Global analysis of protein lysine 2-hydroxyisobutyrylation (Khib) profiles in Chinese herb rhubarb (Dahuang).

BACKGROUND: Lysine 2-hydroxyisobutyrylation (Khib) is a newly discovered protein posttranslational modification (PTM) and is involved in the broad-spectrum regulation of cellular processes that are found in both prokaryotic and eukaryotic cells, including in plants. The Chinese herb rhubarb (Dahuang) is one of the most widely used traditional Chinese medicines in clinical applications. To better understand the physiological activities and mechanism of treating diseases with the herb, it is necessary to conduct intensive research on rhubarb. However, Khib modification has not been reported thus far in rhubarb. RESULTS: In this study, we performed the first global analysis of Khib-modified proteins in rhubarb by using sensitive affinity enrichment combined with high-accuracy HPLC-MS/MS tandem spectrometry. A total of 4333 overlapping Khib modification peptides matched on 1525 Khib-containing proteins were identified in three independent tests. Bioinformatics analysis showed that these Khib-containing proteins are involved in a wide range of cellular processes, particularly in protein biosynthesis and central carbon metabolism and are distributed mainly in chloroplasts, cytoplasm, nucleus and mitochondria. In addition, the amino acid sequence motif analysis showed that a negatively charged side chain residue (E), a positively charged residue (K), and an uncharged residue with the smallest side chain (G) were strongly preferred around the Khib site, and a total of 13 Khib modification motifs were identified. These identified motifs can be classified into three motif patterns, and some motif patterns are unique to rhubarb and have not been identified in other plants to date. CONCLUSIONS: A total of 4333 Khib-modified peptides on 1525 proteins were identified. The Khib-modified proteins are mainly distributed in the chloroplast, cytoplasm, nucleus and mitochondria, and involved in a wide range of cellular processes. Moreover, three types of amino acid sequence motif patterns, including EKhib/KhibE, GKhib and k.kkk….Khib….kkkkk, were extracted from a total of 13 Khib-modified peptides. This study provides comprehensive Khib-proteome resource of rhubarb. The findings from the study contribute to a better understanding of the physiological roles of Khib modification, and the Khib proteome data will facilitate further investigations of the roles and mechanisms of Khib modification in rhubarb.

The Microstructure, Proteomics and Crystallization of the Limpet Teeth.

Limpets are marine mollusks that use mineralized teeth, one of the hardest and strongest biomaterials, to feed on algae on intertidal rocks. However, most of studies only focus on the ultrastructure and chemical composition of the teeth while the molecular information is largely unknown, limiting our understanding of this unique and fundamental biomineralization process. The study investigates the microstructure, proteomics, and crystallization in the teeth of limpet Cellana toreuma. It is found that the limpets formed alternatively tricuspid teeth and unicuspid teeth. Small nanoneedles are densely packed at the tips or leading regions of the cusps. In contrast, big nanoneedles resembling chemically synthesized goethite are loosely packed in the trailing regions of the cusps. Proteins extracted from the whole radula, such as ferritin, peroxiredoxin, arginine kinase, GTPase-Rabs, and clathrin, are identified by proteomics. A goethite-binding experiment coupled with proteomics and RNA-seq highlights six chitin-binding proteins (CtCBPs). Furthermore, the extracted proteins from the cusps of radula or the framework chitin induce packing of crystals and possibly affect crystal polymorphs in vitro. This study provides insight into the unique biomineralization process in the limpet teeth at the molecular levels, which may guide biomimetic strategies aimed at designing hard materials at room temperature.

Effects of Environmental Organic Pollutants on Environment and Human Health: The Latest Updates.

This editorial introduces the Special Issue "Effects of Environmental Organic Pollutants on Environment and Human Health: The Latest Updates" [...].

Chinese Technical Guideline for Deriving Water Quality Criteria for Protection of Freshwater Organisms.

