The Association of Frailty and Neighborhood Disadvantage with Emergency Department Visits and Hospitalizations in Older Adults.

BACKGROUND: Risk stratification and population management strategies are critical for providing effective and equitable care for the growing population of older adults in the USA. Both frailty and neighborhood disadvantage are constructs that independently identify populations with higher healthcare utilization and risk of adverse outcomes. OBJECTIVE: To examine the joint association of these factors on acute healthcare utilization using two pragmatic measures based on structured data available in the electronic health record (EHR). DESIGN: In this retrospective observational study, we used EHR data to identify patients aged ≥ 65 years at Atrium Health Wake Forest Baptist on January 1, 2019, who were attributed to affiliated Accountable Care Organizations. Frailty was categorized through an EHR-derived electronic Frailty Index (eFI), while neighborhood disadvantage was quantified through linkage to the area deprivation index (ADI). We used a recurrent time-to-event model within a Cox proportional hazards framework to examine the joint association of eFI and ADI categories with healthcare utilization comprising emergency visits, observation stays, and inpatient hospitalizations over one year of follow-up. KEY RESULTS: We identified a cohort of 47,566 older adults (median age = 73, 60% female, 12% Black). There was an interaction between frailty and area disadvantage (P = 0.023). Each factor was associated with utilization across categories of the other. The magnitude of frailty's association was larger than living in a disadvantaged area. The highest-risk group comprised frail adults living in areas of high disadvantage (HR 3.23, 95% CI 2.99-3.49; P < 0.001). We observed additive effects between frailty and living in areas of mid- (RERI 0.29; 95% CI 0.13-0.45; P < 0.001) and high (RERI 0.62, 95% CI 0.41-0.83; P < 0.001) neighborhood disadvantage. CONCLUSIONS: Considering both frailty and neighborhood disadvantage may assist healthcare organizations in effectively risk-stratifying vulnerable older adults and informing population management strategies. These constructs can be readily assessed at-scale using routinely collected structured EHR data.

Extracellular Interaction of Bacillus thuringiensis, ATP and Phage 0105phi7-2: A Potential New Anti-Bacterial Strategy.

The following hypothesis proposes non-diffusive, environmental bacteriophage (phage) motion. (1) Some phage-hosting, motile bacteria undergo chemotaxis down ATP concentration gradients to escape lysis-inducing conditions, such as phage infection. (2) Some phages respond by non-infective binding to the motile bacteria. (3) When the bacteria reach a lower ATP concentration, which is a condition that signals increased density of phage-susceptible bacteria, the phage converts, Trojan-horse-like, to productive binding and infection. This hypothesis was previously proposed for Bacillus thuringiensis siphophage 0105phi7-2. It is tested here and confirmed with the following observations. (1) B. thuringiensis is found, macroscopically, preferentially located at low ATP concentrations when propagated in-gel after inoculation in the center of an artificially generated ATP concentration gradient. (2) Inoculating phage 0105phi7-2 at the bacteria inoculation site, 2-3 h after inoculation of bacteria, results in cell lysing activity that moves with the bacteria, without a visible trail of lysis. Trojan-horse-like behavior is consistent with only biofilm-inhabiting phages because environmental selection for this behavior requires limited fluid flows. We propose using artificial ATP concentration gradients to instigate Trojan-horse-like phage behavior during phage therapy of bacterial biofilms.

Siphophage 0105phi7-2 of Bacillus thuringiensis: Novel Propagation, DNA, and Genome-Implied Assembly.

