167 results on '"Kramer, Susanne"'
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2. Is mRNA decapping by ApaH like phosphatases present in eukaryotes beyond the Kinetoplastida?
- Author
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Castañeda Londoño, Paula Andrea, Banholzer, Nicole, Bannermann, Bridget, and Kramer, Susanne
- Published
- 2021
- Full Text
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3. Faster Sensitivity Loss around Dense Scotomas than for Overall Macular Sensitivity in Stargardt Disease: ProgStar Report No. 14
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Scholl, Hendrik P.N., Strauss, Rupert W., Wolfson, Yulia, Bittencourt, Millena, Shah, Syed Mahmood, Ahmed, Mohamed, Schönbach, Etienne, Fujinami, Kaoru, Traboulsi, Elias, Ehlers, Justis, Marino, Meghan, Crowe, Susan, Briggs, Rachael, Borer, Angela, Pinter, Anne, Fecko, Tami, Burgnoni, Nikki, Sunness, Janet S., Applegate, Carol, Russell, Leslie, Michaelides, Michel, Degli Esposti, Simona, Moore, Anthony, Webster, Andrew, Connor, Sophie, Barnfield, Jade, Salchi, Zaid, Alfageme, Clara, McCudden, Victoria, Pefkianaki, Maria, Aboshiha, Jonathan, Liew, Gerald, Holder, Graham, Robson, Anthony, King, Alexa, Cajas Narvaez, Daniela Ivanova, Barnard, Katy, Grigg, Catherine, Dunbar, Hannah, Obadeyi, Yetunde, Girard-Claudon, Karine, Swann, Hilary, Rughani, Avani, Amoah, Charles, Carrington, Dominic, Bibi, Kanom, Ting, Emerson, Illiyas, Mohamed Nafaz, Begum, Hamida, Carter, Andrew, Georgiou, Anne, Lewism, Selma, Shaheen, Saddaf, Shinmar, Harpreet, Burton, Linda, Bernstein, Paul, Wegner, Kimberley, Sawyer, Briana Lauren, Carlstrom, Bonnie, Farnsworth, Kellian, Fry, Cyrie, Chandler, Melissa, Jenkins, Glen, Creel, Donnel, Birch, David, Wang, Yi-Zhong, Rodriguez, Luis, Locke, Kirsten, Klein, Martin, Mejia, Paulina, Cideciyan, Artur V., Jacobson, Samuel G., Schwartz, Sharon B., Matsui, Rodrigo, Gruzensky, Michaela, Charng, Jason, Roman, Alejandro J., Zrenner, Eberhart, Nasser, Fadi, Hahn, Gesa Astrid, Wilhelm, Barbara, Peters, Tobias, Beier, Benjamin, Koenig, Tilman, Kramer, Susanne, Sahel, José-Alain, Mohand-Said, Saddek, Audo, Isabelle, Laurent-Coriat, Caroline, Sliesoraityte, Ieva, Zeitz, Christina, Boyard, Fiona, Tran, Minh Ha, Chapon, Mathias, Chaumette, Céline, Amaudruz, Juliette, Ganem, Victoria, Sancho, Serge, Girmens, Aurore, Wojciechowski, Robert, Khan, Shazia, Emmert, David G., Cain, Dennis, Herring, Mark, Bassinger, Jennifer, Liberto, Lisa, West, Sheila, Ervin, Ann-Margret, Munoz, Beatriz, Kong, Xiangrong, Dreger, Kurt, Jones, Jennifer, Sadda, Srinivas, Ip, Michael S., Jha, Anamika, Ho, Alex, Kramer, Brendan, Lam, Ngoc, Tawdros, Rita, Zhou, Yong Dong, Carmona, Johana, Uji, Akihito, Hariri, Amirhossein, Lock, Amy, Elshafei, Anthony, Ganegoda, Anushika, Petrossian, Christine, Jenkins, Dennis, Strnad, Edward, Baghdasaryan, Elmira, Ito, Eric, Samson, Feliz, Blanquel, Gloria, Akil, Handan, Melendez, Jhanisus, Lei, Jianqin, Huang, Jianyan, Chau, Jonathan, Falavarjani, Khalil G., Espino, Kristina, Li, Manfred, Mendoza, Maria, Nittala, Muneeswar Gupta, Roded, Netali, Saleh, Nizar, Huang, Ping, Pitetta, Sean, Balasubramanian, Siva, Leahy, Sophie, Srinivas, Sowmya J., Velaga, Swetha B., Margaryan, Teresa, Tepelus, Tudor, Brown, Tyler, Fan, Wenying, Murillo, Yamileth, Shi, Yue, Aguilar, Katherine, Chan, Cynthia, Santos, Lisa, Seo, Brian, Sison, Christopher, Perez, Silvia, Chao, Stephanie, Miyasato, Kelly, Higgins, Julia, Luna, Zoila, Menchaca, Anita, Gonzalez, Norma, Robledo, Vicky, Carig, Karen, Baker, Kirstie, Ellenbogen, David, Bluemel, Daniel, Sanford, Theo, Linares, Daisy, Tran, Mei, Nava, Lorane, Oberoi, Michelle, Romero, Mark, Chiguil, Vivian, Bynum-Bain, Grantley, Kim, Monica, Mendiguren, Carolina, Huang, Xiwen, Smith, Monika, Sarreal, Natalie, Schönbach, Etienne M., Ibrahim, Mohamed A., Janes, Jessica L., Birch, David G., Muñoz, Beatriz, and Sadda, SriniVas R.
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- 2020
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4. Small but active — pool size does not matter for carbon incorporation in below-ground food webs
- Author
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Pausch, Johanna, Kramer, Susanne, Scharroba, Anika, Scheunemann, Nicole, Butenschoen, Olaf, Kandeler, Ellen, Marhan, Sven, Riederer, Michael, Scheu, Stefan, Kuzyakov, Yakov, and Ruess, Liliane
- Published
- 2016
5. Nucleoside analogue activators of cyclic AMP-independent protein kinase A of Trypanosoma
- Author
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Bachmaier, Sabine, Volpato Santos, Yuri, Kramer, Susanne, Githure, George Boniface, Klöckner, Thomas, Pepperl, Julia, Baums, Cordula, Schenk, Robin, Schwede, Frank, Genieser, Hans-Gottfried, Dupuy, Jean-William, Forné, Ignasi, Imhof, Axel, Basquin, Jerôme, Lorentzen, Esben, and Boshart, Michael
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- 2019
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6. A unique mRNA decapping complex in trypanosomes.
- Author
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Kramer, Susanne, Karolak, Natalia Katarzyna, Odenwald, Johanna, Gabiatti, Bernardo, Castañeda Londoño, Paula Andrea, Zavřelová, Anna, Freire, Eden Ribeiro, Almeida, Kayo Schemiko, Braune, Silke, Moreira, Claudia, Eder, Amelie, Goos, Carina, Field, Mark, Carrington, Mark, Holetz, Fabiola, Górna, Maria Wiktoria, and Zoltner, Martin
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- 2023
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7. Resource Type and Availability Regulate Fungal Communities Along Arable Soil Profiles
- Author
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Moll, Julia, Goldmann, Kezia, Kramer, Susanne, Hempel, Stefan, Kandeler, Ellen, Marhan, Sven, Ruess, Liliane, Krüger, Dirk, and Buscot, Francois
- Published
- 2015
8. Imaging-Based Assay for Identification and Characterization of Inhibitors of CXCR4-Tropic HIV-1 Envelope-Dependent Cell-Cell Fusion
- Author
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Kramer, Susanne, Buontempo, Peter, Agrawal, Sony, and Ralston, Robert
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- 2011
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9. Trans-acting proteins regulating mRNA maturation, stability and translation in trypanosomatids
- Author
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Kramer, Susanne and Carrington, Mark
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- 2011
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10. Parallel monitoring of RNA abundance, localization and compactness with correlative single molecule FISH on LR White embedded samples
- Author
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Kramer, Susanne, Meyer-Natus, Elisabeth, Stigloher, Christian, Thoma, Hanna, Schnaufer, Achim, and Engstler, Markus
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RNA, Spliced Leader ,AcademicSubjects/SCI00010 ,Trypanosoma brucei brucei ,Fluorescent Antibody Technique ,Microscopy, Electron ,ddc:570 ,Methods Online ,Animals ,RNA Editing ,RNA, Messenger ,RNA, Helminth ,Caenorhabditis elegans ,In Situ Hybridization, Fluorescence ,RNA, Protozoan - Abstract
Single mRNA molecules are frequently detected by single molecule fluorescence in situ hybridization (smFISH) using branched DNA technology. While providing strong and background-reduced signals, the method is inefficient in detecting mRNAs within dense structures, in monitoring mRNA compactness and in quantifying abundant mRNAs. To overcome these limitations, we have hybridized slices of high pressure frozen, freeze-substituted and LR White embedded cells (LR White smFISH). mRNA detection is physically restricted to the surface of the resin. This enables single molecule detection of RNAs with accuracy comparable to RNA sequencing, irrespective of their abundance, while at the same time providing spatial information on RNA localization that can be complemented with immunofluorescence and electron microscopy, as well as array tomography. Moreover, LR White embedding restricts the number of available probe pair recognition sites for each mRNA to a small subset. As a consequence, differences in signal intensities between RNA populations reflect differences in RNA structures, and we show that the method can be employed to determine mRNA compactness. We apply the method to answer some outstanding questions related to trans-splicing, RNA granules and mitochondrial RNA editing in single-cellular trypanosomes and we show an example of differential gene expression in the metazoan Caenorhabditis elegans.
