Accepted: 08/30/2022] [Indexed: 11/27/2022]
Abstract
Metatranscriptomics allows profiling of community messenger RNA (mRNA) and ribosomal RNA (rRNA) transcript abundance under certain environmental conditions. However, variations in the proportion of RNA transcripts across different community size structures remain less explained, thus limiting the possible applications of metatranscriptomics in community studies. Here, we extended the assumptions of the growth-rate hypothesis (GRH) and the metabolic theory of ecology (MTE) to validate the allometric scaling of interspecific RNA transcript (mRNA and rRNA) abundance through metatranscriptomic analysis of mock communities consisting of model organisms. Results suggest that body size imposes significant constraints on RNA transcript abundance. Interestingly, the relationship between the total mitochondrial transcript abundance (mRNA and rRNA slopes were -0.30 and -0.28, respectively) and body size aligned with the MTE assumptions with slopes close to -¼, while the nuclear transcripts displayed much steeper slopes (mRNA and rRNA slopes were -0.33 and -0.40, respectively). The assumed temperature dependence was not observed in this study. At the gene level, the allometric slopes range from 0 to -1. Overall, the above results showed that larger individuals have lesser RNA transcript abundance per tissue mass than smaller ones regardless of temperature. Analyses of field-collected microcrustacean zooplankton samples demonstrated that the correction of size effect, using the allometric exponents derived from the model organism mock community, explains better the patterns of interspecific RNA transcripts abundance within the metatranscriptome. Integrating allometry with metatranscriptomics can extend the use of RNA transcript reads in estimating ecological processes within complex communities.
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Affiliation(s)
- Mark Louie D Lopez
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan.,Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Ya-Ying Lin
- Biodiversity Research Center, Academia Sinica, Nankang District, Taipei, Taiwan
| | - Stephan Q Schneider
- Institute of Organismic and Cellular Biology, Academia Sinica, Nankang District, Taipei, Taiwan
| | - Chih-Hao Hsieh
- Institute of Oceanography, National Taiwan University, Da'an District, Taipei, Taiwan.,Environmental Change Research Center, Academia Sinica, Nankang District, Taipei, Taiwan
| | - Fuh-Kwo Shiah
- Environmental Change Research Center, Academia Sinica, Nankang District, Taipei, Taiwan
| | - Ryuji J Machida
- Biodiversity Research Center, Academia Sinica, Nankang District, Taipei, Taiwan
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4
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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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5
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de Gunst M, Mandjes M, Sollie B. Statistical inference for a quasi birth–death model of RNA transcription. BMC Bioinformatics 2022; 23:105. [PMID: 35346020 PMCID: PMC8961911 DOI: 10.1186/s12859-022-04638-6] [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: 09/28/2021] [Accepted: 03/11/2022] [Indexed: 11/25/2022] Open
Abstract
Background A birth–death process of which the births follow a hypoexponential distribution with L phases and are controlled by an on/off mechanism, is a population process which we call the on/off-seq-L process. It is a suitable model for the dynamics of a population of RNA molecules in a single living cell. Motivated by this biological application, our aim is to develop a statistical method to estimate the model parameters of the on/off-seq-L process, based on observations of the population size at discrete time points, and to apply this method to real RNA data. Methods It is shown that the on/off-seq-L process can be seen as a quasi birth–death process, and an Erlangization technique can be used to approximate the corresponding likelihood function. An extensive simulation-based numerical study is carried out to investigate the performance of the resulting estimation method. Results and conclusion A statistical method is presented to find maximum likelihood estimates of the model parameters for the on/off-seq-L process. Numerical complications related to the likelihood maximization are identified and analyzed, and solutions are presented. The proposed estimation method is a highly accurate method to find the parameter estimates. Based on real RNA data, the on/off-seq-3 process emerges as the best model to describe RNA transcription.
