1
|
Putri R, Allende-Ballestero C, Luque D, Klem R, Rousou KA, Liu A, Traulsen CHH, Rurup WF, Koay MST, Castón JR, Cornelissen JJLM. Structural Characterization of Native and Modified Encapsulins as Nanoplatforms for in Vitro Catalysis and Cellular Uptake. ACS Nano 2017; 11:12796-12804. [PMID: 29166561 PMCID: PMC6150732 DOI: 10.1021/acsnano.7b07669] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Recent years have witnessed the emergence of bacterial semiorganelle encapsulins as promising platforms for bio-nanotechnology. To advance the development of encapsulins as nanoplatforms, a functional and structural basis of these assemblies is required. Encapsulin from Brevibacterium linens is known to be a protein-based vessel for an enzyme cargo in its cavity, which could be replaced with a foreign cargo, resulting in a modified encapsulin. Here, we characterize the native structure of B. linens encapsulins with both native and foreign cargo using cryo-electron microscopy (cryo-EM). Furthermore, by harnessing the confined enzyme (i.e., a peroxidase), we demonstrate the functionality of the encapsulin for an in vitro surface-immobilized catalysis in a cascade pathway with an additional enzyme, glucose oxidase. We also demonstrate the in vivo functionality of the encapsulin for cellular uptake using mammalian macrophages. Unraveling both the structure and functionality of the encapsulins allows transforming biological nanocompartments into functional systems.
Collapse
Affiliation(s)
- Rindia
M. Putri
- Department
of Biomolecular Nanotechnology, MESA+ Institute for Nanotechnology, University of Twente, 7500 AE Enschede, The Netherlands
| | - Carolina Allende-Ballestero
- Department
of Structure of Macromolecules, Centro Nacional
de Biotecnología/CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Daniel Luque
- Department
of Structure of Macromolecules, Centro Nacional
de Biotecnología/CSIC, Cantoblanco, 28049 Madrid, Spain
- Centro
Nacional de Microbiología/Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain
| | - Robin Klem
- Department
of Biomolecular Nanotechnology, MESA+ Institute for Nanotechnology, University of Twente, 7500 AE Enschede, The Netherlands
| | - Katerina-Asteria Rousou
- Department
of Biomolecular Nanotechnology, MESA+ Institute for Nanotechnology, University of Twente, 7500 AE Enschede, The Netherlands
| | - Aijie Liu
- Department
of Biomolecular Nanotechnology, MESA+ Institute for Nanotechnology, University of Twente, 7500 AE Enschede, The Netherlands
| | - Christoph H.-H. Traulsen
- Department
of Biomolecular Nanotechnology, MESA+ Institute for Nanotechnology, University of Twente, 7500 AE Enschede, The Netherlands
| | - W. Frederik Rurup
- Department
of Biomolecular Nanotechnology, MESA+ Institute for Nanotechnology, University of Twente, 7500 AE Enschede, The Netherlands
| | - Melissa S. T. Koay
- Department
of Biomolecular Nanotechnology, MESA+ Institute for Nanotechnology, University of Twente, 7500 AE Enschede, The Netherlands
| | - José R. Castón
- Department
of Structure of Macromolecules, Centro Nacional
de Biotecnología/CSIC, Cantoblanco, 28049 Madrid, Spain
- E-mail:
| | - Jeroen J. L. M. Cornelissen
- Department
of Biomolecular Nanotechnology, MESA+ Institute for Nanotechnology, University of Twente, 7500 AE Enschede, The Netherlands
- E-mail:
| |
Collapse
|
2
|
Ivanova EP, Christen R, Alexeeva YV, Zhukova NV, Gorshkova NM, Lysenko AM, Mikhailov VV, Nicolau DV. Brevibacterium celere sp. nov., isolated from degraded thallus of a brown alga. Int J Syst Evol Microbiol 2004; 54:2107-2111. [PMID: 15545442 DOI: 10.1099/ijs.0.02867-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two whitish yellow, Gram-positive, non-motile, aerobic bacteria were isolated from enrichment culture during degradation of the thallus of the brown alga Fucus evanescens. The bacteria studied were chemo-organotrophic, mesophilic and grew well on nutrient media containing up to 15 % (w/v) NaCl. The DNA G+C content was 61 mol%. The two isolates exhibited a conspecific DNA-DNA relatedness value of 98 %, indicating that they belong to the same species. A comparative analysis of 16S rRNA gene sequences revealed that strain KMM 3637(T) formed a distinct phyletic lineage in the genus Brevibacterium (family Brevibacteriaceae, class Actinobacteria) and showed the highest sequence similarity (about 97 %) to Brevibacterium casei. DNA-DNA hybridization experiments demonstrated 45 % binding with the DNA of B. casei DSM 20657(T). Physiological and chemotaxonomic characteristics (meso-diaminopimelic acid in the peptidoglycan, major cellular fatty acids 15 : 0ai and 17 : 0ai) of the bacteria studied were consistent with the genomic and phylogenetic data. On the basis of the results of this study, a novel species, Brevibacterium celere sp. nov., is proposed. The type strain is KMM 3637(T) (=DSM 15453(T)=ATCC BAA-809(T)).
