The Arabidopsis Functional Genomics Network
The Arabidopsis Functional Genomics Network
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and Hans-Hubert
Kirch
Summary
Due to their chemical reactivity, many aldehydes are toxic for organisms at low concentrations. It is therefore important that metabolic aldehyde levels are strictly controlled. Many biologically important aldehydes are metabolized by the superfamily of NAD(P)+-dependent aldehyde dehydrogenases [aldehyde:NAD(P)+ oxidoreductases, EC 1.2.1]. Currently, 555 genes encoding ALDH proteins have been identified throughout all taxa (Sophos and Vasiliou, 2003). At least 172 ALDH genes have been discovered in eukaryotes and encode enzymes that belong to more than 20 distinct protein families. Many of these families are substrate specific enzymes as the non-phosphorylating glyceraldehyde-3-phosphate dehydrogenases (GAPDH, EC 1.2.1.9), methylmalonate semialdehyde dehydrogenases (MMSALDH, EC 1.2.1.27), succinic semialdehyde dehydrogenases (SSALDH, EC 1.2.1.16) or betaine aldehyde dehydrogenases (BADH, EC 1.2.1.8), whereas the variable substrate aldehyde dehydrogenases (class-1/2 and class-3 ALDHs) catalyze the oxidation of a broad spectrum of aliphatic and aromatic aldehydes to their corresponding carboxylic acids and are either NAD-dependent (EC 1.2.1.3) or NADP-linked (EC 1.2.1.5).
Plants have several distinct ALDHs, but information on their biological role is limited. Database analyses reveal 14 ALDH genes in Arabidopsis. The ALDH Gene Nomenclature Committee (http://www.uchsc.edu/sp/sp/alcdbase/aldhcov.html) has established specific criteria for cataloguing ALDH deduced polypeptide sequences (Vasiliou et al., 1999). In cooperation with two other research groups (P. Schnable, Iowa State University; A. Wood, Southern Illinois University-Carbondale) we have established a new unified nomenclature for the Arabidopsis ALDH genes which has been approved by the ALDH Gene Nomenclature Committee. According to this nomenclature each family is represented by the root symbol ALDH followed by a family number, a capital letter specifying the sub-family and a number identifying the individual gene. The Arabidopsis ALDH genes can be divided into nine families: Six variable-substrate ALDHs - two mitochondrial and one cytosolic localized tetrameric class-1/2 enzymes (ALDH2C4, ALDH2B4 and ALDH2B3) and three dimeric class-3 enzymes (ALDH3I1, ALDH3H1 and ALDH3F1) - belonging to two different families, one member each of the SS-ALDH- (ALDH5F1) and MMS-ALDH- (ALDH6B2) families, one antiquitin-related or turgor-ALDH (ALDH7B4), two putative BADHs (ALDH10A8, ALDH10A9), one member each of the GAPDH- (ALDH11A3), P5CDH- (ALDH12A1) families, and finally the ALDH22 family.
Several ALDHs from Arabidopsis have been investigated so far. The genes ALDH3I1 and ALDH3H1 encode two novel aldehyde dehydrogenases belonging to class-3 ALDHs (Kirch et al., 2001) and overexpression of ALDH3I1 in trangenic Arabidopsis plants improves tolerance to diverse environmental stresses (Sunkar et al., 2003). SSADH1 (ALDH5F1) encodes the first cloned succinic semialdehyde dehydrogenase from plants, is localized in mitochondria and constitutes a member of the GABA-shunt in Arabidopsis (Busch and Fromm, 1999). T-DNA mutants of SSADH1 are dwarfs with necrotic lesions and display an enhanced sensitivity to both UV-B light and heat stress that is correlated with an increase in H2O2 levels, suggesting that this gene may restrict levels of ROS intermediates in plant defense against environmental stress (Bouché et al., 2003). A mitochondrial D1-pyrroline-5-carboxylate dehydro-genase (P5CDH, ALDH12A1) was identified by complementing the yeast Dput2 mutant and probably is involved in the prevention of proline toxicity (Deuschle et al., 2001). Three class-1/2 ALDH genes (ALDH2B3, ALDH2B4 and ALDH2C4) were identified in a comparative study on ALDH genes from Arabidopsis and maize (Skibbe et al., 2002). Two of these ALDHs are predicted to be localized in mitochondria. Enzymatic activity of all three enzymes has been demonstrated and a recent study suggests that ALDH2C4 is involved in ferulic acid and sinapic acid biosynthesis (Nair et al., 2004).
