Journal of Bacteriology, September 1998, p. 4325-4331, Vol. 180, No. 17
NSF Center for Microbial Ecology, Michigan
State University, East Lansing, Michigan 48824
Received 25 July 1997/Accepted 6 March 1998
Genetic rearrangements within a population of bacteria were
analyzed to understand the degree of divergence occurring after experimental evolution. We used 18 replicate populations founded from
Ralstonia sp. strain TFD41 that had been propagated for
1,000 generations with 2,4-dichlorophenoxyacetic acid (2,4-D) as the carbon source. Genetic divergence was examined by restriction fragment
length polymorphism analysis of the incumbent plasmid that carries the
2,4-D catabolic genes and by amplification of random regions of the
genome via PCR. In 18 evolved clones examined, we observed duplication
within the plasmid, including the tfdA gene, which encodes
a 2,4-D dioxygenase that catalyzes the first step in the 2,4-D
catabolic pathway. In 71 of 72 evolved clones, a common 2.4-kb PCR
product was lost when genomic fingerprints produced by PCR
amplification using degenerate primers based on repetitive extragenic
palindromic (REP) sequences (REP-PCR) were compared. The nucleotide
sequence of the 2.4-kb PCR product has homology to the TRAP (tripartite
ATP-independent periplasmic) solute transporter gene family.
Hybridization of the 2.4-kb REP-PCR product from the ancestor to
genomic DNA from the evolved populations showed that the loss of the
PCR product resulted from deletions in the genome. Deletions in the
plasmid and presence and/or absence of other REP-PCR products were also
found in these clones but at much lower frequencies. The common and
uncommon genetic changes observed show that both parallel and divergent
genotypic evolution occurred in replicate populations of this
bacterium.
Experimental evolution of bacteria
has been an instrumental approach used to gain a greater understanding
of the fundamental processes involved in adaptive evolution (7,
19, 23, 43, 44). These studies have shown that phenotypically
similar populations evolve but underlying genetic divergence may exist
because different adaptive mutations can result in similar phenotypic
changes. The similarity or difference in genetic changes among
replicate populations during adaptive evolution is a function of both
the number of different possible adaptive mutations and the frequency
at which they occur (21, 22, 44, 46). There are many
potential sources of genetic variations (e.g., point mutations and
genomic rearrangements) (14, 29, 32), and thus the
likelihood of truly parallel (identical) genetic changes occurring
would appear to be small, given the uncertainties of mutation and
fixation. By observing the genetic changes that occur in experimentally evolved populations, we should be able to gain a better understanding of the genetic mechanisms used in adaptive evolution.
The objective of this study was to examine genetic changes that
occurred in laboratory-evolved replicate populations of
Ralstonia sp. strain TFD41 to determine if changes could be
observed and, if so, whether these changes can be correlated with the
observed phenotypic changes (23, 24). This is a potentially
difficult process because improved fitness can result from genetic
changes associated with a number of different aspects of bacterial
growth, including but not limited to the phases of bacterial growth in batch culture (lag, logarithmic, stationary, and death), a particular cell structure (e.g., cell wall or ribosome), or a particular aspect of
nutrient utilization (uptake or catabolism). To facilitate the search
for genetic changes, we have pursued a top-down analysis, looking for
genetic changes resulting from genome rearrangements. The approaches
for genetic analysis were chosen because recent studies suggest that
the role of recombination and genetic rearrangements in adaptive
mutation and gene evolution may be greater than previously realized
(3, 4, 18, 32, 35).
The genes (tfdA through tfdF) required for the
catabolism of the carbon source 2,4-dichlorophenoxyacetic acid (2,4-D)
(13, 31, 41) are plasmid encoded; therefore, we first
examined rearrangements of the plasmid by restriction fragment length
polymorphism and hybridization with the gene probes. Our second
analysis was to look for genomic changes without regard to a particular
locus by genome fingerprinting using degenerate primers based on
repetitive extragenic palindromic (REP) sequences and PCR (REP-PCR)
(12, 45). Potentially any number of different genetic
changes could be responsible for improved fitness, and focusing on a
single specific locus might cause one to overlook major genetic
changes. This technique is simple, such that many replicate assays can be performed, and unbiased, such that random regions of the bacterial genome can be sampled. REP elements are just one example of many highly
repeated sequences that are distributed throughout the genome of
phylogenetically diverse bacteria (28). There are 581 copies
of the REP sequence distributed throughout the Escherichia coli chromosome (8), allowing random amplification of
the genome.
In this study, we demonstrated that genetic changes after experimental
evolution of populations of Ralstonia sp. strain TFD41 can
be observed by the various methods that we used. With the genetic
information obtained from comparative analysis of plasmid fingerprints
and REP-PCR-generated genomic fingerprints, we were able to show
parallel and divergent evolution in the genotype of replicate
populations of a bacterium.
