Search for: All records

Abstract While most studies of biomolecular phase separation have focused on the condensed phase, relatively little is known about the dilute phase. Theory suggests that stable complexes form in the dilute phase of two-component phase-separating systems, impacting phase separation; however, these complexes have not been interrogated experimentally. We show that such complexes indeed exist, using an in vitro reconstitution system of a phase-separated organelle, the algal pyrenoid, consisting of purified proteins Rubisco and EPYC1. Applying fluorescence correlation spectroscopy (FCS) to measure diffusion coefficients, we found that complexes form in the dilute phase with or without condensates present. The majority of these complexes contain exactly one Rubisco molecule. Additionally, we developed a simple analytical model which recapitulates experimental findings and provides molecular insights into the dilute phase organization. Thus, our results demonstrate the existence of protein complexes in the dilute phase, which could play important roles in the stability, dynamics, and regulation of condensates. 

Pump-probe microscopy of melanin in tumors has been proposed to improve diagnosis of malignant melanoma, based on the hypothesis that aggressive cancers disaggregate melanin structure. However, measured signals of melanin are complex superpositions of multiple nonlinear processes, which makes interpretation challenging. Polarization control during measurement and data fitting are used to decompose signals of melanin into their underlying molecular mechanisms. We then identify the molecular mechanisms that are most susceptible to melanin disaggregation and derive false-coloring schemes to highlight these processes in biological tissue. We demonstrate that false-colored images of a small set of melanoma tumors correlate with clinical concern. More generally, our systematic approach of decomposing pump-probe signals can be applied to a multitude of different samples.

 

Many eukaryotic photosynthetic organisms enhance their carbon uptake by supplying concentrated CO₂to the CO₂-fixing enzyme Rubisco in an organelle called the pyrenoid. Ongoing efforts seek to engineer this pyrenoid-based CO₂-concentrating mechanism (PCCM) into crops to increase yields. Here we develop a computational model for a PCCM on the basis of the postulated mechanism in the green algaChlamydomonas reinhardtii. Our model recapitulates allChlamydomonasPCCM-deficient mutant phenotypes and yields general biophysical principles underlying the PCCM. We show that an effective and energetically efficient PCCM requires a physical barrier to reduce pyrenoid CO₂leakage, as well as proper enzyme localization to reduce futile cycling between CO₂and HCO₃⁻. Importantly, our model demonstrates the feasibility of a purely passive CO₂uptake strategy at air-level CO₂, while active HCO₃⁻uptake proves advantageous at lower CO₂levels. We propose a four-step engineering path to increase the rate of CO₂fixation in the plant chloroplast up to threefold at a theoretical cost of only 1.3 ATP per CO₂fixed, thereby offering a framework to guide the engineering of a PCCM into land plants.

 

Biogenic volatile organic compounds (VOCs) play crucial roles in ecosystems at multiple scales, ranging from mediating soil microbial interactions to contributing to atmospheric chemistry. However, soil VOCs and how they respond to environmental change remains understudied. We aimed to assess how 2 abiotic global change drivers, soil warming and simulated nitrogen (N) deposition, impact soil VOC emissions over time in a temperate forest. We characterized the effect of warming, N deposition, and their interaction on the composition and emissions of soil VOCs during the growing season of 2 consecutive years. We found that chronic warming and N deposition enhanced total VOC emissions at certain times of the year (as high as 332.78 µg m–2 h–1), but that overall VOC composition was not strongly affected by these global change treatments. However, certain compounds, particularly sesquiterpenoids and alkanes, were sensitive to these treatments, with their emissions increasing under both chronic warming and N deposition. Moreover, specific signature VOCs—α-pinene, β-thujone, β-caryophyllene, and 2,4-dimethylheptane—were consistently found under chronic warming and N deposition. This suggests that emissions of specific VOC classes/compounds may increase under global change.