The aim of this research project is to determine the biological function of the ALDH genes from A. thaliana focusing on members of the class-3 ALDH, BADH and turgor-responsive ALDH genes, because of their potential role in osmotic stress adaptation.
The following experimental approaches will be pursued: Knock-Out mutations for the identified ALDH genes will be isolated to study their effects on physiological and morphological characteristics. In addition, transgenic plants with a modified ALDH gene expression will be constructed. ALDH expression will be analyzed in wild-type, mutant and transgenic plants under defined physiological conditions. Recombinant proteins will be used to determine enzymatic properties of the ALDHs. To identify putative in vivo substrates, metabolite profiling of wild-type, mutant and transgenic plants and a substrate trapping strategy will be used in the future.
References:
Busch, K. B. and Fromm, H. (1999). Plant Succinic Semialdehyde Dehydrogenase. Cloning, purification, localization in mitochondria, and regulation by adenine nucleotides. Plant Physiol. 121, 589-598.
Bouché, N., Fait, A., Bouchez, D., Møller, S.G. and Fromm, H. (2003). Mitochondrial succinic-semialdehyde dehydrogenase of the gamma-aminobutyrate shunt is required to restrict levels of reactive oxygen intermediates in plants. Proc. Natl. Acad. Sci. USA 100, 6843-6849.
Deuschle, K., Funck, D., Hellmann, H., Däschner, K., Binder, S. and Frommer, W.B. (2001). A nuclear gene encoding mitochondrial Delta-pyrroline-5-carboxylate dehydrogenase and its potential role in protection from proline toxicity. Plant J. 27, 345-356.
Kirch, H.H., Nair, A. and Bartels, D. (2001). Novel ABA- and dehydration-inducible aldehyde dehydrogenase genes isolated from the resurrection plant Craterostigma plantagineum and Arabidopsis thaliana. Plant J. 28, 555-567.
Nair, R.B., Bastress, K.L., Ruegger, M.O., Denault, J.W. and Chapple C (2004). The Arabidopsis thaliana REDUCED EPIDERMAL FLUORESCENCE1 gene encodes an aldehyde dehydrogenase involved in ferulic acid and sinapic acid biosynthesis. Plant Cell 16, 544-554.
Skibbe, D.S., Liu, F., Wen, Tsui-Jung, Yandeau, M.D., Xiangqin, C., Cao, J., Simmons, C.R. and Schnable, P.S. (2002). Characterization of the aldehyde dehydrogenase gene families of Zea mays and Arabidopsis thaliana. Plant Mol. Biol. 48, 751-764.
Sophos, N.A. and Vasiliou, V. (2003). Aldehyde dehydrogenase gene superfamily: The 2002 update. Chem. Biol. Interact. 143-144, 5-22.
Sunkar, R., Bartels, D. and Kirch, H.H. (2003). Overexpression of a stress-inducible aldehyde dehydrogenase gene from Arabidopsis thaliana in transgenic plants improves stress tolerance. Plant J. 35, 452-464.
Vasiliou, V., Bairoch, A., Tipton, K.F. and Nebert, D.W. (1999). Eucaryotic aldehyde dehydrogenase (ALDH) genes: human polymorphisms, and recommended nomenclature based on divergent evolution and chromosomal mapping. Pharmacogenet. 9, 421-434.
