Amino Acids

, Volume 30, Issue 2, pp 163–171 | Cite as

In silico assessment of gene function involved in cysteine biosynthesis in Arabidopsis: expression analysis of multiple isoforms of serine acetyltransferase

  • M. Noji
  • C. Goulart Kawashima
  • T. Obayashi
  • K. Saito


In plants, the inorganic sulfur is first fixed into cysteine by the cysteine biosynthetic pathway. This biosynthetic pathway of cysteine involves several enzymatic reactions. In Arabidopsis thaliana, multiple isoforms seem to participate in each enzymatic step for cysteine biosynthesis. To obtain more insights on the specific role of each isoform involved in the cysteine biosynthesis, in silico analysis of these isoforms using Arabidopsis expressed sequence tags (EST) database was carried out. This EST database analysis revealed distinct population distribution of ESTs among multiple isoforms, suggesting that each isoform has its particular expression pattern, presumably associated with its specific role in cysteine biosynthesis. As another in silico analysis, co-expression analysis of genes involved in sulfur metabolism in Arabidopsis was performed using a public transcriptome database of DNA microarrays. This co-expression analysis also suggested specific function and co-regulation of some isoform genes for cysteine biosynthesis by consideration on the clustering of co-expressed genes. From the results of sensitivity to feedback regulation, subcellular localization and expression of mRNA analyses, each serine acetyltransferase (SATase) isoform seems to have its specific role for cysteine biosynthesis. Similar expression patterns were observed between the experimental results of expression data for SATase isoforms and the in silico results of “digital northern” analysis using EST database.

Keywords: Cysteine biosynthesis – Serine acetyltransferase – In silico – Expressed sequence tags – Co-expression analysis 



