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Background
Mycobacterium colombiense is an acid-fast, non-motile, rod-shaped mycobacterium confirmed to cause respiratory disease and disseminated infection in immune-compromised patients, and lymphadenopathy in immune-competent children. It has virulence mechanisms that allow them to adapt, survive, replicate, and produce diseases in the host. To...
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... the relationships among the sequences without regard to the host species, inferring the functions of genes that have not been studied experimentally and elucidating mechanisms that lead to microbial outbreaks [27]. Here, a phylogenetic tree was constructed using the neighbor-joining method and minimum-evolution method of MEGA-X as shown in Fig. 3. Even though homologous evolutionary ancestor supported with 100% bootstrap was shown in the (2022) 20:53 following phylogenetic tree, different closely related clusters and sister groups were ...
Citations
... The transcriptional start site (TSS) and promoter regions were determined by the methods described (Hamde et al., 2022) with modification ( Figure 1). For the current study, after searching the database for drug-resistance genes in Staphylococcus aureus, the twelve genes were identified as being associated with antibiotic resistance in the bacterium. ...
... coli). The matched transcription factors were found to be in good agreement with the regulatory functions means that their activity aligns well with the expected outcomes for antibacterial development (Hamde et al., 2022). ...
... [53] (Fig. 1K). To achieve this, genes were searched for, and their promoter annotations were copied into a table [54,55] from the "General information" section. The NCBI reference sequences of the primary promoters were downloaded in FASTA format (see Table S9). ...
... Primary promoter sequences that did not yield significant results in the biological pathway enrichment analyses were examined using the Multiple Expectation Maximization for Motif Elicitation (MEME suite) version 5.5.2 (https://meme-suite.org/meme/tools/ meme) [55] (Fig. 1L), selecting five motifs. Results were opened in MEME HTML format to discover motifs and their locations. ...
... The motifs were subjected to the TomTom platform for comparison with the JASPAR2022_CORE_vertebrates_non-redundant_v2 motif database to determine if a newly discovered putative motif resembled any of the previously discovered regulatory motifs for transcription factors (TFs), using the statistical measure of motif-motif similarity. TFs of the motifs with the lowest E-value were compiled for further analysis [55] (Fig. 1L). ...
Obesity is currently one of the most alarming pathological conditions due to the progressive increase in its prevalence. In the last decade, it has been associated with fine particulate matter suspended in the air (PM2.5). The purpose of this study was to explore the mechanistic interaction of PM2.5 with a high-fat diet (HFD) through the differential regulation of transcriptional signatures, aiming to identify the association of these particles with metabolically abnormal obesity. The research design was observational, using bioinformatic methods and an explanatory approach based on Rothman's causal model. We propose three new transcriptional signatures in murine adipose tissue. The sum of transcriptional differences between the group exposed to an HFD and PM2.5, compared to the control group, were 0.851, 0.265, and −0.047 (p > 0.05). The HFD group increased body mass by 20% with two positive biomarkers of metabolic impact. The group exposed to PM2.5 maintained a similar weight to the control group but exhibited three positive biomarkers. Enriched biological pathways (p < 0.05) included PPAR signaling, small molecule transport, adipogenesis genes, cytokine-cytokine receptor interaction, and HIF-1 signaling. Transcriptional regulation predictions revealed CpG islands and common transcription factors. We propose three new transcriptional signatures: FAT-PM2.5-CEJUS, FAT-PM2.5-UP, and FAT-PM2.5-DN, whose transcriptional regulation profile in adipocytes was statistically similar by dietary intake and HFD and exposure to PM2.5 in mice; suggesting a mechanistic interaction between both factors. However, HFD-exposed murines developed moderate metabolically abnormal obesity, and PM2.5-exposed murines developed severe abnormal metabolism without obesity. Therefore, in Rothman's terms, it is concluded that HFD is a sufficient cause of the development of obesity, and PM2.5 is a component cause of severe abnormal metabolism of obesity. These signatures would be integrated into a systemic biological process that would induce transcriptional regulation in trans, activating obesogenic biological pathways, restricting lipid mobilization pathways, decreasing adaptive thermogenesis and angiogenesis, and altering vascular tone thus inducing a severe metabolically abnormal obesity.
... This result indicates that the promoter region of the Mer operon genes has rich CpG islands that play a crucial role in gene regulation applications while compared to the gene bodies as indicated above. Hande and his colleagues reported similar finding in the Mycobacterium colombiense CECT 3035 [25]. The current finding agreed with the finding of gene expression in the promoter-associated CpG islands in the human methylome [26]. ...
