Biology Reference
In-Depth Information
4.2. SAR clade
The SAR clade is represented by 24 stramenopile, 30 alveolate and
11 rhizarian genomes (
Table 9.3
). The stramenopile genomes are globin
rich, with 2-7 globins, including FHbs, SDgbs, TrHb1s and TrHb2s. Only
Blastocystis hominis
and
Hyaloperonospora arabidopsidis
appear to lack globins,
and one,
Phythophtora capsicis
, has a putative TrHb3 (
Table 9.3
). A curious
chimeric nitrite reductase comprising a central TrHb2 domain is found in
the raphidophyte
Heterosigma akashiwo
(
Stewart & Coyne, 2011
). Of the
30 alveolate genomes, 17 are apicomplexans, obligate intracellular animal
parasites that share a unique organelle, the apicoplast and an apical complex
structure used in host cell penetration. They have complex life cycles that
include sexual and asexual reproduction and appear to lack globins, except
for the coccidian
Hammonia hammondi
that has a larger than usual genome
(67.5 Mbp) and an SDgb (see Supplementary Table S1 at
http://www.
elsevierdirect.com/companions/9780124076938
). Some of these fungi
are discussed in more detail in
Section 6
. The ciliates, the second group
of alveolates, are represented by six genomes (
Table 9.3
), of which only
one,
Stylonychia lemnae
, lacks globins. Their salient characteristic is having
numerous TrHb1s, including many chimeric multidomain proteins, with
up to seven covalently linked TrHb1 domains (see Supplementary
Table S1 at
http://www.elsevierdirect.com/companions/9780124076938
).
The common fish parasite
Ichthyophthirius multifiliis
has four TrHb1s, three
of which have three to four TrHb1 domains and an N-terminal
thioredoxin-like domain, identified specifically as a two-Cys peroxiredoxin
(PFAM cd 3015).
Tetrahymena thermophila
has 20 TrHb1 domains in 20 pro-
teins, 3 being chimeric, with an N-terminal peroxiredoxin and 3-7 TrHb1
domains.
Paramecium tetraurelia
comprises 92 globin domains in 42 proteins,
of which 18 are chimeric. Of the latter, 2 have an N-terminal serine kinase
with a C-terminal TrHb1; the remaining 16 have an unidentified
N-terminals linked with 2-4 TrHb1 domains. The genome of
Perkinsus mar-
inus
, a dominant parasite of oysters and clams, has 39 globin domains in 30 pro-
teins, 14 of them chimeric. Of the 16 single-domain proteins, all are TrHb1s,
except for 2 TrHb2s, that also score high as TrHb1s in FUGUE searches (see
Supplementary Table S1 at
http://www.elsevierdirect.com/companions/
9780124076938
). The largest chimeric protein is a 2145-residue-long protein
(XP_002778565.1) with an unknown 140-residue N-terminal followed by a
350-residue serine/threonine metallophosphatase, an unidentified 1050 resi-
dues domain, and seven consecutive TrHb1 domains. The Spirotrichean,
