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Evolution and functional diversification of the GLI family of transcription factors in vertebrates.

Abbasi AA, Goode DK, Amir S, Grzeschik KH - Evol. Bioinform. Online (2009)

Bottom Line: A relative rate test suggested that the majority of the paralogous copies of the GLI family analyzed evolved with similar evolutionary rates except GLI1 which evolved at a significantly faster rate than its paralogous counterparts in tetrapods.Our analysis shows that sequence evolutionary patterns of GLI family members are largely correlated with the reported similarities and differences in the functionality of GLI proteins within and between the various vertebrate species.We propose that duplication and divergence of GLI genes has increased in the complexity of vertebrate body plan by recruiting the hedgehog signalling for the novel developmental tasks.

View Article: PubMed Central - PubMed

Affiliation: National Center for Bioinformatics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan. abbasiam@qau.edu.pk

ABSTRACT

Background: In vertebrates the "SONIC HEDGEHOG" signalling pathway has been implicated in cell-fate determination, proliferation and the patterning of many different cell types and organs. As the GLI family members (GLI1, GLI2 and GLI3) are key mediators of hedgehog morphogenetic signals, over the past couple of decades they have been extensively scrutinized by genetic, molecular and biochemical means. Thus, a great deal of information is currently available about the functional aspects of GLI proteins in various vertebrate species. To address the roles of GLI genes in diversifying the repertoire of the Hh signalling and deploying them for the vertebrate specifications, in this study we have examined the evolutionary patterns of vertebrate GLI sequences within and between species.

Results: Phylogenetic tree analysis suggests that the vertebrate GLI1, GLI2 and GLI3 genes diverged after the separation of urochordates from vertebrates and before the tetrapods-bony fishes split. Lineage specific duplication events were also detected. Estimation of mode and strength of selection acting on GLI orthologs demonstrated that all members of the GLI gene family experienced more relaxed selection in teleost fish than in the mammalian lineage. Furthermore, the GLI1 gene appeared to have been exposed to different functional constraints in fish and tetrapod lineages, whilst a similar level of functional constraints on GLI2 and GLI3 was suggested by comparable average non-synonymous (Ka) substitutions across the lineages. A relative rate test suggested that the majority of the paralogous copies of the GLI family analyzed evolved with similar evolutionary rates except GLI1 which evolved at a significantly faster rate than its paralogous counterparts in tetrapods.

Conclusions: Our analysis shows that sequence evolutionary patterns of GLI family members are largely correlated with the reported similarities and differences in the functionality of GLI proteins within and between the various vertebrate species. We propose that duplication and divergence of GLI genes has increased in the complexity of vertebrate body plan by recruiting the hedgehog signalling for the novel developmental tasks.

No MeSH data available.


Related in: MedlinePlus

Neighbor-joining tree of the GLI family members. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. All positions containing gaps and missing data were eliminated from the dataset. Black arrowheads show duplication events that occurred before the tetrapod-fish divergence whereas the open arrows indicate lineage specific duplications. Scale bar shows substitutions per site.
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f1-ebo-2009-005: Neighbor-joining tree of the GLI family members. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. All positions containing gaps and missing data were eliminated from the dataset. Black arrowheads show duplication events that occurred before the tetrapod-fish divergence whereas the open arrows indicate lineage specific duplications. Scale bar shows substitutions per site.

Mentions: The phylogenetic history of vertebrate GLI genes was analyzed by including the sequences from representative members of teleost and tetrapod lineages (Fig. 1). The tree was rooted with orthologous genes from invertebrate species. A phylogenetic tree of multigene family members provides several types of useful information for studying the evolution and diversification of function of genes across various species. First, it can work as tool to provide support for or against direct orthologous relationships between genes from different species. Second, it can provide information on the likely status of members of gene family in animals that are ancestral to groups of currently extant species. Finally, the phylogenetic tree can provide an estimate of the relative time elapsed since the divergence of any two gene sequences from their most recent common ancestor.


