Evolutionary Bioinformatics
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Evolution and Functional Diversification of the GLI Family of Transcription Factors in Vertebrates
Authors: Amir Ali Abbasi, Debbie K. Goode, Saneela Amir and Karl-Heinz Grzeschik
Publication Date: 18 May 2009
Evolutionary Bioinformatics 2009:5 5-13
Amir Ali Abbasi1,2, Debbie K. Goode3, Saneela Amir4 and Karl-Heinz Grzeschik2
1National Center for Bioinformatics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan. 2Institute of Human Genetics, Philipps-University, Bahnhofstrasse 7 D35037 Marburg, Germany. 3School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, U.K. 4COMSATS Institute of Information Technology, Abbottabad, 22060, Pakistan.
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.
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Robust Model Selection for Classification of Microarrays - 25/Jun/2009
Angiotensin II Type 1 Receptor Blockers Reduce Urinary Angiotensinogen Excretion and the Levels of Urinary Markers of Oxidative Stress and Inflammation in Patients with Type 2 Diabetic Nephropathy - 23/Jun/2009