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6
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Jones TS, Oliveira SMD, Myers CJ, Voigt CA, Densmore D. Genetic circuit design automation with Cello 2.0. Nat Protoc 2022; 17:1097-1113. [PMID: 35197606 DOI: 10.1038/s41596-021-00675-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 11/29/2021] [Indexed: 11/09/2022]
Abstract
Cells interact with their environment, communicate among themselves, track time and make decisions through functions controlled by natural regulatory genetic circuits consisting of interacting biological components. Synthetic programmable circuits used in therapeutics and other applications can be automatically designed by computer-aided tools. The Cello software designs the DNA sequences for programmable circuits based on a high-level software description and a library of characterized DNA parts representing Boolean logic gates. This process allows for design specification reuse, modular DNA part library curation and formalized circuit transformations based on experimental data. This protocol describes Cello 2.0, a freely available cross-platform software written in Java. Cello 2.0 enables flexible descriptions of the logic gates' structure and their mathematical models representing dynamic behavior, new formal rules for describing the placement of gates in a genome, a new graphical user interface, support for Verilog 2005 syntax and a connection to the SynBioHub parts repository software environment. Collectively, these features expand Cello's capabilities beyond Escherichia coli plasmids to new organisms and broader genetic contexts, including the genome. Designing circuits with Cello 2.0 produces an abstract Boolean network from a Verilog file, assigns biological parts to each node in the Boolean network, constructs a DNA sequence and generates highly structured and annotated sequence representations suitable for downstream processing and fabrication, respectively. The result is a sequence implementing the specified Boolean function in the organism and predictions of circuit performance. Depending on the size of the design space and users' expertise, jobs may take minutes or hours to complete.
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Affiliation(s)
- Timothy S Jones
- Biological Design Center, Boston University, Boston, MA, USA.,Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
| | - Samuel M D Oliveira
- Biological Design Center, Boston University, Boston, MA, USA.,Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
| | - Chris J Myers
- Electrical, Computer & Energy Engineering, University of Colorado Boulder, Boulder, CO, USA
| | - Christopher A Voigt
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Douglas Densmore
- Biological Design Center, Boston University, Boston, MA, USA. .,Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA.
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7
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Chen L, Lin G, Jiao F. Using average transcription level to understand the regulation of stochastic gene activation. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211757. [PMID: 35223065 PMCID: PMC8847896 DOI: 10.1098/rsos.211757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/24/2022] [Indexed: 05/03/2023]
Abstract
Gene activation is a random process, modelled as a framework of multiple rate-limiting steps listed sequentially, in parallel or in combination. Together with suitably assumed processes of gene inactivation, transcript birth and death, the step numbers and parameters in activation frameworks can be estimated by fitting single-cell transcription data. However, current algorithms require computing master equations that are tightly correlated with prior hypothetical frameworks of gene activation. We found that prior estimation of the framework can be facilitated by the traditional dynamical data of mRNA average level M(t), presenting discriminated dynamical features. Rigorous theory regarding M(t) profiles allows to confidently rule out the frameworks that fail to capture M(t) features and to test potential competent frameworks by fitting M(t) data. We implemented this procedure for a large number of mouse fibroblast genes under tumour necrosis factor induction and determined exactly the 'cross-talking n-state' framework; the cross-talk between the signalling and basal pathways is crucial to trigger the first peak of M(t), while the following damped gentle M(t) oscillation is regulated by the multi-step basal pathway. This framework can be used to fit sophisticated single-cell data and may facilitate a more accurate understanding of stochastic activation of mouse fibroblast genes.
