Genomes and Genes
Experts and Doctors on bacterial proteins in Heidelberg, Baden Württemberg, Germany
Locale: Heidelberg, Baden Württemberg, Germany
Topic: bacterial proteins
- Ettema T, van der Oost J, Huynen M. Modularity in the gain and loss of genes: applications for function prediction. Trends Genet. 2001;17:485-7 pubmed..Hence, this can be used to divide predicted clusters of functionally interacting proteins into sub-clusters, and as such, to refine the prediction of their function and functional interactions. ..
- Zhang Y, Hoffmeister M, Weck M, Chang Claude J, Brenner H. Helicobacter pylori infection and colorectal cancer risk: evidence from a large population-based case-control study in Germany. Am J Epidemiol. 2012;175:441-50 pubmed publisher..22 (95% CI: 1.02, 1.45), suggesting that H. pylori infection may be associated with a small yet relevant risk increase in the left colorectum. ..
- Gupta S, Gross R, Dandekar T. An antibiotic target ranking and prioritization pipeline combining sequence, structure and network-based approaches exemplified for Serratia marcescens. Gene. 2016;591:268-278 pubmed publisher..This supports reliable drug target identification and prioritization for infectious agents (bacteria, parasites, fungi) by these bundled complementary criteria. ..
- Griffiths G, Roos N, Schleich S, Locker J. Structure and assembly of intracellular mature vaccinia virus: thin-section analyses. J Virol. 2001;75:11056-70 pubmed..All of the images presented here can be rationalized with respect to the model put forward for the assembly of the IMV in the accompanying paper. ..
- Lommel M, Strahl S. Protein O-mannosylation: conserved from bacteria to humans. Glycobiology. 2009;19:816-28 pubmed publisher..In this review, we summarize the observations that have opened up the field and highlight characteristics of O-mannosylation in the different domains/kingdoms of life. ..
- Gunderson S, Polycarpou Schwarz M, Mattaj I. U1 snRNP inhibits pre-mRNA polyadenylation through a direct interaction between U1 70K and poly(A) polymerase. Mol Cell. 1998;1:255-64 pubmed..Conservation of the U1 70K inhibitory domains suggests that polyadenylation regulation via PAP inhibition may be more widespread than previously thought. ..
- Bilan D, Matlashov M, Gorokhovatsky A, Schultz C, Enikolopov G, Belousov V. Genetically encoded fluorescent indicator for imaging NAD(+)/NADH ratio changes in different cellular compartments. Biochim Biophys Acta. 2014;1840:951-7 pubmed publisher..Our results show that normalizing the signal of the sensor to the pH changes is a good strategy for overcoming pH-induced artifacts in imaging. ..
- Udvarhelyi A, Domratcheva T. Glutamine rotamers in BLUF photoreceptors: a mechanistic reappraisal. J Phys Chem B. 2013;117:2888-97 pubmed publisher..Finally, we demonstrate that the tautomerized glutamine is consistent with our criteria and observations of the BLUF light state...
- Wendt C, Schutt S, Dalpke A, Konrad M, Mieth M, Trierweiler Hauke B, et al. First outbreak of Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae in Germany. Eur J Clin Microbiol Infect Dis. 2010;29:563-70 pubmed publisher..Typing revealed that all patients were colonised by the same strain. KPC-K. pneumoniae has been introduced to Germany possibly from Greece and transmission to other institutions is likely. ..
- Mutschler H, Gebhardt M, Shoeman R, Meinhart A. A novel mechanism of programmed cell death in bacteria by toxin-antitoxin systems corrupts peptidoglycan synthesis. PLoS Biol. 2011;9:e1001033 pubmed publisher..Finally, we discuss how phosphorylated UNAG likely poisons additional pathways of bacterial cell wall synthesis, making it an attractive lead compound for development of new antibiotics. ..
