Genomic neighborhoods around vertebrate <i>GCKR</i> genes.

<p>Relative order and orientation of genes near the <i>GCKR</i> genes in human, chicken, Chinese softshell turtle, coelacanth, zebrafish and takifugu genomes. Gene names, as annotated in the human genome, are shown above the arrows, with the arrowhead indicating direction of transcription. Gene sizes and distance between genes are not to scale. Human is representative of the gene organization in mammals, while chicken is representative of birds. <i>GCKR</i> gene was not found in bird genomes. In fish, two distinct gene organizations were found – one found in zebrafish, and a second found in other fish genomes and represented by takifugu. The Chinese softshell turtle GCKR gene was distributed over two genomic contigs, with the slashes (/) indicating the ends of contigs.</p

Evolution of Hepatic Glucose Metabolism: Liver-Specific Glucokinase Deficiency Explained by Parallel Loss of the Gene for Glucokinase Regulatory Protein (GCKR)

<div><p>Background</p><p>Glucokinase (GCK) plays an important role in the regulation of carbohydrate metabolism. In the liver, phosphorylation of glucose to glucose-6-phosphate by GCK is the first step for both glycolysis and glycogen synthesis. However, some vertebrate species are deficient in GCK activity in the liver, despite containing <i>GCK</i> genes that appear to be compatible with function in their genomes. Glucokinase regulatory protein (GCKR) is the most important post-transcriptional regulator of GCK in the liver; it participates in the modulation of GCK activity and location depending upon changes in glucose levels. In experimental models, loss of GCKR has been shown to associate with reduced hepatic GCK protein levels and activity.</p> <p>Methodology/Principal Findings</p><p><i>GCKR</i> genes and <i>GCKR</i>-like sequences were identified in the genomes of all vertebrate species with available genome sequences. The coding sequences of <i>GCKR</i> and <i>GCKR</i>-like genes were identified and aligned; base changes likely to disrupt coding potential or splicing were also identified.</p> <p>Conclusions/Significance</p><p><i>GCKR</i> genes could not be found in the genomes of 9 vertebrate species, including all birds. In addition, in multiple mammalian genomes, whereas <i>GCKR</i>-like gene sequences could be identified, these genes could not predict a functional protein. Vertebrate species that were previously reported to be deficient in hepatic GCK activity were found to have deleted (birds and lizard) or mutated (mammals) <i>GCKR</i> genes. Our results suggest that mutation of the <i>GCKR</i> gene leads to hepatic GCK deficiency due to the loss of the stabilizing effect of GCKR.</p> </div

Exons bearing inactivating mutation in mammalian <i>GCKR</i> genes.

<p>Exons bearing inactivating mutation in mammalian <i>GCKR</i> genes.</p

Genomic location of vertebrate <i>GCKR</i> genes.

1<p>Sequences identified/searched for in the PreEnsembl database (some represent newer genome assemblies than those in Ensembl)</p>2<p>Protein ID from the NCBI database</p

Vertebrate <i>GCKR</i> genes.

*<p>Predicted genes have a single frame shift mutation that may be a sequencing error.</p

Relative rate tests.

1<p>– Number of unique amino acid substitutions on the lineages to species A and B when the Tasmanian devil sequence was used as the outgroup.</p>2<p>– Chi square value for the expectation that an equal number of substitutions occurred on each lineage.</p

Evolution of <i>GCKR</i> genes and hepatic GCK activity in vertebrates.

<p>Summary of information on the structure of <i>GCKR</i> genes and hepatic GCK activity are placed on a phylogeny of vertebrates with available genome sequences (with the common names of the species shown on the right). Higher-level taxonomic groups of species are indicated to the right, with their composition indicated by the vertical bars. The phylogenetic relationship is from Ensembl (<a href="http://www.ensembl.org" target="_blank">www.ensembl.org</a>). <i>Xenopus laevis</i> is added to the tree as it has an intact <i>GCKR</i> cDNA. Genes are labeled as intact (I), likely intact (I?) or mutated (M), with the types of mutation indicated: fs = frame shift, sm = splice mutation, Δ = deletion, and Δ? = likely deletion (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060896#pone-0060896-t002" target="_blank">Tables 2</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060896#pone-0060896-t003" target="_blank">3</a>). The phylogenetic placement of gene inactivation events (Ψ, with type of inactivation indicated) was determined by parsimony. Possible inactivations, or events with unresolved locations (i.e., on the bird lineage), are indicated by the ? symbol. Hepatic GCK activity is from references 27-31, with Y = activity found, N = no or very low activity, and nd = not determined.</p

Phylogeny of mammalian GCKR protein sequences.

<p>Phylogeny of mammalian GCKR protein sequences generated from full length <i>GCKR</i> coding sequences (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060896#pone.0060896.s001" target="_blank">Figure S1</a>). The bootstrapped (1000 replications) neighbor-joining distance tree was generated using JTT protein distances. The sequence from the Tasmanian devil was used as the outgroup. Similar trees were generated when different protein distance measures, or distance measures based on nonsynonymous distances calculated from aligned DNA sequences, were used or if trees were built by other methods, such as parsimony or maximum likelihood.</p

Phylogeny of vertebrate GCKR protein sequences.

<p>Phylogeny of vertebrate GCKR protein sequences generated from intact and near-full length <i>GCKR</i> coding sequences (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060896#pone.0060896.s001" target="_blank">Figure S1</a>). Only select mammals were included in the analysis. The bootstrapped (1000 replications) neighbor-joining distance tree was generated using JTT protein distances. The Lamprey (jawless fish) sequence was used as the outgroup. Similar trees were generated when different protein distance measures were used or if other tree building methods, such as parsimony or maximum likelihood, were used.</p