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Santillán O, Ramírez-Romero MA, Dávila G. CAPRRESI: Chimera Assembly by Plasmid Recovery and Restriction Enzyme Site Insertion. J Vis Exp 2017. [DOI: 10.3791/55526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
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Santillán O, Ramírez-Romero MA, Lozano L, Checa A, Encarnación SM, Dávila G. Region 4 of Rhizobium etli Primary Sigma Factor (SigA) Confers Transcriptional Laxity in Escherichia coli. Front Microbiol 2016; 7:1078. [PMID: 27468278 PMCID: PMC4943231 DOI: 10.3389/fmicb.2016.01078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 06/27/2016] [Indexed: 11/13/2022] Open
Abstract
Sigma factors are RNA polymerase subunits engaged in promoter recognition and DNA strand separation during transcription initiation in bacteria. Primary sigma factors are responsible for the expression of housekeeping genes and are essential for survival. RpoD, the primary sigma factor of Escherichia coli, a γ-proteobacteria, recognizes consensus promoter sequences highly similar to those of some α-proteobacteria species. Despite this resemblance, RpoD is unable to sustain transcription from most of the α-proteobacterial promoters tested so far. In contrast, we have found that SigA, the primary sigma factor of Rhizobium etli, an α-proteobacteria, is able to transcribe E. coli promoters, although it exhibits only 48% identity (98% coverage) to RpoD. We have called this the transcriptional laxity phenomenon. Here, we show that SigA partially complements the thermo-sensitive deficiency of RpoD285 from E. coli strain UQ285 and that the SigA region σ4 is responsible for this phenotype. Sixteen out of 74 residues (21.6%) within region σ4 are variable between RpoD and SigA. Mutating these residues significantly improves SigA ability to complement E. coli UQ285. Only six of these residues fall into positions already known to interact with promoter DNA and to comprise a helix-turn-helix motif. The remaining variable positions are located on previously unexplored sites inside region σ4, specifically into the first two α-helices of the region. Neither of the variable positions confined to these helices seem to interact directly with promoter sequence; instead, we adduce that these residues participate allosterically by contributing to correct region folding and/or positioning of the HTH motif. We propose that transcriptional laxity is a mechanism for ensuring transcription in spite of naturally occurring mutations from endogenous promoters and/or horizontally transferred DNA sequences, allowing survival and fast environmental adaptation of α-proteobacteria.
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Affiliation(s)
- Orlando Santillán
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México Cuernavaca, Mexico
| | | | - Luis Lozano
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México Cuernavaca, Mexico
| | - Alberto Checa
- Programa de Genómica Funcional de Procariontes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México Cuernavaca, Mexico
| | - Sergio M Encarnación
- Programa de Genómica Funcional de Procariontes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México Cuernavaca, Mexico
| | - Guillermo Dávila
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de MéxicoCuernavaca, Mexico; Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de MéxicoJuriquilla, Mexico
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López-Leal G, Tabche ML, Castillo-Ramírez S, Mendoza-Vargas A, Ramírez-Romero MA, Dávila G. RNA-Seq analysis of the multipartite genome of Rhizobium etli CE3 shows different replicon contributions under heat and saline shock. BMC Genomics 2014; 15:770. [PMID: 25201548 PMCID: PMC4167512 DOI: 10.1186/1471-2164-15-770] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 09/03/2014] [Indexed: 12/23/2022] Open
Abstract
Background Regulation of transcription is essential for any organism and Rhizobium etli (a multi-replicon, nitrogen-fixing symbiotic bacterium) is no exception. This bacterium is commonly found in the rhizosphere (free-living) or inside of root-nodules of the common bean (Phaseolus vulgaris) in a symbiotic relationship. Abiotic stresses, such as high soil temperatures and salinity, compromise the genetic stability of R. etli and therefore its symbiotic interaction with P. vulgaris. However, it is still unclear which genes are up- or down-regulated to cope with these stress conditions. The aim of this study was to identify the genes and non-coding RNAs (ncRNAs) that are differentially expressed under heat and saline shock, as well as the promoter regions of the up-regulated loci. Results Analysing the heat and saline shock responses of R. etli CE3 through RNA-Seq, we identified 756 and 392 differentially expressed genes, respectively, and 106 were up-regulated under both conditions. Notably, the set of genes over-expressed under either condition was preferentially encoded on plasmids, although this observation was more significant for the heat shock response. In contrast, during either saline shock or heat shock, the down-regulated genes were principally chromosomally encoded. Our functional analysis shows that genes encoding chaperone proteins were up-regulated during the heat shock response, whereas genes involved in the metabolism of compatible solutes were up-regulated following saline shock. Furthermore, we identified thirteen and nine ncRNAs that were differentially expressed under heat and saline shock, respectively, as well as eleven ncRNAs that had not been previously identified. Finally, using an in silico analysis, we studied the promoter motifs in all of the non-coding regions associated with the genes and ncRNAs up-regulated under both conditions. Conclusions Our data suggest that the replicon contribution is different for different stress responses and that the heat shock response is more complex than the saline shock response. In general, this work exemplifies how strategies that not only consider differentially regulated genes but also regulatory elements of the stress response provide a more comprehensive view of bacterial gene regulation. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-770) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gamaliel López-Leal
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Apartado Postal 565-A, Cuernavaca, Morelos C,P 62210, México.
