Molecular mechanisms of durg inhibition of DNA gyrase

DNA gyrase, an enzyme unique to prokaryotes, has been implicated in almost all processes that involve DNA. Although efficient inhibitors of this protein have been known for more than 20 years, none of them have enjoyed prolonged pharmaceutical success. It is only recently that the mechanisms of inhibition for some of these classes of drugs have been established unequivocally by X-ray crystallography. It is hoped that this detailed structural information will assist the design of novel, effective inhibitors of DNA gyrase.     

Evolutionary dynamics of spliceosomal intron revealed by <Emphasis Type="Italic">in silico</Emphasis> analyses of the P-Type ATPase superfamily genes

It has been long debated whether spliceosomal introns originated in the common ancestor of eukaryotes and prokaryotes. In this study, we tested the possibility that extant introns were inherited from the common ancestor of eukaryotes and prokaryotes using in silico simulation. We first identified 21 intron positions that are shared among different families of the P-Type ATPase superfamily, some of which are known to have diverged before the separation of prokaryotes and eukaryotes. Theoretical estimates of the expected number of intron positions shared by different genes suggest that the introns at those 21 positions were inserted independently. There seems to be no intron that arose from before the diversification of the P-Type ATPase superfamily. Namely, the present introns were inserted after the separation of eukaryotes and prokaryotes.     

Aerobiosis increases the genomic guanine plus cytosine content (GC%) in prokaryotes

The huge variation in the genomic guanine plus cytosine content (GC%) among prokaryotes has been explained by two mutually exclusive hypotheses, namely, selectionist and neutralist. The former proposals have in common the assumption that this feature is a form of adaptation to some ecological or physiological condition. On the other hand, the neutralist interpretation states that the variations are due only to different mutational biases. Since all of the traits that have been proposed by the selectionists either appeared to be limited to certain genera or were invalidated by the availability of more data, they cannot be considered as a selective force influencing the genomic GC% across all prokaryotes. In this report we show that aerobic prokaryotes display a significant increment in genomic GC% in relation to anaerobic ones. This is the first time that a link between a metabolic character and GC% has been found, independently of phylogenetic relationships and with a statistically significant amount of data.     

Evidence for the symbiotic origin of mitochondria

There are numerous characteristics in which mitochondria resemble bacteria and differ from the enveloping eukaryotic cell. These similarities and differences have been offered in support of the symbiotic origin of mitochondria. Such evidence, no matter how striking, can be faulted as representing retained primitive genome if the characteristics being compared evolved prior to the divergence of protoeukaryotes from prokaryotes. In contrast, if a characteristic evolved after this evolutionary divergence, in response to a relatively recent environmental change, it could serve as a clear marker of the symbiotic event. The enzyme superoxide dismutase, which serves as a defense against oxygen toxicity, need not have existed prior to the accumulation of photosynthetic oxygen. It probably evolved after the appearance of blue-green algae and it was apparently evolved independently by prokaryotes and by protoeukaryotes. The superoxide dismutases found in prokaryotes and in mitochondria are remarkably similar in gross properties and in amino acid sequence; whereas the corresponding enzyme of the eukaryotic cytoplasm is entirely different. This represents support for the symbiotic origin of mitochondria which is not easily argued away.     

Calcium signalling in bacteria

Whereas the importance of calcium as a cell regulator is well established in eukaryotes, the role of calcium in prokaryotes is still elusive. Over the past few years, there has been an increased interest in the role of calcium in bacteria. It has been demonstrated that as in eukaryotic organisms, the intracellular calcium concentration in prokaryotes is tightly regulated ranging from 100 to 300 nM. It has been found that calcium ions are involved in the maintenance of cell structure, motility, transport and cell differentiation processes such as sporulation, heterocyst formation and fruiting body development. In addition, a number of calcium-binding proteins have been isolated in several prokaryotic organisms. The characterization of these proteins and the identification of other factors suggest the possibility that calcium signal transduction exists in bacteria. This review presents recent developments of calcium in bacteria as it relates to signal transduction.     

Why Can’t Vertebrates Synthesize Trehalose?

