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Pirkalkhoran S, Grabowska WR, Kashkoli HH, Mirhassani R, Guiliano D, Dolphin C, Khalili H. Bioengineering of Antibody Fragments: Challenges and Opportunities. Bioengineering (Basel) 2023; 10:bioengineering10020122. [PMID: 36829616 PMCID: PMC9952581 DOI: 10.3390/bioengineering10020122] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
Antibody fragments are used in the clinic as important therapeutic proteins for treatment of indications where better tissue penetration and less immunogenic molecules are needed. Several expression platforms have been employed for the production of these recombinant proteins, from which E. coli and CHO cell-based systems have emerged as the most promising hosts for higher expression. Because antibody fragments such as Fabs and scFvs are smaller than traditional antibody structures and do not require specific patterns of glycosylation decoration for therapeutic efficacy, it is possible to express them in systems with reduced post-translational modification capacity and high expression yield, for example, in plant and insect cell-based systems. In this review, we describe different bioengineering technologies along with their opportunities and difficulties to manufacture antibody fragments with consideration of stability, efficacy and safety for humans. There is still potential for a new production technology with a view of being simple, fast and cost-effective while maintaining the stability and efficacy of biotherapeutic fragments.
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Affiliation(s)
- Sama Pirkalkhoran
- School of Biomedical Science, University of West London, London W5 5RF, UK
| | | | | | | | - David Guiliano
- School of Life Science, College of Liberal Arts and Sciences, University of Westminster, London W1W 6UW, UK
| | - Colin Dolphin
- School of Biomedical Science, University of West London, London W5 5RF, UK
| | - Hanieh Khalili
- School of Biomedical Science, University of West London, London W5 5RF, UK
- School of Pharmacy, University College London, London WC1N 1AX, UK
- Correspondence:
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Pepi MJ, Chacko S, Marqus GM, Singh V, Wang Z, Planck K, Cullinane RT, Meka PN, Gollapalli DR, Ioerger TR, Rhee KY, Cuny GD, Boshoff HI, Hedstrom L. A d-Phenylalanine-Benzoxazole Derivative Reveals the Role of the Essential Enzyme Rv3603c in the Pantothenate Biosynthetic Pathway of Mycobacterium tuberculosis. ACS Infect Dis 2022; 8:330-342. [PMID: 35015509 DOI: 10.1021/acsinfecdis.1c00461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
New drugs and new targets are urgently needed to treat tuberculosis. We discovered that d-phenylalanine-benzoxazole Q112 displays potent antibacterial activity against Mycobacterium tuberculosis (Mtb) in multiple media and in macrophage infections. A metabolomic profiling indicates that Q112 has a unique mechanism of action. Q112 perturbs the essential pantothenate/coenzyme A biosynthetic pathway, depleting pantoate while increasing ketopantoate, as would be expected if ketopantoate reductase (KPR) were inhibited. We searched for alternative KPRs, since the enzyme annotated as PanE KPR is not essential in Mtb. The ketol-acid reductoisomerase IlvC catalyzes the KPR reaction in the close Mtb relative Corynebacterium glutamicum, but Mtb IlvC does not display KPR activity. We identified the essential protein Rv3603c as an orthologue of PanG KPR and demonstrated that a purified recombinant Rv3603c has KPR activity. Q112 inhibits Rv3603c, explaining the metabolomic changes. Surprisingly, pantothenate does not rescue Q112-treated bacteria, indicating that Q112 has an additional target(s). Q112-resistant strains contain loss-of-function mutations in the twin arginine translocase TatABC, further underscoring Q112's unique mechanism of action. Loss of TatABC causes a severe fitness deficit attributed to changes in nutrient uptake, suggesting that Q112 resistance may derive from a decrease in uptake.
