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Are plant formins integral membrane proteins?

Cvrcková F - Genome Biol. (2000)

Bottom Line: I found eight putative formin-coding genes in the publicly available part of the Arabidopsis genome sequence and analyzed their predicted protein sequences.Surprisingly, some of them lack parts of the conserved formin-homology 2 (FH2) domain and the majority of them seem to have signal sequences and putative transmembrane segments that are not found in yeast or animals formins.Plant formins define a distinct subfamily.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Plant Physiology, Faculty of Sciences, Charles University, Vinicná 5, CZ 128 44 Praha 2, Czech Republic. fatima@natur.cuni.cz.

ABSTRACT

Background: The formin family of proteins has been implicated in signaling pathways of cellular morphogenesis in both animals and fungi; in the latter case, at least, they participate in communication between the actin cytoskeleton and the cell surface. Nevertheless, they appear to be cytoplasmic or nuclear proteins, and it is not clear whether they communicate with the plasma membrane, and if so, how. Because nothing is known about formin function in plants, I performed a systematic search for putative Arabidopsis thaliana formin homologs.

Results: I found eight putative formin-coding genes in the publicly available part of the Arabidopsis genome sequence and analyzed their predicted protein sequences. Surprisingly, some of them lack parts of the conserved formin-homology 2 (FH2) domain and the majority of them seem to have signal sequences and putative transmembrane segments that are not found in yeast or animals formins.

Conclusions: Plant formins define a distinct subfamily. The presence in most Arabidopsis formins of sequence motifs typical or transmembrane proteins suggests a mechanism of membrane attachment that may be specific to plant formins, and indicates an unexpected evolutionary flexibility of the conserved formin domain.

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Alignment of the FH2 domain of selected formins and definition of the subdomain modules. Subdomain modules (a-j) are marked in color. Red dots denote the position of introns (not shown in MFORMIN, for which only mRNA sequence is available). The consensus line shows 80% consensus of the EMBL DS39866 alignment. Numbers indicate positions within the sequence and the size of unaligned insertions; residues corresponding to unambiguous consensus and/or shared by all Arabidopsis formins are highlighted. For gene terminology see Table 1 and Materials and methods.
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Figure 1: Alignment of the FH2 domain of selected formins and definition of the subdomain modules. Subdomain modules (a-j) are marked in color. Red dots denote the position of introns (not shown in MFORMIN, for which only mRNA sequence is available). The consensus line shows 80% consensus of the EMBL DS39866 alignment. Numbers indicate positions within the sequence and the size of unaligned insertions; residues corresponding to unambiguous consensus and/or shared by all Arabidopsis formins are highlighted. For gene terminology see Table 1 and Materials and methods.

Mentions: Sequence comparison with known formins revealed the presence of genuine FH2 domain in all Arabidopsis formins (Figure 1). However, even the longest predicted proteins, encoded by the AtFORMIN 3, -4 and -5 genes, lack parts of the FH2 region ubiquitously conserved among corresponding genes of fungi and metazoa (Figures 1 and 2), although not necessarily among their protein products, because some formin mRNAs undergo complex splicing [24]. Sequence motifs corresponding to the missing regions were found in all cases within the predicted introns by visual inspection of three-frame translation data. Because the reliability of mRNA structure prediction is limited [25], failure to identify exons correctly may explain the apparent deletion of this region of the FH2 domain. The possibly mispredicted intron encoding subdomain g of AtFORMIN4 is split by a frameshift mutation, however. Although this could reflect a sequencing error, the possibility remains that plant formin homologs have a modular structure within the FH2 domain at the gene level, and that at least some of the FH2-related sequences within predicted introns are vestiges of exons lost by mutation.


Are plant formins integral membrane proteins?

Cvrcková F - Genome Biol. (2000)

Alignment of the FH2 domain of selected formins and definition of the subdomain modules. Subdomain modules (a-j) are marked in color. Red dots denote the position of introns (not shown in MFORMIN, for which only mRNA sequence is available). The consensus line shows 80% consensus of the EMBL DS39866 alignment. Numbers indicate positions within the sequence and the size of unaligned insertions; residues corresponding to unambiguous consensus and/or shared by all Arabidopsis formins are highlighted. For gene terminology see Table 1 and Materials and methods.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC31918&req=5

Figure 1: Alignment of the FH2 domain of selected formins and definition of the subdomain modules. Subdomain modules (a-j) are marked in color. Red dots denote the position of introns (not shown in MFORMIN, for which only mRNA sequence is available). The consensus line shows 80% consensus of the EMBL DS39866 alignment. Numbers indicate positions within the sequence and the size of unaligned insertions; residues corresponding to unambiguous consensus and/or shared by all Arabidopsis formins are highlighted. For gene terminology see Table 1 and Materials and methods.
Mentions: Sequence comparison with known formins revealed the presence of genuine FH2 domain in all Arabidopsis formins (Figure 1). However, even the longest predicted proteins, encoded by the AtFORMIN 3, -4 and -5 genes, lack parts of the FH2 region ubiquitously conserved among corresponding genes of fungi and metazoa (Figures 1 and 2), although not necessarily among their protein products, because some formin mRNAs undergo complex splicing [24]. Sequence motifs corresponding to the missing regions were found in all cases within the predicted introns by visual inspection of three-frame translation data. Because the reliability of mRNA structure prediction is limited [25], failure to identify exons correctly may explain the apparent deletion of this region of the FH2 domain. The possibly mispredicted intron encoding subdomain g of AtFORMIN4 is split by a frameshift mutation, however. Although this could reflect a sequencing error, the possibility remains that plant formin homologs have a modular structure within the FH2 domain at the gene level, and that at least some of the FH2-related sequences within predicted introns are vestiges of exons lost by mutation.

Bottom Line: I found eight putative formin-coding genes in the publicly available part of the Arabidopsis genome sequence and analyzed their predicted protein sequences.Surprisingly, some of them lack parts of the conserved formin-homology 2 (FH2) domain and the majority of them seem to have signal sequences and putative transmembrane segments that are not found in yeast or animals formins.Plant formins define a distinct subfamily.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Plant Physiology, Faculty of Sciences, Charles University, Vinicná 5, CZ 128 44 Praha 2, Czech Republic. fatima@natur.cuni.cz.

ABSTRACT

Background: The formin family of proteins has been implicated in signaling pathways of cellular morphogenesis in both animals and fungi; in the latter case, at least, they participate in communication between the actin cytoskeleton and the cell surface. Nevertheless, they appear to be cytoplasmic or nuclear proteins, and it is not clear whether they communicate with the plasma membrane, and if so, how. Because nothing is known about formin function in plants, I performed a systematic search for putative Arabidopsis thaliana formin homologs.

Results: I found eight putative formin-coding genes in the publicly available part of the Arabidopsis genome sequence and analyzed their predicted protein sequences. Surprisingly, some of them lack parts of the conserved formin-homology 2 (FH2) domain and the majority of them seem to have signal sequences and putative transmembrane segments that are not found in yeast or animals formins.

Conclusions: Plant formins define a distinct subfamily. The presence in most Arabidopsis formins of sequence motifs typical or transmembrane proteins suggests a mechanism of membrane attachment that may be specific to plant formins, and indicates an unexpected evolutionary flexibility of the conserved formin domain.

Show MeSH