Trehalose facilitates DNA melting: a single-molecule optical tweezers study

Bezrukavnikov, Sergey; Mashaghi, Alireza; Wijk, Roeland J. van; Gu, Chan; Yang, Li Jiang; Gao, Yi Qin; Tans, Sander J.

doi:10.1039/c4sm01532k

Cited by 17 publications

(12 citation statements)

References 50 publications

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“…Correspondingly, phosphates were down-regulated in groups AA, F, and H in response to the stress of inhibitors (Table 1 ). Furthermore, trehalose is synthesized specially upon different stresses to protect various cellular components, and it can also directly interact with nucleic acids to facilitate melting of double-stranded DNA and stabilize single-stranded nucleic acids [ 65 ]. Hence, the up-regulation of trehalose in groups F, P, and C were consistent with its positive effects.…”

Section: Resultsmentioning

confidence: 99%

Proteomic and metabolomic analysis of the cellular biomarkers related to inhibitors tolerance in Zymomonas mobilis ZM4

Chang

Islam

French

et al. 2018

Biotechnol Biofuels

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BackgroundToxic compounds present in both the hydrolysate and pyrolysate of lignocellulosic biomass severely hinder the further conversion of lignocellulose-derived fermentable sugars into useful chemicals by common biocatalysts like Zymomonas mobilis, which has remarkable advantages over yeast. Although the extra detoxification treatment prior to fermentation process can help biocatalysts to eliminate the inhibitory environment, it is not environment friendly and cost effective for industrial application. As also reported by previous studies, an ideal and holistic approach to solve this issue is to develop microbial strains with inhibitor tolerance. However, previously engineered strains had the limitation that they could not cope well with the synergistic effect of multiple inhibitors as they are resistant only to a single inhibitor. Hence, understanding the universal cellular responses of Z. mobilis to various inhibitors may guide the designing of rational strategies to obtain more robust engineered strains for biofuel production from lignocellulosic biomass.ResultsQuantitative proteomics and metabolomics approaches were used to determine the cellular responses of Z. mobilis ZM4 to representative biomass-derived inhibitors like formic acid, acetic acid, furfural, 5-hydroxymethylfurfural, and phenol. The differentially expressed proteins identified under the challenge of single and combined inhibitors were involved in cell wall/membrane biogenesis, energy production, DNA replication, DNA recombination, DNA repair, DNA transcription, RNA translation, posttranslational modification, biosynthesis of amino acids, central carbon metabolism, etc. Metabolomics analysis showed that the up- or down-regulation pattern of metabolites was changed consistently with that of relevant proteins.ConclusionFifteen up-regulated proteins (e.g., Isopropylmalate isomerase LeuC, transcription-repair-coupling factor Mfd, and phosphoglucose isomerase PGI) and thirteen down-regulated proteins (e.g., TonB-dependent transporter ZMO1522, transcription termination factor Rho, and S1/P1 nuclease ZMO0127) were identified as candidate proteins related to all the stress conditions, implying that these proteins are potential biomarkers for the improvement of Z. mobilis ZM4 to resist complex biomass-derived inhibitors. These data can be used to generate a database of inhibitor-tolerance biomarkers, which could provide a basis for engineering Z. mobilis that would be able to grow in the presence of multiple inhibitors and directly ferment the biomass-derived sugars into biofuels.Electronic supplementary materialThe online version of this article (10.1186/s13068-018-1287-5) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

Proteomic and metabolomic analysis of the cellular biomarkers related to inhibitors tolerance in Zymomonas mobilis ZM4

Chang

Islam

French

et al. 2018

Biotechnol Biofuels

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“…In a previously published report on M. smegmatis it has also been shown that trehalose confers protection during elevated temperature (Woodruff et al, 2004). Trehalose is also an effective protectant of biological macromolecules including DNA (Woodruff et al, 2004; Bezrukavnikov et al, 2014). Trehalose prevents denaturation and aggregation of damaged proteins and thus facilitates their repair at a later stage (Strøm and Kaasen, 1993).…”

