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Tamman H, Ernits K, Roghanian M, Ainelo A, Julius C, Perrier A, Talavera A, Ainelo H, Dugauquier R, Zedek S, Thureau A, Pérez J, Lima-Mendez G, Hallez R, Atkinson GC, Hauryliuk V, Garcia-Pino A. Structure of SpoT reveals evolutionary tuning of catalysis via conformational constraint. Nat Chem Biol 2023; 19:334-345. [PMID: 36470996 PMCID: PMC9974481 DOI: 10.1038/s41589-022-01198-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 10/05/2022] [Indexed: 12/12/2022]
Abstract
Stringent factors orchestrate bacterial cell reprogramming through increasing the level of the alarmones (p)ppGpp. In Beta- and Gammaproteobacteria, SpoT hydrolyzes (p)ppGpp to counteract the synthetase activity of RelA. However, structural information about how SpoT controls the levels of (p)ppGpp is missing. Here we present the crystal structure of the hydrolase-only SpoT from Acinetobacter baumannii and uncover the mechanism of intramolecular regulation of 'long'-stringent factors. In contrast to ribosome-associated Rel/RelA that adopt an elongated structure, SpoT assumes a compact τ-shaped structure in which the regulatory domains wrap around a Core subdomain that controls the conformational state of the enzyme. The Core is key to the specialization of long RelA-SpoT homologs toward either synthesis or hydrolysis: the short and structured Core of SpoT stabilizes the τ-state priming the hydrolase domain for (p)ppGpp hydrolysis, whereas the longer, more dynamic Core domain of RelA destabilizes the τ-state priming the monofunctional RelA for efficient (p)ppGpp synthesis.
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Affiliation(s)
- Hedvig Tamman
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles (ULB), Boulevard du Triomphe, Brussels, Belgium.
| | - Karin Ernits
- Department of Experimental Medicine, University of Lund, Lund, Sweden
- Department of Chemistry, Umeå University, Umeå, Sweden
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Mohammad Roghanian
- Department of Experimental Medicine, University of Lund, Lund, Sweden
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Departement of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
| | - Andres Ainelo
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles (ULB), Boulevard du Triomphe, Brussels, Belgium
| | | | - Anthony Perrier
- Biology of Microorganisms Research Unit, Namur Research Institute for Life Science, University of Namur, Namur, Belgium
- Bacterial Cell Cycle and Development, Biology of Microorganisms Research Unit, Namur Research Institute for Life Science, University of Namur, Namur, Belgium
| | - Ariel Talavera
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles (ULB), Boulevard du Triomphe, Brussels, Belgium
| | - Hanna Ainelo
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles (ULB), Boulevard du Triomphe, Brussels, Belgium
| | - Rémy Dugauquier
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles (ULB), Boulevard du Triomphe, Brussels, Belgium
- Biology of Microorganisms Research Unit, Namur Research Institute for Life Science, University of Namur, Namur, Belgium
| | - Safia Zedek
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles (ULB), Boulevard du Triomphe, Brussels, Belgium
| | | | - Javier Pérez
- Synchrotron SOLEIL, Saint-Aubin - BP 48, Gif sur Yvette, France
| | - Gipsi Lima-Mendez
- Biology of Microorganisms Research Unit, Namur Research Institute for Life Science, University of Namur, Namur, Belgium
| | - Régis Hallez
- Biology of Microorganisms Research Unit, Namur Research Institute for Life Science, University of Namur, Namur, Belgium
- Bacterial Cell Cycle and Development, Biology of Microorganisms Research Unit, Namur Research Institute for Life Science, University of Namur, Namur, Belgium
- WELBIO, Brussels, Belgium
| | - Gemma C Atkinson
- Department of Experimental Medicine, University of Lund, Lund, Sweden
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Vasili Hauryliuk
- Department of Experimental Medicine, University of Lund, Lund, Sweden.
