Specific Gene Expression Responses Research Articles

Evaluation of cold growth and related gene transcription responses associated with Listeria monocytogenes strains of different origins

The cold growth phenotypes and transcriptional activation of cold stress adaptation genes was evaluated amongst Listeria monocytogenes strains from human listeriosis cases, food products and associated production environments. Significant cold growth phenotypic variation was observed during growth of such strains in rich (BHI) as well as chemically defined minimal (MDM) nutrient conditions. While all twenty analyzed strains grew in BHI at 4 °C, only eight of these strains, mostly those recovered from human listeriosis cases, were also able to grow in MDM under similar cold stress. The cold growth phenotypes observed in BHI were used to define two categories of five strains each, which either displayed enhanced and poor cold tolerance relative to the rest of the strain collection. The first group (GP1) consisted of strains characterized by short lag times, whilst the second group (GP2) comprised of strains displaying prolonged lag times before growth resumption during incubation in BHI cultures at 4 °C. Transcription level activation of sigB, cspA and pgpH gene expression associated with cold stress exposure in a selection of GP1 and GP2 strains was assessed. Despite similar cold dependent sigB transcript induction between these two strain groups, there were significant differences observed in cold stress dependent induction of cspA and pgpH transcripts. Cold tolerant GP1 strains displayed relatively higher transcriptional activation of cspA and pgpH after cold stress exposure compared to the cold sensitive GP2 strains. This study highlights strain variability in cold stress tolerance phenotypes, as well as in strain capacity to activate specific cold adaptation gene expression responses. In addition the study also shows that enhanced and poor cold growth phenotypes are associated with particular strain capacity to activate important cold stress gene expression responses upon transition of L. monocytogenes into low temperature environments.

Transcriptional differences between triploid and diploid Chinook salmon (Oncorhynchus tshawytscha) during live Vibrio anguillarum challenge

Understanding how organisms function at the level of gene expression is becoming increasingly important for both ecological and evolutionary studies. It is evident that the diversity and complexity of organisms are not dependent solely on their number of genes, but also the variability in gene expression and gene interactions. Furthermore, slight differences in transcription control can fundamentally affect the fitness of the organism in a variable environment or during development. In this study, triploid and diploid Chinook salmon (Oncorhynchus tshawytscha) were used to examine the effects of polyploidy on specific and genome-wide gene expression response using quantitative real-time PCR (qRT-PCR) and microarray technology after an immune challenge with the pathogen Vibrio anguillarum. Although triploid and diploid fish had significant differences in mortality, qRT-PCR revealed no differences in cytokine gene expression response (interleukin-8, interleukin-1, interleukin-8 receptor and tumor necrosis factor), whereas differences were observed in constitutively expressed genes, (immunoglobulin (Ig) M, major histocompatibility complex (MHC) -II and beta-actin) upon live Vibrio anguillarum exposure. Genome-wide microarray analysis revealed that, overall, triploid gene expression is similar to diploids, consistent with their similar phenotypes. This pattern, however, can subtly be altered under stress (for example, handling, V. anguillarum challenge) as we have observed at some housekeeping genes. Our results are the first report of dosage effect on gene transcription in a vertebrate, and they support the observation that diploid and triploid salmon are generally phenotypically indistinguishable, except under stress, when triploids show reduced performance.

Identification of regulatory elements in 16S rRNA gene of Acinetobacter species isolated from water sample

A bacterial strain, designated AcBz01, was isolated from a water sample collected from Gomti River, Lucknow, India, and identified using a molecular approach. On the basis of the bacterial 16S rRNA gene sequence phylogeny and comparison of this gene sequence with sequences in Ribosomal Database project II, evidence given in this study, it is proposed that isolate is closely related to members of the genus Acinetobacter. Identification and annotation of regulatory elements in the 16S rRNA gene and characterization of their interaction with the respective transcription factor can provide basis for better understanding of the mechanism of network of gene interaction of functionally related genes. The identification of such sites is relevant for locating promoter boundary of a gene and it also allows the prediction of specific gene expression pattern and response to disturbances in a known signaling pathway. Computational identification of regulatory elements and Transcription Factor with their binding sites in 16S rRNA gene of Acinetobacter sp. was performed using BPROM tool. We predicted the regulatory elements are TSS, -10 box, -35 box and three Transcription Factor (narP, ompR and fadR) with their binding sites in the upstream region of 16S rRNA gene of Acinetobacter sp. AcBz01. The GenBank accession number for 16S rRNA gene of Acinetobacter sp. AcBz01 is EU931637.

