The new MATH: homology suggests shared binding surfaces in meprin tetramers and TRAF trimers

Sunnerhagen, Maria; Pursglove, Sharon E.; Fladvad, Malin

doi:10.1016/s0014-5793(02)03330-6

Cited by 35 publications

(22 citation statements)

References 22 publications

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“…The MATH motif comprises around 150 amino acids forming eight b-sheets. Like the BTB/ POZ motif, it was found primarily in eukaryotes (Sunnerhagen et al, 2002). The domain was only recently noted based on homology of a COOHterminal region of meprins A and B and the TRAF-C domain (Uren and Vaux, 1996).…”

Section: Discussionmentioning

confidence: 99%

“…The domain was only recently noted based on homology of a COOHterminal region of meprins A and B and the TRAF-C domain (Uren and Vaux, 1996). Although the specific function of the MATH domain is still unknown, Sunnerhagen et al (2002) have suggested that the domain is an independent folding motif that participates in various modular arrangements based on other multimerization domains linked to it. The name for the MATH domain is composed of meprins and TRAFs, which participate in a broad variety of cellular processes, such as cell growth signaling and apoptosis (Bond and Beynon, 1995;Baker and Reddy, 1996;Arch et al, 1998;Bauvois, 2001;Bertenshaw et al, 2001).…”

Section: Discussionmentioning

confidence: 99%

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Arabidopsis AtCUL3a and AtCUL3b Form Complexes with Members of the BTB/POZ-MATH Protein Family

et al. 2005

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The ubiquitin proteasome pathway in plants has been shown to be important for many developmental processes. The E3 ubiquitin-protein ligases facilitate transfer of the ubiquitin moiety to substrate proteins. Many E3 ligases contain cullin proteins as core subunits. Here, we show that Arabidopsis (Arabidopsis thaliana) AtCUL3 proteins interact in yeast two-hybrid and in vitro pull-down assays with proteins containing a BTB/POZ (broad complex, tramtrack, bric-a-brac/pox virus and zinc finger) motif. By changing specific amino acid residues within the proteins, critical parts of the cullin and BTB/POZ proteins are defined that are required for these kinds of interactions. In addition, we show that AtCUL3 proteins assemble with the RINGfinger protein AtRBX1 and are targets for the RUB-conjugation pathway. The analysis of AtCUL3a and AtCUL3b expression as well as several BTB/POZ-MATH genes indicates that these genes are expressed in all parts of the plant. The results presented here provide strong evidence that AtCUL3a and AtCUL3b can assemble in Arabidopsis with BTB/POZ-MATH and AtRBX1 proteins to form functional E3 ligases.The ubiquitin proteasome pathway participates in a broad variety of physiologically and developmentally controlled processes in plants (for an overview, see Smalle and Vierstra, 2004). A critical step involves E3 ubiquitin ligases that facilitate the transfer of ubiquitin moieties to a substrate protein, leading to degradation via the 26S proteasome.In Arabidopsis (Arabidopsis thaliana), the bestcharacterized E3s are the SCF (Skp1-cullin-F-box) complexes that consist of at least four subunits: a cullin protein (AtCUL1), an ASK (Arabidopsis Skp1 ortholog) protein, a RING finger protein (RBX1), and an F-box protein (Gray et al., 1999Lechner et al., 2002;Shen et al., 2002). The cullin is a scaffolding subunit for the SCF and binds the ASK-F-box and RBX1 subunits within NH 2 -and COOH-terminal domains, respectively (Zheng et al., 2002). F-box proteins are substrate adaptors that confer specificity to the assembled SCF complexes (Gagne et al., 2002). AtCUL1-dependent E3s are crucial regulators for phytohormone responses, flowering, embryo development, and other processes (Smalle and Vierstra, 2004).At least 11 cullins are encoded in the Arabidopsis genome . However, only six members contain the conserved RUB (related to ubiquitin)-modification site characteristic of cullins that assemble into an SCF or related E3 complex (del Querido et al., 2001;del Pozo et al., 2002). Based on homology to cullins in other organisms, these six Arabidopsis cullins can be classified into three groups. The first group is the CUL1 family, which includes AtCUL1 (At4g02570), AtCUL2 (At1g02980), and AtCUL5 (At1g43140). It is likely that all three members participate in an SCF complex Risseeuw et al., 2003). The second group comprises the CUL3 family with AtCUL3a (At1g26830) and AtCUL3b (At1g69670). These two cullins are approximately 88% identical to each other and represent potential Arabidopsis orthologs of Caenorhabditis...

