Table 1.
Data sets contributing to the Cyanothece 51142 proteome coverage.
Figure 1.
Hierarchical clustered heat map of proteins with diurnal abundance changes.
The samples were taken from cultures grown under nitrogen fixing conditions in alternating light/dark cycles over a period of 48 hours. Each colored area in the template represents the relative spectral counts of the associated proteins. White colored areas reveal absence of data.
Figure 2.
Functional category breakdown for all cyclic proteins.
The graph shows the percentage of cyclic proteins within each functional category, calculated based on the total number of predicted proteins in each functional category. The number of cyclic proteins vs. the total number of proteins from each functional category is shown in bold. Functional categories for each gene are assigned as [6].
Figure 3.
Venn diagram representing all transcripts and proteins with and without oscillating abundance profiles during a diurnal cycle.
(A) Transcripts present on the microarray and (B) proteins detected under diurnal conditions. Transcripts identified as cyclic are shaded in green, while proteins identified as cyclic are in blue.
Figure 4.
Integration of transcriptomic and proteomic data.
(A) Co-expression network of previously obtained transcriptomic data which contains all genes with cyclic mRNA abundance that changed by at least 1.3-fold over the entire time course [5]. The network was visualized using Cytoscape version 2.5.1 [43]. Genes with Pearson correlation coefficients ≥0.9 are connected and each node corresponds to one gene. The genes are colored according to their relative mRNA abundance at time point L5 (five hours in the light cycle). (B) All genes in the co-expression network from panel A for which cyclically expressed proteins were detected are colored according to the relative protein abundance levels at time point L5. Genes without corresponding cyclic proteins are shown in grey. Other time points are shown in Figure S5.
Figure 5.
Overview of diurnal changes in the abundance of proteins involved in central metabolic pathways during a circadian cycle.
Enzymatic steps involving proteins with maximal abundance during the dark are shown in blue, while proteins with peak expression during the light period are represented by red arrows. Dark grey colored arrows indicate proteins without significant changes in their abundance during a diurnal period while light grey colored arrows represent proteins that were not detected. GlgA1: glycogen synthase, GlgB2: 1,4-alpha-glucan branching enzyme, GlgC1,2: glucose-1-phosphate adenylyltransferase, GlgP1: glycogen phosphorylase, Zwf: glucose-6-phosphate dehydrogenase, TalA: transaldolase AB family, Fbp: fructose 1,6 bisphosphatase I, GpmI: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase, EnoI: Enolase, Ppc: Phosphoenolpyruvate carboxylase, Me: malic oxidoreductase, Mdh: Malate dehydrogenase, FumC: fumarate hydratase, SdhA: succinate dehydrogenase subunit A, NifHDK nitrogenase subunits HDK, HupL: uptake hydrogenase large subunit, GlsF: ferredoxin-dependent glutamate synthase, CarA: carbamoyl phosphate synthase, PyrD: dihydroorotate dehydrogenase, Prk: phosphoribulokinase, Rpe: ribulose-phosphate 3-epimerase, GlpX: fructose-1,6-bisphosphatase II, Spt: serine:pyruvate/alanine:glyoxylate aminotransferase, GcvP: glycine carboxylase, LpdA: dihydrolipoamide dehydrogenase, 3-PGA: 3-phosphoglycerate, 1,3-bis PGA: 1,3 bis-phosphoglycerate, GAD-3P: glyceraldehyde-3-phosphate, DHAP: dihydroxy acetone phosphate.