Experimental evolution conditions.
Ralstonia (formerly
Alcaligenes) sp. strain TFD41 was isolated from an
agricultural soil and shown to utilize 2,4-D as a sole carbon source
(42). This strain was formerly called Comamonas sp. strain TFD41, but 16S rRNA sequence determination shows that it is
a Ralstonia strain (29b). The protocol used to
experimentally evolve Ralstonia sp. strain TFD41 has
previously been described (24). Briefly, 18 independent
populations initiated from a single ancestral clone were grown for
1,000 generations (250 days) in minimal defined medium (MMO)
(40) with 2 mM 2,4-D as the carbon source. All populations
improved in competitive fitness, relative to their common ancestor, by
approximately 40% whether they were propagated in mass-action (6 populations in liquid batch) or structured (12 populations on solid
agar substrate) environments. The ancestral strain was designated
generation 0. Representative samples of each population were harvested
every 100 generations through to generation 1000 and preserved as
glycerol stocks (15% [final concentration]) at Hybridization analyses.
The tfdA through
-F genes carried on plasmid pJP4 of Ralstonia
eutropha (formerly Alcaligenes eutrophus) JMP134 are
involved in the initial steps of 2,4-D catabolism and have been well
described (13, 31, 41). E. coli strains carrying
the cloned structural genes tfdA through -F were
used to generate probes for the hybridization experiments
(20). All E. coli strains were grown at 37°C in Luria-Bertani broth plus ampicillin (50 mg/liter) (33).
Plasmid DNA was isolated by the alkaline lysis method (33)
and labeled by using PCR amplification primers and conditions described
by Holben et al. (20) except that the standard
deoxynucleoside triphosphate mix was replaced with the nonradioactive
label, digoxigenin-dUTP-deoxynucleoside triphosphate mixture
(Boehringer Mannheim).
0021-9193/98/$04.00+0
Copyright © 1998, American Society for Microbiology. All rights reserved.
Parallel and Divergent Genotypic Evolution in
Experimental Populations of Ralstonia sp.
ABSTRACT
Top
Abstract
Introduction
Materials & Methods
Results
Discussion
References
INTRODUCTION
Top
Abstract
Introduction
Materials & Methods
Results
Discussion
References
MATERIALS AND METHODS
Top
Abstract
Introduction
Materials & Methods
Results
Discussion
References
80°C. Individual
clones were randomly chosen for genetic analysis by streaking the
glycerol stocks onto 2,4-D-MMO, agar plates. Each clone was grown in
2,4-D-MMO medium and preserved in glycerol at 80°C, allowing us to
confirm experiments by performing replicate analysis.
Genome fingerprinting. The genomic organization of ancestral and evolved populations of TFD41 was determined by DNA fingerprinting using REP-PCR. The fingerprints of four clones from each population were determined after 1,000 generations and compared to that of the ancestral strain. To determine if trends in genetic changes could be observed and if the small sample size was representative of the populations, an additional four clones from every 100 generations of populations 5 and 15 were analyzed, except at generations 500 and 1000, where 50 clones were examined. One microliter of frozen glycerol stock of each clone was amplified in a Perkin-Elmer Gene Amp 9600 system, using conditions and reagents described by de Bruijn (12). Fingerprint patterns were confirmed by repeating the amplification at least twice.
Genetic distances.
Genetic distances between pairs of the
four clones analyzed by REP-PCR from each of the 18 evolved populations
after 1,000 generations of experimental evolution (73 × 72/2 = 2,628 pairs), as well as the ancestral strain, were determined. The
genetic distance between clones based on the REP-PCR fingerprints was calculated by determining the number of different PCR fragments (either
present or absent) between every pair of clones and then dividing by
the total number of PCR fragments observed. The average genetic
distance was determined for three different comparisons: (i) among
clones from the same evolved population (4 × 3 × 18/2 = 108 pairs), (ii) among clones from two different evolved populations (4 × 4 × 18 × 17/2 = 2,448 pairs), and (iii)
between the ancestor and evolved clones (1 × 72 = 72 pairs).
For comparisons i and iii, confidence limits (95%) were calculated
based on t distribution using 17 degrees of freedom
(n 1, where n = 18 independently evolved populations). To obtain the confidence limits for comparison ii, we used the jackknife technique (37) to determine the
contribution of each population to the overall average. All values are
reported as the mean ± standard error of the mean.
