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A phylogenetic survey of myotubularin genes of eukaryotes: distribution, protein structure, evolution, and gene expression.

Kerk D, Moorhead GB - BMC Evol. Biol. (2010)

Bottom Line: This study presents an overall framework of eukaryotic myotubularin gene evolution.Inactive myotubularin homologues with distinct domain architectures appear to have arisen on three separate occasions in different eukaryotic lineages.The large and distinctive set of myotubularin genes found in an important pathogen species suggest that in this organism myotubularins might present important new targets for basic research and perhaps novel therapeutic strategies.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biological Sciences, University of Calgary, Alberta, Canada.

ABSTRACT

Background: Phosphorylated phosphatidylinositol (PtdIns) lipids, produced and modified by PtdIns kinases and phosphatases, are critical to the regulation of diverse cellular functions. The myotubularin PtdIns-phosphate phosphatases have been well characterized in yeast and especially animals, where multiple isoforms, both catalytically active and inactive, occur. Myotubularin mutations bring about disruption of cellular membrane trafficking, and in humans, disease. Previous studies have suggested that myotubularins are widely distributed amongst eukaryotes, but key evolutionary questions concerning the origin of different myotubularin isoforms remain unanswered, and little is known about the function of these proteins in most organisms.

Results: We have identified 80 myotubularin homologues amidst the completely sequenced genomes of 30 organisms spanning four eukaryotic supergroups. We have mapped domain architecture, and inferred evolutionary histories. We have documented an expansion in the Amoebozoa of a family of inactive myotubularins with a novel domain architecture, which we dub "IMLRK" (inactive myotubularin/LRR/ROCO/kinase). There is an especially large myotubularin gene family in the pathogen Entamoeba histolytica, the majority of them IMLRK proteins. We have analyzed published patterns of gene expression in this organism which indicate that myotubularins may be important to critical life cycle stage transitions and host infection.

Conclusions: This study presents an overall framework of eukaryotic myotubularin gene evolution. Inactive myotubularin homologues with distinct domain architectures appear to have arisen on three separate occasions in different eukaryotic lineages. The large and distinctive set of myotubularin genes found in an important pathogen species suggest that in this organism myotubularins might present important new targets for basic research and perhaps novel therapeutic strategies.

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Alignment of ROCO Domain Sequences. ROCO domain sequences were identified and aligned as detailed in Methods. The alignment presents the sequences of six ROCO domain reference proteins: "Ct_ROCO" (Chlorobium tepidum); "Ns_LRRP1" (Nostoc sp. PCC 7120); "Mb_ROCO1" (Methanosarcina barkeri str. Fusaro); "Hs_LRK1" (Homo sapiens); "Hs_LRRK2" (Homo sapiens); and "Ce_LRK1" (Caenorhabditis elegans). Most of the other sequences are designated by an organism prefix, followed by a number from the appropriate organism-specific protein database. Several Dictyostelium ("Dd") sequences are referred to by their gene names. Further information about the reference and candidate ROCO sequences, including organism prefixes and database accession numbers, are provided in Additional File 6. Conserved residues shown by Gotthardt et al. [15] as being critical to the functioning of both the bacterial protein and the human ROCO protein homologue LRRK2 are marked with blue lettering outlining and blue arrows. These positions are as follows: "T484" (our T53); "L487" (our L61); "G518" (our G110); and "Y804" (our Y642). Above the alignment is shown in red the secondary structure of the solved structure of the ROCO domain of Chlorobium tepidum (PDB: 3dpu_A). "A" indicates alpha helix, "B" indicates beta strand, and arrowhead symbols ("<" and ">") denote the beginning and ending of secondary structure regions. The functionally important "Switch I" ("SW1") and "Switch II" ("SW2") regions are indicated. Areas with "+++" symbols in purple represent poorly aligned sequence regions which have been edited from the alignment. The initial sequence region (positions 1-365) represents the ROC domain. The beginning of the COR domain is indicated.
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Figure 4: Alignment of ROCO Domain Sequences. ROCO domain sequences were identified and aligned as detailed in Methods. The alignment presents the sequences of six ROCO domain reference proteins: "Ct_ROCO" (Chlorobium tepidum); "Ns_LRRP1" (Nostoc sp. PCC 7120); "Mb_ROCO1" (Methanosarcina barkeri str. Fusaro); "Hs_LRK1" (Homo sapiens); "Hs_LRRK2" (Homo sapiens); and "Ce_LRK1" (Caenorhabditis elegans). Most of the other sequences are designated by an organism prefix, followed by a number from the appropriate organism-specific protein database. Several Dictyostelium ("Dd") sequences are referred to by their gene names. Further information about the reference and candidate ROCO sequences, including organism prefixes and database accession numbers, are provided in Additional File 6. Conserved residues shown by Gotthardt et al. [15] as being critical to the functioning of both the bacterial protein and the human ROCO protein homologue LRRK2 are marked with blue lettering outlining and blue arrows. These positions are as follows: "T484" (our T53); "L487" (our L61); "G518" (our G110); and "Y804" (our Y642). Above the alignment is shown in red the secondary structure of the solved structure of the ROCO domain of Chlorobium tepidum (PDB: 3dpu_A). "A" indicates alpha helix, "B" indicates beta strand, and arrowhead symbols ("<" and ">") denote the beginning and ending of secondary structure regions. The functionally important "Switch I" ("SW1") and "Switch II" ("SW2") regions are indicated. Areas with "+++" symbols in purple represent poorly aligned sequence regions which have been edited from the alignment. The initial sequence region (positions 1-365) represents the ROC domain. The beginning of the COR domain is indicated.

