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The ubiquilin gene family: evolutionary patterns and functional insights.

Marín I - BMC Evol. Biol. (2014)

Bottom Line: This exceptional mammalian-specific expansion is the result of the recent emergence of four new genes, three of them (UBQLN3, UBQLN5 and UBQLNL) with precise testis-specific expression patterns that indicate roles in the postmeiotic stages of spermatogenesis.The ubiquilin gene family is highly conserved in eukaryotes.The infrequent lineage-specific amplifications observed may be linked to the emergence of novel functions in particular tissues.

View Article: PubMed Central - HTML - PubMed

Affiliation: Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), Valencia, Spain. imarin@ibv.csic.es.

ABSTRACT

Background: Ubiquilins are proteins that function as ubiquitin receptors in eukaryotes. Mutations in two ubiquilin-encoding genes have been linked to the genesis of neurodegenerative diseases. However, ubiquilin functions are still poorly understood.

Results: In this study, evolutionary and functional data are combined to determine the origin and diversification of the ubiquilin gene family and to characterize novel potential roles of ubiquilins in mammalian species, including humans. The analysis of more than six hundred sequences allowed characterizing ubiquilin diversity in all the main eukaryotic groups. Many organisms (e. g. fungi, many animals) have single ubiquilin genes, but duplications in animal, plant, alveolate and excavate species are described. Seven different ubiquilins have been detected in vertebrates. Two of them, here called UBQLN5 and UBQLN6, had not been hitherto described. Significantly, marsupial and eutherian mammals have the most complex ubiquilin gene families, composed of up to 6 genes. This exceptional mammalian-specific expansion is the result of the recent emergence of four new genes, three of them (UBQLN3, UBQLN5 and UBQLNL) with precise testis-specific expression patterns that indicate roles in the postmeiotic stages of spermatogenesis. A gene with related features has independently arisen in species of the Drosophila genus. Positive selection acting on some mammalian ubiquilins has been detected.

Conclusions: The ubiquilin gene family is highly conserved in eukaryotes. The infrequent lineage-specific amplifications observed may be linked to the emergence of novel functions in particular tissues.

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Related in: MedlinePlus

Classification of vertebrate ubiquilins. This figure corresponds to the subtree indicated as a triangle labelled “Vertebrates” in Figure 2, which has been expanded here, to show all the main types of ubiquilins. In brackets, the number of sequences in each group and the different types of vertebrates that have each ubiquilin gene. Bootstrap support (NJ/MP/ML) as in previous figures. Scale bar as in Figure 1.
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Figure 3: Classification of vertebrate ubiquilins. This figure corresponds to the subtree indicated as a triangle labelled “Vertebrates” in Figure 2, which has been expanded here, to show all the main types of ubiquilins. In brackets, the number of sequences in each group and the different types of vertebrates that have each ubiquilin gene. Bootstrap support (NJ/MP/ML) as in previous figures. Scale bar as in Figure 1.

Mentions: Figures 2 and 3 summarize the results for all animal species for which ubiquilin sequences have been found. Figure 2 details phylogenetic trees, derived again from the sequences of the UBL and UBA domains, summarizing the relationships among 349 animal ubiquilins. It turned out that many animal species have single ubiquilin genes. More precisely, I found that only vertebrates and (as it was shown already in Figure 1) species of the Drosophila genus have two or more. As indicated above, the choanoflagellate Monosiga brevicollis, which is the closest animal relative among all protozoans for which data are available, also has a single ubiquilin gene. Thus, it is likely that only one gene of this family was present when animals originated.


The ubiquilin gene family: evolutionary patterns and functional insights.

Marín I - BMC Evol. Biol. (2014)

Classification of vertebrate ubiquilins. This figure corresponds to the subtree indicated as a triangle labelled “Vertebrates” in Figure 2, which has been expanded here, to show all the main types of ubiquilins. In brackets, the number of sequences in each group and the different types of vertebrates that have each ubiquilin gene. Bootstrap support (NJ/MP/ML) as in previous figures. Scale bar as in Figure 1.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4230246&req=5

Figure 3: Classification of vertebrate ubiquilins. This figure corresponds to the subtree indicated as a triangle labelled “Vertebrates” in Figure 2, which has been expanded here, to show all the main types of ubiquilins. In brackets, the number of sequences in each group and the different types of vertebrates that have each ubiquilin gene. Bootstrap support (NJ/MP/ML) as in previous figures. Scale bar as in Figure 1.
Mentions: Figures 2 and 3 summarize the results for all animal species for which ubiquilin sequences have been found. Figure 2 details phylogenetic trees, derived again from the sequences of the UBL and UBA domains, summarizing the relationships among 349 animal ubiquilins. It turned out that many animal species have single ubiquilin genes. More precisely, I found that only vertebrates and (as it was shown already in Figure 1) species of the Drosophila genus have two or more. As indicated above, the choanoflagellate Monosiga brevicollis, which is the closest animal relative among all protozoans for which data are available, also has a single ubiquilin gene. Thus, it is likely that only one gene of this family was present when animals originated.

Bottom Line: This exceptional mammalian-specific expansion is the result of the recent emergence of four new genes, three of them (UBQLN3, UBQLN5 and UBQLNL) with precise testis-specific expression patterns that indicate roles in the postmeiotic stages of spermatogenesis.The ubiquilin gene family is highly conserved in eukaryotes.The infrequent lineage-specific amplifications observed may be linked to the emergence of novel functions in particular tissues.

View Article: PubMed Central - HTML - PubMed

Affiliation: Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), Valencia, Spain. imarin@ibv.csic.es.

ABSTRACT

Background: Ubiquilins are proteins that function as ubiquitin receptors in eukaryotes. Mutations in two ubiquilin-encoding genes have been linked to the genesis of neurodegenerative diseases. However, ubiquilin functions are still poorly understood.

Results: In this study, evolutionary and functional data are combined to determine the origin and diversification of the ubiquilin gene family and to characterize novel potential roles of ubiquilins in mammalian species, including humans. The analysis of more than six hundred sequences allowed characterizing ubiquilin diversity in all the main eukaryotic groups. Many organisms (e. g. fungi, many animals) have single ubiquilin genes, but duplications in animal, plant, alveolate and excavate species are described. Seven different ubiquilins have been detected in vertebrates. Two of them, here called UBQLN5 and UBQLN6, had not been hitherto described. Significantly, marsupial and eutherian mammals have the most complex ubiquilin gene families, composed of up to 6 genes. This exceptional mammalian-specific expansion is the result of the recent emergence of four new genes, three of them (UBQLN3, UBQLN5 and UBQLNL) with precise testis-specific expression patterns that indicate roles in the postmeiotic stages of spermatogenesis. A gene with related features has independently arisen in species of the Drosophila genus. Positive selection acting on some mammalian ubiquilins has been detected.

Conclusions: The ubiquilin gene family is highly conserved in eukaryotes. The infrequent lineage-specific amplifications observed may be linked to the emergence of novel functions in particular tissues.

Show MeSH
Related in: MedlinePlus