Regulatory Gene Products Research Articles

Antimicrobial efficacy of eravacycline against emerging extensively drug-resistant (XDR) Acinetobacter baumannii isolates

PurposeDrug-resistant Acinetobacter baumannii is an emerging threat. This study has been conducted to observe the efficacy of eravacycline along with the RND-efflux pump system. MethodsA cross-sectional study was done collecting 48 clinical isolates of Acinetobacter baumannii. MICs of 15 antibiotics were detected along with BMD of tigecycline and eravacycline. PCR products of drug-resistant regulatory genes were sequenced and analyzed. ResultsOf the total 48 Isolates, 35 (72.91%) were XDR and 13 (27.08%) were MDR. Out of all, 60.41% of isolates were found to be susceptible to eravacycline by BMD according to both FDA and EUCAST guidelines. A 2-fold decline of MIC50/90 was observed with the use of eravacycline compared to tigecycline. RND-efflux genes like AdeC in 30 (62.5%) isolates and Regulatory gene AdeS in 29 (60.41%) isolates were detected, explaining the existing resistance mechanism. ConclusionsXDR Acinetobacter poses an escalating threat due to its resistance to multiple antibiotics, raising serious concerns in healthcare settings. Eravacycline is an encouraging new drug for empirical use in severe infection caused due to the same. Molecular investigation and strict antimicrobial stewardship should be followed to control the emergence, and a better understanding of mechanisms of resistance to prevent the spread of drug-resistant isolates.

Listeria monocytogenes two component system PieRS regulates secretion chaperones PrsA1 and PrsA2 and enhances bacterial translocation across the intestine.

Listeria monocytogenes (Lm) is a widespread environmental Gram‐positive bacterium that can transition into a pathogen following ingestion by a susceptible host. To cross host barriers and establish infection, Lm is dependent upon the regulated secretion and activity of many proteins including PrsA2, a peptidyl‐prolyl cis‐trans isomerase with foldase activity. PrsA2 contributes to the stability and activity of a number of secreted virulence factors that are required for Lm invasion, replication, and cell‐to‐cell spread within the infected host. In contrast, a second related secretion chaperone, PrsA1, has thus far no identified contributions to Lm pathogenesis. Here we describe the characterization of a two‐component signal transduction system PieRS that regulates the expression of a regulon that includes the secretion chaperones PrsA1 and PrsA2. PieRS regulated gene products are required for bacterial resistance to ethanol exposure and are important for bacterial survival during transit through the gastrointestinal tract. PrsA1 was also found to make a unique contribution to Lm survival in the GI tract, revealing for the first time a non‐overlapping requirement for both secretion chaperones PrsA1 and PrsA2 during the process of intra‐gastric infection.

Modeling Transport Regulation in Gene Regulatory Networks.

A gene regulatory network summarizes the interactions between a set of genes and regulatory gene products. These interactions include transcriptional regulation, protein activity regulation, and regulation of the transport of proteins between cellular compartments. DSGRN is a network modeling approach that builds on traditions of discrete-time Boolean models and continuous-time switching system models. When all interactions are transcriptional, DSGRN uses a combinatorial approximation to describe the entire range of dynamics that is compatible with network structure. Here we present an extension of the DGSRN approach to transport regulation across a boundary between compartments, such as a cellular membrane. We illustrate our approach by searching a model of the p53-Mdm2 network for the potential to admit two experimentally observed distinct stable periodic cycles.

Sensory Systems and Transcriptional Regulation in Escherichia coli.

