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  • 1
    Language: English
    In: Molecular microbiology, June 2011, Vol.80(6), pp.1479-95
    Description: The photosynthetic alphaproteobacterium Rhodobacter sphaeroides has to cope with photooxidative stress that is caused by the bacteriochlorophyll a-mediated formation of singlet oxygen ((1)O(2)). Exposure to (1)O(2) induces the alternative sigma factors RpoE and RpoH(II) which then promote transcription of photooxidative stress-related genes, including small RNAs (sRNAs). The ubiquitous RNA chaperone Hfq is well established to interact with and facilitate the base-pairing of sRNAs and target mRNAs to influence mRNA stability and/or translation. Here we report on the pleiotropic phenotype of a Δhfq mutant of R. sphaeroides, which is less pigmented, produces minicells and is more sensitive to (1)O(2). The higher (1)O(2) sensitivity of the Δhfq mutant is paralleled by a reduced RpoE activity and a disordered induction of RpoH(II)-dependent genes. We used co-immunoprecipitation of FLAG-tagged Hfq combined with RNA-seq to identify association of at least 25 sRNAs and of mRNAs encoding cell division proteins and ribosomal proteins with Hfq. Remarkably, 〉 70% of the Hfq-bound sRNAs are (1)O(2)-affected. Proteomics analysis of the Hfq-deficient strain revealed an impact of Hfq on amino acid transport and metabolic functions. Our data demonstrate for the first time an involvement of Hfq in regulation of photosynthesis genes and in the photooxidative stress response.
    Keywords: Gene Expression Regulation, Bacterial ; Oxidative Stress ; Protein Binding ; Bacterial Proteins -- Metabolism ; Host Factor 1 Protein -- Metabolism ; Rhodobacter Sphaeroides -- Metabolism
    ISSN: 0950382X
    E-ISSN: 1365-2958
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  • 2
    Language: English
    In: Environmental microbiology, March 2011, Vol.13(3), pp.775-91
    Description: Roseobacter clade aerobic anoxygenic phototrophic bacteria (AAnP) are abundant in photic zone environments of marine ecosystems. These bacteria form a photosynthetic apparatus at oxygen saturation, a situation expected to generate high levels of singlet oxygen (¹O₂) when light is present. Rhodobacter sphaeroides, an anaerobic anoxygenic phototroph, represses photosynthesis genes at high oxygen tension. Here we report that Roseobacter denitrificans showed higher sensitivity to ¹O₂ compared with Rhb. sphaeroides. While photosynthetic membranes of Rsb. denitrificans generated more ¹O₂ during light exposure, key regulator genes rpoE and rpoH(II) were more strongly induced in response to ¹O₂ stress compared with Rhb. sphaeroides. The regulon controlled by RpoE was different in Rsb. denitrificans and Rhb. sphaeroides. Patterns of synthesized soluble proteins strongly changed upon high light exposure in Rsb. denitrificans but not in Rhb. sphaeroides, and most changes were not further promoted by artificial ¹O₂ generation. The strong increase of small RNA RDs2461 levels by photooxidative stress implies a role for sRNAs in post-transcriptional regulation of the response to ¹O₂ in AAnPs. Our data reveal similarities but also significant differences in the response of Rsb. denitrificans and Rhb. sphaeroides to ¹O₂, most likely a consequence of their different lifestyles.
    Keywords: Light ; Oxidative Stress ; Photosynthesis ; Roseobacter -- Metabolism
    ISSN: 14622912
    E-ISSN: 1462-2920
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  • 3
    Language: English
    In: Biochemistry, 05/1983, Vol.22(10), pp.2339-2346
    Description: The detailed surface topography of the Escherichia coli 30S ribosomal subunit has been investigated, with iodination catalyzed by immobilized lactoperoxidase as the surface probe. Under mild conditions, only proteins S3, S7, S9, S18, and S21 were iodinated to a significant and reproducible extent. These proteins were isolated from the iodinated subunits, and in each case, the individual tyrosine residues that had reacted were identified by standard protein sequencing techniques. The targets of iodination that could be positively established were as follows: in protein S3 (232 amino acids), the tyrosines at positions 167 and 192; in S7 (153 amino acids), tyrosines 84 and 152; in S9 (128 amino acids), tyrosine 89; in S18 (74 amino acids), tyrosine 3 (tentative); in S21 (70 amino acids), tyrosines 37 and 70. The results represent part of a broader program to investigate ribosomal topography at the amino acid-nucleotide level.
