Traceless Protein-Selective Glycan Labeling and Chemical Modification.

Executing glycan editing at a molecular level not only is pivotal for the elucidation of complicated mechanisms involved in glycan-relevant biological processes but also provides a promising solution to potentiate disease therapy. However, the precision control of glycan modification or glyco-editing on a selected glycoprotein is by far a grand challenge. Of note is to preserve the intact cellular glycan landscape, which is preserved after editing events are completed. We report herein a versatile, traceless glycan modification methodology for customizing the glycoforms of targeted proteins (subtypes), by orchestrating chemical- and photoregulation in a protein-selective glycoenzymatic system. This method relies on a three-module, ligand-photocleavable linker-glycoenzyme (L-P-G) conjugate. We demonstrated that RGD- or synthetic carbohydrate ligand-containing conjugates (RPG and SPG) would not activate until after the ligand-receptor interaction is accomplished (chemical regulation). RPG and SPG can both release the glycoenzyme upon photoillumination (photoregulation). The adjustable glycoenzyme activity, combined with ligand recognition selectivity, minimizes unnecessary glycan editing perturbation, and photolytic cleavage enables precise temporal control of editing events. An altered target protein turnover and dimerization were observed in our system, emphasizing the significance of preserving the native physiological niche of a particular protein when precise modification on the carbohydrate epitope occurs.

Recent Advances in Protein-Specific Glycan Imaging and Editing.

Glycosylation in live cell and animal modulate a constellation of biological functions. The advent of Chemical Biology has revolutionized the analysis and tailoring of glycans, by introducing myriads of glycan engineering methods. However, the ideal scenario to achieve glycan monitoring and structural manipulation at any hierarchical levels is unmet yet. Herein we review recent advances in the methodological innovation and the versatile applications of the protein-specific glycan visualization and editing in deciphering the biological functions of glycans. An outlook for future directions toward specific sugar-chain editing is also included.

Butyrate mitigates metabolic dysfunctions via the ERα-AMPK pathway in muscle in OVX mice with diet-induced obesity.

The higher prevalence of metabolic syndrome (MetS) in women after menopause is associated with a decrease in circulating 17ß-oestradiol. To explore novel treatments for MetS in women with oestrogen deficiency, we studied the effect of exogenous butyrate on diet-induced obesity and metabolic dysfunctions using ovariectomized (OVX) mice as a menopause model. Oral administration of sodium butyrate (NaB) reduced the body fat content and blood lipids, increased whole-body energy expenditure, and improved insulin sensitivity. Additionally, NaB induced oestrogen receptor alpha (ERα) expression, activated the phosphorylation of AMPK and PGC1α, and improved mitochondrial aerobic respiration in cultured skeletal muscle cells. In conclusion, oral NaB improves metabolic parameters in OVX mice with diet-induced obesity. Oral supplementation with NaB might provide a novel therapeutic approach to treating MetS in women with menopause. Video Abstract.

Vitamin D supplementation improved physical growth and neurologic development of Preterm Infants receiving Nesting Care in the neonatal Intensive Care Unit.

OBJECTIVE: To study the effects of vitamin D supplementation on physical growth and neurologic development of very preterm infants receiving nesting intervention in the neonatal intensive care unit (NICU). METHODS: A total of 196 preterm infants had been hospitalized in NICU with the gestational age (GA) between 28 and 32 weeks. Among them, 98 preterm infants received nesting intervention, and the other 98 cases received both nesting and vitamin D supplementation (400 IU). The interventions were continued until 36 weeks postmenstrual age (PMA). The 25(OH)D serum levels, anthropometric parameters, and Premie-Neuro (PN) scores were compared at 36 weeks PMA. RESULTS: Higher median serum level of 25(OH)D was found in the nesting + vitamin D [38.40 ng/mL (IQR: 17.20 ~ 70.88) ng/mL] as compared to the nesting group [15.95 ng/mL (IQR: 10.80 ~ 24.30) ng/mL] at 36 weeks PMA. Besides, infants receiving combined nesting intervention and vitamin D supplementation had less proportion of vitamin D deficiency [VDD, 25(OH)D levels < 20 ng/mL] than those receiving nesting intervention alone. After intervention, the anthropometric parameters of infants, including weight, length, BMI and head circumference were improved in the nesting + vitamin D group as compared to the nesting group at 36 weeks PMA, with higher scores of neurological, movement and responsiveness. CONCLUSIONS: Vitamin D supplementation effectively decreased the prevalence of VDD and led to higher concentrations of 25(OH)D at 36 weeks PMA. This was one more study that supported the necessity of vitamin D supplementation to improve physical growth and neurologic development of preterm-born newborns who received nesting intervention in the NICU.

