How a motile cytoskeleton drives bacterial cell division

Posted on 25 May, 2017 by Kevin

In a recent issue of Science, the discovery of a key mechanism for bacterial cell division was reported. This work was carried out by Dr Seamus Holden’s lab (ICaMB) in collaboration with Professor Cees Dekker (TU Delft), Professor Yves Brun (Indiana University), Professor Mike VanNieuwenhze (Indiana University) and Professor Ethan Garner (Harvard University). Here, Seamus tells us about this discovery and what its implications could be for antimicrobial research.

Bacterial cell division is a lovely mechanistic problem in biology: how do the simplest living organisms build a crosswall at mid cell, against very high outwards pressure (think of a racing bike tyre), without bursting? A ring of protein filaments forms around the future division site, and enzymes associated with this ring build a new crosswall that cleaves the bacteria in half. But what has remained completely mysterious is how these proteins work together as a single nanoscale machine to cut the bacterial balloon skin (cell wall) in two.

Cytoskeletal proteins FtsZ in live bacteria imaged in vertical nanocages

Working together with collaborators in Delft, Indiana and Harvard, we tracked the organization and motion of key division proteins as they build the dividing crosswall, and the organization of the newly built crosswall itself. We began by examining the motion of FtsZ, a cytoskeletal filament that is required for cell division – cytokinesis – in bacteria and is related to the tubulin cytoskeletal protein found in eukaryotic cells. Using high-resolution microscopy techniques, we found that FtsZ filaments move around the division site, traveling around the division ring. We imaged the motion of individual cell wall synthesis enzymes, and saw that the synthesis enzymes ride on FtsZ filaments, building new cell wall as they travel along the division site. This causes the cell wall to be synthesized in discrete sites that travel around the division site during cytokinesis, a process which we were able to observe directly by using dyes that label the bacterial cell wall. Using a variety of experimental techniques, we were able to speed up or slow down how fast FtsZ rotated around the cell. Strikingly, we found that the speed of FtsZ filament motion determines how fast the cell can divide. When FtsZ moves more rapidly, cell wall is produced more quickly, and cytokinesis happens faster. This shows that the motion of FtsZ is the critical overall controller of cell division.

One challenge that we faced was trying to look at the division proteins in actively dividing cells. At the earliest stages of division, it was possible to image division protein organization because the proteins in the partially assembled ring are sparsely distributed. However, a new strategy was required to measure how the dense protein network of actively dividing cells was organized. Normally, bacteria are immobilized flat on a microscope slide, and imaged from underneath, but unfortunately this places the division ring side-on, obscuring the motion and organization of division proteins. To solve this problem, we used nanofabrication technology, originally developed to manufacture computer chips, to create tiny gel nanocages to trap bacteria in an upright position.

Bacteria trapped in vertical nanocages

By trapping individual bacteria upright, we were able to rotate the cell division ring so that it was fully visible on our high resolution microscope. This revealed the dynamic motion of FtsZ filaments as they travel around the entire division site:

Together, these results revealed the basic mechanistic principles of bacterial cell division: that the building of the division crosswall is orchestrated by moving cytoskeletal filaments. Previously, the cytoskeleton was thought to serve as a static scaffold, recruiting other molecules and perhaps exerting some force to divide the cell. This new work demonstrates that all the components of cell division are in constant, controlled motion around the division site, driven by the fundamental dynamics of the cytoskeleton.

In the longer term, this study could open up novel antibiotic targets. Based on the discovery that the treadmilling motion of the bacterial cytoskeleton is critical for division, it may be possible to develop new drugs that specifically inhibit this motion, similar to how the chemotherapy drug taxol suppresses the motion of the cytoskeleton in cancer cells.

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Links

Explanatory animation: https://youtu.be/6dq2_gqKPfU (Animation credit TU Delft / Scixel)

Nanocage Video: nanocage-movie-2.

Science report: http://science.sciencemag.org/content/355/6326/739

Press release: http://bit.ly/2kwsnJf

Any excuse to drink red wine

Posted on 22 March, 2017 by Elisabeth

By Elisabeth Lowe

I’m writing this blog from an interesting perspective – though a member of the lab I’m not involved in the project, except through the (exhaustive!) discussions at coffee time with Harry Gilbert and the rest of the authors on the paper. This work, published today in Nature, describes the way in which one particular species of human gut bacteria is able to degrade a complex plant polysaccharide. Why is this new, you might well ask? Well, after being talked to death on the project, so much so I’d be glad never to hear a word about it again, I’ve actually come to appreciate what a great piece of work it is. The Bolam and Gilbert labs have published quite a bit on plant polysaccharide degradation over the years, but this one is a little different, because the polysaccharide involved – Rhamnogalacturonan-II (RGII) – is thought to be the most complex glycan found in nature. It contains ~13 different sugars linked by 21 different linkages, and all but one can be broken by a single bacterial species, Bacteroides thetaiotaomicron (Bt).