In free-living bacteria, the ability to regulate gene expression is at the core of adapting and interacting with the environment. For these systems to have a logic, a signal must trigger a genetic change that helps the cell to deal with what implies its presence in the environment; briefly, the response is expected to include a feedback to the signal. Thus, it makes sense to think of genetic sensory mechanisms of gene regulation. Escherichia coli K-12 is the bacterium model for which the largest number of regulatory systems and its sensing capabilities have been studied in detail at the molecular level. In this special issue focused on biomolecular sensing systems, we offer an overview of the transcriptional regulatory corpus of knowledge for E. coli that has been gathered in our database, RegulonDB, from the perspective of sensing regulatory systems. Thus, we start with the beginning of the information flux, which is the signal’s chemical or physical elements detected by the cell as changes in the environment; these signals are internally transduced to transcription factors and alter their conformation. Signals transduced to effectors bind allosterically to transcription factors, and this defines the dominant sensing mechanism in E. coli. We offer an updated list of the repertoire of known allosteric effectors, as well as a list of the currently known different mechanisms of this sensing capability. Our previous definition of elementary genetic sensory-response units, GENSOR units for short, that integrate signals, transport, gene regulation, and the biochemical response of the regulated gene products of a given transcriptional factor fit perfectly with the purpose of this overview. We summarize the functional heterogeneity of their response, based on our updated collection of GENSORs, and we use them to identify the expected feedback as part of their response. Finally, we address the question of multiple sensing in the regulatory network of E. coli. This overview introduces the architecture of sensing and regulation of native components in E.coli K-12, which might be a source of inspiration to bioengineering applications.

An integrated transcriptomic and proteomic approach to dynamically study the mechanism of pollen-pistil interactions during jasmine crossing

Jasmine (Jasminum sambac Aiton, Oleaceae) flowers are widely consumed in many countries for their tea-making, medicinal and ornamental properties. To improve the quality and yield of flowers, it is very important to carry out cross-breeding between different petal types of jasmine. However, because of the difficulty of sexual reproduction, there is no report on the success of jasmine crosses. In this paper, single- and double-petal jasmine plants were crossed artificially. The stigmas of single-petal plants post pollination, including those at 0 h after pollination (CK), 1 h after pollination (T1) and 6 h after pollination (T2), were sequenced by transcriptomic combined with proteomic analyses. A total of 178,098 gene products were assembled. Simultaneously, a total of 2337 protein species were identified. Some regulatory gene products and functional protein species were identified that may be involved in the process of pollen-pistil interactions. These findings suggest that the identified differentially expressed gene products and differentially accumulated protein species may play vital roles in jasmine plants in response to pollen-pistil interactions, providing important genetic resources for further functional dissection of the molecular mechanisms of these interactions. SignificanceThese results have important scientific significance to take effective measures to overcome pre-fertilization barriers and to guide the cross breeding of jasmine. Further, they can also be used for reference in other plant breeding with the same fertilization barriers.

Characteristics and diversity of mutations in regulatory genes of resistance-nodulation-cell division efflux pumps in association with drug-resistant clinical isolates of Acinetobacter baumannii

BackgroundThis study was aimed to characterize the genetic diversity and expression of three putative resistance-nodulation-cell division (RND)-type efflux systems and their contribution to multidrug efflux in clinical isolates of Acinetobacter baumannii.MethodsAntimicrobial susceptibility testing of 95 A. baumannii isolates was determined by Kirby-Bauer disk diffusion for 18 antibiotics and minimum inhibitory concentration (MIC) of colistin was determined by the broth microdilution method. Moreover, the MIC of five classes of antibiotics was assessed using E-test strips in the presence and absence of phenylalanine-arginine beta-naphthylamide (PAβN). Regulatory genes of the RND efflux pumps (adeRS, adeL, adeN and baeSR) were subjected to sequencing. The relative expression of adeB, adeG and adeJ genes was determined by quantitative real-time PCR (qRT-PCR).ResultsOverall, the majority of isolates (94%) were extensively drug-resistant (XDR). In the phenotypic assay, efflux pump activity was observed in 40% of the isolates against multiple antibiotics mainly tigecycline. However, we found no efflux activity against imipenem. Several amino acid substitutions were detected in the products of regulatory genes; except in AdeN. Of note, G186V mutation in AdeS was found to be associated with overexpression of its efflux pump. No insertion sequences were detected.ConclusionsOur findings outlined the role of RND efflux pumps in resistance of A. baumannii to multiple antibiotics particularly tigecycline, and pointed out the importance of a variety of single mutations in the corresponding regulatory systems. Further studies are required to decipher the precise role of RND efflux pumps in multidrug-resistant clinical isolates of A. baumannii.

Molecular Mechanisms of the Floral Biology of Jatropha curcas: Opportunities and Challenges as an Energy Crop.

