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Hartmann AK, Krajenbrink A, Le Doussal P. Probing the large deviations for the beta random walk in random medium. Phys Rev E 2024; 109:024122. [PMID: 38491613 DOI: 10.1103/physreve.109.024122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 01/11/2024] [Indexed: 03/18/2024]
Abstract
We consider a discrete-time random walk on a one-dimensional lattice with space- and time-dependent random jump probabilities, known as the beta random walk. We are interested in the probability that, for a given realization of the jump probabilities (a sample), a walker starting at the origin at time t=0 is at position beyond ξsqrt[T/2] at time T. This probability fluctuates from sample to sample and we study the large-deviation rate function, which characterizes the tails of its distribution at large time T≫1. It is argued that, up to a simple rescaling, this rate function is identical to the one recently obtained exactly by two of the authors for the continuum version of the model. That continuum model also appears in the macroscopic fluctuation theory of a class of lattice gases, e.g., in the so-called KMP model of heat transfer. An extensive numerical simulation of the beta random walk, based on an importance sampling algorithm, is found in good agreement with the detailed analytical predictions. A first-order transition in the tilted measure, predicted to occur in the continuum model, is also observed in the numerics.
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Affiliation(s)
| | - Alexandre Krajenbrink
- Quantinuum, Terrington House, 13-15 Hills Road, Cambridge CB2 1NL, United Kingdom
- Le Lab Quantique, 58 rue d'Hauteville, 75010, Paris, France
| | - Pierre Le Doussal
- Laboratoire de Physique de l'École Normale Supérieure, PSL University, CNRS, Sorbonne Universités, 24 rue Lhomond, 75231 Paris, France
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2
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Fusco F, Pires MC, Lopes APY, Alves VDS, Gonçalves VM. Influence of the mRNA initial region on protein production: a case study using recombinant detoxified pneumolysin as a model. Front Bioeng Biotechnol 2024; 11:1304965. [PMID: 38260740 PMCID: PMC10800503 DOI: 10.3389/fbioe.2023.1304965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 12/12/2023] [Indexed: 01/24/2024] Open
Abstract
Recombinant proteins are of great importance in modern society, mostly as biopharmaceutical products. However, challenging and complex processes with low production yield are major drawbacks. Normally, the optimization to overcome these obstacles is focused on bioreactor and purification processes, and the biomolecular aspects are neglected, seen as less important. In this work, we present how the 5' mRNA secondary structure region can be relevant for translation and, therefore, protein production. For this, Escherichia coli BL21(DE3) clones, producing recombinant detoxified pneumolysin (PdT) with and without the N-terminal His-tag, were cultivated in 10-L bioreactors. Another version of the pdt gene (version 2) with synonymous changes in the 5'-end nucleotide sequence was also obtained. Protein production, plasmid stability, carbon sources, and acetic acid were quantified during the cultures. Furthermore, in silico mRNA analyses were performed using TIsigner and RNAfold. The results showed that the His-tag presence at the N-terminus generated a minimum 1.5-fold increase in target protein synthesis, which was explained by the in silico mRNA analyses that returned an mRNA secondary structure easier to translate and, therefore, higher protein production than without the His-tag. The pdt gene version 2 showed lower 5' mRNA opening energy than version 1, allowing higher PdT production even without a tag. This work reveals that simple mRNA analyses during heterologous gene design and production steps can help reach high-recombinant protein titers in a shorter time than using only traditional bioprocess optimization strategies.
