Functional analysis of novel Rab GTPases identified in the proteome of purified Legionella-containing vacuoles from macrophages: Macrophage LCV proteome
Open accessAbstract
The opportunistic pathogen Legionella pneumophila employs the Icm/Dot type IV secretion system and ∼300 different effector proteins to replicate in macrophages and amoebae in a distinct 'Legionella-containing vacuole' (LCV). LCVs from infected RAW 264.7 macrophages were enriched by immuno-affinity separation and density gradient centrifugation, using an antibody against the L. pneumophila effector SidC, which specifically binds to the phosphoinositide PtdIns(4)P on the pathogen vacuole membrane. The proteome of purified LCVs was determined by mass spectro-metry (data are available via ProteomeXchange with identifier PXD000647). The proteomics analysis revealed more than 1150 host proteins, including 13 small GTPases of the Rab family. Using fluorescence microscopy, 6 novel Rab proteins were confirmed to localize on pathogen vacuoles harbouring wild-type but not ΔicmT mutant L. pneumophila. Individual depletion of 20 GTPases by RNA interference indicated that endocytic GTPases (Rab5a, Rab14 and Rab21) restrict intracellular growth of L. pneumophila, whereas secretory GTPases (Rab8a, Rab10 and Rab32) implicated in Golgi-endosome trafficking promote bacterial replication. Upon silencing of Rab21 or Rab32, fewer LCVs stained positive for Rab4 or Rab9, implicated in secretory or retrograde trafficking respectively. Moreover, depletion of Rab8a, Rab14 or Rab21 significantly decreased the number of SidC-positive LCVs, suggesting that PtdIns(4)P is reduced under these conditions. L. pneumophila proteins identified in purified LCVs included proteins putatively implicated in phosphorus metabolism and as many as 60 Icm/Dot-translocated effectors, which are likely required early during infection. Taken together, the phagocyte and Legionella proteomes of purified LCVs lay the foundation for further hypothesis-driven investigations of the complex process of pathogen vacuole formation.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Rab 3, 4, 5, 7, 9, 10, 11, and 14 are associated with pathogen-containing phagosomes and allocated to individual maturation stages.
“A number of Rab proteins have been associated with pathogen-containing phagosomes including Rab 3, 4, 5, 7, 9, 10, 11, and 14 (14, 15) and allocated to individual maturation stages.”
From Macrophage defense mechanisms against intracellular bacteria (2015) · cites this paper as [15]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Rab GTPases as coordinators of vesicle traffic
Stenmark, H. (2009) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2728 · Cited by 3,413 · see citing works
Rab proteins as membrane organizers
Zerial, M., & McBride, H. (2001) · Nature Reviews Molecular Cell Biology · doi:10.1038/35052055 · Cited by 3,381 · see citing works
The Proteomics Identifications (PRIDE) database and associated tools: status in 2013
Vizcaíno, J. A., Côté, R. G., Csordas, A., Dianes, J. A., Fabregat, A., Foster, J. M., Griss, J., Alpi, E., Birim, M., Contell, J., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1262 · Cited by 1,918 · see citing works
Garin, J., Diez, R., Kieffer‐Jaquinod, S., Dermine, J.-F., Duclos, S., Gagnon, É., Sadoul, R., Rondeau, C., & Desjardins, M. (2001) · The Journal of Cell Biology · doi:10.1083/jcb.152.1.165 · Cited by 686 · see citing works
Immune Control of Tuberculosis by IFN-γ-Inducible LRG-47
MacMicking, J. D., Taylor, G. A., & McKinney, J. D. (2003) · Science · doi:10.1126/science.1088063 · Cited by 685 · cited 1× · see citing works
“Moreover, 4 IFN-γ-induced genes were identified in the LCV proteome, including LRG-47 implicated in cellular immunity against Mycobacterium tuberculosis (MacMicking et al., 2003).”
