1
|
Knoops A, Ledesma-García L, Waegemans A, Lamontagne M, Decat B, Degand H, Morsomme P, Soumillion P, Delvigne F, Hols P. Competence shut-off by intracellular pheromone degradation in salivarius streptococci. PLoS Genet 2022; 18:e1010198. [PMID: 35613247 PMCID: PMC9173638 DOI: 10.1371/journal.pgen.1010198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 06/07/2022] [Accepted: 04/12/2022] [Indexed: 11/18/2022] Open
Abstract
Competence for DNA transformation is a major strategy for bacterial adaptation and survival. Yet, this successful tactic is energy-consuming, shifts dramatically the metabolism, and transitory impairs the regular cell-cycle. In streptococci, complex regulatory pathways control competence deactivation to narrow its development to a sharp window of time, a process known as competence shut-off. Although characterized in streptococci whose competence is activated by the ComCDE signaling pathway, it remains unclear for those controlled by the ComRS system. In this work, we investigate competence shut-off in the major human gut commensal Streptococcus salivarius. Using a deterministic mathematical model of the ComRS system, we predicted a negative player under the control of the central regulator ComX as involved in ComS/XIP pheromone degradation through a negative feedback loop. The individual inactivation of peptidase genes belonging to the ComX regulon allowed the identification of PepF as an essential oligoendopeptidase in S. salivarius. By combining conditional mutants, transcriptional analyses, and biochemical characterization of pheromone degradation, we validated the reciprocal role of PepF and XIP in ComRS shut-off. Notably, engineering cleavage site residues generated ultra-resistant peptides producing high and long-lasting competence activation. Altogether, this study reveals a proteolytic shut-off mechanism of competence in the salivarius group and suggests that this mechanism could be shared by other ComRS-containing streptococci. The human oral cavity is one of the most challenging ecological niches for bacteria. In this ecosystem, hundreds of species compete for food and survival in a physicochemical fluctuating environment. To outcompete, Streptococcus salivarius has developed a particular physiological state called competence during which antibacterial compounds are produced together with the uptake of external DNA that can be integrated in its own genome. Although this strategy is of main importance for evolution and adaptation, its short-term cost in terms of energy and metabolism reprogramming are important. To restrain competence activation to a sharp window of time, bacteria use a process known as shut-off. Although described in some species, this process is still mostly unknown in streptococci. In this work, we used predictive mathematical simulations to infer the role of a pheromone-degradation machinery involved in the exit from competence. We confirmed experimentally this mechanism by identifying PepF as a competence-induced oligoendopeptidase with a specific activity towards the XIP pheromone. Importantly, we show that this peptidase is not only shutting down competence but also preventing its development under inappropriate conditions.
Collapse
Affiliation(s)
- Adrien Knoops
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-La-Neuve, Belgium
| | - Laura Ledesma-García
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-La-Neuve, Belgium
| | - Alexandra Waegemans
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-La-Neuve, Belgium
| | - Morgane Lamontagne
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-La-Neuve, Belgium
| | - Baptiste Decat
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-La-Neuve, Belgium
| | - Hervé Degand
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-La-Neuve, Belgium
| | - Pierre Morsomme
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-La-Neuve, Belgium
| | - Patrice Soumillion
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-La-Neuve, Belgium
| | - Frank Delvigne
- Microbial Processes and Interactions, TERRA Research and Teaching Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Pascal Hols
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-La-Neuve, Belgium
- * E-mail:
| |
Collapse
|
2
|
Gain G, Vega de Luna F, Cordoba J, Perez E, Degand H, Morsomme P, Thiry M, Baurain D, Pierangelini M, Cardol P. Trophic state alters the mechanism whereby energetic coupling between photosynthesis and respiration occurs in Euglena gracilis. New Phytol 2021; 232:1603-1617. [PMID: 34392544 PMCID: PMC9292222 DOI: 10.1111/nph.17677] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 08/06/2021] [Indexed: 06/13/2023]
Abstract
The coupling between mitochondrial respiration and photosynthesis plays an important role in the energetic physiology of green plants and some secondary-red photosynthetic eukaryotes (diatoms), allowing an efficient CO2 assimilation and optimal growth. Using the flagellate Euglena gracilis, we first tested if photosynthesis-respiration coupling occurs in this species harbouring secondary green plastids (i.e. originated from an endosymbiosis between a green alga and a phagotrophic euglenozoan). Second, we tested how the trophic state (mixotrophy and photoautotrophy) of the cell alters the mechanisms involved in the photosynthesis-respiration coupling. Energetic coupling between photosynthesis and respiration was determined by testing the effect of respiratory inhibitors on photosynthesis, and measuring the simultaneous variation of photosynthesis and respiration rates as a function of temperature (i.e. thermal response curves). The mechanism involved in the photosynthesis-respiration coupling was assessed by combining proteomics, biophysical and cytological analyses. Our work shows that there is photosynthesis-respiration coupling and membrane contacts between mitochondria and chloroplasts in E. gracilis. However, whereas in mixotrophy adjustment of the chloroplast ATP/NADPH ratio drives the interaction, in photoautotrophy the coupling is conditioned by CO2 limitation and photorespiration. This indicates that maintenance of photosynthesis-respiration coupling, through plastic metabolic responses, is key to E. gracilis functioning under changing environmental conditions.
Collapse
Affiliation(s)
- Gwenaëlle Gain
- InBioS – PhytoSYSTEMSLaboratoire de Génétique et Physiologie des MicroalguesULiègeLiègeB‐4000Belgium
| | - Félix Vega de Luna
- InBioS – PhytoSYSTEMSLaboratoire de Génétique et Physiologie des MicroalguesULiègeLiègeB‐4000Belgium
| | - Javier Cordoba
- InBioS – PhytoSYSTEMSLaboratoire de Génétique et Physiologie des MicroalguesULiègeLiègeB‐4000Belgium
| | - Emilie Perez
- InBioS – PhytoSYSTEMSLaboratoire de Génétique et Physiologie des MicroalguesULiègeLiègeB‐4000Belgium
| | - Hervé Degand
- Louvain Institute of Biomolecular Science and Technology (LIBST)UCLouvainLouvain‐la‐NeuveB‐1348Belgium
| | - Pierre Morsomme
- Louvain Institute of Biomolecular Science and Technology (LIBST)UCLouvainLouvain‐la‐NeuveB‐1348Belgium
| | - Marc Thiry
- Laboratoire de Biologie Cellulaire et TissulaireGiga‐NeurosciencesULiègeLiègeB‐4000Belgium
| | - Denis Baurain
- InBioS – PhytoSYSTEMSEukaryotic PhylogenomicsULiègeLiègeB‐4000Belgium
| | - Mattia Pierangelini
- InBioS – PhytoSYSTEMSLaboratoire de Génétique et Physiologie des MicroalguesULiègeLiègeB‐4000Belgium
| | - Pierre Cardol
- InBioS – PhytoSYSTEMSLaboratoire de Génétique et Physiologie des MicroalguesULiègeLiègeB‐4000Belgium
| |
Collapse
|
3
|
Delmez V, Degand H, Poleunis C, Moshkunov K, Chundak M, Dupont-Gillain C, Delcorte A. Deposition of Intact and Active Proteins In Vacuo Using Large Argon Cluster Ion Beams. J Phys Chem Lett 2021; 12:952-957. [PMID: 33443416 DOI: 10.1021/acs.jpclett.0c02510] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Providing inert materials with a biochemical function, for example using proteins, is a cornerstone technology underlying many applications. However, the controlled construction of protein thin films remains a major challenge. Here, an innovative solvent-free approach for protein deposition is reported, using lysozyme as a model. By diverting a time-of-flight secondary ion mass spectrometer (ToF-SIMS) from its standard analytical function, large argon clusters were used to achieve protein transfer. A target consisting of a pool of proteins was bombarded with 10 keV Ar5000+ ions, and the ejected proteins were collected on a silicon wafer. The ellipsoidal deposition pattern was evidenced by ToF-SIMS analysis, while SDS-PAGE electrophoresis confirmed the presence of intact lysozyme on the collector. Finally, enzymatic activity assays demonstrated the preservation of the three-dimensional structure of the transferred proteins. These results pave the way to well-controlled protein deposition using ion beams and to the investigation of more complex multilayer architectures.