Cloning and nucleotide sequencing of the 2.4-kb REP-PCR fragment. Genomic DNA from the ancestral strain was amplified by REP-PCR, and the resulting DNA fragments were separated on a 1.5% low-melting-point agarose gel (SeaPlaque; FMC). The 2.4-kb amplified fragment that was lost in the majority of evolved clones was cut out of the gel, purified by using a Gene Clean kit (Biolabs 101), inserted into the pCRII cloning vector (Invitrogen), and introduced into E. coli as instructed by the manufacturers. Recombinant plasmid DNA was isolated by the alkaline lysis technique (33), digested with EcoRI, and resolved by agarose gel electrophoresis. The 2.4-kb fragment was purified (Gene Clean) and labeled with digoxigenin-dUTP according to the instructions supplied by the manufacturer (Boehringer Mannheim). The 2.4-kb REP-PCR fragment was hybridized to genomic DNA digested with BamHI and prepared as described above. Hybridization to the REP-PCR fingerprints was also determined by the method described above. Nucleotide sequence of the cloned fragment was determined by using Amersham's ThermoSequenase fluorescent primer sequencing kit and an ALFexpress automatic sequencer (Pharmacia). Nucleotide sequences were compared to entries in the available databases at the National Institutes of Health, using the BLAST (basic local alignment search tool) program (2).
Nucleotide sequence accession number. The nucleotide sequence of the 2.4-kb REP-PCR product has been deposited in the GenBank database under accession no. AF045553.
| |
RESULTS |
|---|
|
Top
Abstract
Introduction
Materials & Methods
Results
Discussion
References
|
|---|
Plasmid and 2,4-D catabolic gene analyses. The ancestral strain of Ralstonia sp. strain TFD41 carries a large plasmid (~200 kb), designated pTFD41 that carries the genes required for catabolism of 2,4-D, the carbon source used in these experiments. Restriction enzyme digestion of the plasmid and fragment density plots revealed 14 BamHI fragments, consisting of 12 unique and two duplicated sizes (Fig. 1). The three largest fragments (66.8, 29.6, and 27.2 kb) were resolved by pulsed-field electrophoretic separation (CHEF mapper system). The density plot of the BamHI digest of the ancestral plasmid (Fig. 1B, lane 1) illustrates that the peak height and area of the 6.7- and 3.6-kb fragments were greater than those of the preceding fragments (8.6 and 3.7 kb, respectively) of larger size, suggesting greater numbers of copies of these fragments. All 18 clones from the evolved populations at generation 1000 maintained the catabolic plasmid. In each of the evolved plasmids examined, the 6.7- and 3.6-kb BamHI fragments also had a greater peak height and area relative to the adjacent fragments (Fig. 1, lanes 2 to 6). In addition, the peak height and area of the 10.5-kb fragment were similar to those of the 9.9-kb fragment in the ancestral strain but noticeably higher than those in the evolved plasmids; therefore, this fragment may have been duplicated.
|
REP-PCR fingerprint analyses. Genome organization of ancestral and evolved clones of Ralstonia sp. strain TFD41 were determined by REP-PCR fingerprint analyses (Fig. 2A). Nine unique REP-PCR fingerprint patterns were observed from the 337 evolved clones examined. These unique genotypes were distinguished by the presence or absence of specific REP-PCR amplification products. Of the 337 clones examined, 296 (88%) had REP-PCR fingerprints different from those of their ancestor. The majority of clones with ancestor-like REP-PCR fingerprints were from generation 500 or earlier (28% [37 of the 134 clones] versus 2% [4 of 171 clones] at generation 1000). Ten REP-PCR-amplified fragments were common to all clones examined. Table 1 characterizes the four REP-PCR genotypes that were detected most frequently during this study, including the ancestral genotype. They varied in the presence of the 2.4-, 2.0-, and 1.9-kb amplification products. Seventy-two evolved clones were analyzed after 1,000 generations of experimental evolution, and 48, 7, 15, 1, and 1 clones had genotypes I, II, III, ancestral, and unique, respectively. Note that 71 of the 72 clones lacked the 2.4-kb fragment. Evidently, in all 18 independently evolving populations of Ralstonia sp. strain TFD41, one or more genotypes that lacked the 2.4-kb REP-PCR fragment appeared and achieved high frequency.
|
|
|
|
) and evolved genotypes I (
), II
(
), and III plus other (
) are described in Table Genetic distances. Genetic distances between pairs of the four clones analyzed by REP-PCR from each of the 18 evolved populations after 1,000 generations of evolution as well as the ancestral strain were determined (summarized in Fig. 5). The average genetic distances determined were (i) 0.333 ± 0.094, among clones from the same evolved population; (ii) 0.848 ± 0.077, among clones from two different evolved populations; and (iii) 1.528 ± 0.161, between the ancestor and evolved clones. The larger values for genetic distances indicate a greater genetic divergence between the populations being compared. As one would expect, there was greater divergence between clones from different evolved populations (0.848 ± 0.077) than between clones from a single population (0.333 ± 0.094). One would expect that as independent populations evolve, the genetic distance between these populations (0.848 ± 0.077) would be greater than the distance between the evolved clones and their ancestor (1.528 ± 0.161). However, the values were opposite, suggesting that the independently evolved populations underwent parallel evolution. Most of this evolutionary convergence can be attributed to the loss of the 2.4-kb fragment; therefore, when it is excluded from these analyses, the average genetic distance between the evolved and ancestral genotypes is reduced by almost 1 (to ~0.5), whereas the average genetic distance between clones from different populations is hardly changed (~0.8). Then the average genetic distance between clones from two independently evolved populations was substantially greater than the average distance between evolved clones and their common ancestor, consistent with expectations for phylogenetically informative molecular characters.
