The exogenous gene expression and its impacts on the bacterial population are important to study quorum sensing systems and synthetic biology industry. However, the behavior of exogenous protein expressing bacteria remains poorly understood. To find out which factors are playing a critical role in the growth of population and exogenous gene expression, we measured Lux-type receptor-regulated exogenous gene expression under the induction of N-acyl homoserine lactone (N-AHL) signaling molecules and impacts on the bacterial population dynamics after such stimulation. To analyze the cause of fitness burden of bacteria, we set up a hypothetical mathematical model. Previous studies often arrogate this phenomenon to the synthesis cost and the toxicity of N-AHL signaling molecule. However, we suggested another possible cause of the fitness burden.
Bacteria ; Gene Expression ; Gene Expression Regulation, Bacterial ; Quorum Sensing

In order to understand the role of the upstream region of the Mycobacterium leprae 18-kDa gene on the gene regulation, the region was divided into two at the -50 position from the first start codon of the gene and their effect on transcription was examined by using a LacZ transcriptional reporter gene assay. The presence of each of these two regions conferred transcription repression not only on its cognate M. lepraerae 18-kDa gene promoter, but also on a heterologous promoter such as the Mycobacterium bovis BCG hsp65 gene promoter. Moreover, it was found that these regions could confer transcription repression activity in both cases in an orientation-independent manner. Thus, these results indicate that the upstream region of the M. leprae 18-kDa gene harbors transcription repression responsive element(s) acting as an operator and can be further divided into two separately functional regions, suggesting a bipartite structure of the element(s). The identification of transcription repression activity of the upstream region in the M. leprae 18-kDa gene will contribute greatly for the understanding of the 18-kDa gene regulation mechanism, and provide also useful information for the manipulation of mycobacterium gene expression.
Bacterial Proteins/*genetics ; Down-Regulation/*genetics ; *Gene Expression Regulation, Bacterial ; Mycobacterium leprae/*genetics ; Response Elements/*genetics ; Transcription, Genetic

OBJECTIVETo screen and verify differentially expressed genes in prostate cancer.

METHODSUsing DNA microarray, we screened differentially expressed genes in prostate cancer tissue and its adjacent tissue followed by verification by PCR.

RESULTSA total of 1 444 genes were found to be differentially expressed (differentiation ≥ 1.5-fold; P≤ 0.05) in the prostate cancer tissue, of which 769 (53%) were up-regulated and 675 (47%) down-regulated. Fifty percent of the differentially expressed genes showed a 1.5- to 2-fold differentiation, including 396 up-regulated and 182 down-regulated ones. Additionally, 308 up-regulated and 334 down-regulated genes exhibited a >2- to 5-fold, 46 up-regulated and 78 down-regulated genes a > 5- to 10-fold, and 19 up-regulated and 81 down-regulated genes a > 10-fold differentiation. Verification by subjecting 15 most significantly up-regulated and another 15 most markedly down-regulated genes to quantitative real-time PCR (qRT-PCR) showed that most of the genes had a transcriptional profile similar to that in the microarray data, with a Pearson correction coefficient of 0.83 between the microarray data and qRT-PCR results. Totally, 10 significantly differentially expressed genes were identified.

CONCLUSIONDNA microarray analysis provides reliable information on differentially expressed genes in prostate cancer and benign tissues. The 10 significantly differentially expressed genes verified by qRT-PCR could possibly become new bio-markers and specific molecules for tumor identification.

Cell Differentiation ; Down-Regulation ; Gene Expression ; Gene Expression Regulation, Neoplastic ; Humans ; Male ; Oligonucleotide Array Sequence Analysis ; Polymerase Chain Reaction ; Prostatic Neoplasms ; genetics ; Transcriptional Activation ; Up-Regulation

Long non-coding RNAs (lncRNAs) reportedly function as important modulators of gene regulation and malignant processes in the development of human cancers. The lncRNA JPX is a novel molecular switch for X chromosome inactivation and differentially expressed JPX has exhibited certain clinical correlations in several cancers. Notably, JPX participates in cancer growth, metastasis, and chemoresistance, by acting as a competing endogenous RNA for microRNA, interacting with proteins, and regulating some specific signaling pathways. Moreover, JPX may serve as a potential biomarker and therapeutic target for the diagnosis, prognosis, and treatment of cancer. The present article summarizes our current understanding of the structure, expression, and function of JPX in malignant cancer processes and discusses its molecular mechanisms and potential applications in cancer biology and medicine.
Humans ; RNA, Long Noncoding/genetics* ; Neoplasms/genetics* ; MicroRNAs/genetics* ; Gene Expression Regulation ; X Chromosome Inactivation

