Methylation Warfare: Interaction of Pneumococcal Bacteriophages with Their Host.

Virus-host interactions are regulated by complex coevolutionary dynamics. In Streptococcus pneumoniae, phase-variable type I restriction-modification (R-M) systems are part of the core genome. We hypothesized that the ability of the R-M systems to switch between six target DNA specificities also has a key role in preventing the spread of bacteriophages. Using the streptococcal temperate bacteriophage SpSL1, we show that the variants of both the SpnIII and SpnIV R-M systems are able to restrict invading bacteriophage with an efficiency approximately proportional to the number of target sites in the bacteriophage genome. In addition to restriction of lytic replication, SpnIII also led to abortive infection in the majority of host cells. During lytic infection, transcriptional analysis found evidence of phage-host interaction through the strong upregulation of the nrdR nucleotide biosynthesis regulon. During lysogeny, the phage had less of an effect on host gene regulation. This research demonstrates a novel combined bacteriophage restriction and abortive infection mechanism, highlighting the importance that the phase-variable type I R-M systems have in the multifunctional defense against bacteriophage infection in the respiratory pathogen S. pneumoniaeIMPORTANCE With antimicrobial drug resistance becoming an increasing burden on human health, much attention has been focused on the potential use of bacteriophages and their enzymes as therapeutics. However, the investigations into the physiology of the complex interactions of bacteriophages with their hosts have attracted far less attention, in comparison. This work describes the molecular characterization of the infectious cycle of a bacteriophage in the important human pathogen Streptococcus pneumoniae and explores the intricate relationship between phase-variable host defense mechanisms and the virus. This is the first report showing how a phase-variable type I restriction-modification system is involved in bacteriophage restriction while it also provides an additional level of infection control through abortive infection.

Altered carbon turnover processes and microbiomes in soils under long-term extremely high CO2 exposure.

There is only limited understanding of the impact of high p(CO2) on soil biomes. We have studied a floodplain wetland where long-term emanations of temperate volcanic CO2 (mofettes) are associated with accumulation of carbon from the Earth's mantle. With an integrated approach using isotope geochemistry, soil activity measurements and multi-omics analyses, we demonstrate that high (nearly pure) CO2 concentrations have strongly affected pathways of carbon production and decomposition and therefore carbon turnover. In particular, a promotion of dark CO2 fixation significantly increased the input of geogenic carbon in the mofette when compared to a reference wetland soil exposed to normal levels of CO2. Radiocarbon analysis revealed that high quantities of mofette soil carbon originated from the assimilation of geogenic CO2 (up to 67%) via plant primary production and subsurface CO2 fixation. However, the preservation and accumulation of almost undegraded organic material appeared to be facilitated by the permanent exclusion of meso- to macroscopic eukaryotes and associated physical and/or ecological traits rather than an impaired biochemical potential for soil organic matter decomposition. Our study shows how CO2-induced changes in diversity and functions of the soil community can foster an unusual biogeochemical profile.

Ephrin-B3 binds to a sulfated cell-surface receptor.

The ephrins are a family of proteins known to bind the Eph (erythropoietin-producing hepatocellular) receptor tyrosine kinase family. In the present paper, we provide data showing that ephrin-B3 binds a sulfated cell-surface protein on HEK-293T (human embryonic kidney-293 cells expressing the large T-antigen of simian virus 40) and HeLa cells, a binding that is nearly completely blocked by treatment of these cell lines with chlorate or heparinase, or by addition of the heavily sulfated glycosaminoglycan heparin. This indicates that heparan sulfate on these cells is essential for cell-surface binding of ephrin-B3. Heparin did not affect ephrin-B3 binding to EphB receptors expressed on transfected HEK-293T cells, indicating further that ephrin-B3 binds an alternative receptor which is a heparan sulfate proteoglycan. Site-directed mutagenesis analysis revealed that Arg178 and Lys179 are important for heparin binding of ephrin-B3 and also for ephrin-B3 binding to cells. These amino acids, when introduced in the non-heparin-binding ephrin-B1, conferred the heparin-binding property. Functional studies reveal that ephrin-B3 binding to cells induces cellular signalling and influences cell rounding and cell spreading. In conclusion, our data provide evidence for an unknown ephrin-B3-binding cell-surface proteoglycan involved in cellular signalling.

Evidence for the involvement of FAM110C protein in cell spreading and migration.

A number of factors, including protein kinases, Rho GTPases and actin and microtubule cytoskeletons play a crucial role in cell migration and spreading. We have recently shown that ectopic expression of FAM110C can alter cellular morphology by mechanisms yet to be determined. In this study, a FAM110C antiserum has been developed and used to study endogenously expressed FAM110C. Our data show that FAM110C is expressed by different cell lines and it can be detected throughout the cell. Interestingly, depletion of FAM110C by short interfering RNA reduced integrin-mediated filopodia formation, hepatocyte growth factor-induced migration, and phosphorylation of the Akt1 kinase in the epithelial cell line HepG2. Furthermore, co-immunoprecipitation and co-localization studies show that both ectopically and endogenously expressed FAM110C interact, or is part of a protein complex, with the Akt1 kinase. This interaction is transient and follows the activation of Akt1. In addition, we show that alpha-tubulin co-precipitates with FAM110C which further supports an interaction with the microtubule cytoskeleton. Collectively, these findings suggest a new function for FAM110C in the regulation of cell spreading, migration and filopodia induction.

A homozygote splice site PMS2 mutation as cause of Turcot syndrome gives rise to two different abnormal transcripts.

Turcot syndrome is a rare, inherited disease predisposing of tumours in the central nerve system and in the colorectal system. This report describes a Turcot patient with an extraordinary clinical history. The patient is still alive at the age of 43. She was operated at the age of 10 by brain tumour and at the age of 16 by colorectal cancer. She has since then been treated for multiple cancers (gastrointestinal, endometrial, basal cell carcinomas), and removal of adenomatous polyps at several occasions. The aim of this work was to investigate if there was any specific genotype that explains her remarkable clinical history. Microsatellite instability and immunohistochemistry analysis for four DNA mismatch repair proteins were performed. DNA mutation analysis was done for genes involved in polyposis and mismatch repair by denaturing high performance liquid chromatography and sequencing. cDNA analysis was carried out for the mismatch repair gene PMS2. The patients genotype was found to be a homozygous splice site mutation in the PMS2 gene, c.989-1G