Transcription Needs Translation Initiation of the Downstream Gene to Continue Downstream at Intercistronic Junctions in E. Coli

We have reported a gal mutant called galE stop0, wherein the galE stop codon was changed to a sense codon. The experiment results demonstrated that preventing galE translation termination inhibited the production of galE 3' ends. This implies that when the galE translation termination was prevented, the galE 3' ends generation was reduced or impaired. We anticipated that the translation of galE would continue to galT, producing a chimeric protein GalE-GalT. This study verified that the chimeric protein was produced, but unexpectedly, we found that the GalT protein was also synthesized in the mutant, and its amount equaled that in the wild-type. In the wild-type, we also found that the GalE-GalT chimeric protein was produced in an amount equal to that of the GalE protein. These results suggest that translation termination of galE and translation initiation of galT occur independently, thus, corroborating our transcription-translation model: At the cistron junction, transcription, decoupled from translation due to the translation termination of galE, needs translation initiation of galT to continue downstream; otherwise, transcription would be terminated by Rho. RNase E-mediated transcript cleavage also produces the 3' ends of pre-galE mRNA. These findings indicated that RNase E produces the 3' end of mRNA and establishes gene expression polarity.

Reporter Gene-Based qRT-PCR Assay for Rho-Dependent Termination In Vivo

In bacteria, the Rho protein mediates Rho-dependent termination (RDT) by identifying a non-specific cytosine-rich Rho utilization site on the newly synthesized RNA. As a result of RDT, downstream RNA transcription is reduced. Due to the bias in reverse transcription and PCR amplification, we could not identify the RDT site by directly measuring the amount of mRNA upstream and downstream of RDT sites. To overcome this difficulty, we employed a 77 bp reporter gene argX, (coding tRNAarg) from Brevibacterium albidum, and we transcriptionally fused it to the sequences to be assayed. We constructed a series of plasmids by combining a segment of the galactose (gal) operon sequences, both with and without the RDT regions at the ends of cistrons (galE, galT, and galM) upstream of argX. The RNA polymerase will transcribe the gal operon sequence and argX unless it encounters the RDT encoded by the inserted sequence. Since the quantitative real-time PCR (qRT-PCR) method detects the steady state following mRNA synthesis and degradation, we observed that tRNAarg is degraded at the same rate in these transcriptional fusion plasmids. Therefore, the amount of tRNAarg can directly reflect the mRNA synthesis. Using this approach, we were able to effectively assay the RDTs and Rho-independent termination (RIT) in the gal operon by quantifying the relative amount of tRNAarg using qRT-PCR analyses. The resultant RDT% for galET, galTK, and at the end of galM were 36, 26, and 63, individually. The resultant RIT% at the end of the gal operon is 33%. Our findings demonstrate that combining tRNAarg with qRT-PCR can directly measure RIT, RDT, or any other signal that attenuates transcription efficiencies in vivo, making it a useful tool for gene expression research.

Identification of a Rho-Dependent Termination Site In Vivo Using Synthetic Small RNA

Rho promotes Rho-dependent termination (RDT) at the Rho-dependent terminator, producing a variable-length region without secondary structure at the 3' end of mRNA. Determining the exact RDT site in vivo is challenging, because the 3' end of mRNA is rapidly removed after RDT by 3'-to-5' exonuclease processing. Here, we applied synthetic small RNA (sysRNA) to identify the RDT region in vivo by exploiting its complementary base-pairing ability to target mRNA. Through the combined analyses of rapid amplification of cDNA 3' ends, primer extension, and capillary electrophoresis, we could precisely map and quantify mRNA 3' ends. We found that complementary double-stranded RNA (dsRNA) formed between sysRNA and mRNA was efficiently cleaved by RNase III in the middle of the dsRNA region. The formation of dsRNA appeared to protect the cleaved RNA 3' ends from rapid degradation by 3'-to-5' exonuclease, thereby stabilizing the mRNA 3' end. We further verified that the signal intensity at the 3' end was positively correlated with the amount of mRNA. By constructing a series of sysRNAs with close target sites and comparing the difference in signal intensity at the 3' end of wild-type and Rho-impaired strains, we finally identified a region of increased mRNA expression within the 21-bp range, which was determined as the RDT region. Our results demonstrated the ability to use sysRNA as a novel tool to identify RDT regions in vivo and expand the range of applications of sysRNA. IMPORTANCE sysRNA, which was formerly widely employed, has steadily lost popularity as more novel techniques for suppressing gene expression come into existence because of issues such as unstable inhibition effect and low inhibition efficiency. However, it remains an interesting topic as a regulatory tool due to its ease of design and low metabolic burden on cells. Here, for the first time, we discovered a new method to identify RDT regions in vivo using sysRNA. This new feature is important because since the discovery of the Rho protein in 1969, specific identification of RDT sites in vivo has been difficult due to the rapid processing of RNA 3' ends by exonucleases, and sysRNA might provide a new approach to address this challenge.

sRNA expedites polycistronic mRNA decay in Escherichia coli

In bacteria, most small RNA (sRNA) elicits RNase E-mediated target mRNA degradation by binding near the translation initiation site at the 5' end of the target mRNA. Spot 42 is an sRNA that binds in the middle of the gal operon near the translation initiation site of galK, the third gene of four, but it is not clear whether this binding causes degradation of gal mRNA. In this study, we measured the decay rate of gal mRNA using Northern blot and found that Spot 42 binding caused degradation of only a specific group of gal mRNA that shares their 3' end with full-length mRNA. The results showed that in the MG1655Δspf strain in which the Spot 42 gene was removed, the half-life of each gal mRNA in the group increased by about 200% compared to the wild type. Since these mRNA species are intermediate mRNA molecules created by the decay process of the full-length gal mRNA, these results suggest that sRNA accelerates the mRNA decaying processes that normally operate, thus revealing an unprecedented role of sRNA in mRNA biology.

