AnatomyOrganismsDiseasesChemicals and DrugsAnalytical, Diagnostic and Therapeutic Techniques and EquipmentPhenomena and ProcessesInformation ScienceHealth Care
Ubiquitin-Protein LigasesCoenzyme ACoenzymesDNA LigasesSKP Cullin F-Box Protein LigasesCoenzyme A LigasesCullin ProteinsUbiquinoneUbiquitinationAcetyl Coenzyme APolynucleotide LigasesUbiquitinRING Finger DomainsUbiquitin-Conjugating EnzymesCobamidesCoenzyme A-TransferasesRNA Ligase (ATP)Hydroxymethylglutaryl CoA ReductasesMesnaMolecular Sequence DataAmino Acid SequenceSubstrate SpecificityF-Box ProteinsNADEndosomal Sorting Complexes Required for TransportPeptide SynthasesPantothenic AcidUbiquitinsProteasome Endopeptidase ComplexKineticsProtein BindingProtein Structure, TertiaryUbiquitin-Protein Ligase ComplexesPolyubiquitinEuryarchaeotaUbiquitin-Activating EnzymesPropanediol DehydrataseCarbon-Oxygen LigasesCatalysisSequence Homology, Amino AcidBinding SitesProto-Oncogene Proteins c-cblMethanosarcina barkeriMutationNADPAcetate-CoA LigaseProteolysisMevalonic AcidHydroxymethylglutaryl-CoA Reductase InhibitorsAlcohol OxidoreductasesS-Phase Kinase-Associated ProteinsRiboflavinProtein Inhibitors of Activated STATPantetheineSUMO-1 ProteinSmall Ubiquitin-Related Modifier ProteinsAdenosine MonophosphateEscherichia coliPalmitoyl Coenzyme AModels, MolecularMethanobacteriumLovastatinMalonyl Coenzyme ASequence AlignmentCloning, MolecularSaccharomyces cerevisiaeSumoylationCarrier ProteinsSaccharomyces cerevisiae ProteinsAmino Acid MotifsOxidoreductasesPyridoxal PhosphateHydroxymethylglutaryl-CoA-Reductases, NADP-dependentMethylmalonyl-CoA MutaseCrystallography, X-RayBase SequenceLysineRecombinant ProteinsCell LineBacterial ProteinsMultienzyme ComplexesMuscular AtrophyAdenosine TriphosphateSuccinate-CoA LigasesOxidation-ReductionAcyltransferasesBiocatalysisProtein ConformationMultiprotein ComplexesMethaneCell Cycle ProteinsAcetatesHeLa CellsCorrinoidsSimvastatinModels, BiologicalVitamin B 12Receptors, Autocrine Motility FactorPhosphate AcetyltransferaseAnaphase-Promoting Complex-Cyclosome
Long-chain-MetabolismSubunitProteinsFattyBiosynthesisOntologyEnzymeMitochondrialCarboxylaseGenomeRequired for the synthesisEncodesMalonylLigninEssential genesSucla2ExpressionAnnotationPathwayUniProtSpeciesSequences1.12DeficiencyNucleotideAccessionBacteriaSymbolEnzymes involvedFunctionalPseudomonasEukaryotesNovoPrevalenceMutationsFamilyColiChemical reactionDownstreamAminoPathwaysActivityOrganism
Long-chain-1
  • We have cloned previously the human long-chain fatty acid-CoA ligase 4 (FACL4), which is a central enzyme in controlling the free arachidonic acid level in cells and thereby regulating eicosanoid production. (nih.gov)
Metabolism6
  • At T1, the significantly more abundant enzyme-coding genes were related to threonine metabolism and those genes related to the glycolytic pathway, explained by the abundance of sugars in the medium. (frontiersin.org)
  • At T2, the genes linked to the metabolism of ceramides and hopanoids lipids were clearly dominant, which are associated with the resistance of microbial species to extreme temperatures and pH values. (frontiersin.org)
  • In T3, genes linked to trehalose metabolism, related to the response to heat stress, dominated. (frontiersin.org)
  • The significant module (royal blue) identified was associated with TC, TG and non-HDL-C. GO and KEGG enrichment analyses revealed that the genes in the royal blue module were associated with carbon metabolism, steroid biosynthesis, fatty acid metabolism and biosynthesis pathways of unsaturated fatty acids. (biomedcentral.com)
  • As the affinity of folate-dependent enzymes increases markedly with the number of glutamic residues, the tetrahydropteroyl polyglutamates are the preferred coenzymes of C(1) metabolism. (cathdb.info)
  • These disorders are due to a deficiency of the adenosylcobalamin-dependent enzyme methylmalonyl-CoA mutase (apoenzyme deficiency), a defect in intracellular cobalamin metabolism (coenzyme deficiency), transcobalamin II deficiency, intrinsic factor deficiency, or dietary cobalamin deficiency, which is found in vegetarians. (medscape.com)
Subunit3
  • The SUCLA2 and SUCLG1 genes each provide instructions for making one part (subunit) of an enzyme called succinate-CoA ligase. (medlineplus.gov)
