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1.
Cell ; 176(6): 1310-1324.e10, 2019 03 07.
Article in English | MEDLINE | ID: mdl-30827684

ABSTRACT

DNA rearrangements resulting in human genome structural variants (SVs) are caused by diverse mutational mechanisms. We used long- and short-read sequencing technologies to investigate end products of de novo chromosome 17p11.2 rearrangements and query the molecular mechanisms underlying both recurrent and non-recurrent events. Evidence for an increased rate of clustered single-nucleotide variant (SNV) mutation in cis with non-recurrent rearrangements was found. Indel and SNV formation are associated with both copy-number gains and losses of 17p11.2, occur up to ∼1 Mb away from the breakpoint junctions, and favor C > G transversion substitutions; results suggest that single-stranded DNA is formed during the genesis of the SV and provide compelling support for a microhomology-mediated break-induced replication (MMBIR) mechanism for SV formation. Our data show an additional mutational burden of MMBIR consisting of hypermutation confined to the locus and manifesting as SNVs and indels predominantly within genes.


Subject(s)
Chromosomes, Human, Pair 17 , Mutation , Abnormalities, Multiple/genetics , Chromosome Breakpoints , Chromosome Disorders/genetics , Chromosome Duplication/genetics , DNA Copy Number Variations , DNA Repair/genetics , DNA Replication , Gene Rearrangement , Genome, Human , Genomic Structural Variation , Humans , INDEL Mutation , Models, Genetic , Polymorphism, Single Nucleotide , Recombination, Genetic , Sequence Analysis, DNA/methods , Smith-Magenis Syndrome/genetics
2.
Cell ; 168(5): 830-842.e7, 2017 02 23.
Article in English | MEDLINE | ID: mdl-28235197

ABSTRACT

De novo copy number variants (dnCNVs) arising at multiple loci in a personal genome have usually been considered to reflect cancer somatic genomic instabilities. We describe a multiple dnCNV (MdnCNV) phenomenon in which individuals with genomic disorders carry five to ten constitutional dnCNVs. These CNVs originate from independent formation incidences, are predominantly tandem duplications or complex gains, exhibit breakpoint junction features reminiscent of replicative repair, and show increased de novo point mutations flanking the rearrangement junctions. The active CNV mutation shower appears to be restricted to a transient perizygotic period. We propose that a defect in the CNV formation process is responsible for the "CNV-mutator state," and this state is dampened after early embryogenesis. The constitutional MdnCNV phenomenon resembles chromosomal instability in various cancers. Investigations of this phenomenon may provide unique access to understanding genomic disorders, structural variant mutagenesis, human evolution, and cancer biology.


Subject(s)
Chromosome Aberrations , DNA Copy Number Variations , Genetic Diseases, Inborn/embryology , Genetic Diseases, Inborn/genetics , Genomic Instability , Mutation , Chromosome Breakpoints , Chromosome Duplication , DNA Replication , Embryonic Development , Female , Gametogenesis , Humans , Male
3.
EMBO J ; 42(4): e111549, 2023 02 15.
Article in English | MEDLINE | ID: mdl-36598329

ABSTRACT

YAP/TAZ transcriptional co-activators play pivotal roles in tumorigenesis. In the Hippo pathway, diverse signals activate the MST-LATS kinase cascade that leads to YAP/TAZ phosphorylation, and subsequent ubiquitination and proteasomal degradation by SCFß-TrCP . When the MST-LATS kinase cascade is inactive, unphosphorylated or dephosphorylated YAP/TAZ translocate into the nucleus to mediate TEAD-dependent gene transcription. Hippo signaling-independent YAP/TAZ activation in human malignancies has also been observed, yet the mechanism remains largely elusive. Here, we report that the ubiquitin E3 ligase HERC3 can promote YAP/TAZ activation independently of its enzymatic activity. HERC3 directly binds to ß-TrCP, blocks its interaction with YAP/TAZ, and thus prevents YAP/TAZ ubiquitination and degradation. Expression levels of HERC3 correlate with YAP/TAZ protein levels and expression of YAP/TAZ target genes in breast tumor cells and tissues. Accordingly, knockdown of HERC3 expression ameliorates tumorigenesis of breast cancer cells. Our results establish HERC3 as a critical regulator of the YAP/TAZ stability and a potential therapeutic target for breast cancer.


