Comparative Proteomic Analysis of saccharopolyspora spinosa SP06081 and PR2 strains reveals the differentially expressed proteins correlated with the increase of spinosad yield

Table 1 Summary of the identified proteins directly related to spinosad biosynthesis pathway from Saccharopolyspora spinosa SP06081 and PR2 strains during RG1 in SM

Accession number ¹⁾	Protein description	Gene ²⁾	Possible function ³⁾	emPAI value⁴⁾		Sequence coverage (%)		SEQUEST Score ⁵⁾
				PR2	SP06081	PR2	SP06081	PR2	SP06081
gi134098110	acyl carrier protein	ACP	Polyketide synthesis	0.93	0.93	13	13	40	48
gi134100839	modular polyketide synthase	MPS	Polyketide synthesis	0.01	0.01	5	5	48	35
gi30795006	lankamycin synthase, modules 3 and 4	LSM3-4	Polyketide synthesis	0.013	0.018	2	1	70	63
gi30795005	lankamycin synthase, modules 5 and 6	LSM5-6	Polyketide synthesis	0.007	0.007	2	1	55	62
gi10179853	megalomicin 6-deoxy- erythronolide B synthase 2	M6DBS2	Polyketide synthesis	0.006	0.006	3	1	57	81
gi10179852	megalomicin 6-deoxy- erythronolide B synthase 1	M6DBS1	Polyketide synthesis	0.01	/	4	/	100	/
gi30795014	putative NDP-3-keto-6- deoxyhexose 3- ketoreductase	PNDP-DK	Forosamine synthesis	0.04	/	10	/	37	/
gi68270876	BusQ	BusQ	Forosamine synthesis	0.04	/	4	/	20	/
gi13162634	polyketide synthase extender modules 8-10	PSEM8-10	Polyketide synthesis	/	0.004	/	1	/	176
gi13162637	polyketide synthase extender module 2	PSEM2	Polyketide synthesis	/	0.02	/	2	/	115
gi581651	6-deoxyerythronolide B synthase II	6DBSII	Polyketide synthesis	/	0.006	/	2	/	32
gi10179846	TDP-4-keto-6-deoxyhexose 3,5-epimerase	TDP-DE	Rhamnose synthesis	/	0.12	/	11	/	26

1) Protein database accession numbers were obtained on NCBI database.
2) Gene product acronym
3) Functional clustering realized according to Gene Ontology classification http://www.uniprot.org/ and hypothetical pathway for the biosynthesis of spinosyn (see reference 4).
4) The exponentially modified protein abundance index value (emPAI) is the transformed ratio of the number of experimentally observed peptides to the total number of peptides obtained after in silico trypsinization of the protein by using IPEP online proteolysis http://ipep.moffitt.org/searchProtein.cgi.
5) The Score is a sum of the individual peptide scores from all six proteomics run (see Additional file 2 and file 3: Tables S2 and S3).

ISSN: 1477-5956