Plant cell walls are comprised largely of the polysaccharides cellulose, hemicellulose, and pecti... more Plant cell walls are comprised largely of the polysaccharides cellulose, hemicellulose, and pectin, along with ∼10% protein and up to 40% lignin. These wall polymers interact covalently and noncovalently to form the functional cell wall. Characterized cross-links in the wall include covalent linkages between wall glycoprotein extensins between rhamnogalacturonan II monomer domains and between polysaccharides and lignin phenolic residues. Here, we show that two isoforms of a purified Arabidopsis thaliana arabinogalactan protein (AGP) encoded by hydroxyproline-rich glycoprotein family protein gene At3g45230 are covalently attached to wall matrix hemicellulosic and pectic polysaccharides, with rhamnogalacturonan I (RG I)/homogalacturonan linked to the rhamnosyl residue in the arabinogalactan (AG) of the AGP and with arabinoxylan attached to either a rhamnosyl residue in the RG I domain or directly to an arabinosyl residue in the AG glycan domain. The existence of this wall structure, n...
ABSTRACTThis research was initiated to search for novel antimicrobial compounds produced by food ... more ABSTRACTThis research was initiated to search for novel antimicrobial compounds produced by food or environmental microorganisms. A new bacterial strain, designated OSY-SE, which produces a unique and potent antimicrobial agent was isolated from soil. The isolate was identified as aPaenibacillussp. through cultural, biochemical, and genetic analyses. An antimicrobial compound was extracted fromPaenibacillusOSY-SE with acetonitrile and purified using liquid chromatography. After analyses by mass spectrometry (MS) and nuclear magnetic resonance (NMR), the antimicrobial compound was determined to be a cyclic lipopeptide consisting of a C15fatty acyl (FA) chain and 13 amino acids. The deduced sequence is FA-Orn-Val-Thr-Orn-Ser-Val-Lys-Ser-Ile-Pro-Val-Lys-Ile. The carboxyl-terminal Ile is connected to Thr by ester linkage. The new compound, designated paenibacterin, showed antagonistic activities against most Gram-positive and Gram-negative bacteria tested, includingListeria monocytogene...
Applied and environmental microbiology, Jan 26, 2016
A new environmental bacterial strain exhibited strong antimicrobial characteristics against methi... more A new environmental bacterial strain exhibited strong antimicrobial characteristics against methicillin-resistant Staphylococcus aureus, vancomycin-resistant strains of Enterococcus faecalis and Lactobacillus plantarum, and other Gram-positive bacteria. The producer strain, designated as OSY-I1, was determined to be Brevibacillus laterosporus via morphological, biochemical and genetic analyses. The antimicrobial agent was extracted from cells of OSY-I1 with isopropanol, purified by high-performance liquid chromatography, and structurally analyzed using mass spectrometry (MS) and nuclear magnetic resonance (NMR). The MS and NMR results, taken together, uncovered a linear lipopeptide consisting of 13 amino acids and an N-terminal C6-fatty acid chain (FA), 2-hydroxy-3-methylpentanoic acid. The lipopeptide (FA- Dhb - Leu - Orn - Ile - Ile - Val - Lys - Val - Val - Lys - Tyr - Leu - Valinol) has a molecular mass of 1583.0794 Da and contains three modified amino acid residues; α,β-didehyd...
DksA controls transcription of genes associated with diverse stress responses, such as amino acid... more DksA controls transcription of genes associated with diverse stress responses, such as amino acid and carbon starvation, oxidative stress, and iron starvation. DksA binds within the secondary channel of RNA polymerase, extending its long coiled-coil domain towards the active site. The cellular expression of DksA remains constant due to a negative feedback autoregulation, raising the question of whether DksA activity is directly modulated during stress. Here, we show that Escherichia coli DksA is essential for survival in acidic conditions and that, while its cellular levels do not change significantly, DksA activity and binding to RNA polymerase are increased at lower pH, with a concomitant decrease in its stability. NMR data reveal pH-dependent structural changes centered at the interface of the N and C-terminal regions of DksA. Consistently, we show that a partial deletion of the N-terminal region and substitutions of a histidine 39 residue at the domain interface abolish pH sensi...
