Evolutionary conservation of nested MIR159 structural microRNA genes and their promoter characterization in Arabidopsis thaliana

MicroRNAs (miRNAs) are endogenous small RNAs, that are vital for gene expression regulation in eukaryotes. Whenever a pri-miRNA precursor includes another miRNA precursor, and both of these precursors may generate independent, non-overlapping mature miRNAs, we named them nested miRNAs. However, the extent of nested miR159 structural evolutionary conservation and its promoter characterization remains unknown. In this study, the sequence alignment and phylogenetic analysis reveal that the MIR159 family is ancient, and its nested miR159 structures are evolutionary conserved in different plant species. The overexpression of ath-MIR159a, including the 1.2 kb downstream region, has no effect on rescuing the mir159ab phenotype. The promoter truncation results revealed that the 1.0 kb promoter of ath-MIR159a is sufficient for rescuing the mir159ab phenotype. The cis-regulatory elements in the ath-miR159a promoters indicated functions related to different phytohormones, abiotic stresses, and transcriptional activation. While the MybSt1 motif-containing region is not responsible for activating the regulation of the miR159a promoter. The qRT-PCR results showed that overexpression of ath-MIR159a led to high expression levels of miR159a.1–5 and miR159a.1–3 and complemented the growth defect of mir159ab via downregulation of MYB33 and MYB65. Furthermore, continuously higher expression of the miR159a.2 duplex in transgenic lines with the curly leaf phenotype indicates that miR159a.2 is functional in Arabidopsis and suggests that it is possible for a miRNA precursor to encode several regulatory small RNAs in plants. Taken together, our study demonstrates that the nested miR159 structure is evolutionary conserved and miRNA-mediated gene regulation is more complex than previously thought

Comparative transcriptomic and metabolomic analyses reveal differences in flavonoid biosynthesis between PCNA and PCA persimmon fruit

The fruit of the persimmon (Diospyros kaki.) has high economic and nutritional value and is rich in flavonoids. Flavonoids are essential secondary metabolisms in plants. The association between persimmon astringency and changes in the proanthocyanidins (a flavonoid subclass) content is well-known. However, information on the relationships between different astringency types and other flavonoid subclasses and biosynthetic genes is more limited. In this study, an initial correlation analysis between total flavonoids and fruit astringency type, and KEGG analysis of metabolites showed that flavonoid-related pathways were linked to differences between mature pollination-constant non-astringent (PCNA) varieties (‘Jiro’ and ‘Yohou’) and pollination-constant astringent (PCA) fruit varieties (‘Zhongshi5’ and ‘Huojing’). Based on these findings, variations in the expression of genes and metabolites associated with flavonoid biosynthesis were investigated between typical PCNA (‘Jiro’) and PCA (‘Huojing’) persimmons during fruit development. The flavonoid concentration in ‘Huojing’ fruit was significantly higher than that of ‘Jiro’ fruit, especially, in levels of proanthocyanin precursor epicatechin and anthocyanin cyanidin derivatives. Combined WGCNA and KEGG analyses showed that genes such as PAL, C4H, CHI, CHS, F3H, F3’5’H, FLS, DFR, ANR, ANS, and UF3GT in the phenylpropanoid and flavonoid biosynthesis pathways may be significant factors impacting the proanthocyanin precursor and anthocyanin contents. Moreover, interactions between the R2R3MYB (evm.TU.contig7272.598) and WD40 (evm.TU.contig3208.5) transcription factors were found to be associated with the above structural genes. These findings provide essential information on flavonoid biosynthesis and its regulation in the persimmon and lay a foundation for further investigation into how astringency types affect flavor components in PCNA and PCA persimmons

Water management affects arsenic and cadmium accumulation in different rice cultivars

Paddy rice (Oryza sativa L.) is a staple food and one of the major sources of dietary arsenic (As) and cadmium (Cd) in Asia. A field experiment was conducted to investigate the effects of four water management regimes (aerobic, intermittent irrigation, conventional irrigation and flooding) on As and Cd accumulation in seven major rice cultivars grown in Zhejiang province, east China. With increasing irrigation from aerobic to flooded conditions, the soil HCl-extractable As concentrations increased significantly and the HCl-extractable Cd concentrations decreased significantly. These trends were consistent with the As and Cd concentrations in the straw, husk and brown rice. Water management both before and after the full tillering stage affected As and Cd accumulation in the grains. The intermittent and conventional treatments produced higher grain yields than the aerobic and flooded treatments. Cd concentrations in brown rice varied 13.1-40.8 times and As varied 1.75-8.80 times among the four water management regimes. Cd and As accumulation in brown rice varied among the rice cultivars, with Guodao 6 (GD6) was a low Cd but high-As-accumulating cultivar while Indonesia (IR) and Yongyou 9 (YY9) were low As but high-Cd-accumulating cultivars. Brown rice Cd and As concentrations in the 7 cultivars were significantly negatively correlated. The results indicate that As and Cd accumulated in rice grains with opposite trends that were influenced by both water management and rice cultivar. Production of 'safe' rice with respect to As and Cd might be possible by balancing water management and rice cultivar according to the severity of soil pollution.Paddy rice (Oryza sativa L.) is a staple food and one of the major sources of dietary arsenic (As) and cadmium (Cd) in Asia. A field experiment was conducted to investigate the effects of four water management regimes (aerobic, intermittent irrigation, conventional irrigation and flooding) on As and Cd accumulation in seven major rice cultivars grown in Zhejiang province, east China. With increasing irrigation from aerobic to flooded conditions, the soil HCl-extractable As concentrations increased significantly and the HCl-extractable Cd concentrations decreased significantly. These trends were consistent with the As and Cd concentrations in the straw, husk and brown rice. Water management both before and after the full tillering stage affected As and Cd accumulation in the grains. The intermittent and conventional treatments produced higher grain yields than the aerobic and flooded treatments. Cd concentrations in brown rice varied 13.1-40.8 times and As varied 1.75-8.80 times among the four water management regimes. Cd and As accumulation in brown rice varied among the rice cultivars, with Guodao 6 (GD6) was a low Cd but high-As-accumulating cultivar while Indonesia (IR) and Yongyou 9 (YY9) were low As but high-Cd-accumulating cultivars. Brown rice Cd and As concentrations in the 7 cultivars were significantly negatively correlated. The results indicate that As and Cd accumulated in rice grains with opposite trends that were influenced by both water management and rice cultivar. Production of 'safe' rice with respect to As and Cd might be possible by balancing water management and rice cultivar according to the severity of soil pollution