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Affiliation(s)
- Michael J. Pepi
- Graduate Program in Chemistry, Brandeis University, Waltham 02453, Massachusetts, United States
| | - Shibin Chacko
- Department of Biology, Brandeis University, Waltham 02453, Massachusetts, United States
| | - Gary M. Marqus
- Graduate Program in Chemistry, Brandeis University, Waltham 02453, Massachusetts, United States
| | - Vinayak Singh
- Drug Discovery and Development Centre (H3D), and South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa
| | - Zhe Wang
- Division of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medical College, New York 10065, New York, United States
| | - Kyle Planck
- Division of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medical College, New York 10065, New York, United States
| | - Ryan T. Cullinane
- Department of Biology, Brandeis University, Waltham 02453, Massachusetts, United States
| | - Penchala N. Meka
- Department of Biology, Brandeis University, Waltham 02453, Massachusetts, United States
| | | | - Thomas R. Ioerger
- Department of Computer Science and Engineering, Texas A&M University, College Station 77843, Texas, United States
| | - Kyu Y. Rhee
- Division of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medical College, New York 10065, New York, United States
| | - Gregory D. Cuny
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston 77204, Texas, United States
| | - Helena I.M. Boshoff
- Tuberculosis Research Section, National Institute of Allergy and Infectious Diseases, Bethesda 20892, Maryland, United States
| | - Lizbeth Hedstrom
- Department of Biology, Brandeis University, Waltham 02453, Massachusetts, United States
- Department of Chemistry, Brandeis University, Waltham 02453, Massachusetts, United States
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Budowa i znaczenie II systemu sekrecji białek w ekologii i patogenezie Legionella pneumophila. POSTEP HIG MED DOSW 2021. [DOI: 10.2478/ahem-2021-0034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
Pałeczki Legionella pneumophila pasożytują w komórkach odległych filogenetycznie gospodarzy, w środowisku wodnym w pierwotniakach, a w organizmie człowieka w makrofagach alweolarnych. Zdolność tych bakterii do wewnątrzkomórkowego namnażania się w komórkach fagocytujących, wyspecjalizowanych do niszczenia mikroorganizmów, ma podstawowe znaczenie dla rozwoju nietypowego zapalenia płuc zwanego chorobą legionistów. Umiejscowione na kilku różnych loci chromosomu bakteryjnego geny II systemu sekrecji L. pneumophila kodują co najmniej 25 białek, w tym enzymy o aktywności lipolitycznej, proteolitycznej, rybonukleazy oraz białka unikalne bakterii Legionella. W środowisku naturalnym T2SS L. pneumophila odgrywa decydującą rolę w ekologii tych drobnoustrojów determinując ich zdolność do przeżycia zarówno w postaci planktonicznej, jak i w strukturach biofilmu w słodkowodnych zbiornikach o niskiej temperaturze. Białka T2SS umożliwiają L. pneumophila zakażenie różnych gatunków pierwotniaków, a substraty tego systemu określają zakres pierwotniaczego gospodarza. Namnażanie się bakterii w różnorodnych pierwotniakach przyczynia się do ich rozsiewania oraz transmisji do antropogenicznych źródeł. Białka wydzielane za pomocą II systemu sekrecji determinują również zdolność L. pneumophila do zakażania mysich makrofagów alweolarnych i szpiku kostnego, ludzkich makrofagów linii U937 i THP-1 oraz komórek nabłonkowych pęcherzyków płucnych. Enzymy wydzielane za pomocą tego systemu, takie jak: proteazy, aminopeptydazy czy fosfolipazy umożliwiają pozyskanie substancji pokarmowych oraz powodują destrukcję tkanki płucnej myszy. W organizmie człowieka białka T2SS przyczyniają się do osłabienia wrodzonej odpowiedzi immunologicznej na zakażenie L. pneumophila przez hamowanie indukcji prozapalnych cytokin (IL-6, TNF-α, IL-1 oraz IL-8).
