Hypoxia-inducible factor 1 recruits FACT and RNF20/40 to mediate histone ubiquitination and transcriptional activation of target genes.

Hypoxia-inducible factor 1 (HIF-1) is a transcriptional activator that mediates cellular adaptation to decreased oxygen availability. HIF-1 recruits chromatin-modifying enzymes leading to changes in histone acetylation, citrullination, and methylation at target genes. Here, we demonstrate that hypoxia-inducible gene expression in estrogen receptor (ER)-positive MCF7 and ER-negative SUM159 human breast cancer cells requires the histone H2A/H2B chaperone facilitates chromatin transcription (FACT) and the H2B ubiquitin ligase RING finger protein 20/40 (RNF20/40). Knockdown of FACT or RNF20/40 expression leads to decreased transcription initiation and elongation at HIF-1 target genes. Mechanistically, FACT and RNF20/40 are recruited to hypoxia response elements (HREs) by HIF-1 and stabilize binding of HIF-1 (and each other) at HREs. Hypoxia induces the monoubiquitination of histone H2B at lysine 120 at HIF-1 target genes in an HIF-1-dependent manner. Together, these findings delineate a cooperative molecular mechanism by which FACT and RNF20/40 stabilize multiprotein complex formation at HREs and mediate histone ubiquitination to facilitate HIF-1 transcriptional activity.

Readthrough events in plants reveal plasticity of stop codons.

Stop codon readthrough (SCR) has important biological implications but remains largely uncharacterized. Here, we identify 1,009 SCR events in plants using a proteogenomic strategy. Plant SCR candidates tend to have shorter transcript lengths and fewer exons and splice variants than non-SCR transcripts. Mass spectrometry evidence shows that stop codons involved in SCR events can be recoded as 20 standard amino acids, some of which are also supported by suppressor tRNA analysis. We also observe multiple functional signals in 34 maize extended proteins and characterize the structural and subcellular localization changes in the extended protein of basic transcription factor 3. Furthermore, the SCR events exhibit non-conserved signature, and the extensions likely undergo protein-coding selection. Overall, our study not only characterizes that SCR events are commonly present in plants but also identifies the recoding plasticity of stop codons, which provides important insights into the flexibility of genetic decoding.

Plexin-B3 expression stimulates MET signaling, breast cancer stem cell specification, and lung metastasis.

Intratumoral hypoxia is a microenvironmental feature that promotes breast cancer progression and is associated with cancer mortality. Plexin B3 (PLXNB3) is highly expressed in estrogen receptor-negative breast cancer, but the underlying mechanisms and consequences have not been thoroughly investigated. Here, we report that PLXNB3 expression is increased in response to hypoxia and that PLXNB3 is a direct target gene of hypoxia-inducible factor 1 (HIF-1) in human breast cancer cells. PLXNB3 expression is correlated with HIF-1α immunohistochemistry, breast cancer grade and stage, and patient mortality. Mechanistically, PLXNB3 is required for hypoxia-induced MET/SRC/focal adhesion kinase (FAK) and MET/SRC/STAT3/NANOG signaling as well as hypoxia-induced breast cancer cell migration, invasion, and cancer stem cell specification. PLXNB3 knockdown impairs tumor formation and lung metastasis in orthotopic breast cancer mouse models.

NARF is a hypoxia-induced coactivator for OCT4-mediated breast cancer stem cell specification.

Hypoxia is a key characteristic of the breast cancer microenvironment that promotes expression of the transcriptional activator hypoxia-inducible factor 1 (HIF-1) and is associated with poor patient outcome. HIF-1 increases the expression or activity of stem cell pluripotency factors, which control breast cancer stem cell (BCSC) specification and are required for cancer metastasis. Here, we identify nuclear prelamin A recognition factor (NARF) as a hypoxia-inducible, HIF-1 target gene in human breast cancer cells. NARF functions as an essential coactivator by recruiting the histone demethylase KDM6A to OCT4 bound to genes encoding the pluripotency factors NANOG, KLF4, and SOX2, leading to demethylation of histone H3 trimethylated at lysine-27 (H3K27me3), thereby increasing the expression of NANOG, KLF4, and SOX2, which, together with OCT4, mediate BCSC specification. Knockdown of NARF significantly decreased the BCSC population in vitro and markedly impaired tumor initiation capacity and lung metastasis in orthotopic mouse models.

A Review of Vector-Borne Rice Viruses.

