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1.
JACS Au ; 4(5): 1811-1823, 2024 May 27.
Article in English | MEDLINE | ID: mdl-38818059

ABSTRACT

Single-cell proteomics offers unparalleled insights into cellular diversity and molecular mechanisms, enabling a deeper understanding of complex biological processes at the individual cell level. Here, we develop an integrated sample processing on an active-matrix digital microfluidic chip for single-cell proteomics (AM-DMF-SCP). Employing the AM-DMF-SCP approach and data-independent acquisition (DIA), we identify an average of 2258 protein groups in single HeLa cells within 15 min of the liquid chromatography gradient. We performed comparative analyses of three tumor cell lines: HeLa, A549, and HepG2, and machine learning was utilized to identify the unique features of these cell lines. Applying the AM-DMF-SCP to characterize the proteomes of a third-generation EGFR inhibitor, ASK120067-resistant cells (67R) and their parental NCI-H1975 cells, we observed a potential correlation between elevated VIM expression and 67R resistance, which is consistent with the findings from bulk sample analyses. These results suggest that AM-DMF-SCP is an automated, robust, and sensitive platform for single-cell proteomics and demonstrate the potential for providing valuable insights into cellular mechanisms.

2.
JACS Au ; 4(5): 2005-2018, 2024 May 27.
Article in English | MEDLINE | ID: mdl-38818065

ABSTRACT

Core fucosylation, a special type of N-linked glycosylation, is important in tumor proliferation, invasion, metastatic potential, and therapy resistance. However, the core-fucosylated glycoproteome has not been extensively profiled due to the low abundance and poor ionization efficiency of glycosylated peptides. Here, a "one-step" strategy has been described for protein core-fucosylation characterization in biological samples. Core-fucosylated peptides can be selectively labeled with a glycosylated probe, which is linked with a temperature-sensitive poly(N-isopropylacrylamide) (PNIPAM) polymer, by mutant endoglycosidase (EndoF3-D165A). The labeled probe can be further removed by wild-type endoglycosidase (EndoF3) in a traceless manner for mass spectrometry (MS) analysis. The feasibility and effectiveness of the "one-step" strategy are evaluated in bovine serum albumin (BSA) spiked with standard core-fucosylated peptides, H1299, and Jurkat cell lines. The "one-step" strategy is then employed to characterize core-fucosylated sites in human lung adenocarcinoma, resulting in the identification of 2494 core-fucosylated sites distributed on 1176 glycoproteins. Further data analysis reveals that 196 core-fucosylated sites are significantly upregulated in tumors, which may serve as potential drug development targets or diagnostic biomarkers. Together, this "one-step" strategy has great potential for use in global and in-depth analysis of the core-fucosylated glycoproteome to promote its mechanism research.

3.
Sci Rep ; 14(1): 3214, 2024 Feb 08.
Article in English | MEDLINE | ID: mdl-38332171

ABSTRACT

In recent decades, rising air temperatures (AT) and apparent temperatures (AP) have posed growing health risks. In the context of China's rapid urbanization and global climate change, it is crucial to understand the impact of urban land use/land cover (LULC) changes on AP. This study investigates the spatial distribution and long-term variation patterns of AT and AP, using data from 834 meteorological stations across China from 1996 to 2020. It also explores the relationship between AT, AP, and LULC in the urban core areas of 30 major cities. Study reveals that AT and AP exhibit overall high spatial similarity, albeit with greater spatial variance in AP. Notably, regions with significant disparities between the two have been identified. Furthermore, it's observed that the spatial range of high AP change rates is wider than that of AT. Moreover, the study suggests a potential bivariate quadratic function relationship between ΔT (the difference between AT and AP) and Wa_ratio and Ar_ratio, indicating the presence of a Least Suitable Curve (LSC), [Formula: see text]. Urban LULC planning should carefully avoid intersecting with this curve. These findings can provide valuable insights for urban LULC planning, ultimately enhancing the thermal comfort of urban residents.