|
Nucleotide sequence analysis of the 2.4-kb REP-PCR fragment. Comparison of the DNA sequence of the 2.4-kb (actual length, 2,420 bp) REP-PCR fragment nucleotide sequence to the GenBank database revealed homology to tripartite ATP-independent periplasmic transporter genes identified in Rhodobacter capsulatus and deduced to exist in E. coli, Salmonella typhimurium, Haemophilus influenzae, and Synechocystis spp. (16). The greatest amino acid sequence similarity is to the deduced YiaN (58% identical and 78% similar) protein in E. coli (8) and YiaM (33% identical and 62% similar) and YiaO (39% identical and 59% similar) in H. influenzae (15, 36). The termini of the 2.4-kb PCR product were located within the genes with sequence similarity to yiaN and yiaO. This finding is unusual because the REP sequences are typically extragenic. The REP nucleotide sequences delineating the PCR products were not found in the homologous sequences from the database search.
| |
DISCUSSION |
|---|
|
Top
Abstract
Introduction
Materials & Methods
Results
Discussion
References
|
|---|
After propagation under identical environmental conditions for 1,000 generations (250 days), replicate populations of a 2,4-D-degrading environmental isolate, Ralsonia sp. strain TFD41, were found to undergo both parallel and divergent evolution. Phenotypic analysis suggested that parallel evolution had occurred because of the systematic increases in competitive mean fitness relative to that of the common ancestor of each of the evolved populations (24). At the same time, divergence was observed by the variance of mean fitness values and changes in colony and cell morphology (23, 24). In this study, we were able to show that the organization of the genome had been altered and could be detected in these populations by using relatively simple genetic analysis techniques. The genotypic analysis showed that common genetic changes occurred in these populations but the resulting genotypes were not identical.
Parallel genotypic evolution was suggested by the duplication of a common segment of the plasmid and by the deletion of a common fragment in the fingerprint pattern of the REP-PCR amplification products. Using DNA hybridization experiments and restriction digest analyses, we determined that there is an apparent duplication in the plasmid that occurred in all of the clones examined, suggesting that it is a determinant of competitive fitness in these populations. It may first appear unusual that the duplication in the plasmid is not accompanied by the addition of a new fragment. However, preliminary evidence indicates that the region is over 10 kb in size and is flanked by insertion sequence (IS) elements (10). We believe that recombination between the IS elements created the duplication and an additional copy of the IS element; therefore, the restriction fragments between and within the IS elements have been duplicated but no new fragments are created because the region external to the elements remains unchanged. By digestion with XbaI, an enzyme without a restriction site in the IS element, a unique fragment is observed in the evolved plasmids (29a).
It was not surprising to find that the apparent duplication in the plasmid included the tfdA gene, encoding the first enzyme in the 2,4-D catabolic pathway. DNA duplication not only is common in bacteria but has been observed frequently in many other organisms (9, 25, 27, 30). Duplications are believed to arise as a primitive regulatory mechanism to increase metabolism under extreme conditions (32). If the duplicated tfdA genes in the evolved Ralstonia populations are functional, then their fitness could be improved by increased enzyme activity. However, the duplicated region is large; therefore, in addition to the tfdA gene, other genes unrelated and related to 2,4-D utilization (e.g., gene regulation and substrate transport) are likely to be present in this region. This observation is similar to those of Sonti and Roth (38), who found that under limited-carbon conditions, large regions of the S. typhimurium chromosome were duplicated. The region duplicated included the permease genes for the carbon sources tested, but the duplication was also large and included other unknown genes.
