The Pin2 genes encode potato type II proteinase inhibitors that act against pathogenic attack. The first examples were found only in the Solanaceae family, but, using new EST and genomic data, we have found 11 homologous genes dispersed through almost the w hole range of mono- and di-cotyledonous plants. In contrast to the repetitive precursor sequences of the Solanaceae Pin2 genes, the new homologs have only a single repeat unit. The gene family appears to have evolved from a single-domain ancestral gene through a series of gene-duplication and domain-duplication steps. A number of unequal cross-over and gene conversion events could explain the current gene and domain pattern of the Solanaceae Pin2 subfamily. Published online: 23 September 2002 The Pin2 family of proteinase inhibitors is present in seeds, leaves and other organs of the Solanaceae. Perhaps the best known representatives are the wound-induced proteinase inhibitors [1,2], which contain up to eight sequence-repeats (the ‘IP repeats’) coded by the second exon of the gene (e.g. [3]). The 3D structure of the mature inhibitor from potato is known [4], and recently it was shown that some engineered Pin2 precursors are able to form a circularly permuted structure [5–7] that was thought to correspond to the ancestral, single-repeat protein of this family. Subsequently, a naturally occurring Pin2 protein, PSI-1.2, with this ‘ancestral’ circularly permuted structure was isolated [3]. Circular permutation of sequences had been reported in other cases (for reviews see [8,9]). But until the discovery of PSI-1.2, circular TRENDS in Genetics Vol.18 No.12 December 2002 http://tig.trends.com 0168-9525/02/$ – see front matter © 2002 Elsevier Science Ltd. All rights reserved. PII: S0168-9525(02)02771-3 600 Research Update Genome Analysis Repeats with variations: accelerated evolution of the Pin2 family of proteinase inhibitors Endre Barta, Alessandro Pintar and Sándor Pongor 3 Yang, M. and Sack, F.D. (1995) The too many mouths and four lips mutations affect stomatal production in Arabidopsis. Plant Cell 7, 2227–2239 4 Geisler, M. et al. (1998) Divergent regulation of stomatal initiation and patterning in organ and suborgan regions of the Arabidopsis mutants too many mouths and four lips. Planta 205, 522–530 5 Serna, L. et al. (2002) Specification of stomatal fate in Arabidopsis: evidences for cellular interactions. New Phytol. 153, 399–404 6 Kobe, B. and Deisenhofer, J. (1994) The leucine-rich repeat: a versatile binding motif. Trends Biochem. Sci. 19, 415–421 7 Kayes, J.M. and Clark, S.E. (1998) CLAVATA2, a regulator of meristem and organ development in Arabidopsis. Development 125, 3843–3851 8 Jeong, S. et al. (1999) The Arabidopsis CLAVATA2 gene encodes a receptor-like protein required for the stability of CLAVATA1 receptor-like kinase. Plant Cell 11, 1925–1934 9 Berger, D. and Altmann, T. (2000) A subtilisin-like serine protease involved in the regulation of stomatal density and distribution in Arabidopsis thaliana. Genes Dev. 14, 1119–1131 10 von Groll, U. and Altmann, T. (2001) Stomatal cell biology. Curr. Opin. Plant Biol. 4, 555–560 11 Clark, S.E. (2001) Cell signalling at the shoot meristem. Nat. Rev. Mol. Cell Biol. 2, 276–284 12 The Arabidopsis Genome Initiative. (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796–815 Laura Serna* Carmen Fenoll Universidad de Castilla-La Mancha, Facultad de Ciencias del Medio Ambiente. Avda. Carlos III, s/n, 45071 Toledo, Spain. * e-mail: laura.serna@uclm.es TRENDS in Genetics IP2 IP3′ PSI-1.1 PSI-X R2 R1 R4 R3 R6 R5 R8 R7 IP3 IP4 IP6 IP8 IP2 + IP1 PSI-1.2? Exon 1 Exon 2 Phase 1 intron 100–200 nucleotides R1 R2 etc Fig. 1. The domain structure of the potato type II proteinase inhibitor (Pin2) family of precursors. The inset shows the consensus protein structure. IP1...IP8 designate the total number of IP repeats (green boxes) within each precursor. The IP1 molecules were identified while searching genomic databases for the purposes of this review (sequences shown in Fig. 2). Yellow box, signal peptide; black vertical lines, Cys residues; gray lines, sequence identity (>98%). The presence of adjacent, identical repeats is a recurrent pattern. PSI-1.1 [17] PSI-X (N. Antcheva and S. Pongor, unpublished) and PSI-1.2 [3] are paprika seed inhibitors, the gene corresponding to the major seed inhibitor PSI-1.2 is unknown. See Fig. 3 and Supplementary Material for the gene accession numbers.