Complex structure of RG-II from red wine

Wade Abbott, a post-doc in Harry’s lab when he was at the Complex Carbohydrate Research Centre, in Athens, Georgia, which is incidentally where the structure of RG-II was determined in the first place by Alan Darvil and Malcolm O’Neill in the 1980s, initiated this project. We knew which loci were upregulated during growth on RG-II from earlier work by myself, Dave Bolam and Eric Martens, so Wade set about cloning and expressing the 30 genes in these loci, and looking for activity with a PhD student, Jeff Xhang. It was a tough job, and little progress was made. When Harry came back to the UK he decided he absolutely had to crack it, and put two post-docs onto the project, Art Rogowski and Didier Ndeh. Though as the project has progressed, more and more people from the lab were sucked in, including the post-docs Alan Cartmell and Aurore Labourel, and Harry’s last PhD student, Ana Sofia Luis. All worked incredibly hard, assisted by Arnaud Baslé from SBL, and between them discovered the activities of 26 enzymes, including seven entirely new glycoside hydrolase families, three new activities, and seven crystal structures, with all the active site mutations, and ligand soaks that go along with a new crystal structure.

Working out the enzyme activities on a polysaccharide as complex as RG-II poses some problems, in that you can’t really buy it, so you have to make it. RGII is concentrated in red wine, so Harry put 150 litres of Asda’s not so finest wine on Dave Bolam’s credit card (don’t ask) and with Art and Didier, took it to Prozomix in Haltwhistle, to use their industrial concentrators.

Starting to concentrate 150 L of wine

As you can see, this did not end well.

It’s all gone horribly wrong

Art then turned to apple concentrate and managed to purify some through an intensive multiple two-week process. Making or buying oligosaccharides is also extremely difficult, so Didier devised a way of killing two birds with one stone – identifying which unknown open reading frames (ORFs) were enzymes, and making oligos at the same time. By deleting the gene of interest, RG-II degradation (which is mainly exo-acting) was halted at the point at which that enzyme acted. Taking the supernatant from these strains grown on RG-II and purifying the sugars released by the bacterium yielded partial breakdown products which could be identified by mass spectrometry with tremendous help from Joe Gray, and then used as a substrate for the enzyme in question.

Getting the data in a format suitable for the tight space restrictions imposed by Nature was almost as challenging as doing the work. Given that Harry is not very artistic, and certainly has no idea how to use Adobe Illustrator, he was fortunate to have three talented artists Ana, Art and Aurore, who ended up doing all the figures. They are now referred to as the art department. This project was definitely a labour of love (for Harry, if no-one else!) and by carefully characterising the breakdown of this polysaccharide, one linkage at a time, has actually revealed new features of the structure of this critical plant polysaccharide. Finding and characterising the vast repertoire of enzymes produced by gut microbes is not only interesting in its own right, but can provide tools to understand complex glycan structure. It’s a fantastic achievement, and I pity the poor lab member who has to try and bake the RG-II cake for the celebrations this week!

Link to paper

A novel copper storage protein discovered by ICaMB scientists

Posted on 17 September, 2015 by Kevin

In a recent issue of Nature the discovery of a new family of proteins that store copper ions inside bacterial cells was reported. This work was carried out by Prof. Chris Dennison’s lab (ICaMB) in collaboration with Dr. Kevin Waldron (ICaMB), Dr. Arnaud Baslé (ICaMB), Dr. Neil Paterson (Diamond Light Source) and Prof. Colin Murrell (UEA). Here, Kevin tells us about this discovery and what its implications could be for the biotechnological exploitation of methane.

Methane, the main component of natural gas, is produced by both geological and anthropogenic processes on Earth, and can be released into the atmosphere. The biosphere’s primary mechanism for limiting the amount of methane (a powerful ‘greenhouse gas’) that escapes into the atmosphere is through its consumption by methane-oxidising bacteria, or methanotrophs (literally ‘methane-eating’), who utilise methane as both a carbon and energy source.

