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  • 1
    Language: English
    In: Plant physiology, November 2013, Vol.163(3), pp.1191-202
    Description: The NAD(P)H oxidoreductase or complex I (NDH1) complex participates in many processes such as respiration, cyclic electron flow, and inorganic carbon concentration in the cyanobacterial cell. Despite immense progress in our understanding of the structure-function relation of the cyanobacterial NDH1 complex, the subunits catalyzing NAD(P)H docking and oxidation are still missing. The gene sml0013 of Synechocystis 6803 encodes for a small protein of unknown function for which homologs exist in all completely known cyanobacterial genomes. The protein exhibits weak similarities to the NDH-dependent flow6 (NDF6) protein, which was reported from Arabidopsis (Arabidopsis thaliana) chloroplasts as a NDH subunit. An sml0013 inactivation mutant of Synechocystis 6803 was generated and characterized. It showed only weak differences regarding growth and pigmentation in various culture conditions; most remarkably, it exhibited a glucose-sensitive phenotype in the light. The genome-wide expression pattern of the Δsml0013::Km mutant was almost identical to the wild type when grown under high CO2 conditions as well as after shifts to low CO2 conditions. However, measurements of the photosystem I redox kinetic in cells of the Δsml0013::Km mutant revealed differences, such as a decreased capability of cyclic electron flow as well as electron flow into respiration in comparison with the wild type. These results suggest that the Sml0013 protein (named NdhP) represents a novel subunit of the cyanobacterial NDH1 complex, mediating its coupling either to the respiratory or the photosynthetic electron flow.
    Keywords: Bacterial Proteins -- Genetics ; Cyanobacteria -- Genetics ; Nadph Oxidases -- Genetics ; Photosystem I Protein Complex -- Genetics ; Synechocystis -- Genetics
    ISSN: 00320889
    E-ISSN: 1532-2548
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  • 2
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 2011, Vol.108(5), pp.2124-2129
    Description: There has been an increasing interest in cyanobacteria because these photosynthetic organisms convert solar energy into biomass and because of their potential for the production of biofuels. However, the exploitation of cyanobacteria for bioengineering requires knowledge of their transcriptional organization. Using differential RNA sequencing, we have established a genome-wide map of 3,527 transcriptional start sites (TSS) of the model organism Synechocystis sp. PCC6803. One-third of all TSS were located upstream of an annotated gene; another third were on the reverse complementary strand of 866 genes, suggesting massive antisense transcription. Orphan TSS located in intergenic regions led us to predict 314 noncoding RNAs (ncRNAs). Complementary microarray-based RNA profiling verified a high number of noncoding transcripts and identified strong ncRNA regulations. Thus, ~64% of all TSS give rise to antisense or ncRNAs in a genome that is to 87% protein coding. Our data enhance the information on promoters by a factor of 40, suggest the existence of additional small peptide-encoding mRNAs, and provide corrected 5' annotations for many genes of this cyanobacterium. The global TSS map will facilitate the use of Synechocystis sp. PCC6803 as a model organism for further research on photosynthesis and energy research. ; Includes references ; p. 2124-2129.
    Keywords: Transcription (Genetics) -- Physiological Aspects ; Cyanobacteria -- Genetic Aspects ; Genetic Regulation -- Research ; Rna Polymerases -- Properties;
    ISSN: 0027-8424
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  • 3
    Language: English
    In: Biological chemistry, April 2011, Vol.392(4), pp.291-7
    Description: Cyanobacteria are the only prokaryotes which directly convert solar energy into biomass using oxygenic photosynthesis. Therefore, these bacteria are of interest for the production of biofuels, biotechnology and are of tremendous relevance for primary carbon fixation in many ecosystems. Mechanisms controlling gene expression cannot be understood entirely without information on the numbers and functions of regulatory RNAs. In cyanobacteria, non-coding RNAs have been characterized from simple unicellular species such as Prochlorococcus up to complex species such as Anabaena. Several of these RNAs function in the control of stress responses, photosynthesis, outer cell membrane protein biosynthesis and the differentiation of cells.
