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genomes. To achieve that, it is essential to broaden this analysis to a larger
group of cyanobacterial strains, which will provide a robust basis for the
reconstruction of the phylogenetic history of cyanobacterial EPS-related
genes, and consequently, allow the optimization of the EPS production
mechanisms.
3.1. Phylogeny of Genes Encoding Proteins Involved
in Cyanobacterial EPS Assembly and Export
The recent high-throughput sequencing techniques have generated large
amounts of genetic data that can be used to reconstruct the evolutionary
history of the EPS-related genes in cyanobacteria. To guarantee a through-
out analysis, 24 cyanobacterial genome sequences (available at NCBI -
National Centre for Biotechnology Information; database March 2012)
were selected. The genomes belong to strains from different orders/subsec-
tions, displaying distinct morphologies, and that were isolated from various
ecological niches.
To start our study, the conserved domains present on the proteins involved
in well-characterized systems of bacterial EPS assembly and export, and
that follow the Wzy- (Wz_ homologues) or ABC-dependent (Kps_ homo-
logues) pathways (see above, sections 2.1. and 2.2.), were identified using
the InterProScan Sequence Search available at the EMBL-EBI (European
Bioinformatics Institute) (
Hunter et al., 2012
). Once the domains were
identified, their presence or absence was investigated in the selected cyano-
bacterial strains, using the InterPro Protein Sequence Analysis & Classifica-
tion Tool, also available at the EMBL-EBI. This analysis yield a large number
of putative cyanobacterial Wz_ and Kps_ homologues (
Tables 7.1 and 7.2
).
Interestingly, proteins possessing the Wzy characteristic domain were
found in all strains analysed, suggesting that cyanobacterial EPS assembly and
export should, in most cases, proceed via this mechanism. This hypothesis
is supported by the higher abundance of Wz_ homologues in cyanobacte-
ria, with several strains possessing all the Wz_ surveyed. Despite that, nine
strains, from unicellular to filamentous heterocystous, lack identifiable Wzx
homologues, raising the hypothesis that the cyanobacterial EPS assembly
and export systems may not fit exactly in the existing models. The postula-
tion of a Wzy-dependent related pathway in cyanobacteria is reinforced by
the low number of putative KpsC and KpsS identified, which could only
be found in
Synechocystis
sp. PCC 6803,
Nostoc punctiforme
PCC 73102, and
Cylindrospermopsis raciborskii
CS-505. Although the exact functions of these
proteins are yet undetermined, in
E. coli
, they were shown to be essential for