Rice (Oryza sativa L.) is one of the major staple foods for global consumption. A major roadblock to global rice production is persistent loss of crops caused by plant diseases, including rice blast, sheath blight, bacterial blight, and particularly various vector-borne rice viral diseases. Since the late 19th century, 19 species of rice viruses have been recorded in rice-producing areas worldwide and cause varying degrees of damage on the rice production. Among them, southern rice black-streaked dwarf virus (SRBSDV) and rice black-streaked dwarf virus (RBSDV) in Asia, rice yellow mottle virus (RYMV) in Africa, and rice stripe necrosis virus (RSNV) in America currently pose serious threats to rice yields. This review systematizes the emergence and damage of rice viral diseases, the symptomatology and transmission biology of rice viruses, the arm races between viruses and rice plants as well as their insect vectors, and the strategies for the prevention and control of rice viral diseases.

HIF inhibitor 32-134D eradicates murine hepatocellular carcinoma in combination with anti-PD1 therapy.

Hepatocellular carcinoma (HCC) is a major cause of cancer mortality worldwide and available therapies, including immunotherapies, are ineffective for many patients. HCC is characterized by intratumoral hypoxia, and increased expression of hypoxia-inducible factor 1α (HIF-1α) in diagnostic biopsies is associated with patient mortality. Here we report the development of 32-134D, a low-molecular-weight compound that effectively inhibits gene expression mediated by HIF-1 and HIF-2 in HCC cells, and blocks human and mouse HCC tumor growth. In immunocompetent mice bearing Hepa1-6 HCC tumors, addition of 32-134D to anti-PD1 therapy increased the rate of tumor eradication from 25% to 67%. Treated mice showed no changes in appearance, behavior, body weight, hemoglobin, or hematocrit. Compound 32-134D altered the expression of a large battery of genes encoding proteins that mediate angiogenesis, glycolytic metabolism, and responses to innate and adaptive immunity. This altered gene expression led to significant changes in the tumor immune microenvironment, including a decreased percentage of tumor-associated macrophages and myeloid-derived suppressor cells, which mediate immune evasion, and an increased percentage of CD8+ T cells and natural killer cells, which mediate antitumor immunity. Taken together, these preclinical findings suggest that combining 32-134D with immune checkpoint blockade may represent a breakthrough therapy for HCC.

Ascorbate peroxidase 1 confers resistance to southern corn leaf blight in maize.

Southern corn leaf blight (SCLB), caused by Bipolaris maydis, is one of the most devastating diseases affecting maize production. However, only one SLCB resistance gene, conferring partial resistance, is currently known, underscoring the importance of isolating new SCLB resistance-related genes. Here, we performed a comparative proteomic analysis and identified 258 proteins showing differential abundance during the maize response to B. maydis. These proteins included an ascorbate peroxidase (Zea mays ascorbate peroxidase 1 (ZmAPX1)) encoded by a gene located within the mapping interval of a previously identified quantitative trait locus associated with SCLB resistance. ZmAPX1 overexpression resulted in lower H2 O2 accumulation and enhanced resistance against B. maydis. Jasmonic acid (JA) contents and transcript levels for JA biosynthesis and responsive genes increased in ZmAPX1-overexpressing plants infected with B. maydis, whereas Zmapx1 mutants showed the opposite effects. We further determined that low levels of H2 O2 are accompanied by an accumulation of JA that enhances SCLB resistance. These results demonstrate that ZmAPX1 positively regulates SCLB resistance by decreasing H2 O2 accumulation and activating the JA-mediated defense signaling pathway. This study identified ZmAPX1 as a potentially useful gene for increasing SCLB resistance. Furthermore, the generated data may be relevant for clarifying the functions of plant APXs.

HIF-1 Interacts with TRIM28 and DNA-PK to release paused RNA polymerase II and activate target gene transcription in response to hypoxia.

Hypoxia-inducible factor-1 (HIF-1) is a transcription factor that acts as a regulator of oxygen (O2) homeostasis in metazoan species by binding to hypoxia response elements (HREs) and activating the transcription of hundreds of genes in response to reduced O2 availability. RNA polymerase II (Pol II) initiates transcription of many HIF target genes under non-hypoxic conditions but pauses after approximately 30-60 nucleotides and requires HIF-1 binding for release. Here we report that in hypoxic breast cancer cells, HIF-1 recruits TRIM28 and DNA-dependent protein kinase (DNA-PK) to HREs to release paused Pol II. We show that HIF-1α and TRIM28 assemble the catalytically-active DNA-PK heterotrimer, which phosphorylates TRIM28 at serine-824, enabling recruitment of CDK9, which phosphorylates serine-2 of the Pol II large subunit C-terminal domain as well as the negative elongation factor to release paused Pol II, thereby stimulating productive transcriptional elongation. Our studies reveal a molecular mechanism by which HIF-1 stimulates gene transcription and reveal that the anticancer effects of drugs targeting DNA-PK in breast cancer may be due in part to their inhibition of HIF-dependent transcription.