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Affiliation(s)
- Liang Chen
- Guangzhou Center for Applied Mathematics, Guangzhou University, Guangzhou, People’s Republic of China
- School of Mathematics and Information Sciences, Guangzhou University, Guangzhou, People’s Republic of China
| | - Genghong Lin
- Guangzhou Center for Applied Mathematics, Guangzhou University, Guangzhou, People’s Republic of China
- School of Mathematics and Information Sciences, Guangzhou University, Guangzhou, People’s Republic of China
| | - Feng Jiao
- Guangzhou Center for Applied Mathematics, Guangzhou University, Guangzhou, People’s Republic of China
- School of Mathematics and Information Sciences, Guangzhou University, Guangzhou, People’s Republic of China
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8
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Chen L, Zhu C, Jiao F. A generalized moment-based method for estimating parameters of stochastic gene transcription. Math Biosci 2022; 345:108780. [DOI: 10.1016/j.mbs.2022.108780] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/27/2021] [Accepted: 01/13/2022] [Indexed: 12/22/2022]
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9
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Thangaraj S, Giordano M, Sun J. Comparative Proteomic Analysis Reveals New Insights Into the Common and Specific Metabolic Regulation of the Diatom Skeletonema dohrnii to the Silicate and Temperature Availability. FRONTIERS IN PLANT SCIENCE 2020; 11:578915. [PMID: 33224167 PMCID: PMC7674209 DOI: 10.3389/fpls.2020.578915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/28/2020] [Indexed: 05/12/2023]
Abstract
Silicate (Si) and temperature are essential drivers for diatom growth and development in the ocean. Response of diatoms to these particular stress has been investigated; however, their common and specific responses to regulate intracellular development and growth are not known. Here, we investigated the combination of physiological characteristics and comparative proteomics of the diatom Skeletonema dohrnii grown in silicate- and temperature-limited conditions. Results show that cell carbon and lipid quotas were higher at lower-temperature cells, whereas cellular phosphate was higher in cells grown with lower Si. In silicate-limited cells, nitrate transporters were downregulated and resulted in lower nitrate assimilation, whereas the phosphate transporters and its assimilation were reduced in lower-temperature conditions. In photosynthesis, lower silicate caused impact in the linear electron flow and NADPH production, whereas cycling electron transport and ATP production were affected by the lower temperature. Concerning cell cycle, imbalances in the translation process were observed in lower-silicate cells, whereas impact in the transcription mechanism was observed in lower-temperature cells. However, proteins associated with carbon fixation and photorespiration were downregulated in both stress conditions, while the carbohydrate and lipid synthesis proteins were upregulated. Our results showed new insights into the common and specific responses on the proteome and physiology of S. dohrnii to silicate and temperature limitation, providing particular nutrient (Si)- and temperature-dependent mechanisms in diatoms.
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Affiliation(s)
- Satheeswaran Thangaraj
- College of Marine Science and Technology, China University of Geosciences (Wuhan), Wuhan, China
| | - Mario Giordano
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Jun Sun
- College of Marine Science and Technology, China University of Geosciences (Wuhan), Wuhan, China
- *Correspondence: Jun Sun,
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10
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Häkkinen A, Oliveira SMD, Neeli-Venkata R, Ribeiro AS. Transcription closed and open complex formation coordinate expression of genes with a shared promoter region. J R Soc Interface 2019; 16:20190507. [PMID: 31822223 DOI: 10.1098/rsif.2019.0507] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Many genes are spaced closely, allowing coordination without explicit control through shared regulatory elements and molecular interactions. We study the dynamics of a stochastic model of a gene-pair in a head-to-head configuration, sharing promoter elements, which accounts for the rate-limiting steps in transcription initiation. We find that only in specific regions of the parameter space of the rate-limiting steps is orderly coexpression exhibited, suggesting that successful cooperation between closely spaced genes requires the coevolution of compatible rate-limiting step configuration. The model predictions are validated using in vivo single-cell, single-RNA measurements of the dynamics of pairs of genes sharing promoter elements. Our results suggest that, in E. coli, the kinetics of the rate-limiting steps in active transcription can play a central role in shaping the dynamics of gene-pairs sharing promoter elements.
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Affiliation(s)
- Antti Häkkinen
- BioMediTech Institute and Department of Signal Processing, Tampere University of Technology, PO Box 553 33101, Tampere, Finland
| | - Samuel M D Oliveira
- BioMediTech Institute and Department of Signal Processing, Tampere University of Technology, PO Box 553 33101, Tampere, Finland
| | - Ramakanth Neeli-Venkata
- BioMediTech Institute and Department of Signal Processing, Tampere University of Technology, PO Box 553 33101, Tampere, Finland
| | - Andre S Ribeiro
- BioMediTech Institute and Department of Signal Processing, Tampere University of Technology, PO Box 553 33101, Tampere, Finland
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11
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Estimating RNA numbers in single cells by RNA fluorescent tagging and flow cytometry. J Microbiol Methods 2019; 166:105745. [PMID: 31654657 DOI: 10.1016/j.mimet.2019.105745] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 10/11/2019] [Accepted: 10/15/2019] [Indexed: 12/13/2022]
Abstract
Estimating the statistics of single-cell RNA numbers has become a key source of information on gene expression dynamics. One of the most informative methods of in vivo single-RNA detection is MS2d-GFP tagging. So far, it requires microscopy and laborious semi-manual image analysis, which hampers the amount of collectable data. To overcome this limitation, we present a new methodology for quantifying the mean, standard deviation, and skewness of single-cell distributions of RNA numbers, from flow cytometry data on cells expressing RNA tagged with MS2d-GFP. The quantification method, based on scaling flow-cytometry data from microscopy single-cell data on integer-valued RNA numbers, is shown to readily produce precise, big data on in vivo single-cell distributions of RNA numbers and, thus, can assist in studies of transcription dynamics.
