Toxin-antitoxin systems in bacteria: Apoptotic tools or metabolic regulators?

The results of recent (10–12 years) research in the functions of two-gene chromosomal modules are considered and generalized. One of the genes encodes a toxin protein; the product of the other gene is an antitoxin protein. In the course of balanced bacterial growth, the toxin is constantly neutralized by the antitoxin; however, certain metabolic changes (amino acid starvation, etc.) disturb the balance and then the toxin “poisons” the cell (in most cases, by destroying mRNA). As a result, bacterial growth ceases. In accordance with one group of the data, long-term inhibition of growth of most cells results in their programmed death and destruction, corresponding to apoptosis; this allows a minor part of the population to survive due to an additional nutrient source. The results of other works show that growth inhibition is mostly reversible and the functions of the relevant gene modules are restricted to the regulation of cell metabolism, i.e., transition of bacteria to the hypometabolic state. There is also a compromise point of view. The possibilities of biotechnological applications for “toxin-antitoxin” systems are discussed.     

Antimicrobial peptides versus parasitic infections?

Reports of antimicrobial peptides generally have evaluations of their antibacterial and antifungal activities. By contrast, little is known of their activities against protozoan and metazoan parasites. In vitro antiparasitic assays suggest that antimicrobial peptides could represent a powerful tool for the development of novel drugs to fight the parasite in the vertebrate host, or to complement current therapeutic strategies.     

Methylglyoxal production in bacteria: suicide or survival?

Methylglyoxal is a toxic electrophile. In Escherichia coli cells, the principal route of methylglyoxal production is from dihydroxyacetone phosphate by the action of methylglyoxal synthase. The toxicity of methylglyoxal is believed to be due to its ability to interact with the nucleophilic centres of macromolecules such as DNA. Bacteria possess an array of detoxification pathways for methylglyoxal. In E. coli, glutathione-based detoxification is central to survival of exposure to methylglyoxal. The glutathione-dependent glyoxalase I-II pathway is the primary route of methylglyoxal detoxification, and the glutathione conjugates formed can activate the KefB and KefC potassium channels. The activation of these channels leads to a lowering of the intracellular pH of the bacterial cell, which protects against the toxic effects of electrophiles. In addition to the KefB and KefC systems, E. coli cells are equipped with a number of independent protective mechanisms whose purpose appears to be directed at ensuring the integrity of the DNA. A model of how these protective mechanisms function will be presented. The production of methylglyoxal by cells is a paradox that can be resolved by assigning an important role in adaptation to conditions of nutrient imbalance. Analysis of a methylglyoxal synthase-deficient mutant provides evidence that methylglyoxal production is required to allow growth under certain environmental conditions. The production of methylglyoxal may represent a high-risk strategy that facilitates adaptation, but which on failure leads to cell death. New strategies for antibacterial therapy may be based on undermining the detoxification and defence mechanisms coupled with deregulation of methylglyoxal synthesis. Received: 30 March 1998 / Accepted: 22 June 1998     

How many signal peptides are there in bacteria?

Over the last 5 years proteogenomics (using mass spectroscopy to identify proteins predicted from genomic sequences) has emerged as a promising approach to the high‐throughput identification of protein N‐termini, which remains a problem in genome annotation. Comparison of the experimentally determined N‐termini with those predicted by sequence analysis tools allows identification of the signal peptides and therefore conclusions on the cytoplasmic or extracytoplasmic (periplasmic or extracellular) localization of the respective proteins. We present here the results of a proteogenomic study of the signal peptides in Escherichia coli K‐12 and compare its results with the available experimental data and predictions by such software tools as SignalP and Phobius. A single proteogenomics experiment recovered more than a third of all signal peptides that had been experimentally determined during the past three decades and confirmed at least 31 additional signal peptides, mostly in the known exported proteins, which had been previously predicted but not validated. The filtering of putative signal peptides for the peptide length and the presence of an eight‐residue hydrophobic patch and a typical signal peptidase cleavage site proved sufficient to eliminate the false‐positive hits. Surprisingly, the results of this proteogenomics study, as well as a re‐analysis of the E. coli genome with the latest version of SignalP program, show that the fraction of proteins containing signal peptides is only about 10%, or half of previous estimates.     

