Catabolism of strigolactones by a carboxylesterase
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ABSTRACT:
PROVIDER: PRJNA734575 | ENA |
REPOSITORIES: ENA
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Project description:Strigolactones (SLs) are carotenoid-derived plant hormones that control shoot branching and communications between host plants and symbiotic fungi or root parasitic plants. Extensive studies have identified the key components participating in SL biosynthesis and signaling, whereas the catabolism or deactivation of endogenous SLs in planta remains largely unknown. Here we report that the Arabidopsis carboxylesterase 15 (AtCXE15) and its orthologues function as efficient hydrolases of SLs. We show that overexpression of AtCXE15 promotes shoot branching by dampening SL-inhibited axillary bud outgrowth. We further demonstrate that AtCXE15 could bind and efficiently hydrolyze SLs both in vitro and in planta. We also provide evidence that AtCXE15 is capable to catalyze hydrolysis of diverse SL analogues and that such CXE15-dependent catabolism of SLs is evolutionarily conserved in seed plants. These results disclose a catalytic mechanism underlying homeostatic regulation of SLs in plants, which also provides a rational approach to spatial-temporally manipulate the endogenous SLs and thus architecture of crops and ornamental plants.
2021-08-05 | GSE176007 | GEO
Project description:Impaired branched-chain amino acid (BCAA) catabolism has recently been implicated in the development of mechanical pain, but the underlying molecular mechanisms are unclear. Here we report that defective BCAA catabolism in dorsal root ganglion (DRG) neurons sensitizes mice to mechanical pain by increasing lactate production and expression of the mechanotransduction channel Piezo2. In high-fat diet-fed obese mice, we observe downregulation of PP2Cm, a key regulator of the BCAA catabolic pathway, in DRG neurons. Mice with conditional knockout of PP2Cm in DRG neurons exhibit mechanical allodynia under normal or SNI-induced neuropathic injury conditions. Furthermore, the VAS scores in the plasma of patients with peripheral neuropathic pain are positively correlated with BCAA contents. Mechanistically, defective BCAA catabolism in DRG neurons promotes lactate production through glycolysis, which increases H3K18la modification and drives Piezo2 expression. Inhibition of lactate production or Piezo2 silencing attenuates the pain phenotype of knockout mice in response to mechanical stimuli. Therefore, our study demonstrates a causal role of defective BCAA catabolism in mechanical pain by enhancing metabolite-mediated epigenetic regulation.
2023-08-27 | GSE235230 | GEO
Project description:Sphingolipids are required for diverse biological functions and are degraded by specific catabolic enzymes. However, the mechanisms that regulate sphingolipid catabolism are not known. Here we characterize a transcriptional axis that regulates sphingolipid breakdown to control resistance against bacterial infection. From an RNAi screen for transcriptional regulators of pathogen resistance in the nematode C. elegans, we identified the nuclear hormone receptor nhr-66, a ligand-gated transcription factor homologous to human hepatocyte nuclear factor 4. Tandem chromatin immunoprecipitation-sequencing (ChIP-seq) and RNA sequencing (RNA-seq) experiments revealed that NHR-66 is a transcriptional repressor, which directly targets sphingolipid catabolism genes. Transcriptional de-repression of two sphingolipid catabolic enzymes in nhr-66 loss-of-function mutants drives the breakdown of sphingolipids, which enhances host susceptibility to infection with the bacterial pathogen Pseudomonas aeruginosa. These data define transcriptional control of sphingolipid catabolism in the regulation of cellular sphingolipids, a process that is necessary for pathogen resistance.
2023-09-08 | GSE240426 | GEO
Project description:While Neanderthals are extinct, fragments of their genome still persist in the genomes of contemporary humans. Here, we show that such Neanderthal-like sequences are not distributed randomly in contemporary human genomes. Specifically, while genome-wide frequency of Neanderthal-like sites is close to 6% in all out-of-Africa populations, genes involved in lipid catabolism contain large excess Neanderthal-like sequences in Europeans (24.3%), but not in Asians (12.4%). While lipid catabolism cannot be assayed in Neanderthals, we took advantage of genetic divergence between human populations, chimpanzees and Neanderthals to predict metabolic divergence expected from the observed excess of Neanderthal gene flow into Europeans. We confirmed predicted changes in lipid catabolism using hydrophobic metabolome measurements in the brain tissue and further linked these metabolic changes to gene expression divergence. 14 human and 6 chimpanzee samples were sequenced.
2014-03-31 | E-GEOD-45263 | biostudies-arrayexpress
Project description:Here, we identified a long-chain acyl-CoA-responsive transcriptional repressor, FdmR, as the key regulator of mycobacterial fatty acid catabolism. We employed ChIP-Seq to identify the genomic binding regions for FdmR. FdmR was found to bind upstream of fadA2, fabG4, fadE24, fixA, MMAR_1683, fadE5, icl, desA3, desA3_1, and MMAR_2730.We then demonstrated that FdmR acts as a valve to direct the fatty acid flux from β-oxidation towards lipid biosynthesis, thereby avoiding the overactive catabolism and accumulation of biologically toxic intermediates. This regulatory mechanism enables a high rate of cell growth with modest consumption of fatty acid substrates.
