Imaging

@article{scheer_tutase_2021,

title = {The TUTase URT1 connects decapping activators and prevents the accumulation of excessively deadenylated mRNAs to avoid siRNA biogenesis},

author = {Hélène Scheer and Caroline Almeida and Emilie Ferrier and Quentin Simonnot and Laure Poirier and David Pflieger and François M. Sement and Sandrine Koechler and Christina Piermaria and Paweł Krawczyk and Seweryn Mroczek and Johana Chicher and Lauriane Kuhn and Andrzej Dziembowski and Philippe Hammann and Hélène Zuber and Dominique Gagliardi},

doi = {10.1038/s41467-021-21382-2},

issn = {2041-1723},

year  = {2021},

date = {2021-02-01},

journal = {Nature Communications},

volume = {12},

number = {1},

pages = {1298},

abstract = {Uridylation is a widespread modification destabilizing eukaryotic mRNAs. Yet, molecular mechanisms underlying TUTase-mediated mRNA degradation remain mostly unresolved. Here, we report that the Arabidopsis TUTase URT1 participates in a molecular network connecting several translational repressors/decapping activators. URT1 directly interacts with DECAPPING 5 (DCP5), the Arabidopsis ortholog of human LSM14 and yeast Scd6, and this interaction connects URT1 to additional decay factors like DDX6/Dhh1-like RNA helicases. Nanopore direct RNA sequencing reveals a global role of URT1 in shaping poly(A) tail length, notably by preventing the accumulation of excessively deadenylated mRNAs. Based on in vitro and in planta data, we propose a model that explains how URT1 could reduce the accumulation of oligo(A)-tailed mRNAs both by favoring their degradation and because 3' terminal uridines intrinsically hinder deadenylation. Importantly, preventing the accumulation of excessively deadenylated mRNAs avoids the biogenesis of illegitimate siRNAs that silence endogenous mRNAs and perturb Arabidopsis growth and development.},

keywords = {Arabidopsis, Arabidopsis Proteins, Co-Repressor Proteins, DEAD-box RNA Helicases, Gene Expression Regulation, Humans, messenger, Plant, PPSE, Proto-Oncogene Proteins, Ribonucleoproteins, RNA, RNA Nucleotidyltransferases, RNA Stability, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Small Interfering, Tobacco, transcriptome, Uridine},

pubstate = {published},

tppubtype = {article}

}

@article{C2021c,

title = {Structure-Switching RNAs: From Gene Expression Regulation to Small Molecule Detection},

author = {C Husser and N Dentz and M Ryckelynck},

url = {https://doi.org/10.1002/sstr.202000132},

doi = {10.1002/sstr.202000132},

year  = {2021},

date = {2021-01-01},

journal = {Small Structures},

volume = {2},

number = {4},

pages = {2000132},

abstract = {RNA is instrumental to cell life in many aspects, especially gene expression regulation. Among the various known regulatory RNAs, riboswitches are particularly interesting cis‐acting molecules as they do not need cellular factor to achieve their function and are therefore highly portable from one organism to the other. These molecules usually found in the 5′ untranslated region of bacterial messenger RNAs are able to specifically sense a target ligand via an aptamer domain prior to transmitting this recognition event to an expression platform that turns on, or off, the expression of downstream genes. In addition to their obvious scientific interest, these modular molecules can also serve for the development of synthetic RNA devices with applications ranging from the control of transgene expression in gene therapy to the specific biosensing of small molecules. The engineering of such nanomachines is greatly facilitated by the proper understanding of their structure as well as the introduction of new technologies. Herein, a general overview of the current knowledge on natural riboswitches prior to explaining the main strategies used to develop new synthetic structure‐switching molecules (riboswitches or biosensors) controlled by small molecules is given.},

keywords = {biosensing, Gene Expression Regulation, riboswitches, RNA aptamers, RYCKELYNCK, Synthetic Biology, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{meteignier_arabidopsis_2021,

title = {Arabidopsis mTERF9 protein promotes chloroplast ribosomal assembly and translation by establishing ribonucleoprotein interactions in vivo},

author = {Louis-Valentin Méteignier and Rabea Ghandour and Aude Zimmerman and Lauriane Kuhn and Jörg Meurer and Reimo Zoschke and Kamel Hammani},