- Department of Molecular Biology, Umeå University, Umeå, Sweden.
- University of Tartu, Institute of Technology, Tartu, Estonia.
| | - Abel Garcia-Pino
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles (ULB), Boulevard du Triomphe, Brussels, Belgium.
- WELBIO, Brussels, Belgium.
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2
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Koller TO, Turnbull KJ, Vaitkevicius K, Crowe-McAuliffe C, Roghanian M, Bulvas O, Nakamoto JA, Kurata T, Julius C, Atkinson G, Johansson J, Hauryliuk V, Wilson D. Structural basis for HflXr-mediated antibiotic resistance in Listeria monocytogenes. Nucleic Acids Res 2022; 50:11285-11300. [PMID: 36300626 PMCID: PMC9638945 DOI: 10.1093/nar/gkac934] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 09/28/2022] [Accepted: 10/26/2022] [Indexed: 08/09/2023] Open
Abstract
HflX is a ubiquitous bacterial GTPase that splits and recycles stressed ribosomes. In addition to HflX, Listeria monocytogenes contains a second HflX homolog, HflXr. Unlike HflX, HflXr confers resistance to macrolide and lincosamide antibiotics by an experimentally unexplored mechanism. Here, we have determined cryo-EM structures of L. monocytogenes HflXr-50S and HflX-50S complexes as well as L. monocytogenes 70S ribosomes in the presence and absence of the lincosamide lincomycin. While the overall geometry of HflXr on the 50S subunit is similar to that of HflX, a loop within the N-terminal domain of HflXr, which is two amino acids longer than in HflX, reaches deeper into the peptidyltransferase center. Moreover, unlike HflX, the binding of HflXr induces conformational changes within adjacent rRNA nucleotides that would be incompatible with drug binding. These findings suggest that HflXr confers resistance using an allosteric ribosome protection mechanism, rather than by simply splitting and recycling antibiotic-stalled ribosomes.
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Affiliation(s)
| | | | - Karolis Vaitkevicius
- Department of Molecular Biology and Umeå Centre for Microbial Research (UCMR), Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90187 Umeå, Sweden
| | - Caillan Crowe-McAuliffe
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Mohammad Roghanian
- Department of Molecular Biology and Umeå Centre for Microbial Research (UCMR), Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90187 Umeå, Sweden
- Department of Clinical Microbiology, Rigshospitalet, 2200 Copenhagen, Denmark
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | - Ondřej Bulvas
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technicka 5, 166 28 Prague 6, Czech Republic
| | - Jose A Nakamoto
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | - Tatsuaki Kurata
- Department of Molecular Biology and Umeå Centre for Microbial Research (UCMR), Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90187 Umeå, Sweden
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | - Christina Julius
- Department of Molecular Biology and Umeå Centre for Microbial Research (UCMR), Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90187 Umeå, Sweden
| | - Gemma C Atkinson
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | - Jörgen Johansson
- Department of Molecular Biology and Umeå Centre for Microbial Research (UCMR), Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90187 Umeå, Sweden
| | | | - Daniel N Wilson
- To whom correspondence should be addressed. Tel: +49 40 42838 2841;
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3
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Julius C, Pletz MW, Rupp J, Witzenrath M, Barten-Neiner G, Rohde G. Pneumonia in the third year of the pandemic: One eye on the pathogens, the other on the host. Am J Physiol Lung Cell Mol Physiol 2022; 323:L611-L614. [PMID: 36218260 DOI: 10.1152/ajplung.00330.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
| | - Mathias W Pletz
- CAPNETZ STIFTUNG Geschäftsstelle, Hannover, Germany.,Institute of Infectious Diseases and Infection Control, University Hospital, Jena, Germany
