Biomedical subjects

Francisco J Silva

Publications and source records attributed to Francisco J Silva.

At least 19 recordsLinked to original sources

PubMed2006

Differential annotation of tRNA genes with anticodon CAT in bacterial genomes.

We have developed three strategies to discriminate among the three types of tRNA genes with anticodon CAT (tRNA(Ile), elongator tRNA(Met) and initiator tRNA(fMet)) in bacterial genomes. With these strategies, we have classified the tRNA genes from 234 bacterial and several organellar genomes. These sequences, in an aligned or unaligned format, may be used for the identification and annotation of tRNA (CAT) genes in other genomes. The first strategy is based on the position of the problem sequences in a phenogram (a tree-like network), the second on the minimum average number of differences against the tRNA sequences of the three types and the third on the search for the highest score value against the profiles of the three types of tRNA genes. The species with the maximum number of tRNA(fMet) and tRNA(Met) was Photobacterium profundum, whereas the genome of one Escherichia coli strain presented the maximum number of tRNA(Ile) (CAT) genes. This last tRNA gene and tilS, encoding an RNA-modifying enzyme, are not essential in bacteria. The acquisition of a tRNA(Ile) (TAT) gene by Mycoplasma mobile has led to the loss of both the tRNA(Ile) (CAT) and the tilS genes. The new tRNA has appropriated the function of decoding AUA codons.

Anticodon↗

PubMed2006

Genome reduction of the aphid endosymbiont Buchnera aphidicola in a recent evolutionary time scale.

Genome reduction, a typical feature of symbiotic bacteria, was analyzed in the last stages of evolution of Buchnera aphidicola, the primary aphid endosymbiont, in two neutrally evolving regions: the pseudogene cmk and an intergenic region. These two regions were examined in endosymbionts from several lineages of their aphid host Rhopalosiphum padi, and different species of the same genus, whose divergence times ranged from 0.62 to 19.51 million years. Estimates of nucleotide substitution rates were between 4.3 and 6.7x10(-9) substitution/site/year, with G or C nucleotides being substituted around four times more frequently than A or T. Two different types of indel events were detected, of which many were small (1-10 nt) but one was large (about 200 nucleotides). With respect to the large one and considering the proportion and size of the deletions and insertions, the reduction rate was 1.3x10(-8) lost nucleotides/site/year. We propose a stepwise scenario for the last stages of evolution in B. aphidicola: together with a very slow and gradual degradation, considerable indels would punctually emerge. The only restriction to large deletion fixation is that the lost fragment does not contain essential genes.

Animals↗

PubMed2006

A small microbial genome: the end of a long symbiotic relationship?

Intracellular bacteria are characterized by genome reduction. The 422,434-base pair genome of Buchnera aphidicola BCc, primary endosymbiont of the aphid Cinara cedri, is approximately 200 kilobases smaller than the previously sequenced B. aphidicola genomes. B. aphidicola BCc has lost most metabolic functions, including the ability to synthesize the essential amino acid tryptophan and riboflavin. In addition, most retained genes are evolving rapidly. Possibly, B. aphidicola BCc is losing its symbiotic capacity and is being complemented (and might be replaced) by the highly abundant coexisting secondary symbiont.

Amino Acids↗

PubMed2006

Plasmids in the aphid endosymbiont Buchnera aphidicola with the smallest genomes. A puzzling evolutionary story.

Buchnera aphidicola, the primary endosymbiont of aphids, has undergone important genomic and biochemical changes as an adaptation to intracellular life. The most important structural changes include a drastic genome reduction and the amplification of genes encoding key enzymes for the biosynthesis of amino acids by their translocation to plasmids. Molecular characterization through different aphid subfamilies has revealed that the genes involved in leucine and tryptophan biosynthesis show a variable fate, since they can be located on plasmids or on the chromosome in different lineages. This versatility contrasts with the genomic stasis found in three distantly related B. aphidicola strains already sequenced. We present the analysis of three B. aphidicola strains (BTg, BCt and BCc) belonging to aphids from different tribes of the subfamily Lachninae, that was estimated to harbour the bacteria with the smallest genomes. The presence of both leucine and tryptophan plasmids in BTg, a chimerical leucine-tryptophan plasmid in BCt, and only a leucine plasmid in BCc, indicates the existence of many recombination events in a recA minus bacterium. In addition, these B. aphidicola plasmids are the simplest described in this species, indicating that plasmids are also involved in the genome shrinkage process.

