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Rens Voesenek Department of Plant Ecophysiology Utrecht University, The Netherlands http://www.bio.uu.nl/ecophysiology/
www.dartmouth.edu/~floods/
Problems: Energy crisis Carbohydrate starvation Reactive oxygen species Toxicity Water status
Contents
Sensing of low oxygen levels in plants Two Rumex species: an ecological model in flooding research Regulation of fast petiole growth to escape from submergence
Overexpression of RAP2.12 results in increased submergence survival and enhanced expression of hypoxia core genes
Air
Sub De-sub
Removal of 13 amino acids at the N terminal side of RAP2.12 affects expression of hypoxia marker genes and submergence survival
Air
Sub
De-sub
Oxygen sensing in plants is mediated by an N-end rule pathway for protein destabilisation O2 %
Normoxia
MCRAP2.12
Anoxia
Methionine aminopeptidase
O2
C*RAP2.12
C-
RAP2.12
26S proteasome
Oxygen sensing in plants mediated by an N-end rule pathway for protein destabilisation
Contents
Sensing of low oxygen levels in plants Two Rumex species: an ecological model in flooding research Regulation of fast petiole growth to escape from submergence
Rumex species are exposed to different flooding intensities and show contrasting elongation responses upon submergence
# floods Ra Rp Ra Rp
Transient-deep floods
Rarely flooded
Long-shallow floods
Shallow floods
Short floods
Long floods
Voesenek et al., 2004. Ecology 85: 16-27
Submerged petioles of R. palustris and R. acetosa do not have low oxygen concentrations
R. palustris
25
20
15
Light
10
Dark
0 200 400 600 800 1000
R. acetosa
22
Light
Dark
Contents
Sensing of low oxygen levels in plants Two Rumex species: an ecological model in flooding research Regulation of fast petiole growth to escape from submergence
Rumex palustris
Rumex acetosa
[IAA] pg/mg FW
Adaxial
R. palustris
Petiole elongation (mm/48 h)
50 40 30
20 10
Control
25
c s
S S + GA Paclobutrazol
R. palustris
20
15
Submerged
10
Control
0 0 5 10 15 20 25 30 35 40 45 50
R. acetosa
Summary
Submergence
Auxin
Ethylene
NCED
GA Expansin proteins
Petiole elongation
Reference transcriptome
(blast against Arabidopsis for annotation)
submerged
air
submerged
R. acetosa
R. palustris
3,116
11,036
2,992
39
33
42
10 116
R. palustris 97
11
68 R. palustris
48
R. acetosa 39 75 10 73 R. palustris 48
R. acetosa 16
158
R. palustris
97
Log2(Fold Change)
R. acetosa
Air Sub
R. palustris
Air Sub
R. acetosa R.palustris
R.pal
2.49 2.85
3.78 4.90
XTH 33 ATEXLA3
KIDARI Peroxidase 32
0.54 0.98
-0.55 0.80
II
II
III IV
III
Ammonium Tr.2
-0.36
-2.16
IV V
V
VI
VI VII VIII IX X
VII
VIII
Alpha-amylase1
3.73
NA
IX X
GA2OX ATEXPB1
-2.29 NA
-2.78 -2.03
R. communis
A. thaliana
R. acetosa R. palustris
name basic helix-loop-helix (bHLH) dehydration responsive protein (RD22) peroxidase no hit MAPKK HSP/Chaperone SAM-dependent methyltransferase transposon protein bHLH/kidari peroxidase GTP binding (RHD) protein kinase AUX/IAA protein kinase (WAG1) lipid transfer protein/protease inhibitor zinc finger (COP1) germin no hit NAD+ ADP-ribosyltransferase (SRO5) non symbiotic haemoglobin chitinase 2OG-Fe(II) oxygenase subtilase SnRK1 beta subunit endopeptidase inhibitor unknown dehydrogenase/reductase unknown protein MYB (59) lipoxygenase glutathion S-transferase dehydration responvive related glutathion S-transferase haloacid dehalogenase hydrolase glycoside hydrolase/chitinase WD40 beta propeller sulfotransferase cytochrome P450 aspartyl protease unknown protein no hit UDP-glycosyltransferase pectin methylesterase inhibitor WRKY (54) annexin basic helix-loop-helix (bHLH)
