Vacuole phase-partitioning boosts mitochondria activity and cell lifespan through an inter-organelle lipid pipeline

Functional linkage between mitochondria and lysosomes is crucial for survival under starvation and lifespan extension. Despite such co-dependency, the supportive pathways connecting mitochondria and lysosomes remain unclear. Here, we identify an inter-organelle lipid trafficking pathway linking yeast vacuole and mitochondria that results in increased mitochondria growth and respiratory activity under glucose starvation. The pathway depends on vacuolar phase-separated, lipid domains, which provide zones for: activation of the vacuolar proton pump; lipid droplet (LD) docking and internalization; and, lipid transfer from vacuole-to-ER-to-mitochondria. Partitioned vacuolar domains form through a specialized type of macro-autophagy, triggered only under acute glucose starvation, that delivers sterol-rich, endosomal-derived lipids to the vacuole. To balance this lipid influx, the vacuole reroutes lipids back to the ER to support both LD biogenesis and mitochondria growth and activity. Energy produced by enhanced mitochondrial activity then feeds back to support the inter-organelle lipid trafficking pathways to ensure survival under nutrient stress.

Obszary intensywnych powiązań funkcjonalnych miast na prawach powiatu w Polsce – autorska metoda delimitacji = Areas of strong functional linkage of Polish cities granted county status – the authors’ own method of delimitation

Spatial mobility of the population is a key factor allowing for the delimitation of functional areas and the identification of ranges of impact of given spatial units. The work detailed here has built on this idea by seeking to identify areas of strong functional linkage in the cities in Poland that have been granted the status of powiat (i.e. unit at the “county” level of administration). In this context, the paper also offers a critical analysis of other, best-known approaches to the delimitation of towns and cities in Poland. The identification of areas characterised by strong functional linkage is achieved by reference to generally-available data, i.e. statistics relating to commutes to work, as well as internal migration leading to permanent residency status. Overall, areas of srong functional linkage are here delimited by reference to: (1) areas of emigration or immigration relating to thecities granted county status, where these are the source and/or destination when it comes to internal migration leading to permanent residency; (2) areas of departure and arrival where commutes to and from the aforesaid cities granted county status are concerned, with account taken of additional relations relating to volumes of flows in a ‘city–rural area’ configuration. Our analysis was performed at NUTS-5 level, hence the exclusion of cities not enjoying county status. It is against the background of existing literature reports on means of identifying areas of functional linkage for Polish cities that the work detailed here may establish a basis for discussing alternative approaches. Here the authors offer their own method of identifying areas of strong functional linkage, from the point of view of people’s spatial mobility. This approach takes account of specifically Polish aspects of the phenomenon’s development. Indeed, analyses confirm that the approach proposed is very much linked to the functional urban areas of regional centres. However, complete objectivisation (i.e. a lack of subjectivity or even arbitrary decisions) represents a significant attribute of the approach in question, with this being desirable when it comes to research being replicated.

We need to keep a reproducible trace of facts, predictions, and hypotheses from gene to function in the era of big data

How do we scale biological science to the demand of next generation biology and medicine to keep track of the facts, predictions, and hypotheses? These days, enormous amounts of DNA sequence and other omics data are generated. Since these data contain the blueprint for life, it is imperative that we interpret it accurately. The abundance of DNA is only one part of the challenge. Artificial Intelligence (AI) and network methods routinely build on large screens, single cell technologies, proteomics, and other modalities to infer or predict biological functions and phenotypes associated with proteins, pathways, and organisms. As a first step, how do we systematically trace the provenance of knowledge from experimental ground truth to gene function predictions and annotations? Here, we review the main challenges in tracking the evolution of biological knowledge and propose several specific solutions to provenance and computational tracing of evidence in functional linkage networks.

The relationship between protein domains and homopeptides in the Plasmodium falciparum proteome

The proteome of the malaria parasite Plasmodium falciparum is notable for the pervasive occurrence of homopeptides or low-complexity regions (i.e., regions that are made from a small subset of amino-acid residue types). The most prevalent of these are made from residues encoded by adenine/thymidine (AT)-rich codons, in particular asparagine. We examined homopeptide occurrences within protein domains in P. falciparum. Homopeptide enrichments occur for hydrophobic (e.g., valine), or small residues (alanine or glycine) in short spans (<5 residues), but these enrichments disappear for longer lengths. We observe that short asparagine homopeptides (<10 residues long) have a dramatic relative depletion inside protein domains, indicating some selective constraint to keep them from forming. We surmise that this is possibly linked to co-translational protein folding, although there are specific protein domains that are enriched in longer asparagine homopeptides (≥10 residues) indicating a functional linkage for specific poly-asparagine tracts. Top gene ontology functional category enrichments for homopeptides associated with diverse protein domains include “vesicle-mediated transport”, and “DNA-directed 5′-3′ RNA polymerase activity”, with various categories linked to “binding” evidencing significant homopeptide depletions. Also, in general homopeptides are substantially enriched in the parts of protein domains that are near/in IDRs. The implications of these findings are discussed.

Role of the I16-D194 ionic interaction in the trypsin fold

Activity in trypsin-like proteases is the result of proteolytic cleavage at R15 followed by an ionic interaction that ensues between the new N terminus of I16 and the side chain of the highly conserved D194. This mechanism of activation, first proposed by Huber and Bode, organizes the oxyanion hole and primary specificity pocket for substrate binding and catalysis. Using the clotting protease thrombin as a relevant model, we unravel contributions of the I16-D194 ionic interaction to Na+ binding, stability of the transition state and the allosteric E*-E equilibrium of the trypsin fold. The I16T mutation abolishes the I16-D194 interaction and compromises the architecture of the oxyanion hole. The D194A mutation also abrogates the I16-D194 interaction but, surprisingly, has no effect on the architecture of the oxyanion hole that remains intact through a new H-bond established between G43 and G193. In both mutants, loss of the I16-D194 ionic interaction compromises Na+ binding, reduces stability of the transition state, collapses the 215–217 segment into the primary specific pocket and abrogates the allosteric E*-E equilibrium in favor of a rigid conformation that binds ligand at the active site according to a simple lock-and-key mechanism. These findings refine the structural role of the I16-D194 ionic interaction in the Huber-Bode mechanism of activation and reveal a functional linkage with the allosteric properties of the trypsin fold like Na+ binding and the E*-E equilibrium.