ProGlycProt V3.0: updated insights into prokaryotic glycoproteins and their glycosyltransferases

ProGlycProt is a comprehensive database of experimentally validated information about protein glycosylation in prokaryotes, including the glycoproteins, glycosyltransferases, and their accessory enzymes. The first release of ProGlycProt featured experimentally validated information on glycoproteins only. For the second release in 2019, the size and scope of the database were expanded twofold, and experimental data on cognate glycosyltransferases and their accessory proteins was incorporated. The growing research and technology interest in microbial glycoproteins and their enzymes is evident from the steady rise in academic publications and patents in this area. Accordingly, the third update comprises a new section on patents related to glycosylation methods, novel glycosyltransferases, and technologies developed therefrom. The structure gallery is reorganized, wherein the number and quality of the models are upgraded with the help of AlphaFold2. Over the years, the influx of experimental proteomics data into public repositories like PRIDE has surged. Harnessing this legacy data for in-silico glycoprotein identification is a smart approach. Version 3.0 adds 45 N-glycoprotein entries annotated from MS datasets available on PRIDE and reviewed by independent research groups. With a 67% rise in entries corresponding to 119 genera of prokaryotes, the ProGlycProt continues to be the exclusive database of experimentally validated comprehensive information about protein glycosylation in prokaryotes.

Dinucleotide biases in the genomes of prokaryotic and eukaryotic dsDNA viruses and their hosts

The genomes of cellular organisms display CpG and TpA dinucleotide composition biases. Such biases have been poorly investigated in dsDNA viruses. Here, we show that in dsDNA virus, bacterial, and eukaryotic genomes, the representation of TpA and CpG dinucleotides is strongly dependent on genomic G + C content. Thus, the classical observed/expected ratios do not fully capture dinucleotide biases across genomes. Because a larger portion of the variance in TpA frequency was explained by G + C content, we explored which additional factors drive the distribution of CpG dinucleotides. Using the residuals of the linear regressions as a measure of dinucleotide abundance and ancestral state reconstruction across eukaryotic and prokaryotic virus trees, we identified an important role for phylogeny in driving CpG representation. Nonetheless, phylogenetic ANOVA analyses showed that few host associations also account for significant variations. Among eukaryotic viruses, most significant differences were observed between arthropod-infecting viruses and viruses that infect vertebrates or unicellular organisms. However, an effect of viral DNA methylation status (either driven by the host or by viral-encoded methyltransferases) is also likely. Among prokaryotic viruses, cyanobacteria-infecting phages resulted to be significantly CpG-depleted, whereas phages that infect bacteria in the genera Burkolderia and Staphylococcus were CpG-rich. Comparison with bacterial genomes indicated that this effect is largely driven by the general tendency for phages to resemble the host's genomic CpG content. Notably, such tendency is stronger for temperate than for lytic phages. Our data shed light into the processes that shape virus genome composition and inform manipulation strategies for biotechnological applications.

Clustering predicted structures at the scale of the known protein universe

Proteins are key to all cellular processes and their structure is important in understanding their function and evolution. Sequence-based predictions of protein structures have increased in accuracy1, and over 214 million predicted structures are available in the AlphaFold database2. However, studying protein structures at this scale requires highly efficient methods. Here, we developed a structural-alignment-based clustering algorithm-Foldseek cluster-that can cluster hundreds of millions of structures. Using this method, we have clustered all of the structures in the AlphaFold database, identifying 2.30 million non-singleton structural clusters, of which 31% lack annotations representing probable previously undescribed structures. Clusters without annotation tend to have few representatives covering only 4% of all proteins in the AlphaFold database. Evolutionary analysis suggests that most clusters are ancient in origin but 4% seem to be species specific, representing lower-quality predictions or examples of de novo gene birth. We also show how structural comparisons can be used to predict domain families and their relationships, identifying examples of remote structural similarity. On the basis of these analyses, we identify several examples of human immune-related proteins with putative remote homology in prokaryotic species, illustrating the value of this resource for studying protein function and evolution across the tree of life.

Generalised interrelations among mutation rates drive the genomic compliance of Chargaff's second parity rule

Chargaff's second parity rule (PR-2), where the complementary base and k-mer contents are matching within the same strand of a double stranded DNA (dsDNA), is a phenomenon that invited many explanations. The strict compliance of nearly all nuclear dsDNA to PR-2 implies that the explanation should also be similarly adamant. In this work, we revisited the possibility of mutation rates driving PR-2 compliance. Starting from the assumption-free approach, we constructed kinetic equations for unconstrained simulations. The results were analysed for their PR-2 compliance by employing symbolic regression and machine learning techniques. We arrived to a generalised set of mutation rate interrelations in place in most species that allow for their full PR-2 compliance. Importantly, our constraints explain PR-2 in genomes out of the scope of the prior explanations based on the equilibration under mutation rates with simpler no-strand-bias constraints. We thus reinstate the role of mutation rates in PR-2 through its molecular core, now shown, under our formulation, to be tolerant to previously noted strand biases and incomplete compositional equilibration. We further investigate the time for any genome to reach PR-2, showing that it is generally earlier than the compositional equilibrium, and well within the age of life on Earth.

Natural Enantiomers: Occurrence, Biogenesis and Biological Properties

The knowledge that natural products (NPs) are potent and selective modulators of important biomacromolecules (e.g., DNA and proteins) has inspired some of the world’s most successful pharmaceuticals and agrochemicals. Notwithstanding these successes and despite a growing number of reports on naturally occurring pairs of enantiomers, this area of NP science still remains largely unexplored, consistent with the adage “If you don’t seek, you don’t find”. Statistically, a rapidly growing number of enantiomeric NPs have been reported in the last several years. The current review provides a comprehensive overview of recent records on natural enantiomers, with the aim of advancing awareness and providing a better understanding of the chemical diversity and biogenetic context, as well as the biological properties and therapeutic (drug discovery) potential, of enantiomeric NPs.

Structure Basis for Shaping the Nse4 Protein by the Nse1 and Nse3 Dimer within the Smc5/6 Complex

The Smc5/6 complex facilitates chromosome replication and DNA break repair. Within this complex, a subcomplex composed of Nse1, Nse3 and Nse4 is thought to play multiple roles through DNA binding and regulating ATP-dependent activities of the complex. However, how the Nse1-Nse3-Nse4 subcomplex carries out these multiple functions remain unclear. To address this question, we determine the crystal structure of the Xenopus laevis Nse1-Nse3-Nse4 subcomplex at 1.7 Å resolution and examine how it interacts with DNA. Our structural analyses show that the Nse1-Nse3 dimer adopts a closed conformation and forms three interfaces with a segment of Nse4, forcing it into a Z-shaped conformation. The Nse1-Nse3-Nse4 structure provides an explanation for how the lung disease immunodeficiency and chromosome breakage syndrome-causing mutations could dislodge Nse4 from Nse1-Nse3. Our DNA binding and mutational analyses reveal that the N-terminal and the middle region of Nse4 contribute to DNA interaction and cell viability. Integrating our data with previous crosslink mass spectrometry data, we propose potential roles of the Nse1-Nse3-Nse4 complex in binding DNA within the Smc5/6 complex.

