Pichia pastoris regulates its gene-specific response to different carbon sources at the transcriptional, rather than the translational, level

Table 3 P. pastoris gene statistics of long, medium and short genes

	Long	Medium	Short	All
Number of genes	1262	2538	1265	5065
ORF length [bp]	>1807	770-1807	<770	141-14853
Mean ORF length [bp]	2786	1235	524	1444
Median ORF length [bp]	2412	1206	540	1203
Mean expression intensity	5081	7141	12092	7864
Median expression intensity	2600	2591	3416	2736
Mean SCUO	0.078	0.105	0.198	0.123
Median SCUO	0.069	0.093	0.165	0.096
Genes with 5′UTR	628	257	29	914
Genes with 5′UTR [%]	50%	10%	2%	18%
5′UTR length mean	238	253	320	245
Mean translational state	−0.22	−0.01	0.18	−0.02

Based on the information published by Liang et al. [2], all P. pastoris genes were split into 3 groups comprising the 25% longest (>1807 bp), the 25% shortest (<770 bp) and the remaining (50%, <1807 and >770 bp) medium length genes. Gene groups are not exactly the same size because they were split by length cut-off (some genes possess equal ORF lengths). 5′UTR information was also taken from Liang et al. [2]. Expression intensities were obtained from our total RNA microarray data which were normalized as described in the Methods section. Synonymous codon usage order (SCUO) was obtained from the CodonO platform [35].

ISSN: 1471-2164