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Life sciences up-date. Do we need to rethink our ideas on the mechanisms of inducible processes in bacteria?

It is confirmed that for a large number of inducible stress tolerance and sensitization responses in Escherichia coli, induction is associated with the secretion of components, often proteins, which can induce related responses in other organisms under normally non-inducing conditions. For most responses, the original induction is also dependent on the functioning of the extracellular agent. It is proposed that the extracellular induction components (EICs) not only induce appropriate responses in organisms in the vicinity of those challenged by the stress, but also act as extracellular alarmones. It is predicted that the switching-on of all other inducible stress tolerances and stress cross-protection and cross-sensitization responses will be found to require similar EICs produced on exposure to appropriate stresses. It is also suggested that cultures will respond to many inhibitory chemicals such as antibiotics, chlorine, other biocides and NO (and possibly to inhibitory biological agents) by producing appropriate EICs i.e. that organisms have evolved so that on exposure to any lethal challenge or a challenge that might be expected to become lethal, they produce diffusible secreted components (EIC alarmones) which both act as a warning to other potentially vulnerable organisms and prepare those organisms to resist the expected challenge. One major stress involves transfer to higher oxygen levels and it is suggested that EIC alarmones will be involved in the rapid habituation to such conditions; such EICs may function not only to induce protection against oxidative components formed as the O2 level rises, but may also be involved in induction/repression of metabolic pathways needed to accomodate to the conditions by giving the most favourable growth at high O2. It is also predicted that envelope alterations induced by environmental changes will prove to be dependent on secreted EICs. The possibility that other inducible processes, including those involving induction or repression of enzymes or pathways by changes in nutrient level, might need EICs has also been discussed. It is concluded that the evolution of EICs now allows organisms to make a meaningful response to almost all inhibitory chemical, physical and, possibly, biological agents and agencies. Also, however, it can be argued that it would be beneficial if nutrient-regulated inducible and repressible processes involving changes in enzyme levels also depended on EICs and, accordingly, in view of such advantages, evolution may have ensured that enzyme inductions and repressions commonly involve such extracellular induction components. It is essential that this be tested. Even those responses unlikely to be associated with EIC secretion (e.g., rapid and reversible processes such as chemotactic responses) may be indirectly influenced by EICs.

Adaptation, Physiological↗

Microbial glycosaminoglycan glycosyltransferases.

Glycosaminoglycans, a class of linear polysaccharides composed of repeating disaccharide units containing a hexosamine, are important carbohydrates found in many organisms. Vertebrates utilize glycosaminoglycans in structural, recognition, adhesion, and signaling roles. Certain pathogenic bacteria produce extracellular capsules composed of glycosaminoglycans or glycosaminoglycan-like polymers that enhance the microbes' ability to infect or to colonize the host. In the period from 1993 to 2001, bacterial enzymes were discovered that catalyze the polymerization of the repeating unit of hyaluronan, chondroitin, or N-acetylheparosan (unsulfated, unepimerized heparin). Depending on the specific carbohydrate and the microorganism, either a dual-action enzyme (synthase) that transfers two distinct monosaccharides or a pair of single-action transferases are utilized to synthesize the glycosaminoglycan polymer. Current views on the enzymology, structures, potential evolution, and the roles of the known glycosyltransferases from Streptococcus, Pasteurella, and Escherichia are discussed.

Bacteria↗

Prokaryotic Genome Size and SSU rDNA Copy Number: Estimation of Microbial Relative Abundance from a Mixed Population.

> Abstract Determination of the relative abundance of a specific prokaryote in an environmental sample is of major interest in applied and environmental microbiology. Relative abundance can be calculated using knowledge of SSU rDNA copy number, amount of SSU rDNA in the sample, and a weighted average estimate of the genome sizes for organisms in the original sample. By surveying the literature, we provide estimates of genome size and SSU rDNA copy number for 303 and 101 prokaryotes, respectively. This compilation can be used to make reasonable estimates for a wide range of organisms in the calculation of relative abundance. A statistical analysis suggests that no correlation exists between genome size and SSU rDNA copy number. A phylogenetic analysis is used to offer insights into the evolution of both genome size and SSU rDNA copy number.http://link.springer-ny.com/link/service/journals/00248/bibs/38n2p93.html

Journal Article↗

Identification of a stomatin orthologue in vacuoles induced in human erythrocytes by malaria parasites. A role for microbial raft proteins in apicomplexan vacuole biogenesis.

