Donor substrate recognition in the raffinose-bound E342A mutant of fructosyltransferase <Emphasis Type="Italic">Bacillus subtilis</Emphasis> levansucrase

Background  

Fructans – β-D-fructofuranosyl polymers with a sucrose starter unit – constitute a carbohydrate reservoir synthesised by a considerable number of bacteria and plant species. Biosynthesis of levan (αGlc(1–2)βFru [(2–6)βFru]_n), an abundant form of bacterial fructan, is catalysed by levansucrase (sucrose:2,6-β-D-fructan-6-β-D-fructosyl transferase), utilizing sucrose as the sole substrate. Previously, we described the tertiary structure of Bacillus subtilis levansucrase in the ligand-free and sucrose-bound forms, establishing the mechanistic roles of three invariant carboxylate side chains, Asp86, Asp247 and Glu342, which are central to the double displacement reaction mechanism of fructosyl transfer. Still, the structural determinants of the fructosyl transfer reaction thus far have been only partially defined.     

<Emphasis Type="Italic">Gdt</Emphasis>2 regulates the transition of <Emphasis Type="Italic">Dictyostelium</Emphasis>cells from growth to differentiation

Background  

Dictyostelium life cycle consists of two distinct phases – growth and development. The control of growth-differentiation transition in Dictyostelium is not completely understood, and only few genes involved in this process are known.     

Viable nonsense mutants for the essential gene <Emphasis Type="Italic">SUP45</Emphasis> of <Emphasis Type="Italic">Saccharomyces cerevisiae</Emphasis>

Background  

Termination of protein synthesis in eukaryotes involves at least two polypeptide release factors (eRFs) – eRF1 and eRF3. The highly conserved translation termination factor eRF1 in Saccharomyces cerevisiae is encoded by the essential gene SUP45.     

Differentially expressed genes in embryonic cardiac tissues of mice lacking <Emphasis Type="Italic">Folr1</Emphasis>gene activity

Background  

Heart anomalies are the most frequently observed among all human congenital defects. As with the situation for neural tube defects (NTDs), it has been demonstrated that women who use multivitamins containing folic acid peri-conceptionally have a reduced risk for delivering offspring with conotruncal heart defects [1–3]. Cellular folate transport is mediated by a receptor or binding protein and by an anionic transporter protein system. Defective function of the Folr1 (also known as Folbp1; homologue of human FRα) gene in mice results in inadequate transport, accumulation, or metabolism of folate during cardiovascular morphogenesis.     

Nucleotide diversity in the mitochondrial and nuclear compartments of <Emphasis Type="Italic">Chlamydomonas reinhardtii</Emphasis>: investigating the origins of genome architecture

Background  

The magnitude of intronic and intergenic DNA can vary substantially both within and among evolutionary lineages; however, the forces responsible for this disparity in genome compactness are conjectural. One explanation, termed the mutational-burden hypothesis, posits that genome compactness is primarily driven by two nonadaptive processes: mutation and random genetic drift – the effects of which can be discerned by measuring the nucleotide diversity at silent sites (π_silent), defined as noncoding sites and the synonymous sites of protein-coding regions. The mutational-burden hypothesis holds that π_silent is negatively correlated to genome compactness. We used the model organism Chlamydomonas reinhardtii, which has a streamlined, coding-dense mitochondrial genome and an noncompact, intron-rich nuclear genome, to investigate the mutational-burden hypothesis. For measuring π_silent we sequenced the complete mitochondrial genome and portions of 7 nuclear genes from 7 geographical isolates of C. reinhardtii.     

