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Bioprospecting of Microbial Diversity for Sustainable Agriculture and Environment
Published in Vineet Kumar, Vinod Kumar Garg, Sunil Kumar, Jayanta Kumar Biswas, Omics for Environmental Engineering and Microbiology Systems, 2023
Hiren K. Patel, Nensi K. Thumar, Priyank D. Patel, Azaruddin V. Gohil
N-acyl-L-homoserine lactones (AHLs) are molecules involved in quorum sensing widely produced by gram-negative bacteria. Plants also produce and secrete compounds similar to AHLs, which affect bacterial quorum sensing. For example, plant-secreted natural N-acylethanolamines (NAEs) are similar to bacterial AHLs. In response to elicitors, N-acylethanolamines production is enhanced in leaves and gets accumulated in seeds that are desiccated. The application of alkamide, which is another bacterial AHL similar to signalling molecules and NAEs, to seedlings of Arabidopsis affects morphogenesis in a concentration-dependent way by altering the growth of root and shoot. Mutant Pseudomonas fluorescens 2P24 having the deletion of AHLs-encoding gene pcoI failed to colonize the rhizosphere of wheat, while pcoI complementation could successfully restore the wild-type activity. Systemic defence against Alternaria alternata fungi in tomato could be achieved through the enhanced synthesis of ethylene and salicylic acid by AHLs-secreting bacteria in soil (Ortiz-Castro et al. 2009). Two different but conserved homoserine-based quorum sensing systems were detected in PGPR Paraburkholderia sp., i.e. BpI.1/R.1 and BpI.2/R.2. BpI.1/R.1 has an important role in colonization for Arabidopsis thaliana. The present study indicates that BpI.1/R.1 quorum sensing system has a vital role in biofilm production control via regulation of expression of ecf26.1 gene, which is responsible for the encoding of sigma factor, having an extra cytoplasmic function (Zuniga et al. 2017).
Pseudomonas aeruginosa to Hydrocarbon-Rich Jet Fuel
Published in Kenneth Wunch, Marko Stipaničev, Max Frenzel, Microbial Bioinformatics in the Oil and Gas Industry, 2021
Fuel-adapted P. aeruginosa ATCC 33988 strain employs a rapid heat shock response as a mechanism to tolerate stresses produced by the hydrocarbons (Gunasekera et al., 2017). The well-known genes encoding the heat shock proteins, DnaK and GroES, were induced along with katA, which encodes a catalase, and sodB, which encodes superoxide dismutase. Induction of heat shock proteins is primarily caused by increased cellular levels of the heat shock sigma-factor sigma32 encoded by the rpoH gene. Induction of rpoH gene in fuel-resistant ATCC 33988 strain further validates the heat shock response during growth in a fuel environment. Upregulation of genes encoding heat shock/chaperone proteins suggest that ATCC 33988 cells have developed efficient adaptive mechanisms to prevent protein mis-folding and to degrade the irreversibly denatured proteins (Gunasekera et al., 2017).
Bacterial Small RNA and Nanotechnology
Published in Sunil K. Deshmukh, Mandira Kochar, Pawan Kaur, Pushplata Prasad Singh, Nanotechnology in Agriculture and Environmental Science, 2023
The process of gene transcription requires proteins known as sigma factors which serve as the master regulators (Bose et al., 2008; Seshasayee et al., 2011; Ron, 2013). The sigma-factor (a-factor) is the dissociable subunit of the RNA-polymerase which is essential for the recognition of the proper promoter sequence upstream of the gene to be transcribed, followed by recruitment of the RNA-polymerase holoenzyme at the promoter to initiate the process of transcription. Two evolutionarily distinct a-factor families exist: 670 and 654 (Merrick, 1993; Shingler, 1996, 2011; Buck et al., 2000; Guo et al., 2000). They play an essential role in modulating the gene expression of sets of genes when the cell encounters stress conditions or undergoes growth transformations (Chung et al., 2006; Seshasayee et al., 2011). Extensive studies have been carried out with model organisms, Bacillus subtilis and Escherichia coli, to elucidate the regulatory role of these factors. E. coli K12 is known to possess six members of the 670 family (RpoD, RpoH, RpoS, RpoE, and F1iA) and one 654 protein (RpoN) (Seshasayee et al., 2011; Ron, 2013). The onset of stationary phase in E. coli, elicits drastic changes in its morphology, physiology, and membrane composition. In 1993, Hengge-Aronis, established the role of RpoS (σs) as the central regulator of gene expression in the early stationary phase in E. coli. RpoS in-turn is influenced by small molecules such as guanosine 5’-diphosphate 3’-diphosphate (ppGpp) and quorum sensing signalling molecules (homo serine lactones). In gram-negative bacteria, elevated temperature is mediated by heat-shock proteins which are influenced by 632 and 6E (Ron, 2013). The process of nitrogen-fixation is regulated by nif genes which are under the control of 654 (Arsene et al., 1996). Chemotaxis and flagella synthesis is under the control of 628 (Ding et al., 2009). Similarly, different 6 factors control different cellular functions in all bacterial strains.
Genomic-wide analysis approach revealed genomic similarity for environmental Mexican S. Oranienburg genomes
Published in International Journal of Environmental Health Research, 2023
J. R. Aguirre-Sanchez, I. F. Vega-Lopez, N. Castro Del Campo, J. A. medrano-Felix, J. Martínez-Urtaza, C. Chaidez-Quiroz
The application of WGS to S. Oranienburg made possible the punctual identification of core genome changes allowing associations establishment considering strains from different isolation sources. This may impact Salmonella epidemiological outbreaks in timely detection. Although genomic-wide analysis based on SNPs has shown to have an important role in epidemiological outbreaks definitions, it is important to consider basic aspects of outbreaks nature such as source types, routes of infection (Gymoese et al. 2017), and patterns of migration. The genotype of S. Oranienburg population presents a conserved virulence profile. Genes involved in Type III secretion system (T3SS) assembly, magnesium uptake, adhesion, and stress response were consistently found for all genomes. This category has been observed in well-known pathogenic Salmonella serovar as Typhi (Kaur and Jain 2012; Al-Khafaji et al. 2021) and Typhimurium (Johnson et al. 2018; Dos Santos et al. 2019) as an essential gene repertory to invade, survive, reproduce and cause a gastrointestinal clinical profile (Jajere 2019). For example, the sigma factor RpoS, has been described as in control of the adaptative response to environmental stress, virulence, and biofilm formation (Lago et al. 2017). The presence of type 1 fimbria plays an important role in the initial attachment to host intestinal mucosa causing persistence and pathogenesis (Kolenda et al. 2019). The punctual identification of previously mentioned virulence markers suggests that this serotype has the potential to infect a host and trigger a pathogenesis process in it.