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Open Access Research article

The footprint of metabolism in the organization of mammalian genomes

Luisa Berná12, Ankita Chaurasia1, Claudia Angelini3, Concetta Federico4, Salvatore Saccone4 and Giuseppe D'Onofrio1*

Author Affiliations

1 Genome Evolution and Organization - Department Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy

2 Sección Biomatematica, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo, Uruguay

3 Istituto per le Applicazioni del Calcolo "Mauro Picone", IAC-CNR, Via Pietro Castellino, 111-80131 Naples, Italy

4 Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Catania Sezione Biologia.Animale "M. La Greca", Via Androne, 81-95124 Catania, Italy

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BMC Genomics 2012, 13:174  doi:10.1186/1471-2164-13-174

Published: 8 May 2012

Abstract

Background

At present five evolutionary hypotheses have been proposed to explain the great variability of the genomic GC content among and within genomes: the mutational bias, the biased gene conversion, the DNA breakpoints distribution, the thermal stability and the metabolic rate. Several studies carried out on bacteria and teleostean fish pointed towards the critical role played by the environment on the metabolic rate in shaping the base composition of genomes. In mammals the debate is still open, and evidences have been produced in favor of each evolutionary hypothesis. Human genes were assigned to three large functional categories (as well as to the corresponding functional classes) according to the KOG database: (i) information storage and processing, (ii) cellular processes and signaling, and (iii) metabolism. The classification was extended to the organisms so far analyzed performing a reciprocal Blastp and selecting the best reciprocal hit. The base composition was calculated for each sequence of the whole CDS dataset.

Results

The GC3 level of the above functional categories was increasing from (i) to (iii). This specific compositional pattern was found, as footprint, in all mammalian genomes, but not in frog and lizard ones. Comparative analysis of human versus both frog and lizard functional categories showed that genes involved in the metabolic processes underwent the highest GC3 increment. Analyzing the KOG functional classes of genes, again a well defined intra-genomic pattern was found in all mammals. Not only genes of metabolic pathways, but also genes involved in chromatin structure and dynamics, transcription, signal transduction mechanisms and cytoskeleton, showed an average GC3 level higher than that of the whole genome. In the case of the human genome, the genes of the aforementioned functional categories showed a high probability to be associated with the chromosomal bands.

Conclusions

In the light of different evolutionary hypotheses proposed so far, and contributing with different potential to the genome compositional heterogeneity of mammalian genomes, the one based on the metabolic rate seems to play not a minor role. Keeping in mind similar results reported in bacteria and in teleosts, the specific compositional patterns observed in mammals highlight metabolic rate as unifying factor that fits over a wide range of living organisms.