A SAM-key domain required for enzymatic activity of the Fun30 nucleosome remodeler

Fun30 is the prototype of the Fun30-SMARCAD1-ETL subfamily of nucleosome remodelers involved in DNA repair and gene silencing. These proteins appear to act as single-subunit nucleosome remodelers, but their molecular mechanisms are, at this point, poorly understood. Using multiple sequence alignment and structure prediction, we identify an evolutionarily conserved domain that is modeled to contain a SAM-like fold with one long, protruding helix, which we term SAM-key. Deletion of the SAM-key within budding yeast Fun30 leads to a defect in DNA repair and gene silencing similar to that of the fun30Δ mutant. In vitro, Fun30 protein lacking the SAM-key is able to bind nucleosomes but is deficient in DNA-stimulated ATPase activity and nucleosome sliding and eviction. A structural model based on AlphaFold2 prediction and verified by crosslinking-MS indicates an interaction of the long SAM-key helix with protrusion I, a subdomain located between the two ATPase lobes that is critical for control of enzymatic activity. Mutation of the interaction interface phenocopies the domain deletion with a lack of DNA-stimulated ATPase activation and a nucleosome-remodeling defect, thereby confirming a role of the SAM-key helix in regulating ATPase activity. Our data thereby demonstrate a central role of the SAM-key domain in mediating the activation of Fun30 catalytic activity, thus highlighting the importance of allosteric activation for this class of enzymes.

Mars, a molecule archive suite for reproducible analysis and reporting of single-molecule properties from bioimages

The rapid development of new imaging approaches is generating larger and more complex datasets, revealing the time evolution of individual cells and biomolecules. Single-molecule techniques, in particular, provide access to rare intermediates in complex, multistage molecular pathways. However, few standards exist for processing these information-rich datasets, posing challenges for wider dissemination. Here, we present Mars, an open-source platform for storing and processing image-derived properties of biomolecules. Mars provides Fiji/ImageJ2 commands written in Java for common single-molecule analysis tasks using a Molecule Archive architecture that is easily adapted to complex, multistep analysis workflows. Three diverse workflows involving molecule tracking, multichannel fluorescence imaging, and force spectroscopy, demonstrate the range of analysis applications. A comprehensive graphical user interface written in JavaFX enhances biomolecule feature exploration by providing charting, tagging, region highlighting, scriptable dashboards, and interactive image views. The interoperability of ImageJ2 ensures Molecule Archives can easily be opened in multiple environments, including those written in Python using PyImageJ, for interactive scripting and visualization. Mars provides a flexible solution for reproducible analysis of image-derived properties, facilitating the discovery and quantitative classification of new biological phenomena with an open data format accessible to everyone.

The fork protection complex recruits FACT to reorganize nucleosomes during replication

Chromosome replication depends on efficient removal of nucleosomes by accessory factors to ensure rapid access to genomic information. Here, we show this process requires recruitment of the nucleosome reorganization activity of the histone chaperone FACT. Using single-molecule FRET, we demonstrate that reorganization of nucleosomal DNA by FACT requires coordinated engagement by the middle and C-terminal domains of Spt16 and Pob3 but does not require the N-terminus of Spt16. Using structure-guided pulldowns, we demonstrate instead that the N-terminal region is critical for recruitment by the fork protection complex subunit Tof1. Using in vitro chromatin replication assays, we confirm the importance of these interactions for robust replication. Our findings support a mechanism in which nucleosomes are removed through the coordinated engagement of multiple FACT domains positioned at the replication fork by the fork protection complex.

Isolation and characterization of heat-stable allergens from shrimp (Penaeus indicus)

Shrimp are among the more common causes of immediate hypersensitivity reactions to food. To characterize better the allergenic substances within shrimp, extracts from heated shrimp were systematically examined with solid-phase radioimmunoassay and sera from patients clinically sensitive to shrimp. Two heat-stable protein allergens, designated as Sa-I and Sa-II, were identified from boiled shrimp (Penaeus indicus) extracts. Sa-I was isolated by ultrafiltration, Sephadex G-25, and diethylaminoethyl-Sephacel chromatography, whereas, Sa-II, the major allergen, was purified by successive chromatography on diethylaminoethyl-Sephacel, Bio-Gel P-200, and Sepharose 4B columns. Sa-I, was homogeneous by polyacrylamide gel electrophoresis (PAGE), elicited a single band on sodium dodecyl sulfate-PAGE corresponding to a molecular weight of 8.2 kd. Sa-II was also found to be homogeneous by PAGE, crossed immunoelectrophoresis, and immunoblotting. On sodium dodecyl sulfate- PAGE, it elicited a single band with a molecular weight of 34 kd. Sa-II was found to contain 301 amino acid residues and was particularly rich in glutamate/glutamate and aspartate/asparagine. Solid-phase radioimmunoassay-inhibition studies revealed that Sa-I and Sa-II share 54% of the allergenic epitopes, suggesting that Sa-I may be a fragment of Sa-II.