Ancient horizontal gene transfer and the last common ancestors

Background The genomic history of prokaryotic organismal lineages is marked by extensive horizontal gene transfer (HGT) between groups of organisms at all taxonomic levels. These HGT events have played an essential role in the origin and distribution of biological innovations. Analyses of ancient gene families show that HGT existed in the distant past, even at the time of the organismal last universal common ancestor (LUCA). Most gene transfers originated in lineages that have since gone extinct. Therefore, one cannot assume that the last common ancestors of each gene were all present in the same cell representing the cellular ancestor of all extant life. Results Organisms existing as part of a diverse ecosystem at the time of LUCA likely shared genetic material between lineages. If these other lineages persisted for some time, HGT with the descendants of LUCA could have continued into the bacterial and archaeal lineages. Phylogenetic analyses of aminoacyl-tRNA synthetase protein families support the hypothesis that the molecular common ancestors of the most ancient gene families did not all coincide in space and time. This is most apparent in the evolutionary histories of seryl-tRNA synthetase and threonyl-tRNA synthetase protein families, each containing highly divergent “rare” forms, as well as the sparse phylogenetic distributions of pyrrolysyl-tRNA synthetase, and the bacterial heterodimeric form of glycyl-tRNA synthetase. These topologies and phyletic distributions are consistent with horizontal transfers from ancient, likely extinct branches of the tree of life. Conclusions Of all the organisms that may have existed at the time of LUCA, by definition only one lineage is survived by known progeny; however, this lineage retains a genomic record of heterogeneous genetic origins. The evolutionary histories of aminoacyl-tRNA synthetases (aaRS) are especially informative in detecting this signal, as they perform primordial biological functions, have undergone several ancient HGT events, and contain many sites with low substitution rates allowing deep phylogenetic reconstruction. We conclude that some aaRS families contain groups that diverge before LUCA. We propose that these ancient gene variants be described by the term “hypnologs”, reflecting their ancient, reticulate origin from a time in life history that has been all but erased”.National Science Foundation (U.S.) (Grant DEB 0830024)Exobiology Program (U.S.) (Grant NNX10AR85G)United States. National Aeronautics and Space Administration (Postdoctoral Program

Effect of winemaking treatment and wine aging on phenolic content in Vranec wines

Phenolic compounds and colour stability of red wines produced from Vranec Vitis vinifera L. grape variety were investigated by means of different maceration times (3, 6 and 10 days), two doses of SO2 (30 and 70 mg/L SO2), two yeasts for fermentation (Vinalco and Levuline), temperature of storage and time of aging (3, 6 and 16 months). In general, maceration time influenced the phenolics extraction from the grapes into the wine. Highest concentrations of phenolic components were observed in the wines produced with 6 days of maceration, except for the flavan-3-ols which were present in highest amounts in the wines macerated for 10 days. Higher doses of SO2 increased the extraction of polyphenols, preventing the wines from oxidation, while the effect of yeast on phenolics extraction was not significant. Wine aging affected the phenolic content of wines produced with 3 days of maceration and caused intensive decrease of anthocyanins during the storage period. Wines aged at higher temperature showed lower anthocyanin levels and less intense coloration. Principal component analysis revealed that separation of the wines was performed according to the hue value in correlation with the maceration time and time of wine aging

Fate of 4 anthocyanins in presence of inactivated yeasts and yeast cell walls during simulation of wine aging

In the present research, two inactivated yeast strains (W13 and BM45) and a commercial yeast cell wall preparation (YCW) already tested for their ability to removal ochratoxin A were used to simulate the wine aging. During the simulated aging, the concentrations of the main 4 anthocyanins decreased in both the control wine and the wines added with yeasts, although at rates depending on the type of yeast and on the nature of anthocyanins. Peonidin-3-O-glucoside decreased by about 20% in the control wine and by ~ 50% in the wines added with yeast strains or the commercial yeast preparation. Malvidin-3-O-glucoside decreased by about 80% in the control wine and in the wine added with YCW and by about 96% in the wines added with W13 and BM45 strains. Cyanidin-3-O-glucoside decreased by 47% in the control wine, by 65–66% in the wines added with W13 and BM45 strains, and by 73% in the wine added with YCW. Delphinidin-3-O-glucoside decreased by 100% already after 21–28 days of aging in all the wines

Anthocyanins enhance yeast’s adsorption of Ochratoxin A during the alcoholic fermentation

Ochratoxin A (OTA) is a mycotoxin that can be present in food products and beverages such as wine, in which the European Union has regulated its maximum concentration. Since yeasts can adsorb OTA during the alcoholic fermentation (AF), we have analyzed whether anthocyanins influence the reduction of OTA in wine during AF carried out by two Saccharomyces cerevisiae strains. Laboratory experiments were conducted with one white must and two red musts that were obtained by adding to the white must two different concentrations of anthocyanins extract. Musts were supplemented with OTA and tested at two pHs. A reduction of OTA was observed in all wines, being higher in red wines. These data point that a chemical bond between anthocyanins and OTA is probably responsible for enhanced adsorption of OTA by yeast. On the other hand, the removal of OTA between the two inoculated yeast strains was different. This result cannot be only attributed to differences in the yeasts’ cell wall composition, because differences were not detected in white wines