Interbacterial Chemical Communication-Triggered Nascent Proteomics.

Metabolic labeling with clickable noncanonical amino acids has enabled nascent proteome profiling, which can be performed in a cell-type-specific manner. However, nascent proteomics in an intercellular communication-dependent manner remains challenging. Here we develop communication-activated profiling of protein expression (CAPPEX), which integrates the LuxI/LuxR quorum sensing circuit with the cell-type-specific nascent proteomics method to enable selective click-labeling of newly synthesized proteins in a specific bacterium upon receiving chemical signals from another reporter bacterium. CAPPEX reveals that E. coli competes with Salmonella for tryptophan as the precursor for indole, and the resulting indole suppressed the expression of virulence factors in Salmonella. This tryptophan-indole axis confers attenuation of Salmonella invasion in host cells and living mice. The CAPPEX strategy should be widely applicable for investigating various interbacterial communication processes.

Metabolic RNA labeling for probing RNA dynamics in bacteria.

Metabolic labeling of RNAs with noncanonical nucleosides that are chemically active, followed by chemoselective conjugation with imaging probes or enrichment tags, has emerged as a powerful method for studying RNA transcription and degradation in eukaryotes. However, metabolic RNA labeling is not applicable for prokaryotes, in which the complexity and distinctness of gene regulation largely remain to be explored. Here, we report 2'-deoxy-2'-azidoguanosine (AzG) as a noncanonical nucleoside compatible with metabolic labeling of bacterial RNAs. With AzG, we develop AIR-seq (azidonucleoside-incorporated RNA sequencing), which enables genome-wide analysis of transcription upon heat stress in Escherichia coli. Furthermore, AIR-seq coupled with pulse-chase labeling allows for global analysis of bacterial RNA degradation. Finally, we demonstrate that RNAs of mouse gut microbiotas can be metabolically labeled with AzG in living animals. The AzG-enabled metabolic RNA labeling should find broad applications in studying RNA biology in various bacterial species.

Transcriptome-wide discovery of coding and noncoding RNA-binding proteins.

Transcriptome-wide identification of RNA-binding proteins (RBPs) is a prerequisite for understanding the posttranscriptional gene regulation networks. However, proteomic profiling of RBPs has been mostly limited to polyadenylated mRNA-binding proteins, leaving RBPs on nonpoly(A) RNAs, including most noncoding RNAs (ncRNAs) and pre-mRNAs, largely undiscovered. Here we present a click chemistry-assisted RNA interactome capture (CARIC) strategy, which enables unbiased identification of RBPs, independent of the polyadenylation state of RNAs. CARIC combines metabolic labeling of RNAs with an alkynyl uridine analog and in vivo RNA-protein photocross-linking, followed by click reaction with azide-biotin, affinity enrichment, and proteomic analysis. Applying CARIC, we identified 597 RBPs in HeLa cells, including 130 previously unknown RBPs. These newly discovered RBPs can likely bind ncRNAs, thus uncovering potential involvement of ncRNAs in processes previously unknown to be ncRNA-related, such as proteasome function and intermediary metabolism. The CARIC strategy should be broadly applicable across various organisms to complete the census of RBPs.

Chemical Tagging of Protein Lipoylation.

Protein lipoylation is a post-translational modification of emerging importance in both prokaryotes and eukaryotes. However, labeling and large-scale profiling of protein lipoylation remain challenging. Here, we report the development of iLCL (iodoacetamide-assisted lipoate-cyclooctyne ligation), a chemoselective reaction that enables chemical tagging of protein lipoylation. We demonstrate that the cyclic disulfide of lipoamide but not linear disulfides can selectively react with iodoacetamide to produce sulfenic acid, which can be conjugated with cyclooctyne probes. iLCL enables tagging of lipoylated proteins for gel-based detection and cellular imaging. Furthermore, we apply iLCL for proteomic profiling of lipoylated proteins in both bacteria and mammalian cells. In addition to all of the eight known lipoylated proteins, we identified seven candidates for novel lipoylated proteins. The iLCL strategy should facilitate uncovering the biological function of protein lipoylation.