The unconventional Xer recombination machinery of Streptococci/Lactococci

Homologous recombination between circular sister chromosomes during DNA replication in bacteria can generate chromosome dimers that must be resolved into monomers prior to cell division. In Escherichia coli, dimer resolution is achieved by site-specific recombination, Xer recombination, involving two paralogous tyrosine recombinases, XerC and XerD, and a 28-bp recombination site (dif) located at the junction of the two replication arms. Xer recombination is tightly controlled by the septal protein FtsK. XerCD recombinases and FtsK are found on most sequenced eubacterial genomes, suggesting that the Xer recombination system as described in E. coli is highly conserved among prokaryotes. We show here that Streptococci and Lactococci carry an alternative Xer recombination machinery, organized in a single recombination module. This corresponds to an atypical 31-bp recombination site (dif_SL) associated with a dedicated tyrosine recombinase (XerS). In contrast to the E. coli Xer system, only a single recombinase is required to recombine dif_SL, suggesting a different mechanism in the recombination process. Despite this important difference, XerS can only perform efficient recombination when dif_SL sites are located on chromosome dimers. Moreover, the XerS/dif_SL recombination requires the streptococcal protein FtsK_SL, probably without the need for direct protein-protein interaction, which we demonstrated to be located at the division septum of Lactococcus lactis. Acquisition of the XerS recombination module can be considered as a landmark of the separation of Streptococci/Lactococci from other firmicutes and support the view that Xer recombination is a conserved cellular function in bacteria, but that can be achieved by functional analogs.     

Field Metabolic Rate Is Dependent on Time-Activity Budget in Ring-Billed Gulls (Larus delawarensis) Breeding in an Anthropogenic Environment

Environmental and behavioral factors have long been assumed to affect variation in avian field metabolic rate (FMR). However, due to the difficulties in measuring continuous behavior of birds over prolonged periods of time, complete time-activity budgets have rarely been examined in relation to FMR. Our objective was to determine the effect of activity (measured by detailed time-activity budgets) and a series of extrinsic and intrinsic factors on FMR of the omnivorous ring-billed gull (Larus delawarensis). The experiment was conducted during the incubation period when both members of the pair alternate between attending the nest-site and leaving the colony to forage in aquatic and anthropogenic environments (city, agricultural). FMR was determined using the doubly labeled water method. Time-activity budgets were extrapolated from spatio-temporal data (2-5 days) obtained from bird-borne GPS data loggers. Gulls had low FMRs compared to those predicted by allometric equations based on recorded FMRs from several seabird species. Gulls proportioned their time mainly to nest-site attendance (71% of total tracking time), which reduced FMR/g body mass, and was the best variable explaining energy expenditure. The next best variable was the duration of foraging trips, which increased FMR/g; FMR/g was also elevated by the proportion of time spent foraging or flying (17% and 8% of tracking time respectively). Most environmental variables measured did not impact FMR/g, however, the percent of time birds were subjected to temperatures below their lower critical temperature increased FMR. Time-activity budgets varied between the sexes, and with temperature and capture date suggesting that these variables indirectly affected FMR/g. The gulls foraged preferentially in anthropogenic-related habitats, which may have contributed to their low FMR/g due to the high availability of protein- and lipid-rich foods. This study demonstrates that activities were the best predictors of FMR/g in ring-billed gulls, thus providing strong support for this long-standing theory in bioenergetics.     

Staphylococcus aureus Bloodstream Infection and Endocarditis - A Prospective Cohort Study

ObjectivesTo update the epidemiology of S. aureus bloodstream infection (SAB) in a high-income country and its link with infective endocarditis (IE).MethodsAll consecutive adult patients with incident SAB (n = 2008) were prospectively enrolled between 2009 and 2011 in 8 university hospitals in France.ResultsSAB was nosocomial in 54%, non-nosocomial healthcare related in 18% and community-acquired in 26%. Methicillin resistance was present in 19% of isolates. SAB Incidence of nosocomial SAB was 0.159/1000 patients-days of hospitalization (95% confidence interval [CI] 0.111-0.219). A deep focus of infection was detected in 37%, the two most frequent were IE (11%) and pneumonia (8%). The higher rates of IE were observed in injecting drug users (IE: 38%) and patients with prosthetic (IE: 33%) or native valve disease (IE: 20%) but 40% of IE occurred in patients without heart disease nor injecting drug use. IE was more frequent in case of community-acquired (IE: 21%, adjusted odds-ratio (aOR) = 2.9, CI = 2.0-4.3) or non-nosocomial healthcare-related SAB (IE: 12%, aOR = 2.3, CI = 1.4-3.5). S. aureus meningitis (IE: 59%), persistent bacteremia at 48 hours (IE: 25%) and C-reactive protein > 190 mg/L (IE: 15%) were also independently associated with IE. Criteria for severe sepsis or septic shock were met in 30% of SAB without IE (overall in hospital mortality rate 24%) and in 51% of IE (overall in hospital mortality rate 35%).ConclusionSAB is still a severe disease, mostly related to healthcare in a high-income country. IE is the most frequent complication and occurs frequently in patients without known predisposing conditions.     

