The plant s1-like nuclease family has evolved a highly diverse range of catalytic capabilities

Plant Cell Physiol. 2013 Jul;54(7):1064-78. doi: 10.1093/pcp/pct061. Epub 2013 Apr 24.


Plant S1-like nucleases, often referred to as nuclease I enzymes, are the main class of enzymes involved in nucleic acid degradation during plant programmed cell death. The catalytically active site of these enzymes shows a significant similarity to the well-described P1 nuclease from Penicillium citrinum. Previously published studies reported that plant S1-like nucleases possess catalytic activities similar to their fungal orthologs, i.e. they hydrolyze single-stranded DNA and RNA, and less efficiently double-stranded DNA, in the presence of zinc ions. Here we describe a comprehensive study of the nucleolytic activities of all Arabidopsis S1-like paralogs. Our results revealed that different members of this family are characterized by a surprisingly large variety of catalytic properties. We found that, in addition to Zn(2+)-dependent enzymes, this family also comprises nucleases activated by Ca(2+) and Mn(2+), which implies that the apparently well-known S1 nuclease active site in plant nucleases is able to cooperate with different activatory ions. Moreover, particular members of this class differ in their optimum pH value and substrate specificity. These results shed new light on the widely accepted classification of plant nucleases which is based on the assumption that the catalytic requirements of plant nucleases reflect their phylogenetic origin. Our results imply the need to redefine the understanding of the term 'nuclease I'. Analysis of the phylogenetic relationships between S1-like enzymes shows that plant representatives of this family evolve toward an increase in catalytic diversity. The importance of this process for the biological functions of plant S1-type enzymes is discussed.

Keywords: Arabidopsis thaliana; Gene family evolution; Metallonucleases; Nuclease I; Programmed cell death; S1-like nucleases.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Arabidopsis / enzymology
  • Arabidopsis / genetics*
  • Arabidopsis / metabolism
  • Arabidopsis Proteins / chemistry
  • Arabidopsis Proteins / genetics*
  • Arabidopsis Proteins / metabolism
  • Biocatalysis / drug effects
  • Blotting, Western
  • Calcium / pharmacology
  • Catalytic Domain
  • DNA, Single-Stranded / metabolism
  • Endonucleases / chemistry
  • Endonucleases / classification
  • Endonucleases / genetics*
  • Endonucleases / metabolism
  • Evolution, Molecular*
  • Hydrogen-Ion Concentration
  • Isoenzymes / classification
  • Isoenzymes / genetics
  • Isoenzymes / metabolism
  • Manganese / pharmacology
  • Models, Molecular
  • Molecular Sequence Data
  • Phylogeny
  • RNA / metabolism
  • Sequence Homology, Amino Acid
  • Substrate Specificity
  • Zinc / pharmacology


  • Arabidopsis Proteins
  • DNA, Single-Stranded
  • Isoenzymes
  • Manganese
  • RNA
  • ENDO2 protein, Arabidopsis
  • Endonucleases
  • Zinc
  • Calcium