Bases immediate upstream of the TATAAT box of the sigma 70 promoter of Escherichia coli significantly influence the activity of a model promoter by altering the bending angle of DNA

Sharma, Surbhi; Pant, Pawan Kumar; Arya, Ranjana; Jayaram, B.; Das, H.

doi:10.1016/j.gene.2022.146968

Cited by 7 publications

(3 citation statements)

References 35 publications

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“…E. coli adopts the same RNAP which can associate with different sigma factors to initiate gene transcription. [ 42 ] Among these sigma factors, sigma70 is the housekeeping sigma factor that induces transcription of essential bacterial growth‐related genes. [ 19 ] The design of sigma70 promoters was previously reported, [ 11 ] and the conserved sigma70 motifs were suggested to benefit RNAP binding and transcription efficiency.…”

Section: Resultsmentioning

confidence: 99%

Deep Learning‐Assisted Design of Novel Promoters in Escherichia coli

Wang,

Xu,

Tan

et al. 2023

Advanced Genetics

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Deep learning (DL) approaches have the ability to accurately recognize promoter regions and predict their strength. Here, the potential for controllably designing active Escherichia coli promoter is explored by combining multiple deep learning models. First, “DRSAdesign,” which relies on a diffusion model to generate different types of novel promoters is created, followed by predicting whether they are real or fake and strength. Experimental validation showed that 45 out of 50 generated promoters are active with high diversity, but most promoters have relatively low activity. Next, “Ndesign,” which relies on generating random sequences carrying functional −35 and −10 motifs of the sigma70 promoter is introduced, and their strength is predicted using the designed DL model. The DL model is trained and validated using 200 and 50 generated promoters, and displays Pearson correlation coefficients of 0.49 and 0.43, respectively. Taking advantage of the DL models developed in this work, possible 6‐mers are predicted as key functional motifs of the sigma70 promoter, suggesting that promoter recognition and strength prediction mainly rely on the accommodation of functional motifs. This work provides DL tools to design promoters and assess their functions, paving the way for DL‐assisted metabolic engineering.

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Section: Resultsmentioning

confidence: 99%

Deep Learning‐Assisted Design of Novel Promoters in Escherichia coli

Wang,

Xu,

Tan

et al. 2023

Advanced Genetics

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“…All the modified nucleic acid–p19 complexes (along with the control/reference complex) were simulated using all-atom explicit-solvent molecular dynamics (MD) simulations (400 ns, 3 replicates each) followed by structure, dynamic, and energetic analysis. MD simulations are a powerful tool for providing insights into the structure, function, and dynamics of biomolecules at the molecular level. − In recent years, MD simulations have been thoroughly utilized to predict the stability, conformational changes, and dynamics of nucleic acids/modified nucleic acids and their interactions with other biological systems. − Strikingly, we noticed that a few modified nucleic acid molecules designed in this study retained double-helical structural integrity and displayed enhanced p19 binding. Such molecules can preferentially interact with the viral p19 protein, resulting in the availability of the plant siRNA for RISC formation, leading to viral mRNA degradation.…”

Section: Introductionmentioning

confidence: 81%

Probing the Nucleic Acid Flexibility to Disarm the Viral Counter-Defense Machinery: Design and Characterization of Potent p19 Inhibitors

Pant,

Leese

2023

J. Phys. Chem. B

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Plant viruses are highly destructive and significant contributors to several global pandemics and epidemics in plants. A viral disease outbreak in plants can cause a scarcity of food supply and is a severe concern to humanity. The siRNA (small interfering RNA)-mediated RNA-induced silencing complex (RISC) formation is a primary defense mechanism in plants against viruses, where the RISC binds and degrades viral mRNAs. As a counter-defense, many viruses encode RNA-silencing suppressor proteins (e.g., the p19 protein from the Tombusviridae family) for viral proliferation in plants. The functional form of p19 (homodimer) binds to plant siRNA with high affinities, thereby interrupting the RISC formation and thus preventing the viral mRNA silencing in plants. By altering the RISC formation, the p19 protein helps the virus invasion in the plant and ultimately stunts host growth. In this study, we designed several modified siRNA-based molecules for p19 inhibition. The viral p19 protein is known to interact predominantly through H-bonds with 2′-OH and phosphates of the plant siRNA. We utilized this information and in silico-designed flexible substituents of siRNA, where we removed the C2′−C3′ bond in each nucleotide unit. We performed all-atom explicit-solvent molecular dynamics simulations (400 ns, 3 replicates each) for control/modified siRNA�p19 complexes (8 in total) followed by energetic estimations. Strikingly, in a few modified complexes, the siRNA not only retained the double-helical structural integrity but also displayed remarkably enhanced p19 binding compared to the control siRNA; hence, we consider it important to perform biological and chemical in vitro and in vivo studies on proposed flexible nucleic acids as p19 inhibitors for crop protection.

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“…In recent years, computer simulations have been thoroughly used to investigate the structure/dynamics of DNA/modified DNA molecules and their interactions with other macromolecules. − MD simulations have also been utilized to explore the B-DNA to Z-DNA transition, and the stability of Z-DNA in varying salt concentrations, and to study the effect of surrounding water molecules on Z-DNA. ,,, In the present Article, we investigated the conformational stability of locked-sugar-composed Z-DNA in high salt conditions (4 M) and in counterion-deprived conditions (no counterions were added to the system). We then compared the stability of the model system with the control Z-DNA molecules.…”

Section: Introductionmentioning

confidence: 99%

Harmonizing Interstrand Electrostatic Repulsion by Conformational Rigidity in Counterion-Deprived Z-DNA: A Molecular Dynamics Study

Sharma

2022

J. Phys. Chem. B

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Deoxyribonucleic acid (DNA) is a vital biomacromolecule. Although the right-handed B-DNA type helical structure is the most abundant and extensively studied form of DNA, several noncanonical forms, such as triplex, quadruplex, Z-DNA, A-DNA, and ss-DNA, have been probed from time to time to gain insights into the DNA's function. Z-DNA was recently found to be involved in cancer and several autoimmune diseases. In the present Article, we evaluated the conformational stability of locked-sugar-based Z-DNA via all-atom explicit-solvent molecular dynamics simulations and found that the modified DNA maintained the left-handed conformation even in the absence of counterions, wherein the structural rigidity dominates over the electrostatic repulsion between the complementary strands. The control Z-DNA without counterions, as expected, instantaneously resulted in unfolded states. The remarkable stability of the conformationally locked model system was thoroughly investigated via structural and energetic perspectives and was probably the result of the backbone widening in tandem with enhanced electrostatics between complementary strands. We believe that the design of the proposed modified Z-DNA construct could help understand the otherwise delicate Z-DNA conformation even in salt-deprived conditions. The design could also motivate the medicinal use of short segments of such modified nucleotides and could be utilized in more advanced modeling techniques, such as DNA origami which has gained popularity in recent years.

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Bases immediate upstream of the TATAAT box of the sigma 70 promoter of Escherichia coli significantly influence the activity of a model promoter by altering the bending angle of DNA

Cited by 7 publications

References 35 publications

Deep Learning‐Assisted Design of Novel Promoters in Escherichia coli

Deep Learning‐Assisted Design of Novel Promoters in Escherichia coli

Probing the Nucleic Acid Flexibility to Disarm the Viral Counter-Defense Machinery: Design and Characterization of Potent p19 Inhibitors

Harmonizing Interstrand Electrostatic Repulsion by Conformational Rigidity in Counterion-Deprived Z-DNA: A Molecular Dynamics Study

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