Harvesting electricity with Geobacter bremensis isolated from compost

Electrochemically active (EA) biofilms were formed on metallic dimensionally stable anode-type electrode (DSA), embedded in garden compost and polarized at +0.50 V/SCE. Analysis of 16S rRNA gene libraries revealed that biofilms were heavily enriched in Deltaproteobacteria in comparison to control biofilms formed on non-polarized electrodes, which were preferentially composed of Gammaproteobacteria and Firmicutes. Among Deltaproteobacteria, sequences affiliated with Pelobacter and Geobacter genera were identified. A bacterial consortium was cultivated, in which 25 isolates were identified as Geobacter bremensis. Pure cultures of 4 different G. bremensis isolates gave higher current densities (1400 mA/m(2) on DSA, 2490 mA/m(2) on graphite) than the original multi-species biofilms (in average 300 mA/m(2) on DSA) and the G. bremensis DSM type strain (100-300 A/m(2) on DSA; 2485 mA/m(2) on graphite). FISH analysis confirmed that G. bremensis represented a minor fraction in the original EA biofilm, in which species related to Pelobacter genus were predominant. The Pelobacter type strain did not show EA capacity, which can explain the lower performance of the multi-species biofilms. These results stressed the great interest of extracting and culturing pure EA strains from wild EA biofilms to improve the current density provided by microbial anodes.     

Demographic crash associated with high parasite load in an experimental roe deer (<Emphasis Type="Italic">Capreolus capreolus</Emphasis>) population

In March 2002, ten roe deer (Capreolus capreolus) were released in a partly wooded 14.2-ha enclosure to investigate the effect of high population density on vegetation cover and demographic parameters. However, in mid 2003, five animals died after rapid emaciation. Two other deer were killed to carry out further post-mortem examination. In addition to a general loss of body mass and injuries in males caused by the healthiest of them, we found a high level of parasitism. The remaining animals received anti-parasite treatment, and four other treated roe deer were added into the enclosure. All the deer were then captured and treated against parasites twice a year, the fawns being removed when first captured. Four years after the crash, the population seemed healthy: deaths no longer occurred; mean adult body mass reached 27.6 kg in March; females produced on average 1.6 fawns per year, with a mean body mass of 13.8 kg in October and 16.7 kg in March. Furthermore, undergrowth cover changed little since March 2004. These results suggest that outbursts of parasites may cause population crashes in high-density situations before the onset of nutritive stress and may explain certain cases of ‘abnormal’ (massive) mortality recorded in roe deer.     

TIMP-1 binding to proMMP-9/CD44 complex localized at the cell surface promotes erythroid cell survival

Besides its ability to inhibit MMP activity, TIMP-1 exhibits other biological functions. We earlier reported that TIMP-1 induced UT-7 erythroid cell survival through activation of the JAK2/PI 3-kinase/Akt pathway and we now aim to determine whether the TIMP-1 anti-apoptotic effect requires MMP involvement. We first show that proMMP-9 was expressed in UT-7 cells and associated with the cell plasma membrane. Such proMMP-9 localization was crucial for TIMP-1 intracellular signalling since (i) TIMP-1 specifically bound to proMMP-9 and (ii) proMMP-9 silencing abrogated the TIMP-1 effect. We also demonstrated that TIMP-1 anti-apoptotic effect was independent on MMP inhibition since MMP-9 function blocking antibodies as well as a synthetic MMP inhibitor were unable to reproduce TIMP-1 effect. Nevertheless, these compounds prevented TIMP-1 binding to proMMP-9 and subsequently abolished TIMP-1-induced cell survival. We finally demonstrated that CD44 anchored proMMP-9 to the plasma membrane and enabled TIMP-1-mediated signal transduction. Therefore, our results indicate that the anti-apoptotic signalling of TIMP-1 depends on the formation of a ternary complex between TIMP-1, proMMP-9 and CD44 at the UT-7 erythroid cell surface.     

Recombination between Polioviruses and Co-Circulating Coxsackie A Viruses: Role in the Emergence of Pathogenic Vaccine-Derived Polioviruses

Ten outbreaks of poliomyelitis caused by pathogenic circulating vaccine-derived polioviruses (cVDPVs) have recently been reported in different regions of the world. Two of these outbreaks occurred in Madagascar. Most cVDPVs were recombinants of mutated poliovaccine strains and other unidentified enteroviruses of species C. We previously reported that a type 2 cVDPV isolated during an outbreak in Madagascar was co-circulating with coxsackieviruses A17 (CA17) and that sequences in the 3′ half of the cVDPV and CA17 genomes were related. The goal of this study was to investigate whether these CA17 isolates can act as recombination partners of poliovirus and subsequently to evaluate the major effects of recombination events on the phenotype of the recombinants. We first cloned the infectious cDNA of a Madagascar CA17 isolate. We then generated recombinant constructs combining the genetic material of this CA17 isolate with that of the type 2 vaccine strain and that of the type 2 cVDPV. Our results showed that poliovirus/CA17 recombinants are viable. The recombinant in which the 3′ half of the vaccine strain genome had been replaced by that of the CA17 genome yielded larger plaques and was less temperature sensitive than its parental strains. The virus in which the 3′ portion of the cVDPV genome was replaced by the 3′ half of the CA17 genome was almost as neurovirulent as the cVDPV in transgenic mice expressing the poliovirus cellular receptor gene. The co-circulation in children and genetic recombination of viruses, differing in their pathogenicity for humans and in certain other biological properties such as receptor usage, can lead to the generation of pathogenic recombinants, thus constituting an interesting model of viral evolution and emergence.     