Amino Acids↗

PubMed2006

Analysis of and function predictions for previously conserved hypothetical or putative proteins in Blochmannia floridanus.

BACKGROUND: There is an increasing interest to better understand endosymbiont capabilities in insects both from an ecological point of view and for pest control. Blochmannia floridanus provides important nutrients for its host, the ant Camponotus, while the bacterium in return is provided with a niche to proliferate. Blochmannia floridanus proteins and metabolites are difficult to study due to its endosymbiontic life style; however, its complete genome sequence became recently available. RESULTS: Improved sequence analysis algorithms, databanks and gene and pathway context methods allowed us to reveal new information on various enzyme and pathways from the Blochmannia floridanus genome sequence [EMBL-ID BX248583]. Furthermore, these predictions are supported and linked to experimental data for instance from structural genomics projects (e.g. Bfl341, Bfl 499) or available biochemical data on proteins from other species which we show here to be related. We were able to assign a confirmed or at least a putative molecular function for 21 from 27 previously conserved hypothetical proteins. For 48 proteins of 66 with a previous putative assignment the function was further clarified. Several of these proteins occur in many proteobacteria and are found to be conserved even in the compact genome of this endosymbiont. To extend and re-test predictions and links to experimentally verified protein functions, functional clusters and interactions were assembled. These included septum initiation and cell division (Bfl165, Bfl303, Bfl248 et al.); translation; transport; the ubiquinone (Bfl547 et al.), the inositol and nitrogen pathways. CONCLUSION: Taken together, our data allow a better and more complete description of the pathway capabilities and life style of this typical endosymbiont.

Animals↗

PubMed2006

Humans' folk physics is not enough to explain variations in their tool-using behavior.

Two experiments examined adult humans' folk physics (i.e., their naturally occurring and spontaneous understanding of the physical world) using variations of trap-table problems used to study chimpanzees' folk physics. When presented with these problems, people unnecessarily avoided retrieving a reward by pulling a rake on the side of a table with a trapping hole--even though it was highly unlikely that the hole would trap the reward. However, when the distance between the reward and the trap was sufficiently large and the distance that the reward had to travel to be retrieved was sufficiently short, people preferred to retrieve a reward by pulling the rake on the side of the table with the trap. These results underscore that behavior during tool-use tasks has many possible causes, only one of which might be a subject's folk physics.

Choice Behavior↗

PubMed2005

Gene expression levels influence amino acid usage and evolutionary rates in endosymbiotic bacteria.

Most endosymbiotic bacteria have extremely reduced genomes, accelerated evolutionary rates, and strong AT base compositional bias thought to reflect reduced efficacy of selection and increased mutational pressure. Here, we present a comparative study of evolutionary forces shaping five fully sequenced bacterial endosymbionts of insects. The results of this study were three-fold: (i) Stronger conservation of high expression genes at not just nonsynonymous, but also synonymous, sites. (ii) Variation in amino acid usage strongly correlates with GC content and expression level of genes. This pattern is largely explained by greater conservation of high expression genes, leading to their higher GC content. However, we also found indication of selection favoring GC-rich amino acids that contrasts with former studies. (iii) Although the specific nutritional requirements of the insect host are known to affect gene content of endosymbionts, we found no detectable influence on substitution rates, amino acid usage, or codon usage of bacterial genes involved in host nutrition.

AT Rich Sequence↗

PubMed2005

Genome rearrangement distances and gene order phylogeny in gamma-Proteobacteria.