- Doerks T, van Noort V, Minguez P, Bork P. Annotation of the M. tuberculosis hypothetical orfeome: adding functional information to more than half of the uncharacterized proteins. PLoS ONE. 2012;7:e34302 pubmed publisher..All together, we have raised the fraction of the proteome with at least some functional annotation to 88% which should considerably enhance the interpretation of large-scale experiments targeting this medically important organism. ..
- Jung A, Domratcheva T, Tarutina M, Wu Q, Ko W, Shoeman R, et al. Structure of a bacterial BLUF photoreceptor: insights into blue light-mediated signal transduction. Proc Natl Acad Sci U S A. 2005;102:12350-5 pubmed publisher..The structure suggests a unique photochemical signaling switch in which the absorption of light induces a structural change in the rim surrounding the hook, thereby changing the protein interface between BLUF and the output domain...
- Dougan D, Mogk A, Zeth K, Turgay K, Bukau B. AAA+ proteins and substrate recognition, it all depends on their partner in crime. FEBS Lett. 2002;529:6-10 pubmed
- Ouzonis C, Kyrpides N, Sander C. Novel protein families in archaean genomes. Nucleic Acids Res. 1995;23:565-70 pubmed..In addition, with the detection of proteins in various metabolic and genetic processes in archaea, we can further predict the presence of additional proteins involved in these processes...
- Santarella Mellwig R, Pruggnaller S, Roos N, Mattaj I, Devos D. Three-dimensional reconstruction of bacteria with a complex endomembrane system. PLoS Biol. 2013;11:e1001565 pubmed publisher..Our results have implications for our definition and understanding of bacterial cell organization, the genesis of complex structure, and the origin of the eukaryotic endomembrane system. ..
- Rippe K, Guthold M, von Hippel P, Bustamante C. Transcriptional activation via DNA-looping: visualization of intermediates in the activation pathway of E. coli RNA polymerase x sigma 54 holoenzyme by scanning force microscopy. J Mol Biol. 1997;270:125-38 pubmed
- Wagner A, Schultz S, Bomke J, Pils T, Lehmann W, Knappe J. YfiD of Escherichia coli and Y06I of bacteriophage T4 as autonomous glycyl radical cofactors reconstituting the catalytic center of oxygen-fragmented pyruvate formate-lyase. Biochem Biophys Res Commun. 2001;285:456-62 pubmed
- Neumann S, Hansen C, Wingreen N, Sourjik V. Differences in signalling by directly and indirectly binding ligands in bacterial chemotaxis. EMBO J. 2010;29:3484-95 pubmed publisher..Overall, our data suggest that the distinction between signalling by directly and indirectly binding ligands is more physiologically important than the traditional distinction between high- and low-abundance receptors. ..
- Eberle W, Pastore A, Sander C, Rosch P. The structure of ColE1 rop in solution. J Biomol NMR. 1991;1:71-82 pubmed..W., Kokkinidis, M. and Tsernoglou, D. (1987) J. Mol. Biol., 196, 657-675), although there are minor differences in regions where packing forces appear to influence the crystal structure. ..
- Sourjik V, Vaknin A, Shimizu T, Berg H. In vivo measurement by FRET of pathway activity in bacterial chemotaxis. Methods Enzymol. 2007;423:365-91 pubmed
- Gibson T, Thompson J, Heringa J. The KH domain occurs in a diverse set of RNA-binding proteins that include the antiterminator NusA and is probably involved in binding to nucleic acid. FEBS Lett. 1993;324:361-6 pubmed..All KH-containing proteins are linked with RNA and the KH motif most probably functions as a nucleic acid binding domain. ..
- Asmah N, Eberspächer B, Regnath T, Arvand M. Prevalence of erythromycin and clindamycin resistance among clinical isolates of the Streptococcus anginosus group in Germany. J Med Microbiol. 2009;58:222-7 pubmed publisher..The implications of these findings for susceptibility testing and antimicrobial therapy of SAG infections are discussed...