| | - Jan Rupp
- CAPNETZ STIFTUNG Geschäftsstelle, Hannover, Germany.,Department of Infectious Diseases and Microbiology, University Hospital Schleswig-Holstein, Lübeck Germany
| | - Martin Witzenrath
- CAPNETZ STIFTUNG Geschäftsstelle, Hannover, Germany.,Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany.,German Center for Lung Research (DZL), Gießen, Germany
| | - Grit Barten-Neiner
- CAPNETZ STIFTUNG Geschäftsstelle, Hannover, Germany.,Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), Hannover, Germany
| | - Gernot Rohde
- CAPNETZ STIFTUNG Geschäftsstelle, Hannover, Germany.,Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), Hannover, Germany.,Goethe-Universität Frankfurt am Main, Department of Respiratory Medicine, Medical Clinic I, Frankfurt/Main, Germany
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Abstract
Recent years witnessed the discovery of ubiquitous and diverse 5'-end RNA cap-like modifications in prokaryotes as well as in eukaryotes. These non-canonical caps include metabolic cofactors, such as NAD+/NADH, FAD, cell wall precursors UDP-GlcNAc, alarmones, e.g. dinucleotides polyphosphates, ADP-ribose and potentially other nucleoside derivatives. They are installed at the 5' position of RNA via template-dependent incorporation of nucleotide analogues as an initiation substrate by RNA polymerases. However, the discovery of NAD-capped processed RNAs in human cells suggests the existence of alternative post-transcriptional NC capping pathways. In this review, we compiled growing evidence for a number of these other mechanisms which produce various non-canonically capped RNAs and a growing repertoire of capping small molecules. Enzymes shown to be involved are ADP-ribose polymerases, glycohydrolases and tRNA synthetases, and may potentially include RNA 3'-phosphate cyclases, tRNA guanylyl transferases, RNA ligases and ribozymes. An emerging rich variety of capping molecules and enzymes suggests an unrecognized level of complexity of RNA metabolism.
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Affiliation(s)
| | | | - Yulia Yuzenkova
- Medical School, NUBI, Newcastle University, Newcastle upon Tyne, UK
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5
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Julius C, Salgado PS, Yuzenkova Y. Metabolic cofactors NADH and FAD act as non-canonical initiating substrates for a primase and affect replication primer processing in vitro. Nucleic Acids Res 2020; 48:7298-7306. [PMID: 32463447 PMCID: PMC7367122 DOI: 10.1093/nar/gkaa447] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 05/13/2020] [Accepted: 05/14/2020] [Indexed: 11/17/2022] Open
Abstract
To initiate replication on a double-stranded DNA de novo, all organisms require primase, an RNA polymerase making short RNA primers which are then extended by DNA polymerases. Here, we show that primase can use metabolic cofactors as initiating substrates, instead of its canonical substrate ATP. DnaG primase of Escherichia coli initiates synthesis of RNA with NADH (the reduced form of nicotinamide adenine dinucleotide) and FAD (flavin adenine dinucleotide) in vitro. These cofactors consist of an ADP core covalently bound to extra moieties. The ADP component of these metabolites base-pairs with the DNA template and provides a 3′-OH group for RNA extension. The additional cofactors moieties apparently contact the ‘basic ridge’ domain of DnaG, but not the DNA template base at the –1 position. ppGpp, the starvation response regulator, strongly inhibits the initiation with cofactors, hypothetically due to competition for overlapping binding sites. Efficient RNA primer processing is a prerequisite for Okazaki fragments maturation, and we find that the efficiency of primer processing by DNA polymerase I in vitro is specifically affected by the cofactors on its 5′-end. Together these results indicate that utilization of cofactors as substrates by primase may influence regulation of replication initiation and Okazaki fragments processing.