An in vitro Assay of mRNA 3' end Using the E. coli Cell-free Expression System

At the end of about 80% of the operon in Escherichia coli, translation termination decouples transcription, leading to Rho-dependent transcription termination (RDT). However, no in vitro or in vivo assay system has proven to be good enough to see the 3' end of the mRNA generated by RDT. Here, we present a cell-free assay system that could provide detailed information on the 3' end of a transcript RNA generated by RDT. Our protocol shows how to extract transcript RNA generated by transcription reactions from a cell-free extract, followed by an RNA oligomer ligation to the 3' end of a transcript RNA of interest. The 3' end of the RNA is amplified using RT-PCR. Its genetic location can be determined using a gene-specific primer extension reaction. The 3' ends of mRNA can be visualized and quantified by polyacrylamide gel electrophoresis. One significant advantage of a cell-free assay system is that factors involved in the generation of the 3' end, such as proteins and sRNA, can be directly assayed by exogenously adding factor(s) to the reaction. Graphic abstract: An illustration of the experimental methodology.

sRNA-mediated regulation of gal mRNA in E. coli: Involvement of transcript cleavage by RNase E together with Rho-dependent transcription termination

In bacteria, small non-coding RNAs (sRNAs) bind to target mRNAs and regulate their translation and/or stability. In the polycistronic galETKM operon of Escherichia coli, binding of the Spot 42 sRNA to the operon transcript leads to the generation of galET mRNA. The mechanism of this regulation has remained unclear. We show that sRNA-mRNA base pairing at the beginning of the galK gene leads to both transcription termination and transcript cleavage within galK, and generates galET mRNAs with two different 3'-OH ends. Transcription termination requires Rho, and transcript cleavage requires the endonuclease RNase E. The sRNA-mRNA base-paired segments required for generating the two galET species are different, indicating different sequence requirements for the two events. The use of two targets in an mRNA, each of which causes a different outcome, appears to be a novel mode of action for a sRNA. Considering the prevalence of potential sRNA targets at cistron junctions, the generation of new mRNA species by the mechanisms reported here might be a widespread mode of bacterial gene regulation.

Indole-3-carbinol inhibits the proliferation of colorectal carcinoma LoVo cells through activation of the apoptotic signaling pathway

Indole-3-carbinol (I3C) is a phytochemical that exhibits growth-inhibitory activity against various cancer cells. However, there are limited studies on the effects of I3C on colon cancer cells. In this study, the growth-inhibitory activity of I3C against the human colorectal carcinoma cell line (LoVo) was examined. The results of the 3-(4,5-dimethylthiazol-2yl)-2,5-diphenyltetrazolium bromide, colony formation, and cell counting assays revealed that I3C suppressed the proliferation of LoVo cells. Microscopy and wound-healing analyses revealed that I3C affected the morphology and inhibited the migration of LoVo cells, respectively. I3C induced apoptosis and DNA fragmentation as evidenced by the results of fluorescein isothiocyanate-conjugated annexin V staining and terminal deoxynucleotidyl transferase-mediated dUTP-biotin nick-end labeling assay, respectively. Additionally, I3C arrested the cell cycle at the G0/G1 phase and enhanced the reactive oxygen species levels. Western blotting analysis revealed that treatment with I3C resulted in the activation of apoptotic proteins, such as poly(ADP-ribose) polymerase, caspase-3, caspase-7, caspase-9, Bax, Bim, and p53 in LoVo cells. These results indicate that I3C induces apoptosis in LoVo cells by upregulating p53, leading to the activation of Bax and caspases. Taken together, I3C exerts cytotoxic effects on LoVo cells by activating apoptosis.

Translation Initiation Control of RNase E-Mediated Decay of Polycistronic gal mRNA

In bacteria, mRNA decay is a major mechanism for regulating gene expression. In Escherichia coli, mRNA decay initiates with endonucleolytic cleavage by RNase E. Translating ribosomes impede RNase E cleavage, thus providing stability to mRNA. In transcripts containing multiple cistrons, the translation of each cistron initiates separately. The effect of internal translation initiations on the decay of polycistronic transcripts remains unknown, which we have investigated here using the four-cistron galETKM transcript. We find that RNase E cleaves a few nucleotides (14-36) upstream of the translation initiation site of each cistron, generating decay intermediates galTKM, galKM, and galM mRNA with fewer but full cistrons. Blocking translation initiation reduced stability, particularly of the mutated cistrons and when they were the 5'-most cistrons. This indicates that, together with translation failure, the location of the cistron is important for its elimination. The instability of the 5'-most cistron did not propagate to the downstream cistrons, possibly due to translation initiation there. Cistron elimination from the 5' end was not always sequential, indicating that RNase E can also directly access a ribosome-free internal cistron. The finding in gal operon of mRNA decay by cistron elimination appears common in E. coli and Salmonella.

A c-di-AMP riboswitch controlling kdpFABC operon transcription regulates the potassium transporter system in Bacillus thuringiensis

The intracellular K+ level in bacteria is strictly controlled by K+ uptake and efflux systems. Among these, KdpFABC is a high-affinity K+ transporter system that is generally activated by the KdpDE two-component system in response to K+ limitation stress. However, the regulatory mechanism remains obscure in bacteria lacking the kdpDE genes. Here we report that the transcription of a kdpFABC operon is distinctively regulated by a cyclic diadenylate monophosphate (c-di-AMP) riboswitch located at the 5'-untranslated region of kdp transcript, and binding of c-di-AMP to the riboswitch promotes its intrinsic termination that blocks the kdpFABC transcription. Further, the intracellular c-di-AMP concentration was found to decrease under the K+ limitation stress, leading to transcriptional read-through over the terminator to allow kdpFABC expression. This regulatory element is found predominantly in the Bacillus cereus group and correlate well with the K+ and c-di-AMP homeostasis that affects a variety of crucial cellular functions.