When the human malaria parasite Plasmodium falciparum infects erythrocytes, proteins associated with host-derived detergent-resistant membrane (DRM) rafts are selectively recruited into the newly formed vacuole, but parasite proteins that contribute to raft-based vacuole development are unknown. In mammalian cells, DRM-associated integral membrane proteins such as caveolin-1 and flotillin-1 that form oligomers have been linked to the formation of DRM-based invaginations called caveolae. Here we show that the P. falciparum genome does not encode caveolins or flotillins but does contain an orthologue of human band 7 stomatin, a protein known to oligomerize, associate with non-caveolar DRMs and is distantly related to flotillins. Stomatins are members of a large protein family conserved in evolution and P. falciparum (Pf) stomatin appears to be a prokaryotic-like molecule. Evidence is presented that it associates with DRMs and may oligomerize, suggesting that these features are conserved in the stomatin family. Further, Pfstomatin is an integral membrane protein concentrated at the apical end of extracellular parasites, where it co-localizes with invasion-associated rhoptry organelles. A resident rhoptry protein, RhopH2 also resides in DRMs. This provides the first evidence that rhoptries of an apicomplexan parasite contain DRM rafts. Further, when the parasite invades erythrocytes, rhoptry Pfstomatin and RhopH2 are inserted into the newly formed vacuole. Thus, like caveolin-1 and flotillin-1, a stomatin may also associate with non-clathrin coated, DRM-enriched vacuoles. We propose a new model of invasion and vacuole formation involving DRM-based interactions of both host and parasite molecules.

Amino Acid Sequence↗

[Uncomplicated urinary tract infections, what about fosfomycin and nitrofurantoin in 2006?].

Since 2000 to 2005 we assessed the prevalence of antimicrobial resistance among uropathogens causing acute uncomplicated urinary tract infections (UTI). A total of 19 618 bacteria were studied, fosfomycin, fluoroquinolones, nitrofurantoin were in vitro the most potent drugs with more than 80% of susceptibility. If we compare year 2000 to 2005 we observed a significant decrease of susceptibility for fluoroquinolones. For the same point of comparison, fosfomycin and nitrofurantoin showed a favourable evolution. Rationale and prudent use of antibiotics must now moved us to prescribe parsimoniously fluoroquinolones especially for some indications such as uncomplicated UTI though there are some others "old antibiotics" with a role may be underestimated for this specific indication.

Anti-Bacterial Agents↗

Heat shock (stress) proteins and autoimmunity in rheumatic diseases.

The rheumatic diseases (RDs) are characterized by acute and chronic inflammation, and autoimmunity plays a major role in their pathogenesis. RDs are for the most part of unknown etiology, but recent evidence indicates that heat shock or stress proteins (HSPs) may have an important role in the etiology/pathogenesis of RDs. HSPs are produced by prokaryotic and eukaryotic cells and are grouped according to molecular weight. Phylogenetically, HSPs are very old and are remarkably conserved molecules in evolution from bacteria to humans. HSPs are induced by a variety of cellular stresses in addition to heat; cognates are expressed constitutively and are essential in a number of normal functions. Some HSPs serve as molecular chaperones, the latter defined as proteins that mediate folding of other polypeptides and either promote their assembly into oligomeric structures or disassemble the final product. Conservation of structure and function of many HSPs may provide a link between immunity to infection and the autoimmune features of RDs. Evidence is reviewed from clinical and laboratory observations that diverse microbial agents, including viruses, bacteria, and parasites, may have putative roles in the development and pathogenesis of some RDs. HSPs also are discussed in relation to the major histocompatibility complex, HLA antigens, and disease associations and how they may alter the balance between tolerance and autoimmunity. Studies are reviewed that are supportive or nonsupportive of the concept of microbial infection associated with autoimmunity; individuals first react to microbial immunizations or infections with enhanced cellular/humoral responses to the agent's HSPs. With the enhanced immune response, cross-reactivity may occur with an HSP of the stressed host because of structural similarities to the microbial HSP. If all of these events occur, the host's homologous HSP or stressed cells now become true autoantigen(s). This sequence has implications for the etiology of immune-mediated RDs, the concept of epitope sharing, and the accompanying autoimmunity. A recurring theme emphasized in some reports to understand better the role of HSPs in autoimmunity is the need to select patients with early-onset disease. A minor subpopulation of T lymphocytes express a CD3-associated T-cell receptor (TCR) heterodimer composed of gamma and delta polypeptide chains. The gamma delta + T cells have several unique features. When analyzed by the polymerase chain reaction, lymphocytes with TCR-gamma delta appear to reflect the polyclonal expansion of preexisting gamma delta clones. They are found in peripheral lymphoid tissue in very low percentage (< 5%) but may represent the majority of T cells within epithelial tissue.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗

Evolving concepts of pharmaceutical company-sponsored surveillance studies.