Diversity of phage propagation, physical properties, and assembly promotes the use of phages in ecological studies and biomedicine. However, observed phage diversity is incomplete. Bacillus thuringiensis siphophage, 0105phi-7-2, first described here, significantly expands known phage diversity, as seen via in-plaque propagation, electron microscopy, whole genome sequencing/annotation, protein mass spectrometry, and native gel electrophoresis (AGE). Average plaque diameter vs. plaque-supporting agarose gel concentration plots reveal unusually steep conversion to large plaques as agarose concentration decreases below 0.2%. These large plaques sometimes have small satellites and are made larger by orthovanadate, an ATPase inhibitor. Phage head-host-cell binding is observed by electron microscopy. We hypothesize that this binding causes plaque size-increase via biofilm evolved, ATP stimulated ride-hitching on motile host cells by temporarily inactive phages. Phage 0105phi7-2 does not propagate in liquid culture. Genomic sequencing/annotation reveals history as temperate phage and distant similarity, in a virion-assembly gene cluster, to prototypical siphophage SPP1 of Bacillus subtilis. Phage 0105phi7-2 is distinct in (1) absence of head-assembly scaffolding via either separate protein or classically sized, head protein-embedded peptide, (2) producing partially condensed, head-expelled DNA, and (3) having a surface relatively poor in AGE-detected net negative charges, which is possibly correlated with observed low murine blood persistence.

Effectiveness and implementation of mPATH™-CRC: a mobile health system for colorectal cancer screening.

BACKGROUND: Screening for colorectal cancer (CRC) is widely recommended but underused, even though CRC is the third most diagnosed cancer and the second leading cause of cancer death in the USA. The mPATH™ program is an iPad-based application designed to identify patients due for CRC screening, educate them on the commonly used screening tests, and help them select their best option, with the goal of increasing CRC screening rates. METHODS: The mPATH™ program consists of questions asked of all adult patients at check-in (mPATH™-CheckIn), as well as a module specific for patients due for CRC screening (mPATH™-CRC). In this study, the mPATH™ program is evaluated through a Type III hybrid implementation-effectiveness design. Specifically, the study consists of three parts: (1) a cluster-randomized controlled trial of primary care clinics comparing a "high touch" evidence-based implementation strategy with a "low touch" implementation strategy; (2) a nested pragmatic study evaluating the effectiveness of mPATH-CRC™ on completion of CRC screening; and (3) a mixed-methods study evaluating factors that facilitate or impede the maintenance of interventions like mPATH-CRC™. The primary objective is to compare the proportion of patients aged 50-74 who are eligible for CRC screening who complete mPATH™-CRC in the 6th month following implementation between the "high touch" and "low touch" implementation strategies. Effectiveness of mPATH™-CRC is evaluated by comparing the proportion who complete CRC screening within 16 weeks of their visit to the clinic between a pre-implementation cohort (8 months before implementation) and a post-implementation cohort (8 months after implementation). DISCUSSION: This study will provide data on both the implementation of the mPATH™ program and its effectiveness in improving screening rates for CRC. In addition, this work has the potential to have an even broader impact by identifying strategies to support the sustained use of other similar technology-based primary care interventions. TRIAL REGISTRATION: ClinicalTrials.gov NCT03843957. Registered on 18 February 2019.

Exploring the consequences of food insecurity and harnessing the power of peer navigation and mHealth to reduce food insecurity and cardiometabolic comorbidities among persons with HIV: protocol for development and implementation trial of weCare/Secure.

BACKGROUND: Food insecurity, or the lack of consistent access to nutritionally adequate and safe foods, effects up to 50% of people living with HIV (PWH) in the United States (US). PWH who are food insecure have lower antiretroviral adherence, are less likely to achieve viral suppression, and are at increased risk developing of serious illnesses, including cardiometabolic comorbidities. The objectives of this study are to better understand how food insecurity contributes to the development of cardiometabolic comorbidities among PWH and to test a novel bilingual peer navigation-mHealth intervention (weCare/Secure) designed to reduce these comorbidities in food-insecure PWH with prediabetes or Type 2 diabetes (T2DM). METHODS: In Aim 1, we will recruit a longitudinal cohort of 1800 adult (≥18 years) PWH from our clinic-based population to determine the difference in the prevalence and incidence of cardiometabolic comorbidities between food-secure and food-insecure PWH. Food insecurity screening, indicators of cardiometabolic comorbidities, and other characteristics documented in the electronic health record (EHR) will be collected annually for up to 3 years from this cohort. In Aim 2, we will conduct a randomized controlled trial among a sample of food-insecure PWH who have prediabetes or T2DM to compare changes in insulin sensitivity over 6 months between participants in weCare/Secure and participants receiving usual care. In Aim 3, we will conduct semi-structured individual in-depth interviews to explore the effect of the intervention among intervention participants with varying insulin sensitivity outcomes. TRIAL STATUS: Aim 1 (longitudinal cohort) recruitment began in May 2022 and is ongoing. Aim 2 (intervention) recruitment is planned for spring 2023 and is expected to be completed in spring 2024. Aim 3 (process evaluation) data collection will occur after sufficient completion of the 6-month assessment in Aim 2. Final results are anticipated in fall 2025. CONCLUSIONS: This research seeks to advance our understanding of how food insecurity impacts the development of cardiometabolic comorbidities among PWH and how food insecurity interventions may alleviate relevant comorbidities. Given the growing interest among health systems in addressing food insecurity, if the intervention is found to be efficacious, it could be broadly disseminated across HIV clinical care settings. TRIAL REGISTRATION: ClinicalTrials.gov NCT04943861 . Registered on June 29, 2021.

Additions to Alpha-Sheet Based Hypotheses for the Cause of Alzheimer's Disease.

Protein amyloid-ß (Aß) oligomers with ß-sheet-like backbone (ß-structured) form extracellular amyloid plaques associated with Alzheimer's disease (AD). However, the relationship to AD is not known. Some investigations suggest that the toxic Aß component has α-sheet-like backbone (α-structured) subsequently detoxified by intracellular α-to-ß conversion before plaque formation. Our objective is to compare this latter hypothesis with observations made by electron microscopy of thin sections of AD-cerebral cortex. We observe irregular, 200-2,000 nm, intracellular, lipofuscin-like inclusions. Some are light-staining and smooth. Others are dark-staining and made granular by fibers that are usually overlapping and are sometimes individually seen. Aspects unusual for lipofuscin include 1) dark and light inclusions interlocking as though previously one inclusion, 2) dark inclusion-contained 2.6 nm thick sub-fibers that are bent as though α-structured, and 3) presence of inclusions in lysosomes and apparent transfer of dark inclusion material to damaged, nearby lysosomal membranes. These data suggest the following additions to α-structure-based hypotheses: 1) Lipofuscin-associated, α-structured protein toxicity to lysosomal membranes is in the chain of AD causation; 2) α-to-ß detoxification of α-structured protein occurs in lipofuscin and causes dark-to-light transition that, when incomplete, is the origin of cell-to-cell transmission essential for development of AD.

Ankle Dorsiflexion Affects Hip and Knee Biomechanics During Landing.

BACKGROUND: Restricted ankle dorsiflexion range of motion (DFROM) has been linked to lower extremity biomechanics that place an athlete at higher risk for injury. Whether reduced DFROM during dynamic movements is due to restrictions in joint motion or underutilization of available ankle DFROM motion is unclear. HYPOTHESIS: We hypothesized that both lesser total ankle DFROM and underutilization of available motion would lead to high-risk biomechanics (ie, greater knee abduction, reduced knee flexion). STUDY DESIGN: Cross-sectional study. LEVEL OF EVIDENCE: Level 3. METHODS: Nineteen active female athletes (age, 20.0 ± 1.3 years; height, 1.61 ± 0.06 m; mass, 67.0 ± 10.7 kg) participated. Maximal ankle DFROM (clinical measure of ankle DFROM [DF-CLIN]) was measured in a weightbearing position with the knee flexed. Lower extremity biomechanics were measured during a drop vertical jump with 3-dimensional motion and force plate analysis. The percent of available DFROM used during landing (DF-%USED) was calculated as the peak DFROM observed during landing divided by DF-CLIN. Univariate linear regressions were performed to identify whether DF-CLIN or DF-%USED predicted knee and hip biomechanics commonly associated with injury risk. RESULTS: For every 1.0° less of DF-CLIN, there was a 1.0° decrease in hip flexion excursion (r2 = 0.21, P = 0.05), 1.2° decrease in peak knee flexion angles (r2 = 0.37, P = 0.01), 0.9° decrease in knee flexion excursion (r2 = 0.40, P = 0.004), 0.002 N·m·N-1·cm-1 decrease in hip extensor work (r2 = 0.28, P = 0.02), and 0.001 N·m·N-1·cm-1 decrease in knee extensor work (r2 = 0.21, P = 0.05). For every 10% less of DF-%USED, there was a 3.2° increase in peak knee abduction angles (r2 = 0.26, P = 0.03) and 0.01 N·m·N-1·cm-1 lesser knee extensor work (r2 = 0.25, P = 0.03). CONCLUSION: Lower levels of both ankle DFROM and DF-%USED are associated with biomechanics that are considered to be associated with a higher risk of sustaining injury. CLINICAL RELEVANCE: While total ankle DFROM can predict some aberrant movement patterns, underutilization of available ankle DFROM can also lead to higher risk movement strategies. In addition to joint specific mobility training, clinicians should incorporate biomechanical interventions and technique feedback to promote the utilization of available motion.

Structural Studies of the Phage G Tail Demonstrate an Atypical Tail Contraction.

Phage G is recognized as having a remarkably large genome and capsid size among isolated, propagated phages. Negative stain electron microscopy of the host-phage G interaction reveals tail sheaths that are contracted towards the distal tip and decoupled from the head-neck region. This is different from the typical myophage tail contraction, where the sheath contracts upward, while being linked to the head-neck region. Our cryo-EM structures of the non-contracted and contracted tail sheath show that: (1) The protein fold of the sheath protein is very similar to its counterpart in smaller, contractile phages such as T4 and phi812; (2) Phage G's sheath structure in the non-contracted and contracted states are similar to phage T4's sheath structure. Similarity to other myophages is confirmed by a comparison-based study of the tail sheath's helical symmetry, the sheath protein's evolutionary timetree, and the organization of genes involved in tail morphogenesis. Atypical phase G tail contraction could be due to a missing anchor point at the upper end of the tail sheath that allows the decoupling of the sheath from the head-neck region. Explaining the atypical tail contraction requires further investigation of the phage G sheath anchor points.

Basics for Improved Use of Phages for Therapy.

Blood-borne therapeutic phages and phage capsids increasingly reach therapeutic targets as they acquire more persistence, i.e., become more resistant to non-targeted removal from blood. Pathogenic bacteria are targets during classical phage therapy. Metastatic tumors are potential future targets, during use of drug delivery vehicles (DDVs) that are phage derived. Phage therapy has, to date, only sometimes been successful. One cause of failure is low phage persistence. A three-step strategy for increasing persistence is to increase (1) the speed of lytic phage isolation, (2) the diversity of phages isolated, and (3) the effectiveness and speed of screening phages for high persistence. The importance of high persistence-screening is illustrated by our finding here of persistence dramatically higher for coliphage T3 than for its relative, coliphage T7, in murine blood. Coliphage T4 is more persistent, long-term than T3. Pseudomonas chlororaphis phage 201phi2-1 has relatively low persistence. These data are obtained with phages co-inoculated and separately assayed. In addition, highly persistent phage T3 undergoes dispersal to several murine organs and displays tumor tropism in epithelial tissue (xenografted human oral squamous cell carcinoma). Dispersal is an asset for phage therapy, but a liability for phage-based DDVs. We propose increased focus on phage persistence-and dispersal-screening.

Phage G Structure at 6.1 ŠResolution, Condensed DNA, and Host Identity Revision to a Lysinibacillus.

Phage G has the largest capsid and genome of any known propagated phage. Many aspects of its structure, assembly, and replication have not been elucidated. Herein, we present the dsDNA-packed and empty phage G capsid at 6.1 and 9 Šresolution, respectively, using cryo-EM for structure determination and mass spectrometry for protein identification. The major capsid protein, gp27, is identified and found to share the HK97-fold universally conserved in all previously solved dsDNA phages. Trimers of the decoration protein, gp26, sit on the 3-fold axes and are thought to enhance the interactions of the hexameric capsomeres of gp27, for other phages encoding decoration proteins. Phage G's decoration protein is longer than what has been reported in other phages, and we suspect the extra interaction surface area helps stabilize the capsid. We identified several additional capsid proteins, including a candidate for the prohead protease responsible for processing gp27. Furthermore, cryo-EM reveals a range of partially full, condensed DNA densities that appear to have no contact with capsid shell. Three analyses confirm that the phage G host is a Lysinibacillus, and not Bacillus megaterium: identity of host proteins in our mass spectrometry analyses, genome sequence of the phage G host, and host range of phage G.

In-Gel Isolation and Characterization of Large (and Other) Phages.

We review some aspects of the rapid isolation of, screening for and characterization of jumbo phages, i.e., phages that have dsDNA genomes longer than 200 Kb. The first aspect is that, as plaque-supporting gels become more concentrated, jumbo phage plaques become smaller. Dilute agarose gels are better than conventional agar gels for supporting plaques of both jumbo phages and, prospectively, the even larger (>520 Kb genome), not-yet-isolated mega-phages. Second, dilute agarose gels stimulate propagation of at least some jumbo phages. Third, in-plaque techniques exist for screening for both phage aggregation and high-in-magnitude, negative average electrical surface charge density. The latter is possibly correlated with high phage persistence in blood. Fourth, electron microscopy of a thin section of a phage plaque reveals phage type, size and some phage life cycle information. Fifth, in-gel propagation is an effective preparative technique for at least some jumbo phages. Sixth, centrifugation through sucrose density gradients is a relatively non-destructive jumbo phage purification technique. These basics have ramifications in the development of procedures for (1) use of jumbo phages for phage therapy of infectious disease, (2) exploration of genomic diversity and evolution and (3) obtaining accurate metagenomic analyses.

Electron Microscopy of In-Plaque Phage T3 Assembly: Proposed Analogs of Neurodegenerative Disease Triggers.

Increased knowledge of virus assembly-generated particles is needed for understanding both virus assembly and host responses to virus infection. Here, we use a phage T3 model and perform electron microscopy (EM) of thin sections (EM-TS) of gel-supported T3 plaques formed at 30 °C. After uranyl acetate/lead staining, we observe intracellular black particles, some with a difficult-to-see capsid. Some black particles (called LBPs) are larger than phage particles. The LBP frequency is increased by including proflavine, a DNA packaging inhibitor, in the growth medium and increasing plaque-forming temperature to 37 °C. Acidic phosphotungstate-precipitate (A-PTA) staining causes LBP substitution by black rings (BRs) that have the size and shape expected of hyper-expanded capsid containers for LBP DNA. BRs are less frequent in liquid cultures, suggesting that hyper-expanded capsids evolved primarily for in-gel (e.g., in-biofilm) propagation. BR-specific A-PTA staining and other observations are explained by α-sheet intense structure of the major subunit of hyper-expanded capsids. We hypothesize that herpes virus triggering of neurodegenerative disease occurs via in-gel propagation-promoted (1) generation of α-sheet intense viral capsids and, in response, (2) host production of α-sheet intense, capsid-interactive, innate immunity amyloid protein that becomes toxic. We propose developing viruses that are therapeutic via detoxifying interaction with this innate immunity protein.

High murine blood persistence of phage T3 and suggested strategy for phage therapy.

OBJECTIVE: Our immediate objective is to determine whether infectivity of lytic podophage T3 has a relatively high persistence in the blood of a mouse, as suggested by previous data. Secondarily, we determine whether the T3 surface has changed during this mouse passage. The surface is characterized by native agarose gel electrophoresis (AGE). Beyond our current data, the long-term objective is optimization of phages chosen for therapy of all bacteremias and associated sepsis. RESULTS: We find that the persistence of T3 in mouse blood is higher by over an order of magnitude than the previously reported persistence of (1) lysogenic phages lambda and P22, and (2) lytic phage T7, a T3 relative. We explain these differences via the lysogenic character of lambda and P22, and the physical properties of T7. For the future, we propose testing a new, AGE-based strategy for rapidly screening for high-persistence, lytic, environmental podophages that have phage therapy-promoting physical properties.

Cell-gel interactions of in-gel propagating bacteria.

OBJECTIVE: Our immediate objective is to test the data-suggested possibility that in-agarose gel bacterial propagation causes gel fiber dislocation and alteration of cell distribution. We also test the further effect of lowering water activity. We perform these tests with both Gram-negative and Gram-positive bacteria. Data are obtained via electron microscopy of thin sections, which provides the first images of both bacteria and gel fibers in gel-supported bacterial lawns. The long-term objective is analysis of the effects of in-gel propagation on the DNA packaging of phages. RESULTS: We find that agarose gel-supported cells in lawns of Escherichia coli and Lysinibacillus (1) are primarily in clusters that increase in size with time and are surrounded by gel fibers, and (2) sometimes undergo gel-induced, post-duplication rotation and translation. Bacterial growth-induced dislocation of gel fibers is observed. One reason for clustering is that clustering promotes growth by increasing the growth-derived force applied to the gel fibers. Reactive force exerted by gel on cells explains cell movement. Finally, addition to growth medium of 0.94 M sucrose causes cluster-associated E. coli cells to become more densely packed and polymorphic. Shape is determined, in part, by neighboring cells, a novel observation to our knowledge.

Nanomedicine and Phage Capsids.

Studies of phage capsids have at least three potential interfaces with nanomedicine. First, investigation of phage capsid states potentially will provide therapies targeted to similar states of pathogenic viruses. Recently detected, altered radius-states of phage T3 capsids include those probably related to intermediate states of DNA injection and DNA packaging (dynamic states). We discuss and test the idea that some T3 dynamic states include extensive α-sheet in subunits of the capsid’s shell. Second, dynamic states of pathogenic viral capsids are possible targets of innate immune systems. Specifically, α-sheet-rich innate immune proteins would interfere with dynamic viral states via inter-α-sheet co-assembly. A possible cause of neurodegenerative diseases is excessive activity of these innate immune proteins. Third, some phage capsids appear to have characteristics useful for improved drug delivery vehicles (DDVs). These characteristics include stability, uniformity and a gate-like sub-structure. Gating by DDVs is needed for (1) drug-loading only with gate opened; (2) closed gate-DDV migration through circulatory systems (no drug leakage-generated toxicity); and (3) drug release only at targets. A gate-like sub-structure is the connector ring of double-stranded DNA phage capsids. Targeting to tumors of phage capsid-DDVs can possibly be achieved via the enhanced permeability and retention effect.

States of phage T3/T7 capsids: buoyant density centrifugation and cryo-EM.

Mature double-stranded DNA bacteriophages have capsids with symmetrical shells that typically resist disruption, as they must to survive in the wild. However, flexibility and associated dynamism assist function. We describe biochemistry-oriented procedures used to find previously obscure flexibility for capsids of the related phages, T3 and T7. The primary procedures are hydration-based buoyant density ultracentrifugation and purified particle-based cryo-electron microscopy (cryo-EM). We review the buoyant density centrifugation in detail. The mature, stable T3/T7 capsid is a shell flexibility-derived conversion product of an initially assembled procapsid (capsid I). During DNA packaging, capsid I expands and loses a scaffolding protein to form capsid II. The following are observations made with capsid II. (1) The in vivo DNA packaging of wild type T3 generates capsid II that has a slight (1.4%), cryo-EM-detected hyper-expansion relative to the mature phage capsid. (2) DNA packaging in some altered conditions generates more extensive hyper-expansion of capsid II, initially detected by hydration-based preparative buoyant density centrifugation in Nycodenz density gradients. (3) Capsid contraction sometimes occurs, e.g., during quantized leakage of DNA from mature T3 capsids without a tail.

ATP-Driven Contraction of Phage T3 Capsids with DNA Incompletely Packaged In Vivo.

Adenosine triphosphate (ATP) cleavage powers packaging of a double-stranded DNA (dsDNA) molecule in a pre-assembled capsid of phages that include T3. Several observations constitute a challenge to the conventional view that the shell of the capsid is energetically inert during packaging. Here, we test this challenge by analyzing the in vitro effects of ATP on the shells of capsids generated by DNA packaging in vivo. These capsids retain incompletely packaged DNA (ipDNA) and are called ipDNA-capsids; the ipDNA-capsids are assumed to be products of premature genome maturation-cleavage. They were isolated via preparative Nycodenz buoyant density centrifugation. For some ipDNA-capsids, Nycodenz impermeability increases hydration and generates density so low that shell hyper-expansion must exist to accommodate associated water. Electron microscopy (EM) confirmed hyper-expansion and low permeability and revealed that 3.0 mM magnesium ATP (physiological concentration) causes contraction of hyper-expanded, lowpermeability ipDNA-capsids to less than mature size; 5.0 mM magnesium ATP (border of supraphysiological concentration) or more disrupts them. Additionally, excess sodium ADP reverses 3.0 mM magnesium ATP-induced contraction and re-generates hyper-expansion. The Nycodenz impermeability implies assembly perfection that suggests selection for function in DNA packaging. These findings support the above challenge and can be explained via the assumption that T3 DNA packaging includes a back-up cycle of ATP-driven capsid contraction and hyper-expansion.

Testing a proposed paradigm shift in analysis of phage DNA packaging.

We argue that a paradigm shift is needed in the analysis of phage DNA packaging. We then test a prediction of the following paradigm shift-engendering hypothesis. The motor of phage DNA packaging has two cycles: (1) the well-known packaging ATPase-driven (type 1) cycle and (2) a proposed back-up, shell expansion/contraction-driven (type 2) cycle that reverses type 1 cycle stalls by expelling accidentally packaged non-DNA molecules. We test the prediction that increasing the cellular concentration of all macromolecules will cause packaging-active capsids to divert to states of hyper-expansion and contraction. We use a directed evolution-derived, 3-site phage T3 mutant, adapted to propagation in concentrated bacterial cytoplasm. We find this prediction correct while discovering novel T3 capsids previously obscure.

Capsid expansion mechanism of bacteriophage T7 revealed by multistate atomic models derived from cryo-EM reconstructions.

Many dsDNA viruses first assemble a DNA-free procapsid, using a scaffolding protein-dependent process. The procapsid, then, undergoes dramatic conformational maturation while packaging DNA. For bacteriophage T7 we report the following four single-particle cryo-EM 3D reconstructions and the derived atomic models: procapsid (4.6-Å resolution), an early-stage DNA packaging intermediate (3.5 Å), a later-stage packaging intermediate (6.6 Å), and the final infectious phage (3.6 Å). In the procapsid, the N terminus of the major capsid protein, gp10, has a six-turn helix at the inner surface of the shell, where each skewed hexamer of gp10 interacts with two scaffolding proteins. With the exit of scaffolding proteins during maturation the gp10 N-terminal helix unfolds and swings through the capsid shell to the outer surface. The refolded N-terminal region has a hairpin that forms a novel noncovalent, joint-like, intercapsomeric interaction with a pocket formed during shell expansion. These large conformational changes also result in a new noncovalent, intracapsomeric topological linking. Both interactions further stabilize the capsids by interlocking all pentameric and hexameric capsomeres in both DNA packaging intermediate and phage. Although the final phage shell has nearly identical structure to the shell of the DNA-free intermediate, surprisingly we found that the icosahedral faces of the phage are slightly (∼4 Å) contracted relative to the faces of the intermediate, despite the internal pressure from the densely packaged DNA genome. These structures provide a basis for understanding the capsid maturation process during DNA packaging that is essential for large numbers of dsDNA viruses.