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1.
Micromachines (Basel) ; 14(9)2023 Aug 26.
Article in English | MEDLINE | ID: mdl-37763830

ABSTRACT

In this paper, diamond-based vertical p-n junction diodes with step edge termination are investigated using a Silvaco simulation (Version 5.0.10.R). Compared with the conventional p-n junction diode without termination, the step edge termination shows weak influences on the forward characteristics and helps to suppress the electric field crowding. However, the breakdown voltage of the diode with simple step edge termination is still lower than that of the ideal parallel-plane one. To further enhance the breakdown voltage, we combine a p-n junction-based junction termination extension on the step edge termination. After optimizing the structure parameters of the device, the depletion regions formed by the junction termination extension overlap with that of the p-n junction on the top mesa, resulting in a more uniform electric field distribution and higher device performance.

2.
J Biol Chem ; 292(4): 1374-1384, 2017 01 27.
Article in English | MEDLINE | ID: mdl-27974467

ABSTRACT

The high-affinity biosynthetic pathway for converting acetate to acetyl-coenzyme A (acetyl-CoA) is catalyzed by the central metabolic enzyme acetyl-coenzyme A synthetase (Acs), which is finely regulated both at the transcriptional level via cyclic AMP (cAMP)-driven trans-activation and at the post-translational level via acetylation inhibition. In this study, we discovered that cAMP directly binds to Salmonella enterica Acs (SeAcs) and inhibits its activity in a substrate-competitive manner. In addition, cAMP binding increases SeAcs acetylation by simultaneously promoting Pat-dependent acetylation and inhibiting CobB-dependent deacetylation, resulting in enhanced SeAcs inhibition. A crystal structure study and site-directed mutagenesis analyses confirmed that cAMP binds to the ATP/AMP pocket of SeAcs, and restrains SeAcs in an open conformation. The cAMP contact residues are well conserved from prokaryotes to eukaryotes, suggesting a general regulatory mechanism of cAMP on Acs.


Subject(s)
Adenosine Monophosphate/chemistry , Adenosine Triphosphate/chemistry , Coenzyme A Ligases/chemistry , Cyclic AMP/chemistry , Salmonella enterica/enzymology , Adenosine Monophosphate/genetics , Adenosine Monophosphate/metabolism , Adenosine Triphosphate/genetics , Adenosine Triphosphate/metabolism , Binding Sites , Coenzyme A Ligases/genetics , Coenzyme A Ligases/metabolism , Crystallography, X-Ray , Cyclic AMP/genetics , Cyclic AMP/metabolism , Salmonella enterica/genetics
3.
J Biol Chem ; 289(22): 15413-25, 2014 May 30.
Article in English | MEDLINE | ID: mdl-24733389

ABSTRACT

The OmpR/PhoB subfamily protein GlnR of actinomycetes is an orphan response regulator that globally coordinates the expression of genes related to nitrogen metabolism. Biochemical and genetic analyses reveal that the functional GlnR from Amycolatopsis mediterranei is unphosphorylated at the potential phosphorylation Asp(50) residue in the N-terminal receiver domain. The crystal structure of this receiver domain demonstrates that it forms a homodimer through the α4-ß5-α5 dimer interface highly similar to the phosphorylated typical response regulator, whereas the so-called "phosphorylation pocket" is not conserved, with its space being occupied by an Arg(52) from the ß3-α3 loop. Both in vitro and in vivo experiments confirm that GlnR forms a functional homodimer via its receiver domain and suggest that the charge interactions of Asp(50) with the highly conserved Arg(52) and Thr(9) in the receiver domain may be crucial in maintaining the proper conformation for homodimerization, as also supported by molecular dynamics simulations of the wild type GlnR versus the deficient mutant GlnR(D50A). This model is backed by the distinct phenotypes of the total deficient GlnR(R52A/T9A) double mutant versus the single mutants of GlnR (i.e. D50N, D50E, R52A and T9A), which have only minor effects upon both dimerization and physiological function of GlnR in vivo, albeit their DNA binding ability is weakened compared with that of the wild type. By integrating the supportive data of GlnRs from the model Streptomyces coelicolor and the pathogenic Mycobacterium tuberculosis, we conclude that the actinomycete GlnR is atypical with respect to its unphosphorylated conserved Asp residue being involved in the critical Arg/Asp/Thr charge interactions, which is essential for maintaining the biologically active homodimer conformation.


Subject(s)
Bacterial Proteins/metabolism , Streptomyces coelicolor/metabolism , Trans-Activators/metabolism , Actinomycetales/chemistry , Actinomycetales/metabolism , Amino Acid Sequence , Aspartic Acid/metabolism , Bacterial Proteins/chemistry , Crystallography, X-Ray , Dimerization , Gene Expression Regulation, Bacterial , Molecular Sequence Data , Mycobacterium tuberculosis/chemistry , Mycobacterium tuberculosis/metabolism , Phosphorylation/physiology , Structure-Activity Relationship , Trans-Activators/chemistry
4.
Cell Res ; 20(10): 1096-108, 2010 Oct.
Article in English | MEDLINE | ID: mdl-20567260

ABSTRACT

Amycolatopsis mediterranei is used for industry-scale production of rifamycin, which plays a vital role in antimycobacterial therapy. As the first sequenced genome of the genus Amycolatopsis, the chromosome of strain U32 comprising 10,236,715 base pairs, is one of the largest prokaryotic genomes ever sequenced so far. Unlike the linear topology found in streptomycetes, this chromosome is circular, particularly similar to that of Saccharopolyspora erythraea and Nocardia farcinica, representing their close relationship in phylogeny and taxonomy. Although the predicted 9,228 protein-coding genes in the A. mediterranei genome shared the greatest number of orthologs with those of S. erythraea, it was unexpectedly followed by Streptomyces coelicolor rather than N. farcinica, indicating the distinct metabolic characteristics evolved via adaptation to diverse ecological niches. Besides a core region analogous to that common in streptomycetes, a novel 'quasi-core' with typical core characteristics is defined within the non-core region, where 21 out of the total 26 gene clusters for secondary metabolite production are located. The rifamycin biosynthesis gene cluster located in the core encodes a cytochrome P450 enzyme essential for the conversion of rifamycin SV to B, revealed by comparing to the highly homologous cluster of the rifamycin B-producing strain S699 and further confirmed by genetic complementation. The genomic information of A. mediterranei demonstrates a metabolic network orchestrated not only for extensive utilization of various carbon sources and inorganic nitrogen compounds but also for effective funneling of metabolic intermediates into the secondary antibiotic synthesis process under the control of a seemingly complex regulatory mechanism.


Subject(s)
Actinomycetales/genetics , Anti-Bacterial Agents/biosynthesis , Genome, Bacterial , Rifamycins/biosynthesis , Actinomycetales/classification , Actinomycetales/metabolism , Carbon/metabolism , Metabolic Networks and Pathways , Multigene Family , Nitrogen/metabolism , Phylogeny
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