Unique plasmids generated via pUC replicon mutagenesis in an error-prone thermophile derived from Geobacillus kaustophilus HTA426.

The plasmid pGKE75-catA138T, which comprises pUC18 and the catA138T gene encoding thermostable chloramphenicol acetyltransferase with an A138T amino acid replacement (CATA138T), serves as an Escherichia coli-Geobacillus kaustophilus shuttle plasmid that confers moderate chloramphenicol resistance on G. kaustophilus HTA426. The present study examined the thermoadaptation-directed mutagenesis of pGKE75-catA138T in an error-prone thermophile, generating the mutant plasmid pGKE75(αß)-catA138T responsible for substantial chloramphenicol resistance at 65°C. pGKE75(αß)-catA138T contained no mutation in the catA138T gene but had two mutations in the pUC replicon, even though the replicon has no apparent role in G. kaustophilus. Biochemical characterization suggested that the efficient chloramphenicol resistance conferred by pGKE75(αß)-catA138T is attributable to increases in intracellular CATA138T and acetyl-coenzyme A following a decrease in incomplete forms of pGKE75(αß)-catA138T. The decrease in incomplete plasmids may be due to optimization of plasmid replication by RNA species transcribed from the mutant pUC replicon, which were actually produced in G. kaustophilus. It is noteworthy that G. kaustophilus was transformed with pGKE75(αß)-catA138T using chloramphenicol selection at 60°C. In addition, a pUC18 derivative with the two mutations propagated in E. coli at a high copy number independently of the culture temperature and high plasmid stability. Since these properties have not been observed in known plasmids, the outcomes extend the genetic toolboxes for G. kaustophilus and E. coli.

Post-transcriptional regulation by distal Shine-Dalgarno sequences in the grpE-dnaK intergenic region of Streptococcus mutans.

A unique 373 bp region (igr66) between grpE and dnaK of Streptococcus mutans lacks a promoter but is required for optimal production of DnaK. Northern blotting using probes specific to hrcA, igr66 or dnaK revealed multiple transcripts produced from the dnaK operon and 5'-RACE mapped 5' termini of multiple dnaK transcripts within igr66. One product mapped to a predicted 5'-SL (stem-loop) and two others mapped just 5' to Shine-Dalgarno (SD)-like sequences located immediately upstream to dnaK and to a predicted SL 120 bp upstream of the dnaK start codon (3'-SL). A collection of cat reporter-gene strains containing mutant derivatives of igr66 were engineered. Chloramphenicol acetyltransferase (CAT) activity varied greatly between strains, but there were no correlative changes in cat mRNA levels. Interestingly, mutations introduced into the SD-like sequences 5' to the 3'-SL resulted in an 83-98% decrease in CAT activity. Markerless point mutations introduced upstream of dnaK in the SD-like sequences impaired growth at elevated temperatures and resulted in up to a 40% decrease in DnaK protein after heat shock. Collectively, these results indicate processing within igr66 enhances translation in a temperature dependent manner via non-canonical ribosome binding sites positioned >120 bp upstream of dnaK.

The innate growth bistability and fitness landscapes of antibiotic-resistant bacteria.

To predict the emergence of antibiotic resistance, quantitative relations must be established between the fitness of drug-resistant organisms and the molecular mechanisms conferring resistance. These relations are often unknown and may depend on the state of bacterial growth. To bridge this gap, we have investigated Escherichia coli strains expressing resistance to translation-inhibiting antibiotics. We show that resistance expression and drug inhibition are linked in a positive feedback loop arising from an innate, global effect of drug-inhibited growth on gene expression. A quantitative model of bacterial growth based on this innate feedback accurately predicts the rich phenomena observed: a plateau-shaped fitness landscape, with an abrupt drop in the growth rates of cultures at a threshold drug concentration, and the coexistence of growing and nongrowing populations, that is, growth bistability, below the threshold.

Expression and regulation of transient receptor potential cation channel, subfamily M, member 2 (TRPM2) in human endometrium.