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Affiliation(s)
- Christina Julius
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle upon Tyne, NE2 4AX, UK
| | - Paula S Salgado
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle upon Tyne, NE2 4AX, UK
| | - Yulia Yuzenkova
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle upon Tyne, NE2 4AX, UK
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6
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Julius C, Yuzenkova Y. Noncanonical RNA-capping: Discovery, mechanism, and physiological role debate. Wiley Interdiscip Rev RNA 2018; 10:e1512. [PMID: 30353673 DOI: 10.1002/wrna.1512] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 09/11/2018] [Accepted: 09/27/2018] [Indexed: 11/12/2022]
Abstract
Recently a new type of 5'-RNA cap was discovered. In contrast to the specialized eukaryotic m7 G cap, the novel caps are abundant cellular cofactors like NAD+ . RNAs capped with cofactors are found in prokaryotes and eukaryotes. Unlike m7 G cap, installed by specialized enzymes, cofactors are attached by main enzyme of transcription, RNA polymerase (RNAP). Cofactors act as noncanonical initiating substrates, provided cofactor's nucleoside base-pairs with template DNA at the transcription start site. Adenosine-containing NAD(H), flavin adenine dinucleotide (FAD), and CoA modify transcripts on promoters starting with +1A. Similarly, uridine-containing cell wall precursors, for example, uridine diphosphate-N-acetylglucosamine were shown to cap RNA in vitro on +1U promoters. Noncanonical capping is a universal feature of evolutionary unrelated RNAPs-multisubunit bacterial and eukaryotic RNAPs, and single-subunit mitochondrial RNAP. Cellular concentrations of cofactors, for example, NAD(H) are significantly higher than their Km in transcription. Yet, only a small proportion of a given cellular RNA is noncanonically capped (if at all). This proportion is a net balance between capping, seemingly stochastic, and decapping, possibly determined by RNA folding, protein binding and transcription rate. NUDIX hydrolases in bacteria and eukaryotes, and DXO family proteins eukaryotes act as decapping enzymes for noncanonical caps. The physiological role of noncanonical RNA capping is only starting to emerge. It was demonstrated to affect RNA stability in vivo in bacteria and eukaryotes and to stimulate RNAP promoter escape in vitro in Escherichia coli. NAD+ /NADH capping ratio may connect transcription to cellular redox state. Potentially, noncanonical capping affects mRNA translation, RNA-protein binding and RNA localization. This article is categorized under: RNA Processing > Capping and 5' End Modifications RNA Export and Localization > RNA Localization RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry.
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Affiliation(s)
- Christina Julius
- Centre for Bacterial Cell Biology, Newcastle University, Newcastle upon Tyne, UK
| | - Yulia Yuzenkova
- Centre for Bacterial Cell Biology, Newcastle University, Newcastle upon Tyne, UK
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7
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Abstract
Recently, it was found that bacterial and eukaryotic transcripts are capped with cellular cofactors installed by their respective RNA polymerases (RNAPs) during transcription initiation. We now show that mitochondrial RNAP efficiently caps transcripts with ADP - containing cofactors. However, a functional role of universal RNAP - catalysed capping is not yet clear.
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Affiliation(s)
- Christina Julius
- a Centre for Bacterial Cell Biology , Institute for Cell and Molecular Biosciences , Newcastle University , Newcastle upon Tyne , NE2 4AX , UK
| | - Amber Riaz-Bradley
- a Centre for Bacterial Cell Biology , Institute for Cell and Molecular Biosciences , Newcastle University , Newcastle upon Tyne , NE2 4AX , UK
| | - Yulia Yuzenkova
- a Centre for Bacterial Cell Biology , Institute for Cell and Molecular Biosciences , Newcastle University , Newcastle upon Tyne , NE2 4AX , UK
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8
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Julius C, Yuzenkova Y. Bacterial RNA polymerase caps RNA with various cofactors and cell wall precursors. Nucleic Acids Res 2017; 45:8282-8290. [PMID: 28531287 PMCID: PMC5737558 DOI: 10.1093/nar/gkx452] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 05/09/2017] [Indexed: 01/19/2023] Open
Abstract
Bacterial RNA polymerase is able to initiate transcription with adenosine-containing cofactor NAD+, which was proposed to result in a portion of cellular RNAs being ‘capped’ at the 5′ end with NAD+, reminiscent of eukaryotic cap. Here we show that, apart from NAD+, another adenosine-containing cofactor FAD and highly abundant uridine-containing cell wall precursors, UDP-Glucose and UDP-N-acetylglucosamine are efficiently used to initiate transcription in vitro. We show that the affinity to NAD+ and UDP-containing factors during initiation is much lower than their cellular concentrations, and that initiation with them stimulates promoter escape. Efficiency of initiation with NAD+, but not with UDP-containing factors, is affected by amino acids of the Rifampicin-binding pocket, suggesting altered RNA capping in Rifampicin-resistant strains. However, relative affinity to NAD+ does not depend on the −1 base of the template strand, as was suggested earlier. We show that incorporation of mature cell wall precursor, UDP-MurNAc-pentapeptide, is inhibited by region 3.2 of σ subunit, possibly preventing targeting of RNA to the membrane. Overall, our in vitro results propose a wide repertoire of potential bacterial RNA capping molecules, and provide mechanistic insights into their incorporation.
