A5013655804- Genomics and Phylogenetic Studies
- CRISPR and Genetic Engineering
- RNA and protein synthesis mechanisms
- Bacterial Genetics and Biotechnology
- Bacteriophages and microbial interactions
- Evolution and Genetic Dynamics
- Vibrio bacteria research studies
- Cancer Research and Treatments
- RNA modifications and cancer
- 3D Printing in Biomedical Research
- Escherichia coli research studies
- Salmonella and Campylobacter epidemiology
- Viral Infectious Diseases and Gene Expression in Insects
Harvard University
2014-2021
Ginkgo BioWorks (United States)
2020
University of Delaware
2010
Recoding and repurposing genetic codons By recoding bacterial genomes, it is possible to create organisms that can potentially synthesize products not commonly found in nature. systematic replacement of seven with synonymous alternatives for all protein-coding genes, Ostrov et al. recoded the Escherichia coli genome. The number E. code was reduced from 64 57 by removing instances UAG stop codon excising two arginine codons, leucine serine codons. Over 90% functionality successfully retained....
Significance This work presents the genome-wide replacement of all rare AGR (AGA and AGG) arginine codons in essential genes Escherichia coli with synonymous CGN alternatives. Synonymous codon substitutions can lethally impact noncoding function by disrupting mRNA secondary structure ribosomal binding site-like motifs. Here we quantitatively define range tolerable deviation these metrics use this relationship to provide critical insight into choice recoded genomes. demonstrates that removal...
Abstract Selection has been invaluable for genetic manipulation, although counter-selection historically exhibited limited robustness and convenience. TolC, an outer membrane pore involved in transmembrane transport E. coli, implemented as a selectable/counter-selectable marker, but escape frequency using colicin E1 precludes tolC inefficient manipulations and/or with large libraries. Here, we leveraged unbiased deep sequencing of 96 independent lineages exhibiting to identify...
A synthetic auxotroph does not escape from biocontainment after evolution, demonstrating that life always find a way.
Abstract Background Vibrio Pathogenicity Island-2 (VPI-2) is a 57 kb region present in choleragenic V. cholerae isolates that required for growth on sialic acid as sole carbon source. non-O1/O139 pathogenic strains also contain VPI-2, which addition to catabolism genes encodes type 3 secretion system these strains. VPI-2 integrates into chromosome 1 at tRNA-serine site and an integrase intV2 (VC1758) belongs the tyrosine recombinase family. IntV2 excision from 1, occurs very low levels,...
Inexpensive DNA sequencing and advances in genome editing have made computational analysis a major rate-limiting step adaptive laboratory evolution microbial engineering. We describe Millstone, web-based platform that automates genotype comparison visualization for projects with up to hundreds of genomic samples. To enable iterative engineering, Millstone allows users design oligonucleotide libraries create successive versions reference genomes. is open source easily deployable cloud...
Abstract Inexpensive DNA sequencing and advances in genome editing have made computational analysis a major rate-limiting step adaptive laboratory evolution microbial engineering. We describe Millstone, web-based platform which automates genotype comparison visualization for projects with up to hundreds of genomic samples. To enable iterative engineering, Millstone allows users design oligonucleotide libraries create successive versions reference genomes. is open source easily deployable...
Abstract Understanding the evolutionary stability and possible context-dependence of biological containment techniques is critical as engineered microbes are increasingly under consideration for applications beyond biomanufacturing. While batch cultures synthetic auxotrophic Escherichia coli previously exhibited undetectable escape throughout 14 days monitoring, long-term effectiveness auxotrophy unknown. Here, we report automated continuous evolution a auxotroph using custom chemostats that...
Abstract The degeneracy of the genetic code allows nucleic acids to encode amino acid identity as well non-coding information for gene regulation and genome maintenance. rare arginine codons AGA AGG (AGR) present a case study in codon choice, with AGRs encoding important transcriptional translational properties distinct from other synonymous alternatives (CGN). We created strain Escherichia coli all 123 instances AGR removed essential genes. readily replaced 110 CGU, but remaining thirteen...
The evolution and emergence of pathogenic bacteria is tightly linked to the horizontal transfer pathogenicity islands (PAIs) bacteriophages encoding a range virulence factors. We studied evolutionary relationships between integrases excisionases from group islands, used VPI‐2 as model for island excision. determined functional role VPI‐2‐encoded integrase (int ) two putative (vefA vefB) in found negligible levels excision measured by attB Δint strain whereas overexpression int showed an...