scholarly journals Total Synthesis of a Functional Designer Eukaryotic Chromosome

Science ◽  
2014 ◽  
Vol 344 (6179) ◽  
pp. 55-58 ◽  
Author(s):  
Narayana Annaluru ◽  
Héloïse Muller ◽  
Leslie A. Mitchell ◽  
Sivaprakash Ramalingam ◽  
Giovanni Stracquadanio ◽  
...  
Keyword(s):  
Total Synthesis ◽  
Base Pair ◽  
Stop Codon ◽  
Bacterial Genomes ◽  
Transfer Rnas ◽  
Eukaryotic Chromosome ◽  
Design And Synthesis ◽  
Biochemical Pathways ◽  
Chromosome Iii ◽  
Subtelomeric Regions

Rapid advances in DNA synthesis techniques have made it possible to engineer viruses, biochemical pathways and assemble bacterial genomes. Here, we report the synthesis of a functional 272,871–base pair designer eukaryotic chromosome, synIII, which is based on the 316,617–base pair native Saccharomyces cerevisiae chromosome III. Changes to synIII include TAG/TAA stop-codon replacements, deletion of subtelomeric regions, introns, transfer RNAs, transposons, and silent mating loci as well as insertion of loxPsym sites to enable genome scrambling. SynIII is functional in S. cerevisiae. Scrambling of the chromosome in a heterozygous diploid reveals a large increase in a-mater derivatives resulting from loss of the MATα allele on synIII. The complete design and synthesis of synIII establishes S. cerevisiae as the basis for designer eukaryotic genome biology.

scholarly journals Nonrecombinant meiosis I nondisjunction in Saccharomyces cerevisiae induced by tRNA ochre suppressors.

Genetics ◽  
1989 ◽  
Vol 123 (1) ◽  
pp. 81-95 ◽  
Author(s):  
E J Louis ◽  
J E Haber
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Mitotic Chromosome ◽  
Stop Codon ◽  
Fold Increase ◽  
Wild Type ◽  
Yeast Saccharomyces Cerevisiae ◽  
Nonsense Mutations ◽  
Chromosome Iii ◽  
Meiosis I ◽  
Chromosome Nondisjunction

Abstract The presence of the tRNA ochre suppressors SUP11 and SUP5 is found to induce meiosis I nondisjunction in the yeast Saccharomyces cerevisiae. The induction increases with increasing dosage of the suppressor and decreases in the presence of an antisuppressor. The effect is independent of the chromosomal location of SUP11. Each of five different chromosomes monitored exhibited nondisjunction at frequencies of 0.1%-1.1% of random spores, which is a 16-160-fold increase over wild-type levels. Increased nondisjunction is reflected by a marked increase in tetrads with two and zero viable spores. In the case of chromosome III, for which a 50-cM map interval was monitored, the resulting disomes are all in the parental nonrecombinant configuration. Recombination along chromosome III appears normal both in meioses that have no nondisjunction and in meioses for which there was nondisjunction of another chromosome. We propose that a proportion of one or more proteins involved in chromosome pairing, recombination or segregation are aberrant due to translational read-through of the normal ochre stop codon. Hygromycin B, an antibiotic that can suppress nonsense mutations via translational read-through, also induces nonrecombinant meiosis I nondisjunction. Increases in mistranslation, therefore, increase the production of aneuploids during meiosis. There was no observable effect of SUP11 on mitotic chromosome nondisjunction; however some disomes caused SUP11 ade2-ochre strains to appear white or red, instead of pink.

scholarly journals Sense codon reassignment enables viral resistance and encoded polymer synthesis

Science ◽  
2021 ◽  
Vol 372 (6546) ◽  
pp. 1057-1062
Author(s):  
Wesley E. Robertson ◽  
Louise F. H. Funke ◽  
Daniel de la Torre ◽  
Julius Fredens ◽  
Thomas S. Elliott ◽  
...  
Keyword(s):  
Stop Codon ◽  
Synonymous Codon ◽  
Viral Resistance ◽  
Release Factor ◽  
Codon Reassignment ◽  
Efficient Synthesis ◽  
Noncanonical Amino Acids ◽  
Laboratory Evolution ◽  
Transfer Rnas ◽  
Sense Codon

It is widely hypothesized that removing cellular transfer RNAs (tRNAs)—making their cognate codons unreadable—might create a genetic firewall to viral infection and enable sense codon reassignment. However, it has been impossible to test these hypotheses. In this work, following synonymous codon compression and laboratory evolution in Escherichia coli, we deleted the tRNAs and release factor 1, which normally decode two sense codons and a stop codon; the resulting cells could not read the canonical genetic code and were completely resistant to a cocktail of viruses. We reassigned these codons to enable the efficient synthesis of proteins containing three distinct noncanonical amino acids. Notably, we demonstrate the facile reprogramming of our cells for the encoded translation of diverse noncanonical heteropolymers and macrocycles.