Recovery of subtropical coastal intertidal system prokaryotes from a destruction event and the role of extracellular polymeric substances in the presence of endocrine disrupting chemicals

Intertidal sediments constitute the micro-environment for the co-existence of endocrine disrupting chemicals (EDCs) and biofilms consisting of the microbial community and extracellular polymeric substances (EPS). However, the interactions and the resulting eco-function of this community are complex and poorly characterized, especially after a destruction event. This study evaluates the re-construction of biofilms in terms of the abundance of prokaryotic cells and related EPS characterization in two destroyed sedimentary matrices from subtropical environments simulated by sterilization in the presence of EDCs and investigates the role of EPS. The results show that benthic prokaryotes recover from the deposition of active prokaryotes in natural seawater and form biofilms after sterilization. Sterilization triggers the release of polysaccharides and protein from lysed native microbial cells and bound EPS in sedimentary organic matter, thus increasing their concentrations. The increased portion of EPS also acts as a persistent stress on re-colonizing prokaryotes and leads to the overproduction of sedimentary EPS. Due to the protective role mediated by EPS, the effect of EDCs on biofilm composition in sterilized sediment is not significant. The sedimentary matrix is the most important determinant of the composition of the biofilm and the occurrence of EDCs. At the end of an 84-day experiment, the abundance of prokaryotic cells and the concentrations of polysaccharides and protein in mangrove sediment are 1.6-1.8 times higher than those in sandflat sediment, regardless of EDCs. Sandflat sediment exhibits higher concentrations of nonylphenol and bisphenol A but a lower concentration of 17α-ethinylestradiol than mangrove sediment. This study enhances our understanding of the role of sedimentary biofilms and the fate of EDCs in intertidal systems and highlights the benefit of a destructive event in enhancing ecosystem function, particularly tolerance to EDC adversity due to EPS production.

Exploring the potentials of halophilic prokaryotes from a solar saltern for synthesizing nanoparticles: The case of silver and selenium

Halophiles are the organisms that thrive in extreme high salt environments. Despite the extensive studies on their biotechnological potentials, the ability of halophilic prokaryotes for the synthesis of nanoparticles has remained understudied. In this study, the archaeal and bacterial halophiles from a solar saltern were investigated for the intracellular/extracellular synthesis of silver and selenium nanoparticles. Silver nanoparticles were produced by the archaeal Haloferax sp. (AgNP-A, intracellular) and the bacterial Halomonas sp. (AgNP-B, extracellular), while the intracellular selenium nanoparticles were produced by the archaeal Halogeometricum sp. (SeNP-A) and the bacterial Bacillus sp. (SeNP-B). The nanoparticles were characterized by various techniques including UV-Vis spectroscopy, XRD, DLS, ICP-OES, Zeta potentials, FTIR, EDX, SEM, and TEM. The average particle size of AgNP-A and AgNP-B was 26.34 nm and 22 nm based on TEM analysis. Also, the characteristic Bragg peaks of face-centered cubic with crystallite domain sizes of 13.01 nm and 6.13 nm were observed in XRD analysis, respectively. Crystallographic characterization of SeNP-A and SeNP-B strains showed a hexagonal crystallite structure with domain sizes of 30.63 nm and 29.48 nm and average sizes of 111.6 nm and 141.6 nm according to TEM analysis, respectively. The polydispersity index of AgNP-A, AgNP-B, SeNP-A, and SeNP-B was determined as 0.26, 0.28, 0.27, and 0.36 and revealed high uniformity of the nanoparticles. All of the synthesized nanoparticles were stable and their zeta potentials were calculated as (mV): -33.12, -35.9, -31.2, and -29.34 for AgNP-A, AgNP-B, SeNP-A, and SeNP-B, respectively. The nanoparticles showed the antibacterial activity against various bacterial pathogens. The results of this study suggested that the (extremely) halophilic prokaryotes have great potentials for the green synthesis of nanoparticles.

Regulation of Low and High Nucleic Acid Fluorescent Heterotrophic Prokaryote Subpopulations and Links to Viral-Induced Mortality Within Natural Prokaryote-Virus Communities

Flow cytometric analysis of marine prokaryotes routinely reveals two distinct clusters of heterotrophic cells referred to as high nucleic acid fluorescent (HNA) and low nucleic acid fluorescent (LNA) populations. Evidence suggests that these may represent physiologically and ecologically distinct prokaryote populations. According to the "kill the winner" hypothesis, viral lysis reduces the efficiency of the microbial loop by decreasing the biomass and activity of the most abundant and active members of a population (i.e., competition specialist). Thus, viral-induced mortality may vary according to the physiology of HNA and LNA cells, with implications for the marine carbon cycle. Here, the abundance and production of heterotrophic prokaryotic populations were assessed in the North Atlantic during two phases of the annual plankton cycle and related to bottom-up (i.e., organic carbon variability) and top-down processes (i.e., viral abundance and lytic production). Our results demonstrate that the relative abundance of HNA and LNA heterotrophic cells and heterotrophic prokaryote production vary according to organic carbon variability in the water column, which can be strongly influenced by the physical eddy field (i.e., type of eddy: cyclonic, anticyclonic, or no eddy). In addition, the abundance and lytic production of virus subpopulations were correlated with  the cellular production and abundance of heterotrophic HNA and LNA prokaryote communities. Our data suggest group- and activity-specific linkages between hosts and viruses (i.e., HNA-V1 and LNA-V2). Specifically, V1 had a greater contribution to total viral production (i.e., 2.6-fold higher than V2 viruses), similar to their putative host. Finally, we explore potential implications of group- and activity-specific linkages between host and virus groups on the flux of carbon through the microbial food web.

The Chemical Transformation of the Cellular Toxin INT (2-(4-Iodophenyl)-3-(4-Nitrophenyl)-5-(Phenyl) Tetrazolium Chloride) as an Indicator of Prior Respiratory Activity in Aquatic Bacteria

In the ocean, the prokaryote respiration rates dominate the oxidation of organics, but the measurements may be biased due to pre-incubation size filtration and long incubation times. To overcome these difficulties, proxies for microbial respiration rates have been proposed, such as the in vitro and in vivo estimation of electron transport system rates (ETS) based on the reduction of tetrazolium salts. INT (2-(4-Iodophenyl)-3-(4-Nitrophenyl)-5-(Phenyl) Tetrazolium Chloride) is the most commonly applied tetrazolium salt, although it is toxic on time scales of less than 1 h for prokaryotes. This toxicity invalidates the interpretation of the rate of in vivo INT reduction to formazan as a proxy for oxygen consumption rates. We found that with aquatic bacteria, the amount of reduced INT (F; µmol/L formazan) showed excellent relation with the respiration rates prior to INT addition (R; O₂ µmol/L/hr), using samples of natural marine microbial communities and cultures of bacteria (V. harveyi) in batch and continuous cultures. We are here relating a physiological rate with the reductive potential of the poisoned cell with units of concentration. The respiration rate in cultures is well related to the cellular potential of microbial cells to reduce INT, despite the state of intoxication.

BUSCA: an integrative web server to predict subcellular localization of proteins

Here, we present BUSCA (http://busca.biocomp.unibo.it), a novel web server that integrates different computational tools for predicting protein subcellular localization. BUSCA combines methods for identifying signal and transit peptides (DeepSig and TPpred3), GPI-anchors (PredGPI) and transmembrane domains (ENSEMBLE3.0 and BetAware) with tools for discriminating subcellular localization of both globular and membrane proteins (BaCelLo, MemLoci and SChloro). Outcomes from the different tools are processed and integrated for annotating subcellular localization of both eukaryotic and bacterial protein sequences. We benchmark BUSCA against protein targets derived from recent CAFA experiments and other specific data sets, reporting performance at the state-of-the-art. BUSCA scores better than all other evaluated methods on 2732 targets from CAFA2, with a F1 value equal to 0.49 and among the best methods when predicting targets from CAFA3. We propose BUSCA as an integrated and accurate resource for the annotation of protein subcellular localization.

