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Related Concept Videos

Gene Regulation in Microbial Communities: Quorum Sensing01:28

Gene Regulation in Microbial Communities: Quorum Sensing

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Quorum sensing is a mechanism of bacterial communication that enables coordinated gene expression in response to changes in population density. This facilitates collective behaviors that enhance survival, resource acquisition, and ecological adaptation. This process relies on small signaling molecules called autoinducers that accumulate as bacterial populations grow. When a critical threshold concentration of autoinducers is reached, bacterial cells collectively modify gene expression,...
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Constitutive and Regulated Gene Expression01:27

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Gene expression in prokaryotes is governed by constitutive and regulated systems, allowing cells to balance the production of essential proteins with adaptive responses to environmental changes.Constitutive Gene ExpressionConstitutive, or housekeeping, genes are continuously expressed as they encode proteins vital for fundamental cellular processes. These include enzymes for glycolysis, ribosomal components for protein synthesis, and proteins involved in DNA replication. Their constant...
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Regulation of Expression at Multiple Steps01:23

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The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the...
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The DNA replication, transcription, and translation processes are intricately coupled in bacteria, allowing efficient gene expression and rapid protein synthesis. While this physical and functional coordination is advantageous, it introduces challenges that bacteria overcome through specific regulatory mechanisms.Coupling of Replication, Transcription, and TranslationThe coupling of replication, transcription, and translation is a hallmark of bacterial gene expression. As the replisome unwinds...
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Translational Regulation01:29

Translational Regulation

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Translational regulation in prokaryotes ensures efficient protein synthesis by controlling ribosome access to mRNA. This regulation is mediated by secondary RNA structures, including translational riboswitches, RNA thermometers, and small RNAs (sRNAs), which respond to intracellular and environmental signals to modulate gene expression.Translational RiboswitchesRiboswitches in the leader region of mRNAs can regulate translation by altering the accessibility of the Shine-Dalgarno (SD) sequence,...
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A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is comprised  of nucleotides and proteins are comprised of amino acids, a mediator is required to convert the information encoded in DNA into proteins. This mediator is the messenger RNA (mRNA). mRNA copies the blueprint from DNA by a process called transcription. In eukaryotes, transcription occurs in the nucleus by complementary base-pairing with the DNA template. The mRNA is then...
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Modulating Gene Expression within a Microbiome Based on Computational Models.

Liyam Chitayat Levi1, Ido Rippin2, Moran Ben Tulila1

  • 1Department of Biomedical Engineering, Tel-Aviv University, Tel Aviv 997801, Israel.

Biology
|September 23, 2022
PubMed
Summary
This summary is machine-generated.

This study introduces a computational framework for engineering microbiomes, enhancing genetic information transfer specificity and biosafety. It addresses horizontal gene transfer challenges for safer microbiome engineering applications.

Keywords:
evolutionary systems biologygene expressionhorizontal gene transfermicrobiome engineeringpopulation genomicssynthetic biology

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Area of Science:

  • Bioinformatics and Molecular Biology
  • Synthetic Biology
  • Microbiome Engineering

Background:

  • Microbiomes exhibit complex host-symbiotic interactions, with horizontal gene transfer (HGT) driving genetic variation.
  • The 'plasmidome' represents an additional layer of genetic information within microbiomes, influenced by HGT.
  • Current genetic engineering methods for microbiomes lack specificity and biosafety, failing to account for HGT and long-term interactions.

Purpose of the Study:

  • To design microbiome-specific engineered genetic information for enhanced compatibility with existing techniques.
  • To develop a computational framework for engineering microbiomes that is agnostic to specific species or genes.
  • To improve the biosafety of microbiome engineering by controlling gene expression and preventing off-target effects.

Main Methods:

  • A computational engineering framework was developed, defining microbiome species as either 'wanted' or 'unwanted' hosts.
  • Novel algorithms were used to individually examine and engineer gene expression elements (promoters, coding regions) for desired expression preferences.
  • Engineered gene blocks were combined synergistically to enhance robustness against random mutations.

Main Results:

  • The computational framework successfully designed microbiome-specific genetic information.
  • The engineered elements demonstrated defined expression preferences and robustness against mutations.
  • Validation was achieved through both computational simulations and experimental testing, including iGEM 2021 research.

Conclusions:

  • The developed framework offers a novel computational approach to microbiome engineering.
  • This method enhances specificity and biosafety in genetic engineering of microbiomes.
  • The research provides a foundation for more controlled and predictable microbiome modification.