The Evolving Genome of
            <i>Salmonella enterica</i>
            Serovar Pullorum

Liu, Guirong; Rahn, Andrea; Liu, Weiqiao; Sanderson, Kenneth E.; Johnston, Randal N.; Liu, Shulin

doi:10.1128/jb.184.10.2626-2633.2002

Cited by 67 publications

(63 citation statements)

References 48 publications

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“…As shown in Fig. 1, serovar Gallinarum SARB21 has a rearranged genome, with the seven I-CeuI fragments being organized differently than those in serovar Typhimurium LT2, a situation that has been seen in a number of other hostadapted Salmonella serovars (19,25,30). Although the partial digestion products, such as EϩF, EϩD, FϩC, and etc.…”

Section: Resultsmentioning

confidence: 99%

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The Genome of Salmonella enterica Serovar Gallinarum: Distinct Insertions/Deletions and Rare Rearrangements

Wu¹,

Liu

Liu³

et al. 2005

J Bacteriol

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Salmonella enterica serovar Gallinarum is a fowl-adapted pathogen, causing typhoid fever in chickens. It has the same antigenic formula (1,9,12:-:-) as S. enterica serovar Pullorum, which is also adapted to fowl but causes pullorum disease (diarrhea). The close relatedness but distinct pathogeneses make this pair of fowl pathogens good models for studies of bacterial genomic evolution and the way these organisms acquired pathogenicity. To locate and characterize the genomic differences between serovar Gallinarum and other salmonellae, we constructed a physical map of serovar Gallinarum strain SARB21 by using I-CeuI, XbaI, and AvrII with pulsed-field gel electrophoresis techniques. In the 4,740-kb genome, we located two insertions and six deletions relative to the genome of S. enterica serovar Typhimurium LT2, which we used as a reference Salmonella genome. Four of the genomic regions with reduced lengths corresponded to the four prophages in the genome of serovar Typhimurium LT2, and the others contained several smaller deletions relative to serovar Typhimurium LT2, including regions containing srfJ, std, and stj and gene clusters encoding a type I restriction system in serovar Typhimurium LT2. The map also revealed some rare rearrangements, including two inversions and several translocations. Further characterization of these insertions, deletions, and rearrangements will provide new insights into the molecular basis for the specific host-pathogen interactions and mechanisms of genomic evolution to create a new pathogen.

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Section: Resultsmentioning

confidence: 99%

“…To this end, we mapped the genome of serovar Gallinarum SARB21 and compared it to the previously mapped genomes of serovars Typhimurium (23) and Pullorum (19). This map and its comparisons with those of the genomes of the other Salmonella serovars revealed several insertions, deletions, and rearrangements in serovar Gallinarum SARB21.…”

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confidence: 99%

The Genome of Salmonella enterica Serovar Gallinarum: Distinct Insertions/Deletions and Rare Rearrangements

Wu¹,

Liu

Liu³

et al. 2005

J Bacteriol

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“…In previous work, we observed high degree of conservation in physical structure of the bacterial genomes and pointed out the potential importance of this phenomenon in both theoretical and applied areas of study, such as in elucidating the mode of bacterial evolution and in bacterial phylogenetic studies (17,19,30). As the first step toward exploring the mechanisms behind such a high degree of genomic conservation, we needed to analyze the genomes of archival mutator strains of serovar Typhimurium, attempting to capture the genomic changes that would escape detection under natural conditions.…”

Section: Discussionmentioning

confidence: 99%

“…The second issue is about the significance of genome diversification in bacterial evolution and, more specifically, speciation. In a model of bacterial speciation, the Adopt-Adapt Model (17,30), we hypothesize that bacteria speciate by acquisition of exogenous DNA (the "adopt" step) and the ensuing adaptive genomic rearrangements (the "adapt" step). In fact, the bacterial speciation process involves a special kind of genomic diversification that ultimately leads to a new bacterial species.…”

Section: Discussionmentioning

confidence: 99%

Genomic Diversification among Archival Strains of Salmonella enterica Serovar Typhimurium LT7

