Structural basis of mitochondrial protein import by the TIM23 complex.

Mitochondria import nearly all of their approximately 1,000-2,000 constituent proteins from the cytosol across their double-membrane envelope1-5. Genetic and biochemical studies have shown that the conserved protein translocase, termed the TIM23 complex, mediates import of presequence-containing proteins (preproteins) into the mitochondrial matrix and inner membrane. Among about ten different subunits of the TIM23 complex, the essential multipass membrane protein Tim23, together with the evolutionarily related protein Tim17, has long been postulated to form a protein-conducting channel6-11. However, the mechanism by which these subunits form a translocation path in the membrane and enable the import process remains unclear due to a lack of structural information. Here we determined the cryo-electron microscopy structure of the core TIM23 complex (heterotrimeric Tim17-Tim23-Tim44) from Saccharomyces cerevisiae. Contrary to the prevailing model, Tim23 and Tim17 themselves do not form a water-filled channel, but instead have separate, lipid-exposed concave cavities that face in opposite directions. Our structural and biochemical analyses show that the cavity of Tim17, but not Tim23, forms the protein translocation path, whereas Tim23 probably has a structural role. The results further suggest that, during translocation of substrate polypeptides, the nonessential subunit Mgr2 seals the lateral opening of the Tim17 cavity to facilitate the translocation process. We propose a new model for the TIM23-mediated protein import and sorting mechanism, a central pathway in mitochondrial biogenesis.

P5-ATPases: Structure, substrate specificities, and transport mechanisms.

P5A- and P5B- ATPases, or collectively P5-ATPases, are eukaryotic-specific ATP-dependent transporters that are important for the function of the endoplasmic reticulum (ER) and endo-/lysosomes. However, their substrate specificities had remained enigmatic for many years. Recent cryo-electron microscopy (cryo-EM) and biochemical studies of P5-ATPases have revealed their substrate specificities and transport mechanisms, which were found to be markedly different from other members of the P-type ATPase superfamily. The P5A-ATPase extracts mistargeted or mis-inserted transmembrane helices from the ER membrane for protein quality control, while the P5B-ATPases mediate export of polyamines from late endo-/lysosomes into the cytosol. In this review, we discuss the mechanisms of their substrate recognition and transport based on the cryo-EM structures of the yeast and human P5-ATPases. We highlight how structural diversification of the transmembrane domain has enabled the P5-ATPase subfamily to adapt for transport of atypical substrates.

Structural basis of polyamine transport by human ATP13A2 (PARK9).

Polyamines are small, organic polycations that are ubiquitous and essential to all forms of life. Currently, how polyamines are transported across membranes is not understood. Recent studies have suggested that ATP13A2 and its close homologs, collectively known as P5B-ATPases, are polyamine transporters at endo-/lysosomes. Loss-of-function mutations of ATP13A2 in humans cause hereditary early-onset Parkinson's disease. To understand the polyamine transport mechanism of ATP13A2, we determined high-resolution cryoelectron microscopy (cryo-EM) structures of human ATP13A2 in five distinct conformational intermediates, which together, represent a near-complete transport cycle of ATP13A2. The structural basis of the polyamine specificity was revealed by an endogenous polyamine molecule bound to a narrow, elongated cavity within the transmembrane domain. The structures show an atypical transport path for a water-soluble substrate, in which polyamines may exit within the cytosolic leaflet of the membrane. Our study provides important mechanistic insights into polyamine transport and a framework to understand the functions and mechanisms of P5B-ATPases.

Information-based analysis of the relationship between brain and facial muscle activities in response to static visual stimuli.

BACKGROUND: Human facial muscles react differently to different visual stimuli. It is known that the human brain controls and regulates the activity of the muscles. OBJECTIVE: In this research, for the first time, we investigate how facial muscle reaction is related to the reaction of the human brain. METHODS: Since both electromyography (EMG) and electroencephalography (EEG) signals, as the features of muscle and brain activities, contain information, we benefited from the information theory and computed the Shannon entropy of EMG and EEG signals when subjects were exposed to different static visual stimuli with different Shannon entropies (information content). RESULTS: Based on the obtained results, the variations of the information content of the EMG signal are related to the variations of the information content of the EEG signal and the visual stimuli. Statistical analysis also supported the results indicating that the visual stimuli with greater information content have a greater effect on the variation of the information content of both EEG and EMG signals. CONCLUSION: This investigation can be further continued to analyze the relationship between facial muscle and brain reactions in case of other types of stimuli.

The endoplasmic reticulum P5A-ATPase is a transmembrane helix dislocase.

