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Antonio Lazcano

Publications and source records attributed to Antonio Lazcano.

17 recordsLinked to original sources
PubMed2006

Molecular evolution of peptide methionine sulfoxide reductases (MsrA and MsrB): on the early development of a mechanism that protects against oxidative damage.

Methionine sulfoxide reductases, enzymes that reverse the oxidation of methionine residues, have been described in a wide range of species. The reduction of the diastereoisomers of oxidized methionine is catalyzed by two different monomeric methionine sulfoxide reductases (MsrA and MsrB) and is best understood as an evolutionary response to high levels of oxygen either in the Earth's atmosphere or possibly in more localized environments. Phylogenetic analyses of these proteins suggest that their distribution is the outcome of a complex history including many paralogy and lateral gene transfer events.

Animals↗
PubMed2005

The last common ancestor: what's in a name?

Twenty completely sequenced cellular genomes from the three major domains were analyzed using twice one-way BLAST searches in order to define the set of the most conserved protein-encoding sequences to characterize the gene complement of the last common ancestor of extant life. The resulting set is dominated by different putative ATPases, and by molecules involved in gene expression and RNA metabolism. DEAD-type RNA helicase and enolase genes, which are known to be part of the RNA degradosome, are as conserved as many transcription and translation genes. This suggests the early evolution of a control mechanism for gene expression at the RNA level, providing additional support to the hypothesis that during early cellular evolution RNA molecules played a more prominent role. Conserved sequences related to biosynthetic pathways include those encoding putative phosphoribosyl pyrophosphate synthase and thioredoxin, which participate in nucleotide metabolism. Although the information contained in the available databases corresponds only to a minor portion of biological diversity, the sequences reported here are likely to be part of an essential and highly conserved pool of proteins domains common to all organisms.

Evolution, Molecular↗
PubMed2005

An investigation of prebiotic purine synthesis from the hydrolysis of HCN polymers.

The polymerization of concentrated NH4CN solutions has been studied at various temperatures and ammonia concentrations. The products of the oligomerization of ammonium cyanide include adenine and guanine, as well as trace amounts of 2,6-diaminopurine. Our results indicate that the adenine yield is not strongly dependent on temperature. Guanine is produced in lower yield. The original studies by Oró and Kimball (1961) showed that the 6 N HCl hydrolysis of the NH4CN polymerization supernatant greatly increased the adenine yield. However, this hydrolysis also decomposes adenine and other purines. Therefore, we have measured the yields from an NH4CN polymerization as a function of hydrolysis time, and found that shorter hydrolytic periods give higher yields of adenine. We have also investigated the hydrolysis of the supernatant at pH 8, which is a more reasonable model of primitive oceanic conditions, and found that the adenine yield is comparable to that obtained with acid hydrolysis (approximately 0.1%). The yield of adenine does not decline at longer hydrolysis times because of the greater stability of adenine at pH 8. The insoluble black polymer formed from NH4CN has been analyzed by both acid and neutral hydrolysis. In both cases adenine yields of approximately 0.05% were obtained. This suggests that the polymer may have been as important a prebiotic source of purines as the usually analyzed supernatant.

Adenine↗
PubMed2005

Polyamino acids as synthetic enzymes: mechanism, applications and relevance to prebiotic catalysis.

Polyamino acids, such as polyleucine, behave as synthetic enzymes in the asymmetric epoxidation of chalcone and other electron-deficient alkenes (the Julià-Colonna reaction). The influences of reaction conditions, of the molecular structure of the catalysts and of the scaling-up of the process on the enantioselectivity of the reaction have been determined. The kinetics and mechanism have been investigated using a soluble PEG-polyleucine conjugate, which behaves in a similar way to an enzyme, showing saturation kinetics for both chalcone and HOO-. Enantioselective catalysis is achieved with peptides with as few as five residues and scalemic catalysts show high chiral amplification. Here, we discuss the relevance of these-enzyme like catalysts to prebiotic processes, such as the role of small peptides in the formation of optically active cyanohydrins.

Amino Acids↗
PubMed2005

Comparative analysis of methodologies for the detection of horizontally transferred genes: a reassessment of first-order Markov models.

With the advent of larger genome databases detection of horizontal gene transfer events has been transformed into an increasingly important issue. Here we present a simple theoretical analysis based on the in silico artificial addition of known foreign genes from different prokaryotic groups into the genome of Escherichia coli K12 MG1655. Using this dataset as a control, we have tested the efficiency of four methodologies commonly employed to detect HTG (Horizontally transferred genes), which are based on (a) the codon adaptation index, codon usage, and GC percentage (CAI/GC); (b) a distributional profile (DP) approach made by a gene search in the closely related phylogenetic genomes; (c) a Bayesian model (BM); and (d) a first-order Markov model (MM). All methods exhibit limitations although, as shown here, the BM and the MM are better approximations. Moreover, the MM has demonstrated a more accurate rate of detections when genes from closely related organisms are evaluated. The application of the MM to detect recently transferred genes in the genomes of E. coli strains K12 MG1655, O157 EDL933, and Salmonella typhimurium, shows that these organisms have undergone a rather significant amount of HTG, most of which appear to be pseudogenes. Few of these sequences that have undergone HGT appear to have well defined functions and may be involved in the organism's adaptation.