Transmission electron micrograph of a M. trichosporium OB3b cell showing the intracytoplasmic membranes that house the copper-dependent enzyme pMMO.

The key enzyme that methanotrophs use to oxidise methane to produce methanol is called methane monooxygenase (MMO). Almost all methanotrophs possess a membrane-bound form of MMO that requires copper (Cu) for activity, called pMMO (some strains also possess an iron-requiring alternative soluble enzyme, called sMMO). Therefore, these bacteria have an unusually high demand for copper, a metal that is essential for most organisms but is used rather sparingly, mainly because it can also be extremely toxic.

Previous studies of methanotrophs have revealed that they utilise unusual mechanisms for acquiring the copper they need for pMMO. For example, they produce and secrete a small, modified peptide called methanobactin that is involved in high affinity copper uptake, analogous to the more familiar siderophore iron uptake systems.

The model methanotroph, Methylosinus trichosporium OB3b, was analysed in the hope of uncovering novel copper proteins. Soluble extracts were resolved by two-dimensional liquid chromatography, with the copper content of resulting fractions monitored. The most abundant copper pool was found to contain a small, cysteine-rich protein that had not been studied previously and Chris Dennison (PI) and I (Co-I) obtained a BBSRC grant to investigate this and related proteins.

The presence of 13 cysteine residues in a mature protein (after cleavage of its signal peptide) with only 122 amino acids was immediately significant, as its thiol sidechain is often found in copper-binding sites. The recombinant protein was extensively studied using a suite of biochemical and biophysical methods to determine its in vitro properties This novel tetrameric protein is capable of binding up to 52 Cu(I) ions with high affinity, consistent with a potential role in the storage of this essential metal and was therefore named Csp1 (copper storage protein 1). A mutant strain of M. trichosporium OB3b that lacks this Csp1 protein (as well as a closely-related protein, Csp2) shows a phenotype consistent with a copper storage role of these proteins in vivo.

The crystal structure shows that the apo-monomer adopts a well-characterised four-helix bundle motif with all 13 cysteine sidechains pointing into the core of the bundle. The protein structure is essentially unchanged in the presence of copper, except that the core of each monomer has filled with 13 Cu(I) ions, bound by the cysteine sidechains. This is an unprecedented structure for metal storage.

The structure of the Cu(I)-Csp1 tetramer, with the 13 Cu(I) ions bound within the core of each four-helix bundle shown as orange spheres.

The implications of this discovery could be of wide impact. There is a great deal of interest in using methanotrophs and MMOs in industrial biotechnology. Available methane is on the increase due to ‘fracking’, but importantly methane can also be produced from sustainable sources such as through the degradation of biomatter (biogas). Methanotrophs and the MMOs could in future be exploited using synthetic biology approaches for gas-to-liquid conversion, for the production of liquid fuels as well as bulk and fine chemicals from renewable methane.

Any such biotechnological applications require an understanding of how the production of pMMO is regulated and how this complex enzyme is assembled, including the cellular delivery and insertion of the essential copper cofactor. The work published in Nature shows that Csps are an important piece in that assembly jigsaw.

Furthermore, bioinformatics has shown that cytosolic members of the Csp family are also encoded in other bacterial genomes. Most bacteria are thought not to require copper in their cytoplasm, so the presence of cytosolic Csp homologues in their genomes could re-write our basic understanding of their use and homeostasis of copper.

Links:

Nature article: http://www.nature.com/nature/journal/v525/n7567/full/nature14854.html

News & Views: http://www.nature.com/nchembio/journal/v11/n10/full/nchembio.1918.html

BBSRC website: http://www.bbsrc.ac.uk/news/fundamental-bioscience/2015/150827-pr-bacteria-that-could-protect-our-environment/

ACS Chemical & Engineering news: http://cen.acs.org/articles/93/web/2015/08/Protein-Stores-Copper-Methane-Digesting.html

Press release: http://www.ncl.ac.uk/press.office/press.release/item/could-bacteria-help-protect-our-environment

Beer, Bread and Bacteria

Posted on 8 January, 2015 by Kevin

Prof. Harry Gilbert

The diverse organisms that live in our gut, collectively termed the gut microbiota, can have a major impact on our health. A new paper from Prof. Harry Gilbert’s lab in ICaMB, published today in Nature, shows that one member of our gut microflora uses a ’selfish’ mechanism to degrade a component of the cell wall of the yeast in our diet.