- Published
- 2021
11. A novel SNF2 ATPase complex in Trypanosoma brucei with a role in H2A.Z-mediated chromatin remodelling.
- Author
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Vellmer, Tim, Hartleb, Laura, Fradera Sola, Albert, Kramer, Susanne, Meyer-Natus, Elisabeth, Butter, Falk, and Janzen, Christian J.
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TRYPANOSOMA brucei ,CHROMATIN ,ADENOSINE triphosphatase ,CHROMATIN-remodeling complexes ,AFRICAN trypanosomiasis ,GENETIC transcription regulation - Abstract
A cascade of histone acetylation events with subsequent incorporation of a histone H2A variant plays an essential part in transcription regulation in various model organisms. A key player in this cascade is the chromatin remodelling complex SWR1, which replaces the canonical histone H2A with its variant H2A.Z. Transcriptional regulation of polycistronic transcription units in the unicellular parasite Trypanosoma brucei has been shown to be highly dependent on acetylation of H2A.Z, which is mediated by the histone-acetyltransferase HAT2. The chromatin remodelling complex which mediates H2A.Z incorporation is not known and an SWR1 orthologue in trypanosomes has not yet been reported. In this study, we identified and characterised an SWR1-like remodeller complex in T. brucei that is responsible for Pol II-dependent transcriptional regulation. Bioinformatic analysis of potential SNF2 DEAD/Box helicases, the key component of SWR1 complexes, identified a 1211 amino acids-long protein that exhibits key structural characteristics of the SWR1 subfamily. Systematic protein-protein interaction analysis revealed the existence of a novel complex exhibiting key features of an SWR1-like chromatin remodeller. RNAi-mediated depletion of the ATPase subunit of this complex resulted in a significant reduction of H2A.Z incorporation at transcription start sites and a subsequent decrease of steady-state mRNA levels. Furthermore, depletion of SWR1 and RNA-polymerase II (Pol II) caused massive chromatin condensation. The potential function of several proteins associated with the SWR1-like complex and with HAT2, the key factor of H2A.Z incorporation, is discussed. Author summary: Trypanosoma brucei is the causative agent of African trypanosomiasis (sleeping sickness) in humans and nagana in cattle. Its unusual genomic organisation featuring large polycistronic units requires a general mechanism of transcription initiation, because individual gene promoters are mostly absent. Despite the fact that the histone variant H2A.Z has previously been identified as a key player of transcription regulation, the complex responsible for correct H2A.Z incorporation at transcription start sites (TSS) remains elusive. In other eukaryotes, SWR1, a SNF2 ATPase-associated chromatin remodelling complex, is responsible for correct incorporation of this histone variant. This study identified a SWR1-like complex in T. brucei. Depletion of the SNF2 ATPase resulted in a reduction of H2A.Z incorporation at the TSS and decreased steady-state mRNA levels accompanied by chromatin condensation. In addition to the SWR1-like complex, we also identified a trypanosome-specific HAT2 complex that includes the histone acetyltransferases HAT2, a key player in the H2A.Z incorporation process. This complex has a trypanosome-specific composition that is different from the NuA4/TIP60 complex in Saccharomyces cerevisiae. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
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12. How do trypanosomes change gene expression in response to the environment?
- Author
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Schwede, Angela, Kramer, Susanne, and Carrington, Mark
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- 2012
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13. Uptake of deoxynivalenol by earthworms from Fusarium-infected wheat straw
- Author
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Schrader, Stefan, Kramer, Susanne, Oldenburg, Elisabeth, and Weinert, Joachim
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- 2009
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14. Nocathiacin, Thiazomycin, and Polar Analogs Are Highly Effective Agents against Toxigenic Clostridioides difficile.
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Singh, Sheo B., Miesel, Lynn, Kramer, Susanne, Xu, Libo, Li, Fangbio, Lan, Jing, Lipari, Phillip, Polishook, Jon D., Liu, Gongjie, Liang, Lianzhu, and Flattery, Amy M.
- Published
- 2022
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15. Visual Evoked Potentials Used to Evaluate a Commercially Available Superabsorbent Polymer as a Cheap and Efficient Material for Preparation-Free Electrodes for Recording Electrical Potentials of the Human Visual Cortex
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Straßer, Torsten, Kramer, Susanne, Kempf, Melanie, Peters, Tobias, Kurtenbach, Anne, and Zrenner, Eberhart
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genetic structures ,Polymers ,superabsorbent polymer gel ,lcsh:Chemical technology ,Article ,visual electrophysiology ,Electrodes, Implanted ,Electrophysiology ,biomedical electrodes ,brain–computer interfaces ,Evoked Potentials, Visual ,Humans ,lcsh:TP1-1185 ,Visual Cortex - Abstract
The aim of this study was to investigate the use of inexpensive and easy-to-use hydrogel &ldquo, marble&rdquo, electrodes for the recording of electrical potentials of the human visual cortex using visual evoked potentials (VEPs) as example. Top hat-shaped holders for the marble electrodes were developed with an electrode cap to acquire the signals. In 12 healthy volunteers, we compared the VEPs obtained with conventional gold-cup electrodes to those obtained with marble electrodes. Checkerboards of two check sizes&mdash, 0.8°, and 0.25°, &mdash, were presented. Despite the higher impedance of the marble electrodes, the line noise could be completely removed by averaging 64 single traces, and VEPs could be recorded. Linear mixed-effect models using electrode type, stimulus, and recording duration revealed a statistically significant effect of the electrode type on only VEP N75 peak latency (mean ±, SEM: 1.0 ±, 1.2 ms) and amplitude (mean ±, SEM: 0.8 ±, 0.9 µ, V) The mean amplitudes of the delta, theta, alpha, beta, and gamma frequency bands of marble electrodes were statistically significantly different and, on average, 25% higher than those of gold-cup electrodes. However, the mean amplitudes showed a statistically significant strong correlation (Pearson&rsquo, s r = 0.8). We therefore demonstrate the potential of the inexpensive and efficient hydrogel electrode to replace conventional gold-cup electrodes for the recording of VEPs and possibly other recordings from the human cortex.
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- 2019
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16. Control of HIV replication in astrocytes by a family of highly conserved host proteins with a common Rev-interacting domain (Risp)
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Vincendeau, Michelle, Kramer, Susanne, Hadian, Kamyar, Rothenaigner, Ina, Bell, Jeanne, Hauck, Stefanie M, Bickel, Christian, Nagel, Daniel, Kremmer, Elisabeth, Werner, Thomas, Leib-Mösch, Christine, and Brack-Werner, Ruth
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- 2010
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17. The nucleolar DExD/H protein Hel66 is involved in ribosome biogenesis in Trypanosoma brucei.
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Bakari-Soale, Majeed, Ikenga, Nonso Josephat, Scheibe, Marion, Butter, Falk, Jones, Nicola G., Kramer, Susanne, and Engstler, Markus
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ORGANELLE formation ,TRYPANOSOMA brucei ,RIBOSOMAL RNA ,KINETOPLASTIDA ,NUCLEOLUS - Abstract
The biosynthesis of ribosomes is a complex cellular process involving ribosomal RNA, ribosomal proteins and several further trans-acting factors. DExD/H box proteins constitute the largest family of trans-acting protein factors involved in this process. Several members of this protein family have been directly implicated in ribosome biogenesis in yeast. In trypanosomes, ribosome biogenesis differs in several features from the process described in yeast. Here, we have identified the DExD/H box helicase Hel66 as being involved in ribosome biogenesis. The protein is unique to Kinetoplastida, localises to the nucleolus and its depletion via RNAi caused a severe growth defect. Loss of the protein resulted in a decrease of global translation and accumulation of rRNA processing intermediates for both the small and large ribosomal subunits. Only a few factors involved in trypanosome rRNA biogenesis have been described so far and our findings contribute to gaining a more comprehensive picture of this essential process. [ABSTRACT FROM AUTHOR]
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- 2021
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18. Trypanosomes can initiate nuclear export co-transcriptionally
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Goos, Carina, Dejung, Mario, Wehman, Ann M., M-Natus, Elisabeth, Schmidt, Johannes, Sunter, Jack, Engstler, Markus, Butter, Falk, and Kramer, Susanne
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ddc:570 - Abstract
The nuclear envelope serves as important messenger RNA (mRNA) surveillance system. In yeast and human, several control systems act in parallel to prevent nuclear export of unprocessed mRNAs. Trypanosomes lack homologues to most of the involved proteins and their nuclear mRNA metabolism is non-conventional exemplified by polycistronic transcription and mRNA processing by trans-splicing. We here visualized nuclear export in trypanosomes by intra- and intermolecular multi-colour single molecule FISH. We found that, in striking contrast to other eukaryotes, the initiation of nuclear export requires neither the completion of transcription nor splicing. Nevertheless, we show that unspliced mRNAs are mostly prevented from reaching the nucleus-distant cytoplasm and instead accumulate at the nuclear periphery in cytoplasmic nuclear periphery granules (NPGs). Further characterization of NPGs by electron microscopy and proteomics revealed that the granules are located at the cytoplasmic site of the nuclear pores and contain most cytoplasmic RNA-binding proteins but none of the major translation initiation factors, consistent with a function in preventing faulty mRNAs from reaching translation. Our data indicate that trypanosomes regulate the completion of nuclear export, rather than the initiation. Nuclear export control remains poorly understood, in any organism, and the described way of control may not be restricted to trypanosomes.
