Yitzel Gama-Martínez’s research while affiliated with National Autonomous University of Mexico and other places

Salmonella enterica serovar Typhi, the etiological agent of Typhoid fever in humans, contains 44 LysR-type transcriptional regulators (LTTRs), most of which are annotated as hypothetical proteins whose roles are not yet described. In this work we demonstrated by mutants, growth evaluation in bile salts, transcriptional fusions, EMSAs, outer membrane protein profiles and motility assays, that the S. Typhi LTTR STY2660 is involved in two regulatory networks: FNR-STY2660-OmpR-OmpC for porin synthesis and bile resistance and FNR-STY2660-OmpR-FliD for motility. Thus, the LTTR STY2660 is able to establish genetic communication with master regulatory proteins to promote and efficiently respond to adverse conditions present in the host.

The LysR-type transcriptional regulators (LTTRs) are DNA-binding proteins present in bacteria, archaea, and in algae. Knowledge about their distribution, abundance, evolution, structural organization, transcriptional regulation, fundamental roles in free life, pathogenesis, and bacteria-plant interaction has been generated. This review focuses on these aspects and provides a current picture of LTTR biology.

Introduction. Salmonella enterica serovar Typhi ( S . Typhi) is the etiological agent of typhoid fever. To establish an infection in the human host, this pathogen must survive the presence of bile salts in the gut and gallbladder. Hypothesis. S . Typhi uses multiple genetic elements to resist the presence of human bile. Aims. To determine the genetic elements that S . Typhi utilizes to tolerate the human bile salt sodium deoxycholate. Methodology. A collection of S . Typhi mutant strains was evaluated for their ability to growth in the presence of sodium deoxycholate and ox-bile. Additionally, transcriptomic and proteomic responses elicited by sodium deoxycholate on S . Typhi cultures were also analysed. Results. Multiple transcriptional factors and some of their dependent genes involved in central metabolism, as well as in cell envelope, are required for deoxycholate resistance. Conclusion. These findings suggest that metabolic adaptation to bile is focused on enhancing energy production to sustain synthesis of cell envelope components exposed to damage by bile salts.

Methyl parathion (MP) is a highly toxic organophosphorus pesticide associated with water, soil, and air pollution events. The identification and characterization of microorganisms capable of biodegrading pollutants are an important environmental task for bioremediation of pesticide impacted sites. The strain Burkholderia cenocepacia CEIB S5-2 is a bacterium capable of efficiently hydrolyzing MP and biodegrade p-nitrophenol (PNP), the main MP hydrolysis product. Due to the high PNP toxicity over microbial living forms, the reports on bacterial PNP biodegradation are scarce. According to the genomic data, the MP- and PNP-degrading ability observed in B. cenocepacia CEIB S5-2 is related to the presence of the methyl parathion-degrading gene (mpd) and the gene cluster pnpABA’E1E2FDC, which include the genes implicated in the PNP degradation. In this work, the transcriptomic analysis of the strain in the presence of MP revealed the differential expression of 257 genes, including all genes implicated in the PNP degradation, as well as a set of genes related to the sensing of environmental changes, the response to stress, and the degradation of aromatic compounds, such as translational regulators, membrane transporters, efflux pumps, and oxidative stress response genes. These findings suggest that these genes play an important role in the defense against toxic effects derived from the MP and PNP exposure. Therefore, B. cenocepacia CEIB S5-2 has a great potential for application in pesticide bioremediation approaches due to its biodegradation capabilities and the differential expression of genes for resistance to MP and PNP.

Theory ecology is applied to comprehend how genetic variation within tree dominant species may be an important driver of ecological processes. In this sense, studies performed suggest that the genetic diversity of the foundation species can have robust organizational influence at the population, community and ecosystem levels. Foundation species are a small subset of the total species in an ecosystem; it has been suggested that they should capture most of the variation of the community structure and ecosystem processes. The trees of forest ecosystems are excellent candidates to be considered as foundation species because their architectural, functional, and physiological characteristics define the structure of the forests and can influence the microclimate; their biomass contributes significantly to ecosystem processes. Species of the genus Quercus (Fagaceae) are one of the most important tree canopy groups, due to its diversity and dominance in temperate forests in particular. In ecological terms, oaks are important for their ecological functions, also their canopy function as habitats for a wide variety of biological groups, including epiphytic plants, mammals, birds, fungi and arthropods. In particular, the gall-forming wasp belonging to the Cynipidae family (Cynipini Tribe) associated with the genus Quercus are considered one of the most specialized groups of herbivorous insects. The galls produced by cynipids form a microcosm with great ecological activity, harboring a closely associated community of guest organisms (including non-gall-inducing cynipids, flies, moths and beetles) and parasitoids. The parasitoids associated with cynipids are specific to them. It has been reported that their communities may be affected by the genetic attributes of plants. Therefore, oaks and the insects associated with the galls oak canopy represent an excellent system to study the effect of genetic variation of foundation species on cynipid communities, their associated parasitoids, and secondary fauna. Mexico is considered one of the most important centers of diversification of the genus Quercus, with 161 species (30%). Quercus crassipes and Q. castanea are two species of red oak, which are a canopy dominant elements of different forest types that support a wide variety of associated species. Therefore, the aim of this chapter is to determine if Q. crassipes and Q. castanea can be recognized as foundation species. This review denotes that both species are dominant oaks of Mexican temperate forests. They have wide geographic distribution and both species act as important reservoirs of canopy arthropod fauna. Also, we have shown that genetic diversity in both oak species results in extended phenotypes that extends to the community and ecosystem levels, in particular, on the associated community structure of oak – gall – inducing wasp –parasitoids and secondary fauna associated with oak canopy.

Pesticides are xenobiotic molecules necessary to control pests in agriculture, home, and industry. However, water and soil can become contaminated as a consequence of their extensive use. Therefore, because of its eco-friendly characteristics and efficiency, bioremediation of contaminated sites is a powerful tool with advantages over other kinds of treatments. For an efficient pesticides bioremediation, it is necessary to take into account different aspects related to the microbial metabolism and physiology. In this respect, OMICs studies such as genomics, transcriptomics, proteomics, and metabolomics are essential to generate relevant information about the genes and proteins involved in pesticide degradation, the metabolites generated by microbial pesticide degradation, and the cellular strategies to contend against stress caused by pesticide exposition. Pesticides as organochlorines and organophosphorus are the more commonly studied using OMIC approaches. To date, many genomes of microorganisms capable of degrading pesticides have been published, mainly bacterial strains from Burkholderia, Pseudomonas, and Rhodococcus genera. Following the genomic reports, transcriptomic studies, using microarrays and more recently next-generation sequencing technology RNA-Seq, in pesticide microbial degradation are the most numerous. Proteomics, metabolomics, as well as studies that combine different OMIC are gained interest. This review aims to describe a brief overview of pesticide biodegradation mechanisms; new tools to study microorganisms in natural environments; basic concepts of the OMICs approaches; as well as advances in methodologies associated with the analysis of that tools. Additionally, the most recent reports on genomics, transcriptomics, proteomics, and metabolomics during the degradation of pesticides are also analyzed.