In bacteria, transcriptional regulation is a key step in cellular gene expression. All bacteria contain a core RNA polymerase that is catalytically competent but requires an additional σ factor for specific promoter recognition and correct transcriptional initiation. The RNAP core is not able to selectively bind to a given σ factor. In contrast, different σ factors have different affinities for the RNAP core. As a consequence, the concentration of alternate σ factors requires strict regulation in order to properly control the delicate interplay among them, which favors the competence for the RNAP core. This control is archived by different σ/anti-σ controlling mechanisms that shape complex regulatory networks and cascades, and enable the response to sudden environmental cues, whose global understanding is a current challenge for systems biology. Although there have been a number of excellent studies on each of these σ/anti-σ post-transcriptional regulatory systems, no comprehensive comparison of these mechanisms in a single model organism has been conducted. Here, we survey all these systems in E. coli dissecting and analyzing their inner workings and highlightin their differences. Then, following an integral approach, we identify their commonalities and outline some of the principles exploited by the cell to effectively and globally reprogram the transcriptional machinery. These principles provide guidelines for developing biological synthetic circuits enabling an efficient and robust response to sudden stimuli.

Searching for new and better biocatalysts is an area of study in constant development. In nature, mechanisms generally occurring in evolution, such as genetic duplication, recombination, and natural selection processes, produce various enzymes with different architectures and properties. The recombination of genes that code proteins produces multidomain chimeric enzymes that contain two or more domains that sometimes enhance their catalytic properties. Protein engineering has mimicked this process to enhance catalytic activity and the global stability of enzymes, searching for new and better biocatalysts. Here, we present and discuss examples from both natural and synthetic multidomain chimeric enzymes and how additional domains heighten their stability and catalytic activity. Moreover, we also describe progress in developing new biocatalysts using synthetic fusion enzymes and revise some methodological strategies to improve their biological fitness.

Currently there is a growing concern about the presence of emerging contaminants (EC) in water bodies and their potential ecotoxicological effects. Pharmaceuticals, a type of EC, are widely distributed in the environment and their main entry is through wastewater from treatment plants, since these systems are not designed to remove EC. In this sense, the photo-Fenton process, an advanced oxidation process, has proven to be highly efficient in degrading new potentially harmful contaminants. However, this process is affected by multiple factors, which makes it necessary to implement a methodological strategy to optimize the photo-Fenton process. Within these, the Taguchi method provides robust and low-cost solutions with the least number of experiments, providing knowledge of the contribution of each of the factors studied to the response variable. In addition to the above, the Taguchi method can be coupled to a Grey relational analysis (Grey–Taguchi method), which will allow the optimization of more than one response variable at the same time. This paper discusses the parameters that affect the photo-Fenton process and the application of designs of experiments to optimize the process.

Pentachlorophenol is the most toxic and recalcitrant chlorophenol because both aspects are directly proportional to the halogenation degree. Biological and abiotic pentachlorophenol degradation generates p-chloranil, which in neutral to lightly alkaline environmental conditions is hydrolyzed to chloranilic acid that present a violet-reddish coloration in aqueous solution. Several genes of the degradation pathway, cadR-cadCDX, as well as other uncharacterized genes (ORF5 and 6), were isolated from a chloranilic acid degrading bacterium, Pseudomonas putida strain TQ07. The disruption by random mutagenesis of the cadR and cadC genes in TQ07 resulted in a growth deficiency in the presence of chloranilic acid, indicating that these genes are essential for TQ07 growth with chloranilic acid as the sole carbon source. Complementation assays demonstrated that a transposon insertion in mutant CAD82 (cadC) had a polar effect on other genes contained in cosmid pLG3562. These results suggest that at least one of these genes, cadD and cadX, also takes part in chloranilic acid degradation. Based on molecular modeling and function prediction, we strongly suggest that CadC is a pyrone dicarboxylic acid hydrolase and CadD is an aldolase enzyme like dihydrodipicolinate synthase. The results of this study allowed us to propose a novel pathway that offers hypotheses on chloranilic acid degradation (an abiotic by-product of pentachlorophenol) by means of a very clear phenotype that is narrowly related to the capability of Pseudomonas putida strain TQ07 to degrade this benzoquinone.

A Gram-negative bacterium designated as strain TQ07 was isolated from a sawdust sample collected from a sawmill in the community of ''El Salto'' in the state of Durango, Mexico. This strain was previously reported for its ability to degrade chloranilic acid, a derivative of both biotic and abiotic degradation of pentachlorophenol. Genome sequencing was carried out using the Illumina NextSeq 500 platform. The draft genome of strain TQ07 was 5016,215 bp in length, with 4,504 protein-coding sequences and an average G + C content of 60.3 mol%. A phylogenetic tree supports the assignment of strain TQ07 as a member of the genus Herbaspirillum. Comparison of average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values revealed that strain TQ07 shared 98.02% and 84.3% identity, respectively, with the genome of H. lusitanum P6-12 (DSM-17,154^T^). These values indicate that strain TQ07 belongs to the same species as strain P6-12. Other bacterial strains were found to contain all or some orthologs of genes involved in chloranilic acid degradation. Additionally, strain TQ07 possesses genes encoding proteins for Cd²⁺, Cu²⁺, Cr⁶⁺, and As⁵⁺ tolerance. The draft genome sequence of H. lusitanum TQ07 has been deposited in the DDBJ/EMBL/GenBank databases under the accession number PRJNA484228. This genome sequence data provides insightful information for taxonomic characterization and further biotechnological exploitation of H. lusitanum TQ07 for the bioremediation of treated wood.