Collapse
Affiliation(s)
- Vincent Delmez
- Institute of Condensed Matter and Nanosciences-Bio & Soft Matter, Université catholique de Louvain, Place Louis Pasteur, 1 bte L4.01.10, B-1348 Louvain-la-Neuve, Belgium
| | - Hervé Degand
- Institute of Biomolecular Science and Technology, Group of Molecular Physiology, Université catholique de Louvain, Croix du Sud 4-5, B-1348 Louvain-la-Neuve, Belgium
| | - Claude Poleunis
- Institute of Condensed Matter and Nanosciences-Bio & Soft Matter, Université catholique de Louvain, Place Louis Pasteur, 1 bte L4.01.10, B-1348 Louvain-la-Neuve, Belgium
| | - Konstantin Moshkunov
- Institute of Condensed Matter and Nanosciences-Bio & Soft Matter, Université catholique de Louvain, Place Louis Pasteur, 1 bte L4.01.10, B-1348 Louvain-la-Neuve, Belgium
| | - Mykhailo Chundak
- Institute of Condensed Matter and Nanosciences-Bio & Soft Matter, Université catholique de Louvain, Place Louis Pasteur, 1 bte L4.01.10, B-1348 Louvain-la-Neuve, Belgium
| | - Christine Dupont-Gillain
- Institute of Condensed Matter and Nanosciences-Bio & Soft Matter, Université catholique de Louvain, Place Louis Pasteur, 1 bte L4.01.10, B-1348 Louvain-la-Neuve, Belgium
| | - Arnaud Delcorte
- Institute of Condensed Matter and Nanosciences-Bio & Soft Matter, Université catholique de Louvain, Place Louis Pasteur, 1 bte L4.01.10, B-1348 Louvain-la-Neuve, Belgium
| |
Collapse
|
4
|
Fox AR, Scochera F, Laloux T, Filik K, Degand H, Morsomme P, Alleva K, Chaumont F. Plasma membrane aquaporins interact with the endoplasmic reticulum resident VAP27 proteins at ER-PM contact sites and endocytic structures. New Phytol 2020; 228:973-988. [PMID: 33410187 PMCID: PMC7586982 DOI: 10.1111/nph.16743] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 06/01/2020] [Indexed: 05/24/2023]
Abstract
Plasma membrane (PM) intrinsic proteins (PIPs) are aquaporins facilitating the diffusion of water and small solutes. The functional importance of the PM organisation of PIPs in the interaction with other cellular structures is not completely understood. We performed a pull-down assay using maize (Zea mays) suspension cells expressing YFP-ZmPIP2;5 and validated the protein interactions by yeast split-ubiquitin and bimolecular fluorescence complementation assays. We expressed interacting proteins tagged with fluorescent proteins in Nicotiana benthamiana leaves and performed water transport assays in oocytes. Finally, a phylogenetic analysis was conducted. The PM-located ZmPIP2;5 physically interacts with the endoplasmic reticulum (ER) resident ZmVAP27-1. This interaction requires the ZmVAP27-1 cytoplasmic major sperm domain. ZmPIP2;5 and ZmVAP27-1 localise in close vicinity in ER-PM contact sites (EPCSs) and endocytic structures upon exposure to salt stress conditions. This interaction enhances PM water permeability in oocytes. Similarly, the Arabidopsis ZmVAP27-1 paralogue, AtVAP27-1, interacts with the AtPIP2;7 aquaporin. Together, these data indicate that the PIP2-VAP27 interaction in EPCSs is evolutionarily conserved, and suggest that VAP27 might stabilise the aquaporins and guide their endocytosis in response to salt stress.
Collapse
Affiliation(s)
- Ana Romina Fox
- Louvain Institute of Biomolecular Science and TechnologyUCLouvainLouvain‐la‐Neuve1348Belgium
- Facultad de Farmacia y BioquímicaInstituto de Química y Fisicoquímica Biológica (IQUIFIB)CONICETUniversidad de Buenos AiresBuenos Aires1113Argentina
| | - Florencia Scochera
- Facultad de Farmacia y BioquímicaInstituto de Química y Fisicoquímica Biológica (IQUIFIB)CONICETUniversidad de Buenos AiresBuenos Aires1113Argentina
- Facultad de Farmacia y BioquímicaDepartamento de FisicomatemáticaUniversidad de Buenos AiresBuenos Aires1113Argentina
| | - Timothée Laloux
- Louvain Institute of Biomolecular Science and TechnologyUCLouvainLouvain‐la‐Neuve1348Belgium
| | - Karolina Filik
- Louvain Institute of Biomolecular Science and TechnologyUCLouvainLouvain‐la‐Neuve1348Belgium
| | - Hervé Degand
- Louvain Institute of Biomolecular Science and TechnologyUCLouvainLouvain‐la‐Neuve1348Belgium
| | - Pierre Morsomme
- Louvain Institute of Biomolecular Science and TechnologyUCLouvainLouvain‐la‐Neuve1348Belgium
| | - Karina Alleva
- Facultad de Farmacia y BioquímicaInstituto de Química y Fisicoquímica Biológica (IQUIFIB)CONICETUniversidad de Buenos AiresBuenos Aires1113Argentina
- Facultad de Farmacia y BioquímicaDepartamento de FisicomatemáticaUniversidad de Buenos AiresBuenos Aires1113Argentina
| | - François Chaumont
- Louvain Institute of Biomolecular Science and TechnologyUCLouvainLouvain‐la‐Neuve1348Belgium
| |
Collapse
|
5
|
Miranda-Astudillo HV, Yadav KNS, Colina-Tenorio L, Bouillenne F, Degand H, Morsomme P, Boekema EJ, Cardol P. The atypical subunit composition of respiratory complexes I and IV is associated with original extra structural domains in Euglena gracilis. Sci Rep 2018; 8:9698. [PMID: 29946152 PMCID: PMC6018760 DOI: 10.1038/s41598-018-28039-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 06/14/2018] [Indexed: 11/10/2022] Open
Abstract
In mitochondrial oxidative phosphorylation, electron transfer from NADH or succinate to oxygen by a series of large protein complexes in the inner mitochondrial membrane (complexes I-IV) is coupled to the generation of an electrochemical proton gradient, the energy of which is utilized by complex V to generate ATP. In Euglena gracilis, a non-parasitic secondary green alga related to trypanosomes, these respiratory complexes totalize more than 40 Euglenozoa-specific subunits along with about 50 classical subunits described in other eukaryotes. In the present study the Euglena proton-pumping complexes I, III, and IV were purified from isolated mitochondria by a two-steps liquid chromatography approach. Their atypical subunit composition was further resolved and confirmed using a three-steps PAGE analysis coupled to mass spectrometry identification of peptides. The purified complexes were also observed by electron microscopy followed by single-particle analysis. Even if the overall structures of the three oxidases are similar to the structure of canonical enzymes (e.g. from mammals), additional atypical domains were observed in complexes I and IV: an extra domain located at the tip of the peripheral arm of complex I and a "helmet-like" domain on the top of the cytochrome c binding region in complex IV.
Collapse
Affiliation(s)
- H V Miranda-Astudillo
- Laboratoire de Génétique et Physiologie des microalgues, InBioS/Phytosystems, Institut de Botanique, Université de Liège, Liege, Belgium
| | - K N S Yadav
- Department of Electron Microscopy, Groningen Biological Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - L Colina-Tenorio
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico, Mexico
| | - F Bouillenne
- InBioS/Center for Protein Engineering, Université de Liège, Liege, Belgium
| | - H Degand
- Institut des Sciences de la Vie, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - P Morsomme
- Institut des Sciences de la Vie, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - E J Boekema
- Department of Electron Microscopy, Groningen Biological Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - P Cardol
- Laboratoire de Génétique et Physiologie des microalgues, InBioS/Phytosystems, Institut de Botanique, Université de Liège, Liege, Belgium.
| |
Collapse
|
6
|
Draime A, Bridoux L, Belpaire M, Pringels T, Degand H, Morsomme P, Rezsohazy R. The O-GlcNAc transferase OGT interacts with and post-translationally modifies the transcription factor HOXA1. FEBS Lett 2018; 592:1185-1201. [PMID: 29465778 DOI: 10.1002/1873-3468.13015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 01/26/2018] [Accepted: 02/13/2018] [Indexed: 11/06/2022]
Abstract
HOXA1 belongs to the HOX family of transcription factors which are key regulators of animal development. Little is known about the molecular pathways controlling HOXA1. Recent data from our group revealed distinct partner proteins interacting with HOXA1. Among them, OGT is an O-linked N-acetylglucosamine (O-GlcNAc) transferase modifying a variety of proteins involved in different cellular processes including transcription. Here, we confirm OGT as a HOXA1 interactor, we characterise which domains of HOXA1 and OGT are required for the interaction, and we provide evidence that OGT post-translationally modifies HOXA1. Mass spectrometry experiments indeed reveal that HOXA1 can be phosphorylated on the AGGTVGSPQYIHHSY peptide and that upon OGT expression, the phosphate adduct is replaced by an O-GlcNAc group.