4.
Biomaterials ; 304: 122403, 2024 01.
Article in English | MEDLINE | ID: mdl-38016335

ABSTRACT

Gene therapy has been adapted, from the laboratory to the clinic, to treat retinopathies. In contrast to subretinal route, intravitreal delivery of AAV vectors displays the advantage of bypassing surgical injuries, but the viral particles are more prone to be nullified by the host neutralizing factors. To minimize such suppression of therapeutic effect, especially in terms of AAV2 and its derivatives, we introduced three serine-to-glycine mutations, based on the phosphorylation sites identified by mass spectrum analysis, to the XL32 capsid to generate a novel serotype named AAVYC5. Via intravitreal administration, AAVYC5 was transduced more effectively into multiple retinal layers compared with AAV2 and XL32. AAVYC5 also enabled successful delivery of anti-angiogenic molecules to rescue laser-induced choroidal neovascularization and astrogliosis in mice and non-human primates. Furthermore, we detected fewer neutralizing antibodies and binding IgG in human sera against AAVYC5 than those specific for AAV2 and XL32. Our results thus implicate this capsid-optimized AAVYC5 as a promising vector suitable for a wide population, particularly those with undesirable AAV2 seroreactivity.


Subject(s)
Capsid , Choroidal Neovascularization , Humans , Mice , Animals , Capsid/metabolism , Dependovirus/genetics , Serogroup , Transduction, Genetic , Choroidal Neovascularization/therapy , Tropism , Capsid Proteins/metabolism , Genetic Vectors/genetics
5.
Analyst ; 148(21): 5435-5444, 2023 Oct 23.
Article in English | MEDLINE | ID: mdl-37750326

ABSTRACT

We developed a highly sensitive and stable SERS-active substrate of Au@Ag@Ag core/shell/shell nanorods, formed by encapsulating Au nanorods (Au NRs) into a bilayer silver shell with Raman reporter molecules (4-mercaptobenzoic acid (4-MBA) and thiram) in the shell-shell gap. The core/shell/shell nanostructures demonstrated a high SERS enhancement and easy assembly. The important role of the bilayer silver shell in boosting the SERS intensity and detection sensitivity was revealed by comparing the performances of the Au@Ag@4-MBA@Ag NRs, Au@Ag@4-MBA NRs, and Au@4-MBA NRs. The obtained Au@Ag@4-MBA@Ag NRs exhibited a significantly promoted SERS intensity, which could reach around 2.6 times and 240 times that of the Au@Ag@4-MBA NRs and Au@4-MBA NRs, where the enhancement factor was found to be strongly correlated with the shell thickness. The controllable plasma properties and SERS effect of the Au@Ag@4-MBA@Ag NRs could be optimized by adjusting the dose of silver nitrate. The SERS substrate comprising core/shell/shell nanorods was highly reproducible and stable (retaining 83% SERS intensity after one month). Moreover, the highly sensitive detection of the pesticide thiram with a detection limit as low as 1.74 × 10-9 M was achieved by taking advantage of the great SERS response of the core/shell/shell nanostructures, which was 1-2 orders of magnitude lower than for other SERS substrates. The developed SERS substrate could be readily extended to embed other target analytes into the core/shell/shell nanostructure for novel and sensitive detection. This study could enable fresh approaches toward next-generation ultrasensitive analyte detection.

6.
Nanotechnology ; 34(45)2023 Aug 25.
Article in English | MEDLINE | ID: mdl-37527639

ABSTRACT

As the price of the precious metal cobalt continues to rise, there is an urgent need for a cobalt-free or low-cobalt electrode material to reduce the cost of lithium-ion batteries, which are widely used commercially, while maintaining their performance as much as possible. With the introduction of the new concept of high entropy (HE) materials into the battery field, low cobalt and cobalt free HE novel lithium-ion batteries have attracted great attention. It possesses important research value to use HE materials to reduce the use of cobalt metal in electrode materials. In this perspective, the comparison between the new cathode materials of low cobalt and cobalt-free HE lithium-ion battery and traditional cathode materials and the latest progress in maintaining structural stability and conductivity are introduced. It is believed that low cobalt and cobalt-free and HE layered oxides can be used to replace the function of cobalt in the cathode materials of lithium-ion batteries. Finally, the future research directions and the synthesis method of HE cathode materials for lithium-ion batteries are also discussed.

