Leaf Senescence DataBase

Basic information

Locus name

AT4G15530

Alias

PPDK

Organism

Arabidopsis thaliana

Taxonomic identifier

[NCBI]

Function category

Nutrient recycling:nitrogen remobilization

Effect for Senescence

promote

Gene Description

The enzyme pyruvate,orthophosphate dikinase (PPDK) interconverts pyruvate and phosphoenolpyruvate. PPDK are up-regulated in naturally senescing leaves. The abundance of PPDK protein increases during natural senescence.

Evidence

Genetic evidence:Transgene [Ref 1]; Genomic evidence:microarray data [Ref 2]

References

1: Taylor L, Nunes-Nesi A, Parsley K, Leiss A, Leach G, Coates S, Wingler A, Fernie AR, Hibberd JM
Cytosolic pyruvate,orthophosphate dikinase functions in nitrogen remobilization during leaf senescence and limits individual seed growth and nitrogen content.
Plant J. 2010 May 1;62(4):641-52

2: Buchanan-Wollaston V, Page T, Harrison E, Breeze E, Lim PO, Nam HG, Lin JF, Wu SH, Swidzinski J, Ishizaki K, Leaver CJ
Comparative transcriptome analysis reveals significant differences in gene expression and signalling pathways between developmental and dark/starvation-induced senescence in Arabidopsis.
Plant J. 2005 May;42(4):567-85

Gene Ontology

biological process	phosphorylation pyruvate metabolic process
molecular function	ATP binding kinase activity pyruvate, phosphate dikinase activity transferase activity, transferring phosphorus-containing groups

Pathway

KEGG	map00620 (EC 2.7.9.1) map00710 (EC 2.7.9.1)
MetaCyc	PWY-241

Sequence

Mutant information

Mutant name

PPDK overexpression line

Mutant/Transgenic

transgenic

Ecotype

Col-0

Mutagenesis type

transgene

Microarray

Sampling

Buchanan-Wollaston V, Page T, Harrison E, Breeze E, Lim PO, Nam HG, Lin JF, Wu SH, Swidzinski J, Ishizaki K, Leaver CJ.
Comparative transcriptome analysis reveals significant differences in gene expression and signalling pathways between developmental and dark/starvation-induced senescence in Arabidopsis.
Plant J. 2005 May;42(4)

Comparation

Legends:
Col: wild type, indicates the ratio of expression in senescing leaves/green leaves.
NahG, coi1 and ein2: indicates the ratio of expression in senescing leaves of mutant/senescing wild type.
D/L: ratio of DARK 5d/control.
CD: Cell Death, ratio of starved cell suspension culture/control.
Genes showing at least 3 fold (ratio) up regulation during leaf senescence.

miRNA Interaction

Details

target: AT4G15530.1
miRNA: ath-miR159a
miRNA: ath-miR159a
mfe: -32.9 kcal/mol
p-value: 0.003840

position:  949
target 5' A             G       G 3'
           AGAGUUUCCUUCA AUCCAAA
           UCUCGAGGGAAGU UAGGUUU
miRNA  3' A                       5'

target: AT4G15530.1
miRNA: ath-miR159b
miRNA: ath-miR159b
mfe: -33.1 kcal/mol
p-value: 0.003375

position:  948
target 5' C              G       G 3'
           AAGAGUUUCCUUCA AUCCAAA
           UUCUCGAGGGAAGU UAGGUUU
miRNA  3'                          5'

target: AT4G15530.1
miRNA: ath-miR2112-5p
miRNA: ath-miR2112-5p
mfe: -24.7 kcal/mol
p-value: 0.014632

position:  2356
target 5' U        U      G    A 3'
           GC UUGGU UCCGCG UUGC
           UG AACUA AGGCGU AACG
miRNA  3'    U     U      A    C 5'

target: AT4G15530.2
miRNA: ath-miR159a
miRNA: ath-miR159a
mfe: -32.9 kcal/mol
p-value: 0.003449

