A layered effect in bacterial defense

Defense systems that protect bacteria from invaders, such as viruses, are believed to be multi-layered and driven by interactions. In this issue of Cell Host & Microbe, Wu, Garushyants et al.1 delve into the dynamics between these safeguard mechanisms and unravel synergistic interactions.

Phage-plasmids promote recombination and emergence of phages and plasmids

Phages and plasmids are regarded as distinct types of mobile genetic elements that drive bacterial evolution by horizontal gene transfer. However, the distinction between both types is blurred by the existence of elements known as prophage-plasmids or phage-plasmids, which transfer horizontally between cells as viruses and vertically within cellular lineages as plasmids. Here, we study gene flow between the three types of elements. We show that the gene repertoire of phage-plasmids overlaps with those of phages and plasmids. By tracking recent recombination events, we find that phage-plasmids exchange genes more frequently with plasmids than with phages, and that direct gene exchange between plasmids and phages is less frequent in comparison. The results suggest that phage-plasmids can mediate gene flow between plasmids and phages, including exchange of mobile element core functions, defense systems, and antibiotic resistance. Moreover, a combination of gene transfer and gene inactivation may result in the conversion of elements. For example, gene loss turns P1-like phage-plasmids into integrative prophages or into plasmids (that are no longer phages). Remarkably, some of the latter have acquired conjugation-related functions to became mobilisable by conjugation. Thus, our work indicates that phage-plasmids can play a key role in the transfer of genes across mobile elements within their hosts, and can act as intermediates in the conversion of one type of element into another.

A manually curated compendium of expression profiles for the microbial cell factory Corynebacterium glutamicum

Corynebacterium glutamicum is the major host for the industrial production of amino acids and has become one of the best studied model organisms in microbial biotechnology. Rational strain construction has led to an improvement of producer strains and to a variety of novel producer strains with a broad substrate and product spectrum. A key factor for the success of these approaches is detailed knowledge of transcriptional regulation in C. glutamicum. Here, we present a large compendium of 927 manually curated microarray-based transcriptional profiles for wild-type and engineered strains detecting genome-wide expression changes of the 3,047 annotated genes in response to various environmental conditions or in response to genetic modifications. The replicates within the 927 experiments were combined to 304 microarray sets ordered into six categories that were used for differential gene expression analysis. Hierarchical clustering confirmed that no outliers were present in the sets. The compendium provides a valuable resource for future fundamental and applied research with C. glutamicum and contributes to a systemic understanding of this microbial cell factory.

Measurement(s)	Gene Expression Analysis
Technology Type(s)	Two Color Microarray
Factor Type(s)	WT condition A vs. WT condition B • Plasmid-based gene overexpression in parental strain vs. parental strain with empty vector control • Deletion mutant vs. parental strain
Sample Characteristic - Organism	Corynebacterium glutamicum
Sample Characteristic - Environment	laboratory environment
Sample Characteristic - Location	Germany

Causes and Consequences of Bacteriophage Diversification via Genetic Exchanges across Lifestyles and Bacterial Taxa

Bacteriophages (phages) evolve rapidly by acquiring genes from other phages. This results in mosaic genomes. Here, we identify numerous genetic transfers between distantly related phages and aim at understanding their frequency, consequences, and the conditions favoring them. Gene flow tends to occur between phages that are enriched for recombinases, transposases, and nonhomologous end joining, suggesting that both homologous and illegitimate recombination contribute to gene flow. Phage family and host phyla are strong barriers to gene exchange, but phage lifestyle is not. Even if we observe four times more recent transfers between temperate phages than between other pairs, there is extensive gene flow between temperate and virulent phages, and between the latter. These predominantly involve virulent phages with large genomes previously classed as low gene flux, and lead to the preferential transfer of genes encoding functions involved in cell energetics, nucleotide metabolism, DNA packaging and injection, and virion assembly. Such exchanges may contribute to the observed twice larger genomes of virulent phages. We used genetic transfers, which occur upon coinfection of a host, to compare phage host range. We found that virulent phages have broader host ranges and can mediate genetic exchanges between narrow host range temperate phages infecting distant bacterial hosts, thus contributing to gene flow between virulent phages, as well as between temperate phages. This gene flow drastically expands the gene repertoires available for phage and bacterial evolution, including the transfer of functional innovations across taxa.