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Affiliation(s)
- Christina Julius
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Baddiley-Clark Building, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Yulia Yuzenkova
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Baddiley-Clark Building, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
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9
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Nagler K, Julius C, Moeller R. Germination of Spores of Astrobiologically Relevant Bacillus Species in High-Salinity Environments. Astrobiology 2016; 16:500-512. [PMID: 27304705 DOI: 10.1089/ast.2015.1419] [Citation(s) in RCA: 6] [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] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
UNLABELLED In times of increasing space exploration and search for extraterrestrial life, new questions and challenges for planetary protection, aiming to avoid forward contamination of different planets or moons with terrestrial life, are emerging. Spore-forming bacteria such as Bacillus species have a high contamination potential due to their spores' extreme resistance, enabling them to withstand space conditions. Spores require liquid water for their conversion into a growing cell (i.e., spore germination and subsequent growth). If present, water on extraterrestrial planets or moons is likely to be closely associated with salts (e.g., in salty oceans or brines), thus constituting high-salinity environments. Spores of Bacillus subtilis can germinate despite very high salt concentrations, although salt stress does exert negative effects on this process. In this study, germination and metabolic reactivation ("outgrowth") of spores of five astrobiologically relevant Bacillus species (B. megaterium, B. pumilus SAFR-032, B. nealsonii, B. mojavensis, and B. vallismortis) in high salinity (≤3.6 M NaCl) were investigated. Spores of different species exhibited different germination and outgrowth capabilities in high salinity, which strongly depended on germination conditions, especially the exact composition of the medium. In this context, a new "universal" germination trigger for Bacillus spores, named KAGE (KCl, L-alanine, D-glucose, ectoine), was identified, which will be very useful for future comparative germination and outgrowth studies on different Bacillus species. Overall, this study yielded interesting new insights on salt stress effects on spore germination and points out the difficulty of predicting the potential of spores to contaminate salty environments on extraterrestrial celestial bodies. KEY WORDS Bacillus species-Spores-Germination-High salinity-Salt stress-NaCl-Inhibition. Astrobiology 16, 500-512.