To identify estrogen-responsive genes, we previously isolated estrogen receptor (ER)-binding DNA fragments from human genomic DNA using a recombinant ER protein. Six DNA fragments, each including a perfect palindromic estrogen response element (ERE), were obtained. The nucleotide sequence of one of the six fragments (E1 fragment) showed that the ERE of the E1 fragment is located in the 3'-untranslated region (UTR) of transient receptor potential cation channel, subfamily M, member 2 (TRPM2). Here, we confirmed the estrogen-dependent enhancer activity of the ERE of the E1 fragment by chloramphenicol acetyltransferase assay. TRPM2 mRNA expression was investigated in human endometrium, cultured human endometrial stromal cells (ESCs), and cultured human endometrial epithelial cells (EECs) using RT-PCR. Quantitative RT-PCR revealed that TRPM2 mRNA expression in ESCs increased after 17ß-estradiol (E2) treatment. This study demonstrated for the first time that TRPM2 is an estrogen-responsive gene expressed in human endometrial cells.

Drosophila Bicoid is a substrate of sumoylation and its activator function is subject to inhibition by this post-translational modification.

Bicoid (Bcd) is a Drosophila morphogenetic protein and a transcriptional activator. Genetic studies have suggested a role of sumoylation in Bcd function, but it is unknown how Bcd activity is affected specifically by its own sumoylation status. Here we show that Bcd is sumoylated in Drosophila cells. We identify a lysine residue of Bcd as the primary sumoylation site. Using a Bcd mutant defective in being sumoylated, we show that sumoylation of Bcd is inhibitory to its ability to activate transcription. We provide evidence suggesting that the SUMO moiety has an intrinsic inhibitory activity for the activator function of Bcd.

Development and characterization of a xylose-inducible gene expression system for Clostridium perfringens.

A xylose-inducible gene expression vector for Clostridium perfringens was developed. Plasmid pXCH contains a chromosomal region from Clostridium difficile (xylR-P(xy)(lB)): xylR, encoding the xylose repressor, xylO, the xyl operator sequence, and P(xylB), the divergent promoter upstream of xylBA encoding xylulo kinase and xylose isomerase. pXCH allows tightly regulated expression of the chloramphenicol acetyltransferase reporter and the α-toxin genes in response to the inducer concentration. Thus, pXCH could constitute a new valuable genetic tool for study of C. perfringens.

Identification and characterization of novel and potent transcription promoters of Francisella tularensis.

Two alternative promoter trap libraries, based on the green fluorescence protein (gfp) reporter and on the chloramphenicol acetyltransferase (cat) cassette, were constructed for isolation of potent Francisella tularensis promoters. Of the 26,000 F. tularensis strain LVS gfp library clones, only 3 exhibited visible fluorescence following UV illumination and all appeared to carry the bacterioferritin promoter (Pbfr). Out of a total of 2,000 chloramphenicol-resistant LVS clones isolated from the cat promoter library, we arbitrarily selected 40 for further analysis. Over 80% of these clones carry unique F. tularensis DNA sequences which appear to drive a wide range of protein expression, as determined by specific chloramphenicol acetyltransferase (CAT) Western dot blot and enzymatic assays. The DNA sequence information for the 33 unique and novel F. tularensis promoters reported here, along with the results of in silico and primer extension analyses, suggest that F. tularensis possesses classical Escherichia coli σ(70)-related promoter motifs. These motifs include the -10 (TATAAT) and -35 [TTGA(C/T)A] domains and an AT-rich region upstream from -35, reminiscent of but distinct from the E. coli upstream region that is termed the UP element. The most efficient promoter identified (Pbfr) appears to be about 10 times more potent than the F. tularensis groEL promoter and is probably among the strongest promoters in F. tularensis. The battery of promoters identified in this work will be useful, among other things, for genetic manipulation in the background of F. tularensis intended to gain better understanding of the mechanisms involved in pathogenesis and virulence, as well as for vaccine development studies.

An improved shuttle vector constructed for metabolic engineering research in Corynebacterium glutamicum.