7.
Natl Sci Rev ; 10(8): nwad167, 2023 Aug.
Article in English | MEDLINE | ID: mdl-37575948

ABSTRACT

Normal adjacent tissues (NATs) of hepatocellular carcinoma (HCC) differ from healthy liver tissues and their heterogeneity may contain biological information associated with disease occurrence and clinical outcome that has yet to be fully evaluated at the proteomic level. This study provides a detailed description of the heterogeneity of NATs and the differences between NATs and healthy livers and revealed that molecular features of tumor subgroups in HCC were partially reflected in their respective NATs. Proteomic data classified HCC NATs into two subtypes (Subtypes 1 and 2), and Subtype 2 was associated with poor prognosis and high-risk recurrence. The pathway and immune features of these two subtypes were characterized. Proteomic differences between the two NAT subtypes and healthy liver tissues were further investigated using data-independent acquisition mass spectrometry, revealing the early molecular alterations associated with the progression from healthy livers to NATs. This study provides a high-quality resource for HCC researchers and clinicians and may significantly expand the knowledge of tumor NATs to eventually benefit clinical practice.

8.
J Am Chem Soc ; 145(29): 15879-15887, 2023 07 26.
Article in English | MEDLINE | ID: mdl-37340703

ABSTRACT

Core fucosylation and O-GlcNAcylation are the two most famous protein glycosylation modifications that regulate diverse physiological and pathological processes in living organisms. Here, a "two birds one stone" strategy has been described for the site-specific analysis of core fucosylation and O-GlcNAcylation. Taking advantage of two mutant endoglycosidases (EndoF3-D165A and EndoCC-N180H), which efficiently and specifically recognize core fucose and O-GlcNAc, glycopeptides can be labeled using a biantennary N-glycan probe bearing azido and oxazoline groups. Then, a temperature-sensitive poly(N-isopropylacrylamide) polymer functionalized with dibenzocyclooctyne was introduced to facilitate the enrichment of the labeled glycopeptides from the complex mixture. The captured glycopeptides can be further released enzymatically by wild-type endoglycosidases (EndoF3 and EndoCC) in a traceless manner for mass spectrometry (MS) analysis. The described strategy allows simultaneous profiling of core-fucosylated glycoproteome and O-GlcNAcylated glycoproteome from one complex sample by MS technology and searching the database using different variable modifications.


Subject(s)
Glycopeptides , Glycoside Hydrolases , Glycosylation , Mass Spectrometry/methods , Glycopeptides/chemistry , Glycoside Hydrolases/metabolism
9.
Anal Chim Acta ; 1251: 340978, 2023 Apr 22.
Article in English | MEDLINE | ID: mdl-36925279

ABSTRACT

Antibody-drug conjugates (ADCs) are formed by binding of cytotoxic drugs to monoclonal antibodies (mAbs) through chemical linkers. A comprehensive evaluation of the critical quality attributes (CQAs) of ADCs is vital for drug development but remains challenging owing to ADC structural heterogeneity than mAbs. Drug conjugation sites can considerably affect ADC properties, such as stability and pharmacokinetics, however, few studies have focused on method development in this area owing to technical challenges. Hybrid electron-transfer/higher-energy collision dissociation (EThcD) produces more fragment ions than conventional higher-energy collision dissociation (HCD) fragmentation, which aids in identifying and localizing post-translational modifications. Herein, we systematically employ EThcD to assess the fragmentation mode impact on conjugation site characterization for randomly conjugated and site-specific ADCs. EThcD generates more fragment ions in tandem mass spectrometry (MS/MS) spectra compared with HCD. Additional ions aid in pinpointing the correct conjugation sites that bear complex linker payload structures. Our study may contribute to the quality control of various preclinical and clinical ADCs.


Subject(s)
Immunoconjugates , Immunoconjugates/analysis , Tandem Mass Spectrometry/methods , Electrons , Antibodies, Monoclonal/chemistry , Ions
10.
Environ Sci Pollut Res Int ; 30(19): 55662-55677, 2023 Apr.
Article in English | MEDLINE | ID: mdl-36897454

ABSTRACT

The assessment of nutrients' fate from source to sink is critical to water quality control. As an important ecological reserve in the arid and semi-arid regions of China, the Luanhe River Basin (LRB) has suffered from the deterioration of water quality, thus leading to the urgent management and control. However, few studies have devoted to exploring the fate of N/P contaminations for the entire watershed, due possibly to the large drainage area and heterogeneous watershed composition. Here, we attempt to illustrate N/P contaminations delivery and retention processes using the SPAtially Referenced Regression On Watershed attributes (SPARROW) model. The model reveals 97% of the spatial variability in the TN load and 81% in the TP load, verifying its availability and credibility. The results indicate that anthropogenic sources are dominating the N/P load, which account for 68.5% of N and 74.6% of P inputs. The results highlight the significant retention effects of streams and reservoirs, with 16.4% of N and 13.4% of P removals by streams and 24.3% of N and 10.7% of P removals by reservoirs, respectively. Ultimately, only 49,045.2 t yr-1 (or 16.9%) of N and 1668.7 t yr-1 (or 17.1%) of P being transported to the Bohai Sea. In addition, the analysis of influencing factors showed that regional characteristics (e.g., topography, rainfall), stream size, and delivery distance are potential factors affecting the riverine transport, whereas flow rate and surface area are primarily affecting the reservoirs attenuation. In the future, the watershed water quality management should pay more attention to source management and pollution legacy risks to achieve sustainable and healthy watershed development.