  • Association between a G-protein beta3 subunit gene polymorphism and the symptomatology and treatment responses of major depressive disorders. (neurotransmitter.net)
  • The aim of the present study was to test a possible effect of the G-protein beta3-subunit (Gbeta3) C825T gene variant on the antidepressant activity of selective serotonin reuptake inhibitors (SSRIs) in a sample of major and bipolar depressives, with or without psychotic features. (neurotransmitter.net)
Proteins4
  • Expression of this gene is regulated by sterol regulatory element-binding proteins, transcription factors that activate genes required for the synthesis of cholesterol and unsaturated fatty acids. (prosci-inc.com)
  • There are many possible applications for these genes: you could try to recreate essential gene pathways in-vitro, or purify the proteins for functional studies, or create a synthetic MoClo-compatible Bacillus subtilis genome using these genes and the sgRNAs available from the Bacillus Genetic Stock Center. (freegenes.org)
  • The codon table used was the FreqB table from " Design Parameters to Control Synthetic Gene Expression in Escherichia coli ", which was used because it was shown to express proteins well and was recommended to us by JCVI. (freegenes.org)
  • Kornberg became an authority on the biochemistry of enzymes, including the production of coenzymes-the proteins that assist enzymes by transferring chemicals from one group of enzymes to another. (encyclopedia.com)
Fatty4
  • Mice homozygous for disruptions in this gene display organic aciduria and develop hypoglycemia and fatty livers after fasting. (jax.org)
  • The protein encoded by this gene is an isozyme of the long-chain fatty-acid-coenzyme A ligase family. (thermofisher.com)
  • This gene functions in mediating fatty acid-induced glioma cell growth. (thermofisher.com)
  • Fatty acid utilization is initiated by fatty acid-CoA ligase, which converts free fatty acids into fatty acyl-CoA esters. (nih.gov)
Biosynthesis4
  • 4-coumarate-CoA ligase intermediate in the biosynthesis of polyketides such as flavonoids (pigmentation) and other natural organic compounds. (cdc.gov)
  • These results suggest that the genes involved in lignin biosynthesis are down-regulated by higher nitrogen fertilizer, which causes lignin deficiency in the secondary cell walls and the weakening of mechanical tissue structure. (springer.com)
  • Hirano K, Aya K, Kondo M, Okuno A, MorinakaY, Matsuoka M (2012) OsCAD2 is the major CAD gene responsible for monolignol biosynthesis in rice culm. (springer.com)
  • A pathway for stilbene biosynthesis was constructed in Escherichia coli with 4-coumaroyl CoA ligase 1 4CL1) from Arabidopsis thaliana and stilbene synthase (STS) cloned from Arachis hypogaea . (biomedcentral.com)
Ontology1
  • Number of Gene Ontology (GO) annotations for this target, consisting of the sum of GO Functions and GO Processes. (nih.gov)
Enzyme3
  • The present study used shotgun metagenomics to determine the enzyme-coding genes of the microbiota found in two different groups of cocoa beans varieties during the fermentation process. (frontiersin.org)
  • Changes in the microbiota enzyme-coding genes over time pointed to the distinct ordering of fermentation at 24-48 h (T1), 72-96 h (T2), and 120-144 h (T3). (frontiersin.org)
  • This gene encodes a cytosolic enzyme that catalyzes the activation of acetate for use in lipid synthesis and energy generation. (prosci-inc.com)
Mitochondrial1
  • Succinate-CoA ligase is involved in producing and maintaining the building blocks of mitochondrial DNA. (medlineplus.gov)
Carboxylase2
  • We found a highly transcribed gene cluster encoding a presumed anaerobic benzene carboxylase (AbcA and AbcD) and a benzoate-coenzyme A ligase (BzlA). (deltares.nl)
  • Genes for two subunits of acetyl coenzyme A carboxylase of Anabaena sp. (uchicago.edu)
Genome2
  • Integrated analysis of differential gene expression, previously reported quantitative trait loci, and genome-wide association studies indicated that TRIB3 , SAA ( SAA1 , SAA3 , and M-SAA3.2 ), VEGFA, PTHLH , and RPL23A were the most promising candidate genes affecting milk protein and fat percentage. (biomedcentral.com)
