Porcine circovirus 2 (PCV2) is the smallest pathogenic virus capable of autonomous replication within its host. Infections result in immunosuppression and subsequent death of the host and are initiated via the attachment of the PCV2 icosahedral capsid to heparan sulfate (HS) and chondroitin sulfate B (CSB) glycosaminoglycans on the cell surface. However, the underlying mechanism of structural recognition remains to be explored. Using heparin, a routinely used analog of heparan sulfate, we demonstrate that increasing lengths of heparin exhibit a greater affinity toward PCV2. Our competition assays indicate that dextran sulfate (8 kDa) has a higher affinity for PCV2 than heparin (12 kDa), chondroitin sulfate B (41 kDa), hyaluronic acid (1.6 MDa), and dextran (6 kDa). This suggests that polymers high in sulfate content are capable of competing with the PCV2-heparan sulfate interaction and, thus, have the potential to inhibit PCV2 infection. Finally, we visualized the interaction between heparin and the PCV2 capsid using cryo-electron microscopy single-particle analysis, symmetry expansion, and focused classification. The image reconstructions provide the first example of an asymmetric distribution of heparin on the surface of an icosahedral virus capsid. We demonstrate that each of the 60 capsid subunits that generate the T=1 capsid can bind heparin via one of five binding sites. However, not all of the binding sites were occupied by heparin, and only one-third to two-thirds of the binding sites were occupied. The binding sites are defined by arginine, lysine, and polar amino acids. Mutating the arginine, lysine, and polar amino acids to alanine diminished the binding capacity of PCV2 to heparin. IMPORTANCE It has been demonstrated that porcine circovirus 2 (PCV2) attaches to cells via heparan sulfate (HS) and chondroitin sulfate B (CSB) glycosaminoglycans; however, the underlying structural mechanism describing the HS/CSB recognition by PCV2 remains to be explored. We used cryo-electron microscopy with single-particle analysis, symmetry expansion, and focused classification to visualize the interaction between the PCV2 capsid and heparin, an analog of heparan sulfate, to better than 3.6-Å resolution. We observed that the interaction between PCV2 and heparin does not adhere to the icosahedral symmetry of the capsid. To the best of our knowledge, this is the first example where the interaction between heparin and an icosahedral capsid does not follow the symmetry elements of the capsid. Our findings also suggest that anionic polymers, such as dextran sulfate, may act to inhibit PCV2 infection.

Enterococcus faecalis is a gram-positive organism responsible for serious infections in humans, but as with many bacterial pathogens, resistance has rendered a number of commonly used antibiotics ineffective. Here, we report the cryo-EM structure of the E. faecalis 70S ribosome to a global resolution of 2.8 Å. Structural differences are clustered in peripheral and solvent exposed regions when compared with Escherichia coli, whereas functional centres, including antibiotic binding sites, are similar to other bacterial ribosomes. Comparison of intersubunit conformations among five classes obtained after three-dimensional classification identifies several rotated states. Large ribosomal subunit protein bL31, which forms intersubunit bridges to the small ribosomal subunit, assumes different conformations in the five classes, revealing how contacts to the small subunit are maintained throughout intersubunit rotation. A tRNA observed in one of the five classes is positioned in a chimeric pe/E position in a rotated ribosomal state. The 70S ribosome structure of E. faecalis now extends our knowledge of bacterial ribosome structures and may serve as a basis for the development of novel antibiotic compounds effective against this pathogen.

20Porcine circovirus 2 (PCV2) is the smallest autonomously replicating virus and thus defines the minimum amount 21 of genetic and biochemical information needed for infection. PCV2 infects nearly every tissue within its host, 22 and infections result in immunosuppression and subsequent death of the host. Infection is initiated via the 23 attachment of the PCV2 capsid to heparan sulfate and chondroitin sulfate B glycosaminoglycan (GAG) on the 24 surface of the cell. We demonstrate that the PCV2 capsid does not recognize the pyranose backbone of a GAG, 25 and solely interacts with the sulfates of GAG. We visualize the interaction between heparin sulfate, an analog 26 for heparan sulfate, and the PCV2 capsid using cryo--electron microscopy. The image reconstructions provide 27 the first example of an asymmetric distribution of heparin sulfate on the surface of a virus capsid. We 28 demonstrate that each subunit possesses six heparin sulfate binding sites, but binding at any site occludes 29 binding at the other five sites. The binding sites are defined by arginine, lysine, and polar amino acids. Mutation 30 of these arginine and lysine to alanine diminishes the binding capacity of the PCV2 to heparin sulfate. A third to 31 two--thirds of the binding sites (subunits) in each PCV2 is occupied by segments of one or multiple 12kDa heparin 32 sulfate chains -leaving the remaining subunits unliganded. We discuss the significance of the unliganded 33 subunits in the life cycle of PCV2. 34Keywords. Circovirus, heparan sulfate, chondroitin sulfate B, glycosamino glycan, heparin sulfate, cellular 35 attachment, electron microscopy, symmetry expansion, focused classification. 36 37. CC-BY-NC-ND 4.0 International license It is made available under a was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/370411 doi: bioRxiv preprint first posted online Jul. 16, 2018; Significance statement: 38 Studies describing the interaction between heparan sulfate (a cellular attachment factor) and non--enveloped 39 icosahedral viruses have adhered to the symmetry elements of the viral capsid. Here we provide the first 40 example where the interaction between heparan sulfate and a non--enveloped icosahedral virus does not follow 41 the symmetry elements of the viral capsid. We use cryo--electron microscopy, symmetry expansion, and focused 42 classification to visualize the interaction between the porcine circovirus 2 (PCV2) capsid. The non symmetric 43 interactions observed in our studies is likely to be true for all non--enveloped viruses, and more accurately 44 representative of what occurs during infection. We discuss how such interaction may be important to the life 45 cycle of PCV2. 46 47

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