Comparisons of dN/dS are time dependent for closely related bacterial genomes

The ratio of non-synonymous (dN) to synonymous (dS) changes between taxa is frequently computed to assay the strength and direction of selection. Here we note that for comparisons between closely related strains and/or species a second parameter needs to be considered, namely the time since divergence of the two sequences under scrutiny. We demonstrate that a simple time lag model provides a general, parsimonious explanation of the extensive variation in the dN/dS ratio seen when comparing closely related bacterial genomes. We explore this model through simulation and comparative genomics, and suggest a role for hitch-hiking in the accumulation of non-synonymous mutations. We also note taxon-specific differences in the change of dN/dS over time, which may indicate variation in selection, or in population genetics parameters such as population size or the rate of recombination. The effect of comparing intra-species polymorphism and inter-species substitution, and the problems associated with these concepts for asexual prokaryotes, are also discussed. We conclude that, because of the critical effect of time since divergence, inter-taxa comparisons are only possible by comparing trajectories of dN/dS over time and it is not valid to compare taxa on the basis of single time points.     

Heterologous production and secretion of Clostridium perfringens beta-toxoid in closely related Gram-positive hosts

The spore forming bacterium Clostridium perfringens is a widely occurring pathogen. Vaccines against C. perfringens type B and C are currently manufactured using beta-toxin secreted by virulent C. perfringens strains. Large-scale production of vaccines from virulent strains requires stringent safety conditions and costly detoxification and control steps. Therefore, it would be beneficial to produce this toxin in a safe production host and in an immunogenic, but non-toxic form (toxoid). For high-level expression of beta-toxoid, we cloned the highly active ribosomal rpsF promoter of Bacillus subtilis in a broad host range multicopy plasmid. In B. subtilis, we obtained high intracellular production, up to 200 microg ml(-1) culture. However, the beta-toxoid was poorly secreted. The employed rpsF expression system allowed using the same expression plasmids in other heterologous hosts such as Lactococcus lactis and Streptococcus pneumoniae. In these organisms secretion of beta-toxoid was ten times higher compared to the best producing B. subtilis strain. These results show the usefulness of the rpsF based broad host range expression system.     

The amino acid sequences of frog heart atrial natriuretic-like peptide and mammalian ANF are closely related

Despite few studies conducted in non-mammalian species, there has been a number of reports pertaining to the occurrence of a natriuretic-like substance in lower organisms. Thus, an immunoreactive substance reacting with antibodies directed against mammalian atrial natriuretic factor has previously been detected both in heart atria and ventricles of a chordate, the frog. This substance was isolated and purified from frog heart atria and its amino acid sequence established. The sequence, Ala-Pro-Arg-Ser-Ser-Asp-Cys-Phe-Gly-Ser-Arg-Ile-Asp-Arg-Ile-Gly-Ala-Gln- Ser-Gly - Met-Gly-Cys-Gly-Arg-(Phe), is highly homologous to known mammalian ANF sequences. However, when aligned with the complete mammalian ANF precursor sequence at positions 121 to 151, it exhibits a single amino acid insertion at position 129 and other substitutions at positions 121, 125, 133, 135, 144, 147 and 148. Some evidence is also presented concerning the occurrence of uncleaved frog pronatriodilatin, the precursor form of ANF. This study represents the first report pertaining to the structure of a non-mammalian ANF and its precursor.     

Growth and potential photosynthesis of cyanobacteria are stimulated by viable gut passage in crucian carp

Growth and potential photosynthetic activity of phytoplankton passed through intestine of crucian carp (Carassius auratus) from a small Siberian reservoir were compared with those of phytoplankton taken the directly from the reservoir. The dominant phytoplankton species in the reservoir, Microcystis aeruginosa, showed a significant increase of growth after the passage. Subdominant Planktothrix agardhii also showed an increase in growth rate, while subdominants Anabaena flos-aquae and Aphanizomenon flos-aquae were not stimulated by the gut passage.     

