Computational protocol: The role of the glucose-sensing transcription factor carbohydrate-responsive element-binding protein pathway in termite queen fertility

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Protocol publication

[…] We obtained 45 amino acid sequences of ChREBP (also called ‘Mondo B’, ‘WBSCR14’, ‘MLXIPL’ or ‘MLX interacting protein-like’) for two vertebrates (human and mouse), one mollusc and 42 arthropods (wasps/sawflies, ants, bees, beetles, bugs, flies, moths, butterflies and a horseshoe crab) and amino acid sequences of Mondo A for two vertebrates (human and mouse) from the database at NCBI. Sequence searches were performed using ‘ChREBP alpha’, ‘WBSCR14’, ‘MLXIPL’, ‘MLX interacting protein-like’, ‘MondoB’, ‘Mondo’, ‘dMondo’, ‘dChREBP’ and ‘Mio’ keywords.Amino acid sequences from the termites Zootermopsis nevadensis [] and Macrotermes natalensis [] and from the NCBI protein database were aligned using two different algorithms, Muscle and ClustalW2, with the Seaview software [], and the alignment was checked manually. ChREBP is a multi-domain protein and some of its regions are highly conserved among the Mondo proteins, such as the Mondo conserved region (MCR) and the glucose-sensing module (GSM) that is the most important region in terms of glucose sensing and regulation [,]. Owing to its high conservation and structural role in the glucose response, only the GSM region was used in the phylogenetic study and alignment was trimmed according to the Mus musculus GSM region boundaries (accession no. NP067430) [].The best model of evolution was selected using ProtTest v. 3.3 software [] and following the corrected Akaike Information Criterion. The best model of evolution identified by ProtTest was JTT + G (Jones Taylor Thornton model []). ML analyses were performed by PhyML [] using an input tree generated by bioNJ, the JTT + G model of amino acid substitution and 1000 repetitions of bootstraps. BI analyses were performed by running two parallel analyses in MrBayes [], each consisting of four Markov chains of 1 000 000 generations, each with a sampling frequency of one tree every one thousand generations and the JTT + G model of amino acid substitution. Convergence of the parameters was evaluated using Tracer v. 1.5.0 []. A consensus tree was then calculated after omitting the first 25% trees as burn-in. […]

Pipeline specifications

Software tools Clustal W, SeaView, ProtTest, PhyML, MrBayes
Application Phylogenetics
Organisms Mus musculus, Drosophila melanogaster
Chemicals Acetyl Coenzyme A, Glucose