doi = {10.1093/nar/gkaa1244},

issn = {1362-4962},

year  = {2021},

date = {2021-01-01},

journal = {Nucleic Acids Research},

volume = {49},

number = {2},

pages = {1114--1132},

abstract = {The mitochondrial transcription termination factor proteins are nuclear-encoded nucleic acid binders defined by degenerate tandem helical-repeats of ∼30 amino acids. They are found in metazoans and plants where they localize in organelles. In higher plants, the mTERF family comprises ∼30 members and several of these have been linked to plant development and response to abiotic stress. However, knowledge of the molecular basis underlying these physiological effects is scarce. We show that the Arabidopsis mTERF9 protein promotes the accumulation of the 16S and 23S rRNAs in chloroplasts, and interacts predominantly with the 16S rRNA in vivo and in vitro. Furthermore, mTERF9 is found in large complexes containing ribosomes and polysomes in chloroplasts. The comprehensive analysis of mTERF9 in vivo protein interactome identified many subunits of the 70S ribosome whose assembly is compromised in the null mterf9 mutant, putative ribosome biogenesis factors and CPN60 chaperonins. Protein interaction assays in yeast revealed that mTERF9 directly interact with these proteins. Our data demonstrate that mTERF9 integrates protein-protein and protein-RNA interactions to promote chloroplast ribosomal assembly and translation. Besides extending our knowledge of mTERF functional repertoire in plants, these findings provide an important insight into the chloroplast ribosome biogenesis.},

keywords = {16S, 23S, Arabidopsis, Arabidopsis Proteins, Chloroplast Proteins, Chloroplasts, Gene Expression Regulation, Organelle Biogenesis, Peptide Termination Factors, Plant, Polyribosomes, PPSE, Protein Biosynthesis, Recombinant Proteins, Ribonucleoproteins, Ribosomal, ribosomes, RNA, Substrate Specificity},

pubstate = {published},

tppubtype = {article}

}

@article{fillatre_teads_2019,

title = {TEADs, Yap, Taz, Vgll4s transcription factors control the establishment of Left-Right asymmetry in zebrafish},

author = {Jonathan Fillatre and Jean-Daniel Fauny and Jasmine Alexandra Fels and Cheng Li and Mary Goll and Christine Thisse and Bernard Thisse},

doi = {10.7554/eLife.45241},

issn = {2050-084X},

year  = {2019},

date = {2019-01-01},

journal = {eLife},

volume = {8},

abstract = {In many vertebrates, establishment of Left-Right (LR) asymmetry results from the activity of a ciliated organ functioning as the LR Organizer (LRO). While regulation of the formation of this structure by major signaling pathways has been described, the transcriptional control of LRO formation is poorly understood. Using the zebrafish model, we show that the transcription factors and cofactors mediating or regulating the transcriptional outcome of the Hippo signaling pathway play a pivotal role in controlling the expression of genes essential to the formation of the LRO including ligands and receptors of signaling pathways involved in this process and most genes required for motile ciliogenesis. Moreover, the transcription cofactor, Vgll4l regulates epigenetic programming in LRO progenitors by controlling the expression of writers and readers of DNA methylation marks. Altogether, our study uncovers a novel and essential role for the transcriptional effectors and regulators of the Hippo pathway in establishing LR asymmetry.},

keywords = {Animals, Body Patterning, Developmental, developmental biology, Gene Expression Regulation, Hippo pathway, I2CT, Imagerie, Left-Right asymmetry, Left-Right Organizer, Signal Transduction, Taz, Transcription Factors, Vgll4, Yap, Zebrafish},

pubstate = {published},

tppubtype = {article}

}

@article{frechin_expression_2014,

title = {Expression of nuclear and mitochondrial genes encoding ATP synthase is synchronized by disassembly of a multisynthetase complex.},

author = {Mathieu Frechin and Ludovic Enkler and Emmanuel Tetaud and Daphné Laporte and Bruno Senger and Corinne Blancard and Philippe Hammann and Gaétan Bader and Sandra Clauder-Münster and Lars M Steinmetz and Robert Pierre Martin and Jean-Paul di Rago and Hubert Dominique Becker},