Evolution and functional diversification of the GLI family of transcription factors in vertebrates.

Abbasi AA, Goode DK, Amir S, Grzeschik KH - Evol. Bioinform. Online (2009)

Neighbor-joining tree of the GLI family members. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. All positions containing gaps and missing data were eliminated from the dataset. Black arrowheads show duplication events that occurred before the tetrapod-fish divergence whereas the open arrows indicate lineage specific duplications. Scale bar shows substitutions per site.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC2747127&req=5

f1-ebo-2009-005: Neighbor-joining tree of the GLI family members. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. All positions containing gaps and missing data were eliminated from the dataset. Black arrowheads show duplication events that occurred before the tetrapod-fish divergence whereas the open arrows indicate lineage specific duplications. Scale bar shows substitutions per site.
Mentions: The phylogenetic history of vertebrate GLI genes was analyzed by including the sequences from representative members of teleost and tetrapod lineages (Fig. 1). The tree was rooted with orthologous genes from invertebrate species. A phylogenetic tree of multigene family members provides several types of useful information for studying the evolution and diversification of function of genes across various species. First, it can work as tool to provide support for or against direct orthologous relationships between genes from different species. Second, it can provide information on the likely status of members of gene family in animals that are ancestral to groups of currently extant species. Finally, the phylogenetic tree can provide an estimate of the relative time elapsed since the divergence of any two gene sequences from their most recent common ancestor.

Bottom Line: A relative rate test suggested that the majority of the paralogous copies of the GLI family analyzed evolved with similar evolutionary rates except GLI1 which evolved at a significantly faster rate than its paralogous counterparts in tetrapods.Our analysis shows that sequence evolutionary patterns of GLI family members are largely correlated with the reported similarities and differences in the functionality of GLI proteins within and between the various vertebrate species.We propose that duplication and divergence of GLI genes has increased in the complexity of vertebrate body plan by recruiting the hedgehog signalling for the novel developmental tasks.

View Article: PubMed Central - PubMed

Affiliation: National Center for Bioinformatics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan. abbasiam@qau.edu.pk

ABSTRACT

Background: In vertebrates the "SONIC HEDGEHOG" signalling pathway has been implicated in cell-fate determination, proliferation and the patterning of many different cell types and organs. As the GLI family members (GLI1, GLI2 and GLI3) are key mediators of hedgehog morphogenetic signals, over the past couple of decades they have been extensively scrutinized by genetic, molecular and biochemical means. Thus, a great deal of information is currently available about the functional aspects of GLI proteins in various vertebrate species. To address the roles of GLI genes in diversifying the repertoire of the Hh signalling and deploying them for the vertebrate specifications, in this study we have examined the evolutionary patterns of vertebrate GLI sequences within and between species.

Results: Phylogenetic tree analysis suggests that the vertebrate GLI1, GLI2 and GLI3 genes diverged after the separation of urochordates from vertebrates and before the tetrapods-bony fishes split. Lineage specific duplication events were also detected. Estimation of mode and strength of selection acting on GLI orthologs demonstrated that all members of the GLI gene family experienced more relaxed selection in teleost fish than in the mammalian lineage. Furthermore, the GLI1 gene appeared to have been exposed to different functional constraints in fish and tetrapod lineages, whilst a similar level of functional constraints on GLI2 and GLI3 was suggested by comparable average non-synonymous (Ka) substitutions across the lineages. A relative rate test suggested that the majority of the paralogous copies of the GLI family analyzed evolved with similar evolutionary rates except GLI1 which evolved at a significantly faster rate than its paralogous counterparts in tetrapods.

Conclusions: Our analysis shows that sequence evolutionary patterns of GLI family members are largely correlated with the reported similarities and differences in the functionality of GLI proteins within and between the various vertebrate species. We propose that duplication and divergence of GLI genes has increased in the complexity of vertebrate body plan by recruiting the hedgehog signalling for the novel developmental tasks.

No MeSH data available.


Related in: MedlinePlus