The eukaryotic phylum Apicomplexa encompasses thousands of obligate intracellular parasites of humans and animals with immense socio-economic and health impacts. We sequenced nuclear genomes of Chromera velia and Vitrella brassicaformis, free-living non-parasitic photosynthetic algae closely related to apicomplexans. Proteins from key metabolic pathways and from the endomembrane trafficking systems associated with a free-living lifestyle have been progressively and non-randomly lost during adaptation to parasitism. The free-living ancestor contained a broad repertoire of genes many of which were repurposed for parasitic processes, such as extracellular proteins, components of a motility apparatus, and DNA- and RNA-binding protein families. Based on transcriptome analyses across 36 environmental conditions, Chromera orthologs of apicomplexan invasion-related motility genes were co-regulated with genes encoding the flagellar apparatus, supporting the functional contribution of flagella to the evolution of invasion machinery. This study provides insights into how obligate parasites with diverse life strategies arose from a once free-living phototrophic marine alga.DOI: http://dx.doi.org/10.7554/eLife.06974.001

The emergence of SARS-CoV-2 variants threatens current vaccines and therapeutic antibodies and urgently demands powerful new therapeutics that can resist viral escape. We therefore generated a large nanobody repertoire to saturate the distinct and highly conserved available epitope space of SARS-CoV-2 spike, including the S1 receptor binding domain, N-terminal domain, and the S2 subunit, to identify new nanobody binding sites that may reflect novel mechanisms of viral neutralization. Structural mapping and functional assays show that indeed these highly stable monovalent nanobodies potently inhibit SARS-CoV-2 infection, display numerous neutralization mechanisms, are effective against emerging variants of concern, and are resistant to mutational escape. Rational combinations of these nanobodies that bind to distinct sites within and between spike subunits exhibit extraordinary synergy and suggest multiple tailored therapeutic and prophylactic strategies.

Peroxisome proliferation occurs by at least two routes, division of existing peroxisomes and de novo biogenesis from the endoplasmic reticulum (ER). The proteins and molecular mechanisms governing peroxisome emergence from the ER are poorly characterized. In this study, we report that two integral membrane peroxins (proteins required for peroxisome biogenesis) in Saccharomyces cerevisiae, Pex29 and Pex30, reside in distinct regions of the ER and associate with Rtn1 and Yop1, reticulon family members that contribute to ER morphology, to govern peroxisome emergence from the ER. In vivo and in vitro analyses reveal that peroxisome proliferation is therefore not restricted to the peroxisome but begins at the level of the ER.Peroxisomes are organelles found across the diversity of eukaryotes. Bound by a single lipid bilayer, peroxisomes contain enzymes involved in lipid metabolism that are coupled to the production of hydrogen peroxide and the scavenging of reactive oxygen species. Peroxisome number, size, and volume are dynamically linked to cell type, its developmental state, and environmental stimuli. Control of these processes is critical to human health. Defects in peroxisome membrane formation, protein import, and organelle proliferation cause severe pathologies in humans, and peroxisome function is linked to numerous human health issues (1-4). Studies in many different model systems, including notably different species of yeast, have led to the identification of peroxins, which are defined as proteins involved in peroxisome biogenesis (5). The mechanisms of action of the more than 30 peroxins in peroxisomal biogenesis and proliferation are the subject of intense investigation.There has been much debate as to whether peroxisomes are semi-autonomous organelles like mitochondria or are derived from internal membrane systems such as the secretory pathway. Evidence supports that peroxisome biogenesis occurs through two separate pathways, de novo biogenesis in which new peroxisomes bud from the ER 3 and the division of existing peroxisomes (6 -12). These biogenesis pathways are tightly regulated spatially and temporally and involve a host of molecular interactions that mediate the assembly of proteins and lipids at the peroxisome membrane and the ER (13-16). In the budding yeast Saccharomyces cerevisiae, growth and division of peroxisomes are the dominant forms of peroxisome proliferation. However, contribution from the ER is an essential albeit poorly understood process. When peroxisomes are absent, cells form peroxisomes de novo from the ER. Presumably, interactions between proteins and lipids at the ER result in de novo biogenesis of nascent preperoxisomes that undergo a series of steps to ultimately form mature peroxisomes. Several peroxisomal membrane proteins (PMPs) insert into the ER dependent on components of the Sec61 complex, and the subsequent formation of preperoxisomes is dependent on the peroxins Pex3 and Pex19. Pex3 is an integral membrane protein that accumulates initially at an ER subdomain and is t...