Computer Simulation↗
PubMed2004

Reconstructing evolutionary relationships from functional data: a consistent classification of organisms based on translation inhibition response.

The last two decades have witnessed an unsurpassed effort aimed at reconstructing the history of life from the genetic information contained in extant organisms. The availability of many sequenced genomes has allowed the reconstruction of phylogenies from gene families and its comparison with traditional single-gene trees. However, the appearance of major discrepancies between both approaches questions whether horizontal gene transfer (HGT) has played a prominent role in shaping the topology of the Tree of Life. Recent attempts at solving this controversy and reaching a consensus tree combine molecular data with additional phylogenetic markers. Translation is a universal cellular function that involves a meaningful, highly conserved set of genes: both rRNA and r-protein operons have an undisputed phylogenetic value and rarely undergo HGT. Ribosomal function reflects the concerted expression of that genetic network and consequently yields information about the evolutionary paths followed by the organisms. Here we report on tree reconstruction using a measure of the performance of the ribosome: antibiotic sensitivity of protein synthesis. A large database has been used where 33 ribosomal systems belonging to the three major cellular lineages were probed against 38 protein synthesis inhibitors. Different definitions of distance between pairs of organisms have been explored, and the classical algorithm of bootstrap evaluation has been adapted to quantify the reliability of the reconstructions obtained. Our analysis returns a consistent phylogeny, where archaea are systematically affiliated to eukarya, in agreement with recent reconstructions which used information-processing systems. The integration of the information derived from relevant functional markers into current phylogenetic reconstructions might facilitate achieving a consensus Tree of Life.

Archaea↗
PubMed2004

Comparative genomics and the gene complement of a minimal cell.

The concept of a minimal cell is discussed from the viewpoint of comparative genomics. Analysis of published DNA content values determined for 641 different archaeal and bacterial species by pulsed field gel electrophoresis has lead to a more precise definition of the genome size ranges of free-living and host-associated organisms. DNA content is not an indicator of phylogenetic position. However, the smallest genomes in our sample do not have a random distribution in rRNA-based evolutionary trees, and are found mostly in (a) the basal branches of the tree where thermophiles are located; and (b) in late clades, such as those of Gram positive bacteria. While the smallest-known genome size for an endosymbiont is only 450 kb, no free-living prokaryote has been described to have genomes < 1450 kb. Estimates of the size of minimal gene complement can provide important insights in the primary biological functions required for a sustainable, reproducing cell nowadays and throughout evolutionary times, but definitions of the minimum cell is dependent on specific environments.

Cells↗
PubMed2003

Hyperthermophily and the origin and earliest evolution of life.

The possibility of a high-temperature origin of life has gained support based on indirect evidence of a hot, early Earth and on the basal position of hyperthermophilic organisms in rRNA-based phylogenies. However, although the availability of more than 80 completely sequenced cellular genomes has led to the identification of hyperthermophilic-specific traits, such as a trend towards smaller genomes, reduced protein-encoding gene sizes, and glutamic-acid-rich simple sequences, none of these characteristics are in themselves an indication of primitiveness. There is no geological evidence for the physical setting in which life arose, but current models suggest that the Earth's surface cooled down rapidly. Moreover, at 100 degrees C the half-lives of several organic compounds, including ribose, nucleobases, and amino acids, which are generally thought to have been essential for the emergence of the first living systems, are too short to allow for their accumulation in the prebiotic environment. Accordingly, if hyperthermophily is not truly primordial, then heat-loving lifestyles may be relics of a secondary adaptation that evolved after the origin of life, and before or soon after separation of the major lineages.

Adaptation, Physiological↗
PubMed2003

The roads to and from the RNA world.

The historical existence of the RNA world, in which early life used RNA for both genetic information and catalytic ability, is widely accepted. However, there has been little discussion of whether protein synthesis arose before DNA or what preceded the RNA world (i.e. the pre-RNA world). We outline arguments of what route life may have taken out of the RNA world: whether DNA or protein followed. Metabolic arguments favor the possibility that RNA genomes preceded the use of DNA as the informational macromolecule. However, the opposite can also be argued based on the enhanced stability, reactivity, and solubility of 2-deoxyribose as compared to ribose. The possibility that DNA may have come before RNA is discussed, although it is a less parsimonious explanation than DNA following RNA.

Animals↗