The primordial metabolism: an ancestral interconnection between leucine, arginine, and lysine biosynthesis

<p>Abstract</p> <p>Background</p> <p>It is generally assumed that primordial cells had small genomes with simple genes coding for enzymes able to react with a wide range of chemically related substrates, interconnecting different metabolic routes. New genes coding for enzymes with a narrowed substrate specificity arose by paralogous duplication(s) of ancestral ones and evolutionary divergence. In this way new metabolic pathways were built up by primordial cells. Useful hints to disclose the origin and evolution of ancestral metabolic routes and their interconnections can be obtained by comparing sequences of enzymes involved in the same or different metabolic routes. From this viewpoint, the lysine, arginine, and leucine biosynthetic routes represent very interesting study-models. Some of the <it>lys</it>, <it>arg </it>and <it>leu </it>genes are paralogs; this led to the suggestion that their ancestor genes might interconnect the three pathways. The aim of this work was to trace the evolutionary pathway leading to the appearance of the extant biosynthetic routes and to try to disclose the interrelationships existing between them and other pathways in the early stages of cellular evolution.</p> <p>Results</p> <p>The comparative analysis of the genes involved in the biosynthesis of lysine, leucine, and arginine, their phylogenetic distribution and analysis revealed that the extant metabolic "grids" and their interrelationships might be the outcome of a cascade of duplication of ancestral genes that, according to the patchwork hypothesis, coded for unspecific enzymes able to react with a wide range of substrates. These genes belonged to a single common pathway in which the three biosynthetic routes were highly interconnected between them and also to methionine, threonine, and cell wall biosynthesis. A possible evolutionary model leading to the extant metabolic scenarios was also depicted.</p> <p>Conclusion</p> <p>The whole body of data obtained in this work suggests that primordial cells synthesized leucine, lysine, and arginine through a single common metabolic pathway, whose genes underwent a set of duplication events, most of which can have predated the appearance of the last common universal ancestor of the three cell domains (Archaea, Bacteria, and Eucaryotes). The model proposes a relative timing for the appearance of the three routes and also suggests a possible evolutionary pathway for the assembly of bacterial cell-wall.</p

Unexpected presence of Fagus orientalis complex in Italy as inferred from 45,000-year-old DNA pollen samples from Venice lagoon

<p>Abstract</p> <p>Background</p> <p>Phylogeographic analyses on the Western Euroasiatic <it>Fagus </it>taxa (<it>F. orientalis</it>, <it>F. sylvatica</it>, <it>F. taurica </it>and <it>F. moesiaca</it>) is available, however, the subdivision of <it>Fagus </it>spp. is unresolved and there is no consensus on the phylogeny and on the identification (both with morphological than molecular markers) of <it>Fagus </it>Eurasiatic taxa.</p> <p>For the first time molecular analyses of ancient pollen, dated at least 45,000 years ago, were used in combination with the phylogeny analysis on current species, to identify the <it>Fagus </it>spp. present during the Last Interglacial period in Italy.</p> <p>In this work we aim at testing if the <it>trn</it>L-<it>trn</it>F chloroplast DNA (cpDNA) region, that has been previously proved efficient in discriminating different <it>Quercus </it>taxa, can be employed in distinguishing the <it>Fagus </it>species and in identifying the ancient pollen.</p> <p>Results</p> <p>86 populations from 4 Western Euroasistic taxa were sampled, and sequenced for the <it>trn</it>L-<it>trn</it>F region to verify the efficiency of this cpDNA region in identifying the <it>Fagus </it>spp.. Furthermore, <it>Fagus crenata </it>(2 populations), <it>Fagus grandifolia </it>(2 populations), <it>Fagus japonica</it>, <it>Fagus hayatae</it>, <it>Quercus </it>species and <it>Castanea </it>species were analysed to better resolve the phylogenetic inference.</p> <p>Our results show that this cpDNA region harbour some informative sites that allow to infer relationships among the species within the Fagaceae family. In particular, few specific and fixed mutations were able to discriminate and identify all the different <it>Fagus </it>species.</p> <p>Considering a short fragment of 176 base pairs within the <it>trn</it>L intron, 2 transversions were found able in distinguishing the <it>F. orientalis </it>complex taxa (<it>F. orientalis</it>, <it>F. taurica </it>and <it>F. moesiaca</it>) from the remaining <it>Fagus </it>spp. (<it>F. sylvatica</it>, <it>F. japonica</it>, <it>F. hayataea</it>, <it>F. crenata </it>and <it>F. grandifolia</it>). This permits to analyse this fragment also in ancient samples, where DNA is usually highly degraded.</p> <p>The sequences data indicate that the DNA recovered from ancient pollen belongs to the <it>F. orientalis </it>complex since it displays the informative sites characteristic of this complex.</p> <p>Conclusion</p> <p>The ancient DNA sequences demonstrate for the first time that, in contrast to current knowledge based on palynological and macrofossil data, the <it>F. orientalis </it>complex was already present during the Tyrrhenian period in what is now the Venice lagoon (Italy).</p> <p>This is a new and important insight considering that nowadays West Europe is not the natural area of <it>Fagus orientalis </it>complex, and up to now nobody has hypothesized the presence during the Last Interglacial period of <it>F. orientalis </it>complex in Italy.</p

Valorizzazione della produzione legnosa dei boschi di castagno

In Italy chestnut stands evolution has been historically and strictly linked to both ecological and socioeconomic factors and the changes over the centuries have nowadays led to three main stands types: cultivated orchards, abandoned orchards and stands managed for wood production, mainly coppices. This last type is spread on 593,242 hectares and the importance of these forests consists of the high production potential in quantitative and qualitative terms and of the variety of timber assortments they can provide. Suitable silvicultural systems, based on diversified rotation length, can be adopted to improve wood production both from a quantitative and qualitative point of view

Evaluating impact of possible transgenic poplar cultivation on protected areas

Plant biodiversity studies have been performed in the Migliarino-San Rossore-Massaciuccoli Regional Park in Tuscany (Italy) within the framework of the European project LIFE08 NAT/IT/342.This project aims at developing a quick monitoring index (QMI) to rapidly assess the potential risk generated by transgenic plants in characterized ecosystems or biotopes. For this reason test areas have been selected inside the protected area to evaluate plant (weeds and trees), animal, and soil microoganisms biodiversity. The proximity of the selected test area to cropped surfaces where Genetically Modified Plants (GMPs) might be cultivated has been taken into account. GMPs could spread pollen and contaminate natural populations. To avoid this risk, an efficient monitoring system is required taking into account genetic diversity and breeding study. As far as tree biodiversity concern, Populus species were identified in the test areas. Two populations of Populus present into two different ecosystems (forest and wetland areas) were examined together with two cultivated varieties. The two ecosystems were characterized for the vegetation. Nuclear microsatellites were used to evaluate genetic diversity of poplar populations and level of breeding between natural and cultivated Populus. In addition the insect populations present on male and female poplars during flowering period have been studied