Tracing the phylogenetic history of the Crl regulon through the Bacteria and Archaea genomes
Abstract Background Crl, identified for curli production, is a small transcription factor that stimulates the association of the σS factor (RpoS) with the RNA polymerase core through direct and specific interactions, increasing the transcription rate of genes during the transition from exponential t...
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| Format: | Article |
| Language: | English |
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BMC
2019-04-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-019-5619-z |
| _version_ | 1819068703532122112 |
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| author | A. Santos-Zavaleta E. Pérez-Rueda M. Sánchez-Pérez D. A. Velázquez-Ramírez J. Collado-Vides |
| author_facet | A. Santos-Zavaleta E. Pérez-Rueda M. Sánchez-Pérez D. A. Velázquez-Ramírez J. Collado-Vides |
| author_sort | A. Santos-Zavaleta |
| collection | DOAJ |
| description | Abstract Background Crl, identified for curli production, is a small transcription factor that stimulates the association of the σS factor (RpoS) with the RNA polymerase core through direct and specific interactions, increasing the transcription rate of genes during the transition from exponential to stationary phase at low temperatures, using indole as an effector molecule. The lack of a comprehensive collection of information on the Crl regulon makes it difficult to identify a dominant function of Crl and to generate any hypotheses concerning its taxonomical distribution in archaeal and bacterial organisms. Results In this work, based on a systematic literature review, we identified the first comprehensive dataset of 86 genes under the control of Crl in the bacterium Escherichia coli K-12; those genes correspond to 40% of the σS regulon in this bacterium. Based on an analysis of orthologs in 18 archaeal and 69 bacterial taxonomical divisions and using E. coli K-12 as a framework, we suggest three main events that resulted in this regulon’s actual form: (i) in a first step, rpoS, a gene widely distributed in bacteria and archaea cellular domains, was recruited to regulate genes involved in ancient metabolic processes, such as those associated with glycolysis and the tricarboxylic acid cycle; (ii) in a second step, the regulon recruited those genes involved in metabolic processes, which are mainly taxonomically constrained to Proteobacteria, with some secondary losses, such as those genes involved in responses to stress or starvation and cell adhesion, among others; and (iii) in a posterior step, Crl might have been recruited in Enterobacteriaceae; because its taxonomical pattern constrained to this bacterial order, however further analysis are necessary. Conclusions Therefore, we suggest that the regulon Crl is highly flexible for phenotypic adaptation, probably as consequence of the diverse growth environments associated with all organisms in which members of this regulatory network are present. |
| first_indexed | 2024-12-21T16:38:22Z |
| format | Article |
| id | doaj.art-be2ac2c21c81474b8d216a6c3d03da04 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-21T16:38:22Z |
| publishDate | 2019-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-be2ac2c21c81474b8d216a6c3d03da042022-12-21T18:57:10ZengBMCBMC Genomics1471-21642019-04-0120111310.1186/s12864-019-5619-zTracing the phylogenetic history of the Crl regulon through the Bacteria and Archaea genomesA. Santos-Zavaleta0E. Pérez-Rueda1M. Sánchez-Pérez2D. A. Velázquez-Ramírez3J. Collado-Vides4Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de MéxicoInstituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Sede Mérida, Universidad Nacional Autónoma de México, Unidad Académica de Ciencias y TecnologíaPrograma de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de MéxicoPrograma de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de MéxicoPrograma de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de MéxicoAbstract Background Crl, identified for curli production, is a small transcription factor that stimulates the association of the σS factor (RpoS) with the RNA polymerase core through direct and specific interactions, increasing the transcription rate of genes during the transition from exponential to stationary phase at low temperatures, using indole as an effector molecule. The lack of a comprehensive collection of information on the Crl regulon makes it difficult to identify a dominant function of Crl and to generate any hypotheses concerning its taxonomical distribution in archaeal and bacterial organisms. Results In this work, based on a systematic literature review, we identified the first comprehensive dataset of 86 genes under the control of Crl in the bacterium Escherichia coli K-12; those genes correspond to 40% of the σS regulon in this bacterium. Based on an analysis of orthologs in 18 archaeal and 69 bacterial taxonomical divisions and using E. coli K-12 as a framework, we suggest three main events that resulted in this regulon’s actual form: (i) in a first step, rpoS, a gene widely distributed in bacteria and archaea cellular domains, was recruited to regulate genes involved in ancient metabolic processes, such as those associated with glycolysis and the tricarboxylic acid cycle; (ii) in a second step, the regulon recruited those genes involved in metabolic processes, which are mainly taxonomically constrained to Proteobacteria, with some secondary losses, such as those genes involved in responses to stress or starvation and cell adhesion, among others; and (iii) in a posterior step, Crl might have been recruited in Enterobacteriaceae; because its taxonomical pattern constrained to this bacterial order, however further analysis are necessary. Conclusions Therefore, we suggest that the regulon Crl is highly flexible for phenotypic adaptation, probably as consequence of the diverse growth environments associated with all organisms in which members of this regulatory network are present.http://link.springer.com/article/10.1186/s12864-019-5619-zCrl regulonStress responseTranscription factorsComparative genomicsBacteriaArchaea |
| spellingShingle | A. Santos-Zavaleta E. Pérez-Rueda M. Sánchez-Pérez D. A. Velázquez-Ramírez J. Collado-Vides Tracing the phylogenetic history of the Crl regulon through the Bacteria and Archaea genomes BMC Genomics Crl regulon Stress response Transcription factors Comparative genomics Bacteria Archaea |
| title | Tracing the phylogenetic history of the Crl regulon through the Bacteria and Archaea genomes |
| title_full | Tracing the phylogenetic history of the Crl regulon through the Bacteria and Archaea genomes |
| title_fullStr | Tracing the phylogenetic history of the Crl regulon through the Bacteria and Archaea genomes |
| title_full_unstemmed | Tracing the phylogenetic history of the Crl regulon through the Bacteria and Archaea genomes |
| title_short | Tracing the phylogenetic history of the Crl regulon through the Bacteria and Archaea genomes |
| title_sort | tracing the phylogenetic history of the crl regulon through the bacteria and archaea genomes |
| topic | Crl regulon Stress response Transcription factors Comparative genomics Bacteria Archaea |
| url | http://link.springer.com/article/10.1186/s12864-019-5619-z |
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