Visualization of RNA 3' ends in Escherichia coli Using 3' RACE Combined with Primer Extension

In this assay, 3' RACE (Rapid Amplification of cDNA 3' Ends) followed by PE (primer extension), abbreviated as 3' RACE-PE is used to identify the mRNA 3' ends. The following protocol describes the amplification of the mRNA 3' ends at the galactose operon in E. coli and the corresponding visualization of the PCR products through PE. In PE, the definite primer is 5' end-labeled using [γ-(32) P] ATP and T4 polynucleotide kinase, which anneals to the specific DNA molecules within the PCR product of the 3' RACE. The conventional PE can only be used to locate the 5' end of an mRNA transcript since reverse transcriptase (RTase) polymerizes only in the 5' → 3' direction. Thus, Taq polymerase is used instead of RTase, PCR is performed. Therefore, we are able to locate the 3' end of the mRNA using this assay. The relative amount of the 3' end can be directly visualized and quantified by way of separating DNA products in a denaturing 8% urea-PAGE (Polyacrylamide Gel Electrophoresis) gel. The exact position of the 3' ends can be sequenced by comparison of these final DNA products with the corresponding DNA sequencing ladder.

The Korean version of the Carpal Tunnel Questionnaire. Cross cultural adaptation, reliability, validity and responsiveness

The purpose of this study was to translate and culturally adapt the Carpal Tunnel Questionnaire to produce an equivalent Korean version. A total of 53 patients completed the Korean version of the Carpal Tunnel Questionnaire pre-operatively and 3 months after open carpal tunnel release. All 53 also completed the Korean version of the Disabilities of Arm, Shoulder, and Hand questionnaire pre-operatively and 3 months post-operatively. Reliability was measured by determining the test-retest reliability and internal consistency. Test-retest reliability was assessed using intraclass correlation coefficients and paired t-tests, and internal consistency using Cronbach's alpha coefficients. Pearson correlation analysis was carried out on the Korean version of the Carpal Tunnel Questionnaire scores and the Korean version of the Disabilities of Arm, Shoulder, and Hand scores to assess construct validity. Responsiveness was evaluated using effect sizes and standardized response means. The reliability of the Korean version of the Carpal Tunnel Questionnaire was good. The scores in the Korean version of the Disabilities of Arm, Shoulder, and Hand strongly correlated with the scores in the Korean version of the Carpal Tunnel Questionnaire. Standardized response mean and effect size were both large for the Korean version of the Carpal Tunnel Questionnaire. The study shows that the Korean version of the Carpal Tunnel Questionnaire is a reliable, valid and responsive instrument for measuring outcomes in carpal tunnel syndrome.

Decision support for ecological river rehabilitation using fish habitat database

After the recent success of several river rehabilitation projects including the Cheong-gye river case, a large number of local governments have been promoting their own projects in Korea. Most of the projects are aimed at securing the soundness of aquatic ecosystems according to the guidelines presented by the Korea Ministry of Environment. However, there is no clear guidance for the management goals of water quality and quantity. In this study, we have made an attempt to construct a habitat database (DB) for each domestic freshwater fish species. The fish population, and physical and physicochemical properties of the habitat of 70 domestic freshwater fish species were investigated using field monitoring data. After the statistical processing, the inhabitable range and optimal range of each species were suggested. Furthermore, based on the DB, a decision support system for ecological river restoration and rehabilitation has been developed, and applied for field tests. It became clear that the decision support procedure based on the fish habitat DB is useful in the planning stage of river rehabilitation projects to select the flagship fish, to decide the restoration goals considering their appropriate habitat and to suggest the optimum quantitative combination of each available water resource.

The CnuK9E H-NS complex antagonizes DNA binding of DicA and leads to temperature-dependent filamentous growth in E. coli

Cnu (an OriC-binding nucleoid protein) associates with H-NS. A variant of Cnu was identified as a key factor for filamentous growth of a wild-type Escherichia coli strain at 37°C. This variant (CnuK9E) bears a substitution of a lysine to glutamic acid, causing a charge reversal in the first helix. The temperature-dependent filamentous growth of E. coli bearing CnuK9E could be reversed by either lowering the temperature to 25°C or lowering the CnuK9E concentration in the cell. Gene expression analysis suggested that downregulation of dicA by CnuK9E causes a burst of dicB transcription, which, in turn, elicits filamentous growth. In vivo assays indicated that DicA transcriptionally activates its own gene, by binding to its operator in a temperature-dependent manner. The antagonizing effect of CnuK9E with H-NS on DNA-binding activity of DicA was stronger at 37°C, presumably due to the lower operator binding of DicA at 37°C. These data suggest that the temperature-dependent negative effect of CnuK9E on DicA binding plays a major role in filamentous growth. The C-terminus of DicA shows significant amino acid sequence similarity to the DNA-binding domains of RovA and SlyA, regulators of pathogenic genes in Yersinia and Salmonella, respectively, which also show better DNA-binding activity at 25°C.

PI3K-ERK1/2 activation contributes to extracellular H2O2 generation in amyloid β toxicity

Amyloid β peptide (Aβ) induces hydrogen peroxide (H2O2) and superoxide generation, leading to neuronal death. Many studies have shown the involvement of NADPH oxidase, but the isotype-specific role was not assessed. Moreover, the activation status of phosphoinositide 3-kinase (PI3K) and extracellular signal-regulated kinase (ERK) 1/2 is unclear in extracellular H2O2 generation. In this paper, we showed that Aβ1-42 induced extracellular H2O2 generation and the resulting cytotoxicity in a concentration-dependent manner. Nox2- and Nox4-specific siRNAs suppressed H2O2 and superoxide generation. LY294002 and U0126, inhibitors of PI3K and ERK1/2, respectively, reduced H2O2 generation in concentration-dependent manners. Furthermore, PI3K activation is responsible for ERK1/2 phosphorylation. An additional increase in H2O2 generation and corresponding cytotoxicity was observed after treatment with Aβ1-42 and glutamate. These results suggest that Aβ1-42 enhances the neuronal vulnerability to oxidative injury in Alzheimer's disease (AD) by increasing H2O2 generation.

XAGE-1a and XAGE-1d are potential biomarkers of lung squamous cell carcinoma

BACKGROUND

Lung cancer is the leading cause of cancer deaths worldwide. We evaluated the diagnostic potential of sera XAGE-1a and XAGE-1d in lung cancer, both of which are variants of the X antigen family, member 1.

