17772
2019
eng
e02504-18
1
10
article
1
2019-03-01
--
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The major RNA-binding protein ProQ impacts virulence gene expression in Salmonella enterica serovar Typhimurium
FinO domain proteins such as ProQ of the model pathogen Salmonella enterica have emerged as a new class of major RNA-binding proteins in bacteria. ProQ has been shown to target hundreds of transcripts, including mRNAs from many virulence regions, but its role, if any, in bacterial pathogenesis has not been studied. Here, using a Dual RNA-seq approach to profile ProQ-dependent gene expression changes as Salmonella infects human cells, we reveal dysregulation of bacterial motility, chemotaxis, and virulence genes which is accompanied by altered MAPK (mitogen-activated protein kinase) signaling in the host. Comparison with the other major RNA chaperone in Salmonella, Hfq, reinforces the notion that these two global RNA-binding proteins work in parallel to ensure full virulence. Of newly discovered infection-associated ProQ-bound small noncoding RNAs (sRNAs), we show that the 3′UTR-derived sRNA STnc540 is capable of repressing an infection-induced magnesium transporter mRNA in a ProQ-dependent manner. Together, this comprehensive study uncovers the relevance of ProQ for Salmonella pathogenesis and highlights the importance of RNA-binding proteins in regulating bacterial virulence programs.
IMPORTANCE
The protein ProQ has recently been discovered as the centerpiece of a previously overlooked “third domain” of small RNA-mediated control of gene expression in bacteria. As in vitro work continues to reveal molecular mechanisms, it is also important to understand how ProQ affects the life cycle of bacterial pathogens as these pathogens infect eukaryotic cells. Here, we have determined how ProQ shapes Salmonella virulence and how the activities of this RNA-binding protein compare with those of Hfq, another central protein in RNA-based gene regulation in this and other bacteria. To this end, we apply global transcriptomics of pathogen and host cells during infection. In doing so, we reveal ProQ-dependent transcript changes in key virulence and host immune pathways. Moreover, we differentiate the roles of ProQ from those of Hfq during infection, for both coding and noncoding transcripts, and provide an important resource for those interested in ProQ-dependent small RNAs in enteric bacteria.
mBio
10.1128/mBio.02504-18
urn:nbn:de:bvb:20-opus-177722
mBio 2019, 10(1):e02504-18. DOI: 10.1128/mBio.02504-18
false
true
CC BY: Creative-Commons-Lizenz: Namensnennung 4.0 International
Alexander J. Westermann
Elisa Venturini
Mikael E. Sellin
Konrad U. Förstner
Wolf-Dietrich Hardt
Jörg Vogel
eng
uncontrolled
Hfq
eng
uncontrolled
noncoding RNA
eng
uncontrolled
ProQ
eng
uncontrolled
RNA-seq
eng
uncontrolled
bacterial pathogen
eng
uncontrolled
posttranscriptional control
Biowissenschaften; Biologie
open_access
Institut für Molekulare Infektionsbiologie
Förderzeitraum 2018
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/17772/Westermann_mBio.pdf
17894
2018
eng
7
article
1
2019-04-05
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ANNOgesic: a Swiss army knife for the RNA-seq based annotation of bacterial/archaeal genomes
To understand the gene regulation of an organism of interest, a comprehensive genome annotation is essential. While some features, such as coding sequences, can be computationally predicted with high accuracy based purely on the genomic sequence, others, such as promoter elements or noncoding RNAs, are harder to detect. RNA sequencing (RNA-seq) has proven to be an efficient method to identify these genomic features and to improve genome annotations. However, processing and integrating RNA-seq data in order to generate high-resolution annotations is challenging, time consuming, and requires numerous steps. We have constructed a powerful and modular tool called ANNOgesic that provides the required analyses and simplifies RNA-seq-based bacterial and archaeal genome annotation. It can integrate data from conventional RNA-seq and differential RNA-seq and predicts and annotates numerous features, including small noncoding RNAs, with high precision. The software is available under an open source license (ISCL) at https://pypi.org/project/ANNOgesic/.
GigaScience
10.1093/gigascience/giy096
urn:nbn:de:bvb:20-opus-178942
GigaScience, 7, 2018. DOI: 10.1093/gigascience/giy096
false
true
CC BY: Creative-Commons-Lizenz: Namensnennung 4.0 International
Sung-Huan Yu
Jörg Vogel
Konrad U. Förstner
eng
uncontrolled
genome annotation
eng
uncontrolled
RNA-seq
eng
uncontrolled
transcriptomics
Medizin und Gesundheit
open_access
Institut für Molekulare Infektionsbiologie
Förderzeitraum 2018
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/17894/Yu_GigaScience.pdf
16456
2016
eng
302
17
article
1
2018-07-16
--
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Genome-wide transcription start site mapping of Bradyrhizobium japonicum grown free-living or in symbiosis - a rich resource to identify new transcripts, proteins and to study gene regulation
Background
Differential RNA-sequencing (dRNA-seq) is indispensable for determination of primary transcriptomes. However, using dRNA-seq data to map transcriptional start sites (TSSs) and promoters genome-wide is a bioinformatics challenge. We performed dRNA-seq of Bradyrhizobium japonicum USDA 110, the nitrogen-fixing symbiont of soybean, and developed algorithms to map TSSs and promoters.