Genome rearrangements have been studied in 30 gamma-proteobacterial complete genomes by comparing the order of a reduced set of genes on the chromosome. This set included those genes fulfilling several characteristics, the main ones being that an ortholog was present in every genome and that none of them had been acquired by horizontal gene transfer. Genome rearrangement distances were estimated based on either the number of breakpoints or the minimal number of inversions separating two genomes. Breakpoint and inversion distances were highly correlated, indicating that inversions were the main type of rearrangement event in gamma-Proteobacteria. In general, the progressive increase in sequence-based distances between genome pairs was associated with the increase in their rearrangement-based distances but with several groups of distances not following this pattern. Compared with free-living enteric bacteria, the lineages of Pasteurellaceae were evolving, on average, to relatively higher rates of between 2.02 and 1.64, while the endosymbiotic bacterial lineages of Buchnera aphidicola and Wigglesworthia glossinidia were evolving at moderately higher rates of 1.38 and 1.35, respectively. Because we know that the rearrangement rate in the Bu. aphidicola lineage was close to zero during the last 100-150 Myr of evolution, we deduced that a much higher rate took place in the first period of lineage evolution after the divergence of the Escherichia coli lineage. On the other hand, the lineage of the endosymbiont Blochmannia floridanus did present an almost identical rate to free-living enteric bacteria, indicating that the increase in the genome rearrangement rate is not a general change associated with bacterial endosymbiosis. Phylogenetic reconstruction based on rearrangement distances showed a different topology from the one inferred by sequence information. This topology broke the proposed monophyly of the three endosymbiotic lineages and placed Bl. floridanus as a closer relative to E. coli than Yersinia pestis. These results indicate that the phylogeny of these insect endosymbionts is still an open question that will require the development of specific phylogenetic methods to confirm whether the sisterhood of the three endosymbiotic lineages is real or a consequence of a long-branch attraction phenomenon.

Biological Evolution↗

PubMed2005

Methodological-conceptual problems in the study of chimpanzees' folk physics: how studies with adult humans can help.

In three experiments, we examined humans' folk physics (i.e., a naturally occurring and spontaneous understanding of the physical world), using variations of problems used to study chimpanzees' folk physics. Presented with trap-tube problems in two experiments, adult humans showed an unnecessary bias to insert a stick into the end of the tube farthest from the reward to push it out the other end. When presented with trap-table problems with ineffective trapping holes, people unnecessarily avoided the side with the hole. The similarity of humans' and chimpanzees' behavior on these tasks highlights methodological and conceptual problems in studies of chimpanzees' folk physics and suggests alternative explanations for their behavior.

Adult↗

PubMed2004

Identification and separation of PCR products based on their GC content by denaturing high-performance liquid chromatography.

We show that denaturing high-performance liquid chromatography is a suitable method for the separation of DNA molecules of similar sizes but with different GC contents. A mixture of homologous molecules coming from different bacterial species may be obtained when PCR with degenerate primers is used for the amplification of a specific gene from an environmental sample. We have observed that, by selecting an appropriate temperature for the partial denaturation of the molecules, we are able to separate them according to the GC content of each DNA product. This allows us to determine if one or several types of molecules are amplified in the course of a PCR reaction. In the latter case it is possible, even with minority products, to isolate them by collecting the eluted volumes, followed by cloning, sequencing or reamplifying them by PCR, depending on the DNA concentration. We have applied this analysis to the amplification of a fragment of the ribA gene in the bacterial endosymbionts of insects, obtaining a high correlation coefficient (0.978) between retention time and the GC content of the molecules.

Chromatography, High Pressure Liquid↗

PubMed2004

The evolutionary fate of nonfunctional DNA in the bacterial endosymbiont Buchnera aphidicola.