Corynebacterium glutamicum is an industrial microorganism for production of amino acids. However, the metabolic engineering in C. glutamicum has been retarded due to lack of suitable vectors. In this study, we have constructed a shuttle vector pDXW-10 which harbors a large multiple cloning site suitable for cloning multiple genes, and a tac-M promoter suitable for constitutive gene expression in C. glutamicum. The cat gene was subcloned into the vector and the expression levels of the CAT protein were found different in Escherichia coli and C. glutamicum; high-level in the former but moderate-level in the latter. The pDXW-10 would be an ideal vector for research on metabolic engineering in C. glutamicum.

Transcriptional regulation of histidine biosynthesis genes in Corynebacterium glutamicum.

Corynebacterium glutamicum, a gram-positive bacterium, has been widely used for industrial amino acid production. Corynebacterium glutamicum his genes are located and transcribed in two unlinked loci, hisEG and hisDCB-orf1-orf2-hisHA-impA-hisFI. The latter his operon starts the transcription at the C residue localized 196 bp upstream of the hisD ATG start codon. Our computer-based sequence analysis showed that the region corresponding to the untranslated 5' end of the transcript, named the hisD leader region, displays the typical features of the T-box transcriptional attenuation mechanism. Therefore, expression of the cat reporter gene under the control of the wild-type or mutated hisD leader regions was tested in multi-copy (pProm and pTer series) and in single-copy (pInt series) systems under conditions of sufficient or limited histidine. Our mutational studies led to the conclusion that the CAU histidine specifier and 5'-UGGA-3' sequence in the hisD leader region are required for the hisDCB-orf1-orf2-hisHA-impA-hisFI gene regulation. The cat gene expression from the wild-type leader region was negatively regulated by histidine. However, the cat gene expression from mutated leader regions was irresponsive to the level of histidine in the growth medium. Taken together, we propose that a T-box mediated attenuation mechanism is responsible for the gene expression of the hisDCB-orf1-orf2-hisHA-impA-hisFI operon in C. glutamicum.

Supernatants from oral epithelial cells and gingival fibroblasts modulate human immunodeficiency virus type 1 promoter activation induced by periodontopathogens in monocytes/macrophages.

Bacterial and host cell products during coinfections of Human Immunodeficiency Virus type 1-positive (HIV-1(+)) patients regulate HIV-1 recrudescence in latently infected cells (e.g. T cells, monocytes/macrophages), impacting highly active antiretroviral therapy (HAART) failure and progression of acquired immunodeficiency syndrome. A high frequency of oral opportunistic infections (e.g. periodontitis) in HIV-1(+) patients has been demonstrated; however, their potential to impact HIV-1 exacerbation is unclear. We sought to determine the ability of supernatants derived from oral epithelial cells (OKF4) and human gingival fibroblasts (Gin-4) challenged with periodontal pathogens, to modulate the HIV-1 promoter activation in monocytes/macrophages. BF24 monocytes/macrophages transfected with the HIV-1 promoter driving the expression of chloramphenicol acetyltransferase (CAT) were stimulated with Porphyromonas gingivalis, Fusobacterium nucleatum, or Treponema denticola in the presence of supernatants from OKF4 or Gin4 cells either unstimulated or previously pulsed with bacteria. CAT levels were determined by enzyme-linked immunosorbent assay and cytokine production was evaluated by Luminex beadlyte assays. OKF4 and Gin4 supernatants enhanced HIV-1 promoter activation particularly related to F. nucleatum challenge. An additive effect was observed in HIV-1 promoter activation when monocytes/macrophages were simultaneously stimulated with gingival cell supernatants and bacterial extracts. OKF4 cells produced higher levels of granulocyte-macrophage colony-stimulating factor (GM-CSF) and interleukins -6 and -8 in response to F. nucleatum and P. gingivalis. Preincubation of OKF4 supernatants with anti-GM-CSF reduced the additive effect in periodontopathogen-induced HIV-1 promoter activation. These results suggest that soluble mediators produced by gingival resident cells in response to periodontopathogens could contribute to HIV-1 promoter activation in monocytes/macrophages, albeit this effect is most notable following direct stimulation of the cells with oral gram-negative bacteria.

AmpC promoter and attenuator mutations affect function of three Escherichia coli strains.