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Martínez-Salazar JM, Sandoval-Calderón M, Guo X, Castillo-Ramírez S, Reyes A, Loza MG, Rivera J, Alvarado-Affantranger X, Sánchez F, González V, Dávila G, Ramírez-Romero MA. The Rhizobium etli RpoH1 and RpoH2 sigma factors are involved in different stress responses. Microbiology (Reading) 2009; 155:386-397. [PMID: 19202087 DOI: 10.1099/mic.0.021428-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The physiological role and transcriptional expression of Rhizobium etli sigma factors rpoH1 and rpoH2 are reported in this work. Both rpoH1 and rpoH2 were able to complement the temperature-sensitive phenotype of an Escherichia coli rpoH mutant. The R. etli rpoH1 mutant was sensitive to heat shock, sodium hypochlorite and hydrogen peroxide, whereas the rpoH2 mutant was sensitive to NaCl and sucrose. The rpoH2 rpoH1 double mutant had increased sensitivity to heat shock and oxidative stress when compared with the rpoH1 single mutant. This suggests that in R. etli, RpoH1 is the main heat-shock sigma factor, but a more complete protective response could be achieved with the participation of RpoH2. Conversely, RpoH2 is involved in osmotic tolerance. In symbiosis with bean plants, the R. etli rpoH1 and rpoH2 rpoH1 mutants still elicited nodule formation, but exhibited reduced nitrogenase activity and bacterial viability in early and late symbiosis compared with nodules produced by rpoH2 mutants and wild-type strains. In addition, nodules formed by R. etli rpoH1 and rpoH2 rpoH1 mutants showed premature senescence. It was also determined that fixNf and fixKf expression was affected in rpoH1 mutants. Both rpoH genes were induced under microaerobic conditions and in the stationary growth phase, but not in response to heat shock. Analysis of the upstream region of rpoH1 revealed a sigma70 and a probable sigmaE promoter, whereas in rpoH2, one probable sigmaE-dependent promoter was detected. In conclusion, the two RpoH proteins operate under different stress conditions, RpoH1 in heat-shock and oxidative responses, and RpoH2 in osmotic tolerance.
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Affiliation(s)
- Jaime M Martínez-Salazar
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Apartado Postal 565-A, CP 62210 Cuernavaca, Morelos, México
| | - Mario Sandoval-Calderón
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Apartado Postal 565-A, CP 62210 Cuernavaca, Morelos, México
| | - Xianwu Guo
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Apartado Postal 565-A, CP 62210 Cuernavaca, Morelos, México
| | - Santiago Castillo-Ramírez
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Apartado Postal 565-A, CP 62210 Cuernavaca, Morelos, México
| | - Alma Reyes
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Apartado Postal 565-A, CP 62210 Cuernavaca, Morelos, México
| | - Maria G Loza
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Apartado Postal 565-A, CP 62210 Cuernavaca, Morelos, México
| | - Javier Rivera
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Apartado Postal 565-A, CP 62210 Cuernavaca, Morelos, México
| | - Xochitl Alvarado-Affantranger
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apartado Postal 510-3, CP 62271 Cuernavaca, Morelos, México
| | - Federico Sánchez
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apartado Postal 510-3, CP 62271 Cuernavaca, Morelos, México
| | - Víctor González
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Apartado Postal 565-A, CP 62210 Cuernavaca, Morelos, México
| | - Guillermo Dávila
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Apartado Postal 565-A, CP 62210 Cuernavaca, Morelos, México
| | - Miguel A Ramírez-Romero
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Apartado Postal 565-A, CP 62210 Cuernavaca, Morelos, México
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Abstract
A collection of Rhizobium etli promoters was isolated from a genomic DNA library constructed in the promoter-trap vector pBBMCS53, by their ability to drive the expression of a gusA reporter gene. Thirty-seven clones were selected, and their transcriptional start-sites were determined. The upstream sequence of these 37 start-sites, and the sequences of seven previously identified promoters were compared. On the basis of sequence conservation and mutational analysis, a consensus sequence CTTGACN16–23TATNNT was obtained. In this consensus sequence, nine on of twelve bases are identical to the canonical Escherichia coli σ70 promoter, however the R.etli promoters only contain 6.4 conserved bases on average. We show that the R.etli sigma factor SigA recognizes all R.etli promoters studied in this work, and that E.coli RpoD is incapable of recognizing them. The comparison of the predicted structure of SigA with the known structure of RpoD indicated that regions 2.4 and 4.2, responsible for promoter recognition, are different only by a single amino acid, whereas the region 1 of SigA contains 72 extra residues, suggesting that the differences contained in this region could be related to the lax promoter recognition of SigA.
