Artikkeli animaalisista BTB/Kelch proteiineista . Kelch toiston omaavan superperheen fylogeniaa.

BMC Bioinformatics
December 2003, 4:42 | Cite as
Molecular phylogeny of the kelch-repeat superfamily reveals an expansion of BTB/kelch proteins in animals Authors Soren Prag, Josephine C Adams, .Dept. of Cell Biology, Lerner Research InstituteCleveland Clinic FoundationClevelandUSA
Open Access
Research article

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Abstract. Background

The kelch motif is an ancient and evolutionarily-widespread sequence motif of 44–56 amino acids in length. It occurs as five to seven repeats that form a β-propeller tertiary structure. Over 28 kelch-repeat proteins have been sequenced  (2003) and functionally characterised from diverse organisms spanning from viruses, plants and fungi to mammals and it is evident from expressed sequence tag, domain and genome databases that many additional hypothetical proteins contain kelch-repeats. In general, kelch-repeat β-propellers are involved in protein-protein interactions, however the modest sequence identity between kelch motifs, the diversity of domain architectures, and the partial information on this protein family in any single species, all present difficulties to developing a coherent view of the kelch-repeat domain and the kelch-repeat protein superfamily. To understand the complexity of this superfamily of proteins, we have analysed by bioinformatics the complement of kelch-repeat proteins encoded in the human genome and have made comparisons to the kelch-repeat proteins encoded in other sequenced genomes.

Results  We identified 71 kelch-repeat proteins encoded in the human genome, whereas 5 or 8 members were identified in yeasts and around 18 in C. elegans, D. melanogaster and A. gambiae. Multiple domain architectures were identified in each organism, including previously unrecognised forms. The vast majority of kelch-repeat domains are predicted to form six-bladed β-propellers. The most prevalent domain architecture in the metazoan animal genomes studied was the BTB/kelch domain organisation and we uncovered 3 subgroups of human BTB/kelch proteins. Sequence analysis of the kelch-repeat domains of the most robustly-related subgroups identified differences in β-propeller organisation that could provide direction for experimental study of protein-binding characteristics.

Conclusion The kelch-repeat superfamily constitutes a distinct and evolutionarily-widespread family of β-propeller domain-containing proteins. Expansion of the family during the evolution of multicellular animals is mainly accounted for by a major expansion of the BTB/kelch domain architecture. BTB/kelch proteins constitute 72 % of the kelch-repeat superfamily of H. sapiens and form three subgroups, one of which appears the most-conserved during evolution. Distinctions in propeller blade organisation between subgroups 1 and 2 were identified that could provide new direction for biochemical and functional studies of novel kelch-repeat proteins.

Keywords

Domain Architecture Galactose Oxidase Biology Workbench Eucaryotic Organism Identity Consensus Sequence 

These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Abbreviations

BLAST

basic local alignment search tool

BTB/POZ

Broad-Complex, Tramtrack, and Bric-a-Brac/ Poxvirus and Zincfinger domain

CDD

conserved domain database

EST

expressed sequence tag

ORF

open reading frame, Pfam, Protein families database of alignments and HMMs

SMART

simple modular architecture research tool.

Electronic supplementary material

The online version of this article (doi: 10.1186/1471-2105-4-42) contains supplementary material, which is available to authorized users.

Background

The kelch motif is an ancient and evolutionarily-widespread sequence motif of 44–56 amino acids in length. Eight residues within the motif are highly-conserved and constitute a consensus sequence [1, 2, 3] (Fig. 1A). Kelch motifs occur as groups of five to seven repeats and have been identified in proteins of otherwise distinct molecular architecture, termed the kelch-repeat superfamily. Currently, over 28 kelch-repeat proteins have been sequenced and functionally characterised in diverse organisms including viruses, plants, fungi and mammals [3]. Several kelch repeat-containing proteins have been recognised in Bacteria and Archaea (GenBank NP_713516, NP_639451 and Pfam01344 species distribution link), revealing the universal nature of the repeats. On the basis of the crystal structure determined for a single kelch-repeat protein, Hypomyces rosellus galactose oxidase (PDB 1GOF), the sets of repeated kelch motifs are predicated to form a β-propeller structure [2, 4].

