Characterization of a Mycobacterium tuberculosis Nanocompartment and Its Potential Cargo Proteins

doi:10.1074/JBC.M114.570119

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Characterization of a Mycobacterium tuberculosis Nanocompartment and Its Potential Cargo Proteins

Journal Article•DOI•

Characterization of a Mycobacterium tuberculosis Nanocompartment and Its Potential Cargo Proteins

Heidi Contreras, Matthew S. Joens¹, Lisa M. McMath, Vincent P. Le, Michael V. Tullius², Jacqueline M. Kimmey², Neda Bionghi², Marcus A. Horwitz², James A. J. Fitzpatrick¹, Celia W. Goulding³ - Show less +6 more•Institutions (3)

Salk Institute for Biological Studies¹, University of California, Los Angeles², University of California, Irvine³

27 Jun 2014-Journal of Biological Chemistry (American Society for Biochemistry and Molecular Biology)-Vol. 289, Iss: 26, pp 18279-18289

TL;DR: It is shown by co-purification and electron microscopy that mycobacteria via Mt-Enc can encapsulate Mt-DyP, Mt-BfrB, and Mt-FolB, which may aid in detoxification of the local environment to ensure long term survival.

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About: This article is published in Journal of Biological Chemistry.The article was published on 2014-06-27 and is currently open access. It has received 82 citations till now. The article focuses on the topics: Mycobacterium tuberculosis.

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Journal Article•DOI•

Bacterial enzymes involved in lignin degradation.

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Gonzalo de Gonzalo¹, Dana I. Colpa, Mohamed H. Habib², Mohamed H. Habib³, Marco W. Fraaije - Show less +1 more•Institutions (3)

University of Seville¹, University of Groningen², Cairo University³

17 Aug 2016-Journal of Biotechnology

TL;DR: An overview of recent advances in the identification and use of bacterial enzymes acting on lignin or lignIn-derived products is provided, including DyP-type peroxidases and laccases.

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393 citations

Cites background from "Characterization of a Mycobacterium..."

...Enzymes containing this Cerminal extension, for instance DyPB, BlDyP and MtDyP, are targets or encapsulation by a protein-based cages, the so-called encapulins (Sutter et al., 2008; Contreras et al., 2014)....
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Journal Article•DOI•

DyP‑type peroxidases: a promising and versatile class of enzymes

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Dana I. Colpa, Marco W. Fraaije, Edwin van Bloois

01 Jan 2014-Journal of Industrial Microbiology & Biotechnology

TL;DR: DyPs are bifunctional enzymes displaying not only oxidative activity but also hydrolytic activity, which makes them potentially interesting for a variety of biocatalytic applications.

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Abstract: DyP peroxidases comprise a novel superfamily of heme-containing peroxidases, which is unrelated to the superfamilies of plant and animal peroxidases. These enzymes have so far been identified in the genomes of fungi, bacteria, as well as archaea, although their physiological function is still unclear. DyPs are bifunctional enzymes displaying not only oxidative activity but also hydrolytic activity. Moreover, these enzymes are able to oxidize a variety of organic compounds of which some are poorly converted by established peroxidases, including dyes, β-carotene, and aromatic sulfides. Interestingly, accumulating evidence shows that microbial DyP peroxidases play a key role in the degradation of lignin. Owing to their unique properties, these enzymes are potentially interesting for a variety of biocatalytic applications. In this review, we deal with the biochemical and structural features of DyP-type peroxidases as well as their promising biotechnological potential.

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160 citations

Journal Article•DOI•

Ferritin family proteins and their use in bionanotechnology

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Didi He¹, Jon Marles-Wright¹•Institutions (1)

University of Edinburgh¹

25 Dec 2015-New Biotechnology

TL;DR: Ferritin family proteins are able to mineralise a range of metal ions and can be used in semi-conductor patterning and a commercial application of ferritin as a phosphate removal system for water purification is explored.

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155 citations

Cites background from "Characterization of a Mycobacterium..."

...It is in fact possible to sequester ferritin within an encapsulin shell [65] and while this has been demonstrated in a recombinant system it is not clear whether this is a physiologically relevant...
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Journal Article•DOI•

Widespread distribution of encapsulin nanocompartments reveals functional diversity.