Bacteria have numerous distinctive groups of phage-plasmids with conserved phage and variable plasmid gene repertoires

Plasmids and temperate phages are key contributors to bacterial evolution. They are usually regarded as very distinct. However, some elements, termed phage–plasmids, are known to be both plasmids and phages, e.g. P1, N15 or SSU5. The number, distribution, relatedness and characteristics of these phage–plasmids are poorly known. Here, we screened for these elements among ca. 2500 phages and 12000 plasmids and identified 780 phage–plasmids across very diverse bacterial phyla. We grouped 92% of them by similarity of gene repertoires to eight defined groups and 18 other broader communities of elements. The existence of these large groups suggests that phage–plasmids are ancient. Their gene repertoires are large, the average element is larger than an average phage or plasmid, and they include slightly more homologs to phages than to plasmids. We analyzed the pangenomes and the genetic organization of each group of phage–plasmids and found the key phage genes to be conserved and co-localized within distinct groups, whereas genes with homologs in plasmids are much more variable and include most accessory genes. Phage–plasmids are a sizeable fraction of the sequenced plasmids (∼7%) and phages (∼5%), and could have key roles in bridging the genetic divide between phages and other mobile genetic elements.

HrrSA orchestrates a systemic response to heme and determines prioritization of terminal cytochrome oxidase expression

Heme is a multifaceted molecule. While serving as a prosthetic group for many important proteins, elevated levels are toxic to cells. The complexity of this stimulus has shaped bacterial network evolution. However, only a small number of targets controlled by heme-responsive regulators have been described to date. Here, we performed chromatin affinity purification and sequencing to provide genome-wide insights into in vivo promoter occupancy of HrrA, the response regulator of the heme-regulated two-component system HrrSA of Corynebacterium glutamicum. Time-resolved profiling revealed dynamic binding of HrrA to more than 200 different genomic targets encoding proteins associated with heme biosynthesis, the respiratory chain, oxidative stress response and cell envelope remodeling. By repression of the extracytoplasmic function sigma factor sigC, which activates the cydABCD operon, HrrA prioritizes the expression of genes encoding the cytochrome bc1-aa3 supercomplex. This is also reflected by a significantly decreased activity of the cytochrome aa3 oxidase in the ΔhrrA mutant. Furthermore, our data reveal that HrrA also integrates the response to heme-induced oxidative stress by activating katA encoding the catalase. These data provide detailed insights in the systemic strategy that bacteria have evolved to respond to the versatile signaling molecule heme.

Impact of Xenogeneic Silencing on Phage-Host Interactions

Phages, viruses that prey on bacteria, are the most abundant and diverse inhabitants of the Earth. Temperate bacteriophages can integrate into the host genome and, as so-called prophages, maintain a long-term association with their host. The close relationship between host and virus has significantly shaped microbial evolution and phage elements may benefit their host by providing new functions. Nevertheless, the strong activity of phage promoters and potentially toxic gene products may impose a severe fitness burden and must be tightly controlled. In this context, xenogeneic silencing (XS) proteins, which can recognize foreign DNA elements, play an important role in the acquisition of novel genetic information and facilitate the evolution of regulatory networks. Currently known XS proteins fall into four classes (H-NS, MvaT, Rok and Lsr2) and have been shown to follow a similar mode of action by binding to AT-rich DNA and forming an oligomeric nucleoprotein complex that silences gene expression. In this review, we focus on the role of XS proteins in phage-host interactions by highlighting the important function of XS proteins in maintaining the lysogenic state and by providing examples of how phages fight back by encoding inhibitory proteins that disrupt XS functions in the host. Sequence analysis of available phage genomes revealed the presence of genes encoding Lsr2-type proteins in the genomes of phages infecting Actinobacteria. These data provide an interesting perspective for future studies to elucidate the impact of phage-encoded XS homologs on the phage life cycle and phage-host interactions.

Cytometry meets next-generation sequencing - RNA-Seq of sorted subpopulations reveals regional replication and iron-triggered prophage induction in Corynebacterium glutamicum

Phenotypic diversification is key to microbial adaptation. Currently, advanced technological approaches offer insights into cell-to-cell variation of bacterial populations at a spatiotemporal resolution. However, the underlying molecular causes or consequences often remain obscure. In this study, we developed a workflow combining fluorescence-activated cell sorting and RNA-sequencing, thereby allowing transcriptomic analysis of 106 bacterial cells. As a proof of concept, the workflow was applied to study prophage induction in a subpopulation of Corynebacterium glutamicum. Remarkably, both the phage genes and flanking genomic regions of the CGP3 prophage revealed significantly increased coverage upon prophage induction - a phenomenon that to date has been obscured by bulk approaches. Genome sequencing of prophage-induced populations suggested regional replication at the CGP3 locus in C. glutamicum. Finally, the workflow was applied to unravel iron-triggered prophage induction in early exponential cultures. Here, an up-shift in iron levels resulted in a heterogeneous response of an SOS (PdivS) reporter. RNA-sequencing of the induced subpopulation confirmed induction of the SOS response triggering also activation of the CGP3 prophage. The fraction of CGP3-induced cells was enhanced in a mutant lacking the iron regulator DtxR suffering from enhanced iron uptake. Altogether, these findings demonstrate the potential of the established workflow to gain insights into the phenotypic dynamics of bacterial populations.