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Arabidopsis AtCUL3a and AtCUL3b Form Complexes with Members of the BTB/POZ-MATH Protein Family

et al. 2005

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“…to interact with human tumor necrosis factor receptors (Rothe et al, 1994) and share with meprins a conserved region of about 180 residues, named the MATH domain (Sunnerhagen et al, 2002). Using the INTERPRO database (http://www.ebi.ac.uk/interpro), a MATH domain is predicted in RTM3 between amino acid positions 13 and 136.…”

Section: Rtm3 Belongs To a New Gene Familymentioning

confidence: 99%

RTM3, Which Controls Long-Distance Movement of Potyviruses, Is a Member of a New Plant Gene Family Encoding a Meprin and TRAF Homology Domain-Containing Protein

Cosson

Sofer

et al. 2010

Plant Physiology

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Restriction of long-distance movement of several potyviruses in Arabidopsis (Arabidopsis thaliana) is controlled by at least three dominant restricted TEV movement (RTM) genes, named RTM1, RTM2, and RTM3. RTM1 encodes a protein belonging to the jacalin family, and RTM2 encodes a protein that has similarities to small heat shock proteins. In this article, we describe the positional cloning of RTM3, which encodes a protein belonging to an undescribed protein family of 29 members that has a meprin and TRAF homology (MATH) domain in its amino-terminal region and a coiled-coil domain at its carboxy-terminal end. Involvement in the RTM resistance system is the first biological function experimentally identified for a member of this new gene family in plants. Our analyses showed that the coiled-coil domain is not only highly conserved between RTM3-homologous MATH-containing proteins but also in proteins lacking a MATH domain. The cluster organization of the RTM3 homologs in the Arabidopsis genome suggests the role of duplication events in shaping the evolutionary history of this gene family, including the possibility of deletion or duplication of one or the other domain. Protein-protein interaction experiments revealed RTM3 self-interaction as well as an RTM1-RTM3 interaction. However, no interaction has been detected involving RTM2 or the potyviral coat protein previously shown to be the determinant necessary to overcome the RTM resistance. Taken together, these observations strongly suggest the RTM proteins might form a multiprotein complex in the resistance mechanism to block the long-distance movement of potyviruses.

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“…The domain probably functions in protein-protein interactions (Sunnerhagen et al 2002). C. elegans MATH-domain cluster-5 genes are predominantly of two sorts.…”

Section: Detection Of Gene Clustersmentioning

confidence: 99%

Analysis of Homologous Gene Clusters inCaenorhabditis elegansReveals Striking Regional Cluster Domains

Thomas

2006

Genetics

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An algorithm for detecting local clusters of homologous genes was applied to the genome of Caenorhabditis elegans. Clusters of two or more homologous genes are abundant, totaling 1391 clusters containing 4607 genes, over one-fifth of all genes in C. elegans. Cluster genes are distributed unevenly in the genome, with the large majority located on autosomal chromosome arms, regions characterized by higher genetic recombination and more repeat sequences than autosomal centers and the X chromosome. Cluster genes are transcribed at much lower levels than average and very few have gross phenotypes as assayed by RNAimediated reduction of function. The molecular identity of cluster genes is unusual, with a preponderance of nematode-specific gene families that encode putative secreted and transmembrane proteins, and enrichment for genes implicated in xenobiotic detoxification and innate immunity. Gene clustering in Drosophila melanogaster is also substantial and the molecular identity of clustered genes follows a similar pattern. I hypothesize that autosomal chromosome arms in C. elegans undergo frequent local gene duplication and that these duplications support gene diversification and rapid evolution in response to environmental challenges. Although specific gene clusters have been documented in C. elegans, their abundance, genomic distribution, and unusual molecular identities were previously unrecognized. IT is widely appreciated that genes of related function tend to reside in clusters in eubacteria and archaea, often arranged in coregulated operons. Functional clusters in eukaryotes are less common, although there are various indications that such clusters may be more common than was first apparent from genetic studies. For example, in Caenorhabditis elegans 15% of genes are members of cotranscribed operons (Blumenthal et al. 2002). The two to eight genes in each of the 1050 operons are subject to similar transcriptional regulation (Lercher et al. 2003), and genes within an operon are often involved in related biological processes (Blumenthal et al. 2002). Such operon clusters are not generally composed of homologous genes, but instead seem to group distinct gene sequences for transcriptional coregulation (Blumenthal et al. 2002). In addition to such functional clustering, specific examples of clusters of homologous genes have also been reported in C. elegans (e.g., Gotoh 1998;Robertson 1998Robertson , 2000Sluder et al. 1999) and in a wide variety of other metazoans (e.g., Fritsch et al. 1980;Akam 1989;Hofker et al. 1989;Del Punta et al. 2000;Glusman et al. 2001). A cursory global analysis of homologous gene clusters was reported in the C. elegans genome sequence report (C. elegans Sequencing Consortium 1998). To investigate homologous gene clusters systematically, I developed an algorithm for scanning the genome for locally abundant gene families. This method identified 1391 cases of local clusters of two or more homologous genes, 216 of which had five or more members. The larger families tend to share a v...

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The new MATH: homology suggests shared binding surfaces in meprin tetramers and TRAF trimers

Cited by 35 publications

References 22 publications

Arabidopsis AtCUL3a and AtCUL3b Form Complexes with Members of the BTB/POZ-MATH Protein Family

Arabidopsis AtCUL3a and AtCUL3b Form Complexes with Members of the BTB/POZ-MATH Protein Family

RTM3, Which Controls Long-Distance Movement of Potyviruses, Is a Member of a New Plant Gene Family Encoding a Meprin and TRAF Homology Domain-Containing Protein

Analysis of Homologous Gene Clusters inCaenorhabditis elegansReveals Striking Regional Cluster Domains

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