To investigate the correlation between mutations in promoter, attenuator, and the AmpC enzyme overproduction in Escherichia coli. ampC Promoters from 4 Escherichia coli clinical isolates were cloned upstream to the chloramphenicol acetyltransferase (CAT) gene in pCAT3 reporter plasmid. Promoter strengths were measured by chloramphenicol MIC and gene sequencing was done on the cloned ampC promoter and attenuator. The strength of promoters from AmpC hyperproducers were 8- to 64-fold higher than those from a low-level AmpC producers. In one of the high-strength promoters, the mutations were located at positions -32, +22, +26, +32 (attenuator), -76, and +79. In another promoter, the mutations were located at positions -88, -82, -18, -1, and +58. In the third promoter, mutations were found at positions -1, +58, -80, -73, -28, and +82. Mutations in Escherichia coli promoter and attenuator sequences promoted Chloramphenicol MICs, which may be the primary causal mechanism for resistance to beta-lactams antibiotics.

Transcription activity of individual rrn operons in Bacillus subtilis mutants deficient in (p)ppGpp synthetase genes, relA, yjbM, and ywaC.

In Bacillus subtilis a null mutation of the relA gene, whose gene product is involved in the synthesis and/or hydrolysis of (p)ppGpp, causes a growth defect that can be suppressed by mutation(s) of yjbM and/or ywaC coding for small (p)ppGpp synthetases. All 35 suppressor mutations newly isolated were classified into two groups, either yjbM or ywaC, by mapping and sequencing their mutations, suggesting that there are no (p)ppGpp synthetases other than RelA, YjbM, and YwaC in B. subtilis. In order to understand better the relation between RelA and rRNA synthesis, we studied in the relA mutant the transcriptional regulation of seven rRNA operons (rrnO, -A, -J, -I, -E, -D, or -B) individually after integration of a promoter- and terminatorless cat gene. We identified the transcriptional start sites of each rrn operon (a G) and found that transcription of all rrn operons from their P1 promoters was drastically reduced in the relA mutant while this was almost completely restored in the relA yjbM ywaC triple mutant. Taken together with previous results showing that the intracellular GTP concentration was reduced in the relA mutant while it was restored in the triple mutant, it seems likely that continuous (p)ppGpp synthesis by YjbM and/or YwaC at a basal level causes a decrease in the amounts of intracellular GTP.

The C, V and W proteins of Nipah virus inhibit minigenome replication.

Nipah virus (NiV) is a recently emergent, highly pathogenic, zoonotic paramyxovirus of the genus Henipavirus. Like the phosphoprotein (P) gene of other paramyxoviruses, the P gene of NiV is predicted to encode three additional proteins, C, V and W. When the C, V and W proteins of NiV were tested for their ability to inhibit expression of the chloramphenicol acetyltransferase (CAT) reporter gene in plasmid-based, minigenome replication assays, each protein inhibited CAT expression in a dose-dependent manner. The C, V and W proteins of NiV also inhibited expression of CAT from a measles virus (MV) minigenome, but not from a human parainfluenzavirus 3 (hPIV3) minigenome. Interestingly, the C and V proteins of MV, which have previously been shown to inhibit MV minigenome replication, also inhibited NiV minigenome replication; however, they were not able to inhibit hPIV3 minigenome replication. In contrast, the C protein of hPIV3 inhibited minigenome replication of hPIV3, NiV and MV. Although there is very limited amino acid sequence similarity between the C, V and W proteins within the paramyxoviruses, the heterotypic inhibition of replication suggests that these proteins may share functional properties.

Mutations generated in human immunodeficiency virus type 1 long terminal repeat during vertical transmission correlate with viral gene expression.

