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Conservation of the TRAPPII-specific subunits of a Ypt/Rab exchanger complex.

Cox R, Chen SH, Yoo E, Segev N - BMC Evol. Biol. (2007)

Bottom Line: However, we show here that the yeast Trs130 does not function as a trans-membrane protein, and the human TMEM1 does not contain putative TMDs.We suggest that the function of both NIBP and TMEM1 in the regulation of intra-cellular trafficking is conserved from yeast to man.The conserved domains and amino acids discovered here can be used for functional analysis that should help to resolve the differences in the assigned functions of these proteins in fungi and animals.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biological Sciences, Laboratory for Molecular Biology, University of Illinois at Chicago, Chicago, IL 60607, USA. randal@randalcox.net <randal@randalcox.net>

ABSTRACT

Background: Ypt/Rab GTPases and their GEF activators regulate intra-cellular trafficking in all eukaryotic cells. In S. cerivisiae, the modular TRAPP complex acts as a GEF for the Golgi gatekeepers: Ypt1 and the functional pair Ypt31/32. While TRAPPI, which acts in early Golgi, is conserved from fungi to animals, not much is known about TRAPPII, which acts in late Golgi and consists of TRAPPI plus three additional subunits.

Results: Here, we show a phylogenetic analysis of the three TRAPPII-specific subunits. One copy of each of the two essential subunits, Trs120 and Trs130, is present in almost every fully sequenced eukaryotic genome. Moreover, the primary, as well as the predicted secondary, structure of the Trs120- and Trs130-related sequences are conserved from fungi to animals. The mammalian orthologs of Trs120 and Trs130, NIBP and TMEM1, respectively, are candidates for human disorders. Currently, NIBP is implicated in signaling, and TMEM1 is suggested to have trans-membrane domains (TMDs) and to function as a membrane channel. However, we show here that the yeast Trs130 does not function as a trans-membrane protein, and the human TMEM1 does not contain putative TMDs. The non-essential subunit, Trs65, is conserved only among many fungi and some unicellular eukaryotes. Multiple alignment analysis of each TRAPPII-specific subunit revealed conserved domains that include highly conserved amino acids.

Conclusion: We suggest that the function of both NIBP and TMEM1 in the regulation of intra-cellular trafficking is conserved from yeast to man. The conserved domains and amino acids discovered here can be used for functional analysis that should help to resolve the differences in the assigned functions of these proteins in fungi and animals.

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Trs130 is conserved in almost all eukaryotes. Same as Figure 2 except that A-bottom shows the domain structure for worm proteins, because these sequences have a deletion of domain III. Also, only a C-terminal-truncated temperature-sensitive mutant is shown. HC amino acids are detailed in Table S3. Whole sequence alignment of all sequences from the NCBI nr database is shown in Figure S2.
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Figure 3: Trs130 is conserved in almost all eukaryotes. Same as Figure 2 except that A-bottom shows the domain structure for worm proteins, because these sequences have a deletion of domain III. Also, only a C-terminal-truncated temperature-sensitive mutant is shown. HC amino acids are detailed in Table S3. Whole sequence alignment of all sequences from the NCBI nr database is shown in Figure S2.

Mentions: Multiple alignments and the domain structure of the TRAPPII-specific subunits are shown in Figures 2, 3, 4 and Figures S1-S3 (see Additional File 1). Domains were defined by inspection of the raw alignment and Figures S1-S3. Highly conserved (HC) amino acids in the alignment (see Methods) are shown at the bottom of the diagram as short vertical lines, and are detailed in the corresponding supplementary tables (Tables S2-S4, respectively, see Additional File 1). There is a number of particularly interesting HC amino acids, including those that are invariant and rare (e.g., prolines) or invariant and potentially catalytic (e.g., aspartic or glutamic acids). These HC amino acids are indicated with asterisks in the multiple alignment and in the supplemental tables (Tables S1-S3, see Additional File 1). Finally, conserved domains, as indicated by alignment strength and HC amino acids are boxed (Figures S1-S3) and the alignment of these conserved domains from representative organisms is shown in Figures 2, 3, 4.


