Comparative Transcriptome Analysis Revealed Genes Involved in Sexual and Polyploid Growth Dimorphisms in Loach (Misgurnus anguillicaudatus)

Sexual and polyploidy size dimorphisms are widespread phenomena in fish, but the molecular mechanisms remain unclear. Loach (Misgurnus anguillicaudatus) displays both sexual and polyploid growth dimorphism phenomena, and are therefore ideal models to study these two phenomena. In this study, RNA-seq was used for the first time to explore the differentially expressed genes (DEGs) between both sexes of diploid and tetraploid loaches in four tissues (brain, gonad, liver, and muscle). Results showed that 21,003, 17, and 1 DEGs were identified in gonad, liver, and muscle tissues, respectively, between females and males in both diploids and tetraploids. Regarding the ploidy levels, 4956, 1496, 2187, and 1726 DEGs were identified in the brain, gonad, liver, and muscle tissues, respectively, between tetraploids and diploids of the same sex. When both sexual and polyploid size dimorphisms were considered simultaneously in the four tissues, only 424 DEGs were found in the gonads, indicating that these gonadal DEGs may play an important regulatory role in regulating sexual and polyploid size dimorphisms. Regardless of the sex or ploidy comparison, the significant DEGs involved in glycolysis/gluconeogenesis and oxidative phosphorylation pathways were upregulated in faster-growing individuals, while steroid hormone biosynthesis-related genes and fatty acid degradation and elongation-related genes were downregulated. This suggests that fast-growing loaches (tetraploids, females) have higher energy metabolism levels and lower steroid hormone synthesis and fatty acid degradation abilities than slow-growing loaches (diploids, males). Our findings provide an archive for future systematic research on fish sexual and polyploid dimorphisms.

A Label-Free Proteomic Strategy to Investigate the Intramuscular fat Proteomic Differences Between Biceps Femoris and Longissimus Dorsi in Inner Mongolian Cashmere Goats

Background: As a major raw-cashmere-producing province in China. Nearly 700,000 Aerbasi cashmere goats are fed per year, and the corresponding meat production is nearly 10,000 tons. However, there are no reports on the meat of this goat. To better understand the molecular variations underlying intramuscular fat (IMF) anabolism and catabolism in Inner Mongolian cashmere goats, the proteomic differences between the biceps femoris (BF) and longissimus dorsi (LD) were investigated by a label-free strategy. Then, the identified proteins were verified as being involved in IMF anabolism and catabolism by Western blot analysis.Results: The IMF content was significantly higher in the BF than in the LD, suggesting that IMF accumulated more in the BF or was metabolized more in the LD. We performed proteomic analysis of IMF anabolism and catabolism at the proteomic level, and 1209 proteins were identified in the BF (high-IMF) and LD (low-IMF) groups. Among them, 110 were differentially expressed proteins (DEPs), 81 of which were upregulated in the high-IMF group, while 29 were upregulated in the low-IMF group. Gene ontology (GO) classification showed that the 110 DEPs were functionally classified into 100 annotation clusters. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the 110 DEPs covered 34 KEGG pathways. Three pathways were related to IMF metabolism and deposition—fatty acid metabolism, fatty acid degradation and fatty acid elongation—and included 7 proteins.Conclusion: GO and KEGG analyses showed that differentially expressed HADHA, HADHB, ACSL1, ACADS, ACAT1 and ACAA2 in the mitochondria act via fatty acid metabolism, fatty acid degradation and fatty acid elongation to influence the metabolism and synthesis of long-, short- and medium-chain fatty acids and modulate IMF anabolism and catabolism. Protein-protein interaction (PPI) network analysis showed that IMF accumulation in different muscle tissues of Inner Mongolian cashmere goats was affected not only by 5 key enzymes and proteins involved in fatty acid synthesis and metabolism but also by five DEPs (SUCLG1, SUCLG2, CS, DLST, and ACO2) in the TCA cycle. Our results provide new insights into IMF deposition in goats and improve our understanding of the molecular mechanisms underlying IMF anabolism and catabolism.

Expanded roles of pyruvate-sensing PdhR in transcription regulation of the Escherichia coli K-12 genome: fatty acid catabolism and cell motility

The transcription factor PdhR has been recognized as the master regulator of the pyruvate catabolism pathway in Escherichia coli , including both NAD-linked oxidative decarboxylation of pyruvate to acetyl-CoA by PDHc (pyruvate dehydrogenase complex) and respiratory electron transport of NADH to oxygen by Ndh-CyoABCD enzymes. To identify the whole set of regulatory targets under the control of pyruvate-sensing PdhR, we performed genomic SELEX (gSELEX) screening in vitro. A total of 35 PdhR-binding sites were identified along the E. coli K-12 genome, including previously identified targets. Possible involvement of PdhR in regulation of the newly identified target genes was analysed in detail by gel shift assay, RT-qPCR and Northern blot analysis. The results indicated the participation of PdhR in positive regulation of fatty acid degradation genes and negative regulation of cell mobility genes. In fact, GC analysis indicated an increase in free fatty acids in the mutant lacking PdhR. We propose that PdhR is a bifunctional global regulator for control of a total of 16–23 targets, including not only the genes involved in central carbon metabolism but also some genes for the surrounding pyruvate-sensing cellular pathways such as fatty acid degradation and flagella formation. The activity of PdhR is controlled by pyruvate, the key node between a wide variety of metabolic pathways, including generation of metabolic energy and cell building blocks.

Transcriptomic Analysis of Fuzi Lizhong Decoction for the Treatment of Stomach Ulcers

This study aims to understand the treatment of stomach ulcers with FLD and to identify its potential target genes as well as related pathways by transcriptomic analysis. Rat stomach mRNA from a blank group (BG), a model group (MG), an untreated-model group (u-MG), and a treated group (TG) was sequenced. A partial least-squares discriminant analysis (PLS-DA) was used to differentiate the MG from the BG, and the Deseq2 R Package was used to identify differentially expressed genes between these groups. Furthermore, t-tests based on transcripts per million (TPM) were used to select different genes between MG and BG and significantly retrieved genes in TG, except for self-retrieved genes in u-MG. Finally, pathways regulated by retrieved genes were analyzed with KEGG database. Results showed that 327 of the 32,623 total detected genes were different (p<0.05) between the MG and BG. Among these genes, eighteen genes were significantly retrieved after rats were treated with FLD in TG, and they were considered as target genes on which FLD acted. In conclusion, FLD was deduced to cure stomach ulcers by affecting glycerolipid metabolism, fatty acid degradation, circadian entrainment, circadian rhythm, and dopaminergic synapse.