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12
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Munshi S, Gopi S, Subramanian S, Campos LA, Naganathan AN. Protein plasticity driven by disorder and collapse governs the heterogeneous binding of CytR to DNA. Nucleic Acids Res 2019. [PMID: 29538715 PMCID: PMC5934615 DOI: 10.1093/nar/gky176] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The amplitude of thermodynamic fluctuations in biological macromolecules determines their conformational behavior, dimensions, nature of phase transitions and effectively their specificity and affinity, thus contributing to fine-tuned molecular recognition. Unique among large-scale conformational changes in proteins are temperature-induced collapse transitions in intrinsically disordered proteins (IDPs). Here, we show that CytR DNA-binding domain, an IDP that folds on binding DNA, undergoes a coil-to-globule transition with temperature in the absence of DNA while exhibiting energetically decoupled local and global structural rearrangements, and maximal thermodynamic fluctuations at the optimal bacterial growth temperature. The collapse is shown to be a continuous transition through a combination of statistical-mechanical modeling and all-atom implicit solvent simulations. Surprisingly, CytR binds single-site cognate DNA with negative cooperativity, described by Hill coefficients less than one, resulting in a graded binding response. We show that heterogeneity arising from varying binding-competent CytR conformations or orientations at the single-molecular level contributes to negative binding cooperativity at the level of bulk measurements due to the conflicting requirements of collapse transition, large fluctuations and folding-upon-binding. Our work reports strong evidence for functionally driven thermodynamic fluctuations in determining the extent of collapse and disorder with implications in protein search efficiency of target DNA sites and regulation.
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Affiliation(s)
- Sneha Munshi
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Soundhararajan Gopi
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Sandhyaa Subramanian
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Luis A Campos
- National Biotechnology Center, Consejo Superior de Investigaciones Científicas, Darwin 3, Campus de Cantoblanco, 28049 Madrid, Spain
| | - Athi N Naganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
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13
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Tremblay J, Fortin N, Elias M, Wasserscheid J, King TL, Lee K, Greer CW. Metagenomic and metatranscriptomic responses of natural oil degrading bacteria in the presence of dispersants. Environ Microbiol 2019; 21:2307-2319. [PMID: 30927379 DOI: 10.1111/1462-2920.14609] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 03/21/2019] [Accepted: 03/24/2019] [Indexed: 01/02/2023]
Abstract
Oil biodegradation has been extensively studied in the wake of the deepwater horizon spill, but the application of dispersant to oil spills in marine environments remains controversial. Here, we report metagenomic (MG) and metatranscriptomic (MT) data mining from microcosm experiments investigating the oil degrading potential of Canadian west and east coasts to estimate the gene abundance and activity of oil degrading bacteria in the presence of dispersant. We found that the addition of dispersant to crude oil mainly favours the abundance of Thalassolituus in the summer and Oleispira in the winter, two key natural oil degrading bacteria. We found a high abundance of genes related not only to n-alkane and aromatics degradation but also associated with transporters, two-component systems, bacterial motility, secretion systems and bacterial chemotaxis.
