A genome-wide screen for essential yeast genes that affect telomere length maintenance

Telomeres are structures composed of repetitive DNA and proteins that protect the chromosomal ends in eukaryotic cells from fusion or degradation, thus contributing to genomic stability. Although telomere length varies between species, in all organisms studied telomere length appears to be controlled by a dynamic equilibrium between elongating mechanisms (mainly addition of repeats by the enzyme telomerase) and nucleases that shorten the telomeric sequences. Two previous studies have analyzed a collection of yeast deletion strains (deleted for nonessential genes) and found over 270 genes that affect telomere length (Telomere Length Maintenance or TLM genes). Here we complete the list of TLM by analyzing a collection of strains carrying hypomorphic alleles of most essential genes (DAmP collection). We identify 87 essential genes that affect telomere length in yeast. These genes interact with the nonessential TLM genes in a significant manner, and provide new insights on the mechanisms involved in telomere length maintenance. The newly identified genes span a variety of cellular processes, including protein degradation, pre-mRNA splicing and DNA replication.     

Diffusion in a Fluid Membrane with a Flexible Cortical Cytoskeleton

We calculate the influence of a flexible network of long-chain proteins, which is anchored to a fluid membrane, on protein diffusion in this membrane. This is a model for the cortical cytoskeleton and the lipid bilayer of the red blood cell, which we apply to predict the influence of the cytoskeleton on the diffusion coefficient of a mobile band 3 protein. Using the pressure field that the cytoskeleton exerts on the membrane, from the steric repulsion between the diffusing protein and the cytoskeletal filaments, we define a potential landscape for the diffusion within the bilayer. We study the changes to the diffusion coefficient on removal of one type of anchor proteins, e.g., in several hemolytic anemias, as well as for isotropic and anisotropic stretching of the cytoskeleton. We predict an overall increase of the diffusion for a smaller number of anchor proteins and increased diffusion for anisotropic stretching in the direction of the stretch, because of the decrease in the spatial frequency as well as in the height of the potential barriers.     

RNA Editing Genes Associated with Extreme Old Age in Humans and with Lifespan in C. elegans

Background

The strong familiality of living to extreme ages suggests that human longevity is genetically regulated. The majority of genes found thus far to be associated with longevity primarily function in lipoprotein metabolism and insulin/IGF-1 signaling. There are likely many more genetic modifiers of human longevity that remain to be discovered.

Methodology/Principal Findings

Here, we first show that 18 single nucleotide polymorphisms (SNPs) in the RNA editing genes ADARB1 and ADARB2 are associated with extreme old age in a U.S. based study of centenarians, the New England Centenarian Study. We describe replications of these findings in three independently conducted centenarian studies with different genetic backgrounds (Italian, Ashkenazi Jewish and Japanese) that collectively support an association of ADARB1 and ADARB2 with longevity. Some SNPs in ADARB2 replicate consistently in the four populations and suggest a strong effect that is independent of the different genetic backgrounds and environments. To evaluate the functional association of these genes with lifespan, we demonstrate that inactivation of their orthologues adr-1 and adr-2 in C. elegans reduces median survival by 50%. We further demonstrate that inactivation of the argonaute gene, rde-1, a critical regulator of RNA interference, completely restores lifespan to normal levels in the context of adr-1 and adr-2 loss of function.

Conclusions/Significance

Our results suggest that RNA editors may be an important regulator of aging in humans and that, when evaluated in C. elegans, this pathway may interact with the RNA interference machinery to regulate lifespan.     

Transmembrane protein structures without X-rays

Transmembrane (TM) proteins constitute 15-30% of the genome, but <1% of the structures in the Protein Data Bank. This discrepancy is disturbing, and emphasizes that structure determination of TM proteins remains challenging. The challenge is greatest for proteins from eukaryotes, the structures of which remain intractable despite tremendous advances that have been made towards structure determination of bacterial TM proteins. Notably, >50% of the membrane protein families in eukaryotes lack bacterial homologs. Therefore, it is conceivable that many more years will elapse before high-resolution structures of eukaryotic TM proteins emerge. Until then, integrated approaches that combine biochemical and computational analyses with low-resolution structures are likely to have increasingly important roles in providing frameworks for the mechanistic understanding of membrane-protein structure and function.     