Fossil fuel sources are a limited resource and could eventually be depleted. Biofuels have emerged as a renewable alternative to fossil fuels. Jatropha has grown in significance as a potential bioenergy crop due to its high content of seed oil. However, Jatropha’s lack of high-yielding seed genotypes limits its potential use for biofuel production. The main cause of lower seed yield is the low female to male flower ratio (1:25–10), which affects the total amount of seeds produced per plant. Here, we review the genetic factors responsible for floral transitions, floral organ development, and regulated gene products in Jatropha. We also summarize potential gene targets to increase seed production and discuss challenges ahead.

The neonatal microenvironment programs innate γδ T cells through the transcription factor STAT5.

IL-17-producing RORγt+ γδ T cells (γδT17 cells) are innate lymphocytes that participate in type 3 immune responses during infection and inflammation. Herein, we show that γδT17 cells rapidly proliferate within neonatal lymph nodes and gut, where, upon entry, they upregulate T-bet and coexpress IL-17, IL-22, and IFN-γ in a STAT3- and retinoic acid-dependent manner. Neonatal expansion was halted in mice conditionally deficient in STAT5, and its loss resulted in γδT17 cell depletion from all adult organs. Hyperactive STAT5 mutant mice showed that the STAT5A homolog had a dominant role over STAT5B in promoting γδT17 cell expansion and downregulating gut-associated T-bet. In contrast, STAT5B preferentially expanded IFN-γ-producing γδ populations, implying a previously unknown differential role of STAT5 gene products in lymphocyte lineage regulation. Importantly, mice lacking γδT17 cells as a result of STAT5 deficiency displayed a profound resistance to experimental autoimmune encephalomyelitis. Our data identify that the neonatal microenvironment in combination with STAT5 is critical for post-thymic γδT17 development and tissue-specific imprinting, which is essential for infection and autoimmunity.

A267 ROLE OF INTESTINAL EPITHELIAL NUCLEAR RECEPTOR HNF4A DURING METABOLIC DISORDERS

Abstract Background HNF4α belongs to the hormone nuclear receptor family and is expressed in liver, intestinal epithelium and pancreas where it regulates genes involved in the control of metabolism. Inactivating mutations in the HNF4A gene cause several forms of maturity-onset diabetes of the young (MODY). However, the specific deletion of Hnf4a in mouse pancreatic beta cells does not lead to diabetes, suggesting the contribution of other tissues, such as the intestine, are necessary for the progression of the disease. Aims Our main hypothesis was that intestinal epithelial HNF4α regulates gene products that act through a paracrine mode of communication in the context of glucose metabolism. The aims of this study were to investigate the impact of deleting Hnf4a in the mouse intestinal epithelium during glucose homeostasis and to identify molecular mechanisms involved during glucose-induced obesity resistance. Methods The Villin-Cre recombinase transgenic mouse model was used to conditionally delete Hnf4a in the intestinal epithelium (Hnf4adeltaIEC). Hnf4adeltaIEC mice were put on a high sugar diet for 8 to 12 weeks, using a 30% sucrose supplemented ab lithium water. Blood glucose values in controls and mutants were measured from whole venous blood from fasted mice or during glucose and insulin tolerance tests. Mouse serum hormone levels (Ghrelin, Fibroblast-growth factor-15 (Fgf15), Insulin, Cholecystokinin (CCK), etc.) were measured using mouse ELISA kits. The Promethion High-Definition Room Calorimetry System was used for indirect calorimetry and metabolic studies. Results Both male and female Hnf4adeltaIEC mice displayed a metabolic resistance to develop obesity under sucrose supplementation when compared to control mice. While male mutant mice showed a resistance to obesity after only 2 weeks of treatment, female mutant mice took at least 6 weeks to display some resistance. The gut hormones ghrelin and Fgf15 were also found modified in fasted mutant mice. Female mutant mice presented a significant increase of 1.8 fold in circulating Fgf15 and an increase of 1.4 fold in circulating ghrelin. Similar changes were observed in male mutant mice. However, only male mutant mice presented an insulin resistance and an oral glucose tolerance after between 6 and 8 weeks. Brown adipose tissue (BAT) whitening was observed after 8 weeks of sucrose treatment in control obese animals, a condition that was prevented in Hnf4adeltaIEC mice. Conclusions The identification of paracrine intestinal targets for HNF4α in association with glucose metabolism will provide a better understanding of the molecular nature of tissues crosstalk in energy balance and in metabolism disorders including diabetes and obesity. Funding Agencies CIHR

Protein Expression Profiling Identifies Key Proteins and Pathways Involved in Growth Inhibitory Effects Exerted by Guggulsterone in Human Colorectal Cancer Cells.

