Organization of carboxysome genes and the genes of related polyhedra. Gene similarity is indicated by the different fill patterns. Gene homologies were assigned based on multiple sequence alignments that considered residue and positional identities. The deduced ORFA and ORFB peptides are 22 to 30% identical to CcmL gene products; CsoS1-like peptides are 50 to 99% identical (62). All of the genes are read from left to right. We have taken the liberty of calling the Prochlorococcus carboxysome genes csoS1, ORFAB, csoS2, and csoS3 instead of ccmK, ccmL, ccmM, and ccmN, respectively, since they are more closely related to the former. Abbreviations: cbb, Calvin-Benson-Bassham cycle in eubacteria and archaea cbbL and cbbS, large and small subunits of RuBisCO; cso, carboxysome; ORF, unidentified open reading frame; ccm, carbon-concentrating mechanism; rbcL and rbcS, large and small subunits of RuBisCO in cyanobacteria; pdu, propanediol utilization; eut, ethanolamine utilization. ∗, Two different sulfur bacteria exhibit the same organization, and a third exhibits the same except that the cso genes are not located downstream of cbbLS. ∗∗, Synechococcus strain PCC 7002 has the same organization as Synechococcus strain PCC7942, except that ccmO is missing from the cluster and rbcX resides between rbcL and rbcS. The ccmO gene may reside elsewhere on the genome of PCC7002 (see Synechocystis strain PCC6803). Additional ccmK genes could potentially reside elsewhere on the genome in both PCC7942 and PCC7002. Synechococcus strains PCC6301 possesses two ORFs immediately upstream of rbcL and rbcS, which appear to be equivalent to ccmO. Additional upstream sequencing has not been reported. ∗∗∗, Synechocystis strain PCC6803 possesses two additional ccmK genes and a ccmO gene completely separate from the ccmKLMN cluster. Nostoc punctiforme exhibits the same organization as Synechocystis strain PCC6803, except that ccmO is found immediately downstream of ccmN and not elsewhere on the genome. Furthermore, ccmO possess only a single ccmK homolog rather than two, as is the case with the other ccmO. ∗∗∗∗, Prochlorococcus strain MED4 shows the same organization as MIT9313, except the downstream csoS1 is missing. Synechococcus WH8102 shows the same organization as Prochlorococcus MIT9313. It seems likely that Synechococcus strain WH7803 will also show the same organization, but the downstream region has not been sequenced.