A pleiotropic mutant of Rhodopseudomonas capsulata defective in nitrogen metabolism

Wild type strains of Rhodopseudomonas capsulata typically can use N₂, NH ₄ ⁺ , or various nitrogenous organic compounds as N sources for photosynthetic growth. One class of mutants selected for inability to grow on N₂ (Nif^–) also shows simultaneous loss of capacity to obtain N from numerous organic substrates. When supplied at relatively high concentrations, ammonia can be used as the sole N source for growth of such strains. Enzymatic analysis of one mutant (W11) indicates that the pleiotropic effect on N nutrition is neither due to detectable alteration in the activities of nitrogenase or the initial enzymes responsible for bulk assimilation of ammonia (glutamine synthetase and glutamate synthase) nor to absence of systems required for catabolism of organic N sources. The phenotype of W11 (Nit^–; defective in N metabolism) appears to result from loss of ability to grow using low concentrations of ammonia (supplied externally or generated in vivo).     

Crystal structure of CTP-ligated T state aspartate transcarbamoylase at 2.5 Å resolution: Implications for ATCase mutants and the mechanism of negative cooperativity

The X-ray crystal structure of CTP-ligated T state aspartate transcarbamoylase has been refined to an R factor of 0.182 at 2.5 Å resolution using the computer program X-PLOR. The structure contains 81 sites for solvent and has rms deviations from ideality in bond lengths and bond angles of 0.018 Å and 3.722°, respectively. The cytosine base of CTP interacts with the main chain carbonyl oxygens of rTyr-89 and rIle-12, the main chain NH of rIle-12, and the amino group of rLys-60. The ribose hydroxyls form polar contacts with the amino group of rLys-60, a carboxylate oxygen of rAsp-19, and the main chain carbonyl oxygen of rVal-9. The phosphate oxygens of CTP interact with the amino group of rLys-94, the hydroxyl of rThr-82, and an imidazole nitrogen of rHis-20. Recent mutagenesis experiments evaluated in parallel with the structure reported here indicate that alterations in the hydrogen bonding environment of the side chain of rAsn-111 may be responsible for the homotropic behavior of the pAR5 mutant of ATCase. The location of the first seven residues of the regulatory chain has been identified for the first time in a refined ATCase crystal structure, and the proximity of this portion of the regulatory chain to the allosteric site suggests a potential role for these residues in nucleotide binding to the enzyme. Finally, a series of amino acid side chain rearrangements leading from the R1 CTP allosteric to the R6 CTP allosteric site has been identified which may constitute the molecular mechanism of distinct CTP binding sites on ATCase. © 1993 Wiley-Liss, Inc.     

High-frequency electrically stimulated skeletal muscle contractions increase p70 phosphorylation independent of known IGF-I sensitive signaling pathways

Insulin-like growth factor (IGF-I) is hypothesized to be a critical upstream regulator of mammalian target of rapamycin (mTOR)-regulated protein synthesis with muscle contraction. We utilized a mouse model that expresses a skeletal muscle specific dominant-negative IGF-I receptor to investigate the role of IGF-I signaling of protein synthesis in response to unilateral lengthening contractions (10 sets, 6 repetitions, 100 Hz) at 0 and 3 h following the stimulus. Our results indicate that one session of high frequency muscle contractions can activate mTOR signaling independent of signaling components directly downstream of the receptor.     

Endoplasmic reticulum microenvironment and conserved histidines govern ELOVL4 fatty acid elongase activity