Collapse
Affiliation(s)
- Amandine Draime
- Animal Molecular and Cellular Biology, Institut des Sciences de la Vie (ISV), Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Laure Bridoux
- Animal Molecular and Cellular Biology, Institut des Sciences de la Vie (ISV), Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Magali Belpaire
- Animal Molecular and Cellular Biology, Institut des Sciences de la Vie (ISV), Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Tamara Pringels
- Animal Molecular and Cellular Biology, Institut des Sciences de la Vie (ISV), Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Hervé Degand
- Molecular Physiology, Institut des Sciences de la Vie (ISV), Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Pierre Morsomme
- Molecular Physiology, Institut des Sciences de la Vie (ISV), Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - René Rezsohazy
- Animal Molecular and Cellular Biology, Institut des Sciences de la Vie (ISV), Université catholique de Louvain, Louvain-la-Neuve, Belgium
| |
Collapse
|
7
|
Villers J, Savocco J, Szopinska A, Degand H, Nootens S, Morsomme P. Study of the Plasma Membrane Proteome Dynamics Reveals Novel Targets of the Nitrogen Regulation in Yeast. Mol Cell Proteomics 2017; 16:1652-1668. [PMID: 28679684 PMCID: PMC5587864 DOI: 10.1074/mcp.m116.064923] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [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: 11/07/2016] [Revised: 06/26/2017] [Indexed: 12/19/2022] Open
Abstract
Yeast cells, to be able to grow on a wide variety of nitrogen sources, regulate the set of nitrogen transporters present at their plasma membrane. Such regulation relies on both transcriptional and post-translational events. Although microarray studies have identified most nitrogen-sensitive genes, nitrogen-induced post-translational regulation has only been studied for very few proteins among which the general amino acid permease Gap1. Adding a preferred nitrogen source to proline-grown cells triggers Gap1 endocytosis and vacuolar degradation in an Rsp5-Bul1/2-dependent manner. Here, we used a proteomic approach to follow the dynamics of the plasma membrane proteome after addition of a preferred nitrogen source. We identified new targets of the nitrogen regulation and four transporters of poor nitrogen sources-Put4, Opt2, Dal5, and Ptr2-that rapidly decrease in abundance. Although the kinetics is different for each transporter, we found that three of them-Put4, Dal5, and Ptr2-are endocytosed, like Gap1, in an Rsp5-dependent manner and degraded in the vacuole. Finally, we showed that Gap1 stabilization at the plasma membrane, through deletion of Bul proteins, regulates the abundance of Put4, Dal5 and Ptr2.
Collapse
Affiliation(s)
- Jennifer Villers
- From the ‡Université catholique de Louvain, Institut des Sciences de la Vie, Croix du Sud 4-5, B-1348 Louvain-la-Neuve
| | - Jérôme Savocco
- From the ‡Université catholique de Louvain, Institut des Sciences de la Vie, Croix du Sud 4-5, B-1348 Louvain-la-Neuve
| | - Aleksandra Szopinska
- From the ‡Université catholique de Louvain, Institut des Sciences de la Vie, Croix du Sud 4-5, B-1348 Louvain-la-Neuve
| | - Hervé Degand
- From the ‡Université catholique de Louvain, Institut des Sciences de la Vie, Croix du Sud 4-5, B-1348 Louvain-la-Neuve
| | - Sylvain Nootens
- From the ‡Université catholique de Louvain, Institut des Sciences de la Vie, Croix du Sud 4-5, B-1348 Louvain-la-Neuve
| | - Pierre Morsomme
- From the ‡Université catholique de Louvain, Institut des Sciences de la Vie, Croix du Sud 4-5, B-1348 Louvain-la-Neuve
| |
Collapse
|
8
|
Renoz F, Champagne A, Degand H, Faber AM, Morsomme P, Foray V, Hance T. Toward a better understanding of the mechanisms of symbiosis: a comprehensive proteome map of a nascent insect symbiont. PeerJ 2017; 5:e3291. [PMID: 28503376 PMCID: PMC5426354 DOI: 10.7717/peerj.3291] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 04/10/2017] [Indexed: 12/18/2022] Open
Abstract
Symbiotic bacteria are common in insects and can affect various aspects of their hosts’ biology. Although the effects of insect symbionts have been clarified for various insect symbiosis models, due to the difficulty of cultivating them in vitro, there is still limited knowledge available on the molecular features that drive symbiosis. Serratia symbiotica is one of the most common symbionts found in aphids. The recent findings of free-living strains that are considered as nascent partners of aphids provide the opportunity to examine the molecular mechanisms that a symbiont can deploy at the early stages of the symbiosis (i.e., symbiotic factors). In this work, a proteomic approach was used to establish a comprehensive proteome map of the free-living S. symbiotica strain CWBI-2.3T. Most of the 720 proteins identified are related to housekeeping or primary metabolism. Of these, 76 were identified as candidate proteins possibly promoting host colonization. Our results provide strong evidence that S. symbiotica CWBI-2.3T is well-armed for invading insect host tissues, and suggest that certain molecular features usually harbored by pathogenic bacteria are no longer present. This comprehensive proteome map provides a series of candidate genes for further studies to understand the molecular cross-talk between insects and symbiotic bacteria.
Collapse
Affiliation(s)
- François Renoz
- Biodiversity Reasearch Center, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Antoine Champagne
- Institute of Life Sciences, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Hervé Degand
- Institute of Life Sciences, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Anne-Marie Faber
- Institute of Life Sciences, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Pierre Morsomme
- Institute of Life Sciences, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Vincent Foray
- Centre de Recherche de Biochimie Macromoléculaire, Centre National de la Recherche Scientifique, Montpellier, France
| | - Thierry Hance
- Biodiversity Reasearch Center, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| |
Collapse
|
9
|
Yadav KS, Miranda-Astudillo HV, Colina-Tenorio L, Bouillenne F, Degand H, Morsomme P, González-Halphen D, Boekema EJ, Cardol P. Atypical composition and structure of the mitochondrial dimeric ATP synthase from Euglena gracilis. Biochimica et Biophysica Acta (BBA) - Bioenergetics 2017; 1858:267-275. [DOI: 10.1016/j.bbabio.2017.01.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 12/22/2016] [Accepted: 01/10/2017] [Indexed: 11/26/2022]
|
10
|
Hachez C, Laloux T, Reinhardt H, Cavez D, Degand H, Grefen C, De Rycke R, Inzé D, Blatt MR, Russinova E, Chaumont F. Arabidopsis SNAREs SYP61 and SYP121 coordinate the trafficking of plasma membrane aquaporin PIP2;7 to modulate the cell membrane water permeability. Plant Cell 2014; 26:3132-47. [PMID: 25082856 PMCID: PMC4145137 DOI: 10.1105/tpc.114.127159] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 06/24/2014] [Accepted: 07/08/2014] [Indexed: 05/19/2023]
Abstract
Plant plasma membrane intrinsic proteins (PIPs) are aquaporins that facilitate the passive movement of water and small neutral solutes through biological membranes. Here, we report that post-Golgi trafficking of PIP2;7 in Arabidopsis thaliana involves specific interactions with two syntaxin proteins, namely, the Qc-SNARE SYP61 and the Qa-SNARE SYP121, that the proper delivery of PIP2;7 to the plasma membrane depends on the activity of the two SNAREs, and that the SNAREs colocalize and physically interact. These findings are indicative of an important role for SYP61 and SYP121, possibly forming a SNARE complex. Our data support a model in which direct interactions between specific SNARE proteins and PIP aquaporins modulate their post-Golgi trafficking and thus contribute to the fine-tuning of the water permeability of the plasma membrane.
