Cao, L.-Y. | Search bioRxiv

bioRxiv2023

Hsa_circ_0005397 could promote hepatocellular carcinoma progression and metastasis through EIF4A3

PurposeThe purpose was to explore the expression and potential mechanism of hsa_circ_0005397 in hepatocellular carcinoma metabolism. MethodsThe quantitative real-time PCR (qPCR) was used to measure the expression of hsa_circ_0005397 and EIF4A3. The specificity of primers was confirmed by agarose gel electrophoresis. The ROC curve was draw to analysis clinical value. The actinomycin D assay and Nuclear and Cytoplasmic Extraction assay were utilized to evaluate the characteristic of hsa_circ_0005397. The CCK-8 and colony formation assays were performed to detect cell proliferation. The flow cytometry analysis was used to detect the cycle distribution. The transwell assays and Xenograft tumor model were conducted to explore cell metabolism. The RNA-binding proteins of hsa_circ_0005397 in HCC were explored in bioinformatics websites. The relationship between hsa_circ_0005397 and EIF4A3 was verified by RIP assays and rescue experiments. ResultsHsa_circ_0005397 and EIF4A3 were overexpressed in HCC. Through ROC analysis, hsa_circ_0005397 shown a big role in diagnosis and prognosis. Hsa_circ_0005397 was stable and almost distributed in the cytoplasm. The upregulation of hsa_circ_0005397 generally resulted in stronger proliferative ability, clonality, metastatic potency of HCC cells, while downregulation of hsa_circ_0005397 yielded opposite results. Tumor volume and size were notably reduced while downregulation of hsa_circ_0005397, showing significant difference in tumor growth. EIF4A3 was the RNA-binding protein of hsa_circ_0005397, the expression of hsa_circ_0005397 decreased equally when depletion of EIF4A3. Knockdown of EIF4A3 could reverse the function on HCC progression. ConclusionsHsa_circ_0005397 could promote the progression of hepatocellular carcinoma through EIF4A3. These research findings may present a novel clinical value for HCC.

cancer biology↗

bioRxiv2021

Exploration of molecular mechanism underlying the self-flocculation of Zymomonas mobilis through comparative omics analyses and experimental validations for developing robust production systems

Zymomonas mobilis metabolizes sugar through the Entner-Doudoroff pathway with less ATP generated for lower biomass accumulation and more substrate to product formation with improved yield, since ATP is dissipated predominately through growth for intracellular energy homeostasis, making it a platform to be engineered as microbial cell factories, particularly for producing bulk commodities with major cost from feedstock consumption. ZM401, a self-flocculating mutant, presents advantages for production including cost-effective biomass recovery through gravity sedimentation, self-immobilization within bioreactors for high cell density to improve productivity and enhanced tolerance to environmental stresses for high product titers, but molecular mechanism underlying this phenotype is largely unknown. In this work, we sequenced and assembled the genome of ZM401 to explore genetic basis for the self-flocculation of the bacterial cells through comparative genomic and transcriptomic analyses, molecular docking simulations for enzymes encoded by functional genes and their substrates/activators, and experimental validations. Our results demonstrated that the single nucleotide deletion in ZMO1082 disrupted its stop codon for the putative gene being fused with ZMO1083, which created an exciting gene encoding the subunit A of the bacterial cellulose synthase with unique function for synthesizing cellulose microfibrils to flocculate the bacterial cells, and the single nucleotide mutation in ZMO1055 compromised the function of bifunctional diguanylate cyclase/phosphodiesterase encoded by the gene on the degradation of c-di-GMP for its intracellular accumulation to activate the cellulose biosynthesis. These discoveries are significant not only for optimizing the self-flocculation of Z. mobilis, but also engineering other bacteria with the self-flocculating phenotype for robust production.

microbiology↗