  • Integrated analysis of differential gene expression and the reported quantitative trait loci and genome-wide association study data permitted the identification of candidate key genes for milk composition traits. (biomedcentral.com)
Required for the synthesis1
  • One such essential nutrient is pantothenate, also known as vitamin B5, which the parasite cannot synthesize de novo and is required for the synthesis of coenzyme A (CoA) in the parasite. (mdpi.com)
Encodes1
  • The pqsABCDE operon has been identified as being necessary for PQS production, and the pqsA gene encodes a predicted protein with homology to acyl coenzyme A (acyl-CoA) ligases. (ecu.edu)
Malonyl2
  • Flavonoids and stilbenes are synthesized from a coenzyme A (CoA) activated phenylpropanoid starter unit and three malonyl-CoA extender units (Fig. 1 ). (biomedcentral.com)
  • The basic skeleton of pinosylvin is composed of a B ring from a trans -cinnamoyl coenzyme A ( trans -cinnamoyl-CoA) and an A ring formed by the cyclization of three malonyl coenzyme A (malonyl-CoA) molecules. (biomedcentral.com)
Lignin1
  • Down-regulation of the 4-Coumarate:coenzyme A ligase gene (reduced lignin content and altered monomer composition) generally resulted in less stiff and weaker stems. (biomedcentral.com)
Essential genes8
  • 261 essential genes from Bacillus subtilis , codon optimized for Escherichia coli in MoClo-compatible high-copy ampicillin resistance backbones. (freegenes.org)
  • The Bacillus subtilis community has done an amazing job in curating a list of essential genes , and while the first published list goes back to 2003, the Bacillus subtilis community has continuously updated this list with results from new experiments. (freegenes.org)
  • In 2016, a paper was published using a CRISPR-based method for knocking down essential genes in Bacillus subtilis . (freegenes.org)
  • All the sgRNAs are available through the Bacillus Genetic Stock Center , which would allow for knockdown of native-sequence essential genes. (freegenes.org)
  • We took the list of essential genes from that 2016 paper and synthesized 261 of the 289 genes through Twist Biosciences. (freegenes.org)
  • All the essential genes have been recorded for expression in Escherichia coli and have been made MoClo compatible. (freegenes.org)
  • 261 of the 289 essential genes from 2016 essential gene list are included in this distribution. (freegenes.org)
  • The essential genes included in the distribution at attached in essential_included.csv , while the essential genes not included are in essential_not_included.csv . (freegenes.org)
Sucla22
  • Succinate-CoA ligase deficiency results from mutations in the SUCLA2 or SUCLG1 gene. (medlineplus.gov)
  • Mutations in either the SUCLA2 or SUCLG1 gene disrupt the normal function of succinate-CoA ligase. (medlineplus.gov)
Expression13
  • GXD's primary emphasis is on endogenous gene expression during development. (jax.org)
  • Here, using a combination of RNA-seq and proteomic LC-MS/MS analyses, we investigated the effect of anesthetic diethyl ether on gene expression and downstream consequences in plant Arabidopsis thaliana . (frontiersin.org)
  • Differential expression analyses revealed reprogramming of gene expression under anesthesia: 6,168 genes were upregulated, 6,310 genes were downregulated, while 9,914 genes were not affected in comparison with control plants. (frontiersin.org)
  • Weighted gene co-expression network (WGCNA) analysis was used to analyse the gene expression profile, and the royal blue module was considered to have the highest correlation. (biomedcentral.com)
  • Gene co-expression network-based methods have been widely used in processing microarray data and have especially been used to identify meaningful functional modules [ 18 , 19 ]. (biomedcentral.com)
  • Weighted gene co-expression network analysis (WGCNA) is one of the most effective methods of gene co-expression network analysis. (biomedcentral.com)
  • We report here the expression of this gene in tissues, particularly in different parts of the brain. (nih.gov)
