Scientists from the National Centre for Biological Sciences (NCBS), Bangalore, and the National Institutes of Health (NIH), USA, have elucidated genome-wide patterns in the complex structures formed by the DNA of bacteria in different environmental conditions. These complex structures in DNA could be playing important roles in regulating gene expression.
"A bend and a twist, then stretch and turn, now relax". What sounds like a series of exercise instructions, are also words that describe the various shapes a piece of DNA can assume. The classic double helix structure that one associates with DNA is but an extremely limited view of its physical 'shape'. The molecule that holds the codes of life is capable of further winding itself into myriad complex shapes called 'supercoils' that are capable of affecting gene expression patterns. Now, researchers from the National Centre for Biological Sciences (NCBS), Bangalore, and the National Institutes of Health (NIH), USA, have elucidated this pattern of supercoiling across the genome of the much studied bacterium E. coli.
DNA molecules are wound and rewound into complex structures that condense their immense lengths to a fraction of their actual size in order to fit their long strings of information into microscopic cells. But this 'packed' DNA that fits neatly into a cell also needs to be 'unpacked' periodically for gene expression and replication. When a gene is expressed, it is 'read' by protein machineries to create a messenger transcript that codes for more proteins. This requires DNA to be unwound from its double helix - a process that causes further twisting and coiling or 'overwinding' in regions of DNA elsewhere on the genome. Similarly, unwinding and overwinding also occurs when the genome replicates during reproduction. Therefore, at any given time, a cell's genetic material is in a constant state of structural flux - coils, supercoils, bends, twists and turns are formed, lost and reformed depending on the cell's state of activity.
A bacterial cell can be exposed to various environmental changes which include periods of starvation, lack of oxygen and unfavourable temperatures. Surviving these situations would require the bacterium to change its protein repertoire by altering the corresponding genetic expression profiles. Scientists have long thought that these changes could be effected through variations in the supercoiled structure of DNA. For example, the genomes of actively dividing cells under rich-nutrient conditions are known to be more underwound than the genomes of cells from the stationary phase when nutrients are scarce. In other words, supercoiling is likely to be sensitive to changes in the environment.
Although recent advancements in methodology have allowed researchers to study DNA supercoiling in human and yeast cells at local scales, this methodology has never been applied to bacterial genomes. Researchers from Aswin S. N. Seshasayee's group at NCBS and Prof. Sankar Adhya's team at NIH have currently applied these methods to study DNA supercoiling in bacteria at a fine-scale level. Using the chemical trimethylpsoralen, exposure to UV light and microarray technology, the research team have gained information on section-specific variations in genomic supercoiling within bacteria exposed to different external conditions.
"We have measured DNA supercoiling at a fine-scale resolution in bacteria for the first time. This study provides proof-of-concept that the supercoiling of a genome is not uniform and that it varies locally across genes. It also provides evidence to support the hypothesis that bacterial cells could be regulating gene expression and their own physiologies by altering the structure of their genomes," says Avantika Lal, the first author of the publication in the journal Nature Communications that details these findings.
In order to study the effect of environmental stimuli on the supercoiling status of the bacterial genome, two populations of E. coli were used to simulate two different external conditions. One simulated a nutrient-rich situation where actively dividing cells represented a growing population; whereas the other represented a condition where a population had exhausted its nutrients and was in a 'stationary' phase. Since the binding of trimethylpsoralen to DNA is proportional to the amount of supercoiling in the DNA, one could study genome-wide patterns of winding under these two settings. The results have shown that E. coli cells in the 'stationary' phase display a gradient of supercoiling across their circular genomes. In actively dividing cells, however, this gradient was missing though the entire genome was more supercoiled than the genomes of cells from the 'stationary' phase.
"It is very early days yet, but this work paves the way to understanding which genes' expression are affected by the environment," says Avantika. "This work can potentially teach us how we could control cell physiology by altering genetic expression via changes to DNA supercoiling by altering external conditions," she adds.
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Avantika Lal et al. Genome scale patterns of supercoiling in a bacterial chromosome, Nature Communications (2016). DOI: 10.1038/ncomms11055