doi = {10.1016/j.molcel.2014.10.015},

issn = {1097-4164 1097-2765},

year  = {2014},

date = {2014-12-01},

journal = {Molecular cell},

volume = {56},

number = {6},

pages = {763--776},

abstract = {In eukaryotic cells, oxidative phosphorylation involves multisubunit complexes of mixed genetic origin. Assembling these complexes requires an organelle-independent synchronizing system for the proper expression of nuclear and mitochondrial genes. Here we show that proper expression of the F1FO ATP synthase (complex V) depends on a cytosolic complex (AME) made of two aminoacyl-tRNA synthetases (cERS and cMRS) attached to an anchor protein, Arc1p. When yeast cells adapt to respiration the Snf1/4 glucose-sensing pathway inhibits ARC1 expression triggering simultaneous release of cERS and cMRS. Free cMRS and cERS relocate to the nucleus and mitochondria, respectively, to synchronize nuclear transcription and mitochondrial translation of ATP synthase genes. Strains releasing asynchronously the two aminoacyl-tRNA synthetases display aberrant expression of nuclear and mitochondrial genes encoding subunits of complex V resulting in severe defects of the oxidative phosphorylation mechanism. This work shows that the AME complex coordinates expression of enzymes that require intergenomic control.},

note = {Place: United States},

keywords = {Cell Nucleus/genetics, Fungal, Gene Expression, Gene Expression Regulation, Mitochondria/genetics, Multienzyme Complexes, PPSE, Protein Multimerization, Proton-Translocating ATPases/*genetics/metabolism, RNA-Binding Proteins/physiology, Saccharomyces cerevisiae Proteins/physiology, Saccharomyces cerevisiae/enzymology/*genetics},

pubstate = {published},

tppubtype = {article}

}

@article{tartey_akirin2_2014,

title = {Akirin2 is critical for inducing inflammatory genes by bridging IκB-ζ and the SWI/SNF complex},

author = {Sarang Tartey and Kazufumi Matsushita and Alexis Vandenbon and Daisuke Ori and Tomoko Imamura and Takashi Mino and Daron M Standley and Jules A Hoffmann and Jean-Marc Reichhart and Shizuo Akira and Osamu Takeuchi},

doi = {10.15252/embj.201488447},

issn = {1460-2075},

year  = {2014},

date = {2014-10-01},

journal = {EMBO J.},

volume = {33},

number = {20},

pages = {2332--2348},

abstract = {Transcription of inflammatory genes in innate immune cells is coordinately regulated by transcription factors, including NF-κB, and chromatin modifiers. However, it remains unclear how microbial sensing initiates chromatin remodeling. Here, we show that Akirin2, an evolutionarily conserved nuclear protein, bridges NF-κB and the chromatin remodeling SWI/SNF complex by interacting with BRG1-Associated Factor 60 (BAF60) proteins as well as IκB-ζ, which forms a complex with the NF-κB p50 subunit. These interactions are essential for Toll-like receptor-, RIG-I-, and Listeria-mediated expression of proinflammatory genes including Il6 and Il12b in macrophages. Consistently, effective clearance of Listeria infection required Akirin2. Furthermore, Akirin2 and IκB-ζ recruitment to the Il6 promoter depend upon the presence of IκB-ζ and Akirin2, respectively, for regulation of chromatin remodeling. BAF60 proteins were also essential for the induction of Il6 in response to LPS stimulation. Collectively, the IκB-ζ-Akirin2-BAF60 complex physically links the NF-κB and SWI/SNF complexes in innate immune cell activation. By recruiting SWI/SNF chromatin remodellers to IκB-ζ, transcriptional coactivator for NF-κB, the conserved nuclear protein Akirin2 stimulates pro-inflammatory gene promoters in mouse macrophages during innate immune responses to viral or bacterial infection.},

keywords = {Adaptor Proteins, Animals, Cell Nucleus, Chromatin Assembly and Disassembly, chromatin remodeling, Chromosomal Proteins, cytokine, Cytokines, Female, Gene Expression Regulation, gene regulation, Genetic, hoffmann, Humans, Immunity, Innate, innate immunity, Knockout, Listeria monocytogenes, M3i, Macrophages, Male, Mice, Multiprotein Complexes, Non-Histone, Nuclear Proteins, Promoter Regions, Protein Binding, reichhart, Repressor Proteins, Sequence Deletion, Signal Transducing, Transcriptional Activation},