METHODS

The expression levels of XAGE-1a and XAGE-1d in cell lines were determined using western blot analysis. Competitive ELISA was used to analyze XAGE-1a and XAGE-1d levels in culture supernatants and sera from 194 lung cancer patients and 194 healthy sex- and age-group-matched controls. To evaluate the diagnostic performance of these proteins, we also analyzed carcinoembryonic antigen (CEA) and cytokeratin 19 fragment (CYFRA 21-1) in culture supernatants and 388 sera using commercial ELISA kits.

RESULTS

XAGE-1a and XAGE-1d proteins were expressed in both breast cancer and lung cancer cell lines, but they were only secreted by the latter. The areas under the curves (AUCs) for XAGE-1a and XAGE-1d were 0.787 and 0.806, respectively. The cutoff values (sensitivity, specificity) for XAGE-1a and XAGE-1d were 1.62 ng/ml (0.866, 0.572) and 2.51 ng/ml (0.871, 0.613), respectively. The diagnostic performance was improved for patients with squamous cell carcinoma. The AUC values for XAGE-1a and XAGE-1d for patients with squamous cell carcinoma versus a group containing all healthy participants and patients with any illness other than squamous cell carcinoma were similar to those for CEA and CYFRA 21-1. Better performance (AUC: 0.914) for all patients was obtained when using a combination of four markers (Random Forest).

CONCLUSIONS

Sera XAGE-1a and XAGE-1d are potential biomarkers for lung cancer; they display a diagnostic performance comparable to that of CEA or CYFRA 21-1. Further studies are needed to evaluate the diagnostic and prognostic potential of XAGE-1a and XAGE-1d in lung cancer.

A mutational study of Cnu reveals attractive forces between Cnu and H-NS

Cnu is a small 71-amino acid protein that complexes with H-NS and binds to a specific sequence in the replication origin of the E. coli chromosome. To understand the mechanism of interaction between Cnu and H-NS, we used bacterial genetics to select and analyze Cnu variants that cannot complex with H-NS. Out of 2,000 colonies, 40 Cnu variants were identified. Most variants (82.5%) had a single mutation, but a few variants (17.5%) had double amino acid changes. An in vitro assay was used to identify Cnu variants that were truly defective in H-NS binding. The changes in these defective variants occurred exclusively at charged amino acids (Asp, Glu, or Lys) on the surface of the protein. We propose that the attractive force that governs the Cnu-H-NS interaction is an ionic bond, unlike the hydrophobic interaction that is the major attractive force in most proteins.

In vivo transcription dynamics of the galactose operon: a study on the promoter transition from P1 to P2 at onset of stationary phase

Quantitative analyses of the 5′ end of gal transcripts indicate that transcription from the galactose operon P1 promoter is higher during cell division. When cells are no longer dividing, however, transcription is initiated more often from the P2 promoter. Escherichia coli cells divide six times before the onset of the stationary phase when grown in LB containing 0.5% galactose at 37°C. Transcription from the two promoters increases, although at different rates, during early exponential phase (until the third cell division, OD₆₀₀ 0.4), and then reaches a plateau. The steady-state transcription from P1 continues in late exponential phase (the next three cell divisions, OD₆₀₀ 3.0), after which transcription from this promoter decreases. However, steady-state transcription from P2 continues 1 h longer into the stationary phase, before decreasing. This longer steady-state P2 transcription constitutes the promoter transition from P1 to P2 at the onset of the stationary phase. The intracellular cAMP concentration dictates P1 transcription dynamics; therefore, promoter transition may result from a lack of cAMP-CRP complex binding to the gal operon. The decay rate of gal-specific transcripts is constant through the six consecutive cell divisions that comprise the exponential growth phase, increases at the onset of the stationary phase, and is too low to be measured during the stationary phase. These data suggest that a regulatory mechanism coordinates the synthesis and decay of gal mRNAs to maintain the observed gal transcription. Our analysis indicates that the increase in P1 transcription is the result of cAMP-CRP binding to increasing numbers of galactose operons in the cell population.

Quantification of the galactose-operon mRNAs 5 bases different in their 5'-ends

Three assay methods for quantification of the two galactoseoperon mRNAs that only differ by 5 bases in their 5'-end are presented. The 5' ends of each mRNA were extended by ligating the 3'-end of the abundant 5S rRNA. This ligation extends the 5' ends of the two gal mRNAs long enough to be distinguished by the specific PCR primers in the following quantification reactions. Quantification of the corresponding cDNAs was performed either by primer extension assay or real-time qPCR. To circumvent the problem of the RNA ligation reaction (i.e. very low ligation efficiency), we devised a new method that employs real-time qPCR directly for the quantification of the gal transcripts which differ by 5 bases in their 5'-ends.

Extracellular hydrogen peroxide contributes to oxidative glutamate toxicity

Oxidative glutamate toxicity is characterized by the inhibition of cystine uptake, the depletion of intracellular glutathione, and increased levels of intracellular reactive oxygen species, factors that lead to neuronal injury. We found that the presence of extracellular catalase protected cultured neuronal cells, such as HT22, SH-SY5Y and PC12 cells, from glutamate-induced cytotoxicity. Extracellular hydrogen peroxide (H₂O₂) accumulated in a time- and concentration-dependent manner in HT22 cells during prolonged exposure to glutamate. To investigate the involvement of NADPH oxidase in glutamate-induced H₂O₂ generation, we used small interference RNA (siRNA). Knockdown of Nox2 and Nox4 expression reduced H₂O₂ accumulation and increased cell survival. siRNA specific for Nox4 reduced the production of H₂O₂ by ~74% compared with control siRNA. Furthermore, H₂O₂ accumulation was also suppressed by U0126, a MEK/ERK inhibitor, in a concentration-dependent manner. These results suggest that glutamate triggers the Nox-dependent generation of extracellular H₂O₂ via ERK1/2 activation, which contributes to oxidative glutamate toxicity.