By Drs. Elisabeth Lowe and Fiona Cuskin.

Have you over-indulged this Christmas? One too many ales, or too many turkey sandwiches?

Beer: full of yeast.

The good news is that, while your waist line may be expanding and you may be feeling a little the worse for wear, the organisms of your gut microbiota are thriving!

Some of the bacteria in the human gut, called Bacteroides, can break down the complex carbohydrates in our diet into simple sugars, which they use for energy.

: Bread: full of yeast

Our work, published in Nature today, shows that one of these bacteria can also break down some of the carbohydrate cell wall of yeasts, called mannan, a polymer of mannose. This includes mannan from Saccharomyces cerevisiae (Baker’s yeast), and the pathogenic gut fungus, Candida albicans. The current understanding of polysaccharide digestion by gut bacteria suggests a cooperative environment, in which break-down products are shared between different members of the microbiota. However our data shows that this species (Bacteroides thetaiotaomicron) is ‘selfish’ when it degrades mannan, and doesn’t share any of the digestion products with other bacteria.

Turkey: er… full of yeast?

To achieve this selfish degradation, the large and multiply-branched mannan structure undergoes only very limited degradation in the extracellular space (see figure). The resulting processed mannan fragments are then imported into the Bacteroides periplasmic space, where they are further degraded by a suite of glycoside hydrolase enzymes to yield the sugar mannose. Achieving complete breakdown within the periplasm prevents the mannose from being shared with competing bacteria.

This selfish approach to mannan utilisation could offer the opportunity to design bespoke prebiotics targeted to a specific bacterial population within the gut. Food products containing yeast mannan would be expected to promote growth of B. thetaiotamicron, whereas other complex polysaccharides may specifically promote other members of the microbiota.

Complex polysaccharide mannan is sequentially degraded by a ‘selfish’ mechanism to yield periplasmic mannose.

A number of inflammatory bowel diseases such as Crohn’s disease are associated with intolerance to yeast, and particularly cell wall polysaccharides, and have also been linked to low levels of Bacteroides species in the gut. Our work provides a potential mechanism for how Bacteroides might be able to influence the effect of yeast on patients with Crohn’s disease, and in fact a drug named Thetanix (which is a live formulation of Bacteroides thetaiotaomicron) has been licensed for treatment of paediatric Crohn’s disease in the USA.

Researchers Max Temple, Lis Lowe and Fiona Cuskin of the Gilbert lab.

Yeast is commonly in our diet in the form of some of our favourite things: bread, beer, wine and fermented food products. So it may be dry January but if your willpower fails and you succumb to an alcoholic beverage, then make sure it’s an unfiltered one with plenty of yeast!

This research in the Gilbert lab was funded by the Wellcome Trust and the European Research Council.

Links:

Nature article: http://www.nature.com/nature/journal/v517/n7533/full/nature13995.html

Press release: http://www.ncl.ac.uk/press.office/press.release/item/beer-and-bread-yeast-eating-bacteria-aid-human-health

Gilbert Lab: http://www.ncl.ac.uk/camb/staff/profile/harry.gilbert

Pruning the Tree of Life

Posted on 13 December, 2013 by Neil

Dr Tom WIlliams

Anyone who has studied biology has seen an image of the tree of life in the text books. Most of us think of this as being set in stone, one of the rock solid foundations on which evolutionary biology is built. However, all is not quite as settled as it seems. Recently, a Nature article from the laboratory of ICaMB’s Professor Martin Embley challenges the traditional three domain structure of the root of life. Here, first author on the paper, Dr Tom Williams, tells us the story.

By Dr Tom Williams

Our modern understanding of the tree of life began in 1977 when Carl Woese and his colleagues discovered the Archaea, a group of prokaryotes originally isolated from extremely hot or salty environments. Although Archaea looked indistinguishable from Bacteria under the microscope, their gene sequences were at least as different to those of Bacteria as from the eukaryotes – the group of organisms, including fungi, animals and plants, whose cells contain a mitochondrion and a nucleus. According to these analyses, living cells should be classified into three main groups: Bacteria, Archaea and eukaryotes – rather than the two (prokaryotes and eukaryotes) that had previously been established based on cell structure. In 1990, Woese and his colleagues published another seminal paper in which they argued for this “three domains” classification. This three-domains tree has become an iconic image in biology, and is often found in the popular science literature, as well as many textbooks – you’ve probably seen it before. Here it is from a 1997 review by Norman Pace:

