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Related Concept Videos

Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

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The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
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RNA Editing02:23

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RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...
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While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
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Gene Conversion02:08

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Other than maintaining genome stability via DNA repair, homologous recombination plays an important role in diversifying the genome. In fact, the recombination of sequences forms the molecular basis of genomic evolution. Random and non-random permutations of genomic sequences create a library of new amalgamated sequences. These newly formed genomes can determine the fitness and survival of cells. In bacteria, homologous and non-homologous types of recombination lead to the evolution of new...
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DNA replication is a well-evolved process that copies millions of base pairs with high fidelity during each cell division. Occasionally a wrong base or a long stretch of wrong bases may get added to the daughter strands. If the errors are left unchecked, cells might accumulate several mutations that might endanger their  survival. Therefore, the copying errors are checked and repaired at three levels.
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Related Experiment Video

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BEST: Barcode Enabled Sequencing of Tetrads
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Random Base Editing for Genome Evolution in Saccharomyces cerevisiae.

Yingjia Pan1, Siyang Xia1, Chang Dong1,2

  • 1Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China.

ACS Synthetic Biology
|September 20, 2021
PubMed
Summary

A new random base editing (rBE) system enables genome-wide C to T mutations in yeast. This tool advances microbial cell factory engineering for industrial biotechnology applications.

Keywords:
Saccharomyces cerevisiaebase editinggenome evolutionmicrobial cell factoriesssDNA binding proteins

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Area of Science:

  • Synthetic biology
  • Molecular biology
  • Biotechnology

Background:

  • Rational engineering of microbial cell factories for industrial traits is challenging due to limited understanding of cellular metabolism and regulatory networks.
  • Development of simple, efficient, and programmable genome evolution techniques is crucial for industrial biotechnology.
  • Existing genome engineering methods may lack the efficiency and programmability required for complex trait development.

Discussion:

  • A novel random base editing (rBE) system was established in *Saccharomyces cerevisiae* for genome evolution.
  • The rBE system utilizes a cytidine deaminase fused to an ssDNA-binding protein to introduce C to T mutations genome-wide.
  • Specific DNA replication proteins (RFA1-3, PRI1, HCS1, TOP1) were employed to mediate deamination of genomic ssDNA.

Key Insights:

  • The rBE system's mutation rate was estimated using a *CAN1* reporter system.
  • rBE demonstrated efficacy in enhancing resistance to isobutanol and acetate, and increasing beta-carotene production.
  • An optimized rBE was successfully used for continuous genome evolution of a yeast strain resistant to 9% isobutanol.

Outlook:

  • The rBE system's reliance on conserved DNA replication mechanisms suggests broad applicability across diverse organisms.
  • This technology holds potential for continuous genome evolution in various microbial platforms.
  • Further research can explore rBE applications for engineering complex industrial traits in other microbial species.