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Affiliation(s)
- Julien Tremblay
- Energy, Mining and Environment, National Research Council Canada, 6100 Royalmount Avenue, Montreal, Quebec, H4P2R2, Canada
| | - Nathalie Fortin
- Energy, Mining and Environment, National Research Council Canada, 6100 Royalmount Avenue, Montreal, Quebec, H4P2R2, Canada
| | - Miria Elias
- Energy, Mining and Environment, National Research Council Canada, 6100 Royalmount Avenue, Montreal, Quebec, H4P2R2, Canada
| | - Jessica Wasserscheid
- Energy, Mining and Environment, National Research Council Canada, 6100 Royalmount Avenue, Montreal, Quebec, H4P2R2, Canada
| | - Thomas L King
- Centre for Offshore Oil, Gas and Energy Research (COOGER), Fisheries and Oceans Canada, Dartmouth, Nova Scotia, B2Y4A2, Canada
| | - Kenneth Lee
- Fisheries and Oceans Canada, Bedford Institute of Oceanography, PO Box 1006, Dartmouth, Nova Scotia, B2Y4A2, Canada
| | - Charles W Greer
- Energy, Mining and Environment, National Research Council Canada, 6100 Royalmount Avenue, Montreal, Quebec, H4P2R2, Canada
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14
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Millius A, Ode KL, Ueda HR. A period without PER: understanding 24-hour rhythms without classic transcription and translation feedback loops. F1000Res 2019; 8. [PMID: 31031966 PMCID: PMC6468715 DOI: 10.12688/f1000research.18158.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/09/2019] [Indexed: 01/08/2023] Open
Abstract
Since Ronald Konopka and Seymour Benzer's discovery of the gene Period in the 1970s, the circadian rhythm field has diligently investigated regulatory mechanisms and intracellular transcriptional and translation feedback loops involving Period, and these investigations culminated in a 2017 Nobel Prize in Physiology or Medicine for Michael W. Young, Michael Rosbash, and Jeffrey C. Hall. Although research on 24-hour behavior rhythms started with Period, a series of discoveries in the past decade have shown us that post-transcriptional regulation and protein modification, such as phosphorylation and oxidation, are alternatives ways to building a ticking clock.
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Affiliation(s)
- Arthur Millius
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Laboratory of Systems Immunology and Laboratory of Host Defense, Immunology Frontier Research Center, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Koji L Ode
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hiroki R Ueda
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
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15
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Oliveira SMD, Goncalves NSM, Kandavalli VK, Martins L, Neeli-Venkata R, Reyelt J, Fonseca JM, Lloyd-Price J, Kranz H, Ribeiro AS. Chromosome and plasmid-borne P LacO3O1 promoters differ in sensitivity to critically low temperatures. Sci Rep 2019; 9:4486. [PMID: 30872616 PMCID: PMC6418193 DOI: 10.1038/s41598-019-39618-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 01/28/2019] [Indexed: 12/31/2022] Open
Abstract
Temperature shifts trigger genome-wide changes in Escherichia coli's gene expression. We studied if chromosome integration impacts on a gene's sensitivity to these shifts, by comparing the single-RNA production kinetics of a PLacO3O1 promoter, when chromosomally-integrated and when single-copy plasmid-borne. At suboptimal temperatures their induction range, fold change, and response to decreasing temperatures are similar. At critically low temperatures, the chromosome-integrated promoter becomes weaker and noisier. Dissection of its initiation kinetics reveals longer lasting states preceding open complex formation, suggesting enhanced supercoiling buildup. Measurements with Gyrase and Topoisomerase I inhibitors suggest hindrance to escape supercoiling buildup at low temperatures. Consistently, similar phenomena occur in energy-depleted cells by DNP at 30 °C. Transient, critically-low temperatures have no long-term consequences, as raising temperature quickly restores transcription rates. We conclude that the chromosomally-integrated PLacO3O1 has higher sensitivity to low temperatures, due to longer-lasting super-coiled states. A lesser active, chromosome-integrated native lac is shown to be insensitive to Gyrase overexpression, even at critically low temperatures, indicating that the rate of escaping positive supercoiling buildup is temperature and transcription rate dependent. A genome-wide analysis supports this, since cold-shock genes exhibit atypical supercoiling-sensitivities. This phenomenon might partially explain the temperature-sensitivity of some transcriptional programs of E. coli.