- Meyle E, Brenner Weiss G, Obst U, Prior B, Hänsch G. Immune defense against S. epidermidis biofilms: components of the extracellular polymeric substance activate distinct bactericidal mechanisms of phagocytic cells. Int J Artif Organs. 2012;35:700-12 pubmed publisher..In the present study we identified in the bacteria-free extracellular substance of Staphylococcus epidermidis biofilms protein fractions that activated PMN in vitro. ..
- Filimonov V, Prieto J, Martinez J, Bruix M, Mateo P, Serrano L. Thermodynamic analysis of the chemotactic protein from Escherichia coli, CheY. Biochemistry. 1993;32:12906-21 pubmed..The reversible dimerization of "molten globules" might explain such peculiarities as the increased stability or the cooperative unfolding found for the molten globule state of some proteins. ..
- Schulz A, Mücke N, Langowski J, Rippe K. Scanning force microscopy of Escherichia coli RNA polymerase.sigma54 holoenzyme complexes with DNA in buffer and in air. J Mol Biol. 1998;283:821-36 pubmed..sigma54-DNA complexes at the promoter as compared to the contour length of the free DNA was 22 nm for the dried samples as opposed to only 6 nm for the undried samples imaged in buffer. This suggests an artefact of the drying process. ..
- Guenebaut V, Schlitt A, Weiss H, Leonard K, Friedrich T. Consistent structure between bacterial and mitochondrial NADH:ubiquinone oxidoreductase (complex I). J Mol Biol. 1998;276:105-12 pubmed
- Noble M, Musacchio A, Saraste M, Courtneidge S, Wierenga R. Crystal structure of the SH3 domain in human Fyn; comparison of the three-dimensional structures of SH3 domains in tyrosine kinases and spectrin. EMBO J. 1993;12:2617-24 pubmed..These loops are different in tyrosine kinase and spectrin SH3 domains. They could modulate the binding properties of the aromatic surface. ..
- Werbeck N, Zeymer C, Kellner J, Reinstein J. Coupling of oligomerization and nucleotide binding in the AAA+ chaperone ClpB. Biochemistry. 2011;50:899-909 pubmed publisher..In this way, they provide a basis for intersubunit communication within the functional ClpB complex. ..
- Bange G, Petzold G, Wild K, Parlitz R, Sinning I. The crystal structure of the third signal-recognition particle GTPase FlhF reveals a homodimer with bound GTP. Proc Natl Acad Sci U S A. 2007;104:13621-5 pubmed..Our results provide insights into SRP GTPases and their roles in two fundamentally different protein-targeting routes that both rely on efficient protein delivery to a secretion channel. ..
- Bange G, Kümmerer N, Grudnik P, Lindner R, Petzold G, Kressler D, et al. Structural basis for the molecular evolution of SRP-GTPase activation by protein. Nat Struct Mol Biol. 2011;18:1376-80 pubmed publisher..Our study exemplifies the evolutionary transition from RNA- to protein-driven activation in SRP-GTPases and suggests that the current view on SRP-mediated protein targeting is incomplete. ..
- S raphin B. The HIT protein family: a new family of proteins present in prokaryotes, yeast and mammals. DNA Seq. 1992;3:177-9 pubmed..The function of these proteins is unknown but they share a characteristic histidine triad that may be involved in zinc binding. This group of protein has been named the HIT protein family...
- Brehmer D, Gässler C, Rist W, Mayer M, Bukau B. Influence of GrpE on DnaK-substrate interactions. J Biol Chem. 2004;279:27957-64 pubmed..These findings suggest that the ATP-triggered dissociation of GrpE and substrates from DnaK occurs in a concerted fashion. ..
- Baumann S, Hess J, Eichhorst S, Krueger A, Angel P, Krammer P, et al. An unexpected role for FosB in activation-induced cell death of T cells. Oncogene. 2003;22:1333-9 pubmed..Thus, our results demonstrate an important novel function for FosB dimerized with c-Jun in TCR/CD3-mediated AICD in human T cells. ..