An additional novel antimicrobial resistance gene cluster in Salmonella genomic island 1 of a Salmonella enterica serovar Typhimurium DT104 human isolate

The multi-antimicrobial resistance gene cluster and its derivatives have been detected in Salmonella genomic island 1 (SGI1), which has been identified in the Salmonella enterica serovar Typhimurium, phage types DT104, DT12, DT120, and U302, as well as other Salmonella serovars, including Agona, Paratyphi B, Albany, Meleagridis, Newport, Cerro, Derby, Dusseldorf, Infantis, Kiambu, and Emek. We acquired 53 Salmonella Typhimurium DT104 isolates from diarrheal patients in Korea. From these isolates, we identified a novel antimicrobial resistance gene cluster as an additional gene cassette in SGI1 from a multi-antimicrobial resistant isolate. The minimum inhibitory concentration for this isolate against ampicillin and chloramphenicol was two to four times higher than those for other multi-antimicrobial-resistant Salmonella Typhimurium DT104 isolates. The new antimicrobial resistance gene cluster detected in this isolate consisted of bla(PSE-1), sul1 Delta, floR, and tetR, in that order. The order of this gene cluster was shuffled as compared to that of the known In104 in SGI1. This report is, to the best of our knowledge, the first to identify and describe an additional shuffled antimicrobial resistance gene cluster in SGI1.

Establishment of an mRNA gradient depends on the promoter: an investigation of polarity in gene expression

We found six mRNA species specific to the galactose operon of Escherichia coli. Analyses of both ends of the mRNAs indicated that while the 5' ends are fixed at the promoter region, the 3' ends vary along the operon. The resulting gal mRNA map suggests generation of an mRNA concentration gradient that is higher in the promoter-proximal region and lower toward the distal region. Real-time RT-PCR analyses of the amount of each mRNA species confirmed the existence of the gradient. This gradient of mRNA concentration could serve as an underlying mechanism for the long known phenomenon "natural polarity." Further analyses of the 3' ends of the mRNAs showed that they are generated by either an unknown mRNA processing/transcription termination mechanism(s) or Rho-dependent intra-cistronic transcription termination. The results showed also that transcription from the P2 promoter can yield a more severe mRNA gradient than that from the P1 promoter, suggesting that the slope of the mRNA gradient depends on which promoter the transcription has initiated from. These results led us to suggest a novel gene regulation model in which transcription initiation is tightly coupled to mRNA processing and/or transcription termination.

Structural and dynamic basis of a supercoiling-responsive DNA element

In both eukaryotes and prokaryotes, negative supercoiling of chromosomal DNA acts locally to regulate a variety of cellular processes, such as transcription, replication, recombination and response to environmental stresses. While studying the interaction between the Hin recombinase and mutated versions of its cognate DNA-binding site, we identified a mutated DNA site that binds Hin only when the DNA is supercoiled. To understand the mechanism of this supercoiling-responsive DNA site, we used NMR spectroscopy and fluorescence resonance energy transfer to determine the solution structures and dynamics of three related DNA oligonucleotides. The supercoiling-responsive DNA site formed a partially unwound and stretched helix and showed significant flexibility and base pair opening kinetics. The single CAG/CTG triplet contained in this DNA sequence displayed the same characteristics as do multiple CAG/CTG repeats, which are associated with several hereditary neuromuscular diseases. It is known that short DNA sequence motifs that have either very high or low bending flexibility occur preferentially at supercoiling-sensitive bacterial and eukaryotic promoters. From our results and these previous data, we propose a model in which supercoiling utilizes the intrinsic flexibility of a short DNA site to switch the local DNA structure from an inefficient conformation for protein binding to an efficient one, or vice versa.

Cnu, a novel oriC-binding protein of Escherichia coli

We have found, using a newly developed genetic method, a protein (named Cnu, for oriC-binding nucleoid-associated) that binds to a specific 26-base-pair sequence (named cnb) in the origin of replication of Escherichia coli, oriC. Cnu is composed of 71 amino acids (8.4 kDa) and shows extensive amino acid identity to a group of proteins belonging to the Hha/YmoA family. Cnu was previously discovered as a protein that, like Hha, complexes with H-NS in vitro. Our in vivo and in vitro assays confirm the results and further suggest that the complex formation with H-NS is involved in Cnu/Hha binding to cnb. Unlike the hns mutants, elimination of either the cnu or hha gene did not disturb the growth rate, origin content, and synchrony of DNA replication initiation of the mutants compared to the wild-type cells. However, the cnu hha double mutant was moderately reduced in origin content. The Cnu/Hha complex with H-NS thus could play a role in optimal activity of oriC.

Effect of varying the supercoiling of DNA on transcription and its regulation

The effect of superhelicity of DNA templates on transcription is well documented in several cases. However, the amount of supercoiling that is needed to bring about any changes and the steps at which such effects are exerted were not systematically studied. We investigated the effect of DNA supercoiling on transcription from a set of promoters present on a plasmid by using a series of topoisomers with different superhelical densities ranging from totally relaxed to more than physiological. In vitro transcription assays with these topoisomers in the absence and presence of gene regulatory proteins showed that the effect of negative supercoiling on intrinsic transcription varies from promoter to promoter. Some of those promoters, in which DNA superhelicity stimulated transcription, displayed specific optima of superhelical density while others did not. The results also showed that the amounts of abortive RNA synthesis from two of the promoters decreased and full-length RNA increased with increasing supercoiling, indicating for the first time an inverse relationship between full-length and abortive RNA synthesis and supporting a role of DNA superhelicity in promoter clearance. DNA supercoiling might also influence the point of RNA chain termination. Furthermore, the effect of varying the amount of supercoiling on the action of gene regulatory proteins suggested the mode of action, which is consistent with previous results. Our results underscore the importance of DNA supercoiling in fine-tuning promoter activities, which should be relevant in cell physiology given that local changes in chromosomal supercoiling must occur in different environments.

A "master" in base unpairing during isomerization of a promoter upon RNA polymerase binding

Isomerization of a closed to open complex of a promoter upon RNA polymerase binding involves base unpairing at the -10 region. After potassium permanganate sensitivity of unpaired thymine residues, we studied base unpairing at the -10 region during isomerization upon RNA polymerase binding at the P1 and P3 promoters of the gal operon. Substitution of adenine by 2-amino purine (2-AP) at the invariable A small middle dotT base pair at the -11 position of P1 and P3 prevented unpairing not only at that position but also at the other downstream positions, suggesting a "master" role of the adenine base at -11 of the template strand in overall base unpairing. 2-AP at -11 did not inhibit the formation of RNA polymerase small middle dotpromoter complex and subsequent isomerization of the polymerase. Substitution of adenine by 2-AP at several other positions did not affect thymine unpairing. Changing the position of the amino group from C6 in adenine to C2 in 2-AP is mutational only at the master switch position, -11.