The traditional 3 domain Tree of Life. From: A molecular view of diversity and the biosphere. Pace NR Science (1997) 276: 734-740

Professor Martin Embley

This was certainly the tree of life that I was familiar with, first as an undergrad and later as a Ph.D. student at Trinity College Dublin. So I was surprised and very intrigued when a certain Martin Embley came to talk at an Irish bioinformatics meeting, claiming that support for the three-domains tree was not as strong as you might expect. New work from his lab instead favoured the “eocyte tree”, in which the eukaryotes (or, at least, some of their genes) actually evolved from within the Archaea. If true, this tree would imply that there were originally only two types of cells – Bacteria and Archaea – and that the eukaryotes (i.e., us!) originated later in a partnership between the two primary domains.

The new model of the Tree of Life proposed by the Embley lab

Fast-forward a couple of years, and I was thinking about where I wanted to do my postdoc. I remembered Martin not only from that talk, but also from some interesting work (2nd link) he had done on a group of parasitic fungi called Microsporidia. I joined his group and began working on microsporidians, but I was still very interested in the tree of life and the origin of eukaryotes. In the meantime, DNA sequencing technology had been improving, and microbial ecologists were beginning to publish genomes from new groups of Archaea that could not be grown in the lab, and so had never been studied before. One of the really exciting findings from these studies was that some Archaea contained genes that looked very similar to fundamental components of our own cells, such as actin and tubulin – two proteins that help to define the microscopic “skeleton” of eukaryotic cells. When we added these new genomes to our analyses, we found even stronger support for the eocyte tree; those findings were reported last year in Proceedings B. At about the same time, a number of other researchers were reporting something similar: as our view of archaeal biodiversity increased, support for the three-domains tree was on the wane. Given the prominent position of the three-domains tree in the literature, and the importance of this question for understanding early life on Earth, we decided to write a review summarizing these recent developments in the field – it came out in Nature this week, and it’s the reason for this blog post!

As we delved back into the 30 years of literature on the molecular tree of life, one of the most interesting discoveries for me was a seam of eocyte literature that I hadn’t been aware of previously. Although many analyses over the past three decades have recovered the three-domains tree, and it appears in all the textbooks, the literature has actually never been unanimous in its support. Nonetheless, it is only in the last five years or so that support for the eocyte hypothesis has reached critical mass, perhaps due to improvements in our statistical methods and, more recently, sampling of archaeal biodiversity.

The Embley lab: Back row, left-to-right: Kacper Sendra, Martin Embley, Tom Williams, Robert Hirt. Front row: Shaojun Long, Ekaterina Kozhevnikova, Andrew Watson, Paul Dean, Maxine Geggie,Alina Goldberg-Cavalleri, Sirintra Nakjang.

Of course, our latest work is almost certainly not going to be the last word on the relationship between eukaryotes and other cells. Our methods are getting better – in part thanks to the statisticians we are collaborating with here in Newcastle – but there is much room for improvement, and so much about the microbial world that we still have to discover. Still, if the eocyte tree is correct – and it appears to be the best-supported tree on the current evidence – then that has important implications for how we understand early life on Earth and the origin of our own cells. For one thing, it rules out the eukaryotes as a primordial cellular lineage, as old as the Bacteria and Archaea. Instead, it suggests that the Bacteria and Archaea were established and diversifying on Earth before the origin of eukaryotes, resurrecting the concept of an “Age of Prokaryotes” on the early Earth. Of course, when you think about the phenomenal number of Bacteria and Archaea that live in your own body, never mind the wider environment, you might well argue that it never ended…

This work was supported by a Marie Curie postdoctoral fellowship to Tom Williams. Martin Embley acknowledges support from the European Research Council Advanced Investigator Programme and the Wellcome Trust.