- Zapun A, Bardwell J, Creighton T. The reactive and destabilizing disulfide bond of DsbA, a protein required for protein disulfide bond formation in vivo. Biochemistry. 1993;32:5083-92 pubmed..This implies that the disulfide bond destabilizes the folded conformation of DsbA. This was confirmed by demonstrating that the reduced protein was 3.6 +/- 1.4 kcal.mol-1 more stable than that with the disulfide bond. ..
- Stemmann O, Neidig A, Kocher T, Wilm M, Lechner J. Hsp90 enables Ctf13p/Skp1p to nucleate the budding yeast kinetochore. Proc Natl Acad Sci U S A. 2002;99:8585-90 pubmed..skp1 mutants exhibit growth defects on media containing geldanamycin. A skp1 mutation together with Hsp90 mutations exhibits synthetic lethality. An Hsp90 mutant contains decreased levels of active Ctf13p/Skp1p. ..
- Rizzato C, Kato I, Plummer M, Munoz N, Stein A, Jan van Doorn L, et al. Risk of advanced gastric precancerous lesions in Helicobacter pylori infected subjects is influenced by ABO blood group and cagA status. Int J Cancer. 2013;133:315-22 pubmed publisher..We showed that SNPs in the ABO gene, predictive of ABO blood groups, are associated with risk of advanced precancerous gastric lesions in individuals infected with Hp, but the assessment of the risk is strictly dependent on cagA status. ..
- Parlitz R, Eitan A, Stjepanovic G, Bahari L, Bange G, Bibi E, et al. Escherichia coli signal recognition particle receptor FtsY contains an essential and autonomous membrane-binding amphipathic helix. J Biol Chem. 2007;282:32176-84 pubmed..Deletion experiments showed that this helix is essential for FtsY function in vivo, thus offering, for the first time, clear evidence for the functionally important, physiologically relevant interaction of FtsY with lipids. ..
- Sandaltzopoulos R, Bonte E. Elimination of background in footprinting analysis by template selection. Biotechniques. 1995;18:773, 776 pubmed
- Santarella Mellwig R, Franke J, Jaedicke A, Gorjanacz M, Bauer U, Budd A, et al. The compartmentalized bacteria of the planctomycetes-verrucomicrobia-chlamydiae superphylum have membrane coat-like proteins. PLoS Biol. 2010;8:e1000281 pubmed publisher..Our results demonstrate similarities between bacterial and eukaryotic compartmentalization machinery, suggesting that the bacterial PVC superphylum contributed significantly to eukaryogenesis. ..
- Montoya G, Svensson C, Luirink J, Sinning I. Crystal structure of the NG domain from the signal-recognition particle receptor FtsY. Nature. 1997;385:365-8 pubmed..It also identifies regions potentially involved in the transmission of signals between domains and in interactions with regulatory proteins. ..
- Jung A, Reinstein J, Domratcheva T, Shoeman R, Schlichting I. Crystal structures of the AppA BLUF domain photoreceptor provide insights into blue light-mediated signal transduction. J Mol Biol. 2006;362:717-32 pubmed publisher..We propose that the blue light signal is transmitted towards the surface of the BLUF domain via His44, which serves as a reporter of active site changes...
- Kulik V, Hartmann E, Weyand M, Frey M, Gierl A, Niks D, et al. On the structural basis of the catalytic mechanism and the regulation of the alpha subunit of tryptophan synthase from Salmonella typhimurium and BX1 from maize, two evolutionarily related enzymes. J Mol Biol. 2005;352:608-20 pubmed publisher..The latter is caused by a substitution of the residues that stabilize the inactive conformation in TRPS...
- Tews I, Findeisen F, Sinning I, Schultz A, Schultz J, Linder J. The structure of a pH-sensing mycobacterial adenylyl cyclase holoenzyme. Science. 2005;308:1020-3 pubmed..Two alpha helices serve as molecular switches. Mutagenesis is consistent with a regulatory role of the structural transition, and we suggest that the transition is regulated by pH. ..