Subject(s)
Adaptor Proteins, Signal Transducing , Breast Neoplasms , Humans , Female , Adaptor Proteins, Signal Transducing/genetics , Adaptor Proteins, Signal Transducing/metabolism , Trans-Activators/genetics , Trans-Activators/metabolism , Intracellular Signaling Peptides and Proteins/genetics , Intracellular Signaling Peptides and Proteins/metabolism , YAP-Signaling Proteins , beta-Transducin Repeat-Containing Proteins/genetics , beta-Transducin Repeat-Containing Proteins/metabolism , Transcriptional Coactivator with PDZ-Binding Motif Proteins , Transcription Factors/genetics , Transcription Factors/metabolism , Cell Transformation, Neoplastic/genetics , Carcinogenesis/genetics , Ubiquitination , Breast Neoplasms/genetics , Ubiquitins/metabolism , Ligases/genetics , Phosphoproteins/genetics , Phosphoproteins/metabolism
4.
Am J Hum Genet ; 111(3): 509-528, 2024 Mar 07.
Article in English | MEDLINE | ID: mdl-38412861

ABSTRACT

Neurodevelopmental disorders (NDDs) result from impaired development and functioning of the brain. Here, we identify loss-of-function (LoF) variation in ZFHX3 as a cause for syndromic intellectual disability (ID). ZFHX3 is a zinc-finger homeodomain transcription factor involved in various biological processes, including cell differentiation and tumorigenesis. We describe 42 individuals with protein-truncating variants (PTVs) or (partial) deletions of ZFHX3, exhibiting variable intellectual disability and autism spectrum disorder, recurrent facial features, relative short stature, brachydactyly, and, rarely, cleft palate. ZFHX3 LoF associates with a specific methylation profile in whole blood extracted DNA. Nuclear abundance of ZFHX3 increases during human brain development and neuronal differentiation. ZFHX3 was found to interact with the chromatin remodeling BRG1/Brm-associated factor complex and the cleavage and polyadenylation complex, suggesting a function in chromatin remodeling and mRNA processing. Furthermore, ChIP-seq for ZFHX3 revealed that it predominantly binds promoters of genes involved in nervous system development. We conclude that loss-of-function variants in ZFHX3 are a cause of syndromic ID associating with a specific DNA methylation profile.


Subject(s)
Autism Spectrum Disorder , Intellectual Disability , Neurodevelopmental Disorders , Humans , Intellectual Disability/genetics , Intellectual Disability/complications , Haploinsufficiency/genetics , Neurodevelopmental Disorders/genetics , Brain/metabolism , Homeodomain Proteins/genetics , Homeodomain Proteins/metabolism
5.
Nat Methods ; 21(3): 531-540, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38279009

ABSTRACT

Analysis across a growing number of single-cell perturbation datasets is hampered by poor data interoperability. To facilitate development and benchmarking of computational methods, we collect a set of 44 publicly available single-cell perturbation-response datasets with molecular readouts, including transcriptomics, proteomics and epigenomics. We apply uniform quality control pipelines and harmonize feature annotations. The resulting information resource, scPerturb, enables development and testing of computational methods, and facilitates comparison and integration across datasets. We describe energy statistics (E-statistics) for quantification of perturbation effects and significance testing, and demonstrate E-distance as a general distance measure between sets of single-cell expression profiles. We illustrate the application of E-statistics for quantifying similarity and efficacy of perturbations. The perturbation-response datasets and E-statistics computation software are publicly available at scperturb.org. This work provides an information resource for researchers working with single-cell perturbation data and recommendations for experimental design, including optimal cell counts and read depth.