Links

The Nature Article: http://www.nature.com/nature/journal/v504/n7479/full/nature12779.html?WT.ec_id=NATURE-20131212

The Proceedings B paper: http://rspb.royalsocietypublishing.org/content/279/1749/4870

The Embley lab website: http://research.ncl.ac.uk/microbial_eukaryotes/

Microsporidia papers: http://www.nature.com/nature/journal/v452/n7187/full/nature06606.html

http://www.nature.com/nature/journal/v453/n7194/full/nature06903.html

A ‘tail’ to tell – Lakey lab discovery could lead to a new class of antibiotics

Posted on 12 July, 2013 by Neil

Dr Chris Johnson

“Most of us know that we should wash our hands after being around animals but do most of us know the reasons why? As a researcher who spends most of his time in the lab killing E. coli, using E. coli specific antibiotics I should be well aware of the dangers of this often underestimated Gram-negative bacteria. However when my youngest daughter contracted E. coli O157 after visiting an agricultural show in Scotland in 2011 (even though we had followed the hand washing procedure), I realised that I did not appreciate how nasty this bacteria can be. Thankfully after 6 weeks in hospital including a lengthy stretch on dialysis my daughter made a full recovery but not everyone is so lucky.”

Professor Jeremy Lakey

The urgent need to develop new drugs to target pathogenic bacteria has been a theme of the ICaMB blog since its inception in early 2013. However, these words from Dr Chris Johnson, a postdoc in Jeremy Lakey’s laboratory, bring home the seriousness of the problem. Fortunately, Chris is in a position to do something about this.

Many of you will have realised that last week saw another potential breakthrough in ICaMB’s ongoing ‘War on bacteria’ (and here, here and here). This time the PI making the news, with data demonstrating the possibility of a whole new class of antibiotics, was Professor Jeremy Lakey. And when we say making the news, we mean that literally. The ITV interview of Jeremy and his team can be viewed here

This story has made news around the world and has been featured in newspapers in Australia and India (and here), as well as closer to home. Here is the official university press release.

So what’s going on? If you want to read the primary paper it is here

The unstructured domain of colicin N kills Escherichia coli. Mol Micro 89:84-95

Chris Johnson, who was the lead author on this manuscript explains:

“E. coli produces protein antibiotics called colicins which are used to kill E. coli and closely related bacteria in the eternal bacterial arms race. In order to further understand how one of these, colicin N (ColN), works, we dissected the protein into its individual domains to see how each part behaved in isolation. Quite by chance we found that part of the protein, THE TAIL, was actually toxic to them. Although far less efficient than the entire ColN molecule, it remains specific for E. coli and furthermore, the specificity is housed within an intrinsically unfolded domain (a domain which has no defined 3D structure). Although this is a very basic discovery in its early stages, it allows us to appreciate novel mechanisms to kill E. coli.” (see the full version of this at the bottom of the page)

Some more about Jeremy

Any of you who were bioscience undergraduates in Newcastle will know Jeremy Lakey from his famous recreations of protein structure using party balloons. Others may know him for co-founding Orla Protein technologies. Some of us know him as a man who will always buy his round in the pub. All of us know him as a great scientist and colleague. Furthermore, Jeremy is a leading supporter of Leading Edge and recently a group of 6 Year 9 school pupils from St Cuthberts RC School looked at how ColN acts against E.coli when you start changing the amount of salt they are grown in. As many ICaMB scientists may know Jeremy also runs a workshop with Ponteland Community High School to explore bacterial shape and their surfaces using LEGO.

But did any of us think that one day Jeremy Lakey may SAVE THE WORLD from antibiotic resistant bacteria? Possibly.

The detailed science

Most Gram- negative bacteria produce protein antibiotics which are used as weapons in the battle between competing populations of bacteria. E. coli produces protein antibiotics called colicins which are use to kill E. coli and closely related bacteria. Once colicins are released into the extracellular milleu they dock onto their targets via specific outer-membrane receptors and then seek out an internal, periplasmic, binding partner (the Tol or Ton proteins) which helps them translocate into the cell. We study colicin N (ColN) which comprises of an intrinsically unfolded N-terminal translocation (T) domain, involved in TolA and OmpF binding. Its central receptor binding (R) domain binds lipopolysaccharide whilst its C-terminal 200 amino acids define the cytotoxic pore-forming (P) domain. This latter feature is common to all pore-forming colicins and forms a channel in the inner-membrane causing K⁺ release and cell death. Other colicins have C-terminal domains which display cytotoxic activities that include DNAase or RNase activity. Irrespective of the particular cytotoxic activity, all colicins are comprised of three domains (T-R-P) and it was assumed that the sole role of the T and R domains was to deliver the cytotoxic C-terminal domain across the outer-membrane.