Colorectal cancer (CRC) is a leading killer cancer worldwide and one of the most common malignancies with increasing incidences of mortality. Guggulsterone (GS) is a plant sterol used for treatment of various ailments such as obesity, hyperlipidemia, diabetes, and arthritis. In the current study, anti-cancer effects of GS in human colorectal cancer cell line HCT 116 was tested, potential targets identified using mass spectrometry-based label-free shotgun proteomics approach and key pathways validated by proteome profiler antibody arrays. Comprehensive proteomic profiling identified 14 proteins as significantly dysregulated. Proteins involved in cell proliferation/migration, tumorigenesis, cell growth, metabolism, and DNA replication were downregulated while the protein with functional role in exocytosis/tumor suppression was found to be upregulated. Our study evidenced that GS treatment altered expression of Bcl-2 mediated the mitochondrial release of cytochrome c which triggered the formation of apoptosome as well as activation of caspase-3/7 leading to death of HCT 116 cells via intrinsic apoptosis pathway. GS treatment also induced expression of p53 protein while p21 expression was unaltered with no cell cycle arrest. In addition, GS was found to inhibit NF-kB signaling in colon cancer cells by quelling the expression of its regulated gene products Bcl-2, cIAP-1, and survivin.

28 The functional annotation of the sheep genome project

Abstract Reference genomes for some agricultural animals have been available for almost a decade; however, the annotation of these genomes remain an ongoing process. As a result, a detailed understanding of gene and gene product regulation that impart biological traits and physiological systems remains elusive. Through the Functional Annotation of ANimal Genomes (FAANG) consortium, coordinated efforts of the international scientific community are addressing this deficiency. The overarching goal of the Ovine FAANG project is to generate comprehensive transcriptome and chromatin state data sets from a large variety of adult tissues to accurately map functional elements of the ovine genome. In total, 100 tissues were collected (snap & slow frozen) from Benz 2616, the new reference genome, Oar_rambouillet_v1.0. Three methods of RNA sequencing have been utilized to fully understand tissue specific gene expression profiles. Transcript sequencing using poly-A+ messenger RNA has been completed for 60 tissues, whereas small microRNA as well as long read Iso-Sequencing data have been generated in a subset of these tissues. To further complement the gene expression data and to identify active promoters and confirm transcription start sites, Cap Analysis of Gene Expression (CAGE) has been completed. Histone modifications are being examined through Chromatin Immuno-precipitation (ChIP) sequencing to define different regulatory features. We are capitalizing on the knowledge that H3K4me3 and H3K27ac are enriched at transcription start sites and H3K4me1 at enhancer sites of actively transcribed genes, whereas H3K27me3 represses gene transcription. To determine chromatin accessibility, ATAC-seq is being performed for the 60 highest priority tissues. DNA methylation assays, specifically whole genome bisulfite and reduced representation bisulfite sequencing, are being performed on these tissues. This project will provide the first detailed understanding of tissue-specific gene regulatory signals and gene products, imparting a greater understanding of the mechanisms for genome to functional phenotype variation within sheep.

Combined genetic disruption of K-Cl cotransporters and Gardos channel KCNN4 rescues erythrocyte dehydration in the SAD mouse model of sickle cell disease