A hydrogen-bonding network formed by the B10–E7–E11 residues of a truncated hemoglobin from <Emphasis Type="Italic">Tetrahymena pyriformis</Emphasis> is critical for stability of bound oxygen and nitric oxide detoxification

Abstract  

Truncated hemoglobins (trHbs) are distributed from bacteria to unicellular eukaryotes and have roles in oxygen transport and nitric oxide detoxification. It is known that trHbs exist in ciliates of the Tetrahymena group, but trHb structure and function remain poorly understood. To investigate trHb function with respect to stability of bound oxygen and protein structure, we measured the oxygen binding kinetics of Tetrahymena pyriformis trHb, and determined the crystal structure of the protein. The O₂ association and dissociation rate constants of T. pyriformis trHb were 5.5 μM⁻¹ s⁻¹ and 0.18 s⁻¹, respectively. The autooxidation rate constant was 3.8 × 10⁻³ h⁻¹. These values are similar to those of HbN from Mycobacterium tuberculosis. The three-dimensional structure of an Fe(II)–O₂ complex of T. pyriformis trHb was determined at 1.73-? resolution. Tyr25 (B10) and Gln46 (E7) were hydrogen-bonded to a heme-bound O₂ molecule. Tyr25 donated a hydrogen bond to the terminal oxygen atom, whereas Gln46 hydrogen-bonded to the proximal oxygen atom. Furthermore, Tyr25 was hydrogen-bonded to the Gln46 and Gln50 (E11) residues. Mutations at Tyr25, Gln46, and Gln50 increased the O₂ dissociation and autooxidation rate constants. An Fe(III)–H₂O complex of T. pyriformis trHb was formed following reaction of the Fe(II)–O₂ complex of T. pyriformis trHb, in a crystal state, with nitric oxide. This suggests that T. pyriformis trHb functions in nitric oxide detoxification.     

A canonical FtsZ protein in <Emphasis Type="Italic">Verrucomicrobium spinosum</Emphasis>, a member of the Bacterial phylum <Emphasis Type="Italic">Verrucomicrobia</Emphasis> that also includes tubulin-producing <Emphasis Type="Italic">Prosthecobacter</Emphasis> species

Background  

The origin and evolution of the homologous GTP-binding cytoskeletal proteins FtsZ typical of Bacteria and tubulin characteristic of eukaryotes is a major question in molecular evolutionary biology. Both FtsZ and tubulin are central to key cell biology processes – bacterial septation and cell division in the case of FtsZ and in the case of tubulins the function of microtubules necessary for mitosis and other key cytoskeleton-dependent processes in eukaryotes. The origin of tubulin in particular is of significance to models for eukaryote origins. Most members of domain Bacteria possess FtsZ, but bacteria in genus Prosthecobacter of the phylum Verrucomicrobia form a key exception, possessing tubulin homologs BtubA and BtubB. It is therefore of interest to know whether other members of phylum Verrucomicrobia possess FtsZ or tubulin as their FtsZ-tubulin gene family representative.     

Climate change and recent genetic flux in populations of <Emphasis Type="Italic">Drosophila robusta</Emphasis>

Background  

Studied since the early 1940's, chromosomal polymorphisms in the deciduous woods species Drosophila robusta have been characterized by well-defined latitudinal, longitudinal, and elevational clines, but – until at least ten years ago – stable, local population frequencies. Recent biogeographical analyses indicate that D. robusta invaded North America from southeast Asia and has persisted in eastern temperate forests for at least 20–25 my without speciating. The abundant chromosome polymorphisms found across the range of D. robusta are thus likely to be relatively ancient, having accumulated over many well known climatic cycles in North America. Sufficient long-term data are now available such that we can now gauge the rate of these evolutionary changes in natural populations due to environmental change.     

The diversity of reproductive parasites among arthropods: <Emphasis Type="Italic">Wolbachia</Emphasis>do not walk alone

Background  

Inherited bacteria have come to be recognised as important components of arthropod biology. In addition to mutualistic symbioses, a range of other inherited bacteria are known to act either as reproductive parasites or as secondary symbionts. Whilst the incidence of the α-proteobacterium Wolbachia is relatively well established, the current knowledge of other inherited bacteria is much weaker. Here, we tested 136 arthropod species for a range of inherited bacteria known to demonstrate reproductive parasitism, sampling each species more intensively than in past surveys.     

