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Transcript
Supplementary Table 4. COMPARISON OF DYNAMIC AND ADAPTIVE RESPONSE OF S. cerevisiae WITH
OTHER ORGANISMS
Pathway/
Biological
Process
Reference
behavior in S.
cerevisiae
Closer
Organism
Behavior of
process in closer
organism
Either
Glycosidase-I or
Glycosidase-II is
required for
growth of S.
cerevisiae cells.
[1,2,3,4]
Cell wall
organization
Meiosis
Glycosidase-I
does not play
role in outer
chain formation
or mannosylation
and elongation of
oligosaccharide
residues in cell
wall organization.
[4,5]
S. cerevisiae has
two silent mating
cassettes (HML &
HMR) and an
active MAT locus.
The
morphogenesis is
regulated by
MAPK signaling
pathway.
[6,7,8,9]
Candida
glabrata
Candida
glabrata
Candida
glabrata
C. glabrata has
two silent mating
cassettes and an
active MAT locus
and undergoes
mating-type
interconversions
via a Ho-type
endonuclease,
regulated by a
MAP kinase
cascade.
Ideal
temperature for
Pheromone
stimulated
growth is
between 24º C
and 37º C. [7,10]
Only diploid cells
of S. cerevisiae
shows bipolar
budding pattern.
[11,12]
More distant
organism
Candida
albicans
Candida
albicans
Kluyveromyces
lactis
Both haploid and
diploid cells of K.
lactis shows
bipolar budding
pattern.
Candida
albicans
Behavior of process
in more distant
organism
Glycosidase-I AND
Glycosidase-II is
required for growth
of C. albicans cells.
Glycosidase-I or
Glycosidase-II play
important role in
mobility of β-Nacetylhexosaminidas
e to initiate outer-Nchain elongation in
cell wall
organization.
C. albicans has one
MAT locus and a
mating-type
pleiotropic switching
event is required for
mating to occur.
Pheromone causes
smoothing, the initial
step in the mating
process, only in a/a
cells expressing the
opaque phenotype.
Does not grow at
37º C.
Axial budding
pattern.
Supplementary Table 4 continued.
Switching from
axial to bipolar
Pseudohyphal mode is required
growth
for germ tube
emission. [12]
Thiamine
metabolism
Nonhomologous
end-joining
(NHEJ)
recombination
Thiamine
biosynthetic
pathway
component plays
dual role,
cooperating with
repair mechanisms
in mitochondria.
[13,14,15]
Haploid strain
performs NHEJ
efficiently and
diploid strain
performs NHEJ
inefficiently.
[16,17]
Illegitimate
recombination (IR)
by NHEJ pathway
occurs at rate of 15 transformants/μg
[17]
IR mechanism is
based on
microhomology
and the target site
is near to the
consensus
sequence for TOP1
binding
(Topoisomerase-1).
[14,18,19]
Candida
albicans
Arabidopsis
thaliana
Switching from
axial to bipolar
mode is
required for
germ tube
emission
because the
mechanism
requires a polar
budding
pattern.
Thiamine
biosynthetic
pathway
component
probably plays
dual role,
cooperating
with repair
mechanisms.
Candida
glabrata
Candida
glabrata
Candida
glabrata
IR mechanism is
based on
microhomology
and the target
site is near to
the consensus
sequence for
TOP1 binding.
Yarrowia
lipolytica
Pseudomonas
fluorescens
Switch from axial to
bipolar mode is not
necessary because Y.
lipolytica shows
budding pattern in
haploid and diploid
form.
Thiamine
biosynthetic
pathway component
does not play any
role in repair
mechanisms.
Kluyveromyces
lactis
NHEJ transcription is
not regulated by cell
type (both haploid
and diploid show
same efficiency in
repair).
Kluyveromyces
lactis
Illegitimate
recombination (IR)
by NHEJ pathway
occurs 1000 fold
faster than in S.
cerevisiae.
Kluyveromyces
lactis
IR mechanism is not
based on
microhomology and
the target site is not
specific to the
consensus sequence
for TOP1 binding.