Less expected, but most important and revealing, was the loss of a common 2.4-kb PCR amplification product in almost all (71 of 72) of the evolved clones examined (Fig. 2 and 3). The results were not expected because it seemed very unlikely that the same region of the chromosome would be deleted in virtually every genotype in each population. These findings are important because this technique allowed the screening of a great number of clones from independently evolved populations; therefore, it seems certain that the loss of the 2.4-kb REP-PCR fragment is causally related to the improvements in competitive fitness demonstrated in our previous study (24). The loss of the 2.4-kb product from REP-PCR fingerprints resulted from a deletion in the chromosome and not a point mutation or rearrangement into an alternate locus as shown by the lack of hybridization of the 2.4-kb PCR product to total genomic DNA from these evolved strains. All 18 experimental populations independently led to genotypes that had lost this fragment, and in all cases these genotypes reached high frequencies. We stress that these changes in the REP-PCR fingerprint must have evolved independently in each case because each population was founded from a single colony (and hence a single cell) of the ancestral strain. Moreover, we can exclude the possibility that the parallel changes in the 2.4-kb fragment resulted from cross-contamination among the experimental populations because the replicate populations possessed different antibiotic resistance markers that were strictly alternated during the serial propagation of cultures and remained distinct from one another (24). It is possible that the parallel changes at this locus indicate that it is hypermutable (6, 11, 29), but the fact that the deletion mutation achieved high frequency in every population implies that the deletion was under strong positive selection during the evolution experiment.
Nucleotide sequencing revealed that the 2.4-kb fragment carries genes related to the tripartite ATP-independent periplasmic transporter genes, encoding a high-affinity transport system for the C4 dicarboxylates malate, succinate, and fumarate (16). We do not know if these genes are functional in Ralstonia; the REP primer sequences were intragenic and may have disrupted the genes. Also, the extent of the genomic deletion associated with the loss of the 2.4-kb PCR fragment is unknown; therefore, other genes that contribute to the fitness changes may have been lost. The deletion of this region can improve fitness if genes carry detrimental information or provide no selective advantage but are a costly genetic load (1). Further research is required to determine why and how this genetic change affects fitness.
It is important to recognize the fact that although common genetic events were observed, the resultant populations were not genetically identical. Genetic diversification was indicated by the different REP-PCR fingerprints observed in clones at generation 1000 and as early as generation 100. These differences showed that genetic divergence occurred both within and between the independently evolved populations. Genetic diversification was also indicated by the deletions that were observed in 4 of the 18 plasmids from evolved populations. These changes may be less frequent and/or provide less of a selective advantage than loss of the 2.4-kb DNA segment. Future research can elucidate if these genetic differences contribute to the variation in mean fitness observed within populations, produce an alternate phenotype (e.g., physiology or morphology), or are neutral mutations.
The results of this study suggest that the role of genetic rearrangements in adaptive evolution may be greater than is presently realized. The parallel genotypic changes observed in this study arose from some form of genetic recombination (26, 32, 34) that resulted in both duplications and deletions of relatively large spans of DNA sequences. Finding two genotypic changes associated with improved fitness reinforces the fact that a number of physiological factors affects the fitness of a population and that studies are not complete when single gene changes are found. More importantly, the study shows that genetic analysis of experimentally evolved populations with a known ancestor provides a means to begin interpreting genetic events that led to organisms as we see them now and to understand the underlying genetic mechanism.
| |
ACKNOWLEDGMENTS |
|---|
We are indebted to M. Travisano for critical reading of the manuscript and helpful, insightful discussions. We are grateful to M. Schneider for technical advice on the use of the REP-PCR technique and J. Lindell for technical assistance.
This work was supported by National Research Foundation grant BIR9120006 to the Center for Microbial Ecology at Michigan State University.
| |
FOOTNOTES |
|---|
* Corresponding author. Present address: Department of Agronomy, Purdue University, West Lafayette, IN 47907-1150. Phone: (765) 496-2997. Fax: (765) 496-2926. E-mail: cnakatsu{at}purdue.edu.
Present address: Institute of Environmental Biology, Jagiellonian
University, 30-060 Krakow, Poland.
Present address: Department of Microbiology, University of
Groningen, Kerklaan 30, 9750 AA Haren, The Netherlands.
| |
REFERENCES |
|---|
|
Top
Abstract
Introduction
Materials & Methods
Results
Discussion
References
|
|---|
| 1. | Ajioka, J. W., and D. L. Hartl. 1989. Population dynamics of transposable elements, p. 939-958. In D. E. Berg, and M. M. Howe (ed.), Mobile DNA. ASM Press, Washington, D.C. |
| 2. | Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410[Medline]. |
| 3. | Arber, W. 1991. Elements in microbial evolution. J. Mol. Evol. 33:4-12[Medline]. |
| 4. | Arber, W. 1993. Evolution of prokaryotic genomes. Gene 135:49-56[Medline]. |
| 5. | Ausubel, F. M., R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, J. A. Smith, and K. Struhl (ed.). 1989. Short protocols in molecular biology. John Wiley & Sons, New York, N.Y. |
| 6. | Bachellier, S., J. M. Clement, M. Hofnung, and E. Gilson. 1997. Bacterial interspersed mosaic elements (BIMES) are a major source of sequence polymorphism in Escherichia coli intergenic regions including specific associations with a new insertion sequence. Genetics 145:551-562[Abstract]. |
| 7. | Bennett, A. F., and R. E. Lenski. 1996. Evolutionary adaptation to temperature. 5. Adaptive mechanisms and correlated responses in experimental lines of Escherichia coli. Evolution 50:493-503. |
| 8. |
Blattner, F. R.,
G. Plunkett III,
C. A. Bloch,
N. T. Perna,
V. Burland,
M. Riley,
J. Collado-Vides,
J. D. Glasner,
C. K. Rode,
G. F. Mayhew,
J. Gregor,
N. W. Davis,
H. A. Kirkpatrick,
M. A. Goeden,
D. J. Rose,
B. Mau, and Y. Shao.
1997.