Distinguishing importation from diversification of quinolone-resistant <Emphasis Type="Italic">Neisseria gonorrhoeae</Emphasis> by molecular evolutionary analysis

Background  

Distinguishing the recent introduction of quinolone resistant gonococci into a population from diversification of resistant strains already in the population is important for planning effective infection control strategies. We applied molecular evolutionary analyses to DNA sequences from 9 housekeeping genes and gyrA, parC and porB of 24 quinolone resistant N. gonorrhoeae (QRNG) and 24 quinolone sensitive isolates collected in Israel during 2000–2001.     

Pulse perturbations from bacterial decomposition of <Emphasis Type="Italic">Chrysaora</Emphasis><Emphasis Type="Italic">quinquecirrha</Emphasis> (Scyphozoa: Pelagiidae)

Bacteria decomposed damaged and moribund Chrysaora quinquecirrha Desor, 1848 releasing a pulse of carbon and nutrients. Tissue decomposed in 5–8 days, with 14 g of wet biomass exhibiting a half-life of 3 days at 22°C, which is 3× longer than previous reports. Decomposition raised mean concentrations of organic carbon and nutrients above controls by 1–2 orders of magnitude. An increase in nitrogen (16,117 μg l⁻¹) occurred 24 h after increases in phosphorus (1,365 μg l⁻¹) and organic carbon (25 mg l⁻¹). Cocci dominated control incubations, with no significant increase in numbers. In incubations of tissue, bacilli increased exponentially after 6 h to become dominant, and cocci reproduced at a rate that was 30% slower. These results, and those from previous studies, suggested that natural assemblages may include bacteria that decompose medusae, as well as bacteria that benefit from the subsequent release of carbon and nutrients. This experiment also indicated that proteins and other nitrogenous compounds are less labile in damaged medusae than in dead or homogenized individuals. Overall, dense patches of decomposing medusae represent an important, but poorly documented, component of the trophic shunt that diverts carbon and nutrients incorporated by gelatinous zooplankton into microbial trophic webs.     

DNA sequence diversity and the origin of cultivated safflower (<Emphasis Type="Italic">Carthamus tinctorius</Emphasis>L.; Asteraceae)

Background  

Safflower (Carthamus tinctorius L.) is a diploid oilseed crop whose origin is largely unknown. Safflower is widely believed to have been domesticated over 4,000 years ago somewhere in the Fertile Crescent. Previous hypotheses regarding the origin of safflower have focused primarily on two other species from sect. Carthamus – C. oxyacanthus and C. palaestinus – as the most likely progenitors, although some attention has been paid to a third species (C. persicus) as a possible candidate. Here, we describe the results of a phylogenetic analysis of the entire section using data from seven nuclear genes.     

Genetic surveillance of endemic bovine <Emphasis Type="Italic">Salmonella</Emphasis> Infantis infection

Background  

Salmonella serovar Infantis is endemic in Finnish food-producing animals since the 1970s. The purpose of this study was to describe the molecular epidemiology of the infection in cattle during 1985–2005, to follow the persistence of the feed-related outbreak strain from 1995 in the cattle population, and to analyse the stability of Xba I-banding patterns in individual herds during long-lasting infections.     

Transcriptional regulation of mouse alpha <Emphasis Type="Italic">A-crystallin</Emphasis> gene in a 148kb <Emphasis Type="Italic">Cryaa</Emphasis> BAC and its derivates

Background  

αA-crystallin is highly expressed in the embryonic, neonatal and adult mouse lens. Previously, we identified two novel distal control regions, DCR1 and DCR3. DCR1 was required for transgenic expression of enhanced green fluorescent protein, EGFP, in lens epithelium, whereas DCR3 was active during "late" stages of lens primary fiber cell differentiation. However, the onset of transgenic EGFP expression was delayed by 12–24 hours, compared to the expression of the endogenous Cryaa gene.     

