Engineering the ribosomal DNA in a megabase synthetic chromosome

Journal of bacteriology, 1978

The intragenic organization of ribosomal DNA from a diploid strain of Saccharomyces cerevisiae was analyzed by using recombinant DNA molecules constructed in vitro. Restriction analysis of the yeast ribosomal DNA with the EcoRI restriction enzyme indicated that eight restriction fragments were present in the ribosomal DNA of this strain: X' (1.87 X 10(6) daltons), A (1.77 X 10(6) daltons), B (1.48 X 10(6) daltons), C (1.22 X 10(6) daltons), D (0.39 X 10(6) daltons), E (0.36 X 10(6) daltons), F (0.22 X 10(6) daltons), and G (0.17 X 10(6) daltons). These fragments were distributed between two different types of ribosomal DNA genes, which had the restriction maps: (formula: see text) in which the underlined region shows the repeating unit. The diploid yeast strain contained approximately equal amounts of each of these two types of genes. The analysis of the recombinant DNA molecules also indicated that the yeast ribosomal genes are homogeneous and extensively clustered.

Hereditas, 2004

Nature Communications, 2022

The Synthetic Yeast Genome Project (Sc2.0) represents the first foray into eukaryotic genome engineering and a framework for designing and building the next generation of industrial microbes. However, the laboratory strain S288c used lacks many of the genes that provide phenotypic diversity to industrial and environmental isolates. To address this shortcoming, we have designed and constructed a neo-chromosome that contains many of these diverse pan-genomic elements and which is compatible with the Sc2.0 design and test framework. The presence of this neo-chromosome provides phenotypic plasticity to the Sc2.0 parent strain, including expanding the range of utilizable carbon sources. We also demonstrate that the induction of programmable structural variation (SCRaMbLE) provides genetic diversity on which further adaptive gains could be selected. The presence of this neo-chromosome within the Sc2.0 backbone may therefore provide the means to adapt synthetic strains to a wider variety of environments, a process which will be vital to transitioning Sc2.0 from the laboratory into industrial applications.

YAC Protocols, 2006

Mammalian Genome, 1992

We describe methods for rapid production and screening of yeast artificial chromosome (YAC) libraries. Utilizing complete restriction digests of mouse genomic DNA for ligations in agarose, a 32,000clone library was produced and screened in seven weeks. Screening was accomplished by subdividing primary transformation plates into pools of approximately 100 clones which were transferred into a master glycerol stock. These master stocks were used to inoculate liquid cultures to produce culture "pools," and ten pools of 100 clones were then combined to yield superpools of 1,000 clones. Both pool and superpool DNA was screened by polymerase chain reaction (PCR) and positive pools representing 100 clones were then plated on selective medium and screened by in situ hybridization. Screening by the two tiered PCR assay and by in situ hybridization was completed in 4-5 days. Utilizing this methodology we have isolated a 150 kb clone spanning the al(I) collagen (Collal) gene as well as 40 kb clones from the Hox-2 locus. To characterize the representation of the YAC library, the size distribution of genomic Sal I fragments was compared to that of clones picked at random from the library. The results demonstrate significant biasing of the cloned fragment distribution, resulting in a loss of representation for larger fragments.

Proceedings of the National Academy of Sciences, 1996

DNA molecules undergoing transformation into yeast are highly recombinogenic, even when diverged. We reasoned that transformation-associated recombination (TAR) could be employed to clone large DNAs containing repeat sequences, thereby eliminating the need for in vitro enzymatic reactions such as restriction and ligation and reducing the amount of DNA handling. Gently isolated human DNA was transformed directly into yeast spheroplasts along with two genetically marked (Ml and M2) linearized vectors that contained a human Alu sequence at one end and a telomere sequence at the other end (Alu-CEN-MI-TEL and Alu-M2-TEL). Nearly all the Mi-selected transformants had yeast artificial chromosomes (YACs) containing human DNA inserts that varied in size from 70 kb to >600 kb. Approximately half of these had also acquired the unselected M2 marker. The mitotic segregational stability of YACs generated from one (Ml) or two (Ml and M2) vector(s) was comparable, suggesting de novo generation of telomeric ends. Since no YACs were isolated when rodent DNAs or a vector lacking an Alu sequence was used, the YACs were most likely the consequence of TAR between the repeat elements on the vector(s) and the human DNA. Using the BLUR13 Alu-containing vector, we demonstrated that human DNA could be efficiently cloned from mouse cells that contained a single human chromosome 16. The distribution of cloned DNAs on chromosome 16 was determined by fluorescence in situ hybridization. We propose that TAR cloning can provide an efficient means for generating YACs from specific chromosomes and subchromosome fragments and that TAR cloning may be useful for isolating families of genes and specific genes from total genome DNA.

Proceedings of The National Academy of Sciences, 1974

In vivo, ribosomal RNA of Saccharomyces cerevisiae is transcribed from the light strand of γ DNA. In vitro, γ DNA is transcribed with equal efficiency by both of the yeast nuclear RNA polymerases, polymerase I and polymerase II; however the RNA products synthesized by the two enzymes differ from each other both in size and in the relative composition of guanine and cytosine. RNA synthesized by polymerase I hybridizes preferentially to the light strand, while that synthesized by polymerase II hybridizes equally well to either strand. Selective transcription of the light strand of the ribosomal DNA also occurs when high-molecular-weight total nuclear DNA is used as template.

Biotechnology Techniques, 1996

Yeast chromosomal DNA was prepared under different conditions. Treatment of intact cells with proteinase I( (1 mg/ml) resultes in appropriate electrophoretic karyotypes; when protoplasts were formed III s&r, the presence of both sodium lauroylsarcosine and EDTA was essential. Further, the duration of cell wall lysis (12 h) and the concentrations of lytic enzymes (0.5% snail enzyme and 0.25% Novozym)had to be kept at a minimum.

Fungal Genetics Reports, 1994

A yeast artificial chromosome (YAC) library of Neurospora crassa strain 74-OR23-1A has been constructed. This library has been used to clone 750 kb of contiguous DNA sequences from the centromere region of linkage group VII (M. Centola and J. Carbon. 1994. Mol. Cell. Biol. 14:1510-1519). The purpose of this article is explicitly to outline procedures that have been developed for library screening and chromosome walking.

FEBS Letters, 1982