Structure and membrane binding properties of the endosomal tetratricopeptide repeat (TPR) domain-containing sorting nexins SNX20 and SNX21

Sorting nexins (SNX) orchestrate membrane trafficking and signaling events required for the proper distribution of proteins within the endosomal network. Their phox homology (PX) domain acts as a phosphoinositide (PI) recognition module that targets them to specific endocytic membrane domains. The modularity of SNX proteins confers a wide variety of functions from signaling to membrane deformation and cargo binding, and many SNXs are crucial modulators of endosome dynamics and are involved in a myriad of physiological and pathological processes such as neurodegenerative diseases, cancer, and inflammation. Here, we have studied the poorly characterized SNX20 and its paralogue SNX21, which contain an N-terminal PX domain and a C-terminal PX-associated B (PXB) domain of unknown function. The two proteins share similar PI-binding properties and are recruited to early endosomal compartments by their PX domain. The crystal structure of the SNX21 PXB domain reveals a tetratricopeptide repeat (TPR)-fold, a module that typically binds short peptide motifs, with three TPR α-helical repeats. However, the C-terminal capping helix adopts a highly unusual and potentially self-inhibitory topology. SAXS solution structures of SNX20 and SNX21 show that these proteins adopt a compact globular architecture, and membrane interaction analyses indicate the presence of overlapping PI-binding sites that may regulate their intracellular localization. This study provides the first structural analysis of this poorly characterized subfamily of SNX proteins, highlighting a likely role as endosome-associated scaffolds

SopB-Mediated Recruitment of SNX18 Facilitates Salmonella Typhimurium Internalization by the Host Cell

To invade epithelial cells, Salmonella enterica serovar Typhimurium (S. Typhimurium) induces macropinocytosis through the action of virulence proteins delivered across the host cell membrane via a type III secretion system. We show that after docking at the plasma membrane S. Typhimurium triggers rapid recruitment of cytosolic SNX18, a SH3-PX-BAR domain sorting nexin protein, to the bacteria-induced membrane ruffles and to the nascent Salmonella-containing vacuole. SNX18 recruitment required the inositol-phosphatase activity of the Salmonella effector SopB and an intact phosphoinositide-binding site within the PX domain of SNX18, but occurred independently of Rho-GTPases Rac1 and Cdc42 activation. SNX18 promotes formation of the SCV from the plasma membrane by acting as a scaffold to recruit Dynamin-2 and N-WASP in a process dependent on the SH3 domain of SNX18. Quantification of bacteria uptake revealed that overexpression of SNX18 increased bacteria internalization, whereas a decrease was detected in cells overexpressing the phosphoinositide-binding mutant R303Q, the ΔSH3 mutant, and in cells where endogenous levels of SNX18 were knocked-down. This study identifies SNX18 as a novel target of SopB and suggests a mechanism where S. Typhimurium engages host factors via local manipulation of phosphoinositide composition at the site of invasion to orchestrate the internalization process

Numerical simulation and feasibility assessment of acid gas injection in a carbonate formation of the Tarim Basin, China

An enormous amount of acid gas, containing carbon dioxide (CO2) and hydrogen sulfide (H2S), is generated in the exploitation of oil and gas reservoirs in the Tarim Basin, China. An appropriate management plan is required to safely dispose of the acid gas, and common strategy considered for the safe disposal of acid gas is the injection of it into deep formations – this strategy mitigates greenhouse gas emissions and avoids costs associated with desulfurization. A feasibility assessment of acid gas injection requires a detailed investigation of the potential physical and geochemical impacts. Reactive transport simulations based on the mineralogical composition and the hydrochemical characteristics of a carbonate formation in the Tarim Basin were conducted to identify the physical and geochemical interactions of acid gas with the mineral matrix and formation water. Acid gas (59% CO2 and 41% H2S) was injected at a constant rate of 19 200 Nm3/d for 25 years, and the simulation was run by the TMVR_EOSG module of the TOUGHREACT code for a period of 10 000 years. The results indicate that the minimum liquid saturation is much larger than the residual water saturation, and the pressure buildup is below the allowable pressure increase. Additionally, the porosity change is found to be negligible due to the small changes in calcite and quartz in the volume fraction. From this perspective, acid gas injection in the carbonate formation of the Tarim Basin seems feasible. Furthermore, the fast breakthrough of CO2 can provide an advanced warning of a potential breakthrough of acid gas. Last, the injection rate can be increased to accelerate acid gas trapping, and the results could be used as guidance for future acid gas injection operations

Effects of Different Penetration Patterns on a Fault during Underground Fluid Injection

