Molecular and Cellular Mechanisms of Lipid Droplet Breakdown in the Liver of Chinese Soft-Shelled Turtle (Pelodiscus sinensis)

The Chinese soft-shelled turtle (Pelodiscus sinensis) is among the most primitive amphibians and reptiles in nature. On account of its environmental suitability and unique hibernation habit, the peculiar physiological phenomenon in P. sinensis attracted the attention of researchers in the field of marine science. The present study aimed to investigate the molecular mechanisms underlying the periodic variation of lipid droplet (LD) in the liver of P. sinensis. Histological results indicated that accumulated LD in the liver of P. sinensis during non-hibernation was gradually consumed during hibernation. RNA-Seq results revealed that genes responsible for carbohydrate catabolism were down-regulated during hibernation, while genes involved in lipid oxidation were up-regulated. These results suggest that energy metabolism in the liver of P. sinensis changes during hibernation, i.e., the energy generation mode shifted from carbohydrate catabolism to lipid oxidation. Further analysis of RNA-Seq results indicated that both lipolysis and autophagy could promote the degradation of hepatic LD during hibernation. To further determine the relationship between lipolysis and autophagy in the process of LD breakdown, we applied the inhibitors of lipolysis and autophagy (diethylumbelliferyl phosphate and 3-Methyladenine) in cultured primary hepatocytes of P. sinensis. The results indicated that lipolysis is the main way for LD degradation in the hepatocyte of P. sinensis. These data provide clear evidence about the seasonal changes in hepatocytes, corresponding with the different energy generation mode in the liver of P. sinensis.

Identification of Nitrogen Fixation Genes in Lactococcus Isolated from Maize Using Population Genomics and Machine Learning

Sierra Mixe maize is a landrace variety from Oaxaca, Mexico, that utilizes nitrogen derived from the atmosphere via an undefined nitrogen fixation mechanism. The diazotrophic microbiota associated with the plant’s mucilaginous aerial root exudate composed of complex carbohydrates was previously identified and characterized by our group where we found 23 lactococci capable of biological nitrogen fixation (BNF) without containing any of the proposed essential genes for this trait (nifHDKENB). To determine the genes in Lactococcus associated with this phenotype, we selected 70 lactococci from the dairy industry that are not known to be diazotrophic to conduct a comparative population genomic analysis. This showed that the diazotrophic lactococcal genomes were distinctly different from the dairy isolates. Examining the pangenome followed by genome-wide association study and machine learning identified genes with the functions needed for BNF in the maize isolates that were absent from the dairy isolates. Many of the putative genes received an ‘unknown’ annotation, which led to the domain analysis of the 135 homologs. This revealed genes with molecular functions needed for BNF, including mucilage carbohydrate catabolism, glycan-mediated host adhesion, iron/siderophore utilization, and oxidation/reduction control. This is the first report of this pathway in this organism to underpin BNF. Consequently, we proposed a model needed for BNF in lactococci that plausibly accounts for BNF in the absence of the nif operon in this organism.

The permeabilized SecY protein-translocation channel can serve as a nonspecific sugar transporter

As the initial step in carbohydrate catabolism in cells, the substrate-specific transporters via active transport and facilitated diffusion play a decisive role in passage of sugars through the plasma membrane into the cytoplasm. The SecY complex (SecYEG) in bacteria forms a membrane channel responsible for protein translocation. This work demonstrates that weakening the sealability of the SecY channel allowed free diffusion of sugars, including glucose, fructose, mannose, xylose, arabinose, and lactose, into the engineered cells, facilitating its rapid growth on a wide spectrum of monosaccharides and bypassing/reducing stereospecificity, transport saturation, competitive inhibition, and carbon catabolite repression (CCR), which are usually encountered with the specific sugar transporters. The SecY channel is structurally conserved in prokaryotes, thus it may be engineered to serve as a unique and universal transporter for bacteria to passage sugars as demonstrated inEscherichia coliandClostridium acetobutylicum.