Figure 1.
Streptomyces coelicolor development stages and sample preparation.
(A) Liquid non-sporulating cultures. (B) Solid sporulating cultures. Mycelial structures (MI, first compartmentalized mycelium; MII, second multinucleated mycelium). The classical nomenclature of substrate, aerial mycelium, and hydrophobic layers are indicated. Three independent biological replicates and two developmental stages (MI and MII) were processed and cDNA was labeled with Cy3 while chromosomal S. coelicolor DNA was used as reference and labeled with Cy5. The scheme was adapted from Manteca et al. [12].
Table 1.
Transcripts showing opposite (positive values in solid and negative in liquid or vice versa) and significant (coefficient of variation between solid and liquid cultures higher than 0.7) abundances (Fig. 4C, F, I, L, O, R, U; Fig. 5C, F, I, L).
Table 2.
Transcripts up- or down- regulated in MI or MII liquid and solid cultures, showing differences in their abundances (coefficient of variation between liquid and solid higher than 0.7).
Figure 2.
Quantitative transcriptomic data analysis.
Correlation of transcription abundance values (log2 ratio against chromosomal DNA). Upper panels - biological replicates: (A) MIL vs. MIL, (B) MIIL vs. MIIL, (C) MIL vs. MIIL (three biological replicates compared in pairs). Lower panels - developmental stages (average abundance values from three biological replicates: (D) MIL vs. MIS, (E) MIIL vs. MIIS, (F) MIL vs. MIIS and MIS vs. MIIL.
Figure 3.
Comparison between transcriptomics (this work) and proteomics [12].
Transcription and protein abundance values correspond to log2 MIIL/MIL and are the average of two (in the case of proteomics) or three (in the case of transcriptomics) biological replicates. Dashed lines indicate the limit for considering abundance variations as significant (log2 abundances greater than ±1). (A) Proteins and transcripts significantly up-regulated in MIIL (positive abundance values higher than 1) or in MIL (negative abundance values lower than −1). (B) Proteins and transcripts without significant variations (log 2 abundances within ±1 interval). (C) Proteins and transcripts showing divergent abundance values (positive values in MIL and negative in MIIL or vice versa).
Figure 4.
Abundance values of transcripts quantified in solid and liquid cultures (1901 in total) and grouped into functional categories.
Abundance values (average of log2 MII/MI from three biological replicates) and transcripts with significant variations in MIIL and/or MIIS (log2 abundance greater than ±1) are shown. Transcripts without significant (log2 abundance within the ±1interval) are indicated into squares and labeled as “No variation”. Functional categories: primary metabolism (DNA/RNA replication, aerobic and anaerobic energy production, glycolysis and glyconeogenesis, pentose phosphate pathway, amino acid metabolism, nucleotide metabolism, translation, protein folding, RNA/protein processing, nucleases/RM methylases); secondary metabolism (secondary metabolite synthesis); differentiation (TTA bldA targets, Bld and Whi proteins); regulatory genes (transcriptional regulators, kinases, other regulatory genes); transposons - insertion sequences; conjugation, recombination, mutagenesis; stress and defense proteins. Dashed lines indicate the limit for considering abundance variations significant (log2 abundance ±1).
Figure 5.
Transcripts abundance values (log2 MII/MI) grouped in functional categories (continuation).
Functional categories: catabolism and degradation; lipid metabolism; transporters and secreted (ABC transporters, transporters and secreted proteins); genes with unknown function. Dashed lines indicate the limit for considering abundance variations significant (log2 abundance ±1).
Table 3.
Summary of well characterized genes whose transcripts showed similar abundances in liquid and solid cultures (coefficient of variation between liquid and solid cultures lower than 0.7) (Fig. 4A, D, G, J, M, P, S; Fig. 5A, D, G, J).