BackgroundThe Legionella pneumophila replication vacuole: making a cosy niche inside host cells
Isberg, R. R., O’Connor, T. J., & Heidtman, M. I. (2008) · Nature Reviews Microbiology · doi:10.1038/nrmicro1967 · Cited by 675 · see citing works
Horwitz, M. A. (1983) · The Journal of Experimental Medicine · doi:10.1084/jem.158.4.1319 · Cited by 659 · see citing works
A Bacterial Guanine Nucleotide Exchange Factor Activates ARF on Legionella Phagosomes
Nagai, H., Kagan, J. C., Zhu, X., Kahn, R., & Roy, C. R. (2002) · Science · doi:10.1126/science.1067025 · Cited by 551 · see citing works
Association of Legionella pneumophila with the macrophage endoplasmic reticulum
Swanson, M. S., & Isberg, R. R. (1995) · Infection and Immunity · doi:10.1128/iai.63.9.3609-3620.1995 · Cited by 540 · see citing works
Molecular Pathogenesis of Infections Caused by Legionella pneumophila
Newton, H. J., Ang, D. K. Y., van Driel, I. R., & Hartland, E. L. (2010) · Clinical Microbiology Reviews · doi:10.1128/cmr.00052-09 · Cited by 493 · see citing works
Luo, Z., & Isberg, R. R. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0304916101 · Cited by 479 · see citing works
The <i>Legionella</i> Effector RavZ Inhibits Host Autophagy Through Irreversible Atg8 Deconjugation
Choy, A., Dancourt, J., Mugo, B., O’Connor, T. J., Isberg, R. R., Melia, T. J., & Roy, C. R. (2012) · Science · doi:10.1126/science.1227026 · Cited by 473 · see citing works
Legionella phagosomes intercept vesicular traffic from endoplasmic reticulum exit sites
Kagan, J. C., & Roy, C. R. (2002) · Nature Cell Biology · doi:10.1038/ncb883 · Cited by 448 · see citing works
Modulation of Host Cell Function byLegionella pneumophilaType IV Effectors
Hubber, A. M., & Roy, C. R. (2010) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-100109-104034 · Cited by 427 · see citing works
The Legionella pneumophila effector protein DrrA is a Rab1 guanine nucleotide-exchange factor
Murata, T., Delprato, A., Ingmundson, A., et al. (2006) · Nature Cell Biology · doi:10.1038/ncb1463 · Cited by 366 · see citing works
Tilney, L. G., Harb, O. S., Connelly, P. S., Robinson, C. G., & Roy, C. R. (2001) · Journal of Cell Science · doi:10.1242/jcs.114.24.4637 · Cited by 345 · see citing works
Small GTPase Rab21 regulates cell adhesion and controls endosomal traffic of β1-integrins
Pellinen, T. S., Arjonen, A., Vuoriluoto, K., Kallio, K., Fransen, J. A. M., & Ivaska, J. (2006) · The Journal of Cell Biology · doi:10.1083/jcb.200509019 · Cited by 343 · see citing works
Targeting of Host Rab GTPase Function by the Intravacuolar Pathogen Legionella pneumophila
Machner, M. P., & Isberg, R. R. (2006) · Developmental Cell · doi:10.1016/j.devcel.2006.05.013 · Cited by 340 · see citing works
Zhu, W., Banga, S., Tan, Y., Zheng, C. C., Stephenson, R. E., Gately, J. M., & Luo, Z. (2011) · PLoS ONE · doi:10.1371/journal.pone.0017638 · Cited by 304 · see citing works
Legionella Effectors That Promote Nonlytic Release from Protozoa
Chen, J. Y.-S., de Felipe, K. S., Clarke, M., Lu, H. X., Anderson, O. R., Segal, G., & Shuman, H. A. (2004) · Science · doi:10.1126/science.1094226 · Cited by 294 · see citing works
Weber, S. S., Ragaz, C., Reus, K., Nyfeler, Y., & Hilbi, H. (2006) · PLoS Pathogens · doi:10.1371/journal.ppat.0020046 · Cited by 292 · see citing works
Self-citationRab38 and Rab32 control post-Golgi trafficking of melanogenic enzymes
Wasmeier, C., Romao, M., Plowright, L., Bennett, D. C., Raposo, G., & Seabra, M. C. (2006) · The Journal of Cell Biology · doi:10.1083/jcb.200606050 · Cited by 291 · see citing works
Legionella Subvert the Functions of Rab1 and Sec22b to Create a Replicative Organelle
Kagan, J. C., Stein, M., Pypaert, M., & Roy, C. R. (2004) · The Journal of Experimental Medicine · doi:10.1084/jem.20031706 · Cited by 281 · see citing works