At underground fluid injection sites with natural faults, understanding how to avoid the subsequent fault reactivation and induced seismicity plays a crucial role in the success of subsurface anthropogenic activities. In this work, with the objective of avoiding risky faults in site selection in the Shengli Oilfield, we investigated the faults that are usually encountered in the target demonstration zone; based on the geophysical observations of fault structures, we designed different fault tectonic scenarios to investigate the different penetration patterns of faults. We used the finite element-based numerical method to assess the influence of the effective lateral and vertical reservoir transmissivity in each fault penetration pattern. Our results indicate that when a permeable fault intersects into the target reservoir, it presents both barrier effect to reservoir transmissivity within the target reservoir and hydraulic connection between reservoirs. The effective lateral reservoir transmissivity is dominated by the barrier effect of the fault, and the effective vertical reservoir transmissivity is dominated by the hydraulic connection between reservoirs. Relatively impermeable faults with less contact with the target aquifer make higher effective lateral reservoir transmissivity and lower effective vertical reservoir transmissivity, which would mitigate the risk of caprock failure and the magnitude of the induced seismicity

SopB-mediated recruitment of SNX18 facilitates Salmonella typhimurium internalization by the host cell

To invade epithelial cells, Salmonella enterica serovar Typhimurium (S. Typhimurium) induces macropinocytosis through the action of virulence proteins delivered across the host cell membrane via a type Ill secretion system. We show that after docking at the plasma membrane S. Typhimurium triggers rapid recruitment of cytosolic SNX18, a SH3-PX-BAR domain sorting nexin protein, to the bacteria-induced membrane ruffles and to the nascent Salmonella-containing vacuole. SNX18 recruitment required the inositol-phosphatase activity of the Salmonella effector SopB and an intact phosphoinositide-binding site within the PX domain of SNX18, but occurred independently of Rho-GTPases Rac1 and Cdc42 activation. SNX18 promotes formation of the SCV from the plasma membrane by acting as a scaffold to recruit Dynamin-2 and N-WASP in a process dependent on the SH3 domain of SNX1 8. Quantification of bacteria uptake revealed that overexpression of SNX18 increased bacteria internalization, whereas a decrease was detected in cells overexpressing the phosphoinositide-binding mutant R303Q, the Delta SH3 mutant, and in cells where endogenous levels of SNX18 were knocked-down. This study identifies SNX1 8 as a novel target of SopB and suggests a mechanism where S. Typhimurium engages host factors via local manipulation of phosphoinositide composition at the site of invasion to orchestrate the internalization process

Retromer is required for apoptotic cell clearance by phagocytic receptor recycling

The cell surface receptor CED-1 mediates apoptotic cell recognition by phagocytic cells, enabling cell corpse clearance in Caenorhabditis elegans. Here, we found that the C. elegans intracellular protein sorting complex, retromer, was required for cell corpse clearance by mediating the recycling of CED-1. Retromer was recruited to the surfaces of phagosomes containing cell corpses, and its loss of function caused defective cell corpse removal. The retromer probably acted through direct interaction with CED-1 in the cell corpse recognition pathway. In the absence of retromer function, CED-1 associated with lysosomes and failed to recycle from phagosomes and cytosol to the plasma membrane. Thus, retromer is an essential mediator of apoptotic cell clearance by regulating phagocytic receptor(s) during cell corpse engulfment

Clathrin and AP2 are required for phagocytic receptor-mediated apoptotic cell clearance in Caenorhabditis elegans

Clathrin and the multi-subunit adaptor protein complex AP2 are central players in clathrin-mediated endocytosis by which the cell selectively internalizes surface materials. Here, we report the essential role of clathrin and AP2 in phagocytosis of apoptotic cells. In Caenorhabditis elegans, depletion of the clathrin heavy chain CHC-1 and individual components of AP2 led to a significant accumulation of germ cell corpses, which resulted from defects in both cell corpse engulfment and phagosome maturation required for corpse removal. CHC-1 and AP2 components associate with phagosomes in an inter-dependent manner. Importantly, we found that the phagocytic receptor CED-1 interacts with the α subunit of AP2, while the CED-6/Gulp adaptor forms a complex with both CHC-1 and the AP2 complex, which likely mediates the rearrangement of the actin cytoskeleton required for cell corpse engulfment triggered by the CED-1 signaling pathway. In addition, CHC-1 and AP2 promote the phagosomal association of LST-4/Snx9/18/33 and DYN-1/dynamin by forming a complex with them, thereby facilitating the maturation of phagosomes necessary for corpse degradation. These findings reveal a non-classical role of clathrin and AP2 and establish them as indispensable regulators in phagocytic receptor-mediated apoptotic cell clearance