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Morosov X, Davoudi CF, Baumgart M, Brocker M, Bott M. The copper-deprivation stimulon of Corynebacterium glutamicum comprises proteins for biogenesis of the actinobacterial cytochrome bc 1- aa 3 supercomplex. J Biol Chem 2018; 293:15628-15640. [PMID: 30154248 DOI: 10.1074/jbc.ra118.004117] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 08/21/2018] [Indexed: 01/01/2023] Open
Abstract
Aerobic respiration in Corynebacterium glutamicum involves a cytochrome bc 1-aa 3 supercomplex with a diheme cytochrome c 1, which is the only c-type cytochrome in this species. This organization is considered as typical for aerobic Actinobacteria. Whereas the biogenesis of heme-copper type oxidases like cytochrome aa 3 has been studied extensively in α-proteobacteria, yeast, and mammals, nothing is known about this process in Actinobacteria. Here, we searched for assembly proteins of the supercomplex by identifying the copper-deprivation stimulon, which might include proteins that insert copper into cytochrome aa 3 Using gene expression profiling, we found two copper starvation-induced proteins for supercomplex formation. The Cg2699 protein, named CtiP, contained 16 predicted transmembrane helices, and its sequence was similar to that of the copper importer CopD of Pseudomonas syringae in the N-terminal half and to the cytochrome oxidase maturation protein CtaG of Bacillus subtilis in its C-terminal half. CtiP deletion caused a growth defect similar to that produced by deletion of subunit I of cytochrome aa 3, increased copper tolerance, triggered expression of the copper-deprivation stimulon under copper sufficiency, and prevented co-purification of the supercomplex subunits. The secreted Cg1884 protein, named CopC, had a C-terminal transmembrane helix and contained a Cu(II)-binding motif. Its absence caused a conditional growth defect, increased copper tolerance, and also prevented co-purification of the supercomplex subunits. CtiP and CopC are conserved among aerobic Actinobacteria, and we propose a model of their functions in cytochrome aa 3 biogenesis. Furthermore, we found that the copper-deprivation response involves additional regulators besides the ECF sigma factor SigC.
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Affiliation(s)
- Xenia Morosov
- From the Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Cedric-Farhad Davoudi
- From the Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Meike Baumgart
- From the Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Melanie Brocker
- From the Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Michael Bott
- From the Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
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Arginine-deprivation-induced oxidative damage sterilizes Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 2018; 115:9779-9784. [PMID: 30143580 PMCID: PMC6166831 DOI: 10.1073/pnas.1808874115] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Reactive oxygen species (ROS)-mediated oxidative stress and DNA damage have recently been recognized as contributing to the efficacy of most bactericidal antibiotics, irrespective of their primary macromolecular targets. Inhibitors of targets involved in both combating oxidative stress as well as being required for in vivo survival may exhibit powerful synergistic action. This study demonstrates that the de novo arginine biosynthetic pathway in Mycobacterium tuberculosis (Mtb) is up-regulated in the early response to the oxidative stress-elevating agent isoniazid or vitamin C. Arginine deprivation rapidly sterilizes the Mtb de novo arginine biosynthesis pathway mutants ΔargB and ΔargF without the emergence of suppressor mutants in vitro as well as in vivo. Transcriptomic and flow cytometry studies of arginine-deprived Mtb have indicated accumulation of ROS and extensive DNA damage. Metabolomics studies following arginine deprivation have revealed that these cells experienced depletion of antioxidant thiols and accumulation of the upstream metabolite substrate of ArgB or ArgF enzymes. ΔargB and ΔargF were unable to scavenge host arginine and were quickly cleared from both immunocompetent and immunocompromised mice. In summary, our investigation revealed in vivo essentiality of the de novo arginine biosynthesis pathway for Mtb and a promising drug target space for combating tuberculosis.