[A cryobank as an attribute of omics technologies]

Biobanks are systematic and annotated collections of biological samples based on the system of standard operating procedures (SOP) and corresponding to the recommendations of the International Society for Biological and Environmental Repositories (ISBER). Standardization of conditions of obtaining, processing, storage of samples and providing to an end user are crucial in the activities of the biobank. The attributes of biobanks include common principles of labeling and annotation of biological samples using specialized software, an automated monitoring system of storage conditions, and registration of biosamples. Cryobanks are the biobanks maintained at the storage conditions from -196°C to -150°C that provide better cell viability and the highest preservation of biological molecules. Cryobanking is the most essential part of the infrastructure of population and personalized medicine, pharmaceuticals and biopharmacology, conservation of rare and endangered species, as well as biotechnology in general. Next Generation Biobanking, a concept especially designed for omics technologies, involves annotating biological samples on many biomarkers based on Next Generation Sequencing techniques, as well as collecting biological material from the same patient at different time points (for example, at different stages of the disease, before and after the operation, at different periods of therapy) with a detailed annotation of physiological, biochemical and clinical data. Epigenetic studies (DNA methylation, microRNA, etc.), as well as bioinformatic data analysis are of great importance in the activity of Next Generation Biobanking. Such biobanks should function based on the new ethical principles of the post-genomic era.

Dom34 Links Translation to Protein O-mannosylation

In eukaryotes, Dom34 upregulates translation by securing levels of activatable ribosomal subunits. We found that in the yeast Saccharomyces cerevisiae and the human fungal pathogen Candida albicans, Dom34 interacts genetically with Pmt1, a major isoform of protein O-mannosyltransferase. In C. albicans, lack of Dom34 exacerbated defective phenotypes of pmt1 mutants, while they were ameliorated by Dom34 overproduction that enhanced Pmt1 protein but not PMT1 transcript levels. Translational effects of Dom34 required the 5′-UTR of the PMT1 transcript, which bound recombinant Dom34 directly at a CA/AC-rich sequence and regulated in vitro translation. Polysomal profiling revealed that Dom34 stimulates general translation moderately, but that it is especially required for translation of transcripts encoding Pmt isoforms 1, 4 and 6. Because defective protein N- or O-glycosylation upregulates transcription of PMT genes, it appears that Dom34-mediated specific translational upregulation of the PMT transcripts optimizes cellular responses to glycostress. Its translational function as an RNA binding protein acting at the 5′-UTR of specific transcripts adds another facet to the known ribosome-releasing functions of Dom34 at the 3′-UTR of transcripts.

Fungi respond to damages of their glycostructures in their cell wall by transcriptional upregulation of genes that specify compensatory activities. Upon block of protein N-glycosylation, the human fungal pathogen Candida albicans increases transcription of PMT1 encoding a major isoform of protein O-mannosyltransferase. Here we demonstrate that the Dom34 protein aids in glycostress responses by upregulating the translation of several PMT isoform transcripts. Dom34 has previously been implicated in mechanisms to secure high levels of ribosomal subunits that promote translation in general, e. g. by no-go decay at the 3′-UTR of transcripts. By binding to the 5′-UTR and activating translational initiation of PMT transcripts we add a novel mode of action and suggest a preferred class of targets for the translational activities of the Dom34 protein. The combination of transcriptional and Dom34-mediated translational upregulation of PMT genes optimizes effective recovery and survival of fungal cells upon glycostress.

Preoperative Renal Tumor Embolization

The medical reports of 113 patients operated upon for renal tumors were retrospectively reviewed to assess the value of preoperative embolization. Coils or ethanol were used preoperatively in 55 patients while 58 patients underwent nephrectomy without embolization. The tumors were staged according to the TNM and the Robson staging classification. T1 and T2 tumors as well as T3 and T4 tumors were grouped together for statistical evaluation. There was no significant difference in intraoperative blood loss, operation time and survival rate between patients undergoing preoperative embolization and those who had only nephrectomy. Duration of hospital stay was always longer in the preoperatively embolized group. Preoperative embolization of renal tumors neither improved the patients' outcome nor reduced the surgical risk. Robson's classification, stage III/IV, did not show any significant differences for embolized patients or for those nephrectomized without embolization.

