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Search for "biosynthesis" in Full Text gives 320 result(s) in Beilstein Journal of Organic Chemistry. Showing first 200.
A systems-based framework to computationally describe putative transcription factors and signaling pathways regulating glycan biosynthesis
Beilstein J. Org. Chem. 2021, 17, 1712–1724, doi:10.3762/bjoc.17.119
- , State University of New York, Buffalo, NY 14260, USA 10.3762/bjoc.17.119 Abstract Glycosylation is a common posttranslational modification, and glycan biosynthesis is regulated by a set of glycogenes. The role of transcription factors (TFs) in regulating the glycogenes and related glycosylation
- health and disease may affect multiple carbohydrate structures. Upon applying the Fisher’s exact test along with glycogene pathway classification, we identified TFs that may specifically regulate the biosynthesis of individual glycan types. Integration with Reactome DB knowledge provided an avenue to
- various sources in literature [45][46]. The following is a summary of the pathways studied and the enzymes involved: 1) Glycolipid core: The enzymes in this group are involved in the biosynthesis of the glucosylceramide (GlcCer) and galactosylceramide (GalCer) lipid core. Here, the GlcCer core is formed
Volatile emission and biosynthesis in endophytic fungi colonizing black poplar leaves
Beilstein J. Org. Chem. 2021, 17, 1698–1711, doi:10.3762/bjoc.17.118
- stronger defense response against the beet armyworm (Spodoptera exigua) [81]. In these cases, it is not known whether the increased terpene emission results from biosynthesis by the plant or the fungus. Future work should include measurements of plant and fungal TPS expression to determine the origin of
- two terpene synthases from one of the endophytic fungi to lay the groundwork for comparing the biosynthesis of plant vs fungal volatiles. More knowledge about the formation of these compounds could contribute to the greater understanding of their roles in plant–insect, plant–plant and plant–microbe
Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications
Beilstein J. Org. Chem. 2021, 17, 1641–1688, doi:10.3762/bjoc.17.116
A new glance at the chemosphere of macroalgal–bacterial interactions: In situ profiling of metabolites in symbiosis by mass spectrometry
Beilstein J. Org. Chem. 2021, 17, 1313–1322, doi:10.3762/bjoc.17.91
- high concentrations during saline stress conditions [32]. It has not yet been described in the Ulva–bacteria symbiosis. Not all essential genes for ectoine biosynthesis reported by [33] were found in the U. mutabilis genome [34], providing further support for the bacterial origin of ectoine. Homologs
- aspartokinase (ask_ect). Aspartokinase (Ask), along with ʟ-aspartate-β-semialdehyde-dehydrogenase (Asd), provides the precursor ʟ-ASA for ectoine biosynthesis [33][44][45]. Homologs of the enzymes of the ectoine pathway from Halorhodospira halochloris were identified by BLAST searches of the U. mutabilis genome
Synthesis of multiply fluorinated N-acetyl-D-glucosamine and D-galactosamine analogs via the corresponding deoxyfluorinated glucosazide and galactosazide phenyl thioglycosides
Beilstein J. Org. Chem. 2021, 17, 1086–1095, doi:10.3762/bjoc.17.85
- biomedical applications due to their ability to inhibit the glycan and glycosaminoglycan biosynthesis [34][35][36][37]. The fluorine substituent has typically been introduced into these GlcNAc and GalNAc analogues using nucleophilic fluorination. The primary position (C6 hydroxy group) was fluorinated by
Simulating the enzymes of ganglioside biosynthesis with Glycologue
Beilstein J. Org. Chem. 2021, 17, 739–748, doi:10.3762/bjoc.17.64
- those of the central nervous system, where they function in intercellular recognition and communication. We describe an in silico method for determining the metabolic pathways leading to the most common gangliosides, based on the known enzymes of their biosynthesis. A network of 41 glycolipids is
- ganglioside biosynthesis, and altered ganglioside status in cancer, and the effects on network structure are predicted. The simulator is available at the Glycologue website, https://glycologue.org/. Keywords: gangliosides; Glycologue; glycosyltransferases; neuropathy; Svennerholm nomenclature; Introduction
