Photoperiodic effect on protein profiles of potato petiole
Shweta Shah1, Young Jin-Lee2, David J. Hannapel3 and A. Gururaj Rao*1
1
Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011
2
Department of Chemistry, Iowa State University, Ames, Iowa 50011
3
Plant Biology Major, Iowa State University, Ames, Iowa 50011
Abstract
In potato (Solanum tuberosum), StBEL5 mRNA is a mobile RNA that is involved in the signaling system that activates tuber
formation. Short-day (SD) conditions induce tuberization and long-day (LD) inhibits the process. The transcriptional source of this
mobile RNA is leaf veins and leaf stalks designated, petioles. Transport of StBEL5 RNA is induced by a SD photoperiod that leads to
tuber formation. It is likely that the movement of StBEL5 is facilitated by the formation of RNA-protein complex(s). To further
understand this proposed mechanism of downstream signaling we have undertaken a detailed proteomic analysis of proteins isolated
from potato petioles (PP) grown under LD and SD photoperiod conditions using 2-dimensional gel electrophoresis (2-DE) followed
by MALDI MS/MS and/or LC MS/MS. Proteins that were differentially expressed in response to changes in photoperiods were
analyzed by Progenesis SameSpots software. Phosphoproteins and RNA-binding proteins were enriched using immobilized metal
affinity chromatography and poly(U) Sepharose columns respectively from SD and LD PP protein extracts and similarly analyzed. In
addition to establishing a catalog of PP proteins, we have so far identified nearly sixty-seven proteins that are differentially expressed
in response to SD or LD photoperiods. Significantly, the RNA-binding protein, elF-5A, has been detected in multiple isoforms
specifically under LD conditions. Numerous other poly(U)-binding proteins which contain RNA recognition motifs have also been
isolated and identified. This is the first comprehensive proteomics study that examines and catalogs the proteins that are present in the
potato petiole and are potentially differentially regulated by photoperiod.
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Table 3: Catalogue of Poly(U) binding proteins enriched from potato petiole extract from plants grown under LD
and SD photoperiod. RNA-binding proteins are highlighted in red.
Spot
#
Accession #
1
gi|27883932
MW % coverage MOWSE
TAIR
Blast
(kDa) / # unique
Score
accession #
Epeptide
value
69.8
13/6
342
AT1G78900 0
Annotation
2
gi|13235340
69.1
8/5
233
AT1G78900 0
Vacuolar ATP
synthase subunit A
3
gi|27883932
68.8
18/6
483
AT1G78900 0
Vacuolar ATP
synthase subunit A
4
gi|28261702
55.4
17/6
446
AT2G07698 2E-163
ATP synthase alpha
subunit
5
gi|28261702
55.4
11/5
320
AT2G07698 2E-163
ATP synthase alpha
subunit
Vacuolar ATP
synthase subunit A
Putative function
hydrogen ion transporting
ATP synthase activity,
rotational mechanism,
proton-transporting ATPase
activity
hydrogen ion transporting
ATP synthase activity,
rotational mechanism,
proton-transporting ATPase
activity
hydrogen ion transporting
ATP synthase activity,
rotational mechanism,
proton-transporting ATPase
activity
hydrogen ion transporting
ATP synthase activity,
rotational mechanism,
Poly(U) binding
hydrogen ion transporting
ATP synthase activity,
rotational mechanism,
poly(U) binding
6
gi|3850926
52.7
25/6
599
AT5G08680 0
ATP synthase beta
chain
hydrogen ion transporting
ATP synthase activity,
rotational mechanism, copper
ion binding
hydrogen ion transporting
ATP synthase activity,
rotational mechanism, copper
ion binding
7
gi|3850926
52.7
20/7
421
AT5G08680 0
ATP synthase beta
chain
8
gi|21633353
52.9
11/5
186
AT5G08680 0
ATP synthase beta
chain
9
gi|114421
59.9
32/9
461
AT5G08680 0
10
11
12
13
gi|1762130
gi|15429015
gi|15429015
gi|22094840
63
56
56
36.7
17/7
13/5
7/3
13/5
341
192
217
AT3G13470
AT2G07698 0
