Genomic and metagenomic surveys of hydrogenase distribution indicate H2 is a widely utilised energy source for microbial growth and survival

Recent physiological and ecological studies have challenged the long-held belief that microbial metabolism of molecular hydrogen (H₂) is a niche process. To gain a broader insight into the importance of microbial H₂ metabolism, we comprehensively surveyed the genomic and metagenomic distribution of hydrogenases, the reversible enzymes that catalyse the oxidation and evolution of H₂. The protein sequences of 3286 non-redundant putative hydrogenases were curated from publicly available databases. These metalloenzymes were classified into multiple groups based on (1) amino acid sequence phylogeny, (2) metal-binding motifs, (3) predicted genetic organisation and (4) reported biochemical characteristics. Four groups (22 subgroups) of [NiFe]-hydrogenase, three groups (6 subtypes) of [FeFe]-hydrogenases and a small group of [Fe]-hydrogenases were identified. We predict that this hydrogenase diversity supports H₂-based respiration, fermentation and carbon fixation processes in both oxic and anoxic environments, in addition to various H₂-sensing, electron-bifurcation and energy-conversion mechanisms. Hydrogenase-encoding genes were identified in 51 bacterial and archaeal phyla, suggesting strong pressure for both vertical and lateral acquisition. Furthermore, hydrogenase genes could be recovered from diverse terrestrial, aquatic and host-associated metagenomes in varying proportions, indicating a broad ecological distribution and utilisation. Oxygen content (pO₂) appears to be a central factor driving the phylum- and ecosystem-level distribution of these genes. In addition to compounding evidence that H₂ was the first electron donor for life, our analysis suggests that the great diversification of hydrogenases has enabled H₂ metabolism to sustain the growth or survival of microorganisms in a wide range of ecosystems to the present day. This work also provides a comprehensive expanded system for classifying hydrogenases and identifies new prospects for investigating H₂ metabolism.     

How Salmonella oxidises H(2) under aerobic conditions

Salmonella enterica serovar Typhimurium is a Gram negative bacterial pathogen and a common cause of food-borne illness. Molecular hydrogen has been shown to be a key respiratory electron donor during infection and H(2) oxidation can be catalysed by three genetically-distinct [NiFe] hydrogenases. Of these, hydrogenases-1 (Hyd-1) and Hyd-2 have well-characterised homologues in Escherichia coli. The third, designated Hyd-5 here, is peculiar to Salmonella and is expressed under aerobic conditions. In this work, Salmonella was genetically modified to enable the isolation and characterisation of Hyd-5. Electrochemical analysis established that Hyd-5 is a H(2)-oxidising enzyme that functions in very low levels of H(2) and sustains this activity in high levels of O(2). In addition, electron paramagnetic resonance spectroscopy of the Hyd-5 isoenzyme reveals a complex paramagnetic FeS signal at high potentials which is comparable to that observed for other O(2)-tolerant respiratory [NiFe] hydrogenases. Taken altogether, Hyd-5 can be classified as an O(2)-tolerant hydrogenase that confers upon Salmonella the ability to use H(2) as an electron donor in aerobic respiration.     

A new and widely distributed species of Pseudoarachniotus

Summary A new species ofPseudoarachniotus, P. hyalinosporus, is described and illustrated. A total of 54 isolates of this species was studied and their growth was compared on several media.Although certain differences appeared in colonial coloration and growth characteristics, all strains were similar in 2 fundamental characteristics, viz., type of ascospore and type of gametangial initials and their subsequent development. The initials in early stages are often so closely appressed one to another that they give the appearance of a single structure. Further development takes place by the elongation of the ascogonium which forms a loop around the male initial at right angles to the linear plane of that initial. The ascospores ofP. hyalinosporus are small, about 2.2 × 3.3µ, thin-walled, oval, hyaline to very pale yellow, and smooth, thereby differing fromPseudoarachniotus reticulatus which has globose, echinulate-reticulate ascospores, andP. roseus andP. citrinus which have large, thick-walled, oval to oblate ascospores. Furthermore, the colonies ofP. roseus are red, those ofP. citrinus are yellow, and inP. hyalinosporus colonies are white with pale yellow asciferous areas and usually with a great deal of green pigment both above and reverse. Of the 54 strains of this new species, 25 were isolated from rodent lungs, 9 from dung, 19 from soil and one from a tinea pedis condition.Pseudoarachniotus hyalinosporus was found in two collections from India and it appears to be widely distributed in California.Supported in part by Botany Department Research Grant # 1344, University of California, Los Angeles, California.A portion of this study was made possible through laboratory facilities provided by Dr.B. Samantarai, Ravenshaw College, Cuttuck, Orissa, India.     