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Velasco-García R, Villalobos MA, Ramírez-Romero MA, Mújica-Jiménez C, Iturriaga G, Muñoz-Clares RA. Betaine aldehyde dehydrogenase from Pseudomonas aeruginosa: cloning, over-expression in Escherichia coli, and regulation by choline and salt. Arch Microbiol 2005; 185:14-22. [PMID: 16315011 DOI: 10.1007/s00203-005-0054-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2005] [Revised: 10/06/2005] [Accepted: 11/03/2005] [Indexed: 10/25/2022]
Abstract
In the human pathogen Pseudomonas aeruginosa, betaine aldehyde dehydrogenase (BADH) may play a dual role assimilating carbon and nitrogen from choline or choline precursors--abundant at infection sites--and producing glycine betaine, which protects the bacteria against the high-osmolarity stress prevalent in the infected tissues. We cloned the P. aeruginosa BADH gene and expressed the BADH protein in Escherichia coli. The recombinant protein appears identical to its native counterpart, as judged by Western blot, N-terminal amino acid sequence, tryptophan-fluorescence emission spectra, circular-dichroism spectroscopy, size-exclusion chromatography, and kinetic properties. Computational analysis indicated that the promoter sequence of the putative operon that includes the BADH gene has a consensus-binding site for the choline-sensing transcription repressor BetI, and putative boxes for ArcA and Lrp transcription factors but no known elements of response to osmotic stress. This is consistent with the strong induction of BADH expression by choline and with the lack of effect of NaCl. As there were significant amounts of BADH protein and activity in P. aeruginosa cells grown on glucose plus choline, as well as the BADH activity exhibiting tolerance to salt, it is likely that glycine betaine is synthesized in vivo and could play an important osmoprotectant role under conditions of infection.
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Affiliation(s)
- Roberto Velasco-García
- Laboratorio de Osmorregulación, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, México, Mexico
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Izquierdo J, Venkova-Canova T, Ramírez-Romero MA, Téllez-Sosa J, Hernández-Lucas I, Sanjuan J, Cevallos MA. An antisense RNA plays a central role in the replication control of a repC plasmid. Plasmid 2005; 54:259-77. [PMID: 16005966 DOI: 10.1016/j.plasmid.2005.05.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2005] [Revised: 05/17/2005] [Accepted: 05/17/2005] [Indexed: 11/23/2022]
Abstract
The widespread replicons of repABC and repC families from alpha-proteobacteria share high similarity in their replication initiator proteins (RepC). Here we describe the minimal region required for stable replication of a member of the repC family, the low copy-number plasmid pRmeGR4a from Sinorizobium meliloti GR4. This region contains only two genes: one encoding the initiator protein RepC (46.8 kDa) and other, an antisense RNA (67 nt). Mapping of transcriptional start sites and promoter regions of both genes showed that the antisense RNA is nested within the repC mRNA leader. The constitutively expressed countertranscribed RNA (ctRNA) forms a single stem-loop structure that acts as an intrinsic rho-independent terminator. The ctRNA is a strong trans-incompatibility factor and negative regulator of repC expression. Based on structural and functional similarities between members of the repC and repABC families we propose a model of their evolutionary relationship.