Collapse
Affiliation(s)
- Charles Hachez
- Institut des Sciences de la Vie, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Timothée Laloux
- Institut des Sciences de la Vie, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Hagen Reinhardt
- Institut des Sciences de la Vie, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Damien Cavez
- Institut des Sciences de la Vie, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Hervé Degand
- Institut des Sciences de la Vie, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Christopher Grefen
- Zentrum für Molekularbiologie der Pflanzen, Developmental Genetics, University of Tuebingen, D-72076 Tuebingen, Germany
| | - Riet De Rycke
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Dirk Inzé
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Michael R Blatt
- Laboratory of Plant Physiology and Biophysics, Institute of Molecular, Cell, and Systems Biology, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Eugenia Russinova
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - François Chaumont
- Institut des Sciences de la Vie, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| |
Collapse
|
11
|
Rolain T, Bernard E, Beaussart A, Degand H, Courtin P, Egge-Jacobsen W, Bron PA, Morsomme P, Kleerebezem M, Chapot-Chartier MP, Dufrêne YF, Hols P. O-glycosylation as a novel control mechanism of peptidoglycan hydrolase activity. J Biol Chem 2013; 288:22233-47. [PMID: 23760506 DOI: 10.1074/jbc.m113.470716] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Acm2, the major autolysin of Lactobacillus plantarum, is a tripartite protein. Its catalytic domain is surrounded by an O-glycosylated N-terminal region rich in Ala, Ser, and Thr (AST domain), which is of low complexity and unknown function, and a C-terminal region composed of five SH3b peptidoglycan (PG) binding domains. Here, we investigate the contribution of these two accessory domains and of O-glycosylation to Acm2 functionality. We demonstrate that Acm2 is an N-acetylglucosaminidase and identify the pattern of O-glycosylation (21 mono-N-acetylglucosamines) of its AST domain. The O-glycosylation process is species-specific as Acm2 purified from Lactococcus lactis is not glycosylated. We therefore explored the functional role of O-glycosylation by purifying different truncated versions of Acm2 that were either glycosylated or non-glycosylated. We show that SH3b domains are able to bind PG and are responsible for Acm2 targeting to the septum of dividing cells, whereas the AST domain and its O-glycosylation are not involved in this process. Notably, our data reveal that the lack of O-glycosylation of the AST domain significantly increases Acm2 enzymatic activity, whereas removal of SH3b PG binding domains dramatically reduces this activity. Based on this antagonistic role, we propose a model in which access of the Acm2 catalytic domain to its substrate may be hindered by the AST domain where O-glycosylation changes its conformation and/or mediates interdomain interactions. To the best of our knowledge, this is the first time that O-glycosylation is shown to control the activity of a bacterial enzyme.
Collapse
Affiliation(s)
- Thomas Rolain
- Institut des Sciences de la Vie, Université catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
12
|
Galka P, Santabarbara S, Khuong TTH, Degand H, Morsomme P, Jennings RC, Boekema EJ, Caffarri S. Functional analyses of the plant photosystem I-light-harvesting complex II supercomplex reveal that light-harvesting complex II loosely bound to photosystem II is a very efficient antenna for photosystem I in state II. Plant Cell 2012; 24:2963-78. [PMID: 22822202 PMCID: PMC3426126 DOI: 10.1105/tpc.112.100339] [Citation(s) in RCA: 165] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 06/20/2012] [Accepted: 07/02/2012] [Indexed: 05/19/2023]
Abstract
State transitions are an important photosynthetic short-term response that allows energy distribution balancing between photosystems I (PSI) and II (PSII). In plants when PSII is preferentially excited compared with PSI (State II), part of the major light-harvesting complex LHCII migrates to PSI to form a PSI-LHCII supercomplex. So far, little is known about this complex, mainly due to purification problems. Here, a stable PSI-LHCII supercomplex is purified from Arabidopsis thaliana and maize (Zea mays) plants. It is demonstrated that LHCIIs loosely bound to PSII in State I are the trimers mainly involved in state transitions and become strongly bound to PSI in State II. Specific Lhcb1-3 isoforms are differently represented in the mobile LHCII compared with S and M trimers. Fluorescence analyses indicate that excitation energy migration from mobile LHCII to PSI is rapid and efficient, and the quantum yield of photochemical conversion of PSI-LHCII is substantially unaffected with respect to PSI, despite a sizable increase of the antenna size. An updated PSI-LHCII structural model suggests that the low-energy chlorophylls 611 and 612 in LHCII interact with the chlorophyll 11145 at the interface of PSI. In contrast with the common opinion, we suggest that the mobile pool of LHCII may be considered an intimate part of the PSI antenna system that is displaced to PSII in State I.
Collapse
Affiliation(s)
- Pierre Galka
- Aix Marseille Université, Biologie Végétale et Microbiologie Environnementales, Laboratoire de Génétique et Biophysique des Plantes, 13288 Marseille, France
- Commissariat à l’Energie Atomique, Direction des Sciences du Vivant, Institut de Biologie Environnementale et Biotechnologie, 13288 Marseille, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7265 Biologie Végétale et Microbiologie Environnementales, 13288 Marseille, France
- Institut des Sciences de la Vie, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Stefano Santabarbara
- Consiglio Nazionale delle Ricerche, Istituto di Biofisica, 20133 Milan, Italy
- Dipartimento di Biologia, Università degli Studi di Milano, 20133 Milan, Italy
| | - Thi Thu Huong Khuong
- Aix Marseille Université, Biologie Végétale et Microbiologie Environnementales, Laboratoire de Génétique et Biophysique des Plantes, 13288 Marseille, France
- Commissariat à l’Energie Atomique, Direction des Sciences du Vivant, Institut de Biologie Environnementale et Biotechnologie, 13288 Marseille, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7265 Biologie Végétale et Microbiologie Environnementales, 13288 Marseille, France
| | - Hervé Degand
- Institut des Sciences de la Vie, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Pierre Morsomme
- Institut des Sciences de la Vie, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Robert C. Jennings
- Consiglio Nazionale delle Ricerche, Istituto di Biofisica, 20133 Milan, Italy
- Dipartimento di Biologia, Università degli Studi di Milano, 20133 Milan, Italy
| | - Egbert J. Boekema
- Groningen University, Department of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute, 9747 AG Groningen, The Netherlands
| | - Stefano Caffarri
- Aix Marseille Université, Biologie Végétale et Microbiologie Environnementales, Laboratoire de Génétique et Biophysique des Plantes, 13288 Marseille, France
- Commissariat à l’Energie Atomique, Direction des Sciences du Vivant, Institut de Biologie Environnementale et Biotechnologie, 13288 Marseille, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7265 Biologie Végétale et Microbiologie Environnementales, 13288 Marseille, France
| |
Collapse
|
13
|
Szopinska A, Degand H, Hochstenbach JF, Nader J, Morsomme P. Rapid response of the yeast plasma membrane proteome to salt stress. Mol Cell Proteomics 2011; 10:M111.009589. [PMID: 21825281 DOI: 10.1074/mcp.m111.009589] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The plasma membrane separates the cell from the external environment and plays an important role in the stress response of the cell. In this study, we compared plasma membrane proteome modifications of yeast cells exposed to mild (0.4 m NaCl) or high (1 m NaCl) salt stress for 10, 30, or 90 min. Plasma membrane-enriched fractions were isolated, purified, and subjected to iTRAQ labeling for quantitative analysis. In total, 88-109 plasma membrane proteins were identified and quantified. The quantitative analysis revealed significant changes in the abundance of several plasma membrane proteins. Mild salt stress caused an increase in abundance of 12 plasma membrane proteins, including known salt-responsive proteins, as well as new targets. Interestingly, 20 plasma membrane proteins, including the P-type H(+)-ATPase Pma1, ABC transporters, glucose and amino acid transporters, t-SNAREs, and proteins involved in cell wall biogenesis showed a significant and rapid decrease in abundance in response to both 0.4 m and 1 m NaCl. We propose that rapid protein internalization occurs as a response to hyper-osmotic and/or ionic shock, which might affect plasma membrane morphology and ionic homeostasis. This rapid response might help the cell to survive until the transcriptional response takes place.
