1
|
Dequivre M, Diel B, Villard C, Sismeiro O, Durot M, Coppée JY, Nesme X, Vial L, Hommais F. Small RNA Deep-Sequencing Analyses Reveal a New Regulator of Virulence in Agrobacterium fabrum C58. Mol Plant Microbe Interact 2015; 28:580-589. [PMID: 26024442 DOI: 10.1094/mpmi-12-14-0380-fi] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Novel ways of regulating Ti plasmid functions were investigated by studying small RNAs (sRNAs) that are known to act as posttranscriptional regulators in plant pathogenic bacteria. sRNA-seq analyses of Agrobacterium fabrum C58 allowed us to identify 1,108 small transcripts expressed in several growth conditions that could be sRNAs. A quarter of them were confirmed by bioinformatics or by biological experiments. Antisense RNAs represent 24% of the candidates and they are over-represented on the pTi (with 62% of pTi sRNAs), suggesting differences in the regulatory mechanisms between the essential and accessory replicons. Moreover, a large number of these pTi antisense RNAs are transcribed opposite to those genes involved in virulence. Others are 5'- and 3'-untranslated region RNAs and trans-encoded RNAs. We have validated, by rapid amplification of cDNA ends polymerase chain reaction, the transcription of 14 trans-encoded RNAs, among which RNA1111 is expressed from the pTiC58. Its deletion decreased the aggressiveness of A. fabrum C58 on tomatoes, tobaccos, and kalanchoe, suggesting that this sRNA activates virulence. The identification of its putative target mRNAs (6b gene, virC2, virD3, and traA) suggests that this sRNA may coordinate two of the major pTi functions, the infection of plants and its dissemination among bacteria.
Collapse
Affiliation(s)
- M Dequivre
- 1Université de Lyon, F-69622, Lyon, France
- 2Université Lyon 1, F-69622 Villeurbanne, France
- 3CNRS, UMR 5240 Microbiologie Adaptation et Pathogénie, F-69622 Villeurbanne, France
| | - B Diel
- 1Université de Lyon, F-69622, Lyon, France
- 2Université Lyon 1, F-69622 Villeurbanne, France
- 3CNRS, UMR 5240 Microbiologie Adaptation et Pathogénie, F-69622 Villeurbanne, France
- 4CNRS, UMR 5557 Ecologie Microbienne, F-69622 Villeurbanne, France
- 5INRA, USC 1364 Ecologie Microbienne, F-69622 Villeurbanne, France
| | - C Villard
- 1Université de Lyon, F-69622, Lyon, France
- 2Université Lyon 1, F-69622 Villeurbanne, France
- 3CNRS, UMR 5240 Microbiologie Adaptation et Pathogénie, F-69622 Villeurbanne, France
| | - O Sismeiro
- 6Plate-forme Transcriptome et Epigénome, Département Génomes et Génétique, Institut Pasteur, 25 rue du Dr. Roux, F75015 Paris, France
| | - M Durot
- 7CEA/DSV/FAR/IG/Genoscope and CNRS UMR8030 Laboratoire d'Analyses Bioinformatiques en Métabolisme et Génomique, 2 rue Gaston Crémieux 91057 Evry cedex, France
- 8Total New Energies USA, 5858 Horton Street, Emeryville, CA 94608, U.S.A
| | - J Y Coppée
- 6Plate-forme Transcriptome et Epigénome, Département Génomes et Génétique, Institut Pasteur, 25 rue du Dr. Roux, F75015 Paris, France
| | - X Nesme
- 1Université de Lyon, F-69622, Lyon, France
- 2Université Lyon 1, F-69622 Villeurbanne, France
- 4CNRS, UMR 5557 Ecologie Microbienne, F-69622 Villeurbanne, France
- 5INRA, USC 1364 Ecologie Microbienne, F-69622 Villeurbanne, France
| | - L Vial
- 1Université de Lyon, F-69622, Lyon, France
- 2Université Lyon 1, F-69622 Villeurbanne, France
- 4CNRS, UMR 5557 Ecologie Microbienne, F-69622 Villeurbanne, France
- 5INRA, USC 1364 Ecologie Microbienne, F-69622 Villeurbanne, France
| | - F Hommais
- 1Université de Lyon, F-69622, Lyon, France
- 2Université Lyon 1, F-69622 Villeurbanne, France
- 3CNRS, UMR 5240 Microbiologie Adaptation et Pathogénie, F-69622 Villeurbanne, France
| |
Collapse
|
2
|
Abstract
We describe a rapid method for determining nucleotide sequences directly from total genomic DNA. This technique was used to determine genomic DNA sequences in various prokaryotic and eukaryotic microorganisms with a G+C content between 40 and 50%, e.g. Escherichia coli, Vibrio cholerae, Bacillus subtilis and Saccharomyces cerevisiae. Furthermore, the method was applied to accurately sequence up to 300 DNA base pairs in Photorhabdus luminescens, whose genome sequencing is currently under way. Taken together, these results provide evidence that our technique can be widely used to easily and efficiently determine genomic DNA sequences.