The complete genome sequence of Escherichia coli K-12.
Science
277:1453-1474 |
| 9. | Brenner, S. E., T. Hubbard, A. Murzin, and C. Chothia. 1995. Gene duplications in H. influenzae. Nature 387:140. |
| 10. | Bulinski, D. A., and C. H. Nakatsu. 1997. Presented at the 97th General Meeting of American Society of Microbiology, 4-8 May, 1997, Miami Beach, Fla . |
| 11. | Cunningham, C. W., K. Jeng, J. Husti, M. Badgett, I. J. Molineux, D. M. Hillis, and J. J. Bull. 1997. Parallel molecular evolution of deletions and nonsense mutations in bacteriophage T7. Mol. Biol. Evol. 14:113-116[Medline]. |
| 12. |
de Bruijn, F.
1992.
Use of repetitive (repetitive extragenic palindromic and enterobacterial repetitive intergeneric consensus) sequences and the polymerase chain reaction to fingerprint the genomes of Rhizobium meliloti isolates and other soil bacteria.
Appl. Environ. Microbiol.
58:2180-2187 |
| 13. |
Don, R. H., and J. M. Pemberton.
1985.
Genetic and physical map of the 2,4-dichlorophenoxyacetic acid degrative plasmid pJP4.
J. Bacteriol.
161:466-468 |
| 14. | Dybvig, K. 1993. DNA rearrangements and phenotypic switching in prokaryotes. Mol. Microbiol. 10:465-471[Medline]. |
| 15. |
Fleischmann, R. D.,
M. D. Adams,
O. White,
R. A. Clayton,
E. F. Kirkness,
A. R. Kerlavage,
C. J. Bult,
J.-F. Tomb,
B. A. Dougherty,
J. M. Merrick,
K. McKenney,
G. Sutton,
W. FitzHugh,
C. A. Fields,
J. D. Gocayne,
J. D. Scott,
R. Shirley,
L.-I. Liu,
A. Glodek,
J. M. Kelley,
J. F. Weidman,
C. A. Phillips,
T. Spriggs,
E. Hedblom,
M. D. Cotton,
T. R. Utterback,
M. C. Hanna,
D. T. Nguyen,
D. M. Saudek,
R. C. Brandon,
L. D. Fine,
J. L. Fritchman,
J. L. Fuhrmann,
N. S. M. Geoghagen,
C. L. Gnehm,
L. A. McDonald,
K. V. Small,
C. M. Fraser,
H. O. Smith, and J. C. Venter.
1995.
Whole-genome random sequencing and assembly of Haemophilus influenzae.
Science
269:496-512 |
| 16. |
Forward, J. A.,
M. C. Behrendt,
N. R. Wyborn,
R. Cross, and D. J. Kelly.
1997.
TRAP transporters a new family of periplasmic solute transport systems encoded by the dctPQM genes of Rhodobacter capsulatus and by homologs in diverse gram-negative bacteria.
J. Bacteriol.
179:5482-5493 |
| 17. | Fulthorpe, R. R., C. McGowan, O. V. Maltseva, W. H. Holben, and J. M. Tiedje. 1995. 2,4-Dichlorophenoxyacetic acid-degrading bacteria contain mosaics of catabolic genes. Appl. Environ. Microbiol. 61:3274-3281[Abstract]. |
| 18. | Guttman, D. S., and D. E. Dykhuizen. 1994. Detecting selective sweeps in naturally occurring Escherichia coli. Genetics 138:993-1003[Abstract]. |
| 19. |
Helling, R. B.,
C. N. Vargas, and J. Adams.
1987.
Evolution of Escherichia coli during growth in a constant environment.
Genetics
116:349-358 |
| 20. |
Holben, W. E.,
B. M. Schroeter,
V. G. M. Calabrese,
R. H. Olsen,
J. K. Kukor,
V. O. Biederbeck,
A. E. Smith, and J. M. Tiedje.
1992.
Gene probe analysis of soil microbial populations selected by amendment with 2,4-dichlorophenoxyacetic acid.
Appl. Environ. Microbiol.
58:3941-3948 |
| 21. |
Johnson, P. A.,
R. E. Lenski, and F. C. Hoppensteadt.
1995.
Theoretical analysis of divergence in mean fitness between initially identical populations.