AT2G07698 0
AT1G13440 0
ATP synthase beta
chain
Chaperonin, putative
ATPase subunit 1
ATPase subunit 1
Glyceraldehyde-3phosphate
dehydrogenase C2
14
gi|22094840
36.7
15/4
197
AT1G13440 0
Glyceraldehyde-3phosphate
dehydrogenase C2
Glyceraldehyde-3-phosphate
dehydrogenase
(phosphorylating) activity
15
No hit
16
gi|225433414
36.8
8/2
152
AT1G04690 1E-178
Oxidoreductase activity
17
gi|73808794
16.2
34/3
451
AT4G09320 2E-69
Potassium channel !subunit
Nnucleoside
diphosphate kinase 1
hydrogen ion transporting
ATP synthase activity,
rotational mechanism, copper
ion binding
Hydrogen ion transporting
ATP synthase activity
protein binding, ATP binding
ATP bnding
ATP binding
NAD or NADH binding,
glyceraldehyde-3-phosphate
dehydrogenase
(phosphorylating) activity
Nucleoside diphosphate
kinase activity, ATP binding
18
gi|537313
40.9
6/2
105
AT5G11420 2E-163
19
gi|255549002
40.2
10/3
175
AT5G11420 2E-178
20
gi|118486160
40.1
7/2
106
AT5G11420 4E-171
21
gi|118486160
40.1
7/2
106
AT5G11420 4E-171
22
gi|118486160
40.1
7/2
141
AT5G11420 4E-171
23
gi|10720247
50.8
6/2
121
AT2G39730 0
Uunknown protein
DUF 642
Unknown protein
DUF 642
Unknown protein
DUF 642
Unknown protein
DUF 642
Unknown protein
DUF 642
RuBisCO activase
24
gi|10720247
50.8
6/2
121
AT2G39730 0
RuBisCO activase
25
gi|10720247
50.8
6/2
121
AT2G39730 0
RuBisCO activase
gi|75338883
62.1
10/5
300
AT1G60900 0
26
gi|4139264
41.8
10/5
123
AT5G09810 0
U2 snRNP auxiliary
factor large subunit,
putative
Actin 7
27
gi|182409985
41.8
25/7
123
AT5G09810 0
Actin 7
28
gi|3328122
50.4
12/5
212
AT1G56190 0
29
gi|475736
52.4
10/5
275
0
30
gi|475736
52.4
10/5
275
0
31
gi|32332101
52.3
8/4
228
0
Phosphoglycerate
kinase, putative
RuBisCO large
subunit
RuBisCO large
subunit
RuBisCO large
subunit
Molecular function unknown
Molecular function unknown
Molecular function unknown
Molecular function unknown
Molecular function unknown
ADP binding / ATP binding /
enzyme regulator
ADP binding / ATP binding /
enzyme regulator
ADP binding / ATP binding /
enzyme regulator
RNA binding, nucleotide
binding
Structural constituent of
cytoskeleton
Structural constituent of
cytoskeleton
phosphoglycerate kinase
activity
32
gi|6715512
52
10/5
210
AT4G38510 0
Vacuolar ATP
synthase subunit B,
putative
Eukaryotic release
factor 1-3
embryo sacdevelopment arrest 9
Glucose -6-phosphate
dehydrogenase 6
Hydrogen ion transporting
ATP synthase activity
33
gi|82623383
49.1
5/2
230
AT3G26618 0
34
gi|224105607
57
36/6
420
AT4G34200 0
35
gi|585165
58
6/2
108
AT5G40760 0
36
gi|11386828
47.7
10/3
123
AT5G35630
Glutamine synthetase
2
Glutamate-ammonia ligase
activity
37
gi|77416937
18
23/3
215
AT4G34412 2.00E62
AT1G06680 3.00E144
AT5G26360 0
Unknown protein
molecular_function unknown
38
gi|11134035
28.1
59/5
500
Photosystem II
subunit P-1
Chaperonin, putative
Poly(U) binding
39
gi|159464215
61
2/2
58
40
gi|19032260
32.9
10/3
106
41
gi|37780996
16.8
18/3
186
42
43
gi|15239049
gi|76160947
39.9
22.1
5/2
57/7
78
300
44
gi|78191462
26.4
12/3
113
AT4G24770 1.00E93
AT2G37270 9.00E81
AT5G11420 0
AT1G48830 7.00E90
AT1G66680
45
gi|313129
67
17/8
215
AT3G52600 0
Translation release factor
activity
ATP binding
Glucose-6-phosphate
dehydrogenase activity
Unfolded protein binding,
protein binding, ATP binding
31-KDa RNA
RNA binding, poly(U)
binding protein
binding
Ribosomal protein 5B Structural constituent of
ribosome
Unknown protein
Molecular_function unknown
40S ribosomal
Structural constituent of
protein S7
ribosome
Sadenosylmethioninedependent
methyltransferases
Arabidopsis thaliana
Hydrolase activity
cell wall invertase 2
46
gi|24745945
49.5
30/8
192
AT5G60390 0
Elongation factor 1alpha
47
gi|255538240
71.9
13/6
188
AT4G34110 0
Poly (A) binding 2
48
gi|6752880
49
42/11
162
AT5G19990 0
Regulatory particle
triple –A ATPase 6A
49
gi|197260357
51.2
27/6
397
AT3G55430 3.00E132