Accessory polypeptides in phycobilisomes of red algae and cyanobacteria

Phycobilisomes of red algae and cyanobacteria contain small amounts of nonpigmented polypeptides in addition to the major constituent biliprotein pigments. The localization of these polypeptides is analyzed by gel electrophoresis of phycobilisome fragments obtained by selective dissociation and subsequent separation. Five groups of biliprotein aggregates are determined, belonging to the 6, 11, 16, 18 and 23 S categories. Accessory nonpigmented high molecular weight proteins (80,000 MW) are exclusively bound to phycobilisome core fractions and thylakoids, thus apparently serving as links between the phycobilisomes and the photosynthetic units of the thylakoids. In contrast, smaller nonpigmented accessory polypeptides of 20,000 to 60,000 MW are preferably found in the peripheral biliprotein stacks. They may either form a compatible link between the phycobilisome core and periphery or bind and co-polymerize with hexameric biliproteins in the peripheral stacks to enhance or effect binding of the aggregates. Furthermore, they may determine the arrangement and composition of the phycobilisomes during development and chromatic adaptation.Abbreviations PE phycoerythrin - PEC phycoerythrocyanin - PC phycocyanin - APC allophycocyanin     

Genes controlling circadian rhythm are widely distributed in cyanobacteria

Destruction of alveolar surfactant phospholipids by bacterial phospholipases is suggested to be a major virulence factor involved in bacterial pneumonia. Since Legionella pneumophila secretes phospholipase A, we analyzed phospholipid degradation in natural bovine surfactant by L. pneumophila. Phospholipids were reduced in amount after incubation with bacteria or culture supernatant of L. pneumophila serogroup 6. Free fatty acids and lysophosphatidylcholine were formed, the latter is known to be highly cytotoxic. Surface tension of surfactant as determined by pulsating bubble surfactometer increased significantly compared to the control. Phospholipase A activity seems to be a powerful agent of legionellae in causing lung disease.     

Sodium requirement and metabolism in nitrogen-fixing cyanobacteria

Sodium affects the metabolism of eukaryotes and prokaryotes in several ways. This review collates information on the effects of Na⁺ on the metabolism of cyanobacteria with emphasis on the N₂,fixing filamentous species. Na⁺ is required for nitrogenase activity inAnabaena torulosa, Anabaena L-31 andPlectonema boryanum. The features of this requirement have been mainly studied inAnabaena torulosa. The need for Na⁺ is specific and cannot be replaced by K⁺, Li⁺, Ca 2 + or Mg²⁺. Processes crucial for expression of nitrogenase such as molybdenum uptake, protection of the enzyme from oxygen inactivation and conformational activation of the enzyme are not affected by Na⁺. Mo-Fe protein and Fe protein, the two components of nitrogenase are synthesized in the absence of Na⁺ but the enzyme complex is catalytically inactive. Photoevolution of O₂ and CO₂ fixation, which are severely inhibited in the absence of Na⁺, are quickly restored by glutamine or glutamate indicating that Na⁺ deprivation affects photosynthesis indirectly due to deficiency in the products of N₂ fixation. Na⁺ deprivation decreases phosphate uptake, nucleoside phosphate pool and nitrogenase activity. These effects are reversed by the addition of Na⁺ suggesting that a limitation of available ATP caused by reduced phosphate uptake results in loss of nitrogenase activity during Na⁺ starvation. Na⁺ influx inAnabaena torulosa andAnabaena L-31 is unaffected by low K⁺ concentration, is carrier mediated, follows Michaelis-Menten kinetics and is modulated mainly by membrane potential. Treatments which cause membrane depolarisation and hyperpolarisation inhibit and enhance Na⁺ influx respectively. These cyanobacteria exhibit rapid active efflux of Na⁺, in a manner different from the Na⁺/H⁺ antiporter mechanism found inAnacystis nidulans. Na⁺ requirement in nitrogen metabolism including nitrate assimilation, synthesis of amino acids and proteins, in respiration and oxidative phosphorylation, in transport of sugars and amino acids, cellular distribution of absorbed sodium, physiological basis of salt tolerance and prospects of reclamation of saline soils by cyanobacteria are the other aspects discussed in this review.     

Dark-induced mRNA instability involves RNase E/G-type endoribonuclease cleavage at the AU-box and SD sequences in cyanobacteria

Light-responsive gene expression is crucial to photosynthesizing organisms. Here, we studied functions of cis-elements (AU-box and SD sequences) and a trans-acting factor (ribonuclease, RNase) in light-responsive expression in cyanobacteria. The results indicated that AU-rich nucleotides with an AU-box, UAAAUAAA, just upstream from an SD confer instability on the mRNA under darkness. An RNase E/G homologue, Slr1129, of the cyanobacterium Synechocystis sp. strain PCC 6803 was purified and confirmed capable of endoribonucleolytic cleavage at the AU- (or AG)-rich sequences in vitro. The cleavage depends on the primary target sequence and secondary structure of the mRNA. Complementation tests using Escherichia coli rne/rng mutants showed that Slr1129 fulfilled the functions of both the RNase E and RNase G. An analysis of systematic mutations in the AU-box and SD sequences showed that the cis-elements also affect significantly mRNA stability in light-responsive genes. These results strongly suggested that dark-induced mRNA instability involves RNase E/G-type cleavage at the AU-box and SD sequences in cyanobacteria. The mechanical impact and a possible common mechanism with RNases for light-responsive gene expression are discussed. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Two overlapping SOS-boxes in ColE operons are responsible for the viability of cells harboring the Col plasmid