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Affiliation(s)
- Katja Nagler
- German Aerospace Center (DLR e.V.), Institute of Aerospace Medicine , Radiation Biology Department, Space Microbiology Research Group, Cologne, Germany
| | - Christina Julius
- German Aerospace Center (DLR e.V.), Institute of Aerospace Medicine , Radiation Biology Department, Space Microbiology Research Group, Cologne, Germany
| | - Ralf Moeller
- German Aerospace Center (DLR e.V.), Institute of Aerospace Medicine , Radiation Biology Department, Space Microbiology Research Group, Cologne, Germany
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10
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Julius C, Heikenwalder M, Schwarz P, Marcel A, Karin M, Prinz M, Pasparakis M, Aguzzi A. Prion propagation in mice lacking central nervous system NF-κB signalling. J Gen Virol 2008; 89:1545-1550. [DOI: 10.1099/vir.0.83622-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Prions induce highly typical histopathological changes including cell death, spongiosis and activation of glia, yet the molecular pathways leading to neurodegeneration remain elusive. Following prion infection, enhanced nuclear factor-κB (NF-κB) activity in the brain parallels the first pathological changes. The NF-κB pathway is essential for proliferation, regulation of apoptosis and immune responses involving induction of inflammation. The IκB kinase (IKK) signalosome is crucial for NF-κB signalling, consisting of the catalytic IKKα/IKKβ subunits and the regulatory IKKγ subunit. This study investigated the impact of NF-κB signalling on prion disease in mouse models with a central nervous system (CNS)-restricted elimination of IKKβ or IKKγ in nearly all neuroectodermal cells, including neurons, astrocytes and oligodendrocytes, and in mice containing a non-phosphorylatable IKKα subunit (IKKα
AA/AA). In contrast to previously published data, the observed results showed no evidence supporting the hypothesis that impaired NF-κB signalling in the CNS impacts on prion pathogenesis.
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Affiliation(s)
- C. Julius
- Institute of Neuropathology, University Hospital of Zürich, Zürich, Switzerland
| | - M. Heikenwalder
- Institute of Neuropathology, University Hospital of Zürich, Zürich, Switzerland
| | - P. Schwarz
- Institute of Neuropathology, University Hospital of Zürich, Zürich, Switzerland
| | - A. Marcel
- Institute of Neuropathology, University Hospital of Zürich, Zürich, Switzerland
| | - M. Karin
- Laboratory of Gene Regulation and Signal Transduction, Department of Pharmacology, School of Medicine, University of California, San Diego, USA
| | - M. Prinz
- Department of Neuropathology, University of Freiburg, Freiburg, Germany
| | - M. Pasparakis
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - A. Aguzzi
- Institute of Neuropathology, University Hospital of Zürich, Zürich, Switzerland
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11
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Brachmann A, König J, Julius C, Feldbrügge M. A reverse genetic approach for generating gene replacement mutants in Ustilago maydis. Mol Genet Genomics 2004. [DOI: 10.1007/s00438-004-1067-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Brachmann A, König J, Julius C, Feldbrügge M. A reverse genetic approach for generating gene replacement mutants in Ustilago maydis. Mol Genet Genomics 2004; 272:216-26. [PMID: 15316769 DOI: 10.1007/s00438-004-1047-z] [Citation(s) in RCA: 122] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2003] [Accepted: 07/19/2004] [Indexed: 10/26/2022]
Abstract
We describe a versatile strategy for generating gene replacement mutants in the phytopathogenic fungus Ustilago maydis. The system includes the choice of 32 different insertion cassettes for genetic engineering purposes, such as gene disruption and more sophisticated insertions of reporter genes, heterologous promoters or combinations of the two. PCR-amplified flanking sequences needed for homologous recombination are ligated to the respective insertion cassettes via SfiI sites. As proof of principle we generated two replacement mutants in which the endogenous promoter of the pheromone gene mfa1 drives expression of the Green Fluorescent Protein gene (gfp). Simultaneously, expression of the mfa1 ORF is controlled either by the carbon source-regulated crg1 promoter or the nitrogen source-regulated nar1 promoter. In both cases gfp expression was pheromone-inducible and pheromone expression was only detected when the heterologous promoters were active.