Toxin-antitoxin pairs in bacteria: killers or stress regulators?

Plasmid toxin-antitoxin systems, which kill daughter cells that fail to inherit the plasmid genome, have chromosomal homologs in eubacteria and archaea. In this issue of Cell, Pederson et al. show that the E. coli RelE toxin cleaves mRNA in the ribosomal A site, potentially allowing it to function as a stress regulator during amino acid starvation.     

Denitrification in pathogenic bacteria: for better or worst?

A large variety of physiological and taxonomic groups have the ability to use nitrogen oxides as alternative electron acceptors. Brucella spp. is an alpha-proteobacteriaceae that induces a persistent disease in some mammals. Recent work has revealed that a denitrifying gene cluster is important in the interaction of Brucella neotomoae with its host.     

How do bacteria resist human antimicrobial peptides?

Cationic antimicrobial peptides (CAMPs), such as defensins, cathelicidins and thrombocidins, are an important human defense mechanism, protecting skin and epithelia against invading microorganisms and assisting neutrophils and platelets. Staphylococcus aureus, Salmonella enterica and other bacterial pathogens have evolved countermeasures to limit the effectiveness of CAMPs, including the repulsion of CAMPs by reducing the net negative charge of the bacterial cell envelope through covalent modification of anionic molecules (e.g. teichoic acids, phospholipids and lipid A); expelling CAMPs through energy-dependent pumps; altering membrane fluidity; and cleaving CAMPs with proteases. Mutants susceptible to CAMPs are more efficiently inactivated by phagocytes and are virulence-attenuated, indicating that CAMP resistance plays a key role in bacterial infections.     

OmpA: a pore or not a pore? Simulation and modeling studies

The bacterial outer membrane protein OmpA is composed of an N-terminal 171-residue beta-barrel domain (OmpA(171)) that spans the bilayer and a periplasmic, C-terminal domain of unknown structure. OmpA has been suggested to primarily serve a structural role, as no continuous pore through the center of the barrel can be discerned in the crystal structure of OmpA(171). However, several groups have recorded ionic conductances for bilayer-reconstituted OmpA(171). To resolve this apparent paradox we have used molecular dynamics (MD) simulations on OmpA(171) to explore the conformational dynamics of the protein, in particular the possibility of transient formation of a central pore. A total of 19 ns of MD simulations of OmpA(171) have been run, and the results were analyzed in terms of 1) comparative behavior of OmpA(171) in different bilayer and bilayer-mimetic environments, 2) solvation states of OmpA(171), and 3) pore characteristics in different MD simulations. Significant mobility was observed for residues and water molecules within the beta-barrel. A simulation in which putative gate region side chains of the barrel interior were held in a non-native conformation led to an open pore, with a predicted conductance similar to experimental measurements. The OmpA(171) pore has been shown to be somewhat more dynamic than suggested by the crystal structure. A gating mechanism is proposed to explain its documented channel properties, involving a flickering isomerization of Arg138, forming alternate salt bridges with Glu52 (closed state) and Glu128 (open state).     

The pore of TRP channels: trivial or neglected?

Ultimate proof that a protein contributes to the pore of an ion channel is demonstrating that pore properties can be altered by mutations to the putative pore-forming region. To date this has only been achieved for a few TRP proteins, and only within the TRPV subfamily. The location and structure of the pore region and selectivity filter of most TRP proteins, including all members of the TRPM and TRPC subfamilies, is currently unknown. In this review we give a short overview of the limited current knowledge about TRP channel pores and argue that further study is needed, not only for a better understanding of the mechanisms underlying cation permeation, but also to establish that all members of the TRP superfamily indeed function as bona fide ion channels.     

Cyclooxygenase-2 inhibitors: promise or peril?