[14, 59,70]
Supplementary Table 4 continued.
Mitotic and ORF IR
Nonare equally
homologous
compromised by
end-joining
HR (homologous
(NHEJ)
recombination) and
recombination NHEJ. [17]
Isoleucine
biosynthesis
One carbon
pool by folate
1-butanol
production flux
comes mostly from
an intermediate of
the isoleucine
biosynthesis
pathway produced
through the use of
threonine.
[20,21,22,23]
One-carbon pool in
cytoplasm required
for synthesis of
purines,
thymidylate and
regeneration of
methionine.
[24,25,26]
Candida
glabrata
Escherichia
coli
Rattus
norvegicus
Mitotic and ORF
IR are equally
compromised
by HR and NHEJ.
1-butanol
production flux
comes mostly
from an
intermediate of
the isoleucine
biosynthesis
pathway
produced
through the use
of threonine.
One-carbon
pool in
cytoplasm
required for
synthesis of
purines,
thymidylate and
regeneration of
methionine.
Kluyveromyces
lactis
Laptospira
interrogans,
Methanococcus
jannaschii,
Geobacter
sulfurreducens
Arabidopsis
thaliana
Mitotic (cell cycle
error) IR occurs 6
folds more
frequently than in
ORFs (transcription
error).
1-butanol production
is only observed
when threoninemediated isoleucine
biosynthesis is shut
down and pyruvate
mediated isoleucine
biosynthesis is
overexpressed.
[5, 29, 56, 68]
One-carbon pool in
cytoplasm is only
requiring for
regeneration of
methylation. It is not
required for purine
synthesis.
Supplementary Table 4 continued.
Kluyveromy
ces lactis
Production of
different
terpenoids from
the same
substrate has a
flux and a time
course similar to
that in S.
cerevisiae.
Chlamydomonas
reinhardtii
Terpenoids
C. reinhardtii is
resistant to singlet
oxygen, while
S .cerevisiae is not.
Probably due to
different levels of
carotenoid
(terpenoids)
biosynthesis.
biosynthesis
[27]
[28,29]
Kluyveromy
ces lactis
Production of
different
trepenoids from
the same
substrate has a
flux and a time
course similar to
that in S.
cerevisiae.
Chlamydomonas
reinhardtii
C. reinhardtii is
resistent to singlet
oxygen, while
S.cerevisiae is not.
Probably due to
different levels of
carotenoid
(terpenoids)
biosynthesis.
Supplementary Table 4 continued.
One-carbon pool in
cytoplasm required
for synthesis of
One carbon
purines,
pool by folate thymidylate and
regeneration of
methionine.
[24,25,26]
[30]
Steroid
biosynthesis
Hsp70/Hsp90
organizing
protein coordinates
interactions during
assembly of steroid
receptor
complexes.
Supports
maturation of
Glucocorticoid
receptor (GR)
function. [31]
Rattus
norvegicus
Kluyveromy
ces lactis
Homo
sapiens
One-carbon
pool in
cytoplasm
required for
synthesis of
purines,
thymidylate and
regeneration of
methionine.
Time course and
flux amount for
Ergosterol and
phytate
production is
the same
between
S. cerevisiae and
K. lactis.
Hsp70/Hsp90
organizing
protein coordin
ates
interactions
during assembly
of steroid
receptor
complexes.
Supports
maturation of
Glucocorticoid
receptor (GR)
function.
Arabidopsis
thaliana
Drosophila
melanogaster
One-carbon pool in
cytoplasm is only
requiring for
regeneration of
methylation. It is
not required for
purine synthesis.
Hsp70/Hsp90
organizing
protein coordinates
interactions during
assembly of steroid
receptor
complexes. Does
not support
maturation of
Glucocorticoid
receptor (GR)
function.
Supplementary Table 4: A comparison of dynamic and adaptive responses of different organisms with S.
cerevisiae. We find that organisms that are more distant to S. cerevisiae in Figures 2-5 (Supplementary Figures 1 4) with respect to some biological process also have phenotypic behavior that is more different from the yeast
than those that are predicted to be closer with respect to that process, whose references have been found in the
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