- Grosskinsky S, Schott M, Brenner C, Cutler S, Kraiczy P, Zipfel P, et al. Borrelia recurrentis employs a novel multifunctional surface protein with anti-complement, anti-opsonic and invasive potential to escape innate immunity. PLoS ONE. 2009;4:e4858 pubmed publisher..recurrentis to escape innate immunity and to persist in human tissues, including the brain, may help to understand the pathological processes underlying louse-borne relapsing fever. ..
- Blasche S, Wuchty S, Rajagopala S, Uetz P. The protein interaction network of bacteriophage lambda with its host, Escherichia coli. J Virol. 2013;87:12745-55 pubmed publisher..Lambda appears to dramatically differ from other phages, such as T7, because of its unusually large number of modified and processed proteins, which reduces the number of host-virus interactions detectable by yeast two-hybrid screens. ..
- Cuylen S, Haering C. Deciphering condensin action during chromosome segregation. Trends Cell Biol. 2011;21:552-9 pubmed publisher..In this review we discuss possible mechanisms that could explain the variety of condensin actions during chromosome segregation...
- Schulmeister S, Grosse K, Sourjik V. Effects of receptor modification and temperature on dynamics of sensory complexes in Escherichia coli chemotaxis. BMC Microbiol. 2011;11:222 pubmed publisher..coli. ..
- Munoz V, Serrano L. Elucidating the folding problem of helical peptides using empirical parameters. III. Temperature and pH dependence. J Mol Biol. 1995;245:297-308 pubmed..The inclusion of these terms allow us to calculate the helical behaviour of polyalanine-based peptides, as well as of complex natural sequences, under different experimental conditions. ..
- Lombardi D, Soldati T, Riederer M, Goda Y, Zerial M, Pfeffer S. Rab9 functions in transport between late endosomes and the trans Golgi network. EMBO J. 1993;12:677-82 pubmed..Moreover, our results confirm the observation that a given organelle may bear multiple rab proteins with different biological functions. ..
- Shanmugam R, Aklujkar M, Schafer M, Reinhardt R, Nickel O, Reuter G, et al. The Dnmt2 RNA methyltransferase homolog of Geobacter sulfurreducens specifically methylates tRNA-Glu. Nucleic Acids Res. 2014;42:6487-96 pubmed publisher..Interestingly, the same loss of activity was observed with human DNMT2, indicating that the variable loop functions as a specificity determinant in tRNA recognition of Dnmt2 enzymes. ..
- Yang Y, Sourjik V. Opposite responses by different chemoreceptors set a tunable preference point in Escherichia coli pH taxis. Mol Microbiol. 2012;86:1482-9 pubmed publisher..We further demonstrate that the inversion point of the pH response can be adjusted in response to changes in the cell density...
- Winkler A, Heintz U, Lindner R, Reinstein J, Shoeman R, Schlichting I. A ternary AppA-PpsR-DNA complex mediates light regulation of photosynthesis-related gene expression. Nat Struct Mol Biol. 2013;20:859-67 pubmed publisher..We discuss implications of these results for regulation by light and oxygen, highlighting new insights into blue light-mediated signal transduction. ..
- Liberman L, Berg H, Sourjik V. Effect of chemoreceptor modification on assembly and activity of the receptor-kinase complex in Escherichia coli. J Bacteriol. 2004;186:6643-6 pubmed..Thus, changes in receptor activity do not appear to be mediated by changes in receptor-kinase assembly. ..
- Rashid M, Schäfer H, Gonzalez J, Wink M. Genetic diversity of rhizobia nodulating lentil (Lens culinaris) in Bangladesh. Syst Appl Microbiol. 2012;35:98-109 pubmed publisher..These clades differ from the R. etli-R. leguminosarum group and may correspond to novel species in the genus Rhizobium. ..
