The SWIRM domain: a conserved module found in chromosomal proteins points to novel chromatin-modifying activities

Abstract

Background: Eukaryotic chromosomal components, especially histones, are subject to a wide array of covalent modifications and catalytic reorganization. These modifications have an important role in the regulation of chromatin structure and are mediated by large multisubunit complexes that contain modular proteins with several conserved catalytic and noncatalytic adaptor domains.

Results: Using computational sequence-profile analysis methods, we identified a previously uncharacterized, predicted alpha-helical domain of about 85 residues in chromosomal proteins such as Swi3p, Rsc8p, Moira and several other uncharacterized proteins. This module, termed the SWIRM domain, is predicted to mediate specific protein-protein interactions in the assembly of chromatin-protein complexes. In one group of proteins, which are highly conserved throughout the crown-group eukaryotes, the SWIRM domain is linked to a catalytic domain related to the monoamine and polyamine oxidases. Another human protein has the SWIRM domain linked to a JAB domain that is involved in protein degradation through the ubiquitin pathway.

Conclusions: Identification of the SWIRM domain could help in directed experimental analysis of specific interactions in chromosomal proteins. We predict that the proteins in which it is combined with an amino-oxidase domain define a novel class of chromatin-modifying enzymes, which are likely to oxidize either the amino group of basic residues in histones and other chromosomal proteins or the polyamines in chromatin, and thereby alter the charge distribution. Other forms, such as KIAA1915, may link chromatin modification to ubiquitin-dependent protein degradation.

Figure 1

Multiple sequence alignment of the SWIRM domain. Proteins are designated by their gene names followed by the species abbreviations and GenBank (gi) numbers. The coloring represents the conservation profile of amino-acid residues at 90% consensus distinguished by the following amino-acid classes: h, hydrophobic residues (LIYFMWACV (in the single-letter amino-acid code)), a, aromatic residues (FHYW) and l, aliphatic (LIAV) residues, all shaded yellow; c, charged (KERDH) residues (basic (KRH) residues and acidic (DE) residues) colored magenta; p, polar (STEDRKHNQC) residues colored blue; s, small (SACGDNPVT) residues colored green; u, tiny (GAS) residues shaded green (in positions that are always glycine, this is indicated with a G); b, big (LIYERFMWQ) residues shaded gray. The predicted secondary structure is shown above the alignment: H or h, α helix; E or e, β strand. Species abbreviations: At, Arabidopsis thaliana; Bna, Brassica napus; Ce, Caenorhabditis elegans; Ddi, Dictyostelium discoideum; Dm, Drosophila melanogaster; Ecu, Encephalitozoon cuniculi; Hs, Homo sapiens; Osa, Oryza sativa; Sc, Saccharomyces cerevisiae; Sp, Schizosaccharomyces pombe; Zm, Zea mays. A subset of Rsc8p orthologs is represented in the automatically generated, uncurated PFAM-B entry 3680.

Figure 2

Domain architectures of proteins predicted to have the SWIRM domain. Proteins are designated by their gene names, species abbreviations and gi numbers. The phyletic distribution of a particular domain architecture is additionally given in brackets, where A represents animals; P, plants; F, fungi; D, D. discoideum and Pf, Plasmodium falciparum. Domains are typically represented by their standard names or abbreviations. ZZ represents the ZZ-type of zinc finger, and 'helical' designates the conserved α-helical domain found at the carboxyl terminus of proteins with a Myb (SANT) and an RSC8-like SWIRM domain.

Figure 3

Multiple sequence alignment of the polyamine oxidase domain. Amino-acid residues are colored at 100% consensus. The protein designations, coloring scheme and consensus abbreviations are as described in Figure 1; +, acidic residues. The crystal-structure-derived secondary-structure assignments are shown above the alignment with positions involved in cofactor or substrate binding marked by an asterisk. Inserts in individual sequences are given as brown numbers. Species abbreviations: At, A. thaliana; Ce, C. elegans; Dm, D. melanogaster; Hs, Homo sapiens; Mm, Mus musculus; Mtu, Mycobacterium tuberculosis; Rn, Rattus norvegicus; Sp, S. pombe; Zma, Z. mays.