Agriculture Reference
In-Depth Information
Table 7.1 (continued)
Saccharomyces
cerevisiae
(number of
residues)
Selected
references
related to plant
phenotypes
Homo sapiens
(number of
residues)
Arabidopsis
thaliana
(number
of residues, gene)
Loss of function
phenotype in
plants
Not studied in
plants. No phe-
notype data.
Exact homo-
logue still
unclear
Some of the proteins cited in this table are represented by more than one alternative spliced
isoform; only the longest one is indicated in brackets. For the function description of most of the
proteins shown here see Klionsky et al. (
2011
)
a
FRAP1 [
FK
BP12-
r
apamycin complex-
a
ssociated
p
rotein (
FK
506-
b
inding
p
rotein 12-rapamycin
c
omplex-
a
ssociated
p
rotein
1
)], mTOR (
ma
mmalian
t
arget
o
f
r
apamycin), ATG (
au
tophagy-
r
elated
p
rotein), ULK1 (
U
nc-51-
l
ike
k
inase 1), ATG1s ATG1t is represented longer than in Suttangkakul et
al. (2011) because manual removing of the introns in this locus reveals cDNA predicted to encode
408 aa protein (instead of 267 aa). After ELM (EukarioticLinear Motif) domain search a conflict
with Li and Vierstra 2012 appears because the regulatory domain exists although the protein is
shorten in the middle (mostly disordered region), C (carbon), N (nitrogen), LST8 (
L
ethal with
S
EC13 protein
8
), RAPTOR (
r
egulatory-
as
sociated
p
rotein of
TOR
), FIP200 (FAK family kinase-
interacting protein of 200 kDa), RBCC1 (RB1-inducible coiled-coil protein 1)
b
Bph1p (2167)
ALFY (3601)
At4g02660;
At1g03060
Suttangkakul et al. (2011) comment to have found possible ATG17 and ATG101 orthologues but
do not state exactly which one. Similarly we failed to identify the ATG29 and ATG31 plant
orthologues but we propose homologues of AtATG101, AtATG11, AtATG17, and ATG32
(At4g29060 has mitochondrial and chloroplastic location based on BLAST, MOTIFSCAN,
TMPRED and ELM search/predictions). Souval et al. (2007) showed oxidative stress sensitivity
in atg4 mutants (a and b) of mammal cells
c
ATG9 in plant ATG9 no transmembrane region is predicted by ELM (weakly by TMPRED),
hypothetically plant ATG9 may attach to the membrane by means of ATG27, WIPI1 (
W
D repeat
domain,
phosphoinositide i
nteracting
1
)
d
BECN1 (
BEC
LI
N
1), BARKOR (
B
eclin 1-
a
ssociated autophagy-
r
elated
k
ey
r
egulator), PIK3R4
(
p
hospho
i
nositide
3
-kinase
r
egulatory subunit
4
), VPS15 (
v
acuolar
p
rotein
s
orting-associated
protein
15
), ATG27 according to Yen et al. (2007) the N terminus is in the vesicular lumen while
that C terminus is in the cytosolic part in yeast; TM and ELM predicts that and plant Nt also ends into
the membrane and has a Ct TM. PIK3c3
(p
hosphatidyl
i
nositol
3
-
k
inase
c
atalytic/
cl
ass subunit type
3
)
e
LC3 (
l
ight
c
hain
3
), GABARAP (
g
amma-
am
ino
b
utyrate
re
ceptor
a
ssociated
p
rotein), GATE16
(
g
olgi-
a
ssociated A
T
Pase
e
nhancer of
16
kDa), GEF2 (
g
anglioside
e
xpression
f
actor
2
)
f
BNIP3L (
B
CL2/
N
IP3-
l
ike), SQSTM (
S
e
q
ue
st
roso
m
e), NBR1 [
n
ext to
BR
CA1 (
br
east
ca
ncer)
g
ene
1
], TBK (
t
ank
b
inding
k
inase), UBQL4 (
Ub
i
q
ui
l
in4), Bph1p (
b
eige
p
rotein
h
omologue
1
),
ALFY (
a
utophagy
l
inked
FYV
E protein)
How Many Autophagy Forms Exist in Plants?
The process of autophagy in plants was initially considered as non-selective bulk
degradation of cellular contents, however now it is clear that the process is selective
(Floyd et al.
2012
; Li and Vierstra
2012a
). For example, the following specific
forms of autophagy were reported each involved in degradation of a specific target,
