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21.
Nonrandom location of IS1 elements in the genomes of natural isolates of Escherichia coli 总被引:2,自引:0,他引:2
We have studied the spatial distribution of IS1 elements in the genomes of
natural isolates comprising the ECOR reference collection of Escherichia
coli. We find evidence for nonrandomness at three levels. Many pairs of IS1
elements are in much closer proximity (< 10 kb) than can be accounted
for by chance. IS1 elements in close proximity were identified by
long-range PCR amplification of the genomic sequence between them. Each
amplified region was sequenced and its map location determined by database
screening of DNA hybridization. Among the ECOR strains with at least two
IS1 elements, 54% had one or more pairs of elements separated by < 10
kb. We propose that this type of clustering is a result of "local hopping,"
in which we assume that a significant proportion of tranposition events
leads to the insertion of a daughter IS element in the vicinity of the
parental element. A second level of nonrandomness is found in strains with
a modest number of IS1 elements that are mapped through the use of inverse
PCR to amplify flanking genomic sequences: in these strains, the insertion
sites tend to be clustered over a smaller region of chromosome than would
be expected by chance. A third level of nonrandomness is observed in the
composite distribution of IS elements across strains: among 20 mapped IS1
elements, none were found in the region of 48-77 minutes, a significant
gap. One region of the E. coli chromosome, at 98 min, had a cluster of IS1
elements in seven ECOR strains of diverse phylogenetic origin. We deduce
from sequence analysis that this pattern of distribution is a result of
initial insertion in the most recent common ancestor of these strains and
therefore not a hot spot of insertion. Analysis using long- range PCR with
primers for IS2 and IS3 also yielded pairs of elements in close proximity,
suggesting that these elements may also occasionally transpose by local
hopping.
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23.
Fitness effects of amino acid replacements in the beta-galactosidase of Escherichia coli 总被引:7,自引:1,他引:6
Two genetic procedures were used to obtain amino acid replacements in the
lacZ-encoded beta-galactosidase in Escherichia coli. Amino acid
replacements could be obtained without regard to their effects on lactase
activity by selecting spontaneous mutations that relieved the strong
polarity of six nonsense mutations. When streaked on MacConkey- lactose
indicator plates, approximately 75% of these mutants gave strong red
lactose-fermenting colonies, and 25% gave white nonfermenting colonies.
Mutants from 11 other nonsense codons were isolated directly using
MacConkey-lactose indicator plates, on which positive color indication
requires only 0.5% of the wildtype lactase activity. Among the total of 17
codons, 25 variant beta-galactosidases were identified using
electrophoresis and thermal denaturation studies. The fitness effects of
these variant beta-galactosidases were determined using competition
experiments conducted with lactose as the sole nutrient limiting the growth
rate in chemostat cultures. Three of the replacements were deleterious, one
was selectively advantageous, and the selective effects of the remaining 21
were undetectable under conditions in which the smallest detectable
selection coefficient was approximately 0.4%/generation.
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24.
Introns and reading frames: correlation between splicing sites and their codon positions 总被引:4,自引:1,他引:3
Computer analyses of the entire GenBank database were conducted to examine
correlation between splicing sites and codon positions in reading frames.
Intron insertion patterns (i.e., splicing site locations with respect to
codon positions) have been analyzed for all of the 74 codons of all the
eukaryote taxonomic groups: primates, rodents mammals, vertebrates,
invertebrates, and plants. We found that reading frames are interrupted by
an intron at a codon boundary (as opposed to the middle of a codon)
significantly more often than expected. This observation is consistent with
the exon shuffling hypothesis, because exons that end at codon boundaries
can be concatenated without causing a frame shift and thus are
evolutionarily advantageous. On the other hand, when introns interrupt at
the middles of codons, they exist in between the first and second bases
much more frequently than between the second and third bases, despite the
fact that boundaries between the first and second bases of codons are
generally far more important than those between the second and third bases.
The reason for this is not clear and yet to be explained. We also show that
the length of an exon is a multiple of 3 more frequently than expected.
Furthermore, the total length of two consecutive exons is also more
frequently a multiple of 3. All the observations above are consistent with
results recently published by Long, Rosenberg, and Gilbert (1995).
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25.