MT1‐MMP proinvasive activity is regulated by a novel Rab8‐dependent exocytic pathway
Bravo‐Cordero, J. J., Marrero‐Diaz, R., Megı́as, D., Genı́s, L., García‐Grande, A., García, M. Á., Arroyo, A. G., & Montoya, M. C. (2007) · The EMBO Journal · doi:10.1038/sj.emboj.7601606 · Cited by 269 · see citing works
Brombacher, E., Urwyler, S., Ragaz, C., Weber, S. S., Kami, K., Overduin, M., & Hilbi, H. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.m807505200 · Cited by 261 · see citing works
Self-citationFaix, J. (2004) · Nucleic Acids Research · doi:10.1093/nar/gnh136 · Cited by 258 · see citing works
De-AMPylation of the Small GTPase Rab1 by the Pathogen Legionella pneumophila
Neunuebel, M. R., Chen, Y., Gaspar, A. H., et al. (2011) · Science · doi:10.1126/science.1207193 · Cited by 227 · see citing works
Legionella pneumophila SidD is a deAMPylase that modifies Rab1
Tan, Y., & Luo, Z. (2011) · Nature · doi:10.1038/nature10307 · Cited by 226 · see citing works
Inhibition of Host Vacuolar H+-ATPase Activity by a Legionella pneumophila Effector
Xu, L., Shen, X., Bryan, A. B., Banga, S., Swanson, M. S., & Luo, Z. (2010) · PLoS Pathogens · doi:10.1371/journal.ppat.1000822 · Cited by 218 · see citing works
Manipulation of Rab GTPase Function by Intracellular Bacterial Pathogens
Brumell, J. H., & Scidmore, M. A. (2007) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00023-07 · Cited by 217 · see citing works
Derré, I., & Isberg, R. R. (2004) · Infection and Immunity · doi:10.1128/iai.72.5.3048-3053.2004 · Cited by 213 · see citing works
Ragaz, C., Pietsch, H., Urwyler, S., Tiaden, A. N., Weber, S. S., & Hilbi, H. (2008) · Cellular Microbiology · doi:10.1111/j.1462-5822.2008.01219.x · Cited by 207 · see citing works
Self-citationLegionella pneumophila regulates the small GTPase Rab1 activity by reversible phosphorylcholination
Tan, Y., Arnold, R. J., & Luo, Z. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1114023109 · Cited by 203 · see citing works
The protein SdhA maintains the integrity of the Legionella -containing vacuole
Creasey, E. A., & Isberg, R. R. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1121286109 · Cited by 198 · see citing works
Tiaden, A. N., Spirig, T., Weber, S. S., Brüggemann, H., Bosshard, R., Buchrieser, C., & Hilbi, H. (2007) · Cellular Microbiology · doi:10.1111/j.1462-5822.2007.01005.x · Cited by 175 · see citing works
Self-citationRab14 is critical for maintenance of Mycobacterium tuberculosis phagosome maturation arrest
Kyei, G. B., Vergne, I., Chua, J., Roberts, E. A., Harris, J., Junutula, J. R., & Deretic, V. P. (2006) · The EMBO Journal · doi:10.1038/sj.emboj.7601407 · Cited by 171 · see citing works
Urwyler, S., Nyfeler, Y., Ragaz, C., Lee, H., Mueller, L. N., Aebersold, R. H., & Hilbi, H. (2008) · Traffic · doi:10.1111/j.1600-0854.2008.00851.x · Cited by 168 · see citing works
Self-citationThe Legionella Effector RidL Inhibits Retrograde Trafficking to Promote Intracellular Replication
Finsel, I., Ragaz, C., Hoffmann, C., Harrison, C. F., Weber, S., van Rahden, V. A., Johannes, L., & Hilbi, H. (2013) · Cell Host & Microbe · doi:10.1016/j.chom.2013.06.001 · Cited by 149 · see citing works
Self-citationClemens, D. L., Lee, B., & Horwitz, M. A. (2000) · Infection and Immunity · doi:10.1128/iai.68.9.5154-5166.2000 · Cited by 135 · see citing works
Weber, S. S., Ragaz, C., & Hilbi, H. (2008) · Cellular Microbiology · doi:10.1111/j.1462-5822.2008.01266.x · Cited by 133 · see citing works
Self-citationPathogen trafficking pathways and host phosphoinositide metabolism
Weber, S. S., Ragaz, C., & Hilbi, H. (2009) · Molecular Microbiology · doi:10.1111/j.1365-2958.2009.06608.x · Cited by 133 · see citing works