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Affiliation(s)
- Samuel M D Oliveira
- Laboratory of Biosystem Dynamics and Multi-Scaled Biodata Analysis and Modelling Research Community, Faculty of Medicine and Health Technology, Tampere University, Korkeakoulunkatu 7, 33720, Tampere, Finland
| | - Nadia S M Goncalves
- Laboratory of Biosystem Dynamics and Multi-Scaled Biodata Analysis and Modelling Research Community, Faculty of Medicine and Health Technology, Tampere University, Korkeakoulunkatu 7, 33720, Tampere, Finland
| | - Vinodh K Kandavalli
- Laboratory of Biosystem Dynamics and Multi-Scaled Biodata Analysis and Modelling Research Community, Faculty of Medicine and Health Technology, Tampere University, Korkeakoulunkatu 7, 33720, Tampere, Finland
| | - Leonardo Martins
- Laboratory of Biosystem Dynamics and Multi-Scaled Biodata Analysis and Modelling Research Community, Faculty of Medicine and Health Technology, Tampere University, Korkeakoulunkatu 7, 33720, Tampere, Finland
- CA3 CTS/UNINOVA. Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, 2829-516, Caparica, Portugal
| | - Ramakanth Neeli-Venkata
- Laboratory of Biosystem Dynamics and Multi-Scaled Biodata Analysis and Modelling Research Community, Faculty of Medicine and Health Technology, Tampere University, Korkeakoulunkatu 7, 33720, Tampere, Finland
| | - Jan Reyelt
- Gene Bridges, Im Neuenheimer Feld 584, 69120, Heidelberg, Germany
| | - Jose M Fonseca
- CA3 CTS/UNINOVA. Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, 2829-516, Caparica, Portugal
| | - Jason Lloyd-Price
- Biostatistics Department, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA, 02142, USA
| | - Harald Kranz
- Gene Bridges, Im Neuenheimer Feld 584, 69120, Heidelberg, Germany
| | - Andre S Ribeiro
- Laboratory of Biosystem Dynamics and Multi-Scaled Biodata Analysis and Modelling Research Community, Faculty of Medicine and Health Technology, Tampere University, Korkeakoulunkatu 7, 33720, Tampere, Finland.
- CA3 CTS/UNINOVA. Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, 2829-516, Caparica, Portugal.
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16
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Startceva S, Kandavalli VK, Visa A, Ribeiro AS. Regulation of asymmetries in the kinetics and protein numbers of bacterial gene expression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:119-128. [DOI: 10.1016/j.bbagrm.2018.12.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 12/04/2018] [Accepted: 12/05/2018] [Indexed: 01/21/2023]
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17
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Prajapat MK, Ribeiro AS. Added value of autoregulation and multi-step kinetics of transcription initiation. ROYAL SOCIETY OPEN SCIENCE 2018; 5:181170. [PMID: 30564410 PMCID: PMC6281912 DOI: 10.1098/rsos.181170] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 11/01/2018] [Indexed: 06/09/2023]
Abstract
Bacterial gene expression regulation occurs mostly during transcription, which has two main rate-limiting steps: the close complex formation, when the RNA polymerase binds to an active promoter, and the subsequent open complex formation, after which it follows elongation. Tuning these steps' kinetics by the action of e.g. transcription factors, allows for a wide diversity of dynamics. For example, adding autoregulation generates single-gene circuits able to perform more complex tasks. Using stochastic models of transcription kinetics with empirically validated parameter values, we investigate how autoregulation and the multi-step transcription initiation kinetics of single-gene autoregulated circuits can be combined to fine-tune steady state mean and cell-to-cell variability in protein expression levels, as well as response times. Next, we investigate how they can be jointly tuned to control complex behaviours, namely, time counting, switching dynamics and memory storage. Overall, our finding suggests that, in bacteria, jointly regulating a single-gene circuit's topology and the transcription initiation multi-step dynamics allows enhancing complex task performance.
