Prediction, Identification, and Artificial Selection of DNA Rearrangements in Rhizobium: Toward a Natural Genomic Design

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 2000 Aug 2

PMID 10922070

Citations 31

Authors

M Flores

P Mavingui

X Perret

W J Broughton

D Romero

G Hernandez

G Davila

R Palacios

Affiliations

Soon will be listed here.

Abstract

Based on the DNA sequence of the symbiotic plasmid of Rhizobium strain NGR234, we predicted potential rearrangements generated by homologous recombination. All predicted rearrangements were identified experimentally by using a PCR-based methodology. Thus, the predicted and the actual dynamic maps of the replicon coincide. By using an approach that does not involve the introduction of exogenous genetic elements, derivative populations that are pure for specific rearrangements were obtained. We propose that knowledge of the DNA sequence of a genome offers the possibility of designing pathways of sequential rearrangements leading to alternative genomic structures. An experimental strategy to isolate bacterial populations containing the desired structures is discussed.

Citing Articles

Heteroresistance in Enterobacter cloacae complex caused by variation in transient gene amplification events.

Kupke J, Brombach J, Fang Y, Wolf S, Thrukonda L, Ghazisaeedi F NPJ Antimicrob Resist. 2025; 3(1):13.

PMID: 39987221 PMC: 11846870. DOI: 10.1038/s44259-025-00082-7.

How Latin America's genomics revolution began - and why the field is under threat.

Arnold C Nature. 2023; 615(7953):754-756.

PMID: 36941379 DOI: 10.1038/d41586-023-00794-8.

Gene amplification mutations originate prior to selective stress in Acinetobacter baylyi.

Herrmann J, Koprowska A, Winters T, Villanueva N, Nikityuk V, Pek F G3 (Bethesda). 2022; 13(3).

PMID: 36504387 PMC: 9997567. DOI: 10.1093/g3journal/jkac327.

Intracellular Competitions Reveal Determinants of Plasmid Evolutionary Success.

Hulter N, Wein T, Effe J, Garona A, Dagan T Front Microbiol. 2020; 11:2062.

PMID: 33013753 PMC: 7500096. DOI: 10.3389/fmicb.2020.02062.

Unstable Mechanisms of Resistance to Inhibitors of Escherichia coli Lipoprotein Signal Peptidase.

Pantua H, Skippington E, Braun M, Noland C, Diao J, Peng Y mBio. 2020; 11(5).

PMID: 32900806 PMC: 7482066. DOI: 10.1128/mBio.02018-20.

References

Romero D, Martinez-Salazar J, Ortiz E, Rodriguez C, Valencia-Morales E . Repeated sequences in bacterial chromosomes and plasmids: a glimpse from sequenced genomes. Res Microbiol. 2000; 150(9-10):735-43. DOI: 10.1016/s0923-2508(99)00119-9. View

Shapiro J . Genome system architecture and natural genetic engineering in evolution. Ann N Y Acad Sci. 1999; 870:23-35. DOI: 10.1111/j.1749-6632.1999.tb08862.x. View

Sapienza C, Rose M, Doolittle W . High-frequency genomic rearrangements involving archaebacterial repeat sequence elements. Nature. 1982; 299(5879):182-5. DOI: 10.1038/299182a0. View

Morrison N, Cen Y, Chen H, Plazinski J, Ridge R, Rolfe B . Mobilization of a Sym plasmid from a fast-growing cowpea Rhizobium strain. J Bacteriol. 1984; 160(1):483-7. PMC: 214752. DOI: 10.1128/jb.160.1.483-487.1984. View

Flores M, Gonzalez V, Brom S, Martinez E, Pinero D, Romero D . Reiterated DNA sequences in Rhizobium and Agrobacterium spp. J Bacteriol. 1987; 169(12):5782-8. PMC: 214138. DOI: 10.1128/jb.169.12.5782-5788.1987. View

Flores M, Gonzalez V, Pardo M, Leija A, Martinez E, Romero D . Genomic instability in Rhizobium phaseoli. J Bacteriol. 1988; 170(3):1191-6. PMC: 210891. DOI: 10.1128/jb.170.3.1191-1196.1988. View

Petes T, HILL C . Recombination between repeated genes in microorganisms. Annu Rev Genet. 1988; 22:147-68. DOI: 10.1146/annurev.ge.22.120188.001051. View

Hynes M, McGregor N . Two plasmids other than the nodulation plasmid are necessary for formation of nitrogen-fixing nodules by Rhizobium leguminosarum. Mol Microbiol. 1990; 4(4):567-74. DOI: 10.1111/j.1365-2958.1990.tb00625.x. View

Campbell A . Genome organization in prokaryotes. Curr Opin Genet Dev. 1993; 3(6):837-44. DOI: 10.1016/0959-437x(93)90002-7. View

10.

Romero D, Martinez-Salazar J, Girard L, Brom S, DAVILLA G, Palacios R . Discrete amplifiable regions (amplicons) in the symbiotic plasmid of Rhizobium etli CFN42. J Bacteriol. 1995; 177(4):973-80. PMC: 176691. DOI: 10.1128/jb.177.4.973-980.1995. View

11.

Koonin E, Mushegian A . Complete genome sequences of cellular life forms: glimpses of theoretical evolutionary genomics. Curr Opin Genet Dev. 1996; 6(6):757-62. DOI: 10.1016/s0959-437x(96)80032-3. View

12.

Freiberg C, Fellay R, Bairoch A, Broughton W, Rosenthal A, Perret X . Molecular basis of symbiosis between Rhizobium and legumes. Nature. 1997; 387(6631):394-401. DOI: 10.1038/387394a0. View

13.

Lashkari D, McCusker J, Davis R . Whole genome analysis: experimental access to all genome sequenced segments through larger-scale efficient oligonucleotide synthesis and PCR. Proc Natl Acad Sci U S A. 1997; 94(17):8945-7. PMC: 22974. DOI: 10.1073/pnas.94.17.8945. View

14.

Romero D, Palacios R . Gene amplification and genomic plasticity in prokaryotes. Annu Rev Genet. 1997; 31:91-111. DOI: 10.1146/annurev.genet.31.1.91. View

15.

Flores M, Mavingui P, Girard L, Perret X, Broughton W, Martinez-Romero E . Three replicons of Rhizobium sp. Strain NGR234 harbor symbiotic gene sequences. J Bacteriol. 1998; 180(22):6052-3. PMC: 107684. DOI: 10.1128/JB.180.22.6052-6053.1998. View

16.

Casjens S . The diverse and dynamic structure of bacterial genomes. Annu Rev Genet. 1999; 32:339-77. DOI: 10.1146/annurev.genet.32.1.339. View

17.

Papadopoulos D, Schneider D, Arber W, Lenski R, Blot M . Genomic evolution during a 10,000-generation experiment with bacteria. Proc Natl Acad Sci U S A. 1999; 96(7):3807-12. PMC: 22376. DOI: 10.1073/pnas.96.7.3807. View

18.

Pueppke S, Broughton W . Rhizobium sp. strain NGR234 and R. fredii USDA257 share exceptionally broad, nested host ranges. Mol Plant Microbe Interact. 1999; 12(4):293-318. DOI: 10.1094/MPMI.1999.12.4.293. View

19.

Anderson R, Roth J . Tandem genetic duplications in phage and bacteria. Annu Rev Microbiol. 1977; 31:473-505. DOI: 10.1146/annurev.mi.31.100177.002353. View