For PPI degree, gene sequence conservation, cell-cycle expression variation, and protein abundance, relationships between HI and gene properties were significant among both essential and nonessential genes.
Because HI associates with PPI degree, gene sequence conservation, cell-cycle expression variation, and protein abundance among both essential and nonessential genes, we can infer that although a confounding effect exists between gene essentiality and HI, gene essentiality does not fully explain the relationships between the gene properties and HI.
In addition, conserved cell cycle regulatory motifs across these two species are more nucleosome-depleted compared to those that are not conserved, suggesting that the degree of conservation of regulatory sites varies, and is reflected by nucleosome occupancy patterns.
The analysis described above reveals combined effects of the presence of a motif and the levels of nucleosome occupancy on the conservation of cell cycle expression.
We also assessed the conservation of cell cycle specific gene expression using the 800 genes previously identified by a different dataset [ 55] as periodically expressed in synchrony with the cell cycle in S. cerevisiae, and observed that 226 of these orthologs were periodically expressed in synchronous cultures of S. bayanus (p<0.001).
Conservation of cell cycle-regulation is defined as in both species, the periodicity difference is smaller than that of the inflection point.
The phenotypes, including chromosome hypercondensation, aberrant segregation, and polyploidy, are reminiscent of the defects observed in Ubc9-deficient mouse embryos and Drosophila embryos mutant for pias, a possible SUMO ligase [13], [72], indicating conservation of SUMO cell cycle functions in metazoan evolution.
An assay of cell size of all nonessential homozygous and all 1166 essential heterozygous deletion mutants identified a much smaller set of 49 genes that dramatically alter cell size, 88% of which have human homologs (Zhang et al. 2002), underscoring the remarkably high level of conservation in core cell cycle control genes.
Given the conservation across phyla between cell cycle proteins, we herein applied the DIVEC approach to perform a biochemical screen for APC substrates in Xenopus interphase egg extract and identified Drosophila Microcephalin (dMCPH1) as a candidate.
To investigate whether there is a correlation between nucleosome and motif interaction to cell-cycle expression conservation, we ranked the orthologous cell cycle regulated genes with conserved MBP1 motifs according to whether they are cyclically expressed in S. bayanus.
This modeling is essential in order to underline differences and conservation of several features of cell cycle regulation in alpha proteobacteria.
