BackgroundPhenolic aldehydes generated from lignocellulose pretreatment exhibited severe toxic inhibitions on microbial growth and fermentation. Numerous tolerance studies against furfural, 5-hydroxymethyl-2-furaldehyde (HMF), acetate, and ethanol were reported, but studies on inhibition of phenolic aldehyde inhibitors are rare. For ethanologenic strains, Zymomonas mobilis ZM4 is high in ethanol productivity and genetic manipulation feasibility, but sensitive to phenolic aldehyde inhibitors. Molecular mechanisms of tolerance for Z. mobilis toward phenolic aldehydes are not known.ResultsWe took the first insight into genomic response of Z. mobilis ZM4 to the phenolic aldehyde inhibitors derived from lignocellulose pretreatment. The results suggest that the toxicity to cells is caused by the functional group of phenolic aldehyde, similar to furfural and HMF, rather than aromatic groups or phenolic hydroxyl groups. Transcriptome response against 4-hydroxybenzaldehyde, syringaldehyde, and vanillin, representing phenolic groups H, S, and G, respectively, was investigated. The atlas of the important genes responsible for significantly enhanced and repressed genes at the genomic level was illustrated. 272 genes with twofold greater expressions than non-treated controls and 36 gene clusters in response to challenges of these phenolic aldehydes were identified. Several reductases encoded by ZMO1116, ZMO1696, and ZMO1885 were found to play the key roles in reducing phenolic aldehydes into the corresponding phenolic alcohols. Reduction of phenolic aldehydes by overexpression of ZMO1116, ZMO1696, and ZMO1885 in Z. mobilis ZM4 resulted in the increased inhibitor conversion and ethanol productivity, especially for 4-hydroxybenzaldehyde and vanillin. Several transporter genes such as ZMO0282, ZMO0283, ZMO0798, ZMO0799, and ZMO0800 was also displayed significantly increased expressions against the phenolic aldehydes.ConclusionsThe genes encoding reductases are with potentials on phenolic aldehydes-tolerant genes contributing to the reduction of phenolic aldehydes into the corresponding phenolic alcohols forms for Z. mobilis ZM4. Overexpression of the key genes improved the conversion ratio and ethanol productivity of 4-hydroxybenzaldehyde and vanillin with high toxicity. New knowledge obtained from this research aids understanding the mechanisms of bacterial tolerance and the development of the next-generation biocatalysts for advanced biofuels production.Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-015-0333-9) contains supplementary material, which is available to authorized users.

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Adipogenesis, a physiological process initiated with the committed preadipocytes expressing adipocyte-specific genes and terminated in mature, differentiated and functional adipocytes, mainly involved with energy homeostasis. Abnormal distributionchanges and dysfunctions in adipogenesis may lead to complex physiopathological disorders. However, it remains unclear for the key players working for the whole complex differentiating process of adipogenesis. Here, it investigated transcriptional profiling of adipogenesis from human mesenchymal stem cells (hMSCs) by RNA-Seq transcriptome technique. Oil Red O staining assays were performed to assess adipogenic potential.Quantitative real-time PCR (qRT-PCR) and lentivirus transfection assays by small interference RNA (siRNA) were conducted to confirm the function of the candidate genes. A total of 1,078 differentially expressed genes shared at 7, 14, 21, and 28 days during adipogenesis from hMSCs, and 706 genes were significantly differentially expressed. It identified 20 potential key genes responsible for adipogenesis with four genes downregulating. The candidate gene, coagulation factor II thrombin receptor (F2R), encoding coagulation factor II thrombin receptor involving with a 7-transmembrane receptor involved in the regulation of thrombotic response, also known as proteinaseactivated receptor-1, contributed to adipogenesis, especially at Day 14, by Oil Red O staining, qRT-PCR, and western blot after siRNA. A unique discovery shed new light to understand the key players of the whole processes of adipogenesis from hMSCs. The gene F2R might be used as an adipogenic marker to provide a potential target for understanding the metabolic syndromes like obesity, type-2 diabetes, steatosis, atherosclerosis, and osteoporosis.

Background Fast, complete, and ultimate removal of inhibitory compounds derived from lignocellulose pretreatment is the prerequisite for efficient production of cellulosic ethanol and biochemicals. Biodetoxification is the most promising method for inhibitor removal by its unique advantages. The biodetoxification mechanisms of a unique diploid fungus responsible for highly efficient biodetoxification in solid-state culture was extensively investigated in the aspects of cellular structure, genome sequencing, transcriptome analysis, and practical biodetoxification. Results The inborn heterozygous diploid structure of A. resinae ZN1 uniquely contributed to the enhancement of inhibitor tolerance and conversion. The co-expression of gene pairs contributed to the enhancement of the degradation of lignocellulose-derived model inhibitors. The ultimate inhibitors degradation pathways and sugar conservation were elucidated by microbial degradation experimentation as well as the genomic and transcriptomic sequencing analysis. Conclusions The finding of the heterozygous diploid structure in A. resinae ZN1 on biodetoxification took the first insight into the global overview of biodetoxification mechanism of lignocellulose-derived inhibitors. This study provided a unique and practical biodetoxification biocatalyst of inhibitor compounds for lignocellulose biorefinery processing, as well as the synthetic biology tools on biodetoxification of biorefinery fermenting strains. Electronic supplementary material The online version of this article (10.1186/s13068-019-1466-z) contains supplementary material, which is available to authorized users.