Silencing of cryptic prophages in Corynebacterium glutamicum

DNA of viral origin represents a ubiquitous element of bacterial genomes. Its integration into host regulatory circuits is a pivotal driver of microbial evolution but requires the stringent regulation of phage gene activity. In this study, we describe the nucleoid-associated protein CgpS, which represents an essential protein functioning as a xenogeneic silencer in the Gram-positive Corynebacterium glutamicum. CgpS is encoded by the cryptic prophage CGP3 of the C. glutamicum strain ATCC 13032 and was first identified by DNA affinity chromatography using an early phage promoter of CGP3. Genome-wide profiling of CgpS binding using chromatin affinity purification and sequencing (ChAP-Seq) revealed its association with AT-rich DNA elements, including the entire CGP3 prophage region (187 kbp), as well as several other elements acquired by horizontal gene transfer. Countersilencing of CgpS resulted in a significantly increased induction frequency of the CGP3 prophage. In contrast, a strain lacking the CGP3 prophage was not affected and displayed stable growth. In a bioinformatics approach, cgpS orthologs were identified primarily in actinobacterial genomes as well as several phage and prophage genomes. Sequence analysis of 618 orthologous proteins revealed a strong conservation of the secondary structure, supporting an ancient function of these xenogeneic silencers in phage-host interaction.

Live cell imaging of SOS and prophage dynamics in isogenic bacterial populations

Almost all bacterial genomes contain DNA of viral origin, including functional prophages or degenerated phage elements. A frequent but often unnoted phenomenon is the spontaneous induction of prophage elements (SPI) even in the absence of an external stimulus. In this study, we have analyzed SPI of the large, degenerated prophage CGP3 (187 kbp), which is integrated into the genome of the Gram-positive Corynebacterium glutamicum ATCC 13032. Time-lapse fluorescence microscopy of fluorescent reporter strains grown in microfluidic chips revealed the sporadic induction of the SOS response as a prominent trigger of CGP3 SPI but also displayed a considerable fraction (∼30%) of RecA-independent SPI. Whereas approx. 20% of SOS-induced cells recovered from this stress and resumed growth, the spontaneous induction of CGP3 always led to a stop of growth and likely cell death. A carbon source starvation experiment clearly emphasized that SPI only occurs in actively proliferating cells, whereas sporadic SOS induction was still observed in resting cells. These data highlight the impact of sporadic DNA damage on the activity of prophage elements and provide a time-resolved, quantitative description of SPI as general phenomenon of bacterial populations.

A prophage-encoded actin-like protein required for efficient viral DNA replication in bacteria

In host cells, viral replication is localized at specific subcellular sites. Viruses that infect eukaryotic and prokaryotic cells often use host-derived cytoskeletal structures, such as the actin skeleton, for intracellular positioning. Here, we describe that a prophage, CGP3, integrated into the genome of Corynebacterium glutamicum encodes an actin-like protein, AlpC. Biochemical characterization confirms that AlpC is a bona fide actin-like protein and cell biological analysis shows that AlpC forms filamentous structures upon prophage induction. The co-transcribed adaptor protein, AlpA, binds to a consensus sequence in the upstream promoter region of the alpAC operon and also interacts with AlpC, thus connecting circular phage DNA to the actin-like filaments. Transcriptome analysis revealed that alpA and alpC are among the early induced genes upon excision of the CGP3 prophage. Furthermore, qPCR analysis of mutant strains revealed that both AlpA and AlpC are required for efficient phage replication. Altogether, these data emphasize that AlpAC are crucial for the spatio-temporal organization of efficient viral replication. This is remarkably similar to actin-assisted membrane localization of eukaryotic viruses that use the actin cytoskeleton to concentrate virus particles at the egress sites and provides a link of evolutionary conserved interactions between intracellular virus transport and actin.

Referral to autopsy: effect of antemortem cardiovascular disease: a population-based study in Olmsted County, Minnesota

PURPOSE

Autopsy studies can provide insight into disease trends and their determinants, including data on the prevalence of atherosclerosis. However, such studies are subject to autopsy bias, which limits their generalizability to the source population. The impact of this bias on autopsy based estimates of time trends in heart disease prevalence is unknown. To report on the trends over time in autopsy rates in Olmsted County, MN, to examine the association between clinical diagnoses of cardiovascular diseases (CVDs) and referral to autopsy and how this association may have changed over time.

METHODS

We examined the trends in autopsy rates between 1979 and 1994 in Olmsted County, and the association between antemortem characteristics including cardiovascular diagnoses and autopsy referral.