Collapse
MESH Headings
- Aerobiosis
- Bacterial Typing Techniques
- Base Composition
- Brevibacterium/classification
- Brevibacterium/cytology
- Brevibacterium/isolation & purification
- Brevibacterium/physiology
- DNA, Bacterial/chemistry
- DNA, Bacterial/isolation & purification
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/isolation & purification
- Diaminopimelic Acid/analysis
- Diaminopimelic Acid/isolation & purification
- Fatty Acids/analysis
- Fatty Acids/isolation & purification
- Fucus/microbiology
- Genes, rRNA
- Gentian Violet
- Molecular Sequence Data
- Movement
- Nucleic Acid Hybridization
- Organic Chemicals/metabolism
- Peptidoglycan/chemistry
- Peptidoglycan/isolation & purification
- Phenazines
- Phylogeny
- Pigments, Biological/biosynthesis
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Saline Solution, Hypertonic
- Sequence Analysis, DNA
- Temperature
Collapse
Affiliation(s)
- Elena P Ivanova
- Pacific Institute of Bioorganic Chemistry of the Far-Eastern Branch of the Russian Academy of Sciences, Prospekt 100 Let Vladivostoku 159, Russia
- Industrial Research Institute, Swinburne University of Technology, PO Box 218, Hawthorn, Victoria 3122, Australia
| | - Richard Christen
- UMR6543 CNRS - Université de Nice Sophia Antipolis, Centre de Biochimie, Parc Valrose, F06108 Nice cedex 2, France
| | - Yulia V Alexeeva
- Industrial Research Institute, Swinburne University of Technology, PO Box 218, Hawthorn, Victoria 3122, Australia
| | - Natalia V Zhukova
- Institute of Marine Biology of the Far-Eastern Branch of the Russian Academy of Sciences, 690041, Vladivostok, Russia
| | - Natalia M Gorshkova
- Pacific Institute of Bioorganic Chemistry of the Far-Eastern Branch of the Russian Academy of Sciences, Prospekt 100 Let Vladivostoku 159, Russia
| | - Anatoly M Lysenko
- Institute of Microbiology of the Russian Academy of Sciences, 117811 Moscow, Russia
| | - Valery V Mikhailov
- Pacific Institute of Bioorganic Chemistry of the Far-Eastern Branch of the Russian Academy of Sciences, Prospekt 100 Let Vladivostoku 159, Russia
| | - Dan V Nicolau
- Industrial Research Institute, Swinburne University of Technology, PO Box 218, Hawthorn, Victoria 3122, Australia
| |
Collapse
|
3
|
Abstract
Structurally identical teichoic acids were detected in cell walls of two soil isolates assigned to Brevibacterium linens based on phylogenetic data. Both cell walls contain unsubstituted 1,3-poly(glycerol phosphate) and poly(glycosylglycerol phosphate). Repeating units of the latter--alpha-D-GlcpNAc-(1-->4)-beta-D-Galp-(1-->1)-Gro--are bound by phosphodiester bonds including OH-3 of galactose and OH-3 of glycerol. Some of the N-acetylglucosamine residues have 4,6-pyruvic acid acetal, amounts of the latter in the two strains being unequal. Species-specificity of the structures of teichoic acids in the genus Brevibacterium is discussed.
Collapse
Affiliation(s)
- A S Shashkov
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow 117913, Russia
| | | | | | | |
Collapse
|
4
|
Siebert J, Hirsch P. Characterization of 15 selected coccal bacteria isolated from Antarctic rock and soil samples from the McMurdo-Dry Valleys (South-Victoria Land). Polar Biol 2001; 9:37-44. [PMID: 11538335 DOI: 10.1007/bf00441762] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Approximately 1500 cultures of microorganisms were isolated from rocks and soils of the Ross Desert (McMurdo-Dry Valleys). From these, 15 coccoid strains were chosen for more detailed investigation. They were characterized by morphological, physiological and chemotaxonomical properties. All isolates were Gram-positive, catalase-positive and nonmotile. Six strains showed red pigmentation and could be identified as members of the genera Micrococcus (M. roseus, M. agilis) or Deinococcus. In spite of their coccoid morphology, the remaining nine strains had to be associated with coryneform bacteria (Arthrobacter, Brevibacterium), because of their cell wall composition and G+C ratios. Most of the strains were psychrotrophic, but one strain was even obligately psychrophilic, with a temperature maximum below 20 degrees C. Red cocci had in vitro pH optima above 9.0 although they generally originated from acid samples. Most isolates showed a preference for sugar alcohols and organic acids, compounds which are commonly known to be released by lichens, molds and algae, the other components of the cryptoendolithic ecosystem. These properties indicate that our strains are autochthonous members of the natural Antarctic microbial population.