Charged multivesicular body protein 5 (CHMP5) has a key role in multivesicular body biogenesis and a critical role in the downregulation of signaling pathways through receptor degradation. However, the role of CHMP5 in T-cell receptor (TCR)-mediated signaling has not been previously investigated. In this study, we utilized a short hairpin RNA-based RNA interference approach to investigate the functional role of CHMP5. Upon TCR stimulation, CHMP5-knockdown (CHMP5(KD)) Jurkat T cells exhibited activation of TCR downstream signaling molecules, such as PKCθ and IKKαβ, and resulted in the activation of nuclear factor-κB and the marked upregulation of TCR-induced gene expression. Moreover, we found that activator protein-1 and nuclear factor of activated T-cells transcriptional factors were markedly activated in CHMP5(KD) Jurkat cells in response to TCR stimulation, which led to a significant increase in interleukin-2 secretion. Biochemical studies revealed that CHMP5 endogenously forms high-molecular-weight complexes, including TCR molecules, and specifically interacts with TCRβ. Interestingly, flow cytometry analysis also revealed that CHMP5(KD) Jurkat T cells exhibit upregulation of TCR expression on the cell surface compared with control Jurkat T cells. Taken together, these findings demonstrated that CHMP5 might be involved in the homeostatic regulation of TCR on the cell surface, presumably through TCR recycling or degradation. Thus CHMP5 is implicated in TCR-mediated signaling.
Down-Regulation ; Flow Cytometry ; Gene Expression ; Humans ; Interleukin-2 ; Jurkat Cells ; Multivesicular Bodies ; Receptors, Antigen, T-Cell* ; Recycling ; RNA Interference ; T-Lymphocytes* ; Transcription Factor AP-1 ; Up-Regulation

OBJECTIVEThis research aimed to detect the expression levels of ffh gene in Streptococcus mutans (S. mutans) UA159 under different pH conditions, analyze the effect of pH on the expression of ffh gene in S. mutans, and identify the factors regulating the ffh gene expression.

METHODSSamples of S. mutans were collected at different growth stages (4 h, 18 h) and pH values (pH 4.0-7.0). Fluorescence quantitative real-time polymerase chain reaction (qRT-PCR) was used to measure the relative mRNA expression and trend of the target gene ffh in S. mutans at different growth stages and pH values.

RESULTSqRT-PCR results showed that the ffh gene expression decreased along with pH at 4 h, but the expression increased with decreasing pH at 18 h. Under the same pH conditions, the ffh gene expression was significantly different between 4 h and 18 h (P < 0.05).

CONCLUSIONGrowth stage and pH value influenced the ffh gene expression in S. mutans.

Bacterial Proteins ; Gene Expression ; Gene Expression Regulation, Bacterial ; Hydrogen-Ion Concentration ; Streptococcus mutans

Protein phosphorylation on tyrosine has emerged as a key device in the control of numerous cellular functions in bacteria. In this article, we review the structure and function of bacterial tyrosine kinases and phosphatases. Phosphorylation is catalyzed by autophosphorylating adenosine triphosphate-dependent enzymes (bacterial tyrosine (BY) kinases) that are characterized by the presence of Walker motifs. The reverse reaction is catalyzed by three classes of enzymes: the eukaryotic-like phosphatases (PTPs) and dual-specific phosphatases; the low molecular weight protein-tyrosine phosphatases (LMW-PTPs); and the polymerase-histidinol phosphatases (PHP). Many BY kinases and tyrosine phosphatases can utilize host cell proteins as substrates, thereby contributing to bacterial pathogenicity. Bacterial tyrosine phosphorylation/dephosphorylation is also involved in biofilm formation and community development. The Porphyromonas gingivalis tyrosine phosphatase Ltp1 is involved in a restraint pathway that regulates heterotypic community development with Streptococcus gordonii. Ltp1 is upregulated by contact with S. gordonii and Ltp1 activity controls adhesin expression and levels of the interspecies signal AI-2.
Bacteria ; enzymology ; Bacterial Proteins ; genetics ; metabolism ; Biofilms ; growth & development ; Gene Expression Regulation, Bacterial ; Host-Pathogen Interactions ; Phosphorylation ; Polysaccharides, Bacterial ; biosynthesis ; Porphyromonas gingivalis ; enzymology ; Protein Processing, Post-Translational ; Protein Structure, Tertiary ; Protein Tyrosine Phosphatases ; chemistry ; genetics ; metabolism ; Protein-Tyrosine Kinases ; chemistry ; genetics ; metabolism ; Quorum Sensing ; Signal Transduction ; Streptococcus gordonii ; enzymology ; Virulence Factors ; metabolism

Gene Expression Regulation, Bacterial ; Genes, Regulator ; Humans ; Streptococcus mutans ; genetics

OBJECTIVETo determine the distribution and the predominant gene carrying model of drug inactive enzyme genes in bacterial isolates, and the mechanism of its induction and inhibition.