Computational identification of composite regulatory sites in 16s-rRNA gene promoters of Mycobacterium species.

The availability of completely sequenced genomes allow the use of computational techniques to investigate cis-acting sequences controlling transcription regulation associated with groups of functionally related genes. Theoretical analysis was performed to assign functions to regulatory systems. The identification of such sites is relevant for locating a promoter at the 5' boundary of a gene. They also allow the prediction of specific gene-expression pattern and response to disturbances in a known signaling pathway. Here, we describe the identification of composite transcription factor (TF) binding sites over promoter regions in16s-rRNA gene for mycobacterium species strains ICC47, ICC67, ICC43 and CMVL700. It is established that the ribosomal gene comprises of sequences that are conserved during evolution and interspersed with divergent regions. Computational identification of known TF-binding sites was performed using TFSITESCAN tool and ooTFD database. The ICC67, ICC47, ICC43 and CMYL700 strains showed 12, 13, 9 and 15 known TF binding sites, respectively. Comparison between strains suggests 9 known TF predicted binding sites to be conserved among them. These data provide basis for the understanding of promoter regulation in 16s-rRNA.

Transcriptomics and adaptive genomics of the asymptomatic bacteriuria Escherichia coli strain 83972

Escherichia coli strains are the major cause of urinary tract infections in humans. Such strains can be divided into virulent, UPEC strains causing symptomatic infections, and asymptomatic, commensal-like strains causing asymptomatic bacteriuria, ABU. The best-characterized ABU strain is strain 83972. Global gene expression profiling of strain 83972 has been carried out under seven different sets of environmental conditions ranging from laboratory minimal medium to human bladders. The data reveal highly specific gene expression responses to different conditions. A number of potential fitness factors for the human urinary tract could be identified. Also, presence/absence data of the gene expression was used as an adaptive genomics tool to model the gene pool of 83972 using primarily UPEC strain CFT073 as a scaffold. In our analysis, 96% of the transcripts filtered present in strain 83972 can be found in CFT073, and genes on six of the seven pathogenicity islands were expressed in 83972. Despite the very different patient symptom profiles, the two strains seem to be very similar. Genes expressed in CFT073 but not in 83972 were identified and can be considered as virulence factor candidates. Strain 83972 is a deconstructed pathogen rather than a commensal strain that has acquired fitness properties.

Gene Expression Profiling of Mouse Bladder Inflammatory Responses to LPS, Substance P, and Antigen-Stimulation

Inflammatory bladder disorders such as interstitial cystitis (IC) deserve attention since a major problem of the disease is diagnosis. IC affects millions of women and is characterized by severe pain, increased frequency of micturition, and chronic inflammation. Characterizing the molecular fingerprint (gene profile) of IC will help elucidate the mechanisms involved and suggest further approaches for therapeutic intervention. Therefore, in the present study we used established animal models of cystitis to determine the time course of bladder inflammatory responses to antigen, Escherichia coli lipopolysaccharide (LPS), and substance P (SP) by morphological analysis and cDNA microarrays. The specific aim of the present study was to compare bladder inflammatory responses to antigen, LPS, and SP by morphological analysis and cDNA microarray profiling to determine whether bladder responses to inflammation elicit a specific universal gene expression response regardless of the stimulating agent. During acute bladder inflammation, there was a predominant infiltrate of polymorphonuclear neutrophils into the bladder. Time-course studies identified early, intermediate, and late genes that were commonly up-regulated by all three stimuli. These genes included: phosphodiesterase 1C, cAMP-dependent protein kinase, iNOS, beta-NGF, proenkephalin B and orphanin, corticotrophin-releasing factor (CRF) R, estrogen R, PAI2, and protease inhibitor 17, NFkB p105, c-fos, fos-B, basic transcription factors, and cytoskeleton and motility proteins. Another cluster indicated genes that were commonly down-regulated by all three stimuli and included HSF2, NF-kappa B p65, ICE, IGF-II and FGF-7, MMP2, MMP14, and presenilin 2. Furthermore, we determined gene profiles that identify the transition between acute and chronic inflammation. During chronic inflammation, the urinary bladder presented a predominance of monocyte/macrophage infiltrate and a concomitant increase in the expression of the following genes: 5-HT 1c, 5-HTR7, beta 2 adrenergic receptor, c-Fgr, collagen 10 alpha 1, mast cell factor, melanocyte-specific gene 2, neural cell adhesion molecule 2, potassium inwardly-rectifying channel, prostaglandin F receptor, and RXR-beta cis-11-retinoic acid receptor. We conclude that microarray analysis of genes expressed in the bladder during experimental inflammation may be predictive of outcome. Further characterization of the inflammation-induced gene expression profiles obtained here may identify novel biomarkers and shed light into the etiology of cystitis.