- Published
- 2019
19. Long-term HIV-1 infection of neural progenitor populations
- Author
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Rothenaigner, Ina, Kramer, Susanne, Ziegler, Manja, Wolff, Horst, Kleinschmidt, Andrea, and Brack-Werner, Ruth
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- 2007
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20. Trypanosoma brucei Polo-like kinase is essential for basal body duplication, kDNA segregation and cytokinesis
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Hammarton, Tansy C., Kramer, Susanne, Tetley, Laurence, Boshart, Michael, and Mottram, Jeremy C.
- Published
- 2007
21. Epstein–Barr virus associated acute retinal necrosis
- Author
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KRAMER, SUSANNE, BRUMMER, CHRISTOF, and ZIERHUT, MANFRED
- Published
- 2001
22. Comparative proteomics of the two T. brucei PABPs suggests that PABP2 controls bulk mRNA
- Author
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Zoltner, Martin, Krienitz, Nina, Field, Mark C., and Kramer, Susanne
- Subjects
Proteomics ,Trypanosoma ,Cell Physiology ,lcsh:Arctic medicine. Tropical medicine ,lcsh:RC955-962 ,Trypanosoma brucei brucei ,Protozoan Proteins ,Gene Expression ,Fractional Precipitation ,RNA-binding proteins ,Research and Analysis Methods ,Poly(A)-Binding Protein I ,Poly(A)-Binding Protein II ,Biochemistry ,Cell Fusion ,Genetics ,Trypanosoma Brucei ,ddc:610 ,RNA, Messenger ,Protozoans ,Translation Initiation ,Salting Out ,Messenger RNA ,lcsh:Public aspects of medicine ,Organisms ,Biology and Life Sciences ,Eukaryota ,Proteins ,lcsh:RA1-1270 ,Cell Biology ,Parasitic Protozoans ,Precipitation Techniques ,Nucleic acids ,Eukaryotic Initiation Factor-4E ,RNA ,Protein Translation ,Protein Binding ,Research Article ,Trypanosoma Brucei Gambiense - Abstract
Poly(A)-binding proteins (PABPs) regulate mRNA fate by controlling stability and translation through interactions with both the poly(A) tail and eIF4F complex. Many organisms have several paralogs of PABPs and eIF4F complex components and it is likely that different eIF4F/PABP complex combinations regulate distinct sets of mRNAs. Trypanosomes have five eIF4G paralogs, six of eIF4E and two PABPs, PABP1 and PABP2. Under starvation, polysomes dissociate and the majority of mRNAs, most translation initiation factors and PABP2 reversibly localise to starvation stress granules. To understand this more broadly we identified a protein interaction cohort for both T. brucei PABPs by cryo-mill/affinity purification-mass spectrometry. PABP1 very specifically interacts with the previously identified interactors eIF4E4 and eIF4G3 and few others. In contrast PABP2 is promiscuous, with a larger set of interactors including most translation initiation factors and most prominently eIF4G1, with its two partners TbG1-IP and TbG1-IP2. Only RBP23 was specific to PABP1, whilst 14 RNA-binding proteins were exclusively immunoprecipitated with PABP2. Significantly, PABP1 and associated proteins are largely excluded from starvation stress granules, but PABP2 and most interactors translocate to granules on starvation. We suggest that PABP1 regulates a small subpopulation of mainly small-sized mRNAs, as it interacts with a small and distinct set of proteins unable to enter the dominant pathway into starvation stress granules and localises preferentially to a subfraction of small polysomes. By contrast PABP2 likely regulates bulk mRNA translation, as it interacts with a wide range of proteins, enters stress granules and distributes over the full range of polysomes., Author summary Poly(A)-binding proteins (PABPs) bind to the poly(A) tails of eukaryotic mRNAs and function in regulating mRNA fate. Many eukaryotes have several PABP paralogs and the current view is that each PABP binds a specific subset of mRNAs. Trypanosoma brucei has two PABPs, and to understand the differential functionality of these paralogs we identified interacting proteins for each. We found unique interactors for both PABPs, and significant differences between the two interaction cohorts. Our data indicate that the two PABP paralogs of trypanosomes have very distinct roles in mediating mRNA fate.
- Published
- 2018
23. Nuclear mRNA maturation and mRNA export control: from trypanosomes to opisthokonts.
- Author
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Kramer, Susanne
- Subjects
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EXPORT controls , *TRYPANOSOMA brucei , *TRYPANOSOMA , *RNA - Abstract
The passage of mRNAs through the nuclear pores into the cytoplasm is essential in all eukaryotes. For regulation, mRNA export is tightly connected to the full machinery of nuclear mRNA processing, starting at transcription. Export competence of pre-mRNAs gradually increases by both transient and permanent interactions with multiple RNA processing and export factors. mRNA export is best understood in opisthokonts, with limited knowledge in plants and protozoa. Here, I review and compare nuclear mRNA processing and export between opisthokonts and Trypanosoma brucei. The parasite has many unusual features in nuclear mRNA processing, such as polycistronic transcription and trans-splicing. It lacks several nuclear complexes and nuclear-pore-associated proteins that in opisthokonts play major roles in mRNA export. As a consequence, trypanosome mRNA export control is not tight and export can even start co-transcriptionally. Whether trypanosomes regulate mRNA export at all, or whether leakage of immature mRNA to the cytoplasm is kept to a low level by a fast kinetics of mRNA processing remains to be investigated. mRNA export had to be present in the last common ancestor of eukaryotes. Trypanosomes are evolutionary very distant from opisthokonts and a comparison helps understanding the evolution of mRNA export. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
24. Genome-wide in silico screen for CCCH-type zinc finger proteins of Trypanosoma brucei, Trypanosoma cruzi and Leishmania major
- Author
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Carrington Mark, Kimblin Nicola C, and Kramer Susanne
- Subjects
Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background CCCH type zinc finger proteins are RNA binding proteins with regulatory functions at all stages of mRNA metabolism. The best-characterized member, tritetraproline (TTP), binds to AU rich elements in 3' UTRs of unstable mRNAs, mediating their degradation. In kinetoplastids, CCCH type zinc finger proteins have been identified as being involved in the regulation of the life cycle and possibly the cell cycle. To date, no systematic listing of CCCH proteins in kinetoplastids is available. Results We have identified the complete set of CCCH type zinc finger proteins in the available genomes of the kinetoplastid protozoa Trypanosoma brucei, Trypanosoma cruzi and Leishmania major. One fifths (20%) of all CCCH motifs fall into non-conventional classes and many had not been previously identified. One third of all CCCH proteins have more than one CCCH motif, suggesting multivalent RNA binding. One third have additional recognizable domains. The vast majority are unique to Kinetoplastida or to a subgroup within. Two exceptions are of interest: the putative orthologue of the mRNA nuclear export factor Mex67 and a 3'-5' exoribonuclease restricted to Leishmania species. CCCH motifs are absent from these proteins in other organisms and might be unique, novel features of the Kinetoplastida homologues. Of the others, several have a predicted, and in one case experimentally confirmed, connection to the ubiquitination pathways, for instance a HECT-type E3 ubiquitin ligase. The total number of kinetoplastid CCCH proteins is similar to the number in higher eukaryotes but lower than in yeast. A comparison of the genomic loci between the Trypanosomatidae homologues provides insight into both the evolution of the CCCH proteins as well as the CCCH motifs. Conclusion This study provides the first systematic listing of the Kinetoplastida CCCH proteins. The number of CCCH proteins with more then one CCCH motif is larger than previously estimated, due to the identification of non-conventional CCCH motifs. Experimental approaches are now necessary to examine the functions of the many unique CCCH proteins as well as the function of the putative Mex67 and the Leishmania 3'-5' exoribonuclease.