We determined the effect of mutations generated in HIV-1 LTR on viral gene expression in six mother-infant pairs following vertical transmission. We show that the functional domains critical for LTR function, the promoter (TATAA), enhancers (three SpI and two NFkappaB sites), the modulatory region (two AP-I sites, two NFAT, one NF-IL6 site, one Ets-1, and one USF-1) and the TAR region were generally conserved among mother-infant pairs, although we observed several patient and pair specific mutations in these important domains. We then determined the promoter activity of our mother-infant LTR sequences by measuring CAT gene expression, which was driven by these LTRs and found that most of these HIV-1 LTRs derived from 6 mother-infant pairs were functional. However, mutations in the important transcription factor binding sites, including TATAA, SpI, NFkappaB, AP-I, NFAT, NF-IL6, Ets-1, USF-1 and TAR resulted in reduced LTR driven CAT gene expression. Taken together, conservation of functional domains in the LTR during vertical transmission supports the notion that a functional LTR is critical in viral replication and pathogenesis and mutations generated during the course of infection correlated with HIV-1 gene expression.

Regulation of an amino acid transporter mRNA in Trypanosoma brucei.

Trypanosoma brucei regulates gene expression by post-transcriptional mechanisms, such as mRNA turnover and translation control. This regulation frequently requires specific sequences located in the 3'-untranslated region. Microarray analysis and Northern blot hybridization showed that the amino acid transporter 11 mRNA is up-regulated in insect stages of the parasite. By RT-PCR and sequencing, the AATP11 polyadenylation site was mapped. We show that this 3'-UTR causes higher expression of the chloramphenicol acetyltransferase (CAT) reporter gene in procyclic trypanosomes than in bloodstream forms. Results of deletion analysis suggested that multiple elements located between nucleotides 141 and 618 of the 3'-untranslated region are required for this control.

Effects of some new antiepileptic drugs and progabide on glucocorticoid receptor-mediated gene transcription in LMCAT cells.

Antiepileptic drugs affect endocrine and immune system activity, however, it is not clear whether these effects are indirect, via interference with neurotransmitters, membrane receptors and ion channels or maybe independent of neuronal mechanisms. In order to shed more light on this problem, in the present study, we evaluated effects of some new-generation antiepileptic drugs and progabide as a GABA-mimetic on the corticosterone-induced chloramphenicol acetyltransferase (CAT) activity in mouse fibroblast cells stably transfected with mouse mammary tumor virus (MMTV)-CAT plasmid. Treatment of cells with felbamate for five days inhibited in a concentration-dependent manner (3-100 microM) the corticosterone-induced reporter gene transcription. Progabide and loreclezole also inhibited the corticosterone-induced CAT activity, but with lower potency, and significant effects were observed at 10 to 100 microM concentration. Tiagabine and stiripentol showed less potent inhibitory effect on functional activity of glucocorticoid receptors (GR). In contrast, topiramate and lamotrigine (3-100 microM) failed to affect the corticosterone-induced gene transcription. These data indicate that some new antiepileptic drugs and progabide may suppress glucocorticoid effects via the inhibition of GR-mediated gene transcription. In turn, attenuation of GR function could influence antiepileptic drug effect on seizures, neuronal degeneration and immune system activity.

Pitfalls of the CAT reporter gene for analyzing translational regulation in Leishmania.

Heterologous reporter genes are widely used for the characterization of gene expression in many organisms. Particularly, constructs bearing reporter genes have greatly contributed to our understanding of gene regulation in kinetoplastids. In some specific circumstances, however, such heterologous reporter has a risk of resulting in irrelevant observations and conclusions, which are primarily due to the introduction of foreign sequence elements. This communication describes our recent experience using the chloramphenicol acetyltransferase (CAT) gene as a reporter for analysis of the translational regulation of HSP70 genes in Leishmania infantum. We show that chimeric mRNAs consisting of the CAT open reading frame (ORF) and the untranslated regions (UTRs) from HSP70-II genes behave differently as endogenous HSP70-II mRNAs and that this difference is due to the presence of CAT sequences. Thus, the main purpose of this communication is to alert researchers working in gene regulation to be cautious when interpreting results based on heterologous reporter genes.

Marek's disease virus unique genes pp38 and pp24 are essential for transactivating the bi-directional promoters for the 1.8 kb mRNA transcripts.

