How does the TOM complex mediate insertion of precursor proteins into the mitochondrial outer membrane?

A multisubunit translocase of the outer mitochondrial membrane (TOM complex) mediates both the import of mitochondrial precursor proteins into the internal compartments of the organelle and the insertion of proteins residing in the mitochondrial outer membrane. The proposed β-barrel structure of Tom40, the pore-forming component of the translocase, raises the question of how the apparent uninterrupted β-barrel topology can be compatible with a role of Tom40 in releasing membrane proteins into the lipid core of the bilayer. In this review, I discuss insertion mechanisms of proteins into the outer membrane and present alternative models based on the opening of a multisubunit β-barrel TOM structure or on the interaction of outer membrane precursors with the outer face of the Tom40 β-barrel structure

Biogenesis of β-barrel membrane proteins in bacteria and eukaryotes: evolutionary conservation and divergence

Membrane-embedded β-barrel proteins span the membrane via multiple amphipathic β-strands arranged in a cylindrical shape. These proteins are found in the outer membranes of Gram-negative bacteria, mitochondria and chloroplasts. This situation is thought to reflect the evolutionary origin of mitochondria and chloroplasts from Gram-negative bacterial endosymbionts. β-barrel proteins fulfil a variety of functions; among them are pore-forming proteins that allow the flux of metabolites across the membrane by passive diffusion, active transporters of siderophores, enzymes, structural proteins, and proteins that mediate protein translocation across or insertion into membranes. The biogenesis process of these proteins combines evolutionary conservation of the central elements with some noticeable differences in signals and machineries. This review summarizes our current knowledge of the functions and biogenesis of this special family of proteins

Climate change and its implications on stored food grains: Presentation

Safe food grain storages are considered as a measure to adapt to the changing global climates and as a channel to food security, particularly in periods when agriculture fails. However, grain storage themselves can be heavily affected by changing global climates. One main aspect of the ‘climate change’ is the rise of global temperature that may lead to an increase in atmospheric humidity. This climate change, warm and humid, are not suitable for grain storage. At such a scenario, stored grain is at a risk due to the favorable conditions developed for the growth of insect pests. Predicting the future ecological impact of climate change drivers requires understanding how these same drivers have acted in the past on the dynamics of insect's population. In the past ten years there has been a detailed documentation on the biotic and abiotic conditions of two storage sites in Israel. This historical ecological data can reveal long-term consequences of multiple drivers of climate change. The changes can be evident at the level of the species and at the level of the societies of insect-pest in the grain storage. The differences between two storages located at different climate regions in Israel further predict the direction current IPM practice may lead to. Following this understanding, we hope to develop feasible mitigation strategies that might overcome the changes ahead of us.Safe food grain storages are considered as a measure to adapt to the changing global climates and as a channel to food security, particularly in periods when agriculture fails. However, grain storage themselves can be heavily affected by changing global climates. One main aspect of the ‘climate change’ is the rise of global temperature that may lead to an increase in atmospheric humidity. This climate change, warm and humid, are not suitable for grain storage. At such a scenario, stored grain is at a risk due to the favorable conditions developed for the growth of insect pests. Predicting the future ecological impact of climate change drivers requires understanding how these same drivers have acted in the past on the dynamics of insect's population. In the past ten years there has been a detailed documentation on the biotic and abiotic conditions of two storage sites in Israel. This historical ecological data can reveal long-term consequences of multiple drivers of climate change. The changes can be evident at the level of the species and at the level of the societies of insect-pest in the grain storage. The differences between two storages located at different climate regions in Israel further predict the direction current IPM practice may lead to. Following this understanding, we hope to develop feasible mitigation strategies that might overcome the changes ahead of us

Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data

A large number of computational methods have been developed for analyzing differential gene expression in RNA-seq data. We describe a comprehensive evaluation of common methods using the SEQC benchmark dataset and ENCODE data. We consider a number of key features, including normalization, accuracy of differential expression detection and differential expression analysis when one condition has no detectable expression. We find significant differences among the methods, but note that array-based methods adapted to RNA-seq data perform comparably to methods designed for RNA-seq. Our results demonstrate that increasing the number of replicate samples significantly improves detection power over increased sequencing depth

The C-terminal domain of Fcj1 is required for formation of crista junctions and interacts with the TOB/SAM complex in mitochondria

Crista junctions (CJs) are tubular invaginations of the inner membrane of mitochondria that connect the inner boundary with the cristae membrane. These architectural elements are critical for mitochondrial function. The yeast inner membrane protein Fcj1, called mitofilin in mammals, was reported to be preferentially located at CJs and crucial for their formation. Here we investigate the functional roles of individual domains of Fcj1. The most conserved part of Fcj1, the C-terminal domain, is essential for Fcj1 function. In its absence, formation of CJ is strongly impaired and irregular, and stacked cristae are present. This domain interacts with full-length Fcj1, suggesting a role in oligomer formation. It also interacts with Tob55 of the translocase of outer membrane β-barrel proteins (TOB)/sorting and assembly machinery (SAM) complex, which is required for the insertion of β-barrel proteins into the outer membrane. The association of the TOB/SAM complex with contact sites depends on the presence of Fcj1. The biogenesis of β-barrel proteins is not significantly affected in the absence of Fcj1. However, down-regulation of the TOB/SAM complex leads to altered cristae morphology and a moderate reduction in the number of CJs. We propose that the C-terminal domain of Fcj1 is critical for the interaction of Fcj1 with the TOB/SAM complex and thereby for stabilizing CJs in close proximity to the outer membrane. These results assign novel functions to both the C-terminal domain of Fcj1 and the TOB/SAM complex