- Published
- 2010
- Full Text
- View/download PDF
25. A quorum sensing-independent path to stumpy development in Trypanosoma brucei
- Author
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Zimmermann, Henriette, Subota, Ines, Batram, Christopher, Kramer, Susanne, Janzen, Christian J., Jones, Nicola G., and Engstler, Markus
- Subjects
Life Cycles ,Disease Vectors ,Parasitic Cell Cycles ,Antibiotics ,Medicine and Health Sciences ,Cell Cycle and Cell Division ,lcsh:QH301-705.5 ,Mammals ,Staining ,Membrane Glycoproteins ,Antimicrobials ,Quorum Sensing ,Drugs ,Cell Differentiation ,Antigenic Variation ,Specimen preparation and treatment ,Insects ,Infectious Diseases ,Cell Processes ,Tetracyclines ,Hyperexpression Techniques ,Variant Surface Glycoproteins, Trypanosoma ,Research Article ,lcsh:Immunologic diseases. Allergy ,Glossina ,Tsetse Flies ,Arthropoda ,Tsetse Fly ,Parasitic Life Cycles ,Trypanosoma brucei brucei ,Research and Analysis Methods ,Microbiology ,Microbial Control ,Gene Expression and Vector Techniques ,Parasitic Diseases ,Animals ,ddc:610 ,Molecular Biology Techniques ,Molecular Biology ,Pharmacology ,Molecular Biology Assays and Analysis Techniques ,DAPI staining ,Organisms ,Biology and Life Sciences ,Cell Biology ,Invertebrates ,Insect Vectors ,Species Interactions ,Trypanosomiasis, African ,Gene Expression Regulation ,lcsh:Biology (General) ,Nuclear staining ,Parasitology ,lcsh:RC581-607 ,Developmental Biology ,Cloning - Abstract
For persistent infections of the mammalian host, African trypanosomes limit their population size by quorum sensing of the parasite-excreted stumpy induction factor (SIF), which induces development to the tsetse-infective stumpy stage. We found that besides this cell density-dependent mechanism, there exists a second path to the stumpy stage that is linked to antigenic variation, the main instrument of parasite virulence. The expression of a second variant surface glycoprotein (VSG) leads to transcriptional attenuation of the VSG expression site (ES) and immediate development to tsetse fly infective stumpy parasites. This path is independent of SIF and solely controlled by the transcriptional status of the ES. In pleomorphic trypanosomes varying degrees of ES-attenuation result in phenotypic plasticity. While full ES-attenuation causes irreversible stumpy development, milder attenuation may open a time window for rescuing an unsuccessful antigenic switch, a scenario that so far has not been considered as important for parasite survival., Author summary African trypanosomes escape the mammalian host’s immune system by antigenic variation of their variant surface glycoprotein (VSG) coat. VSGs are expressed from a specialized region in the genome, the expression site (ES), that contains essential expression site associated genes (ESAGs). So far, it was assumed that only successful antigenic switches to an intact expression site are viable. Here we show that unsuccessful VSG switches are not a dead-end, but may rather contribute to the persistence of the trypanosomes at the population level. We have simulated an unsuccessful VSG switch in pleomorphic trypanosomes by expression of a second VSG from a locus without ESAGs. The parasites responded with surprising phenotypic plasticity. All parasites immediately exchanged the surface coat and reduced the abundance of ES-derived transcripts. However, depending on the degree of ES-attenuation, the transgenic trypanosomes either resumed growth, or stopped proliferation. We show that the growth-arrested populations synchronously differentiate to the stumpy life cycle stage and become infective for the tsetse fly. This occurs at low cell densities and in the absence of the quorum sensing factor SIF. Thus, unsuccessful VSG switches are not lethal and cell density-dependent quorum sensing is not the only path to the tsetse fly competence.
- Published
- 2017
26. Simultaneous detection of mRNA transcription and decay intermediates by dual colour single mRNA FISH on subcellular resolution
- Author
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Kramer, Susanne
- Subjects
Cell Nucleus ,Cytoplasm ,Mice ,Transcription, Genetic ,RNA Stability ,ddc:570 ,Trypanosoma brucei brucei ,NIH 3T3 Cells ,Methods Online ,Animals ,RNA, Messenger ,In Situ Hybridization, Fluorescence - Abstract
The detection of mRNAs undergoing transcription or decay is challenging, because both processes are fast. However, the relative proportion of an mRNA in synthesis or decay increases with mRNA size and decreases with mRNA half-life. Based on this rationale, I have exploited a 22 200 nucleotide-long, short-lived endogenous mRNA as a reporter for mRNA metabolism in trypanosomes. The extreme 5΄ and 3΄ ends were labeled with red- and green-fluorescent Affymetrix® single mRNA FISH probes, respectively. In the resulting fluorescence images, yellow spots represent intact mRNAs; red spots are mRNAs in transcription or 3΄-5΄ decay, and green spots are mRNAs in 5΄-3΄ degradation. Most red spots were nuclear and insensitive to transcriptional inhibition and thus likely transcription intermediates. Most green spots were cytoplasmic, confirming that the majority of cytoplasmic decay in trypanosomes is 5΄-3΄. The system showed the expected changes at inhibition of transcription or translation and RNAi depletion of the trypanosome homologue to the 5΄-3΄ exoribonuclease Xrn1. The method allows to monitor changes in mRNA metabolism both on cellular and on population/tissue wide levels, but also to study the subcellular localization of mRNA transcription and decay pathways. I show that the system is applicable to mammalian cells.
- Published
- 2016
27. Polycistronic trypanosome mRNAs are a target for the exosome
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Kramer, Susanne, Piper, Sophie, Estevez, Antonio, Carrington, Mark, German Research Foundation, Wellcome Trust, Ministerio de Economía y Competitividad (España), Estévez, Antonio M., Carrington, Mark, Carrington, Mark [0000-0002-6435-7266], Apollo - University of Cambridge Repository, and Estévez, Antonio M. [0000-0002-8272-5405]
- Subjects
Cell Nucleus ,trans-splicing ,Exosome Multienzyme Ribonuclease Complex ,Short Communication ,Trypanosoma brucei brucei ,Exosome ,ddc:570 ,Trypanosomes ,Polycistronic mRNA ,NMD ,Parasitology ,Trypanosoma brucei ,RNA, Messenger ,Molecular Biology ,RNA, Protozoan ,ComputingMethodologies_COMPUTERGRAPHICS - Abstract
Eukaryotic cells have several mRNA quality control checkpoints to avoid the production of aberrant proteins. Intron-containing mRNAs are actively degraded by the nuclear exosome, prevented from nuclear exit and, if these systems fail, degraded by the cytoplasmic NMD machinery. Trypanosomes have only two introns. However, they process mRNA5 from long polycistronic precursors by trans-splicing and polycistronic mRNA molecules frequently arise from any missed splice site. Here, we show that RNAi depletion of the trypanosome exosome, but not of the cytoplasmic 5'-3' exoribonuclease XRNA or the NMD helicase UPF1, causes accumulation of oligocistronic mRNA5. We have also revisited the localization of the trypanosome exosome by expressing eYFP-fusion proteins of the exosome subunits RRP44 and RRP6. Both proteins are significantly enriched in the nucleus. Together with published data, our data suggest a major nuclear function of the trypanosome exosome in rRNA, snoRNA and mRNA quality control. (C) 2016 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.orgilicensesiby/4.0/)., This work was funded by the DFG (Kr4017/1-1 and Kr4017/1-2 to SK), by the Wellcome trust (grant number 085956/Z/08/Z to MC) and by the Spanish Ministerio de Economia e Innovacion (BFU2014-55193-P to AE). Markus Engstler (University of Wurzburg) is acknowledged for mentoring and providing lab space and research infrastructure. Anti-BiP was kindly provided by Jay Bangs (University of Wisconsin-Madison, Madison, US).
- Published
- 2016
28. Novel insights into RNP granules by employing the trypanosome's microtubule skeleton as a molecular sieve
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Fritz, Melanie, Vanselow, Jens, Sauer, Nadja, Lamer, Stephanie, Goos, Carina, Siegel, T. Nicolai, Subota, Ines, Schlosser, Andreas, Carrington, Mark, and Kramer, Susanne
- Subjects
ddc:610 - Abstract
RNP granules are ribonucleoprotein assemblies that regulate the post-transcriptional fate of mRNAs in all eukaryotes. Their exact function remains poorly understood, one reason for this is that RNP granule purification has not yet been achieved. We have exploited a unique feature of trypanosomes to prepare a cellular fraction highly enriched in starvation stress granules. First, granules remain trapped within the cage-like, subpellicular microtubule array of the trypanosome cytoskeleton while soluble proteins are washed away. Second, the microtubules are depolymerized and the granules are released. RNA sequencing combined with single molecule mRNA FISH identified the short and highly abundant mRNAs encoding ribosomal mRNAs as being excluded from granules. By mass spectrometry we have identified 463 stress granule candidate proteins. For 17/49 proteins tested by eYFP tagging we have confirmed the localization to granules, including one phosphatase, one methyltransferase and two proteins with a function in trypanosome life-cycle regulation. The novel method presented here enables the unbiased identification of novel RNP granule components, paving the way towards an understanding of RNP granule function.
- Published
- 2015
29. The complex enzymology of mRNA decapping: Enzymes of four classes cleave pyrophosphate bonds.
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Kramer, Susanne and McLennan, Alexander G.