Subject(s)
Proteomics , Software , Gene Expression Profiling/methods , Epigenomics , Single-Cell Analysis
6.
Am J Hum Genet ; 110(8): 1229-1248, 2023 08 03.
Article in English | MEDLINE | ID: mdl-37541186

ABSTRACT

Despite advances in clinical genetic testing, including the introduction of exome sequencing (ES), more than 50% of individuals with a suspected Mendelian condition lack a precise molecular diagnosis. Clinical evaluation is increasingly undertaken by specialists outside of clinical genetics, often occurring in a tiered fashion and typically ending after ES. The current diagnostic rate reflects multiple factors, including technical limitations, incomplete understanding of variant pathogenicity, missing genotype-phenotype associations, complex gene-environment interactions, and reporting differences between clinical labs. Maintaining a clear understanding of the rapidly evolving landscape of diagnostic tests beyond ES, and their limitations, presents a challenge for non-genetics professionals. Newer tests, such as short-read genome or RNA sequencing, can be challenging to order, and emerging technologies, such as optical genome mapping and long-read DNA sequencing, are not available clinically. Furthermore, there is no clear guidance on the next best steps after inconclusive evaluation. Here, we review why a clinical genetic evaluation may be negative, discuss questions to be asked in this setting, and provide a framework for further investigation, including the advantages and disadvantages of new approaches that are nascent in the clinical sphere. We present a guide for the next best steps after inconclusive molecular testing based upon phenotype and prior evaluation, including when to consider referral to research consortia focused on elucidating the underlying cause of rare unsolved genetic disorders.


Subject(s)
Exome , Genetic Testing , Humans , Exome/genetics , Sequence Analysis, DNA , Phenotype , Exome Sequencing , Rare Diseases
7.
Proc Natl Acad Sci U S A ; 120(9): e2216810120, 2023 02 28.
Article in English | MEDLINE | ID: mdl-36812201

ABSTRACT

Mitochondria provide essential metabolites and adenosine triphosphate (ATP) for the regulation of energy homeostasis. For instance, liver mitochondria are a vital source of gluconeogenic precursors under a fasted state. However, the regulatory mechanisms at the level of mitochondrial membrane transport are not fully understood. Here, we report that a liver-specific mitochondrial inner-membrane carrier SLC25A47 is required for hepatic gluconeogenesis and energy homeostasis. Genome-wide association studies found significant associations between SLC25A47 and fasting glucose, HbA1c, and cholesterol levels in humans. In mice, we demonstrated that liver-specific depletion of SLC25A47 impaired hepatic gluconeogenesis selectively from lactate, while significantly enhancing whole-body energy expenditure and the hepatic expression of FGF21. These metabolic changes were not a consequence of general liver dysfunction because acute SLC25A47 depletion in adult mice was sufficient to enhance hepatic FGF21 production, pyruvate tolerance, and insulin tolerance independent of liver damage and mitochondrial dysfunction. Mechanistically, SLC25A47 depletion leads to impaired hepatic pyruvate flux and malate accumulation in the mitochondria, thereby restricting hepatic gluconeogenesis. Together, the present study identified a crucial node in the liver mitochondria that regulates fasting-induced gluconeogenesis and energy homeostasis.


Subject(s)
Genome-Wide Association Study , Gluconeogenesis , Humans , Mice , Animals , Gluconeogenesis/physiology , Glucose/metabolism , Liver/metabolism , Energy Metabolism/physiology , Pyruvates/metabolism
8.
Nucleic Acids Res ; 51(20): e105, 2023 11 10.
Article in English | MEDLINE | ID: mdl-37843111