Cj0596 is a periplasmic peptidyl prolyl cis-trans isomerase involved in Campylobacter jejuni motility, invasion, and colonization

Background  

Campylobacter jejuni is a gastrointestinal pathogen of humans, but part of the normal flora of poultry, and therefore grows well at the respective body temperatures of 37°C and 42°C. Proteomic studies on temperature regulation in C. jejuni strain 81–176 revealed the upregulation at 37°C of Cj0596, a predicted periplasmic chaperone that is similar to proteins involved in outer membrane protein folding and virulence in other bacteria.     

BVPaP-3, a T7-Like Lytic Phage of <Emphasis Type="Italic">Pseudomonas aeruginosa</Emphasis>: Its Isolation and Characterisation

The increasing emergence of antibiotic-resistant bacteria has produced a growing interest among scientists in bacteriophages as alternative antimicrobial agents. This article reports a lytic phage against an antibiotic-resistant strain of Pseudomonas aeruginosa. Phage BVPaP-3 is a member of the Podoviridae family and morphologically similar to the T7-like phage gh-1. The phage has a hexagonal head of 58–59 nm in diameter and a short tail of 10 × 8 nm. It is stable at a wide range of pH (6–10) and temperatures (4–40°C). Its optimal growth temperature is 37°C and the adsorption rate constant is 1.19 × 10⁻⁹. Latent and eclipse periods are 20 and 15 min, respectively, and the burst size is 44 after 35 min at 37°C. The phage has a DNA size of 41.31 kb and a proteome of 11 proteins. The major protein is 33 kDa in size.     

Geminiviruses: a tale of a plasmid becoming a virus

Background  

Geminiviruses (family Geminiviridae) are small single-stranded (ss) DNA viruses infecting plants. Their virion morphology is unique in the known viral world – two incomplete T = 1 icosahedra are joined together to form twinned particles. Geminiviruses utilize a rolling-circle mode to replicate their genomes. A limited sequence similarity between the three conserved motifs of the rolling-circle replication initiation proteins (RCR Reps) of geminiviruses and plasmids of Gram-positive bacteria allowed Koonin and Ilyina to propose that geminiviruses descend from bacterial replicons.     

Rapid acid treatment of <Emphasis Type="Italic">Escherichia coli</Emphasis>: transcriptomic response and recovery

Background  

Many E. coli genes show pH-dependent expression during logarithmic growth in acid (pH 5–6) or in base (pH 8–9). The effect of rapid pH change, however, has rarely been tested. Rapid acid treatment could distinguish between genes responding to external pH, and genes responding to cytoplasmic acidification, which occurs transiently following rapid external acidification. It could reveal previously unknown acid-stress genes whose effects are transient, as well as show which acid-stress genes have a delayed response.     

Nicotine degradation by two novel bacterial isolates of <Emphasis Type="Italic">Acinetobacter</Emphasis> sp. TW and <Emphasis Type="Italic">Sphingomonas</Emphasis> sp. TY and their responses in the presence of neonicotinoid insecticides

Two novel nicotine-degrading bacterial strains were isolated from tobacco waste and identified as Acinetobacter sp. TW and Sphingomonas sp. TY based on morphology, physiological and biochemical tests, Biolog analysis and 16S rDNA sequencing. The 16S rDNA sequences have been deposited in GenBank under the accession numbers FJ753401 for TW and FJ754274 for TY. The best culture conditions for nicotine degradation were 25–37°C and pH 7.0–8.0 for strain TW and 25–30°C and pH 6.0–7.0 for strain TY. Under the best conditions, the cell growth and nicotine-degradation kinetics of the two isolates were assessed, and 1.0 g/l nicotine was completely degraded within 12 and 18 h for TW and TY, respectively. Moreover, the presence of four widely-used commercial neonicotinoid insecticides in the medium had no effects on nicotine degradation by TW; among the four tested neonicotinoids, only thiamethoxam significantly delayed nicotine degradation by TY. TW and TY were also able to degrade selected neonicotinoids. This is the first report of nicotine degradation by Acinetobacter sp. and Sphingomonas sp. This study showed that these two newly isolated bacteria may be suitable for the disposal of tobacco waste and the reduction of nicotine in tobacco leaves.