HIF-1 recruits NANOG as a coactivator for TERT gene transcription in hypoxic breast cancer stem cells.

Breast cancer stem cells (BCSCs) play essential roles in tumor formation, drug resistance, relapse, and metastasis. NANOG is a protein required for stem cell self-renewal, but the mechanisms by which it performs this function are poorly understood. Here, we show that hypoxia-inducible factor 1α (HIF-1α) is required for NANOG-mediated BCSC enrichment. Mechanistically, NANOG is recruited by HIF-1 to cooperatively activate transcription of the TERT gene encoding the telomerase reverse transcriptase that maintains telomere length, which is required for stem cell self-renewal. NANOG stimulates HIF-1 transcriptional activity by recruitment of the deubiquitinase USP9X, which inhibits HIF-1α protein degradation, and by stabilizing HIF-1α interaction with the coactivator p300, which mediates histone acetylation. Our results delineate a cooperative transcriptional mechanism by which HIF-1 and NANOG mediate BCSC self-renewal.

Histone citrullination by PADI4 is required for HIF-dependent transcriptional responses to hypoxia and tumor vascularization.

Hypoxia-inducible factors (HIFs) activate transcription of target genes by recruiting coactivators and chromatin-modifying enzymes. Peptidylarginine deiminase 4 (PADI4) catalyzes the deimination of histone arginine residues to citrulline. Here, we demonstrate that PADI4 expression is induced by hypoxia in a HIF-dependent manner in breast cancer and hepatocellular carcinoma cells. PADI4, in turn, is recruited by HIFs to hypoxia response elements (HREs) and is required for HIF target gene transcription. Hypoxia induces histone citrullination at HREs that is PADI4 and HIF dependent. RNA sequencing revealed that almost all HIF target genes in breast cancer cells are PADI4 dependent. PADI4 is required for breast and liver tumor growth and angiogenesis in mice. PADI4 expression is correlated with HIF-1α expression and vascularization in human breast cancer biopsies. Thus, HIF-dependent recruitment of PADI4 to target genes and local histone citrullination are required for transcriptional responses to hypoxia.

Hypoxia-inducible factor-dependent ADAM12 expression mediates breast cancer invasion and metastasis.

Breast cancer patients with increased expression of hypoxia-inducible factors (HIFs) in primary tumor biopsies are at increased risk of metastasis, which is the major cause of breast cancer-related mortality. The mechanisms by which intratumoral hypoxia and HIFs regulate metastasis are not fully elucidated. In this paper, we report that exposure of human breast cancer cells to hypoxia activates epidermal growth factor receptor (EGFR) signaling that is mediated by the HIF-dependent expression of a disintegrin and metalloprotease 12 (ADAM12), which mediates increased ectodomain shedding of heparin-binding EGF-like growth factor, an EGFR ligand, leading to EGFR-dependent phosphorylation of focal adhesion kinase. Inhibition of ADAM12 expression or activity decreased hypoxia-induced breast cancer cell migration and invasion in vitro, and dramatically impaired lung metastasis after orthotopic implantation of MDA-MB-231 human breast cancer cells into the mammary fat pad of immunodeficient mice.

Theoretical Characterization of Catalytically Active Species in Reductive Hydroxymethylation of Styrene with CO2 over a Bisphosphine-Ligated Copper Complex.