Expression of a vegetative-storage-protein gene from Arabidopsis is regulated by copper, senescence and ozone.

Emerging data suggest that the mechanisms regulating plant copper homeostasis could be implicated in stress and senescence signal transduction pathways. To gain insight into copper-modulated patterns of gene expression, copper-treated Arabidopsis thaliana (L.) Heynh. plants were analysed by mRNA differential display. The experimental conditions were selected using aggregation of ribulose-1,5-bisphosphate carboxylase-oxygenase (Rubisco) as a molecular sensor to monitor copper-induced oxidative stress. Two copper-induced messengers encoding a vegetative storage protein (VSP2) were isolated by this technique. Both clones differed in the length of their 3'-untranslated region according to the presence of two polyadenylation signals in this region. VSP2 expression was further studied under natural senescence and various conditions causing oxidative stress, such as ozone exposure, paraquat and H2O2 treatments. The expression of other messengers related to copper homeostasis and detoxification processes was followed in parallel to that of VSP2. Here, we describe specific gene-expression responses to copper treatment, and present arguments connecting copper homeostasis, senescence and antioxidative responses in plants. Our results are consistent with the role of VSPs as temporary nitrogen-storage proteins which accumulate if nutrients are abundant, either in developing organs or in cotyledons and mature leaves subjected to generalized protein mobilization, such as those conditions created under severe oxidative stress.

In the cellular garden of forking paths: how p38 MAPKs signal for downstream assistance.

Mitogen-activated protein kinases (MAPKs) are evolutionarily conserved enzymes which connect cell-surface receptors to regulatory targets within cells and convert receptor signals into various outputs. In mammalian cells, four distinct MAPKs have been identified: the extracellular signal-related kinases (ERK)-1/2, the c-jun N-terminal kinases or stress-activated protein kinases 1 (JNK1/2/3, or SAPK1s), the p38 MAPKs (p38 alpha/beta/gamma/delta, or SAPK2s), and the ERK5 or big MAP kinase 1 (BMK1). The p38 MAPK cascade is activated by stress or cytokines and leads to phosphorylation of its central elements, the p38 MAPKs. Downstream of p38 MAPKs there is a diversification and extensive branching of signalling pathways. For that reason, we will focus in this review on the different signalling events that are triggered by p38 activity, and analyse how these events contribute to specific gene expression and cellular responses.

Emerging targets: Molecular mechanisms of cell contact-mediated growth control

Contact inhibition of cell proliferation evokes a unique cellular program of growth arrest compared with stress, age, or other physical constraints. The last decade of research on genes activated by cell-cell contact has uncovered features of transmembrane signaling, cytoskeletal reorganization, and transcriptional control that initiate and maintain a quiescent phenotype. This review will focus on mechanisms controlling contact inhibition of cell proliferation, highlighting specific gene expression responses that are activated by cell-cell contact. Although a temporal framework for imposition of these mechanisms has not yet been well described, contact inhibition of cell proliferation clearly requires their coordinated function. Novel targets for intervention in proliferative disorders are emerging from these studies.