Impact of pyrene and cadmium co-contamination on prokaryotic community in coastal sediment microcosms

Acute ecological impacts of co-contamination of polycyclic aromatic hydrocarbons (PAHs) and heavy metals on diversity and composition of coastal benthic prokaryotes were unclear. We took pyrene (Pyr) and cadmium (Cd) as the representatives and mimicked an eight-week exposure of moderate and high levels of Pyr, Cd and their mixtures. 16S rRNA amplicon sequencing was used to investigate interaction of the contaminants in temporal succession of prokaryotes. Generally, concentrations of Pyr and HCl-extractable Cd in the sediments were stable over time. Effects and interaction of Pyr and Cd on prokaryotic α-diversity were temporally- and dose-dependent with a decreasing trend in richness and Shannon index under various contamination regimes, particularly in the single-Cd contaminated groups at the early stage. Temporal variability and Pyr-induced pattern in prokaryotic composition were observed. However, Pyr and Cd showed a persistent interaction in prokaryotic composition after 7 days, altering successional trajectories of communities. The communities under Pyr contamination regardless of Cd could be at a developing stage for an active PAH-degrading community with appearance of a pioneer Cycloclasticus phylotype, persistently showing a strong correlation with Pyr level. The associations of phylotypes and Cd level were short-lived and weak, corresponding to the overall resistance of prokaryotic composition to Cd. In the high-throughput sequencing era, using microcosm experiment, we renewed the knowledge about how prokaryotes vary in terms of α-diversity, composition and specific taxa in response to co-contamination of model contaminants at a temporal scale.

Geochemical constraints on the Hadean environment from mineral fingerprints of prokaryotes

The environmental conditions on the Earth before 4 billion years ago are highly uncertain, largely because of the lack of a substantial rock record from this period. During this time interval, known as the Hadean, the young planet transformed from an uninhabited world to the one capable of supporting, and inhabited by the first living cells. These cells formed in a fluid environment they could not at first control, with homeostatic mechanisms developing only later. It is therefore possible that present-day organisms retain some record of the primordial fluid in which the first cells formed. Here we present new data on the elemental compositions and mineral fingerprints of both Bacteria and Archaea, using these data to constrain the environment in which life formed. The cradle solution that produced this elemental signature was saturated in barite, sphene, chalcedony, apatite, and clay minerals. The presence of these minerals, as well as other chemical features, suggests that the cradle environment of life may have been a weathering fluid interacting with dry-land silicate rocks. The specific mineral assemblage provides evidence for a moderate Hadean climate with dry and wet seasons and a lower atmospheric abundance of CO2 than is present today.

Selective intra-dinucleotide interactions and periodicities of bases separated by K sites: a new vision and tool for phylogeny analyses

Direct tests of the random or non-random distribution of nucleotides on genomes have been devised to test the hypothesis of neutral, nearly-neutral or selective evolution. These tests are based on the direct base distribution and are independent of the functional (coding or non-coding) or structural (repeated or unique sequences) properties of the DNA. The first approach described the longitudinal distribution of bases in tandem repeats under the Bose-Einstein statistics. A huge deviation from randomness was found. A second approach was the study of the base distribution within dinucleotides whose bases were separated by 0, 1, 2… K nucleotides. Again an enormous difference from the random distribution was found with significances out of tables and programs. These test values were periodical and included the 16 dinucleotides. For example a high "positive" (more observed than expected dinucleotides) value, found in dinucleotides whose bases were separated by (3K + 2) sites, was preceded by two smaller "negative" (less observed than expected dinucleotides) values, whose bases were separated by (3K) or (3K + 1) sites. We examined mtDNAs, prokaryote genomes and some eukaryote chromosomes and found that the significant non-random interactions and periodicities were present up to 1000 or more sites of base separation and in human chromosome 21 until separations of more than 10 millions sites. Each nucleotide has its own significant value of its distance to neutrality; this yields 16 hierarchical significances. A three dimensional table with the number of sites of separation between the bases and the 16 significances (the third dimension is the dinucleotide, individual or taxon involved) gives directly an evolutionary state of the analyzed genome that can be used to obtain phylogenies. An example is provided.

Cache Domains That are Homologous to, but Different from PAS Domains Comprise the Largest Superfamily of Extracellular Sensors in Prokaryotes

Cellular receptors usually contain a designated sensory domain that recognizes the signal. Per/Arnt/Sim (PAS) domains are ubiquitous sensors in thousands of species ranging from bacteria to humans. Although PAS domains were described as intracellular sensors, recent structural studies revealed PAS-like domains in extracytoplasmic regions in several transmembrane receptors. However, these structurally defined extracellular PAS-like domains do not match sequence-derived PAS domain models, and thus their distribution across the genomic landscape remains largely unknown. Here we show that structurally defined extracellular PAS-like domains belong to the Cache superfamily, which is homologous to, but distinct from the PAS superfamily. Our newly built computational models enabled identification of Cache domains in tens of thousands of signal transduction proteins including those from important pathogens and model organisms. Furthermore, we show that Cache domains comprise the dominant mode of extracellular sensing in prokaryotes.

Cell-surface receptors control multiple cellular functions and are attractive targets for drug design. These receptors often have dedicated extracellular domains that bind signaling molecules, such as hormones and nutrients. Computational identification of these ligand-binding domains in genomic sequences is a pre-requisite for their further experimental characterization. Using available three-dimensional structures of several bacterial cell-surface receptors, we built computational models that enabled identification of the Cache domain, as the most common extracellular sensor module in prokaryotes, including many important pathogens. We also demonstrated that the Cache domain is homologous to, but sufficiently different from the most common intracellular sensor module, the PAS domain. These findings provide a unified view on molecular principles of signal recognition by extra- and intracellular receptors.

Thiol-based redox switches in prokaryotes

Bacteria encounter reactive oxygen species (ROS) as a consequence of the aerobic life or as an oxidative burst of activated neutrophils during infections. In addition, bacteria are exposed to other redox-active compounds, including hypochloric acid (HOCl) and reactive electrophilic species (RES) such as quinones and aldehydes. These reactive species often target the thiol groups of cysteines in proteins and lead to thiol-disulfide switches in redox-sensing regulators to activate specific detoxification pathways and to restore the redox balance. Here, we review bacterial thiol-based redox sensors that specifically sense ROS, RES and HOCl via thiol-based mechanisms and regulate gene transcription in Gram-positive model bacteria and in human pathogens, such as Staphylococcus aureus and Mycobacterium tuberculosis. We also pay particular attention to emerging widely conserved HOCl-specific redox regulators that have been recently characterized in Escherichia coli. Different mechanisms are used to sense and respond to ROS, RES and HOCl by 1-Cys-type and 2-Cys-type thiol-based redox sensors that include versatile thiol-disulfide switches (OxyR, OhrR, HypR, YodB, NemR, RclR, Spx, RsrA/RshA) or alternative Cys phosphorylations (SarZ, MgrA, SarA), thiol-S-alkylation (QsrR), His-oxidation (PerR) and methionine oxidation (HypT). In pathogenic bacteria, these redox-sensing regulators are often important virulence regulators and required for adapation to the host immune defense.

New Advances in Chromosome Architecture

Our knowledge of the "architecture" of chromosomes has grown enormously in the past decade. This new insight has been enabled largely through advances in interdisciplinary research methods at the cutting-edge interface of the life and physical sciences. Importantly this has involved several state-of-the-art biophysical tools used in conjunction with molecular biology approaches which enable investigation of chromosome structure and function in living cells. Also, there are new and emerging interfacial science tools which enable significant improvements to the spatial and temporal resolution of quantitative measurements, such as in vivo super-resolution and powerful new single-molecule biophysics methods, which facilitate probing of dynamic chromosome processes hitherto impossible. And there are also important advances in the methods of theoretical biophysics which have enabled advances in predictive modeling of this high quality experimental data from molecular and physical biology to generate new understanding of the modes of operation of chromosomes, both in eukaryotic and prokaryotic cells. Here, I discuss these advances, and take stock on the current state of our knowledge of chromosome architecture and speculate where future advances may lead.