Collapse
Affiliation(s)
- Aleksandra Szopinska
- Université Catholique de Louvain, Institut des Sciences de la Vie, Croix du Sud 5/15, B-1348 Louvain-la-Neuve, Belgium
| | | | | | | | | |
Collapse
|
14
|
Van Cutsem E, Simonart G, Degand H, Faber AM, Morsomme P, Boutry M. Gel-based and gel-free proteomic analysis of Nicotiana tabacum trichomes identifies proteins involved in secondary metabolism and in the (a)biotic stress response. Proteomics 2011; 11:440-54. [PMID: 21268273 DOI: 10.1002/pmic.201000356] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2010] [Revised: 11/09/2010] [Accepted: 11/17/2010] [Indexed: 12/22/2022]
Abstract
Nicotiana tabacum leaves are covered by trichomes involved in the secretion of large amounts of secondary metabolites, some of which play a major role in plant defense. However, little is known about the metabolic pathways that operate in these structures. We undertook a proteomic analysis of N. tabacum trichomes in order to identify their protein complement. Efficient trichome isolation was obtained by abrading frozen leaves. After homogenization, soluble proteins and a microsomal fraction were prepared by centrifugation. Gel-based and gel-free proteomic analyses were then performed. 2-DE analysis of soluble proteins led to the identification of 1373 protein spots, which were digested and analyzed by MS/MS, leading to 680 unique identifications. Both soluble proteins and microsomal fraction were analyzed by LC MALDI-MS/MS after trypsin digestion, leading to 858 identifications, many of which had not been identified after 2-DE, indicating that the two methods complement each other. Many enzymes putatively involved in secondary metabolism were identified, including enzymes involved in the synthesis of terpenoid precursors and in acyl sugar production. Several transporters were also identified, some of which might be involved in secondary metabolite transport. Various (a)biotic stress response proteins were also detected, supporting the role of trichomes in plant defense.
Collapse
Affiliation(s)
- Emmanuel Van Cutsem
- Institut des Sciences de la Vie, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | | | | | | | | | | |
Collapse
|
15
|
Vanhee C, Guillon S, Masquelier D, Degand H, Deleu M, Morsomme P, Batoko H. A TSPO-related protein localizes to the early secretory pathway in Arabidopsis, but is targeted to mitochondria when expressed in yeast. J Exp Bot 2011; 62:497-508. [PMID: 20847098 PMCID: PMC3003801 DOI: 10.1093/jxb/erq283] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2010] [Revised: 08/16/2010] [Accepted: 08/19/2010] [Indexed: 05/29/2023]
Abstract
AtTSPO is a TspO/MBR domain-protein potentially involved in multiple stress regulation in Arabidopsis. As in most angiosperms, AtTSPO is encoded by a single, intronless gene. Expression of AtTSPO is tightly regulated both at the transcriptional and post-translational levels. It has been shown previously that overexpression of AtTSPO in plant cell can be detrimental, and the protein was detected in the endoplasmic reticulum (ER) and Golgi stacks, contrasting with previous findings and suggesting a mitochondrial subcellular localization for this protein. To ascertain these findings, immunocytochemistry and ABA induction were used to demonstrate that, in plant cells, physiological levels of AtTSPO colocalized with AtArf1, a mainly Golgi-localized protein in plant cells. In addition, fluorescent protein-tagged AtTSPO was targeted to the secretory pathway and did not colocalize with MitoTracker-labelled mitochondria. These results suggest that the polytopic membrane protein AtTSPO is cotranslationally targeted to the ER in plant cells and accumulates in the Trans-Golgi Network. Heterologous expression of AtTSPO in Saccharomyces cerevisiae, yeast devoid of TSPO-related protein, resulted in growth defects. However, subcellular fractionation and immunoprecipitation experiments showed that AtTSPO was targeted to mitochondria where it colocalized and interacted with the outer mitochondrial membrane porin VDAC1p, reminiscent of the subcellular localization and activity of mammalian translocator protein 18 kDa TSPO. The evolutionarily divergent AtTSPO appears therefore to be switching its sorting mode in a species-dependent manner, an uncommon peculiarity for a polytopic membrane protein in eukaryotic cells. These results are discussed in relation to the recognition and organelle targeting mechanisms of polytopic membrane proteins in eukaryotic cells.
Collapse
Affiliation(s)
- Celine Vanhee
- Institut des Sciences de la Vie (ISV), Molecular Physiology Group (FYMO), Université catholique de Louvain, Croix du Sud 4-15, 1348 Louvain-la-Neuve, Belgium
| | - Stéphanie Guillon
- Institut des Sciences de la Vie (ISV), Molecular Physiology Group (FYMO), Université catholique de Louvain, Croix du Sud 4-15, 1348 Louvain-la-Neuve, Belgium
| | - Danièle Masquelier
- Institut des Sciences de la Vie (ISV), Molecular Physiology Group (FYMO), Université catholique de Louvain, Croix du Sud 4-15, 1348 Louvain-la-Neuve, Belgium
| | - Hervé Degand
- Institut des Sciences de la Vie (ISV), Molecular Physiology Group (FYMO), Université catholique de Louvain, Croix du Sud 4-15, 1348 Louvain-la-Neuve, Belgium
| | - Magali Deleu
- Unité de Chimie Biologique Industrielle, Université de Liège, Gembloux Agro-BioTech (GxABT), Passage des Déportés 2, 5030 Gembloux, Belgium
| | - Pierre Morsomme
- Institut des Sciences de la Vie (ISV), Molecular Physiology Group (FYMO), Université catholique de Louvain, Croix du Sud 4-15, 1348 Louvain-la-Neuve, Belgium
| | - Henri Batoko
- Institut des Sciences de la Vie (ISV), Molecular Physiology Group (FYMO), Université catholique de Louvain, Croix du Sud 4-15, 1348 Louvain-la-Neuve, Belgium
| |
Collapse
|
16
|
Deschuyteneer G, Garcia S, Michiels B, Baudoux B, Degand H, Morsomme P, Soumillion P. Intein-mediated cyclization of randomized peptides in the periplasm of Escherichia coli and their extracellular secretion. ACS Chem Biol 2010; 5:691-700. [PMID: 20527881 DOI: 10.1021/cb100072u] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Split-inteins can be used to generate backbone cyclized peptide as a source of new bioactive molecules. In this work we show that cysteine-mediated splicing can be performed in the oxidative environment of the periplasm of Escherichia coli. Cyclization of the TEM-1 beta-lactamase and of small randomized peptides was demonstrated using an artificially permuted version of the DnaB mini-intein from Synechocystis sp. PCC6803 strain fused to a signal sequence. For small peptides, a signal sequence that promotes cotranslational translocation had to be used. Efficient backbone cyclization was observed for more than 50% of combinatorial peptides featuring a fully randomized sequence inserted between a serine and glycine that are necessary for fast splicing. Furthermore, by coexpressing a mutant of the pIV outer membrane pore protein of fd bacteriophage, we showed that peptides can diffuse in the extracellular medium. These results open new routes for searching compounds acting on new targets such as exported and membrane proteins or pathogen microorganisms.
Collapse
Affiliation(s)
| | | | | | | | - Hervé Degand
- Physiologie Moléculaire, Institut des Sciences de la Vie, Université catholique de Louvain, Place Croix du Sud 4-5, B-1348 Louvain-la-Neuve, Belgium
| | - Pierre Morsomme
- Physiologie Moléculaire, Institut des Sciences de la Vie, Université catholique de Louvain, Place Croix du Sud 4-5, B-1348 Louvain-la-Neuve, Belgium
| | | |
Collapse
|
17
|
Duby G, Degand H, Faber AM, Boutry M. The proteome complement of Nicotiana tabacum Bright-Yellow-2 culture cells. Proteomics 2010; 10:2545-50. [PMID: 20405476 DOI: 10.1002/pmic.200900527] [Citation(s) in RCA: 8] [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] [Received: 07/21/2009] [Accepted: 04/08/2010] [Indexed: 12/16/2023]
Abstract
The Nicotiana tabacum Bright-Yellow-2 (BY2) cell line is one of most commonly used plant suspension cell lines and offers interesting properties, such as fast growth, amenability to genetic transformation, and synchronization of cell division. To build a proteome reference map of BY2 cell proteins, we isolated the soluble proteins from N. tabacum BY2 cells at the end of the exponential growth phase and analyzed them by 2-DE and MALDI TOF-TOF. Of the 1422 spots isolated, 795 were identified with a significant score, corresponding to 532 distinct proteins.