Clifford DL Folmes D Kent Arrell Jelena Zlatkovic-Lindor Almudena Martinez-Fernandez Carmen Perez-Terzic Timothy J Nelson Andre Terzic 《Cell cycle (Georgetown, Tex.)》2013,12(15):2355-2365
Nuclear reprogramming resets differentiated tissue to generate induced pluripotent stem (iPS) cells. While genomic attributes underlying reacquisition of the embryonic-like state have been delineated, less is known regarding the metabolic dynamics underscoring induction of pluripotency. Metabolomic profiling of fibroblasts vs. iPS cells demonstrated nuclear reprogramming-associated induction of glycolysis, realized through augmented utilization of glucose and accumulation of lactate. Real-time assessment unmasked downregulated mitochondrial reserve capacity and ATP turnover correlating with pluripotent induction. Reduction in oxygen consumption and acceleration of extracellular acidification rates represent high-throughput markers of the transition from oxidative to glycolytic metabolism, characterizing stemness acquisition. The bioenergetic transition was supported by proteome remodeling, whereby 441 proteins were altered between fibroblasts and derived iPS cells. Systems analysis revealed overrepresented canonical pathways and interactome-associated biological processes predicting differential metabolic behavior in response to reprogramming stimuli, including upregulation of glycolysis, purine, arginine, proline, ribonucleoside and ribonucleotide metabolism, and biopolymer and macromolecular catabolism, with concomitant downregulation of oxidative phosphorylation, phosphate metabolism regulation, and precursor biosynthesis processes, prioritizing the impact of energy metabolism within the hierarchy of nuclear reprogramming. Thus, metabolome and metaboproteome remodeling is integral for induction of pluripotency, expanding on the genetic and epigenetic requirements for cell fate manipulation. 相似文献
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The Acochlidia are unique among opisthobranch gastropods in combining extremely high morphological and ecological diversity with modest species diversity. The phylogeny of acochlidians has never been addressed by cladistic means, as their evolution has remained unknown. This study gives a first overview on more than 150 biological and morphological characters that are potentially useful for phylogenetic analysis. Based on 107 characters, a parsimony analysis (PAUP) was performed for all 27 valid acochlidian species together with 11 (plus two) outgroup taxa. The resulting strict consensus tree shows a moderate overall resolution, with at least some bootstrap support for most resolved nodes. The Acochlidia are clearly monophyletic, and originate from an unresolved basal opisthobranch level. The Acochlidia split into the Hedylopsacea (Tantulum (Hedylopsis (Pseudunela (Strubellia (‘Acochlidium’, ‘Palliohedyle’))))) and Microhedylacea (Asperspina (Pontohedyle, ‘Parhedyle’, ‘Microhedyle’, (Ganitus, Paraganitus))). The formerly enigmatic Ganitidae, resembling sacoglossan opisthobranchs by having dagger‐like rachidian radular teeth, are likely to be highly derived microhedylids. The paraphyly of some of the traditionally recognized family level taxa induced a preliminary reclassification. From the phylogenetic hypothesis obtained, we conclude that the acochlidian ancestor was marine mesopsammic. The colonization of limnic systems occurred twice, independently: first in the Caribbean (with the development of the small interstitial Tantulum elegans), and second in the Indo‐Pacific, with a radiation of large‐sized benthic acochlidian species. The evolution of extraordinary reproductive features, such as hypodermic impregnation by a complex copulative aparatus in hedylopsaceans, cutaneous insemination via spermatophores in microhedylaceans, and gonochorism in Microhedylidae s.l. (including Ganitidae), is discussed. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 158 , 124–154. 相似文献
28.
Chromosomal DNA from 23 closely related, pathogenic strains of Escherichia
coli was digested and probed for the insertion sequences IS1, IS2, IS4,
IS5, and IS30. Under the assumption that elements residing in DNA
restriction fragments of the same apparent length are identical by descent,
parsimony analysis of these characters yielded a unique phylogenetic tree.
This analysis not only distinguished among bacterial strains that were
otherwise identical in their biochemical characteristics and enzyme
electrophoretic mobilities, but certain aspects of the topology of the tree
were consistent across several unrelated insertion elements. The
distribution of IS elements was then reexamined in light of the inferred
phylogenetic relationships to investigate the biological properties of the
elements, such as rates of insertion and deletion, and to discover apparent
recombinational events. The analysis shows that the pattern of distribution
of insertion elements in the bacterial genome is sufficiently stable for
epidemiological studies. Although the rate of recombination by conjugation
has been postulated to be low, at least two such events appear to have
taken place.
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29.
TL Kieft EM Murphy DL Haldeman PS Amy BN Bjornstad EV McDonald DB Ringelberg DC White J Stair RP Griffiths TC Gsell WE Holben DR Boone 《Microbial ecology》1998,36(3):336-348
Abstract Two chronosequences of unsaturated, buried loess sediments, ranging in age from <10,000 years to >1 million years, were investigated to reconstruct patterns of microbial ecological succession that have occurred since sediment burial. The relative importance of microbial transport and survival to succession was inferred from sediment ages, porewater ages, patterns of abundance (measured by direct counts, counts of culturable cells, and total phospholipid fatty acids), activities (measured by radiotracer and enzyme assays), and community composition (measured by phospholipid fatty acid patterns and Biolog substrate usage). Core samples were collected at two sites 40 km apart in the Palouse region of eastern Washington State, near the towns of Washtucna and Winona. The Washtucna site was flooded multiple times during the Pleistocene by glacial outburst floods; the Winona site elevation is above flood stage. Sediments at the Washtucna site were collected from near surface to 14.9 m depth, where the sediment age was approximately 250 ka and the porewater age was 3700 years; sample intervals at the Winona site ranged from near surface to 38 m (sediment age: approximately 1 Ma; porewater age: 1200 years). Microbial abundance and activities declined with depth at both sites; however, even the deepest, oldest sediments showed evidence of viable microorganisms. Same-age sediments had equal quantities of microorganisms, but different community types. Differences in community makeup between the two sites can be attributed to differences in groundwater recharge and paleoflooding. Estimates of the microbial community age can be constrained by porewater and sediment ages. In the shallower sediments (<9 m at Washtucna, <12 m at Winona), the microbial communities are likely similar in age to the groundwater; thus, microbial succession has been influenced by recent transport of microorganisms from the surface. In the deeper sediments, the populations may be considerably older than the porewater ages, since microbial transport is severely restricted in unsaturated sediments. This is particularly true at the Winona site, which was never flooded. 相似文献
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