METHODSThe β-lactam, aminoglycosides and macrolides inactive enzyme genes were detected by PCR and sequencing in S. aureus, E.coli, K. pneumoniae, A. baumannii and E. cloacae isolates. The expression of inactive enzyme genes were examined by real-time fluorescent quantitative RT-PCR when the bacterial isolates were treated with antibiotics or a histidine kinase blocker closantel.

RESULTSIn 63 isolates of E.coli, 4 kinds of β-lactam, 2 aminoglycosides and 1 macrolides inactive enzyme-encoding genes were detected and the predominant gene-carrying models were [TEM+CTX-M]+aac(3)-II+mphA (25.4 %) and [TEM+CTX-M]+ aac (6')-I b (20.6%). In 24 isolates of S.aureus, 2 kinds of β-lactam and 3 aminoglycosides inactive enzyme-encoding genes were detected and the predominant gene-carrying models were aph (3')(41.7%) or aac (6)-I e-aph (2)-I a (25.0%). In 28 isolates of K.pneumoniae, 4 kinds of β-lactam and 2 aminoglycosides inactive enzyme-encoding genes were detected and the predominant gene-carrying models were [TEM+SHV]+[aac(6')-I b+aac (3)-II](28.6 %) and [TEM+SHV]+[aac(6')-I b+aac (3)-II]+ mphA (17.8 %). The isolates of A.baumannii and E.cloacae also had a predominant model to carry 2 or 3 kinds of inactive enzyme-encoding genes. 1/4 MIC of penicillin, cefotaxime or streptomycin induced the up-regulation of expression of 3 β-lactam or 4 aminoglycosides inactive enzyme-encoding genes (P<0.05), and this effect was inhibited by closantel (P<0.05).

CONCLUSIONThe bacterial isolates frequently carry multiple kinds of inactive enzyme-encoding genes with different predominant gene-carrying models.Low concentration antibiotics can induce the up-regulation of inactive enzyme gene expression, which can be inhibited by histidine kinase blocker.

Anti-Bacterial Agents ; pharmacology ; Bacteria ; enzymology ; genetics ; Drug Resistance, Multiple, Bacterial ; genetics ; Gene Expression Regulation, Bacterial ; Up-Regulation ; drug effects ; beta-Lactamases ; genetics

Promoter, an essential regulatory element, is widely used for metabolic engineering of industrial strains. Corynebacterium glutamicum is an important industrial workhorse to produce various amino acids. However, strong constitutive promoters that are applicable to C. glutamicum are rarely reported. In this study, we first performed a time-series transcriptome analysis of a glutamate hyper-producing strain C. glutamicum SL4 by using RNA-Seq. Overall, we picked 10 samples at different time during the fermentation process. By analyzing the time-series transcriptome data, we selected 10 candidate genes with the highest transcriptional level. These genes were all transcribed stably during the fermentation process. We subsequently cloned the promoter sequences and evaluated the promoters' strength in strain SL4 using a red fluorescent protein reporter system. To evaluate the universality of the promoters in different C. glutamicum strains, we further tested the performance of some promoters in wild type C. glutamicum strains, including ATCC 13869 and ATCC 13032. The strongest promoter was further characterized using LacZ as a reporter in all the three C. glutamicum strains. Finally, we successfully obtained three constitutive promoters with universality, PcysK, PgapA and PfumC. PcysK is the most efficient promoter among the three C. glutamicum strains. In strains SL4 and ATCC 13869, the strength of PcysK is 2-fold of the strong inducible promoter Ptac using the red fluorescent protein as a reporter and 4-fold of Ptac using LacZ as a reporter. Moreover, the strength of PcysK reaches 30%-40% of Ptac in strain ATCC 13032. The promoter PcysK is identified as a strong promoter for the first time, which can be used as an efficient biobrick for metabolic engineering of synthesis pathways in C. glutamicum.
Corynebacterium glutamicum ; genetics ; Gene Expression Profiling ; Gene Expression Regulation, Bacterial ; Metabolic Engineering ; Promoter Regions, Genetic ; Transcriptome