position:  677
target 5' A             G       G 3'
           AGAGUUUCCUUCA AUCCAAA
           UCUCGAGGGAAGU UAGGUUU
miRNA  3' A                       5'

target: AT4G15530.2
miRNA: ath-miR159b
miRNA: ath-miR159b
mfe: -33.1 kcal/mol
p-value: 0.003010

position:  676
target 5' C              G       G 3'
           AAGAGUUUCCUUCA AUCCAAA
           UUCUCGAGGGAAGU UAGGUUU
miRNA  3'                          5'

target: AT4G15530.2
miRNA: ath-miR2112-5p
miRNA: ath-miR2112-5p
mfe: -24.7 kcal/mol
p-value: 0.013186

position:  2084
target 5' U        U      G    A 3'
           GC UUGGU UCCGCG UUGC
           UG AACUA AGGCGU AACG
miRNA  3'    U     U      A    C 5'

target: AT4G15530.3
miRNA: ath-miR159a
miRNA: ath-miR159a
mfe: -32.9 kcal/mol
p-value: 0.003892

position:  985
target 5' A             G       G 3'
           AGAGUUUCCUUCA AUCCAAA
           UCUCGAGGGAAGU UAGGUUU
miRNA  3' A                       5'

target: AT4G15530.3
miRNA: ath-miR159b
miRNA: ath-miR159b
mfe: -33.1 kcal/mol
p-value: 0.003424

position:  984
target 5' C              G       G 3'
           AAGAGUUUCCUUCA AUCCAAA
           UUCUCGAGGGAAGU UAGGUUU
miRNA  3'                          5'

target: AT4G15530.3
miRNA: ath-miR2112-5p
miRNA: ath-miR2112-5p
mfe: -24.7 kcal/mol
p-value: 0.014822

position:  2392
target 5' U        U      G    A 3'
           GC UUGGU UCCGCG UUGC
           UG AACUA AGGCGU AACG
miRNA  3'    U     U      A    C 5'

target: AT4G15530.4
miRNA: ath-miR159a
miRNA: ath-miR159a
mfe: -32.9 kcal/mol
p-value: 0.003802

position:  922
target 5' A             G       G 3'
           AGAGUUUCCUUCA AUCCAAA
           UCUCGAGGGAAGU UAGGUUU
miRNA  3' A                       5'

target: AT4G15530.4
miRNA: ath-miR159b
miRNA: ath-miR159b
mfe: -33.1 kcal/mol
p-value: 0.003339

position:  921
target 5' C              G       G 3'
           AAGAGUUUCCUUCA AUCCAAA
           UUCUCGAGGGAAGU UAGGUUU
miRNA  3'                          5'

target: AT4G15530.4
miRNA: ath-miR2112-5p
miRNA: ath-miR2112-5p
mfe: -24.7 kcal/mol
p-value: 0.014489

position:  2329
target 5' U        U      G    A 3'
           GC UUGGU UCCGCG UUGC
           UG AACUA AGGCGU AACG
miRNA  3'    U     U      A    C 5'

target: AT4G15530.5
miRNA: ath-miR159a
miRNA: ath-miR159a
mfe: -32.9 kcal/mol
p-value: 0.003776

position:  904
target 5' A             G       G 3'
           AGAGUUUCCUUCA AUCCAAA
           UCUCGAGGGAAGU UAGGUUU
miRNA  3' A                       5'

target: AT4G15530.5
miRNA: ath-miR159b
miRNA: ath-miR159b
mfe: -33.1 kcal/mol
p-value: 0.003315

position:  903
target 5' C              G       G 3'
           AAGAGUUUCCUUCA AUCCAAA
           UUCUCGAGGGAAGU UAGGUUU
miRNA  3'                          5'

target: AT4G15530.5
miRNA: ath-miR2112-5p
miRNA: ath-miR2112-5p
mfe: -24.7 kcal/mol
p-value: 0.014394

position:  2311
target 5' U        U      G    A 3'
           GC UUGGU UCCGCG UUGC
           UG AACUA AGGCGU AACG
miRNA  3'    U     U      A    C 5'