pubstate = {published},

tppubtype = {article}

}

@article{lamiable_induced_2014,

title = {Induced antiviral innate immunity in Drosophila},

author = {Olivier Lamiable and Jean-Luc Imler},

doi = {10.1016/j.mib.2014.05.006},

issn = {1879-0364},

year  = {2014},

date = {2014-08-01},

journal = {Current Opinion in Microbiology},

volume = {20},

pages = {62--68},

abstract = {Immunity to viral infections in the model organism Drosophila melanogaster involves both RNA interference and additional induced responses. The latter include not only cellular mechanisms such as programmed cell death and autophagy, but also the induction of a large set of genes, some of which contribute to the control of viral replication and resistance to infection. This induced response to infection is complex and involves both virus-specific and cell-type specific mechanisms. We review here recent developments, from the sensing of viral infection to the induction of signaling pathways and production of antiviral effector molecules. Our current understanding, although still partial, validates the Drosophila model of antiviral induced immunity for insect pests and disease vectors, as well as for mammals.},

keywords = {Animals, Gene Expression Regulation, Host-Pathogen Interactions, imler, Immunity, Innate, M3i, RNA Viruses, Signal Transduction},

pubstate = {published},

tppubtype = {article}

}

@article{lacotte_early_2013,

title = {Early differentiated CD138(high) MHCII+ IgG+ plasma cells express CXCR3 and localize into inflamed kidneys of lupus mice},

author = {Stéphanie Lacotte and Marion Decossas and Carole Le Coz and Susana Brun and Sylviane Muller and Hélène Dumortier},

doi = {10.1371/journal.pone.0058140},

issn = {1932-6203},

year  = {2013},

date = {2013-01-01},

journal = {PloS One},

volume = {8},

number = {3},

pages = {e58140},

abstract = {Humoral responses are central to the development of chronic autoimmune diseases such as systemic lupus erythematosus. Indeed, autoantibody deposition is responsible for tissue damage, the kidneys being one of the main target organs. As the source of pathogenic antibodies, plasma cells are therefore critical players in this harmful scenario, both at systemic and local levels. The aim of the present study was to analyze plasma cells in NZB/W lupus mice and to get a better understanding of the mechanisms underlying their involvement in the renal inflammation process. Using various techniques (i.e. flow cytometry, quantitative PCR, ELISpot), we identified and extensively characterized three plasma cell intermediates, according to their B220/CD138/MHCII expression levels. Each of these cell subsets displays specific proliferation and antibody secretion capacities. Moreover, we evidenced that the inflammation-related CXCR3 chemokine receptor is uniquely expressed by CD138(high)MHCII(+) plasma cells, which encompass both short- and long-lived cells and mostly produce IgG (auto)antibodies. Expression of CXCR3 allows efficient chemotactic responsiveness of these cells to cognate chemokines, which production is up-regulated in the kidneys of diseased NZB/W mice. Finally, using fluorescence and electron microscopy, we demonstrated the presence of CD138(+)CXCR3(+)IgG(+) cells in inflammatory areas in the kidneys, where they are very likely involved in the injury process. Thus, early differentiated CD138(high)MHCII(+) rather than terminally differentiated CD138(high)MHCII(low) plasma cells may be involved in the renal inflammatory injury in lupus, due to CXCR3 expression and IgG secretion.},

keywords = {Animals, Autoantibodies, Cell Differentiation, CXCR3, Dumortier, Gene Expression Regulation, Histocompatibility Antigens Class II, I2CT, Immunoglobulin G, Inbred BALB C, Kidney, Leukocyte Common Antigens, Lupus Nephritis, Mice, Plasma Cells, Receptors, Syndecan-1, Team-Dumortier},

pubstate = {published},

tppubtype = {article}

}

@article{lemaitre_pillars_2012,

title = {Pillars article: the dorsoventral regulatory gene cassette spätzle/Toll/cactus controls the potent antifungal response in Drosophila adults. Cell. 1996. 86: 973-983},

author = {Bruno Lemaitre and Emmanuelle Nicolas and Lydia Michaut and Jean-Marc Reichhart and Jules A Hoffmann},

issn = {1550-6606},

year  = {2012},

date = {2012-06-01},

journal = {J. Immunol.},

volume = {188},

number = {11},

pages = {5210--5220},

abstract = {The cytokine-induced activation cascade of NF-kappaB in mammals and the activation of the morphogen dorsal in Drosophila embryos show striking structural and functional similarities (Toll/IL-1, Cactus/I-kappaB, and dorsal/NF-kappaB). Here we demonstrate that these parallels extend to the immune response of Drosophila. In particular, the intracellular components of the dorsoventral signaling pathway (except for dorsal) and the extracellular Toll ligand, spätzle regulatory gene cassette, control expression of the antifungal peptide gene drosomycin in adults. We also show that mutations in the Toll signaling pathway dramatically reduce survival after fungal infection. Antibacterial genes are induced either by a distinct pathway involving the immune deficiency gene (imd) or by combined activation of both imd and dorsoventral pathways.},