Proceedings of the National Academy of Sciences of the United States of America, Jan 8, 2016
The bromodomain and extraterminal domain (BET) protein family are promising therapeutic targets f... more The bromodomain and extraterminal domain (BET) protein family are promising therapeutic targets for a range of diseases linked to transcriptional activation, cancer, viral latency, and viral integration. Tandem bromodomains selectively tether BET proteins to chromatin by engaging cognate acetylated histone marks, and the extraterminal (ET) domain is the focal point for recruiting a range of cellular and viral proteins. BET proteins guide γ-retroviral integration to transcription start sites and enhancers through bimodal interaction with chromatin and the γ-retroviral integrase (IN). We report the NMR-derived solution structure of the Brd4 ET domain bound to a conserved peptide sequence from the C terminus of murine leukemia virus (MLV) IN. The complex reveals a protein-protein interaction governed by the binding-coupled folding of disordered regions in both interacting partners to form a well-structured intermolecular three-stranded β sheet. In addition, we show that a peptide compr...
Three new rotenoids (1-3), two new isoflavonoids (4 and 5), and six known analogues (6-11) were i... more Three new rotenoids (1-3), two new isoflavonoids (4 and 5), and six known analogues (6-11) were isolated from an n-hexane partition of a methanol extract of the fruits of Millettia caerulea, with the structures of the new compounds elucidated by analysis of their spectroscopic data. The relative configurations of the rotenoids were determined by interpretation of their NMR spectroscopic data, and their absolute configurations were established using electronic circular dichroism spectra and specific rotation values. All compounds isolated were evaluated for their cell growth inhibitory activity against the HT-29 human colon cancer cell line, and the known compounds, (-)-3-hydroxyrotenone (6) and (-)-rotenone (7), were found to be potently active. When tested in an NF-κB inhibition assay, compound 6 showed activity. This compound, along with the new compound, (-)-caeruleanone D (1), and the known compound, ichthynone (8), exhibited K-Ras inhibitory potency. Further bioactivity studies...
In spite of its central roles in cell cycle progression, senescence, and aging, knowledge about t... more In spite of its central roles in cell cycle progression, senescence, and aging, knowledge about the posttranslational regulation of P16 (also known as INK4A and MTS1) remains limited. While it has been reported that P16 could be phosphorylated at Ser7, Ser8, Ser140, and Ser152, the corresponding kinases have not been identified yet. Here we report that IKKβ, a primary kinase for IκBα phosphorylation, is involved in P16 phosphorylation. Immunoprecipitation and kinase assays showed that IKKβ specifically binds to P16 and phosphorylates P16 at Ser8 in WI38 cells. Biochemical characterization of phosphomimetic Ser → Glu P16 mutants demonstrated that phosphorylation at Ser8 of P16 brings about a significant loss of its cyclin-dependent kinase (CDK) 4-inhibitory activity while P16 retains structurally and functionally intact upon phosphorylation at Ser7, Ser140, and Ser152. Our results reveal the novel role of IKKβ in P16 phosphorylation and broaden our understanding of the regulation of P16.
Protein science : a publication of the Protein Society, Jan 7, 2016
It was recently discovered that the NRAS isoform 5 (20 amino acids) is expressed in melanoma and ... more It was recently discovered that the NRAS isoform 5 (20 amino acids) is expressed in melanoma and results in a more aggressive cell phenotype. This novel isoform is responsible for increased phosphorylation of downstream targets such as AKT, MEK and ERK as well as increased cellular proliferation. This structure report describes the NMR solution structure of NRAS isoform 5 to be used as a starting point to understand its biophysical interactions. The isoform is highly flexible in aqueous solution, but forms a helix-turn-coil structure in the presence of trifluoroethanol as determined by NMR and CD spectroscopy. This article is protected by copyright. All rights reserved.