    Keywords: Escherichia Coli -- Analysis ; Ribosomal Proteins -- Analysis ; Ribosomes -- Analysis ; Tyrosine -- Analysis;
    ISSN: 0006-2960
    E-ISSN: 1520-4995
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  • 4
    Language: English
    In: Biochemistry, 06/21/1983, Vol.22(13), pp.3157-3162
    Description: Further to our studies on the Escherichia coli 30S ribosomal subunit, the detailed surface topography of both 50S subunits and 70S ribosomes has been investigated by using iodination catalyzed by immobilized lactoperoxidase as the surface probe. In the 50S subunit, only proteins L2, L5, L10, and L11 were iodinated to a significant and reproducible extent. The targets of iodination were identified, after isolation of the individual iodinated proteins, and were as follows: in protein L2 (271 amino acids), tyrosine-102 and -160; in protein L5 (178 amino acids), tyrosine-142; in protein L10 (165 amino acids), tyrosine-132; in protein L11 (142 amino acids), tyrosine-7 and -61. In the 70S ribosome, only protein L5 was still iodinated to a significant extent from the 50S subunit, whereas in the 30S subunit the same spectrum of iodinated proteins was observed as that from iodinated isolated 30S subunits, with the exception that S21 was no longer present.
    Keywords: Ribosomal Proteins ; Ribosomes -- Ultrastructure;
    ISSN: 0006-2960
    E-ISSN: 1520-4995
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  • 5
    Language: English
    In: Journal of Molecular Biology, 1986, Vol.191(1), pp.135-138
    Description: "In vivo" cross-links were introduced into ribosomal RNA by direct ultraviolet irradiation of intact Escherichia coli cells, during growth in a 32P-labelled medium. Ribosomes were isolated from the irradiated cultures, dissociated into subunits and subjected to partial digestion with cobra venom nuclease. The intra-RNA cross-linked fragments were separated by two-dimensional gel electrophoresis and the sites of cross-linking determined, using our published methodology. A comparison with the data previously obtained by this procedure, after irradiation of isolated 30 S and 50 S subunits, showed that in the case of the 50 S subunit nine out of the ten previous cross-links in the 23 S RNA could be identified in the "in vivo" experiments, and correspondingly in the 30 S subunit five out of the six previous cross-links in the 16 S RNA were identified. Some new cross-links were found, as well as two cross-links in the 16 S RNA, which had hitherto only been observed after partial digestion of irradiated 30 S subunits with ribonuclease T1. The relevance of these data to the tertiary folding of the rRNA in situ is discussed, with particular reference to the work of other authors, in which "naked" RNA was used as the substrate for cross-linking and model-building studies.
    Keywords: Biology ; Chemistry
    ISSN: 0022-2836
    E-ISSN: 1089-8638
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  • 6
    Language: English
    In: Journal of proteome research, July 2007, Vol.6(7), pp.2460-71
    Description: Singlet oxygen (1O2) is a stress factor and signal in the facultative phototrophic bacterium Rhodobacter sphaeroides. In vivo protein labeling with L-[35S]-methionine and analysis by two-dimensional gel electrophoresis revealed that the synthesis of 61 proteins was changed in response to 1O2. After 1O2 treatment, protein synthesis patterns were distinct from those after H2O2 treatment but similar to those after high light exposure. This indicates regulatory mechanisms selective for different reactive oxygen species (ROS) and a response to light partly mediated by 1O2. Analysis of mutant strains support that the response to 1O2 is regulated mainly by rpoE (sigma E), but also a modulation of the sigma E dependent response by other factors and the existence of sigma E independent responses. The involvement of the RNA chaperon Hfq in the 1O2 response implies a role of small regulatory RNAs.
    Keywords: Bacterial Proteins -- Metabolism ; Protein Biosynthesis -- Drug Effects ; Proteome -- Metabolism ; Rhodobacter Sphaeroides -- Drug Effects ; Singlet Oxygen -- Pharmacology
    ISSN: 1535-3893
    E-ISSN: 15353907
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  • 7
    Language: English
    In: Molecular & cellular proteomics : MCP, December 2009, Vol.8(12), pp.2827-42
    Description: Proteome-based technologies represent powerful tools for the analysis of protein expression profiles, including the identification of potential cancer candidate biomarkers. Thus, here we provide a comprehensive protein expression map for clear cell renal cell carcinoma established by systematic comparative two-dimensional gel electrophoresis-based protein expression profiling of 16 paired tissue systems comprising clear cell renal cell carcinoma lesions and corresponding tumor-adjacent renal epithelium using overlapping narrow pH gradients. This approach led to the mapping of 348 distinct spots corresponding to 248 different protein identities. By implementing restriction criteria concerning their detection frequency and overall regulation mode, 28 up- and 56 down-regulated single target spots were considered as potential candidate biomarkers. Based on their gene ontology information, these differentially expressed proteins were classified into distinct functional groups and according to their cellular distribution. Moreover, three representative members of this group, namely calbindin, gelsolin, and heart fatty acid-binding protein, were selected, and their expression pattern was analyzed by immunohistochemistry using tissue microarrays. Thus, this pilot study provides a significant update of the current renal cell carcinoma map and defines a number of differentially expressed proteins, but both their potential as candidate biomarkers and clinical relevance has to be further explored in tissues and for body fluids like serum and urine.
