scholarly journals Author Correction: In vivo and in vitro reconstitution of unique key steps in cystobactamid antibiotic biosynthesis

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Sebastian Groß ◽  
Bastien Schnell ◽  
Patrick A. Haack ◽  
David Auerbach ◽  
Rolf Müller
Keyword(s):  
Antibiotic Biosynthesis ◽  
In Vitro Reconstitution ◽  
Key Steps

scholarly journals In vivo and in vitro reconstitution of unique key steps in cystobactamid antibiotic biosynthesis

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Sebastian Groß ◽  
Bastien Schnell ◽  
Patrick A. Haack ◽  
David Auerbach ◽  
Rolf Müller
Keyword(s):  
Biosynthetic Gene Cluster ◽  
Antibiotic Biosynthesis ◽  
Gene Deletions ◽  
Aminobenzoic Acids ◽  
In Vitro Reconstitution ◽  
Peptide Synthetase ◽  
Nrps Module ◽  
Key Steps

AbstractCystobactamids are myxobacteria-derived topoisomerase inhibitors with potent anti-Gram-negative activity. They are formed by a non-ribosomal peptide synthetase (NRPS) and consist of tailored para-aminobenzoic acids, connected by a unique α-methoxy-l-isoasparagine or a β-methoxy-l-asparagine linker moiety. We describe the heterologous expression of the cystobactamid biosynthetic gene cluster (BGC) in Myxococcus xanthus. Targeted gene deletions produce several unnatural cystobactamids. Using in vitro experiments, we reconstitute the key biosynthetic steps of linker formation and shuttling via CysB to the NRPS. The biosynthetic logic involves a previously uncharacterized bifunctional domain found in the stand-alone NRPS module CysH, albicidin biosynthesis and numerous BGCs of unknown natural products. This domain performs either an aminomutase (AM) or an amide dehydratase (DH) type of reaction, depending on the activity of CysJ which hydroxylates CysH-bound l-asparagine. Furthermore, CysQ O-methylates hydroxyl-l-(iso)asparagine only in the presence of the AMDH domain. Taken together, these findings provide direct evidence for unique steps in cystobactamid biosynthesis.

scholarly journals Intermediate step of cohesin’s ATPase cycle allows cohesin to entrap DNA

2018 ◽  
Vol 115 (39) ◽  
pp. 9732-9737 ◽  
Author(s):  
Gamze Ö. Çamdere ◽  
Kristian K. Carlborg ◽  
Douglas Koshland
Keyword(s):  
Atp Hydrolysis ◽  
Intermediate Step ◽  
Mutant Form ◽  
In Vitro Reconstitution ◽  
Chromatid Cohesion ◽  
The Family ◽  
Structural Maintenance Of Chromosomes ◽  
Dna Substrate

Cohesin is a four-subunit ATPase in the family of structural maintenance of chromosomes (SMC). Cohesin promotes sister chromatid cohesion, chromosome condensation, DNA repair, and transcription regulation. Cohesin performs these functions as a DNA tether and potentially a DNA-based motor. At least one of its DNA binding activities involves entrapment of DNA within a lumen formed by its subunits. This activity can be reconstituted in vitro by incubating cohesin with DNA, ATP, and cohesin loader. Previously we showed that a mutant form of cohesin (DE-cohesin) possesses the ability to bind and tether DNA in vivo. Using in vitro reconstitution assays, we show that DE-cohesin can form stable complexes with DNA without ATP hydrolysis. We show that wild-type cohesin with ADP aluminum fluoride (cohesinADP/AlFx) can also form stable cohesin–DNA complexes. These results suggest that an intermediate nucleotide state of cohesin, likely cohesinADP-Pi, is capable of initially dissociating one interface between cohesin subunits to allow DNA entry into a cohesin lumen and subsequently interacting with the bound DNA to stabilize DNA entrapment. We also show that cohesinADP/AlFx binding to DNA is enhanced by cohesin loader, suggesting a function for loader other than stimulating the ATPase. Finally, we show that loader remains stably bound to cohesinADP/AlFx after DNA entrapment, potentially revealing a function for loader in tethering the second DNA substrate. These results provide important clues on how SMC complexes like cohesin can function as both DNA tethers and motors.

