Salmonella enterica serovar Typhi has a 134-kb island of DNA identified as salmonella pathogenicity island 7 (SPI7), inserted between pheU and pheU (truncated), two genes for tRNA Phe . SPI7 has genes for Vi exopolysaccharide, for type IVB pili, for putative conjugal transfer, and for sopE bacteriophage. Pulsed-field gel electrophoresis following digestion with the endonuclease I-CeuI, using DNA from a set of 120 wild-type strains of serovar Typhi assembled from several sources, identified eight strains in which the I-CeuI G fragment, which contains SPI7, had a large deletion. In addition, agglutination tests with Vi antiserum and phage typing with Vi phages show that all eight strains are Vi negative. We therefore tested these strains for deletion of SPI7 by multiplex PCR, by microarray analysis, and by sequencing of PCR amplicons. Data show that seven of the eight strains are precise deletions of SPI7: a primer pair flanking SPI7 results in a PCR amplicon containing a single pheU gene; microarrays show that all SPI7 genes are deleted. Two of the strains produce amplicons which have A derived from pheU at bp 27, while five have C derived from pheU at this position; thus, the position of the crossover which results in the deletion can be inferred. The deletion in the eighth strain, TYT1669, removes 175 kb with junction points in genes STY4465 and STY4664; the left junction of SPI7 and adjacent genes, as well as part of SPI7 including the viaB operon for Vi exopolysaccharide, was removed, while the right junction of SPI7 was retained. We propose that these deletions occurred during storage following isolation.Of the more than 2,300 closely related Salmonella serovars recognized, Salmonella enterica serovar Typhi (referred to hereafter as serovar Typhi) is the only one which grows exclusively in humans and causes typhoid enteric fever. The closely related serovar S. enterica serovar Typhimurium is a host-generalist able to grow on a wide range of animals, and is causal agent of gastroenteritis rather than enteric fevers. In most enteric bacteria there is a strong conservation of chromosomal gene order, but serovar Typhi is an exception, because its chromosome shows major rearrangements in gene order in wild-type strains due to homologous recombination between the rrn operons (23). These rearrangements were detected by pulsed-field gel electrophoresis (PFGE) analysis involving complete and partial digestion of genomic DNA with intron-encoded endonuclease I-CeuI which cuts only in the rrn genes (20). PFGE analysis also revealed the presence of insertions in serovar Typhi, one predicted to be about 120 kb, carrying the viaB locus for Vi exopolysaccharide synthesis which is missing from most other Salmonella species (21, 23). Further analysis showed that this island contains genes for the type IV pili (37,38).This island is now shown in strain CT18 to be a 134-kb pathogenicity island, identified as SPI7, which is inserted between two genes which code for tRNA Phe , pheU and ЈpheU (truncated) (29, 31) (Fig. 1A). Distri...