Mentions: To confirm the identity of the ROCO domains of these Entamoeba sequences we performed iterative multiple sequence alignments, HMM construction, database searches and realignment, to assemble the data presented as Figure 4. During this process, we identified several previously unreported ROCO proteins (2 from Monosiga and 9 from Trichoplax). The alignment presents a comparison between our set of newly identified ROCO domain sequences and those from previously characterized Dictyostelium proteins. In their report of the solved structure of a bacterial ROCO protein, Gotthardt et al. [15] identified residues important to both the function of the bacterial protein, and animal ROCO protein homologues. These include residues in the ROC domain important for GTPase binding and residues in both the ROC and COR domains important for domain interactions and GTPase activity (see Legend to Figure 4). It is evident by inspection of the alignment in Figure 4 that on the whole, conservation of this critical residue set for the Entamoeba IMLRK sequences is poor. Despite the overall apparent similarity of these sequences to the rest of the comparison set, several of the Entamoeba sequences have deletions in these critical residues, and would therefore presumably lack GTPase activity. Only one Entamoeba sequence (EHI_048230) has a set of residues which might confer enzymatic activity.


A phylogenetic survey of myotubularin genes of eukaryotes: distribution, protein structure, evolution, and gene expression.

Kerk D, Moorhead GB - BMC Evol. Biol. (2010)

Alignment of ROCO Domain Sequences. ROCO domain sequences were identified and aligned as detailed in Methods. The alignment presents the sequences of six ROCO domain reference proteins: "Ct_ROCO" (Chlorobium tepidum); "Ns_LRRP1" (Nostoc sp. PCC 7120); "Mb_ROCO1" (Methanosarcina barkeri str. Fusaro); "Hs_LRK1" (Homo sapiens); "Hs_LRRK2" (Homo sapiens); and "Ce_LRK1" (Caenorhabditis elegans). Most of the other sequences are designated by an organism prefix, followed by a number from the appropriate organism-specific protein database. Several Dictyostelium ("Dd") sequences are referred to by their gene names. Further information about the reference and candidate ROCO sequences, including organism prefixes and database accession numbers, are provided in Additional File 6. Conserved residues shown by Gotthardt et al. [15] as being critical to the functioning of both the bacterial protein and the human ROCO protein homologue LRRK2 are marked with blue lettering outlining and blue arrows. These positions are as follows: "T484" (our T53); "L487" (our L61); "G518" (our G110); and "Y804" (our Y642). Above the alignment is shown in red the secondary structure of the solved structure of the ROCO domain of Chlorobium tepidum (PDB: 3dpu_A). "A" indicates alpha helix, "B" indicates beta strand, and arrowhead symbols ("<" and ">") denote the beginning and ending of secondary structure regions. The functionally important "Switch I" ("SW1") and "Switch II" ("SW2") regions are indicated. Areas with "+++" symbols in purple represent poorly aligned sequence regions which have been edited from the alignment. The initial sequence region (positions 1-365) represents the ROC domain. The beginning of the COR domain is indicated.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2927912&req=5

