The footprint of metabolism in the organization of mammalian genomes

<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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.</p> <p>Conclusions</p> <p>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.</p

Identification of differentially expressed genes from multipotent epithelia at the onset of an asexual development

© The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 6 (2016): 27357, doi:10.1038/srep27357.Organisms that have evolved alternative modes of reproduction, complementary to the sexual mode, are found across metazoans. The chordate Botryllus schlosseri is an emerging model for asexual development studies. Botryllus can rebuild its entire body from a portion of adult epithelia in a continuous and stereotyped process called blastogenesis. Anatomy and ontogenies of blastogenesis are well described, however molecular signatures triggering this developmental process are entirely unknown. We isolated tissues at the site of blastogenesis onset and from the same epithelia where this process is never triggered. We linearly amplified an ultra-low amount of mRNA (<10ng) and generated three transcriptome datasets. To provide a conservative landscape of transcripts differentially expressed between blastogenic vs. non-blastogenic epithelia we compared three different mapping and analysis strategies with a de novo assembled transcriptome and partially assembled genome as references, additionally a self-mapping strategy on the dataset. A subset of differentially expressed genes were analyzed and validated by in situ hybridization. The comparison of different analyses allowed us to isolate stringent sets of target genes, including transcripts with potential involvement in the onset of a non-embryonic developmental pathway. The results provide a good entry point to approach regenerative event in a basal chordate.This work was supported by AFM Telethon grant (#16611), IRG Marie Curie grant (#276974), ANR (ANR-14-CE02-0019-01) and IDEX Super (INDIBIO). L.R. was supported by an UPMC-EMREGENCE grant and by a FRM grant (#FDT20140931163). A.C. was supported by a FRM grant (ING 20140129231)

Length and GC Content Variability of Introns among Teleostean Genomes in the Light of the Metabolic Rate Hypothesis

A comparative analysis of five teleostean genomes, namely zebrafish, medaka, three-spine stickleback, fugu and pufferfish was performed with the aim to highlight the nature of the forces driving both length and base composition of introns (i.e., bpi and GCi). An inter-genome approach using orthologous intronic sequences was carried out, analyzing independently both variables in pairwise comparisons. An average length shortening of introns was observed at increasing average GCi values. The result was not affected by masking transposable and repetitive elements harbored in the intronic sequences. The routine metabolic rate (mass specific temperature-corrected using the Boltzmann\u27s factor) was measured for each species. A significant correlation held between average differences of metabolic rate, length and GC content, while environmental temperature of fish habitat was not correlated with bpi and GCi. Analyzing the concomitant effect of both variables, i.e., bpi and GCi, at increasing genomic GC content, a decrease of bpi and an increase of GCi was observed for the significant majority of the intronic sequences (from ~40% to ~90%, in each pairwise comparison). The opposite event, concomitant increase of bpi and decrease of GCi, was counter selected (from <1% to ~10%, in each pairwise comparison). The results further support the hypothesis that the metabolic rate plays a key role in shaping genome architecture and evolution of vertebrate genomes

Testing the Metabolic Rate Hypothesis by Analyzing Vertebrate Genomes.

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

Evaluation of bacteriological profile of bladder calculi and its association with urinary tract infection in a tertiary health care centre

Background: The occurrence of urinary tract infection in presence of urolithiasis (urinary calculi) is frequent. Bladder calculi comprise approximately 5-10% cases of renal or urinary calculi. However, microbial agents of urolithiasis and their association with urinary tract infection are under investigated.Objectives: This study was aimed to evaluate the bacteriological profile of bladder calculi and its association with urinary tract infection.Material &amp; Methods: This descriptive study was conducted in the Department of Microbiology at a tertiary care hospital from September 2018 to September 2019. A sample size of 100 (61 males and 39 females, presenting with bladder calculi) was calculated at 95% confidence interval at 5% acceptable margin of error by Epi Info software version 7.2. Preoperative urine culture and postoperative stone culture were performed. Isolation and identification of bacteria was done using standard microbiological techniques.Results: Urinary tract infection was present in 53% cases which included 26 males and 27 females. The mean age of patients was 42 ± 6.2 years. In majority of cases the reaction of urine was acidic (76%). The most common organism isolated in urine culture was E. coli (28%), followed by Staphylococcus aureus(8%), Pseudomonas aeruginosa (4%), Klebsiellaaerogenes (3%), Proteus mirabilis (2%) and mixed organisms (8%). On bladder stone core culture growth was observed in 50% cases including 22 males and 28 females. The most common organism isolated was E. coli (28%), followed by Staphylococcus aureus (6%), Klebsiellaaerogenes (8%) and mixed organisms (8%). E. coli was the predominant organism found both in urine and core culture of stone.Conclusion: The present study showed that urinary infection was present among majority of cases that presented with bladder calculi and E. coli was the most common type of organism associated. The association of microorganisms isolated from urine and stone core culture was considerable and can predict the source of infective stone. This study highlights the importance of microbiological analysis of stones for complete sterilization of urinary system and prevention of recurrence

Extensive amplification of the E2F transcription factor binding sites by transposons during evolution of Brassica species

Transposable elements (TEs) are major players in genome evolution. The effects of their movement vary from gene knockouts to more subtle effects such as changes in gene expression. It has recently been shown that TEs may contain transcription factor binding sites (TFBSs), and it has been proposed that they may rewire new genes into existing transcriptional networks. However, little is known about the dynamics of this process and its effect on transcription factor binding. Here we show that TEs have extensively amplified the number of sequences that match the E2F TFBS during Brassica speciation, and, as a result, as many as 85% of the sequences that fit the E2F TFBS consensus are within TEs in some Brassica species. We show that these sequences found within TEs bind E2Fa in vivo, which indicates a direct effect of these TEs on E2F-mediated gene regulation. Our results suggest that the TEs located close to genes may directly participate in gene promoters, whereas those located far from genes may have an indirect effect by diluting the effective amount of E2F protein able to bind to its cognate promoters. These results illustrate an extreme case of the effect of TEs in TFBS evolution, and suggest a singular way by which they affect host genes by modulating essential transcriptional networks.This work was supported by the Ministerio de Ciencia e Innovación (grant BFU2009-11932 to J.M.C. and grants BFU2009-9783 and BFU2012-34821 to C.G.), and by an institutional grant from the Fundacion Ramon Areces to Centro de Biologia Molecular Severo Ochoa (to C.G.).Peer reviewe

Average bp% and GC% of repetitive elements removed by Repeat Masker.

<p>S.E.  =  standard error.</p

The histograms show the base composition distribution of the intronic sequences (GCi) in the five teleostean genomes.

<p>In each panel, the average GCi and the skewness (SK) of the distribution are reported.</p

Average values of genome (GCg) and intron (GCi) base composition, intron lenght (bpi) and metabolic rate temperature-corrected by Boltzmann's factor (MR) in fish genomes.

<p>Average values of genome (GCg) and intron (GCi) base composition, intron lenght (bpi) and metabolic rate temperature-corrected by Boltzmann's factor (MR) in fish genomes.</p

The histogram shows the percents of orthologous intronic sequences increasing in length (Δbpi, blue bars) and GC content (ΔGCi, red bars) in each pairwise comparison.

<p>Data before (bRM) and after (aRM) RepeatMasker are reported. In cluster A: comparison of medaka, stickleback, fugu and pufferfish against zebrafish. In cluster B: comparison of stickleback, fugu and pufferfish against medaka. In cluster C: comparison of fugu and pufferfish against stickleback. Within each cluster pairwise comparisons were ordered according to the increasing phylogenetic distance.</p