Glycosyl hydrolase
family 17 protein
Cation binding, hydrolase
activity
50
gi|83283995
38.8
54/8
116
77999255
Fructose-bisphosphate
aldolase activity
51
gi|77416923
34.6
40/7
453
AT4G13010 3.00E143
52
gi|6689892
63.4
22/6
514
AT3G14310 0
53
gi|24745880
54
55
gi|22326994
gi|62870979
54.5
25.8
2/1
12/3
57
147
AT5G22610 0
AT4G11010 4.00E123
Fructosebisphosphate
aldolase, putative
Zinc-binding
dehydrogenase
family protein
ATPME3;
pectinesterase
Regulatory particle
triple –A ATPase 4A
F-box family protein
Nucleoside
diphosphate kinase 3
56
gi|38604456
41
9/3
134
AT1G66430 4.00E172
Kinase activity, ribokinase
activity
57
gi|38604456
41
10/3
254
AT1G66430 4.00E172
pfkB-type
carbohydrate kinase
family protein
pfkB-type
carbohydrate kinase
family protein
2.00E179
AT5G43010 0
Calmodulin binding,
translation elongation factor
activity
RNA binding, translation
initiation factor activity
ATPase activity
Oxidoreductase activity
Pectinesterase activity
ATPase activity
Molecular_function unknown
ATP binding
Kinase activity, ribokinase
activity
58
gi|38604456
41
26/7
376
AT1G66430 4.00E172
59
gi|17432522
31.3
39/6
245
60
gi|133246
30.7
14/3
188
61
gi|6015063
24.7
6/2
154
61
gi|15748154
29
6/2
126
AT2G37220 3.00E79
AT4G24770 1.00E83
AT2G18110 3.00E82
AT2G42590 5.00E120
62
gi|12229923
26.1
37/6
152
63
gi|82623423
17.5
23/4
154
64
gi|82623423
17.5
17/3
88
65
Q03878
15.7
23/3
117
66
Q03878
15.7
23/3
102
67
Q03878
15.7
23/3
100
68
Q03878
15.7
23/3
124
69
gi|82623423
17.5
34/3
247
70
gi|82623423
17.5
33/4
181
AT3G14290 2.00E135
AT4G39260 8.00E38
AT4G39260 8.00E38
AT4G39260 1.00E41
AT4G39260 1.00E41
AT4G39260 1.00E41
AT4G39260 1.00E41
AT4G39260 8.00E38
AT4G39260 8.00E38
pfkB-type
carbohydrate kinase
family protein
29 kDa
Ribonucleoprotein
31-KDa RNA
binding protein
Elongation factor 1beta, putative
General regulatory
factor 9/14-3-3
protein
Threonine-type
endopeptidase
AtRBP8
AtRBP8
GR-RBP8
GR-RBP8
GR-RBP8
GR-RBP8
GR-RBP8
GR-RBP8
Kinase activity, ribokinase
activity
RNA binding, poly(U)
binding
RNA binding / poly(U)
binding
Translation elongation factor
activity
Protein phosphorylated
amino acid binding
Peptidase activity
RNA binding / nucleic acid
binding / nucleotide binding
RNA binding / nucleic acid
binding / nucleotide binding
RNA binding / nucleic acid
binding / nucleotide binding
RNA binding / nucleic acid
binding / nucleotide binding
RNA binding / nucleic acid
binding / nucleotide binding
RNA binding / nucleic acid
binding / nucleotide binding
RNA binding / nucleic acid
binding / nucleotide binding
RNA binding / nucleic acid
binding / nucleotide binding
71
gi|224142804
47.1
38/10
411
AT3G13920 0
72
gi|25809054
47.1
34/9
363
AT3G13920 0
73
gi|50400860
47.1
44/12
751
AT3G52880 0
74
gi|6580762
70.8
9/5
219
75
gi|78191424
33.9
34/7
343
76
gi|8247363
35.9
63/13
413
77
gi|2565436
43.6
11/4
122
AT3G22640 1.00E80
AT2G40010 3.00E143
AT1G35720 2.00E122
AT3G27925 0
78
gi|1934994
15.8
18/2
150
79
gi|224102217
21
23/3
80
No hit
81
gi|132071
20.5
18/2
111
82
gi|132080
20.6
19/2
197
!
!
AT2G21660 3.00E34
AT4G14300 2.00E75
AT5G38410 4.00E79
AT5G38410 1.00E78
Eukaryotic
translation initiation
factor 4A1
Eukaryotic
translation initiation
factor 4A1
Monodehydroascorba
te reductase, putative
PAP85; nutrient
reservoir
60S acidic ribosomal
protein P0
Annexin Arabidopsis
1
DegP protease 1
ATP-dependent helicase
activity
Heterogeneous
nuclear
ribonucleoprotein,
putative
RNA binding, nucleotide
binding
RuBisCO small
subunit
RuBisCO small
subunit
ribulose-bisphosphate
carboxylase activity
ribulose-bisphosphate
carboxylase activity
ATP-dependent helicase
activity
Monodehydroascorbate
reductase (NADH) activity
Nutrient reservoir activity
structural constituent of
ribosome
ATP binding / Protein
homodimerization
Serine-type endopeptidase
activity
Glycine rich protein 7 DNA/ RNA binding