- negative charge. Figure 1 shows the structure of the monosialylated ganglioside GM1a. The biosynthesis of gangliosides occurs in the endoplasmic reticulum and Golgi, where specific glycosyltransferases act, in stepwise fashion, by adding monosaccharides from sugar nucleotide donors, first to ceramide, and
Biochemistry of fluoroprolines: the prospect of making fluorine a bioelement
Beilstein J. Org. Chem. 2021, 17, 439–460, doi:10.3762/bjoc.17.40
- first protein-biosynthesis-generated structures are based on variable backbone elements; proline (cyclic and chiral), glycine (acyclic and achiral) or alanine (acyclic and chiral). Subsequent acquisition of the functional side-chains for this repertoire led to the recruitment of amino acids that are
- pathways for proline biosynthesis involve the synthesis from either glutamate or ornithine [61]. Both sources of amino acids are derived from the core metabolic processes. The connection to the central metabolism makes it difficult to make interventions in the production of proline in the cells. For
- entry into the citric acid cycle. The dehydrogenation of proline is involved in numerous biochemical processes. For example, the dehydrogenation of proline linked to an acyl carrier protein makes a first step in the biosynthesis of some neurotoxins from cyanobacteria (ana gene cluster) [68]. The
Identification of volatiles from six marine Celeribacter strains
Beilstein J. Org. Chem. 2021, 17, 420–430, doi:10.3762/bjoc.17.38
- from the roseobacter group is the production of the sulfur-containing antibiotic tropodithietic acid (TDA) in Phaeobacter piscinae DSM 103509T [28], a compound that is in equilibrium with its tautomer thiotropocin [29] that was first described from Pseudomonas sp. CB-104 [30]. Its biosynthesis depends
- experiments also led to a suggestion for the mechanism for sulfur incorporation, but further research is required for a deep understanding of TDA biosynthesis. Besides its function as an antibiotic, TDA acts as a signaling molecule, similar to N-acylhomoserine lactones, at concentrations 100 times lower than
- required for a significant antibiotic activity [34]. The biosynthesis of tropone [35] and of the algicidal sulfur-containing roseobacticides [36] are most likely connected to the TDA pathway. Interestingly, in the interaction with marine algae P. inhibens can change its lifestyle from a symbiotic
Synthesis of legonmycins A and B, C(7a)-hydroxylated bacterial pyrrolizidines
Beilstein J. Org. Chem. 2021, 17, 334–342, doi:10.3762/bjoc.17.31
- papers addressed their biosynthesis. Thus, the investigation of the metabolites of Streptomyces sp. MA37 (from a soil sample obtained in Legon, Ghana) revealed the production of legonmycins A (3) and B (4) (Figure 2) and found that just four genes (lgnA–D) were necessary for their biosynthesis [22
- . These species include both Gram-positive and Gram-negative bacteria, indicating that pyrrolizidines are potential secondary metabolites of a variety of bacterial genera. The most recent addition to the bacterial pyrrolizidine literature also concerns their biosynthesis and addresses the origin of the
- . The clazamycins, and selected bacterial pyrrolizidines of the vinylogous urea type. For consistency, the standard numbering convention used for the plant pyrrolizidines, as depicted for the clazamycins, is used throughout. Key species in the biosynthesis of legonmycins A (3) and B (4), and the
19F NMR as a tool in chemical biology
Beilstein J. Org. Chem. 2021, 17, 293–318, doi:10.3762/bjoc.17.28
- biosynthesis and biodegradation of fluorinated organic compounds is also described. Keywords: biotransformation; chemical biology; fluorine; 19F NMR; probes; protein structure; Introduction Although fluorine is abundant in the environment, it is not a nutrient nor is it a feature of biochemistry for most
- biosynthesis through hBBOX-catalysed GBBNF hydroxylation, both in vitro and in cell lysates [43]. Moreover, by using a competitive substrate for the enzyme, inhibition experiments could be directly employed to determine the IC50 values in the basis of fluoride release, and the extent of GBBNF turnover
