The LysR-type transcriptional regulator VtlR/LsrB controls expression of multiple small RNA and small protein genes in Agrobacterium tumefaciens
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ABSTRACT:
PROVIDER: PRJNA670952 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12884751_1.fastq.gz | Fastqsanger.gz | |||
| SRR12884751_2.fastq.gz | Fastqsanger.gz | |||
| SRR12884752_1.fastq.gz | Fastqsanger.gz | |||
| SRR12884752_2.fastq.gz | Fastqsanger.gz | |||
| SRR12884753_1.fastq.gz | Fastqsanger.gz |
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Project description:We investigated the role of the LysR-type transcriptional regulator VtlR/LsrB (Atu2186) from Agrobacterium tumefaciens C58 (alias A. fabrum C58), which regulates the expression of small-regulatory-RNA (sRNA) genes such as AbcR1 and the expression of genes encoding small proteins with a domain of unknown function DUF1127. For this purpose, we constructed a vtlR/lsrB deletion mutant. Total RNA was isolated from this mutant as well as from an AbcR1 deletion mutant (Wilms et al., 2011) at optical densities (OD) of 0.5 or 0.5 and 1.5, respectively. Sequencing was done on the Illumina NovaSeq 6000 platform. In addition to annotated genes (NCBI genome: 13606), almost 700 previously described sRNA genes (Wilms et al., 2012; Lee et al., 2013; Möller et al., 2014) were also considered within our data analysis. Wild-type samples that derived from the same experiment were published previously (Kraus et al., 2020) (GEO accession: GSE150941). In the vtlR/lsrB mutant a total of 542 genes were downregulated and 665 were upregulated at least three-fold (p value ≤ 0.05). Among those were 25 downregulated sRNA genes (including AbcR1) and 77 upregulated sRNA genes. In the AbcR1 mutant 8 or 20 genes were downregulated at ODs 0.5 or 1.5, respectively, and 72 or 31 were upregulated. A total of 39 differentially expressed genes from the vtlR/lsrB mutant also displayed identical regulation in the AbcR1 mutant and thus are controlled indirectly by VtlR/LsrB via the sRNA AbcR1. Overall, the results demonstrate the complex network of VtlR/LsrB and regulatory sRNAs, which has a great impact on the transcriptome of A. tumefaciens. Kraus, A., Weskamp, M., Zierles, J., Balzer, M., Busch, R., Eisfeld, J., et al. (2020) Arginine-rich small proteins with a domain of unknown function DUF1127 play a role in phosphate and carbon metabolism of Agrobacterium tumefaciens. J Bacteriol 202: e00309-20. Lee, K., Huang, X., Yang, C., Lee, D., Ho, V., Nobuta, K., et al. (2013) A genome-wide survey of highly expressed non-coding RNAs and biological validation of selected candidates in Agrobacterium tumefaciens. PLoS One 8: e70720. Möller, P., Overlöper, A., Förstner, K.U., Wen, T.N., Sharma, C.M., Lai, E.M., and Narberhaus, F. (2014) Profound impact of Hfq on nutrient acquisition, metabolism and motility in the plant pathogen Agrobacterium tumefaciens. PLoS One 9: e110427. Wilms, I., Overlöper, A., Nowrousian, M., Sharma, C.M., and Narberhaus, F. (2012) Deep sequencing uncovers numerous small RNAs on all four replicons of the plant pathogen Agrobacterium tumefaciens. RNA Biol 9: 446–57. Wilms, I., Voss, B., Hess, W.R., Leichert, L.I., and Narberhaus, F. (2011) Small RNA-mediated control of the Agrobacterium tumefaciens GABA binding protein. Mol Microbiol 80: 492–506.
2020-10-24 | GSE159961 | GEO
Project description:We investigated the role of the LysR-type transcriptional regulator LsrB (Atu2186) from Agrobacterium tumefaciens C58 (alias A. fabrum C58), which regulates the expression of small-regulatory-RNA (sRNA) and several protein-coding genes, such as ampD (atu2113). In our current study we invesigated the role of LsrB in beta-lactam resistance. For this purpose, we constructed a vtlR/lsrB deletion mutant. Total RNA was isolated from this mutant. Sequencing was done on the Illumina NovaSeq 6000 platform. Wild-type samples that derived from the same experiment were published previously (Kraus et al., 2020) (GEO accession: GSE150941). In the vtlR/lsrB mutant around 800 protein coding genes and around 80 sRNA coding genes were downregulated or upregulated at least three-fold (p value ≤ 0.05). Overall, the results demonstrate the huge regulatory effect of LsrB on the transcriptome of A. tumefaciens. Kraus, A., Weskamp, M., Zierles, J., Balzer, M., Busch, R., Eisfeld, J., et al. (2020) Arginine-rich small proteins with a domain of unknown function DUF1127 play a role in phosphate and carbon metabolism of Agrobacterium tumefaciens. J Bacteriol 202: e00309-20.