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Affiliation(s)
- Filipe Fusco
- Laboratory of Vaccine Development, Butantan Institute, Sao Paulo, Brazil
- Interunits Graduate Program in Biotechnology, University of Sao Paulo, Sao Paulo, Brazil
| | - Manuella Cazelato Pires
- Laboratory of Vaccine Development, Butantan Institute, Sao Paulo, Brazil
- Interunits Graduate Program in Biotechnology, University of Sao Paulo, Sao Paulo, Brazil
| | | | - Vítor dos Santos Alves
- Laboratory of Vaccine Development, Butantan Institute, Sao Paulo, Brazil
- Interunits Graduate Program in Biotechnology, University of Sao Paulo, Sao Paulo, Brazil
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Mutharasu G, Murugesan A, Kondamani S, Thiyagarajan R, Yli-Harja O, Kandhavelu M. Signaling landscape of mitochondrial non-coding RNAs. J Biomol Struct Dyn 2023; 41:12016-12025. [PMID: 36617957 DOI: 10.1080/07391102.2022.2164520] [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: 10/07/2022] [Accepted: 12/27/2022] [Indexed: 01/10/2023]
Abstract
Human mitochondria are the vital cell organelle acting as a storehouse of energy generation and diverse regulatory functions. Mitochondrial DNA comprises 93% coding region and 7% non-coding regions, in which the non-coding region hypothesized as responsible for signaling is our specific interest. Here, we explored the unknown functions of mitochondrial non-coding RNAs by studying their respective signaling pathways. We retrieved conserved motifs of interactions from known experimental protein-RNA complexes to model unknown mitochondrial ncRNA sequences. Our results provide the ncRNAs list and show their involvement in four crucial pathways, such as (i) Processing of Capped Intron-Containing Pre-mRNA, (ii) Spliceosome, (iii) Spliceosomal assembly, and (iv) RNA Polymerase II Transcription, respectively. The interactome analysis revealed that the SRSF2 and U2AF2 proteins interact with ncRNAs. Further, we have simulated the selected ncRNA-protein complexes in cell-like environmental conditions and found them stable in terms of energetics. Through our study, we have identified an apparent interaction of mitochondrial ncRNAs with proteins and their role in critical signaling pathways, providing new insights into mitochondrial ncRNA-dependent gene regulation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gnanavel Mutharasu
- BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Akshaya Murugesan
- BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Molecular Signaling Group, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Biotechnology, Lady Doak College, Thallakulam, Madurai, Tamil Nadu, India
| | - Saravnan Kondamani
- Department of Biotechnology, Bharath Institute of Higher Education and Research, Chennai, Tamil Nadu, India
| | - Ramesh Thiyagarajan
- Department of Basic Medical Sciences, College of Medicine, Prince Sattam Bin Abdulaziz University, Kingdom of Saudi Arabia
| | - Olli Yli-Harja
- Computaional Systems Biology Group, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Institute for Systems Biology, Seattle, WA, USA
| | - Meenakshisundaram Kandhavelu
- BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Molecular Signaling Group, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
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Baliga P, Shekar M, Tg P, Sk G. Investigation into the prevalent CRISPR-Cas systems among the Aeromonas genus. J Basic Microbiol 2021; 61:874-882. [PMID: 34486151 DOI: 10.1002/jobm.202100234] [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: 05/11/2021] [Revised: 08/12/2021] [Accepted: 08/21/2021] [Indexed: 01/15/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) is a prokaryotic adaptive immune system that checks invasion by mobile genetic elements through nuclease targeting. In this study, we investigated the occurrence, diversity, and features of the CRISPR system in the genus Aeromonas using bioinformatics tools. Only 13 out of 122 complete genomes (10.66%) of the genus Aeromonas from the NCBI GenBank database harbored the CRISPR system. The Type I-F system was the most prevalent CRISPR system among the Aeromonads, followed by the Type I-E system. Only one strain harbored a Type I-C CRISPR system. Among the Aeromonads, Aeromonas caviae (22.7%) and Aeromonas veronii (20%) had a higher prevalence rate of the complete CRISPR system. The analysis of direct repeat (DR) sequences showed that all could form stable RNA secondary structures. A phylogenetic tree generated for the Cas1 protein classified CRISPR subtypes into three distinct clusters. Among the 748 spacers investigated, 41.98% and 17.25% showed perfect homology to phage and plasmid sequences, respectively. Some arrays had duplicated spacers. The CRISPR loci are closely linked to antibiotic resistance genes in most strains. Collectively, our results would contribute to research on antibiotic resistance in the Aeromonas group, and provide new insights into the diversity and evolution of the CRISPR-Cas system.