Figure 4: Alignment of ROCO Domain Sequences. ROCO domain sequences were identified and aligned as detailed in Methods. The alignment presents the sequences of six ROCO domain reference proteins: "Ct_ROCO" (Chlorobium tepidum); "Ns_LRRP1" (Nostoc sp. PCC 7120); "Mb_ROCO1" (Methanosarcina barkeri str. Fusaro); "Hs_LRK1" (Homo sapiens); "Hs_LRRK2" (Homo sapiens); and "Ce_LRK1" (Caenorhabditis elegans). Most of the other sequences are designated by an organism prefix, followed by a number from the appropriate organism-specific protein database. Several Dictyostelium ("Dd") sequences are referred to by their gene names. Further information about the reference and candidate ROCO sequences, including organism prefixes and database accession numbers, are provided in Additional File 6. Conserved residues shown by Gotthardt et al. [15] as being critical to the functioning of both the bacterial protein and the human ROCO protein homologue LRRK2 are marked with blue lettering outlining and blue arrows. These positions are as follows: "T484" (our T53); "L487" (our L61); "G518" (our G110); and "Y804" (our Y642). Above the alignment is shown in red the secondary structure of the solved structure of the ROCO domain of Chlorobium tepidum (PDB: 3dpu_A). "A" indicates alpha helix, "B" indicates beta strand, and arrowhead symbols ("<" and ">") denote the beginning and ending of secondary structure regions. The functionally important "Switch I" ("SW1") and "Switch II" ("SW2") regions are indicated. Areas with "+++" symbols in purple represent poorly aligned sequence regions which have been edited from the alignment. The initial sequence region (positions 1-365) represents the ROC domain. The beginning of the COR domain is indicated.
Mentions: To confirm the identity of the ROCO domains of these Entamoeba sequences we performed iterative multiple sequence alignments, HMM construction, database searches and realignment, to assemble the data presented as Figure 4. During this process, we identified several previously unreported ROCO proteins (2 from Monosiga and 9 from Trichoplax). The alignment presents a comparison between our set of newly identified ROCO domain sequences and those from previously characterized Dictyostelium proteins. In their report of the solved structure of a bacterial ROCO protein, Gotthardt et al. [15] identified residues important to both the function of the bacterial protein, and animal ROCO protein homologues. These include residues in the ROC domain important for GTPase binding and residues in both the ROC and COR domains important for domain interactions and GTPase activity (see Legend to Figure 4). It is evident by inspection of the alignment in Figure 4 that on the whole, conservation of this critical residue set for the Entamoeba IMLRK sequences is poor. Despite the overall apparent similarity of these sequences to the rest of the comparison set, several of the Entamoeba sequences have deletions in these critical residues, and would therefore presumably lack GTPase activity. Only one Entamoeba sequence (EHI_048230) has a set of residues which might confer enzymatic activity.

Bottom Line: This study presents an overall framework of eukaryotic myotubularin gene evolution.Inactive myotubularin homologues with distinct domain architectures appear to have arisen on three separate occasions in different eukaryotic lineages.The large and distinctive set of myotubularin genes found in an important pathogen species suggest that in this organism myotubularins might present important new targets for basic research and perhaps novel therapeutic strategies.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biological Sciences, University of Calgary, Alberta, Canada.

ABSTRACT

Background: Phosphorylated phosphatidylinositol (PtdIns) lipids, produced and modified by PtdIns kinases and phosphatases, are critical to the regulation of diverse cellular functions. The myotubularin PtdIns-phosphate phosphatases have been well characterized in yeast and especially animals, where multiple isoforms, both catalytically active and inactive, occur. Myotubularin mutations bring about disruption of cellular membrane trafficking, and in humans, disease. Previous studies have suggested that myotubularins are widely distributed amongst eukaryotes, but key evolutionary questions concerning the origin of different myotubularin isoforms remain unanswered, and little is known about the function of these proteins in most organisms.

Results: We have identified 80 myotubularin homologues amidst the completely sequenced genomes of 30 organisms spanning four eukaryotic supergroups. We have mapped domain architecture, and inferred evolutionary histories. We have documented an expansion in the Amoebozoa of a family of inactive myotubularins with a novel domain architecture, which we dub "IMLRK" (inactive myotubularin/LRR/ROCO/kinase). There is an especially large myotubularin gene family in the pathogen Entamoeba histolytica, the majority of them IMLRK proteins. We have analyzed published patterns of gene expression in this organism which indicate that myotubularins may be important to critical life cycle stage transitions and host infection.

Conclusions: This study presents an overall framework of eukaryotic myotubularin gene evolution. Inactive myotubularin homologues with distinct domain architectures appear to have arisen on three separate occasions in different eukaryotic lineages. The large and distinctive set of myotubularin genes found in an important pathogen species suggest that in this organism myotubularins might present important new targets for basic research and perhaps novel therapeutic strategies.

Show MeSH
Related in: MedlinePlus