Programmatic access to bioinformatics tools from EMBL-EBI update: 2017

Chojnacki, Szymon; Cowley, Andrew Peter; Lee, Joon; Foix, Anna; López, Rodrigo

doi:10.1093/nar/gkx273

Cited by 281 publications

(216 citation statements)

References 34 publications

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“…E. coli and S. enterica proteins used for comparison with M. xanthus proteins are listed in Table S3. Clustal Omega (Chojnacki et al, 2017) was used to align protein sequences.…”

Section: Bioinformaticsmentioning

confidence: 99%

Identification of the lipopolysaccharide O‐antigen biosynthesis priming enzyme and the O‐antigen ligase in Myxococcus xanthus: critical role of LPS O‐antigen in motility and development

Pérez‐Burgos

García‐Romero

Jung

et al. 2019

Molecular Microbiology

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Summary Myxococcus xanthus is a model bacterium to study social behavior. At the cellular level, the different social behaviors of M. xanthus involve extensive cell–cell contacts. Here, we used bioinformatics, genetics, heterologous expression and biochemical experiments to identify and characterize the key enzymes in M. xanthus implicated in O‐antigen and lipopolysaccharide (LPS) biosynthesis and examined the role of LPS O‐antigen in M. xanthus social behaviors. We identified WbaPMx (MXAN_2922) as the polyisoprenyl‐phosphate hexose‐1‐phosphate transferase responsible for priming O‐antigen synthesis. In heterologous expression experiments, WbaPMx complemented a Salmonella enterica mutant lacking the endogenous WbaP that primes O‐antigen synthesis, indicating that WbaPMx transfers galactose‐1‐P to undecaprenyl‐phosphate. We also identified WaaLMx (MXAN_2919), as the O‐antigen ligase that joins O‐antigen to lipid A‐core. Our data also support the previous suggestion that WzmMx (MXAN_4622) and WztMx (MXAN_4623) form the Wzm/Wzt ABC transporter. We show that mutations that block different steps in LPS O‐antigen synthesis can cause pleiotropic phenotypes. Also, using a wbaPMx deletion mutant, we revisited the role of LPS O‐antigen and demonstrate that it is important for gliding motility, conditionally important for type IV pili‐dependent motility and required to complete the developmental program leading to the formation of spore‐filled fruiting bodies.

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“…E. coli and S. enterica proteins used for comparison with M. xanthus proteins are listed in Table S3. Clustal Omega (Chojnacki et al, 2017) was used to align protein sequences.…”

Section: Bioinformaticsmentioning

confidence: 99%

Identification of the lipopolysaccharide O‐antigen biosynthesis priming enzyme and the O‐antigen ligase in Myxococcus xanthus: critical role of LPS O‐antigen in motility and development

Pérez‐Burgos

García‐Romero

Jung

et al. 2019

Molecular Microbiology

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“…The highest degree of similarity was observed for the N‐terminal RRMs of human MSI2 (residues 21‐187) which are 87% and 86% identical to the RNA‐binding domains (RBDs) (residues 20‐186) of human MSI1 and mouse MSI1, respectively. A multiple sequence alignment of human MSI2, human MSI1, and mouse MSI1 using Clustal Omega is shown in Figure . The C‐terminal region of MSI2 has no known motifs or specific function, while the N‐terminal RRMs mediate the binding to mRNAs, including those involved in the proliferation of certain cancers.…”

Section: Introductionmentioning

confidence: 99%

Crystal and solution structures of human oncoprotein Musashi‐2 N‐terminal RNA recognition motif 1

et al. 2019

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Musashi‐2 (MSI2) belongs to Musashi family of RNA binding proteins (RBP). Like Musashi‐1 (MSI1), it is overexpressed in a variety of cancers and is a promising therapeutic target. Both MSI proteins contain two N‐terminal RNA recognition motifs and play roles in posttranscriptional regulation of target mRNAs. Previously, we have identified several inhibitors of MSI1, all of which bind to MSI2 as well. In order to design MSI2‐specific inhibitors and compare the differences of binding mode of the inhibitors, we set out to solve the structure of MSI2‐RRM1, the key motif that is responsible for the binding. Here, we report the crystal structure and the first NMR solution structure of MSI2‐RRM1, and compare these to the structures of MSI1‐RBD1 and other RBPs. A high degree of structural similarity was observed between the crystal and solution NMR structures. MSI2‐RRM1 shows a highly similar overall folding topology to MSI1‐RBD1 and other RBPs. The structural information of MSI2‐RRM1 will be helpful for understanding MSI2‐RNA interaction and for guiding rational drug design of MSI2‐specific inhibitors.

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“… Multiple sequence alignment (CLUSTAL Omega 1.2.4) of amino acid sequences of T 4 HNR and various ketoreductases. Three‐dimensional information for T 4 HNR (PDB ID: 1JA9) and ActIII KR (PDB ID: 1W4Z) was accessed by using iCn3D Structure Viewer at NCBI.…”

Section: Methodsmentioning

confidence: 99%

Insights into the Role of Ketoreductases in the Biosynthesis of Partially Reduced Bacterial Aromatic Polyketides*

et al. 2019

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Partially reduced aromatic polyketides are bioactive secondary metabolites or intermediates in the biosynthesis of deoxygenated aromatics. For the antibiotic GTRI‐02 (mensalone) in different Streptomyces spp., biosynthesis involving the reduction of a fully aromatized acetyltrihydroxynaphthalene by a naphthol reductase has been proposed and shown in vitro with a fungal enzyme. However, more recently, GTRI‐02 has been identified as a product of the ActIII biosynthetic gene cluster from Streptomyces coelicolor A3(2), for which the reduction of a linear polyketide precursor by ActIII ketoreductase, prior to cyclization and aromatization, has been suggested. We have examined three different ketoreductases from bacterial producer strains of GTRI‐02 for their ability to reduce mono‐, bi‐, and tricyclic aromatic substrates. The enzymes reduced 1‐ and 2‐tetralone but not other aromatic substrates. This strongly suggests a reduction of a cyclized but not yet aromatic polyketide intermediate in the biosynthesis of GTRI‐02. Implications of the results for the biosynthesis of other secondary polyketidic metabolites are discussed.

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Programmatic access to bioinformatics tools from EMBL-EBI update: 2017

Cited by 281 publications

References 34 publications

Identification of the lipopolysaccharide O‐antigen biosynthesis priming enzyme and the O‐antigen ligase in Myxococcus xanthus: critical role of LPS O‐antigen in motility and development

Identification of the lipopolysaccharide O‐antigen biosynthesis priming enzyme and the O‐antigen ligase in Myxococcus xanthus: critical role of LPS O‐antigen in motility and development

Crystal and solution structures of human oncoprotein Musashi‐2 N‐terminal RNA recognition motif 1

Insights into the Role of Ketoreductases in the Biosynthesis of Partially Reduced Bacterial Aromatic Polyketides*

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