The non-reducing disaccharide trehalose is a singular molecule, which has been strictly conserved throughout evolution in prokaryotes (bacteria and archaea), lower eukaryotes, plants, and invertebrates, but is absent in vertebrates and—more specifically—in mammals. There are notable differences regarding the pivotal roles played by trehalose among distantly related organisms as well as in the specific metabolic pathways of trehalose biosynthesis and/or hydrolysis, and the regulatory mechanisms that control trehalose expression genes and enzymatic activities. The success of trehalose compared with that of other structurally related molecules is attributed to its exclusive set of physical properties, which account for its physiological roles and have also promoted important biotechnological applications. However, an intriguing question still remains: why are vertebrates in general, and mammals in particular, unable (or have lost the capacity) to synthesize trehalose? The search for annotated genomes of vertebrates reveals the absence of any functional trehalose synthase gene. Indeed, this is also true for the human genome, which contains, however, two genes encoding for isoforms of the hydrolytic activity (trehalase). Although we still lack a convincing answer, this striking difference might reflect the divergent evolutionary lineages followed by invertebrates and vertebrates. Alternatively, some clinical data point to trehalose as a toxic molecule when stored inside the human body.     

Evidence for protein kinase activities in the prokaryote Salmonella typhimurium.

Evidence for phosphorylation of proteins by protein kinases has been found in Salmonella typhimurium despite previous indications that protein kinase action is absent in prokaryotes. At least four proteins have been found to be phosphorylated. Serine and threonine phosphates have been isolated from acid hydrolysates of these proteins after in vivo and in vitro labeling. The kinases do not phosphorylate histones, casein, or phosvitin. It would appear that phosphorylation as a regulatory control exists in prokaryotes.     

Mycoplasma and bacterial proteins resembling contractile proteins: a review

The basis of gliding motility in prokaryotes including certain mycoplasmas and the ability of mycoplasmas to retain their characteristic cell shapes in the absence of a supporting cell wall is unexplained. This review examines the available studies describing proteins resembling contractile proteins and cytoskeletal proteins in prokaryotes. Proteins with a significant degree of amino acid sequence homology to the myofibrillar proteins actin and myosin Al light chain and to tropomyosin have been described in prokaryotes. In addition, protein preparations from Mycoplasma pneumoniae have been shown to bind heavy meromyosin fragments, anti-actin antibody, and phalloidin; however, it remains to be proved that proteins in these preparations sharing properties with actin are synthesized by the mycoplasma.     

Zn(II) metabolism in prokaryotes

It is difficult to over-state the importance of Zn(II) in biology. It is a ubiquitous essential metal ion and plays a role in catalysis, protein structure and perhaps as a signal molecule, in organisms from all three kingdoms. Of necessity, organisms have evolved to optimise the intracellular availability of Zn(II) despite the extracellular milieu. To this end, prokaryotes contain a range of Zn(II) import, Zn(II) export and/or binding proteins, some of which utilise either ATP or the chemiosmotic potential to drive the movement of Zn(II) across the cytosolic membrane, together with proteins that facilitate the diffusion of this ion across either the outer or inner membranes of prokaryotes. This review seeks to give an overview of the systems currently classified as altering Zn(II) availability in prokaryotes.     

Comparative genomics analysis of completely sequenced microbial genomes reveals the ubiquity of N-linked glycosylation in prokaryotes

Glycosylation of proteins in prokaryotes has been known for the last few decades. Glycan structures and/or the glycosylation pathways have been experimentally characterized in only a small number of prokaryotes. Even this has become possible only during the last decade or so, primarily due to technological and methodological developments. Glycosylated proteins are diverse in their function and localization. Glycosylation has been shown to be associated with a wide range of biological phenomena. Characterization of the various types of glycans and the glycosylation machinery is critical to understand such processes. Such studies can help in the identification of novel targets for designing drugs, diagnostics, and engineering of therapeutic proteins. In view of this, the experimentally characterized pgl system of Campylobacter jejuni, responsible for N-linked glycosylation, has been used in this study to identify glycosylation loci in 865 prokaryotes whose genomes have been completely sequenced. Results from the present study show that only a small number of organisms have homologs for all the pgl enzymes and a few others have homologs for none of the pgl enzymes. Most of the organisms have homologs for only a subset of the pgl enzymes. There is no specific pattern for the presence or absence of pgl homologs vis-à-vis the 16S rRNA sequence-based phylogenetic tree. This may be due to differences in the glycan structures, high sequence divergence, horizontal gene transfer or non-orthologous gene displacement. Overall, the presence of homologs for pgl enzymes in a large number of organisms irrespective of their habitat, pathogenicity, energy generation mechanism, etc., hints towards the ubiquity of N-linked glycosylation in prokaryotes.     