Effects of dimer interface mutations in Hin recombinase on DNA binding and recombination

Previous biochemical assays and a structural model of the protein have indicated that the dimer interface of the Hin recombinase is composed of two alpha-helices. To elucidate the structure and function of the helix, amino acids at the N-terminal end of the helix, where the two helices make their most extensive contact, were randomized, and inversion-incompetent mutants were selected. To investigate why the mutants lost their inversion activities, the DNA binding, hix pairing, invertasome formation, and DNA cleavage activities were assayed using in vivo and in vitro methodologies. The results indicated that the mutants could be divided into four classes based on their DNA binding activity. We propose that the alpha-helices might serve to place a DNA binding motif of Hin in the correct spatial relationship to the minor groove of the recombination site. All the mutants except those that failed to bind DNA were able to perform hix pairing and invertasome formation, suggesting that the dimer interface is not involved in either of these processes. The inversion-incompetent phenotype of the binders was caused by the inability of mutants to perform DNA cleavage. The mutants that showed less binding ability than the wild type nevertheless exhibited a wild-type level of hix pairing activity, because the hix pairing activity overcomes the defect in DNA binding. This phenotype of the mutants that are impaired in DNA binding suggests that the binding domains of Hin may mediate Hin-Hin interaction during hix pairing.

Kainate-induced neuronal injury leads to persistent phosphorylation of cAMP response element-binding protein in glial and endothelial cells in the hippocampus

Intracerebroventricular kainate treatment in rats induces neuronal cell death, followed by proliferation and hypertrophy of glial cells in the lesioned area. To further understand the activated signal transduction pathways and to get insights into potential target gene activation, the present study aims to elucidate long-term effects on the phosphorylation state of cAMP response element-binding protein (CREB) in the hippocampal formation. One to four weeks after kainate injection, we found high levels of phosphorylated and hence activated CREB (pCREB) in glial cells of the degenerating CA fields. As shown by electron microscopy, pCREB immunoreactivity was present in reactive astrocytes, oligodendrocyte precursor cells and endothelial cells of blood vessels. It is postulated that pCREB could drive the expression of downstream genes in these cells to promote cell proliferation and survival.

In vivo assay of protein-protein interactions in Hin-mediated DNA inversion

In order to form the catalytic nucleoprotein complex called the invertasome in the Hin-mediated DNA inversion reaction, interactions of the DNA-binding proteins Hin and Fis are required. Assays for these protein-protein interactions have been exploited with protein cross-linkers in vitro. In this study, an in vivo assay system that probes protein-protein interactions was developed. The formation of a DNA loop generated by protein interactions resulted in transcriptional repression of an artificially designed operon, which in turn increased the chance of survival of Escherichia coli host cells in a streptomycin-containing medium. Using this system, we were able to assay the Hin-Hin interaction that results in the pairing of the two recombination sites and protein interactions that result in the formation of the invertasome. This assay system also led us to find that an individual Hin dimer bound on a recombination site can form a stable complex with Fis bound on the recombinational enhancer; this finding has never been observed in in vitro studies. Possible pathways toward the formation of the invertasome are discussed based on the assay results for a previously reported Hin mutant.

The role of polarization of Xe by di- and monovalent cations in 129Xe NMR studies in zeolite A

We consider the role of polarization in the adsorption of Xe in zeolites of type A by direct comparative analysis of the adsorption isotherms, distributions of occupancies, and 129Xe NMR chemical shifts of Xe(n) in cages containing CaxNa12-2x ions per alpha cage (x = 0, 1, 2, 3, 5). We find that the qualitative trends in the adsorption isotherms, and in the progressions of Xe(n) chemical shifts (for n = 0-8 in cages with x = 0, 1 Ca2+ ions and for n = 0-5 in cages with x = 2, 3 Ca2+ ions) upon increasing the level of Ca2+ ion for Na+ ion substitution could only be accounted for by including polarization of the Xe atom by the zeolite framework and its ions. This system, which permits observation of individual Xe(n) peaks and of directly comparable adsorption isotherms in several cage types, provides a good model system for the interpretation of the more general case in which only the overall average 129Xe NMR chemical shift is observed in open network zeolites, arising from free exchange of Xe among cavities of variable occupancy and variable cation distribution.

Hin-mediated inversion on positively supercoiled DNA

Hin recombinase requires negatively supercoiled DNA for an efficient inversion. We have generated positively supercoiled plasmid DNA using reverse gyrase from Sulfolobus shibatae and subjected it to the Hin-mediated inversion reaction. Both Hin and Fis showed the same DNA binding activity regardless of the superhelical handedness of the substrate plasmid. However, inversion activity on positively supercoiled DNA was less than 1% of negatively supercoiled DNA. Assays designed to probe steps in inversion, showed that on positively supercoiled DNA, Hin was able to cleave the recombination sites with the same efficiency shown on negatively supercoiled DNA but was not able to exchange the cleaved DNA. Based on the theoretical differences between positive and negative supercoiling, our data may suggest that unwinding of the double helix at recombination sites is needed after DNA cleavage for strand exchange to occur.

A clinical investigation of the efficacy of low level laser therapy in reducing orthodontic postadjustment pain

Low level laser therapy (LLLT) has been shown to produce analgesic effects in many clinical applications. The aim of this clinical study was to test the efficacy of LLLT in controlling orthodontic postadjustment pain. Thirty-nine volunteers were selected for this study that used a double-blind design with placebo control. Elastomeric separators were placed at the proximal contacts of one premolar in each quadrant of the dentition to induce orthodontic pain. The tip of a 30 mW gallium-arsenide-aluminium (830 nm) diode laser probe was then placed at the buccal gingiva and directed at the middle third of the root. Three different treatment durations of 15, 30, and 60 seconds and one placebo treatment of 30 seconds were tested within each subject. The study was conducted over 5 days, and the visual analogue scale (VAS) was used to quantify the pain experienced by the subjects before and after laser applications for each day. Analysis of the VAS median scores showed that teeth exposed to laser treatment had lower levels of pain as compared with those with the placebo treatment. However, nonparametric statistical analysis of the data showed that the differences between treatments and placebo within each subject were not statistically significant.