The genomes of most strains of Salmonella and Escherichia coli are highly conserved. In contrast, all 136 wild-type strains of Salmonella enterica serovar Typhi analyzed by partial digestion with I-CeuI (an endonuclease which cuts within the rrn operons) and pulsed-field gel electrophoresis and by PCR have rearrangements due to homologous recombination between the rrn operons leading to inversions and translocations. Recombination between rrn operons in culture is known to be equally frequent in S. enterica serovar Typhi and S. enterica serovar Typhimurium; thus, the recombinants in S. enterica serovar Typhi, but not those in S. enterica serovar Typhimurium, are able to survive in nature. However, even in S. enterica serovar Typhi the need for genome balance and the need for gene dosage impose limits on rearrangements. Of 100 strains of genome types 1 to 6, 72 were only 25.5 kb off genome balance (the relative lengths of the replichores during bidirectional replication from oriC to the termination of replication [Ter]), while 28 strains were less balanced (41 kb off balance), indicating that the survival of the best-balanced strains was greater. In addition, the need for appropriate gene dosage apparently selected against rearrangements which moved genes from their accustomed distance from oriC. Although rearrangements involving the seven rrn operons are very common in S. enterica serovar Typhi, other duplicated regions, such as the 25 IS200 elements, are very rarely involved in rearrangements. Large deletions and insertions in the genome are uncommon, except for deletions of Salmonella pathogenicity island 7 (usually 134 kb) from fragment I-CeuI-G and 40-kb insertions, possibly a prophage, in fragment I-CeuI-E. The phage types were determined, and the origins of the phage types appeared to be independent of the origins of the genome types.Salmonella enterica serovar Typhi is host restricted, for it grows only in humans, where it causes typhoid enteric fever (13, 51). The annual global incidence of typhoid fever is estimated to be 21.6 million cases, with more than 220,000 deaths (10). The emergence of antibiotic-resistant strains (8) and the increased incidence of typhoid fever in human immunodeficiency virus type 1-infected persons are causes for concern. The genus Salmonella is separated into two species and more than 2,500 serovars (52) on the basis of the somatic and flagellar antigens. Many of the serovars, such as S. enterica serovar Typhimurium, are host generalists, growing in many different animal species and humans and causing gastroenteritis.S. enterica serovar Typhi is more homogeneous than most serovars of Salmonella. Using multilocus enzyme electrophoresis, Reeves et al. (54) and Selander et al. (58) showed that S. enterica serovar Typhi strains constitute only one or two clones that are widely separated from the other serovars in subspecies I. Membrane protein profiles (15, 17) and plasmids (42) show homogeneity. Multilocus sequence typing of housekeeping genes has suggested that S. enterica ser...

We compared the stem elongation response and anthocyanin accumulation between alpine and prairie plants of Stellaria longipes Goldie under different red/far-red light ratios (R/FR) of 0.7 and 1.9 while all other environmental conditions were uniform. Both ecotypes responded to light quality. The prairie ecotype, considered to be the shade avoider, showed greater stem elongation in response to low R/FR (0.7) than under high R/FR (1.9) as compared with the alpine ecotype. The levels of anthocyanin in prairie plants, as compared with alpine plants, were significantly higher under high R/FR. Under low R/FR, both showed almost the same levels of anthocyanin. Also, the two ecotypes upon etiolation showed differences in the sites of anthocyanin accumulation under different R/FR. The results of the present study show that the extent of the stem elongation response and anthocyanin accumulation in the two ecotypes of S. longipes is likely a result of their origins in two contrasting habitats.Résumé : Tout en maintenant les autres conditions du milieu uniformes, les auteurs ont soumis des plants de Stellaria longipes Goldie alpins et de prairie, à des ratios lumière rouge/rouge sombre (R/FR) de 0,7 et 1,9, et ils en ont comparé les effets sur l'élongation de la tige et l'accumulation des anthocyanes. Les deux écotypes réagissent à la qualité de la lumière. Comparativement à l'écotype alpin, l'écotype de prairie, considéré comme évitant l'ombre, montre une plus grande élongation de la tige en réaction au rapport R/FR faible (0,7) que sous le rapport R/FR plus élevé (1,9). Comparativement aux plants alpins également, les teneurs en anthocyanes chez les plants de prairie sont significativement plus élevées sous le régime R/FR le plus élevé. Sous le régime R/FR le plus faible, les deux écotypes ont des teneurs en anthocyanes équivalentes. De plus, sous étiolation avec différents régimes R/FR, les deux écotypes montrent des différences dans les sites d'accumulation des anthocyanes. Les résultats montrent que l'importance de la réaction d'élongation de la tige et de l'accumulation des anthocyanes, chez les deux écotypes du Stellatia longipes, résulte vraisemblablement du fait qu'ils proviennent de deux habitats contrastants.

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...

We studied mRNA accumulation and enzyme activity of phenylalanine ammonia-lyase (PAL) and chalcone synthase (CHS) in alpine and prairie ecotypes of Stellaria longipes.The results show that light is required for the induction of PAL and CHS and accumulation of anthocyanins. Although both the ecotypes showed higher levels of anthocyanins under high R/FR (1.9) than under low R/FR (0.7), neither of the ecotypes showed any significant difference in the transcript