Non-contiguous finished genome sequence and description of Oceanobacillus massiliensis sp. nov.

Oceanobacillus massiliensis strain N’Diop^T sp. nov. is the type strain of O. massiliensis sp. nov., a new species within the genus Oceanobacillus. This strain, whose genome is described here, was isolated from the fecal flora of a healthy patient. O. massiliensis is an aerobic rod. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,532,675 bp long genome contains 3,519 protein-coding genes and 72 RNA genes, including between 6 and 8 rRNA operons.     

2-Amino-6-chloro-3,4-dihydroquinazoline: A novel 5-HT3 receptor antagonist with antidepressant character

2-Amino-6-chloro-3,4-dihydroquinazoline HCl (A6CDQ, 4) binds at 5-HT₃ serotonin receptors and displays antidepressant-like action in the mouse tail suspension test (TST). Empirically, 4 was demonstrated to be a 5-HT₃ receptor antagonist (two-electrode voltage clamp recordings using frog oocytes; IC₅₀ = 0.26 μM), and one that should readily penetrate the blood–brain barrier (log P = 1.86). 5-HT₃ receptor antagonists represent a potential approach to the development of new antidepressants, and 4 is an example of a structurally novel 5-HT₃ receptor antagonist that is active in a preclinical antidepressant model (i.e., the mouse TST).     

Inhibition of autophagy by TAB2 and TAB3

Autophagic responses are coupled to the activation of the inhibitor of NF-κB kinase (IKK). Here, we report that the essential autophagy mediator Beclin 1 and TGFβ-activated kinase 1 (TAK1)-binding proteins 2 and 3 (TAB2 and TAB3), two upstream activators of the TAK1-IKK signalling axis, constitutively interact with each other via their coiled-coil domains (CCDs). Upon autophagy induction, TAB2 and TAB3 dissociate from Beclin 1 and bind TAK1. Moreover, overexpression of TAB2 and TAB3 suppresses, while their depletion triggers, autophagy. The expression of the C-terminal domain of TAB2 or TAB3 or that of the CCD of Beclin 1 competitively disrupts the interaction between endogenous Beclin 1, TAB2 and TAB3, hence stimulating autophagy through a pathway that requires endogenous Beclin 1, TAK1 and IKK to be optimally efficient. These results point to the existence of an autophagy-stimulatory 'switch' whereby TAB2 and TAB3 abandon inhibitory interactions with Beclin 1 to engage in a stimulatory liaison with TAK1.     

Towards an accurate identification of mosaic genes and partial horizontal gene transfers

Many bacteria and viruses adapt to varying environmental conditions through the acquisition of mosaic genes. A mosaic gene is composed of alternating sequence polymorphisms either belonging to the host original allele or derived from the integrated donor DNA. Often, the integrated sequence contains a selectable genetic marker (e.g. marker allowing for antibiotic resistance). An effective identification of mosaic genes and detection of corresponding partial horizontal gene transfers (HGTs) are among the most important challenges posed by evolutionary biology. We developed a method for detecting partial HGT events and related intragenic recombination giving rise to the formation of mosaic genes. A bootstrap procedure incorporated in our method is used to assess the support of each predicted partial gene transfer. The proposed method can be also applied to confirm or discard complete (i.e. traditional) horizontal gene transfers detected by any HGT inferring method. While working on a full-genome scale, the new method can be used to assess the level of mosaicism in the considered genomes as well as the rates of complete and partial HGT underlying their evolution.     

Late steps of ribosome assembly in E. coli are sensitive to a severe heat stress but are assisted by the HSP70 chaperone machine

The late stages of 30S and 50S ribosomal subunits biogenesis have been studied in a wild-type (wt) strain of Escherichia coli (MC4100) subjected to a severe heat stress (45-46°C). The 32S and 45S ribosomal particles (precursors to 50S subunits) and 21S ribosomal particles (precursors to 30S subunits) accumulate under these conditions. They are authentic precursors, not degraded or dead-end particles. The 21S particles are shown, by way of a modified 3'5' RACE procedure, to contain 16S rRNA unprocessed, or processed at its 5' end, and not at the 3' end. This implies that maturation of 16S rRNA is ordered and starts at its 5'-terminus, and that the 3'-terminus is trimmed at a later step. This observation is not limited to heat stress conditions, but it also can be verified in bacteria growing at a normal temperature (30°C), supporting the idea that this is the general pathway. Assembly defects at very high temperature are partially compensated by plasmid-driven overexpression of the DnaK/DnaJ chaperones. The ribosome assembly pattern in wt bacteria under a severe heat stress is therefore reminiscent of that observed at lower temperatures in E. coli mutants lacking the chaperones DnaK or DnaJ.     