Subject(s)
Environmental Monitoring , Water Pollutants, Chemical , Environmental Monitoring/methods , Water Pollutants, Chemical/analysis , Nitrogen/analysis , Phosphorus/analysis , China , Rivers
11.
J Proteome Res ; 22(5): 1446-1454, 2023 05 05.
Article in English | MEDLINE | ID: mdl-36751022

ABSTRACT

The global proteome analysis was limited by the identification of peptides with low abundance or specific physiochemical properties. Here, a one-dimensional online alkaline-pH reverse phase nanoelectrospray-tandem mass spectrometry (alkaline-pH-MS/MS) method was developed and optimized for global proteomic analysis. In this method, peptides were separated on a nanoflow C18 column with an alkaline-pH mobile phase (pH = 8.0) and directly injected into the mass spectrometer. The unique peptides overlapped between alkaline-pH-MS/MS and conventional online low-pH reverse phase nanoelectrospray-tandem mass spectrometry (low-pH-MS/MS) were as low as 45%, strongly indicating that these two methods were complementary to each other. In addition, alkaline-pH-MS/MS showed identification capacity for a higher proportion of peptides with negative grand average of hydropathy (GRAVY) or high isoelectric point (pI). Compared to low-pH-MS/MS, alkaline-pH-MS/MS enabled enrichment preference toward histidine-, lysine-, methionine-, and proline-containing peptides. The complementarity of alkaline-pH-MS/MS and low-pH-MS/MS was further demonstrated for the analysis of tryptic digests from 15 intrahepatic cholangiocarcinoma (iCCA) cell lines. The alternating 60 min alkaline-pH-MS/MS plus 60 min low-pH-MS/MS method outperformed the conventional 120 min low-pH-MS/MS method in both the identification of amino acid variants and protein groups. Therefore, we established the alkaline-pH-MS/MS method as a simple, competitive, alternative method to low-pH-MS/MS for global proteomic analysis.


Subject(s)
Proteomics , Tandem Mass Spectrometry , Tandem Mass Spectrometry/methods , Chromatography, High Pressure Liquid , Proteomics/methods , Peptides/analysis , Complement System Proteins , Proteome/analysis , Hydrogen-Ion Concentration
12.
Proteomics ; 23(3-4): e2100407, 2023 02.
Article in English | MEDLINE | ID: mdl-35689503

ABSTRACT

Phosphorylation is one of the most common post-translational modifications (PTMs) and is closely related to protein activity and function, playing a critical role during cancer development. Quantitative phosphoproteomic strategies have been widely used to study the underlying mechanisms of cancer progression or drug resistance. In this report, we analyzed the association of phosphosite levels originated from our previously reported proteogenomic study in hepatocellular carcinoma (HCC) with clinical parameters, including prognosis, recurrence, and Tumor-Node-Metastasis (TNM) stages. By using both the log-rank test and univariate Cox proportional hazards regression analysis, we found that the abundance levels of 1712 phosphosites were associated with prognosis and those of 393 phosphosites associated with recurrence. Besides, 692 phosphosites had different abundance levels among TNM stages (I, II, III+IV) by Analysis of Variance (ANOVA) test. Gene ontology (GO) biological process and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed using proteins with these statistically significant phosphosites. In conclusion, we provided a dataset resource for clinically associated phosphosites in HCC, which may be beneficial to liver cancer related basic research.


