Biology subjects

Petras, D.

Publications and source records attributed to Petras, D..

43 records · Page 3Linked to original sources

bioRxiv2019

Laboratory evolution of Escherichia coli enables life based on fluorinated amino acids

Organofluorine compounds are toxic to various living beings in different habitats. On the other hand, fluorine incorporation into single proteins via related amino acid analogues has become common practice in protein engineering. Thus, an essential question remains: can fluorinated amino acids generally be used as xeno-nutrients to build up biomass, or do large amounts of fluorine in the cells render them nonviable? To gain information about the effect of long-term exposure of a cellular proteome to fluorinated organic compounds, we constructed an experiment based on bacterial adaptation in artificial fluorinated habitats. We propagated Escherichia coli (E. coli) in the presence of either 4- or 5-fluoroindole as essential precursors for the in situ synthesis of tryptophan (Trp) analogues. We found that full adaptation requires astonishingly few genetic mutations but is accompanied by large rearrangements in regulatory networks, membrane integrity and quality control of protein folding. These findings highlight the cellular mechanisms of the evolutionary adaption process to unnatural amino acids and provide the molecular foundation for novel and innovative bioengineering of microbial strains with potential for biotechnological applications.\n\nOne Sentence SummaryLaboratory evolution enabled for the first time Escherichia coli to use fluorinated indoles as essential precursors for protein synthesis by introducing few genetic mutations but large rearrangements in regulatory networks, membrane integrity and quality control of protein folding.

synthetic biology↗

bioRxiv2019

MASST: A Web-based Basic Mass Spectrometry Search Tool for Molecules to Search Public Data.

CorrespondenceWe introduce a web-enabled small-molecule mass spectrometry (MS) search engine. To date, no tool can query all the public small-molecule tandem MS data in metabolomics repositories, greatly limiting the utility of these resources in clinical, environmental and natural product applications. Therefore, we introduce a Mass Spectrometry Search Tool (MASST) (https://proteosafe-extensions.ucsd.edu/masst/), that enables the discovery of molecular relationships among accessible public metabolomics and natural product tandem mass spectrometry data (MS/MS).

bioinformatics↗

bioRxiv2018

Community venomics reveals intra-species variations in venom composition of a local population of Vipera kaznakovi in Northeastern Turkey

We report on the variable venom composition of a population of the Caucasus viper (Vipera kaznakovi) in Northeastern Turkey. We applied a combination of venom gland transcriptomics, as well as de-complexing bottom-up and top-down venomics, enabling the comparison of the venom proteomes from multiple individuals. In total, we identified peptides and proteins from 15 toxin families, including snake venom metalloproteinases (svMP; 37.8%), phospholipases A2 (PLA2; 19.0%), snake venom serine proteinases (svSP; 11.5%), C-type lectins (CTL; 6.9%) and cysteine-rich secretory proteins (CRISP; 5.0%), in addition to several low abundant toxin families. Furthermore, we identified intra-species variations of the V. kaznakovi venom composition, and find these were mainly driven by the age of the animals, with lower svSP abundance in juveniles. On a proteoform level, several small molecular weight toxins between 5 and 8 kDa in size, as well as PLA2s, drove the difference between juvenile and adult individuals. This study provides first insights into venom variability of V. kaznakovi and highlights the utility of intact mass profiling for a fast and detailed comparison of snake venoms of individuals from a community.\n\nBiological SignificancePopulation level and ontogenetic venom variation (e.g. diet, habitat, sex or age) can cause a loss of antivenom efficacy against snake bites from wide ranging snake populations. The state of the art for the analysis of snake venoms are de-complexing bottom-up proteomics approaches. While useful, these have the significant drawback of being time-consuming and following costly protocols, and consequently are often applied to pooled venom samples. To overcome these shortcomings and to enable rapid and detailed profiling of large numbers of individual venom samples, we integrated an intact protein analysis workflow into a transcriptomics-guided bottom-up approach. The application of this workflow to snake individuals of a local population of V. kaznakovi revealed intra-species variations in venom composition, which are primarily explained by the age of the animals, and highlighted svSP abundance to be one of the molecular drivers for the compositional differences.\n\nHighlightsO_LIFirst community venomic analysis of a local population of the Caucasian viper (Vipera kaznakovi).\nC_LIO_LIThe venom gland transcriptome of V. kaznakovi identified 46 toxin genes relating to 15 venom toxin families.\nC_LIO_LIBottom-up venomics revealed the identification of 25 proteins covering 7 toxin families mainly dominated by snake venom metalloproteinases (svMP).\nC_LIO_LICommunity venomics by top-down mass profiling revealed ontogenetic shifts between juvenile and adult snakes.\nC_LI

biochemistry↗

bioRxiv2018

Extracellular matrix components are required to protect Bacillus subtilis colonies from T6SS-dependent Pseudomonas invasion and modulate co-colonization of plant

