15 November 2019
The nucleus of each and every cell in our bodies is packed with DNA that is 2 metres in length. So, how do you package all of that DNA into something less than the width of a single hair? The answer. Histones. DNA is wrapped around these proteins to form a complex called chromatin and allows the DNA to be packaged up and condensed into a smaller and smaller space.
In almost all eukaryotes, histone-based chromatin is the standard, yet in bacteria, there are no histones. So, how and why have histones become so entrenched in our chromatin structures during evolution, but bacterial genomes don’t need them. Interestingly, another branch of life called archaea – another type of single-celled organism – are even more flexible as some do have histones and some don’t. This makes archaea a great model to help us try and understand how you can build chromatin and whether there is anything special about histones. Can we still get chromatin-like structure if we swap histones for some other protein? Two new research studies published in eLife on 6 November and 11 November by the Molecular Systems group at the LMS shared insights into these questions.
Molecular surface of histones is shown in blue and the DNA in orange wrapped around. Image by Thomas Splettstoesser – Own work, CC BY-SA 3.0 – //commons.wikimedia.org/w/index.php?curid=15327175
Building chromatin-like structures
The archaeon Thermoplasma acidophilum grows optimally in very acidic conditions with high temperatures. It doesn’t have histones, but interestingly its ancestors did, so how does this archaeon package its genome without histones? Previous studies had shown that Thermoplasma gained a bacterial protein via horizontal gene transfer – the movement of genetic material between unicellular or multicellular organisms other than through reproduction. Research by Antoine Hocher in the Molecular Systems lab has demonstarted that this bacterial protein has converged to act like a histone in Thermoplasma. Like histones, it prefers binding DNA rich in C and G nucleotides and protects the DNA from nuclease digestion. This shows that you can make similar chromatin structures using different proteins and is a striking case of convergent evolution across different kingdoms of life.
Escherichia coli is a bacterium, which doesn’t have any histones. It is a system that is naïve to histones and hasn’t evolved to deal with histone:DNA structures. The second paper, led by PhD student Maria Rojec, asks the question how this system copes when you add an archaeal histone into the mix. Excitingly, these histones, when expressed in E. coli, bind the genome nearly everywhere in sequence-specific ways and formed repressive structures down-regulating the expression of some genes. The bacteria, however, don’t seem to care much that these histone proteins are bound to its DNA. This research shows that packaging up the DNA into chromatin isn’t completely shutting down gene expression. Instead, histones are being incorporated in the bacterial genome without affecting key processes in the cell, like replication or transcription. It suggests that histones in present day eukaryotes may have evolved initially without interfering with these key DNA processes, and only later became global repressive forces.
Tobias Warnecke, Head of the Molecular Systems Group at the MRC LMS and senior author of both these papers, discussed the next steps for this research:
“We want to explore more ‘odd systems’ with exceptional cases where there are interesting combinations of proteins and we don’t know what the chromatin structure looks like. We want to look at other archaea, algae and other natural histone mutants and dissect chromatin diversity across the tree of life.”
‘Chromatinization of Escherichia coli with archaeal histones’ was published on 6 November in eLife. Read the full article here.
‘The DNA-binding protein HTa from Thermoplasma acidophilum is an archael histone analog’ was published on 11 November in eLife. Read the full article here.
DNA Structure DNA Replication Eukaryotic Chromosome Structure
Study Questions DNA Structure, Replication and Eukaryotic Chromatin Structure Overheads DNA Structure, Replication
and Eukaryotic Chromatin Structure WWW Links Genetic Topics DNA replication is semi-conservative, one strand serves as the template for the second strand. Furthermore, DNA replication only occurs at a specific step in the cell cycle. The following table describes the cell cycle for a hypothetical cell with a 24 hr cycle. 10 hr 8 hr 5 hr 1 hr DNA replication has two requirements that must be met: In addition to these proteins, several other enzymes are involved in bacterial DNA replication. The second two activities of DNA Pol I are important for replication, but DNA Polymerase III (Pol III) is the enzyme that performs the 5'-3' polymerase function. Stage Activity Duration G1
Growth and increase in cell size
S
DNA synthesis
G2
Post-DNA synthesis
M
Mitosis
Proteins of DNA Replication
DNA exists in the nucleus as a condensed, compact structure. To prepare DNA for replication, a series of proteins aid in the unwinding and separation of the double-stranded DNA molecule. These proteins are required because DNA must be single-stranded before replication can proceed.
A General Model for DNA Replication
- The DNA molecule is unwound and prepared for synthesis by the action of DNA gyrase, DNA helicase and the single-stranded DNA binding proteins.
- A free 3'OH group is required for replication, but when the two chains separate no group of that nature exists. RNA primers are synthesized, and the free 3'OH of the primer is used to begin replication.
- The replication fork moves in one direction, but DNA replication only goes in the 5' to 3' direction. This paradox is resolved by the use of Okazaki fragments. These are short, discontinuous replication products that are produced off the lagging strand. This is in comparison to the continuous strand that is made off the leading strand.
- The final product does not have RNA stretches in it. These are removed by the 5' to 3' exonuclease action of Polymerase I.
- 5. The final product does not have any gaps in the DNA that result from the removal of the RNA primer. These are filled in by the action of DNA Polymerase I.
- 6. DNA polymerase does not have the ability to form the final bond. This is done by the enzyme DNA ligase.
Genetics of E. coli DNA Replication
Mutants are powerful tools to study any biochemical process. But to be useful, the scienctist must be able to maintain mutant in a viable state. This poses a problem for mutants ofa essential processes such as DNA replication. If the mutated gene is re quired for DNA replication, it is obvious that the mutant will not last more than one generation. The use of conditional mutants has helped to solve this problem. Conditional mutants express their mutant phenotype only under restricted conditons. A popular form of conditional mutant is the temperature sensitive mutant. Temperature sensitive mutants only express their mutant phenotype at a temperature the organism normally does not confront. Many of these mutants are expressed at elevate d temperatures. Therefore the mutant will grow normally at the permissive temperature and express the mutant phenotype at the elevetated tempterature.The analysis of temperature-sensitive mutants of E. coli has defined a series of genes and their role in DNA synthesis. The following table list some of the genes and their role in E. coli DNA replication.
| dnaA,I,P | Initiation |
| dnaB,C | Helicase at oriC |
| dnaE,N,Q,X,Z | Subunits of DNA polymerase III |
| dnaG | Primase |
| gyrA,B | Subunits of gyrase |
| lig | Ligase |
| oriC | Origin of Replication |
| polA | DNA polymerase I |
| polB | DNA polymerase II |
| rep | Helicase |
| ssb | Single-stranded DNA binding proteins |
Copyright © 1997. Phillip McClean