TABLE 2.

Proteins upregulated in cells grown on cDCE compared to cells grown on glycolate

Sample	Locus tag	Putative enzyme functiona	Protein scoreb	Peptide countc
1	Bpro0645	GST-like protein	325	8
2	Bpro2715	2-C-methyl-d-erythritol 2,4-cyclodiphosphate synthase	109	2
3	Bpro5186	HAD, type II (plasmid 1)	663	11
3	Bpro0530	HAD, type II (chromosome)	638	9
4	Bpro5186	HAD, type II (plasmid 1)	582	11
4	Bpro0530	HAD, type II (chromosome)	534	9
5	Bpro5186	HAD, type II (plasmid 1)	721	14
5	Bpro0530	HAD, type II (chromosome)	559	11
6	Bpro0646	PNPox-related protein	280	7
7	Bpro2322	2-Isopropylmalate synthase	146	2
8	Bpro5565	CMO	186	3
8	Bpro2322	2-Isopropylmalate synthase	123	2
8	Bpro0759	Chaperonin GroEL	70	1
9	Bpro2029	Trigger factor	404	9
9	Bpro3157	Protein of unknown function DUF404	265	5
9	Bpro5565	CMO	70	1
9	Bpro1807	Glutamine synthetase, type I	68	1
11	Bpro0646	PNPox-related protein	207	6
13 DCEd	Bpro4562	Hydroxypyruvate isomerase	790	16
13 GLYd	Bpro4562	Hydroxypyruvate isomerase	722	16

^aProteins upregulated by both reference substrates are indicated by bold type. Annotations were derived from the DOE Joint Genome Institute Integrated Microbial Genomes database.

^bSamples 2 and 7 to 9 were identified using LC-MS/MS. All other samples were identified using MALDI-TOF/TOF MS. Spot 10 had 12 protein matches, which are not listed.

^cNumber of significant peptides with an expectation value of <0.001 for MALDI-TOF/TOF MS samples and an expectation value of <0.01 for LC-MS/MS samples.

^dAll proteins were from 2D gel spots that were present only in cDCE gels, with the exception of samples 13 DCE and 13 GLY, which were highly upregulated in the cDCE gel.