Microbial genes and their product were diverse and beneficial for heavy metal bioremediation from the contaminated sites. Screening of genes and gene products plays a significant role in the detoxification of pollutants. Understanding of the promoter region and its regulatory elements is a vital implication of microbial genes. To the best of our knowledge, there is no in silico study reported so far on mer gene families used for heavy metal bioremediation. The motif distribution was observed densely upstream of the TSSs (transcription start sites) between +1 and -350 bp and sparsely distributed above -350 bp, according to the current study. MEME identified the best common candidate motifs of TFs (transcription factors) binding with the lowest e value (7.2 e -033) and is the most statistically significant candidate motif. The EXPREG output of the 11 TFs with varying degrees of function such as activation, repression, transcription, and dual purposes was thoroughly examined. Data revealed that transcriptional gene regulation in terms of activation and repression was observed at 36.4% and 54.56%, respectively. This shows that most TFs are involved in transcription gene repression rather than activation. Likewise, EXPREG output revealed that transcriptional conformational modes, such as monomers, dimers, tetramers, and other factors, were also analyzed. The data indicated that most of the transcriptional conformation mode was dual, which accounts for 96%. CpG island analysis using online and offline tools revealed that the gene body had fewer CpG islands compared to the promoter regions. Understanding the common candidate motifs, transcriptional factors, and regulatory elements of the mer operon gene cluster using a machine learning approach could help us better understand gene expression patterns in heavy metal bioremediation.
... This result indicates that the promoter region of the Mer operon genes has rich CpG islands that play a crucial role in gene regulation applications while compared to the gene bodies as indicated above. Hande and his colleagues reported similar finding in the Mycobacterium colombiense CECT 3035 [25]. The current finding agreed with the finding of gene expression in the promoter-associated CpG islands in the human methylome [26]. ...
Background: Microbial gene and gene production were diverse and beneficial for heavy metal bioremediation from the contaminated sites. Screening of genes and gene products plays an important role in the detoxification of pollutants. Understanding of promoter region and its regulatory elements is a vital implication of microbial genes. To the best of our knowledge, there is no in silico analysis report so far on mer genes families used for heavy metal bioremediation.
Results: The motif distribution was observed densely upstream of the TSS from +1 to -400bp and sparsely distributed above -500bp, according to the current study. MEME identified the best common candidate motifs of TFs binding with the lowest e value (7.2e 033) and is the most statistically significant candidate motif. The EXPREG output of the 11 TFs with varying degrees of function as activation, repression transcriptions, and dual purposes was thoroughly examined. Data revealed that transcriptional gene regulation in terms of activation and repression was observed at 36.4% and 54.56% respectively. This shows that the vast majority of TFs are involved in the transcription gene repression rather than activation. Likewise, EXPREG output revealed that transcriptional conformational modes, such as monomer, dimer, tetramer, and other factors, were also analyzed. The data indicated that the majority of transcriptional conformation mode was dual which accounts for 96%. CpG island analysis using online and offline tools revealed that the gene body had fewer CpG islands as compared with the promoter regions.
Conclusion: Understanding the common candidate motifs, transcriptional factors binding sites, and regulatory elements of the mer operon gene cluster using a machine learning approach could help us better understand gene expression patterns in heavy metal bioremediation.
The evolution of microbes in response to conventional antimicrobials leads to antimicrobial resistance (AMR) and multidrug resistance (MDR), and it is a global threat to public health. Natural products are possible solutions to this massive challenge. In this study, the potential of Acanthus polystachyus extracts was investigated for phytochemical composition and biological properties as antimicrobials. Gas chromatography-mass spectra (GC-MS) analysis of methanol extract (ME) and essential oil (EO) detected 79 and 20 compounds, respectively. The major compounds identified in ME and their abundance were β-sitosterol acetate (16.06%), cholest-5-en-3-yl (9Z)-9-octadecenoate (9.54%), 1-dodecanol (7.57%), (S)-(E)-(−)-4-acetoxy-1-phenyl-2-dodecen-1-one (6.03%), neophytadiene (5.7%), (E)-2-nonadecene (3.9%), hexanol-4-D2 (2.92%), and decane (2.4%). Most compounds have known bioactive functions. In EO, the major compounds were stearyl alcohol (25.38%); cis-9-tetradecenoic acid, isobutyl ester (22.95%); butyl 9-tetradecenoate (10.62%); 11,13-dimethyl-12-tetradecen-1-ol acetate (10.14%); ginsenol (3.48%); and diisooctyl phthalate (2.54%). All compounds are known to be bioactive. The antioxidant activity of ME and EO ranged from 48.3 to 84.2% radical scavenging activity (RSA) and 45.6 to 82% RSA, respectively, with dose dependency. The disc diffusion assay for the antimicrobial activity of ME revealed high inhibition against Acenetobacter baumannii (130.2%), Pseudomonas aeruginosa (100.3%), and Staphylococcus aureus (87.7%). The MIC, MBC/MFC, and MBIC values for ME were 0.5–1.0, 2–4, and 0.5–1.0 mg/mL and for EO were 0.31–0.62, 1.25–2.5, and 0.31–0.62 μL/mL, respectively, indicating inhibition potential as well as inhibition of biofilm formation. The tolerance test values indicated bactericidal activity against most strains and bacteriostatic/fungistatic activity against A. baumannii, E. faecalis, and C. albicans. The antiquorum sensing activity of ME achieved by pyocyanin inhibition assay on P. aeruginosa showed a 51.6% inhibition at 500 μg/mL. These results suggest that ME and EO derived from A. polystachyus leaves are potent, valuable, cost-effective antioxidants and antimicrobials. Both extracts may effectively combat pathogenic and resistant microbes.
