Evidence for symmetric chromosomal inversions around the replication origin in bacteria.

BackgroundWhole-genome comparisons can provide great insight into many aspects of biology. Until recently, however, comparisons were mainly possible only between distantly related species. Complete genome sequences are now becoming available from multiple sets of closely related strains or species.ResultsBy comparing the recently completed genome sequences of Vibrio cholerae, Streptococcus pneumoniae and Mycobacterium tuberculosis to those of closely related species - Escherichia coli, Streptococcus pyogenes and Mycobacterium leprae, respectively - we have identified an unusual and previously unobserved feature of bacterial genome structure. Scatterplots of the conserved sequences (both DNA and protein) between each pair of species produce a distinct X-shaped pattern, which we call an X-alignment. The key feature of these alignments is that they have symmetry around the replication origin and terminus; that is, the distance of a particular conserved feature (DNA or protein) from the replication origin (or terminus) is conserved between closely related pairs of species. Statistically significant X-alignments are also found within some genomes, indicating that there is symmetry about the replication origin for paralogous features as well.ConclusionsThe most likely mechanism of generation of X-alignments involves large chromosomal inversions that reverse the genomic sequence symmetrically around the origin of replication. The finding of these X-alignments between many pairs of species suggests that chromosomal inversions around the origin are a common feature of bacterial genome evolution

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The regional-scale surface mass balance of Pine Island Glacier, West Antarctica, over the period 2005--2014, derived from airborne radar soundings and neutron probe measurements

We derive recent surface mass balance (SMB) estimates from airborne radar observations along the iSTAR traverse (2013, 2014) at Pine Island Glacier (PIG), West Antarctica. Ground-based neutron probe measurements provide information of snow and firn density with depth at 22 locations and were used to date internal annual reflection layers. The 2005 layer was traced for a total distance of 2367 km to determine annual mean SMB for the period 2005–2014. Using complementary SMB estimates from two regional climate models, RACMO2.3p2 and MAR, and a geostatistical kriging scheme, we determine a regional-scale SMB distribution with similar main characteristics to that determined for the period 1985–2009 in previous studies. Local departures exist for the northern PIG slopes, where the orographic precipitation shadow effect appears to be more pronounced in our observations, and the southward interior, where the SMB gradient is more pronounced in previous studies. We derive total mass inputs of 79.9 +/- 19.2 and 82.1 +/- 19.2 Gt yr-1 to the PIG basin based on complementary ASIRAS–RACMO and ASIRAS–MAR SMB estimates, respectively. These are not significantly different to the value of 78.3 +/- 6.8 Gt yr-1 for the period 1985–2009. Thus, there is no evidence of a secular trend at decadal scales in total mass input to the PIG basin. We note, however, that our estimated uncertainty is more than twice the uncertainty for the 1985–2009 estimate on total mass input. Our error analysis indicates that uncertainty estimates on total mass input are highly sensitive to the selected krige methodology and assumptions made on the interpolation error, which we identify as the main cause for the increased uncertainty range compared to the 1985–2009 estimates

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Whole genome sequence analysis reveals the broad distribution of the RtxA type 1 secretion system and four novel putative type 1 secretion systems throughout the Legionella genus.

Type 1 secretion systems (T1SSs) are broadly distributed among bacteria and translocate effectors with diverse function across the bacterial cell membrane. Legionella pneumophila, the species most commonly associated with Legionellosis, encodes a T1SS at the lssXYZABD locus which is responsible for the secretion of the virulence factor RtxA. Many investigations have failed to detect lssD, the gene encoding the membrane fusion protein of the RtxA T1SS, in non-pneumophila Legionella, which has led to the assumption that this system is a virulence factor exclusively possessed by L. pneumophila. Here we discovered RtxA and its associated T1SS in a novel Legionella taurinensis strain, leading us to question whether this system may be more widespread than previously thought. Through a bioinformatic analysis of publicly available data, we classified and determined the distribution of four T1SSs including the RtxA T1SS and four novel T1SSs among diverse Legionella spp. The ABC transporter of the novel Legionella T1SS Legionella repeat protein secretion system shares structural similarity to those of diverse T1SS families, including the alkaline protease T1SS in Pseudomonas aeruginosa. The Legionella bacteriocin (1-3) secretion systems T1SSs are novel putative bacteriocin transporting T1SSs as their ABC transporters include C-39 peptidase domains in their N-terminal regions, with LB2SS and LB3SS likely constituting a nitrile hydratase leader peptide transport T1SSs. The LB1SS is more closely related to the colicin V T1SS in Escherichia coli. Of 45 Legionella spp. whole genomes examined, 19 (42%) were determined to possess lssB and lssD homologs. Of these 19, only 7 (37%) are known pathogens. There was no difference in the proportions of disease associated and non-disease associated species that possessed the RtxA T1SS (p = 0.4), contrary to the current consensus regarding the RtxA T1SS. These results draw into question the nature of RtxA and its T1SS as a singular virulence factor. Future studies should investigate mechanistic explanations for the association of RtxA with virulence

