• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.421-426
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• 2005

In this paper, we investigate the nonlinear dynamic behavior of TPP (thiamine pyrophosphate) riboswitches in E. coli (Escherichia coli). TPP riboswitches are highly conserved RNA regulatory elements, embedded within the 5’'untranslated region of three TPP biosynthesis operons. The three operons thiCEFSGH, thiMD, and thiBPQ are involved in the biosynthesis, salvage, and transport of TPP, respectively. TPP riboswitches modulate their expressions in response to changing TPP concentration, without involving protein cofactors. Interestingly, the expression of thiMD is regulated at the translational level, while that of thiCEFSGH at both levels of transcription and translation. We develop a mathematical model of the TPP riboswitch’s regulatory system possessed by thiCEFSGH and thiMD, so as to simulate the time-course experiments of TPP biosynthesis in E. coli. The simulation results are validated against three sets of reported experimental data in order to gain insight into the nature of steady states and the stability of TPP riboswitches, and to explain the biological significance of regulating at level of transcription or translation, or even both. Our findings suggest that in the TPP biosynthesis pathway of E. coli, the biological effect of down-regulating thiCEFSGH operon at the translational level by TPP riboswitch is less prominent than that at the transcriptional level.

• Journal of the Korean Magnetic Resonance Society
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• v.19 no.3
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• pp.143-148
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• 2015

In some pathogenic bacteria, there are RNA thermometers, which regulate the production of virulence associated factors or heat shock proteins depending on temperature changes. Like a riboswitches, RNA thermometers are located in the 5'-untranslated region and involved translational gene regulatory mechanism. RNA thermometers block the ribosome-binding site and start codon area under the $37^{\circ}C$ within their secondary structure. After bacterial infection, increased the temperature in the host causes conformations changes of RNA, and the ribosome-binding site is exposed for translational initiation. Because structural differences between open and closed forms of RNA thermometers are mainly mediated by base pairing changes, NMR spectroscopy is a very useful method to study these thermodynamically changing RNA structure. In this review, we briefly provide a fundamental function of RNA thermometers, and also suggest a proper NMR experiments for studying RNA thermometers.

• Journal of Life Science
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• v.30 no.3
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• pp.304-312
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• 2020

Agarase can be used in the field of basic science, as well as for production of agar-derived high-functional oligosaccharides and bioenergy production using algae. In 2012, we summarized the classification, origin, production, and applications of agar. In this paper, we briefly review the literature on the recombinant expression of agarases from 2012 to the present. Agarase genes originated from 19 genera, including Agarivorans, Flammeovirga, Pseudoalteromonas, Gayadomonas, Catenovulum, Microbulbifer, Cellulophaga, Saccharophagus, Simiduia, and Vibrio. Of the 47 recombinant agarases, there were only two α-agarases, while the rest were β-agarases. All α-agarases produced agarotetraose, while β-agarases yielded many neoagarooligosaccharides ranging from neoagarobiose to neoagarododecaose. The optimum temperature ranged between 25 and 60℃, and the optimum pH ranged from 3.0 to 8.5. There were 14 agarases with an optimum temperature of 50℃ or higher, where agar is in sol state after melting. Artificial mutations, including manipulation of carbohydrate-binding modules (CBM), increased thermostability and simultaneously raised the optimum temperature and activity. Many hosts and secretion signals or riboswitches have been used for recombinant expression. In addition to gene recombination based on the amino acid sequence after agarase purification, recombinant expression of the putative agarase genes after genome sequencing and metagenome-derived agarases have been studied. This study is expected to be actively used in the application fields of agarase and agarase itself.