Collapse
Affiliation(s)
- J Siebert
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität Kiel, Federal Republic of Germany
| | | |
Collapse
|
5
|
Honrubia MP, Ramos A, Gil JA. The cell division genes ftsQ and ftsZ, but not the three downstream open reading frames YFIH, ORF5 and ORF6, are essential for growth and viability in Brevibacterium lactofermentum ATCC 13869. Mol Genet Genomics 2001; 265:1022-30. [PMID: 11523774 DOI: 10.1007/s004380100497] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
The three ORFs (YFIH, ORF5 and ORF6) located downstream of the cell division genes ftsQ and ftsZ in Brevibacterium lactofermentum were disrupted by single homologous recombination events between internal fragments of the corresponding genes and the chromosomal sequences. The phenotypes of the disrupted mutants were similar to that of the wild type, suggesting that these genes are dispensable for growth and viability. However, using different plasmid constructs, it was not possible to obtain disrupted ftsZ or ftsQ mutants by single crossover events. When the ftsZ or ftsQ gene sequence was disrupted in vitro and used to replace the homologous chromosomal gene by double recombination, only single recombination events took place, and therefore no disruptants were obtained. It may be concluded therefore that, as in Escherichia coli, the cell division genes ftsQ and ftsZ are indispensable for growth and viability of B. lactofermentum. Northern hybridisation analyses performed using internal fragments of the genes coding for YFIH, ORF5 and ORF6 allowed us to dissect their transcriptional organization and to confirm the disruption of these genes.
Collapse
Affiliation(s)
- M P Honrubia
- Departamento de Ecología, Genética y Microbiología, Facultad de Biología, Universidad de León, Spain
| | | | | |
Collapse
|
6
|
Kobayashi M, Asai Y, Hatakeyama K, Kijima N, Wachi M, Nagai K, Yukawa H. Cloning, sequencing, and characterization of the ftsZ gene from coryneform bacteria. Biochem Biophys Res Commun 1997; 236:383-8. [PMID: 9240446 DOI: 10.1006/bbrc.1997.6930] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Taking advantage of highly conserved domains present in the ftsZ genes from Escherichia coli, Rhizobium meliloti, and Bacillus subtilis, we designed degenerate oligonucleotides (oligos) corresponding to these regions. These oligos were used as primers in PCR in order to amplify DNA sequences from Brevibacterium flavum MJ233 chromosomal DNA. The PCR product was used as a probe to recover genomic fragments from a lambda library of Br. flavum MJ233. The complete nucleotide sequence (nt) of the cloned 4.2-kb EcoRI fragment containing the ftsZ homolog from Br. flavum MJ233 indicated that the deduced gene product of the Br. flavum ftsZ homolog is composed of 438 amino acids (aa) with a deduced molecular weight of 46.9 kDa. This size of molecular weight was also confirmed by the in vitro protein synthesis assay. Comparison of this aa sequence to the corresponding sequences from E. coli, Rh. meliloti, B. subtilis, and Streptomyces coelicolor revealed a high degree of conservation and suggested that the Br. flavum ftsZ homolog has a putative GTP binding motif and a GTP hydrolizing region. Expression of Br. flavum ftsZ gene in E. coli, JM109 inhibited its cell division, leading to filamentation. This suggested that the Br. flavum ftsZ product competed with the E. coli ftsZ product.
Collapse
Affiliation(s)
- M Kobayashi
- Tsukuba Research Center, Mitsubishi Chemical Corporation, Inashiki, Ibaraki, Japan
| | | | | | | | | | | | | |
Collapse
|
7
|
McBride ME, Ellner KM, Black HS, Clarridge JE, Wolf JE. A new Brevibacterium sp. isolated from infected genital hair of patients with white piedra. J Med Microbiol 1993; 39:255-61. [PMID: 8411085 DOI: 10.1099/00222615-39-4-255] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
A new aerobic gram-positive non-sporeforming bacillus has been isolated from infected genital hair of patients with white piedra in association with Trichosporon beigelii. This species has been characterised morphologically, nutritionally, by DNA base composition, cell-wall analysis and cellular fatty-acid profile on the basis of 14 isolates. The G+C content of DNA is 63.05 mol%. Cell walls possess meso-diaminopimelic acid (Type IV) and the sugars glucose, galactose, xylose and ribose; mycolic acids are not present. The species has a distinct colonial and microscopic morphology, is strongly proteolytic and produces methanethiol. These findings and the cellular fatty-acid profile are compatible with the genus Brevibacterium. A new species is proposed based on the following characters: colonial and microscopic growth and morphology; conditions for rod-to-coccus cycle; ribose utilisation; and tellurite reduction. The type strain has been named Brevibacterium mcbrellneri E2cr (ATCC 49030). The strong proteolytic properties may be the mechanism of pathogenesis.