Conservation of the TRAPPII-specific subunits of a Ypt/Rab exchanger complex.

Cox R, Chen SH, Yoo E, Segev N - BMC Evol. Biol. (2007)

Trs130 is conserved in almost all eukaryotes. Same as Figure 2 except that A-bottom shows the domain structure for worm proteins, because these sequences have a deletion of domain III. Also, only a C-terminal-truncated temperature-sensitive mutant is shown. HC amino acids are detailed in Table S3. Whole sequence alignment of all sequences from the NCBI nr database is shown in Figure S2.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1803778&req=5

Figure 3: Trs130 is conserved in almost all eukaryotes. Same as Figure 2 except that A-bottom shows the domain structure for worm proteins, because these sequences have a deletion of domain III. Also, only a C-terminal-truncated temperature-sensitive mutant is shown. HC amino acids are detailed in Table S3. Whole sequence alignment of all sequences from the NCBI nr database is shown in Figure S2.
Mentions: Multiple alignments and the domain structure of the TRAPPII-specific subunits are shown in Figures 2, 3, 4 and Figures S1-S3 (see Additional File 1). Domains were defined by inspection of the raw alignment and Figures S1-S3. Highly conserved (HC) amino acids in the alignment (see Methods) are shown at the bottom of the diagram as short vertical lines, and are detailed in the corresponding supplementary tables (Tables S2-S4, respectively, see Additional File 1). There is a number of particularly interesting HC amino acids, including those that are invariant and rare (e.g., prolines) or invariant and potentially catalytic (e.g., aspartic or glutamic acids). These HC amino acids are indicated with asterisks in the multiple alignment and in the supplemental tables (Tables S1-S3, see Additional File 1). Finally, conserved domains, as indicated by alignment strength and HC amino acids are boxed (Figures S1-S3) and the alignment of these conserved domains from representative organisms is shown in Figures 2, 3, 4.

Bottom Line: However, we show here that the yeast Trs130 does not function as a trans-membrane protein, and the human TMEM1 does not contain putative TMDs.We suggest that the function of both NIBP and TMEM1 in the regulation of intra-cellular trafficking is conserved from yeast to man.The conserved domains and amino acids discovered here can be used for functional analysis that should help to resolve the differences in the assigned functions of these proteins in fungi and animals.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biological Sciences, Laboratory for Molecular Biology, University of Illinois at Chicago, Chicago, IL 60607, USA. randal@randalcox.net <randal@randalcox.net>

ABSTRACT

Background: Ypt/Rab GTPases and their GEF activators regulate intra-cellular trafficking in all eukaryotic cells. In S. cerivisiae, the modular TRAPP complex acts as a GEF for the Golgi gatekeepers: Ypt1 and the functional pair Ypt31/32. While TRAPPI, which acts in early Golgi, is conserved from fungi to animals, not much is known about TRAPPII, which acts in late Golgi and consists of TRAPPI plus three additional subunits.

Results: Here, we show a phylogenetic analysis of the three TRAPPII-specific subunits. One copy of each of the two essential subunits, Trs120 and Trs130, is present in almost every fully sequenced eukaryotic genome. Moreover, the primary, as well as the predicted secondary, structure of the Trs120- and Trs130-related sequences are conserved from fungi to animals. The mammalian orthologs of Trs120 and Trs130, NIBP and TMEM1, respectively, are candidates for human disorders. Currently, NIBP is implicated in signaling, and TMEM1 is suggested to have trans-membrane domains (TMDs) and to function as a membrane channel. However, we show here that the yeast Trs130 does not function as a trans-membrane protein, and the human TMEM1 does not contain putative TMDs. The non-essential subunit, Trs65, is conserved only among many fungi and some unicellular eukaryotes. Multiple alignment analysis of each TRAPPII-specific subunit revealed conserved domains that include highly conserved amino acids.

Conclusion: We suggest that the function of both NIBP and TMEM1 in the regulation of intra-cellular trafficking is conserved from yeast to man. The conserved domains and amino acids discovered here can be used for functional analysis that should help to resolve the differences in the assigned functions of these proteins in fungi and animals.

Show MeSH