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- 2019
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30. Effects of resource availability and quality on soil microorganisms and their carbon assimilation
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Kramer, Susanne
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arable field ,Kohlenstoffkreislauf ,Nahrungsnetze ,Pilze ,Stabile Isotope ,Wurzel ,food webs ,ddc:630 ,stable isotopes ,Agrarfläche ,Agriculture ,Streu ,Bakterien - Abstract
Soil microorganisms play a pivotal role in decomposition processes and therefore influence nutrient cycling and ecosystem function. Availability and quality of resources determines activity, growth and identity of substrate users. In agricultural systems, availability of resources is dependent on, for example, crop type, management, season, and depth. At depth substrate availability and microbial biomass decrease. However, there remain gaps in our understanding of C turnover in subsoil and how processes in the topsoil may influence abundance, activity, and function of microorganisms in deeper soil layers. With respect to substrate quality it is thought that bacteria are the dominant users of high quality substrates and more labile components whereas fungi are more important for the degradation of low quality and more recalcitrant substrates (i.e. cellulose, lignin). Therefore, this thesis was designed to increase our understanding of C turnover and the influence of both availability and quality of substrates on microorganisms in an agricultural soil. In the first and second studies, a recently established C3-C4 plant exchange field experiment was used to investigate the C flow from belowground (root) and aboveground (shoot litter) resources into the belowground food web. Maize plants were cultivated to introduce a C4 signal into the soil both by plant growth (belowground / root channel) and also by applying shoot litter (aboveground litter channel). To separate C flow from the shoot litter versus the root channel, maize litter was applied on wheat cultivated plots, while on half of the maize planted plots no maize litter was returned. Wheat cultivated plots without additional maize litter application served as a reference for the calculation of incorporated maize-C into different soil pools. Soil samplings took place in two consecutive years in summer, autumn and winter. Three depths were considered (0-10 cm: topsoil, 40-50 cm: rooted zone beneath the plough layer, 60-70 cm: unrooted zone). In the third study a microcosm experiment with substrates of different recalcitrance and complexity was carried out to identify primary decomposers of different plant litter materials (leaves and roots) during early stages of decomposition (duration of 32 days) and to follow the C flow into the next higher trophic level (protozoa). Bodenmikroorganismen spielen eine zentrale Rolle im Abbau von organischer Substanz und beeinflussen somit Nährstoffkreisläufe und die Funktion von Ökosystemen. Die Verfügbarkeit und Qualität von Ressourcen bestimmt die Aktivität, das Wachstum und die Identität der entsprechenden Substratnutzer. In Agrarökosystemen ist die Verfügbarkeit von Ressourcen zum Beispiel abhängig von Kulturpflanzenart, Bodenbearbeitung, Jahreszeit und Bodentiefe. In der Tiefe ist die Substratverfügbarkeit und somit auch die mikrobielle Biomasse verringert. Aber es ist immer noch wenig bekannt über den C-Umsatz im Unterboden und wie und ob Prozesse im Oberboden die Abundanz, Aktivität und Funktion von Mikroorganismen im Unterboden beeinflussen. In Bezug auf die Substratqualität wird davon ausgegangen, dass Bakterien vor allem am Abbau hoch qualitativer und leicht abzubauender Substrate beteiligt sind, während Pilze eine wichtigere Rolle beim Abbau von qualitativ minderwertigeren und schwerer abzubauenden Substraten (z.B. Cellulose, Lignin) spielen. Die vorliegende Arbeit wurde durchgeführt, um das Verständnis des C-Umsatzes und den Einfluss von Verfügbarkeit und Qualität von Substraten auf Mikroorganismen in einer Agrarfläche zu verbessern. In der ersten und zweiten Studie wurde ein Feldversuch genutzt, der angelegt wurde, um mit Hilfe eines C3-C4 Pflanzenwechsels den C-Fluss von unterirdischen (Wurzel) und oberirdischen (Streu) Ressourcen ins unterirdische Nahrungsnetz zu untersuchen. Maispflanzen wurden angebaut, um das C4-bürtige Signal in den Boden einzuführen. Dies geschah einerseits durch Pflanzenwachstum (unterirdisch / Wurzelkanal) und andererseits durch das Rückführen von Streu auf die Flächen (oberirdischer Streukanal). Um den C-Fluss des Wurzel- und Streu-Kanals zu trennen, wurde Streu auf Flächen aufgebracht, auf denen Weizen angebaut wurde, während auf der Hälfte der Flächen, auf denen Mais angebaut wurde, keine Streu zurückgeführt wurde. Weizenflächen auf denen keine zusätzliche Maisstreu aufgebracht wurde, wurden als Referenz für die Berechnung des C-Eintrags in die unterschiedlichen Bodenpools genutzt. Bodenproben wurden in 2 aufeinanderfolgenden Jahren im Sommer, Herbst und Winter genommen. Es wurden 3 unterschiedliche Bodentiefen betrachtet (0-10 cm: Oberboden, 40-50 cm: durchwurzelte Zone unter dem Pflughorizont, 60-70 cm: nicht durchwurzelte Zone). In der dritten Studie wurde ein Mikrokosmenexperiment mit Substraten unterschiedlicher Qualität und Komplexität durchgeführt, um primäre Nutzer von unterschiedlichem Pflanzenmaterial (Blätter und Wurzeln) während der frühen Abbauphase (32 Tage) zu identifizieren und den C-Fluss in eine nächst höhere trophische Ebene (Protozoen) zu untersuchen.
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- 2014
31. Multispecies reconstructions uncover widespread conservation, and lineage-specific elaborations in eukaryotic mRNA metabolism.
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Bannerman, Bridget P., Kramer, Susanne, Dorrell, Richard G., and Carrington, Mark
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- *
EUKARYOTES , *MESSENGER RNA , *CYTOPLASMIC inheritance , *EXONS (Genetics) , *INTRONS - Abstract
The degree of conservation and evolution of cytoplasmic mRNA metabolism pathways across the eukaryotes remains incompletely resolved. In this study, we describe a comprehensive genome and transcriptome-wide analysis of proteins involved in mRNA maturation, translation, and mRNA decay across representative organisms from the six eukaryotic super-groups. We demonstrate that eukaryotes share common pathways for mRNA metabolism that were almost certainly present in the last eukaryotic common ancestor, and show for the first time a correlation between intron density and a selective absence of some Exon Junction Complex (EJC) components in eukaryotes. In addition, we identify pathways that have diversified in individual lineages, with a specific focus on the unique gene gains and losses in members of the Excavata and SAR groups that contribute to their unique gene expression pathways compared to other organisms. [ABSTRACT FROM AUTHOR]
- Published
- 2018
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32. The nuclear proteome of Trypanosoma brucei.
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Goos, Carina, Dejung, Mario, Janzen, Christian J., Butter, Falk, and Kramer, Susanne
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TRYPANOSOMA brucei ,PROTEOMICS ,TSETSE-flies ,AFRICAN trypanosomiasis ,RNA polymerase I - Abstract
Trypanosoma brucei is a protozoan flagellate that is transmitted by tsetse flies into the mammalian bloodstream. The parasite has a huge impact on human health both directly by causing African sleeping sickness and indirectly, by infecting domestic cattle. The biology of trypanosomes involves some highly unusual, nuclear-localised processes. These include polycistronic transcription without classical promoters initiated from regions defined by histone variants, trans-splicing of all transcripts to the exon of a spliced leader RNA, transcription of some very abundant proteins by RNA polymerase I and antigenic variation, a switch in expression of the cell surface protein variants that allows the parasite to resist the immune system of its mammalian host. Here, we provide the nuclear proteome of procyclic Trypanosoma brucei, the stage that resides within the tsetse fly midgut. We have performed quantitative label-free mass spectrometry to score 764 significantly nuclear enriched proteins in comparison to whole cell lysates. A comparison with proteomes of several experimentally characterised nuclear and non-nuclear structures and pathways confirmed the high quality of the dataset: the proteome contains about 80% of all nuclear proteins and less than 2% false positives. Using motif enrichment, we found the amino acid sequence KRxR present in a large number of nuclear proteins. KRxR is a sub-motif of a classical eukaryotic monopartite nuclear localisation signal and could be responsible for nuclear localization of proteins in Kinetoplastida species. As a proof of principle, we have confirmed the nuclear localisation of six proteins with previously unknown localisation by expressing eYFP fusion proteins. While proteome data of several T. brucei organelles have been published, our nuclear proteome closes an important gap in knowledge to study trypanosome biology, in particular nuclear-related processes. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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33. The ApaH-like phosphatase TbALPH1 is the major mRNA decapping enzyme of trypanosomes.
- Author
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Kramer, Susanne
- Subjects
- *
PHOSPHATASES , *MESSENGER RNA , *EUKARYOTE phylogeny , *DEADENYLATION , *EXORIBONUCLEASES , *RNA interference - Abstract
5’-3’ decay is the major mRNA decay pathway in many eukaryotes, including trypanosomes. After deadenylation, mRNAs are decapped by the nudix hydrolase DCP2 of the decapping complex and finally degraded by the 5’-3’ exoribonuclease. Uniquely, trypanosomes lack homologues to all subunits of the decapping complex, while deadenylation and 5’-3’ degradation are conserved. Here, I show that the parasites use an ApaH-like phosphatase (ALPH1) as their major mRNA decapping enzyme. The protein was recently identified as a novel trypanosome stress granule protein and as involved in mRNA binding. A fraction of ALPH1 co-localises exclusively with the trypanosome 5’-3’ exoribonuclease XRNA to a special granule at the posterior pole of the cell, indicating a connection between the two enzymes. RNAi depletion of ALPH1 is lethal and causes a massive increase in total mRNAs that are deadenylated, but have not yet started 5’-3’ decay. These data suggest that ALPH1 acts downstream of deadenylation and upstream of mRNA degradation, consistent with a function in mRNA decapping. In vitro experiments show that recombinant, N-terminally truncated ALHP1 protein, but not a catalytically inactive mutant, sensitises the capped trypanosome spliced leader RNA to yeast Xrn1, but only if an RNA 5’ polyphosphatase is included. This indicates that the decapping mechanism of ALPH1 differs from the decapping mechanism of Dcp2 by leaving more than one phosphate group at the mRNA’s 5’ end. This is the first reported function of a eukaryotic ApaH-like phosphatase, a bacterial-derived class of enzymes present in all phylogenetic super-groups of the eukaryotic kingdom. The substrates of eukaryotic ApaH-like phosphatases are unknown. However, the substrate of the related bacterial enzyme ApaH, diadenosine tetraphosphate, is highly reminiscent of a eukaryotic mRNA cap. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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34. Contrasting effect of elevated atmospheric CO2 on the C/N ratio of faba bean and spring wheat residues exert only minor changes in the abundance and enzyme activities of soil proteolytic bacteria.