  • Besides genetic data, gene expression profiles and metabolic pathway analysis offer new opportunities to elucidate the underlying mechanisms of complex traits in humans and farm animals. (biomedcentral.com)
  • Recently, along with the rapid development and cost reduction of next generation sequencing (NGS), sequence-based assays of transcriptomes, namely RNA sequencing (RNA-seq), have become a comprehensive and accurate tool for gene expression pattern analyses. (biomedcentral.com)
  • Two studies on the transcriptome of the mammary gland of Holstein cows using an oligonucleotide microarray have been presented, one of which compared the gene expression profile before (dry) and after (milk) parturition, using an Affymetrix cDNA array [ 22 ]. (biomedcentral.com)
  • To understand the mechanism that regulates stem mechanical strength in response to nitrogen, we analysed stem morphology, anatomy, mechanical properties, cell wall components, and expression of cell wall-related genes, in two varieties of japonica rice, namely, Wuyunjing23 (lodging-resistant variety) and W3668 (lodging-susceptible variety). (springer.com)
  • The expression of Ptr4CL4 drastically improved the production of pinosylvin (42.5 ± 1.1 mg/L), achieving values 15.7-fold higher than that of Ptr4CL5 (another 4-Coumarate-CoA ligase from Populus trichocarpa ) in the absence of cerulenin. (biomedcentral.com)
  • A typical scenario is data coming from expression experiments, in which we wish to analyze the promoter region of a bunch of genes that are up- or down-regulated under some condition. (umbc.edu)
Annotation1
Pathway3
  • Fqo can be hypothesized to be operative during sulfate reduction with CO. The Fqo complex receives electrons from the reduced coenzyme F 420 (F 420 H 2 ), generated from the oxidative acetyl-CoA pathway, and transfers electrons to the membrane-bound respiratory chain by the reduction of menaquinone [ 16 - 18 ]. (hindawi.com)
  • In order to elucidate the first step of the 4-quinolone synthesis pathway in P. aeruginosa, we have characterized the function of the pqsA gene product. (ecu.edu)
  • Each pathway is defined by a set of rules based on individual steps or genes. (lbl.gov)
UniProt3
  • Description of the protein which includes the UniProt Function and the NCBI Gene Summary. (nih.gov)
  • A single transcript chosen for a gene which is the most conserved, most highly expressed, has the longest coding sequence and is represented in other key resources, such as NCBI and UniProt. (ensembl.org)
  • The spreadsheet BBF_to_uniprot.csv contains links from our genes to outside resources like uniprot, as well as detailed descriptions. (freegenes.org)
Species2
  • BLAST analyses based on 16S rRNA gene sequence revealed 95.44%-100% sequence identity to recognized species. (bvsalud.org)
  • More recently, motif discovery algorithms that make use of phylogenetic foot-printing (the idea that TF-binding site will be conserved in the promoter sequences for the same gene in different species) have become available. (umbc.edu)
Sequences3
  • The main module page also shows the location of these motifs within the upstream sequences of the module member genes. (systemsbiology.net)
  • cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. (systemsbiology.net)
  • Phylogenetic analysis based 16S rRNA gene sequences showed that strain SCSIO 72103T formed a single clade with M. aquimaris SW105T. (bvsalud.org)
1.121
  • Cinnamic acid is hydroxylated by cinnamate-4-hydroxylase (C4H) (EC 1.14.13.11) to make 4-coumaric acid, which is then activated by 4-coumaroyl:CoA ligase (4CL) (EC 6.2.1.12) to make 4-coumaroyl-CoA. (biomedcentral.com)
Deficiency7
  • Succinate-CoA ligase deficiency is an inherited disorder that affects the early development of the brain and other body systems. (medlineplus.gov)
  • Most children with succinate-CoA ligase deficiency also experience a failure to thrive, which means that they gain weight and grow more slowly than expected. (medlineplus.gov)
  • Succinate-CoA ligase deficiency causes breathing difficulties that often lead to recurrent infections of the respiratory tract. (medlineplus.gov)
  • These infections can be life-threatening, and most people with succinate-CoA ligase deficiency live only into childhood or adolescence. (medlineplus.gov)