RESULTS

From 1979 to 1994, a total of 9110 residents died in Olmsted County. The average annual autopsy rate was 30%. Autopsy rates declined from 36% in 1979 to 23% in 1994, corresponding to an average decline of 0.6%/year (p < 0.01). Referral to autopsy was positively associated with younger age, male sex, in-hospital place of death, antemortem diagnoses of myocardial infarction (MI) or peripheral vascular disease (PVD), and earlier calendar period. There was no evidence of an interaction between calendar period and any of these predictor variables. Antemortem diagnosis of heart failure was associated with a decrease in the odds of referral to autopsy over time as compared to persons without such diagnosis.

CONCLUSIONS

In Olmsted County, autopsy rates, although declining over time, have remained on average approximately 30%. Antemortem diagnoses of MI or PVD are associated with autopsy referral but this association did not change over time. While the greater decline overtime in the use of autopsy observed among decedents with an antemortem diagnosis of congestive heart failure (CHF) deserves further studies, the present findings reduce the concern for bias of time trends in the prevalence of atherosclerosis by changes in the clinical characteristics of decedents referred to autopsy.

Gamma responses and ERPs in a visual classification task

OBJECTIVE

We examined event-related potentials (ERPs) and gamma range EEG activity in a visual classification task to assess which variables affect these responses.

METHODS

Ten subjects silently counted the occurrence of rare Kanizsa squares (targets) among Kanizsa triangles and non-Kanizsa figures (standards). By applying a time-frequency analysis to the data and selectively calculating topographical maps of certain frequencies.

RESULTS

We were able to find 3 different types of gamma responses to Kanizsa figures: an early phase-locked gamma response at 40 Hz in the N100 time range, late phase-locked gamma activity (200-300 ms) at 40 Hz and a continuous phase-locked gamma response at 80 Hz due to the monitor refresh frequency. The two 40 Hz responses were significantly higher for Kanizsa figures than for non-Kanizsa figures and within the Kanizsa figures were higher for the target figure than for the non-target.

CONCLUSION

The phase-locking of these two responses, previously found also as non-phase-locked activity, could be synchronized due to the monitor flicker frequency. Also, our findings suggest that the gamma responses are not solely associated with the binding of stimulus features, but reflect some processes related to target processing.

A MEG analysis of the P300 in visual discrimination tasks

Based on recent research that indicated that P300 scalp topography varies as a function of task and/or information to be processed, this study examined scalp-recorded magnetic fields correlated with the P300 by means of whole-head magnetoencephalography. Subjects performed two discrimination tasks, in which targets, defined on either object or spatial characteristics of the same visual stimuli, had to be discriminated. Based on the across-subject root mean square (RMS) functions a sequence of 4 components could be identified in both tasks, N1m, P3m, and two later components, which, based on their estimated neuronal sources, were classified as representing motor processes during and following the manual responses to target stimuli. Reliable between-task differences in source localization were obtained for the P3m component, but not for the other components. Inferior-medial sources were found for the P3m evoked by both spatial and object targets, with these sources being located about 3.5 cm more anterior for object targets. These results suggest that different neuronal sources, possibly located in subcortical regions in the vicinity of the thalamus, contribute to the P3m evoked by target stimuli defined by either object or spatial stimulus characteristics.

The adenylation domain of tyrocidine synthetase 1--structural and functional role of the interdomain linker region and the (S/T)GT(T/S)GXPKG core sequence

Sequence analysis of peptide synthetases revealed extensive structure similarity with firefly luciferase, whose crystal structure has recently become available, providing evidence for the localization of the active site at the interface between two subdomains separated by a distorted linker region [Conti, E., Franks, N. P. & Brick, P. (1996) Structure 4, 287-298]. The functional importance of two flexible loops, corresponding to the linker region of firefly luciferase and the highly conserved (S/T)GT(T/S)GXPKG core sequence, has been studied in view of the proposed conformational changes by the use of mutant analysis, limited proteolysis and chemical modification of tyrocidine synthetase 1. Substitution of the highly conserved Arg416, residing in the loop separating the subdomains of the adenylation domain, resulted in profound loss of activity. Limited proteolysis of the mutant suggested significant structural changes as manifested by lack of protection to degradation in the presence of substrates, revealing a probable disturbance of the induced-fit mechanism regulating the transformation from an open to a closed conformation. Mutants, obtained by replacement of the conserved Lys186 from the (S/T)GT(T/S)GXPKG core sequence, displayed only minor differences in substrate-binding affinity despite significant reduction of catalytic efficiency. Residue Lys186 appears to play an important role in either stabilization of the bound substrate through charge-charge-interactions, and/or fixing of the loop for maintainance of the active-site conformation.

