Selenium Metabolism and Selenoproteins in Prokaryotes: A Bioinformatics Perspective.

Selenium (Se) is an important trace element that mainly occurs in the form of selenocysteine in selected proteins. In prokaryotes, Se is also required for the synthesis of selenouridine and Se-containing cofactor. A large number of selenoprotein families have been identified in diverse prokaryotic organisms, most of which are thought to be involved in various redox reactions. In the last decade or two, computational prediction of selenoprotein genes and comparative genomics of Se metabolic pathways and selenoproteomes have arisen, providing new insights into the metabolism and function of Se and their evolutionary trends in bacteria and archaea. This review aims to offer an overview of recent advances in bioinformatics analysis of Se utilization in prokaryotes. We describe current computational strategies for the identification of selenoprotein genes and generate the most comprehensive list of prokaryotic selenoproteins reported to date. Furthermore, we highlight the latest research progress in comparative genomics and metagenomics of Se utilization in prokaryotes, which demonstrates the divergent and dynamic evolutionary patterns of different Se metabolic pathways, selenoprotein families, and selenoproteomes in sequenced organisms and environmental samples. Overall, bioinformatics analyses of Se utilization, function, and evolution may contribute to a systematic understanding of how this micronutrient is used in nature.

Prokaryotic and eukaryotic traits support the biological role of the chloroplast outer envelope.

The plastid outer envelope (OE) is a mixture of components inherited from their prokaryotic ancestor like galactolipids, carotenoids and porin type ion channels supplemented with eukaryotic inventions to make the endosymbiotic process successful as well as to control plastid biogenesis and differentiation. In this review we wanted to highlight the importance of the OE proteins and its evolutionary origin. For a long time, the OE was thought to be a diffusion barrier only, but with the recent discoveries of all kinds of different proteins in the OE it has been shown that the OE can modulate various functions within the cell. The phenotypic changes show that channels like the outer envelope proteins OEP40, OEP16 or JASSY have a pronounced ion selectivity that cannot be replaced by other ion channels present in the OE. Eukaryotic additions, like the GTPase receptors Toc33 and Toc159 or the ubiquitin proteasome system for chloroplast protein quality control, round up the profile of the OE.

Prokaryotic viruses impact functional microorganisms in nutrient removal and carbon cycle in wastewater treatment plants.

As one of the largest biotechnological applications, activated sludge (AS) systems in wastewater treatment plants (WWTPs) harbor enormous viruses, with 10-1,000-fold higher concentrations than in natural environments. However, the compositional variation and host-connections of AS viruses remain poorly explored. Here, we report a catalogue of ~50,000 prokaryotic viruses from six WWTPs, increasing the number of described viral species of AS by 23-fold, and showing the very high viral diversity which is largely unknown (98.4-99.6% of total viral contigs). Most viral genera are represented in more than one AS system with 53 identified across all. Viral infection widely spans 8 archaeal and 58 bacterial phyla, linking viruses with aerobic/anaerobic heterotrophs, and other functional microorganisms controlling nitrogen/phosphorous removal. Notably, Mycobacterium, notorious for causing AS foaming, is associated with 402 viral genera. Our findings expand the current AS virus catalogue and provide reference for the phage treatment to control undesired microorganisms in WWTPs.

Hostile Takeover: How Viruses Reprogram Prokaryotic Metabolism.

To reproduce, prokaryotic viruses must hijack the cellular machinery of their hosts and redirect it toward the production of viral particles. While takeover of the host replication and protein synthesis apparatus has long been considered an essential feature of infection, recent studies indicate that extensive reprogramming of host primary metabolism is a widespread phenomenon among prokaryotic viruses that is required to fulfill the biosynthetic needs of virion production. In this review we provide an overview of the most significant recent findings regarding virus-induced reprogramming of prokaryotic metabolism and suggest how quantitative systems biology approaches may be used to provide a holistic understanding of metabolic remodeling during lytic viral infection.

Tellurium: A Rare Element with Influence on Prokaryotic and Eukaryotic Biological Systems.

Metalloid tellurium is characterized as a chemical element belonging to the chalcogen group without known biological function. However, its compounds, especially the oxyanions, exert numerous negative effects on both prokaryotic and eukaryotic organisms. Recent evidence suggests that increasing environmental pollution with tellurium has a causal link to autoimmune, neurodegenerative and oncological diseases. In this review, we provide an overview about the current knowledge on the mechanisms of tellurium compounds' toxicity in bacteria and humans and we summarise the various ways organisms cope and detoxify these compounds. Over the last decades, several gene clusters conferring resistance to tellurium compounds have been identified in a variety of bacterial species and strains. These genetic determinants exhibit great genetic and functional diversity. Besides the existence of specific resistance mechanisms, tellurium and its toxic compounds interact with molecular systems, mediating general detoxification and mitigation of oxidative stress. We also discuss the similarity of tellurium and selenium biochemistry and the impact of their compounds on humans.