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Rasche, Frank, Kramer, Susanne, Enowashu, Esther, Mackie, Katie, Högy, Petra, and Marhan, Sven
- Subjects
- *
PLANT residues , *FAVA bean , *EFFECT of atmospheric carbon dioxide on plants , *SOIL microbiology , *PROTEOLYTIC enzymes , *BACTERIAL enzymes - Abstract
Our primary objective was to follow the effects of altered C/N ratios of two residue materials on the abundance and potential activities of soil proteolytic bacteria during the initial stages of decomposition of organic residue derived nitrogen (N), taking into account the explicit physiological responses of spring wheat (SW; increase of C/N ratio) and faba bean (FB; decrease of C/N ratio) to elevated carbon dioxide (CO 2 ) exposure. FB and SW residues were obtained from a Mini-FACE experiment (ambient (380 μl l −1 ) CO 2 :C/N ratio FB: 100:1; SW: 75:1), elevated (550 μl l −1 ) CO 2 (FB: 42:1; SW: 105:1)) and incubated in a stagnic luvisol (Ap-horizon, 0–10 cm). Soil samples were obtained at 7, 14, 28, and 56 days of incubation and measured for potential activities of thermolysin-like neutral metalloproteases and alanyl-aminopeptidases as well as abundances of corresponding genes (i.e., neutral metalloproteases ( npr ) and alanine aminopeptidases ( pepN )). It was our major finding that distinct C/N ratios revealed only minor and inconsistent effects on gene abundances and potential enzyme activities. There was no relationship between activity potentials of both enzymes and abundances of corresponding genes implying the presence of inactive proteolytic bacteria. Moreover, a likely functional redundancy among proteolytic genes was noticed as explained by the omnipresence of Firmicutes (i.e., npr gene) as well as α- and β-proteobacteria (i.e., pepN gene) in studied soils. It was concluded that for prospective research, a greater variety of organic residue types from crops cultivated under elevated CO 2 with their individual biochemical characteristics should be considered to get a closer understanding of the ecological significance and complex dynamics of hitherto largely overlooked proteolytic bacteria in agricultural ecosystems. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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35. Simultaneous detection of mRNA transcription and decay intermediates by dual colour single mRNA FISH on subcellular resolution.
- Author
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Kramer, Susanne
- Published
- 2017
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36. Characterization of a PKA-like kinase from Trypanosoma brucei
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Kramer, Susanne
- Subjects
FOS: Biological sciences ,Trypanosoma brucei PKA cAMP cGMP - Abstract
The protozoan parasite Trypanosoma brucei causes human sleeping sickness and Nagana in domestic animals and depends on the tsetse fly for dissemination. The complex T. brucei life cycle requires differentiation from the dividing long slender forms via the cell cycle arrested short stumpy forms (both in the mammalian bloodstream) to the procyclic forms of the insect vector. The signaling pathways that regulate differentiation are unknown but there is evidence for an involvement of cAMP. In search of the putative cAMP receptor, three catalytic and one regulatory PKA-like subunits have been previously cloned from T. brucei. The catalytic subunits possess all features of a classical PKA in terms of inhibitor and substrate specificity. It was shown that each of the catalytic PKAlike subunits binds to the regulatory subunit to form a dimeric PKA-like holoenzyme. Most surprisingly, we found that T. brucei PKA-like kinase, despite of its apparent similarities to a PKA, was not activated but instead inhibited by cAMP. Out of several other cyclic nucleotides that were tested on their effects on PKA-like kinase, only cGMP was able to activate the kinase, but in millimolar and thus most likely unphysiological concentrations. Assuming that the activation of PKA-like kinase might depend on its native, subcellular environment, an in vivo kinase assay was established in this work. It is based on the immunological detection of the phosphorylated form of the PKA reporter substrate VASP that was transgenically expressed in T. brucei. Interestingly, results from the in vivo assay did confirm the in vitro data, suggesting that T. brucei PKA-like kinase is in fact inhibited rather than activated by cAMP. Even though these findings challenge the original assumption that T. brucei PKA-like kinase transmits the differentation signal mimicked by cAMP antagonists, data from this work nevertheless provide evidence for an involvement of T. brucei PKA-like kinase in relaying extracellular cues. This is suggested from an increase in in vivo PKA activity in the presence of treatments that have either been shown to induce LS to SS differentiation (etazolate) or to participate in SS to PCF differentiation (cold shock, mild acid stress). In addition, in vivo PKA activity was stimulated with the PDE inhibitor dipyridamole and at hypoosmotic stress. In the context of a putative role for T. brucei PKA-like kinase in the regulation of differentiation, two of the catalytic isoforms (PKAC1 and PKAC2) were of particular interest. We found significant life cycle stage dependent differences in protein expression between the two almost identical isoforms. PKAC1 was nearly exclusively present in bloodstream forms and PKAC2 in procyclic cells. In addition, PKAC1, but not PKAC2 carries a phosphorylation that is restricted to the SS stage. This phosphorylation was mapped to the C-terminal threonine 324 by mass spectrometry. The functions of these life cycle stage dependent differences between PKAC1 and PKAC2 remain unknown. Reverse genetics did not reveal any functional differences between the isoforms, in fact, PKAC1 was even able to complement PKAC2 in procyclic PKAC2 knock-out cells. Results from several reverse genetic experiments indicate that T. brucei PKA-like kinase plays an important role in cell division. Depletion of either PKA-like subunit leads to a cytokinesis block. Depletion of the regulatory PKA-like subunit additionally results in altered basal body segregation. Given that 1) both cytokinesis and basal body movement had been previously suggested to be regulated by the trypanosomal flagellum (Kohl et al., 2003) and 2) the flagellum hosts T. brucei PKA-like kinase (C. Krumbholz, this lab) we propose that trypanosomal flagella act as signaling compartments for coordination of cell division.
- Published
- 2005
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37. Resource Partitioning between Bacteria, Fungi, and Protists in the Detritusphere of an Agricultural Soil.
- Author
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Kramer, Susanne, Dibbern, Dörte, Moll, Julia, Huenninghaus, Maike, Koller, Robert, Krueger, Dirk, Marhan, Sven, Urich, Tim, Wubet, Tesfaye, Bonkowski, Michael, Buscot, François, Lueders, Tillmann, and Kandeler, Ellen
- Subjects
RESOURCE partitioning (Ecology) ,MICROCOSM & macrocosm ,RIBOSOMAL RNA - Abstract
The flow of plant-derived carbon in soil is a key component of global carbon cycling. Conceptual models of trophic carbon fluxes in soil have assumed separate bacterial and fungal energy channels in the detritusphere, controlled by both substrate complexity and recalcitrance. However, detailed understanding of the key populations involved and niche-partitioning between them is limited. Here, a microcosm experiment was performed to trace the flow of detritusphere C from substrate analogs (glucose, cellulose) and plant biomass amendments (maize leaves, roots) in an agricultural soil. Carbon flow was traced by rRNA stable isotope probing and amplicon sequencing across three microbial kingdoms. Distinct lineages within the Actinobacteria, Bacteroidetes, Gammaproteobacteria, Basidiomycota, Ascomycota as well as Peronosporomycetes were identified as important primary substrate consumers. A dynamic succession of primary consumers was observed especially in the cellulose treatments, but also in plant amendments over time. While intra-kingdom niche partitioning was clearly observed, distinct bacterial and fungal energy channels were not apparent. Furthermore, while the diversity of primary substrate consumers did not notably increase with substrate complexity, consumer succession and secondary trophic links to bacterivorous and fungivorous microbes resulted in increased food web complexity in the more recalcitrant substrates. This suggests that rather than substrate-defined energy channels, consumer succession as well as intra- and inter-kingdom cross-feeding should be considered as mechanisms supporting food web complexity in the detritusphere. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
38. Replenishment of type VII collagen and re-epithelialization of chronically ulcerated skin after intradermal administration of allogeneic mesenchymal stromal cells in two patients with recessive dystrophic epidermolysis bullosa
- Author
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Conget, Paulette, Rodriguez, Fernando, Kramer, Susanne, Allers, Carolina, Simon, Valeska, Palisson, Francis, Gonzalez, Sergio, and Yubero, Maria J.
- Published
- 2010
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39. Spatial and temporal variation of resource allocation in an arable soil drives community structure and biomass of nematodes and their role in the micro-food web.
- Author
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Scharroba, Anika, Kramer, Susanne, Kandeler, Ellen, and Ruess, Liliane
- Subjects
- *
SPATIAL variation , *RESOURCE allocation , *ARABLE land , *COMMUNITY organization , *BIOMASS , *NEMATODES , *FOOD chains - Abstract
The assemblages of organisms residing at different soil horizons are important drivers for carbon and nutrient cycle in arable systems, yet knowledge on food web dynamics below the plough zone is sparse. The present study investigated the effects of management practice on the nematode community structure and biomass in the top soil, rooted zone below plough layer, and root free deeper soil in two successive vegetation periods. Resource quality was manipulated by crop plant (maize and wheat) and organic amendment (with/without maize litter), to differently fuel the major soil carbon pathways based on roots, bacteria and fungi. Nematode assemblages were used as model to determine changes in the structure, function and carbon allocation of the soil micro-food web. The biomass of nematode families as well as the fungal to bacterial feeder ratio F/(F + B) assigned a predominance of the bacterial carbon channel in the arable soil. The differences in spatial and temporal availability of major plant resources, i.e. litter (recalcitrant substrate) and rhizodeposits (labile carbon), separated the nematode fauna into meta-communities along the depth profile. The seasonal pattern in population density, and the positive effects of litter amendment predominantly in the top soil, indicated low migration between these patches during crop growth. However, mass-flow as resource subsidy for communities at depth takes place under fallow during winter. Crop type was most important for carbon allocation, with wheat generally resulting in a greater biomass build-up of nematodes. The biomass distribution of trophic groups differed with depth, pointing to a strong bottom-up effect in the root channel, whereas predation likely was the primary regulating force in the fungal channel. Overall, combining nematode community composition with biomass revealed spatially separated micro-food web assemblages, differing in structure and carbon allocation. Thereby transport processes cross community boundaries, linking top soil and subsoil, notably in periods without a crop. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