Reduction of the genome size in endosymbiotic bacteria is the main feature linked to the adaptation to a host-associated lifestyle. We have analyzed the fate of the nonfunctional DNA in Buchnera aphidicola, the primary endosymbiont of aphids. At least 164 gene losses took place during the recent evolution of three B. aphidicola strains, symbionts of the aphids Acyrthosiphon pisum (BAp), Schizaphis graminum (BSg), and Baizongia pistacia (BBp). A typical pattern starts with the inactivation of a gene, which produces a pseudogene, and is followed by the progressive loss of its DNA. Our results show that during the period from the separation of the Aphidinae and Pemphiginae lineages (86-164 MYA) to the divergence of BAp and BSg (50-70 MYA) the half-life of a pseudogene was 23.9 Myr. For the remaining periods of evolution, the ranges of values obtained for this parameter are of the same order of magnitude. These results have revealed that a gene inactivated during B. aphidicola evolution requires 40-60 Myr to become almost completely disintegrated. Moreover, we have shown a positive correlation between the decrease in the GC content and the DNA loss for these nonfunctional DNA regions. When gene losses are classified, based on the detection of a pseudogene or otherwise of an absent gene in the modern B. aphidicola genomes, we have observed a drastic reduction of DNA length in the latter versus the former relative to the functional gene. Finally, we have also detected a slight reduction in size of the intergenic regions in the three B. aphidicola strains, when they are compared with the size of the close relative Escherichia coli.

Buchnera↗

PubMed2004

Evolution of the leucine gene cluster in Buchnera aphidicola: insights from chromosomal versions of the cluster.

In Buchnera aphidicola strains associated with the aphid subfamilies Thelaxinae, Lachninae, Pterocommatinae, and Aphidinae, the four leucine genes (leuA, -B, -C, and -D) are located on a plasmid. However, these genes are located on the main chromosome in B. aphidicola strains associated with the subfamilies Pemphiginae and Chaitophorinae. The sequence of the chromosomal fragment containing the leucine cluster and flanking genes has different positions in the chromosome in B. aphidicola strains associated with three tribes of the subfamily Pemphiginae and one tribe of the subfamily Chaitophorinae. Due to the extreme gene order conservation of the B. aphidicola genomes, the variability in the position of the leucine cluster in the chromosome may be interpreted as resulting from independent insertions from an ancestral plasmid-borne leucine gene. These findings do not support a chromosomal origin for the leucine genes in the ancestral B. aphidicola and do support a back transfer evolutionary scenario from a plasmid to the main chromosome.

Binding Sites↗

PubMed2004

Role of CTCF binding sites in the Igf2/H19 imprinting control region.

A approximately 2.4-kb imprinting control region (ICR) regulates somatic monoallelic expression of the Igf2 and H19 genes. This is achieved through DNA methylation-dependent chromatin insulator and promoter silencing activities on the maternal and paternal chromosomes, respectively. In somatic cells, the hypomethylated maternally inherited ICR binds the insulator protein CTCF at four sites and blocks activity of the proximal Igf2 promoter by insulating it from its distal enhancers. CTCF binding is thought to play a direct role in inhibiting methylation of the ICR in female germ cells and in somatic cells and, therefore, in establishing and maintaining imprinting of the Igf2/H19 region. Here, we report on the effects of eliminating ICR CTCF binding by severely mutating all four sites in mice. We found that in the female and male germ lines, the mutant ICR remained hypomethylated and hypermethylated, respectively, showing that the CTCF binding sites are dispensable for imprinting establishment. Postfertilization, the maternal mutant ICR acquired methylation, which could be explained by loss of methylation inhibition, which is normally provided by CTCF binding. Adjacent regions in cis-the H19 promoter and gene-also acquired methylation, accompanied by downregulation of H19. This could be the result of a silencing effect of the methylated maternal ICR.

Animals↗

PubMed2004

Determination of the core of a minimal bacterial gene set.