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Affiliation(s)
- Mahendra Kumar Prajapat
- Laboratory of Biosystem Dynamics, Faculty of Biomedical Sciences and Engineering, BioMediTech Institute, Tampere University of Technology, 33101 Tampere, Finland
| | - Andre S. Ribeiro
- Laboratory of Biosystem Dynamics, Faculty of Biomedical Sciences and Engineering, BioMediTech Institute, Tampere University of Technology, 33101 Tampere, Finland
- Multi-scaled Biodata Analysis and Modelling Research Community, Tampere University of Technology, 33101 Tampere, Finland
- CA3 CTS/UNINOVA, Faculdade de Ciencias e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, 2829-516 Caparica, Portugal
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18
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Abstract
Fluctuating environments such as changes in ambient temperature represent a fundamental challenge to life. Cells must protect gene networks that protect them from such stresses, making it difficult to understand how temperature affects gene network function in general. Here, we focus on single genes and small synthetic network modules to reveal four key effects of nonoptimal temperatures at different biological scales: (i) a cell fate choice between arrest and resistance, (ii) slower growth rates, (iii) Arrhenius reaction rates, and (iv) protein structure changes. We develop a multiscale computational modeling framework that captures and predicts all of these effects. These findings promote our understanding of how temperature affects living systems and enables more robust cellular engineering for real-world applications. Most organisms must cope with temperature changes. This involves genes and gene networks both as subjects and agents of cellular protection, creating difficulties in understanding. Here, we study how heating and cooling affect expression of single genes and synthetic gene circuits in Saccharomyces cerevisiae. We discovered that nonoptimal temperatures induce a cell fate choice between stress resistance and growth arrest. This creates dramatic gene expression bimodality in isogenic cell populations, as arrest abolishes gene expression. Multiscale models incorporating population dynamics, temperature-dependent growth rates, and Arrhenius scaling of reaction rates captured the effects of cooling, but not those of heating in resistant cells. Molecular-dynamics simulations revealed how heating alters the conformational dynamics of the TetR repressor, fully explaining the experimental observations. Overall, nonoptimal temperatures induce a cell fate decision and corrupt gene and gene network function in computationally predictable ways, which may aid future applications of engineered microbes in nonstandard temperatures.
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19
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Precision in a rush: Trade-offs between reproducibility and steepness of the hunchback expression pattern. PLoS Comput Biol 2018; 14:e1006513. [PMID: 30307984 PMCID: PMC6198997 DOI: 10.1371/journal.pcbi.1006513] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 10/23/2018] [Accepted: 09/14/2018] [Indexed: 11/19/2022] Open
Abstract
Fly development amazes us by the precision and reproducibility of gene expression, especially since the initial expression patterns are established during very short nuclear cycles. Recent live imaging of hunchback promoter dynamics shows a stable steep binary expression pattern established within the three minute interphase of nuclear cycle 11. Considering expression models of different complexity, we explore the trade-off between the ability of a regulatory system to produce a steep boundary and minimize expression variability between different nuclei. We show how a limited readout time imposed by short developmental cycles affects the gene’s ability to read positional information along the embryo’s anterior posterior axis and express reliably. Comparing our theoretical results to real-time monitoring of the hunchback transcription dynamics in live flies, we discuss possible regulatory strategies, suggesting an important role for additional binding sites, gradients or non-equilibrium binding and modified transcription factor search strategies. Despite very limited time, organisms develop in reproducible ways. In the early stages of fly development the information about maternal signals is read out in a few minutes to produce steep and precise gene expression patterns. Motivated by recent live imaging experiments in fly embryos, we explore the consequences of the trade-off between a rushed but reproducible readout and a steep expression pattern on the regulatory modules of gene expression. We show that the current view of one anterior gradient morphogen binding to six binding sites is quantitatively inconsistent with the experimental data given the short readout time, suggesting other regulatory features.
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20
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Wong DCS, O’Neill JS. Non-transcriptional processes in circadian rhythm generation. CURRENT OPINION IN PHYSIOLOGY 2018; 5:117-132. [PMID: 30596188 PMCID: PMC6302373 DOI: 10.1016/j.cophys.2018.10.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
'Biological clocks' orchestrate mammalian biology to a daily rhythm. Whilst 'clock gene' transcriptional circuits impart rhythmic regulation to myriad cellular systems, our picture of the biochemical mechanisms that determine their circadian (∼24 hour) period is incomplete. Here we consider the evidence supporting different models for circadian rhythm generation in mammalian cells in light of evolutionary factors. We find it plausible that the circadian timekeeping mechanism in mammalian cells is primarily protein-based, signalling biological timing information to the nucleus by the post-translational regulation of transcription factor activity, with transcriptional feedback imparting robustness to the oscillation via hysteresis. We conclude by suggesting experiments that might distinguish this model from competing paradigms.