adenosine 5′-phosphosulfate


serine acetyltransferase


Expressed sequence tags




3′-phosphoadenosine 5′-phosphosulfate


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Allona, I, Quinn, M, Shoop, E, Swope, K, St Cyr, S, Carlis, J, Riedl, J, Retzel, E, Campbell, MM, Sederoff, R, Whetten, RW 1998Analysis of xylem formation in pine by cDNA sequencing.Proc Natl Acad Sci USA9596939698CrossRefPubMedGoogle Scholar
  2. Arabidopsis Genome Initiative2000Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.Nature408796815Google Scholar
  3. Ascano, A, Nicholas, DJD 1977Purification and properties of O-acetyl-l-serine sulphydrylase from wheat leaves.Phytochemistry16889893Google Scholar
  4. Brunold, C, Suter, M 1982Intracellular localization of serine acetyltransferase in spinach leaves.Planta155321327CrossRefGoogle Scholar
  5. Brunold, C, Suter, M 1989Localization of enzymes of assimilatory sulfate reduction in pea roots.Planta179228234CrossRefGoogle Scholar
  6. Costa, MA, Collins, RE, Anterola, AM, Cochrane, FC, Davin, LB, Lewis, NG 2003An in silico assessment of gene function and organization of the phenylpropanoid pathway metabolic networks in Arabidopsis thaliana and limitations thereof.Phytochemistry6410971112CrossRefPubMedGoogle Scholar
  7. Dominguez-Solis, JR, Gutierrez-Alcala, G, Romero, LC, Gotor, C 2001The cytosolic O-acetylserine (thiol) lyase gene is regulated by heavy-metals and can function in cadmium tolerance.J Biol Chem27692979302CrossRefPubMedGoogle Scholar
  8. Droux, M, Martin, J, Sajus, P, Douce, R 1992Purification and characterization of O-acetylserine (thiol) lyase from spinach chloroplasts.Arch Biochem Biophys295379390CrossRefPubMedGoogle Scholar
  9. Fielden, MR, Matthews, JB, Fertuck, KC, Halgren, RG, Zacharewski, TR 2002In silico approaches to mechanistic and predictive toxicology: an introduction to bioinformatics for toxicologists.Crit Rev Toxicol3267112CrossRefPubMedGoogle Scholar
  10. Hatzfeld, Y, Lee, S, Lee, M, Leustek, T, Saito, K 2000aFunctional characterization of a gene encoding a fourth ATP sulfurylase isoforms from Arabidopsis thaliana.Gene2485158CrossRefGoogle Scholar
  11. Hatzfeld, Y, Maruyama, A, Schmidt, A, Noji, M, Saito, K 2000bβ-Cyanoalanine synthase is a mitochondrial cysteine synthase-like protein in spinach and Arabidopsis thaliana.Plant Physiol12311631171CrossRefGoogle Scholar
  12. Hell, R, Jost, R, Berkowitz, O, Wirtz, M 2002Molecular and biochemical analysis of the enzymes of cysteine biosynthesis in the plant Arabidopsis thaliana.Amino Acids22245257CrossRefPubMedGoogle Scholar
  13. Hertzberg, M, Aspeborg, H, Schrader, J, Andersson, A, Erlandsson, R, Blomqvist, K, Bhalerao, R, Uhlen, M, Teeri, TT, Lundeberg, J, Sundberg, B, Nilsson, P, Sandberg, G 2001A transcriptional roadmap to wood formation.Proc Natl Acad Sci USA981473214737CrossRefPubMedGoogle Scholar
  14. Hesse, H, Lipke, J, Altmann, T, Hoefgen, R 1999Molecular cloning and expression analyses of mitochondrial and plastidic isoforms of cysteine synthase (O-acetylserine(thiol)lyase) from Arabidopsis thaliana.Amino Acids16113131CrossRefPubMedGoogle Scholar
  15. Hirai, MY, Klein, M, Fujikawa, Y, Yano, M, Goodenowe, DB, Yamazaki, Y, Kanaya, S, Nakamura, Y, Kitayama, M, Suzuki, H, Sakurai, N, Shibata, D, Tokuhisa, J, Reichelt, M, Gershenzon, J, Papenbrock, J, Saito, K 2005Elucidation of gene-to-gene and metabolite-to-gene networks in Arabidopsis by integration of metabolomics and transcriptomics.J Biol Chem2802559025595CrossRefPubMedGoogle Scholar
  16. Jost, R, Berkowitz, O, Wirtz, M, Hopkins, L, Hawkesford, MJ, Hell, R 2000Genomic and functional characterization of the oas gene family encoding O-acetylserine (thiol) lyases, enzymes catalyzing the final step in cysteine biosynthesis in Arabidopsis thaliana.Gene253237247CrossRefPubMedGoogle Scholar
  17. Kataoka, T, Watanabe-Takahashi, A, Hayashi, N, Ohnishi, M, Mimura, T, Buchner, P, Hawkesford, MJ, Yamaya, T, Takahashi, H 2004Vacuolar sulfate transporters are essential determinants controlling internal distribution of sulfate in Arabidopsis.Plant Cell1626932704CrossRefPubMedGoogle Scholar
  18. Kawashima, CG, Noji, M, Nakamura, M, Ogra, Y, Suzuki, KT, Saito, K 2004Heavy metal tolerance of transgenic tobacco plants over-expressing cysteine synthase.Biotech Lett26153157Google Scholar
  19. Kim, H, Hirai, MY, Hayashi, H, Chino, M, Naito, S, Fujiwara, T 1999Role of O-acetyl-l-serine in the coordinated regulation of the expression of a soybean seed storage-protein gene by sulfur and nitrogen nutrition.Planta209282289CrossRefPubMedGoogle Scholar
  20. Klockars, T, Perheentupa, T, Dahl, H-HM 2003In silico analyses of mouse inner-ear transcripts.J Assoc Res Otolaryngol42440CrossRefPubMedGoogle Scholar
  21. Klonus, D, Hoefgen, R, Willmitzer, L, Riesmeier, J 1994Isolation and characterization of two cDNA clones encoding ATP-sulfurylases from potato by complementation of a yeast mutant.Plant J6105112CrossRefPubMedGoogle Scholar