DescribePROT: database of amino acid-level protein structure and function predictions.

We present DescribePROT, the database of predicted amino acid-level descriptors of structure and function of proteins. DescribePROT delivers a comprehensive collection of 13 complementary descriptors predicted using 10 popular and accurate algorithms for 83 complete proteomes that cover key model organisms. The current version includes 7.8 billion predictions for close to 600 million amino acids in 1.4 million proteins. The descriptors encompass sequence conservation, position specific scoring matrix, secondary structure, solvent accessibility, intrinsic disorder, disordered linkers, signal peptides, MoRFs and interactions with proteins, DNA and RNAs. Users can search DescribePROT by the amino acid sequence and the UniProt accession number and entry name. The pre-computed results are made available instantaneously. The predictions can be accesses via an interactive graphical interface that allows simultaneous analysis of multiple descriptors and can be also downloaded in structured formats at the protein, proteome and whole database scale. The putative annotations included by DescriPROT are useful for a broad range of studies, including: investigations of protein function, applied projects focusing on therapeutics and diseases, and in the development of predictors for other protein sequence descriptors. Future releases will expand the coverage of DescribePROT. DescribePROT can be accessed at http://biomine.cs.vcu.edu/servers/DESCRIBEPROT/.

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.

Phosphorus mediates soil prokaryote distribution pattern along a small-scale elevation gradient in Noijin Kangsang Peak, Tibetan Plateau.

Environmental factors that are important in shaping microbe community structure are less explored along elevation in the alpine grassland ecosystem of Tibet Plateau, which is generally phosphorus limited. Here, we examined soil prokaryote communities at three elevations to explore soil prokaryote community distribution and mediation factors in Noijin Kangsang Peak, Tibetan Plateau. Results showed prokaryote community compositions differed significantly by elevations. Topsoil or subsoil prokaryote richness and Shannon diversity were significantly lower at the middle than other elevations, while significantly higher aboveground biomass (AGB) and available P (AP) were found at the middle elevation. The importance of P for both soil layers was discovered by variation partitioning analysis based on redundancy analysis, finding that soil AP and total phosphorus, interacted with pH, explained 43% the variance in topsoil prokaryote community compositions, while soil AP, as well as AGB, explained 44% in subsoil. Consistently, structural equation model also revealed that AP was a mediating factor for prokaryote community diversity. Other than plant beta diversity, soil prokaryote beta diversity positively correlated with AP difference significantly. Taken together, the distribution patterns of soil prokaryote community were distinct along elevations even in a small scale in Noijin Kangsang Peak and was likely mediated predominantly by soil AP in both topsoil and subsoil.

Identification of new promising plant-based lead compounds for inhibition of prokaryotic replicative DNA polymerases: combination of in silico and in vitro studies.

Emerging widespread bacterial resistance to current antibiotics with traditional targets is one of the major global concerns. Therefore, so many investigations are exploring the potential of other druggable macromolecules of bacteria such as replication machinery components that are not addressed by previous antibiotics. DNA polymerase is the major part of this machine. However, a few studies have been done on it so far. In this respect, we report the discovery of four new plant-based leads against DNA polymerase (pol) IIIC (three leads) and pol IIIE (one lead) of Gram-positive and negative bacteria by combining a sequentially constrained high-throughput virtual screenings on Traditional Chinese Medicine Database with in vitro assays. The compounds displayed relatively good levels of inhibitory effect. They were active against their designated targets at micromolar concentrations. The IC50 values for them are ranged from 25 to 111 µM. In addition, they showed minimum inhibitory concentrations in the range of 8-128 µg/mL against five representatives of pathogenic bacteria species. However, they were inactive against Pseudomonas aeruginosa. Given these results, these leads hold promise for future modification and optimization to be more effective in lower concentrations and also against most of the important bacterial species. Communicated by Ramaswamy H. Sarma.

ProAcePred: prokaryote lysine acetylation sites prediction based on elastic net feature optimization.