Subject(s)
Carcinoma, Hepatocellular , Liver Neoplasms , Humans , Carcinoma, Hepatocellular/pathology , Liver Neoplasms/pathology , Prognosis
13.
Small ; 19(3): e2206270, 2023 01.
Article in English | MEDLINE | ID: mdl-36464498

ABSTRACT

Microneedle (MN) patches hold demonstrated prospects in intelligent wound management. Herein, inspired by the highly folded structure of insect wings, a three-dimensional (3D) origami MN patch with superfine miniature needle structures, microfluidic channels, and multiple functions was reported to detect biomarkers, release drugs controllably and monitor motions to facilitate wound healing. By simply replicating the pre-stretched silicone rubber (Ecoflex) molds patterned by a laser engraving machine, the superfine structure MN patch with microfluidic channels was obtained from the restored molds. The bioinspired origami structure endows the MN patch with a high degree of functional integration, including microfluidic channels and electrocircuits. The microfluidic channels combined with the pH value and glucose concentration indicators enable the patch with the capability of biomarker sensing detection. Porous structures, a temperature-responsive hydrogel, and a photothermal-sensitive agent are utilized to form a controllable drug release system on the MN patch. Meanwhile, MXene electrocircuits were printed on the MN patch for motion sensing. In addition, the ability of the MN patch to accelerate wound healing was demonstrated by a mouse model experiment with full-thickness skin wounds. These results indicate that the multifunctional 3D origami MN patch is a valuable intelligent strategy for wound management.


Subject(s)
Microfluidics , Wound Healing , Mice , Animals , Hydrogels/chemistry , Light , Needles
14.
Plant Cell ; 35(2): 700-716, 2023 02 20.
Article in English | MEDLINE | ID: mdl-36423345

ABSTRACT

Light is a major environmental factor for seed germination. Red light-activated phytochrome B (phyB) promotes seed germination by modulating the dynamic balance of two phytohormones, gibberellic acid (GA) and abscisic acid (ABA). How phyB modulates ABA biosynthesis after perceiving a light signal is not yet well understood. Here, we identified the noncoding RNA HIDDEN TREASURE 1 (HID1) as a repressor of ABA biosynthesis acting downstream of phyB during Arabidopsis thaliana seed germination. Loss of HID1 function led to delayed phyB-dependent seed germination. Photoactivated phyB promoted the accumulation of HID1 in the radicle within 48 h of imbibition. Our transcriptomics analysis showed that HID1 and phyB co-regulate the transcription of a common set of genes involved in ABA and GA metabolism. Through a forward genetic screen, we identified three ABA biosynthesis genes, ABA DEFICIENT 1 (ABA1), ABA2, and ABA3, as suppressors of HID1. We further demonstrated that HID1 directly inhibits the transcription of 9-CIS-EPOXYCAROTENOID DIOXYGENASE (NCED9), a gene encoding a key rate-limiting enzyme of ABA biosynthesis. HID1 interacts with ARABIDOPSIS TRITHORAX-RELATED7 (ATXR7), an H3K4me3 methyltransferase, inhibiting its occupancy and H3K4me3 modification at the NCED9 locus. Our study reveals a nuclear mechanism of phyB signaling transmitted through HID1 to control the internal homeostasis of ABA and GA, which gradually optimizes the transcriptional network during seed germination.


Subject(s)
Arabidopsis Proteins , Arabidopsis , Abscisic Acid/metabolism , Phytochrome B/genetics , Phytochrome B/metabolism , Arabidopsis Proteins/metabolism , Germination/genetics , Seeds/genetics , Seeds/metabolism , Arabidopsis/genetics , Arabidopsis/metabolism , Gibberellins/metabolism , Gene Expression Regulation, Plant/genetics
15.
J Integr Plant Biol ; 64(12): 2290-2308, 2022 Dec.
Article in English | MEDLINE | ID: mdl-36453685

ABSTRACT

The development of plants is largely dependent on their growth environment. To better adapt to a particular habitat, plants have evolved various subtle regulatory mechanisms for altering gene expression. Non coding RNAs (ncRNAs) constitute a major portion of the transcriptomes of eukaryotes. Various ncRNAs have been recognized as important regulators of the expression of genes involved in essential biological processes throughout the whole life cycles of plants. In this review, we summarize the current understanding of the biogenesis and contributions of small nucle olar RNA (snoRNA)- and regulatory long non coding RNA (lncRNA)-mediated gene regulation in plant development and environmental responses. Many regulatory ncRNAs appear to be associated with increased yield, quality and disease resistance of various species and cultivars. These ncRNAs may potentially be used as genetic resources for improving agronomic traits and for molecular breeding. The challenges in understanding plant ncRNA biology and the possibilities to make better use of these valuable gene resources in the future are discussed in this review.


