Mechanochemical basis of protein degradation by a double-ring AAA+ machine

Molecular machines containing double or single AAA+ rings power energy-dependent protein degradation and other critical cellular processes, including disaggregation and remodeling of macromolecular complexes. How the mechanical activities of double-ring and single-ring AAA+ enzymes differ is unknown. Using single-molecule optical trapping, we determine how the double-ring ​ClpA enzyme from Escherichia coli, in complex with the ​ClpP peptidase, mechanically degrades proteins. We demonstrate that ​ClpA unfolds some protein substrates substantially faster than does the single-ring ​ClpX enzyme, which also degrades substrates in collaboration with ​ClpP. We find that ​ClpA is a slower polypeptide translocase and that it moves in physical steps that are smaller and more regular than steps taken by ​ClpX. These direct measurements of protein unfolding and translocation define the core mechanochemical behavior of a double-ring AAA+ machine and provide insight into the degradation of proteins that unfold via metastable intermediates.Howard Hughes Medical InstituteNational Institutes of Health (U.S.) (Grant AI-16892

Predictive factors of aneuploidy in infertile patients undergoing IVF: a retrospective analysis in a private IVF practice

Abstract Background PGT-A has become an important part of IVF treatments. Despite its increased use, there are contradicting results on its role in improving reproductive outcomes of ART cycles. Given that aneuploidy is a main limiting factor for IVF success, we aimed to study the predictive factors of aneuploidy in infertile patients undergoing IVF and hence highlight the patients who would benefit the most from genetic testing. Results A retrospective analysis of 1242 blastocysts biopsied in the setting of PGT-A cycles was performed. The euploid group included 703 embryos, while the aneuploid group had 539 embryos. The factors included in the analyses were the couple’s history as well as the embryo characteristics. The primary outcome was the rate of aneuploid embryos per patient’s history as well as per embryo characteristics. The aneuploidy rate (AR) in our cohort was 43.4%. The woman’s age was found to be a significant predictor (OR 1.045, 95% CI 1.008–1.084, p = 0.016). Biopsy on day 5 as well as degree of expansion 3 was also found to affect significantly (OR 0.724, 95% CI .541–.970, p = 0.03 and OR 2.645, 95% CI 1.252–5.585, p = 0.011). Lack of consanguinity decreased the AR by an OR 0.274 with 95% CI .137–.547, p < 0.001. The number of blastocysts available, trophectoderm quality, embryo grade, gonadotropins as well as trigger used were not found to be significant predictors (p = 0.495, 0.649, 0.264, 0.717 and 0.659 respectively). Conclusion Advanced female age, consanguinity, the day of embryo biopsy, and the degree of blastocyst expansion were all found to affect the incidence of AR. The age of the male partner, cause of infertility, and grade of embryo at biopsy were not found to correlate with aneuploidy

Single Molecule Cluster Analysis dissects splicing pathway conformational dynamics

The spliceosome is the dynamic RNA-protein machine responsible for faithfully splicing introns from precursor messenger RNAs (pre-mRNAs). Many of the dynamic processes required for the proper assembly, catalytic activation, and disassembly of the spliceosome as it acts on its pre-mRNA substrate remain poorly understood, a challenge that persists for many biomolecular machines. Here, we developed a fluorescence-based Single Molecule Cluster Analysis (SiMCAn) tool to dissect the manifold conformational dynamics of a pre-mRNA through the splicing cycle. By clustering common dynamic behaviors derived from selectively blocked splicing reactions, SiMCAn was able to identify signature conformations and dynamic behaviors of multiple ATP-dependent intermediates. In addition, it identified a conformation adopted late in splicing by a 3′ splice site mutant, invoking a mechanism for substrate proofreading. SiMCAn presents a novel framework for interpreting complex single molecule behaviors that should prove widely useful for the comprehensive analysis of a plethora of dynamic cellular machines

Distinct Prion Domain Sequences Ensure Efficient Amyloid Propagation by Promoting Chaperone Binding or Processing <i>In Vivo</i>

<div><p>Prions are a group of proteins that can adopt a spectrum of metastable conformations <i>in vivo</i>. These alternative states change protein function and are self-replicating and transmissible, creating protein-based elements of inheritance and infectivity. Prion conformational flexibility is encoded in the amino acid composition and sequence of the protein, which dictate its ability not only to form an ordered aggregate known as amyloid but also to maintain and transmit this structure <i>in vivo</i>. But, while we can effectively predict amyloid propensity <i>in vitro</i>, the mechanism by which sequence elements promote prion propagation <i>in vivo</i> remains unclear. In yeast, propagation of the [<i>PSI</i>^<i>+</i>] prion, the amyloid form of the Sup35 protein, has been linked to an oligopeptide repeat region of the protein. Here, we demonstrate that this region is composed of separable functional elements, the repeats themselves and a repeat proximal region, which are both required for efficient prion propagation. Changes in the numbers of these elements do not alter the physical properties of Sup35 amyloid, but their presence promotes amyloid fragmentation, and therefore maintenance, by molecular chaperones. Rather than acting redundantly, our observations suggest that these sequence elements make complementary contributions to prion propagation, with the repeat proximal region promoting chaperone binding to and the repeats promoting chaperone processing of Sup35 amyloid.</p></div