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Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity

Nature Reviews Genetics volume 11, pages 9–16 (2010)Cite this article

Abstract

Transcriptome-wide studies in eukaryotes have been instrumental in the characterization of fundamental regulatory mechanisms for more than a decade. By contrast, in prokaryotes (bacteria and archaea) whole-transcriptome studies have not been performed until recently owing to the general view that microbial gene structures are simple, as well as technical difficulties in enriching for mRNAs that lack poly(A) tails. Deep RNA sequencing and tiling array studies are now revolutionizing our understanding of the complexity, plasticity and regulation of microbial transcriptomes.

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Figure 1: Contribution of transcriptomics to annotation of functional elements.
Figure 2: Multifunctional RNA elements in Listeria monocytogenes.
Figure 3: Metatranscriptomics: a flow diagram of the steps involved in metatranscriptome sequencing and analysis.

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Acknowledgements

We thank O. Wurtzel and A. Levy for stimulating comments. R.S. is supported, in part, by the Israel Science Foundation Focal Initiatives in Research in Science and Technology (FIRST) program (grant 1615/09), the Crown Human Genome Center, the Y. Leon Benoziyo Institute for Molecular Medicine and the M.D. Moross Institute for Cancer Research at the Weizmann Institute of Science, as well as the Alon Fellowship. P.C. is a Howard Hughes International Scholar. She has received financial support for her work on RNA from the Agence Nationale de la Recherche, the European Union (BacRNA 2005-018618) and recently from the European Research Council.

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Authors and Affiliations

  1. Rotem Sorek is at the Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.,

    Rotem Sorek

  2. Pascale Cossart is at the Institut Pasteur, Unité des Interactions Bactéries-Cellules, Paris F-75015, France; the Institut National de la Santé et de la Recherche Médicale U604, Paris F-75015, France; and the Institut National de la Recherche Agronomique USC2020, Paris F-75015, France.,

    Pascale Cossart

  3. the Institut National de la Santé et de la Recherche Médicale U604, Paris F-75015, France,

    Pascale Cossart

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Correspondence to Rotem Sorek.

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Glossary

Expressed sequence tag

A fragment of cDNA that is generated using random shotgun sequencing of the transcriptome.

Genomic tiling array

A DNA microarray that uses a set of overlapping oligonucleotide probes that cover the whole genome or a proportion of the genome at high resolution.

Polycistronic mRNA

An mRNA (also known as a polycistron) that encodes several polypeptides. Polycistronic transcripts are common in bacteria.

Quorum sensing

A mechanism used by many bacteria to detect a critical bacterial cell density. Some genes are only expressed at high cell density. Cell densities are proportional to the concentration of small molecules or peptides (autoinducers) that are secreted by the bacteria in the medium. These molecules coordinate the expression of specific genes — for example, virulence genes in pathogenic bacteria.

Riboswitch

An RNA element that is located at the 5′ end of an mRNA and that can adopt alternative structures. When a riboswitch binds a metabolite, metal or even a tRNA, the transcription of the downstream gene or, in some cases, the translation of the gene is inhibited.

RNA–seq

An approach for whole-transcriptome profiling in which a population of RNA is converted to cDNA and subjected to high-throughput sequencing. Sequences are mapped to the genome to generate a high-resolution transcriptome map.

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Sorek, R., Cossart, P. Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity. Nat Rev Genet 11, 9–16 (2010). https://doi.org/10.1038/nrg2695

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