Ultrastructural Heterogeneity of Carbonaceous Material in Ancient Cherts: Investigating Biosignature Origin and Preservation

Opaline silica deposits on Mars may be good target sites where organic biosignatures could be preserved. Potential analogues on Earth are provided by ancient cherts containing carbonaceous material (CM) permineralized by silica. In this study, we investigated the ultrastructure and chemical characteristics of CM in the Rhynie chert (c. 410 Ma, UK), Bitter Springs Formation (c. 820 Ma, Australia), and Wumishan Formation (c. 1485 Ma, China). Raman spectroscopy indicates that the CM has experienced advanced diagenesis or low-grade metamorphism at peak metamorphic temperatures of 150-350°C. Raman mapping and micro-Fourier transform infrared (micro-FTIR) spectroscopy were used to document subcellular-scale variation in the CM of fossilized plants, fungi, prokaryotes, and carbonaceous stromatolites. In the Rhynie chert, ultrastructural variation in the CM was found within individual fossils, while in coccoidal and filamentous microfossils of the Bitter Springs and formless CM of the Wumishan stromatolites ultrastructural variation was found between, not within, different microfossils. This heterogeneity cannot be explained by secondary geological processes but supports diverse carbonaceous precursors that experienced differential graphitization. Micro-FTIR analysis found that CM with lower structural order contains more straight carbon chains (has a lower R3/2 branching index) and that the structural order of eukaryotic CM is more heterogeneous than prokaryotic CM. This study demonstrates how Raman spectroscopy combined with micro-FTIR can be used to investigate the origin and preservation of silica-permineralized organics. This approach has good capability for furthering our understanding of CM preserved in Precambrian cherts, and potential biosignatures in siliceous deposits on Mars.

Life Origination Hydrate Theory (LOH-Theory) and the explanation of the biological diversification

The Life Origination Hydrate Theory (LOH-Theory) considers the life origination process as a sequence of thermodynamically caused regular and inevitable chemical transformations regulated by universal physical and chemical laws. The LOH-Theory bears on a number of experimental, thermodynamic, observation, and simulation researches. N-bases, riboses, nucleosides, and nucleotides and DNAs and RNAs are formed repeatedly within structural cavities of localizations of underground and underseabed honeycomb CH4-hydrate deposits from CH4 and nitrate and phosphate ions that diffused into the hydrate structures; proto-cells and their agglomerates originated from these DNAs and from the same minerals in the semi-liquid soup after liquation of the hydrate structures. Each localization gave rise to a multitude of different DNAs and living organisms. The species diversity is caused by the spatial and temporal repeatability of the processes of living matter origination under similar but not identical conditions, multiplicity of the DNA forms in each living matter origination event, variations in the parameters of the native medium, intraspecific variations, and interspecific variations. The contribution of the last to the species diversity is, likely, significant for prokaryotes and those eukaryotes that are only at low steps of their biological organization; however, in the light of the LOH-Theory, of available long-term paleontological investigations, and of studies of reproduction of proliferous organisms, we conclude that, in toto, the contribution of interspecific variations to the species diversity was earlier overestimated by some researchers. The reason of this overestimation is that origination of scores of «spores» of different organisms in any one event and multiple reproductions of such events in time and Earth's space were not taken into consideration.

Investigating the interplay between nucleoid-associated proteins, DNA curvature, and CRISPR elements using comparative genomics

Many prokaryotic and eukaryotic genomes feature a characteristic periodic signal in distribution of short runs of A or T (A-tracts) phased with the DNA helical period of ∼10-11 bp. Such periodic spacing of A-tracts has been associated with intrinsic DNA curvature. In eukaryotes, this periodicity is a major component of the nucleosome positioning signal but its physiological role in prokaryotes is not clear. One hypothesis centers on possible role of intrinsic DNA bends in nucleoid compaction. We use comparative genomics to investigate possible relationship between the A-tract periodicity and nucleoid-associated proteins in prokaryotes. We found that genomes with DNA-bridging proteins tend to exhibit stronger A-tract periodicity, presumably indicative of more prevalent intrinsic DNA curvature. A weaker relationship was detected for nucleoid-associated proteins that do not form DNA bridges. We consider these results an indication that intrinsic DNA curvature acts collaboratively with DNA-bridging proteins in maintaining the compact structure of the nucleoid, and that previously observed differences among prokaryotic genomes in terms DNA curvature-related sequence periodicity may reflect differences in nucleoid organization. We subsequently investigated the relationship between A-tract periodicity and presence of CRISPR elements and we found that genomes with CRISPR tend to have stronger A-tract periodicity. This result is consistent with our earlier hypothesis that extensive A-tract periodicity could help protect the chromosome against integration of prophages, possibly due to its role in compaction of the nucleoid.

MetaMetaDB: a database and analytic system for investigating microbial habitability

MetaMetaDB (http://mmdb.aori.u-tokyo.ac.jp/) is a database and analytic system for investigating microbial habitability, i.e., how a prokaryotic group can inhabit different environments. The interaction between prokaryotes and the environment is a key issue in microbiology because distinct prokaryotic communities maintain distinct ecosystems. Because 16S ribosomal RNA (rRNA) sequences play pivotal roles in identifying prokaryotic species, a system that comprehensively links diverse environments to 16S rRNA sequences of the inhabitant prokaryotes is necessary for the systematic understanding of the microbial habitability. However, existing databases are biased to culturable prokaryotes and exhibit limitations in the comprehensiveness of the data because most prokaryotes are unculturable. Recently, metagenomic and 16S rRNA amplicon sequencing approaches have generated abundant 16S rRNA sequence data that encompass unculturable prokaryotes across diverse environments; however, these data are usually buried in large databases and are difficult to access. In this study, we developed MetaMetaDB (Meta-Metagenomic DataBase), which comprehensively and compactly covers 16S rRNA sequences retrieved from public datasets. Using MetaMetaDB, users can quickly generate hypotheses regarding the types of environments a prokaryotic group may be adapted to. We anticipate that MetaMetaDB will improve our understanding of the diversity and evolution of prokaryotes.

[Prokaryotic expression, purification and antigenicity identification of recombinant human survivin protein]

OBJECTIVE

To construct a prokaryotic expression plasmid pET28a-survivin, optimize the recombinant protein expression conditions in E.coli, and purify the survivin recombinant protein and identify its antigenicity.

METHODS

Survivin cDNA segment was amplified by PCR and cloned into prokaryotic expression vector pET28a(+) to construct the recombinant expression vector pET28a-survivin. The expression vector was transformed into BL21 (DE3) and the fusion protein survivin/His was induced by IPTG. The fusion protein was purified through Ni affinity chromatography. The antigenicity of the purified survivin protein was identified by Western blotting and ELISA.

RESULTS

The recombinant expression vector was verified successfully by BamHI and HindIII. The fusion protein induced by IPTG was obtained with Mr; about 24 000. The purity of the purified protein reached 90% by SDS-PAGE analysis. And the antigenicity of the survivin protein was validated by Western blotting and ELISA.

CONCLUSION

The prokaryotic expression plasmid pET28a-survivin was successfully constructed and the survivin protein was expressed and purified in E.coli. The antigenicity of the purified survivin protein was demonstrated desirable.