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Tobias W. Giessen¹, Pamela A. Silver², Pamela A. Silver¹•Institutions (2)

Harvard University¹, Wyss Institute for Biologically Inspired Engineering²

06 Mar 2017-Nature microbiology

TL;DR: This work experimentally characterize three newly identified encapsulin systems and illustrates their probable involvement in iron mineralization, oxidative and nitrosative stress resistance and anaerobic ammonium oxidation, a process responsible for 30% of the nitrogen lost from the oceans.

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Abstract: Cells organize and regulate their metabolism via membrane- or protein-bound organelles. In this way, incompatible processes can be spatially separated and controlled. In prokaryotes, protein-based compartments are used to sequester harmful reactions and store useful compounds. These protein compartments play key roles in various metabolic and ecological processes, ranging from iron homeostasis to carbon fixation. One of the newest types of protein organelle are encapsulin nanocompartments. They are able to encapsulate specific protein cargo and are proposed to be involved in redox-related processes. We identified more than 900 putative encapsulin systems in bacterial and archaeal genomes. Encapsulins can be found in fifteen bacterial and two archaeal phyla. Our analysis reveals one new capsid type and nine previously unknown cargo proteins targeted to the interior of encapsulins. We experimentally characterize three newly identified encapsulin systems and illustrate their probable involvement in iron mineralization, oxidative and nitrosative stress resistance and anaerobic ammonium oxidation, a process responsible for 30% of the nitrogen lost from the oceans. Bioinformatics analysis identifies 900 encapsulin nanocompartments in prokaryotes that are associated with cargo proteins carrying out diverse functions.

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114 citations

Journal Article•DOI•

A structural and functional perspective of DyP-type peroxidase family.

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Toru Yoshida¹, Yasushi Sugano²•Institutions (2)

Kyoto Sangyo University¹, Japan Women's University²

15 May 2015-Archives of Biochemistry and Biophysics

TL;DR: The differences and similarities of structure and function among this family are reviewed and a reasonable new classification of DyP-type peroxidase family is proposed, that is, class P, I and V.

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108 citations

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Journal Article•

Protein Measurement with the Folin Phenol Reagent

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Oliver H. Lowry¹, Nira J. Rosebrough¹, A. Lewis Farr¹, Rose J. Randall¹•Institutions (1)

Washington University in St. Louis¹

01 Nov 1951-Journal of Biological Chemistry

TL;DR: Procedures are described for measuring protein in solution or after precipitation with acids or other agents, and for the determination of as little as 0.2 gamma of protein.

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289,852 citations

"Characterization of a Mycobacterium..." refers methods in this paper

...Protein concentration was determined by UV-visible spectroscopy, utilizing molar extinction coefficients at 280 nm as predicted by the program Protein Calculator (Scripps) or as determined by either a modified Lowry (18) or Bradford (19) assay using bovine serum albumin as a standard....
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Journal Article•DOI•

A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding

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Marion M. Bradford¹•Institutions (1)

University of Georgia¹

07 May 1976-Analytical Biochemistry

TL;DR: This assay is very reproducible and rapid with the dye binding process virtually complete in approximately 2 min with good color stability for 1 hr with little or no interference from cations such as sodium or potassium nor from carbohydrates such as sucrose.

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225,085 citations

"Characterization of a Mycobacterium..." refers methods in this paper

...Protein concentration was determined by UV-visible spectroscopy, utilizing molar extinction coefficients at 280 nm as predicted by the program Protein Calculator (Scripps) or as determined by either a modified Lowry (18) or Bradford (19) assay using bovine serum albumin as a standard....
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Journal Article•DOI•

NIH Image to ImageJ: 25 years of image analysis

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Caroline A Schneider¹, Wayne Rasband², Kevin W. Eliceiri¹•Institutions (2)

University of Wisconsin-Madison¹, National Institutes of Health²

01 Jul 2012-Nature Methods

TL;DR: The origins, challenges and solutions of NIH Image and ImageJ software are discussed, and how their history can serve to advise and inform other software projects.