In order to investigate the mechanism of ColN activity we dissected the protein into its individual domains. We were attempting to block the toxic activity of full length ColN by pre- incubating E. coli cells with the intrinsically unfolded T-domain. The rationale behind the experiment was that we could block all the available receptor sites on the E. coli target cells by saturating with T-domain, such that when the full length ColN was added to cells it would be non-toxic, as all the essential receptor binding sites would be already sequestered. However rather than protecting the cells, T-domain was found to be toxic and like full length ColN provoked K+ efflux. Although less efficient than full length ColN, T-domain is strictly dependent upon the same receptor proteins, OmpF and TolA for killing. Since these receptors are only found in E. coli-like bacteria, T-domain displays the unusual combination of a generic killing mechanism coupled with extreme specificity housed within an intrinsically unfolded domain.

Links

Jeremy Lakey’s University home page: http://www.ncl.ac.uk/camb/staff/profile/jeremy.lakey

Follow Jeremy Lakey on Twitter: https://twitter.com/JeremyLakey

ICaMB: http://www.ncl.ac.uk/camb/

The Centre for Bacterial cell Biology: http://www.ncl.ac.uk/cbcb/

The official Newcastle University press release: http://www.ncl.ac.uk/press.office/press.release/item/chance-finding-could-lead-to-new-antibiotics

Link to ITV story:

http://www.itv.com/news/tyne-tees/story/2013-07-05/breakthrough-in-combatting-bacterial-infection/

The ‘Australian’ story: http://www.theaustralian.com.au/news/breaking-news/tail-could-be-used-for-new-drugs/story-fn3dxix6-1226674131684

The ‘Times of India’ Story: http://articles.timesofindia.indiatimes.com/2013-07-06/science/40406695_1_escherichia-coli-e-coli-protein

The Northern Echo story: http://www.thenorthernecho.co.uk/news/10524003.Scientists__chance_find_may_develop_new_generation_of_antibiotics/

Jeremy’s company, Orla Proteins: http://www.orlaproteins.com/about-orla/the-board.aspx

ICaMB Research Update: Zenkin lab Science paper

Posted on 28 June, 2013 by Neil

Congratulations to ICaMB and CBCB researchers Soren Nielsen, Yulia Yezenkova and Nikolay Zenkin and who have a paper published in the prestigious journal Science today.

Nikolay Zenkin: RNA Polymerase researcher

There are three RNA Polymerases in Eukaryotic cells and although much attention focuses on the role of RNA Polymerase II, since it transcribes mRNAs from protein encoding genes, it is easy to forget that the majority of transcription in the cell is accomplished by RNA Polymerase III. RNA Polymerase III (or Pol III as it is commonly known) is responsible for the synthesis of ribosomal 5S rRNA, tRNA and other small RNAs.

Soren’s paper, entitled “Mechanism of Eukaryotic RNA polymerase III Transcription” termination solves a long-standing mystery in the field of how transcriptional termination by RNA polymerase III takes place. Their study reveals an elegant scenario, in which co-transcriptional folding of highly-structured RNA polymerase III transcripts causes termination at the end of their genes. This mechanism ensures proper folding of the structural/catalytic RNAs synthesized by RNA polymerase III prior to RNA release. Analogies with bacterial termination suggest that this fundamental mechanism may have emerged before divergence of bacteria and eukaryotes.

Here is the Science Editor’s summary of the paper

It is as important to terminate any biological process as it is to start it. Transcription, copying information encoded in genes into RNA, requires accurate and timely termination. Nielsen et al. (p. 1577) present a mechanism for transcription termination by RNA polymerase III, the enzyme that synthesizes the majority of RNA molecules in eukaryotes. In this scenario, the folding of the RNA as it is transcribed by polymerase into a highly structured transcript causes termination at the end of its synthesis. This mechanism may serve as a control of proper folding of structural or catalytic RNAs synthesized by RNA polymerase III. Comparison with other organisms suggests that this mechanism emerged before divergence of bacteria and eukaryotes.

And here is the abstract of their paper

Gene expression in organisms involves many factors and is tightly controlled. Although much is known about the initial phase of transcription by RNA polymerase III (Pol III), the enzyme that synthesizes the majority of RNA molecules in eukaryotic cells, termination is poorly understood. Here, we show that the extensive structure of Pol III–synthesized transcripts dictates the release of elongation complexes at the end of genes. The poly-T termination signal, which does not cause termination in itself, causes catalytic inactivation and backtracking of Pol III, thus committing the enzyme to termination and transporting it to the nearest RNA secondary structure, which facilitates Pol III release. Similarity between termination mechanisms of Pol III and bacterial RNA polymerase suggests that hairpin-dependent termination may date back to the common ancestor of multisubunit RNA polymerases.