Sub‐angstrom modeling of complexes between flexible peptides and globular proteins

A wide range of regulatory processes in the cell are mediated by flexible peptides that fold upon binding to globular proteins. Computational efforts to model these interactions are hindered by the large number of rotatable bonds in flexible peptides relative to typical ligand molecules, and the fact that different peptides assume different backbone conformations within the same binding site. In this study, we present Rosetta FlexPepDock, a novel tool for refining coarse peptide–protein models that allows significant changes in both peptide backbone and side chains. We obtain high resolution models, often of sub‐angstrom backbone quality, over an extensive and general benchmark that is based on a large nonredundant dataset of 89 peptide–protein interactions. Importantly, side chains of known binding motifs are modeled particularly well, typically with atomic accuracy. In addition, our protocol has improved modeling quality for the important application of cross docking to PDZ domains. We anticipate that the ability to create high resolution models for a wide range of peptide–protein complexes will have significant impact on structure‐based functional characterization, controlled manipulation of peptide interactions, and on peptide‐based drug design. Proteins 2010. © 2010 Wiley‐Liss, Inc.     

Role and regulation of sperm gelsolin prior to fertilization

To acquire fertilization competence, spermatozoa should undergo several biochemical changes in the female reproductive tract, known as capacitation. The capacitated spermatozoon can interact with the egg zona pellucida resulting in the occurrence of the acrosome reaction, a process that allowed its penetration into the egg and fertilization. Sperm capacitation requires actin polymerization, whereas F-actin must disperse prior to the acrosome reaction. Here, we suggest that the actin-severing protein, gelsolin, is inactive during capacitation and is activated prior to the acrosome reaction. The release of bound gelsolin from phosphatidylinositol 4,5-bisphosphate (PIP(2)) by PBP10, a peptide containing the PIP(2)-binding domain of gelsolin, or by activation of phospholipase C, which hydrolyzes PIP(2), caused rapid Ca(2+)-dependent F-actin depolymerization as well as enhanced acrosome reaction. Using immunoprecipitation assays, we showed that the tyrosine kinase SRC and gelsolin coimmunoprecipitate, and activating SRC by adding 8-bromo-cAMP (8-Br-cAMP) enhanced the amount of gelsolin in this precipitate. Moreover, 8-Br-cAMP enhanced tyrosine phosphorylation of gelsolin and its binding to PIP(2(4,5)), both of which inactivated gelsolin, allowing actin polymerization during capacitation. This actin polymerization was blocked by inhibiting the Src family kinases, suggesting that gelsolin is activated under these conditions. These results are further supported by our finding that PBP10 was unable to cause complete F-actin breakdown in the presence of 8-Br-cAMP or vanadate. In conclusion, inactivation of gelsolin during capacitation occurs by its binding to PIP(2) and tyrosine phosphorylation by SRC. The release of gelsolin from PIP(2) together with its dephosphorylation enables gelsolin activation, resulting in the acrosome reaction.     

The Aspergillus fumigatus cspA Gene Encoding a Repeat-Rich Cell Wall Protein Is Important for Normal Conidial Cell Wall Architecture and Interaction with Host Cells

