Table 3.

Proteins Identified in Arabidopsis Leaf Peroxisomes

	Known Proteins			Novel Proteins					Predicted Proteins
	Total	Matrix	Membrane	Total	PTS1	PTS2	PTS-Like	Non-PTS1	PTS1	PTS2
Up to 2007	75	51	24	–	–	–		–	221	60
This study	36	33	3	43	21	2	5	15	311	611

Of the 51 known matrix proteins reported up to 2007 to be targeted to plant peroxisomes, 33 (65%) were identified in this proteome study of Arabidopsis leaf peroxisomes. With respect to membrane proteins, the coverage of known proteins is significantly reduced (3 out of 24), consistent with the low content of membrane proteins in the entire proteome of the organelle. In total, 43 novel peroxisomal proteins were identified (42 by the proteome approach, 6PGL as EYFP fusion protein). Approximately half of the novel proteins (21; 49%) carry a previously defined PTS1 tripeptide (16 proteins; Reumann, 2004) or one of three novel functional PTS1 tripeptides (SSL>, SSI>, and ASL>) identified in this study (five proteins). The identification of three novel PTS1 tripeptides increases the number of putative PTS1 proteins encoded in the Arabidopsis genome by 40%, from 221 to 311. Even though a considerable number of Arabidopsis proteins carry a predicted PTS2 at an internal position, as does TLP (¹, 201 proteins with a major PTS2 and 443 proteins with a minor PTS2), these proteins are not listed because only few bifunctional proteins are expected to expose a functional PTS2 on the protein surface and to represent true positive peroxisomal matrix proteins.