The availability of a large number of complete genome sequences raises the question of how many genes are essential for cellular life. Trying to reconstruct the core of the protein-coding gene set for a hypothetical minimal bacterial cell, we have performed a computational comparative analysis of eight bacterial genomes. Six of the analyzed genomes are very small due to a dramatic genome size reduction process, while the other two, corresponding to free-living relatives, are larger. The available data from several systematic experimental approaches to define all the essential genes in some completely sequenced bacterial genomes were also considered, and a reconstruction of a minimal metabolic machinery necessary to sustain life was carried out. The proposed minimal genome contains 206 protein-coding genes with all the genetic information necessary for self-maintenance and reproduction in the presence of a full complement of essential nutrients and in the absence of environmental stress. The main features of such a minimal gene set, as well as the metabolic functions that must be present in the hypothetical minimal cell, are discussed.

Bacteria↗

PubMed2004

The rich get richer: students' discounting of hypothetical delayed rewards and real effortful extra credit.

The present research compared choices among students with higher or lower grades for rewards that were devalued by imposing a delay to their receipt (Study 1) or by requiring more work for a larger reward (Study 2). In Study 1, students chose between hypothetical and noncontingent smaller immediate or larger delayed monetary rewards. In Study 2, students chose from among different amounts of real, response-contingent academic rewards (extra credit) that required different amounts of work. The results of both studies were similar: The highest scoring students discounted the value of the delayed money less than did their lower scoring counterparts, and the highest scoring students also chose to do and actually did more extra-credit work than lower scoring students did. Differences in the discounting of devalued rewards might represent a fundamental difference between the highest and lower scoring students.

Choice Behavior↗

PubMed2003

The genome sequence of Blochmannia floridanus: comparative analysis of reduced genomes.

Bacterial symbioses are widespread among insects, probably being one of the key factors of their evolutionary success. We present the complete genome sequence of Blochmannia floridanus, the primary endosymbiont of carpenter ants. Although these ants feed on a complex diet, this symbiosis very likely has a nutritional basis: Blochmannia is able to supply nitrogen and sulfur compounds to the host while it takes advantage of the host metabolic machinery. Remarkably, these bacteria lack all known genes involved in replication initiation (dnaA, priA, and recA). The phylogenetic analysis of a set of conserved protein-coding genes shows that Bl. floridanus is phylogenetically related to Buchnera aphidicola and Wigglesworthia glossinidia, the other endosymbiotic bacteria whose complete genomes have been sequenced so far. Comparative analysis of the five known genomes from insect endosymbiotic bacteria reveals they share only 313 genes, a number that may be close to the minimum gene set necessary to sustain endosymbiotic life.

Animals↗

PubMed2003

Reductive genome evolution in Buchnera aphidicola.

We have sequenced the genome of the intracellular symbiont Buchnera aphidicola from the aphid Baizongia pistacea. This strain diverged 80-150 million years ago from the common ancestor of two previously sequenced Buchnera strains. Here, a field-collected, nonclonal sample of insects was used as source material for laboratory procedures. As a consequence, the genome assembly unveiled intrapopulational variation, consisting of approximately 1,200 polymorphic sites. Comparison of the 618-kb (kbp) genome with the two other Buchnera genomes revealed a nearly perfect gene-order conservation, indicating that the onset of genomic stasis coincided closely with establishment of the symbiosis with aphids, approximately 200 million years ago. Extensive genome reduction also predates the synchronous diversification of Buchnera and its host; but, at a slower rate, gene loss continues among the extant lineages. A computational study of protein folding predicts that proteins in Buchnera, as well as proteins of other intracellular bacteria, are generally characterized by smaller folding efficiency compared with proteins of free living bacteria. These and other degenerative genomic features are discussed in light of compensatory processes and theoretical predictions on the long-term evolutionary fate of symbionts like Buchnera.

Base Sequence↗

PubMed2003

Why are the genomes of endosymbiotic bacteria so stable?

The comparative analysis of three strains of the endosymbiotic bacterium Buchnera aphidicola has revealed high genome stability associated with an almost complete absence of chromosomal rearrangements and horizontal gene transfer events during the past 150 million years. The loss of genes involved in DNA uptake and recombination in the initial stages of endosymbiosis probably underlies this stability. Gene loss, which was extensive during the initial steps of Buchnera evolution, has continued in the different Buchnera lineages since their divergence.

Buchnera↗