Longitudinal Serum Proteome Characterization of COVID-19 Patients With Different Severities Revealed Potential Therapeutic Strategies

The COVID-19 pandemic caused by SARS-CoV-2 is exerting huge pressure on global healthcare. Understanding of the molecular pathophysiological alterations in COVID-19 patients with different severities during disease is important for effective treatment. In this study, we performed proteomic profiling of 181 serum samples collected at multiple time points from 79 COVID-19 patients with different severity levels (asymptomatic, mild, moderate, and severe/critical) and 27 serum samples from non-COVID-19 control individuals. Dysregulation of immune response and metabolic reprogramming was found in severe/critical COVID-19 patients compared with non-severe/critical patients, whereas asymptomatic patients presented an effective immune response compared with symptomatic COVID-19 patients. Interestingly, the moderate COVID-19 patients were mainly grouped into two distinct clusters using hierarchical cluster analysis, which demonstrates the molecular pathophysiological heterogeneity in COVID-19 patients. Analysis of protein-level alterations during disease progression revealed that proteins involved in complement activation, the coagulation cascade and cholesterol metabolism were restored at the convalescence stage, but the levels of some proteins, such as anti-angiogenesis protein PLGLB1, would not recovered. The higher serum level of PLGLB1 in COVID-19 patients than in control groups was further confirmed by parallel reaction monitoring (PRM). These findings expand our understanding of the pathogenesis and progression of COVID-19 and provide insight into the discovery of potential therapeutic targets and serum biomarkers worth further validation

Regular Patterns for Proteome-Wide Distribution of Protein Abundance across Species

A proteome of the bio-entity, including cell, tissue, organ, and organism, consists of proteins of diverse abundance. The principle that determines the abundance of different proteins in a proteome is of fundamental significance for an understanding of the building blocks of the bio-entity. Here, we report three regular patterns in the proteome-wide distribution of protein abundance across species such as human, mouse, fly, worm, yeast, and bacteria: in most cases, protein abundance is positively correlated with the protein's origination time or sequence conservation during evolution; it is negatively correlated with the protein's domain number and positively correlated with domain coverage in protein structure, and the correlations became stronger during the course of evolution; protein abundance can be further stratified by the function of the protein, whereby proteins that act on material conversion and transportation (mass category) are more abundant than those that act on information modulation (information category). Thus, protein abundance is intrinsically related to the protein's inherent characters of evolution, structure, and function

Relationships between Hematopoiesis and Hepatogenesis in the Midtrimester Fetal Liver Characterized by Dynamic Transcriptomic and Proteomic Profiles

In fetal hematopoietic organs, the switch from hematopoiesis is hypothesized to be a critical time point for organogenesis, but it is not yet evidenced. The transient coexistence of hematopoiesis will be useful to understand the development of fetal liver (FL) around this time and its relationship to hematopoiesis. Here, the temporal and the comparative transcriptomic and proteomic profiles were observed during the critical time points corresponding to the initiation (E11.5), peak (E14.5), recession (E15.5), and disappearance (3 ddp) of mouse FL hematopoiesis. We found that E11.5-E14.5 corresponds to a FL hematopoietic expansion phase with distinct molecular features, including the expression of new transcription factors, many of which are novel KRAB (Kruppel-associated box)-containing zinc finger proteins. This time period is also characterized by extensive depression of some liver functions, especially catabolism/utilization, immune and defense, classical complement cascades, and intrinsic blood coagulation. Instead, the other liver functions increased, such as xenobiotic and sterol metabolism, synthesis of carbohydrate and glycan, the alternate and lectin complement cascades and extrinsic blood coagulation, and etc. Strikingly, all of the liver functions were significantly increased at E14.5-E15.5 and thereafter, and the depression of the key pathways attributes to build the hematopoietic microenvironment. These findings signal hematopoiesis emigration is the key to open the door of liver maturation