ABSTRACT

Cytosine base editors (CBEs), which enable precise C-to-T substitutions, have been restricted by potential safety risks, including DNA off-target edits, RNA off-target edits and additional genotoxicity such as DNA damages induced by double-strand breaks (DSBs). Though DNA and RNA off-target edits have been ameliorated via various strategies, evaluation and minimization of DSB-associated DNA damage risks for most CBEs remain to be resolved. Here we demonstrate that YE1, an engineered CBE variant with minimized DNA and RNA off-target edits, could induce prominent DSB-associated DNA damage risks, manifested as γH2AX accumulation in human cells. We then perform deaminase engineering for two deaminases lamprey LjCDA1 and human APOBEC3A, and generate divergent CBE variants with eliminated DSB-associated DNA damage risks, in addition to minimized DNA/RNA off-target edits. Furthermore, the editing scopes and sequence preferences of APOBEC3A-derived CBEs could be further diversified by internal fusion strategy. Taken together, this study provides updated evaluation platform for DSB-associated DNA damage risks of CBEs and further generates a series of safer toolkits with diversified editing signatures to expand their applications.


Subject(s)
Cytosine , Gene Editing , Humans , RNA/genetics , DNA Damage , DNA/genetics , CRISPR-Cas Systems
9.
Chem Soc Rev ; 53(1): 227-262, 2024 Jan 02.
Article in English | MEDLINE | ID: mdl-38059509

ABSTRACT

Chiral amines are pivotal building blocks for the pharmaceutical industry. Asymmetric reductive amination is one of the most efficient and atom economic methodologies for the synthesis of optically active amines. Among the various strategies available, NAD(P)H-dependent amine dehydrogenases (AmDHs) and imine reductases (IREDs) are robust enzymes that are available from various sources and capable of utilizing a broad range of substrates with high activities and stereoselectivities. AmDHs and IREDs operate via similar mechanisms, both involving a carbinolamine intermediate followed by hydride transfer from the co-factor. In addition, both groups catalyze the formation of primary and secondary amines utilizing both organic and inorganic amine donors. In this review, we discuss advances in developing AmDHs and IREDs as biocatalysts and focus on evolutionary history, substrate scope and applications of the enzymes to provide an outlook on emerging industrial biotechnologies of chiral amine production.


Subject(s)
NAD , Oxidoreductases , Amination , Oxidoreductases/metabolism , Amines , Biocatalysis , Imines , Stereoisomerism
10.
J Am Chem Soc ; 146(8): 5622-5633, 2024 Feb 28.
Article in English | MEDLINE | ID: mdl-38373280

ABSTRACT

Ethylene glycol is an essential commodity chemical with high demand, which is conventionally produced via thermocatalytic oxidation of ethylene with huge fossil fuel consumption and CO2 emission. The one-step electrochemical approach offers a sustainable route but suffers from reliance on noble metal catalysts, low activity, and mediocre selectivity. Herein, we report a one-step electrochemical oxidation of ethylene to ethylene glycol over an earth-abundant metal-based molecular catalyst, a cobalt phthalocyanine supported on a carbon nanotube (CoPc/CNT). The catalyst delivers ethylene glycol with 100% selectivity and 1.78 min-1 turnover frequency at room temperature and ambient pressure, more competitive than those obtained over palladium catalysts. Experimental data demonstrate that the catalyst orchestrates multiple tasks in sequence, involving electrochemical water activation to generate high-valence Co-oxo species, ethylene epoxidation to afford an ethylene oxide intermediate via oxygen transfer, and eventually ring-opening of ethylene oxide to ethylene glycol facilitated by in situ formed Lewis acid site. This work offers a great opportunity for commodity chemicals synthesis based on a one-step, earth-abundant metal-catalyzed, and renewable electricity-driven route.