Analysis of subunit interaction by introducing disulfide bonds at the dimerization domain of Hin recombinase

The Hin recombinase exists as a homodimer in solution and binds to its recombination site (hix) as a dimer (Glasgow, A. C., Bruist, M. F., and Simon M. I. (1989) J. Biol. Chem. 264, 10072-10082). Previous mutational and structural studies of related proteins suggested the location of a putative dimerization domain. In order to probe the function of this region of the protein, cysteine residues were introduced at each of the seven positions comprising the domain. Proteins containing cysteine substitutions at positions 101 and 104 were able to form disulfide bonds spontaneously in crude extracts. M101C showed wild type inversion activity only if the cysteine residue was not engaged in a disulfide bond. This mutant, which is cross-linked by a disulfide bond at the dimeric interface, was found to be defective in the DNA cleavage step during inversion. H107C displayed the wild type DNA cleavage activity, even though its DNA binding activity was not detected by three different binding assays. This suggests that it maintains specificity for DNA binding but dissociates rapidly after binding. The remaining inversion-defective mutants fell into two groups. One group lost its capacity to specifically bind to DNA (G102C, F105C, and F106C), and the other group (R103C and F104C), while able to bind to DNA, was defective in subsequent steps of the inversion reaction. Characteristics of these mutants led me to postulate that movement of subunits at the dimerization interface is critical during DNA binding and during formation of the invertasome, which is the recombination structure. Furthermore, the relative position of subunits within the dimer may be important for maintaining stable DNA binding.

Molecular cloning and sequencing of sulfated glycoprotein-2 cDNA from testis of mouse: implications of two different mRNAs of SGP-2

We cloned a mouse homolog of sulfated glycoprotein-2 (SGP-2) cDNA by screening a mouse testicular cDNA library and its nucleotide sequence was determined. The predicted amino acid sequence of the cDNA shares 93% identity with that of rat SGP-2. The nucleotide sequences of both cDNAs show extensive homology throughout the open reading frames and 3' untranslated regions. The 5' untranslated regions, however, share homology only up to 28 bp upstream from the start codons; the rest of sequences are quite different. DNA sequence homology search to mouse SGP-2 cDNA through the EMBL/GenBank database and a recent study on the genomic organization of rat TRPM-2 gene suggest a possibility that there are at least two different SGP-2 mRNAs as a result of alternative splicing and/or different promoter usage in mouse.

The role of negative supercoiling in Hin-mediated site-specific recombination

A series of biochemical assays were developed and performed to monitor the molecular events that occur during the Hin-mediated DNA inversion reaction. These events can be divided into five different stages: 1) binding of proteins (Hin, Fis, and HU) to DNA; 2) pairing of Hin-binding sites; 3) invertasome formation; 4) DNA strand cleavage; 5) strand rotation and religation. A series of topoisomers of the wild type DNA substrate plasmid (ranging from fully relaxed molecules to those with more than the physiological superhelical density (the physiological superhelical density of pKH336 from Escherichia coli DH10B is -0.072 in this study)) was generated, and the role of negative supercoiling in each step of the inversion reaction was investigated. We found differences in the dependence of the formation of paired Hin-binding sites and of the invertasome formation on the superhelical density of the substrate plasmid. Pairing of Hin-binding sites occurs independently from invertasome formation, and a relatively low degree of negative supercoiling is enough to promote maximal pairing. However, efficient invertasome formation requires higher levels of negative supercoiling.

The effects of symmetrical recombination site hixC on Hin recombinase function

An artificial recombination site hixC composed of two identical half-sites that bind the Hin recombinase served as a better operator in vivo than the wild type site hixL (Hughes, K. T., Youderian, P., and Simon, M. I (1988) Genes & Dev. 2, 937-948). In vitro binding assays such as gel retardation assay and methylation protection assay demonstrated that Hin binds to hixC as tightly as it binds to hixL, even when the sites are located in negatively supercoiled plasmids. However, hixC served as a poor recombination site when it was subjected to the standard inversion assay in vitro. hixC showed a 16-fold slower inversion rate than the wild type. A series of biochemical assays designed to probe different stages of the Hin-mediated inversion reaction, demonstrated that Hin dimers bound to hixC have difficulty in forming paired hix site intermediates. KMnO4 and S1 nuclease assays detected an anomalous structure of the center of hixC only when the site was in negatively supercoiled plasmids. Mutational analysis in the central region of hixC and assays of paired hix site formation with topoisomers of the hixC substrate plasmid suggested that Hin is not able to pair hixC sites because of the presence of the anomalous structure in the center of the site. The structure does not behave like a DNA "cruciform" since Hin dimers still bind efficiently to the site. It is thought to consist of a short denatured "bubble" encompassing 2 base pairs. During the study of mutations in the center of hixC, it was found that Hin is not able to cleave DNA if a guanine residue is one of the two central nucleotides close to the cleavage site. Furthermore, Hin acts in a concerted fashion and cannot cleave any DNA strand if one of the four strands in the inversion intermediate is not cleavable.

Site-directed mutagenesis of dicarboxylic acids near the active site of Bacillus cereus 5/B/6 beta-lactamase II

An amino acid residue functioning as a general base has been proposed to assist in the hydrolysis of beta-lactam antibiotics by the zinc-containing Bacillus cereus beta-lactamase II [Bicknell & Waley (1985) Biochemistry 24, 6876-6887]. Oligonucleotide-directed mutagenesis of cloned Bacillus cereus 5/B/6 beta-lactamase II was used in an 'in vivo' study to investigate the role of carboxy-group-containing amino acids near the active site of the enzyme. Substitution of asparagine for the wild-type aspartic acid residue at position 81 resulted in fully functional enzyme. An aspartic acid residue at position 90 is essential for beta-lactamase II to confer any detectable ampicillin and cephalosporin C resistance to Escherichia coli. Conversion of Asp90 into Asn90 or Glu90 lead to the synthesis of inactive enzyme, suggesting that the spatial position of the beta-carboxy group of Asp90 is critical for enzyme function.