Autosomal dominant Stargardt-like macular dystrophy (STGD3) in humans results from mutations in elongation of very long chain FAs-like 4 (ELOVL4), which leads to vision loss in young adults. ELOVL4 is an integral endoplasmic reticulum (ER) protein that mediates the elongation of very long chain (VLC) FAs. Mutations in ELOVL4 lead to truncation and mislocalization of the translated protein from the ER, the site of FA elongation. Little is known about the enzymatic elongation of VLC-FAs by ELOVL4. We over-expressed full-length mouse ELOVL4, an N-glycosylation-deficient mutant, an ER-retention mutant, and mutants of active site histidines to parse their individual roles in VLC-FA elongation. ELOVL4 elongated appropriate precursors to the corresponding VLC-FA species ≥28 carbons. Active site histidine mutants of ELOVL4 did not elongate appropriate precursors, establishing ELOVL4 as the elongase. Displacing ELOVL4 from the ER was sufficient to cause loss of condensation activity, while absence of N-glycosylation was irrelevant for enzyme function. This study shows that ELOVL4 enzymatic activity is governed by individual histidines in its active site and the ER microenvironment, both of which are essential for elongation of VLC-FAs.     

Selection and Structure of Hyperactive Inteins: Peripheral Changes Relayed to the Catalytic Center

Inteins are phylogenetically diverse self-splicing proteins that are of great functional, evolutionary, biotechnological, and medical interest. To address the relationship between intein structure and function, particularly with respect to regulating the splicing reaction, and to groom inteins for application, we developed a phage display system to extend current in vivo selection for enhanced intein function to selection in vitro. We thereby isolated inteins that can function under excursions in temperature, pH, and denaturing environment. Remarkably, most mutations mapped to the surface of the intein, remote from the active site. We chose two mutants with enhanced splicing activity for crystallography, one of which was also subjected to NMR analysis. These studies define a “ripple effect”, whereby mutations in peripheral non-catalytic residues can cause subtle allosteric changes in the active-site environment in a way that facilitates intein activity. Altered salt-bridge formation and chemical shift changes of the mutant inteins provide a molecular rationale for their phenotypes. These fundamental insights will advance the utility of inteins in chemical biology, biotechnology, and medicine.     

Biochemical characteristics of functional domains using feline foamy virus integrase mutants

We constructed deletion mutants and seven point mutants by polymerase chain reaction to investigate the specificity of feline foamy virus integrase functional domains. Complementation reactions were performed for three enzymatic activities such as 3’-end processing, strand transfer, and disintegration. The complementation reactions with deletion mutants showed several activities for 3’-end processing and strand transfer. The conserved central domain and the combination of the N-terminal or C-terminal domains increased disintegration activity significantly. In the complementation reactions between deletion and point mutants, the combination between D107V and deletion mutants revealed 3’-end processing activities, but the combination with others did not have any activity, including strand transfer activities. Disintegration activity increased evenly, except the combination with glutamic acid 200. These results suggest that an intact central domain mediates enzymatic activities but fails to show these activities in the absence of the N-terminal or C-terminal domains. [BMB Reports 2013; 46(1):53-58]     

Effects of Mutations of Lys41 and Asp102 of Bacteriorhodopsin

Bacteriorhodopsin (BR) is a retinal protein that functions as a light-driven proton pump. In this study, six novel mutants including K41E and D102K, were obtained to verify or rule out the possibility that residues Lys41 and Asp102 are determinants of the time order of proton release and uptake, because we found that the order was reversed in another retinal protein archaerhodopsin 4 (AR4), which had different 41th and 102th residues. Our results rule out that possibility and confirm that the pK _a of the proton release complex (PRC) determines the time order. Nevertheless, mutations, especially D102K, were found to affect the kinetics of proton uptake substantially and the pK _a of Asp96. Compared to the wild-type BR (BR-WT), the decay of the M intermediate and proton uptake in the photocycle was slowed about 3-fold in D102K. Hence those residues might be involved in proton uptake and delivery to the internal proton donor.     

A Simple Method for Preparation of Poly-mannuronate Using Poly-guluronate Lyase

A simple method for preparation of poly-mannuronate from alginate has been developed. By making the best use of the substrate specificity of a poly-guluronate lyase, we prepared a poly-mannuronate of which the properties were almost identical to those of the poly-mannuronate produced by Haug’s acid hydrolysis method. Our method is very useful in terms of time and labor saving.