Inhibition of the prokaryotic pentameric ligand-gated ion channel ELIC by divalent cations

The modulation of pentameric ligand-gated ion channels (pLGICs) by divalent cations is believed to play an important role in their regulation in a physiological context. Ions such as calcium or zinc influence the activity of pLGIC neurotransmitter receptors by binding to their extracellular domain and either potentiate or inhibit channel activation. Here we have investigated by electrophysiology and X-ray crystallography the effect of divalent ions on ELIC, a close prokaryotic pLGIC homologue of known structure. We found that divalent cations inhibit the activation of ELIC by the agonist cysteamine, reducing both its potency and, at higher concentrations, its maximum response. Crystal structures of the channel in complex with barium reveal the presence of several distinct binding sites. By mutagenesis we confirmed that the site responsible for divalent inhibition is located at the outer rim of the extracellular domain, at the interface between adjacent subunits but at some distance from the agonist binding region. Here, divalent cations interact with the protein via carboxylate side-chains, and the site is similar in structure to calcium binding sites described in other proteins. There is evidence that other pLGICs may be regulated by divalent ions binding to a similar region, even though the interacting residues are not conserved within the family. Our study provides structural and functional insight into the allosteric regulation of ELIC and is of potential relevance for the entire family.

[K+/Na+ in the animal extracellular fluid at weathering of granitoids and problem of the origin of life]

Leaching of granitoids of the paleoproterozoic age was performed from several seconds to 360 days in water solutions (pH < 6.0) in the oxygen or argon medium. Under these conditions the entrance of K+ into the solution has been shown to occur at the higher rate than that of Na+. The obtained data are considered as evidence in favor of a possibility of the existence at the earlier stages of the Earth geologic history of water reservoirs with predominance of K+ over Na+. The K+/Na+ ratio exceeding 1 has been shown in prokaryotes, in cells and tissues of the free living and parasitic species of invertebrate and vertebrate animals. At the same time in the extracellular fluid of the fresh water, marine, and terrestrial animals, in which the Na+ concentration varies from 13 to 482 mmol/l, the K+/Na+ ratio is preserved at the level of 0.034 +/- 0.001. These results are discussed in connection with the problem of origin of protocells and of concentration ratios of monovalent cations in water phases of multicellular organisms.

TBC: a clustering algorithm based on prokaryotic taxonomy

High-throughput DNA sequencing technologies have revolutionized the study of microbial ecology. Massive sequencing of PCR amplicons of the 16S rRNA gene has been widely used to understand the microbial community structure of a variety of environmental samples. The resulting sequencing reads are clustered into operational taxonomic units that are then used to calculate various statistical indices that represent the degree of species diversity in a given sample. Several algorithms have been developed to perform this task, but they tend to produce different outcomes. Herein, we propose a novel sequence clustering algorithm, namely Taxonomy-Based Clustering (TBC). This algorithm incorporates the basic concept of prokaryotic taxonomy in which only comparisons to the type strain are made and used to form species while omitting full-scale multiple sequence alignment. The clustering quality of the proposed method was compared with those of MOTHUR, BLASTClust, ESPRIT-Tree, CD-HIT, and UCLUST. A comprehensive comparison using three different experimental datasets produced by pyrosequencing demonstrated that the clustering obtained using TBC is comparable to those obtained using MOTHUR and ESPRIT-Tree and is computationally efficient. The program was written in JAVA and is available from http://sw.ezbiocloud.net/tbc.

[Preparation of prokaryotic cDNA for high-throughput transcriptome analysis]

High contents of non-coding RNA in total bacteria RNA complicates considerably transcriptome analysis using standard approaches like high-throughput sequencing, gene expression profiles, subtractive hybridization. We suggest a procedure of preparation of bacterial cDNA for transcriptomics that includes rRNA and tRNA depletion with preservation of relative abundance of coding sequences. The method is based on the second order hybridization kinetics and unique properties of Kanchatka crab duplex-specific nuclease. The method efficacy was demonstrated on a model experiments.

Structural disorder in eukaryotes

Based on early bioinformatic studies on a handful of species, the frequency of structural disorder of proteins is generally thought to be much higher in eukaryotes than in prokaryotes. To refine this view, we present here a comparative prediction study and analysis of 194 fully described eukaryotic proteomes and 87 reference prokaryotes for structural disorder. We found that structural disorder does distinguish eukaryotes from prokaryotes, but its frequency spans a very wide range in the two superkingdoms that largely overlap. The number of disordered binding regions and different Pfam domain types also contribute to distinguish eukaryotes from prokaryotes. Unexpectedly, the highest levels--and highest variability--of predicted disorder is found in protists, i.e. single-celled eukaryotes, often surpassing more complex eukaryote organisms, plants and animals. This trend contrasts with that of the number of domain types, which increases rather monotonously toward more complex organisms. The level of structural disorder appears to be strongly correlated with lifestyle, because some obligate intracellular parasites and endosymbionts have the lowest levels, whereas host-changing parasites have the highest level of predicted disorder. We conclude that protists have been the evolutionary hot-bed of experimentation with structural disorder, in a period when structural disorder was actively invented and the major functional classes of disordered proteins established.

[Construction of prokaryotic expression vectors for tandem affinity purification]

OBJECTIVE

To construct prokaryotic expression vectors suitable for tandem affinity purification to study protein-protein interactions in bacteria.

METHODS

Two tandem affinity tag sequences, including the coding sequences of Protein G and streptavidin binding protein (SBP), as the N- and C- terminus of fusion proteins were designed and de novo synthesized. Constitutive expression vectors pNTAP and pCTAP were constructed using pUC18 as the backbone deleted of the lacI gene.

RESULTS

Two expression vectors pNTAP and pCTAP were successfully constructed, pNTAP showed substantial expression of the built-in tag protein GFPuv not only in Escherichia coli BL21 (DE3) but also in enterohemorrhagic Escherichia coli O157:H7 and Shigella flexneri 5a.

CONCLUSION

Of the two recombinant expression vectors successfully constructed, pNTAP can express the model protein for tandem affinity purification and could be used for studies of protein-protein interactions in some gram-negative pathogenic bacteria such as Escherichia coli and Shigella flexneri.

Tumor malignancy is engaged to prokaryotic homolog toolbox

Cancer cells display high proliferation rates and survival provided by high glycolysis, chemoresistance and radioresistance, metabolic features that appear to be activated with malignancy, and seemed to have arisen as early in evolution as in unicellular/prokaryotic organisms. Based on these assumptions, we hypothesize that aggressive phenotypes found in malignant cells may be related to acquired unicellular behavior, launched within a tumor when viral and prokaryotic homologs are overexpressed performing likely robust functions. The ensemble of these expressed viral and prokaryotic close homologs in the proteome of a tumor tissue gives them advantage over normal cells. To assess the hypothesis validity, sequences of human proteins involved in apoptosis, energetic metabolism, cell mobility and adhesion, chemo- and radio-resistance were aligned to homologs present in other life forms, excluding all eukaryotes, using PSI-BLAST, with further corroboration from data available in the literature. The analysis revealed that selected sequences of proteins involved in apoptosis and tumor suppression (as p53 and pRB) scored non-significant (E-value>0.001) with prokaryotic homologs; on the other hand, human proteins involved in cellular chemo- and radio-resistance scored highly significant with prokaryotic and viral homologs (as catalase, E-value=zero). We inferred that such upregulated and/or functionally activated proteins in aggressive malignant cells represent a toolbox of modern human homologs evolved from a similar key set that have granted survival of ancient prokaryotes against extremely harsh environments. According to what has been discussed along this analysis, high mutation rates usually hit hotspots in important conserved protein domains, allowing uncontrolled expansion of more resistant, death-evading malignant clones. That is the case of point mutations in key viral proteins affording viruses escape to chemotherapy, and human homologs of such retroviral proteins (as Ras, Akt and EGFR) can elicit the same phenotype. Furthermore, a corollary to this hypothesis presumes that target-directed anti-cancer therapy should target human protein domains of low similarity to prokaryotic homologs for a well-succeeded anti-cancer therapy.