Collapse
Affiliation(s)
- M E McBride
- Department of Dermatology, Baylor College of Medicine, Houston, Texas 77030
| | | | | | | | | |
Collapse
|
8
|
Kvasnikov EI, Nogina TM, Nesterenko OA, Panchenko LP, Rozynov BV. [Taxonomic position of the lysine producer Brevibacterium flavum]. Mikrobiologiia 1984; 53:93-7. [PMID: 6423939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Brevibacterium flavum 22 and 22L producing lysine and glutamic acid should be reclassified as Corynebacterium glutamicum on the basis of their chemotaxonomic characteristics: the IV type of the cell wall, corynomycolic acids C32--C34, 57.8% of GC in DNA.
Collapse
|
9
|
|
10
|
Abstract
Whole cells of Brevibacterium ammoniagenes IAM 1645 having the polyphosphate NAD-kinase were successfully immobilized in a polyacrylamide gel lattice. The immobilized cells were activated by treatment with organic solvents or detergents. The pH optimum of the immobilized cells for the production of NADP was 7.0, and divalent metal ions were required to maintain the elevated activity of polyphosphate NAD-kinase. Highly pure NADP was continuously produced in high yield by the immobilized cell column. The half-life of this column was about eight days.
Collapse
|
11
|
Golovlev EL, Baryshnikova LM. Differentiation of genera of the coryneform bacteria. Biol Bull Acad Sci USSR 1979; 6:143-9. [PMID: 121544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A scheme of the generic structure of the group of coryneform bacteria, including the genera Arthrobacter, Brevibacterium, Cellulomonas, Corynebacterium, and Rhodococcus, is suggested. Morphological, chemotaxonomic (presence and stereochemical form of diaminopimelic acid, lipid A, and L-arabinose), and physiological features were used as diagnostic criteria. The position of Microbacterum and Mycococcus and of coryneforms with a nocardial wall but giving a positive Hugh-Leifson anaerobic test, and also of Arthrobacter pascens, which may be identical with Mycoplana sp., remains uncertain.
Collapse
|
12
|
Jicinská E. Control of cell division by carbon dioxide in a filamentous mutant of Brevibacterium fulvum. Z Allg Mikrobiol 1974; 14:157-60. [PMID: 4836965 DOI: 10.1002/jobm.3630140211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
|
13
|
Abstract
Two species of marine bacteria with the ability to degrade crude oil were compared ultrastructurally after growing in the presence and absence of oil. Large electron-dense inclusions, which were located predominantly at the cell terminus, characterized species of Flavobacterium and Brevibacterium when growing on oil. Cells of Flavobacterium sp. had smaller inclusions when grown on marine agar, while inclusion bodies were not found in Brevibacterium sp. grown on marine agar. Sudan black B staining indicated the inclusions are stored lipids.
Collapse
|
14
|
|
15
|
|
16
|
Abstract
In the microbial conversion of added hypoxanthine to 5'-inosinic acid, Mn(2+) concentration in the growth medium is known to have a profound effect both on the yield of 5'-inosinic acid and the morphology of cells of Brevibacterium ammoniagenes. To elucidate the mechanism in which Mn(2+) was concerned with cell morphology and 5'-inosinic acid production, effects of Mn(2+) on the macromolecular synthesis were measured. It was found that Mn(2+) strongly governed deoxyribonucleic acid (DNA) synthesis and that, in the medium lacking Mn(2+), DNA synthesis was stopped at the level corresponding to one-fourth to one-third that in the medium supplemented with Mn(2+) (100 mug/liter). On the other hand, cellular ribonucleic acid and protein synthesis was quite indifferent to Mn(2+) concentration. Consequently, cells showed so-called "unbalanced growth death" after 10 hr of culture, losing the ability to form colonies while cell mass was increasing. The elongated cells turned into irregular forms (bulbous, club-shaped, etc.) which finally lysed. Two main reaction components in the conversion of hypoxanthine to 5'-inosinic acid, phosphoribosylpyrophosphate and hypoxanthine phosphoribosyltransferase, were liberated into the medium during lysis. The role of Mn(2+) in the synthesis of DNA and the role of the unbalanced growth death in the conversion of hypoxanthine to 5'-inosinic acid are discussed.
Collapse
|