keywords = {Animals, Antifungal Agents, Developmental, DNA-Binding Proteins, Gene Expression Regulation, history, hoffmann, M3i, Multigene Family, Mycoses, Phosphoproteins, reichhart, Toll-Like Receptors},

pubstate = {published},

tppubtype = {article}

}

@article{deleury_specific_2012,

title = {Specific versus non-specific immune responses in an invertebrate species evidenced by a comparative de novo sequencing study},

author = {Emeline Deleury and Géraldine Dubreuil and Namasivayam Elangovan and Eric Wajnberg and Jean-Marc Reichhart and Benjamin Gourbal and David Duval and Olga Lucia Baron and Jérôme Gouzy and Christine Coustau},

doi = {10.1371/journal.pone.0032512},

issn = {1932-6203},

year  = {2012},

date = {2012-01-01},

journal = {PLoS ONE},

volume = {7},

number = {3},

pages = {e32512},

abstract = {Our present understanding of the functioning and evolutionary history of invertebrate innate immunity derives mostly from studies on a few model species belonging to ecdysozoa. In particular, the characterization of signaling pathways dedicated to specific responses towards fungi and Gram-positive or Gram-negative bacteria in Drosophila melanogaster challenged our original view of a non-specific immunity in invertebrates. However, much remains to be elucidated from lophotrochozoan species. To investigate the global specificity of the immune response in the fresh-water snail Biomphalaria glabrata, we used massive Illumina sequencing of 5'-end cDNAs to compare expression profiles after challenge by Gram-positive or Gram-negative bacteria or after a yeast challenge. 5'-end cDNA sequencing of the libraries yielded over 12 millions high quality reads. To link these short reads to expressed genes, we prepared a reference transcriptomic database through automatic assembly and annotation of the 758,510 redundant sequences (ESTs, mRNAs) of B. glabrata available in public databases. Computational analysis of Illumina reads followed by multivariate analyses allowed identification of 1685 candidate transcripts differentially expressed after an immune challenge, with a two fold ratio between transcripts showing a challenge-specific expression versus a lower or non-specific differential expression. Differential expression has been validated using quantitative PCR for a subset of randomly selected candidates. Predicted functions of annotated candidates (approx. 700 unisequences) belonged to a large extend to similar functional categories or protein types. This work significantly expands upon previous gene discovery and expression studies on B. glabrata and suggests that responses to various pathogens may involve similar immune processes or signaling pathways but different genes belonging to multigenic families. These results raise the question of the importance of gene duplication and acquisition of paralog functional diversity in the evolution of specific invertebrate immune responses.},

keywords = {Animals, Biomphalaria, Calmodulin, Cluster Analysis, Complementary, DNA, Expressed Sequence Tags, Ferritins, Gene Expression Profiling, Gene Expression Regulation, High-Throughput Nucleotide Sequencing, Immunity, Innate, M3i, messenger, Pattern Recognition, Phylogeny, Receptors, reichhart, RNA, Signal Transduction, Zinc Fingers},

pubstate = {published},

tppubtype = {article}

}

@article{bou_aoun_analysis_2011,

title = {Analysis of thioester-containing proteins during the innate immune response of Drosophila melanogaster},

author = {Richard Bou Aoun and Charles Hetru and Laurent Troxler and Daniel Doucet and Dominique Ferrandon and Nicolas Matt},

doi = {10.1159/000321554},

issn = {1662-8128},

year  = {2011},

date = {2011-01-01},

journal = {J Innate Immun},

volume = {3},

number = {1},

pages = {52--64},

abstract = {Thioester-containing proteins (TEPs) are conserved proteins among insects that are thought to be involved in innate immunity. In Drosophila, the Tep family is composed of 6 genes named Tep1-Tep6. In this study, we investigated the phylogeny, expression pattern and roles of these genes in the host defense of Drosophila. Protostomian Tep genes are clustered in 3 distinct branches, 1 of which is specific to mosquitoes. Most D. melanogaster Tep genes are expressed in hemocytes, can be induced in the fat body, and are expressed in specific regions of the hypodermis. This expression pattern is consistent with a role in innate immunity. However, we find that TEP1, TEP2, and TEP4 are not strictly required in the body cavity to fight several bacterial and fungal infections. One possibility is that Drosophila TEPs act redundantly or that their absence can be compensated by other components of the immune response. TEPs may thus provide a subtle selective advantage during evolution. Alternatively, they may be required in host defense against specific as yet unidentified natural pathogens of Drosophila.},