As a result of increasing bacterial resistance to antimicrobial agents, there is a need to conduct studies that monitor changes in susceptibility. In addition to studying the emergence and dissemination of antibacterial resistance, pharmaceutical companies perform surveillance studies for a number of reasons. As an example, the Alexander Project was conducted to study community-acquired respiratory infections internationally over 10 years. The project's findings have been valuable in the study of antimicrobial resistance. The Alexander Project has also been instrumental in the study of the evolution of resistance genes and in predictions of future rates of resistance, as well as in establishing the importance of high-quality data, the complexity of the evolution of resistance, and the need to disseminate the results in a variety of formats. Although there has been a reduction in pharmaceutical company studies, consolidated efforts between industry, government, and private groups have increased. Future surveillance efforts by pharmaceutical companies will likely be more targeted and disease directed.

Bacteria↗

Peptides as weapons against microorganisms in the chemical defense system of vertebrates.

The innate immunity of vertebrates to microbial invasion is arbitrated by a network of host-defense mechanisms involving both the long-lasting highly specific responses of the cell-mediated immune system and a nonspecific chemical defense system based on a series of broad-spectrum antimicrobial peptides that are analogous to those found in insects. Vertebrate antibiotic peptides secreted by nonlymphoid cells of the mucosal surfaces of the respiratory and gastrointestinal tracts as well as by the granular glands of the skin reportedly cause the lysis of numerous pathogenic microorganisms, including viruses, gram-positive and gram-negative bacteria, protozoa, yeasts, and fungi, as well as of cancer cells. Antimicrobial peptides isolated from vertebrates have three characteristic properties: They are relatively small (20-46 amino acid residues), basic (lysine- or arginine-rich), and amphipathic. Although these peptides differ widely in length and amino acid sequences, they may be grouped in four broad families based on characteristic structural features. Although the precise mechanism of action of these peptides remains to be defined, their microbicidal effect very likely results from their capacity to form channels or pores within the microbial membrane in order to permeate the cell and impair its ability to carry out anabolic processes. This secondary, chemical immune system provides vertebrates with a repertoire of small peptides that are promptly synthesized upon induction, easily stored in large amounts, and readily available for antimicrobial warfare.

Amino Acid Sequence↗

Biodegradation of tert-butylphenyl diphenyl phosphate.

The biodegradation of tert-butylphenyl diphenyl phosphate (BPDP) was examined in microcosms containing sediment and water from five different ecosystems as part of our studies to elucidate the environmental fate of phosphate ester flame retardants. Biodegradation of [14C]BPDP was monitored in the environmental microcosms by measuring the evolution of 14CO2. Over 37% of BPDP was mineralized after 8 weeks in microcosms from an ecosystem which had chronic exposure to agricultural chemicals. In contrast, only 1.7% of BPDP was degraded to 14CO2 in samples collected from a noncontaminated site. The exposure concentration of BPDP affected the percentage which was degraded to 14CO2 in microcosms from the two most active ecosystems. Mineralization was highest at a concentration of 0.1 mg of BPDP and was inhibited with 10- and 100-fold higher concentrations of BPDP in these microcosms. Indigenous heterotrophic and BPDP-utilizing microbial populations and phosphoesterase enzyme activities were highest in sediments which had the highest biodegradation of BPDP. We observed adaptive increases in both microbial populations and phosphoesterase enzymes in some sediments acclimated to BPDP. Chemical analyses of the residues in the microcosms indicated undegraded BPDP and minor amounts of phenol, tert-butylphenol, diphenyl phosphate, and triphenyl phosphate as biodegradation products. These data suggest that the microbial degradation of BPDP results from at least three catabolic processes and is highest when low concentrations of BPDP are exposed to sediment microorganisms of eutrophic ecosystems which have high phosphotri- and diesterase activities and previous exposure to anthropogenic chemicals.

Animals↗

Purification of (1-->3)-beta-glucan endohydrolase isoenzyme II from germinated barley and determination of its primary structure from a cDNA clone.