Erratum to: The discovery of potent immunostimulatory CpG-ODNs widely distributed in bacterial genomes

In the article by Liu et al. published in Journal of Microbiology 2020; 58, 153–162, 1# The Supplementary data’s consecutive numbers (Supplementary data Fig. S2) on 9th line of 4th paragraph in the section of ‘Discussion.’ on page 160 should be corrected in (Supplementary data Fig. S1). The sentence should have read: The results showed that the nonspecific internalization of T03 had only a slight competition with CpG-ODNs (Supplementary data Fig. S1). 2# The Supplementary data’s consecutive numbers (Supplementary data Fig. S3) on 13th line of 6th paragraph in the section of ‘Discussion.’ on page 161 should be corrected in (Supplementary data Fig. S2). The sentence should have read: Although the CpG-ODNs screened in this study had no or weak stimulation effect on human PBMCs (Supplementary data Fig. S2), it once again indicated that CpG-ODNs can be species-specific. And the Electronic Supplementary Material should be corrected as below. We apologize for any inconvenience that this may have caused.     

A widely distributed antigen developmentally regulated in the nervous system

We have identified a glycoprotein (BEN) of 95-100 x 10(3) Mr using a monoclonal antibody. This protein is transiently expressed at the cell surface of the peripherally projecting neurons, i.e. motoneurons of the spinal cord and cranial nuclei, sensory neurons of the dorsal root and cranial sensory ganglia and sympathetic, parasympathetic and enteric neurons. In vitro cultures of dorsal root and sympathetic ganglia have shown that BEN is expressed on neurons but not on glial cells. On motor and sensory neurons, BEN first appears at the level of the cell body just after withdrawal from the cell cycle. Soon afterwards, expression of the antigen extends to the elongating axon. After a few days, BEN is no longer expressed by the motor and sensory neurons, disappearing first from the cell body and then progressively from the fibres. The loss of expression is concomitant with the onset of intense proliferation of satellite and Schwann cells. This modulated expression within the nervous system is unlike that of any surface glycoprotein so far described in vertebrates. Preliminary biochemical analysis indicates that, although it bears the adhesion-associated epitope HNK-1, BEN does not share characteristics with any previously described axonal glycoprotein. Consequently, we speculate that this glycoprotein might be a novel molecule implicated in selective adhesion phenomena, such as axonal fasciculation.     

H2 consumption by Escherichia coli coupled via hydrogenase 1 or hydrogenase 2 to different terminal electron acceptors

Hydrogen uptake in the presence of various terminal electron acceptors was examined in Escherichia coli mutants synthesizing either hydrogenase 1 or hydrogenase 2. Both hydrogenases mediated nitrate-dependent H2 consumption but neither of them was coupled with nitrite. Unlike hydrogenase 2, hydrogenase 1 demonstrated poor activity with electron acceptors of low midpoint redox potential. Oxygen-linked H2 uptake via hydrogenase 1 was observed over a wide range of air concentrations. Hydrogenase 2 catalyzed this reaction only at low air concentrations. Thus, hydrogenase 1 works in cells at higher redox potential, being more tolerant to oxygen than hydrogenase 2.     

An epitope of elongation factor Tu is widely distributed within the bacterial and archaeal domains.

A monoclonal antibody (MAb), MAb 900, which detects a 43-kDa protein present on Escherichia coli was found. Subsequently, more than 90 organisms, belonging to either the bacterial, archaeal, or eucaryal domain, were tested for reactivity to this MAb. Of the bacterial and archaeal domains, almost all species proved to be positive, whereas all organisms from the eucaryal domain gave negative results. The 43-kDa protein was purified by affinity chromatography and subsequently analyzed by microsequencing methods. Two peptide sequences which showed a high degree of homology (> 99%) to the prokaryotic elongation factor Tu (EF-Tu) were obtained. Western blot (immunoblot) analysis using both purified EF-Tu and EF-Tu domains confirmed that the unknown protein was EF-Tu. The panbacterial distribution of EF-Tu, which is present in large amounts in every prokaryotic cell, renders this protein a good candidate for a diagnostic approach. In consequence, we have used the anti-EF-Tu MAb 900 to design both a dot blot assay and an enzyme-linked immunosorbent assay. From either blood culture, urine, or gall-bladder fluid, bacterial contamination could be detected. The sensitivity of these tests is currently 10(4) bacteria per ml.     