A dichapetalin-type triterpenoid and a dibenzylbutyrolactone-type lignan, together with five know... more A dichapetalin-type triterpenoid and a dibenzylbutyrolactone-type lignan, together with five known lignans, a known aromatic diterpenoid, and a known acylated phytosterol, were isolated from the aerial parts of Phyllanthus songboiensis, collected in Vietnam. Their structures were determined by interpretation of the spectroscopic data, and the inhibitory activity toward HT-29 human colon cancer cells of all isolates was evaluated by a cytotoxicity assay. The known arylnaphthalene lignan, (+)-acutissimalignan A, was highly cytotoxic toward HT-29 cells, with an IC50 value of 19 nM, but this compound was inactive as a DNA topoisomerase IIα (topo IIα) poison. The known phytosterol, (-)-β-sitosterol-3-O-β-d-(6-O-palmitoyl)glucopyranoside, was found to stimulate natural killer (NK) cells at a concentration of 10μM in the presence of interleukin 12 (IL-12).
An integrated LC-MS and NMR metabolomic study was conducted to investigate metabolites whose form... more An integrated LC-MS and NMR metabolomic study was conducted to investigate metabolites whose formation was induced by lactofen (1), a soybean (Glycine max L.) disease resistance-inducing herbicide. First, LC-MS analyses of control and lactofen (1)-induced soybean extracts were performed. The LC-MS raw data were then processed by a custom designed bioinformatics program to detect the induced metabolites so formed. Finally, structures of unknown induced metabolites were determined on the basis of their 1D and 2D NMR spectroscopic data. Structure of two previously unreported compounds, 7,8-dihydroxy-4'-methoxy-3'-prenylisoflavone (2) and 7-hydroxy-4',8-dimethoxy-3'-prenylisoflavone (3) were elucidated together with four known prenylated compounds, 3'-prenyldaidzein (4), 8-prenyldaidzein (5), 3'-prenylgenistein (6), and 4-prenylcoumestrol (7). Compounds (2-6) are reported for the first time in soybean, as are the (13)C chemical shift assignments for compound (7). Formation of these six prenylated compounds was also induced by the primary defense glucan elicitor from the cell wall of the pathogen Phytophthora sojae (Kauf. and Gerde.), further suggesting a potential role in soybean defense. These results highlight the metabolic flexibility within soybean secondary product pathways and suggest that prenylation may be associated with defense responses. Moreover, this study demonstrates a promising future approach using metabolomics on elicitor-induced plants for discovery of unknown compounds even in relatively well studied plants.
Plant cell walls are comprised largely of the polysaccharides cellulose, hemicellulose, and pecti... more Plant cell walls are comprised largely of the polysaccharides cellulose, hemicellulose, and pectin, along with ∼10% protein and up to 40% lignin. These wall polymers interact covalently and noncovalently to form the functional cell wall. Characterized cross-links in the wall include covalent linkages between wall glycoprotein extensins between rhamnogalacturonan II monomer domains and between polysaccharides and lignin phenolic residues. Here, we show that two isoforms of a purified Arabidopsis thaliana arabinogalactan protein (AGP) encoded by hydroxyproline-rich glycoprotein family protein gene At3g45230 are covalently attached to wall matrix hemicellulosic and pectic polysaccharides, with rhamnogalacturonan I (RG I)/homogalacturonan linked to the rhamnosyl residue in the arabinogalactan (AG) of the AGP and with arabinoxylan attached to either a rhamnosyl residue in the RG I domain or directly to an arabinosyl residue in the AG glycan domain. The existence of this wall structure, n...
ABSTRACTThis research was initiated to search for novel antimicrobial compounds produced by food ... more ABSTRACTThis research was initiated to search for novel antimicrobial compounds produced by food or environmental microorganisms. A new bacterial strain, designated OSY-SE, which produces a unique and potent antimicrobial agent was isolated from soil. The isolate was identified as aPaenibacillussp. through cultural, biochemical, and genetic analyses. An antimicrobial compound was extracted fromPaenibacillusOSY-SE with acetonitrile and purified using liquid chromatography. After analyses by mass spectrometry (MS) and nuclear magnetic resonance (NMR), the antimicrobial compound was determined to be a cyclic lipopeptide consisting of a C15fatty acyl (FA) chain and 13 amino acids. The deduced sequence is FA-Orn-Val-Thr-Orn-Ser-Val-Lys-Ser-Ile-Pro-Val-Lys-Ile. The carboxyl-terminal Ile is connected to Thr by ester linkage. The new compound, designated paenibacterin, showed antagonistic activities against most Gram-positive and Gram-negative bacteria tested, includingListeria monocytogene...