Organelle identity depends on protein composition. How mistargeted proteins are selectively recognized and removed from organelles is incompletely understood. Here, we found that the orphan P5A-adenosine triphosphatase (ATPase) transporter ATP13A1 (Spf1 in yeast) directly interacted with the transmembrane segment (TM) of mitochondrial tail-anchored proteins. P5A-ATPase activity mediated the extraction of mistargeted proteins from the endoplasmic reticulum (ER). Cryo-electron microscopy structures of Saccharomyces cerevisiae Spf1 revealed a large, membrane-accessible substrate-binding pocket that alternately faced the ER lumen and cytosol and an endogenous substrate resembling an α-helical TM. Our results indicate that the P5A-ATPase could dislocate misinserted hydrophobic helices flanked by short basic segments from the ER. TM dislocation by the P5A-ATPase establishes an additional class of P-type ATPase substrates and may correct mistakes in protein targeting or topogenesis.

Information-based analysis of the relation between human muscle reaction and walking path.

BACKGROUND: Walking is one of the important actions of the human body. For this purpose, the human brain communicates with leg muscles through the nervous system. Based on the walking path, leg muscles act differently. Therefore, there should be a relation between the activity of leg muscles and the path of movement. OBJECTIVE: In order to address this issue, we analyzed how leg muscle activity is related to the variations of the path of movement. METHOD: Since the electromyography (EMG) signal is a feature of muscle activity and the movement path has complex structures, we used entropy analysis in order to link their structures. The Shannon entropy of EMG signal and walking path are computed to relate their information content. RESULTS: Based on the obtained results, walking on a path with greater information content causes greater information content in the EMG signal which is supported by statistical analysis results. This allowed us to analyze the relation between muscle activity and walking path. CONCLUSION: The method of analysis employed in this research can be applied to investigate the relation between brain or heart reactions and walking path.

Complexity-based decoding of brain-skin relation in response to olfactory stimuli.

BACKGROUND AND OBJECTIVE: Human body is covered with skin in different parts. In fact, skin reacts to different changes around human. For instance, when the surrounding temperature changes, human skin will react differently. It is known that the activity of skin is regulated by human brain. In this research, for the first time we investigate the relation between the activities of human skin and brain by mathematical analysis of Galvanic Skin Response (GSR) and Electroencephalography (EEG) signals. METHOD: For this purpose, we employ fractal theory and analyze the variations of fractal dimension of GSR and EEG signals when subjects are exposed to different olfactory stimuli in the form of pleasant odors. RESULTS: Based on the obtained results, the complexity of GSR signal changes with the complexity of EEG signal in case of different stimuli, where by increasing the molecular complexity of olfactory stimuli, the complexity of EEG and GSR signals increases. The results of statistical analysis showed the significant effect of stimulation on variations of complexity of GSR signal. In addition, based on effect size analysis, fourth odor with greatest molecular complexity had the greatest effect on variations of complexity of EEG and GSR signals. CONCLUSION: Therefore, it can be said that human skin reaction changes with the variations in the activity of human brain. The result of analysis in this research can be further used to make a model between the activities of human skin and brain that will enable us to predict skin reaction to different stimuli.

Decoding of the relationship between human brain activity and walking paths.

BACKGROUND: The human brain controls all actions of the body. Walking is one of the most important actions that deals with the movement of the body. In fact, the brain controls and regulates human walking based on different conditions. One of the conditions that affects human walking is the complexity of path of movement. Therefore, the brain activity should change when a person walks on a path with different complexities. OBJECTIVE: In this research we benefit from fractal analysis to study the effect of complexity of path of movement on the complexity of human brain reaction. METHODS: For this purpose we calculate the fractal dimension of the electroencephalography (EEG) signal when subjects walk on different paths with different fractal dimensions (complexity). RESULTS: The results of the analysis show that the complexity of brain activity increases with the increment of complexity of path of movement. CONCLUSION: The method of analysis employed in this research can also be employed to analyse the reaction of the human heart and respiration when subjects move on paths with different complexities.

A central role for PBP2 in the activation of peptidoglycan polymerization by the bacterial cell elongation machinery.

Cell elongation in rod-shaped bacteria is mediated by the Rod system, a conserved morphogenic complex that spatially controls cell wall assembly by the glycan polymerase RodA and crosslinking enzyme PBP2. Using Escherichia coli as a model system, we identified a PBP2 variant that promotes Rod system function when essential accessory components of the machinery are inactivated. This PBP2 variant hyperactivates cell wall synthesis in vivo and stimulates the activity of RodA-PBP2 complexes in vitro. Cells with the activated synthase also exhibited enhanced polymerization of the actin-like MreB component of the Rod system. Our results define an activation pathway governing Rod system function in which PBP2 conformation plays a central role in stimulating both glycan polymerization by its partner RodA and the formation of cytoskeletal filaments of MreB to orient cell wall assembly. In light of these results, previously isolated mutations that activate cytokinesis suggest that an analogous pathway may also control cell wall synthesis by the division machinery.

