Chaurasia, Ankita (2011) Testing the Metabolic Rate Hypothesis by Analyzing Vertebrate Genomes. [Tesi di dottorato] (Unpublished)

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Item Type: Tesi di dottorato
Uncontrolled Keywords: GC, Habitat, Fish, Mammals, Genome Evolution
Date Deposited: 06 Dec 2011 14:55
Last Modified: 17 Jun 2014 06:03
URI: http://www.fedoa.unina.it/id/eprint/8802

Abstract

The nature of the forces driving the genomic GC content of both prokaryotes and eukaryotes is a matter of debate among evolutionists. At present several hypotheses have been proposed: the mutational bias, the biased gene conversion (BGC), the thermal stability and the metabolic rate. The thesis mainly focused on testing the role played by the metabolic rate in shaping the base composition of genomes of vertebrates, namely: teleosts and mammals. Interesting results were also obtained analyzing non-vertebrate genomes (tunicates). Focusing on teleostean fish, the mass specific routine metabolic rate temperature-corrected using the Boltzmann's factor (MR) and base composition of genomes (GC%) were re-examined and related with their major habitat: polar, temperate, sub-tropical, tropical and deep-water. Fish of the polar habitat showed the highest MR and that of temperate fish was significantly higher than that of tropical one, showing the lowest average value. The GC% of polar and temperate fish both showed significantly higher values than that of tropical and sub-tropical fish. Plotting MR vs. GC%, a significant correlation was found. The deamination process, transforming the 5-methylcytosine (5mC) to thymine, and thus 5mCpG doublets into the derivative ones, i.e. TpG and CpA, is well known to affect the genomic GC content and to be temperature dependent. The 5mC level was reported to decrease from polar to tropical fish gnomes. The frequencies of CpG, TpG and CpA in five teleostean genomes living in different habitat excluded the temperature effect of 5mC on the genomic GC content in fish, further supporting a link between environmental metabolic adaptation and genome base composition. Several observations reported that GC-rich genes preferably arbor short non-coding sequences. A comparative analysis of orthologous introns (assigned throughout gene orthology) among five sequenced teleostean genomes, was carried out. The preliminary results highlighted a link between GC content and intronic length, hence supporting the energetic cost on transcriptional activity hypothesis. Human genes were assigned to three large functional categories according to the KOG database: information storage and processing, cellular processes and signaling, and metabolism. The GC3 level was significantly increasing from the former to the latter. This specific compositional pattern was found, as footprint, in all mammalian genomes analyzed, but not in frog and lizard ones. In the same comparative analysis among vertebrate genomes, it was found that human genes involved in the metabolic processes underwent to the highest GC3 increment. Compositional analysis of tunicate genomes showed that C. savignyi is GC-richer than C. intestinalis. Interestingly, preliminary data showed a same trend for the oxygen consumption. In conclusion, the data produced in the present thesis, analyzing available vertebrate and non-vertebrate genomes, all converged towards evidences supporting the metabolic rate as one of the key forces driving the base composition variability observed among living organisms. Natural (negative) selection may essentially explain the GC variability among organisms.

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