Collapse
Affiliation(s)
- E Krin
- Unité des Génétique deo Génomes Bactériens, Institut Pasteur, 28 rue du Dr. Roux, 75724 Cedex 15, Paris, France
| | | | | | | | | | | |
Collapse
|
3
|
Hommais F, Krin E, Laurent-Winter C, Soutourina O, Malpertuy A, Le Caer JP, Danchin A, Bertin P. Large-scale monitoring of pleiotropic regulation of gene expression by the prokaryotic nucleoid-associated protein, H-NS. Mol Microbiol 2001; 40:20-36. [PMID: 11298273 DOI: 10.1046/j.1365-2958.2001.02358.x] [Citation(s) in RCA: 319] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Despite many years of intense work investigating the function of nucleoid-associated proteins in prokaryotes, their role in bacterial physiology remains largely unknown. The two-dimensional protein patterns were compared and expression profiling was carried out on H-NS-deficient and wild-type strains of Escherichia coli K-12. The expression of approximately 5% of the genes and/or the accumulation of their protein was directly or indirectly altered in the hns mutant strain. About one-fifth of these genes encode proteins that are involved in transcription or translation and one-third are known to or were in silico predicted to encode cell envelope components or proteins that are usually involved in bacterial adaptation to changes in environmental conditions. The increased expression of several genes in the mutant resulted in a better ability of this strain to survive at low pH and high osmolarity than the wild-type strain. In particular, the putative regulator, YhiX, plays a central role in the H-NS control of genes required in the glutamate-dependent acid stress response. These results suggest that there is a strong relationship between the H-NS regulon and the maintenance of intracellular homeostasis.
Collapse
Affiliation(s)
- F Hommais
- Unité de Régulation de l'Expression Génétique, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris, France
| | | | | | | | | | | | | | | |
Collapse
|
4
|
Bertin P, Hommais F, Krin E, Soutourina O, Tendeng C, Derzelle S, Danchin A. H-NS and H-NS-like proteins in Gram-negative bacteria and their multiple role in the regulation of bacterial metabolism. Biochimie 2001; 83:235-41. [PMID: 11278074 DOI: 10.1016/s0300-9084(01)01247-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
In Escherichia coli, the H-NS protein plays an important role in the structure and the functioning of bacterial chromosome. A homologous protein has also been identified in several enteric bacteria and in closely related organisms such as Haemophilus influenzae. To get information on their structure and their function, we identified H-NS-like proteins in various microorganisms by different procedures. In silico analysis of their amino acid sequence and/or in vivo experiments provide evidence that more than 20 proteins belong to the same class of regulatory proteins. Moreover, large scale technologies demonstrate that, at least in E. coli, the loss of motility in hns mutants results from a lack of flagellin biosynthesis, due to the in vivo repression of flagellar gene expression. In contrast, several genes involved in adaptation to low pH are strongly induced in a H-NS deficient strain, resulting in an increased resistance to acidic stress. Finally, expression profiling and phenotypic analysis suggest that, unlike H-NS, its paralogous protein StpA does not play any role in these processes.
Collapse
Affiliation(s)
- P Bertin
- Unité de Régulation de l' Expression Génétique, Institut Pasteur, 28, rue du Dr.-Roux, 75724 Paris cedex 15, France.
| | | | | | | | | | | | | |
Collapse
|