Biomedical subjects

Dvora Biran

Publications and source records attributed to Dvora Biran.

14 recordsLinked to original sources

PubMed2006

Genetically engineered pfabA pfabR bacteria: an electrochemical whole cell biosensor for detection of water toxicity.

We describe here a bacterial sensor for electrochemical detection of toxic chemicals. The sensor constitutes recombinant bacteria harboring plasmids encoding the fabA and fabR genes and has high-resolution amperometric response to membrane-damaging chemicals. For example, it can detect phenol at concentrations ranging between 1.6 and 16 ppm within 20 min. The high sensitivity is achieved by using the fabA promoter fused to a reporter gene-encoded beta-galactosidase on a low copy number plasmid, under the control of the FabR repressor. The use of electrochemical whole cell sensors enables sensitive, fast, easy to operate, and cost-effective detection of water toxicity threats.

Biosensing Techniques↗

PubMed2006

Requirement for the acetyl phosphate pathway in Escherichia coli ATP-dependent proteolysis.

Protein degradation is a central component of the protein quality control system. Here we show that efficient proteolysis in Escherichia coli requires the active acetyl phosphate pathway. Deletion of this pathway, leading to depletion of acetyl phosphate, results in temperature sensitivity and reduced rate of ATP-dependent proteolysis. The effect on proteolysis is general, as can be seen from the slowing down of the degradation of unstable proteins, including puromycin-derived peptides. In addition, reduced intracellular concentrations of acetyl phosphate brings about an increase in the levels of protein aggregates, which contain a wide range of proteins, as expected if a broad spectrum of substrates are involved. Additional outcomes of acetyl phosphate deficiency are elevation in the transcript levels of heat shock genes and increased thermotolerance. In E. coli the acetyl phosphate pathway is the only source of acetyl phosphate, which is a key metabolic compound involved in major cellular processes. In this communication we present evidence for the general role of the acetyl phosphate pathway in protein degradation.

ATP-Dependent Proteases↗

PubMed2005

Evolutionary plasticity of methionine biosynthesis.

Methionine is an essential cellular constituent, the initiator of protein synthesis and a precursor in many metabolic activities, such as methylation and formylation. Here we investigate the genomic distribution of the methionine biosynthetic pathway and analyze its evolutionary history by reconstructing the phylogeny of its enzymatic components. We demonstrate the evolutionary complexity of methionine synthesis and describe the various mechanisms that have shaped this biosynthetic pathway: gene duplication, functional reassignment, lateral acquisition and gene loss. Lateral gene transfer within and between domains and gene recruitment have played an important role in the evolution of this pathway, especially in its first and third enzymatic steps--homoserine activation and homocysteine methylation. These analyses are also the basis of predictions regarding methionine synthesis in Archaea, where the pathway is yet to be characterized. This study illustrates how diverse molecular solutions can fulfill a conserved function in living beings.

Arabidopsis↗

PubMed2005

The lpf operon of invasive Escherichia coli.

Extraintestinal pathogenic Escherichia coli (ExPEC) strains have been shown to code for several virulence factors involved in adherence to host tissues. Here we show the existence of an additional adherence gene cluster, coding for long polar fimbriae--LPF--in several strains of serotype O78 from septicemia and newborn meningitis. The complete gene cluster was sequenced in strain 789 (lpf789), where it is located between the genes glmS and pstS, and contains four ORFs, lpfA to lpfD. The lpf operon is expressed and is important for adherence to epithelial cells. The lpf operon was found only in four of the ExPEC strains tested and is likely to have been acquired by horizontal gene transfer.

Bacterial Adhesion↗

PubMed2005

Novel integrated electrochemical nano-biochip for toxicity detection in water.

An electrochemical nano-biochip for water toxicity detection is presented. We describe chip design, fabrication, and performance. Bacteria, which have been genetically engineered to respond to environmental stress, act as a sensor element and trigger a sequence of processes, which leads to generation of electrical current. This novel, portable and miniature device provides rapid and sensitive real-time electrochemical detection of acute toxicity in water. A clear signal is produced within less than 10 min of exposure to various concentrations of toxicants, or to stress conditions, with a direct correlation between the toxicant concentration and the induced current.

Biosensing Techniques↗

PubMed2004

Monitoring aromatic hydrocarbons by whole cell electrochemical biosensors.

