chen, Y. | bioRxiv Science

bioRxiv2025

Deconvolution to restore cryo-EM maps with anisotropic resolution

With technological advancements in recent years, single particle cryogenic electron microscopy (cryo-EM) has become a major methodology for structural biology. Structure determination by single particle cryo-EM is premised on randomly orientated particles embedded in a thin layer of vitreous ice to resolve high-resolution structure in all directions. In practice, preferentially distributed particle orientations and/or other imperfections in imaging and data processing deteriorate quality of obtained cryo-EM map. Here we present a deconvolution approach, named AR-Decon, that computationally improves the quality of cryo-EM maps. We tested and validated the procedure, compared its performance with that of machine learning based density modification method, and benchmarked its performance with a wide range of deposited maps. Our results show that AR-Decon is robust and is a generally applicable post-processing procedure for single particle cryo-EM.

biophysics↗

bioRxiv2023

High-level production of nervonic acid in the oleaginous yeast Yarrowia lipolytica by systematic metabolic engineering

Brain and neurological diseases are influencing more than one billion worlds people. Nervonic acid (cis-15-tetracosenoic acid, C24:1 {Delta}15) benefits the treatment of neurological diseases and the health of brain. Currently, the sources of nervonic acid are limited to the seeds of a couple of plants. In this study, we employed the oleaginous yeast Yarrowia lipolytica to overproduce nervonic acid oil by systematic metabolic engineering. First, engineering the fatty acid elongation (FAE) pathway by expressing a heterologous {beta}-ketoacyl-CoA synthase gene CgKCS enabled the production of nervonic acid in Y. lipolytica. Second, modulation of endogenous pathways by expressing a C16:0-acyl-CoA preferred fatty acid elongase gELOVL6 together with a C18:0-acyl-CoA preferred fatty acid desaturase MaOLE2 increased the content of nervonic acid in total fatty acids (TFA). Third, iterative expression of CgKCS, gELOVL6 and MaOLE2 at the genomic loci of rDNA, FAD2, TGL4, GSY1 and SNF1 dramatically improved the production of nervonic acid. Fourth, the biosynthesis of both nervonic acid and lipids were further enhanced by expression of the MaOLE2-CgKCS fusion protein and glycerol-3-phosphate acyltransferases (GPAT) and diacylglycerol acyltransferases (DGAT) from Malania oleifera in the endoplasmic reticulum (ER) membrane. Fifth, an ER structure regulator YlINO2 was identified in Y. lipolytica and the overexpression of YlINO2 led to a 39.3% increase in lipid production. Next, pilot-scale fermentation in 50-L reactor using the strain YLNA9 exhibited a lipid titer of 96.7 g/L and a nervonic acid titer of 17.3 g/L, the highest reported titer to date for de novo nervonic acid production. We also found that disruption of the AMP-activated S/T protein kinase SNF1 increased the ratio of nervonic acid (C24:1) to lignoceric acid (C24:0) by 61.6% and a ratio of 3.5:1 (nervonic acid to lignoceric acid) was achieved in the strain YLNA10. Finally, a proof-of-concept purification and separation of nervonic acid were performed and the purity of it reached 98.7%. This study suggested that oleaginous yeasts are attractive hosts for the cost-efficient production of nervonic acid and possibly other very long-chain fatty acids (VLCFAs).

bioengineering↗