A novel multi-functional role for the MCM8/9 helicase complex in maintaining fork integrity during replication stress

The minichromosome maintenance (MCM) 8/9 helicase is a AAA+ complex involved in DNA replication-associated repair. Despite high sequence homology to the MCM2-7 helicase, an active role for MCM8/9 has remained elusive. We interrogated fork progression in cells lacking MCM8 or 9 and find there is a functional partitioning. Loss of MCM8 or 9 slows overall replication speed and increases markers of genomic damage and fork instability, further compounded upon treatment with hydroxyurea. MCM8/9 acts upstream and antagonizes the recruitment of BRCA1 in nontreated conditions. However, upon treatment with fork stalling agents, MCM9 recruits Rad51 to protect and remodel persistently stalled forks. The helicase function of MCM8/9 aids in normal replication fork progression, but upon excessive stalling, MCM8/9 directs additional stabilizers to protect forks from degradation. This evidence defines novel multifunctional roles for MCM8/9 in promoting normal replication fork progression and promoting genome integrity following stress.

Subspace alignment as a mechanism for binding

To choose between options, we must solve two important binding problems. First, the features that determine each options values must be appropriately combined and kept separate from the corresponding features of other options. Second, options must be associated with the specific actions needed to select them. We hypothesized that the brain solves these problems through use of aligned (for bound dimensions) and orthogonal (for separated dimensions) population subspaces. We examined responses of single neurons in six putative value-coding regions in rhesus macaques performing a risky choice task. In all areas, single neurons encode the features that define the value of each option (stakes and probability) but only very weakly encode value per se. However, the coding dimensions associated with these features are aligned on a single subspace, from which a strong emergent value signal can be read out. Moreover, all six regions use nearly orthogonal subspaces for the left and right options, thereby linking options to their position in space, implementing functional partitioning, and reducing the possibility of misbinding. These results provide a new solution to the neuroeconomic binding problems and suggest that other forms of binding may work through similar principles.

Functional partitioning of a liquid-like organelle during assembly of axonemal dyneins

Ciliary motility is driven by axonemal dyneins that are assembled in the cytoplasm before deployment to cilia. Motile ciliopathy can result from defects in the dyneins themselves or from defects in factors required for their cytoplasmic pre-assembly. Recent work demonstrates that axonemal dyneins, their specific assembly factors, and broadly-acting chaperones are concentrated in liquid-like organelles in the cytoplasm called DynAPs (Dynein Axonemal Particles). Here, we use in vivo imaging in Xenopus to show that inner dynein arm (IDA) and outer dynein arm (ODA) subunits are partitioned into non-overlapping sub-regions within DynAPs. Using affinity- purification mass-spectrometry of in vivo interaction partners, we also identify novel partners for inner and outer dynein arms. Among these, we identify C16orf71/Daap1 as a novel axonemal dynein regulator. Daap1 interacts with ODA subunits, localizes specifically to the cytoplasm, is enriched in DynAPs, and is required for the deployment of ODAs to axonemes. Our work reveals a new complexity in the structure and function of a cell-type specific liquid-like organelle that is directly relevant to human genetic disease.

Genomic analysis reveals an exogenous viral symbiont with dual functionality in parasitoid wasps and their hosts

Insects are known to host a wide variety of beneficial microbes that are fundamental to many aspects of their biology and have substantially shaped their evolution. Notably, parasitoid wasps have repeatedly evolved beneficial associations with viruses that enable developing wasps to survive as parasites that feed from other insects. Ongoing genomic sequencing efforts have revealed that most of these virus-derived entities are fully integrated into the genomes of parasitoid wasp lineages, representing endogenous viral elements (EVEs) that retain the ability to produce virus or virus-like particles within wasp reproductive tissues. All documented parasitoid EVEs have undergone similar genomic rearrangements compared to their viral ancestors characterized by viral genes scattered across wasp genomes and specific viral gene losses. The recurrent presence of viral endogenization and genomic reorganization in beneficial virus systems identified to date suggest that these features are crucial to forming heritable alliances between parasitoid wasps and viruses. Here, our genomic characterization of a mutualistic poxvirus associated with the wasp Diachasmimorpha longicaudata, known as Diachasmimorpha longicaudata entomopoxvirus (DlEPV), has uncovered the first instance of beneficial virus evolution that does not conform to the genomic architecture shared by parasitoid EVEs with which it displays evolutionary convergence. Rather, DlEPV retains the exogenous viral genome of its poxvirus ancestor and the majority of conserved poxvirus core genes. Additional comparative analyses indicate that DlEPV is related to a fly pathogen and contains a novel gene expansion that may be adaptive to its symbiotic role. Finally, differential expression analysis during virus replication in wasps and fly hosts demonstrates a unique mechanism of functional partitioning that allows DlEPV to persist within and provide benefit to its parasitoid wasp host.

Anaerobic microbial degradation of protein and lipid macromolecules in subarctic marine sediment

Microorganisms in marine sediments play major roles in marine biogeochemical cycles by mineralizing substantial quantities of organic matter from decaying cells. Proteins and lipids are abundant components of necromass, yet microorganisms that degrade them remain understudied. Here, we revealed identities, trophic interactions and genomic features of microorganisms that degraded 13C-labelled proteins and lipids in cold anoxic microcosms with sulfidic subarctic marine sediment. Supplemented proteins and lipids were rapidly fermented to various volatile fatty acids within five days. DNA-stable isotope probing (SIP) suggested Psychrilyobacter atlanticus was an important primary degrader of proteins, and Psychromonas members were important primary degraders of both proteins and lipids. Closely related Psychromonas populations, as represented by distinct 16S rRNA gene variants, differentially utilized either proteins or lipids. DNA-SIP also showed 13C-labeling of various Deltaproteobacteria within ten days, indicating trophic transfer of carbon to putative sulfate-reducers. Metagenome-assembled genomes revealed the primary hydrolyzers encoded secreted peptidases or lipases, and enzymes for catabolism of protein or lipid degradation products. Psychromonas were prevalent in diverse marine sediments, suggesting they are important players in organic carbon processing in situ. Together, this study provides an improved understanding of the metabolic processes and functional partitioning of necromass macromolecules among microorganisms in the seafloor.