Proc. R. Soc. Lond. Biol. Sci.
259:125-130 |
| 22. | Kimura, M. 1983. The neutral theory of molecular evolution. Cambridge University Press, Cambridge, England. |
| 23. | Korona, R. 1996. Genetic divergence and fitness convergence under uniform selection in experimental populations of bacteria. Genetics 143:637-644[Abstract]. |
| 24. |
Korona, R.,
C. H. Nakatsu,
L. J. Forney, and R. E. Lenski.
1994.
Evidence for multiple adaptive peaks from populations of bacteria evolving in a structured habitat.
Proc. Natl. Acad. Sci. USA
91:9037-9041 |
| 25. |
Labedan, B., and M. Riley.
1995.
Widespread protein sequence similarities: origins of Escherichia coli genes.
J. Bacteriol.
177:1585-1588 |
| 26. | Lloyd, R. G., and K. B. Low. 1996. Homologous recombination, p. 2236-2255. In F. C. Neidhardt, R. Curtiss III, J. L. Ingraham, E. C. C. Lin, K. B. Low, B. Magasanik, W. S. Reznikoff, M. Riley, M. Schaechter, and H. E. Umbarger (ed.), Escherichia coli and Salmonella: cellular and molecular biology, vol. 2. ASM Press, Washington, D.C. |
| 27. | Lupski, J. R., J. R. Roth, and G. M. Weinstock. 1996. Chromosomal duplications in bacteria, fruit flies, and humans. Am. J. Hum. Genet. 58:21-27[Medline]. |
| 28. |
Lupski, J. R., and G. M. Weinstock.
1992.
Short, interspersed repetitive DNA sequences in prokaryotic genomes.
J. Bacteriol.
174:4525-4529 |
| 29. | Moxon, E. R., P. B. Rainey, M. A. Nowak, and R. E. Lenski. 1994. Adaptive evolution of highly mutable loci in pathogenic bacteria. Curr. Biol. 4:24-33[Medline]. |
| 29a. | Nakatsu, C. H. Unpublished data. |
| 29b. | Nakatsu, C. H., and T. L. Marsh. GenBank accession no. AF067833. |
| 30. | Ohta, T. 1994. Further examples of evolution by gene duplication revealed through DNA sequence comparisons. Genetics 138:1331-1337[Abstract]. |
| 31. |
Perkins, E. J.,
M. P. Gordon,
O. Caceres, and P. F. Lurquin.
1990.
Organization and sequence analysis of the 2,4-dichlorophenol hydroxylase and dichlorocatechol oxidative operons of plasmid pJP4.
J. Bacteriol.
172:2351-2359 |
| 32. | Roth, J. R., N. Benson, T. Galitski, K. Haack, J. G. Lawrence, and L. Miesel. 1996. Rearrangements of the bacterial chromosome: formation and applications, p. 2256-2276. In F. C. Neidhardt, R. Curtiss III, J. L. Ingraham, E. C. C. Lin, K. B. Low, B. Magasanik, W. S. Reznikoff, M. Riley, M. Schaechter, and H. E. Umbarger (ed.), Escherichia coli and Salmonella: cellular and molecular biology, vol. 2. ASM Press, Washington, D.C. |
| 33. | Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. |
| 34. | Shapiro, J. A. 1985. Mechanisms of DNA reorganization in bacteria. Int. Rev. Cytol. 93:25-56[Medline]. |
| 35. | Shapiro, J. A. 1992. Natural genetic engineering in evolution. Genetica 86:99-111[Medline]. |
| 36. | Shaw, J. G., M. J. Hamblin, and D. J. Kelly. 1991. Purification, characterization and nucleotide sequence of the periplasmic C4 dicarboxylate-binding protein (DctP) from Rhodobacter capsulatus. Mol. Microbiol. 5:3055-3062[Medline]. |
| 37. | Sokal, R. R., and F. J. Rohlf. 1981. Biometry, 2nd ed., p. 795-799. W. H. Freeman, San Francisco, Calif. |
| 38. |
Sonti, R. V., and J. R. Roth.
1989.
Role of gene duplication in the adaptation of Salmonella typhimurium to growth on limiting carbon sources.
Genetics
123:19-28 |
| 39. | Southern, E. M. 1975. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J. Mol. Biol. 98:503-517[Medline]. |
| 40. |
Stanier, R. Y.,
N. J. Palleroni, and M. Doudoroff.
1966.
The aerobic pseudomonads: a taxonomic study.
J. Gen. Microbiol.
43:159-271 |
| 41. |
Streber, W. R.,
K. N. Timmis, and M. H. Zenk.
1987.
Analysis, cloning, and high-level expression of 2,4-dichlorophenoxyacetic monooxygenase gene tfdA of Alcaligenes eutrophus JMP134.