- , but only one could be detected (SF5-catechol) despite the 19F NMR analysis showing the presence of multiple fluorometabolites. Detection and biosynthesis of natural organofluorine compounds As naturally-occurring organofluorine compounds are so rare, it is possible to easily detect them in a crude
Progress in the total synthesis of inthomycins
Beilstein J. Org. Chem. 2021, 17, 58–82, doi:10.3762/bjoc.17.7
- biosynthesis [1][4], in vitro antimicrobial activity [4][5], and anticancer activity against human prostate cancer cell lines [6][7]. A recent study suggested that the close analogue (+)-11 of inthomycin C was found to exhibit proteasome inhibition activity [8]. The skeletal structures of inthomycins A–C (1–3
Secondary metabolites of Bacillus subtilis impact the assembly of soil-derived semisynthetic bacterial communities
Beilstein J. Org. Chem. 2020, 16, 2983–2998, doi:10.3762/bjoc.16.248
- ). For the biosynthesis of B. subtilis NRPs, the phosphopantetheinyl transferase Sfp is needed since it has been shown to activate the peptidyl carrier protein domains, converting it from the inactive apo-form to the active holo-form [37]. B. subtilis has four sfp-dependent SMs, of which three are
On the mass spectrometric fragmentations of the bacterial sesterterpenes sestermobaraenes A–C
Beilstein J. Org. Chem. 2020, 16, 2807–2819, doi:10.3762/bjoc.16.231
- rearrangement to a2•+ and a hydride shift to b2•+ (Scheme 3A). This hydride migration is in reverse order compared to a similar step along the cationic cyclisation cascade during the biosynthesis of 2 (Scheme S1 in Supporting Information File 1). The subsequent inductive ring opening to c2•+ and α-cleavage of
- sesterterpenes have a common intrinsic reactivity that is in the first instance reflected by their joint biosynthesis, but also by their similar behaviour in the comparably high-energy chemistry of mass spectrometric fragmentation reactions. Further support for the similar reactivity of the investigated
- compounds during biosynthesis and mass spectrometric fragmentations is given by the notable observation of hydride shifts that occur in both of these processes. However, the three compounds show also some differences in their mass spectrometric fragmentation, e.g., for compound 2 a strong fragment ion is
3-Acetoxy-fatty acid isoprenyl esters from androconia of the ithomiine butterfly Ithomia salapia
Beilstein J. Org. Chem. 2020, 16, 2776–2787, doi:10.3762/bjoc.16.228
- , acylated isoprenyl esters of fatty acids, is described, representing a combination of fatty acid and terpene biosynthesis. We also reveal small but reproducible differences between the two subspecies that could potentially be involved in species recognition and reproductive isolation. Results Extracts from
- formed from hedycaryol (7) during GC/MS analysis by a Cope-rearrangement [20][21], indicating that 7 might be originally present in the hairpencils. That said, we cannot disprove that this rearrangement could also occur in the androconia. Hedycaryol is an early product of sesquiterpene biosynthesis
- originate from the terpene building block 3-methyl-3-butenyl (isoprenyl) pyrophosphate. Because isoprenyl pyrophosphate is partly converted to 3-methyl-2-butenyl (prenyl) pyrophosphate during terpene biosynthesis, the presence of prenyl esters could not be excluded. Nevertheless, the two ester types can be
A consensus-based and readable extension of Linear Code for Reaction Rules (LiCoRR)
Beilstein J. Org. Chem. 2020, 16, 2645–2662, doi:10.3762/bjoc.16.215
- . Krambeck Kiyoko F. Aoki-Kinoshita Nathan E. Lewis See end of main text. 10.3762/bjoc.16.215 Abstract Systems glycobiology aims to provide models and analysis tools that account for the biosynthesis, regulation, and interactions with glycoconjugates. To facilitate these methods, there is a need for a
- , cytoplasm (bacteria and archaea), or lysosome (degradation, Man-6-P dephosphorylation and lysosomal glycoprotein biosynthesis [33][34] or paucimannose recycling [35]), are important constraints on glycosylation [36], therefore, the addition of this information to the Linear Code reaction rules provides