scholarly journals Regulation of peripheral lipogenesis by glucagon. Inability of the hormone to inhibit lipogenesis in rat mammary acini in vitro in the presence or absence of agents which alter its effects on adipocytes

1984 ◽  
Vol 217 (3) ◽  
pp. 743-749 ◽  
Author(s):  
N A Robson ◽  
R A Clegg ◽  
V A Zammit
Keyword(s):  
Concentration Ratio ◽  
Response Curve ◽  
Potent Inhibitor ◽  
Specific Binding ◽  
Insulin Dose ◽  
Mammary Glands ◽  
Key Steps ◽  
Glucagon Concentration

The rate of lipogenesis in acini isolated from mammary glands of mid-lactating rats was studied by measuring the rate of incorporation of 3H from 3H2O into total lipid and fatty acids, with glucose as substrate. Glucagon did not affect the rate of lipogenesis in acini. Glucagon did not antagonize the maximal stimulatory effect of insulin, nor did it alter the insulin dose-response curve. Theophylline, at concentrations up to 20 mM, was a potent inhibitor of lipogenesis in acini. Glucagon did not augment the degree of inhibition of lipogenesis induced by 5 mM-theophylline. The results suggest that mammary-gland acini do not respond to glucagon in vitro under conditions in which the hormone induces inhibition of lipogenesis (the present paper) and of individual key steps in the lipogenic pathway in adipocytes [Zammit & Corstorphine (1982) Biochem. J. 208, 783-788; Green (1983) Biochem. J. 212, 189-195]. In agreement with these observations, we could detect only a minimal degree of specific binding of 125I-labelled glucagon to acini which bound insulin normally. This difference in responsiveness of mammary and adipose cell preparations in vitro to glucagon suggests that the two tissues may be differentially responsive to changes in the circulating insulin/glucagon concentration ratio in vivo. The significance of these findings for the regulation of substrate utilization for lipogenesis in the two tissues during lactation is discussed.

scholarly journals Crystallizing the 6S and 8S spliceosomal assembly intermediates: a complex project

2015 ◽  
Vol 71 (10) ◽  
pp. 2040-2053 ◽  
Author(s):  
Jann-Patrick Pelz ◽  
Hermann Schindelin ◽  
Katharina van Pee ◽  
Jochen Kuper ◽  
Caroline Kisker ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Protein Complexes ◽  
Sm Proteins ◽  
Entropy Reduction ◽  
Multimeric Protein ◽  
Complex Project ◽  
Key Steps ◽  
Small Nuclear Ribonucleoproteins

The small nuclear ribonucleoproteins (snRNPs) U1, U2, U4/6 and U5 are major constituents of the pre-mRNA processing spliceosome. They contain a common RNP core that is formed by the ordered binding of Sm proteins onto the single-stranded Sm site of the snRNA. Although spontaneousin vitro, assembly of the Sm core requires assistance from the PRMT5 and SMN complexesin vivo. To gain insight into the key steps of the assembly process, the crystal structures of two assembly intermediates of U snRNPs termed the 6S and 8S complexes have recently been reported. These multimeric protein complexes could only be crystallized after the application of various rescue strategies. The developed strategy leading to the crystallization and solution of the 8S crystal structure was subsequently used to guide a combination of rational crystal-contact optimization with surface-entropy reduction of crystals of the related 6S complex. Conversely, the resulting high-resolution 6S crystal structure was used during the restrained refinement of the 8S crystal structure.

scholarly journals A stromal region of cytochromeb6fsubunit IV is involved in the activation of the Stt7 kinase inChlamydomonas