Motivation: Lysine acetylation exists extensively in prokaryotes, and plays a vital role in function adjustment. Recent progresses in the identification of prokaryote acetylation substrates and sites provide a great opportunity to explore the difference of substrate site specificity between prokaryotic and eukaryotic acetylation. Motif analysis suggests that prokaryotic and eukaryotic acetylation sites have distinct location-specific difference, and it is necessary to develop a prokaryote-specific acetylation sites prediction tool. Results: Therefore, we collected nine species of prokaryote lysine acetylation data from various databases and literature, and developed a novel online tool named ProAcePred for predicting prokaryote lysine acetylation sites. Optimization of feature vectors via elastic net could considerably improve the prediction performance. Feature analyses demonstrated that evolutionary information played significant roles in prediction model for prokaryote acetylation. Comparison between our method and other tools suggested that our species-specific prediction outperformed other existing works. We expect that the ProAcePred could provide more instructive help for further experimental investigation of prokaryotes acetylation. Availability and implementation: http://computbiol.ncu.edu.cn/ProAcePred. Supplementary information: Supplementary data are available at Bioinformatics online.

Graphene oxide significantly inhibits cell growth at sublethal concentrations by causing extracellular iron deficiency.

Graphene oxide (GO)-based materials are increasingly being used in medical materials and consumer products. However, their sublethal effects on biological systems are poorly understood. Here, we report that GO (at 10 to 160 mg/L) induced significant inhibitory effects on the growth of different unicellular organisms, including eukaryotes (i.e. Saccharomyces cerevisiae, Candida albicans, and Komagataella pastoris) and prokaryotes (Pseudomonas fluorescens). Growth inhibition could not be explained by commonly reported cytotoxicity mechanisms such as plasma membrane damage or oxidative stress. Based on transcriptomic analysis and measurement of extra- and intracellular iron concentrations, we show that the inhibitory effect of GO was mainly attributable to iron deficiency caused by binding to the O-functional groups of GO, which sequestered iron and disrupted iron-related physiological and metabolic processes. This inhibitory mechanism was corroborated with supplementary experiments, where adding bathophenanthroline disulfonate-an iron chelating agent-to the culture medium exerted similar inhibition, whereas removing surface O-functional groups of GO decreased iron sequestration and significantly alleviated the inhibitory effect. These findings highlight a potential indirect detrimental effect of nanomaterials (i.e. scavenging of critical nutrients), and encourage research on potential biomedical applications of GO-based materials to sequester iron and enhance treatment of iron-dependent diseases such as cancer and some pathogenic infections.

Flamingos and drought as drivers of nutrients and microbial dynamics in a saline lake.

Waterbird aggregations and droughts affect nutrient and microbial dynamics in wetlands. We analysed the effects of high densities of flamingos on nutrients and microbial dynamics in a saline lake during a wet and a dry hydrological year, and explored the effects of guano on prokaryotic growth. Concentrations of dissolved organic carbon, total phosphorus and total nitrogen in the surface waters were 2-3 fold higher during the drought and were correlated with salinity. Flamingos stimulated prokaryotic heterotrophic production and triggered cascading effects on prokaryotic abundance, viruses and dissolved nitrogen. This stimulus of heterotrophic prokaryotes was associated with soluble phosphorus inputs from guano, and also from sediments. In the experiments, the specific growth rate and the carrying capacity were almost twice as high after guano addition than in the control treatments, and were coupled with soluble phosphorus assimilation. Flamingo guano was also rich in nitrogen. Dissolved N in lake water lagged behind the abundance of flamingos, but the causes of this lag are unclear. This study demonstrates that intense droughts could lead to increases in total nutrients in wetlands; however, microbial activity is likely constrained by the availability of soluble phosphorus, which appears to be more dependent on the abundance of waterbirds.

Distribution of Prokaryotic Abundance and Microbial Nutrient Cycling Across a High-Alpine Altitudinal Gradient in the Austrian Central Alps is Affected by Vegetation, Temperature, and Soil Nutrients.

Studies of the altitudinal distributions of soil microorganisms are rare or have led to contradictory results. Therefore, we studied archaeal and bacterial abundance and microbial-mediated activities across an altitudinal gradient (2700 to 3500 m) on the southwestern slope of Mt. Schrankogel (Central Alps, Austria). Sampling sites distributed over the alpine (2700 to 2900 m), the alpine-nival (3000 to 3100 m), and the nival altitudinal belts (3200 to 3500 m), which are populated by characteristic plant assemblages. Bacterial and archaeal abundances were measured via quantitative real-time PCR (qPCR). Moreover, microbial biomass C, microbial activity (dehydrogenase), and enzymes involved in carbon (CM-cellulase), nitrogen (protease), phosphorus (alkaline phosphatase), and sulfur (arylsulfatase) cycling were determined. Abundances, microbial biomass C, and activities almost linearly decreased along the gradient. Archaeal abundance experienced a sharper decrease, thus pointing to pronounced sensitivity toward environmental harshness. Additionally, abundance and activities were significantly higher in soils of the alpine belt compared with those of the nival belt, whereas the alpine-nival ecotone represented a transitional area with intermediate values, thus highlighting the importance of vegetation. Archaeal abundance along the gradient was significantly related to soil temperature only, whereas bacterial abundance was significantly related to temperature and dissolved organic carbon (DOC). Soil carbon and nitrogen concentrations explained most of the variance in enzyme activities involved in the cycling of C, N, P, and S. Increasing temperature could therefore increase the abundances and activities of microorganisms either directly or indirectly via expansion of alpine vegetation to higher altitudes and increased plant cover.