11.
Mol Med ; 30(1): 5, 2024 Jan 08.
Article in English | MEDLINE | ID: mdl-38191316

ABSTRACT

BACKGROUND: Soy isoflavones (SI) is a natural bioactive substance exhibiting beneficial effects on human health. This study aims to elucidate the therapeutic potential of SI in the treatment of osteosarcoma (OS) and to investigate the underlying mechanisms, particularly focusing on mitophagy. METHODS: The effects of SI on the proliferation, apoptosis, migration, and invasion of U2OS cells were analyzed. Mitophagy was assessed through multiple parameters: mitochondrial autophagosomes, mitochondrial membrane potential, autophagy-related proteins, reactive oxygen species (ROS), and oxygen consumption rate (OCR). Protein levels related to apoptosis, autophagy, and the AKT/mTOR pathway were analyzed using western blot. The therapeutic efficacy of SI was further identified using a mouse tumor xenograft model. Cell apoptosis and proliferation in tumor xenografts were detected by TUNEL staining and immunohistochemistry (IHC), respectively. RESULTS: SI dose-dependently suppressed the viability, colony formation, migration, and invasion of U2OS cells, and enhanced the apoptosis. SI also dose-dependently induced mitophagy in OS cells, evidenced by an increase in autophagosomes and ROS levels, a decrease in mitochondrial membrane potential and OCR, and concomitant changes in autophagy-related proteins. Mdivi-1, an inhibitor of mitophagy, reversed the anti-tumor effects of SI on U2OS cells. In addition, SI blocked the AKT/mTOR pathway in U2OS cells. SC-79, an AKT agonist, reversed the effect of SI on inducing mitophagy. Moreover, SI also promoted cell apoptosis and mitophagy in tumor xenografts in vivo. CONCLUSIONS: SI induces mitophagy in OS cells by blocking the AKT/mTOR pathway, contributing to the inhibition of OS.


Subject(s)
Bone Neoplasms , Isoflavones , Osteosarcoma , Animals , Humans , Autophagy-Related Proteins , Bone Neoplasms/drug therapy , Disease Models, Animal , Isoflavones/pharmacology , Mitophagy , Osteosarcoma/drug therapy , Proto-Oncogene Proteins c-akt , Reactive Oxygen Species , Signal Transduction , TOR Serine-Threonine Kinases , Glycine max/chemistry , Mice
12.
J Neuroinflammation ; 21(1): 60, 2024 Feb 28.
Article in English | MEDLINE | ID: mdl-38419042

ABSTRACT

BACKGROUND: The spinal inflammatory signal often spreads to distant segments, accompanied by widespread pain symptom under neuropathological conditions. Multiple cytokines are released into the cerebrospinal fluid (CSF), potentially inducing the activation of an inflammatory cascade at remote segments through CSF flow. However, the detailed alteration of CSF in neuropathic pain and its specific role in widespread pain remain obscure. METHODS: A chronic constriction injury of the infraorbital nerve (CCI-ION) model was constructed, and pain-related behavior was observed on the 7th, 14th, 21st, and 28th days post surgery, in both vibrissa pads and hind paws. CSF from CCI-ION rats was transplanted to naïve rats through intracisternal injection, and thermal and mechanical allodynia were measured in hind paws. The alteration of inflammatory cytokines in CCI-ION's CSF was detected using an antibody array and bioinformatic analysis. Pharmacological intervention targeting the changed cytokine in the CSF and downstream signaling was performed to evaluate its role in widespread pain. RESULTS: CCI-ION induced local pain in vibrissa pads together with widespread pain in hind paws. CCI-ION's CSF transplantation, compared with sham CSF, contributed to vibrissa pad pain and hind paw pain in recipient rats. Among the measured cytokines, interleukin-6 (IL-6) and leptin were increased in CCI-ION's CSF, while interleukin-13 (IL-13) was significantly reduced. Furthermore, the concentration of CSF IL-6 was correlated with nerve injury extent, which gated the occurrence of widespread pain. Both astrocytes and microglia were increased in remote segments of the CCI-ION model, while the inhibition of astrocytes in remote segments, but not microglia, significantly alleviated widespread pain. Mechanically, astroglial signal transducer and activator of transcription 3 (STAT3) in remote segments were activated by CSF IL-6, the inhibition of which significantly mitigated widespread pain in CCI-ION. CONCLUSION: IL-6 was induced in the CSF of the CCI-ION model, triggering widespread pain via activating astrocyte STAT3 signal in remote segments. Therapies targeting IL-6/STAT3 signaling might serve as a promising strategy for the widespread pain symptom under neuropathological conditions.


