Comprehensive discovery and characterization of small RNAs in Corynebacterium glutamicum ATCC 13032

Mentz A, Neshat A, Pfeifer-Sancar K, Pühler A, Rückert C, Kalinowski J (2013)
BMC Genomics 14(1): 714.

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Zeitschriftenaufsatz | Veröffentlicht | Englisch
Abstract / Bemerkung
BACKGROUND: Recent discoveries on bacterial transcriptomes gave evidence that small RNAs (sRNAs) have important regulatory roles in prokaryotic cells. Modern high-throughput sequencing approaches (RNA-Seq) enable the most detailed view on transcriptomes offering an unmatched comprehensiveness and single-base resolution. Whole transcriptome data obtained by RNA-Seq can be used to detect and characterize all transcript species, including small RNAs. Here, we describe an RNA-Seq approach for comprehensive detection and characterization of small RNAs from Corynebacterium glutamicum, an actinobacterium of high industrial relevance and model organism for medically important Corynebacterianeae, such as C. diphtheriae and Mycobacterium tuberculosis. RESULTS: In our RNA-Seq approach, total RNA from C. glutamicum ATCC 13032 was prepared from cultures grown in minimal medium at exponential growth or challenged by physical (heat shock, cold shock) or by chemical stresses (diamide, H2O2, NaCl) at this time point. Total RNA samples were pooled and sequencing libraries were prepared from the isolated small RNA fraction. High throughput short read sequencing and mapping yielded over 800 sRNA genes. By determining their 5[prime]- and 3[prime]-ends and inspection of their locations, these potential sRNA genes were classified into UTRs of mRNAs (316), cis-antisense sRNAs (543), and trans-encoded sRNAs (262). For 77 of trans-encoded sRNAs significant sequence and secondary structure conservation was found by a computational approach using a whole genome alignment with the closely related species C. efficiens YS-314 and C. diphtheriae NCTC 13129. Three selected trans-encoded sRNAs were characterized by Northern blot analysis and stress-specific transcript patterns were found. CONCLUSIONS: The study showed comparable numbers of sRNAs known from genome-wide surveys in other bacteria. In detail, our results give deep insight into the comprehensive equipment of sRNAs in C. glutamicum and provide a sound basis for further studies concerning the functions of these sRNAs.
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BMC Genomics
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14
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1
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714
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Article Processing Charge funded by the Deutsche Forschungsgemeinschaft and the Open Access Publication Fund of Bielefeld University.
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Mentz A, Neshat A, Pfeifer-Sancar K, Pühler A, Rückert C, Kalinowski J. Comprehensive discovery and characterization of small RNAs in Corynebacterium glutamicum ATCC 13032. BMC Genomics. 2013;14(1):714.
Mentz, A., Neshat, A., Pfeifer-Sancar, K., Pühler, A., Rückert, C., & Kalinowski, J. (2013). Comprehensive discovery and characterization of small RNAs in Corynebacterium glutamicum ATCC 13032. BMC Genomics, 14(1), 714. doi:10.1186/1471-2164-14-714
Mentz, A., Neshat, A., Pfeifer-Sancar, K., Pühler, A., Rückert, C., and Kalinowski, J. (2013). Comprehensive discovery and characterization of small RNAs in Corynebacterium glutamicum ATCC 13032. BMC Genomics 14, 714.
Mentz, A., et al., 2013. Comprehensive discovery and characterization of small RNAs in Corynebacterium glutamicum ATCC 13032. BMC Genomics, 14(1), p 714.
A. Mentz, et al., “Comprehensive discovery and characterization of small RNAs in Corynebacterium glutamicum ATCC 13032”, BMC Genomics, vol. 14, 2013, pp. 714.
Mentz, A., Neshat, A., Pfeifer-Sancar, K., Pühler, A., Rückert, C., Kalinowski, J.: Comprehensive discovery and characterization of small RNAs in Corynebacterium glutamicum ATCC 13032. BMC Genomics. 14, 714 (2013).
Mentz, Almut, Neshat, Armin, Pfeifer-Sancar, Katharina, Pühler, Alfred, Rückert, Christian, and Kalinowski, Jörn. “Comprehensive discovery and characterization of small RNAs in Corynebacterium glutamicum ATCC 13032”. BMC Genomics 14.1 (2013): 714.
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28 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Improving the genome annotation of the acarbose producer Actinoplanes sp. SE50/110 by sequencing enriched 5'-ends of primary transcripts.
Schwientek P, Neshat A, Kalinowski J, Klein A, Rückert C, Schneiker-Bekel S, Wendler S, Stoye J, Pühler A., J Biotechnol 190(), 2014
PMID: 24642337
Comprehensive analysis of the Corynebacterium glutamicum transcriptome using an improved RNAseq technique.
Pfeifer-Sancar K, Mentz A, Rückert C, Kalinowski J., BMC Genomics 14(), 2013
PMID: 24341750

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