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Table 1 List of metabolic pathways and functional groups whose genes expression was increased/diminished during different periods of germination

From: Changes in activity of metabolic and regulatory pathways during germination of S. coelicolor

Functional group Deactivation in t1-t2 spore rehydration Activation in t2-t3 Activation in t7-t8 first DNA replication Other periods Note
Amino acid metabolism pathways 250 Alanine, aspartate and glutamate 250 Alanine, aspartate and glutamate   
260 Glycine, serine and threonine 260 Glycine, serine and threonine
270 Cysteine and methionine 270 Cysteine and methionine
280 Valine, leucine and isoleucine degradation 280 Valine, leucine and isoleucine degradation
290 Valine, leucine and isoleucine biosynthesis 290 Valine, leucine and isoleucine biosynthesis
300 Lysine biosynthesis 300 Lysine biosynthesis
310 Lysine degradation 330 Arginine and proline
330 Arginine and proline 340 Histidine400 Phenylalanine, tyrosine and tryptophan biosynthesis
340 Histidine
350 Tyrosine 360 Phenylalanine
380 Tryptophan
400 Phenylalanine, tyrosine and tryptophan biosynthesis  
Carbohydrate metabolism TCA cycle/pentose phosphate/glycolysis/gluconeogenesis TCA cycle/pentose phosphate/glycolysis pathways TCA cycle-associated pathways and genes. Deactivated in t7-t8 the majority - 23 of 57 were associated with the TCA cycle/pentose phosphate/glycolysis pathways genes
40 Pentose and glucuronate interconversions 630 Glyoxylate and dicarboxylate metabolism 40 Pentose and glucuronate interconversions (2) 10 of 30 of the TCA cycle-associated pathways
51 Fructose and mannose metabolism 640 Propanoate metabolism 51 Fructose and mannose metabolism 52 Galactose metabolism
500 Starch and sucrose metabolism 650 Butanoate metabolism 500 Starch and sucrose metabolism 500 Starch and sucrose metabolism
520 Amino sugar and nucleotide sugar metabolism 660 C5-Branched dibasic acid metabolism. 52 Galactose metabolism 520 Amino sugar and nucleotide sugar metabolism
562 Inositol phosphate metabolism 53 Ascorbate and aldarate metabolism 562 Inositol phosphate metabolism
630 Glyoxylate and dicarboxylate metabolism 520 Amino sugar and nucleotide sugar metabolism 650 Butanoate metabolism
650 Butanoate metabolism. 562 Inositol phosphate metabolism 660 C5-Branched dibasic acid metabolism
630 Glyoxylate and dicarboxylate metabolism
640 Propanoate metabolism
650 Butanoate metabolism
Energy metabolism 190 Oxidative phosphorylation, 190 Oxidative phosphorylation 190 Oxidative phosphorylatio genes associated with cytochrome C activated in t11-t12 A minor portion of the genes with diminished expression at t7-t8 only, represented catalase (catA and B; SCO379 and 0666) and nitrate and nitrite reductases (SCO4947, 6102 and 6532)
680 Methane 680 Methane metabolism, 680 methane metabolism
910 Nitrogen metabolisms 910 Nitrogen metabolism, 910 nitrogen metabolism
Folding, sorting and degradation 20S Proteasome subunits (SCO1643 and 1644) and a Signal peptidase I (SCO5597 and 5598). 3018 RNA degradation modest activation of chaperone GroEL (SCO4296 and 4762) DnaK and GroEL was for both diminished at t6-t7.  
3060 Protein export
Lipid metabolism and membrane transport Acetyl CoA carboxylase and acetyltransferase (SCO2445, 5399)    activation at (t1-t2) –  
561 Glycerolipid metabolism 61 and 71 Fatty acid biosynthesis pathways
564 Glycerophospholipid metabolism Deactivation at t7-t8 - ABC transporters,membrane transport system.
ABC transporters
genes of the secretion system
Nucleotide metabolism   240 Pyrimidine metabolism    
230 Purine metabolism
Replication and repair 3030 DNA replication 3030 replication
3410 Base excision repair 3430 mismatch repair
3420 Nucleotide excision repair 3440 homologous recombination
3430 Mismatch repair
3440 Homologous recombination
Transcription/translation 970 Aminoacyl-tRNA biosynthesis   Ribosomal proteins Induced in the t2-t4 time interval. RNA polymerase complex genes, ribosomal proteins (L1, L2, L3, L4, L5, L6, L9, L10, L11, L14, L15, L16, L17, L18, L21, L22, L23, L24, L25, L30, S3, S4, S5, S6, S7, S8, S10, S12, S16, S18, S19)  
ribosomal proteins 970 Aminoacyl-tRNA biosynthesis