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      A Dimeric Chlorite Dismutase Exhibits O 2-Generating Activity and Acts as a Chlorite Antioxidant in Klebsiella pneumoniae MGH 78578

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          Abstract

          Chlorite dismutases (Clds) convert chlorite to O 2 and Cl , stabilizing heme in the presence of strong oxidants and forming the O=O bond with high efficiency. The enzyme from the pathogen Klebsiella pneumoniae ( KpCld) represents a subfamily of Clds that share most of their active site structure with efficient O 2-producing Clds, even though they have a truncated monomeric structure, exist as a dimer rather than a pentamer, and come from Gram-negative bacteria without a known need to degrade chlorite. We hypothesized that KpCld, like others in its subfamily, should be able to make O 2 and may serve an in vivo antioxidant function. Here, it is demonstrated that it degrades chlorite with limited turnovers relative to the respiratory Clds, in part because of the loss of hypochlorous acid from the active site and destruction of the heme. The observation of hypochlorous acid, the expected leaving group accompanying transfer of an oxygen atom to the ferric heme, is consistent with the more open, solvent-exposed heme environment predicted by spectroscopic measurements and inferred from the crystal structures of related proteins. KpCld is more susceptible to oxidative degradation under turnover conditions than the well-characterized Clds associated with perchlorate respiration. However, wild-type K. pneumoniae has a significant growth advantage in the presence of chlorate relative to a Δ cld knockout strain, specifically under nitrate-respiring conditions. This suggests that a physiological function of KpCld may be detoxification of endogenously produced chlorite.

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          Simultaneous determination of hemes a, b, and c from pyridine hemochrome spectra.

          Two procedures for analyzing overlapping optical spectra of mixtures of pyridine hemochromes are described, and extinction coefficients of pyridine hemochromes are provided for use with these methods. In the first procedure, absorbance is measured at a number of wavelengths equal to the number of components to be analyzed. This is the minimum amount of spectral data from which the concentration of each species can be calculated. In the second procedure, absorbance is measured at a number of wavelengths greater than the number of components to be analyzed. This redundancy of information makes it impossible to fit spectra which contain contributions from additional components, unless the spectra of the additional components are equal to linear combinations of the spectra of the species being analyzed. These two procedures are generally applicable to analyses of absolute or difference spectra of mixtures of components obeying Beer's law. The sensitivity to error in the absorbance measurements is only slightly greater than that for measuring a pure component at a single wavelength.
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            Modeling protein evolution with several amino acid replacement matrices depending on site rates.

            Most protein substitution models use a single amino acid replacement matrix summarizing the biochemical properties of amino acids. However, site evolution is highly heterogeneous and depends on many factors that influence the substitution patterns. In this paper, we investigate the use of different substitution matrices for different site evolutionary rates. Indeed, the variability of evolutionary rates corresponds to one of the most apparent heterogeneity factors among sites, and there is no reason to assume that the substitution patterns remain identical regardless of the evolutionary rate. We first introduce LG4M, which is composed of four matrices, each corresponding to one discrete gamma rate category (of four). These matrices differ in their amino acid equilibrium distributions and in their exchangeabilities, contrary to the standard gamma model where only the global rate differs from one category to another. Next, we present LG4X, which also uses four different matrices, but leaves aside the gamma distribution and follows a distribution-free scheme for the site rates. All these matrices are estimated from a very large alignment database, and our two models are tested using a large sample of independent alignments. Detailed analysis of resulting matrices and models shows the complexity of amino acid substitutions and the advantage of flexible models such as LG4M and LG4X. Both significantly outperform single-matrix models, providing gains of dozens to hundreds of log-likelihood units for most data sets. LG4X obtains substantial gains compared with LG4M, thanks to its distribution-free scheme for site rates. Since LG4M and LG4X display such advantages but require the same memory space and have comparable running times to standard models, we believe that LG4M and LG4X are relevant alternatives to single replacement matrices. Our models, data, and software are available from http://www.atgc-montpellier.fr/models/lg4x.
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              A rapid method for efficient gene replacement in the filamentous fungus Aspergillus nidulans.

              The construction of mutant fungal strains is often limited by the poor efficiency of homologous recombination in these organisms. Higher recombination efficiencies can be obtained by increasing the length of homologous DNA flanking the transformation marker, although this is a tedious process when standard molecular biology techniques are used for the construction of gene replacement cassettes. Here, we present a two-step technology which takes advantage of an Escherichia coli strain expressing the phage lambda Red(gam, bet, exo) functions and involves (i) the construction in this strain of a recombinant cosmid by in vivo recombination between a cosmid carrying a genomic region of interest and a PCR-generated transformation marker flanked by 50 bp regions of homology with the target DNA and (ii) genetic exchange in the fungus itself between the chromosomal locus and the circular or linearized recombinant cosmid. This strategy enables the rapid establishment of mutant strains carrying gene knock-outs with efficiencies >50%. It should also be appropriate for the construction of fungal strains with gene fusions or promoter replacements.
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                Author and article information

                Journal
                Biochemistry
                Biochemistry
                bi
                bichaw
                Biochemistry
                American Chemical Society
                0006-2960
                1520-4995
                01 December 2015
                01 December 2014
                20 January 2015
                : 54
                : 2
                : 434-446
                Affiliations
                []Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59715, United States
                []Department of Chemistry and Biochemistry, North Dakota State University , Fargo, North Dakota 58102, United States
                [§ ]Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
                []Department of Infection, Immunity and Inflammation, University of Leicester , Leicester LE1 9HN, U.K.
                []CNRS, Unité de Recherche Mixte CNRS/CEA/Université Paris-Sud (UMR 8221), Laboratoire de Bioénergétique, Métalloprotéines et Stress, Centre d’Etudes de Saclay, iBiTec-S, 91191 Gif-sur-Yvette, France
                Author notes
                [* ]E-mail: jdubois@ 123456chemistry.montana.edu . Telephone: (406) 994-2844. Fax: (406) 994-5407.
                [* ]E-mail: gudrun.s.lukat-rodgers@ 123456ndsu.edu . Telephone: (701) 231-8834.
                Article
                10.1021/bi501184c
                4303309
                25437493
                1d23eb07-da49-4248-8528-503a5348972e
                Copyright © 2014 American Chemical Society

                This is an open access article published under an ACS AuthorChoice License, which permits copying and redistribution of the article or any adaptations for non-commercial purposes.

                History
                : 19 September 2014
                : 26 November 2014
                Funding
                National Institutes of Health, United States
                Categories
                Article
                Custom metadata
                bi501184c
                bi-2014-01184c

                Biochemistry
                Biochemistry

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