2023-08-12 | GSE240243 | GEO
Project description:This research focuses on the design, manufacturing and validation of a new Agrobacterium tumefaciens C58 whole-genome tiling microarray platform for novel RNA transcript discovery. A whole-genome tiling microarray allows both annotated genes as well as previously unknown RNA transcripts to be detected and quantified at once. The Agrobacterium tumefaciens C58 genome is re-acquired with next-generation sequencing and then used to design the tilinlg microarray with the thermodynamic analysis program Picky. Validations are performed by subjecting Agrobacterium tumefaciens C58 under various growth conditions and then using the tling microarrays to verify expected gene expression patterns.
2014-09-25 | GSE61737 | GEO
Project description:As sessile organisms, plants require dynamic pathways in order to recognize pathogens and coordinate plant defenses by signalling. Agrobacterium tumefaciens C58 is able to avoid triggering plant defenses prior to entering the cell, and therefore is only detected once infection has begun making Agrobacterium a plant pathogen to numerous plant species. Understanding plant responses to Agrobacterium will be useful in improving plant defenses and potentially may also improve plant transformation efficiency. Microarrays were utilized for detailing the global gene expression pattern in A. thaliana Col-0 roots in response to A. tumefaciens C58 for the identification of differentially expressed genes.
2014-10-28 | GSE62750 | GEO
Project description:As sessile organisms, plants require dynamic pathways in order to recognize pathogens and coordinate plant defenses by signalling. Agrobacterium tumefaciens C58 is able to avoid triggering plant defenses prior to entering the cell, and therefore is only detected once infection has begun making Agrobacterium a plant pathogen to numerous plant species. Understanding plant responses to Agrobacterium will be useful in improving plant defenses and potentially may also improve plant transformation efficiency. Microarrays were utilized for detailing the global gene expression pattern in A. thaliana Col-0 leafs in response to A. tumefaciens C58 for the identification of differentially expressed genes.
2014-10-28 | GSE62749 | GEO
Project description:The genome of Agrobacterium tumefaciens C58 harbors three genes encoding small proteins (<50 aa) with a domain of unknown function DUF1127 (ATU_RS08170, ATU_RS08175, ATU_RS21905). To investigate their function we created a triple-deletion mutant lacking those genes. Total RNA was isolated from A. tumefaciens wild type and from the triple mutant (∆∆∆) at optical densities (OD) of 0.5 and 1.5, and after 24 h of growth (30 °C in YEB medium at 180 rpm) and sequenced on an Illumina platform. For data analysis, 672 small regulatory RNA (sRNA) genes annotated by Wilms et al. (1), Lee et al. (2) and Möller et al. (3) were added to the genome. At OD 0.5 a total of 76 genes showed significantly altered expression in ΔΔΔ. The number increased to 896 and 2,575 genes at OD 1.5 and after 24 h, respectively. 15 genes were upregulated in all three growth phases in ΔΔΔ. At ODs 0.5 and 1.5 numerous genes associated with glycine/serine synthesis were upregulated in the mutant. Additionally, phosphorus starvation and denitrification genes were highly induced at OD 1.5, whereas almost all sugar ABC-transporter genes were downregulated. Overall, the results demonstrate a great impact of DUF1127 proteins on the transcriptome of A. tumefaciens. 1. Wilms I, Overlöper A, Nowrousian M, Sharma CM, Narberhaus F. 2012. Deep sequencing uncovers numerous small RNAs on all four replicons of the plant pathogen Agrobacterium tumefaciens. RNA Biol 9:446–57. 2. Lee K, Huang X, Yang C, Lee D, Ho V, Nobuta K, Fan JB, Wang K. 2013. A genome-wide survey of highly expressed non-coding RNAs and biological validation of selected candidates in Agrobacterium tumefaciens. PLoS One 8:e70720. 3. Möller P, Overlöper A, Förstner KU, Wen TN, Sharma CM, Lai EM, Narberhaus F. 2014. Profound impact of Hfq on nutrient acquisition, metabolism and motility in the plant pathogen Agrobacterium tumefaciens. PLoS One 9:e110427.
2020-05-21 | GSE150941 | GEO
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