Subject(s)
MicroRNAs , RNA, Long Noncoding , RNA, Untranslated/genetics , RNA, Long Noncoding/genetics , RNA, Long Noncoding/metabolism , Plants/genetics , Plants/metabolism , Transcriptome , MicroRNAs/genetics
16.
Angew Chem Int Ed Engl ; 61(49): e202206802, 2022 12 05.
Article in English | MEDLINE | ID: mdl-36224515

ABSTRACT

Core fucosylation, the attachment of α1,6-fucose to the innermost N-acetylglucosamine (GlcNAc) residue of N-glycans, has a strong relationship with tumor growth, invasion, metastasis, prognosis, and immune evasion by regulating many membrane proteins. However, details about the functional mechanism are still largely unknown due to the lack of an effective analytical method to identify cell-surface core-fucosylated glycoproteins, and especially glycosylation sites. Here, we developed a sensitive and reversible labeling strategy for probing core fucosylation, by which core-fucosylated glycoproteins that located on cell-surface were selectively tagged by a biotinylated probe with high sensitivity. The labeled probe can be further broken enzymatically after the capture by affinity resin. The on-bead traceless cleavage allowed the global mapping of core-fucosylated glycoproteins and glycosylation sites by mass spectrometry (MS). The profile of core-fucosylated glycoproteome provides an in-depth understanding of the biological functions of core fucosylation.


Subject(s)
Fucose , Glycoproteins , Glycosylation , Fucose/chemistry , Glycoproteins/chemistry , Mass Spectrometry/methods , Acetylglucosamine/chemistry , Polysaccharides/chemistry , Proteome/metabolism
17.
Talanta ; 248: 123621, 2022 Oct 01.
Article in English | MEDLINE | ID: mdl-35661844

ABSTRACT

By rationally introducing Ce(III) and Tb(III) into a coordination polymer (CP), a series of lanthanide bimetallic coordination polymers (Tb:Ce-BCPs) has been prepared in this work. Compared with pure Tb-CP and Ce-CP, bimetallic Tb:Ce-BCPs show stronger and more stable ECL intensity, which is mainly attributed to the "dual sensitization effect" combined with the energy transfer from Ce(III) to Tb(III) and the antenna effect from the ligand to the center atoms of Ce(III) and Tb(III). In the meantime, after explore the ECL intensity and morphologies of all these Tb:Ce-BCPs, the results show that the morphologies and ECL intensities of Tb:Ce-BCPs can be adjusted by doping different molar ratios of Ce(III) in Tb:Ce-BCP. Excitingly, Ce(III) can also act as a co-reaction accelerator, effectively promoting S2O82- to generate more SO4•-, thereby enhancing the ECL intensity of Tb:Ce-BCP. That is to say, Ce(III) plays a triple role in Tb:Ce-BCP. Furthermore, the ECL strength of Tb:Ce-BCP decreased by only 1.8% and 3.5%, respectively after the modified electrode was scanned for 800 s and stored for one month. Enlightened by the excellent ECL properties of Tb:Ce-BCP, we modified Tb:Ce-BCP directly on the surface of electrode, and explored its application in electroanalytical chemistry through the detection of epinephrine (EP) and the detection limit is 33 fmol L-1. Significantly, our ECL sensing strategy promotes the application of lanthanides in ECL sensor and opens vast possibilities for the synthesis of a new generation of ECL emitter in electroanalytical fields.


Subject(s)
Biosensing Techniques , Lanthanoid Series Elements , Biosensing Techniques/methods , Electrochemical Techniques/methods , Electrodes , Epinephrine , Lanthanoid Series Elements/chemistry , Luminescent Measurements/methods , Polymers/chemistry
18.
Proc Natl Acad Sci U S A ; 119(27): e2206075119, 2022 07 05.
Article in English | MEDLINE | ID: mdl-35759663