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Affiliation(s)
- Pallavi Baliga
- Department of Aquatic Animal Health Management, College of Fisheries, Karnataka Veterinary, Animal and Fisheries Sciences University, Mangalore, Karnataka, India
| | - Malathi Shekar
- Department of Aquatic Animal Health Management, College of Fisheries, Karnataka Veterinary, Animal and Fisheries Sciences University, Mangalore, Karnataka, India
| | - Puneeth Tg
- Department of Aquatic Animal Health Management, College of Fisheries, Karnataka Veterinary, Animal and Fisheries Sciences University, Mangalore, Karnataka, India
| | - Girisha Sk
- Department of Aquatic Animal Health Management, College of Fisheries, Karnataka Veterinary, Animal and Fisheries Sciences University, Mangalore, Karnataka, India
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Hartmann AK, Krajenbrink A, Le Doussal P. Probing large deviations of the Kardar-Parisi-Zhang equation at short times with an importance sampling of directed polymers in random media. Phys Rev E 2020; 101:012134. [PMID: 32069556 DOI: 10.1103/physreve.101.012134] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Indexed: 11/07/2022]
Abstract
The one-point distribution of the height for the continuum Kardar-Parisi-Zhang equation is determined numerically using the mapping to the directed polymer in a random potential at high temperature. Using an importance sampling approach, the distribution is obtained over a large range of values, down to a probability density as small as 10^{-1000} in the tails. The short-time behavior is investigated and compared with recent analytical predictions for the large-deviation forms of the probability of rare fluctuations, showing a spectacular agreement with the analytical expressions. The flat and stationary initial conditions are studied in the full space, together with the droplet initial condition in the half-space.
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Affiliation(s)
| | - Alexandre Krajenbrink
- Laboratoire de Physique de l'École Normale Supérieure, PSL University, CNRS, Sorbonne Universités, 24 rue Lhomond, 75231 Paris, France
| | - Pierre Le Doussal
- Laboratoire de Physique de l'École Normale Supérieure, PSL University, CNRS, Sorbonne Universités, 24 rue Lhomond, 75231 Paris, France
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Pressman A, Moretti JE, Campbell GW, Müller UF, Chen IA. Analysis of in vitro evolution reveals the underlying distribution of catalytic activity among random sequences. Nucleic Acids Res 2017. [PMID: 28645146 PMCID: PMC5737207 DOI: 10.1093/nar/gkx540] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The emergence of catalytic RNA is believed to have been a key event during the origin of life. Understanding how catalytic activity is distributed across random sequences is fundamental to estimating the probability that catalytic sequences would emerge. Here, we analyze the in vitro evolution of triphosphorylating ribozymes and translate their fitnesses into absolute estimates of catalytic activity for hundreds of ribozyme families. The analysis efficiently identified highly active ribozymes and estimated catalytic activity with good accuracy. The evolutionary dynamics follow Fisher's Fundamental Theorem of Natural Selection and a corollary, permitting retrospective inference of the distribution of fitness and activity in the random sequence pool for the first time. The frequency distribution of rate constants appears to be log-normal, with a surprisingly steep dropoff at higher activity, consistent with a mechanism for the emergence of activity as the product of many independent contributions.
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Affiliation(s)
- Abe Pressman
- Department of Chemistry and Biochemistry 9510, University of California, Santa Barbara, CA 93106, USA.,Program in Chemical Engineering, University of California, Santa Barbara, CA 93106, USA
| | - Janina E Moretti
- Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093, USA
| | - Gregory W Campbell
- Department of Chemistry and Biochemistry 9510, University of California, Santa Barbara, CA 93106, USA.,Program in Biomolecular Sciences and Engineering, University of California, Santa Barbara, CA 93106, USA
| | - Ulrich F Müller
- Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093, USA
| | - Irene A Chen
- Department of Chemistry and Biochemistry 9510, University of California, Santa Barbara, CA 93106, USA.,Program in Biomolecular Sciences and Engineering, University of California, Santa Barbara, CA 93106, USA
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Investigating CRISPR-Cas systems in Clostridium botulinum via bioinformatics tools. INFECTION GENETICS AND EVOLUTION 2017; 54:355-373. [DOI: 10.1016/j.meegid.2017.06.027] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 06/19/2017] [Accepted: 06/27/2017] [Indexed: 12/22/2022]
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Jensen KT, Fløe L, Petersen TS, Huang J, Xu F, Bolund L, Luo Y, Lin L. Chromatin accessibility and guide sequence secondary structure affect CRISPR-Cas9 gene editing efficiency. FEBS Lett 2017; 591:1892-1901. [PMID: 28580607 DOI: 10.1002/1873-3468.12707] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 05/29/2017] [Accepted: 05/30/2017] [Indexed: 11/06/2022]
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated protein 9 (CRISPR-Cas9) systems have emerged as the method of choice for genome editing, but large variations in on-target efficiencies continue to limit their applicability. Here, we investigate the effect of chromatin accessibility on Cas9-mediated gene editing efficiency for 20 gRNAs targeting 10 genomic loci in HEK293T cells using both SpCas9 and the eSpCas9(1.1) variant. Our study indicates that gene editing is more efficient in euchromatin than in heterochromatin, and we validate this finding in HeLa cells and in human fibroblasts. Furthermore, we investigate the gRNA sequence determinants of CRISPR-Cas9 activity using a surrogate reporter system and find that the efficiency of Cas9-mediated gene editing is dependent on guide sequence secondary structure formation. This knowledge can aid in the further improvement of tools for gRNA design.