Bacteria adapt to environmental changes and interact with other microorganisms using a wide array of molecules, metabolic plasticity, secretion systems and the formation of biofilms. Some research has looked at changes in the expression of biofilm related genes during interactions between different bacterial species, however no studies have directly demonstrated the functional significance of biofilms in modulating such interactions. In this study, we have explored this fundamental question by studying the interaction between Bacillus subtilis 3610 and Pseudomonas chlororaphis PCL1606. We demonstrate the important role of the extracellular matrix in protecting B. subtilis colonies from infiltration by Pseudomonas. Surprisingly, we find that the Pseudomonas type VI secretion system (T6SS) is required in the cell-to-cell contact with matrix-impaired B. subtilis cells, revealing a novel role for T6SS against Gram-positive bacteria. In response to P. chlororaphis infiltration, we find that B. subtilis activates sporulation and expresses motility-related genes. Experiments using plant organs demonstrate the functional importance of these different bacterial strategies in their coexistence as stable bacterial communities. The findings described here further our understanding of the functional role played by biofilms in mediating bacterial social interactions.

microbiology↗

bioRxiv2018

Adaptation of Bacillus subtilis upon interaction with Setophoma terrestris results in loss of surfactin and plipastatin production

Environmental species of bacteria and fungi coexist and interact showing antagonistic and mutualistic behaviors, mediated by exchange of small diffusible metabolites, driving microbial adaptation to complex communal lifestyles1. Here we show that a wild Bacilus subtilis strain undergoes heritable phenotypic variation following interaction with the soil fungal pathogen Setophoma terrestris (ST) in co-culture. Metabolomics analysis revealed a differential profile in B. subtilis before (pre-ST) and after (post-ST) interacting with the fungus, which paradoxically involved the absence of lipopeptides surfactin and plipastatin and yet acquired antifungal activity in post-ST variants. Metabolic changes were also observed in the profile of volatile compounds, with 2-heptanone and 2-octanone being the most discriminating metabolites present at higher concentrations in post-ST during its interaction with the fungus. Most strikingly, both ketones showed strong antifungal activity against S. terrestris, which was lost with the addition of exogenous surfactin to the medium. Whole-genome analyses showed that mutations in the comA and comP genes of the ComQPXA quorum-sensing system, constituted the genetic bases of post-ST conversion, which allowed the concomitant production of ketones and elimination of surfactin. These findings suggest that mutations in ComQXPA stably rewired B. subtilis metabolism towards the depletion of surfactins and the production of antifungal compounds during its antagonistic interaction with S. terrestris.

microbiology↗

bioRxiv2018

Untargeted Mass Spectrometry-Based Metabolomics Tracks Molecular Changes in Raw and Processed Foods and Beverages

A major aspect of our daily lives is the need to acquire, store and prepare our food. Storage and preparation can have drastic effects on the compositional chemistry of our foods, but we have a limited understanding of the temporal nature of processes such as storage, spoilage, fermentation and brewing on the chemistry of the foods we eat. Here, we performed a temporal analysis of the chemical changes in foods during common household preparations using untargeted mass spectrometry and novel data analysis approaches. Common treatments of foods such as home fermentation of yogurt, brewing of tea, spoilage of meats and ripening of tomatoes altered the chemical makeup through time, through both chemical and biological processes. For example, brewing tea altered its composition by increasing the diversity of molecules, but this change was halted after 4 min of brewing. The results indicate that this is largely due to differential extraction of the material from the tea and not modification of the molecules during the brewing process. This is in contrast to the preparation of yogurt from milk, spoilage of meat and the ripening of tomatoes where biological transformations directly altered the foods molecular composition. Comprehensive assessment of chemical changes using multivariate statistics showed the varied impacts of the different food treatments, while analysis of individual chemical changes show specific alterations of chemical families in the different food types. The methods developed here represent novel approaches to studying the changes in food chemistry that can reveal global alterations in chemical profiles and specific transformations at the chemical level.\n\nO_LSTHighlightsC_LSTO_LIWe created a reference data set for tomato, milk to yogurt, tea, coffee, turkey and beef.\nC_LIO_LIWe show that normal preparation and handling affects the molecular make-up.\nC_LIO_LITea preparation is largely driven by differential extraction.\nC_LIO_LIFormation of yogurt involves chemical transformations.\nC_LIO_LIThe majority of meat molecules are not altered in 5 days at room temperature.\nC_LI

biochemistry↗

bioRxiv2017

Significance estimation for large scale untargeted metabolomics annotations

The annotation of small molecules in untargeted mass spectrometry relies on the matching of fragment spectra to reference library spectra. While various spectrum-spectrum match scores exist, the field lacks statistical methods for estimating the false discovery rates (FDR) of these annotations. We present empirical Bayes and target-decoy based methods to estimate the false discovery rate. Relying on estimations of false discovery rates, we explore the effect of different spectrum-spectrum match criteria on the number and the nature of the molecules annotated. We show that the spectral matching settings needs to be adjusted for each project. By adjusting the scoring parameters and thresholds, the number of annotations rose, on average, by +139% (ranging from -92% up to +5705%) when compared to a default parameter set available at GNPS. The FDR estimation methods presented will enable a user to define the scoring criteria for large scale analysis of untargeted small molecule data that has been essential in the advancement of large scale proteomics, transcriptomics, and genomics science.

bioinformatics↗