    Keywords: Carcinoma, Renal Cell -- Metabolism ; Electrophoresis, Gel, Two-Dimensional -- Methods ; Kidney Neoplasms -- Metabolism ; Neoplasm Proteins -- Metabolism ; Proteomics -- Methods
    ISSN: 15359476
    E-ISSN: 1535-9484
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  • 8
    Language: English
    In: Proteomics, September 2006, Vol.6(18), pp.4950-66
    Description: Within the Human Proteome Organization (HUPO) Brain Proteome Project, a pilot study was launched with reference samples shipped to nine international laboratories (see Hamacher et al., this Special Issue) to evaluate different proteome approaches in neuroscience and to build up a first version of a brain protein database. One part of the study addresses quantitative proteome alterations between three developmental stages (embryonic day 16; postnatal day 7; 8 weeks) of mouse brains. Five brains per stage were differentially analyzed by 2-D DIGE using internal standardization and overlapping pH gradients (pH 4-7 and 6-9). In total, 214 protein spots showing stage-dependent intensity alterations (〉 two-fold) were detected, 56 of which were identified. Several of them, e.g. members of the dihydropyrimidinase family, are known to be associated with brain development. To feed the HUPO BPP brain protein database, a robust 2-D LC-MS/MS method was applied to murine postnatal day 7 and human post-mortem brain samples. Using MASCOT and the IPI database, 350 human and 481 mouse proteins could be identified by at least two different peptides. The data are accessible through the PRIDE database (http://www.ebi.ac.uk/pride/).
    Keywords: Brain -- Metabolism ; Proteome -- Metabolism
    ISSN: 1615-9853
    Source: MEDLINE/PubMed (U.S. National Library of Medicine)
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  • 9
    Language: English
    In: PROTEOMICS, September 2006, Vol.6(18), pp.4950-4966
    Description: Within the Human Proteome Organization (HUPO) Brain Proteome Project, a pilot study was launched with reference samples shipped to nine international laboratories (see Hamacher et al., this Special Issue) to evaluate different proteome approaches in neuroscience and to build up a first version of a brain protein database. One part of the study addresses quantitative proteome alterations between three developmental stages (embryonic day 16; postnatal day 7; 8 weeks) of mouse brains. Five brains stage were differentially analyzed by 2‐D DIGE using internal standardization and overlapping pH gradients (pH 4–7 and 6–9). In total, 214 protein spots showing stage‐dependent intensity alterations (〉two‐fold) were detected, 56 of which were identified. Several of them, . members of the dihydropyrimidinase family, are known to be associated with brain development. To feed the HUPO BPP brain protein database, a robust 2‐D LC‐MS/MS method was applied to murine postnatal day 7 and human post‐mortem brain samples. Using MASCOT and the IPI database, 350 human and 481 mouse proteins could be identified by at least two different peptides. The data are accessible through the PRIDE database (http://www.ebi.ac.uk/pride/).
    Keywords: 2‐D Lc‐Ms/Ms ; Brain ; Development ; Dige ; Proteome
    ISSN: 1615-9853
    E-ISSN: 1615-9861
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  • 10
    Language: English
    In: The Journal of general virology, September 2006, Vol.87(Pt 9), pp.2631-8
    Description: Coxsackievirus B3 (CVB3) is a common factor in human myocarditis. The interplay between host factors and virus components is crucial for the fate of the infected cells. Despite that, host protein responses, which characterize CVB3-induced diseases, have not yet been determined in detail. To investigate the nature of modified protein patterns in infected human cells compared with uninfected cells, two-dimensional gel electrophoresis in combination with matrix-assisted laser desorption/ionization-mass spectrometry were used. The regulated proteins, e.g. nucleophosmin (nucleolar protein B23), lamin, the RNA-binding protein UNR and the p38 mitogen-activated protein kinase, were sorted according to their functional groups and interpreted in the context of the myocarditis process.
    Keywords: Coxsackievirus Infections -- Metabolism ; Enterovirus B, Human -- Pathogenicity ; Proteome -- Metabolism
    ISSN: 0022-1317
    E-ISSN: 14652099
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