CD8+ T lymphocytes regulating Th2 pathology escape neonatal tolerization

Transplantation tolerance induced by neonatal injection of semiallogeneic spleen cells is associated in several strain combinations with a pathological syndrome caused by Th2 differentiation of donor-specific CD4(+) T lymphocytes. We investigated the role of host CD8(+) T cells in the regulation of this Th2 pathology. IgE serum levels and eosinophilia significantly increased in BALB/c mice neonatally injected with (A/J x BALB/c)F(1) spleen cells when CD8(+) T cells were depleted by administration of anti-CD8 mAb or when beta(2)-microglobulin-deficient mice were used as recipients. In parallel, increased serum levels of IL-5 and IL-13 were measured in blood of tolerant CD8(+) T cell-deficient mice. Whereas neonatally injected mice were unable to generate anti-donor cytotoxic effectors, their CD8(+) T cells were as efficient as control CD8(+) T cells in reducing the severity of Th2 pathology and in restoring donor-specific cytotoxicity in vitro after in vivo transfer in beta(2)-microglobulin-deficient mice. Likewise, CD8(+) T cells from control and tolerant mice equally down-regulated the production of Th2 cytokines by donor-specific CD4(+) T cells in vitro. The regulatory activity of CD8(+) T cells depended on their secretion of IFN-gamma for the control of IL-5 production but not for IL-4 or IL-13. Finally, we found that CD8(+) T cells from 3-day-old mice were already able to down-regulate IL-4, IL-5, and IL-13 production by CD4(+) T cells. We conclude that regulatory CD8(+) T cells controlling Th2 responses are functional in early life and escape neonatal tolerization.     

In vitro RNP assembly and methylation guide activity of an unusual box C/D RNA, cis-acting archaeal pre-tRNA(Trp)

Among the large family of C/D methylation guide RNAs, the intron of euryarchaeal pre-tRNA(Trp) represents an outstanding specimen able to guide in cis, instead of in trans, two 2'-O-methylations in the pre-tRNA exons. Remarkably, both sites of methylation involve nucleotides within the bulge-helix-bulge (BHB) splicing motif, while the RNA-guided methylation and pre-tRNA splicing events depend on mutually exclusive RNA folding patterns. Using the three recombinant core proteins of archaeal C/D RNPs, we have analyzed in vitro RNP assembly of the pre-tRNA and tested its site-specific methylation activity. Recognition by L7Ae of hallmark K-turns at the C/D and C'/D' motifs appears as a crucial assembly step required for subsequent binding of a Nop5p-aFib heterodimer at each site. Unexpectedly, however, even without L7Ae but at a higher concentration of Nop5p-aFib, a substantially active RNP complex can still form, possibly reflecting the higher propensity of the cis-acting system to form guide RNA duplex(es) relative to classical trans- acting C/D RNA guides. Moreover, footprinting data of RNPs, consistent with Nop5p interacting with the non-canonical stem of the K-turn, suggest that binding of Nop5p-aFib to the pre-tRNA-L7Ae complex might direct transition from a splicing-competent structure to an RNA conformer displaying the guide RNA duplexes required for site-specific methylation.     

Selective inhibitory DNA aptamers of the human RNase H1

Human RNase H1 binds double-stranded RNA via its N-terminal domain and RNA–DNA hybrid via its C-terminal RNase H domain, the latter being closely related to Escherichia coli RNase HI. Using SELEX, we have generated a set of DNA sequences that can bind efficiently (K_d values ranging from 10 to 80 nM) to the human RNase H1. None of them could fold into a simple perfect double-stranded DNA hairpin confirming that double-stranded DNA does not constitute a trivial ligand for the enzyme. Only two of the 37 DNA aptamers selected were inhibitors of human RNase H1 activity. The two inhibitory oligomers, V-2 and VI-2, were quite different in structure with V-2 folding into a large, imperfect but stable hairpin loop. The VI-2 structure consists of a central region unimolecular quadruplex formed by stacking of two guanine quartets flanked by the 5′ and 3′ tails that form a stem of six base pairs. Base pairing between the 5′ and 3′ tails appears crucial for conferring the inhibitory properties to the aptamer. Finally, the inhibitory aptamers were capable of completely abolishing the action of an antisense oligonucleotide in a rabbit reticulocyte lysate supplemented with human RNase H1, with IC₅₀ ranging from 50 to 100 nM.