The A. thaliana ALDH genes
| No. |
AGI code |
official nameh,
i |
former name |
putative function |
putative subcellular
localization |
protein accession |
DNA accession |
CDS (bp) |
ORF (aa) |
MW (kDa) |
| g1 |
ALDH2C4 |
ALDH1a |
aldehyde dehydrogenase |
cytosol |
AAM27004 |
AF349448 |
1506 |
501 |
54.3 |
|
| g2 |
ALDH2B4 |
ALDH2a |
aldehyde dehydrogenase (NAD+)-like protein |
mitochondria |
AAM27003 BAA96792 |
AF349447 |
1617 |
538 |
58.6 |
|
| g3 |
ALDH2B3 |
ALDH2b |
putative aldehyde dehydrogenase, NAD+ |
mitochondria |
AAL99612 |
AF348416 |
1605 |
534 |
58.1 |
|
| a,c4 |
ALDH3I1 |
ALDH3 |
class-3 aldehyde dehydrogenase |
chloroplast |
CAC84903 |
AJ306961 |
1653 |
550 |
60.2 |
|
| a,b5 |
ALDH3H1 |
ALDH4 |
putative aldehyde dehydrogenase |
nd |
AAL59944 |
AY072122 |
1455 |
484 |
53.2 |
|
| b6 |
ALDH3F1 |
ALDH5 |
aldehyde dehydrogenase like protein |
nd |
CAE48163 |
AJ584644 |
1452 |
483 |
53.5 |
|
| d,e7 |
ALDH5F1 |
SSADH1 |
succinic semialdehyde dehydrogenase 1 |
mitochondria |
AAF23590 |
AF117335 |
1587 |
528 |
56.6 |
|
| 8 |
ALDH6B2 |
MMS-ALDH |
putative methylmalonate semi-aldehyde dehydrogenase |
mitochondria |
AAD25855 |
NM_126989 |
1824 |
607 |
65.9 |
|
| b9 |
ALDH7B4 |
ALDH6 (turgor-ALDH) |
putative aldehyde dehydrogenase homolog |
nd |
CAE48164 |
AJ584645 |
1527 |
508 |
54.2 |
|
| 10 |
ALDH10A8 |
putBADH |
putative betaine aldehyde dehydrogenase |
nd |
AAM13070 |
AY093071 |
1506 |
501 |
54.4 |
|
| 11 |
ALDH10A9 |
putBADH |
betaine aldehyde dehydrogenase-like protein |
mitochondria |
AAK44148 |
AF370333 |
1512 |
503 |
54.9 |
|
| 12 |
ALDH11A3 |
GAPDH |
putative NADP-dependent glyceraldehyde-3-phosphate
dehydrogenase |
nd |
AAK59790 |
AY037205 |
1491 |
496 |
53.1 |
|
| f13 |
ALDH12A1 |
P5CDH |
delta-1-pyrroline-5-carboxylate dehydrogenase precursor |
mitochondria |
AAK73756 |
AY039787 |
1671 |
556 |
61.7 |
|
| b14 |
ALDH22A1 |
ALDH7 |
putative aldehyde dehydrogenase |
secretory pathway |
CAE48165 |
AJ584646 |
1791 |
596 |
66.0 |
a Kirch, H.H. et al. (2001); b Kirch, H.H., Schlingensiepen, S., Kotchoni, S.O., Bartels,
D., in preparation; c Sunkar et al., 2003;
d Busch, K. B. and Fromm, H. (1999); e Bouché
et al., 2003; f Deuschle, K. et al. (2001);
g Skibbe, D.S. et al. (2002); h Vasiliou, V.
et al. (1999); i Kirch, H.H., Bartels, D., Wei, Y., Schnable,
P.S., Wood, A.J., in preparation
.
Prof. Dr. Dorothea Bartels
Phone: +49-228 732070
dbartels@uni-bonn.de
Priv.-Doz. Dr. Hans-Hubert Kirch
Phone: +49-228 732680
hhkirch@uni-bonn.de
Rheinische Friedrich-Wilhelms-Universität
Bonn
Institut für
molekulare Physiologie und Biotechnologie der Pflanzen
Kirschallee 1
D-53115 Bonn,
Germany
Fax: +49-228 731697
Dieter Steinmetz 12.04.2005