    Keywords: Chromosomes, Bacterial -- Genetics ; Cyanobacteria -- Genetics ; RNA, Antisense -- Genetics ; RNA, Bacterial -- Genetics ; Regulatory Sequences, Ribonucleic Acid -- Genetics ; Stress, Physiological -- Genetics
    ISSN: 14316730
    E-ISSN: 1437-4315
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  • 4
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 01 February 2011, Vol.108(5), pp.2124-9
    Description: There has been an increasing interest in cyanobacteria because these photosynthetic organisms convert solar energy into biomass and because of their potential for the production of biofuels. However, the exploitation of cyanobacteria for bioengineering requires knowledge of their transcriptional organization. Using differential RNA sequencing, we have established a genome-wide map of 3,527 transcriptional start sites (TSS) of the model organism Synechocystis sp. PCC6803. One-third of all TSS were located upstream of an annotated gene; another third were on the reverse complementary strand of 866 genes, suggesting massive antisense transcription. Orphan TSS located in intergenic regions led us to predict 314 noncoding RNAs (ncRNAs). Complementary microarray-based RNA profiling verified a high number of noncoding transcripts and identified strong ncRNA regulations. Thus, ∼64% of all TSS give rise to antisense or ncRNAs in a genome that is to 87% protein coding. Our data enhance the information on promoters by a factor of 40, suggest the existence of additional small peptide-encoding mRNAs, and provide corrected 5' annotations for many genes of this cyanobacterium. The global TSS map will facilitate the use of Synechocystis sp. PCC6803 as a model organism for further research on photosynthesis and energy research.
    Keywords: Transcription, Genetic ; Synechocystis -- Genetics
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 5
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 10 November 2015, Vol.112(45), pp.E6243-52
    Description: Glutamine synthetase (GS), a key enzyme in biological nitrogen assimilation, is regulated in multiple ways in response to varying nitrogen sources and levels. Here we show a small regulatory RNA, NsiR4 (nitrogen stress-induced RNA 4), which plays an important role in the regulation of GS in cyanobacteria. NsiR4 expression in the unicellular Synechocystis sp. PCC 6803 and in the filamentous, nitrogen-fixing Anabaena sp. PCC 7120 is stimulated through nitrogen limitation via NtcA, the global transcriptional regulator of genes involved in nitrogen metabolism. NsiR4 is widely conserved throughout the cyanobacterial phylum, suggesting a conserved function. In silico target prediction, transcriptome profiling on pulse overexpression, and site-directed mutagenesis experiments using a heterologous reporter system showed that NsiR4 interacts with the 5'UTR of gifA mRNA, which encodes glutamine synthetase inactivating factor (IF)7. In Synechocystis, we observed an inverse relationship between the levels of NsiR4 and the accumulation of IF7 in vivo. This NsiR4-dependent modulation of gifA (IF7) mRNA accumulation influenced the glutamine pool and thus [Formula: see text] assimilation via GS. As a second target, we identified ssr1528, a hitherto uncharacterized nitrogen-regulated gene. Competition experiments between WT and an ΔnsiR4 KO mutant showed that the lack of NsiR4 led to decreased acclimation capabilities of Synechocystis toward oscillating nitrogen levels. These results suggest a role for NsiR4 in the regulation of nitrogen metabolism in cyanobacteria, especially for the adaptation to rapid changes in available nitrogen sources and concentrations. NsiR4 is, to our knowledge, the first identified bacterial sRNA regulating the primary assimilation of a macronutrient.
    Keywords: Ntca ; Synechocystis ; Glutamine Synthetase Inactivating Factors ; Nitrogen Assimilation ; Regulatory RNA ; Bacterial Proteins -- Metabolism ; DNA-Binding Proteins -- Metabolism ; Glutamate-Ammonia Ligase -- Antagonists & Inhibitors ; Nitrogen Fixation -- Physiology ; Regulatory Sequences, Ribonucleic Acid -- Physiology ; Synechocystis -- Physiology ; Transcription Factors -- Metabolism
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 6
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 10 September 2013, Vol.110(37), pp.E3487-96
    Description: Small RNAs (sRNAs) constitute a large and heterogeneous class of bacterial gene expression regulators. Much like eukaryotic microRNAs, these sRNAs typically target multiple mRNAs through short seed pairing, thereby acting as global posttranscriptional regulators. In some bacteria, evidence for hundreds to possibly more than 1,000 different sRNAs has been obtained by transcriptome sequencing. However, the experimental identification of possible targets and, therefore, their confirmation as functional regulators of gene expression has remained laborious. Here, we present a strategy that integrates phylogenetic information to predict sRNA targets at the genomic scale and reconstructs regulatory networks upon functional enrichment and network analysis (CopraRNA, for Comparative Prediction Algorithm for sRNA Targets). Furthermore, CopraRNA precisely predicts the sRNA domains for target recognition and interaction. When applied to several model sRNAs, CopraRNA revealed additional targets and functions for the sRNAs CyaR, FnrS, RybB, RyhB, SgrS, and Spot42. Moreover, the mRNAs gdhA, lrp, marA, nagZ, ptsI, sdhA, and yobF-cspC were suggested as regulatory hubs targeted by up to seven different sRNAs. The verification of many previously undetected targets by CopraRNA, even for extensively investigated sRNAs, demonstrates its advantages and shows that CopraRNA-based analyses can compete with experimental target prediction approaches. A Web interface allows high-confidence target prediction and efficient classification of bacterial sRNAs.