keywords = {Animals, bioinformatic, DNA, Evolution, ferrandon, Gene Expression Regulation, Hemocytes, Immunity, In Situ Hybridization, Innate, M3i, matt, Molecular, Mutation, Phylogeny, Sequence Analysis},

pubstate = {published},

tppubtype = {article}

}

@article{lee_negative_2011b,

title = {Negative regulation of immune responses on the fly},

author = {Kwang-Zin Lee and Dominique Ferrandon},

doi = {10.1038/emboj.2011.47},

issn = {1460-2075},

year  = {2011},

date = {2011-01-01},

journal = {EMBO J.},

volume = {30},

number = {6},

pages = {988--990},

keywords = {*Gene Expression Regulation, *Homeostasis, Animals, bacteria, Bacteria/*immunology, Biological, Drosophila melanogaster/*immunology, Drosophila Proteins/biosynthesis/metabolism, ferrandon, Gene Expression Regulation, Homeostasis, M3i, Mitogen-Activated Protein Kinases, Mitogen-Activated Protein Kinases/metabolism, Models, NF-kappa B, NF-kappa B/metabolism, ras Proteins, ras Proteins/metabolism, Receptor Protein-Tyrosine Kinases, Receptor Protein-Tyrosine Kinases/metabolism},

pubstate = {published},

tppubtype = {article}

}

@article{hetru_nf-kappab_2009,

title = {NF-kappaB in the immune response of Drosophila},

author = {Charles Hetru and Jules A Hoffmann},

doi = {10.1101/cshperspect.a000232},

issn = {1943-0264},

year  = {2009},

date = {2009-12-01},

journal = {Cold Spring Harb Perspect Biol},

volume = {1},

number = {6},

pages = {a000232},

abstract = {The nuclear factor kappaB (NF-kappaB) pathways play a major role in Drosophila host defense. Two recognition and signaling cascades control this immune response. The Toll pathway is activated by Gram-positive bacteria and by fungi, whereas the immune deficiency (Imd) pathway responds to Gram-negative bacterial infection. The basic mechanisms of recognition of these various types of microbial infections by the adult fly are now globally understood. Even though some elements are missing in the intracellular pathways, numerous proteins and interactions have been identified. In this article, we present a general picture of the immune functions of NF-kappaB in Drosophila with all the partners involved in recognition and in the signaling cascades.},

keywords = {Animals, bacteria, Fungi, Gene Expression Regulation, hoffmann, M3i, NF-kappa B},

pubstate = {published},

tppubtype = {article}

}

@article{kemp_antiviral_2009,

title = {Antiviral immunity in drosophila},

author = {Cordula Kemp and Jean-Luc Imler},

doi = {10.1016/j.coi.2009.01.007},

issn = {1879-0372},

year  = {2009},

date = {2009-02-01},

journal = {Current Opinion in Immunology},

volume = {21},

number = {1},

pages = {3--9},

abstract = {Genetic analysis of the drosophila antiviral response indicates that RNA interference plays a major role. This contrasts with the situation in mammals, where interferon-induced responses mediate innate antiviral host-defense. An inducible response also contributes to antiviral immunity in drosophila, and similarities in the sensing and signaling of viral infection are becoming apparent between drosophila and mammals. In particular, DExD/H box helicases appear to play a crucial role in the cytosolic detection of viral RNAs in flies and mammals.},

keywords = {Animals, Argonaute Proteins, Caspases, DEAD-box RNA Helicases, Evolution, Gene Expression Regulation, Host-Pathogen Interactions, imler, M3i, Membrane Proteins, Molecular, Nuclear Proteins, Ribonuclease III, RNA, RNA Helicases, RNA Interference, RNA Virus Infections, RNA Viruses, RNA-Induced Silencing Complex, Viral, Virulence},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {An overview of RNAs with regulatory functions in gram-positive bacteria},

author = {P Romby and E Charpentier},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19859665},