ABSTRACT

The master transcriptional repressor DREAM (dimerization partner, RB-like, E2F and multivulval class B) complex regulates the cell cycle in eukaryotes, but much remains unknown about how it transmits repressive signals on chromatin to the primary transcriptional machinery (e.g., RNA polymerase II [Pol II]). Through a forward genetic screen, we identified BTE1 (barrier of transcription elongation 1), a plant-specific component of the DREAM complex. The subsequent characterization demonstrated that DREAM complex containing BTE1 antagonizes the activity of Complex Proteins Associated with Set1 (COMPASS)-like complex to repress H3K4me3 occupancy and inhibits Pol II elongation at DREAM target genes. We showed that BTE1 is recruited to chromatin at the promoter-proximal regions of target genes by E2F transcription factors. DREAM target genes exhibit characteristic enrichment of H2A.Z and H3K4me2 modification on chromatin. We further showed that BTE1 directly interacts with WDR5A, a core component of COMPASS-like complex, repressing WDR5A chromatin binding and the elongation of transcription on DREAM target genes. H3K4me3 is known to correlate with the Pol II transcription activation and promotes efficient elongation. Thus, our study illustrates a transcriptional repression mechanism by which the DREAM complex dampens H3K4me3 deposition at a set of genes through its interaction with WDR5A.


Subject(s)
Arabidopsis Proteins , Arabidopsis , Histones , Arabidopsis/genetics , Arabidopsis/metabolism , Arabidopsis Proteins/metabolism , Carrier Proteins/metabolism , Chromatin/genetics , Chromatin/metabolism , Histones/genetics , Histones/metabolism , Transcription Factors/genetics , Transcription Factors/metabolism
19.
Mol Ther Nucleic Acids ; 28: 293-306, 2022 Jun 14.
Article in English | MEDLINE | ID: mdl-35474733

ABSTRACT

Impressive achievements in clinical trials to treat hemophilia establish a milestone in the development of gene therapy. It highlights the significance of AAV-mediated gene delivery to liver. AAV5 is a unique serotype featured by low neutralizing antibody prevalence. Nevertheless, its liver infectivity is relatively weak. Consequently, it is vital to exploit novel AAV5 capsid mutants with robust liver tropism. To this aim, we performed AAV5-NNK library and barcode screening in mice, from which we identified one capsid variant, called AAVzk2. AAVzk2 displayed a similar yield but divergent post-translational modification sites compared with wild-type serotypes. Mice intravenously injected with AAVzk2 demonstrated a stronger liver transduction than AAV5, roughly comparable with AAV8 and AAV9, with undetectable transduction of other tissues or organs such as heart, lung, spleen, kidney, brain, and skeletal muscle, indicating a liver-specific tropism. Further studies showed a superior human hepatocellular transduction of AAVzk2 to AAV5, AAV8 and AAV9, whereas the seroreactivity of AAVzk2 was as low as AAV5. Overall, we provide a novel AAV serotype that facilitates a robust and specific liver gene delivery to a large population, especially those unable to be treated by AAV8 and AAV9.

20.
Plant Cell ; 34(7): 2747-2764, 2022 07 04.
Article in English | MEDLINE | ID: mdl-35385118

ABSTRACT

Many glycine-rich RNA-binding proteins (GR-RBPs) have critical functions in RNA processing and metabolism. Here, we describe a role for the tomato (Solanum lycopersicum) GR-RBP SlRBP1 in regulating mRNA translation. We found that SlRBP1 knockdown mutants (slrbp1) displayed reduced accumulation of total chlorophyll and impaired chloroplast ultrastructure. These phenotypes were accompanied by deregulation of the levels of numerous key transcripts associated with chloroplast functions in slrbp1. Furthermore, native RNA immunoprecipitation-sequencing (nRIP-seq) recovered 61 SlRBP1-associated RNAs, most of which are involved in photosynthesis. SlRBP1 binding to selected target RNAs was validated by nRIP-qPCR. Intriguingly, the accumulation of proteins encoded by SlRBP1-bound transcripts, but not the mRNAs themselves, was reduced in slrbp1 mutants. Polysome profiling followed by RT-qPCR assays indicated that the polysome occupancy of target RNAs was lower in slrbp1 plants than in wild-type. Furthermore, SlRBP1 interacted with the eukaryotic translation initiation factor SleIF4A2. Silencing of SlRBP1 significantly reduced SleIF4A2 binding to SlRBP1-target RNAs. Taking these observations together, we propose that SlRBP1 binds to and channels RNAs onto the SleIF4A2 translation initiation complex and promotes the translation of its target RNAs to regulate chloroplast functions.


Subject(s)
Solanum lycopersicum , Chloroplasts/metabolism , Gene Expression Regulation, Plant/genetics , Solanum lycopersicum/genetics , Photosynthesis/genetics , Polyribosomes/metabolism
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