Collapse
Affiliation(s)
- Geoffrey Duby
- Institut des Sciences de la Vie, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | | | | | | |
Collapse
|
18
|
Lapaille M, Escobar-Ramírez A, Degand H, Baurain D, Rodríguez-Salinas E, Coosemans N, Boutry M, Gonzalez-Halphen D, Remacle C, Cardol P. Atypical subunit composition of the chlorophycean mitochondrial F1FO-ATP synthase and role of Asa7 protein in stability and oligomycin resistance of the enzyme. Mol Biol Evol 2010; 27:1630-44. [PMID: 20156838 DOI: 10.1093/molbev/msq049] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In yeast, mammals, and land plants, mitochondrial F(1)F(O)-ATP synthase (complex V) is a remarkable enzymatic machinery that comprises about 15 conserved subunits. Peculiar among eukaryotes, complex V from Chlamydomonadales algae (order of chlorophycean class) has an atypical subunit composition of its peripheral stator and dimerization module, with nine subunits of unknown evolutionary origin (Asa subunits). In vitro, this enzyme exhibits an increased stability of its dimeric form, and in vivo, Chlamydomonas reinhardtii cells are insensitive to oligomycins, which are potent inhibitors of proton translocation through the F(O) moiety. In this work, we showed that the atypical features of the Chlamydomonadales complex V enzyme are shared by the other chlorophycean orders. By biochemical and in silico analyses, we detected several atypical Asa subunits in Scenedesmus obliquus (Sphaeropleales) and Chlorococcum ellipsoideum (Chlorococcales). In contrast, complex V has a canonical subunit composition in other classes of Chlorophytes (Trebouxiophyceae, Prasinophyceae, and Ulvophyceae) as well as in Streptophytes (land plants), and in Rhodophytes (red algae). Growth, respiration, and ATP levels in Chlorophyceae were also barely affected by oligomycin concentrations that affect representatives of the other classes of Chlorophytes. We finally studied the function of the Asa7 atypical subunit by using RNA interference in C. reinhardtii. Although the loss of Asa7 subunit has no impact on cell bioenergetics or mitochondrial structures, it destabilizes in vitro the enzyme dimeric form and renders growth, respiration, and ATP level sensitive to oligomycins. Altogether, our results suggest that the loss of canonical components of the complex V stator happened at the root of chlorophycean lineage and was accompanied by the recruitment of novel polypeptides. Such a massive modification of complex V stator features might have conferred novel properties, including the stabilization of the enzyme dimeric form and the shielding of the proton channel. In these respects, we discuss an evolutionary scenario for F(1)F(O)-ATP synthase in the whole green lineage (i.e., Chlorophyta and Streptophyta).
Collapse
Affiliation(s)
- Marie Lapaille
- Genetics of Microorganisms, Department of Life Sciences, Université de Liège, Belgium
| | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Linard D, Kandlbinder A, Degand H, Morsomme P, Dietz KJ, Knoops B. Redox characterization of human cyclophilin D: identification of a new mammalian mitochondrial redox sensor? Arch Biochem Biophys 2009; 491:39-45. [PMID: 19735641 DOI: 10.1016/j.abb.2009.09.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [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: 06/16/2009] [Revised: 08/31/2009] [Accepted: 09/01/2009] [Indexed: 12/30/2022]
Abstract
Mitochondria are metabolically highly active cell organelles that are also implicated in reactive oxygen species production and in cell death regulation. Cyclophilin D, the only human mitochondrial isoform of cyclophilins, plays an essential role in the formation of the mitochondrial permeability transition pore leading to cell necrosis. Recently, it has been shown that redox environment modifies structural and functional properties of some plant cyclophilins. Here, it is shown that oxidation of human cyclophilin D influences the conformation of the enzyme but also its activity. Site-directed mutagenized variants of cyclophilin D allowed the identification of cysteine 203 as an important redox-sensitive residue. Moreover, the redox modulation of cyclophilin D was confirmed in human neuroblastoma SH-SY5Y cells exposed to oxidative stress. Altogether, our results suggest that cyclophilin D may play a role as a redox sensor in mitochondria of mammalian cells transmitting information on the redox environment to target proteins.
Collapse
Affiliation(s)
- Dominique Linard
- Laboratory of Cell Biology, Institut des Sciences de la Vie, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | | | | | | | | | | |
Collapse
|
20
|
Degand H, Faber AM, Dauchot N, Mingeot D, Watillon B, Cutsem PV, Morsomme P, Boutry M. Proteomic analysis of chicory root identifies proteins typically involved in cold acclimation. Proteomics 2009; 9:2903-7. [PMID: 19405027 DOI: 10.1002/pmic.200800744] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [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: 09/18/2008] [Accepted: 01/24/2009] [Indexed: 11/09/2022]
Abstract
Chicory (Cichorium intybus) roots contain high amounts of inulin, a fructose polymer used as a storage carbohydrate by the plant and as a human dietary and prebiotic compound. We performed 2-D electrophoretic analysis of proteins from root material before the first freezing period. The proteins were digested with trypsin and the peptides analyzed by MS (MALDI-TOF/TOF). From the 881 protein spots analyzed, 714 proteins corresponded to a database accession, 619 of which were classified into functional categories. Besides expected proteins (e.g. related to metabolism, energy, protein synthesis, or cell structure), other well-represented categories were proteins related to folding and stability (49 spots), proteolysis (49 spots), and the stress response (67 spots). The importance of abiotic stress response was confirmed by the observation that 7 of the 21 most intense protein spots are known to be involved in cold acclimation. These results suggest a major effect of the low temperature period that preceded root harvesting.
Collapse
Affiliation(s)
- Hervé Degand
- Université catholique de Louvain, Institut des Sciences de la Vie, Louvain-la-Neuve, Belgium
| | | | | | | | | | | | | | | |
Collapse
|
21
|
Loumaye E, Andersen AC, Clippe A, Degand H, Dubuisson M, Zal F, Morsomme P, Rees JF, Knoops B. Cloning and characterization of Arenicola marina peroxiredoxin 6, an annelid two-cysteine peroxiredoxin highly homologous to mammalian one-cysteine peroxiredoxins. Free Radic Biol Med 2008; 45:482-93. [PMID: 18503776 DOI: 10.1016/j.freeradbiomed.2008.04.033] [Citation(s) in RCA: 7] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2008] [Revised: 04/14/2008] [Accepted: 04/23/2008] [Indexed: 10/22/2022]
Abstract
Peroxiredoxins (PRDXs) are a superfamily of thiol-dependent peroxidases found in all phyla. PRDXs are mechanistically divided into three subfamilies, namely typical 2-Cys, atypical 2-Cys, and 1-Cys PRDXs. To reduce peroxides, the N-terminal peroxidatic Cys of PRDXs is first oxidized into sulfenic acid. This intermediate is reduced by forming a disulfide bond either with a resolving Cys of another monomeric entity (typical 2-Cys) or of the same molecule (atypical 2-Cys). In 1-Cys PRDXs, the resolving Cys is missing and the sulfenic acid of the peroxidatic Cys is reduced by a heterologous thiol-containing reductant. In search of a homolog of human 1-Cys PRDX6 in Arenicola marina, an annelid worm living in intertidal sediments, we have cloned and characterized a PRDX exhibiting high sequence homology with its mammalian counterpart. However, A. marina PRDX6 possesses five Cys among which two Cys function as peroxidatic and resolving Cys of typical 2-Cys PRDXs. Thus, A. marina PRDX6 belongs to a transient group exhibiting sequence homologies with mammalian 1-Cys PRDX6 but must be mechanistically classified into typical 2-Cys PRDXs. Moreover, PRDX6 is highly expressed in tissues directly exposed to the external environment, suggesting that this PRDX may be of particular importance for protection against exogenous oxidative attacks.