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Affiliation(s)
| | - Lasse Fløe
- Department of Biomedicine, Aarhus University, Denmark
| | | | - Jinrong Huang
- BGI-Shenzhen, China.,China National GeneBank-Shenzhen, BGI-Shenzhen, China
| | - Fengping Xu
- BGI-Shenzhen, China.,China National GeneBank-Shenzhen, BGI-Shenzhen, China.,Biology Department, Copenhagen University, Denmark
| | - Lars Bolund
- Department of Biomedicine, Aarhus University, Denmark.,BGI-Shenzhen, China.,China National GeneBank-Shenzhen, BGI-Shenzhen, China
| | - Yonglun Luo
- Department of Biomedicine, Aarhus University, Denmark
| | - Lin Lin
- Department of Biomedicine, Aarhus University, Denmark
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9
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George TP, Thomas T. Novel Approach to Analyzing MFE of Noncoding RNA Sequences. GENOMICS INSIGHTS 2016; 9:41-49. [PMID: 27695341 PMCID: PMC5029481 DOI: 10.4137/gei.s39995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 08/01/2016] [Accepted: 08/04/2016] [Indexed: 12/30/2022]
Abstract
Genomic studies have become noncoding RNA (ncRNA) centric after the study of different genomes provided enormous information on ncRNA over the past decades. The function of ncRNA is decided by its secondary structure, and across organisms, the secondary structure is more conserved than the sequence itself. In this study, the optimal secondary structure or the minimum free energy (MFE) structure of ncRNA was found based on the thermodynamic nearest neighbor model. MFE of over 2600 ncRNA sequences was analyzed in view of its signal properties. Mathematical models linking MFE to the signal properties were found for each of the four classes of ncRNA analyzed. MFE values computed with the proposed models were in concordance with those obtained with the standard web servers. A total of 95% of the sequences analyzed had deviation of MFE values within ±15% relative to those obtained from standard web servers.
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Affiliation(s)
- Tina P George
- Research Scholar, Department of Electronics, Cochin University of Science and Technology (CUSAT), Kochi, Kerala, India
| | - Tessamma Thomas
- Professor, Department of Electronics, Cochin University of Science and Technology (CUSAT), Kochi, Kerala, India
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Rahmatabadi SS, Nezafat N, Negahdaripour M, Hajighahramani N, Morowvat MH, Ghasemi Y. Studying the features of 57 confirmed CRISPR loci in 29 strains of Escherichia coli. J Basic Microbiol 2016; 56:645-53. [PMID: 26871258 DOI: 10.1002/jobm.201500707] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 01/17/2016] [Indexed: 12/26/2022]
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) system is a novel type of innate defense system in prokaryotes for destruction of exogenous elements. To gain further insight into behavior and organization of the system, the extensive analysis of the available sequenced genomes is necessary. The dynamic nature of CRISPR loci is possibly valuable for typing and relative analyses of strains and microbial population. There are a few orderly bioinformatics investigations about the structure of CRISPR sequences in the Escherichia coli strains. In this study, 57 CRISPR loci were selected from 32 Escherichia coli strains to investigate their structural characteristics and potential functions using bioinformatics tools. Our results showed that most strains contained several loci that mainly included conserved direct repeats, while the spacers were highly variable. Moreover, RNA analysis of the sequences indicated that all loci could form stable RNA secondary structures and showed homology mostly with phages compared to plasmids. Only three strains included cas genes around their loci.
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Affiliation(s)
- Seyyed Soheil Rahmatabadi
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.,Pharmaceutical Science Research Center, Shiraz University of Medical Science, Shiraz, Iran
| | - Navid Nezafat
- Pharmaceutical Science Research Center, Shiraz University of Medical Science, Shiraz, Iran
| | - Manica Negahdaripour
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.,Pharmaceutical Science Research Center, Shiraz University of Medical Science, Shiraz, Iran
| | - Nasim Hajighahramani
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.,Pharmaceutical Science Research Center, Shiraz University of Medical Science, Shiraz, Iran
| | | | - Younes Ghasemi
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.,Pharmaceutical Science Research Center, Shiraz University of Medical Science, Shiraz, Iran.,Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
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