Methylation, sugar puckering and Z-form status of DNA from a heavy metal-acclimated freshwater Gordonia sp.

Gurbanov, Rafig
Tuncer, Sinem
Mingu, Sara
Severcan, Feride
Gözen, Ayşe Gül
Heavy metal acclimation of bacteria is of particular interest in many aspects. It could add to our understanding of adaptation strategies applied by bacteria, as well as help us in devising ways to use such adaptive bacteria for bioremediation. In this study, we have explored the changes in the DNA of an aquatic Gordonia sp. acclimated to silver, cadmium, and lead. We have measured the changes in the DNA extracted from the acclimated bacteria by using ATR-FTIR coupled with unsupervised and supervised pattern recognition algorithms. Although whole-cell FTIR studies do reveal nucleic acid changes, the special care should be taken when considering marker nucleic acid bands in such spectra, as various other cell or tissue constituents also yield IR bands in the same region. An FTIR study on isolated DNA can be used to avoid this problem. The IR spectral profiles of the DNA molecules revealed significant changes in the backbone and sugar conformations of upon acclimation. We then further analyzed the DNA's global cytosine-methylation patterns of the heavy metal-acclimated bacteria. We aimed to find out whether epigenetic mechanisms operate in bacteria for survival and growth in inhibitory heavy metal concentrations or not. We found hypermethylation in Cd acclimation but hypomethylation for both Pb and Ag in Gordonia sp. Our results imply that changes in the conformational and methylation states of DNA seem to let bacteria to thrive in otherwise inhibitory conditions and mark the involvement of epigenetic modulation in acclimation processes.


Biosorption sites for lead [Pb (II)] in phanerochaete chrysosporium
Kaya, Levent; Özcengiz, Gülay; Department of Biology (2004)
Biosorption is a phenomenon involving the mechanisms that basically mediate heavy metal tolerance of microorganisms as well as sequestration of heavy metals from environment. Different classes of microorganisms have different biosorption capacities, as a result of the differences in composition and types of functional groups found on cell surfaces. The present study was undertaken to identify the molecular mechanisms for lead [Pb(II)] biosorption in the white-rot fungus, Phanerochaete chrysosporium. The met...
Structural and functional damages of whole body ionizing radiation on rat brain homogenate membranes and protective effect of amifostine
ÇAKMAK, GÜLGÜN; Severcan, Mete; Zorlu, Faruk; Severcan, Feride (Informa UK Limited, 2016-01-01)
Purpose: To investigate the effects of whole body ionizing radiation at a sublethal dose on rat brain homogenate membranes and the protective effects of amifostine on these systems at molecular level.
Discrimination of heavy metal acclimated environmental strains by chemometric analysis of FTIR spectra
Kepenek, Eda Seyma; Severcan, Mete; Gözen, Ayşe Gül; SEVERCAN, FERİDE (Elsevier BV, 2020-10-01)
Heavy metal acclimated bacteria are profoundly the preferred choice for bioremediation studies. Bacteria get acclimated to toxic concentrations of heavy metals by induction of specific enzymes and genetic selection favoring new metabolic abilities leading to activation of one or several of resistance mechanisms creating bacterial populations with differences in resistance profile and/or level. Therefore, to use in bioremediation processes, it is important to discriminate acclimated bacterial populations and...
Electronic excited states and excitation transfer kinetics in the Fenna-Matthews-Olson protein of the photosynthetic bacterium Prosthecochloris aestuarii at low temperatures
Iseri, EI; Gulen, D (Springer Science and Business Media LLC, 1999-01-01)
The molecular structure-function relationship of the Fenna-Matthews-Olson light-harvesting complex of the photosynthetic green bacterium Prosthecochloris aestuarii has been investigated. It has been assumed that the electronic excited states responsible for the function (transfer of electronic excitation energy) result from the dipole-dipole interactions between the bacteriochlorophyll molecules bound to the polypeptide chain of the complex at a specific three-dimensional geometry. The molecular structure-e...
Use of the isolated problem approach for multi-compartment BEM models of electro-magnetic source imaging
Gençer, Nevzat Güneri (IOP Publishing, 2005-07-07)
The isolated problem approach (IPA) is a method used in the boundary element method (BEM) to overcome numerical inaccuracies caused by the high-conductivity difference in the skull and the brain tissues in the head. Hamalainen and Sarvas (1989 IEEE Trans. Biomed. Eng. 36 165-71) described how the source terms can be updated to overcome these inaccuracies for a three-layer head model. Meijs et al (1989 IEEE Trans. Biomed. Eng. 36 103849) derived the integral equations for the general case where there are an ...
Citation Formats
R. Gurbanov, S. Tuncer, S. Mingu, F. Severcan, and A. G. Gözen, “Methylation, sugar puckering and Z-form status of DNA from a heavy metal-acclimated freshwater Gordonia sp.,” JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY, pp. 0–0, 2019, Accessed: 00, 2020. [Online]. Available: