Protamine folds DNA into flowers and loop stacks

DNA in sperm undergoes an extreme compaction to almost crystalline packing levels. To produce this dense packing, DNA is dramatically reorganized in minutes by protamine proteins. Protamines are positively charged proteins that coat negatively charged DNA and fold it into a series of toroids. The exact mechanism for forming these ∼50-kbp toroids is unknown. Our goal is to study toroid formation by starting at the "bottom" with folding of short lengths of DNA that form loops and working "up" to more folded structures that occur on longer length scales. We previously measured folding of 200-300 bp of DNA into a loop. Here, we look at folding of intermediate DNA lengths (L = 639-3003 bp) that are 2-10 loops long. We observe two folded structures besides loops that we hypothesize are early intermediates in the toroid formation pathway. At low protamine concentrations (∼0.2 μM), we see that the DNA folds into flowers (structures with multiple loops that are positioned so they look like the petals of a flower). Folding at these concentrations condenses the DNA to 25% of its original length, takes seconds, and is made up of many small bending steps. At higher protamine concentrations (≥2 μM), we observe a second folded structure-the loop stack-where loops are stacked vertically one on top of another. These results lead us to propose a two-step process for folding at this length scale: 1) protamine binds to DNA, bending it into loops and flowers, and 2) flowers collapse into loop stacks. These results highlight how protamine uses a bind-and-bend mechanism to rapidly fold DNA, which may be why protamine can fold the entire sperm genome in minutes.

Abstract P644: Engagement With a Weight Loss Program for Postpartum Individuals at Elevated Cardiovascular Risk: A Qualitative Study

Background: Rising rates of postpartum obesity increase risk for cardiovascular (CV) disease, especially among individuals with adverse pregnancy outcomes. Engagement in weight loss programs (WLP) have not been well studied in the postpartum period. Our objective was to understand barriers to engagement in an online behavioral WLP among a racially diverse postpartum population with CV risk factors.

Methods: We conducted a qualitative study of participants enrolled in a clinical trial. We identified individuals who were 3-12 months postpartum, had a body mass index ≥ 27 kg/m2, and had ≥1 of the following: chronic hypertension, hypertensive disorder of pregnancy, gestational or pre-gestational diabetes. We randomized 60 subjects 1:2 to usual care or online WLP based on the Diabetes Prevention Program. We conducted semi-structured virtual interviews with participants in the WLP who completed final assessments to understand barriers to and facilitators of program engagement. Interviews were recorded and transcribed, a codebook was developed iteratively with concurrent interrater reliability assessment, and themes were identified using content analysis.

Results: Of 26 eligible participants, 20 completed interviews (77%). Mean age was 35 years and 45% were Black. Common barriers to program engagement were a lack of time due to competing life priorities and stressors, coupled with insufficient program personalization and peer support (see Table). In terms of facilitators, participants discussed intentionality, creating a routine to complete program requirements (e.g., daily morning weights) and specific aspects of the program structure (e.g., weekly feedback) as playing important roles in maximizing program engagement.

Conclusion: Participants identified several opportunities to improve program engagement and weight loss success among postpartum individuals in future studies. These strategies will be critical to the implementation of future lifestyle interventions using remote technology in this population.

Impact of an inpatient nurse-initiated penicillin allergy delabeling questionnaire

Penicillin allergy delabeling is an important component of antimicrobial stewardship and improves patient outcomes. We demonstrated the successful use of a nurse-initiated questionnaire to remove inappropriate penicillin allergy labels in inpatients. Nurses can play a key role in improving antibiotic allergy assessment and more broadly in interprofessional antimicrobial stewardship.

DNA looping by protamine follows a nonuniform spatial distribution

DNA looping plays an important role in cells in both regulating and protecting the genome. Often, studies of looping focus on looping by prokaryotic transcription factors like lac repressor or by structural maintenance of chromosomes proteins such as condensin. Here, however, we are interested in a different looping method whereby condensing agents (charge ≥+3) such as protamine proteins neutralize the DNA, causing it to form loops and toroids. We considered two previously proposed mechanisms for DNA looping by protamine. In the first mechanism, protamine stabilizes spontaneous DNA fluctuations, forming randomly distributed loops along the DNA. In the second mechanism, protamine binds and bends the DNA to form a loop, creating a distribution of loops that is biased by protamine binding. To differentiate between these mechanisms, we imaged both spontaneous and protamine-induced loops on short-length (≤1 μm) DNA fragments using atomic force microscopy. We then compared the spatial distribution of the loops to several model distributions. A random looping model, which describes the mechanism of spontaneous DNA folding, fit the distribution of spontaneous loops, but it did not fit the distribution of protamine-induced loops. Specifically, it failed to predict a peak in the spatial distribution of loops at an intermediate location along the DNA. An electrostatic multibinding model, which was created to mimic the bind-and-bend mechanism of protamine, was a better fit of the distribution of protamine-induced loops. In this model, multiple protamines bind to the DNA electrostatically within a particular region along the DNA to coordinate the formation of a loop. We speculate that these findings will impact our understanding of protamine’s in vivo role for looping DNA into toroids and the mechanism of DNA condensation by condensing agents more broadly.

Beige fat is dispensable for the metabolic benefits associated with myostatin deletion

OBJECTIVE

Increasing muscle mass and activating beige fat both have great potential for ameliorating obesity and its comorbidities. Myostatin null mice have increased skeletal muscle mass and are protected from obesity and its sequelae. Deletion of myostatin has also been suggested to result in the activation of beige adipocytes, thermogenic fat cells with anti-obesity and anti-diabetes properties. It is not known whether beige fat activation contributes to the protection from obesity in myostatin null mice.

METHODS

To investigate the role of beige fat activation in the metabolic benefits associated with myostatin deletion, we crossed myostatin null mice to adipocyte-specific PRDM16 knockout mice. We analyzed this new mouse model using molecular profiling, whole mount three-dimensional tissue imaging, tissue respiration, and glucose and insulin tolerance tests in models of diet-induced obesity.

RESULTS

Here, we report that PRDM16 is required for the activation of beige fat in the absence of myostatin. However, we show in both male and female mice that beige fat activation is dispensable for the protection from obesity, glucose intolerance, insulin resistance, and hepatic steatosis mediated by myostatin deletion.

CONCLUSION

These findings demonstrate that increasing muscle mass can compensate for the inactivation of beige fat and raise the possibility of targeting muscle mass as a therapeutic approach to offset the deleterious effects of adipose tissue dysfunction in obesity and metabolic syndrome.

Protamine loops DNA in multiple steps

Protamine proteins dramatically condense DNA in sperm to almost crystalline packing levels. Here, we measure the first step in the in vitro pathway, the folding of DNA into a single loop. Current models for DNA loop formation are one-step, all-or-nothing models with a looped state and an unlooped state. However, when we use a Tethered Particle Motion (TPM) assay to measure the dynamic, real-time looping of DNA by protamine, we observe the presence of multiple folded states that are long-lived (∼100 s) and reversible. In addition, we measure folding on DNA molecules that are too short to form loops. This suggests that protamine is using a multi-step process to loop the DNA rather than a one-step process. To visualize the DNA structures, we used an Atomic Force Microscopy (AFM) assay. We see that some folded DNA molecules are loops with a ∼10-nm radius and some of the folded molecules are partial loops—c-shapes or s-shapes—that have a radius of curvature of ∼10 nm. Further analysis of these structures suggest that protamine is bending the DNA to achieve this curvature rather than increasing the flexibility of the DNA. We therefore conclude that protamine loops DNA in multiple steps, bending it into a loop.