In this work, a density functional theory (DFT) study was performed to identify the catalytically active species in the copper-catalyzed three-component reductive hydroxymethylation of styrene with CO2 and hydrosilane. The calculations reveal that the dimeric copper(I) hydride species, formed in a mixture of the bisphosphine ligand, Cu(OAc)2, and hydrosilane, probably acts as the catalyst precursor. In the beginning, this species is catalytically competent to trigger the hydrocupration of styrene, along with the formation of the dimeric copper(I) alkyl intermediate. Subsequently, CO2 insertion into the dimeric copper(I) alkyl intermediate occurs, which is accompanied by the cleavage of the Cu-Cu bond and the generation of the monomeric copper(I) carboxylate intermediate. In the end, the sequential reduction of the monomeric copper(I) carboxylate intermediate with the hydrosilane produces the monomeric copper(I) hydride species as the actual catalyst and turns on the catalytic cycle. On the other hand, the monomeric copper(II) hydride species, yielded as the kinetic product in the initial reaction of the bisphosphine ligand, Cu(OAc)2, and hydrosilane, is also reactive for the hydrocupration of styrene. However, the resulting monomeric copper(II) alkyl intermediate is found to be the catalyst resting state, because of the much higher energy barrier demanded for the subsequent nucleophilic attack toward CO2. On the basis of the results of an activation-strain model (ASM) analysis and charge decomposition analysis (CDA), the low activity of the monomeric copper(II) alkyl intermediate can be ascribed to the more crowded environment around the central copper(II) ion and the weaker nucleophilicity of the alkyl moiety. Furthermore, all of the possible CuH species generated in the system are competent to promote the two-component hydrosilylation of CO2 with hydrosilane, which is an inevitable side reaction along with the reductive hydroxymethylation of styrene with CO2 and hydrosilane.

Molecular mechanism comparison of decarbonylation with deoxygenation and hydrogenation of 5-hydroxymethylfurfural catalyzed by palladium acetate.

The selective removal of oxygen from 5-hydroxymethylfurfural (HMF) is challenging for the effective utilization of biomass. The catalytic mechanisms of palladium acetate toward the conversion of HMF to furfuryl alcohol (FFA), 5-methylfurfural (5-MF) and 2,5-dihydroxymethyl furan (DHMF) have been theoretically investigated. The decarbonylation of HMF to FFA includes (i) migratory extrusion, (ii) metal-acetate-co-assisted deprotonation, (iii) decarbonylation, (iv) metal-assisted deprotonation, and (v) migratory extrusion and catalyst regeneration. Both hydrogenation and deoxidation of HMF with HCOOH as the H-source involve (i) migratory extrusion, (ii) oxidative addition, (iii) reductive elimination, (iv) metal-assisted deprotonation, and (v) migratory extrusion and catalyst regeneration. The C-H bond cleavage is the crucial reaction step, in which the metal-acetate-co-assisted deprotonation is kinetically more preferable than the oxidative addition. Both FFA and DHMF are kinetically superior to 5-MF. In terms of selectivity, increasing the temperature is beneficial to decarbonylation and decreasing the temperature is advantageous to hydrogenation. The present finding provides molecular-level insight into the functions of both the metal-center and coordinated-ligand in the Pd(OAc)2 catalyst, which may drive the novel design of catalytic systems toward both decarbonylation and hydrogenation reactions.

Regular patterns of the effects of hydrogen-containing additives on the formation of CdSe monomer.

It is unclear at the molecular level why HY (HY = RSH, or ROH, or RNH2) with HPPh2 additives kinetically affects the reaction pathway to the formation of different monomers (Ph2P-SeCd-Y or Ph2P-SeCdSe-Y) in the systhesis of semiconductor nanocrystals. In the present work, it was found that in a [Cd(OA)2 + Se[double bond, length as m-dash]P(C8H17)3 + HPPh2 + HY] mixture, HY behaves as a mediator for the formation of the initial kind of monomer, besides as a hydrogen/proton donor in the release of oleic acid and as an accelerant in the Se-P bond cleavage, which follows the mechanism of hydrogen-shift/nucleophilic-attack. The capability of the HY additive to provide a H-source decreases in the order SePPh2H > RSH > HPPh2 > ROH > RNH2, while the performance of HY to accelerate Se-P bond cleavage decreases in the order HPPh2 > RSH > RNH2 > ROH. The capacity of HY to promote the formation of the Ph2P-SeCd-Y monomer decreases in the order RSH > HPPh2 > ROH > RNH2, while the effect of HY to drive the formation of the Ph2P-SeCdSe-Y monomer decreases in the order HPPh2 > RSH > RNH2 > ROH. The activation strain energy plays a key role in both the Se-P and H-Y bond cleavage, which correlates negatively to the size of the coordinated atom radius. When only HPPh2 is present without other HY species (HY = RNH2, or RSH, or ROH), Ph2P-SeCdSe-PPh2 is preferentially formed. Alternatively, when both HY (HY = RNH2, or RSH, or ROH) and HPPh2 are present, Ph2P-SeCd-Y is favorably formed. For the formation of Ph2P-SeCd-Y (Y = -PPh2, -SR, -OR, and -NHR), SePPh2H embodies the catalytic performance, while HPPh2 serves as the catalyst for the formation of Ph2P-SeCdSe-Y (Y = -NHR or -OR). Our study brings a molecular-level insight into the relationship between the CdSe monomer and the phosphorous-containing side-product, which may advance the rational design and synthesis of quantum dots.