2017 ◽  
Vol 114 (45) ◽  
pp. 12063-12068 ◽  
Author(s):  
Louis Dumas ◽  
Francesca Zito ◽  
Stéphanie Blangy ◽  
Pascaline Auroy ◽  
Xenie Johnson ◽  
...  
Keyword(s):  
Random Mutagenesis ◽  
Direct Interaction ◽  
Chloroplast Transformation ◽  
Kinase Domain ◽  
State Transitions ◽  
Light Harvesting Complexes ◽  
Gene Coding ◽  
In Vitro Reconstitution

The cytochrome (cyt)b6fcomplex and Stt7 kinase regulate the antenna sizes of photosystems I and II through state transitions, which are mediated by a reversible phosphorylation of light harvesting complexes II, depending on the redox state of the plastoquinone pool. When the pool is reduced, the cytb6factivates the Stt7 kinase through a mechanism that is still poorly understood. After random mutagenesis of the chloroplastpetDgene, coding for subunit IV of the cytb6fcomplex, and complementation of a ΔpetDhost strain by chloroplast transformation, we screened for impaired state transitions in vivo by chlorophyll fluorescence imaging. We show that residues Asn122, Tyr124, and Arg125 in the stromal loop linking helices F and G of cytb6fsubunit IV are crucial for state transitions. In vitro reconstitution experiments with purified cytb6fand recombinant Stt7 kinase domain show that cytb6fenhances Stt7 autophosphorylation and that the Arg125 residue is directly involved in this process. The peripheral stromal structure of the cytb6fcomplex had, until now, no reported function. Evidence is now provided of a direct interaction with Stt7 on the stromal side of the membrane.

scholarly journals Dissection of goadsporin biosynthesis by in vitro reconstitution leading to designer analogues expressed in vivo

2017 ◽  
Vol 8 (1) ◽  
Author(s):  
Taro Ozaki ◽  
Kona Yamashita ◽  
Yuki Goto ◽  
Morito Shimomura ◽  
Shohei Hayashi ◽  
...  
Keyword(s):  
In Vitro Reconstitution

scholarly journals Improved reconstitution of yeast vacuole fusion with physiological SNARE concentrations reveals an asymmetric Rab(GTP) requirement

2016 ◽  
Vol 27 (16) ◽  
pp. 2590-2597 ◽  
Author(s):  
Michael Zick ◽  
William Wickner
Keyword(s):  
Acyl Chain ◽  
Fatty Acyl ◽  
Fatty Acyl Chain ◽  
Rab Gtpase ◽  
Lower Phase ◽  
Yeast Vacuole ◽  
Vacuole Fusion ◽  
In Vitro Reconstitution

In vitro reconstitution of homotypic yeast vacuole fusion from purified components enables detailed study of membrane fusion mechanisms. Current reconstitutions have yet to faithfully replicate the fusion process in at least three respects: 1) The density of SNARE proteins required for fusion in vitro is substantially higher than on the organelle. 2) Substantial lysis accompanies reconstituted fusion. 3) The Rab GTPase Ypt7 is essential in vivo but often dispensable in vitro. Here we report that changes in fatty acyl chain composition dramatically lower the density of SNAREs that are required for fusion. By providing more physiological lipids with a lower phase transition temperature, we achieved efficient fusion with SNARE concentrations as low as on the native organelle. Although fused proteoliposomes became unstable at elevated SNARE concentrations, releasing their content after fusion had occurred, reconstituted proteoliposomes with substantially reduced SNARE concentrations fused without concomitant lysis. The Rab GTPase Ypt7 is essential on both membranes for proteoliposome fusion to occur at these SNARE concentrations. Strikingly, it was only critical for Ypt7 to be GTP loaded on membranes bearing the R-SNARE Nyv1, whereas the bound nucleotide of Ypt7 was irrelevant on membranes bearing the Q-SNAREs Vam3 and Vti1.

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