Direct evidence for radar reflector originating from changes in crystal-orientation fabric

International audienceThe origin of a strong continuous radar reflector observed with airborne radio-echo sounding (RES) at the EPICA deep-drilling site in Dronning Maud Land, Antarctica, is identified as a transition in crystal fabric orientation from a vertical girdle- to increased single-pole orientation seen along the ice core. The reflector is observed with a 60 ns and 600 ns long pulse at a frequency of 150 MHz, spans one pulse length, is continuous over 5 km, and occurs at a depth of about 2020?2030 m at the drill site. Changes in conductivity as reflector origin are excluded by investigating the ice-core profile and synthetic RES data. Our observations allow to extrapolate the crystal orientation feature along the reflector in space, with implications for ice-sheet dynamics. As the conductivity profile of the EPICA shows no distinctive peak at this depths, we exclude changes in conductivity as the reflector origin. This is supported by application of numerical forward modelling of electromagnetic wave propagation, based on the conductivity profile, which is able to reproduce nearby reflections, but fails to reproduce this one. Because of background noise, the permittivity profile based on dielectric does not show prominent signals at these depths. We therefore interpret the observed reflector to originate from this change in crystal fabric

Direct evidence for continuous radar reflector originating from changes in crystal-orientation fabric

International audienceThe origin of a strong continuous radar reflector observed with airborne radio-echo sounding (RES) at the EPICA deep-drilling site in Dronning Maud Land, Antarctica, is identified as a transition in crystal fabric orientation from a vertical girdle to an increased single-pole orientation seen along the ice core. The reflector is observed with a 60 ns and 600 ns long pulse at a frequency of 150 MHz, spans one pulse length, is continuous over 5 km, and occurs at a depth of about 2025?2045 m at the drill site. Changes in conductivity as reflector origin are excluded by investigating the ice-core profile, synthetic RES data, and a RES profile with different electromagnetic polarisation azimuths. The reflector's magnitude shows maximum values for polarisation parallel to the nearby ice divide and disappears for polarisation perpendicular to it, identifying the orientation of the girdle to lie in the vertical plane parallel to the ice divide. Observations allow us to extrapolate the crystal orientation feature along the reflector in space, with implications for ice-sheet dynamics and modeling

Comparative genomics of the genus porphyromonas identifies adaptations for heme synthesis within the prevalent canine oral species porphyromonas cangingivalis

© 2015 The Author(s). Porphyromonads play an important role inhuman periodontal disease and recently have been shownto be highly prevalent in canine mouths. Porphyromonas cangingivalis is the most prevalent canine oral bacterial species in both plaque from healthy gingiva and plaque from dogs with early periodontitis. The ability of P. cangingivalis to flourish in the different environmental conditions characterized by these two states suggests a degree of metabolic flexibility. To characterize the genes responsible for this, the genomes of 32 isolates (including 18 newly sequenced and assembled) from18Porphyromonad species fromdogs, humans, and other mammals were compared. Phylogenetic trees inferred using core genes largely matched previous findings; however, comparative genomic analysis identified several genes and pathways relating to heme synthesis that were present in P. cangingivalis but not in other Porphyromonads. Porphyromonas cangingivalis has a complete protoporphyrin IX synthesis pathway potentially allowing it to synthesize its own heme unlike pathogenic Porphyromonads such as Porphyromonas gingivalis that acquire heme predominantly from blood. Other pathway differences such as the ability to synthesize siroheme and vitamin B12 point to enhanced metabolic flexibility for P. cangingivalis, which may underlie its prevalence in the canine oral cavity