- Bange G, K mmerer N, Engel C, Bozkurt G, Wild K, Sinning I. FlhA provides the adaptor for coordinated delivery of late flagella building blocks to the type III secretion system. Proc Natl Acad Sci U S A. 2010;107:11295-300 pubmed publisher..Taken together, these results allow to propose a model that explains how the T3SS may switch from the stoichiometric export of FliD to the high-throughput secretion of flagellin...
- Becker A, Oh E, Weissman J, Kramer G, Bukau B. Selective ribosome profiling as a tool for studying the interaction of chaperones and targeting factors with nascent polypeptide chains and ribosomes. Nat Protoc. 2013;8:2212-39 pubmed publisher..Factor-RNC purification and sequencing library preparation takes 7-8 d, and sequencing and data analysis can be completed in 5-6 d. ..
- Luirink J, High S, Wood H, Giner A, Tollervey D, Dobberstein B. Signal-sequence recognition by an Escherichia coli ribonucleoprotein complex. Nature. 1992;359:741-3 pubmed..Here we show that the P48/4.5S RNA ribonucleoprotein complex interacts specifically with the signal sequence of a nascent secretory protein and therefore is a signal recognition particle. ..
- Zeymer C, Werbeck N, Schlichting I, Reinstein J. The molecular mechanism of Hsp100 chaperone inhibition by the prion curing agent guanidinium chloride. J Biol Chem. 2013;288:7065-76 pubmed publisher..We propose that both the interference with the essential glutamate and the modulation of nucleotide binding properties in NBD1 is responsible for the GdmCl-specific inhibition of Hsp100 chaperones. ..
- Benz J, Sendlmeier C, Barends T, Meinhart A. Structural insights into the effector-immunity system Tse1/Tsi1 from Pseudomonas aeruginosa. PLoS ONE. 2012;7:e40453 pubmed publisher..Moreover, it is also the first example of a member of the N1pC/P60 superfamily which becomes inhibited upon binding to its cognate immunity protein...
- Castresana J, L bben M, Saraste M. New archaebacterial genes coding for redox proteins: implications for the evolution of aerobic metabolism. J Mol Biol. 1995;250:202-10 pubmed publisher..A phylogenetic analysis of the new protein sequences gives support to the view that an elaborate aerobic respiratory chain was already present in the last common ancestor of all living organisms...
- Scheuermann M, Murmann A, Richter K, Görisch S, Herrmann H, Lichter P. Characterization of nuclear compartments identified by ectopic markers in mammalian cells with distinctly different karyotype. Chromosoma. 2005;114:39-53 pubmed..Since the distribution of the ectopically expressed protein markers is similar in cells with distinctly different chromosome numbers, the property of the delineated, limited compartment might indeed depend on chromatin organization...
- Budd A, Blandin S, Levashina E, Gibson T. Bacterial alpha2-macroglobulins: colonization factors acquired by horizontal gene transfer from the metazoan genome?. Genome Biol. 2004;5:R38 pubmed..The protease inhibitor alpha2-macroglobulin provides a major metazoan defense against invasive bacteria, trapping attacking proteases required by parasites for successful invasion...
- Schneider S, Bosse F, D Urso D, Muller H, Sereda M, Nave K, et al. The AN2 protein is a novel marker for the Schwann cell lineage expressed by immature and nonmyelinating Schwann cells. J Neurosci. 2001;21:920-33 pubmed..Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis of purified AN2 from early postnatal mouse brain demonstrated that AN2 is the murine homolog of the rat NG2 proteoglycan. ..
- Hahmann M, Maurer T, Lorenz M, Hengstenberg W, Glaser S, Kalbitzer H. Structural studies of histidine-containing phosphocarrier protein from Enterococcus faecalis. Eur J Biochem. 1998;252:51-8 pubmed..A similar observation was made for HPr from E. faecalis phosphorylated at its regulatory site (Ser46). 31P-NMR shows that phosphorylated HPr exists in two conformational substates with nearly equal populations...
- Dreger C, König A, Spring H, Lichter P, Herrmann H. Investigation of nuclear architecture with a domain-presenting expression system. J Struct Biol. 2002;140:100-15 pubmed