A widely distributed gene cluster compensates for uricase loss in hominids

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A widely distributed "CAT" family of repetitive DNA sequences

The yeast genome contains a family of repetitive sequences consisting primarily of a tandemly arranged trinucleotide, CAT, or a closely related CGT sequence. To characterize similar sequences in divergent organisms, a previously isolated "CAT" sequence was used to isolate homologous genomic clones from a human cell line, an insect and a higher plant. Sequence analyses show that comparable repetitive sequences are widely distributed and may be present in all eukaryotic genomes. In situ hybridization analyses indicate that in yeast, the CAT elements are dispersed among all the chromosomes, and a more detailed analysis in Drosophila indicates that at least one of these sequences maps on the X chromosome between known genetic loci which are actively expressed. Repeated searches of yeast cDNA libraries indicate that these CAT clusters are not expressed but substantial effects on the expression of a cloned gene strongly suggest that they play an important role in gene regulation.     

A novel haloarchaeal-related lineage is widely distributed in deep oceanic regions

During our study of the 16S rRNA gene sequence-based archaeal diversity of a deep-sea site located at a 3000 m depth at the Antarctic Polar Front, we detected several phylotypes ascribed to already known Group II and III Euryarchaeota, and a cluster of distinct sequences that branched off at the base of haloarchaea. The position of this lineage (marine Group IV) was very robust using distance (neighbour-joining) and maximum-likelihood methods. Subsequently, we designed specific primers for the detection of this archaeal group in other marine environments using polymerase chain reaction amplification and sequence comparison. Group IV archaea were found in the Antarctic area (across a gradient from the Southern ocean to the South Atlantic), and also in North Atlantic and Mediterranean waters. In all oceanic locations, Group IV archaea were never detected in surface waters, but were vertically distributed in the deepest part of the water column.     

On the redox equilibrium between H2 and hydrogenase.

Redox titrations of the nickel ion in active hydrogenase from Methanobacterium thermoautotrophicum and Chromatium vinosum were performed in the absence of artificial redox mediators, by variation of the H2-partial pressure. These experiments revealed a redox behaviour of the nickel ion which differed remarkably from previous redox titrations in the presence of redox mediators. Notably the EPR signal of the species earlier characterized as monovalent nickel with bound hydrogen, behaved as an n = 2 redox component upon reduction under varying H2-partial pressures. The EPR signal was not a transient one and persisted upon removal of hydrogen. Possible redox processes to explain these observations are discussed. A similar behaviour of nickel was also observed in enzyme as present in intact cells of M. thermoautotrophicum. These results suggest that nickel hydrogenases possess a second site for reaction with H2.     

Phosphoenolpyruvate:glycose phosphotransferase system in species of Vibrio, a widely distributed marine bacterial genus.

The genus Vibrio is one of the most common and widely distributed groups of marine bacteria. Studies on the physiology of marine Vibrio species were initiated by examining 15 species for the bacterial phosphoenolpyruvate:glycose phosphotransferase system (PTS). All species tested contained a PTS analogous to the glucose-specific (IIGlc) system in enteric bacteria. Crude extracts of the cells showed immunological cross-reactivity with antibodies to enzyme I, HPr, and IIIGlc from Salmonella typhimurium when assayed by the rocket-line method. Toluene-permeabilized cells of 11 species were tested and were active in phosphorylating methyl alpha-D-glucoside with phosphoenolpyruvate but not ATP as the phosphoryl donor. Membranes from 10 species were assayed, and they phosphorylated methyl alpha-D-glucoside when supplemented with a phospho-IIIGlc-generating system composed of homogeneous proteins from enteric bacteria. Toluene-permeabilized cells and membranes of seven species were assayed, as were phosphorylated fructose and 2-deoxyglucose. IIIGlc was isolated from Vibrio fluvialis and was active in phosphorylating methyl alpha-D-glucoside when supplemented with a phospho-HPr-generating system composed of homogeneous proteins from Escherichia coli and membranes from either E. coli or V. fluvialis. These results show that the bacterial PTS is widely distributed in the marine environment and that it is likely to have a significant role in marine bacterial physiology and in the marine ecosystem.     