Some factors that influence the plasma lipoprotein 1H NMR spectra of normal and cancer patients: an oncolipid test?

Selected factors have been evaluated in order to determine their influences on the plasma lipoprotein proton NMR spectra of normal and cancer patients. The variables were donor's diet (fasting/non-fasting), temperature and time of sample storage, processing procedure, centrifugation speed, and water pre-saturation time. Plasma samples from fasting individuals that were placed immediately on ice, spun at 1,000 and 3,000 g for 15 minutes, and the proton NMR spectrum acquired with the Carr-Purcell Meiboom-Gill (CPMG) pulse sequence, using a two-second water pre-saturation time, consistently gave reproducible results. Resonances attributed to lactate were minimized under these processing conditions. Centrifugation speed and pre-saturation time did not affect the average line width; however, donor fasting state, processing temperature, and storage time did alter the line width. Most important, blood chemistry analysis revealed an inverse correlation between triglyceride levels and average methyl and methylene line widths. Thus, these factors alone caution against the indiscriminate use of proton NMR spectra to differentiate plasma from normal and cancer patients.

Mutations affecting the catalytic activity of Bacillus cereus 5/B/6 beta-lactamase II

Random in vitro mutagenesis of a cloned Bacillus cereus 5/B/6 beta-lactamase II gene was used to select defective genes unable to confer ampicillin or cephalosporin C resistance to Escherichia coli. DNA sequencing of mutant genes identified histidine at position 28 as important to beta-lactamase II function. In addition, the isolation of six identical frameshift mutants established that the carboxyl-terminal end of beta-lactamase II is critical for enzyme function. Random mutagenesis also revealed that His88 (implicated previously as one of 4 residues acting as a zinc ligand) is crucial to enzymatic activity and that a glycine to glutamic acid substitution at position 148 produced a defective beta-lactamase. Oligonucleotide mutagenesis directed at Glu37 and Glu212 suggests that these residues are inconsequential to enzyme function but that histidine at position 28 may be involved in substrate binding or recognition.

Lichen planus: a study of 72 cases in Singapore

Seventy-two patients attending this hospital with a diagnosis of lichen planus were examined. There was a striking predominance of Indians (69%) and a surprisingly low incidence of Chinese (24%) and Malays (4%) in the study population, compared to the racial composition of the general clinic population. The age distribution curve of the study population was bimodal with peaks at age groups 21-30 (22%) and 41-60 (33%) years. The most common morphologic variant was lichen planus vulgaris (common type) which we observed in 46 (64%) patients, followed by lichen planus hypertrophicus in 8 (11%) and lichen planus atrophicus in 2 (3%). Lichen planus confined to the skin was observed in 49 (68%) patients. Mucous membrane involvement was seen in 21 (29%)-17 (24%) had oral mucosa membrane involvement and 4 (6%) genital mucous membrane involvement. In 16 (22%) cases, mucous membranes were exclusively involved--12 (17%) had oral mucous membrane involvement and 4 (6%) genital mucous membrane involvement. Nail changes were only observed in 2 (3%) patients. Eight (11%) patients had associated diabetes mellitus. Overall, lichen planus appeared to pursue a protracted course with only 4 (6%) patients clearing completely after a disease duration of 5-12 months.

Chicken riboflavin-binding protein. cDNA sequence and homology with milk folate-binding protein

The Rd gene is expressed in the livers and oviducts of laying hens and codes for the riboflavin-binding protein (RfBP) of egg yolk and egg white. A lambda gt11 cDNA library derived from chicken oviduct poly(A)+ RNA was screened with polyclonal rabbit antiserum to chicken RfBP. Positive clones were isolated and rescreened with a mixed oligonucleotide probe corresponding to residues 20-25 of the mature protein. The largest cDNA clone (969 base pairs) was subcloned into plasmid pIBI21, and the nucleotide sequence was determined by the dideoxynucleotide method. This clone contained the entire coding region for RfBP. The published amino acid sequence of the mature protein was confirmed. In addition, the following 17-residue signal peptide was deduced: Met-Leu-Arg-Phe-Ala-Ile-Thr-Leu-Phe-Ala-Val-Ile-Thr-Ser-Ser-Thr-Cys. Unexpectedly, the nucleotide sequence codes for 2 adjacent arginine residues at the carboxyl terminus that are not observed in the mature protein. The amino acid sequence of RfBP is homologous with bovine milk folate-binding protein. Eight of the nine pairs of cysteines involved in disulfide bonds in RfBP are conserved in folate-binding protein, as are all of the tryptophan residues. Sequence identity between homologous regions of these two vitamin-binding proteins is more than 30%.

Cloning, nucleotide sequence, and expression of the Bacillus cereus 5/B/6 beta-lactamase II structural gene

Two forms of heat-stable, zinc-containing beta-lactamase II have been described for strains of Bacillus cereus and have been shown to differ in substrate specificity (R. B. Davies, E. P. Abraham, J. Fleming, and M. R. Pollock, Biochem. J. 145: 409-411, 1975). We report here the nucleotide sequence, inferred amino acid sequence, and expression of beta-lactamase II from B. cereus 5/B/6 and compare our results with those for its homolog characterized in B. cereus 569/H (M. Hussain, C. Anthony, M. J. Madonna, and J. O. Lampen, J. Bacteriol. 164: 223-229, 1985) to document amino acid differences contributing to the specific properties of these enzymes.

Optimal conditions for supercoil DNA sequencing with the Escherichia coli DNA polymerase I large fragment

Sequencing ladders produced from supercoiled DNA templates with the Escherichia coli DNA polymerase Klenow fragment are often unreadable because of a high background and misincorporated nucleotides. This study showed that contaminating RNA molecules can interfere with template:primer hybridization. Procedures are provided for the purification of template DNA and stringent conditions for primer-template hybridization that overcome these problems.