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21
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Neeli-Venkata R, Oliveira SMD, Martins L, Startceva S, Bahrudeen M, Fonseca JM, Minoia M, Ribeiro AS. The precision of the symmetry in Z-ring placement in Escherichia coli is hampered at critical temperatures. Phys Biol 2018; 15:056002. [PMID: 29717708 DOI: 10.1088/1478-3975/aac1cb] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Cell division in Escherichia coli is morphologically symmetric due to, among other things, the ability of these cells to place the Z-ring at midcell. Studies have reported that, at sub-optimal temperatures, this symmetry decreases at the single-cell level, but the causes remain unclear. Using fluorescence microscopy, we observe FtsZ-GFP and DAPI-stained nucleoids to assess the robustness of the symmetry of Z-ring formation and positioning in individual cells under sub-optimal and critical temperatures. We find the Z-ring formation and positioning to be robust at sub-optimal temperatures, as the Z-ring's mean width, density and displacement from midcell maintain similar levels of correlation to one another as at optimal temperatures. However, at critical temperatures, the Z-ring displacement from midcell is greatly increased. We present evidence showing that this is due to enhanced distance between the replicated nucleoids and, thus, reduced Z-ring density, which explains the weaker precision in setting a morphologically symmetric division site. This also occurs in rich media and is cumulative, i.e. combining richer media and critically high temperatures enhances the asymmetries in division, which is evidence that the causes are biophysical. To further support this, we show that the effects are reversible, i.e. shifting cells from optimal to critical, and then to optimal again, reduces and then enhances the symmetry in Z-ring positioning, respectively, as the width and density of the Z-ring return to normal values. Overall, our findings show that the Z-ring positioning in E. coli is a robust biophysical process under sub-optimal temperatures, and that critical temperatures cause significant asymmetries in division.
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Affiliation(s)
- Ramakanth Neeli-Venkata
- Laboratory of Biosystem Dynamics, BioMediTech Institute and Faculty of Biomedical Sciences and Engineering, Tampere University of Technology, 33101, Tampere, Finland
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22
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Goncalves NSM, Startceva S, Palma CSD, Bahrudeen MNM, Oliveira SMD, Ribeiro AS. Temperature-dependence of the single-cell variability in the kinetics of transcription activation in Escherichia coli. Phys Biol 2018; 15:026007. [PMID: 29182518 DOI: 10.1088/1478-3975/aa9ddf] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
From in vivo single-cell, single-RNA measurements of the activation times and subsequent steady-state active transcription kinetics of a single-copy Lac-ara-1 promoter in Escherichia coli, we characterize the intake kinetics of the inducer (IPTG) from the media, following temperature shifts. For this, for temperature shifts of various degrees, we obtain the distributions of transcription activation times as well as the distributions of intervals between consecutive RNA productions following activation in individual cells. We then propose a novel methodology that makes use of deconvolution techniques to extract the mean and the variability of the distribution of intake times. We find that cells, following shifts to low temperatures, have higher intake times, although, counter-intuitively, the cell-to-cell variability of these times is lower. We validate the results using a new methodology for direct estimation of mean intake times from measurements of activation times at various inducer concentrations. The results confirm that E. coli's inducer intake times from the environment are significantly higher following a shift to a sub-optimal temperature. Finally, we provide evidence that this is likely due to the emergence of additional rate-limiting steps in the intake process at low temperatures, explaining the reduced cell-to-cell variability in intake times.
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Affiliation(s)
- Nadia S M Goncalves
- Laboratory of Biosystem Dynamics, BioMediTech Institute and Faculty of Biomedical Sciences and Engineering, Tampere University of Technology, Tampere 33101, Finland
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