Skip to main content
SpringerLink
Log in

The Peroxidase Gene Family in Plants: A Phylogenetic Overview

  • Published:
Journal of Molecular Evolution Aims and scope Submit manuscript

Abstract

The 73 class III peroxidase genes in Arabidopsis thaliana were used for surveying the evolutionary relationships among peroxidases in the plant kingdom. In Arabidopsis, the 73 genes were clustered in robust similarity groups. Comparison to peroxidases from other angiosperms showed that the diversity observed in Arabidopsis preceded the radiation of dicots, whereas some clusters were absent from grasses. Grasses contained some unique peroxidase clusters not seen in dicot plants. We found peroxidases in other major groups of land plants but not in algae. This might indicate that the class III peroxidase gene family appeared with the colonization of land by plants. The present survey may be used as a rational basis for further investigating the functional roles of class III peroxidases.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Figure 1
Figure 2
Figure 3
Figure 4

Similar content being viewed by others

References

  1. SF Altschul W Gish W Miller EW Myers DJ Lipman (1990) ArticleTitleBasic local alignment search tool. J Mol Biol 215 403–410 Occurrence Handle10.1006/jmbi.1990.9999 Occurrence Handle1:CAS:528:DyaK3MXitVGmsA%3D%3D Occurrence Handle2231712

    Article  CAS  PubMed  Google Scholar 

  2. E Asamizu Y Nakamura S Sato H Fukuzawa S Tabata (1999) ArticleTitleA large scale structural analysis of cDNAs in a unicellular green alga, Chlamydomonas reinhardtii. I. Generation of 3433 non-redundant expressed sequence tags. DNA Res 6 369–373 Occurrence Handle10691129

    PubMed  Google Scholar 

  3. WR Atchley WM Fitch (1997) ArticleTitleA natural classification of the basic helix-loop-helix class of transcription factors. Proc Natl Acad Sci USA 94 5172–5176 Occurrence Handle1:CAS:528:DyaK2sXjtlalurk%3D Occurrence Handle9144210

    CAS  PubMed  Google Scholar 

  4. S Barnes (2000) ArticleTitleComparing Arabidopsis to other flowering plants. Curr Opin Plant Biol 5 128–133 Occurrence Handle10.1016/S1369-5266(02)00239-X

    Article  Google Scholar 

  5. GI Berglund GH Carlsson AT Smith H Szoke A Henriksen J Hajdu (2002) ArticleTitleThe catalytic pathway of horseradish peroxidase at high resolution. Nature 417 463–468 Occurrence Handle10.1038/417463a Occurrence Handle1:CAS:528:DC%2BD38XjvVersrw%3D Occurrence Handle12024218

    Article  CAS  PubMed  Google Scholar 

  6. V Charvet-Candela S Hitchin MS Reddy B Cournoyer R Marmeisse G Gay (2002) ArticleTitleCharacterization of a Pinus pinaster cDNA encoding an auxin up-regulated putative peroxidase in roots. Tree Physiol 22 231–238 Occurrence Handle1:CAS:528:DC%2BD38XisVWlsb8%3D Occurrence Handle11874719

    CAS  PubMed  Google Scholar 

  7. M Collinge T Boller (2001) ArticleTitleDifferential induction of two potato genes, Stprx2 and StNAC, in response to infection by Phytophthora infestans and to wounding. Plant Mol Biol 46 521–529 Occurrence Handle1:CAS:528:DC%2BD3MXmt1Shsrs%3D Occurrence Handle11516145

    CAS  PubMed  Google Scholar 

  8. G Drouin F Prat M Ell GD Clarke (1999) ArticleTitleDetecting and characterizing gene conversions between multigene family members. Mol Biol Evol 16 1369–1390 Occurrence Handle1:CAS:528:DyaK1MXms1Ojt7Y%3D Occurrence Handle10563017

    CAS  PubMed  Google Scholar 

  9. JA Eisen (1998) ArticleTitlePhylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Res 8 163–167 Occurrence Handle1:CAS:528:DyaK1cXitlWluro%3D Occurrence Handle9521918

    CAS  PubMed  Google Scholar 

  10. J Felsenstein (2001) PHYLIP v3.6. Department of Genetics. University of Washington Seattle

    Google Scholar 

  11. CG Fossdal P Sharma A Lonneborg (2001) ArticleTitleIsolation of the first putative peroxidase cDNA from a conifer and the local and systemic accumulation of related proteins upon pathogen infection. Plant Mol Biol 47 423–435 Occurrence Handle10.1023/A:1011615328684 Occurrence Handle1:CAS:528:DC%2BD3MXntlGju7s%3D Occurrence Handle11587513