A (1-->3)-beta-D-glucan 3-glucanohydrolase (EC 3.2.1.39) of apparent M(r) 32,000, designated GII, has been purified from germinated barley grain and characterized. The isoenzyme is resolved from a previously purified isoenzyme (GI) on the basis of differences in their isoelectric points; (1-->3)-beta-glucanases GI and GII have pI values of 8.6 and > or = 10.0, respectively. Comparison of the sequences of their 40 NH2-terminal amino acids reveals 68% positional identity. A 1265 nucleotide pair cDNA encoding (1-->3)-beta-glucanase isoenzyme GII has been isolated from a library prepared with mRNA of 2-day germinated barley scutella. Nucleotide sequence analysis of the cDNA has enabled the complete primary structure of the 306 amino acid (1-->3)-beta-glucanase to be deduced, together with that of a putative NH2-terminal signal peptide of 28 amino acid residues. The (1-->3)-beta-glucanase cDNA is characterized by a high (G+C) content, which reflects a strong bias for the use of G or C in the wobble base position of codons. The amino acid sequence of the (1-->3)-beta-glucanase shows highly conserved internal domains and 52% overall positional identity with barley (1-->3, 1-->4)-beta-glucanase isoenzyme EII, an enzyme of related but quite distinct substrate specificity. Thus, the (1-->3)-beta-glucanases, which may provide a degree of protection against microbial invasion of germinated barley grain through their ability to degrade fungal cell wall polysaccharides, appear to share a common evolutionary origin with the (1-->3, 1-->4)-beta-glucanases, which function to depolymerize endosperm cell walls in the germinated grain.

Amino Acid Sequence↗

Manipulation of innate immunity by bacterial pathogens.

The past decade has witnessed tremendous growth in two related fields: innate immunity and microbial pathogenesis. Many pathogens have evolved mechanisms to infect their hosts in the face of a fully functional innate immune system, and there are numerous examples by which pathogens avoid recognition and/or suppress inflammation. In this review, I suggest that pathogens not only survive the innate immune response, but use it to promote their pathogenesis.

Animals↗

The role of viruses in the evolution of antibody diversity.

We propose an alternate concept for the creation of antibody diversity involving the role of viruses as mediators of genetic exchange. We suggest that both species specificity and the diversity of the immune response arose as a consequence of virus co-evolution with host organisms. Processes such as viral transformation, transduction, and integration provide mechanisms of nucleotide exchange with the host leading to antibody diversity. In this model the genes coding for antibodies are stabilized through a process of antigenic and natural selection. Stabilization of genes ensures vertical transmission of appropriate nucleotide sequences.

Antibody Specificity↗

Resistance issues and treatment implications: pneumococcus, Staphylococcus aureus, and gram-negative rods.

During the last decade there has been an unexpectedly rapid evolution of antimicrobial resistance in the respiratory pathogens for community- and hospital-acquired pneumonia. In order to choose the most optimal therapy for their patients, it is essential that physicians be aware of the prevalence and mechanisms of resistance and their implications on the effectiveness of the various antimicrobials.

Anti-Bacterial Agents↗

Thermodynamic efficiency of microbial growth is low but optimal for maximal growth rate.

Thermodynamic efficiency of microbial growth on substrates that are more oxidized than biomass approaches 24%. This is the theoretical value for a linear energy converter optimized for maximal output flow at optimal efficiency. For growth on substrates more reduced than biomass, thermodynamic efficiencies correspond to those predicted for optimization to maximal growth rate (or yield) only.

Bacteria↗

Effects of positively selected sequence variations in human and Macaca fascicularis beta-defensins 2 on antimicrobial activity.

The evolution of orthologous genes coding for beta-defensin 2 (BD2) in primates has been subject to positive selection during the divergence of the platyrrhines from the catarrhines and of the Cercopithecidae from the Hylobatidae, great apes, and humans. Three peptides have been selected for a functional analysis of the effects of sequence variations on the direct antimicrobial activity: human BD2 (hBD2), Macaca fascicularis BD2 (mfaBD2), and a variant of the human peptide lacking Asp(4), (-D)hBD2, which is characteristic only of the human/great ape peptides. hBD2 and mfaBD2 showed a significant difference in specificity, the former being more active towards Escherichia coli and the later towards Staphylococcus aureus and Candida albicans. Asp(4) in the human peptide appears to be important, as (-D)hBD2 was less structured and had a markedly lower antimicrobial activity. The evolution of beta-defensin 2 in primates may thus have been driven, at least in part, by different environmental pressures so as to modulate antimicrobial activity.