Collapse
Affiliation(s)
- Eléonore Loumaye
- Laboratoire de Biologie Cellulaire, Institut des Sciences de la Vie, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Van Wilder V, Miecielica U, Degand H, Derua R, Waelkens E, Chaumont F. Maize Plasma Membrane Aquaporins Belonging to the PIP1 and PIP2 Subgroups are in vivo Phosphorylated. ACTA ACUST UNITED AC 2008; 49:1364-77. [DOI: 10.1093/pcp/pcn112] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
23
|
Abstract
As a consequence of their poor solubility during isoelectric focusing, integral membrane proteins are generally absent from two-dimensional gel proteome maps. In order to analyze the yeast plasma membrane proteome, a plasma membrane purification protocol was optimized in order to reduce contaminating membranes and cytosolic proteins. Specifically, the new fractionation scheme largely depleted the plasma membrane fraction of cytosolic proteins by deoxycholate stripping and ribosomal proteins by sucrose gradient flotation. The plasma membrane complement was resolved by two-dimensional electrophoresis using the cationic detergent cetyl trimethyl ammonium bromide in the first, and sodium dodecyl sulfate in the second dimension, and fifty spots were identified by matrix-assisted laser desorption/ionization-time of flight mass spectometry. In spite of the presence of still contaminating ribosomal proteins, major proteins corresponded to known plasma membrane residents, the ABC transporters Pdr5p and Snq2p, the P-type H(+)-ATPase Pma1p, the glucose transporter Hxt7p, the seven transmembrane-span Mrh1p, the low affinity Fe(++) transporter Fet4p, the twelve-span Ptr2p, and the plasma membrane anchored casein kinase Yck2p. The four transmembrane-span proteins Sur7p and Nce102p were also present in the isolated plasma membranes, as well as the unknown protein Ygr266wp that probably contains a single transmembrane span. Thus, combining subcellular fractionation with adapted two-dimensional electrophoresis resulted in the identification of intrinsic plasma membrane proteins.
Collapse
Affiliation(s)
- Catherine Navarre
- Unité de Biochimie Physiologique, Institut des Sciences de la Vie, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | | | | | | | | | | |
Collapse
|
24
|
Duby G, Degand H, Boutry M. Structure requirement and identification of a cryptic cleavage site in the mitochondrial processing of a plant F1-ATPase beta-subunit presequence. FEBS Lett 2001; 505:409-13. [PMID: 11576538 DOI: 10.1016/s0014-5793(01)02856-3] [Citation(s) in RCA: 9] [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: 11/25/2022]
Abstract
We sought to determine the structural features involved in the processing of the mitochondrial F1-ATPase beta-subunit (F1beta) presequence (54 residues) from Nicotiana plumbaginifolia. The cleavage efficiency of F1beta presequence mutants linked to the green fluorescent protein (GFP) was evaluated in vivo in tobacco by in situ microscopy and Western blotting. The residue at position -1 (Tyr) was required to be an aromatic residue and the residue at position +2 (Thr) was found to be important for F1beta processing, while, unexpectedly, changing the distal (Arg-15) and proximal (Arg-5) arginine residues did not strongly reduce processing. In addition, results also supported the requirement of a helical structure around the cleavage position. Sequencing of the mature form of a precursor containing the first 30 residues of the F1beta presequence linked to GFP revealed the presence of a cryptic cleavage site between residues 26 and 27, which showed the features of a classical mitochondrial processing site, suggesting dual processing of the F1beta presequence. In vitro processing confirmed these data and showed that processing was sensitive to o-phenanthroline, thus catalyzed by mitochondrial processing peptidase.
Collapse
Affiliation(s)
- G Duby
- Unité de Biochimie Physiologique, Université Catholique de Louvain, Croix du Sud 2-20, B-1348, Louvain-la-Neuve, Belgium
| | | | | |
Collapse
|
25
|
Jasiński M, Stukkens Y, Degand H, Purnelle B, Marchand-Brynaert J, Boutry M. A plant plasma membrane ATP binding cassette-type transporter is involved in antifungal terpenoid secretion. Plant Cell 2001; 13:1095-1107. [PMID: 11340184 DOI: 10.1105/tpc.13.5.1095] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
ATP binding cassette (ABC) transporters, which are found in all species, are known mainly for their ability to confer drug resistance. To date, most of the ABC transporters characterized in plants have been localized in the vacuolar membrane and are considered to be involved in the intracellular sequestration of cytotoxins. Working on the assumption that certain ABC transporters might be involved in defense metabolite secretion and their expression might be regulated by the concentration of these metabolites, we treated a Nicotiana plumbaginifolia cell culture with sclareolide, a close analog of sclareol, an antifungal diterpene produced at the leaf surface of Nicotiana spp; this resulted in the appearance of a 160-kD plasma membrane protein, which was partially sequenced. The corresponding cDNA (NpABC1) was cloned and shown to encode an ABC transporter. In vitro and in situ immunodetection showed NpABC1 to be localized in the plasma membrane. Under normal conditions, expression was found in the leaf epidermis. In cell culture and in leaf tissues, NpABC1 expression was strongly enhanced by sclareolide and sclareol. In parallel with NpABC1 induction, cells acquired the ability to excrete a labeled synthetic sclareolide derivative. These data suggest that NpABC1 is involved in the secretion of a secondary metabolite that plays a role in plant defense.
Collapse
Affiliation(s)
- M Jasiński
- Unité de Biochimie Physiologique, Université Catholique de Louvain, Croix du Sud 2-20, B-1348 Louvain-la-Neuve, Belgium
| | | | | | | | | | | |
Collapse
|
26
|
Jasiński M, Stukkens Y, Degand H, Purnelle B, Marchand-Brynaert J, Boutry M. A plant plasma membrane ATP binding cassette-type transporter is involved in antifungal terpenoid secretion. Plant Cell 2001; 13:1095-107. [PMID: 11340184 PMCID: PMC135550] [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] [Subscribe] [Scholar Register] [Received: 10/20/2000] [Accepted: 03/01/2001] [Indexed: 04/16/2023]
Abstract
ATP binding cassette (ABC) transporters, which are found in all species, are known mainly for their ability to confer drug resistance. To date, most of the ABC transporters characterized in plants have been localized in the vacuolar membrane and are considered to be involved in the intracellular sequestration of cytotoxins. Working on the assumption that certain ABC transporters might be involved in defense metabolite secretion and their expression might be regulated by the concentration of these metabolites, we treated a Nicotiana plumbaginifolia cell culture with sclareolide, a close analog of sclareol, an antifungal diterpene produced at the leaf surface of Nicotiana spp; this resulted in the appearance of a 160-kD plasma membrane protein, which was partially sequenced. The corresponding cDNA (NpABC1) was cloned and shown to encode an ABC transporter. In vitro and in situ immunodetection showed NpABC1 to be localized in the plasma membrane. Under normal conditions, expression was found in the leaf epidermis. In cell culture and in leaf tissues, NpABC1 expression was strongly enhanced by sclareolide and sclareol. In parallel with NpABC1 induction, cells acquired the ability to excrete a labeled synthetic sclareolide derivative. These data suggest that NpABC1 is involved in the secretion of a secondary metabolite that plays a role in plant defense.
Collapse
Affiliation(s)
- M Jasiński
- Unité de Biochimie Physiologique, Université Catholique de Louvain, Croix du Sud 2-20, B-1348 Louvain-la-Neuve, Belgium
| | | | | | | | | | | |
Collapse
|
27
|
Santoni V, Rouquié D, Doumas P, Mansion M, Boutry M, Degand H, Dupree P, Packman L, Sherrier J, Prime T, Bauw G, Posada E, Rouzé P, Dehais P, Sahnoun I, Barlier I, Rossignol M. Use of a proteome strategy for tagging proteins present at the plasma membrane. Plant J 1998; 16:633-41. [PMID: 10036779 DOI: 10.1046/j.1365-313x.1998.00335.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
A plasma membrane (PM) fraction was purified from Arabidopsis thaliana using a standard procedure and analyzed by two-dimensional (2D) gel electrophoresis. The proteins were classified according to their relative abundance in PM or cell membrane supernatant fractions. Eighty-two of the 700 spots detected on the PM 2D gels were microsequenced. More than half showed sequence similarity to proteins of known function. Of these, all the spots in the PM-specific and PM-enriched fractions, together with half of the spots with similar abundance in PM fraction and supernatant, have previously been found at the PM, supporting the validity of this approach. Extrapolation from this analysis indicates that (i) approximately 550 polypeptides found at the PM could be resolved on 2D gels; (ii) that numerous proteins with multiple locations are found at the PM; and (iii) that approximately 80% of PM-specific spots correspond to proteins with unknown function. Among the later, half are represented by ESTs or cDNAs in databases. In this way, several unknown gene products were potentially localized to the PM. These data are discussed with respect to the efficiency of organelle proteome approaches to link systematically genomic data to genome expression. It is concluded that generalized proteomes can constitute a powerful resource, with future completion of Arabidopsis genome sequencing, for genome-wide exploration of plant function.