Primary collision tumors of the kidney composed of oncocytoma and papillary renal cell carcinoma: A review.

BACKGROUND: There are well known cases of hybrid tumors of chromophobe renal cell carcinoma (RCC) and oncocytoma in kidney, where both tumors have the same cell of origin - intercalated cell of the collecting duct. However, collision tumors composed of neoplasms originating from different cell lineages such as oncocytoma and papillary RCC are extremely rare. Herein, we made a collective literature review of reported cases of collision tumors composed of oncocytoma and papillary RCC, adding a case that we recently experienced. MATERIAL AND METHODS: A PubMed database was search for collision tumors of the kidney composed of oncocytoma and papillary RCC and a collective literature review was made. To this cohort, we also added a recently encountered case with similar, confirmed by immunohistochemistry, morphological features. RESULTS: To date 8 cases of a collision tumor composed of papillary RCC and oncocytoma have been described in the literature. All of them had a smaller papillary RCC component present within a larger oncocytoma. CONCLUSION: Because of a few cases of such a collision tumors reported, it is difficult to make classification and right clinical management of these patients. None of the reported cases had tumor recurrence or progression on a follow-up. The presence of only small portion of papillary RCC in a large oncocytoma raises a possibility of under-sampling of malignant component in large oncocytomas in core biopsy or surgically resected specimens. We recommend better sampling, particularly at the periphery of otherwise classic oncocytomas to unveil this possible association.

Post-translational modification directs nuclear and hyphal tip localization of Candida albicans mRNA-binding protein Slr1.

The morphological transition of the opportunistic fungal pathogen Candida albicans from budding to hyphal growth has been implicated in its ability to cause disease in animal models. Absence of SR-like RNA-binding protein Slr1 slows hyphal formation and decreases virulence in a systemic candidiasis model, suggesting a role for post-transcriptional regulation in these processes. SR (serine-arginine)-rich proteins influence multiple steps in mRNA metabolism and their localization and function are frequently controlled by modification. We now demonstrate that Slr1 binds to polyadenylated RNA and that its intracellular localization is modulated by phosphorylation and methylation. Wildtype Slr1-GFP is predominantly nuclear, but also co-fractionates with translating ribosomes. The non-phosphorylatable slr1-6SA-GFP protein, in which six serines in SR/RS clusters are substituted with alanines, primarily localizes to the cytoplasm in budding cells. Intriguingly, hyphal cells display a slr1-6SA-GFP focus at the tip near the Spitzenkörper, a vesicular structure involved in molecular trafficking to the tip. The presence of slr1-6SA-GFP hyphal tip foci is reduced in the absence of the mRNA-transport protein She3, suggesting that unphosphorylated Slr1 associates with mRNA-protein complexes transported to the tip. The impact of SLR1 deletion on hyphal formation and function thus may be partially due to a role in hyphal mRNA transport.

Clear cell adenocarcinoma of the colon: a case report and review of the literature.

Clear cell adenocarcinoma of the colon has been described scarcely in the literature. It affects elderly men more commonly than women and usually appears in the left side of the colon. A Hispanic 41-year-old female came to the emergency room with abdominal pain, vomiting, and distension. Physical exam revealed generalized tenderness without peritoneal signs. Laboratory data was unremarkable. A CT scan showed an apple-core lesion in the distal colon. A flexible sigmoidoscopy revealed an obstructive mass that made further evaluation impossible. Exploratory surgery revealed a hard mass obstructing the descending colon, which was resected. Histopathology analysis with immunohistochemistry staining was positive for cytokeratin 20, cytokeratin 10, CDX2, and villin, while it was negative for cytokeratin 7, RCC, vimentin, and CD31. These results confirmed the clear cell variant of the adenocarcinoma. Clear cell adenocarcinomas usually arise from the kidneys and Müllerian organs. Immunohistochemistry is crucial for establishing the origin of these neoplastic cells. A cytokeratin 20+/7- with positive CDX2 is highly specific and sensitive for intestinal neoplastic origin. The main treatment has been surgery alone with moderately good results. More research and information about this malignancy is needed, especially in regard to prognosis and in order to provide the best treatment option.