40. Carbon transfer from maize roots and litter into bacteria and fungi depends on soil depth and time.
- Author
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Müller, Karolin, Kramer, Susanne, Haslwimmer, Heike, Marhan, Sven, Scheunemann, Nicole, Butenschön, Olaf, Scheu, Stefan, and Kandeler, Ellen
- Subjects
- *
CORN , *PLANT roots , *SOIL microbiology , *SOIL fungi , *SOIL depth - Abstract
Plant-derived carbon (C) transfer to soil is one of the important factors controlling the size and structure of the belowground microbial community. The present study quantifies this plant-derived C incorporation into abiotic and biotic C pools in top- and subsoil in an arable field over five years. Stable isotope analysis was used to determine the incorporation of maize root and shoot litter C into soil organic C (SOC), extractable organic C (EOC), total microbial biomass (C mic ), ergosterol and phospholipid fatty acids (PLFAs). The following treatments were investigated: corn maize (CM), providing root- and shoot-derived C (without corncobs), fodder maize (FM), providing only root-derived C, and wheat plus maize shoot litter amendment (WL), providing only shoot-derived maize C. Wheat plants (W) without maize litter amendment served as control. Soil samples were taken each September directly before harvest from 2009 to 2013. During the experiment, the maize-derived C signal increased in SOC, EOC, C mic , ergosterol, bacterial and fungal PLFAs in the topsoil (0–10 cm). Although total maize shoot C input was threefold lower than maize root C input, similar relative amounts of maize C derived from shoots and roots were incorporated into the different C pools in the WL and the FM treatments, indicating the importance of shoot-derived C sources for microorganisms in the topsoil. An additive effect of both C sources was found in the CM treatment with almost twice as much maize-derived C in the respective pools. Furthermore, the proportion of maize-derived C varied between the different pools with lower incorporation into the total SOC (17%) and total EOC (24%) pools and higher incorporation ratios of maize C into PLFAs of different microbial groups (29% in Gram-positive (Gr + ) bacterial PLFA-C, 44% in Gram-negative (Gr − ) bacterial PLFA-C, 69% in fungal PLFA-C and 78% in ergosterol) in the CM treatment in topsoil after five years. After the third and fifth vegetation periods, we also detected maize-derived C in the rooted zone (40–50 cm depth) and the root-free zone (60–70 cm depth). The maize-derived C incorporation was lower in subsoil C pools in comparison to topsoil C pools. In the root-free zone, the maize-derived C was found to be 2% in total SOC, 28% in total EOC, 9% in Gr + bacterial PLFA-C, 20% in Gr − bacterial PLFA-C and 53% in fungal PLFA-C. Saprotrophic fungi incorporated maize-derived C in all soil depths to a greater degree than Gr + and Gr − bacteria, indicating the importance of saprotrophic fungi in this agro-ecosystem. [ABSTRACT FROM AUTHOR]
- Published
- 2016
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41. Modulation of human endogenous retrovirus (HERV) transcription during persistent and de novo HIV-1 infection.
- Author
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Vincendeau, Michelle, Göttesdorfer, Ingmar, Schreml, Julia M. H., Wetie, Armand G. Ngounou, Mayer, Jens, Greenwood, Alex D., Helfer, Markus, Kramer, Susanne, Seifarth, Wolfgang, Hadian, Kamyar, Brack-Werner, Ruth, and Leib-Mösch, Christine
- Subjects
HUMAN endogenous retroviruses ,GENETIC transcription ,MEDICAL microbiology ,HIV infections ,CELL lines - Abstract
Background: The human genome contains multiple LTR elements including human endogenous retroviruses (HERVs) that together account for approximately 8-9% of the genomic DNA. At least 40 different HERV groups have been assigned to three major HERV classes on the basis of their homologies to exogenous retroviruses. Although most HERVs are silenced by a variety of genetic and epigenetic mechanisms, they may be reactivated by environmental stimuli such as exogenous viruses and thus may contribute to pathogenic conditions. The objective of this study was to perform an in-depth analysis of the influence of HIV-1 infection on HERV activity in different cell types. Results: A retrovirus-specific microarray that covers major HERV groups from all three classes was used to analyze HERV transcription patterns in three persistently HIV-1 infected cell lines of different cellular origins and in their uninfected counterparts. All three persistently infected cell lines showed increased transcription of multiple class I and II HERV groups. Up-regulated transcription of five HERV taxa (HERV-E, HERV-T, HERV-K (HML-10) and two ERV9 subgroups) was confirmed by quantitative reverse transcriptase PCR analysis and could be reversed by knock-down of HIV-1 expression with HIV-1-specific siRNAs. Cells infected de novo by HIV-1 showed stronger transcriptional up-regulation of the HERV-K (HML-2) group than persistently infected cells of the same origin. Analysis of transcripts from individual members of this group revealed up-regulation of predominantly two proviral loci (ERVK-7 and ERVK-15) on chromosomes 1q22 and 7q34 in persistently infected KE37.1 cells, as well as in de novo HIV-1 infected LC5 cells, while only one single HML-2 locus (ERV-K6) on chromosome 7p22.1 was activated in persistently infected LC5 cells. Conclusions: Our results demonstrate that HIV-1 can alter HERV transcription patterns of infected cells and indicate a correlation between activation of HERV elements and the level of HIV-1 production. Moreover, our results suggest that the effects of HIV-1 on HERV activity may be far more extensive and complex than anticipated from initial studies with clinical material. [ABSTRACT FROM AUTHOR]
- Published
- 2015
- Full Text
- View/download PDF
42. RNA in development: how ribonucleoprotein granules regulate the life cycles of pathogenic protozoa.
- Author
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Kramer, Susanne
- Published
- 2014
- Full Text
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43. Temporal variation in surface and subsoil abundance and function of the soil microbial community in an arable soil
- Author
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Kramer, Susanne, Marhan, Sven, Haslwimmer, Heike, Ruess, Liliane, and Kandeler, Ellen
- Subjects
- *
SUBSOILS , *SOIL microbiology , *MICROBIAL ecology , *BIOTIC communities , *BIOGEOCHEMICAL cycles , *SOIL management , *CARBON , *TOPSOIL - Abstract
Abstract: Many studies of the microbial ecology of agricultural ecosystems focus on surface soils, whereas the impacts of management practice and season on soil microbial community composition and function below the plough zone are largely neglected. Deep soils have a high potential to store carbon; therefore any management driven stimulation or repression of microorganisms in subsoil could impact biogeochemical cycling in agricultural sites. The aim of this study was to understand whether soil management affects microbial communities in the topsoil (0–10 cm), rooted zone beneath the plough layer (40–50 cm), and the unrooted zone (60–70 cm). In a field experiment with different crops [wheat (Triticum aestivum L.) and maize (Zea mays L.)] and agricultural management strategies (litter amendment) we analysed microbial biomass as phospholipid fatty acids (PLFAs) and enzyme activities involved in the C-cycle (β-glucosidase, N-acetyl-β-d-glucosaminidase, β-xylosidase, phenol- and peroxidase) across a depth transect over a period of two years. Wheat cultivation resulted in higher bacterial and fungal biomass as well as higher enzyme activities at most sampling dates in comparison to maize cultivated plots, and this effect was visible to 50 cm depth. Litter application increased bacterial and fungal biomass as well as hydrolytic enzyme activities but effects were apparent only in the topsoil. In winter high microbial biomass and enzyme activities were measured in all soil layers, possibly due to increased mobilization and translocation of organic matter into deeper soil. Hydrolytic enzyme activities decreased with depth, whereas oxidative enzyme activities showed no decrease or even an increase with depth. This could have been due to differing sorption mechanisms of hydrolytic and oxidative enzymes. Specific enzyme activities (enzyme activity per microbial biomass) were higher in the deeper layers and possible reasons are discussed. [Copyright &y& Elsevier]
- Published
- 2013
- Full Text
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44. Differential Localization of the Two T. brucei Poly(A) Binding Proteins to the Nucleus and RNP Granules Suggests Binding to Distinct mRNA Pools.
- Author
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Kramer, Susanne, Bannerman-Chukualim, Bridget, Ellis, Louise, Boulden, Elizabeth A., Kelly, Steve, Field, Mark C., and Carrington, Mark
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PROTEIN research , *TRYPANOSOMA , *YEAST research , *CARRIER proteins , *GENETIC translation , *MESSENGER RNA - Abstract
The number of paralogs of proteins involved in translation initiation is larger in trypanosomes than in yeasts or many metazoan and includes two poly(A) binding proteins, PABP1 and PABP2, and four eIF4E variants. In many cases, the paralogs are individually essential and are thus unlikely to have redundant functions although, as yet, distinct functions of different isoforms have not been determined. Here, trypanosome PABP1 and PABP2 have been further characterised. PABP1 and PABP2 diverged subsequent to the differentiation of the Kinetoplastae lineage, supporting the existence of specific aspects of translation initiation regulation. PABP1 and PABP2 exhibit major differences in intracellular localization and distribution on polysome fractionation under various conditions that interfere with mRNA metabolism. Most striking are differences in localization to the four known types of inducible RNP granules. Moreover, only PABP2 but not PABP1 can accumulate in the nucleus. Taken together, these observations indicate that PABP1 and PABP2 likely associate with distinct populations of mRNAs. The differences in localization to inducible RNP granules also apply to paralogs of components of the eIF4F complex: eIF4E1 showed similar localization pattern to PABP2, whereas the localisation of eIF4E4 and eIF4G3 resembled that of PABP1. The grouping of translation initiation as either colocalizing with PABP1 or with PABP2 can be used to complement interaction studies to further define the translation initiation complexes in kinetoplastids. [ABSTRACT FROM AUTHOR]
- Published
- 2013
- Full Text
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45. Alterations in DRBD3 Ribonucleoprotein Complexes in Response to Stress in Trypanosoma brucei.