    Keywords: E. Coli ; RNA–RNA Interaction ; Regulatory RNA ; RNA, Bacterial -- Genetics
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 7
    Language: English
    In: Microbiology and Molecular Biology Reviews, 2011, Vol. 75(2), p.286
    Description: Summary: A substantial amount of antisense transcription is a hallmark of gene expression in eukaryotes. However, antisense transcription was first demonstrated in bacteria almost 50 years ago. The transcriptomes of bacteria as different as Helicobacter pylori, Bacillus subtilis, Escherichia coli, Synechocystis sp. strain PCC6803, Mycoplasma pneumoniae, Sinorhizobium meliloti, Geobacter sulfurreducens, Vibrio cholerae, Chlamydia trachomatis, Pseudomonas syringae, and Staphylococcus aureus have now been reported to contain antisense RNA (asRNA) transcripts for a high percentage of genes. Bacterial asRNAs share functional similarities with trans-acting regulatory RNAs, but in addition, they use their own distinct mechanisms. Among their confirmed functional roles are transcription termination, codegradation, control of translation, transcriptional interference, and enhanced stability of their respective target transcripts. Here, we review recent publications indicating that asRNAs occur as frequently in simple unicellular bacteria as they do in higher organisms, and we provide a comprehensive overview of the experimentally confirmed characteristics of asRNA actions and intimately linked quantitative aspects. Emerging functional data suggest that asRNAs in bacteria mediate a plethora of effects and are involved in far more processes than were previously anticipated. Thus, the functional impact of asRNAs should be considered when developing new strategies against pathogenic bacteria and when optimizing bacterial strains for biotechnology.
    Keywords: Gene Expression ; Molecular Biology ; Translations ; Genes ; RNA ; Microbiology ; Transcription ; Biotechnology ; Gene Expression ; Translation ; Data Processing ; RNA ; Transcription Termination ; Gene Regulation ; Reviews ; Antisense RNA ; Vibrio Cholerae ; Synechocystis ; Helicobacter Pylori ; Bacillus Subtilis ; Escherichia Coli ; Sinorhizobium Meliloti ; Chlamydia Trachomatis ; Staphylococcus Aureus ; Mycoplasma Pneumoniae ; Geobacter Sulfurreducens ; Pseudomonas Syringae ; RNA ; Bacteria ; Genetics & Taxonomy ; Prevention and Control ; Public Health, Medicines, Dangerous Organisms;
    ISSN: 1098-5557
    ISSN: 10985557
    ISSN: 10922172
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  • 8
    Language: English
    In: Clinical epidemiology, 2011, Vol.3, pp.213-6
    Description: To evaluate whether the ongoing debate over diagnostic problems and treatment choices for acute rhinosinusitis has had any influence on the management of the disease. We randomly selected 300 Danish general practitioners (GPs) from the files of the Research Unit for General Practice at Aarhus University. Invitations to participate and a questionnaire were sent to the GPs by mail. A total of 149 (49%) GPs answered the questionnaire. When asked about symptoms, the highest priority was given to sinus pain and signs of tenderness. The most frequent examinations were objective examination of the ear-nose-throat (ENT), palpation of the maxillofacial area, and C-reactive protein point-of-care testing (or CRP rapid test). Nearly all GPs prescribed local vasoconstrictors, and in 70% of cases, antibiotics were prescribed. Phenoxymethyl-penicillin was the preferred antibiotic. Use of the CRP rapid test, years in practice, or employment in an ENT department did not have a significant impact on the diagnostic certainty and antibiotic prescribing rate. The clinical diagnoses are based on a few symptoms, signs, and the CRP rapid test. Other examinations, including imaging techniques, are seldom used. Phenoxymethylpenicillin is the preferred antibiotic, and the GPs' diagnostic certainty was 70%.