In this study, oligonucleotide-directed site-specific mutagenesis was used to change the consensus sequences of the LexA binding motifs in either one of the two SOS-boxes of the ColE7 operon. The results indicated that both mutants produced larger amounts of colicin than cells harboring the wild-type ColE7 plasmid. This finding would imply that two biologically functional SOS boxes exist in the ColE7 operon. In the non-induced state, no lysis of cells harboring wild-type plasmids occurred at 37°C, whereas, cells harboring recombinant plasmids containing either one of the mutated SOS boxes underwent lysis within 100 min under the same conditions. This result indicated that adaptation of two SOS boxes of the ColE operon would obviously tightly control the expression of ColE operons. In such a way that it may prevent excessive expression of the lysis (cel) gene, thus safeguard the host cells from being lysed in ordinary living conditions.     

Phylogenetic analysis of Antrodia and related taxa based on partial mitochondrial SSU rDNA sequences

Sequences of mitochondrial SSU rDNA were obtained from six species of Antrodia and related fungal taxa to reveal their phylogenetic relationships. Phylogenetic analysis showed that the species of Antrodia did not cluster into a single clade. Brown rot fungi were separated into two main groups through which Antrodia was dispersed. Antrodia sinuosa, A. serialis, A. heteromorpha and A. malicola clustered with Perenniporia, Fomitopsis, Piptoporus, Daedalea and Melanoporia within one group of brown rot fungi, while A. carbonica and A. vaillantii clustered with Oligoporus, Gloeophyllum and Auriporia within the other group of brown rot fungi, indicating that Antrodia is a heterogeneous genus and that brown rot fungi have evolved convergently. This revised version was published online in June 2006 with corrections to the Cover Date.     

Biotransformation and toxicity of aniline and aniline derivatives in cyanobacteria

Agmenellum quadruplicatum strain PR-6 and Oscillatoria sp. strain JCM grown photoautotrophically in the presence of aniline metabolized the aromatic amine to formanilide, acetanilide and p-aminophenol. The metabolites were isolated by either thin-layer, gas-liquid or high pressure liquid chromatography and identified by comparison of their chromatographic, ultraviolet absorbance and mass spectral properties with those of authentic compounds. The toxicity of aniline derivatives towards Agmenellum quadruplicatum strain PR-6 indicated that the cyanobacterium was extremely sensitive to o-, m- and p-aminophenols, and phenylhydroxylamine.Abbreviations TLC thin layer chromatography - HPLC high pressure liquid chromatography - GC/MS gas chromatography/mass spectrometry - m/e mass to charge ratio     

Diversity and bioactivities of nostocacean cyanobacteria isolated from paddy soil in Vietnam

Nostocacean cyanobacteria are one of the important components of paddy fields due to their ability to fix atmospheric nitrogen and supply phytohormones for crop growth. In this study, 13 Nostoc strains isolated from paddy soils in Vietnam were classified using a polyphasic approach. The results showed a high diversity of the isolated strains that represented seven morphotypes corresponding to five genotypes, with 16S rRNA gene sequence similarity values ranging between 94.97–99.78% compared to the available sequences from GenBank. Bioassay assessment revealed that 11 out of 13 strains possessed antibacterial activities, three of which exhibited cytotoxic activities on MCF7 and HCT116 cells with an IC₅₀ ranging from 47.8 μg mL^?1 to 232.0 μg mL^?1. Interestingly, strains with identical 16S rRNA gene sequences displayed different antibacterial and cytotoxic activity profiles.     