The pp38 and pp24 genes of Marek's diseases virus (MDV) share the same promoter, which controls the transcription of pp38 or pp24 and a 1.8-kb mRNA bi-directionally. To understand the trans-activating activity of pp38 and pp24 on the bi-directional promoter, both genes were cloned into pcDNA-3 or pBudCE4.1 vectors either singly or in combination. These plasmids were expressed in transfected chicken embryonic fibroblast (CEF) cells. Chloramphenicol acetyltransferase (CAT) activity expressed under the control of the promoter in CEF co-transfected with pP(1.8 kb)-CAT and pBud-pp38-pp24 was significantly higher than that following transfection with only pBud-pp38 or pBud-pp24. This indicates the combination of pp24 and pp38 together are essential for the activation of the promoter. In DNA mobility shift assays, the promoter binds to pp38 and pp24 together, but not to pp38 or pp24 alone. By competitive inhibition tests with a set of DNA fragments from the promoter region, the sequence 5'-CTGCTCATTT-3' was identified as the core sequence for binding by pp38-pp24 in up-regulation of the bi-directional promoter activity.

Differences in regulation of type I collagen synthesis in primary and passaged hepatic stellate cell cultures: the role of alpha5beta1-integrin.

Hepatic stellate cells (HSC) differ in their phenotype depending on the initiation and progression of their activation. Our hypothesis was that different mechanisms govern type I collagen synthesis depending on stage of HSC activation. We investigated the role of alpha(5)beta(1)-integrin as a regulator of type I collagen gene COL1A1 expression in primary and passaged HSC cultures using transgenic mouse containing type I collagen gene COL1A1 promoter linked to the chloramphenicol acetyltransferase (CAT) reporter gene. The alpha(5)beta(1) protein levels increased during the activation and were highest in day 6 primary cultures but decreased in passaged HSC. CAT activity, reflecting COL1A1 expression, was upregulated by alpha(5)beta(1)-integrin. Inhibition of alpha(5)beta(1)-integrin by echistatin and blocking antibody resulted in reduced transgene activity only in early primary cultures (compared with the control, 53.3 +/- 12% echistatin and 58.8 +/- 7% blocking antibody, respectively, P < 0.05). Treatment of passaged HSC with either echistatin or blocking antibody had no effect. Fibronectin, an alpha(5)beta(1)-integrin ligand, increased transgene activity in primary (210 +/- 33%, P < 0.05) but not in passaged HSC cultures (119 +/- 8%). This alpha(5)beta(1)-integrin effect appears to be at least in part mediated by CCAAT enhancer binding protein-beta (C/EBPbeta), because fibronectin increased and alpha(5)-gene silencing by small interfering RNA decreased C/EBPbeta levels. In addition, C/EBPbeta knockout mice showed reduced type I collagen synthesis compared with wild-type littermates. Therefore alpha(5)beta(1)-integrin is an important regulator of type I collagen production in early primary HSC cultures but appears to have no direct role once the HSC are fully activated.

Defibrinated bovine plasma inhibits retroviral transcription by blocking p52 activation of the NFkappaB element in the long terminal repeat.

Bovine leukemia virus (BLV) induces a persistent but latent infection in cattle. Viral latency is invoked by a protein known as plasma blocking factor (PBF) that is found in both bovine and human plasma. We report here on pathways that mediate latency in the presence of PBF. Reporter-gene constructs driven by the promoters of 6 retroviruses were used to measure the production of chloramphenicol acetyl transferase (CAT) in cell lines cultured with or without defibrinated bovine plasma. Plasma inhibited CAT production only in constructs containing an NFkappaB-binding element proximal to the initiation site (BLV, human immunodeficiency virus, and human T-cell leukemia virus). The promoters of Bovine immunodeficiency virus, Feline immunodeficiency virus, or Feline leukemia virus were not inhibited in the presence of bovine plasma. Using gel mobility shift assays, we demonstrated that activation of viral transcription upon stimulation with phorbol esters and ionomycin was mediated through the NFkappaB element and that this was abrogated in the presence of plasma. Furthermore, analysis of individual NFkappaB proteins in nuclear extracts of mononuclear cells or Jurkat cells showed that all 5 members of the NFkappaB family were upregulated in response to stimulation, but only p52 was significantly downregulated in the presence of bovine plasma. Thus, we infer that plasma effects are mediated through interference with either p52 translocation to the nucleus or p52 synthesis.