The kelch motif and the β-propeller fold. A, Consensus sequence of the kelch motif. Compiled from [2] and [3]. The sequence motif is shown in relation to the four β-sheets of a propeller blade structure, as determined for the kelch motifs of fungal galactose oxidase [4]. In the consensus, G= glycine, Y = tyrosine, W = tryptophan, s = small residue; l = large residue; h = hydrophobic residue. B, Structure of a kelch-repeat propeller blade. A single blade from the crystal structure of fungal galactose oxidase (1GOF) is shown. β sheets 1–4 are colored as in panel A. The N- and C-termini join to adjacent blades. As indicated by the mapping of the consensus amino acids onto the blade, the most highly-conserved residues are located in the β-sheets. In various examples of β-propeller proteins, the intra- and inter-blade loops have variable sequences and contribute to protein-protein interactions [3]. C, Structure of the kelch-repeat β-propeller domain of fungal galactose oxidase (1GOF). β-sheets 1–4 in each blade are colored as in panel A. As indicated, this β-propeller contains seven blades. The β-4 strand of blade 7 is derived from the amino-terminus of the domain and thus closes the circular structure.

The β-propeller is a widespread and universal protein domain fold, as revealed from crystal structures of diverse proteins [5, 6, 7]. Many unrelated primary sequences can adopt the stereotypical topology of a β-propeller; however, several sequence repeat motifs have been identified in relation to known crystal structures that are predictors of propeller domains. These include the WD motif, the regulator of chromosome condensation 1 (RCC1) motif and the tachylectin-2 repeat, as well as the kelch motif [3, 5, 6, 7, 8, 9]. Each "blade" of a β-propeller structure is formed from a four-stranded antiparallel twisted β-sheet fold, in which each β-sheet packs onto the adjoining sheets through hydrophobic contacts (Fig. 1B). Four to eight of these β-sheet modules are radially arranged around a central axis to form the β-propeller domain, with the twist of the β-sheets within each module producing the propeller-blade appearance (Fig. 1C). Intra- and inter-blade loops of varying lengths protrude above, below, or at the sides of the β-sheets and contribute variability to the binding properties of individual β-propellers [3, 5, 6] (Fig. 1B). The whole structure is closed and stabilised by interactions between the first and last blades. In the four-bladed β-propellers of hemopexin and collagenase this is achieved by disulphide bonding between the first and last blades [10, 11]. In the other examples for which there is crystal structural information, the last blade of the β-propeller is assembled as a composite from sequences at the amino- and carboxy-terminal ends of the domain, that are held together by hydrogen bonds [3, 5, 6, 9] (example of galactose oxidase shown in Fig. 1C).

Kelch-repeat β-propellers undergo a variety of binding interactions with other molecules. Several kelch proteins, including D. melanogaster kelch and mammalian IPP, bind and cross-link F-actin through the β-propeller domain [12, 13]. In contrast, the kelch repeats of other proteins, such as gigaxonin, Keap1, or recombination-activating gene 2, (RAG-2), have unique binding partner proteins [14, 15, 16] and the β-propeller of fungal galactose oxidase corresponds to the catalytic domain of the enzyme [2, 4]. The kelch-repeat β-propeller is thus considered to form a general protein-protein interaction module that associates with diverse and specific binding partners [3]. Several kelch-repeat proteins contain other protein domains, of particular note being the Broad-Complex, Tramtrack, and Bric-a-Brac/Poxvirus and Zincfinger (BTB/POZ) domain (CDD6184, Pfam 00651, SMART0225) [1, 3, 17]. The BTB/POZ domain was first identified as a dimerisation domain of transcription factors and also mediates homodimerisation of kelch and other BTB/kelch domain proteins [10, 17, 18].

As summarised above, the current view of the kelch-repeat superfamily has been compiled from studies of individual kelch-repeat proteins from diverse organisms. The extent and complexity of the kelch-repeat family within an individual species is unknown. An overview of this domain family would be of value in order to make a rational assignment of structural subgroups and to develop a coherent perspective on the evolution of this protein domain between modern organisms. A clear view of kelch-repeat proteins could also open up new possibilities for sequence analysis, prediction and experimental analysis of structure/function relationships, and a greater understanding of the specific properties of kelch-repeat proteins within the large β-propeller fold group. In modern life sciences, such molecular information provides a fundamental context for well-targeted biochemical and biological studies of individual proteins. Building on the availability of complete genome sequence information for H. sapiens, D. melanogaster, A. gambiae, C. elegans, S. cerevisiae, S. pombe and A. thaliana we have addressed these questions through database mining and bioinformatic sequence analyses.

Results