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Freudl R. Signal peptides for recombinant protein secretion in bacterial expression systems. Microb Cell Fact 2018; 17:52. [PMID: 29598818 PMCID: PMC5875014 DOI: 10.1186/s12934-018-0901-3] [Citation(s) in RCA: 141] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 03/27/2018] [Indexed: 02/06/2023] Open
Abstract
The secretion of biotechnologically or pharmaceutically relevant recombinant proteins into the culture supernatant of a bacterial expression host greatly facilitates their downstream processing and significantly reduces the production costs. The first step during the secretion of a desired target protein into the growth medium is its transport across the cytoplasmic membrane. In bacteria, two major export pathways, the general secretion or Sec pathway and the twin-arginine translocation or Tat pathway, exist for the transport of proteins across the plasma membrane. The routing into one of these alternative protein export systems requires the fusion of a Sec- or Tat-specific signal peptide to the amino-terminal end of the desired target protein. Since signal peptides, besides being required for the targeting to and membrane translocation by the respective protein translocases, also have additional influences on the biosynthesis, the folding kinetics, and the stability of the respective target proteins, it is not possible so far to predict in advance which signal peptide will perform best in the context of a given target protein and a given bacterial expression host. As outlined in this review, the most promising way to find the optimal signal peptide for a desired protein is to screen the largest possible diversity of signal peptides, either generated by signal peptide variation using large signal peptide libraries or, alternatively, by optimization of a given signal peptide using site-directed or random mutagenesis strategies.
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Affiliation(s)
- Roland Freudl
- Institut für Bio- und Geowissenschaften 1, Biotechnologie, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany. .,Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.
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Freudl R. Beyond amino acids: Use of the Corynebacterium glutamicum cell factory for the secretion of heterologous proteins. J Biotechnol 2017; 258:101-109. [DOI: 10.1016/j.jbiotec.2017.02.023] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 02/21/2017] [Accepted: 02/21/2017] [Indexed: 11/16/2022]
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Protein Secretion in Gram-Positive Bacteria: From Multiple Pathways to Biotechnology. Curr Top Microbiol Immunol 2017; 404:267-308. [PMID: 27885530 DOI: 10.1007/82_2016_49] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A number of Gram-positive bacteria are important players in industry as producers of a diverse array of economically interesting metabolites and proteins. As discussed in this overview, several Gram-positive bacteria are valuable hosts for the production of heterologous proteins. In contrast to Gram-negative bacteria, proteins secreted by Gram-positive bacteria are released into the culture medium where conditions for correct folding are more appropriate, thus facilitating the isolation and purification of active proteins. Although seven different protein secretion pathways have been identified in Gram-positive bacteria, the majority of heterologous proteins are produced via the general secretion or Sec pathway. Not all proteins are equally well secreted, because heterologous protein production often faces bottlenecks including hampered secretion, susceptibility to proteases, secretion stress, and metabolic burden. These bottlenecks are associated with reduced yields leading to non-marketable products. In this chapter, besides a general overview of the different protein secretion pathways, possible hurdles that may hinder efficient protein secretion are described and attempts to improve yield are discussed including modification of components of the Sec pathway. Attention is also paid to omics-based approaches that may offer a more rational approach to optimize production of heterologous proteins.
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Petrus MLC, Vijgenboom E, Chaplin AK, Worrall JAR, van Wezel GP, Claessen D. The DyP-type peroxidase DtpA is a Tat-substrate required for GlxA maturation and morphogenesis in Streptomyces. Open Biol 2016; 6:150149. [PMID: 26740586 PMCID: PMC4736821 DOI: 10.1098/rsob.150149] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The filamentous bacterium Streptomyces lividans depends on the radical copper oxidase GlxA for the formation of reproductive aerial structures and, in liquid environments, for the formation of pellets. Incorporation of copper into the active site is essential for the formation of a cross-linked tyrosyl-cysteine cofactor, which is needed for enzymatic activity. In this study, we show a crucial link between GlxA maturation and a group of copper-related proteins including the chaperone Sco and a novel DyP-type peroxidase hereinafter called DtpA. Under copper-limiting conditions, the sco and dtpA deletion mutants are blocked in aerial growth and pellet formation, similarly to a glxA mutant. Western blot analysis showed that GlxA maturation is perturbed in the sco and dtpA mutants, but both maturation and morphology can by rescued by increasing the bioavailability of copper. DtpA acts as a peroxidase in the presence of GlxA and is a substrate for the twin-arginine translocation (Tat) translocation pathway. In agreement, the maturation status of GlxA is also perturbed in tat mutants, which can be compensated for by the addition of copper, thereby partially restoring their morphological defects. Our data support a model wherein a copper-trafficking pathway and Tat-dependent secretion of DtpA link to the GlxA-dependent morphogenesis pathway.