isbn = {19859665},

year  = {2009},

date = {2009-01-01},

journal = {Cell Mol Life Sci},

volume = {67},

number = {2},

pages = {217-237},

abstract = {During the last decade, RNA molecules with regulatory functions on gene expression have benefited from a renewed interest. In bacteria, recent high throughput computational and experimental approaches have led to the discovery that 10-20% of all genes code for RNAs with critical regulatory roles in metabolic, physiological and pathogenic processes. The trans-acting RNAs comprise the noncoding RNAs, RNAs with a short open reading frame and antisense RNAs. Many of these RNAs act through binding to their target mRNAs while others modulate protein activity or target DNA. The cis-acting RNAs include regulatory regions of mRNAs that can respond to various signals. These RNAs often provide the missing link between sensing changing conditions in the environment and fine-tuning the subsequent biological responses. Information on their various functions and modes of action has been well documented for gram-negative bacteria. Here, we summarize the current knowledge of regulatory RNAs in gram-positive bacteria.},

note = {1420-9071 (Electronic) 

1420-682X (Linking) 

Journal Article 

Research Support, Non-U.S. Gov't 

Review},

keywords = {Bacterial  Gram-Positive Bacteria/*genetics/pathogenicity  RNA, Bacterial/genetics/*metabolism  RNA, Gene Expression Regulation, ROMBY, Unité ARN, Untranslated/genetics/*metabolism  Virulence/genetics},

pubstate = {published},

tppubtype = {article}

}

@article{deddouche_dexd/h-box_2008,

title = {The DExD/Ħ-box helicase Dicer-2 mediates the induction of antiviral activity in drosophila},

author = {Safia Deddouche and Nicolas Matt and Aidan Budd and Stefanie Mueller and Cordula Kemp and Delphine Galiana-Arnoux and Catherine Dostert and Christophe Antoniewski and Jules A Hoffmann and Jean-Luc Imler},

doi = {10.1038/ni.1664},

issn = {1529-2916},

year  = {2008},

date = {2008-12-01},

journal = {Nature Immunology},

volume = {9},

number = {12},

pages = {1425--1432},

abstract = {Drosophila, like other invertebrates and plants, relies mainly on RNA interference for its defense against viruses. In flies, viral infection also triggers the expression of many genes. One of the genes induced, Vago, encodes a 18-kilodalton cysteine-rich polypeptide. Here we provide genetic evidence that the Vago gene product controlled viral load in the fat body after infection with drosophila C virus. Induction of Vago was dependent on the helicase Dicer-2. Dicer-2 belongs to the same DExD/H-box helicase family as do the RIG-I-like receptors, which sense viral infection and mediate interferon induction in mammals. We propose that this family represents an evolutionary conserved set of sensors that detect viral nucleic acids and direct antiviral responses.},

keywords = {Amino Acid, Animals, Electrophoresis, Fat Body, Gene Expression Regulation, Genetic, Genetically Modified, hoffmann, Humans, imler, M3i, matt, Phylogeny, Polyacrylamide Gel, Reverse Transcriptase Polymerase Chain Reaction, Ribonuclease III, RNA Helicases, Sequence Homology, Transcription, Virus Diseases},

pubstate = {published},

tppubtype = {article}

}

@article{bringel_lactobacillus_2008,

title = {Lactobacillus plantarum response to inorganic carbon concentrations: PyrR2-dependent and -independent transcription regulation of genes involved in arginine and nucleotide metabolism.},

author = {Françoise Bringel and Philippe Hammann and Valérie Kugler and Florence Arsène-Ploetze},

