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Shoaib M, Murugesan A, Devanesan S, AlSalhi MS, Kandhavelu M. Growth phase-dependent ribonucleic acid production dynamics. Int J Biol Macromol 2024; 270:132457. [PMID: 38772467 DOI: 10.1016/j.ijbiomac.2024.132457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 04/18/2024] [Accepted: 05/09/2024] [Indexed: 05/23/2024]
Abstract
Transcriptional events play a crucial role in major cellular processes that specify the activity of an individual cells and influences cell population behavior in response to environment. Active (ON) and an inactive (OFF) states controls the transcriptional burst. Yet, the mechanism and kinetics of ON/OFF-state across the different growth phases of Escherichia coli remains elusive. Here, we have used a single mRNA detection method in live-cells to comprehend the ON/OFF mechanism of the first transcriptional (TF) and consecutive events (TC) controlled by lactose promoters, Plac and Plac/ara1. We determined that the duration of TF ON/OFF has different modes, exhibiting a close to inverse behavior to that of TC ON/OFF. Dynamics of ON/OFF states in fast and slow-dividing cells were affected by the promoter region during the initiation of transcription. Period of TF ON-state defines the behavior of TC by altering the number and the frequency of mRNAs formed. Furthermore, we have shown that delayed OFF-time in TF affects the dynamics of TC in both states, which is mainly determined by the upstream promoter region. Furthermore, using elongation arrest experiments, we independently validate that mRNA noise in TC is governed by the delayed OFF-period in TF. We have identified the position of the regulatory regions that plays a crucial role in noise (Fano) modulation. Taken together, our results suggest that the dynamics of the first transcriptional event, TF, pre-defines the diversity of the population.
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Affiliation(s)
- Muhammad Shoaib
- Molecular Signaling Group, Faculty of Medicine and Health Technology, Tampere University and BioMediTech, P.O. Box 553, 33101 Tampere, Finland
| | - Akshaya Murugesan
- Molecular Signaling Group, Faculty of Medicine and Health Technology, Tampere University and BioMediTech, P.O. Box 553, 33101 Tampere, Finland; Department of Biotechnology, Lady Doak College, Madurai Kamaraj University, Thallakulam, Madurai 625002, India
| | - Sandhanasamy Devanesan
- Department of Physics and Astronomy, College of Science, King Saud University, P. O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Mohamad S AlSalhi
- Department of Physics and Astronomy, College of Science, King Saud University, P. O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Meenakshisundaram Kandhavelu
- Molecular Signaling Group, Faculty of Medicine and Health Technology, Tampere University and BioMediTech, P.O. Box 553, 33101 Tampere, Finland; BioMeditech and Tays Cancer Center, Tampere University, Hospital, P.O. Box 553, 33101 Tampere, Finland.
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Murugesan A, Alshagrawi RA, Thiyagarajan R, Kandhavelu M. A dual fluorescence protein expression system detects cell cycle dependent protein noise. Int J Biol Macromol 2024; 263:130262. [PMID: 38378117 DOI: 10.1016/j.ijbiomac.2024.130262] [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: 12/20/2023] [Revised: 02/14/2024] [Accepted: 02/15/2024] [Indexed: 02/22/2024]
Abstract
Inherently identical cells exhibit significant phenotypic variation. It can be essential for many biological processes and is known to arise from stochastic, 'noisy', gene expression that is determined by intrinsic and extrinsic components. It is now obvious that the noise varies as a function of inducer concentration. However, its fluctuation over the cell cycle is limited. Applying dual colour fluorescence protein reporter system, Cyan Fluorescent Protein (CFP) and Yellow fluorescent protein (YFP) tagged multi-copy plasmids, we determine variation of the noise components over the phases in lac promoter induced by Isopropyl β-D-1-thiogalactopyranoside (IPTG) and in presence of additional Magnesium, Mg2+ ion. We, also, estimate the how such system deviates from observations of single-copy plasmid. Found 25 % difference between multi-copy system and single-copy system clarifies that observed noise is considerable and estimates population behaviour during the cell cycle. We show that total variation in cells induced with IPTG is determined by higher extrinsic than intrinsic noise. It increases from Lag to Exponential phase and decreases from Retardation to Stationary phase. By observing slow and fast dividing cells, we show that 5 mM Mg2+ increases population homogeneity compared to 2.5 mM Mg2+ in the environment. The experimental data obtained using dual colour fluorescence protein reporter system demonstrates that protein expression noise, depending on intra cellular ionic concentration, is tightly controlled by phase of the cell.