    Keywords: Acute Rhinosinusitis ; Antibiotic ; Diagnosis ; General Practice ; Treatment
    E-ISSN: 1179-1349
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  • 9
    In: American Journal of Epidemiology, 2015, Vol. 182(5), pp.451-458
    Description: Longitudinal outcomes following stress or trauma diagnoses are receiving attention, yet population-based studies are few. The aims of the present cohort study were to examine the cumulative incidence of traumatic events and psychiatric diagnoses following diagnoses of severe stress and adjustment disorders categorized using International Classification of Diseases, Tenth Revision , codes and to examine associations of these diagnoses with all-cause mortality and suicide. Data came from a longitudinal cohort of all Danes who received a diagnosis of reaction to severe stress or adjustment disorders ( International Classification of Diseases, Tenth Revision , code F43.x) between 1995 and 2011, and they were compared with data from a general-population cohort. Cumulative incidence curves were plotted to examine traumatic experiences and psychiatric diagnoses during the study period. A Cox proportional hazards regression model was used to examine the associations of the disorders with mortality and suicide. Participants with stress diagnoses had a higher incidence of traumatic events and psychiatric diagnoses than did the comparison group. Each disorder was associated with a higher rate of all-cause mortality than that seen in the comparison cohort, and strong associations with suicide were found after adjustment. This study provides a comprehensive assessment of the associations of stress disorders with a variety of outcomes, and we found that stress diagnoses may have long-lasting and potentially severe consequences.
    Keywords: Cohort Studies ; Stress Disorders ; Traumatic ; Suicide
    ISSN: 0002-9262
    E-ISSN: 1476-6256
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  • 10
    In: Journal of Traumatic Stress, June 2014, Vol.27(3), pp.370-374
    Description: We created a registry of Danish‐born citizens of Denmark with incident (10th ed.; ) severe stress and adjustment disorder diagnoses between 1995 and 2011. A unique personal identifier was used to retrieve and merge data on demographic characteristics and diagnoses (ICD‐10 codes F43.x). Here we report on the incidence of these disorders and the demographic characteristics of the subset of the Danish population who have received 1 of these diagnoses: 111,844 adults and children received a first diagnosis between 1995 and 2011. More women than men (60.1% vs. 39.9%) received a diagnosis. Diagnoses increased during the late teens through early 30s. Adjustment disorder was the most common diagnosis (65.7% of adults and 64% of children). Reaction to severe stress unspecified was the second most common (19.8% of adults and 23.8% of children), and there was a large increase in both, as well as acute stress reaction diagnoses, in 2007 (3,717–5,141, 1,248–2,520, and 348–1,024 in 2006 to 2007, respectively). Findings regarding gender and age of onset are similar to other westernized countries. This registry can be used for future research programs, contributing to the study of stress and trauma. Traditional and Simplified Chinese s by AsianSTSS 標題:丹麥人口中嚴重壓力及適應障礙的診斷 撮要:我們建立了一個在丹麥出生市民的名冊,記錄1995至2011年間患上國際疾病分類(第十版) (ICD‐10) 中嚴重壓力及適應障礙的市民,而有一獨特個人識別碼以搜尋和合併有關人口統計學特性和診斷(ICD‐10碼F43.x)。本文報告這些病症的病發率和患有這些診斷其中一種的丹麥人口子集的人口統計學特性。總括而言,在1995至2011年間有111,848名成人及兒童首先診斷有這些病症,其中女多於男(60.1%比39.9%),而診斷隨青少年晚期到三十歲初期而增多。最常見的診斷是適應障礙(65.7%成人和64%兒童),而第二位是未指定嚴重壓力應激反應(19.8%成人和23.8%兒童)。在2007年兩者和急性壓力應激反應有極大增長(分別是從2006年至2007年3,717升至5,141,1,248升至2,520,和348升至1,024)。關於性別和病發年齡的結果與其他西方國家相似。本名冊有助未來有關壓力和創傷的研究計劃。 标题:丹麦人口中严重压力及适应障碍的诊断 撮要:我们建立了一个在丹麦出生市民的名册,记录1995至2011年间患上国际疾病分类(第十版) (ICD‐10) 中严重压力及适应障碍的市民,而有一独特个人标识号以搜寻和合并有关人口统计学特性和诊断(ICD‐10码F43.x)。本文报告这些病症的病发率和患有这些诊断其中一种的丹麦人口子集的人口统计学特性。总括而言,在1995至2011年间有111,848名成人及儿童首先诊断有这些病症,其中女多于男(60.1%比39.9%),而诊断随青少年晚期到三十岁初期而增多。最常见的诊断是适应障碍(65.7%成人和64%儿童),而第二位是未指定严重压力应激反应(19.8%成人和23.8%儿童)。在2007年两者和急性压力应激反应有极大增长(分别是从2006年至2007年3,717升至5,141,1,248升至2,520,和348升至1,024)。关于性别和病发年龄的结果与其他西方国家相似。本名册有助未来有关压力和创伤的研究计划。
    Keywords: Danes ; Adults ; Children ; Females ; Males ; Adolescents ; Young Adults ; Survivors ; Adjustment Disorder ; PTSD (ICD-10) ; Acute Stress Disorder ; Effects ; Stressors ; Epidemiology;
    ISSN: 0894-9867
    E-ISSN: 1573-6598
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