    Article  CAS  PubMed  Google Scholar 

  12. M Gajhede DJ Schuller A Henriksen AT Smith TL Poulos (1997) ArticleTitleCrystal structure of horseradish peroxidase C at 2.15 A resolution. Nat Struct Biol 4 1032–1038 Occurrence Handle1:CAS:528:DyaK2sXnvV2nsrs%3D Occurrence Handle9406554

    CAS  PubMed  Google Scholar 

  13. DS Heckman DM Geiser BR Eidell RL Stauffer NL Kardos SB Hedges (2001) ArticleTitleMolecular evidence for the early colonization of land by fungi and plants. Science 293 1129–1133 Occurrence Handle1:CAS:528:DC%2BD3MXmtVWrtLk%3D Occurrence Handle11498589

    CAS  PubMed  Google Scholar 

  14. A Henriksen DJ Schuller K Meno KG Welinder AT Smith M Gajhede (1998b) ArticleTitleStructural interactions between horseradish peroxidase C and the substrate benzhydroxamic acid determined by X-ray crystallography. Biochemistry 37 8054–8060 Occurrence Handle1:CAS:528:DyaK1cXivFCis78%3D

    CAS  Google Scholar 

  15. A Henriksen KG Welinder M Gajhede (1998a) ArticleTitleStructure of barley grain peroxidase refined at 1.9-A resolution. A plant peroxidase reversibly inactivated at neutral pH. J Biol Chem 273 2241–2248 Occurrence Handle1:CAS:528:DyaK1cXnsVKlsQ%3D%3D

    CAS  Google Scholar 

  16. A Henriksen O Mirza C Indiana K Teilum G Smulevich K Welinder M Gajhede (2001) ArticleTitleStructure of soybean seed coat peroxidase: A plant peroxidase with unusual stability and haem-apoprotein interactions. Protein Sci 10 108–115 Occurrence Handle10.1110/ps.37301 Occurrence Handle1:CAS:528:DC%2BD3MXksFCjurY%3D Occurrence Handle11266599

    Article  CAS  PubMed  Google Scholar 

  17. S Hiraga K Sasaki H Ito Y Ohashi H Matsui (2001) ArticleTitleA large family of class III plant peroxidases. Plant Cell Physiol 42 462–468

    Google Scholar 

  18. S Hiraga K Yamamoto H Ito K Sasaki H Matsui M Honma Y Nagamura T Sasaki Y Ohashi (2000) ArticleTitleDiverse expression profiles of 21 rice peroxidase genes. FEBS Lett 471 245–250 Occurrence Handle10.1016/S0014-5793(00)01409-5 Occurrence Handle1:CAS:528:DC%2BD3cXitlOlu78%3D Occurrence Handle10767432

    Article  CAS  PubMed  Google Scholar 

  19. HM Jespersen IV Kjærsgård L Østergaard KG Welinder (1997) ArticleTitleFrom sequence analysis of three novel ascorbate peroxidases from Arabidopsis thaliana to structure, function and evolution of seven types of ascorbate peroxidase. Biochem J 326 305–310 Occurrence Handle1:CAS:528:DyaK2sXmt1Gisrg%3D Occurrence Handle9291097

    CAS  PubMed  Google Scholar 

  20. KY Kim GH Huh HS Lee SY Kwon Y Hur SS Kwak (1999) ArticleTitleMolecular characterization of cDNAs for two anionic peroxidases from suspension cultures of sweet potato. Mol Gen Genet 261 941–947 Occurrence Handle10.1007/s004380051041 Occurrence Handle1:CAS:528:DyaK1MXlvFyitb4%3D Occurrence Handle10485284

    Article  CAS  PubMed  Google Scholar 

  21. H Kishino M Hasegawa (1989) ArticleTitleEvaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea. J Mol Evol 29 170–179 Occurrence Handle1:CAS:528:DyaL1MXkvFCnsbc%3D Occurrence Handle2509717

    CAS  PubMed  Google Scholar 

  22. IV Kjærsgård HM Jespersen SK Rasmussen KG Welinder (1997) ArticleTitleSequence and RT-PCR expression analysis of two peroxidases from Arabidopsis thaliana belonging to a novel evolutionary branch of plant peroxidases. Plant Mol Biol 33 699–708 Occurrence Handle10.1023/A:1005707813801 Occurrence Handle1:STN:280:ByiB3sfkslI%3D Occurrence Handle9132061

    Article  CAS  PubMed  Google Scholar 

  23. A Kubo H Saji K Tanaka N Kondo (1993) ArticleTitleGenomic DNA structure of a gene encoding cytosolic ascorbate peroxidase from Arabidopsis thaliana. FEBS Lett 315 313–317 Occurrence Handle1:CAS:528:DyaK3sXlslGjsLk%3D Occurrence Handle8422923