Results
A specialized machine learning procedure for TSS recognition allowed us to map 15,923 TSSs: 14,360 in free-living bacteria, 4329 in symbiosis with soybean and 2766 in both conditions. Further, we provide proteomic evidence for 4090 proteins, among them 107 proteins corresponding to new genes and 178 proteins with N-termini different from the existing annotation (72 and 109 of them with TSS support, respectively). Guided by proteomics evidence, previously identified TSSs and TSSs experimentally validated here, we assign a score threshold to flag 14 % of the mapped TSSs as a class of lower confidence. However, this class of lower confidence contains valid TSSs of low-abundant transcripts. Moreover, we developed a de novo algorithm to identify promoter motifs upstream of mapped TSSs, which is publicly available, and found motifs mainly used in symbiosis (similar to RpoN-dependent promoters) or under both conditions (similar to RpoD-dependent promoters). Mapped TSSs and putative promoters, proteomic evidence and updated gene annotation were combined into an annotation file.
Conclusions
The genome-wide TSS and promoter maps along with the extended genome annotation of B. japonicum represent a valuable resource for future systems biology studies and for detailed analyses of individual non-coding transcripts and ORFs. Our data will also provide new insights into bacterial gene regulation during the agriculturally important symbiosis between rhizobia and legumes.
BMC Genomics
10.1186/s12864-016-2602-9
urn:nbn:de:bvb:20-opus-164565
BMC Genomics (2016) 17:302
false
true
CC BY: Creative-Commons-Lizenz: Namensnennung 4.0 International
Jelena Čuklina
Julia Hahn
Maxim Imakaev
Ulrich Omasits
Konrad U. Förstner
Nikolay Ljubimov
Melanie Goebel
Gabriella Pessi
Hans-Martin Fischer
Christian H. Ahrens
Mikhail S. Gelfand
Elena Evguenieva-Hackenberg
eng
uncontrolled
Bradyrhizobium
eng
uncontrolled
RNA-seq
eng
uncontrolled
Promoter prediction
eng
uncontrolled
Genome re-annotation
eng
uncontrolled
Internal transcription start site
eng
uncontrolled
Nodule
eng
uncontrolled
Transcription start site
eng
uncontrolled
Proteogenomics
eng
uncontrolled
Antisense RNA
Medizin und Gesundheit
open_access
Institut für Molekulare Infektionsbiologie
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/16456/015_Cuklina_BMC-GENOMICS.pdf
13644
2015
eng
1373
6
article
1
2016-07-25
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Phenotypic Heterogeneity Affects Stenotrophomonas maltophilia K279a Colony Morphotypes and \(\beta\)-Lactamase Expression
Phenotypic heterogeneity at the cellular level in response to various stresses, e.g., antibiotic treatment has been reported for a number of bacteria. In a clonal population, cell-to-cell variation may result in phenotypic heterogeneity that is a mechanism to survive changing environments including antibiotic therapy. Stenotrophomonas rnaltophilia has been frequently isolated from cystic fibrosis patients, can cause numerous infections in other organs and tissues, and is difficult to treat due to antibiotic resistances. S. maltophilia K279a produces the Li and L2 beta-lactamases in response to beta-lactam treatment. Here we report that the patient isolate S. rnaltophilia K279a diverges into cellular subpopulations with distinct but reversible morphotypes of small and big colonies when challenged with ampicillin. This observation is consistent with the formation of elongated chains of bacteria during exponential growth phase and the occurrence of mainly rod-shaped cells in liquid media. RNA-seq analysis of small versus big colonies revealed differential regulation of at least seven genes among the colony morphotypes. Among those, bleu and bla(L2) were transcriptionally the most strongly upregulated genes. Promoter fusions of b/a(L1) and b/a(L2) genes indicated that expression of both genes is also subject to high levels of phenotypic heterogeneous expression on a single cell level. Additionally, the comE homolog was found to be differentially expressed in homogenously versus heterogeneously bla(L2) expressing cells as identified by RNA(seq) analysis. Overexpression of cornE in S. maltophilia K279a reduced the level of cells that were in a bla(L2)-ON mode to 1% or lower. Taken together, our data provide strong evidence that S. maltophilia K279a populations develop phenotypic heterogeneity in an ampicillin challenged model. This cellular variability is triggered by regulation networks including b/a(L1), b/a(L2), and comE.
Frontiers in Microbiology
10.3389/fmicb.2015.01373
urn:nbn:de:bvb:20-opus-136446
Frontiers in Microbiology 6:1373. doi:10.3389/fmicb.2015.01373
278864-2
Ebrahim M. Abda
Dagmar Krysciak
Ines Krohn-Molt
Uwe Mamat
Christel Schmeisser
Konrad U. Förstner
Ulrich E. Schaible
Thomas A. Kohi
Stefan Nieman
Wolfgang R. Streit
eng
uncontrolled
xanthomonas maltophilia
eng
uncontrolled
gram-negative bacteria
eng
uncontrolled
RNA-seq
eng
uncontrolled
pseudomas aeruginosa
eng
uncontrolled
antibiotic resistance
eng
uncontrolled
colony morphotypes
eng
uncontrolled
beta-lactamases
eng
uncontrolled
K279a
eng
uncontrolled
Stenotrophomonas maltophilia
eng
uncontrolled
phenotypic heterogeneity
eng
uncontrolled
persister cells
eng
uncontrolled
streptococcus pneumoniae
eng
uncontrolled
nosocomial pathogen
eng
uncontrolled
membrane vesicles
eng
uncontrolled
sinorhizobium fredii NGR234
eng
uncontrolled
red fluorescent protein
eng
uncontrolled
escherichia coli
Medizin und Gesundheit
open_access
Institut für Molekulare Infektionsbiologie
OpenAIRE
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/13644/fmicb-06-01373.pdf