Phenotypic Landscape of a Bacterial Cell

The recent increase in genomic data is revealing an unexpected perspective of gene loss as a pervasive source of genetic variation that can cause adaptive phenotypic diversity. This novel perspective of gene loss is raising new fundamental questions. How relevant has gene loss been in the divergence of phyla? How do genes change from being essential to dispensable and finally to being lost? Is gene loss mostly neutral, or can it be an effective way of adaptation? These questions are addressed, and insights are discussed from genomic studies of gene loss in populations and their relevance in evolutionary biology and biomedicine.

Evolution by gene loss

https://patofyziologie.lf1.cuni.cz/file/100/Aebersold_skoro%20kompletni%20kvasinka%202012.pdf

Quantitative Analysis of Fission Yeast Transcriptomes and Proteomes in Proliferating and Quiescent Cells

In this essay, we revisit the status of yeast as a model system for biology. We first summarize important contributions of yeast to eukaryotic biology that we anticipated in 1988 in our first article on the subject. We then describe transformative developments that we did not anticipate, most of which followed the publication of the complete genomic sequence of Saccharomyces cerevisiae in 1996. In the intervening 23 years it appears to us that yeast has graduated from a position as the premier model for eukaryotic cell biology to become the pioneer organism that has facilitated the establishment of the entirely new fields of study called “functional genomics” and “systems biology.” These new fields look beyond the functions of individual genes and proteins, focusing on how these interact and work together to determine the properties of living cells and organisms.

https://www.genetics.org/content/genetics/189/3/695.full.pdf

Yeast: An Experimental Organism for 21st Century Biology

DNA-Damaging Agents in Cancer Chemotherapy: Serendipity and Chemical Biology

We report the construction and analysis of 4,836 heterozygous diploid deletion mutants covering 98.4% of the fission yeast genome providing a tool for studying eukaryotic biology. Comprehensive gene dispensability comparisons with budding yeast--the only other eukaryote for which a comprehensive knockout library exists--revealed that 83% of single-copy orthologs in the two yeasts had conserved dispensability. Gene dispensability differed for certain pathways between the two yeasts, including mitochondrial translation and cell cycle checkpoint control. We show that fission yeast has more essential genes than budding yeast and that essential genes are more likely than nonessential genes to be present in a single copy, to be broadly conserved and to contain introns. Growth fitness analyses determined sets of haploinsufficient and haploproficient genes for fission yeast, and comparisons with budding yeast identified specific ribosomal proteins and RNA polymerase subunits, which may act more generally to regulate eukaryotic cell growth.

/pdf/analysis-of-a-genome-wide-set-of-gene-deletions-in-the-5citfpy3ix.pdf

Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe

Corrigendum: Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe

/pdf/corrigendum-analysis-of-a-genome-wide-set-of-gene-deletions-1wbbgvgnai.pdf

A method comprising transforming Schizosaccharomyces pombe with a deletion cassette, constructed by four-round serial PCR, block PCR or total gene synthesis, containing a homologous recombination site is provided for preparing gene-targeted heterozygous deletion Schizosaccharomyces pombe Also provided are gene-targeted hetero2ygous deletion Schizosaccharomyces pombe mutants prepared by the method, and a library of gene-targeted heterozygous deletion Schizosaccharomyces pombe mutants Further, the library is useful in constructing a method and a kit for screening a drug's modes of action

Genome-wide construction of Schizosaccharomyces pombe heterozygous deletion mutants containing gene-specific barcodes by the methods of 4-round serial or block PCR, or total gene synthesis thereof

Jo Young Park

Papers

Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe

Corrigendum: Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe

Genome-wide construction of Schizosaccharomyces pombe heterozygous deletion mutants containing gene-specific barcodes by the methods of 4-round serial or block PCR, or total gene synthesis thereof