Applied and environmental microbiology, Jan 26, 2016
A new environmental bacterial strain exhibited strong antimicrobial characteristics against methi... more A new environmental bacterial strain exhibited strong antimicrobial characteristics against methicillin-resistant Staphylococcus aureus, vancomycin-resistant strains of Enterococcus faecalis and Lactobacillus plantarum, and other Gram-positive bacteria. The producer strain, designated as OSY-I1, was determined to be Brevibacillus laterosporus via morphological, biochemical and genetic analyses. The antimicrobial agent was extracted from cells of OSY-I1 with isopropanol, purified by high-performance liquid chromatography, and structurally analyzed using mass spectrometry (MS) and nuclear magnetic resonance (NMR). The MS and NMR results, taken together, uncovered a linear lipopeptide consisting of 13 amino acids and an N-terminal C6-fatty acid chain (FA), 2-hydroxy-3-methylpentanoic acid. The lipopeptide (FA- Dhb - Leu - Orn - Ile - Ile - Val - Lys - Val - Val - Lys - Tyr - Leu - Valinol) has a molecular mass of 1583.0794 Da and contains three modified amino acid residues; α,β-didehyd...
DksA controls transcription of genes associated with diverse stress responses, such as amino acid... more DksA controls transcription of genes associated with diverse stress responses, such as amino acid and carbon starvation, oxidative stress, and iron starvation. DksA binds within the secondary channel of RNA polymerase, extending its long coiled-coil domain towards the active site. The cellular expression of DksA remains constant due to a negative feedback autoregulation, raising the question of whether DksA activity is directly modulated during stress. Here, we show that Escherichia coli DksA is essential for survival in acidic conditions and that, while its cellular levels do not change significantly, DksA activity and binding to RNA polymerase are increased at lower pH, with a concomitant decrease in its stability. NMR data reveal pH-dependent structural changes centered at the interface of the N and C-terminal regions of DksA. Consistently, we show that a partial deletion of the N-terminal region and substitutions of a histidine 39 residue at the domain interface abolish pH sensi...
Proceedings of the National Academy of Sciences of the United States of America, Jan 8, 2016
The bromodomain and extraterminal domain (BET) protein family are promising therapeutic targets f... more The bromodomain and extraterminal domain (BET) protein family are promising therapeutic targets for a range of diseases linked to transcriptional activation, cancer, viral latency, and viral integration. Tandem bromodomains selectively tether BET proteins to chromatin by engaging cognate acetylated histone marks, and the extraterminal (ET) domain is the focal point for recruiting a range of cellular and viral proteins. BET proteins guide γ-retroviral integration to transcription start sites and enhancers through bimodal interaction with chromatin and the γ-retroviral integrase (IN). We report the NMR-derived solution structure of the Brd4 ET domain bound to a conserved peptide sequence from the C terminus of murine leukemia virus (MLV) IN. The complex reveals a protein-protein interaction governed by the binding-coupled folding of disordered regions in both interacting partners to form a well-structured intermolecular three-stranded β sheet. In addition, we show that a peptide compr...
Three new rotenoids (1-3), two new isoflavonoids (4 and 5), and six known analogues (6-11) were i... more Three new rotenoids (1-3), two new isoflavonoids (4 and 5), and six known analogues (6-11) were isolated from an n-hexane partition of a methanol extract of the fruits of Millettia caerulea, with the structures of the new compounds elucidated by analysis of their spectroscopic data. The relative configurations of the rotenoids were determined by interpretation of their NMR spectroscopic data, and their absolute configurations were established using electronic circular dichroism spectra and specific rotation values. All compounds isolated were evaluated for their cell growth inhibitory activity against the HT-29 human colon cancer cell line, and the known compounds, (-)-3-hydroxyrotenone (6) and (-)-rotenone (7), were found to be potently active. When tested in an NF-κB inhibition assay, compound 6 showed activity. This compound, along with the new compound, (-)-caeruleanone D (1), and the known compound, ichthynone (8), exhibited K-Ras inhibitory potency. Further bioactivity studies...