Self-citationHigh-Resolution Dissection of Phagosome Maturation Reveals Distinct Membrane Trafficking Phases
Gotthardt, D. N., Warnatz, H.-J., Henschel, O., Brückert, F., Schleicher, M., & Soldati, T. (2002) · Molecular Biology of the Cell · doi:10.1091/mbc.e02-04-0206 · Cited by 133 · see citing works
Rab8 Regulates Basolateral Secretory, But Not Recycling, Traffic at the Recycling Endosome
Henry, L., & Sheff, D. R. (2008) · Molecular Biology of the Cell · doi:10.1091/mbc.e07-09-0902 · Cited by 122 · see citing works
Structural basis for substrate recognition by a unique Legionella phosphoinositide phosphatase
Hsu, F., Zhu, W., Brennan, L. D., Tao, L., Luo, Z., & Mao, Y. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1207903109 · Cited by 117 · see citing works
A Rab-Centric Perspective of Bacterial Pathogen-Occupied Vacuoles
Sherwood, R. K., & Roy, C. R. (2013) · Cell Host & Microbe · doi:10.1016/j.chom.2013.08.010 · Cited by 110 · see citing works
Legionella spp. outdoors: colonization, communication and persistence
Hilbi, H., Hoffmann, C., & Harrison, C. F. (2011) · Environmental Microbiology Reports · doi:10.1111/j.1758-2229.2011.00247.x · Cited by 107 · see citing works
Self-citationKu, B., Lee, K.-H., Park, W. S., et al. (2012) · PLoS Pathogens · doi:10.1371/journal.ppat.1003082 · Cited by 106 · see citing works
Rothmeier, E., Pfaffinger, G., Hoffmann, C., Harrison, C. F., Grabmayr, H., Repnik, U., Hannemann, M., Wölke, S., Bausch, A. R., Griffiths, G., et al. (2013) · PLoS Pathogens · doi:10.1371/journal.ppat.1003598 · Cited by 105 · see citing works
Self-citationDegtyar, E., Zusman, T., Ehrlich, M., et al. (2009) · Cellular Microbiology · doi:10.1111/j.1462-5822.2009.01328.x · Cited by 104 · see citing works
Proteomics Fingerprinting of Phagosome Maturation and Evidence for the Role of a Gα during Uptake
Gotthardt, D., Blancheteau, V., Bosserhoff, A., Ruppert, T., Delorenzi, M., & Soldati, T. (2006) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m600113-mcp200 · Cited by 98 · see citing works
Function and Mechanism of Action of <i>Dictyostelium</i> Nramp1 (Slc11a1) in Bacterial Infection
Peracino, B., Wagner, C., Balest, A., Balbo, A., Pergolizzi, B., Noegel, A. A., Steinert, M., & Bozzaro, S. (2006) · Traffic · doi:10.1111/j.1600-0854.2005.00356.x · Cited by 96 · see citing works
High‐affinity binding of phosphatidylinositol 4‐phosphate by Legionella pneumophila DrrA
Schoebel, S., Blankenfeldt, W., Goody, R. S., & Itzen, A. (2010) · EMBO Reports · doi:10.1038/embor.2010.97 · Cited by 92 · see citing works
Secretive Bacterial Pathogens and the Secretory Pathway
Hilbi, H., & Haas, A. (2012) · Traffic · doi:10.1111/j.1600-0854.2012.01344.x · Cited by 89 · see citing works
Self-citationAnchors for Effectors: Subversion of Phosphoinositide Lipids by Legionella
Hilbi, H., Weber, S., & Finsel, I. (2011) · Frontiers in Microbiology · doi:10.3389/fmicb.2011.00091 · Cited by 83 · see citing works
Self-citationProtein LidA from Legionella is a Rab GTPase supereffector
Schoebel, S., Cichy, A., Goody, R. S., & Itzen, A. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1113133108 · Cited by 79 · see citing works
Identification and Structural Characterization of a Legionella Phosphoinositide Phosphatase*
Toulabi, L., Wu, X., Cheng, Y., & Mao, Y. (2013) · Journal of Biological Chemistry · doi:10.1074/jbc.m113.474239 · Cited by 78 · see citing works
Fajardo, M., Schleicher, M., Noegel, A., Bozzaro, S., Killinger, S., Heuner, K., Hacker, J., & Steinert, M. (2004) · Microbiology · doi:10.1099/mic.0.27111-0 · Cited by 73 · see citing works
Domain organization of Legionella effector SetA
Jank, T., Böhmer, K. E., Tzivelekidis, T., Schwan, C., Belyi, Y., & Aktories, K. (2012) · Cellular Microbiology · doi:10.1111/j.1462-5822.2012.01761.x · Cited by 72 · see citing works
