FIGURE 2 

Phenotype of parent versus trmB mutant strain during growth. (A) Comparison of growth of the parent strain versus mutant in complete defined medium (CDM) supplemented with various sugars (x-axis). Ratio of ura3 parent to trmB growth doubling time is represented on the y-axis. Error bars represent the s.d. from the mean of at least 3 biological replicate samples, 3 technical replicates each for a total of at least 9 observations and at most 20. Asterisks represent confidence of P<0.001 of mutant versus parent in non-parametric paired t-tests (i.e. mutant grew significantly slower than parent in all cases except for glucose). (B) NAD⁺/H assay shows that energy status is perturbed in mutant cells. 'Glu', glucose was added to cultures. Adding glucose to parent strain cultures did not change NAD⁺/H levels significantly (not shown). Error bars represent the s.d. from at least three biological replicate experiments. Asterisks represent P<0.05 difference between parent and trmB in the absence of glucose in non-parametric paired t-tests. (C) The trmB mutant has a defect in expression of genes associated with diverse metabolic processes. Figure represents results of mRNA expression profiling using microarrays. Log10 expression ratios of trmB and ura3 parent versus the common reference RNA (Materials and methods) (y-axis) are plotted throughout the growth curve (black triangles beneath graph). The three time points depicted in the expression graph represent RNA collected from cultures in early log, mid-log, and stationary phase relative to parent strain in the presence (+) and absence (-) of glucose (x-axis). Colored lines on the graph represent the mean expression profile for genes in each functional category. In the legend, numbers in parentheses indicate the number of genes and the Gene Ontology (GO) P-value of enrichment in each category and colors of corresponding categories are indicated. Those categories with no P-values shown had no annotations in KEGG or GO and were therefore hand annotated based on protein functional information from databases (Materials and methods).