McrD binds asymmetrically to methyl-coenzyme M reductase improving active-site accessibility during assembly.

Methyl-coenzyme M reductase (MCR) catalyzes the formation of methane, and its activity accounts for nearly all biologically produced methane released into the atmosphere. The assembly of MCR is an intricate process involving the installation of a complex set of posttranslational modifications and the unique Ni-containing tetrapyrrole called coenzyme F430. Despite decades of research, details of MCR assembly remain largely unresolved. Here, we report the structural characterization of MCR in two intermediate states of assembly. These intermediate states lack one or both F430 cofactors and form complexes with the previously uncharacterized McrD protein. McrD is found to bind asymmetrically to MCR, displacing large regions of the alpha subunit and increasing active-site accessibility for the installation of F430-shedding light on the assembly of MCR and the role of McrD therein. This work offers crucial information for the expression of MCR in a heterologous host and provides targets for the design of MCR inhibitors.

Location variance of the great vessels while undergoing side-bend positioning changes during lateral interbody fusion.

Background: Minimally invasive lateral lumbar interbody fusion (LLIF) is an increasingly popular surgical technique that facilitates minimally invasive exposure, attenuated blood loss, and potentially improved arthrodesis rates. However, there is a paucity of evidence elucidating the risk of vascular injury associated with LLIF, and no previous studies have evaluated the distance from the lumbar intervertebral space (IVS) to the abdominal vascular structures in a side-bend lateral decubitus position. Therefore, the purpose of this study is to evaluate the average distance, and changes in distance, from the lumbar IVS to the major vessels from supine to side-bend right and left lateral decubitus (RLD and LLD) positions simulating operating room positioning utilizing magnetic resonance imaging (MRI). Methods: We independently evaluated lumbar MRI scans of 10 adult patients in the supine, RLD, and LLD positions, calculating the distance from each lumbar IVS to adjacent major vascular structures. Results: At the cephalad lumbar levels (L1-L3), the aorta lies in closer proximity to the IVS in the RLD position, in contrast to the inferior vena cava (IVC), which is further from the IVS in the RLD. At the L3-S1 vertebral levels, the right and left common iliac arteries (CIA) are both further from the IVS in the LLD position, with the notable exception of the right CIA, which lies further from the IVS in the RLD at the L5-S1 level. At both the L4-5 and L5-S1 levels, the right common iliac vein (CIV) is further from the IVS in the RLD. In contrast, the left CIV is further from the IVS at the L4-5 and L5-S1 levels. Conclusion: Our results suggest that RLD positioning may be safer for LLIF as it affords greater distance away from critical venous structures, however, surgical positioning should be assessed at the discretion of the spine surgeon on a patient-specific basis.

Amino acid sensing and lysosomal signaling complexes.

Amino acid pools in the cell are monitored by dedicated sensors, whose structures are now coming into view. The lysosomal Rag GTPases are central to this pathway, and the regulation of their GAP complexes, FLCN-FNIP and GATOR1, have been worked out in detail. For FLCN-FNIP, the entire chain of events from the arginine transporter SLC38A9 to substrate-specific mTORC1 activation has been visualized. The structure GATOR2 has been determined, hinting at an ordering of amino acid signaling across a larger size scale than anticipated. The centerpiece of lysosomal signaling, mTORC1, has been revealed to recognize its substrates by more nuanced and substrate-specific mechanisms than previous appreciated. Beyond the well-studied Rag GTPase and mTORC1 machinery, another lysosomal amino acid sensor/effector system, that of PQLC2 and the C9orf72-containing CSW complex, is coming into structural view. These developments hold promise for further insights into lysosomal physiology and lysosome-centric therapeutics.

Structural basis of TRAPPIII-mediated Rab1 activation.

The GTPase Rab1 is a master regulator of the early secretory pathway and is critical for autophagy. Rab1 activation is controlled by its guanine nucleotide exchange factor, the multisubunit TRAPPIII complex. Here, we report the 3.7 Å cryo-EM structure of the Saccharomyces cerevisiae TRAPPIII complex bound to its substrate Rab1/Ypt1. The structure reveals the binding site for the Rab1/Ypt1 hypervariable domain, leading to a model for how the complex interacts with membranes during the activation reaction. We determined that stable membrane binding by the TRAPPIII complex is required for robust activation of Rab1/Ypt1 in vitro and in vivo, and is mediated by a conserved amphipathic α-helix within the regulatory Trs85 subunit. Our results show that the Trs85 subunit serves as a membrane anchor, via its amphipathic helix, for the entire TRAPPIII complex. These findings provide a structural understanding of Rab activation on organelle and vesicle membranes.

Structural basis for the initiation of COPII vesicle biogenesis.