Biosystems Engineering of Prokaryotes with Tumor-Killing Capacities.

Certain bacteria selectively attack tumor tissues and trigger tumor shrinkage by producing toxins and modulating the local immune system, but their clinical utility is limited because of the dangers posed by systemic infection. Genetic engineering can be used to minimize the risks associated with tumor-targeting pathogens, as well as to increase their efficiency in killing tumor cells. Advances in genetic circuit design have led to the development of bacterial strains with enhanced tumor-targeting capacities and the ability to secrete therapeutics, cytotoxic proteins and prodrug-cleaving enzymes, which allows their safe and effective use for cancer treatment. The present review details the recent advances in the design and application of these modified bacterial strains.

Evolution of selenophosphate synthetases: emergence and relocation of function through independent duplications and recurrent subfunctionalization.

Selenoproteins are proteins that incorporate selenocysteine (Sec), a nonstandard amino acid encoded by UGA, normally a stop codon. Sec synthesis requires the enzyme Selenophosphate synthetase (SPS or SelD), conserved in all prokaryotic and eukaryotic genomes encoding selenoproteins. Here, we study the evolutionary history of SPS genes, providing a map of selenoprotein function spanning the whole tree of life. SPS is itself a selenoprotein in many species, although functionally equivalent homologs that replace the Sec site with cysteine (Cys) are common. Many metazoans, however, possess SPS genes with substitutions other than Sec or Cys (collectively referred to as SPS1). Using complementation assays in fly mutants, we show that these genes share a common function, which appears to be distinct from the synthesis of selenophosphate carried out by the Sec- and Cys- SPS genes (termed SPS2), and unrelated to Sec synthesis. We show here that SPS1 genes originated through a number of independent gene duplications from an ancestral metazoan selenoprotein SPS2 gene that most likely already carried the SPS1 function. Thus, in SPS genes, parallel duplications and subsequent convergent subfunctionalization have resulted in the segregation to different loci of functions initially carried by a single gene. This evolutionary history constitutes a remarkable example of emergence and evolution of gene function, which we have been able to trace thanks to the singular features of SPS genes, wherein the amino acid at a single site determines unequivocally protein function and is intertwined to the evolutionary fate of the entire selenoproteome.

[Thermophilic prokaryotes from deep subterranean habitats].

The deep continental biosphere consists of geologically isolated ecosystems differing in their physicochemical, geological, and trophic parameters. Most of the deep ecosystems exist at elevated temperatures (50-120 degrees C), which favor the development of thermophilic microorganisms. In many cases, indigenous nature of subsurface microorganisms is questionable due to problems of collecting representative and non-contaminated samples. In spite of the numerous studies on the deep biosphere microbial communities, the number of cultivated thermophiles isolated from subsurface environments not associated with petroleum deposits does not exceed 30 species. More than half of the thermophilic species isolated from deep subsurface belong to the Firmicutes. Majority of the underground thermophiles are subsurface strict or facultative anaerobes, with capacity for sulfate and iron reduction are notably widespread. Most thermophilic subsurface microorganisms are organotrophs, although chemolithoautotrophic thermophiles also have been reported. This review deals with the phylogenetic diversity and physiological properties of the cultivated thermophilic prokaryotes isolated from various deep subterranean habitats.

Modes of deformation of walled cells.

The bewildering morphological diversity found in cells is one of the starkest illustrations of life's ability to self-organize. Yet the morphogenetic mechanisms that produce the multifarious shapes of cells are still poorly understood. The shared similarities between the walled cells of prokaryotes, many protists, fungi, and plants make these groups particularly appealing to begin investigating how morphological diversity is generated at the cell level. In this review, I attempt a first classification of the different modes of surface deformation used by walled cells. Five modes of deformation were identified: inextensional bending, equi-area shear, elastic stretching, processive intussusception, and chemorheological growth. The two most restrictive modes-inextensional and equi-area deformations-are embodied in the exine of pollen grains and the wall-like pellicle of euglenoids, respectively. For these modes, it is possible to express the deformed geometry of the cell explicitly in terms of the undeformed geometry and other easily observable geometrical parameters. The greatest morphogenetic power is reached with the processive intussusception and chemorheological growth mechanisms that underlie the expansive growth of walled cells. A comparison of these two growth mechanisms suggests a possible way to tackle the complexity behind wall growth.

