A Complete Sequence of the <i>T. tengcongensis</i> Genome

Bao, Qiyu; Tian, Yuqing; Li, Wei; Xu, Zuyuan; Xuan, Zhenyu; Hu, Songnian; Dong, Wei; Yang, Jian Feng; Chen, Yanjiong; Xue, Yanfen; Xu, Yi; Lai, Xiaoqin; Huang, Li; Dong, Xiuzhu; Ma, Yanhe; Ling, Leevan; Tan, Huarong; Chen, Runsheng; Wang, Jian; Yu, Jun; Yang, Huanming

doi:10.1101/gr.219302

Cited by 218 publications

(155 citation statements)

References 84 publications

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“…Of these, the E. coli PgaABCD system is involved in formation of an EPS containing a b-1,6-N-acetyl-D-glucosamine polymer, and an EPS with a similar component is also part of the Y. pestis biofilm (Itoh et al, 2005;Wang et al, 2004). Several other proteins related to HmsH, HmsF, HmsR and HmsS are from genome sequence projects (Bao et al, 2002;Methé et al, 2003;Nascimento et al, 2004;Ren et al, 2003). We have used these in amino acid sequence alignments with the Hms proteins to identify highly conserved residues that might be critical to the function of these four Hms proteins.…”

Section: Discussionmentioning

confidence: 99%

Identification of critical amino acid residues in the plague biofilm Hms proteins

et al. 2006

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Yersinia pestis biofilm formation causes massive adsorption of haemin or Congo red in vitro as well as colonization and eventual blockage of the flea proventriculus in vivo. This blockage allows effective transmission of plague from some fleas, like the oriental rat flea, to mammals. Four Hms proteins, HmsH, HmsF, HmsR and HmsS, are essential for biofilm formation, with HmsT and HmsP acting as positive and negative regulators, respectively. HmsH has a β-barrel structure with a large periplasmic domain while HmsF possesses polysaccharide deacetylase and COG1649 domains. HmsR is a putative glycosyltransferase while HmsS has no recognized domains. In this study, specific amino acids within conserved domains or within regions of high similarity in HmsH, HmsF, HmsR and HmsS proteins were selected for site-directed mutagenesis. Some but not all of the substitutions in HmsS and within the periplasmic domain of HmsH were critical for protein function. Substitutions within the glycosyltransferase domain of HmsR and the deacetylase domain of HmsF abolished biofilm formation in Y. pestis. Surprisingly, substitution of highly conserved residues within COG1649 did not affect HmsF function.

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Section: Discussionmentioning

confidence: 99%

Identification of critical amino acid residues in the plague biofilm Hms proteins

et al. 2006

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“…Presumably, the lack of the transferase domain activity is compensated for by the methyltransferase protein (38) also involved in the same reaction (32). This particular adaptation seems to be partly due to either lateral gene transfer (39) or to convergent evolution (17), because it is present in both T. maritima and T. tengcongensis, the latter of which is regarded as a later-diverged thermophile most closely related to mesophilic Bacillus halodurans (17).…”

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confidence: 99%

“…We began by comparing the utilization of structures in proteomes of thermophilic eubacteria (17)(18)(19) living at high temperatures (Ϸ373 K) to those of mesophilic eubacteria (20)(21)(22) living at moderate temperatures (Ϸ310 K). Previously, studies investigating the cause of thermostability (23) in proteins from thermophilic eubacteria have either focused in detail on the variation of relatively small families of folds from thermophile to mesophile (24,25) or else have directed their attention principally toward particular sequence-based means for thermal stabilization (26,27), such as salt-bridge formation (28,29) or disulfide bridges (15).…”

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confidence: 99%

Natural selection of more designable folds: A mechanism for thermophilic adaptation

England

Shakhnovich

2003

Proc. Natl. Acad. Sci. U.S.A.