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Affiliation(s)
- Marloes L C Petrus
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Erik Vijgenboom
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Amanda K Chaplin
- School of Biological Science, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Jonathan A R Worrall
- School of Biological Science, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Dennis Claessen
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
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TatC-dependent translocation of pyoverdine is responsible for the microbial growth suppression. J Microbiol 2016; 54:122-30. [PMID: 26832668 DOI: 10.1007/s12275-016-5542-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 12/21/2015] [Accepted: 12/22/2015] [Indexed: 01/28/2023]
Abstract
Infections are often not caused by a colonization of Pseudomonas aeruginosa alone but by a consortium of other bacteria. Little is known about the impact of P. aeruginosa on the growth of other bacteria upon coinfection. Here, cell-ree culture supernatants obtained from P. aeruginosa suppressed the growth of a number of bacterial strains such as Corynebacterium glutamicum, Bacillus subtilis, Staphylococcus aureus, and Agrobacterium tumefaciens, but had little effect on the growth of Escherichia coli and Salmonella Typhimurium. The growth suppression effect was obvious when P. aeruginosa was cultivated in M9 minimal media, and the suppression was not due to pyocyanin, a well-known antimicrobial toxin secreted by P. aeruginosa. By performing transposon mutagenesis, PA5070 encoding TatC was identified, and the culture supernatant of its mutant did not suppress the growth. HPLC analysis of supernatants showed that pyoverdine was a secondary metabolite present in culture supernatants of the wild-type strain, but not in those of the PA5070 mutant. Supplementation of FeCl2 as a source of iron compromised the growth suppression effect of supernatants and also recovered biofilm formation of S. aureus, indicating that pyoverdine-mediated iron acquisition is responsible for the growth suppression. Thus, this study provides the action of TatC-dependent pyoverdine translocation for the growth suppression of other bacteria, and it might aid understanding of the impact of P. aeruginosa in the complex community of bacterial species upon coinfection.
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Abstract
Twin-arginine protein translocation systems (Tat) translocate fully folded and co-factor-containing proteins across biological membranes. In this review, we focus on the Tat pathway of Gram-positive bacteria. The minimal Tat pathway is composed of two components, namely a TatA and TatC pair, which are often complemented with additional TatA-like proteins. We provide overviews of our current understanding of Tat pathway composition and mechanistic aspects related to Tat-dependent cargo protein translocation. This includes Tat pathway flexibility, requirements for the correct folding and incorporation of co-factors in cargo proteins and the functions of known cargo proteins. Tat pathways of several Gram-positive bacteria are discussed in detail, with emphasis on the Tat pathway of Bacillus subtilis. We discuss both shared and unique features of the different Gram-positive bacterial Tat pathways. Lastly, we highlight topics for future research on Tat, including the development of this protein transport pathway for the biotechnological secretion of high-value proteins and its potential applicability as an antimicrobial drug target in pathogens.
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Affiliation(s)
- Vivianne J Goosens
- MRC Centre for Molecular Bacteriology and Infection, Section of Microbiology, Imperial College London, London, SW7 2AZ, UK
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700, RB, Groningen, The Netherlands.
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