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3D structure of genome of simple bacteria reveals complex organization

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M. pneumoniae cell/Yuhei O. Tahara, CCBY

From ScienceDaily:

Researchers have described the 3D structure of the genome in the extremely small bacteria Mycoplasma pneumoniae. They discovered previously unknown arrangements of DNA within this tiny bacteria, which are also found in larger cells. Their findings suggest that this type of organization is a universal feature of living cells.

DNA contains the instructions for life, encoded within genes. Within all cells, DNA is organised into very long lengths known as chromosomes. In animal and plant cells these are double-ended, like pieces of string or shoelaces, but in bacteria they are circular. Whether stringy or circular, these long chromosomes must be organised and packaged inside a cell so that the genes can be switched on or off when they are required.

The scientists also used the Hi-C technique to study more detailed patterns of organisation within the Mycoplasma genome. In recent years, scientists all over the world have investigated the organisation of chromosomes inside cells from species ranging from larger bacteria to human. Next Generation Sequencing has allowed scientists to ‘read’ the DNA sequence of any genome, but this doesn’t reveal how genetic information is managed and organised in the crowded and bustling biological environment inside a cell. Now, new tools have revealed complex organisational structures within the genomes of larger organisms, with certain regions of chromosomes clustered together to form domains containing genes that are switched on or off together.

However, it was thought that these domains would not be found in Mycoplasma, because its genome is so small and it only makes around 20 different DNA binding proteins responsible for organising the chromosome, compared to the hundreds made by other bacterial species.

Intriguingly, the CRG team found that even the tiny Mycoplasma chromosome is organised into distinct structural domains, each containing genes that are also turned on or off in a co-ordinated way.

Marie Trussart, the lead author on the paper, said: “Studying bacteria with such a small genome was a big technical challenge, especially because we were using super-resolution microscopy, and it took us five years to complete the project. We had suspected that the Mycoplasma genome might have a similar overall organisation to other bacteria, but we were completely surprised to find that it was also organised into domains, which can be considered as regulatory units of chromatin organisation and that we had identified a previously unknown layer of gene regulation. This research shows that the organisation and control of genes cannot be understood by just looking at the linear sequence of DNA in the genome. Indeed, to get the full picture of gene regulation we need to look at the three-dimensional organisation of the chromatin that also coordinates gene activity.” Paper. (public access) – Marie Trussart, Eva Yus, Sira Martinez, Davide Baù, Yuhei O. Tahara, Thomas Pengo, Michael Widjaja, Simon Kretschmer, Jim Swoger, Steven Djordjevic, Lynne Turnbull, Cynthia Whitchurch, Makoto Miyata, Marc A. Marti-Renom, Maria Lluch-Senar, Luís Serrano. Defined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniae. Nature Communications, 2017; 8: 14665 DOI: 10.1038/ncomms14665 More.

These days, even simple bacteria have hidden structures. But it supposedly all just happened via Darwinism (natural selection acting on random mutation) even though we know full well it couldn’t have. No wonder the sea is boiling hot.

See also: Denis Noble’s new book calls for “fundamental revision” of neo-Darwinian theory Darwin apologists can probably convince the New York Times but these days that’s only a participation trophy.

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Comments
Off topic: Interesting article https://www.evolutionnews.org/2017/03/why-understanding-intelligent-design-helps-us-to-understand-physiology/Dionisio
March 25, 2017
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gpuccio, I think you've mentioned the topologically associating domains (TADs) here in this site before. Don't recall exactly when, but it was the first time I heard about them. Now it seems to show up more often in the research literature.Dionisio
March 25, 2017
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Dioniso: I agree. It's definitely an interesting paper. :)gpuccio
March 25, 2017
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[...] borders are characterized by low GC content levels.
interesting, isn’t it?Dionisio
March 24, 2017
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[...] domain borders are correlated with the presence of convergent and divergent gene pairs [...]
interesting, isn’t it?Dionisio
March 24, 2017
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[...] genes inside CIDs tend to be co-regulated, with lower co-expression levels being detected between genes at the domain boundaries.
interesting, isn’t it?Dionisio
March 24, 2017
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[...] supercoiling could be regulating domain formation in bacteria.
interesting, isn’t it?Dionisio
March 24, 2017
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[...] large genome DNA rearrangements can have important effects on the presence, order and expression of genes [...] [...] chromosome domains are a fundamental principle of genome folding.
interesting, isn’t it?Dionisio
March 24, 2017
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[...] the Ori and Ter are preferentially located at opposite poles early on in the cell cycle, and both have an origin proximal region parS (partition system) that assists in the orientation of the chromosome during replication.
interesting, isn’t it?Dionisio
March 24, 2017
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[...] the duplication of the AO was reported to be coordinated with cell division, which is known to occur by binary fission. [...] during cell replication but before nucleoid separation, the migration of the AO to the opposite pole of the cell has been observed in fixed cells, suggesting a coordination between the AO duplication and DNA replication. Once a new organelle has formed, it remains attached to the surface while the old AO pulls the dividing cell away from the nascent organelle, positioning itself at the opposite pole.
interesting, isn’t it?Dionisio
March 24, 2017
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DATCG @5: That's an interesting quote. Thanks. BTW, here's what the "CRG team" represents: Centre for Genomic Regulation (CRG) which includes: EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain Gene Regulation, Stem Cells and Cancer Program. Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona 08028, Spain Advanced Light Microscopy Unit, Centre for Genomic Regulation (CRG), 08003 Barcelona, SpainDionisio
March 24, 2017
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[...] genes inside CIDs tend to be co-regulated [...] [...] the chromosome structure has a role in transcription regulation.
interesting, isn't it?Dionisio
March 24, 2017
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"Intriguingly, the CRG team found that even the tiny Mycoplasma chromosome is organised into distinct structural domains, each containing genes that are also turned on or off in a co-ordinated way." All your unknown gene regulation base coordinations are belong to us. ;-)DATCG
March 24, 2017
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Some abbreviations used in the referenced paper: nucleoid-associated proteins (NAPs) chromosome conformation capture (3C) chromosome interacting domains (CIDs) topologically associating domains (TADs) heat unstable (HU) structural maintenance of chromosomes (SMC) factor for inversion simulation (Fis) integration host factor (IHF) histone-like nucleoid structuring (H-NS) transcription factors (TFs) attachment organelle (AO) single-stranded DNA (ssDNA) origin (Ori) matrix modelling potential (MMP) terminus of replication (Ter) transmission electron microscopy (TEM) 4?6-diamidino-2-phenylindole (DAPI) 3D-structured illumination microscopy (3D-SIM) Fluorescence in situ hybridization imaging (FISH)Dionisio
March 24, 2017
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[...] to get the full picture of gene regulation we need to look at the three-dimensional organisation of the chromatin that also coordinates gene activity.
Sorry to disappoint then, but that's not enough.Dionisio
March 24, 2017
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[...] we were completely surprised to find that [...] we had identified a previously unknown layer of gene regulation.
Did somebody say 'surprised'? :) They ain't seen nothin' yet. Complex complexity.Dionisio
March 24, 2017
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[...] the organisation and control of genes cannot be understood by just looking at the linear sequence of DNA in the genome.
Duh! Of course!Dionisio
March 24, 2017
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