Excessive red cell dehydration contributes to the pathophysiology of sickle cell disease (SCD). The densest fraction of sickle red cells (with the highest corpuscular hemoglobin concentration) undergoes the most rapid polymerization of deoxy-hemoglobin S, leading to accelerated cell sickling and increased susceptibility to endothelial activation, red cell adhesion, and vaso-occlusion. Increasing red cell volume in order to decrease red cell density can thus serve as an adjunct therapeutic goal in SCD. Regulation of circulating mouse red cell volume and density is mediated largely by the Gardos channel, KCNN4, and the K-Cl cotransporters, KCC3 and KCC1. Whereas inhibition of the Gardos channel in subjects with sickle cell disease increased red cell volume, decreased red cell density, and improved other hematological indices in subjects with SCD, specific KCC inhibitors have not been available for testing. We therefore investigated the effect of genetic inactivation of KCC3 and KCC1 in the SAD mouse model of sickle red cell dehydration, finding decreased red cell density and improved hematological indices. We describe here generation of mice genetically deficient in the three major red cell volume regulatory gene products, KCNN4, KCC3, and KCC1 in C57BL6 non-sickle and SAD sickle backgrounds. We show that combined loss-of-function of all three gene products in SAD mice leads to incrementally increased MCV, decreased CHCM and % hyperchromic cells, decreased red cell density (phthalate method), increased resistance to hypo-osmotic lysis, and increased cell K content. The data show that combined genetic deletion of the Gardos channel and K-Cl cotransporters in a mouse SCD model decreases red cell density and improves several hematological parameters, supporting the strategy of combined pharmacological inhibition of these ion transport pathways in the adjunct treatment of human SCD.

Retraction: Modification of Cysteine Residue in p65 Subunit of Nuclear Factor-κB (NF-κB) by Picroliv Suppresses NF-κB–Regulated Gene Products and Potentiates Apoptosis

Retraction: Modification of Cysteine Residue in p65 Subunit of Nuclear Factor-κB (NF-κB) by Picroliv Suppresses NF-κB–Regulated Gene Products and Potentiates Apoptosis

STEAP1 Regulates Tumorigenesis and Chemoresistance During Peritoneal Metastasis of Gastric Cancer.

In China, majority of the mortality in gastric cancer are associated with peritoneal metastasis. Since most gastric tumors are metastatic at initial diagnosis, the treatment of gastric cancer is limited to radical resection. Therefore, it is imperative to identify diagnostic and prognostic biomarkers. From 2014 to 2015, 20 patients were enrolled in the study. To search translationally upregulated genes in the context of epithelial to mesenchymal transition (EMT), polysome profiling was performed. The MTT, migration, and invasion assay were conducted to determine cell proliferation, migration, and invasion ability respectively. Experiments of gain and loss of function were performed using the overexpression plasmid, siRNA, and shRNA. Xenograft assay was established using nude mice to explore the role of targets translationally upregulated gene in vivo. Polysome profiling defined the landscape of translationally regulated gene products with differential expression between non-metastatic and metastatic cohorts. Six-transmembrane epithelial antigen of the prostate 1 (STEAP1) was found to be the most translationally upregulated gene product in either experimental groups. STEAP1 was found to be required for cell proliferation, in vitro migration and invasion, and in vivo tumorigenesis. RNAi-mediated silencing of STEAP1 potentiated chemosensitivity of the MKN45 cells to docetaxel treatment, highlighting the importance of STEAP1 as a novel biomarker in gastric cancer patients with peritoneal metastasis. STEAP1 is thus induced translationally and its expression promotes proliferation, migration, invasiveness, and tumorigenicity of gastric cancer. STEAP1 can be a potent candidate for designing of targeted therapy.

Relative sensitivity analysis of the predictive properties of sloppy models.

Commonly among the model parameters characterizing complex biological systems are those that do not significantly influence the quality of the fit to experimental data, so-called "sloppy" parameters. The sloppiness can be mathematically expressed through saturating response functions (Hill's, sigmoid) thereby embodying biological mechanisms responsible for the system robustness to external perturbations. However, if a sloppy model is used for the prediction of the system behavior at the altered input (e.g. knock out mutations, natural expression variability), it may demonstrate the poor predictive power due to the ambiguity in the parameter estimates. We introduce a method of the predictive power evaluation under the parameter estimation uncertainty, Relative Sensitivity Analysis. The prediction problem is addressed in the context of gene circuit models describing the dynamics of segmentation gene expression in Drosophila embryo. Gene regulation in these models is introduced by a saturating sigmoid function of the concentrations of the regulatory gene products. We show how our approach can be applied to characterize the essential difference between the sensitivity properties of robust and non-robust solutions and select among the existing solutions those providing the correct system behavior at any reasonable input. In general, the method allows to uncover the sources of incorrect predictions and proposes the way to overcome the estimation uncertainties.

Pinus Roxburghii essential oil anticancer activity and chemical composition evaluation.

