The NCBI BioSystems database

105

Tomato flavor is dependent upon a complex mixture of volatiles including multiple acetate esters. Red-fruited species of the tomato clade accumulate a relatively low content of acetate esters in comparison with the green-fruited species. We show that the difference in volatile ester content between the red-and greenfruited species is associated with insertion of a retrotransposon adjacent to the most enzymatically active member of a family of esterases. This insertion causes higher expression of the esterase, resulting in the reduced levels of multiple esters that are negatively correlated with human preferences for tomato. The insertion was evolutionarily fixed in the red-fruited species, suggesting that high expression of the esterase and consequent low ester content may provide an adaptive advantage in the ancestor of the redfruited species. These results illustrate at a molecular level how closely related species exhibit major differences in volatile production by altering a volatile-associated catabolic activity.T he flavor of a food involves integration of the information detected by taste and olfactory receptors (1). In the case of tomato (Solanum lycopersicum), flavor is the sum of the interactions between sugars, acids, and multiple volatile chemicals (2). Although sugars and acids are essential to our appreciation of tomato, the uniqueness and complexity of its flavor are dependent upon the blend of volatiles that can be detected (3, 4). Plants synthesize a vast array of volatile organic compounds. Derived from primary and secondary metabolites, they contribute to functions as diverse as defense against herbivores and pathogens, plant-toplant interactions, and attraction of pollinators and seed dispersers (5-7). Most of the important tomato volatiles are derived from amino acids, fatty acids, and carotenoid precursors (2,8). Despite the importance of these volatiles to fruit quality, regulation of their synthesis still remains poorly understood (4).One approach to identification of genes involved in plant volatile production is based upon characterization of quantitative trait loci (QTL). This method exploits variation between cultivars of the same species or between closely related species (9-11). In tomato, populations of introgression lines (ILs) that contain only a fragment of the genome of a wild species have been useful in the discovery of numerous volatile-associated QTL (10, 12) as well as of QTL affecting yield, carotenoid production, and accumulation of primary metabolites (13,14). From a human flavor perspective, it makes the most sense to concentrate on the volatiles that are most important to consumer preferences. Historically, the most important volatiles have been identified on the basis of odor units, that is, the concentration of a given volatile divided by its odor threshold (2, 15). Although this method has value, recent work has shown that the reality of taste preference is far more complex as interactions between volatiles and other flavor-associated chemicals influence perception....

Section: Resultsmentioning

confidence: 57%

Role of an esterase in flavor volatile variation within the tomato clade

Goulet

Magerøy

Lam

et al. 2012

105

“…A set of publicly available S. aureus genome sequences was downloaded from the NCBI including 48 completely assembled genomes (16). From this set, a phylogenetic tree was constructed using the concatenated sequence of seven conserved housekeeping genes (arcC, aroE, glpF, gmk, pta, tpi, and yqiL) commonly used to define clonal complexes in clinical studies of S. aureus using the MLST approach (Fig.…”

Section: Resultsmentioning

confidence: 99%

Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity

Bosi

Monk

Aziz

et al. 2016

211

196

Staphylococcus aureus is a preeminent bacterial pathogen capable of colonizing diverse ecological niches within its human host. We describe here the pangenome of S. aureus based on analysis of genome sequences from 64 strains of S. aureus spanning a range of ecological niches, host types, and antibiotic resistance profiles. Based on this set, S. aureus is expected to have an open pangenome composed of 7,411 genes and a core genome composed of 1,441 genes. Metabolism was highly conserved in this core genome; however, differences were identified in amino acid and nucleotide biosynthesis pathways between the strains. Genome-scale models (GEMs) of metabolism were constructed for the 64 strains of S. aureus. These GEMs enabled a systems approach to characterizing the core metabolic and panmetabolic capabilities of the S. aureus species. All models were predicted to be auxotrophic for the vitamins niacin (vitamin B3) and thiamin (vitamin B1), whereas strain-specific auxotrophies were predicted for riboflavin (vitamin B2), guanosine, leucine, methionine, and cysteine, among others. GEMs were used to systematically analyze growth capabilities in more than 300 different growth-supporting environments. The results identified metabolic capabilities linked to pathogenic traits and virulence acquisitions. Such traits can be used to differentiate strains responsible for mild vs. severe infections and preference for hosts (e.g., animals vs. humans). Genome-scale analysis of multiple strains of a species can thus be used to identify metabolic determinants of virulence and increase our understanding of why certain strains of this deadly pathogen have spread rapidly throughout the world.systems biology | mathematical modeling | pathogenicity | core genome | pangenome

“…Moreover, because we know the phylogenetic location of ostrich, (26) we attempted to obtain the degree of accuracy in our experiment by conducting a phylogenetic analysis. We infer the position of the ostrich in the tree of life using the de novo proteomics analysis and compare this tree to the taxonomic tree as provided by the National Center for Biotechnology Information (NCBI) (30) (Fig. S3).…”

Section: Resultsmentioning

confidence: 99%

Database independent proteomics analysis of the ostrich and human proteome

Altelaar

Navarro²,

Boekhorst³

et al. 2011

Mass spectrometry (MS)-based proteome analysis relies heavily on the presence of complete protein databases. Such a strategy is extremely powerful, albeit not adequate in the analysis of unpredicted postgenome events, such as posttranslational modifications, which exponentially increase the search space. Therefore, it is of interest to explore "database-free" approaches. Here, we sampled the ostrich and human proteomes with a method facilitating de novo sequencing, utilizing the protease Lys-N in combination with electron transfer dissociation. By implementing several validation steps, including the combined use of collision-induced dissociation/ electron transfer dissociation data and a cross-validation with conventional database search strategies, we identified approximately 2,500 unique de novo peptide sequences from the ostrich sample with over 900 peptides generating full backbone sequence coverage. This dataset allowed the appropriate positioning of ostrich in the evolutionary tree. The described database-free sequencing approach is generically applicable and has great potential in important proteomics applications such as in the analysis of variable parts of endogenous antibodies or proteins modified by a plethora of complex posttranslational modifications.