Mitochondria associate with P-bodies and modulate microRNA-mediated RNA interference

P-bodies are cytoplasmic granules that are linked to mRNA decay, mRNA storage, and RNA interference (RNAi). They are known to interact with stress granules in stressed cells, and with late endosomes. Here, we report that P-bodies also interact with mitochondria, as previously described for P-body-related granules in germ cells. The interaction is dynamic, as a large majority of P-bodies contacts mitochondria at least once within a 3-min interval, and for about 18 s. This association requires an intact microtubule network. The depletion of P-bodies does not seem to affect mitochondria, nor the mitochondrial activity to be required for their contacts with P-bodies. However, inactivation of mitochondria leads to a strong decrease of miRNA-mediated RNAi efficiency, and to a lesser extent of siRNA-mediated RNAi. The defect occurs during the assembly of active RISC and is associated with a specific delocalization of endogeneous Ago2 from P-bodies. Our study reveals the possible involvement of RNAi defect in pathologies involving mitochondrial deficiencies.     

Pseudomonas aeruginosa delays Kupffer cell death via stabilization of the X-chromosome-linked inhibitor of apoptosis protein

Kupffer cells are important for bacterial clearance and cytokine production during infection. We have previously shown that severe infection with Pseudomonas aeruginosa ultimately results in loss of Kupffer cells and hepatic bacterial clearance. This was associated with prolonged hepatic inflammation. However, there is a period of time during which there is both preserved hepatic bacterial clearance and increased circulating TNF-alpha. We hypothesized that early during infection, Kupffer cells are protected against TNF-alpha-induced cell death via activation of survival pathways. KC13-2 cells (a clonal Kupffer cell line) were treated with P. aeruginosa (strain PA103), TNF-alpha, or both. At early time points, TNF-alpha induced caspase-mediated cell death, but PA103 did not. When we combined the two exposures, PA103 protected KC13-2 cells from TNF-alpha-induced cell death. PA103, in the setting of TNF exposure, stabilized the X-chromosome-linked inhibitor of apoptosis protein (XIAP). Stabilization of XIAP can occur via PI3K and Akt. We found that PA103 activated Akt and that pretreatment with the PI3K inhibitor, LY294002, prevented PA103-induced protection against TNF-alpha-induced cell death. The effects of LY294002 included decreased levels of XIAP and increased amounts of cleaved caspase-3. Overexpression of Akt mimicked the effects of PA103 by protecting cells from TNF-alpha-induced cell death and XIAP cleavage. Transfection with a stable, nondegradable XIAP mutant also protected cells against TNF-alpha-induced cell death. These studies demonstrate that P. aeruginosa delays TNF-alpha-induced Kupffer cell death via stabilization of XIAP.     

Reshaping our understanding of species’ roles in landscape‐scale networks

In network ecology, landscape‐scale processes are often overlooked, yet there is increasing evidence that species and interactions spill over between habitats, calling for further study of interhabitat dependencies. Here, we investigate how species connect a mosaic of habitats based on the spatial variation of their mutualistic and antagonistic interactions using two multilayer networks, combining pollination, herbivory and parasitism in the UK and New Zealand. Developing novel methods of network analysis for landscape‐scale ecological networks, we discovered that few plant and pollinator species acted as connectors or hubs, both within and among habitats, whereas herbivores and parasitoids typically have more peripheral network roles. Insect species’ roles depend on factors other than just the abundance of taxa in the lower trophic level, exemplified by larger Hymenoptera connecting networks of different habitats and insects relying on different resources across different habitats. Our findings provide a broader perspective for landscape‐scale management and ecological community conservation.