Event-related potentials reveal topographical and temporal distinct neuronal activation patterns for spatial and object working memory

This study examined whether working memory processes for object and spatial information are associated with different patterns of ERP activity. Subjects performed two versions of a delayed match-to-sample task in which either object forms or two-dimensional spatial configurations (S1) had to be encoded and retained in working memory for 6800 ms for comparison with a subsequent stimulus (S2). Event-related potentials (ERPs) were recorded from 29 electrode sites in the S1-S2 interval. Negative slow wave activity in the ERP varied with both, the type of memory task and the amount of materials held in working memory. When spatial information was maintained in working memory negative slow wave activity rapidly rose at recording sites overlying posterior parietal and occipital cortical areas. At these recording sites, slow wave increased in amplitude with increasing spatial memory load. For object information, load-sensitive negative slow wave activity was obtained approximately 2000 ms later than in the spatial task and it was focused to mid-frontal recording sites. Moreover, in the object memory task more pronounced negative slow wave activity was found at right inferior temporal recording sites indicating a larger involvement of the right temporal lobe in the processing of object as compared to spatial information. The results provide evidence for the notion that encoding and retention processes for object information and for spatial information can be functionally dissociated and involve differential patterns of neuronal activation rapidly shifting in time.

An immunological and genetic study of patients with gestational diabetes mellitus

The aim of the study was to evaluate the frequency of islet cell (ICA) and insulin (IAA) antibodies and of HLA antigen typing in a group of subjects diagnosed with gestational diabetes mellitus (GDM) in a screening-diagnostic program during pregnancy. ICA, complement-fixing (CF) ICA and other autoantibodies, absolute number and percentage of lymphocyte subpopulations, and HLA antigens were evaluated in 68 women with GDM and compared with those of matched controls. ICA were found in 2 (2.9%) and IAA in 1 (1.5%). Both ICA-positive women had CF-ICA; one of them was receiving insulin therapy. while the other was on a special diet. No correlations were found between ICA and IAA, nor between IAA and insulin treatment. As far as lymphocyte subsets were concerned, we found a significant increase in the absolute number of total and activated (CD3+HLA-DR+) T lymphocytes and a significant increase in the absolute number and percentage of suppressor/cytotoxic T lymphocytes (CD8) and NK lymphocytes (CD57) in GDM patients compared with normal pregnant controls. Concerning frequency for HLA A, B, C, DR antigens in the GDM population, only Cw7 was found to be significantly increased and A10 significantly decreased in comparison with controls. Our study suggests that GDM is a heterogeneous disorder in which few patients present with the immunologic and genetic markers of type 1 diabetes.

Characterization of tyrocidine synthetase 1 (TY1): requirement of posttranslational modification for peptide biosynthesis

Tyrocidine synthetase 1 (TY1), produced by Bacillus brevis ATCC 8185, consists of a single multifunctional polypeptide chain catalyzing the activation, thioesterification, and epimerization of phenylalanine. Because we were concerned about possible posttranslational issues, a comparative study between the wild-type isolate and the in Escherichia coli overexpressed protein was performed. Analysis by matrix assisted laser desorption mass spectrometry (MALDI) provided a molecular mass of 122,516 +/- 120 Da for the recombinant protein, which is in agreement with the value of 122,590 Da calculated from the gene sequence. MALDI analysis of the tryptic fragments revealed that in the recombinant TY1 the putative 4'-phosphopantetheine binding site (562Ser) is not modified by the cofactor. The substrate specificity profiles of the amino acid dependent ATP[32P]PPi exchange reactions were identical, including activation of L-phenylserine, L-tyrosine, and L-methionine. However, the rates of the reverse adenylation reaction for the recombinant protein were only 22% relative to those of the wild-type enzyme. The aminoacylation levels of about 60% for TY1 from Bacillus brevis reduced to 1.4% in the overexpressed protein. A similar distribution of the D- and the L-isomer was detected at the thioester attachment site. The pI values of the wild-type and expressed TY1 are 4.9 and 5.0, respectively. In conclusion, it could be established that apo- and holo-TY1 differ in their amino acid activating properties. Posttranslational modification by 4'-phosphopantetheine is an essential requirement for aminoacylation, epimerization, and thus the functioning of the multienzyme in peptide synthesis.