A theoretical study on the unusual square-planar structure of bis(imino)pyridine-ligated Group 13 complexes.

The unusual square-planar (SP) structure of four-coordinate AlIII-complexes with the phenyl-substituted tridentate bis(imino)pyridine (PhI2P) ligand has been studied by a combination of density functional theory (DFT) calculations, frontier molecule orbital (FMO), nucleus-independent chemical shift (NICS) and strain/interaction analyses. The calculations disclose that: (i) the aromaticity shifting from the pyridine ring to the alumina-imidazolate metallacycle, and (ii) the small strain energy imposed on the ligand backbone are two favourable factors for driving the overall SP coordination of the AlIII ion. Meanwhile, the calculations reveal that the SP coordination of the AlIII ion is also influenced by the fourth ligand that is bonded to the AlIII ion. The less steric demanding ligand could ensure the stronger aromaticity of the alumina-imidazolate metallacycle and small strain energy on the ligand backbone. Additionally, the calculations predict that GaIII and InIII ions favour the SP geometry in the analogue PhI2P-ligated complexes, while BIII and TlIII ions are reluctant to adopt the SP coordination with the PhI2P ligand. Overall, all of these findings would be helpful for the synthesis of more unknown low-valent main-group metal complexes bearing the bis(imino)pyridine ligand.

A comparative computational study of N-heterocyclic olefin and N-heterocyclic carbene mediated carboxylative cyclization of propargyl alcohols with CO2.

The carboxylative cyclization of a propargyl alcohol with CO2 mediated by a N-heterocyclic olefin (NHO) or N-heterocyclic carbene (NHC) has been comparatively studied using density functional theory (DFT) calculations. The calculations show that the advantageous catalytic performance of the NHO in the title reaction can be attributed to two aspects: (i) the active site of the NHO extends outside the imidazolium ring, which enhances the reactivity and stability of the [NHOH]+[carbonate]- ionic pair intermediate. Thus, the turnover frequency (TOF)-determining intramolecular cyclization step is kinetically more favorable in the NHO system. (ii) As the basicity of the NHO is weaker than the NHC, deprotonation of the propargyl alcohol by the NHO is relatively more difficult. Consequently, the side reaction of ring-opening transesterification of the α-alkylidene cyclic carbonate with the nucleophilic [NHOH]+[alkoxide]- ionic pair intermediate can be inhibited using the NHO system. The present mechanistic study provides a basis for further application of these promising organocatalysts in more organic transformations.

Theoretical Insights into the Catalytic Mechanism of N-Heterocyclic Olefins in Carboxylative Cyclization of Propargyl Alcohol with CO2.

The mechanism of carboxylative cyclization of propargyl alcohol with CO2 catalyzed by N-heterocyclic olefins (NHOs) has been studied by density functional theory calculations. The calculations reveal that the catalytic reaction tends to proceed via the NHO-mediated basic ionic pair mechanism, in which free NHO primarily acts as a basic precursor to trigger the carboxylation of propargyl alcohol with CO2, leading to a [NHOH](+)[carbonate](-) ion pair intermediate. Then, the catalytic cycle proceeds, including isomerization of the [NHOH](+)[carbonate](-) ion pair intermediate, intramolecular nucleophilic addition of the carbonate oxygen anion to the alkynyl group, and protonation of the alkenyl carbon anion with an external propargyl alcohol molecule. Molecule orbital and nature population analysis discloses that the preference for the basic ionic pair mechanism is due to the favorable orbital and charge interactions between the α-carbon atom of NHO and the hydroxyl hydrogen of propargyl alcohol. The [NHOH](+) cation has proven to be crucial for stabilizing the [carbonate](-) anion, which allows the reaction to proceed through a more thermodynamically stable pathway. The investigations of the effect of substituents of NHOs predict that N-substituents with a strong electron donating effect and a bulky steric effect might improve the catalytic activity of NHOs for the reaction.