Physiological characteristics of cyanobacteria in pulp and paper waste-treatment systems

An investigation was made into the physiological characteristics of the extensive cyanobacterial communities in pulp and paper secondary waste-treatment systems, including the capacity of isolates to biodegrade organic contaminants in these systems. Although pulp and paper waste-treatment systems were found to be severely light-limited, photosynthesis-irradiance curves indicated that shade-adapted cyanobacterial communities could fix conspicuous amounts of inorganic carbon via photosynthesis. Of 21 cyanobacterial strains isolated from pulp and paper waste-treatment systems located in 4 countries, all except one were capable of glucose uptake in the light, and 19 also showed uptake in the dark. In the 6 species tested, glucose and acetate addition stimulated growth in low light in all except one species. Aphanocapsa rivularis grew equally well on glucose and acetate in the dark but Pseudanabaena sp. grew well on acetate, and minimally on glucose. Growth stimulation by glucose and acetate in these two strains was greater in low than in high light. Pseudanabaena sp. and Phormidium animale both accumulated 2,4-dichlorophenol and 3-chlorobenzoate but showed minimal mineralization to CO₂. None of the four species tested could accumulate or degrade phenol or dichloroacetate. It is concluded that, depending on the light conditions, cyanobacteria contribute organic carbon in photosynthesis, and/or remove small organic molecules during mixotrophic and heterotrophic growth but are not important degraders of contaminants in these waste treatment systems.     

Crenactin from Pyrobaculum calidifontis is closely related to actin in structure and forms steep helical filaments

Polymerising proteins of the actin family are nearly ubiquitous. Crenactins, restricted to Crenarchaea, are more closely related to actin than bacterial MreB. Crenactins occur in gene clusters hinting at an unknown, but conserved function. We solved the crystal structure of crenactin at 3.2 Å resolution. The protein crystallises as a continuous right-handed helix with 8 subunits per complete turn, spanning 419 Å. The structure of crenactin shows several loops that are longer than in actin, but overall, crenactin is closely related to eukaryotic actin, with an RMSD of 1.6 Å. Crenactin filaments imaged by electron microscopy showed polymers with very similar helical parameters.     

Colonization and deterioration processes in Roman mortars by cyanobacteria,algae and lichens

The mortars covering some walls of the Roman city of Baelo Claudia (Cadiz, Spain) support an abundant colonization of cyanobacteria, algae and lichens. The distribution of these organisms is closely related to microclimatic parameters. Furthermore, the development, specific composition and biomass of algal cryptoendolithic communities are related to the wall orientation. The effect of these communities on mortar deterioration is discussed.     

Deteriogenic cyanobacteria on historic buildings in Brazil detected by culture and molecular techniques

There are few modern analyses of the cyanobacterial communities in biofilms on external building surfaces. As the classification of cyanobacteria is rapidly changing, we aimed to identify them on historic buildings in Brazil using both established and molecular techniques. In mature biofilms, cyanobacteria of subsections I and II were generally the major biomass; occasionally filamentous genera of the Scytonemataceae, Microchaetaceae and Rivularaceae were dominant. Filamentous organisms of subsections III and IV were more frequently isolated in culture. PCR products using cyanobacteria-specific 16S rDNA primers were sequenced from morphologically identified organisms. Homologies with deposited sequences were generally low. Phylogenetic analysis showed that many isolates were distant from their nearest neighbours, even though they grouped with their appropriate taxa. The majority of cyanobacterial DNA sequences deposited in data banks are aquatic; our results indicate that cyanobacteria from external walls are an ecologically isolated group.     

Stimulation of nitrogenase activity and photosynthesis in some cyanobacteria by glyoxylate

Abstract The effect og glyoxylate on nitrogenase activity (C₂H₂ reduction) and photosynthesis (H¹⁴CO₃ fixation and O₂ evolution) was in vestigated in the three heterocystous cyanobacteria Anabaena cylindrica, A. variabiltis and N. muscorum. Glyoxylate had virtually no effect on the rate of dark respiration and was unable to sustain photoheterotrophic growth, though some slight stimulation (= 30%) of photorophic growth was noted. A considerable stimulation of both nitrogenase and photosynthetic activities was observed in presence of glyoxylate. In the light the stimulation increased with time up to about 15-25 h after adding optimal concentrations of 4–6 mM glyoxylate. Placing glyoxylate treated samples in the dark or adding DCMU (30 μM) in the light, showed that glyoxylate initially supported significantly higher nitrogenase activity than did samples in absence of glyoxylate. However, after a prolonged incubation in the dark or in presence of DCMU glyoxylate is unable to relieve the adverse effects of such conditions. The stimulation of the nitrogenase activity was even more pronounced when the glyoxylate was added to cells preincubated in the dark (“carbon starved”) than for cells kept constantly in light. The results suggest that glyoxylate, or a metabolite, may act as an inhibitor of cyanobacterial photorespiration and this hypothesis is discussed.