Dynamic flexibility in the <i>Escherichia coli</i> genome

Tsai, Lu; Sun, Zhirong

doi:10.1016/s0014-5793(01)02978-7

Cited by 6 publications

(2 citation statements)

References 32 publications

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“…This region has also been found to be highly enriched in sequences favoring DNA curvature in both E. coli and B. subtilis (Pedersen et al 2000), which may favor the fixation of other proteins involved in chromosome condensation, such as H-NS in E. coli (Ussery et al 2001). The resulting structure of this large region encompassing terminus sites may play a role in the segregation of neosynthesized chromosomes in E. coli (Tsai and Sun 2001) and/or the resolution of chromosome dimers at the dif site. These processes have been shown to be highly dependent on flanking sequences (Perals et al 2000).…”

Section: Why Peculiar Patterns For Genes Near the Terminus?mentioning

confidence: 98%

G+C3 Structuring Along the Genome: A Common Feature in Prokaryotes

Daubin

Perrière²

2003

Molecular Biology and Evolution

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The heterogeneity of gene nucleotide content in prokaryotic genomes is commonly interpreted as the result of three main phenomena: (1) genes undergo different selection pressures both during and after translation (affecting codon and amino acid choice); (2) genes undergo different mutational pressure whether they are on the leading or lagging strand; and (3) genes may have different phylogenetic origins as a result of lateral transfers. However, this view neglects the necessity of organizing genetic information on a chromosome that needs to be replicated and folded, which may add constraints to single gene evolution. As a consequence, genes are potentially subjected to different mutation and selection pressures, depending on their position in the genome. In this paper, we analyze the structuring of different codon usage measures along completely sequenced bacterial genomes. We show that most of them are highly structured, suggesting that genes have different base content, depending on their location on the chromosome. A peculiar pattern of genome structure, with a tendency toward an A+T-enrichment near the replication terminus, is found in most bacterial phyla and may reflect common chromosome constraints. Several species may have lost this pattern, probably because of genome rearrangements or integration of foreign DNA. We show that in several species, this enrichment is associated with an increase of evolutionary rate and we discuss the evolutionary implications of these results. We argue that structural constraints acting on the circular chromosome are not negligible and that this natural structuring of bacterial genomes may be a cause of overestimation in lateral gene transfer predictions using codon composition indices.

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Section: Why Peculiar Patterns For Genes Near the Terminus?mentioning

confidence: 98%

G+C3 Structuring Along the Genome: A Common Feature in Prokaryotes

Daubin

Perrière²

2003

Molecular Biology and Evolution

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“…The understanding of mechanical responses of individual macromolecules under a small external force is of unique importance because the induced conformational transitions can result in the change of biological functions, and the investigation of single molecules would inspire new concepts in polymer physics, which go far beyond the classical elastic models. For example, the knowledge of radial compression properties of DNA is helpful in understanding gene regulation and DNA repair (Jimenez et al, 2003; Tsai and Sun, 2001).…”

Section: Introductionmentioning

confidence: 99%

High‐resolution imaging and nano‐manipulation of biological structures on surface

Zhang

Sun

et al. 2010

Microscopy Res & Technique

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In this mini-review we discuss our recent findings on imaging and manipulation of biological macromolecular structures by atomic force microscopy (AFM). In the first part of this review, we focus on high-resolution imaging of selected biological samples. AFM images of membrane proteins have revealed detailed conformational features related to identifiable biological functions. Different self-assembling behaviors of short peptides into supramolecular structures on various substrates under controlled environmental conditions have been systematically studied with AFM imaging. In the second part, we present a novel nano-manipulation technique for manipulating, isolating, amplifying, and sequencing of individual DNA molecules, which may find unique applications in the analysis of difficult sequence structures. Finally, we discuss how to characterize the elasticity of individual biomolecules and live cells. These results demonstrate that not only the high resolution capacity of the AFM is suited to resolve certain biological questions, but can also be applied to single molecule isolation and biomechanical analysis with its unique advantages.

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Sequence-Dependent Flexibility in Promoter Sequences

Tsai

Luo

Sun

2002

Journal of Biomolecular Structure and Dynamics

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The non-neighbor interactions between base-pairs were taken into account to calculate the angular parameters (Omega, rho and tau) describing the orientation of successive base-pair planes and the translation parameters (D(y)) along the long axis of base-pair steps for 36 independent tetramers. A statistical mechanical model was proposed to predict the DNA flexibility that is mainly related to the thermal fluctuations at individual base-pair steps. The DNA flexibility can be described by the root-mean-square deviation of the end-to-end distance of DNA helical structure. The present model was then used to investigate the extreme flexible pattern in prokaryotic and eukaryotic promoter sequences. The results demonstrated several extreme flexible regions related to functionally important elements exist both in prokaryotic promoters and in eukaryotic promoters, DNA flexibility and AT content are highly correlated. The probabilities finding flexibility pattern in promoter sequences were also estimated statistically. The biological implications were discussed briefly.

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Dynamic flexibility in the Escherichia coli genome

Cited by 6 publications

References 32 publications

G+C3 Structuring Along the Genome: A Common Feature in Prokaryotes

G+C3 Structuring Along the Genome: A Common Feature in Prokaryotes

High‐resolution imaging and nano‐manipulation of biological structures on surface

Sequence-Dependent Flexibility in Promoter Sequences

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