The discovery of two isoforms of the cyclooxygenase enzyme, COX-1 and COX-2, and the development of COX-2-specific inhibitors as anti-inflammatories and analgesics have offered great promise that the therapeutic benefits of NSAIDs could be optimized through inhibition of COX-2, while minimizing their adverse side effect profile associated with inhibition of COX-1. While COX-2 specific inhibitors have proven to be efficacious in a variety of inflammatory conditions, exposure of large numbers of patients to these drugs in postmarketing studies have uncovered potential safety concerns that raise questions about the benefit/risk ratio of COX-2-specific NSAIDs compared to conventional NSAIDs. This article reviews the efficacy and safety profiles of COX-2-specific inhibitors, comparing them with conventional NSDAIDs.     

Catecholamine sulfates: end products or metabolic intermediates?

Dopamine-beta-hydroxylase catalyzes the beta-oxidation of dopamine to noradrenaline while phenylethanolamine-N-methyltransferase converts noradrenaline to adrenaline. Since catecholamine sulfates represent the predominant form of catecholamines in human tissues, we have studied the role of dopamine sulfate and noradrenaline sulfate as alternate substrates for dopamine-beta-hydroxylase and phenylethanolamine-N-methyltransferase, respectively. Dopamine 3-sulfate, dopamine 4-sulfate and noradrenaline 3-sulfate were chemically synthesized and exhaustively purified by ion-exchange chromatography. Dopamine-beta-hydroxylase and phenylethanolamine-N-methyltransferase were partially purified from human adrenals. Using tyramine as substrate, dopamine-beta-hydroxylase is slightly inhibited by dopamine 3-sulfate according to some irreversible or mixed mechanisms. When dopamine-beta-hydroxylase was incubated with dopamine 3-sulfate or dopamine 4-sulfate, we were not able to find any synthesis of either noradrenaline sulfate or free noradrenaline. Using phenylethanolamine as substrate, the enzymatic activity of phenylethanolamine-N-methyltransferase remains unchanged with addition of dopamine 3-sulfate, dopamine 4-sulfate or noradrenaline 3-sulfate. It was concluded that dopamine sulfate is not an alternate substrate for either dopamine-beta-hydroxylase or phenylethanolamine-N-methyltransferase nor is noradrenaline 3-sulfate an alternate substrate for phenylethanolamine-N-methyltransferase.     

Protease inhibitors in bacteria: an emerging concept for the regulation of bacterial protein complexes?

Serine protease inhibitors (serpins), the antagonists of serine proteases, were unknown in the bacterial kingdom until recently. Kang et al. in this issue of Molecular Microbiology report the cloning and functional analysis of the three serpin genes from the thermophilic anaerobic bacterium Clostridium thermocellum. Two of the serpins contain a dockerin module for location in the extracellular hydrolytic multienzyme complex, the cellulosome. The susceptibility of cellulosome to proteolytic degradation and the presence of a serine protease in the same complex provoke speculation that protease inhibitor/protease pairs could play hitherto unrecognized roles in protein stability and regulation in bacteria.     

Drosophila melanogaster FMRFamide-containing peptides: redundant or diverse functions?

FMRFamide-related peptides (FaRPs) are expressed throughout the animal kingdom and regulate a multitude of physiological activities. FaRPs have an RFamide C-terminal consensus structure that is important for interaction with the receptor. The ease of genetic manipulation and availability of genomic sequences makes Drosophila melanogaster an important experimental organism. Multiple classes of FaRPs encoded by different genes have been identified within this species. Here, we review FMRFamide-containing peptides encoded by the D. melanogaster FMRFamide gene in order to review the data on the expression, regulation, and activity of these peptides as well as acknowledge further endeavors required to elucidate FaRP signaling.     

Metabolic theory or metabolic models?

The metabolic theory of ecology (MTE) claims to derive ecological relationships from the structure of resource distribution networks, which is assumed to determine the scaling of metabolism with body mass, and from the effect of temperature on the rate of biological processes. MTE is controversial. I propose that some of the controversy stems from the implicit adoption of different views of science by the proponents and critics of MTE. The perspective of proponents is consistent with the theory-centric view of science called the received view, whereas many of the critics implicitly adopt an alternative view consistent with a model-centric view of science. I propose that adopting the model-centric view can help to settle some of the differences among proponents and critics of MTE.