scholarly journals Completion of Replication Map of Saccharomyces cerevisiae Chromosome III

2001 ◽  
Vol 12 (11) ◽  
pp. 3317-3327 ◽  
Author(s):  
Arkadi Poloumienko ◽  
Ann Dershowitz ◽  
Jitakshi De ◽  
Carol S. Newlon
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Dna Replication ◽  
Complete Analysis ◽  
Replication Origins ◽  
Chromosomal Dna ◽  
Chromosomal Replication ◽  
Autonomously Replicating Sequence ◽  
Eukaryotic Chromosome ◽  
Ars Elements ◽  
Chromosome Iii

In Saccharomyces cerevisiae chromosomal DNA replication initiates at intervals of ∼40 kb and depends upon the activity of autonomously replicating sequence (ARS) elements. The identification of ARS elements and analysis of their function as chromosomal replication origins requires the use of functional assays because they are not sufficiently similar to identify by DNA sequence analysis. To complete the systematic identification of ARS elements onS. cerevisiae chromosome III, overlapping clones covering 140 kb of the right arm were tested for their ability to promote extrachromosomal maintenance of plasmids. Examination of chromosomal replication intermediates of each of the seven ARS elements identified revealed that their efficiencies of use as chromosomal replication origins varied widely, with four ARS elements active in ≤10% of cells in the population and two ARS elements active in ≥90% of the population. Together with our previous analysis of a 200-kb region of chromosome III, these data provide the first complete analysis of ARS elements and DNA replication origins on an entire eukaryotic chromosome.

Design and synthesis of a hybrid framework of indanone and chromane: total synthesis of a homoisoflavanoid, brazilane

2018 ◽  
Vol 16 (1) ◽  
pp. 89-100 ◽  
Author(s):  
Jinwoo Kim ◽  
Ikyon Kim
Keyword(s):  
Natural Products ◽  
Total Synthesis ◽  
Hybrid Structure ◽  
Design And Synthesis ◽  
Hybrid Framework

A chemical backbone of tetracyclic homoisoflavanoid natural products such as brazilin inspired us to design a new chemical scaffold, 6a,11b-dihydroindeno[2,1-c]chromen-7(6H)-one, which is a hybrid structure of indanone and chromane.

The replication of yeast chromosomes: lessons fromSaccharomyces cerevisiaechromosome III

1995 ◽  
Vol 73 (S1) ◽  
pp. 208-214 ◽  
Author(s):  
Carol S. Newlon
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Replication Origins ◽  
Chromosomal Replication ◽  
Position Effects ◽  
Autonomously Replicating Sequence ◽  
Systematic Analysis ◽  
Eukaryotic Chromosome ◽  
Ars Elements ◽  
Constant Rate ◽  
Chromosome Iii

To understand how a eukaryotic chromosome is replicated, a systematic analysis of chromosome III of Saccharomyces cerevisiae has been undertaken. Replication origins are specified by autonomously replicating sequence (ARS) elements, whose sequences can be dissected using a simple plasmid assay. Only a subset of ARS elements are active as chromosomal replication origins. Replication origins are required for normal chromosome transmission, but they appear to be redundant; several origins can be deleted without affecting chromosome stability. Replication origin position has been conserved on chromosome III in diverged strains, suggesting that origin position is important for chromosome function. The inability of some ARS elements to function as chromosomal replication origins appears likely to result from chromosomal context or position effects. Replication termination occurs over broad regions between active replication origins. The position of termination can be altered by deleting origins, suggesting that no specific replication termination elements are required. Replication forks appear to move at a relatively constant rate through the chromosome. A replication pause site associated with the centromere results from the kinetochore protein complex that binds the centromere to mediate chromosome segregation. Key words: Saccharomyces cerevisiae, ARS elements, replication origins, replication termination, DNA replication intermediates.

ChemInform Abstract: Design and Synthesis of Heterocyclic Cations for Specific DNA Recognition: From AT-Rich to Mixed-Base-Pair DNA Sequences.

ChemInform ◽  
2014 ◽  
Vol 45 (29) ◽  
pp. no-no
Author(s):  
Yun Chai ◽  
Ananya Paul ◽  
Michael Rettig ◽  
W. David Wilson ◽  
David W. Boykin
Keyword(s):  
Dna Sequences ◽  
Base Pair ◽  
Dna Recognition ◽  
Design And Synthesis ◽  
Heterocyclic Cations

The presence of an RHD pseudogene containing a 37 base pair duplication and a nonsense mutation in Africans with the Rh D-negative blood group phenotype

Blood ◽  
2000 ◽  
Vol 95 (1) ◽  
pp. 12-18 ◽  
Author(s):  
Belinda K. Singleton ◽  
Carole A. Green ◽  
Neil D. Avent ◽  
Peter G. Martin ◽  
Elizabeth Smart ◽  
...  
Keyword(s):  
Blood Group ◽  
Base Pair ◽  
Stop Codon ◽  
Maternal Plasma ◽  
Blood Group System ◽  
Red Cell Membrane ◽  
South Africans ◽  
Cell Membrane Proteins ◽  
Nonsense Mediated Mrna Decay ◽  
Exon 4