    CAS  PubMed  Google Scholar 

  24. WS Li (1997) Molecular evolution. Sinauer Associates Sunderland

    Google Scholar 

  25. O Mirza A Henriksen L Østergaard KG Welinder M Gajhede (2000) ArticleTitle Arabidopsis thaliana peroxidase N: structure of a novel neutral peroxidase. Acta Crystallogr D Biol Crystallogr 56 372–375 Occurrence Handle10.1107/S0907444999016340 Occurrence Handle10713531

    Article  PubMed  Google Scholar 

  26. R Nyffeler (1999) ArticleTitleA new ordinal classification of the flowering plants. Trends Ecol Evol 14 168–170 Occurrence Handle10.1016/S0169-5347(99)01630-4 Occurrence Handle10322527

    Article  PubMed  Google Scholar 

  27. L Østergaard AG Pedersen HM Jespersen S Brunak KG Welinder (1998) ArticleTitleComputational analyses and annotations of the Arabidopsis peroxidase gene family. FEBS Lett 433 98–102 Occurrence Handle10.1016/S0014-5793(98)00849-7 Occurrence Handle9738941

    Article  PubMed  Google Scholar 

  28. L Østergaard K Teilum O Mirza O Mattsson M Petersen KG Welinder et al. (2000) ArticleTitle Arabidopsis ATP A2 peroxidase. Expression and high-resolution structure of a plant peroxidase with implications for lignification. Plant Mol Biol 44 231–243 Occurrence Handle10.1023/A:1006442618860 Occurrence Handle1:CAS:528:DC%2BD3cXovVansro%3D Occurrence Handle11117266

    Article  CAS  PubMed  Google Scholar 

  29. H Philippe J Laurent (1998) ArticleTitleHow good are deep phylogenetic trees?. Curr Opin Genet Dev 8 616–623 Occurrence Handle1:CAS:528:DyaK1MXhs1yjtA%3D%3D Occurrence Handle9914208

    CAS  PubMed  Google Scholar 

  30. YL Qiu JD Palmer (1999) ArticleTitlePhylogeny of early land plants: Insights from genes and genomes. Trends Plant Sci 4 26–30 Occurrence Handle10.1016/S1360-1385(98)01361-2 Occurrence Handle10234267

    Article  PubMed  Google Scholar 

  31. J Quackenbush F Liang I Holt G Pertea J Upton (2000) ArticleTitleThe TIGR gene indices: Reconstruction and representation of expressed gene sequences. Nucleic Acids Res 28 141–145 Occurrence Handle10.1093/nar/28.1.141 Occurrence Handle1:CAS:528:DC%2BD3cXhvVKjsLw%3D Occurrence Handle10592205

    Article  CAS  PubMed  Google Scholar 

  32. N Saitou M Nei (1987) ArticleTitleThe neighbor-joining melhod: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4 406–425 Occurrence Handle1:STN:280:BieC1cbgtVY%3D Occurrence Handle3447015

    CAS  PubMed  Google Scholar 

  33. L Savard P Li SH Strauss MW Chase M Michaud J Bousquet (1994) ArticleTitleChloroplast and nuclear gene sequences indicate late Pennsylvanian time for the last common ancestor of extant seed plants. Proc Natl Acad Sci USA 91 5163–5167 Occurrence Handle1:CAS:528:DyaK2cXktlWgtrk%3D Occurrence Handle8197201

    CAS  PubMed  Google Scholar 

  34. S Sawyer (1989) ArticleTitleStatistical tests for detecting gene conversion. Mol Biol Evol 6 526–538 Occurrence Handle1:CAS:528:DyaL1MXlvFWhtb4%3D Occurrence Handle2677599

    CAS  PubMed  Google Scholar 

  35. DJ Schuller N Ban RB Huystee A McPherson TL Poulos (1996) ArticleTitleThe crystal structure of peanut peroxidase. Structure 4 311–321 Occurrence Handle1:CAS:528:DyaK28XitVensr8%3D Occurrence Handle8805539

    CAS  PubMed  Google Scholar 

  36. AT Smith NC Veitch (1998) ArticleTitleSubstrate binding and catalysis in heme peroxidases. Curr Opin Chem Biol 2 269–278 Occurrence Handle10.1016/S1367-5931(98)80069-0 Occurrence Handle1:CAS:528:DyaK1cXjs1OltLg%3D Occurrence Handle9667928

    Article  CAS  PubMed  Google Scholar 

  37. K Strimmer A von Haeseler (1996) ArticleTitleQuartet puzzling: A quartet maximum likelihood method for reconstructing tree topologies. Mol Biol Evol 13 964–969 Occurrence Handle1:CAS:528:DyaK28XltlSmsLk%3D

    CAS  Google Scholar 

  38. MT Tarkka TA Nyman N Kalkkinen M Raudaskoski (2001) ArticleTitleScots pine expresses short-root-specific peroxidases during development. Eur J Biochem 268 86–92 Occurrence Handle10.1046/j.1432-1327.2001.01853.x Occurrence Handle1:CAS:528:DC%2BD3MXktVOjsA%3D%3D Occurrence Handle11121106

