K, V. | bioRxiv Science

bioRxiv2024

The catabolic nature of fermentative substrates influence proteomic rewiring in Escherichia coli under anoxic growth

During anaerobic batch fermentation by Escherichia coli, there is a decline in cell proliferation rates and a huge demand is placed on cellular proteome to cater its catabolic and anabolic needs under anoxic growth. Previous studies have established a direct relationship between E. coli growth rate and cellular ribosomal content for fast proliferating cells. In this study, we integrated experimental findings with a systemic coarse-grained model of proteome allocation, to characterize the physiological outcomes at slow growth rate during anaerobic fermentative catabolism of different glycolytic and non-glycolytic substrates. The anaerobic catabolism of substrates favored high ribosomal abundances at lower growth rates. Interestingly, a modification of previously discussed "growth law", the ratio of active to inactive ribosomal proteome was found to be linearly related to growth rate for cells proliferating in slow to moderate regime (growth rate < 0.8 h-1). Also, under nutrient- and oxygen-limited growth conditions, the proteome proportion allocated for ribosomal activity was reduced, and resources were channelized towards catabolic and metabolic activities to overcome the limitations imposed while uptake and metabolizing substrate. The energy intensive uptake mechanism or lower substrate affinity, expended more catabolic proteome, which reduced its availability to other cellular functions. Conclusively, the nature of catabolic substrates imposed either uptake limitation or metabolic limitation coupled with ribosomal limitation (arising due to anoxic and nutritional stress), which resulted in higher proteome expenditure leading to sub-optimal phenotype.

systems biology↗

bioRxiv2024

Preferential binding of human BRCA1 protein with open X-like conformation of Holliday junction, a homologous recombination intermediate

BRCA1 is a complex tumor suppressor protein involved in multiple critical cellular processes, e.g., DNA double strand break repair, cell cycle checkpoint, etc. BRCA1 depleted cells are reported to have decreased homologous recombination (HR) and promote error-prone non-homologous end joining for DNA damage repair. Holliday junction (HJ) is an important intermediate of HR. Although BRCA1 is shown to have a very high affinity for HJ and recruits several proteins at the DNA damage site, the question remains what the binding mode of BRCA1 protein with an HJ is. Using single-molecule Fluorescence Correlation Spectroscopy (FCS) we have shown that BRCA1 prefers an open X-like conformation of HJ and has a lesser affinity for stacked HJ. Further, using molecular docking and all-atom molecular dynamics simulation, we show that mostly charged and polar amino acids in the DNA binding region of BRCA1 form complex with HJ. Interestingly, most of those amino acids are reported to be places for missense changes.

biophysics↗