- earliest Krambeck et al. adaptation. Some symbols are only seen in the Krambeck et al. adaptation. Besides the “ # ” as the number symbol, Krambeck et al. also uses “Gnbis” to refer to the specific structure of bisecting GN, which is “Ma3(GNb4)(...Ma6)Mb4.” Several reaction rules for N-glycan biosynthesis
Leveraging glycomics data in glycoprotein 3D structure validation with Privateer
Beilstein J. Org. Chem. 2020, 16, 2523–2533, doi:10.3762/bjoc.16.204
- the lack of carbohydrate-specific modelling tools have often been named as the principal causes for these issues [18]. Heterogeneity of glycoproteins Unlike protein synthesis, which is encoded in the genome and follows a clear template, glycan biosynthesis is not template-directed. A single
- glycoprotein will exist in multiple possibilities of products that can emerge from the glycan biosynthesis pathways, and these are known as glycoforms [22]. More specifically, the variation can appear in terms of which potential glycosylation sites are occupied at any time – macroheterogeneity – or variations
- in the compositions of the glycans added to specific glycosylation sites – microheterogeneity. This variation in the microheterogeneous composition patterns arises due to the competition of glycan-processing enzymes in biosynthesis pathways [23]. Implications for the structure determination of
How and why plants and human N-glycans are different: Insight from molecular dynamics into the “glycoblocks” architecture of complex carbohydrates
Beilstein J. Org. Chem. 2020, 16, 2046–2056, doi:10.3762/bjoc.16.171
- important implications in terms of the N-glycans’ biosynthesis and biodegradation [29]. As an additional interesting point, we found that the folding of the (1-6) arm over the chitobiose region is completely independent of core α(1-6) fucosylation [24], with the result that core-fucosylated and non-core
The biomimetic synthesis of balsaminone A and ellagic acid via oxidative dimerization
Beilstein J. Org. Chem. 2020, 16, 2026–2031, doi:10.3762/bjoc.16.169
- ) [17] and violet-quinone (3) [18] (Figure 1). Similar to those natural products, the biomimetic synthesis of balsaminone A (4) and ellagic acid (5) can be attained using oxidative dimerization reactions, based on their proposed biosynthesis (Scheme 1 and Scheme 2) [19][20]. These pathways, which start
- represent the most efficient routes to these bioactive natural products to date. Selected natural products synthesized via oxidative dimerization. Proposed biosynthesis of balsaminone A (4) [19]. Proposed biosynthesis of ellagic acid (5) [20]. Previous syntheses of balsaminone A (4) [22] and ellagic acid (5
Synthesis of monophosphorylated lipid A precursors using 2-naphthylmethyl ether as a protecting group
Beilstein J. Org. Chem. 2020, 16, 1955–1962, doi:10.3762/bjoc.16.162
- ][8][9]. Various lipid A derivatives have since been synthesized to dissociate endotoxic effects from beneficial immunomodulatory activities. Lipid X, 2-N;3-O-di[(R)-3-hydroxytetradecanoyl]-ᴅ-glucosamine-1-phosphate, is the naturally occurring early monosaccharide precursor of lipid A biosynthesis
Synthesis, docking study and biological evaluation of ᴅ-fructofuranosyl and ᴅ-tagatofuranosyl sulfones as potential inhibitors of the mycobacterial galactan synthesis targeting the galactofuranosyltransferase GlfT2
Beilstein J. Org. Chem. 2020, 16, 1853–1862, doi:10.3762/bjoc.16.152
- substrate of mycobacterial galactofuranosyltransferase GlfT2 in the transition state, we evaluated these compounds by computational methods, as well as in an enzyme assay for the possible inhibition of the mycobacterial galactan biosynthesis. Our data show that despite favorable docking scores to the active
- site of GlfT2, none of these compounds serve as efficient inhibitors of the enzymes involved in the mycobacterial galactan biosynthesis. Keywords: GlfT2; molecular modeling; mycobacterium tuberculosis; synthesis; transition state inhibitors; Introduction Tuberculosis (TB) is one of the most prevalent
- targets for new antitubercular drug developments [6]. Mycobacterial galactan is synthesized by two bifunctional galactofuranosyltransferases, GlfT1 and GlfT2 (Supporting Information File 1, Figure S1). The former one initiates the galactan biosynthesis by addition of the first two Galf residues to