In spite of its central roles in cell cycle progression, senescence, and aging, knowledge about t... more In spite of its central roles in cell cycle progression, senescence, and aging, knowledge about the posttranslational regulation of P16 (also known as INK4A and MTS1) remains limited. While it has been reported that P16 could be phosphorylated at Ser7, Ser8, Ser140, and Ser152, the corresponding kinases have not been identified yet. Here we report that IKKβ, a primary kinase for IκBα phosphorylation, is involved in P16 phosphorylation. Immunoprecipitation and kinase assays showed that IKKβ specifically binds to P16 and phosphorylates P16 at Ser8 in WI38 cells. Biochemical characterization of phosphomimetic Ser → Glu P16 mutants demonstrated that phosphorylation at Ser8 of P16 brings about a significant loss of its cyclin-dependent kinase (CDK) 4-inhibitory activity while P16 retains structurally and functionally intact upon phosphorylation at Ser7, Ser140, and Ser152. Our results reveal the novel role of IKKβ in P16 phosphorylation and broaden our understanding of the regulation of P16.
Protein science : a publication of the Protein Society, Jan 7, 2016
It was recently discovered that the NRAS isoform 5 (20 amino acids) is expressed in melanoma and ... more It was recently discovered that the NRAS isoform 5 (20 amino acids) is expressed in melanoma and results in a more aggressive cell phenotype. This novel isoform is responsible for increased phosphorylation of downstream targets such as AKT, MEK and ERK as well as increased cellular proliferation. This structure report describes the NMR solution structure of NRAS isoform 5 to be used as a starting point to understand its biophysical interactions. The isoform is highly flexible in aqueous solution, but forms a helix-turn-coil structure in the presence of trifluoroethanol as determined by NMR and CD spectroscopy. This article is protected by copyright. All rights reserved.
A dichapetalin-type triterpenoid and a dibenzylbutyrolactone-type lignan, together with five know... more A dichapetalin-type triterpenoid and a dibenzylbutyrolactone-type lignan, together with five known lignans, a known aromatic diterpenoid, and a known acylated phytosterol, were isolated from the aerial parts of Phyllanthus songboiensis, collected in Vietnam. Their structures were determined by interpretation of the spectroscopic data, and the inhibitory activity toward HT-29 human colon cancer cells of all isolates was evaluated by a cytotoxicity assay. The known arylnaphthalene lignan, (+)-acutissimalignan A, was highly cytotoxic toward HT-29 cells, with an IC50 value of 19 nM, but this compound was inactive as a DNA topoisomerase IIα (topo IIα) poison. The known phytosterol, (-)-β-sitosterol-3-O-β-d-(6-O-palmitoyl)glucopyranoside, was found to stimulate natural killer (NK) cells at a concentration of 10μM in the presence of interleukin 12 (IL-12).
An integrated LC-MS and NMR metabolomic study was conducted to investigate metabolites whose form... more An integrated LC-MS and NMR metabolomic study was conducted to investigate metabolites whose formation was induced by lactofen (1), a soybean (Glycine max L.) disease resistance-inducing herbicide. First, LC-MS analyses of control and lactofen (1)-induced soybean extracts were performed. The LC-MS raw data were then processed by a custom designed bioinformatics program to detect the induced metabolites so formed. Finally, structures of unknown induced metabolites were determined on the basis of their 1D and 2D NMR spectroscopic data. Structure of two previously unreported compounds, 7,8-dihydroxy-4'-methoxy-3'-prenylisoflavone (2) and 7-hydroxy-4',8-dimethoxy-3'-prenylisoflavone (3) were elucidated together with four known prenylated compounds, 3'-prenyldaidzein (4), 8-prenyldaidzein (5), 3'-prenylgenistein (6), and 4-prenylcoumestrol (7). Compounds (2-6) are reported for the first time in soybean, as are the (13)C chemical shift assignments for compound (7). Formation of these six prenylated compounds was also induced by the primary defense glucan elicitor from the cell wall of the pathogen Phytophthora sojae (Kauf. and Gerde.), further suggesting a potential role in soybean defense. These results highlight the metabolic flexibility within soybean secondary product pathways and suggest that prenylation may be associated with defense responses. Moreover, this study demonstrates a promising future approach using metabolomics on elicitor-induced plants for discovery of unknown compounds even in relatively well studied plants.
Uploads
Papers by chunhua yuan