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Fernÿndez-Moya, Sandra M., García-Pérez, Angélica, Kramer, Susanne, Carrington, Mark, and Estévez, Antonio M.
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CELL cycle ,CYTOLOGY ,HUMAN genetics ,MESSENGER RNA ,CELL division ,HUMAN cell cycle - Abstract
Regulation of RNA polymerase II transcription initiation is apparently absent in trypanosomes. Instead, these eukaryotes control gene expression mainly at the post-transcriptional level. Regulation is exerted through the action of numerous RNAbinding proteins that modulate mRNA processing, turnover, translation and localization. In this work we show that the RNAbinding protein DRBD3 resides in the cytoplasm, but localizes to the nucleus upon oxidative challenge and to stress granules under starvation conditions. DRBD3 associates with other proteins to form a complex, the composition of which is altered by cellular stress. Interestingly, target mRNAs remain bound to DRBD3 under stress conditions. Our results suggest that DRBD3 transports regulated mRNAs within the cell in the form of ribonucleoprotein complexes that are remodeled in response to environmental cues. [ABSTRACT FROM AUTHOR]
- Published
- 2012
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46. Inhibition of mRNA maturation in trypanosomes causes the formation of novel foci at the nuclear periphery containing cytoplasmic regulators of mRNA fate.
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Kramer, Susanne, Marnef, Aline, Standart, Nancy, and Carrington, Mark
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RNA splicing , *GENETIC regulation , *MESSENGER RNA , *CYTOPLASMIC granules , *CELL membranes , *NUCLEIC acids - Abstract
Maturation of all cytoplasmic mRNAs in trypanosomes involves trans-splicing of a short exon at the 59 end. Inhibition of trans-splicing results in an accumulation of partially processed oligocistronic mRNAs. Here, we show that the accumulation of newly synthesised partially processed mRNAs results in the formation of foci around the periphery of the nucleus. These nuclear periphery granules (NPGs) contain the full complement of P-body proteins identified in trypanosomes to date, as well as poly(A)-binding protein 2 and the trypanosome homologue of the RNA helicase VASA. NPGs resemble perinuclear germ granules from metazoa more than P-bodies because they: (1) are localised around the nuclear periphery; (2) are dependent on active transcription; (3) are not dissipated by cycloheximide; (4) contain VASA; and (5) depend on nuclear integrity. In addition, NPGs can be induced in cells depleted of the P-body core component SCD6. The description of NPGs in trypanosomes provides evidence that there is a perinuclear compartment that can determine the fate of newly transcribed mRNAs and that germ granules could be a specialised derivative. [ABSTRACT FROM AUTHOR]
- Published
- 2012
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47. Restoring Methicillin-Resistant Staphylococcus aureus Susceptibility to β-Lactam Antibiotics.
- Author
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Tan, Christopher M., Therien, Alex G., Lu, Jun, Lee, Sang H., Caron, Alexandre, Gill, Charles J., Lebeau-Jacob, Christian, Benton-Perdomo, Liliana, Monteiro, João M., Pereira, Pedro M., Elsen, Nathaniel L., Wu, Jin, Deschamps, Kathleen, Petcu, Mihai, Wong, Simon, Daigneault, Etienne, Kramer, Susanne, Liang, Lianzhu, Maxwell, Eugene, and Claveau, David
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- 2012
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48. Carbon flow into microbial and fungal biomass as a basis for the belowground food web of agroecosystems
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Kramer, Susanne, Marhan, Sven, Ruess, Liliane, Armbruster, Wolfgang, Butenschoen, Olaf, Haslwimmer, Heike, Kuzyakov, Yakov, Pausch, Johanna, Scheunemann, Nicole, Schoene, Jochen, Schmalwasser, Andreas, Totsche, Kai Uwe, Walker, Frank, Scheu, Stefan, and Kandeler, Ellen
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SOIL microbiology , *AGRICULTURAL ecology , *FOOD chains , *CARBON isotopes , *PLANT roots , *HUMUS - Abstract
Abstract: The origin and quantity of plant inputs to soil are primary factors controlling the size and structure of the soil microbial community. The present study aimed to elucidate and quantify the carbon (C) flow from both root and shoot litter residues into soil organic, extractable, microbial and fungal C pools. Using the shift in C stable isotope values associated with replacing C3 by C4 plants we followed root- vs. shoot litter-derived C resources into different soil C pools. We established the following treatments: Corn Maize (CM), Fodder Maize (FM), Wheat+maize Litter (WL) and Wheat (W) as reference. The Corn Maize treatment provided root- as well as shoot litter-derived C (without corn cobs) whereas Fodder Maize (FM) provided only root-derived C (aboveground shoot material was removed). Maize shoot litter was applied on the Wheat+maize Litter (WL) plots to trace the incorporation of C4 litter C into soil microorganisms. Soil samples were taken three times per year (summer, autumn, winter) over two growing seasons. Maize-derived C signal was detectable after three to six months in the following pools: soil organic C (Corg), extractable organic C (EOC), microbial biomass (Cmic) and fungal biomass (ergosterol). In spite of the lower amounts of root- than of shoot litter-derived C inputs, similar amounts were incorporated into each of the C pools in the FM and WL treatments, indicating greater importance of the root- than shoot litter-derived resources for the soil microorganisms as a basis for the belowground food web. In the CM plots twice as much maize-derived C was incorporated into the pools. After two years, maize-derived C in the CM treatment contributed 14.1, 24.7, 46.6 and 76.2% to Corg, EOC, Cmic and ergosterol pools, respectively. Fungi incorporated maize-derived C to a greater extent than did total soil microbial biomass. [Copyright &y& Elsevier]
- Published
- 2012
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49. Developmental regulation of gene expression in the absence of transcriptional control: The case of kinetoplastids
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Kramer, Susanne
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GENE expression , *KINETOPLASTIDA , *GENETIC transcription , *GENETIC regulation , *TRYPANOSOMA brucei , *TRYPANOSOMA cruzi , *RNA polymerase regulation , *LEISHMANIASIS - Abstract
Abstract: Kinetoplastids, including the human pathogens Trypanosoma brucei, Trypanosoma cruzi and Leishmania, are the only known organisms that do not regulate the transcription of protein coding genes transcribed by RNA polymerase II. Yet, profound changes in gene expression are induced by many different external stimuli and stresses, the extreme example are cascades of changes in gene expression initiated by differentiation triggers that ultimately and irreversibly result in the massive morphological and metabolic changes observed during life-cycle progression. This review explores how kinetoplastids change gene expression by looking at life-cycle stage specific changes in chromatin, mRNA processing, mRNA stability, mRNA translation, protein stability and protein modifications. [Copyright &y& Elsevier]
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- 2012
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50. Genome-wide in silico screen for CCCH-type zinc finger proteins of Trypanosoma brucei, Trypanosoma cruzi and Leishmania major.
- Author
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Kramer, Susanne, Kimblin, Nicola C., and Carrington, Mark
- Subjects
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ZINC-finger proteins , *TRYPANOSOMA cruzi , *CARRIER proteins , *LEISHMANIA , *RNA editing , *MESSENGER RNA - Abstract
Background: CCCH type zinc finger proteins are RNA binding proteins with regulatory functions at all stages of mRNA metabolism. The best-characterized member, tritetraproline (TTP), binds to AU rich elements in 3' UTRs of unstable mRNAs, mediating their degradation. In kinetoplastids, CCCH type zinc finger proteins have been identified as being involved in the regulation of the life cycle and possibly the cell cycle. To date, no systematic listing of CCCH proteins in kinetoplastids is available. Results: We have identified the complete set of CCCH type zinc finger proteins in the available genomes of the kinetoplastid protozoa Trypanosoma brucei, Trypanosoma cruzi and Leishmania major. One fifths (20%) of all CCCH motifs fall into non-conventional classes and many had not been previously identified. One third of all CCCH proteins have more than one CCCH motif, suggesting multivalent RNA binding. One third have additional recognizable domains. The vast majority are unique to Kinetoplastida or to a subgroup within. Two exceptions are of interest: the putative orthologue of the mRNA nuclear export factor Mex67 and a 3'-5' exoribonuclease restricted to Leishmania species. CCCH motifs are absent from these proteins in other organisms and might be unique, novel features of the Kinetoplastida homologues. Of the others, several have a predicted, and in one case experimentally confirmed, connection to the ubiquitination pathways, for instance a HECT-type E3 ubiquitin ligase. The total number of kinetoplastid CCCH proteins is similar to the number in higher eukaryotes but lower than in yeast. A comparison of the genomic loci between the Trypanosomatidae homologues provides insight into both the evolution of the CCCH proteins as well as the CCCH motifs. Conclusion: This study provides the first systematic listing of the Kinetoplastida CCCH proteins. The number of CCCH proteins with more then one CCCH motif is larger than previously estimated, due to the identification of nonconventional CCCH motifs. Experimental approaches are now necessary to examine the functions of the many unique CCCH proteins as well as the function of the putative Mex67 and the Leishmania 3'-5' exoribonuclease. [ABSTRACT FROM AUTHOR]
- Published
- 2010
- Full Text
- View/download PDF
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