et al. 2003

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To document genomic changes during long periods of storage, we analyzed Salmonella enterica serovar Typhimurium LT7, a mutator strain that was previously reported to have higher rates of mutations compared to other serovar Typhimurium strains such as LT2. Upon plating directly from sealed agar stabs that had been stocked at room temperature for up to four decades, many auxotrophic mutants derived from LT7 gave rise to colonies of different sizes. Restreaking from single colonies consistently yielded colonies of diverse sizes even when we repeated single-colony isolation nine times. Colonies from the first plating had diverse genomic changes among and even within individual vials, including translocations, inversions, duplications, and point mutations, which were detected by rare-cutting endonuclease analysis with pulsed-field gel electrophoresis. Interestingly, even though the colony size kept diversifying, all descendents of the same single colonies from the first plating had the same sets of detected genomic changes. We did not detect any colony size or genome structure diversification in serovar Typhimurium LT7 stocked at ؊70°C or in serovar Typhimurium LT2 stocked either at ؊70°C or at room temperature. These results suggest that, although colony size diversification occurred during rapid growth, all detected genomic changes took place during the storage at room temperature and were carried over to their descendents without further changes during rapid growth in rich medium. We constructed a genomic cleavage map on the LT7 strain that had been stocked at ؊70°C and located all of the detected genomic changes on the map. We speculated on the significance of mutators for survival and evolution under environmentally stressed conditions.Comparative studies of bacteria have demonstrated the high level of conservation of the basic genome structure, i.e., the physical arrangement of DNA segments on the genome, in evolution. The earliest known example comes from the comparison of Salmonella enterica serovar Typhimurium and Escherichia coli, bacteria of two genera that have diverged for over 100 million years (6, 8, 39) but still have very similar genome structures (19). Specifically, they have similar genome sizes, similar sets of genes, and similar gene orders on the genome. Bacteria with closer phylogenetic relationships have even greater similarity. For instance, wild-type strains of serovar Typhimurium isolated from different sources have an indistinguishable genome structure as measured by I-CeuI cleavage patterns (25).Genomic diversification does occur among cells of the same clone in culture and presumably also in nature, including duplication and inversion of genomic segments, at frequencies as high as 10 Ϫ5 to 10 Ϫ3 (3, 13). However, most of these types of genomic changes are selected against in nature and therefore cannot be easily detected. In order to capture such genomic changes for the elucidation of the basic rules in genomic diversification during evolution, we examined serovar Typhimurium cultures th...

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“…It is possible, however, that none of the inversions over oriC or TER so far detected in bacteria is exactly symmetrical. Inversions may serve as compensating mechanisms to regain the balance between oriC and TER after the balance is disrupted by insertions or deletions (26).…”

Section: Discussionmentioning

confidence: 99%

Inversions over the Terminus Region inSalmonellaandEscherichia coli: IS200s as the Sites of Homologous Recombination Inverting the Chromosome ofSalmonella entericaSerovar Typhi

Alokam¹,

Liu

Said³

et al. 2002

J Bacteriol

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Genomic rearrangements (duplications and inversions) in enteric bacteria such as Salmonella enterica serovar Typhimurium LT2 and Escherichia coli K12 are frequent (10 ؊3 to 10 ؊5 ) in culture, but in wild-type strains these genomic rearrangements seldom survive. However, inversions commonly survive in the terminus of replication (TER) region, where bidirectional DNA replication terminates; nucleotide sequences from S. enterica serovar Typhimurium LT2, S. enterica serovar Typhi CT18, E. coli K12, and E. coli O157:H7 revealed genomic inversions spanning the TER region. Assuming that S. enterica serovar Typhimurium LT2 represents the ancestral genome structure, we found an inversion of 556 kb in serovar Typhi CT18 between two of the 25 IS200 elements and an inversion of about 700 kb in E. coli K12 and E. coli O157:H7. In addition, there is another inversion of 500 kb in E. coli O157:H7 compared with E. coli K12. PCR analysis confirmed that all S. enterica serovar Typhi strains tested, but not strains of other Salmonella serovars, have an inversion at the exact site of the IS200 insertions. We conclude that inversions of the TER region survive because they do not significantly change replication balance or because they are part of the compensating mechanisms to regain chromosome balance after it is disrupted by insertions, deletions, or other inversions.The order of orthologous genes on the chromosomes of enteric bacteria such as Escherichia coli K12 and Salmonella enterica serovar Typhimurium LT2 was shown by classical genetic exchange methods to be strongly conserved (24, 37), and this has now been confirmed by nucleotide sequence data (6, 30). This conservation was retained even after the genera diverged over 100 million years ago (32) and in spite of base pair divergence of orthologues, which averages about 15%. In addition, lateral genetic transfer has inserted nonorthologous genes that comprise about 30% of the total genetic structure, resulting in mosaic chromosomes. This conservation is surprising, because during growth in culture, chromosome rearrangements such as duplications occur at high frequencies (10 Ϫ3 to 10 Ϫ5 ) (3, 19) and some inversions and translocations, especially those with end points in the rrn operons, are common (36). These rearrangement types must have been selected against in evolution, because they are rarely detected in wildtype strains from nature. In contrast to this conservation within the enteric bacteria, gene order in most bacteria is not conserved during evolution (10, 21, 31), though species of Chlamydia also show striking conservation (35).However, even in the enteric bacteria, two types of genomic rearrangements are often observed. Firstly, inversions and translocations due to homologous recombination between the seven rrn operons are common in species such as Salmonella enterica serovar Typhi; among 127 wild-type strains there were 21 different genome types, based on differences in order of the fragments between the rrn operons (28). Rearrangements were also found in some ot...

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The Evolving Genome of Salmonella enterica Serovar Pullorum

Cited by 67 publications

References 48 publications

The Genome of Salmonella enterica Serovar Gallinarum: Distinct Insertions/Deletions and Rare Rearrangements

The Genome of Salmonella enterica Serovar Gallinarum: Distinct Insertions/Deletions and Rare Rearrangements

Genomic Diversification among Archival Strains of Salmonella enterica Serovar Typhimurium LT7

Inversions over the Terminus Region inSalmonellaandEscherichia coli: IS200s as the Sites of Homologous Recombination Inverting the Chromosome ofSalmonella entericaSerovar Typhi

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