[DNA-topoisomerases and their functions in cell]

DNA-topoisomerases are sophisticated enzymes controlling DNA topology in cells. A lot of new data concerning the structure and functions of topoisomerases was published recently. In this review authors discuss basic features of the different types of topoisomerases with respect to catalytic mechanism and focus at the involvement of topoisomerases in various DNA-related cellular processes, such as replication, transcription, recombination, chromatin condensation and daughter chromatides partitioning.

Mechanisms of Sec61/SecY-mediated protein translocation across membranes

The Sec61 or SecY channel, a universally conserved protein-conducting channel, translocates proteins across and integrates proteins into the eukaryotic endoplasmic reticulum (ER) membrane and the prokaryotic plasma membrane. Depending on channel-binding partners, polypeptides are moved by different mechanisms. In cotranslational translocation, the ribosome feeds the polypeptide chain directly into the channel. In posttranslational translocation, a ratcheting mechanism is used by the ER-lumenal chaperone BiP in eukaryotes, and a pushing mechanism is utilized by the SecA ATPase in bacteria. In prokaryotes, posttranslational translocation is facilitated through the function of the SecD/F protein. Recent structural and biochemical data show how the channel opens during translocation, translocates soluble proteins, releases hydrophobic segments of membrane proteins into the lipid phase, and maintains the barrier for small molecules.

From water and ions to crowded biomacromolecules: in vivo structuring of a prokaryotic cell

The interactions and processes which structure prokaryotic cytoplasm (water, ions, metabolites, and biomacromolecules) and ensure the fidelity of the cell cycle are reviewed from a physicochemical perspective. Recent spectroscopic and biological evidence shows that water has no active structuring role in the cytoplasm, an unnecessary notion still entertained in the literature; water acts only as a normal solvent and biochemical reactant. Subcellular structuring arises from localizations and interactions of biomacromolecules and from the growth and modifications of their surfaces by catalytic reactions. Biomacromolecular crowding is a fundamental physicochemical characteristic of cells in vivo. Though some biochemical and physiological effects of crowding (excluded volume effect) have been documented, crowding assays with polyglycols, dextrans, etc., do not properly mimic the compositional variety of biomacromolecules in vivo. In vitro crowding assays are now being designed with proteins, which better reflect biomacromolecular environments in vivo, allowing for hydrophobic bonding and screened electrostatic interactions. I elaborate further the concept of complex vectorial biochemistry, where crowded biomacromolecules structure the cytosol into electrolyte pathways and nanopools that electrochemically "wire" the cell. Noncovalent attractions between biomacromolecules transiently supercrowd biomacromolecules into vectorial, semiconducting multiplexes with a high (35 to 95%)-volume fraction of biomacromolecules; consequently, reservoirs of less crowded cytosol appear in order to maintain the experimental average crowding of ∼25% volume fraction. This nonuniform crowding model allows for fast diffusion of biomacromolecules in the uncrowded cytosolic reservoirs, while the supercrowded vectorial multiplexes conserve the remarkable repeatability of the cell cycle by preventing confusing cross talk of concurrent biochemical reactions.

Inverse carbon isotope patterns of lipids and kerogen record heterogeneous primary biomass

Throughout the Proterozoic δ(13)C values for preserved n-alkyl lipids are more positive than for syngenetic kerogen. This pattern is the inverse of biosynthetic expectations. It has been suggested that this isotopic inversion results from selective preservation of lipids from (13)C-enriched heterotrophic populations, while the bulk of kerogen derives from primary producers. Here, we formulate a degradation model to calculate the (13)C content of sedimentary total organic carbon and lipid. The model addresses two scenarios. The first scenario explores preferential preservation of heterotrophic lipid, thereby quantifying the existing hypothesis. In the second, we suggest that an inverse signature could be the result of prokaryotic phytoplankton contributing the majority of the total ecosystem biomass. Photosynthetic prokaryotes bearing a relative (13)C enrichment would contribute much of the resulting preserved lipids, while primary eukaryotic biomass would dominate the total organic carbon. We find that our hypothesis of a mixed primary producer community generates inverse isotopic patterns while placing far fewer requirements on specific degradation conditions. It also provides a possible explanation as to why there are large variations in the (13)C content of the isoprenoid lipids pristane and phytane relative to n-alkyl lipid, while the difference between n-alkyl lipid and kerogen is more constant. Our results suggest that the disappearance of the inverse (13)C signature in the late Ediacaran is a natural consequence of the fundamental shift to oceans in which export production has a higher ratio of eukaryotic biomass.

[Prokaryotic expression, purification and biological activity analysis of recombinant β-Lactamase protein]

AIM

To prepare RGD4CβL fusion protein using prokaryotic expression system and evaluate the biological activity of the RGD4CβL.

METHODS

RGD4CβL gene was cloned into pColdII to contruct β-Lactamase prokaryotic expression vector. After transformation, the recombinant vector was induced to express recombinant protein RGD4CβL by IPTG in E.coli BL(DE3). The recombinant protein was purified by Ni-NTA resin under denaturing condition and then dialyzed to renature. The tumor cell targeting ability of the recombinant protein was analyzed by flow cytometric analysis.

RESULTS

After cleavage and purification, β-Lactamase moiety showed the expected size of 42 000 on Tricine-SDS-PAGE, and was further confirmed by Western blotting. Based on flow cytometric analysis, the purified protein specially targeted breast cancer cell line MCF-7.

CONCLUSION

This research successfully estiblished a method for prokaryotic expression and purification of β-lactamase. These results suggest the potential use of the protein as an agent for ADEPT.

Site-specific labeling of proteins with NMR-active unnatural amino acids

A large number of amino acids other than the canonical amino acids can now be easily incorporated in vivo into proteins at genetically encoded positions. The technology requires an orthogonal tRNA/aminoacyl-tRNA synthetase pair specific for the unnatural amino acid that is added to the media while a TAG amber or frame shift codon specifies the incorporation site in the protein to be studied. These unnatural amino acids can be isotopically labeled and provide unique opportunities for site-specific labeling of proteins for NMR studies. In this perspective, we discuss these opportunities including new photocaged unnatural amino acids, outline usage of metal chelating and spin-labeled unnatural amino acids and expand the approach to in-cell NMR experiments.

The eukaryotic cell originated in the integration and redistribution of hyperstructures from communities of prokaryotic cells based on molecular complementarity

In the "ecosystems-first" approach to the origins of life, networks of non-covalent assemblies of molecules (composomes), rather than individual protocells, evolved under the constraints of molecular complementarity. Composomes evolved into the hyperstructures of modern bacteria. We extend the ecosystems-first approach to explain the origin of eukaryotic cells through the integration of mixed populations of bacteria. We suggest that mutualism and symbiosis resulted in cellular mergers entailing the loss of redundant hyperstructures, the uncoupling of transcription and translation, and the emergence of introns and multiple chromosomes. Molecular complementarity also facilitated integration of bacterial hyperstructures to perform cytoskeletal and movement functions.

Prokaryotic and eukaryotic integral membrane proteins have similar architecture

Integral membrane proteins constitute a major constituent of lipid bilayer both in prokaryotes and eukaryotes. The statistical analysis was carried out to determine the bias in amino acid distribution between prokaryotic and eukaryotic integral membrane proteins (pIntMPs and eIntMPs). Our results indicate that both pIntMPs and eIntMPs demonstrate the striking similarity in amino acid distribution in their transmembrane and extramembranous region. pIntMPs have relatively greater functional importance for Gly and Asn in comparison to eIntMPs.