Subject(s)
Interleukin-6 , Neuralgia , Rats , Animals , Interleukin-6/metabolism , Rats, Sprague-Dawley , STAT3 Transcription Factor/metabolism , Gliosis/complications , Constriction , Hyperalgesia/etiology , Hyperalgesia/drug therapy , Neuralgia/drug therapy , Cytokines
13.
Small ; : e2401032, 2024 Apr 15.
Article in English | MEDLINE | ID: mdl-38618652

ABSTRACT

CeO2, particularly in the shape of rod, has recently gained considerable attention for its ability to mimic peroxidase (POD) and haloperoxidase (HPO). However, this multi-enzyme activities unavoidably compete for H2O2 affecting its performance in relevant applications. The lack of consensus on facet distribution in rod-shaped CeO2 further complicates the establishment of structure-activity correlations, presenting challenges for progress in the field. In this study, the HPO-like activity of rod-shaped CeO2 is successfully enhanced while maintaining its POD-like activity through a facile post-calcination method. By studying the spatial distribution of these two activities and their exclusive H2O2 activation pathways on CeO2 surfaces, this study finds that the increased HPO-like activity originated from the newly exposed (111) surface at the tip of the shortened rods after calcination, while the unchanged POD-like activity is attributed to the retained (110) surface in their lateral area. These findings not only address facet distribution discrepancies commonly reported in the literature for rod-shaped CeO2 but also offer a simple approach to enhance its antibacterial performance. This work is expected to provide atomic insights into catalytic correlations and guide the design of nanozymes with improved activity and reaction specificity.

14.
Small ; 20(13): e2308621, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38109130

ABSTRACT

Neuropeptide Y (NPY), as one of the most abundant neuropeptides known, is widely distributed in the central and peripheral nervous system. However, most of the reported NPY-mimetic peptides are hard to cross the blood-brain barrier, target glioma mitochondria, and achieve self-assembly nanostructure in situ. Here, based on the α-helix structure of the novel chiral NPY-mimetic peptides D/LNPY(14), a Y-shaped peptide is designed with the sequences that can be recognized by enterokinase and achieved nanofibers conversion in glioma cell mitochondria. Coupling the Y-shaped NPY-mimetic peptide with the NIR-II fluorophore IR1048, a red-shifting of the fluorescence spectrum beyond 1300 nm is achieved through self-assembly. After the self-assembly in glioma mitochondria, the formed nanofibers can promote intracellular mitochondrial ROS production and extend the NIR-II fluorescence imaging time to at least 7 days in vivo. This work for the first time endows the self-assembly of α-helical-based chiral NPY-mimetic peptides, providing a novel strategy for glioma subcellular regulation enhanced antitumor treatment guided by NIR-II fluorescence imaging.


Subject(s)
Neuropeptide Y , Receptors, Neuropeptide Y , Receptors, Neuropeptide Y/metabolism , Blood-Brain Barrier/metabolism
15.
Small ; : e2308850, 2024 Feb 16.
Article in English | MEDLINE | ID: mdl-38366271

ABSTRACT

Personalized radiotherapy strategies enabled by the construction of hypoxia-guided biological target volumes (BTVs) can overcome hypoxia-induced radioresistance by delivering high-dose radiotherapy to targeted hypoxic areas of the tumor. However, the construction of hypoxia-guided BTVs is difficult owing to lack of precise visualization of hypoxic areas. This study synthesizes a hypoxia-responsive T1 , T2 , T2 mapping tri-modal MRI molecular nanoprobe (SPION@ND) and provides precise imaging of hypoxic tumor areas by utilizing the advantageous features of tri-modal magnetic resonance imaging (MRI). SPION@ND exhibits hypoxia-triggered dispersion-aggregation structural transformation. Dispersed SPION@ND can be used for routine clinical BTV construction using T1 -contrast MRI. Conversely, aggregated SPION@ND can be used for tumor hypoxia imaging assessment using T2 -contrast MRI. Moreover, by introducing T2 mapping, this work designs a novel method (adjustable threshold-based hypoxia assessment) for the precise assessment of tumor hypoxia confidence area and hypoxia level. Eventually this work successfully obtains hypoxia tumor target and accurates hypoxia tumor target, and achieves a one-stop hypoxia-guided BTV construction. Compared to the positron emission tomography-based hypoxia assessment, SPION@ND provides a new method that allows safe and convenient imaging of hypoxic tumor areas in clinical settings.

