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marine picocyanobacterial clade. Nineteen of the 90 genomes that contain
one full-length OCP contain a second or even a third copy (
Synechococcus
sp.PCC7335,
Synechocystis
sp. PCC7509,
Pleurocapsa
sp. PCC7319).
Numerous cyanobacterial genomes also contain separate genes encod-
ing the N- and C-terminal domains (
Fig. 1.3
); in some cases, they are
adjacent to one another on the chromosome (e.g. in
T. elongatus
and the
Fischerella
genomes); in others, they are found in different locations in the
genome (e.g.
Oscillatoria acuminata
PCC6304). Genes for the individual
domains can be found in organisms in addition to full-length OCP or as the
only homologues to the OCP. In general, most organisms are enriched in
additional copies of the N-terminal domain with some diversity in length
and sequence. Most of the genomes encoding genes for the N-terminal
domain also contain a gene encoding the C-terminal domain, but in con-
trast to the N-terminal domain paralogues, these are strongly conserved
and present only in single copies (
Fig. 1.3
). However, some organisms
contain additional genes encoding proteins that adopt the NTF2 fold that
can be detected only by structural similarity (e.g. ava_2261 from
Anabaena
variabilis
, PDB code: 3dmc and npun_r3134 from
Nostoc punctiforme
, PDB
code: 2rqq), yet do not have appreciable sequence homology to the C-ter-
minal domain of the OCP. The function of any of these additional cop-
ies of the N- and C-terminal domains is unknown; it has been proposed
that they could assemble with carotenoids in a modular manner (
Kerfeld,
Sawaya, et al., 2003
) to form OCP variants with different light sensitivities
(receivers) or outputs (affinity for phycobilisome or other response). Such
modularity, as noted above, is well known for other blue-light-responsive
proteins such as those containing BLUF and LOV domains (
Losi, 2007
).
However,
T. elongatus
, in which the N- and C-terminal domains are
encoded by two adjacent genes, does not appear to have a characteristic
OCP-related photoprotective mechanism (
Boulay, Abasova, et al., 2008
),
suggesting that at least some of these modular paralogues have a different
function. It is known that some of the N-terminal domain paralogues are
expressed (
Anderson, Campbell, et al., 2006
;
Stockel, Welsh, et al., 2008
).
In addition to discovering the OCP, David Krogmann's team was also
able to isolate a red protein, dubbed the RCP from
A. maxima
(
Knutson,
1998
). Sequence analysis and mass spectrometry indicated that this was a
short form of the OCP, lacking the first 15 and the last ∼150 amino acids
of the full-length protein. It was assumed to be a proteolytic fragment of
the OCP because the amino acid sequence determined by Edman degra-
dation was otherwise identical to the OCP. Structurally, this corresponds