Bacterial glycoproteins: functions,biosynthesis and applications

Although widely distributed in eukaryotic cells glycoproteins appear to be rare in prokaryotic organisms. The prevalence of the misconception that bacteria do not glycosylate their proteins has been a subject matter of discussion for a long time. Glycoconjugates that are linked to proteins or peptides, generated by the ribosomal translational mechanism have been reported only in the last two to three decades in a few prokaryotic organisms. Most studied prokaryotic glycoproteins are the S-layer glycoproteins of Archeabacteria. Apart from these, membrane-associated, surface-associated, secreted glycoproteins and exoenzymes glycoproteins are also well documented in both, Archea and Eubacteria. From the recent literature, it is now clear that prokaryotes are capable of glycosylating proteins. In general, prokaryotes are deprived of the cellular organelles required for glycosylation. In prokaryotes many different glycoprotein structures have been observed that display much more variation than that observed in eukaryotes. Besides following similar mechanisms in the process of glycosylation, prokaryotes have also been shown to use mechanisms that are different from those found in eukaryotes. The knowledge pertaining to the functional aspects of prokaryotic glycoproteins is rather scarce. This review summarizes developments and understanding relating to characteristics, synthesis, and functions of prokaryotic glycoproteins. An extensive summary of glycosylation that has been reported to occur in bacteria has also been tabulated. Various possible applications of these diverse biomolecules in biotechnology, vaccine development, pharmaceutics and diagnostics are also touched upon.     

The tatC gene cluster is essential for viability in halophilic archaea

In prokaryotes the twin-arginine translocase (Tat) is a unique transport system for the export of folded proteins. The Tat pathway is usually involved in the export of a small proportion of extracytoplasmic proteins. An exception is found in halophilic archaea, in which the majority of secretory proteins have been predicted to be Tat-dependent. All haloarchaea analysed to date contain two genes encoding homologues of the Tat-component TatC. In all of these cases both genes are located adjacently on the chromosome, indicating that they form a functional unit. We show that this gene cluster is essential for viability in haloarchaea, which is in complete contrast to all other prokaryotes that have been tested thus far.     

Identification of microorganisms by PCR amplification and sequencing of a universal amplified ribosomal region present in both prokaryotes and eukaryotes

The small ribosomal subunit contains 16S rRNA in prokaryotes and 18S rRNA in eukaryotes. Even though it has been known that some small ribosomal sequences are conserved in 16S rRNA and 18S rRNA molecules, they have been used separately for taxonomic and phylogenetic studies. Here, we report the existence of two highly conserved ribosomal sequences in all organisms that allow the amplification of a zone containing approximately 495 bp in prokaryotes and 508 bp in eukaryotes which we have named the "Universal Amplified Ribosomal Region" (UARR). Amplification and sequencing of this zone is possible using the same two universal primers (U1F and U1R) designed on the basis of two highly conserved ribosomal sequences. The UARR encompasses the V6, V7 and V8 domains from SSU rRNA in both prokaryotes and eukaryotes. The internal sequence of this zone in prokaryotes and eukaryotes is variable and the differences become less marked on descent from phyla to species. Nevertheless, UARR sequence allows species from the same genus to be differentiated. Thus, by UARR sequence analysis the construction of universal phylogenetic trees is possible, including species of prokaryotic and eukaryotic microorganisms together. Single isolates of prokaryotic and eukaryotic microorganisms from different sources can be identified by amplification and sequencing of UARR using the same pair of primers and the same PCR and sequencing conditions.     

Life: past, present and future

Molecular methods of taxonomy and phylogeny have changed the way in which life on earth is viewed; they have allowed us to transition from a eukaryote-centric (five-kingdoms) view of the planet to one that is peculiarly prokarote-centric, containing three kingdoms, two of which are prokaryotic unicells. These prokaryotes are distinguished from their eukaryotic counterparts by their toughness, tenacity and metabolic diversity. Realization of these features has, in many ways, changed the way we feel about life on earth, about the nature of life past and about the possibility of finding life elsewhere. In essence, the limits of life on this planet have expanded to such a degree that our thoughts of both past and future life have been altered. The abilities of prokaryotes to withstand many extreme conditions has led to the term extremophiles, used to describe the organisms that thrive under conditions thought just a few years ago, to be inconsistent with life. Perhaps the most extensive adaptation to extreme conditions, however, is represented by the ability of many bacteria to survive nutrient conditions not compatible with eukaryotic life. Prokaryotes have evolved to use nearly every redox couple that is in abundance on earth, filling the metabolic niches left behind by the oxygen-using, carbon-eating eukaryotes. This metabolic plasticity leads to a common feature in physically stratified environments of layered microbial communities, chemical indicators of the metabolic diversity of the prokaryotes. Such 'metabolic extremophily' forms a backdrop by which we can view the energy flow of life on this planet, think about what the evolutionary past of the planet might have been, and plan ways to look for life elsewhere, using the knowledge of energy flow on earth.     

