TY  - JOUR
A1  - Schmidtke, Cornelius
A1  - Findeiß, Sven
A1  - Sharma, Cynthia M.
A1  - Kuhfuss, Juliane
A1  - Hoffmann, Steve
A1  - Vogel, Jörg
A1  - Stadler, Peter F.
A1  - Bonas, Ulla
T1  - Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions
JF  - Nucleic Acids Research
N2  - The Gram-negative plant-pathogenic bacterium Xanthomonas campestris pv. vesicatoria (Xcv) is an important model to elucidate the mechanisms involved in the interaction with the host. To gain insight into the transcriptome of the Xcv strain 85-10, we took a differential RNA sequencing (dRNA-seq) approach. Using a novel method to automatically generate comprehensive transcription start site (TSS) maps we report 1421 putative TSSs in the Xcv genome. Genes in Xcv exhibit a poorly conserved -10 promoter element and no consensus Shine-Dalgarno sequence. Moreover, 14% of all mRNAs are leaderless and 13% of them have unusually long 5'-UTRs. Northern blot analyses confirmed 16 intergenic small RNAs and seven cis-encoded antisense RNAs in Xcv. Expression of eight intergenic transcripts was controlled by HrpG and HrpX, key regulators of the Xcv type III secretion system. More detailed characterization identified sX12 as a small RNA that controls virulence of Xcv by affecting the interaction of the pathogen and its host plants. The transcriptional landscape of Xcv is unexpectedly complex, featuring abundant antisense transcripts, alternative TSSs and clade-specific small RNAs.
KW  - SUBSP carotovora
KW  - regulatory RNA
KW  - gene-cluster
KW  - campestris PV vesicatoria
KW  - escherichia coli
KW  - determines pathgenicity
KW  - hypersensitive response
KW  - ralstonia solanacearum
KW  - extracellular enzymes
KW  - secretion systems
KW  - transcription initiation site
KW  - RNA sequence analyses
KW  - messanger RNA
KW  - plants
KW  - libraries
KW  - genome
KW  - genes
KW  - gene expression profiling
KW  - genetic transcription
KW  - northern blotting
KW  - untranslated regions
KW  - xanthomonas
KW  - xanthomonas campestris
KW  - bacteria
KW  - virulence
KW  - pathogenetic organism
KW  - RNA
KW  - small RNA
KW  - pathogenicity
KW  - type III secretion system pathways
KW  - maps
KW  - consesus
KW  - host (organism)
KW  - type III protein secretion system complex
Y1  - 2011
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-131781
VL  - 40
IS  - 5
SP  - 2020
EP  - 2031
ER  - 
TY  - JOUR
A1  - Reynolds, David
A1  - Cliffe, Laura
A1  - Förstner, Konrad U.
A1  - Hon, Chung-Chau
A1  - Siegel, T. Nicolai
A1  - Sabatini, Robert
T1  - Regulation of transcription termination by glucosylated hydroxymethyluracil, base J, in Leishmania major and Trypanosoma brucei
JF  - Nucleic Acids Research
N2  - Base J, beta-d-glucosyl-hydroxymethyluracil, is an epigenetic modification of thymine in the nuclear DNA of flagellated protozoa of the order Kinetoplastida. J is enriched at sites involved in RNA polymerase ( RNAP) II initiation and termination. Reduction of J in Leishmania tarentolae via growth in BrdU resulted in cell death and indicated a role of J in the regulation of RNAP II termination. To further explore J function in RNAP II termination among kinetoplastids and avoid indirect effects associated with BrdU toxicity and genetic deletions, we inhibited J synthesis in Leishmania major and Trypanosoma brucei using DMOG. Reduction of J in L. major resulted in genome-wide defects in transcription termination at the end of polycistronic gene clusters and the generation of antisense RNAs, without cell death. In contrast, loss of J in T. brucei did not lead to genome-wide termination defects; however, the loss of J at specific sites within polycistronic gene clusters led to altered transcription termination and increased expression of downstream genes. Thus, J regulation of RNAP II transcription termination genome-wide is restricted to Leishmania spp., while in T. brucei it regulates termination and gene expression at specific sites within polycistronic gene clusters.
KW  - RNA-polymerase-II
KW  - variant surface glycoprotein
KW  - SWI2/SNF2-like protein
KW  - messenger RNA
KW  - polycistronic transcription
KW  - DNA glycosation
KW  - hela cells
KW  - gene expression
KW  - genome
KW  - 5-bromodeoxyuridine
Y1  - 2014
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-117863
VL  - 42
IS  - 15
ER  -