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MESH Headings
- Amino Acid Sequence
- Conjugation, Genetic
- DNA Replication
- DNA, Bacterial
- Gene Expression Regulation, Bacterial
- Genes, Bacterial
- Glucuronidase/analysis
- Glucuronidase/metabolism
- Molecular Sequence Data
- Molecular Weight
- Mutagenesis, Site-Directed
- Phylogeny
- Plasmids/chemistry
- Plasmids/genetics
- Plasmids/metabolism
- Promoter Regions, Genetic
- RNA, Antisense/genetics
- RNA, Antisense/physiology
- RNA, Bacterial/genetics
- RNA, Bacterial/physiology
- RNA, Messenger/genetics
- Replicon
- Rhizobium etli/genetics
- Sequence Homology, Amino Acid
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Affiliation(s)
- Javier Izquierdo
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Apartado Postal 565-A, Cuernavaca, Morelos, Mexico
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Venkova-Canova T, Soberón NE, Ramírez-Romero MA, Cevallos MA. Two discrete elements are required for the replication of a repABC plasmid: an antisense RNA and a stem-loop structure. Mol Microbiol 2005; 54:1431-44. [PMID: 15554980 DOI: 10.1111/j.1365-2958.2004.04366.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [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: 11/30/2022]
Abstract
The repABC replicons contain an operon encoding the initiator protein (RepC) and partitioning proteins (RepA and RepB). The latter two proteins negatively regulate the transcription of the operon. In this article we have identified two novel regulatory elements, located within the conserved repB-repC intergenic sequence, which negatively modulate the expression of repC, in plasmid p42d of Rhizobium etli. One of them is a small antisense RNA and the other is a stem-loop structure in the repABC mRNA that occludes the Shine-Dalgarno sequence of repC. According to in vivo and in vitro analyses, the small antisense RNA (57-59 nt) resembles canonical negative regulators of replication because: (i) it is transcribed from a strong constitutive promoter (P2), (ii) the transcript overlaps untranslated region upstream of the RepC coding sequences, (iii) the RNA forms one secondary structure acting as a rho-independent terminator, (iv) the antisense RNA is a strong trans-incompatibility factor and (v) its presence reduces the level of repC expression. Surprisingly, both of these seemingly negative regulators are required for efficient plasmid replication.
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MESH Headings
- Base Sequence
- DNA Replication
- DNA, Bacterial/genetics
- DNA, Bacterial/metabolism
- DNA, Intergenic/genetics
- DNA, Intergenic/physiology
- Gene Expression Regulation, Bacterial
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation
- Operon
- Plasmids/genetics
- Plasmids/metabolism
- Promoter Regions, Genetic
- Protein Biosynthesis
- RNA, Antisense/genetics
- RNA, Antisense/physiology
- RNA, Bacterial/genetics
- RNA, Bacterial/physiology
- RNA, Messenger/genetics
- RNA, Messenger/physiology
- Rhizobium etli/genetics
- Sequence Alignment
- Untranslated Regions
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Affiliation(s)
- Tatiana Venkova-Canova
- Programa de Evolución Molecular, Centro de Investigación sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Apartado Postal 565-A, C.P 62210, Cuernavaca, Morelos, Mexico
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Soberón N, Venkova-Canova T, Ramírez-Romero MA, Téllez-Sosa J, Cevallos MA. Incompatibility and the partitioning site of the repABC basic replicon of the symbiotic plasmid from Rhizobium etli. Plasmid 2004; 51:203-16. [PMID: 15109827 DOI: 10.1016/j.plasmid.2004.01.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2003] [Revised: 01/20/2004] [Indexed: 11/19/2022]
Abstract
The basic replicon of the symbiotic plasmid (p42d) of Rhizobium etli CE3 is constituted by the repABC operon. Whereas RepC is essential for plasmid replication, RepA and RepB are involved in plasmid partitioning. Three incompatibility regions have been previously identified in this plasmid: the first one encodes RepA, a partitioning protein that also down-regulates the repABC transcription. The second region is situated within the repB-repC intergenic sequence (inc(alpha)), and the last one, inc(beta), is located in a 502 bp EcoRI fragment spanning the last 72-bp of the coding region of repC and the following downstream sequence. In this paper we show that: (1) The inc(beta) region is required for plasmid partitioning. (2) A 16-bp palindrome sequence, located 40 bp downstream of the repC gene of plasmid p42d, is necessary and sufficient to induce incompatibility towards the parental plasmid, and accounts for all the incompatibility properties of this region (inc(beta)). (3). The palindrome is the DNA target site for RepB binding. With these findings we propose that inc(beta) contains the partitioning site (par site) of the basic replicon of plasmid p42d, and that the 16-bp palindrome is the core sequence to nucleate the RepB binding.
