GENOMES - Cyanobacteria - page 93

genome is attributed due to a loss of a number of genes and the strain-specifi c genes are suggested to
have been acquired through phages. There is one rRNA operon in MED4 while there are two in case
of MIT9313. The number of tRNA genes is 37 in MED4 when compared to 43 present in MIT9313.
The identifi cation of the gene for chlorophyll a oxygenase in the genome of Prochlorococcus has been
confi rmed by a comparative genomic approach (Satoh and Tanaka, 2006).
On the basis of 16S rRNA phylogeny it was suggested that P. marinus MIT9313 branches at the
Prochlorococcus radiation coming closer to Synechococcus group (Fuller et al ., 2003). P. marinus SS120
comes closer to P. marinus MED4 in its genome size being larger by only about 90 kb. Dufresne et
al. (2005) compared the genomes of P. marinus MED4, Prochlorococcus SS120 and P. marinus MIT9313
and Synechococcus sp. strain WH8102. The gene order in MED4 and SS120 is highly conserved with
only fi ve inversions larger than 20 kb having taken place in both these genomes whereas large
number of inversions, translocations and extensive genome rearrangements have taken place in
between Synechococcus and Prochlorococcus , on the one hand, and between MIT9313 and the two
Prochlorococcus strains on the other. These workers are of the view that the divergence of the clade
with MED4 and SS120 is a more recent one than that containing P. marinus MIT9313. They have
identifi ed 1306 orthologous genes that are highly conserved in all marine picocyanobacteria. Total
percentages of protein-coding genes in these four organisms under comparison revealed that
P. marinus MED4 has the highest percentage (73.2%) of such genes with lowest (51.1%) being
represented in Synechococcus sp. strain WH8102. Thus P. marinus MED4 representing HL-clade appears
to be a more recently evolved as it is very less diversifi ed than other LL-clades and the smallest
genome size of this strain is explained on the basis that extensive gene loss had occurred during
its evolution from a Prochlorococcus ancestor with a larger genome. This has been substantiated on
the basis of (i) absence of a number of DNA repair genes in P. marinus MED4 and (ii) the absence of
ada gene that encodes 6-O-metrhylguanine-DNA methyltransferase (in both Prochlorococcus MED4
and P. marinus SS120) that repairs alkylated forms of guanine and thymine in DNA. Due to this, a
mutational pressure to high A+T content exists in these two strains.
Kettler et al . (2007) sequenced the genomes of seven P. marinus strains (MIT9211, MIT 9215,
MIT9515, NATL1A, MIT9301, MIT9303 and AS9601 have been sequenced at JCVI, Maryland,
USA; NATL2A has been sequenced at Joint Genome Institute, USDOE, California) and presented a
comparative account together with those of P. marinus strains MED4, MIT9313 (Rocap et al. , 2003),
SS120 (Dufresne et al ., 2003) and MIT9312 (Coleman et al ., 2006) sequenced earlier. The essential features
of these genomes are presented in Table 2. The smallest genome is that of P. marinus MED4 (with
1.6 Mbp) and the largest is that of MIT9303 (2.7 Mbp). A complete reannotation of the 12 genomes
by a uniform method was carried out by employing gene prediction programmes like CRITICA and
GLIMMER. As a result, there is a progressive reduction in the number of core genes to 1250 (in contrast
to 1352 detected by Rocap et al ., 2003) amounting to 40% to 70% of the genes in any of the 12 strains.
A comparison of these genomes with the genomes of Synechococcus sp. (strains CC9311, CC9902,
WH8102 and CC 9605) revealed 33 genes specifi c to Prochlorococcus (in contrast to 38 noted by Rocap
et al ., 2003) but absent from some or all Synechococcus strains. Of these 33 genes, 13 are exclusively
represented in Prochlorococcus strains only and absent in Synechococcus strains. Eight of these genes
whose putative function has been assigned relate to HL-inducible protein (to overcome high-light
intensity stress), a possible sodium-solute transporter, an iron sulphur protein and a transcription
factor (deoR-like). Signifi cantly, all Prochlorococcus genomes lack genes for divinylprotochlorophyllide
reductase ( dvr ), allophycocyanin ( apcABCDE ), some phycoerythrins, phycobilisome linkers and
molybdoprotein biosynthesis ( mobA , moaABCDE necessary for nitrate reductase).