16.
Chembiochem ; 25(13): e202400328, 2024 Jul 02.
Article in English | MEDLINE | ID: mdl-38742991

ABSTRACT

Baeyer-Villiger monooxygenases belong to a family of flavin-binding proteins that catalyze the Baeyer-Villiger (BV) oxidation of ketones to produce lactones or esters, which are important intermediates in pharmaceuticals or sustainable materials. Phenylacetone monooxygenase (PAMO) from Thermobifida fusca with moderate thermostability catalyzes the oxidation of aryl ketone substrates, but is limited by high specificity and narrow substrate scope. In the present study, we applied loop optimization by loop swapping followed by focused saturation mutagenesis in order to evolve PAMO mutants capable of catalyzing the regioselective BV oxidation of cyclohexanone and cyclobutanone derivatives with formation of either normal or abnormal esters or lactones. We further modulated PAMO to increase enantioselectivity. Crystal structure studies indicate that rotation occurs in the NADP-binding domain and that the high B-factor region is predominantly distributed in the catalytic pocket residues. Computational analyses further revealed dynamic character in the catalytic pocket and reshaped hydrogen bond interaction networks, which is more favorable for substrate binding. Our study provides useful insights for studying enzyme-substrate adaptations.


Subject(s)
Mixed Function Oxygenases , Protein Engineering , Thermobifida , Stereoisomerism , Substrate Specificity , Mixed Function Oxygenases/metabolism , Mixed Function Oxygenases/chemistry , Mixed Function Oxygenases/genetics , Thermobifida/enzymology , Thermobifida/metabolism , Oxidation-Reduction , Biocatalysis , Catalytic Domain , Models, Molecular
17.
Chembiochem ; 25(9): e202400069, 2024 May 02.
Article in English | MEDLINE | ID: mdl-38504591

ABSTRACT

Arylalkylamine N-acetyltransferase (AANAT) serves as a key enzyme in the biosynthesis of melatonin by transforming 5-hydroxytryptamine (5-HT) to N-acetyl-5-hydroxytryptamine (NAS), while its low activity may hinder melatonin yield. In this study, a novel AANAT derived from Sus scrofa (SsAANAT) was identified through data mining using 5-HT as a model substrate, and a rational design of SsAANAT was conducted in the quest to improving its activity. After four rounds of mutagenesis procedures, a triple combinatorial dominant mutant M3 was successfully obtained. Compared to the parent enzyme, the conversion of the whole-cell reaction bearing the best variant M3 exhibted an increase from 50 % to 99 % in the transformation of 5-HT into NAS. Additionally, its catalytic efficiency (kcat/Km) was enhanced by 2-fold while retaining the thermostability (Tm>45 °C). In the up-scaled reaction with a substrate loading of 50 mM, the whole-cell system incorporating variant M3 achieved a 99 % conversion of 5-HT in 30 h with an 80 % yield. Molecular dynamics simulations were ultilized to shed light on the origin of improved activity. This study broadens the repertoire of AANAT for the efficient biosynthesis of melatonin.


Subject(s)
Arylalkylamine N-Acetyltransferase , Serotonin , Arylalkylamine N-Acetyltransferase/metabolism , Arylalkylamine N-Acetyltransferase/genetics , Arylalkylamine N-Acetyltransferase/chemistry , Serotonin/metabolism , Serotonin/chemistry , Serotonin/biosynthesis , Animals , Acetylation , Protein Engineering , Swine
18.
PLoS Comput Biol ; 19(9): e1011447, 2023 09.
Article in English | MEDLINE | ID: mdl-37656740

ABSTRACT

Microbiome sequencing data normalization is crucial for eliminating technical bias and ensuring accurate downstream analysis. However, this process can be challenging due to the high frequency of zero counts in microbiome data. We propose a novel reference-based normalization method called normalization via rank similarity (RSim) that corrects sample-specific biases, even in the presence of many zero counts. Unlike other normalization methods, RSim does not require additional assumptions or treatments for the high prevalence of zero counts. This makes it robust and minimizes potential bias resulting from procedures that address zero counts, such as pseudo-counts. Our numerical experiments demonstrate that RSim reduces false discoveries, improves detection power, and reveals true biological signals in downstream tasks such as PCoA plotting, association analysis, and differential abundance analysis.