Legionella pneumophila LidA Affects Nucleotide Binding and Activity of the Host GTPase Rab1
Neunuebel, M. R., Mohammadi, S., Jarník, M., et al. (2012) · Journal of Bacteriology · doi:10.1128/jb.06306-11 · Cited by 72 · see citing works
Cardoso, C. M. P., Jordão, L., & Vieira, O. V. (2009) · Traffic · doi:10.1111/j.1600-0854.2009.01013.x · Cited by 72 · see citing works
Harris, E. N., & Cardelli, J. A. (2002) · Journal of Cell Science · doi:10.1242/jcs.00050 · Cited by 70 · see citing works
Temesvari, L. A., Rodriguez‐Paris, J., Bush, J., Steck, T. L., & Cardelli, J. A. (1994) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)47307-3 · Cited by 60 · see citing works
Peracino, B., Balest, A., & Bozzaro, S. (2010) · Journal of Cell Science · doi:10.1242/jcs.072124 · Cited by 56 · see citing works
Egami, Y., & Araki, N. (2009) · PLoS ONE · doi:10.1371/journal.pone.0006689 · Cited by 37 · see citing works
Covalent Coercion by Legionella pneumophila
Itzen, A., & Goody, R. S. (2011) · Cell Host & Microbe · doi:10.1016/j.chom.2011.08.002 · Cited by 29 · see citing works
Pathogen Vacuole Purification from Legionella-Infected Amoeba and Macrophages
Hoffmann, C., Finsel, I., & Hilbi, H. (2012) · Methods in molecular biology · doi:10.1007/978-1-62703-161-5_18 · Cited by 25 · see citing works
Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
Macrophage defense mechanisms against intracellular bacteria
Weiss, G., & Schaible, U. E. (2015) · Immunological Reviews · doi:10.1111/imr.12266 · Cited by 989 · see citing works
Naujoks, J., Tabeling, C., Dill, B. D., Hoffmann, C., Brown, A. S., Kunze, M., Kempa, S., Peter, A., Mollenkopf, H.-J., Dorhoi, A., et al. (2016) · PLOS Pathogens · doi:10.1371/journal.ppat.1005408 · Cited by 261 · see citing works
Self-citation
- Authors
- Hoffmann, C., Finsel, I., Otto, A., Pfaffinger, G., Rothmeier, E., Hecker, M., Becher, D., & Hilbi, H.
- Affiliations
- Max-von-Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie (DE)
- Universität Greifswald (DE)
- Corresponding author
- Hilbi, Hubert
- Venue
- Cellular Microbiology
- Publisher
- Hindawi Limited
- Published
- 2014-01-27
- Volume
- 16
- Issue
- 7
- Pages
- n/a-n/a
- ISSN
- 1462-5814 (ISSN-L)
- OpenAlex
- W1542673149
- Cited by
- 126
- References
- 66
- Citations by year
- 2026: 6 · 2025: 1 · 2024: 5 · 2023: 6 · 2022: 5 · 2021: 8 · 2020: 6 · 2019: 9 · 2018: 17 · 2017: 16 · 2016: 14 · 2015: 21 · 2014: 12
- FWCI
- 11.13
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Cellular Microbiology (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Science Foundation
- Imperial College London
- Deutsche Forschungsgemeinschaft (SPP 1580, HI 1511/1-1)
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (31003A, 125369)
- Bundesministerium für Bildung und Forschung (03Z1CN21, 0315834C)
- Eidgenössische Technische Hochschule Zürich
- Turun Yliopisto
- Universidade de Lisboa
- Université de Genève
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Endocrinology › Legionella and Acanthamoeba research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Cellular transport and secretion
- Health Sciences › Medicine › Epidemiology › Autophagy in Disease and Therapy
- Keywords
- Legionella pneumophila, Legionella-containing vacuole, Rab GTPases, phosphatidylinositol 4-phosphate, host-pathogen interaction, macrophages, bacterial replication, endosomal trafficking, secretory trafficking, Rab21, Rab32, Rab8a, Rab14, Rab5a, Rab4, Rab9, phosphorus metabolism, phagosome formation
- MeSH terms
- Animals, Bacterial Proteins, Dictyostelium, Humans, Macrophages, Vacuoles, Legionella pneumophila, Proteome, rab GTP-Binding Proteins, Cell Line, Tumor, Mice, Host-Pathogen Interactions
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
