Global mRNA decay and 23S rRNA fragmentation in Gluconobacter oxydans 621H

BMC Genomics

Table 1 Functional categories or subcategories comprising 1582 assigned protein-coding ORFs with mean mRNA half-lives based on data from 1526 (96%) transcripts (Additional file 1: Table S1)

functional category / pathway ^a)	number of genes
	assigned ^a)	with a calculated mRNA half-life	proportion (%)	half-life ^b) (min)
ATP-proton motive force interconversion	18	18	100	4.0**
RNA metabolism	23	23	100	4.4*
Cell division	26	26	100	4.6
DNA degradation	9	9	100	4.7
Transcription	13	10	77	4.7
Mono/dioxygenase	10	10	100	4.7
Fatty acid and phospholipid metabolism	36	36	100	4.7
Antibiotics resistance	12	12	100	4.7
tRNA metabolism	13	13	100	4.7
Nucleotide metabolism	59	58	98	4.8
Signal transduction	30	29	97	4.8
Cell envelope	134	131	98	4.9
Amino acid metabolism	120	117	98	5.0
Central intermediary metabolism	33	31	94	5.0
Degradation of proteins and peptides	51	48	94	5.0
Ribosome assembly	67	52	78	5.0
DNA replication	26	26	100	5.1
Pyruvate metabolism	12	11	92	5.1
Regulatory functions	99	94	95	5.1
DNA repair	34	34	100	5.2
Transport	232	227	98	5.2
Aminoacyl-tRNA biosynthesis	33	33	100	5.3
Pentose phosphate pathway	13	13	100	5.3
Biosynthesis of cofactors	85	84	99	5.4
Translation factors	20	20	100	5.4
DNA recombination	18	17	94	5.5
Electron transport	53	53	100	5.5
Unknown function	41	40	98	5.5
Detoxification	30	27	90	5.6
Tricarboxylic acid cycle	9	9	100	5.6
Uncharacterized oxidoreductase	66	63	96	5.7
Adaptations to atypical conditions	19	19	100	6.1
Protein folding and stabilization	28	28	100	6.3
Sugar and alcohol degradation	25	24	96	6.3
Biosynthesis and degradation of polymers	11	10	91	6.4
Glycolysis / Gluconeogenesis	17	16	94	6.5
Cell motility	41	39	95	6.6
Entner-Doudoroff pathway	2	2	100	6.7
Ion homeostasis	6	6	100	6.7
DNA restriction and modification	8	8	100	7.0

^a)Functional categories and number of genes are based on assigned gene product functions [11]
^b)Functional categories with significantly shorter or longer mean half-lives than the overall mean half-life (5.7 min) are highlighted by ** (p < 0.001) or * (p < 0.05)

ISSN: 1471-2164