    Article  CAS  PubMed  Google Scholar 

  39. InstitutionalAuthorNameThe Arabidopsis Genome Initiative (2000) ArticleTitleAnalysis of the genome of the flowering plant Arabidopsis thaliana. Nature 408 796–815 Occurrence Handle11130711

    PubMed  Google Scholar 

  40. JD Thompson TJ Gibson F Plewniak F Jeanmougin DG Higgins (1997) ArticleTitleThe CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25 4876–4882 Occurrence Handle1:CAS:528:DyaK1cXntFyntQ%3D%3D Occurrence Handle9396791

    CAS  PubMed  Google Scholar 

  41. JD Thompson F Plewniak O Poch (1999) ArticleTitleA comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Res 27 2682–2690 Occurrence Handle10.1093/nar/27.13.2682 Occurrence Handle1:CAS:528:DyaK1MXksVKqtrY%3D Occurrence Handle10373585

    Article  CAS  PubMed  Google Scholar 

  42. JD Thompson F Plewniak J Thierry O Poch (2000) ArticleTitleDbClustal: Rapid and reliable global multiple alignments of protein sequences detected by database searches. Nucleic Acids Res 28 2919–2926 Occurrence Handle1:CAS:528:DC%2BD3cXlvFCnsb8%3D Occurrence Handle10908355

    CAS  PubMed  Google Scholar 

  43. JD Thompson F Plewniak R Ripp JC Thierry O Poch (2001) ArticleTitleTowards a reliable objective function for multiple sequence alignments. J Mol Biol 314 937–951 Occurrence Handle10.1006/jmbi.2001.5187 Occurrence Handle1:CAS:528:DC%2BD3MXosl2isrY%3D Occurrence Handle11734009

    Article  CAS  PubMed  Google Scholar 

  44. M Tognolli C Penel H Greppin P Simon (2002) ArticleTitleAnalysis and expression of the class III peroxidase large gene family in Arabidopsis thaliana. Gene 288 129–138 Occurrence Handle10.1016/S0378-1119(02)00465-1 Occurrence Handle1:CAS:528:DC%2BD38XjvFGiur8%3D Occurrence Handle12034502

    Article  CAS  PubMed  Google Scholar 

  45. NC Veitch AT Smith (2001) ArticleTitleHorseradish peroxidase. Adv Inorg Chem. 51 107–162 Occurrence Handle1:CAS:528:DC%2BD3cXnvFyktrY%3D

    CAS  Google Scholar 

  46. KG Welinder (1992) ArticleTitleSuperfamily of plant, fungal and bacterial peroxidases. Curr Opin Struc Biol 2 388–393 Occurrence Handle10.1016/0959-440X(92)90230-5 Occurrence Handle1:CAS:528:DyaK38XltVKrsLY%3D

    Article  CAS  Google Scholar 

  47. KG Welinder AF Justesen IV Kjærsgård RB Jensen SK Rasmussen HM Jespersen L Duroux (2002) ArticleTitleStructural diversity and transcription of class III peroxidases from Arabidopsis thaliana. Eur J Biochem 269 6063–6081 Occurrence Handle10.1046/j.1432-1033.2002.03311.x Occurrence Handle1:CAS:528:DC%2BD3sXht1GntQ%3D%3D Occurrence Handle12473102

    Article  CAS  PubMed  Google Scholar 

  48. J Yu S Hu J Wang GK Wong S Li B Liu et al. (2002) ArticleTitleA draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296 79–92 Occurrence Handle1:CAS:528:DC%2BD38XivVSqtr8%3D Occurrence Handle11935017

    CAS  PubMed  Google Scholar 

  49. L Zhang SK Pond BS Gaut (2001) ArticleTitleA survey of the molecular evolutionary dynamics of twenty-five multigene families from four grass taxa. J Mol Evol 52 144–156 Occurrence Handle1:CAS:528:DC%2BD3MXhtlSqu7o%3D Occurrence Handle11231894

    CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This work was supported by the European Commission (FMRX CT98 02000). The authors would like to thank Dr S. McInnis and Dr P. G. Bolwell for having reviewed the manuscript.

Author information

Authors and Affiliations

  1. Department of Life Sciences, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark

    Laurent Duroux & Karen G. Welinder

Authors
  1. Laurent Duroux
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Karen G. Welinder
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Laurent Duroux.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Duroux, L., Welinder, K.G. The Peroxidase Gene Family in Plants: A Phylogenetic Overview . J Mol Evol 57, 397–407 (2003). https://doi.org/10.1007/s00239-003-2489-3

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00239-003-2489-3

Keywords

Search

Navigation