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Affiliation(s)
- Nora Soberón
- Programa de Evolución Molecular, Centro de Investigación sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Apartado Postal 565-A, Cuernavaca, Morelos
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González V, Bustos P, Ramírez-Romero MA, Medrano-Soto A, Salgado H, Hernández-González I, Hernández-Celis JC, Quintero V, Moreno-Hagelsieb G, Girard L, Rodríguez O, Flores M, Cevallos MA, Collado-Vides J, Romero D, Dávila G. The mosaic structure of the symbiotic plasmid of Rhizobium etli CFN42 and its relation to other symbiotic genome compartments. Genome Biol 2003; 4:R36. [PMID: 12801410 PMCID: PMC193615 DOI: 10.1186/gb-2003-4-6-r36] [Citation(s) in RCA: 129] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2002] [Revised: 03/06/2003] [Accepted: 04/02/2003] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Symbiotic bacteria known as rhizobia interact with the roots of legumes and induce the formation of nitrogen-fixing nodules. In rhizobia, essential genes for symbiosis are compartmentalized either in symbiotic plasmids or in chromosomal symbiotic islands. To understand the structure and evolution of the symbiotic genome compartments (SGCs), it is necessary to analyze their common genetic content and organization as well as to study their differences. To date, five SGCs belonging to distinct species of rhizobia have been entirely sequenced. We report the complete sequence of the symbiotic plasmid of Rhizobium etli CFN42, a microsymbiont of beans, and a comparison with other SGC sequences available. RESULTS The symbiotic plasmid is a circular molecule of 371,255 base-pairs containing 359 coding sequences. Nodulation and nitrogen-fixation genes common to other rhizobia are clustered in a region of 125 kilobases. Numerous sequences related to mobile elements are scattered throughout. In some cases the mobile elements flank blocks of functionally related sequences, thereby suggesting a role in transposition. The plasmid contains 12 reiterated DNA families that are likely to participate in genomic rearrangements. Comparisons between this plasmid and complete rhizobial genomes and symbiotic compartments already sequenced show a general lack of synteny and colinearity, with the exception of some transcriptional units. There are only 20 symbiotic genes that are shared by all SGCs. CONCLUSIONS Our data support the notion that the symbiotic compartments of rhizobia genomes are mosaic structures that have been frequently tailored by recombination, horizontal transfer and transposition.
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Affiliation(s)
- Víctor González
- Centro de Investigación Sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México 62210
| | - Patricia Bustos
- Centro de Investigación Sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México 62210
| | - Miguel A Ramírez-Romero
- Centro de Investigación Sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México 62210
| | - Arturo Medrano-Soto
- Centro de Investigación Sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México 62210
| | - Heladia Salgado
- Centro de Investigación Sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México 62210
| | - Ismael Hernández-González
- Centro de Investigación Sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México 62210
| | - Juan Carlos Hernández-Celis
- Centro de Investigación Sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México 62210
| | - Verónica Quintero
- Centro de Investigación Sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México 62210
| | - Gabriel Moreno-Hagelsieb
- Centro de Investigación Sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México 62210
| | - Lourdes Girard
- Centro de Investigación Sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México 62210
| | - Oscar Rodríguez
- Centro de Investigación Sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México 62210
| | - Margarita Flores
- Centro de Investigación Sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México 62210
| | - Miguel A Cevallos
- Centro de Investigación Sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México 62210
| | - Julio Collado-Vides
- Centro de Investigación Sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México 62210
| | - David Romero
- Centro de Investigación Sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México 62210
| | - Guillermo Dávila
- Centro de Investigación Sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México 62210
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Ramírez-Romero MA, Téllez-Sosa J, Barrios H, Pérez-Oseguera A, Rosas V, Cevallos MA. RepA negatively autoregulates the transcription of the repABC operon of the Rhizobium etli symbiotic plasmid basic replicon. Mol Microbiol 2001; 42:195-204. [PMID: 11679078 DOI: 10.1046/j.1365-2958.2001.02621.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [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
The basic replicon of Rhizobium etli CE3, like other members of the repABC plasmid family, is constituted by the repABC operon. RepC is essential for replication, and RepA and RepB play a role in plasmid segregation. It has been shown that deletion derivatives lacking the repAB genes have an increased copy number, indicating that these genes participate in the control of plasmid copy number. RepA is also a trans-incompatibility factor. To understand the regulation of the repABC operon, in this paper: (i) the transcription start site of the repABC operon was determined; (ii) the promoter region was identified by site-directed mutagenesis of the putative -35 and -10 hexameric elements; and (iii) RepA was recognized as a negative regulator of the transcription of the repABC operon.