In recent years, China has determined the national goal of "developing national environmental criteria", thereby promoting the rapid development of environmental quality criteria research in China. In 2017, the Ministry of Ecology and Environment of China (MEEC, formerly the Ministry of Environmental Protection of China) issued the technical guideline for deriving water quality criteria (WQC) for protection of freshwater organisms (HJ 831-2017), and in 2022, they organized the guideline revision and issued an updated version (HJ 831-2022). The primary contents of the revision included the following. The minimum toxicity data requirements were upgraded from 6 to 10, and the species mean toxicity value was replaced by the same effect toxicity value for the criteria calculation. It is now required that the tested organisms must be distributed in China's natural fresh waters, and the toxicity data of non-native model species will no longer be used. The list of freshwater invasive species in China that cannot be used as test species was added into the guideline. The acute/chronic ratio (ACR) method for the criteria derivation and the extreme value model were deleted, and the provisions for testing the toxicity data distribution were also deleted. The exposure time of the toxicity test of various tested organisms was refined, and the priority of the toxicity data was clearly specified. This paper introduces the framework and specific technical requirements of HJ 831-2022 in detail, including data collection, pre-processing of toxicity data, criteria derivation, fitting models, and quality control. This introduction is helpful for international peers to understand the latest research progress of China's WQC.

Impairment of the gut health in Danio rerio exposed to triclocarban.

Triclocarban (TCC) is the principal component in personal and health care products because it is a highly effective, broad-spectrum, and safe antibacterial agent. TCC has recently been discovered in aquatic creatures and has been shown to constitute a health danger to aquatic animals. Although several studies have looked into the toxicological effects of TCC on a variety of aquatic animals from algae to fish, the possible gut-toxicity molecular pathway in zebrafish has never been thoroughly explored. We investigated the gut-toxic effects of TCC on zebrafish by exposing them to different TCC concentrations (100 and 1000 µg/L) for 21 days. We discovered for the first time that the MAPK and TLR signaling pathways related to gut diseases were significantly altered, and inflammation (up-regulation of TNF-α, IL-6, and IL-1ß) caused by TCC was confirmed to be largely mediated by the aryl hydrocarbon receptor (AHR) and its related cytokines. This was found using the results of qPCR, a transcriptome analysis, and molecular docking (AHR, AHRR, CYP1A1 and CYP1B1). Furthermore, high-throughput 16S rDNA sequencing demonstrated that TCC exposure reduced the bacterial diversity and changed the gut microbial composition, with the primary phyla Fusobacteria and Proteobacteria, as well as the genera Cetobacterium and Rhodobacteraceae, being the most affected. TCC exposure also caused damage to the gut tissue, including an increase in the number of goblet cells and a reduction in the height of the columnar epithelium and the thickness of the muscular layer, as shown by hematoxylin and eosin staining. Our findings will aid in understanding of the mechanism TCC-induced aquatic toxicity in aquatic species.

fam20C participates in the shell formation in the pearl oyster, Pinctada fucata.

Kinase-family with sequence similarity 20, member C (Fam20C) is a protein kinase, which can phosphorylate biomineralization related proteins in vertebrate animals. However, the function of Fam20C in invertebrate animals especially the role in biomineralization is still unknown. Herein, we cloned the cDNA of fam20C from the pearl oyster, Pinctada fucata. It is showed that the expression of fam20C in the mantle edge was much higher than other tissues. In situ hybridization showed that fam20C was expressed mostly in the outer epithelial cells of the middle fold, indicating it may play important roles in the shell formation. Besides, fam20C expression increased greatly in the D-shape stage of pearl oyster development, when the shell was first formed. During the shell repair process, the expression level of fam20C increased 1.5 times at 6 h after shell notching. Knockdown of fam20C in vivo by RNA interference resulted in abnormally stacking of calcium carbonate crystals at the edges of nacre tablets, showing direct evidence that fam20C participates in the shell formation. This study provides an insight into the role of kinase protein in the shell formation in mollusk and broaden our understanding of biomineralization mechanism.