*** ** *** *** * ** *** *** ** *** *** *** *** *** *** ** *** *
** ** ** * *** *** *** *** *** *** *** *** ** ** ** *** ** ** ** *** ** *** ** ** *** *** *** *** *** * * ** ** ** ** ** *** *** ***
** ** * * *** *** *** *** * * ** *** * *** *** *** *** ** ** * ** ** ** ** ** ** ** * * * ** * * * *** *** *** *** *** *** *** *** *** ** ** ** * ** ** *** * ** ** ** * *** *** *** *** *** *** *** * *** *** *** *** *** *** *** *** * ** *** *** ** ** ** ** ** ** * ** *** ** *** *** ** * ** * ** ** ** ** * *** * * * *
O. sativa
P. trichocarpa
M. truncatula
B. bistachyon
R. communis
A. thaliana
R. acetosa R. palustris
name basic helix-loop-helix (bHLH) dehydration responsive protein (RD22) peroxidase no hit MAPKK HSP/Chaperone SAM-dependent methyltransferase transposon protein bHLH/kidari peroxidase GTP binding (RHD) protein kinase AUX/IAA protein kinase (WAG1) lipid transfer protein/protease inhibitor zinc finger (COP1) germin no hit NAD+ ADP-ribosyltransferase (SRO5) non symbiotic haemoglobin chitinase 2OG-Fe(II) oxygenase subtilase SnRK1 beta subunit endopeptidase inhibitor unknown dehydrogenase/reductase unknown protein MYB (59) lipoxygenase glutathion S-transferase dehydration responvive related glutathion S-transferase haloacid dehalogenase hydrolase glycoside hydrolase/chitinase WD40 beta propeller sulfotransferase cytochrome P450 aspartyl protease unknown protein WAG1 no KDR SHY2 hit UDP-glycosyltransferase pectin methylesterase inhibitor WRKY (54)
*** ** *** *** * ** *** *** ** *** *** *** *** *** *** ** *** *
** ** ** * *** *** *** *** *** *** *** *** ** ** ** *** ** ** ** *** ** *** ** ** *** *** *** *** *** * * ** ** ** ** ** *** *** *** *
** ** * * *** *** *** *** * * ** *** * *** *** *** *** ** ** * ** ** ** ** ** ** ** * * * ** * * * *** *** *** *** *** *** *** *** *** ** ** ** * ** ** *** * ** ** ** * *** *** *** *** *** *** *** * *** *** *** *** *** *** *** *** * ** *** *** ** ** ** ** ** ** * ** *** ** *** *** ** * ** * ** ** * *** * ** ** * * * *
O. sativa
Degradation
COP1
KIDARI
Major findings:
1. Rumex palustris and R. acetosa have different field locations characterized by contrasting flooding regimes.
2. R. palustris is characterized by ethylene-mediated petiole elongation upon submergence, R. acetosa by ethylene-driven inhibition of elongation. 3. Regulation of endogenous ABA plays an important role in the contrasting elongation responses of the two studied Rumex species. 4. RNA seq transcriptome analysis revealed approx. 14,000 gene families in both species. 5. In R. acetosa 140 families are differentially expressed upon submergence in light, 376 in R. palustris. 6. RNA seq results confirm important roles of ABA, auxin and cell walls in submergenceinduced petiole elongation. 7. Important novel genes are discovered that demonstrate very strong expression differences between the two species.
Acknowledgements
Francesco Licausi Pierdomenico Perata Joost van Dongen Julia Bailey-Serres Eric Visser Rashmi Sasidharan Ronald Pierik Dick Vreugdenhil Ole Pedersen Hans van Veen Divya Vashist Robert Vreeburg Joris Benschop Martijn van Zanten Ankie Ammerlaan Rob Welschen
The Methionine-Cysteine amino acid sequence at the N-terminal part of RAP2.12 qualifies it as a candidate substrate of the N-end rule pathway
Methionine aminopeptidase
Arginine transferase
Proteolysis 6
Ethylene stimulates petiole elongation in R. palustris and inhibits it in R. acetosa Petiole elongation is caused by cell elongation and is equally distributed over the petiole
R.palustris R.acetosa
isotigs with < 50 reads were discarded and isotigs with < 30 reads per kb were discarded significant regulation P < 0.001