Antibacterial scalarane from Doriprismatica stellata nudibranchs (Gastropoda, Nudibranchia), egg ribbons, and their dietary sponge Spongia cf. agaricina (Demospongiae, Dictyoceratida)
Beilstein J. Org. Chem. 2020, 16, 1596–1605, doi:10.3762/bjoc.16.132
- study. Sesterterpenes are a rare terpene class, accounting for less than 2% of all known terpenoids, with only a few reports on their biosynthesis [72][73][74][75][76]. However, their frequent occurrence in marine organisms is striking and sponges are considered as the prime source of these terpenoids
- tempting to argue that the sesterterpene biosynthesis could be performed or mediated by their microbial symbionts. This further indicates a close association, interconnectedness, and probable co-evolution between microorganisms, sponges and nudibranchs [9]. D. stellata was not only found to sequester and
Fabclavine diversity in Xenorhabdus bacteria
Beilstein J. Org. Chem. 2020, 16, 956–965, doi:10.3762/bjoc.16.84
- ), and polyketide synthases (PKS). Selected Xenorhabdus and Photorhabdus mutant strains were generated applying a chemically inducible promoter in front of the suggested fabclavine (fcl) biosynthesis gene cluster (BGC), followed by the analysis of the occurring fabclavines. Subsequently, known and
- actinomycetes and myxobacteria, the genera Photorhabdus and Xenorhabdus are promising sources to discover new SMs since up to 6.5% of their overall genome sequence are associated with SM biosynthesis [5][6]. This includes antimicrobials like isopropylstilbene, xenocoumacins, amicoumacin, and several other SMs
- . budapestensis and X. szentirmaii, and a 50 kb biosynthesis gene cluster (BGC) was identified to be responsible for their formation (Figure 1) [20]. These compounds were of special interest because of their broad-spectrum bioactivity against Gram-positive and -negative bacteria, fungi, and protozoa [20][21
Understanding the role of active site residues in CotB2 catalysis using a cluster model
Beilstein J. Org. Chem. 2020, 16, 50–59, doi:10.3762/bjoc.16.7
- , representing the first committed step in the biosynthesis of the next-generation anti-inflammatory drug cyclooctatin. The intracellular target of cyclooctatin is an as of yet uncharacterized lysophospholipase, which is involved in early steps of the inflammatory signaling cascade [38][39][40]. In the last
- rational biosynthesis of novel terpenes might be possible by careful design of CotB2 mutants. Future studies using multiscale techniques to model the enzyme reaction in a complete enzyme environment will allow careful evaluation of the usefulness of such active site theozyme models. Conclusion In this work
Synthesis of C-glycosyl phosphonate derivatives of 4-amino-4-deoxy-α-ʟ-arabinose
Beilstein J. Org. Chem. 2020, 16, 9–14, doi:10.3762/bjoc.16.2
- the looming antibiotic crisis [5]. 4-Amino-4-deoxy-ʟ-arabinose units are activated as the phosphodiester-linked undecaprenyl derivative [6], which is then transferred by the action of several Ara4N transferases (ArnT, Figure 1) [7]. The synthesis of potential inhibitors of the biosynthesis of Ara4N
Chemical synthesis of tripeptide thioesters for the biotechnological incorporation into the myxobacterial secondary metabolite argyrin via mutasynthesis
Beilstein J. Org. Chem. 2019, 15, 2922–2929, doi:10.3762/bjoc.15.286
- approach where simpler and fully synthetic intermediates of the natural product’s biosynthesis can be biotechnologically incorporated. Here, we report the synthesis of a series of tripeptide thioesters as mutasynthons containing the native sequence with a dehydroalanine (Dha) Michael acceptor attached to a
- has been observed in many cases that exogenous substrates can be incorporated by bacteria into biosynthesis cascades of natural products. The use of substrates which lead to nonnatural derivatives of the natural product coined the field of mutasynthesis, e.g., siderophore analogue biosynthesis by P
- synthetase (NRPS), mutasynthons often carry thioesters to mimic the natural phosphopantetheinyl conjugate [20]. For the argyrins, the Müller group identified the corresponding biosynthetic gene cluster from Cystobacter sp. SBCb004 [21], studied the biosynthesis (Figure 2) and established a heterologous
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