  • A few individuals with succinate-CoA ligase deficiency have had an even more severe form of the disorder known as fatal infantile lactic acidosis. (medlineplus.gov)
  • Although the exact prevalence of succinate-CoA ligase deficiency is unknown, it appears to be very rare. (medlineplus.gov)
  • These problems lead to hypotonia, muscle weakness, and the other characteristic features of succinate-CoA ligase deficiency. (medlineplus.gov)
Nucleotide1
  • While at NIH, he perfected techniques for synthesizing the coenzymes diphosphopyridine nucleotide (DPN) and flavin adenine dinucleotide -two enzymes involved in the production of the energy-rich molecules used by the body. (encyclopedia.com)
Accession1
  • Gene symbols, accession ids and various other target identifiers. (nih.gov)
Bacteria1
  • In some bacteria, a single protein catalyzes both this activity and that of EC 6.3.2.12, the combined activity of which leads to the formation of the coenzyme polyglutamated tetrahydropteroate (H(4)PteGlu(n)), i.e. various tetrahydrofolates (H(4)folate). (cathdb.info)
Symbol1
  • Approved gene symbol with link to HUGO Gene Nomenclature Committee. (nih.gov)
Enzymes involved1
  • The concurrent transcription of genes encoding enzymes involved in oxygenase-mediated aerobic benzene degradation suggested oxygen presence in the culture, possibly formed via a recently identified nitric oxide dismutase (Nod). (deltares.nl)
Functional1
Pseudomonas1
  • Pseudomonas aeruginosa is an opportunistic human pathogen which relies on several intercellular signaling systems for optimum population density-dependent regulation of virulence genes. (ecu.edu)
Eukaryotes1
  • Each isoform is encoded by a separate gene, a situation that is unique among eukaryotes. (cathdb.info)
Novo1
  • cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. (systemsbiology.net)
Prevalence1
  • Jensen Lab generated fractional counting score for the prevalence of this gene in Pubmed articles. (nih.gov)
Mutations3
  • Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene. (jax.org)
  • SUCLG1 gene mutations can cause fatal infantile lactic acidosis, while mutations in either gene can cause the somewhat less severe form of the condition. (medlineplus.gov)
  • which means both copies of the gene in each cell have mutations. (medlineplus.gov)
Family1
Coli2
  • Accumulation of tri- and tetraketide lactones from ferulic acid, regardless of the CoA-ligase expressed in E. coli , suggests that STS cannot properly accommodate and fold the tetraketide intermediate to the corresponding stilbene structure. (biomedcentral.com)
  • Phenylpropionic acids, such as 4-coumaric acid and caffeic acid, can be efficiently converted to stilbene compounds by recombinant E. coli cells expressing plant biosynthetic genes. (biomedcentral.com)
Chemical reaction1
  • To synthesize coenzymes, Kornberg used a chemical reaction called a condensation reaction, in which phosphate is eliminated from the molecule used to form the enzymes. (encyclopedia.com)
Downstream1
  • For subsequent benzoyl-CoA dearomatization, bam-like genes analogous to the ones found in other strict anaerobes were transcribed, whereas gene transcripts involved in downstream benzoyl-CoA degradation were mostly analogous to the ones described in facultative anaerobes. (deltares.nl)
Amino1
  • 96% amino acid identity and similar gene order to the corresponding benzene degradation gene cluster described previously, providing further evidence for anaerobic benzene activation via carboxylation. (deltares.nl)
Pathways2
  • The statistical evaluation of the most abundant genes in each group and time studied allowed us to identify the potential metabolic pathways involved in the success of the different microorganisms. (frontiersin.org)
  • In this study, we report transcription of genes involved in aerobic and anaerobic benzene degradation pathways in a benzene-degrading denitrifying continuous culture. (deltares.nl)
Activity1
  • The PqsA protein was purified as a recombinant His-tagged polypeptide, and this protein was shown to have anthranilate-CoA ligase activity. (ecu.edu)
Organism1
  • Discovery of genes essential for life is the first step in creating a truly synthetic organism. (freegenes.org)