target: AT4G15530.6
miRNA: ath-miR159a
miRNA: ath-miR159a
mfe: -32.9 kcal/mol
p-value: 0.003723

position:  867
target 5' A             G       G 3'
           AGAGUUUCCUUCA AUCCAAA
           UCUCGAGGGAAGU UAGGUUU
miRNA  3' A                       5'

target: AT4G15530.6
miRNA: ath-miR159b
miRNA: ath-miR159b
mfe: -33.1 kcal/mol
p-value: 0.003265

position:  866
target 5' C              G       G 3'
           AAGAGUUUCCUUCA AUCCAAA
           UUCUCGAGGGAAGU UAGGUUU
miRNA  3'                          5'

target: AT4G15530.6
miRNA: ath-miR2112-5p
miRNA: ath-miR2112-5p
mfe: -24.7 kcal/mol
p-value: 0.014197

position:  2274
target 5' U        U      G    A 3'
           GC UUGGU UCCGCG UUGC
           UG AACUA AGGCGU AACG
miRNA  3'    U     U      A    C 5'

Ortholog Group

Ortholog Groups: OG5_127082

Accession	Taxon
NP_001031647	Arabidopsis thaliana
NP_001078395	Arabidopsis thaliana
NP_001078396	Arabidopsis thaliana
NP_001118987 ( AT4G15530 )	Arabidopsis thaliana
NP_193288	Arabidopsis thaliana
NP_849391	Arabidopsis thaliana
CMF012C	Cyanidioschyzon merolae strain 10D
133570	Chlamydomonas reinhardtii
196616	Chlamydomonas reinhardtii
ACO66978	Micromonas sp. RCC299
ACO68660	Micromonas sp. RCC299
NP_001050430	Oryza sativa Japonica Group
NP_001055507	Oryza sativa Japonica Group
estExt_fgenesh1_pm.C_Chr_02.00010080	Ostreococcus tauri
fgenesh1_pm.C_Chr_09.0001000063	Ostreococcus tauri
estExt_gwp_gw1.C_230034	Physcomitrella patens subsp. patens
fgenesh1_pg.scaffold_8195000001	Physcomitrella patens subsp. patens
28796.m000044	Ricinus communis
29726.m003947	Ricinus communis
estExt_fgenesh1_pg.C_chr_80342	Thalassiosira pseudonana CCMP1335
fgenesh1_pg.C_chr_5000542	Thalassiosira pseudonana CCMP1335
XP_002950615	Volvox carteri f. nagariensis
XP_002955807	Volvox carteri f. nagariensis

Cross Link

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PANTHER	PTHR22931	0.0	1	874	No hit	NA
PIRSF	PIRSF000853	0.0	1	875	IPR010121	Pyruvate, phosphate dikinase
SUPERFAMILY	SSF56059	3.9E-138	2	381	No hit	NA
TIGRFAM	TIGR01828	0.0	3	873	IPR010121	Pyruvate, phosphate dikinase
Pfam	PF01326	1.6E-61	20	363	IPR002192	Pyruvate phosphate dikinase, PEP/pyruvate-binding
SUPERFAMILY	SSF52009	1.1E-37	389	511	IPR008279	PEP-utilising enzyme, mobile domain
Pfam	PF00391	1.3E-20	418	505	IPR008279	PEP-utilising enzyme, mobile domain
ProSitePatterns	PS00370	NA	452	463	IPR018274	PEP-utilising enzyme, active site
SUPERFAMILY	SSF51621	4.6E-130	516	872	IPR015813	Pyruvate/Phosphoenolpyruvate kinase-like domain
Pfam	PF02896	1.2E-115	520	872	IPR000121	PEP-utilising enzyme, C-terminal
ProSitePatterns	PS00742	NA	764	782	IPR023151	PEP-utilising enzyme, conserved site

Subcellular Localization

Localization

cytosol,plastid

Evidence

SUBAcon

Pubmed ID

23180787