Subject(s)
Computational Biology , Microbiota , Computational Biology/methods
19.
Int Microbiol ; 2024 Jun 20.
Article in English | MEDLINE | ID: mdl-38900217

ABSTRACT

Chlorobenzene (CB), extensively used in industrial processes, has emerged as a significant contaminant in soil and groundwater. The eco-friendly and cost-effective microbial remediation has been increasingly favored to address this environmental challenge. In this study, a degrading bacterium was isolated from CB-contaminated soil at a pesticide plant, identified as Pandoraea sp. XJJ-1 (CCTCC M 2021057). This strain completely degraded 100 mg·L-1 CB and showed extensive degradability across a range of pH (5.0-9.0), temperature (10-37 °C), and CB concentrations (100-600 mg·L-1). Notably, the degradation efficiency was 85.2% at 15 °C, and the strain could also degrade six other aromatic hydrocarbons, including benzene, toluene, ethylbenzene, and xylene (o-, m-, p-). The metabolic pathway of CB was inferred using ultraperformance liquid chromatography, gas chromatography-mass spectrometry, and genomic analysis. In strain XJJ-1, CB was metabolized to o-chlorophenol and 3-chloroxychol by CB monooxygenase, followed by ortho-cleavage by the action of 3-chlorocatechol 1,2-dioxygenase. Moreover, the presence of the chlorobenzene monooxygenation pathway metabolism in strain XJJ-1 is reported for the first time in Pandoraea. As a bacterium with low-temperature resistance and composite pollutant degradation capacity, strain XJJ-1 has the potential application prospects in the in-situ bioremediation of CB-contaminated sites.

20.
Environ Sci Technol ; 58(5): 2574-2583, 2024 Feb 06.
Article in English | MEDLINE | ID: mdl-38266484

ABSTRACT

To recover multimedia mercury from coal-fired power plants, a novel N-containing conjugated polymer (polyaniline and polypyrrole) functionalized fly ash was prepared, which could continuously adsorb 99.2% of gaseous Hg0 at a high space velocity of 368,500 h-1 and nearly 100% of aqueous Hg2+ in the solution pH range of 2-12. The adsorption capacities of Hg0 and Hg2+ reach 1.62 and 101.36 mg/g, respectively. Such a kind of adsorbent has good environmental applicability, i.e. good resistance to coexisting O2/NO/SO2 and coexisting Na+/K+/Ca2+/Mg2+/SO42-. This adsorbent has very low specific resistances (6 × 106-5 × 109 Ω·cm) and thus can be easily collected by an electrostatic precipitator under low-voltage (0.1-0.8 kV). The Hg-saturated adsorbent can desorb almost 100% Hg under relatively low temperature (<250 °C). Characterization and theoretical calculations reveal that conjugated-N is the critical site for adsorbing both Hg0 and Hg2+ as well as activating chlorine. Gaseous Hg0 is oxidized and adsorbed in the form of HgXClX(ad), while aqueous Hg2+ is adsorbed to form a complex with conjugated-N, and parts of Hg2+ are reduced to Hg+ by conjugated-N. This adsorbent can be easily large-scale manufactured; thus, this novel solid waste functionalization method is promising to be applied in coal-fired power plants and other Hg-involving industrial scenes.


Subject(s)
Air Pollutants , Mercury , Coal Ash/chemistry , Air Pollutants/analysis , Mercury/analysis , Multimedia , Polymers , Coal , Pyrroles , Gases , Power Plants
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