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Affiliation(s)
- Akshaya Murugesan
- Molecular Signaling Group, Faculty of Medicine and Health Technology, Tampere University and BioMediTech, P.O. Box 553, 33101 Tampere, Finland.; Department of Biotechnology, Lady Doak College, Madurai Kamaraj University, Thallakulam, Madurai 625002, India
| | - Reshod A Alshagrawi
- Department of Food Science and Nutrition, College of Food Science and Agriculture, King Saud University, Riyadh, Saudi Arabia
| | - Ramesh Thiyagarajan
- Department of Basic Medical Sciences, College of Medicine, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Meenakshisundaram Kandhavelu
- Molecular Signaling Group, Faculty of Medicine and Health Technology, Tampere University and BioMediTech, P.O. Box 553, 33101 Tampere, Finland..
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Viswanathan A, Anufrieva O, Sala A, Yli-Harja O, Kandhavelu M. Phase-dependent dynamics of the lac promoter under nutrient stress. Res Microbiol 2016; 167:451-61. [PMID: 27106257 DOI: 10.1016/j.resmic.2016.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 04/04/2016] [Accepted: 04/04/2016] [Indexed: 11/26/2022]
Abstract
To survive, a bacterial population must sense nutrient availability and adjust its growth phase accordingly. Few studies have quantitatively analyzed the single-cell behavior of stress and growth phase-related transcriptional changes in Escherichia coli. To investigate the dynamic changes in transcription during different growth phases and starvation, we analyzed the single-cell transcriptional dynamics of the E. coli lac promoter. Cells were grown under different starvation conditions, including glucose, magnesium, phosphate and thiamine limitations, and transcription dynamics was quantified using a single RNA detection method at different phases. Differences in gene expression over conditions and phases indicate that stochasticity in transcription dynamics is directly connected to cell phase and availability of nutrients. Except for glucose, the pattern of transcription dynamics under all starvation conditions appears to be similar. Transcriptional bursts were more prominent in lag and stationary phase cells starved for energy sources. Identical behavior was observed in exponential phase cells starved for phosphate and thiamine. Noise measurements under all nutrient exhaustion conditions indicate that intrinsic noise is higher than extrinsic noise. Our results, obtained in a relA1 mutational background, which led to suboptimal production of ppGpp, suggest that the single-cell transcriptional changes we observed were largely ppGpp-independent. Taken together, we propose that, under different starvation conditions, cells are able to decrease the trend in cell-to-cell variability in transcription as a common means of adaptation.
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Affiliation(s)
- Anisha Viswanathan
- Molecular Signaling Lab, Computational Systems Biology Research Group, Department of Signal Processing, Tampere University of Technology, P.O.Box 553, 33101 Tampere, Finland
| | - Olga Anufrieva
- Molecular Signaling Lab, Computational Systems Biology Research Group, Department of Signal Processing, Tampere University of Technology, P.O.Box 553, 33101 Tampere, Finland
| | - Adrien Sala
- Molecular Signaling Lab, Computational Systems Biology Research Group, Department of Signal Processing, Tampere University of Technology, P.O.Box 553, 33101 Tampere, Finland
| | - Olli Yli-Harja
- Molecular Signaling Lab, Computational Systems Biology Research Group, Department of Signal Processing, Tampere University of Technology, P.O.Box 553, 33101 Tampere, Finland; Institute for Systems Biology, 1441N 34th Street, Seattle, WA, 98103-8904, USA
| | - Meenakshisundaram Kandhavelu
- Molecular Signaling Lab, Computational Systems Biology Research Group, Department of Signal Processing, Tampere University of Technology, P.O.Box 553, 33101 Tampere, Finland.
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Sala A, Shoaib M, Anufrieva O, Mutharasu G, Jahan Hoque R, Yli-Harja O, Kandhavelu M. Transcription closed and open complex dynamics studies reveal balance between genetic determinants and co-factors. Phys Biol 2015; 12:036003. [PMID: 25988584 DOI: 10.1088/1478-3975/12/3/036003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In E. coli, promoter closed and open complexes are key steps in transcription initiation, where magnesium-dependent RNA polymerase catalyzes RNA synthesis. However, the exact mechanism of initiation remains to be fully elucidated. Here, using single mRNA detection and dual reporter studies, we show that increased intracellular magnesium concentration affects Plac initiation complex formation resulting in a highly dynamic process over the cell growth phases. Mg2+ regulates transcription transition, which modulates bimodality of mRNA distribution in the exponential phase. We reveal that Mg2+ regulates the size and frequency of the mRNA burst by changing the open complex duration. Moreover, increasing magnesium concentration leads to higher intrinsic and extrinsic noise in the exponential phase. RNAP-Mg2+ interaction simulation reveals critical movements creating a shorter contact distance between aspartic acid residues and Nucleotide Triphosphate residues and increasing electrostatic charges in the active site. Our findings provide unique biophysical insights into the balanced mechanism of genetic determinants and magnesium ion in transcription initiation regulation during cell growth.
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Affiliation(s)
- Adrien Sala
- Molecular Signaling Lab, Computational Systems Biology Research Group, Signal Processing Department, Tampere University of Technology, PO Box 553, 33101, Tampere, Finland
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