Processing of surgical instruments for minimally invasive surgery

Processing of surgical instruments for Minimally Invasive Surgery (MIS). General information on the development of Minimally Invasive Surgery and MIS instruments is given. The "MIS" scientific study group was formed to discuss and find solutions for design and hygienic problems in MIS. The article describes various groups of MIS instruments, i.e. disposable instruments, instruments with a cleaning channel, and instruments which can be dismantled. Aspects of how the instruments can be processed effectively will be discussed in detail, including an example of a survey carried out in a German hospital with a special monitoring method. Requirements are described for MIS instrumentation with regard to design, material, and surface conditions. Requirements for hygienic processing methods are listed. The article also describes the necessary control and confirmation of cleanliness, which proves to be a very particular problem. Conclusions on the present status of technology and the possibilities for future development with regard to the processing of MIS-instrumentation are given.

Identification of the ATP binding site in tyrocidine synthetase 1 by selective modification with fluorescein 5'-isothiocyanate

Identification of the nucleotide binding site in peptide synthetases has been approached by affinity labeling of tyrocidine synthetase 1 with fluorescein 5'-isothiocyanate. Binding was accompanied by irreversible inhibition of the ATP-dependent phenylalanine activation reaction and was prevented in the presence of MgATP2-. The reaction obeyed pseudo first-order rate kinetics and was accelerated by Mg2+. Complete inhibition corresponded to incorporation of 2.3 mol of fluorescein 5'-isothiocyanate (FITC)/mol of protein. Upon protection by MgATP2-, about 1 mol of FITC is still incorporated; however, this does not affect activity. The modified synthetase was extensively fragmented by tryptic digestion and the labeled fragments isolated by reverse-phase high performance liquid chromatography. Two peptides, DHQVKIR and LDKMPLTPNDKIDR, have been identified by sequencing, and the FITC conjugate of the former peptide has been detected by laser desorption mass spectrometry. The labeled residues, Lys-422 and Lys-505, are located within highly conserved segments of this new class of synthetases.

ATP binding in peptide synthetases: determination of contact sites of the adenine moiety by photoaffinity labeling of tyrocidine synthetase 1 with 2-azidoadenosine triphosphate

Characterization of the nucleotide binding domain in peptide synthetases was approached by photoaffinity labeling of tyrocidine synthetase 1 (TY1) with 2-azidoadenosine triphosphate (2-azido-ATP). Exposure of TY1 in the presence of photolabel to irradiation with ultraviolet light resulted in a time-dependent covalent modification of the enzyme with a concomitant loss of catalytic activity. Inactivation was not observed if incubation was performed in the absence of either light or the nucleotide analogue. Specificity of labeling was indicated by the ability of 2-azido-ATP to serve as a substrate in the amino acid activation reaction. The modified protein was subjected to tryptic digestion, and the fragments labeled by the nucleotide analogue were purified by reverse-phase high-performance liquid chromatography. Sequence analysis identified three tryptic peptides corresponding to residues G373-K384, W405-R416, and L483-K494, derived from the N-terminal half of the TY1 sequence. As this region shows similarity to strongly conserved regions in other peptide synthetases and acyl-CoA synthetases, it is considered to be the region catalyzing aminoacyl adenylate formation. The identified sequences appear to define components of the nucleotide binding domain found in close proximity to the adenine ring in ATP. Conservation of primary structure and homology to other carboxyl-activating enzymes of this superfamily, including peptide synthetases, insect luciferases, and acyl-CoA synthetases, is discussed.

Nucleotide binding by multienzyme peptide synthetases

Peptide synthetases consist of linearly arranged catalytic units, which by sequence alignment show equally spaced amino-acid-activating segments/modules of 600-700 amino acid residues. The consensus sequence comprises a new class of sequence motifs which are shared by some carboxyl-activating enzymes, but which do not occur in aminoacyl-tRNA synthetases. The catalytic properties of peptide synthetases with respect to the nucleotide substrate were investigated by enzyme kinetic studies. In the activation reaction ATP may be substituted by 2'-deoxy-ATP (dATP) and 7-deazaadenosine 5'-triphosphate, substrate analogues which are not recognised by many aminoacyl-tRNA synthetases, and may thus prove useful alternative substrates in the detection of peptide synthetases within complex protein mixtures. ATP derivatives substituted at C2 are substrates, while those substituted at C8 are not, indicating a preference for the anti-conformation in substrate binding. Kinetic studies revealed that coenzyme A is a non-competitive inhibitor of the activation reaction, suggesting the presence of a second nucleotide binding site which accommodates nucleotides with phosphate in the C2' or C3' position. This substrate and inhibition profile is markedly different from that of aminoacyl-tRNA synthetases and indicative of a separate homogeneous family of carboxyl-activating enzymes.