The first stage of the eukaryotic secretory pathway is the packaging of cargo proteins into coat protein complex II (COPII) vesicles exiting the ER. The cytoplasmic COPII vesicle coat machinery is recruited to the ER membrane by the activated, GTP-bound, form of the conserved Sar1 GTPase. Activation of Sar1 on the surface of the ER by Sec12, a membrane-anchored GEF (guanine nucleotide exchange factor), is therefore the initiating step of the secretory pathway. Here we report the structure of the complex between Sar1 and the cytoplasmic GEF domain of Sec12, both from Saccharomyces cerevisiae. This structure, representing a key nucleotide-free activation intermediate, reveals how the potassium ion-binding K loop disrupts the nucleotide-binding site of Sar1. We propose an unexpected orientation of the GEF domain relative to the membrane surface and postulate a mechanism for how Sec12 facilitates membrane insertion of the amphipathic helix exposed by Sar1 upon GTP binding.

In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.

Phosphorylation is one of the most dynamic and widespread post-translational modifications regulating virtually every aspect of eukaryotic cell biology. Here, we assemble a dataset from 75 independent phosphoproteomic experiments performed in our laboratory using Saccharomyces cerevisiae. We report 30,902 phosphosites identified from cells cultured in a range of DNA damage conditions and/or arrested in distinct cell cycle stages. To generate a comprehensive resource for the budding yeast community, we aggregate our dataset with the Saccharomyces Genome Database and another recently published study, resulting in over 46,000 budding yeast phosphosites. With the goal of enhancing the identification of functional phosphorylation events, we perform computational positioning of phosphorylation sites on available 3D protein structures and systematically identify events predicted to regulate protein complex architecture. Results reveal hundreds of phosphorylation sites mapping to or near protein interaction interfaces, many of which result in steric or electrostatic "clashes" predicted to disrupt the interaction. With the advancement of Cryo-EM and the increasing number of available structures, our approach should help drive the functional and spatial exploration of the phosphoproteome.

The TRAPPIII complex activates the GTPase Ypt1 (Rab1) in the secretory pathway.

Rab GTPases serve as molecular switches to regulate eukaryotic membrane trafficking pathways. The transport protein particle (TRAPP) complexes activate Rab GTPases by catalyzing GDP/GTP nucleotide exchange. In mammalian cells, there are two distinct TRAPP complexes, yet in budding yeast, four distinct TRAPP complexes have been reported. The apparent differences between the compositions of yeast and mammalian TRAPP complexes have prevented a clear understanding of the specific functions of TRAPP complexes in all cell types. In this study, we demonstrate that akin to mammalian cells, wild-type yeast possess only two TRAPP complexes, TRAPPII and TRAPPIII. We find that TRAPPIII plays a major role in regulating Rab activation and trafficking at the Golgi in addition to its established role in autophagy. These disparate pathways share a common regulatory GTPase Ypt1 (Rab1) that is activated by TRAPPIII. Our findings lead to a simple yet comprehensive model for TRAPPIII function in both normal and starved eukaryotic cells.

Flexor tendon repair with a knotless, bidirectional barbed suture: an in vivo biomechanical analysis.

PURPOSE: To compare and analyze biomechanical properties and histological characteristics of flexor tendons either repaired by a 4-strand modified Kessler technique or using barbed suture with a knotless repair technique in an in vivo model. METHODS: A total of 25 chickens underwent surgical transection of the flexor digitorum profundus tendon followed by either a 4-strand Kessler repair or a knotless repair with barbed suture. Chickens were randomly assigned to 1 of 3 groups with various postoperative times to death. Harvested tendons were subjected to biomechanical testing or histologic analysis. RESULTS: Harvested tendons revealed failures in 25% of knotless repairs (8 of 32) and 8% of 4-strand Kessler repairs (2 of 24). Biomechanical testing revealed no significant difference in tensile strength between 4-strand Kessler and barbed repairs; however, this lack of difference may be attributed to lower statistical power. We noted a trend toward a gradual decrease in strength over time for barbed repairs, whereas we noticed the opposite for the 4-strand Kessler repairs. Mode of failure during testing differed between repair types. The barbed repairs tended toward suture breakage as opposed to 4-strand Kessler repairs, which demonstrated suture pullout. Histological analysis identified no difference in the degree of inflammation or fibrosis; however, there was a vigorous foreign body reaction around the 4-strand Kessler repair and no such response around the barbed repairs. CONCLUSIONS: In this model, knotless barbed repairs trended toward higher in vivo failure rates and biomechanical inferiority under physiologic conditions, with each repair technique differing in mode of failure and respective histologic reaction. We are unable to recommend the use of knotless barbed repair over the 4-strand modified Kessler technique. CLINICAL RELEVANCE: For the repair techniques tested, surgeons should prefer standard Kessler repairs over the described knotless technique with barbed suture.