Amino Acid Sequence↗

Molecular characterization of extended-spectrum beta-lactamases produced by clinical isolates of Klebsiella pneumoniae and Escherichia coli from a Korean nationwide survey.

To determine the prevalence and genotypes of extended-spectrum beta-lactamases (ESBLs) among clinical isolates of Klebsiella pneumoniae and Escherichia coli, we performed antibiotic susceptibility testing, pI determination, induction testing, transconjugation, and DNA sequencing analysis. Among the 509 isolates collected from 13 university hospitals in Korea, 39.2% produced ESBLs. ESBL-producing isolates were detected in every region in Korea. A total of 44.6% of the isolates produced both TEM- and SHV-type ESBLs, and 52% of ESBL-producing isolates transferred resistance to ceftazidime by transconjugation. The ESBLs were TEM-19, TEM-20, TEM-52, SHV-2a, SHV-12, and one new variant identified for the first time in Korea, namely, TEM-116. TEM-1 and SHV-12 were by far the most common variants. TEM-1, TEM-116, and SHV-12 showed a high prevalence in K. pneumoniae. Two isolates (E. coli SH16 and K. pneumoniae SV3) produced CMY-1-like beta-lactamases, which play a decisive role in resistance to cefoxitin and cefotetan, as well as TEM-type enzymes (TEM-20 and TEM-52, respectively). Using MIC patterns and DNA sequencing analysis, we postulated a possible evolution scheme among TEM-type beta-lactamases in Korea: from TEM-1 to TEM-19, from TEM-19 to TEM-20, and from TEM-20 to TEM-52.

Escherichia coli↗

On the origin of microbial ORFans: quantifying the strength of the evidence for viral lateral transfer.

BACKGROUND: The origin of microbial ORFans, ORFs having no detectable homology to other ORFs in the databases, is one of the unexplained puzzles of the post-genomic era. Several hypothesis on the origin of ORFans have been suggested in the last few years, most of which based on selected, relatively small, subsets of ORFans. One of the hypotheses for the origin of ORFans is that they have been acquired thru lateral transfer from viruses. Here we carry out a comprehensive, genome-wide study on the origins of ORFans to quantify the strength of current evidence supporting this hypothesis. RESULTS: We performed similarity searches by querying all current ORFans against the public virus protein database. Surprisingly, we found that only 2.8% of all microbial ORFans have detectable homologs in viruses, while the percentage of non-ORFans with detectable homologs in viruses is 7.9%, a significantly higher figure. This suggests that the current evidence for the origin of ORFans from lateral transfer from viruses is at best weak. However, an analysis of individual genomes revealed a number of organisms with much higher percentages, many of them belonging to the Firmicutes and Gamma-proteobacteria. We provide evidence suggesting that the current virus database may be biased towards those viruses attacking Firmicutes and Gamma-proteobacteria. CONCLUSION: We conclude that as more viral genomes are sequenced, more microbial ORFans will find homologs in viruses, but this trend may vary much for individual genomes. Thus, lateral transfer from viruses alone is unlikely to explain the origin of the majority of ORFans in the majority of prokaryotes and consequently, other, not necessarily exclusive, mechanisms are likely to better explain the origin of the increasing number of ORFans.

Bacteria↗

[Some aspects of antibiotic resistance of oligotrophic bacteria].

Antibiotic resistance spectra of a large group of oligotrophic and eutrophic bacteria from the open soil and aquatic ecosystems were studied. It was shown that sometimes antibiotic resistance of the oligotrophs was of plasmid nature. A possible transfer of plasmid antibiotic resistance from oligotrophs to pathogenic eutrophic soil and aquatic bacteria in the natural ecosystems is discussed. It was demonstrated that there was no insurmountable transcription/translation barriers between oligotrophic and eutrophic bacteria though the two bacterial groups are taxonomically and evolutionally very distant. A hypothesis was proposed that oligotrophic bacteria are likely to be one of the possible pools of plasmid antibiotic resistance for pathogenic microbes. Plasmid-free strains of some oligotrophic bacteria were selected. With the method of antibioticograms, taxonomic patterns for oligotrophic bacteria of the central group were developed.

Drug Resistance, Microbial↗