MicroRNAs (miRNAs), the potential regulator of adipogenesis, markedly characterized by lipid droplet (LD) formation, play an important role in progenitor-cell differentiation into adipocytes. In recent years, it has excited interests in regulation of miRNAs in adipogenesis. However, no study is available, to our knowledge, regarding the expression of miRNAs on LD formation. Our study provides the first insight into the expression profiling of the miRNA targeting messenger RNAs (mRNAs) involving with LD formation during adipogenesis from human mesenchymal stem cells by RNA-Seq transcriptome technique. It showed that 39, 105, 194, and 112 differentially expressed miRNA appeared at 7, 14, 21, and 28 days, respectively, for LD formation during adipogenesis. Nineteen miRNAs targeted 35 mRNA associated with LDs formation.Except for the known miRNA hsa-miR-1908 regulating adipogenesis, five miRNAs, including hsa-miR-146a-3p, hsa-miR-4495, hsa-miR-4663, hsa-miR-6069, and hsa-miR-675-3p are the latest potential biomarkers for LD formation, targeting ACSL1, APOB, METTL7A, PLIN1, and PLIN4. A comprehensive transcriptome profiling of miRNA reveals the regulatory relationship between miRNA and mRNA relating to LD formation during adipogenesis. Such candidates may represent biomarkers and therapeutic targets for metabolic syndromes like obesity, type-2 diabetes, steatosis, atherosclerosis, and osteoporosis. K E Y W O R D S adipogenesis, hMSCs, lipid droplets, miRNA

Metabolism homeostasis plays an important role in progenitor-cell differentiation to adipocytes, but less is known about the whole transcriptional profiling of cellular metabolism during adipogenesis. We got the first insight into the whole transcriptional profiling of cellular metabolism during adipogenesis from human mesenchymal stem cells (hMSCs) by the RNA-Seq technique. There were 1,998, 2,629, 3,112, and 3,054 differentially expressed genes (DEGs) at Days 7, 14, 21, and 28, respectively, during adipogenesis. The most enriched phosphatidylinositol 3′ kinase-serine/threonine kinase (PI3K-Akt) signaling pathway stimulated and directly regulated cellular metabolism by priming glucose aerobic glycolysis, arginine and proline metabolism, glutathione metabolism, and arachidonic acid metabolism during adipogenesis, targeting the potential key genes, such as fatty acid synthase (FABP4), phosphoenolpyruvate carboxykinase 1 (PKC1), stearoyl-CoA desaturase (SCD), and solute carrier family 2 member 1 of Gluts (SLC2A1). And it confirmed PCK1 as the key player for cellular metabolism by small interfering RNA. A comprehensive understanding of cellular metabolism and its regulatory axis of the signaling pathway during adipogenesis would reveal new study and therapy targets for fat metabolism disorders. K E Y W O R D S adipogenesis, amino acid metabolism, fatty acid metabolism, glucose metabolism, lipid droplets, PI3K-Akt signaling pathway SUPPORTING INFORMATION Additional supporting information may be found online in the Supporting Information section.How to cite this article: Yi X, Liu J, Wu P, Gong Y, Xu X, Li W.The whole transcriptional profiling of cellular metabolism during adipogenesis from hMSCs.

Adipogenesis, the developmental process of progenitor-cell differentiating into adipocytes, leads to fat metabolic disorders. Alternative splicing (AS), a ubiquitous regulatory mechanism of gene expression, allows the generation of more than one unique messenger RNA (mRNA) species from a single gene. Till now, alternative splicing events during adipogenesis from human mesenchymal stem cells (hMSCs) are not yet fully elucidated. We performed RNA-Seq coupled with bioinformatics analysis to identify the differentially expressed AS genes and events during adipogenesis from hMSCs. A global survey separately identified 1262, 1181, 1167, and 1227 ASE involved in the most common types of AS including cassette exon, alt3, and alt5, especially with cassette exon the most prevalent, at 7, 14, 21, and 28 days during adipogenesis. Interestingly, 122 differentially expressed ASE referred to 118 genes, and the three genes including ACTN1 (alt3 and cassette), LRP1 (alt3 and alt5), and LTBP4 (cassette, cassette_multi, and unknown), appeared in multiple AS types of ASE during adipogenesis. Except for all the identified ASE of LRP1 occurred in the extracellular topological domain, alt3 (84) in transmembrane domain significantly differentially expressed was the potential key event during adipogenesis. Overall, we have, for the first time, conducted the global transcriptional profiling during adipogenesis of hMSCs to identify differentially expressed ASE and ASE-related genes. This finding would provide extensive ASE as the regulator of adipogenesis and the potential targets for future molecular research into adipogenesis-related metabolic disorders.

Adipogenesis and osteoblastogenesis (adipo-osteoblastogenesis) are closely related processes involving with the phosphorylation of numerous cytoplasmic proteins and key transcription factors.