Section: Discussionmentioning

confidence: 99%

Free Trehalose Accumulation in Dormant Mycobacterium smegmatis Cells and Its Breakdown in Early Resuscitation Phase

et al. 2017

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Under gradual acidification of growth medium resulting in the formation of dormant Mycobacterium smegmatis, a significant accumulation of free trehalose in dormant cells was observed. According to 1H- and 13C-NMR spectroscopy up to 64% of total organic substances in the dormant cell extract was represented by trehalose whilst the trehalose content in an extract of active cells taken from early stationary phase was not more than 15%. Trehalose biosynthesis during transition to the dormant state is provided by activation of genes involved in the OtsA-OtsB and TreY-TreZ pathways (according to RT-PCR). Varying the concentration of free trehalose in dormant cells by expression of MSMEG_4535 coding for trehalase we found that cell viability depends on trehalose level: cells with a high amount of trehalose survive much better than cells with a low amount. Upon resuscitation of dormant M. smegmatis, a decrease of free trehalose and an increase in glucose concentration occurred in the early period of resuscitation (after 2 h). Evidently, breakdown of trehalose by trehalase takes place at this time as a transient increase in trehalase activity was observed between 1 and 3 h of resuscitation. Activation of trehalase was not due to de novo biosynthesis but because of self-activation of the enzyme from the inactive state in dormant cells. Because, even a low concentration of ATP (2 mM) prevents self-activation of trehalase in vitro and after activation the enzyme is still sensitive to ATP we suggest that the transient character of trehalase activation in cells is due to variation in intracellular ATP concentration found in the early resuscitation period. The negative influence of the trehalase inhibitor validamycin A on the resuscitation of dormant cells proves the importance of trehalase for resuscitation. These experiments demonstrate the significance of free trehalose accumulation for the maintenance of dormant mycobacterial viability and the involvement of trehalose breakdown in early events leading to cell reactivation similar to yeast and fungal spores.

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“…Optical and magnetic tweezers could normally achieve the mechanical information, conformational changes, and interactions of biomolecules, − which were also obtainable through MD simulations. Therefore, some studies used the combination of optical/magnetic tweezers and MD simulation to investigate the structure of biomolecules, − which was a significant approach in scientific research. However, apart from the above information, MD simulation was capable of revealing the interfacial binding details from the atomic level, probably critical to some interactions, which was not easy to acquire by optical/magnetic tweezers.…”

Section: Discussionmentioning

confidence: 99%

Potential Unwinding of Double-Stranded DNA upon Binding to a Carbon Nitride Polyaniline (C₃N) Nanosheet

Zhao

2021

J. Phys. Chem. B

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Recently, carbon nitride polyaniline (C3N) had attracted considerable attention from many scientific fields after its successful synthesis. However, thus far, limited efforts were devoted to reveal its potential effect to biomolecules, which correlated intimately with its further utilization. In this study, by using a molecular dynamics (MD) simulation approach, we investigated in detail the interaction between C3N and a double-stranded DNA (dsDNA) segment to expose the underlying biological effect of C3N to dsDNA and the corresponding molecular basis. MD simulation results demonstrated that dsDNA presented serious damages upon adsorption onto a C3N nanosheet with the terminal base pairs denaturized, unwound, and directly packing on the C3N surface, which implied that C3N was potentially deleterious to biomolecules. This binding/unwinding process was mainly guided by a combination of van der Waals and π–π stacking interactions together with a continuous lateral migration of dsDNA. Moreover, the nanoscale dewetting also played an important role during the adsorption. These findings revealed the potential bio-effect of the C3N nanomaterial and its molecular mechanism, which might benefit the future applications of C3N-based nanostructures.

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Trehalose facilitates DNA melting: a single-molecule optical tweezers study

Cited by 17 publications

References 50 publications

Proteomic and metabolomic analysis of the cellular biomarkers related to inhibitors tolerance in Zymomonas mobilis ZM4

Proteomic and metabolomic analysis of the cellular biomarkers related to inhibitors tolerance in Zymomonas mobilis ZM4

Free Trehalose Accumulation in Dormant Mycobacterium smegmatis Cells and Its Breakdown in Early Resuscitation Phase

Potential Unwinding of Double-Stranded DNA upon Binding to a Carbon Nitride Polyaniline (C₃N) Nanosheet

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Trehalose facilitates DNA melting: a single-molecule optical tweezers study

Cited by 17 publications

References 50 publications

Proteomic and metabolomic analysis of the cellular biomarkers related to inhibitors tolerance in Zymomonas mobilis ZM4

Proteomic and metabolomic analysis of the cellular biomarkers related to inhibitors tolerance in Zymomonas mobilis ZM4

Free Trehalose Accumulation in Dormant Mycobacterium smegmatis Cells and Its Breakdown in Early Resuscitation Phase

Potential Unwinding of Double-Stranded DNA upon Binding to a Carbon Nitride Polyaniline (C3N) Nanosheet

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Potential Unwinding of Double-Stranded DNA upon Binding to a Carbon Nitride Polyaniline (C₃N) Nanosheet