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Affiliation(s)
- A Brachmann
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse, 35043, Marburg, Germany
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13
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Gross P, Julius C, Schmelzer E, Hahlbrock K. Translocation of cytoplasm and nucleus to fungal penetration sites is associated with depolymerization of microtubules and defence gene activation in infected, cultured parsley cells. EMBO J 1993; 12:1735-44. [PMID: 8491167 PMCID: PMC413392 DOI: 10.1002/j.1460-2075.1993.tb05821.x] [Citation(s) in RCA: 114] [Impact Index Per Article: 3.7] [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: 11/06/2022] Open
Abstract
We describe a novel system of reduced complexity for analysing molecular plant-fungus interactions. The system consists of suspension-cultured parsley (Petroselinum crispum) cells infected with a phytopathogenic fungus (Phytophthora infestans) which adheres to a coated glass plate and thus immobilizes the plant cells for live microscopy. Conventional light and electron microscopy as well as time-lapse video microscopy confirmed the virtual identity of fungal infection structures and of several characteristic early plant defence reactions in the cultured cells and whole-plant tissue. Using this new system to approach previously unresolved questions, we made four major discoveries: (i) rapid translocation of plant cell cytoplasm and nucleus to the fungal penetration site was associated with local depolymerization of the microtubular network; (ii) the directed translocation was dependent on intact actin filaments; (iii) a typical plant defence-related gene was activated in the fungus-invaded cell; and (iv) simultaneous activation of this gene in adjacent, non-invaded cells did not require hypersensitive death of the directly affected cell.
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Affiliation(s)
- P Gross
- Max-Planck-Institut für Züchtungsforschung, Abteilung Biochemie, Köln, Germany
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14
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Julius C, Westphal RG. The safety of blood components and derivatives. Hematol Oncol Clin North Am 1992; 6:1057-77. [PMID: 1400072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
An overview of the steps taken to ensure the safety of blood components and derivatives is provided. A brief discussion of hereditary bleeding disorders (hemophilia A, B, and von Willebrand's disease) is included, and the safety of derivatives available for their treatment is discussed, as well as the method of production and the level of safety of derivatives such as factor VIII and factor IX concentrates.
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Affiliation(s)
- C Julius
- Department of Pathology, University of Vermont College of Medicine, Burlington
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Thorneley RN, Ashby GA, Julius C, Hunter JL, Webb MR. Nitrogenase of Klebsiella pneumoniae. Reversibility of the reductant-independent MgATP-cleavage reaction is shown by MgADP-catalysed phosphate/water oxygen exchange. Biochem J 1991; 277 ( Pt 3):735-41. [PMID: 1872810 PMCID: PMC1151306 DOI: 10.1042/bj2770735] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [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: 12/29/2022]
Abstract
The steady-state kinetics of reductant-independent ATP hydrolysis by Klebsiella pneumoniae nitrogenase at 23 degrees C at pH 7.4 were determined as a function of component protein ratio (optimal at an oxidized Fe protein/MoFe protein ratio of 3:1) and MgATP concentration (Km 400 microM). Competitive inhibition was observed for MgADP (Ki 145 microM), [beta gamma-methylene]ATP (Mgp[CH2]ppA) (Ki 115 microM), [beta gamma-monofluoromethylene]ATP (Mgp[CHF]ppA) (Ki 53 microM) and [beta gamma-difluoromethylene]ATP (Mgp[CF2]ppA) (Ki 160 microM). The tighter binding of MgADP to free oxidized Fe protein (KD less than 10 microM) than to the oxidized Fe protein-MoFe protein complex (Ki 145 microM) is proposed as the driving force that induces rate-limiting protein dissociation in the catalytic cycle of nitrogenase. The reversible nature of the reductant-independent MgATP-cleavage reaction was demonstrated by an MgADP-induced enhancement of the rate of the phosphate/water oxygen exchange reaction with 18O-labelled phosphate ion. This enhancement, like the reductant-independent ATPase reaction, only occurred with the complex formed by oxidized Fe protein and MoFe protein and not with the individual proteins. The results are discussed in terms of the mechanism of ATP hydrolysis by nitrogenase and other systems involving protein-protein interactions.
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Affiliation(s)
- R N Thorneley
- A.F.R.C. Institute of Plant Science Research, University of Sussex, Brighton, U.K
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