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An open question of great interest in biophysics is whether variations in structure cause protein folds to differ in the number of amino acid sequences that can fold to them stably, i.e., in their designability. Recently, we have shown that a novel quantitative measure of a fold's tertiary topology, called its contact trace, strongly correlates with the fold's designability. Here, we investigate the relationship between a fold's contact trace and its relative frequency of usage in mesophilic vs. thermophilic eubacteria. We observe that thermophilic organisms exhibit a bias toward using folds of higher contact trace when compared with mesophiles. We establish this difference both for the distributions of folds at the whole-proteome level and also through more focused structural comparisons of orthologous proteins. Our findings suggest that thermophilic adaptation in bacterial genomes occurs in part through natural selection of more designable folds, pointing to designability as a key component of protein fitness.U nderstanding the adaptations that enable thermophilic organisms to survive at extreme temperatures is a challenge that has interested researchers since 1897 (1), and great strides have been made along this line of inquiry since the recent publications of complete genomes for several hyperthermophilic species (2). However, most research in this area has focused on amino acid sequence variations that increase the thermodynamic stability of thermophilic proteins while leaving their structures unchanged (2, 3). Far less is known about what structural differences exist between thermophilic and mesophilic proteomes. One interesting possibility is that a thermophilic bias in structure may manifest as a preference for folds that are able to accommodate a large number of low-energy sequences, because such folds have a higher probability of being able to maintain their stability while adapting by mutation to new pressures. This hypothesis relates to another problem of great interest in biophysics: how the structural topology of a protein fold affects its designability (4-9). Here, we present results that point to an important connection between these two problems. Making use of what is known analytically about the relationship between a fold's topology and its designability and thermostability, we report an adaptation mechanism of thermophillic bacteria: one that proceeds by selection of more designable folds.Recently, a new theoretical treatment of designability has been developed within the framework of a residue-residue contact Hamiltonian (10). This Hamiltonian is a well established model for protein energetics that defines the conformational energy of a polypeptide chain as the sum of the pairwise interaction energies of all of the amino acid pairs whose ␣ carbons are separated by a distance less than some contact cutoff, typically chosen to be Ϸ7.5 Å (11). More formally, for a chain of length N with a monomer alphabet containing M amino acid types (of course, M ϭ 20 for real proteins), we can define the ene...

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“…Here we report the cloning and characterization of the UvrD and MutL proteins from a fully sequenced thermophilic bacterium, Thermoanaerobacter tengcongensis (16). The helicase activity of the Tte-UvrD is described, as are the effects of the Tte-MutL protein on unwinding reactions catalyzed by TteUvrD helicase.…”

mentioning

confidence: 99%

Characterization of a Thermostable UvrD Helicase and Its Participation in Helicase-dependent Amplification

Luo

Tang²,

Ranalli³

et al. 2005

Journal of Biological Chemistry

148

122

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Helicase-dependent amplification (HDA) is an isothermal in vitro DNA amplification method based upon the coordinated actions of helicases to separate doublestranded DNA and DNA polymerases to synthesize DNA. Previously, a mesophilic form of HDA (mHDA) utilizing the Escherichia coli UvrD helicase, DNA polymerase I Klenow fragment, two accessory proteins, MutL and single-stranded DNA-binding protein (SSB), was developed (1). In an effort to improve the specificity and performance of HDA, we have cloned and purified a thermostable UvrD helicase (Tte-UvrD) and the mutL homolog (Tte-MutL) from Thermoanaerobacter tengcongensis. Characterization of the Tte-UvrD helicase shows that it is stable and active from 45 to 65°C. We have found that the Tte-UvrD helicase unwinds blunt-ended DNA duplexes as well as substrates possessing 3-or 5-ssDNA tails.Tte-UvrDwasusedtodevelopathermophilichelicasedependent amplification (tHDA) system to selectively amplify target sequences at 60 -65°C. The tHDA system is more efficient than mHDA, displaying heightened amplification sensitivity without the need for the MutL and SSB accessory proteins. Amplification independent of MutL corresponds with studies demonstrating that maximal Tte-UvrD helicase activity does not require the mutL homolog. The tHDA system allows for rapid amplification and detection of targets present in genomic DNA. The expeditious nature and simplistic design of the tHDA platform makes the technology ideal for use in diagnostic applications requiring rapid identification of organisms at the point-of-need.

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A Complete Sequence of the T. tengcongensis Genome

Cited by 218 publications

References 84 publications

Identification of critical amino acid residues in the plague biofilm Hms proteins

Identification of critical amino acid residues in the plague biofilm Hms proteins

Natural selection of more designable folds: A mechanism for thermophilic adaptation

Characterization of a Thermostable UvrD Helicase and Its Participation in Helicase-dependent Amplification

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