Imaging living cells surface and quantifying its properties at high resolution using AFM in QI™ mode.

Since the last 10 years, AFM has become a powerful tool to study biological samples. However, the classical modes offered (imaging or tapping mode) often damage sample that are too soft or loosely immobilized. If imaging and mechanical properties are required, it requests long recording time as two different experiments must be conducted independently. In this study we compare the new QI™ mode against contact imaging mode and force volume mode, and we point out its benefit in the new challenges in biology on six different models: Escherichia coli, Candida albicans, Aspergillus fumigatus, Chinese hamster ovary cells and their isolated nuclei, and human colorectal tumor cells.

Iron/sulfur proteins biogenesis in prokaryotes: formation, regulation and diversity.

Iron/sulfur centers are key cofactors of proteins intervening in multiple conserved cellular processes, such as gene expression, DNA repair, RNA modification, central metabolism and respiration. Mechanisms allowing Fe/S centers to be assembled, and inserted into polypeptides have attracted much attention in the last decade, both in eukaryotes and prokaryotes. Basic principles and recent advances in our understanding of the prokaryotic Fe/S biogenesis ISC and SUF systems are reviewed in the present communication. Most studies covered stem from investigations in Escherichia coli and Azotobacter vinelandii. Remarkable insights were brought about by complementary structural, spectroscopic, biochemical and genetic studies. Highlights of the recent years include scaffold mediated assembly of Fe/S cluster, A-type carriers mediated delivery of clusters and regulatory control of Fe/S homeostasis via a set of interconnected genetic regulatory circuits. Also, the importance of Fe/S biosynthesis systems in mediating soft metal toxicity was documented. A brief account of the Fe/S biosynthesis systems diversity as present in current databases is given here. Moreover, Fe/S biosynthesis factors have themselves been the object of molecular tailoring during evolution and some examples are discussed here. An effort was made to provide, based on the E. coli system, a general classification associating a given domain with a given function such as to help next search and annotation of genomes. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.

Characterization of the heterotrophic biomass and the endogenous residue of activated sludge.

The activated sludge process generates an endogenous residue (X(E)) as a result of heterotrophic biomass decay (X(H)). A literature review yielded limited information on the differences between X(E) and X(H) in terms of chemical composition and content of extracellular polymeric substances (EPS). The objective of this project was to characterize the chemical composition (x, y, z, a, b and c in C(x)H(y)O(z)N(a)P(b)S(c)) of the endogenous and the active fractions and EPS of activated sludge from well designed experiments. To isolate X(H) and X(E) in this study, activated sludge was generated in a 200L pilot-scale aerobic membrane bioreactor (MBR) fed with a soluble and completely biodegradable synthetic influent of sodium acetate as the sole carbon source. This influent, which contained no influent unbiodegradable organic or inorganic particulate matter, allowed the generation of a sludge composed essentially of two fractions: heterotrophic biomass X(H) and an endogenous residue X(E), the nitrifying biomass being negligible. The endogenous decay rate and the active biomass fraction of the MBR sludge were determined in 21-day aerobic digestion batch tests by monitoring the VSS and OUR responses. Fractions of X(H) and X(E) were respectively 68% and 32% in run 1 (MBR at 5.2 day SRT) and 59% and 41% in run 2 (MBR at 10.4 day SRT). The endogenous residue was isolated by subjecting the MBR sludge to prolonged aerobic batch digestion for 3 weeks, and was characterized in terms of (a) elemental analysis for carbon, nitrogen, phosphorus and sulphur; and (b) content of EPS. The MBR sludge was characterized using the same procedures (a and b). Knowing the proportions of X(H) and X(E) in this sludge, it was possible to characterize X(H) by back calculation. Results from this investigation showed that the endogenous residue had a chemical composition different from that of the active biomass with a lower content of inorganic matter (1:4.2), of nitrogen (1:2.9), of phosphorus (1:5.3) and of sulphur (1:3.2) but a similar content of carbon (1:0.98). Based on these elemental analyses, chemical composition formulae for X(H) and X(E) were determined as CH(1.240)O(0.375)N(0.200)P(0.0172)S(0.0070) and CH(1.248)O(0.492)N(0.068)P(0.0032)S(0.0016), respectively. Data from EPS analyses also confirmed this difference in structure between X(E) and X(H) with an EPS content of 11-17% in X(E)versus 26-40% in X(H).