J. Bacteriol.
169:2950-2955 |
| 42. | Tonso, N. L., V. G. Matheson, and W. E. Holben. 1995. Polyphasic characterization of a suite of bacterial isolates capable of degrading 2,4-D. Microb. Ecol. 30:3-24. |
| 43. | Travisano, M., and R. E. Lenski. 1996. Long-term experimental evolution in Escherichia coli. 4. Targets of selection and the specificity of adaptation. Genetics 143:15-26[Abstract]. |
| 44. |
Travisano, M.,
J. A. Mongold,
A. F. Bennett, and R. E. Lenski.
1995.
Experimental tests of the roles of adaptation, chance, and history in evolution.
Science
267:87-90 |
| 45. |
Versalovic, J.,
T. Koeuth, and J. R. Lupski.
1991.
Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes.
Nucleic Acids Res.
19:6823-6831 |
| 46. | Wright, S. 1932. The roles of mutation, inbreeding, crossbreeding and selection in evolution. Proc. Int. Cong. Genet. 1:356-366. |
| 47. |
Wyndham, R. C.
1986.
Evolved aniline catabolism in Acinetobacter calcoaceticus during continuous culture of river water.
Appl. Environ. Microbiol.
51:781-789 |
Journal of Bacteriology, September 1998, p. 4325-4331, Vol. 180, No. 17
0021-9193/98/$04.00+0
Copyright © 1998, American Society for Microbiology. All rights reserved.
This article has been cited by other articles:
-
Brown, C. J., Wong, M., Davis, C. C., Kanti, A., Zhou, X., Forney, L. J.
(2007). Preliminary characterization of the normal microbiota of the human vulva using cultivation-independent methods. J Med Microbiol
56: 271-276
[Abstract] [Full Text] -
Rath, D., Jawali, N.
(2006). Loss of Expression of cspC, a Cold Shock Family Gene, Confers a Gain of Fitness in Escherichia coli K-12 Strains.. J. Bacteriol.
188: 6780-6785
[Abstract] [Full Text] -
Fong, S. S., Joyce, A. R., Palsson, B. O.
(2005). Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states. Genome Res
15: 1365-1372
[Abstract] [Full Text] -
Plantinga, T. H., van der Does, C., Tomkiewicz, D., van Keulen, G., Konings, W. N., Driessen, A. J. M.
(2005). Deletion of the yiaMNO transporter genes affects the growth characteristics of Escherichia coli K-12. Microbiology
151: 1683-1689
[Abstract] [Full Text] -
Alcantara-Diaz, D., Brena-Valle, M., Serment-Guerrero, J.
(2004). Divergent adaptation of Escherichia coli to cyclic ultraviolet light exposures. Mutagenesis
19: 349-354
[Abstract] [Full Text] -
Zhong, S., Khodursky, A., Dykhuizen, D. E., Dean, A. M.
(2004). Evolutionary genomics of ecological specialization. Proc. Natl. Acad. Sci. USA
101: 11719-11724
[Abstract] [Full Text] -
Mavingui, P., Flores, M., Guo, X., Davila, G., Perret, X., Broughton, W. J., Palacios, R.
(2002). Dynamics of Genome Architecture in Rhizobium sp. Strain NGR234. J. Bacteriol.
184: 171-176
[Abstract] [Full Text] -
Cooper, V. S., Schneider, D., Blot, M., Lenski, R. E.
(2001). Mechanisms Causing Rapid and Parallel Losses of Ribose Catabolism in Evolving Populations of Escherichia coli B. J. Bacteriol.
183: 2834-2841
[Abstract] [Full Text] -
Riley, M. S., Cooper, V. S., Lenski, R. E., Forney, L. J., Marsh, T. L.
(2001). Rapid phenotypic change and diversification of a soil bacterium during 1000 generations of experimental evolution. Microbiology
147: 995-1006
[Abstract] [Full Text] -
Hanczyc, M. M., Dorit, R. L.
(2000). Replicability and Recurrence in the Experimental Evolution of a Group I Ribozyme. Mol Biol Evol
17: 1050-1060
[Abstract] [Full Text] -
Rabus, R., Jack, D. L., Kelly, D. J., Saier, M. H. Jr
(1999). TRAP transporters: an ancient family of extracytoplasmic solute- receptor-dependent secondary active transporters. Microbiology
145: 3431-3445
[Abstract] [Full Text] -
D'Argenio, D. A., Vetting, M. W., Ohlendorf, D. H., Ornston, L. N.
(1999). Substitution, Insertion, Deletion, Suppression, and Altered Substrate Specificity in Functional Protocatechuate 3,4-Dioxygenases. J. Bacteriol.
181: 6478-6487
[Abstract] [Full Text]
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Copyright © 2009 by the American Society for Microbiology. For an alternate route to Journals.ASM.org, visit: http://intl-journals.asm.org | More Info»