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New insights into DNA ‘melting’ reveal chink in bacteria’s armour

Scientists have shed light on DNA ‘melting’ – a crucial process fundamental to all life.

The researchers, from Imperial College London, who used bacteria in their experiments, say these findings may provide new insights into eradicating harmful bugs. 

'How DNA melts is a fundamental part to all life – bacterial and human' Professor Xiaodong ZhangStudy author

DNA encodes information to make proteins, which are key to all processes in life. The DNA molecule is composed of two complementary strands, which are normally wrapped around each other in a helical structure.

When a cell wants to make proteins, the strands need to be pulled apart or 'melted' first, before a fundamental cellular process called transcription takes place.

Because transcription also takes place in human cells, the new findings may provide insights for conditions such as cancer and other diseases.

But although this DNA melting process is fundamental to life, scientists are still in the dark about the intricate details of how the cell’s machinery captures and reads the DNA.

In the new research, published in Molecular Cell, the team used an extremely powerful technique called cryo-electron microscopy to physically see how the DNA melting process happens in detail.


FESEB Conference on Machines on Genes

Xiaodong Zhang and Luke Yates attended the FASEB Machines on Genes meeting last week in Snowmass, Colorado and Xiaodong Zhang gave a keynote lecture whereas Luke's short talk was well received.

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Structure and regulation of the human INO80–nucleosome complex

Rafael Ayala1 na1, Oliver Willhoft, Ricardo J. Aramayo1, Martin Wilkinson, Elizabeth A. McCormack1, Lorraine Ocloo1, Dale B. Wigley1 & Xiaodong Zhang

Access to DNA within nucleosomes is required for a variety of processes in cells including transcription, replication and repair. Consequently, cells encode multiple systems that remodel nucleosomes. These complexes can be simple, involving one or a few protein subunits, or more complicated multi-subunit machines1. Biochemical studies2,3,4 have placed the motor domains of several chromatin remodellers in the superhelical location 2 region of the nucleosome. Structural studies of yeast Chd1 and Snf2—a subunit in the complex with the capacity to remodel the structure of chromatin (RSC)—in complex with nucleosomes5,6,7 have provided insights into the basic mechanism of nucleosome sliding performed by these complexes. However, how larger, multi-subunit remodelling complexes such as INO80 interact with nucleosomes and how remodellers carry out functions such as nucleosome sliding8, histone exchange9 and nucleosome spacing10,11,12 remain poorly understood. Although some remodellers work as monomers13, others work as highly cooperative dimers11, 14, 15. Here we present the structure of the human INO80 chromatin remodeller with a bound nucleosome, which reveals that INO80 interacts with nucleosomes in a previously undescribed manner: the motor domains are located on the DNA at the entry point to the nucleosome, rather than at superhelical location 2. The ARP5–IES6 module of INO80 makes additional contacts on the opposite side of the nucleosome. This arrangement enables the histone H3 tails of the nucleosome to have a role in the regulation of the activities of the INO80 motor domain—unlike in other characterized remodellers, for which H4 tails have been shown to regulate the motor domains.


 Proteins Interaction with the DNA strand       

Proteins Interaction with the DNA strand 

 

 

First-ever look at DNA opening reveals initial stage of reading the genetic code

'Understanding how the fundamental machinery works hopefully gives us additional tools for developing new kinds of antibiotics. As we investigate more steps in the process of transcription, we may find more stages during which we can intervene and attack harmful bacteria.' - Professor Xiaodong Zhang 


 The design of synthetic lifeforms could become a new industry

The design of synthetic lifeforms could become a new industry

IN THE basement of Imperial College sits the London DNA Foundry. The word “foundry” calls forth images of liquid metal being poured into moulds—of the early phase of the Industrial Revolution, in other words. This foundry is, however, determinedly modern. Liquid is indeed being moved around and poured. But it is in minuscule quantities, and it is not metal. Instead, it is an aqueous suspension of the genetic codes of life


Atomic Structure of Type VI Contractile Sheath from Pseudomonas aeruginosa

Pseudomonas aeruginosa has three type VI secretion systems (T6SSs), H1-, H2-, and H3-T6SS, each belonging to a distinct group. The two T6SS components, TssB/VipA and TssC/VipB, assemble to form tubules that conserve structural/functional homology with tail sheaths of contractile bacteriophages and pyocins. Here, we used cryoelectron microscopy to solve the structure of the H1-T6SS P. aeruginosa TssB1C1 sheath at 3.3 Å resolution. Our structure allowed us to resolve some features of the T6SS sheath that were not resolved in the Vibrio cholerae VipAB and Francisella tularensis IglAB structures. Comparison with sheath structures from other contractile machines, including T4 phage and R-type pyocins, provides a better understanding of how these systems have conserved similar functions/mechanisms despite evolution. We used the P. aeruginosa R2 pyocin as a structural template to build an atomic model of the TssB1C1 sheath in its extended conformation, allowing us to propose a coiled-spring-like mechanism for T6SS sheath contraction.