Prokaryotic utilization of the twin-arginine translocation pathway: a genomic survey

The twin-arginine translocation (Tat) pathway, which has been identified in plant chloroplasts and prokaryotes, allows for the secretion of folded proteins. However, the extent to which this pathway is used among the prokaryotes is not known. By using a genomic approach, a comprehensive list of putative Tat substrates for 84 diverse prokaryotes was established. Strikingly, the results indicate that the Tat pathway is utilized to highly varying extents. Furthermore, while many prokaryotes use this pathway predominantly for the secretion of redox proteins, analyses of the predicted substrates suggest that certain bacteria and archaea secrete mainly nonredox proteins via the Tat pathway. While no correlation was observed between the number of Tat machinery components encoded by an organism and the number of predicted Tat substrates, it was noted that the composition of this machinery was specific to phylogenetic taxa.     

Identifying ‘prime suspects’: symbioses and the evolution of multicellularity

The possible involvement of symbioses in the evolution of multicellularity is explored. Evidence is drawn principally from the biology of present day associations of plants and animals with prokaryotes. A particular emphasis is placed on future research opportunities in this area of biology that have been provided by the advent of specific molecular techniques and new model systems. With the application of new approaches that result from these advances, a more holistic understanding of the biology of the coevolved communities, composed of animals or plants and their associated prokaryotes, is within the reach of biologists over the next few decades.     

mRNA decay in prokaryotes and eukaryotes: different approaches to a similar problem

Over the past 15 years considerable progress has been made in understanding the molecular mechanisms of mRNA decay in both prokaryotes and eukaryotes. Interestingly, unlike other important biological reactions such as DNA replication and repair, many features of mRNA decay differ between prokaryotes or eukaryotes. Even when a particular enzyme like poly(A) polymerase has been conserved, polyadenylation of mRNAs in prokaryotes appears to serve a very different function than it does in eukaryotes. Furthermore, while mRNA degrading multiprotein complexes have been identified in both prokaryotes and eukaryotes, their composition and biochemical mechanisms are significantly different. Accordingly, this review seeks to provide a concise comparison of our current knowledge regarding the pathways of mRNA decay in two model organisms, the prokaryote Escherichia coli and the eukaryote Saccharomyces cerevisiae.     

Predatory prokaryotes: an emerging research opportunity

Predatory prokaryotes have evolved a unique strategy of obtaining energy and biosynthetic materials from their surroundings: acquiring them from other living bacterial cells. These types of microbes have been found in a diverse variety of environments, and may play an important role in modulating microbial population structure and dynamics, as has been hypothesized for marine viruses and possibly protists. Only one genus of predatory bacterium, Bdellovibrio, has been extensively described and studied, though several other examples have been reported in the literature. In this review, the four basic strategies used by currently described predatory prokaryotes will be discussed: "wolfpack" group predation, epibiotic attachment, direct cytoplasmic invasion, and periplasmic invasion. Special adaptations to each approach will be considered, and compared overall to the genetic and biochemical characteristics of symbiotic or pathogenic prokaryotes living within eukaryotic cells. Two specific examples of predatory microbes, Bdellovibrio and Ensifer, will be described in terms of predation strategy, association with host cells, and host range. The prospects for bringing to bear the tools of molecular microbial genetics to the study of predatory prokaryotes will be explored, using current research with Bdellovibrio and Ensifer as examples.     

Quorum sensing inhibitors: An overview

Excessive and indiscriminate use of antibiotics to treat bacterial infections has lead to the emergence of multiple drug resistant strains. Most infectious diseases are caused by bacteria which proliferate within quorum sensing (QS) mediated biofilms. Efforts to disrupt biofilms have enabled the identification of bioactive molecules produced by prokaryotes and eukaryotes. These molecules act primarily by quenching the QS system. The phenomenon is also termed as quorum quenching (QQ). In addition, synthetic compounds have also been found to be effective in QQ. This review focuses primarily on natural and synthetic quorum sensing inhibitors (QSIs) with the potential for treating bacterial infections. It has been opined that the most versatile prokaryotes to produce QSI are likely to be those, which are generally regarded as safe. Among the eukaryotes, certain legumes and traditional medicinal plants are likely to act as QSIs. Such findings are likely to lead to efficient treatments with much lower doses of drugs especially antibiotics than required at present.