Strategic thinking and stress

In this study we investigate the behaviour and the performance of experimental subjects, who had to solve a series of tasks of 'strategic thinking' under a stress and a non-stress condition. No significant differences between the conditions could be found with respect to performance and improvement of performance within the series of tasks, but the experimental subjects exhibited under the different conditions different forms of behaviour. Unexpectedly the Ss working under the stress-condition exhibited a more 'analytical' behaviour and increased their workload, instead of decreasing it. Additionally they exhibited a tendency for measures with salient effects and proved to be better in finding the right points of main effort. The results are discussed with respect to a general theory of action regulation.

Event-related brain potentials during natural speech processing: effects of semantic, morphological and syntactic violations

The present study investigated different aspects of auditory language comprehension. The sentences which were presented as connected speech were either correct or incorrect including a semantic error (selectional restriction), a morphological error (verb inflection), or a syntactic error (phrase structure). After each sentence, a probe word was presented auditorily, and subjects had to decide whether this word was part of the preceding sentence or not. Event-related brain potentials (ERPs) were recorded from 7 scalp electrodes. The ERPs evoked by incorrect sentences differed significantly from the correct ones as a function of error type. Semantic anomalies evoked a 'classical' N400 pattern. Morphological errors elicited a pronounced negativity between 300 and 600 ms followed by a late positivity. Syntactic errors, in contrast, evoked an early negativity peaking around 180 ms followed by a negativity around 400 ms. The early negativity was only significant over the left anterior electrode. The present data demonstrate that linguistic errors of different categories evoke different ERP patterns. They indicate that with using connected speech as input, different aspects of language comprehension processes cannot only be described with respect to their temporal structure, but eventually also with respect to possible brain systems subserving these processes.

Delta-(L-alpha-aminoadipyl)-L-cysteinyl-D-valine synthetase from Aspergillus nidulans. Molecular characterization of the acvA gene encoding the first enzyme of the penicillin biosynthetic pathway

The Aspergillus nidulans gene (acvA) encoding the first catalytic steps of penicillin biosynthesis that result in the formation of delta-(L-alpha-aminoadipyl)-L-cysteinyl-D-valine (ACV), has been positively identified by matching a 15-amino acid segment of sequence obtained from an internal CNBr fragment of the purified amino-terminally blocked protein with that predicted from the DNA sequence. acvA is transcribed in the opposite orientation to ipnA (encoding isopenicillin N synthetase), with an intergenic region of 872 nucleotides. The gene has been completely sequenced at the nucleotide level and found to encode a protein of 3,770 amino acids (molecular mass, 422,486 Da). Both fast protein liquid chromatography and native gel estimates of molecular mass are consistent with this predicted molecular weight. The enzyme was identified as a glycoprotein by means of affinity blotting with concanavalin A. No evidence for the presence of introns within the acvA gene has been found. The derived amino acid sequence of ACV synthetase (ACVS) contains three homologous regions of about 585 residues, each of which displays areas of similarity with (i) adenylate-forming enzymes such as parsley 4-coumarate-CoA ligase and firefly luciferase and (ii) several multienzyme peptide synthetases, including bacterial gramicidin S synthetase 1 and tyrocidine synthetase 1. Despite these similarities, conserved cysteine residues found in the latter synthetases and thought to be essential for the thiotemplate mechanism of peptide biosynthesis have not been detected in the ACVS sequence. These observations, together with the occurrence of putative 4'-phosphopantetheine-attachment sites and a putative thioesterase site, are discussed with reference to the reaction sequence leading to production of the ACV tripeptide. We speculate that each of the homologous regions corresponds to a functional domain that recognizes one of the three substrate amino acids.

Preoperative renal tumor embolization. A useful procedure?

The medical reports of 113 patients operated upon for renal tumors were retrospectively reviewed to assess the value of preoperative embolization. Coils or ethanol were used preoperatively in 55 patients while 58 patients underwent nephrectomy without embolization. The tumors were staged according to the TNM and the Robson staging classification. T1 and T2 tumors as well as T3 and T4 tumors were grouped together for statistical evaluation. There was no significant difference in intraoperative blood loss, operation time and survival rate between patients undergoing preoperative embolization and those who had only nephrectomy. Duration of hospital stay was always longer in the preoperatively embolized group. Preoperative embolization of renal tumors neither improved the patients' outcome nor reduced the surgical risk. Robson's classification, stage III/IV, did not show any significant differences for embolized patients or for those nephrectomized without embolization.

Metabolic support: how to form a service

Organizing a metabolic and nutritional support service requires consideration of issues such as departmental affiliation, staffing, and budgeting.