In this article, we describe a bacterial whole cell electrochemical biosensors system that can be used for monitoring aromatic hydrocarbons. These bacterial biosensors are based on fusions of a promoter that is sensitive to aromatic compounds (the promoter region of the xylS gene and the xylR gene coding for the transcriptional regulator of the xyl operon) to reporter genes that can be monitored electrochemically at real-time and on-line. The xylS promoter was fused upstream of two promoterless genes coding the lacZ gene and phoA. These constructs reacted specifically to aromatic compounds but not to nonaromatic compounds, and we could detect, within minutes, micromolar concentrations of different aromatic hydrocarbons such as xylene and toluene. The use of two different reporter genes allows the future construction of a multianalyte detection system for simultaneous monitoring of several pollutants. These whole cell biosensors are potentially useful for on-line and in situ detection of aromatic compounds and as early warning systems of environmental hazards.

Alkaline Phosphatase↗

PubMed2004

Probing the active site of homoserine trans-succinylase.

Homoserine trans-succinylase is the first enzyme in methionine biosynthesis of Escherichia coli and catalyzes the activation of homoserine via a succinylation reaction. The in vivo activity of this enzyme is subject to tight regulation by several mechanisms, including repression and activation of gene expression, feedback inhibition, temperature regulation and proteolysis. This complex regulation reflects the key role of this enzyme in bacterial metabolism. Here, we demonstrate--using proteomics and high-resolution mass spectrometry--that succinyl is covalently bound to one of the two adjacent lysine residues at positions 45 and 46. Replacing these lysine residues by alanine abolished the enzymatic activity. These findings position the lysine residues, one of which is conserved, at the active site.

Acyltransferases↗

PubMed2004

Two-dimensional reference map of Agrobacterium tumefaciens proteins.

Proteomics based on two-dimensional (2-D) gel electrophoresis of proteins followed by spot identification with mass spectrometry is a commonly used method for physiological studies. Physiological proteomics requires 2-D reference maps, on which most of the main proteins are identified. We present a reference map for the bacterial plant pathogen Agrobacterium tumefaciens proteins, which contains more than 300 entries with an isoelectric point (pI) between 4 and 7. The quantitative study of the proteins in the analytical window of the master gel demonstrated unique features, in comparison with other bacteria. In addition, a theoretical analysis of several protein parameters was performed and compared with the experimental results. A comparison of the theoretical molecular weight (MW) of the proteins and their theoretical pI with their vertical and horizontal migration distances, respectively, pointed out the existence of several proteins that strongly diverted from the graph trend-line. These proteins were clearly subjected to post-translational modifications, which changed their pI and/or MW. Additional support for post-translational modifications comes from the identification of multiple spots of the same gene products. Post-translational modifications appear to be more common than expected, at least for soluble proteins, as more than 10% of the proteins were associated with multiple spots.

Agrobacterium tumefaciens↗

PubMed2004

Highly phosphorylated bacterial proteins.

We show in Gram-negative and Gram-positive bacteria the appearance of highly acidic proteins, which are highly phosphorylated. This group of proteins includes many cellular proteins, such as chaperones, biosynthetic, and metabolic enzymes. These proteins accumulate under stress conditions or under conditions, which overload the proteolytic system. Pulse chase experiments using radioactive phosphate indicate that the phosphorylated proteins have a short half-life, suggesting that they could be degradation intermediates. Moreover, results from in vitro experiments in Escherichia coli indicated that ribosomal proteins become susceptible to proteolysis after polyphosphorylation. Therefore, it is possible that the highly phosphorylated proteins represent a group of proteins tagged for degradation by phosphorylation. Such a tagging process may be involved in a general bacterial degradation pathway.

Bacterial Proteins↗

PubMed2004

The Escherichia coli DjlA and CbpA proteins can substitute for DnaJ in DnaK-mediated protein disaggregation.

The DnaJ (Hsp40) protein of Escherichia coli serves as a cochaperone of DnaK (Hsp70), whose activity is involved in protein folding, protein targeting for degradation, and rescue of proteins from aggregates. Two other E. coli proteins, CbpA and DjlA, which exhibit homology with DnaJ, are known to interact with DnaK and to stimulate its chaperone activity. Although it has been shown that in dnaJ mutants both CbpA and DjlA are essential for growth at temperatures above 37 degrees C, their in vivo role is poorly understood. Here we show that in a dnaJ mutant both CbpA and DjlA are required for efficient protein dissaggregation at 42 degrees C.