Collapse
Affiliation(s)
- V Santoni
- Biochimie et Physiologie Moléculaire des Plantes, INRA/ENSA-M/CNRS URA 2133, Montpellier, France
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Maffey L, Degand H, Boutry M. Partial purification of mitochondrial ribosomes from broad bean and identification of proteins encoded by the mitochondrial genome. Mol Gen Genet 1997; 254:365-71. [PMID: 9180689 DOI: 10.1007/s004380050428] [Citation(s) in RCA: 16] [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] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
An approach towards the identification at the protein level of the ribosomal proteins encoded by the mitochondrial genome of broad bean (Vicia faba) has been developed. After Triton X-100 treatment of isolated mitochondria, a fraction enriched in mitochondrial ribosomes was obtained by successive centrifugation, first onto a sucrose cushion, and then in a sucrose gradient. Mitochondrial translation products were labelled in isolated mitochondria with [35S]methionine and added to the enriched mitochondrial ribosomal proteins before separation by two-dimensional gel electrophoresis. Six spots, identified both by Coomassie blue staining and autoradiography, were analysed by protein micro-sequencing. Two of these were shown to correspond to ribosomal proteins S10 and S12. We conclude that these two proteins are encoded by the mitochondrial genome of broad bean and that the method described here can be used to identify other proteins encoded by the mitochondrial genome.
Collapse
Affiliation(s)
- L Maffey
- Unité de Biochimie Physiologique, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | | | | |
Collapse
|
29
|
Gutierres S, Sabar M, Lelandais C, Chetrit P, Diolez P, Degand H, Boutry M, Vedel F, de Kouchkovsky Y, De Paepe R. Lack of mitochondrial and nuclear-encoded subunits of complex I and alteration of the respiratory chain in Nicotiana sylvestris mitochondrial deletion mutants. Proc Natl Acad Sci U S A 1997; 94:3436-41. [PMID: 9096412 PMCID: PMC20388 DOI: 10.1073/pnas.94.7.3436] [Citation(s) in RCA: 146] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/1996] [Accepted: 01/06/1997] [Indexed: 02/04/2023] Open
Abstract
We previously have shown that Nicotiana sylvestris cytoplasmic male sterile (CMS) mutants I and II present large mtDNA deletions and that the NAD7 subunit of complex I (the main dehydrogenase of the mitochondrial respiratory chain) is absent in CMS I. Here, we show that, despite a large difference in size in the mtDNA deletion, CMS I and II display similar alterations. Both have an impaired development from germination to flowering, with partial male sterility that becomes complete under low light. Besides NAD7, two other complex I subunits are missing (NAD9 and the nucleus-encoded, 38-kDa subunit), identified on two-dimensional patterns of mitochondrial proteins. Mitochondria isolated from CMS leaves showed altered respiration. Although their succinate oxidation through complex II was close to that of the wild type, oxidation of glycine, a priority substrate of plant mitochondria, was significantly reduced. The remaining activity was much less sensitive to rotenone, indicating the breakdown of Complex I activity. Oxidation of exogenous NADH (coupled to proton gradient generation and partly sensitive to rotenone) was strongly increased. These results suggest respiratory compensation mechanisms involving additional NADH dehydrogenases to complex I. Finally, the capacity of the cyanide-resistant alternative oxidase pathway was enhanced in CMS, and higher amounts of enzyme were evidenced by immunodetection.
Collapse
Affiliation(s)
- S Gutierres
- Institut de Biotechnologie des Plantes, Centre National de la Recherche Scientifique (Unité de Recherche Associée 1128), Université Paris-Sud, Orsay, France
| | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Blomberg A, Blomberg L, Norbeck J, Fey SJ, Larsen PM, Larsen M, Roepstorff P, Degand H, Boutry M, Posch A. Interlaboratory reproducibility of yeast protein patterns analyzed by immobilized pH gradient two-dimensional gel electrophoresis. Electrophoresis 1995; 16:1935-45. [PMID: 8586069 DOI: 10.1002/elps.11501601320] [Citation(s) in RCA: 114] [Impact Index Per Article: 3.9] [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: 01/31/2023]
Abstract
An interlaboratory comparison was conducted on the positional and quantitative reproducibility of yeast proteins resolved by two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) using isoelectric focusing with immobilized pH gradient (pH 4-7) in the first dimension. The basic experimental set-up was as follows: one laboratory prepared and distributed a [35S]methionine-labeled total yeast protein extract (Göteborg, Sweden), another laboratory prepared the IPG strips to be used by all labs in this study (Munich, Germany), the third laboratory (Aarhus, Denmark) circulated the protocols and coordinated the modest attempts to unify them. Samples were run horizontally in the first dimension and vertically in the second. The gels were sent to Göteborg for processing by phosphoimager technology and computerized image analysis (PDQuest), and the 2-D PAGE resolved proteins were located and quantified automatically. A subset of 470 spots was manually matched in all gels out of an average of 1328 resolved proteins. The positional interlaboratory comparison revealed great pattern reproducibility, the correlation coefficient in no case being less than 0.9994. In absolute terms an average deviation of 2.8 mm (x-position) and 1.8 mm (y-position) were obtained for all nine gels (three gels per lab). The interlaboratory comparison of protein quantitation displayed higher variability, and the best correlation coefficient generated was 0.975. An average standard deviation of 34.5% was calculated for protein quantitation including all three labs, a value slightly higher than the intralaboratory variation (range 20-28%). Thus, despite differences in protocols, chemicals and equipment, the immobilized pH gradient technology gave extremely high positional and quantitative reproducibility. This will greatly facilitate the exchange of data and the establishment of multi-user image-based 2-D gel databases.
Collapse
Affiliation(s)
- A Blomberg
- Department of General and Marine Microbiology, Lundberg Laboratory, University of Göteborg, Sweden.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Decottignies A, Lambert L, Catty P, Degand H, Epping EA, Moye-Rowley WS, Balzi E, Goffeau A. Identification and characterization of SNQ2, a new multidrug ATP binding cassette transporter of the yeast plasma membrane. J Biol Chem 1995; 270:18150-7. [PMID: 7629127 DOI: 10.1074/jbc.270.30.18150] [Citation(s) in RCA: 133] [Impact Index Per Article: 4.6] [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] [Indexed: 01/26/2023] Open
Abstract
The SNQ2 gene of Saccharomyces cerevisiae, which encodes an ATP binding cassette protein responsible for resistance to the mutagen 4-nitroquinoline oxide, is regulated by the DNA-binding proteins PDR1 and PDR3. In a plasma membrane-enriched fraction from a pdr1 mutant, the SNQ2 protein is found in the 160-kDa over-expressed band, together with PDR5. The SNQ2 protein was solubilized with n-dodecyl beta-D-maltoside from the plasma membranes of a PDR5-deleted strain and separated from the PMA1 H(+/-)ATPase by sucrose gradient centrifugation. The enzyme shows a nucleoside triphosphatase activity that differs biochemically from that of PDR5 (Decottignies, A., Kolaczkowski, M., Balzi, E., and Goffeau, A. (1994) J. Biol. Chem. 269, 12797-12803) and is sensitive to vanadate, erythrosine B, and Triton X-100 but not to oligomycin, which inhibits the PDR5 activity only. Disruption of both PDR5 and SNQ2 in a pdr1 mutant decreases the cell growth rate and reveals the presence of at least two other ATP binding cassette proteins in the 160-kDa overexpressed band that have been identified by amino-terminal microsequencing.
Collapse
Affiliation(s)
- A Decottignies
- Unité de Biochimie Physiologique, Université Catholique de Louvain, Belgium
| | | | | | | | | | | | | | | |
Collapse
|