Identification of sitagliptin binding proteins by affinity purification mass spectrometry

Fat-tail allele-specific expression genes may affect fat deposition in tail of sheep

Different sheep breeds show distinct phenotypic plasticity in fat deposition in the tails. The genetic background underlying fat deposition in the tail of sheep is complex, multifactorial, and may involve allele-specific expression (ASE) mechanism to modulate allelic expression. ASE is a common phenomenon in mammals and refers to allelic imbalanced expression modified by cis-regulatory genetic variants that can be observed at heterozygous loci. Therefore, regulatory processes behind the fat-tail formation in sheep may be to some extent explained by cis- regulatory variants, through ASE mechanism, which was investigated in the present study. An RNA-Seq-based variant calling was applied to perform genome-wide survey of ASE genes using 45 samples from seven independent studies comparing the transcriptome of fat-tail tissue between fat- and thin-tailed sheep breeds. Using a rigorous computational pipeline, 115 differential ASE genes were identified, which were narrowed down to four genes (LPL, SOD3, TCP1 and LRPAP1) for being detected in at least two studies. Functional analysis revealed that the ASE genes were mainly involved in fat metabolism. Of these, LPL was of greater importance, as 1) observed in five studies, 2) reported as ASE gene in the previous studies and 3) with a known role in fat deposition. Our findings implied that complex physiological traits, like fat-tail formation, can be better explained by considering various genetic mechanisms, which can be more finely mapped through ASE analyses. The insights gained in this study indicate that biallelic expression may not be a common mechanism in sheep fat-tail development. Hence, allelic imbalance of the fat deposition-related genes can be considered a novel layer of information for future research on genetic improvement and increased efficiency in sheep breeding programs.

Biochemical profiling of the protein encoded by grass carp reovirus genotype II

In this study, we obtained the whole genome sequence of GCRV-DY197 and investigated the localization, post-translational modifications, and host interactions of the 11 viral proteins encoded by GCRV-DY197 in grass carp ovary (GCO) cells. The whole genome sequence is 24,704 kb and contains 11 segments (S1-S11). Subcellular localization showed that the VP1, VP2, VP3, VP5, VP56, and VP35 proteins were localized in both cytoplasm and nucleus, whereas the NS79, VP4, VP41, VP6, and NS38 proteins were localized in the cytoplasm. The NS79 and NS38 proteins were phosphorylated, and the ubiquitination modification sites were identified in VP41 and NS38. An interaction network containing 9 viral proteins and 140 host proteins was also constructed. These results offer a theoretical basis for an in-depth understanding of the biochemical characteristics and pathogenic mechanism of GCRV-II.

Unraveling the enigma: Molecular mechanisms of berberrubine-induced nephrotoxicity reversed by its parent form berberine

BACKGROUND

Berberine is an isoquinoline alkaloid that is extensively applied in the clinic due to its potential therapeutic effects on dysentery and infectious diarrhoea. Its main metabolite, berberrubine, a promising candidate for ameliorating hyperlipidaemia, has garnered more attention than berberine. However, our study revealed that berberrubine induces severe kidney damage, while berberine was proven to be safe.

PURPOSE

Herein, we explored the opposite biological effects of these two compounds on the kidney and elucidated their underlying mechanisms.

METHODS

First, integrated metabolomic and proteomic analyses were conducted to identify relevant signalling pathways. Second, a click chemistry method combined with a cellular thermal shiftassay, a drug affinity responsive target stability assay, and microscale thermophoresis were used to identify the direct target proteins. Moreover, a mutation experiment was performed to study the specific binding sites.

RESULTS

Animal studies showed that berberrubine, but not berberine, induced severe chronic, subchronic, and acute nephrotoxicity. More importantly, berberine reversed the berberrubine-reduced nephrotoxicity. The results indicated that the cPLA2 signalling pathway was highly involved in the nephrotoxicity induced by berberrubine. We further confirmed that the direct target of berberrubine is the BASP1 protein (an upstream factor of cPLA2 signalling). Moreover, berberine alleviated nephrotoxicity by binding cPLA2 and inhibiting cPLA2 activation.

CONCLUSION

This study is the first to revel the opposite biological effects of berberine and its metabolite berberrubine in inducing kidney injury. Berberrubine, but not berberine, shows strong nephrotoxicity. The cPLA2 signalling pathway can be activated by berberrubine through targeting of BASP1, while berberine inhibits this pathway by directly binding with cPLA2. Our study paves the way for studies on the exact molecular targets of herbal ingredients. We also demonstrated that natural small molecules and their active metabolites can have opposite regulatory roles in vivo through the same signalling pathway.

A genome-wide association study identifies 25(OH)D3-associated genetic variants in the prediabetic Chinese population

OBJECTIVES

Diabetes mellitus has been a significant public health problem, associated with high rates of morbidity, disability, and mortality. Prediabetes is a crucial period for preventing and managing diabetes. 25(OH)D3 is an important risk factor for prediabetes. However, there is limited genetic knowledge of 25(OH)D3 in the Chinese population. This study was designed to identify genetic variants associated with 25(OH)D3 and explore the potential pathogenesis of prediabetes.

METHODS

In this study, 451 individuals with prediabetes were recruited to determine the genetic variants associated with 25(OH)D3 through a genome-wide association study (GWAS). Gene mapping and overrepresentation analysis (ORA) were further performed to explore the candidate genes and their biological mechanisms.

RESULTS

In this study, we identified two independent significant loci (rs9457733 and rs11243373, p < 5 × 10-6 and r2 < 0.6) and 37 candidate genes associated with 25(OH)D3 in prediabetes. Furthermore, the ORA analysis revealed that two genes in the gene sets, SLC22A1 and SLC22A3, were found to be significantly enriched in monoamine transmembrane transporter activity and quaternary ammonium group transmembrane transporter activity, as determined by WebGestalt and g:Profiler (padj < 0.05).

CONCLUSION

The identification of potential genes associated with 25(OH)D3 provides a foundation for a better understanding of the pathogenesis, diagnosis, and treatment of prediabetes.