Escherichia coli↗

PubMed2003

On-line and in situ biosensors for monitoring environmental pollution.

Efficient tools for on-line and in situ monitoring of environmental pollutants are required to provide early warning systems. In addition, such tools can contribute important information on the progress of various remediation treatments. One of the recently developed monitoring technologies involves the use of whole-cell biosensors. Such biosensors could be constructed to detect general toxicity or specific toxicity caused by one or more pollutants. Currently, a large spectrum of microbial biosensors have been developed that enable the monitoring of pollutants by measuring light, fluorescence, color or electric current. Electrochemical monitoring is of special interest for in situ measurements as it can be performed using simple, compact and mobile equipment and is easily adaptable for on-line measurements. Here we survey the potential application of electrochemical biosensors in monitoring of general toxicity as well as hydrocarbons and heavy metals.

Bacteria↗

PubMed2002

Protein aggregation in Escherichia coli: role of proteases.

Protein aggregation is involved in several human diseases, and presumed to be an important process in protein quality control. In bacteria, aggregation of proteins occurs during stress conditions, such as heat shock. We studied the protein aggregates of Escherichia coli during heat shock. Our results demonstrate that the concentration and diversity of proteins in the aggregates depend on the availability of proteases. Aggregates obtained from mutants in the Lon (La) protease contain three times more protein than wild-type aggregates and show the broadest protein diversity. The results support the assumption that protein aggregates are formed from partially unfolded proteins that were not refolded by chaperones or degraded by proteases.

ATP-Dependent Proteases↗

PubMed2002

In vivo aggregation of a single enzyme limits growth of Escherichia coli at elevated temperatures.

The formation of protein aggregates is associated with unfolding and denaturation of proteins. Recent studies have indicated that, in Escherichia coli, cellular proteins tend to aggregate when the bacteria are exposed to thermal stress. Here, we show that the aggregation of one single E. coli cytoplasmic protein limits growth at elevated temperatures in minimal media. Homoserine trans-succinylase (HTS), the first enzyme in the methionine biosynthetic pathway, aggregates at temperatures higher than 44 degrees C in vitro. Above this temperature, we can also observe in vivo aggregation that results in the complete disappearance of the enzyme from the soluble fraction. Moreover, reducing the in vivo level of HTS aggregation enables growth at non-permissive temperatures. This is the first demonstration of the physiological role of aggregation of a specific protein in the growth of wild-type bacteria.

Acyltransferases↗

PubMed2002

Identification of the Omega4514 regulatory region, a developmental promoter of Myxococcus xanthus that is transcribed in vitro by the major vegetative RNA polymerase.

Omega4514 is the site of a Tn5 lac insertion in the Myxococcus xanthus genome that fuses lacZ expression to a developmentally regulated promoter. DNA upstream of the insertion site was cloned, and the promoter was localized. The promoter resembles vegetative promoters in sequence, and sigma(A) RNA polymerase, the major form of RNA polymerase in growing M. xanthus, initiated transcription from this promoter in vitro. Two complete open reading frames were identified downstream of the promoter and before the Omega4514 insertion. The first gene product (ORF1) has a putative helix-turn-helix DNA-binding motif and shows sequence similarity to transcriptional regulators. ORF2 is most similar to subunit A of glutaconate coenzyme A (CoA) transferase, which is involved in glutamate fermentation. Tn5 lac Omega4514 is inserted in the third codon of ORF3, which is similar to subunit B of glutaconate CoA-transferase. An orf1 disruption mutant exhibited a mild sporulation defect, whereas neither a disruption of orf2 nor insertion Omega4514 in orf3 caused a defect. Based on DNA sequence analysis, the three genes are likely to be cotranscribed with a fourth gene whose product is similar to alcohol dehydrogenases. ORF1 delays and reduces expression of the operon during development, but relief from this negative autoregulation does not fully explain the regulation of the operon, because expression from a small promoter-containing fragment is strongly induced during development of an orf1 mutant. Also, multiple upstream DNA elements are necessary for full developmental expression. These results suggest that transcriptional activation also regulates the operon. Omega4514 is the first example of a developmentally regulated M. xanthus operon that is transcribed by the major vegetative RNA polymerase, and its regulation appears to involve both negative autoregulation by ORF1 and positive regulation by one or more transcriptional activators.

5' Untranslated Regions↗