2021-03-01 | GSE156432 | GEO
Project description:Endogenous retroviruses (ERVs) are remnants of ancient parasitic viral integrations and comprise a sizable portion of the genome in most organisms. Deregulated expression of ERVs in human is associated with a plethora of disease conditions, such as cancer and neurodegeneration. Epigenetic mechanisms silence most ERVs by generating a local repressive environment (heterochromatin) to prevent their expression. However, the mechanisms controlling the fate of ERVs residing in euchromatic regions of the genome (e.g. MERVL elements) are not well understood. Here, by integrating multidimensional epigenetic and genomic analyses, we demonstrate that silencing of euchromatic MERVL elements is achieved via transcription-coupled RNA degradation. Disrupting RNA catabolism promotes RNAPII elongation from MERVL promoters, increases MERVL expression and exonization, creating novel chimeric gene isoforms, and directing embryonic stem (ES) cells toward a terminal undifferentiated state. Our results indicate that RNA catabolism is a core regulatory module of gene networks that safeguards cell identity and potency, restricts MERVL functionalization and suppresses gene birth.
2023-10-01 | GSE205207 | GEO
Project description:Aromatic compounds are an important renewable source of commodity chemicals traditionally produced from fossil fuels. Aromatics derived from plant lignin can potentially be converted into commodity chemicals through depolymerization followed by microbial funneling of monomers and low molecular weight oligomers. This study investigates the catabolism of the b-5 linked aromatic dimer dehydrodiconiferyl alcohol (DC-A) by the bacterium Novosphingobium aromaticivorans. We used genome wide screens to identify candidate genes involved in DC-A catabolism. Subsequent in vivo and in vitro analyses of these candidates elucidated a catabolic pathway composed of four required gene products and several partially redundant dehydrogenases that convert DC-A to aromatic monomers that can be funneled into the central aromatic metabolic pathway of N. aromaticivorans. Specifically, a newly identified γ-formaldehyde lyase, PcfL, opens the phenylcoumaran ring to form a stilbene and formaldehyde. A lignostilbene dioxygenase, LsdD, then cleaves the stilbene to generate the aromatic monomers, vanillin and 5-formylferulate (5-FF). We also show that an aldehyde dehydrogenase FerD oxidizes 5-FF before it is decarboxylated by LigW, yielding ferulic acid. We found that some enzymes involved in b-5 catabolism pathway can act on multiple substrates and that some steps in the pathway can be mediated by multiple enzymes, providing new insights into the robust flexibility of aromatic catabolism in N. aromaticivorans. We performed a comparative genomic analysis to predict that key enzymes in the newly discovered b-5 aromatic catabolic pathway are common among Sphingomonads.
2024-02-29 | GSE259365 | GEO
Project description:Trichoderma reesei is used to produce saccharifying enzyme cocktails for biofuels. There is limited understanding of the transcription factors (TFs) that regulate the release and catabolism of L-arabinose and D-galactose, as the main TF XYR1 is only partially involved. The T. reesei ortholog of ARA1 from Pyricularia oryzae that regulates L-arabinose release and catabolism, was deleted and characterized by growth profiling and transcriptomics along with a xyr1 mutant and xyr1/ara1 double mutant. Our results show that, in addition to the L-arabinose-related role, T. reesei ARA1 is essential for D-galactose release and catabolism, while XYR1 is not involved in this process.
2017-11-02 | GSE104606 | GEO
Project description:While Neanderthals are extinct, fragments of their genome still persist in the genomes of contemporary humans. Here, we show that such Neanderthal-like sequences are not distributed randomly in contemporary human genomes. Specifically, while genome-wide frequency of Neanderthal-like sites is close to 6% in all out-of-Africa populations, genes involved in lipid catabolism contain large excess Neanderthal-like sequences in Europeans (24.3%), but not in Asians (12.4%). While lipid catabolism cannot be assayed in Neanderthals, we took advantage of genetic divergence between human populations, chimpanzees and Neanderthals to predict metabolic divergence expected from the observed excess of Neanderthal gene flow into Europeans. We confirmed predicted changes in lipid catabolism using hydrophobic metabolome measurements in the brain tissue and further linked these metabolic changes to gene expression divergence.
2014-03-31 | GSE45263 | GEO
Project description:p-Hydroxycinnamates, such as p-coumarate and ferulate, are components of plant cell walls and have a number of commercial applications. Previously, we had shown that the soil Actinobacterium Rhodococcus jostii RHA1 (RHA1) grows on ferulate, catabolizing it via vanillate and the M-NM-2-ketoadipate pathway. We used transcriptomics to identify genes in RHA1 that were specifically up-regulated during growth on ferulate. These include three operons predicted to encode the uptake and M-NM-2-oxidative deacetylation of ferulate and p-coumarate: couHLT, couMNO and couR. A couL mutant did not grow on p-coumarate, ferulate or their dihydro derivatives, but grew on vanillate. Purified CouL catalyzed the thioesterification of several p-hydroxycinnamates. Among the tested substrates, the best were p-coumarate and caffeate (kcat/KM ~400 mM-1s-1), and sinapate was not transformed. Of these, p-coumarate was also RHA1M-bM-^@M-^Ys preferred growth substrate. Although the data indicate that p-hydroxycinnamates are catabolized via M-NM-2-oxidation, the pathway lacks a typical M-NM-2-ketothiolase. The data further suggest the involvement of two formaldehyde detoxification pathways in vanillate catabolism. This study augments our understanding of the bacterial catabolism of biomass and facilitates the production of aromatics from renewable feedstocks. Transcriptomes of R. jostii RHA1 from ferulate and benzoate cultures were analysed using Ion PGMTM system.
2014-09-28 | E-GEOD-56355 | biostudies-arrayexpress