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Abstract: For the past 25 years NIH Image and ImageJ software have been pioneers as open tools for the analysis of scientific images. We discuss the origins, challenges and solutions of these two programs, and how their history can serve to advise and inform other software projects.

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44,587 citations

"Characterization of a Mycobacterium..." refers methods in this paper

...After purification of the Mt-Enc DyP complex, the heme concentration within the complex (and presumably bound to Mt-DyP) was quantified using UV-visible spectroscopy (to determine heme concentration) and SDS-polyacrylamide gel band intensity analysis (to determine Mt-DyP concentration) using ImageJ (32)....
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...The concentration of encapsulated Mt-FolB was estimated by densitometry measurements from SDS-PAGE analysis using ImageJ (32)....
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...The diameter of the Mt-Enc nanocompartment is 220 Å, and its cargo, Mt-DyP, has a diameter ranging from 70 to 90 Å, as measured by ImageJ (32)....
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...To determine if the Mt-Enc BfrB complex maintained ferroxidase activity, we quantified the amount of encapsulated Mt-BfrB by densitometry measurements of SDS-polyacrylamide gel bands using ImageJ (32)....
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...EM analysis revealed that purified Mt-Enc forms a shell-like nanocompartment with a diameter of 220 Å and shell thickness of 25 Å, as determined using ImageJ (32) (Fig....
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Book Chapter•DOI•

The assay of catalases and peroxidases.

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Britton Chance¹, A.C. Maehly¹•Institutions (1)

University of Pennsylvania¹

31 Oct 2006-Methods of biochemical analysis

TL;DR: Two methods are described for the catalase assay by disappearance of peroxide are: ultraviolet spectrophotometry and permanganate titration and indirect measurements of the decrease of light absorption caused by the decomposition of hydrogen peroxide byCatalase.

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Abstract: Publisher Summary This chapter discusses the assay of catalases and peroxidases are: (1) catalase assay by disappearance of peroxide; (2) method for crude cell extracts; (3) direct spectrophotometric assay of catalase and peroxidase in cells and tissues; and (4) peroxidase assay by spectrophotometric measurements of the disappearance of hydrogen donor or the appearance of their colored oxidation products. Two methods are described for the catalase assay by disappearance of peroxide are: ultraviolet spectrophotometry and permanganate titration. Ultraviolet spectrophotometryis a method devised, on the basis of the absorption curves for peroxide solutions, for determining the activity of catalase by direct measurements of the decrease of light absorption in the region 230 to 250 mμ caused by the decomposition of hydrogen peroxide by catalase. In the case of method for crude cell extracts, oxygen evolution caused by the decomposition of hydrogen peroxide is measured with the conventional manometric technique. Peroxidase assay by spectrophotometric measurements of the disappearance of hydrogen donor or the appearance of their colored oxidation products includes the guaiacol test and the pyrogallol test.

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3,917 citations

"Characterization of a Mycobacterium..." refers methods in this paper

...The rate of product formation was calculated using the extinction coefficient of 26,600 M 1 cm 1 of tetraguaiacol at 470 nm (26)....
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Book•

Data for Biochemical Research

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R. M. C. Dawson

01 Jan 1969

TL;DR: Methods for the detection of biochemical compounds on paper and thin layer chromatograms, with some notes on separation Ion exchange, gel filtration, and affinity chromatography media isotopic data.

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Abstract: Amino acids, amines, peptides, and their derivatives Carboxylic acids, alcohols, aldehydes and ketones Phosphate esters exluding nucleotides and coenzymes Constituents of nucleic and related compounds Spectral data and pKa values for purines, pyrimidines, nucleosides, and nucleotides Vitamins and coenzymes Carbohydrates and related compounds Lipids and long-chain fatty acids Steroids Porphyrins and related compounds Carotenoids Plant growth regulators Antimetabolites, antibacterial agents, and enzyme inhibitors Pharmacologically active compounds Artificial and natural substrates Biochemical reagents Stability constants for metal complexes pH, buffers, and physiological media Gel electrophoresis Methods for the detection of biochemical compounds on paper and thin layer chromatograms, with some notes on separation Ion exchange, gel filtration, and affinity chromatography media Isotopic data Biochemical procedures Definitions, formulae, and general information Atomic weights.

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3,269 citations