doi = {10.1099/mic.0.2008/018184-0},

issn = {1350-0872 1350-0872},

year  = {2008},

date = {2008-09-01},

journal = {Microbiology (Reading, England)},

volume = {154},

number = {Pt 9},

pages = {2629--2640},

abstract = {Lactobacillus plantarum susbp. plantarum is a capnophilic Gram-positive heterotroph with optimal growth in 4 % CO(2)-enriched air. At low inorganic carbon (C(i)) concentrations, the pyr genes encoding the enzymes of the pyrimidine biosynthetic pathway were overexpressed, in agreement with a previous study showing that these genes are regulated at the transcription level in response to C(i) via a PyrR(2)-mediated mechanism. A previous study of high-CO(2)-requiring (HCR) mutants revealed an unknown genetic link between arginine regulation and C(i)-dependent nutritional needs. To better understand L. plantarum's adaptation to C(i) availability, additional C(i)-responsive genes were sought in the arginine biosynthetic pathway (arg and car genes) using slot-blot hybridization and a proteomic differential 2D gel electrophoresis (DIGE) global approach. Besides the nine pyr-encoded proteins, 16 new Icr (inorganic-carbon-regulated) proteins accumulated differentially in response to C(i) availability, suggesting that the C(i) response involves several metabolic pathways and adaptation processes. Among these Icr proteins only argininosuccinate lyase, encoded by argH, was involved in arginine biosynthesis. Three proteins involved in the purine biosynthetic pathway and nucleotide conversion, adenylate kinase (Adk), GMP synthase (GuaA), and IMP dehydrogenase (GuaB), accumulated differentially in response to changes in C(i) levels. Expression of the Icr protein-encoding genes argH and guaB was regulated at the transcription level or by RNA stability in response to C(i) availability, as previously demonstrated for the pyr genes. However, PyrR(2) was not essential for the C(i)-regulated transcription of argH and guaB, demonstrating that PyrR(2) modulates only a subset of C(i)-regulated genes. These results suggest that the C(i) response may involve at least two regulatory mechanisms in L. plantarum.},

note = {Place: England},

keywords = {Arginine/*biosynthesis, Argininosuccinate Lyase/genetics, Bacterial, Bacterial Proteins/*genetics, Bacterial/genetics, Carbon Compounds, Carbon Dioxide/metabolism, Electrophoresis, Gel, Gene Expression Regulation, Genetic, IMP Dehydrogenase/genetics, Inorganic/*metabolism, Lactobacillus plantarum/enzymology/genetics/*metabolism, Mass, Matrix-Assisted Laser Desorption-Ionization, Nucleotides/*biosynthesis, Pentosyltransferases/*genetics, PPSE, proteomics, Repressor Proteins/*genetics, Reverse Transcriptase Polymerase Chain Reaction, RNA, Spectrometry, Transcription, Two-Dimensional},

pubstate = {published},

tppubtype = {article}

}

@article{roetzer_candida_2008b,

title = {Candida glabrata environmental stress response involves Saccharomyces cerevisiae Msn2/4 orthologous transcription factors},

author = {Andreas Roetzer and Christa Gregori and Ann Marie Jennings and Jessica Quintin and Dominique Ferrandon and Geraldine Butler and Karl Kuchler and Gustav Ammerer and Christoph Schüller},

doi = {10.1111/j.1365-2958.2008.06301.x},

issn = {1365-2958},

year  = {2008},

date = {2008-01-01},

journal = {Mol. Microbiol.},

volume = {69},

number = {3},

pages = {603--620},

abstract = {We determined the genome-wide environmental stress response (ESR) expression profile of Candida glabrata, a human pathogen related to Saccharomyces cerevisiae. Despite different habitats, C. glabrata, S. cerevisiae, Schizosaccharomyces pombe and Candida albicans have a qualitatively similar ESR. We investigate the function of the C. glabrata syntenic orthologues to the ESR transcription factor Msn2. The C. glabrata orthologues CgMsn2 and CgMsn4 contain a motif previously referred to as HD1 (homology domain 1) also present in Msn2 orthologues from fungi closely related to S. cerevisiae. We show that regions including this motif confer stress-regulated intracellular localization when expressed in S. cerevisiae. Site-directed mutagenesis confirms that nuclear export of CgMsn2 in C. glabrata requires an intact HD1. Transcript profiles of CgMsn2/4 mutants and CgMsn2 overexpression strains show that they regulate a part of the CgESR. CgMsn2 complements a S. cerevisiae msn2 null mutant and in stressed C. glabrata cells, rapidly translocates from the cytosol to the nucleus. CgMsn2 is required for full resistance against severe osmotic stress and rapid and full induction of trehalose synthesis genes (TPS1, TPS2). Constitutive activation of CgMsn2 is detrimental for C. glabrata. These results establish an Msn2-regulated general stress response in C. glabrata.},

keywords = {Animals, Candida glabrata, Candidiasis, DNA-Binding Proteins, ferrandon, Fungal, Fungal Proteins, Gene Expression Profiling, Gene Expression Regulation, Genetic, Humans, M3i, Oligonucleotide Array Sequence Analysis, Osmotic Pressure, Regulon, Saccharomyces cerevisiae Proteins, Transcription, Transcription Factors, Virulence, Yeasts},

pubstate = {published},

tppubtype = {article}

}