Abstract Antigens of the Rh blood group system are encoded by 2 homologous genes, RHD and RHCE, that produce 2 red cell membrane proteins. The D-negative phenotype is considered to result, almost invariably, from homozygosity for a complete deletion ofRHD. The basis of all PCR tests for predicting fetal D phenotype from DNA obtained from amniocytes or maternal plasma is detection of the presence of RHD. These tests are used in order to ascertain the risk of hemolytic disease of the newborn. We have identified an RHD pseudogene (RHD ψ) in Rh D-negative Africans. RHDψ contains a 37 base pair (bp) insert in exon 4, which may introduce a stop codon at position 210. The insert is a sequence duplication across the boundary of intron 3 and exon 4.RHDψ contains another stop codon in exon 6. The frequency ofRHDψ in black South Africans is approximately 0.0714. Of 82 D-negative black Africans, 66% hadRHDψ, 15% had the RHD-CE-D hybrid gene associated with the VS+ V– phenotype, and only 18% completely lackedRHD. RHDψ is present in about 24% of D-negative African Americans and 17% of D-negative South Africans of mixed race. No RHD transcript could be detected in D-negative individuals with RHDψ, probably as a result of nonsense-mediated mRNA decay. Existing PCR-based methods for predicting D phenotype from DNA are not suitable for testing Africans or any population containing a substantial proportion of people with African ethnicity. Consequently, we have developed a new test that detects the 37 bp insert in exon 4 of RHDψ. (Blood. 2000; 95:12-18)

scholarly journals Widespread Distribution of a Group I Intron and Its Three Deletion Derivatives in the Lysin Gene of Streptococcus thermophilus Bacteriophages

2000 ◽  
Vol 74 (2) ◽  
pp. 611-618 ◽  
Author(s):  
Sophie Foley ◽  
Anne Bruttin ◽  
Harald Brüssow
Keyword(s):  
Stop Codon ◽  
Sequence Similarity ◽  
Consensus Sequence ◽  
Gc Content ◽  
Streptococcus Thermophilus ◽  
Variant Form ◽  
Bacterial Genomes ◽  
Stem Loop ◽  
Reading Frame ◽  
Group I

ABSTRACT Of 62 Streptococcus thermophilus bacteriophages isolated from various ecological settings, half contain a lysin gene interrupted by a group IA2 intron. Phage mRNA splicing was demonstrated. Five phages possess a variant form of the intron resulting from three distinct deletion events located in the intron-harbored open reading frame (orf 253). The predicted orf 253 gene sequence showed a significantly lower GC content than the surrounding intron and lysin gene sequences, and the predicted protein shared a motif with endonucleases found in phages from both gram-positive and gram-negative bacteria. A comparison of the phage lysin genes revealed a clear division between intron-containing and intron-free alleles, leading to the establishment of a 14-bp consensus sequence associated with intron possession. The conserved intron was not found elsewhere in the phage or S. thermophilusbacterial genomes. Folding of the intron RNA revealed secondary structure elements shared with other phage introns: first, a 38-bp insertion between regions P3 and P4 that can be folded into two stem-loop structures (shared with introns from Bacillusphage SPO1 and relatives); second, a conserved P7.2 region (shared with all phage introns); third, the location of the stop codon from orf 253 in the P8 stem (shared with coliphage T4 and Bacillus phage SPO1 introns); fourth, orf 253, which has sequence similarity with the H-N-H motif of putative endonuclease genes found in introns fromLactococcus, Lactobacillus, andBacillus phages.

Structure-based synthesis: From natural products to drug prototypes

2009 ◽  
Vol 81 (6) ◽  
pp. 1085-1091 ◽  
Author(s):  
Stephen Hanessian
Keyword(s):  
Natural Products ◽  
Total Synthesis ◽  
Design Element ◽  
X Ray ◽  
Design And Synthesis ◽  
Highly Active ◽  
In Vitro Inhibition ◽  
Inhibitory Activities ◽  
Active Natural

X-ray crystallographic data available from complexes of natural and synthetic molecules with the enzyme thrombin has led to the design and synthesis of truncated and hydrid molecules exhibiting excellent inhibition in vitro. The design element has also been extended to the synthesis and in vitro inhibition of a series of achiral molecules deploying aromatic and heterocyclic core motifs with appropriately functionalized appendages that provide excellent binding interactions at the S1, S2, and S3 sites of thrombin. Excellent selectivity for thrombin over trypsin has also been observed. Thus, studies in total synthesis of highly active natural aeruginosins have inspired further work toward truncated and hybrid analogs with excellent inhibitory activities. Structure-based organic synthesis has guided our research from natural products toward unnatural drug-like prototypes.

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