Diversity and evolution of phycobilisomes in marine Synechococcusspp.: a comparative genomics study

Table 2 Presence or absence of genes encoding linker polypeptides in the different marine Synechococcus genomes

		Allophycocyanin		Phycocyanin			Phycoerythrin I		Phycoerythrin II
Strain	Pigment type	apcC (L_C)	apcE (L_CM)	cpcC (L_R)	cpcD (L_R)	cpcG (L_RC)	cpeC (L_R)	cpeE (L_R)	mpeD* (L_R)^†	mpeC (L_R)^†	mpeE (L_R)^†	mpeF (L_R)^†	mpeG (L_R)^†
WH5701	1	CC	CC^‡	RC (cpcCI^‡) RC (cpcCII^‡) NC (cpcCIII^‡§)	RC	GC (cpcGI)^‡ RC (cpcGII)	-	-	-	-	-	-	-
RS9917	1	CC	CC	RC (cpcCI) RC (cpcCII)	RC	GC (cpcGI) RC (cpcGII)	-	-	-	-	-	-	-
WH7805	2	CC	CC^‡	-	-	GC (cpcGI)^‡ RC (cpcGII)	RC^‡	RC^‡	RC^‡	-	-	-	-
WH7803	3a	CC	CC^‡	-	-	GC (cpcGI)^‡ RC (cpcGII)	RC^‡	RC^‡	RC^‡	-	RC^‡	-	-
RCC307	3b	CC	CC^‡	-	-	GC (cpcGI)^‡ RC (cpcGII)	RC^‡	RC^‡	RC^‡	RC^‡	NC^‡	-	NC
CC9311	3d (CA)	CC	CC	-	-	GC (cpcGI) RC (cpcGII) NC (cpcGIII)	RC	RC	RC	RC	RC	NC	-
CC9902	3d (CA)	CC	CC	-	-	GC (cpcGI) RC (cpcGII) NC (cpcGIII)	RC	RC	RC	RC	NC	NC	-
BL107	3d (CA)	CC	CC	-	-	GC (cpcGI) RC (cpcGII) NC (cpcGIII)	RC	RC	RC	RC	NC	NC	-
RS9916	3d (CA)	CC	CC^‡	-	-	GC (cpcGI)^‡ RC (cpcGII)	RC^‡¶	RC^‡	RC^‡	RC^‡	RC^‡	-	NC
CC9605	3c	CC	CC	-	-	GC (cpcGI) RC (cpcGII) NC (cpcGIII)	RC	RC	RC	RC	NC	-	-
WH8102	3c	CC	CC	-	-	GC (cpcGI) RC (cpcGII)	RC	RC	RC	RC	NC	-	-

CC, gene located within the PBS core gene cluster; GC, gene located within a cluster comprising the cpcGI and cpcS genes; NC, gene unlinked to other PBS genes; RC, gene located within the PBS rod gene cluster. Novel gene names proposed in this study are underlined. The linker polypeptide compositions of Synechococcus spp. WH5701, WH7803, WH7805 and RS9916 were checked by mass spectrometry after cutting the bands out of the LiDS-PAGE gel shown in Figure 5. For annotating paralogs that originated from recent gene duplications and have no obvious differential functional specializations (one-function paralog family), we chose the genetic nomenclature used by Berlyn [77] for Escherichia coli K-12. *MpeD is a chimeric protein made of two linker domains associated with PEI and PEII, respectively [19]. ^†Linkers chromophorylated with PUB. ^‡Linkers that have been identified by mass spectrometry. ^§The product of this cpcC gene has an extended carboxyl terminus showing strong homology to CpcD. ^¶CpeC and MpeC co-eluted in RS9916, explaining the darker band observed at approximately 36 kDa apparent molecular weight in Figure 5. CA, type IV chromatic adapter; L_C, core linker; L_CM, core-membrane linker; L_R, rod linker; L_RC, rod-core linker.

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