SUMO fusion technology for enhanced protein production in prokaryotic and eukaryotic expression systems

In eukaryotic cells, the reversible attachment of small ubiquitin-like modifier (SUMO) protein is a post-translational modification that has been demonstrated to play an important role in various cellular processes. Moreover, it has been found that SUMO as an N-terminal fusion partner enhances functional protein production in prokaryotic and eukaryotic expression systems, based upon significantly improved protein stability and solubility. Following the expression and purification of the fusion protein, the SUMO-tag can be cleaved by specific (SUMO) proteases via their endopeptidase activity in vitro to generate the desired N-terminus of the released protein partner. In addition to its physiological relevance in eukaryotes, SUMO can, thus, be used as a powerful biotechnological tool for protein expression in prokaryotic and eukaryotic cell systems.In this chapter, we will describe the construction of a fusion protein with the SUMO-tag, its expression in Escherichia coli, and its purification followed by the removal of the SUMO-tag by a SUMO-specific protease in vitro.

Intracellular minerals and metal deposits in prokaryotes

Thanks to the work of Terrance J. Beveridge and other pioneers in the field of metal-microbe interactions, prokaryotes are well known to sequester metals and other ions intracellularly in various forms. These forms range from poorly ordered deposits of metals to well-ordered mineral crystals. Studies on well-ordered crystalline structures have generally focused on intracellular organelles produced by magnetotactic bacteria that are ubiquitous in terrestrial and marine environments that precipitate Fe(3)O(4) or Fe(3)S(4), Fe-bearing minerals that have magnetic properties and are enclosed in intracellular membranes. In contrast, studies on less-well ordered minerals have focused on Fe-, As-, Mn-, Au-, Se- and Cd-precipitates that occur intracellularly. The biological and environmental function of these particles remains a matter of debate.

Evolutionary history and functional implications of protein domains and their combinations in eukaryotes

A rapid emergence of animal-specific domains was observed in animals, contributing to specific domain combinations and functional diversification, but no similar trends were observed in other clades of eukaryotes.

Background

In higher multicellular eukaryotes, complex protein domain combinations contribute to various cellular functions such as regulation of intercellular or intracellular signaling and interactions. To elucidate the characteristics and evolutionary mechanisms that underlie such domain combinations, it is essential to examine the different types of domains and their combinations among different groups of eukaryotes.

Results

We observed a large number of group-specific domain combinations in animals, especially in vertebrates. Examples include animal-specific combinations in tyrosine phosphorylation systems and vertebrate-specific combinations in complement and coagulation cascades. These systems apparently underwent extensive evolution in the ancestors of these groups. In extant animals, especially in vertebrates, animal-specific domains have greater connectivity than do other domains on average, and contribute to the varying number of combinations in each animal subgroup. In other groups, the connectivities of older domains were greater on average. To observe the global behavior of domain combinations during evolution, we traced the changes in domain combinations among animals and fungi in a network analysis. Our results indicate that there is a correlation between the differences in domain combinations among different phylogenetic groups and different global behaviors.

Conclusion

Rapid emergence of animal-specific domains was observed in animals, contributing to specific domain combinations and functional diversification, but no such trends were observed in other clades of eukaryotes. We therefore suggest that the strategy for achieving complex multicellular systems in animals differs from that of other eukaryotes.

[Role of heat shock proteins in developing of innate immunity reactions]

Increasing interest to heat shock proteins (HSP) from biologists and medics is connected to widespread distribution of HSP in live nature and reflects their key role in support of life functions which is based on the unique polyfunctionality of these biomolecules. Together with main function, which is defense of biologic systems from stress effects, some HSP in the process of evolution acquired the ability to incorporate in the reactions of the immune system. The in vestmen of this protein in practical reactions of innate immunity system are described. Analysis of mechanisms underlying the adjuvant effect of pro- and eukaryotic HSP in innate immunity system is presented. HSP receptor structures on target cells as well as triggered intracellular signaling pathways are described.

The surface protein Srr-1 of Streptococcus agalactiae binds human keratin 4 and promotes adherence to epithelial HEp-2 cells

Streptococcus agalactiae is frequently the cause of bacterial sepsis and meningitis in neonates. In addition, it is a commensal bacterium that colonizes the mammalian gastrointestinal tract. During its commensal and pathogenic lifestyles, S. agalactiae colonizes and invades a number of host compartments, thereby interacting with different host proteins. In the present study, the serine-rich repeat protein Srr-1 from S. agalactiae was functionally investigated. Immunofluorescence microscopy showed that Srr-1 was localized on the surface of streptococcal cells. The Srr-1 protein was shown to interact with a 62-kDa protein in human saliva, which was identified by matrix-assisted laser desorption ionization-time-of-flight analysis as human keratin 4 (K4). Immunoblot and enzyme-linked immunosorbent assay experiments allowed us to narrow down the K4 binding domain in Srr-1 to a region of 157 amino acids (aa). Furthermore, the Srr-1 binding domain of K4 was identified in the C-terminal 255 aa of human K4. Deletion of the srr-1 gene in the genome of S. agalactiae revealed that this gene plays a role in bacterial binding to human K4 and that it is involved in adherence to epithelial HEp-2 cells. Binding to immobilized K4 and adherence to HEp-2 cells were restored by introducing the srr-1 gene on a shuttle plasmid into the srr-1 mutant. Furthermore, incubation of HEp-2 cells with the K4 binding domain of Srr-1 blocked S. agalactiae adherence to epithelial cells in a dose-dependent fashion. This is the first report describing the interaction of a bacterial protein with human K4.

The major vault protein is related to the toxic anion resistance protein (TelA) family

Vaults are barrel-shaped ribonucleoprotein particles that are abundant in certain tumors and multidrug resistant cancer cells. Prokaryotic relatives of the major vault protein, MVP, have not been identified. We used sequence analysis and molecular modeling to show that MVP and the toxic anion resistance protein, TelA of Rhodobacter sphaeroides strain 2.4.1, share a novel fold that consists of a three-stranded antiparallel beta-sheet. Because of this strong structural correspondence, we examined whether mammalian cell vaults respond to tellurite treatment. In the presence of the oxyanion tellurite, large vault aggregates, or vaultosomes, appear at the cell periphery in 15 min or less. Vaultosome formation is temperature-dependent, reversible, and occurs in normal human umbilical vein endothelial cells as well as transformed HeLa cervical cancer cells. Vaultosome formation is not restricted to tellurite and occurs in the presence of other toxic oxyanions (selenate, selinite, arsenate, arsenite, vanadate). In addition, vaultosomes form independently from other stress-induced ribonucleoprotein complexes, stress granules and aggresomes. Vaultosome formation is therefore a unique cellular response to an environmental toxin.