  22. Kuske, CR, Hill, KK, Guzman, E, Jackson, PJ 1996Subcellular location of O-acetylserine sulfhydrylase isoenzymes in cell cultures and plant tissues of Datura innoxia mill.Plant Physiol112659667PubMedGoogle Scholar
  23. Leustek, T, Saito, K 1999Sulfate transport and assimilation in plants.Plant Physiol120637643CrossRefPubMedGoogle Scholar
  24. Leustek, T, Martin, MN, Bick, J-A, Davies, JP 2000Pathways and regulation of sulfur metabolism revealed through molecular and genetic studies.Annu Rev Plant Physiol Plant Mol Biol51141165CrossRefPubMedGoogle Scholar
  25. Lunn, JE, Droux, M, Martin, J, Douce, R 1990Localization of ATP-sulfurylase and O-acetylserine (thiol) lyase in spinach leaves.Plant Physiol9413451352Google Scholar
  26. Noji, M, Inoue, K, Kimura, N, Gouda, A, Saito, K 1998Isoform-dependent differences in feedback regulation and subcellular localization of serine-acetyltransferase involved in cysteine biosynthesis from Arabidopsis thaliana.J Biol Chem2733273932745CrossRefPubMedGoogle Scholar
  27. Rolland, N, Droux, M, Douce, R 1992Subcellular distribution of O-acetylserine (thiol) lyase in cauliflower (Brassica oleracea L.) inflorescence.Plant Physiol98927935Google Scholar
  28. Renosto, F, Patel, H, Martin, H, Thomassian, C, Zimmerman, G, Segel, I 1993ATP sulfurylase from higher plants: kinetic and structural characterization of the chloroplast and cytosol enzymes from spinach leaf.Arch Biochem Biophys307272285CrossRefPubMedGoogle Scholar
  29. Rotte, C, Leustek, T 2000Differential subcellular localization and expression of ATP sulfurylase and 5′-adenylylsulfate reductase during ontogenesis of Arabidopsis leaves indicates that cytosolic and plastid forms of ATP sulfurylase may have specialized functions.Plant Physiol124715724CrossRefPubMedGoogle Scholar
  30. Ruffet, ML, Droux, M, Douce, R 1994Purification and kinetic properties of serine acetyltransferase free of O-acetylserine(thiol)lyase from spinach chloroplasts.Plant Physiol104597604PubMedGoogle Scholar
  31. Ruffet, ML, Lebrun, M, Droux, M, Douce, R 1995Subcellular distribution of serine acetyltransferase from Pisum sativum and characterization of an Arabidopsis thaliana putative cytosolic isoform.Eur J Biochem227500509CrossRefPubMedGoogle Scholar
  32. Saito, K 2000Regulation of sulfate transport and synthesis of sulfur-containing amino acids.Curr Opin Plant Biol3188195PubMedGoogle Scholar
  33. Saito, K 2004Sulfur assimilatory metabolism. The long and smelling road.Plant Physiol13624432450CrossRefPubMedGoogle Scholar
  34. Seki, M, Narusaka, M, Kamiya, A, Ishida, J, Satou, M, Sakurai, T, Nakajima, M, Enju, A, Akiyama, K, Oono, Y, Muramatsu, M, Hayashizaki, Y, Kawai, J, Carninci, P, Itoh, M, Ishii, Y, Arakawa, T, Shibata, K, Shinagawa, A, Shinozaki, K 2002Functional annotation of a full-length Arabidopsis cDNA collection.Science296141145CrossRefPubMedGoogle Scholar
  35. Smith, IK 1972Studies of L-cysteine biosynthetic enzymes in Phaseolus vulgaris L.Plant Physiol50477479Google Scholar
  36. Sterky, F, Regan, S, Karlsson, J, Hertzberg, M, Rhode, A, Holmberg, A, Amini, B, Bhalerao, R, Larsson, M, Villarroel, R, Van Montagu, M, Sandberg, G, Olsson, O, Teeri, TT, Boerjan, W, Gustafsson, P, Uhlen, M, Sundberg, B, Lundeberg, J 1998Gene discovery in the wood-forming tissues of poplar: analysis of 5692 expressed sequence tags.Proc Natl Acad Sci USA951333013335CrossRefPubMedGoogle Scholar
  37. Takahashi, H, Yamazaki, M, Sasakura, N, Watanabe, A, Leustek, T, de Almeida Engler, J, Engler, G, Van Montagu, M, Saito, K 1997Regulation of sulfur assimilation in higher plants: a sulfate transporter induced in sulfate-starved roots plays a central role in Arabidopsis thaliana.Proc Natl Acad Sci USA941110211107PubMedGoogle Scholar
  38. Warrilow, A, Hawkesford, M 2000Cysteine synthase (O-acetyl-serine (thiol) lyase substrate specificities classify the mitochondrial isoform as a cyanoalanine synthase.J Exp Bot51985993CrossRefPubMedGoogle Scholar
  39. White, JA, Todd, J, Newman, T, Focks, N, Girke, T, Martinez de Ilarduya, O, Jaworski, JG, Ohlrogge, JB, Benning, C 2000A new set of Arabidopsis expressed sequence tags from developing seeds: the metabolic pathway from carbohydrates to seed oil.Plant Physiol12415821594CrossRefPubMedGoogle Scholar
  40. Yamaguchi, T, Masada, M 1995Comparative studies on cysteine synthase isozymes from spinach leaves.Biochem Biophys Acta12519198PubMedGoogle Scholar

Copyright information

© Springer-Verlag/Wien 2006

Authors and Affiliations

  • M. Noji
    • 1
  • C. Goulart Kawashima
    • 1
  • T. Obayashi
    • 1
    • 2
  • K. Saito
    • 1
    • 2
    • 3
  1. 1.Department of Molecular Biology and BiotechnologyGraduate School of Pharmaceutical Sciences, Chiba University, Inage-kuChibaJapan
  2. 2.Core Research for Evolutional Science and Technology, Japan Science and Technology AgencyKawaguchiJapan
  3. 3.RIKEN Plant Science CenterTsurumi-kuJapan

Personalised recommendations