Replicon-Dependent Bacterial Genome Evolution: The Case of Sinorhizobium meliloti

Marco Galardini; Francesco Pini; Marco Bazzicalupo; Emanuele G. Biondi; Alessio Mengoni

doi:10.1093/gbe/evt027

Replicon-Dependent Bacterial Genome Evolution: The Case of Sinorhizobium meliloti

Genome Biology and Evolution ◽

10.1093/gbe/evt027 ◽

2013 ◽

Vol 5 (3) ◽

pp. 542-558 ◽

Cited By ~ 67

Author(s):

Marco Galardini ◽

Francesco Pini ◽

Marco Bazzicalupo ◽

Emanuele G. Biondi ◽

Alessio Mengoni

Keyword(s):

Genome Evolution ◽

Sinorhizobium Meliloti ◽

Bacterial Genome

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The Location of Substitutions and Bacterial Genome Arrangements

Genome Biology and Evolution ◽

10.1093/gbe/evaa260 ◽

2020 ◽

Author(s):

Daniella F Lato ◽

G Brian Golding

Keyword(s):

Sinorhizobium Meliloti ◽

Bacterial Genome ◽

Evolutionary Analysis ◽

Origin Of Replication ◽

Ancestral Reconstruction ◽

Molecular Change ◽

E Coli ◽

A Genome ◽

The Impact ◽

Molecular Evolutionary Analysis

Abstract Increasing evidence supports the notion that different regions of a genome have unique rates of molecular change. This variation is particularly evident in bacterial genomes where previous studies have reported gene expression and essentiality tend to decrease, while substitution rates usually increases with increasing distance from the origin of replication. Genomic reorganization such as rearrangements occur frequently in bacteria and allow for the introduction and restructuring of genetic content, creating gradients of molecular traits along genomes. Here, we explore the interplay of these phenomena by mapping substitutions to the genomes of Escherichia coli, Bacillus subtilis, Streptomyces, and Sinorhizobium meliloti, quantifying how many substitutions have occurred at each position in the genome. Preceding work indicates that substitution rate significantly increases with distance from the origin. Using a larger sample size and accounting for genome rearrangements through ancestral reconstruction, our analysis demonstrates that the correlation between the number of substitutions and distance from the origin of replication is often significant but small and inconsistent in direction. Some replicons had a significantly decreasing trend (E. coli and the chromosome of S. meliloti), while others showed the opposite significant trend (B. subtilis, Streptomyces, pSymA and pSymB in S. meliloti). dN, dS and ω were examined across all genes and there was no significant correlation between those values and distance from the origin. This study highlights the impact that genomic rearrangements and location have on molecular trends in some bacteria, illustrating the importance of considering spatial trends in molecular evolutionary analysis. Assuming that molecular trends are exclusively in one direction can be problematic.

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An algebraic view of bacterial genome evolution

Journal of Mathematical Biology ◽

10.1007/s00285-013-0747-6 ◽

2013 ◽

Vol 69 (6-7) ◽

pp. 1693-1718 ◽

Cited By ~ 7

Author(s):

Andrew R. Francis

Keyword(s):

Genome Evolution ◽

Bacterial Genome

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Bacterial genome evolution within a clonal population: fromin vitroinvestigations toin vivoobservations

Future Microbiology ◽

10.2217/fmb.13.28 ◽

2013 ◽

Vol 8 (5) ◽

pp. 661-674 ◽

Cited By ~ 1

Author(s):

Marie Beaume ◽

Nadezda Monina ◽

Jacques Schrenzel ◽

Patrice François

Keyword(s):

Genome Evolution ◽

Bacterial Genome ◽

Clonal Population

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New Recombination Methods for Sinorhizobium meliloti Genetics

Applied and Environmental Microbiology ◽

10.1128/aem.70.5.2806-2815.2004 ◽

2004 ◽

Vol 70 (5) ◽

pp. 2806-2815 ◽

Cited By ~ 63

Author(s):

Brent L. House ◽

Michael W. Mortimer ◽

Michael L. Kahn

Keyword(s):

Dna Sequences ◽

Sinorhizobium Meliloti ◽

Bacterial Genome ◽

Considerable Time ◽

Deletion Mutations ◽

Flp Recombinase ◽

Symbiotic Plasmid ◽

Cloning Method ◽

Improved Methods

ABSTRACT The availability of bacterial genome sequences has created a need for improved methods for sequence-based functional analysis to facilitate moving from annotated DNA sequence to genetic materials for analyzing the roles that postulated genes play in bacterial phenotypes. A powerful cloning method that uses lambda integrase recombination to clone and manipulate DNA sequences has been adapted for use with the gram-negative α-proteobacterium Sinorhizobium meliloti in two ways that increase the utility of the system. Adding plasmid oriT sequences to a set of vehicles allows the plasmids to be transferred to S. meliloti by conjugation and also allows cloned genes to be recombined from one plasmid to another in vivo by a pentaparental mating protocol, saving considerable time and expense. In addition, vehicles that contain yeast Flp recombinase target recombination sequences allow the construction of deletion mutations where the end points of the deletions are located at the ends of the cloned genes. Several deletions were constructed in a cluster of 60 genes on the symbiotic plasmid (pSymA) of S. meliloti, predicted to code for a denitrification pathway. The mutations do not affect the ability of the bacteria to form nitrogen-fixing nodules on Medicago sativa (alfalfa) roots.

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