Phospholipid metabolism during bacterial growth

Haemophilus parainfluenzae incorporates glycerol and phosphate into the membrane phospholipids without lag during logarithmic growth. In phosphatidyl glycerol (PG), the phosphate and unacylated glycerol moieties turn over and incorporate radioactivity much more rapidly than does the diacylated glycerol. At least half the radioactivity is lost from the phosphate and unacylated glycerol in about 1 doubling. The total fatty acids turn over slightly faster than the diacyl glycerol. In phosphatidyl ethanolamine (PE), which is the major lipid of the bacterium, ethanolamine and phosphate turn over and incorporate radioactivity at least half as fast as the phosphate in PG. The glycerol of PE did not turn over in 4 bacterial doublings. In phosphatidic acid the glycerol turns over at one-third the rate of phosphate turnover. By means of a modified method for the quantitative recovery of 1,3-glycerol diphosphate from cardiolipin, the phosphates and middle glycerol of cardiolipin were shown to turn over more rapidly than the acylated glycerols during bacterial growth. There is no randomization of the radioactivity in the 1- and 3-positions of the glycerol in the course of 1 doubling. The fatty acids of PG turn over faster than those in PE. In both lipids the 2-fatty acids turn over much faster than the 1-fatty acids. At both positions the individual fatty acids have their own rates of turnover. The distribution of fatty acids between the 1- and 2-positions is the same as in other organisms, with more monoenoic and long-chain fatty acids at the 2-position. The different rates of turnover and incorporation of radioactivity into different parts of the lipids suggest that exchange reactions may be important to phospholipid metabolism.     

The mechanisms of H2 activation and CO binding by hydrogenase I and hydrogenase II of Clostridium pasteurianum

Hydrogenase I (bidirectional) and hydrogenase II (uptake) of Clostridium pasteurianum have been investigated by electron paramagnetic resonance (EPR) spectroscopy, in the presence and absence of the inhibitor, CO. These hydrogenases contain both a novel type of iron-sulfur cluster (H), which is the proposed site of H2 catalysis, and ferredoxin-type [4Fe-4S] clusters (F). The results show that the H clusters of these two hydrogenases have very different properties. The H cluster of oxidized hydrogenase II (Hox-II) exhibits three distinct EPR signals, two of which are pH-dependent. Hox-II binds CO reversibly to give a single, pH-independent species with a novel, rhombic EPR spectrum. The H cluster of reduced hydrogenase II (Hred-II) does not react with CO. In contrast, the EPR spectrum of Hox-I appears homogeneous and independent of pH. Hox-I has a much lower affinity for CO than Hox-II, and binds CO irreversibly to give an axial EPR signal. Hred-I also binds CO irreversibly. The EPR spectra of Fred-I and Fred-II show little or no change after CO treatment. Prior exposure to CO does not affect the catalytic activity of the reduced or oxidized hydrogenases when assayed in the absence of CO, but both enzymes are irreversibly inactivated if CO is present during catalysis. Mechanisms for H2 activation by hydrogenase I and hydrogenase II are proposed from the determined midpoint potentials (Em, pH 8.0) of H-I and H-II (Em approximately -400 mV, -CO; approximately -360 mV, +CO), F-I (Em = -420 mV, +/- CO), and F-II (Em = -180 mV, +/- CO). These allow one to rationalize the different modes of CO binding to the two hydrogenases and suggest why hydrogenase II preferentially catalyzes H2 oxidation. The results are discussed in light of recent spectroscopic data on the structures of the two H clusters.     

SPOC: A widely distributed domain associated with cancer,apoptosis and transcription

Background  

The Split ends (Spen) family are large proteins characterised by N-terminal RNA recognition motifs (RRMs) and a conserved SPOC (Spen paralog and ortholog C-terminal) domain. The aim of this study is to characterize the family at the sequence level.     

Evolutionary genetics and biogeographic structure of Rhizobium gallicum sensu lato, a widely distributed bacterial symbiont of diverse legumes

We used phylogenetic and population genetics approaches to evaluate the importance of the evolutionary forces on shaping the genetic structure of Rhizobium gallicum and related species. We analysed 54 strains from several populations distributed in the Northern Hemisphere, using nucleotide sequences of three 'core' chromosomal genes (rrs, glnII and atpD) and two 'auxiliary' symbiotic genes (nifH and nodB) to elucidate the biogeographic history of the species and symbiotic ecotypes (biovarieties) within species. The analyses revealed that strains classified as Rhizobium mongolense and Rhizobium yanglingense belong to the chromosomal evolutionary lineage of R. gallicum and harbour symbiotic genes corresponding to a new biovar; we propose their reclassification as R. gallicum bv. orientale. The comparison of the chromosomal and symbiotic genes revealed evidence of lateral transfer of symbiotic information within and across species. Genetic differentiation analyses based on the chromosomal protein-coding genes revealed a biogeographic pattern with three main populations, whereas the 16S rDNA sequences did not resolve that biogeographic pattern. Both the phylogenetic and population genetic analyses showed evidence of recombination at the rrs locus. We discuss our results in the light of the contrasting views of bacterial species expressed by microbial taxonomist and evolutionary biologists.