Links

Link to the Science paper: http://www.sciencemag.org/content/340/6140/1577.abstract

Nikolay Zenkin laboratory home page: http://www.ncl.ac.uk/camb/staff/profile/nikolay.zenkin#tab_research

Centre for Bacterial Cell Biology: http://www.ncl.ac.uk/cbcb/

Science magazine: http://www.sciencemag.org/

Link to the Science cover: http://www.sciencemag.org/content/340/6140.cover-expansion

Bulging bacteria and the origins of life

Posted on 28 February, 2013 by Paula

Jeff (left), Romain (centre) and Yoshikazu (right), the team of researchers behind these exciting discoveries

In a paper published this week in Cell, Jeff Errington’s team in ICaMB, have discovered new insights into the origin of life on Earth.

Jeff and his team share their results

Bacteria were the first organisms to appear on planet earth. Almost all modern bacteria have a tough protective shell called a cell wall. The structure of the wall and the mechanisms used by cells to manufacture it are conserved, suggesting that the wall was invented right at the beginning of bacterial evolution, and, therefore, when the first true cells emerged.

Production of cell wall is carefully regulated by complex machineries that allow the cell to enlarge and then divide in a controlled manner, all the time maintaining the integrity of the wall intact.

Despite its importance, it seems that many modern bacteria can survive cell wall loss under certain very special conditions, such as when they are treated with certain antibiotics that interfere with its production, like penicillin. Not only that, but a few years ago my lab showed that these “L-form” cells (named after the Lister Institute in London where they were first described) no longer need the complex mechanisms normally needed for bacterial growth and division. Instead, they grow by extrusion of irregular tubes or blebs of cytoplasm, that pinch off into daughter cells.

Our team – me, Yoshikazu Kawai, Romain Mercier – has been working on this problem for some time. “Studying L-form biology is a real technical challenge, and this work could not have succeeded without the strong collaboration established between us“, says Romain. As Yoshikazu explains: “we developed a very simple genetic system to isolate mutations enabling L-form development from non-viable protoplasts.”

We are excited because we think we have now solved the mystery of how L-forms grow and divide. Our latest results, published in Cell, show that the mechanism is remarkably simple: it requires only that cells make excess amounts of membrane – the thin porous layer that acts as the outer boundary of all cells, including our own.

Increasing the membrane surface area beyond the amount needed to contain the cytoplasm causes the cell to buckle and distort. Eventually, this leads to pinching off of membrane bags that are ill formed but nonetheless viable “baby” cells.

Time-lapse photography representing the division of B. subtilis without cell wall (L-form). The images were obtained using light microscopy. Scale bar: 3 μm

At first, we thought this mechanism was too simple to be true, we changed our minds when we were alerted to amazing experiments being done by several groups working on the origins of life, particularly Jack Szostak at Harvard, Saša Svetina in Ljubljana and Peter Walde in Zurich. These groups have been wondering how primitive cells could have arranged to grow and divide efficiently without spilling all of their contents. They recently found that simple membrane bags, called “vesicles”, can be induced to grow and reproduce into multiple smaller vesicles, in the test tube, just by increasing their surface area.

So, in explaining how the bizarre L-form bacteria manage to survive the loss of their beloved cell wall, we think we may now also have glimpsed how the first primitive cells could have duplicated themselves at the dawn of life on earth.

Jeff Errington
Director of the Centre for Bacterial Cell Biology

Cell paper: http://www.cell.com/abstract/S0092-8674(13)00135-9
Cell website: http://www.cell.com/home see PaperFlick
Newcastle University Press Release:http://www.ncl.ac.uk/press.office/press.release/item/how-did-early-primordial-cells-evolve#.US-chen77jQ

Soapbox Science guest blogpost: http://www.blogs.nature.com/soapboxscience/2013/02/28/social-media-from-an-institutional-perspective-why-are-we-on-there

ICaMB website: http://www.ncl.ac.uk/camb/
Facebook: https://www.facebook.com/pages/ICaMB-Newcastle/416200498466481
Twitter: https://twitter.com/ICaMB_NCL
YouTube: http://www.youtube.com/channel/UCSuZgA6URiXTUoHq1tMe-PQ

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