The present study was conducted to appraise the anticancer activity of Pinus roxburghii essential oil along with chemical composition evaluation. MTT assay revealed cytotoxicity induction in colon, leukemia, multiple myeloma, pancreatic, head and neck and lung cancer cells exposed to essential oil. Cancer cell death was also observed through live/dead cell viability assay and FACS analysis. Apoptosis induced by essential oil was confirmed by cleavage of PARP and caspase-3 that suppressed the colony-forming ability of tumor cells and 50 % inhibition occurred at a dose of 25 μg/mL. Moreover, essential oil inhibited the activation of inflammatory transcription factor NF-κB and inhibited expression of NF-κB regulated gene products linked to cell survival (survivin, c-FLIP, Bcl-2, Bcl-xL, c-Myc, c-IAP2), proliferation (Cyclin D1) and metastasis (MMP-9). P. roxburghii essential oil has considerable anticancer activity and could be used as anticancer agent, which needs further investigation to identify and purify the bioactive compounds followed by in vivo studies.

For Want of a Template

For Want of a Template

Correction: Apoptosis by [Pt(O,O′-acac)(γ-acac)(DMS)] requires PKC-δ mediated p53 activation in malignant pleural mesothelioma

[This corrects the article DOI: 10.1371/journal.pone.0181114.].

Bifidobacteria and its rice fermented products on diet induced obese mice: analysis of physical status, serum profile and gene expressions.

Obesity is highly correlated with the dysbiosis of intestinal microbiota, and bifidobacteria are one of the soft targets of this metabolic syndrome. The aim of this study is to evaluate the efficacy of Bifidobacterium sp. MKK4 and rice-based fermented foods on physical, haematological, gut microbiota and lypogenic-lypolytic marker genes in diet-induced obese mice. Adult male mice (21±0.7 g) were randomly divided into four groups (n=10) according to the type of diet: normal diet (ND), high fat diet (HFD), HFD supplemented with Bifidobacterium sp. MKK4 and HFD supplemented with MKK4 associated rice-fermented food. 8 weeks of bacterial therapy in the obese mice resulted in significant reduction of body and organ weights, improved serum levels of glucose, triglyceride and cholesterol, the histological structure of the liver (steatosis), and re-establishment of gut Lactobacillus, Bifidobacterium and Bacteroides species. The bacterial therapy led to up-regulation of lipolytic transcription factors, such as peroxisome proliferator-activated receptor (PPAR)-α, PPAR-δ, and their regulated gene products in fatty acid metabolism and glucose uptake, such as acyl-CoA oxidase, carnitine palmitoyl-transferase-1, uncoupling protein-3 and glucose transporter-4. Concomitantly, both adipocytogenesis and fatty acid synthesis were arrested as reflected by the down-regulation of sterol regulatory element binding protein-1c, acetyl-CoA carboxylase, fatty acid synthase and tumour necrosis factor alpha genes. The effectiveness of the fermented product was more profound than the single bacterium. These data provide experimental support with regard to the use of Bifidobacterium sp. MKK4 as a natural therapeutic agent to control obesity.

Linking Autophagy and the Dysregulated NFκB/ SNAIL/YY1/RKIP/PTEN Loop in Cancer: Therapeutic Implications.

The role of autophagy in the pathogenesis of various cancers has been well documented in many reports. Autophagy in cancer cells regulates cell proliferation, viability, invasion, epithelial-to-mesenchymal transition (EMT), metastasis, and responses to chemotherapeutic and immunotherapeutic treatment strategies. These manifestations are the result of various regulatory gene products that govern autophagic, biochemical, and molecular mechanisms. In several human cancer cell models, the presence of a dysregulated circuit-namely, NFκB/SNAIL/YY1/RKIP/PTEN-that plays a major role in the regulation of tumor cell unique characteristics just listed for autophagy-regulated activities. Accordingly, the autophagic mechanism and the dysregulated circuit in cancer cells share many of the same properties and activities. Thus, it has been hypothesized that there must exist a biochemical/molecular link between the two. The present review describes the link and the association of each gene product of the dysregulated circuit with the autophagic mechanism and delineates the presence of crosstalk. Crosstalk between autophagy and the dysregulated circuit is significant and has important implications in the development of targeted therapies aimed at either autophagy or the dysregulated gene products in cancer cells.