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Affiliation(s)
- M A Ramírez-Romero
- Programa de Evolución Molecular, Centro de Investigación sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Apartado Postal 565-A, Cuernavaca, Morelos, México
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Ramírez-Romero MA, Soberón N, Pérez-Oseguera A, Téllez-Sosa J, Cevallos MA. Structural elements required for replication and incompatibility of the Rhizobium etli symbiotic plasmid. J Bacteriol 2000; 182:3117-24. [PMID: 10809690 PMCID: PMC94497 DOI: 10.1128/jb.182.11.3117-3124.2000] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/1999] [Accepted: 02/25/2000] [Indexed: 11/20/2022] Open
Abstract
The symbiotic plasmid of Rhizobium etli CE3 belongs to the RepABC family of plasmid replicons. This family is characterized by the presence of three conserved genes, repA, repB, and repC, encoded by the same DNA strand. A long intergenic sequence (igs) between repB and repC is also conserved in all members of the plasmid family. In this paper we demonstrate that (i) the repABC genes are organized in an operon; (ii) the RepC product is essential for replication; (iii) RepA and RepB products participate in plasmid segregation and in the regulation of plasmid copy number; (iv) there are two cis-acting incompatibility regions, one located in the igs (incalpha) and the other downstream of repC (incbeta) (the former is essential for replication); and (v) RepA is a trans-acting incompatibility factor. We suggest that incalpha is a cis-acting site required for plasmid partitioning and that the origin of replication lies within incbeta.
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Affiliation(s)
- M A Ramírez-Romero
- Programa de Evolución Molecular, Centro de Investigación sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
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Ramírez-Romero MA, Bustos P, Girard L, Rodríguez O, Cevallos MA, Dávila G. Sequence, localization and characteristics of the replicator region of the symbiotic plasmid of Rhizobium etli. Microbiology (Reading) 1997; 143 ( Pt 8):2825-2831. [PMID: 9274036 DOI: 10.1099/00221287-143-8-2825] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The replicator region of the symbiotic plasmid of Rhizobium etli CFN42 was cloned and sequenced. A plasmid derivative (pH3) harbouring a 5-6 kb HindIII fragment from the symbiotic plasmid was found to be capable of independent replication and eliminated the symbiotic plasmid when introduced into a R. etli CFNX101 strain (a recA derivative). The stability and the copy number of pH3 were the same as that of the symbiotic plasmid, indicating that the information required for stable replication and incompatibility resides in the 5.6 kb HindIII fragment. The sequence analysis of this fragment showed the presence of three ORFs similar in sequence analysis of this fragment showed the presence of three ORFs similar in sequence and organization to repA, repB and repC described for the replicator regions of the Agrobacterium plasmids pTiB653 and pRiA4b and for the R. leguminosarum cryptic plasmid pRL8JI. Hybridization studies showed that p42d-like replicator sequences are found in the symbiotic plasmids of other R. etli strains and in a 'cryptic' plasmid of R. tropici.
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Affiliation(s)
- Miguel A Ramírez-Romero
- Departamento de Genética Molecular, Centro de Investigación sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Apartado Postal 565-A, Cuernavaca, Morelos, Mexico
| | - Patricia Bustos
- Departamento de Genética Molecular, Centro de Investigación sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Apartado Postal 565-A, Cuernavaca, Morelos, Mexico
| | - Lourdes Girard
- Departamento de Genética Molecular, Centro de Investigación sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Apartado Postal 565-A, Cuernavaca, Morelos, Mexico
| | - Oscar Rodríguez
- Departamento de Genética Molecular, Centro de Investigación sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Apartado Postal 565-A, Cuernavaca, Morelos, Mexico
| | - Miguel A Cevallos
- Departamento de Ecología Molecular, Centro de Investigación sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Apartado Postal 565-A, Cuernavaca, Morelos, Mexico
| | - Guillermo Dávila
- Departamento de Genética Molecular, Centro de Investigación sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Apartado Postal 565-A, Cuernavaca, Morelos, Mexico
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