Homologs of eukaryotic Ras superfamily proteins in prokaryotes and their novel phylogenetic correlation with their eukaryotic analogs

Ras superfamily proteins are key regulators in a wide variety of cellular processes. Previously, they were considered to be specific to eukaryotes, and MglA, a group of obviously different prokaryotic proteins, were recognized as their only prokaryotic analogs or even ancestors. Here, taking advantage of quite a current accumulation of prokaryotic genomic databases, we have investigated the existence and taxonomic distribution of Ras superfamily protein homologs in a much wider prokaryotic range, and analyzed their phylogenetic correlation with their eukaryotic analogs. Thirteen unambiguous prokaryotic homologs, which possess the GDP/GTP-binding domain with all the five characteristic motifs of their eukaryotic analogs, were identified in 12 eubacteria and one archaebacterium, respectively. In some other archaebacteria, including four methanogenic archaebacteria and three Thermoplasmales, homologs were also found, but with the GDP/GTP-binding domains not containing all the five characteristic motifs. Many more MglA orthologs were identified than in previous studies mainly in delta-proteobacteria, and all were shown to have common unique features distinct from the Ras superfamily proteins. Our phylogenetic analysis indicated eukaryotic Rab, Ran, Ras, and Rho families have the closest phylogenetic correlation with the 13 unambiguous prokaryotic homologs, whereas the other three eukaryotic protein families (SRbeta, Sar1, and Arf) branch separately from them, but have a relatively close relationship with the methanogenic archaebacterial homologs and MglA. Although homologs were identified in a relative minority of prokaryotes with genomic databases, their presence in a relatively wide variety of lineages, their unique sequence characters distinct from those of eukaryotic analogs, and the topology of our phylogenetic tree altogether do not support their origin from eukaryotes as a result of lateral gene transfer. Therefore, we argue that Ras superfamily proteins might have already emerged at least in some prokaryotic lineages, and that the seven eukaryotic protein families of the Ras superfamily may have two independent prokaryotic origins, probably reflecting the 'fusion' evolutionary history of the eukaryotic cell.

Compositional dynamics of guanine and cytosine content in prokaryotic genomes

Nucleotide compositional analyses of disparities in genomic guanine and cytosine (gGC) content directly relate to the amino acid composition, through the union of the genetic code. Here we analyzed 229 prokaryotic genomes to address the intricate relationships between gGC, amino acids and their codons in the context of genes. First, we not only confirmed the universal rule that the average GC content at codon position 1 (GC1) is always higher than that at codon position 2 (GC2), but also extended the rule to show that it holds true even when codon-position-related GC contents are calculated on a per gene basis. The "GC1>GC2 rule" is attributable essentially to a few dominant amino acids that have GC at one of these two codon positions or the intermediate-GC group of amino acids. Second, we found that gGC fluctuations were largely compensated for at the codon level, when codons belonging to high-GC and low-GC amino acid groups varied accordingly. Finally, we found that prokaryotic genes also have a GC content gradient (Gd) distributed along their transcripts. The gradients at three codon positions (Gd1, Gd2 and Gd3) all correlated with gGC in two different directions: Gd3 was positive, whereas the other two were negative.

Determination of copper binding in Pseudomonas putida CZ1 by chemical modifications and X-ray absorption spectroscopy

Previously performed studies have shown that Pseudomonas putida CZ1 biomass can bind an appreciable amount of Cu(II) and Zn(II) ions from aqueous solutions. The mechanisms of Cu- and Zn-binding by P. putida CZ1 were ascertained by chemical modifications of the biomass followed by Fourier transform infrared and X-ray absorption spectroscopic analyses of the living or nonliving cells. A dramatic decrease in Cu(II)- and Zn(II)-binding resulted after acidic methanol esterification of the nonliving cells, indicating that carboxyl functional groups play an important role in the binding of metal to the biomaterial. X-ray absorption spectroscopy was used to determine the speciation of Cu ions bound by living and nonliving cells, as well as to elucidate which functional groups were involved in binding of the Cu ions. The X-ray absorption near-edge structure spectra analysis showed that the majority of the Cu was bound in both samples as Cu(II). The fitting results of Cu K-edge extended X-ray absorption fine structure spectra showed that N/O ligands dominated in living and nonliving cells. Therefore, by combining different techniques, our results indicate that carboxyl functional groups are the major ligands responsible for the metal binding in P. putida CZ1.

[Functional role of proteins containing ankyrin repeats]

This review describes and discusses new data about the structure and function of proteins which contain ankyrin-like repeats in their structure. These proteins have been found in cells of different organisms but they are not belonging to the cytoskeletal proteins. Many important functions of such proteins are provided by ankyrin repeats which maintain protein-protein interactions involved in the formation of transcription complexes, initiation of immuno-responses, biogenesis and assembly of cation channels in the membranes, regulation of some cell cycle stages, symbiotic interactions and many other processes. Mutations in genes encoding ankyrin-like proteins can cause defects in gene expression leading to diseases onset and progression in animals and humans. Therefore, the structure, dynamics and function of these proteins is an area of extensive research in modern biology.

Compaction of forest soil by logging machinery favours occurrence of prokaryotes

Soil compaction caused by passage of logging machinery reduces the soil air capacity. Changed abiotic factors might induce a change in the soil microbial community and favour organisms capable of tolerating anoxic conditions. The goals of this study were to resolve differences between soil microbial communities obtained from wheel-tracks (i.e. compacted) and their adjacent undisturbed sites, and to evaluate differences in potential anaerobic microbial activities of these contrasting soils. Soil samples obtained from compacted soil had a greater bulk density and a higher pH than uncompacted soil. Analyses of phospholipid fatty acids demonstrated that the eukaryotic/prokaryotic ratio in compacted soils was lower than that of uncompacted soils, suggesting that fungi were not favoured by the in situ conditions produced by compaction. Indeed, most-probable-number (MPN) estimates of nitrous oxide-producing denitrifiers, acetate- and lactate-utilizing iron and sulfate reducers, and methanogens were higher in compacted than in uncompacted soils obtained from one site that had large differences in bulk density. Compacted soils from this site yielded higher iron-reducing, sulfate-reducing and methanogenic potentials than did uncompacted soils. MPN estimates of H2-utilizing acetogens in compacted and uncompacted soils were similar. These results indicate that compaction of forest soil alters the structure and function of the soil microbial community and favours occurrence of prokaryotes.

A new evolutionary paradigm for the Parkinson disease gene DJ-1

The DJ-1 gene is extensively studied because of its involvement in familial Parkinson disease. DJ-1 belongs to a complex superfamily of genes that includes both prokaryotic and eukaryotic representatives. We determine that many prokaryotic groups, such as proteobacteria, cyanobacteria, spirochaetes, firmicutes, or fusobacteria, have genes, often incorrectly called "Thij," that are very close relatives of DJ-1, to the point that they cannot be clearly separated from the eukaryotic DJ-1 genes by phylogenetic analyses of their sequences. In addition, and contrary to a previous study that suggested that DJ-1 genes were animal specific, we show that DJ-1 genes are found in at least 5 of the 6 main eukaryotic groups: opisthokonta (both animals and fungi), plantae, chromalveolata, excavata, and amoebozoa. Our results thus provide strong evidence for DJ-1 genes originating before the origin of eukaryotes. Interestingly, we found that some fungal species, among them the model yeast Schizosaccharomyces pombe, have DJ-1-like genes, most likely orthologous to the animal genes. This finding opens new ways for the analysis of the functions of this group of genes.

Focus on phosphohistidine

Phosphohistidine has been identified as an enzymic intermediate in numerous biochemical reactions and plays a functional role in many regulatory pathways. Unlike the phosphoester bond of its cousins (phosphoserine, phosphothreonine and phosphotyrosine), the phosphoramidate (P-N) bond of phosphohistidine has a high DeltaG degrees of hydrolysis and is unstable under acidic conditions. This acid-lability has meant that the study of protein histidine phosphorylation and the associated protein kinases has been slower to progress than other protein phosphorylation studies. Histidine phosphorylation is a crucial component of cell signalling in prokaryotes and lower eukaryotes. It is also now becoming widely reported in mammalian signalling pathways and implicated in certain human disease states. This review covers the chemistry of phosphohistidine in terms of its isomeric forms and chemical derivatives, how they can be synthesized, purified, identified and the relative stabilities of each of these forms. Furthermore, we highlight how this chemistry relates to the role of phosphohistidine in its various biological functions.