cspA (for cell surface protein A) encodes a repeat-rich glycophosphatidylinositol (GPI)-anchored cell wall protein (CWP) in the pathogenic fungus Aspergillus fumigatus. The number of repeats in cspA varies among isolates, and this trait is used for typing closely related strains of A. fumigatus. We have previously shown that deletion of cspA is associated with rapid conidial germination and reduced adhesion of dormant conidia. Here we show that cspA can be extracted with hydrofluoric acid (HF) from the cell wall, suggesting that it is a GPI-anchored CWP. The cspA-encoded CWP is unmasked during conidial germination and is surface expressed during hyphal growth. Deletion of cspA results in weakening of the conidial cell wall, whereas its overexpression increases conidial resistance to cell wall-degrading enzymes and inhibits conidial germination. Double mutant analysis indicates that cspA functionally interacts with the cell wall protein-encoding genes ECM33 and GEL2. Deletion of cspA together with ECM33 or GEL2 results in strongly reduced conidial adhesion, increased disorganization of the conidial cell wall, and exposure of the underlying layers of chitin and β-glucan. This is correlated with increasing susceptibility of the ΔcspA, ΔECM33, and ΔcspA ΔECM33 mutants to conidial phagocytosis and killing by human macrophages and hyphal damage induced by neutrophils. However, these strains did not exhibit altered virulence in mice with infected lungs. Collectively, these results suggest a role for cspA in maintaining the strength and integrity of the cell wall.The saprophytic mold Aspergillus fumigatus is an emerging pathogen and the major causative agent of invasive aspergillosis, a life-threatening disease primarily affecting immunocompromised patients (12, 16, 38).Molecular analyses have revealed numerous virulence attributes that enable A. fumigatus to infect the human host, including the production of toxins, the ability to acquire nutrients and iron under limiting conditions, and the presence of protective mechanisms that degrade oxygen radicals released by the host immune cells (7).The fungal cell wall plays a crucial role in infection. In A. fumigatus, as in other pathogenic fungi, the cell wall protects the fungus and interacts directly with the host immune system. It is an elastic, dynamic, and highly regulated structure and is essential for growth, viability, and infection. The fungal cell wall is a unique structure and therefore a specific target for antifungal drugs. The cell wall of A. fumigatus is composed of a polysaccharide skeleton interlaced and coated with cell wall proteins (CWPs). The main building blocks of the polysaccharide skeleton are an interconnected network of glucan, chitin, and galactomannan polymers (26). The major class of fungal CWPs is the glycophosphatidylinositol (GPI)-modified proteins (8,–11, 14).We recently identified and characterized A. fumigatus CWPs containing tandem repeats (27). Repeats are hot spots of genetic change: because of replication slippage and recombination, repeats can undergo rapid changes in copy number, leading to natural variability among different isolates and allowing faster adaptation to new environments (23). In Saccharomyces cerevisiae, for example, an increase in the number of coding repeats in the FLO1 adhesin-encoding gene correlates with an increase in adhesion to the plastics used in medical devices (44,–46). Similarly, repeat variation in the Candida albicans ALS3 adhesin changes its cellular binding specificity (34). Moreover, clinical C. albicans isolates show variability in the number of repeats in various cell surface genes, suggesting that this recombination process could play a role during infection, allowing cells to adapt rapidly to a fluctuating environment and/or evade the host immune system (34, 49, 50).We identified four genes encoding putative A. fumigatus GPI-anchored CWPs (AFUA_3G08990 [termed cspA for cell-surface protein A [4], AFUA_2G05150 [MP-2], AFUA_4G09600, and AFUA_6G14090) containing variable numbers of repeats among patient isolates (27). In A. fumigatus WT strain AF 293, cspA encodes a 433-amino-acid-long protein containing a putative leader sequence and GPI modification site. cspA lacks recognizable catalytic domains, and homologous genes are found only in species of Aspergillus. Most interesting is that the gene encodes a 188-amino-acid-long serine-threonine-proline-rich N-terminal region followed by a large size-variable six-amino-acid serine-proline [P-G-Q-P-S-(A/V)]-rich tandem repeat region showing significant homology to the repeat domains found in mammalian type XXI collagen. The number of repeats varies between 18 and 47 (24 to 65% of the length of the protein) in different isolates of A. fumigatus. The strains used in this study, AF 293 and CBS 144.89, contain 32 and 28 repeats, respectively.Deletion of cspA resulted in a phenotype characterized by rapid conidial germination and reduced adhesion to extracellular matrix (ECM), which suggests that cspA participates in defining cell surface properties. Highlighting the importance of this gene, Balajee et al. (4) showed that variations in the cspA nucleotide repeat sequence can be used to type closely related pathogenic isolates of A. fumigatus and identify outbreak clusters occurring in hospitals (3, 4).In this work, we undertook a detailed study of cspA. We analyzed the expression pattern of the protein encoded by cspA and its attachment to the cell wall. We prepared and analyzed A. fumigatus mutant strains in which cspA was overexpressed or deleted in combination with additional cell wall-associated genes. Results indicate that the protein encoded by cspA is GPI anchored to the cell wall and is unmasked during conidial germination. cspA deletion weakens the cell wall and results in rapid conidial germination, whereas cspA overexpression increases conidial resistance to protoplasting and inhibits conidial germination. cspA functionally interacts with the genes ECM33 and GEL2, which encode cell wall-associated proteins, resulting primarily in profound defects in conidial cell wall organization. The cspA ECM33 double mutant exhibited greater susceptibility to killing by human macrophages and hyphal damage induced by neutrophils. The implications of our findings are discussed.