METABOLIC OSCILLATIONS: Cellular decision-making

For this post as part of the “Metabolic oscillations” series, Josi Buerger introduces us to the publications that inspired the creation of this ITN network. The series will focus on the underlying concepts, explain the four main publications stretching from 2010 to 2016, and lay out how the Fellows’ efforts will push this work forward into 2017.

Regulation is at the heart of the cell

Within the cell, genes and proteins are regulated. There are two reasons for this: firstly, a cell can respond to its environment by changing or regulating its internal state. Secondly, it is much more cost-effective if this change happens by modulating existing structures instead of tearing everything down and creating it from scratch. Consider how much less effort it is to dim the lights in the evening as opposed to dismantling the electrical circuits and then reconstruct them in the morning…

The ability to regulate internal states is the basic concept of the first publication featured as part of our “Metabolic oscillations” series, Bacterial adaptation through distributed sensing of metabolic fluxes.  In today’s post we’ll discuss the basic concept of cells responding to their environment and use a textbook example: carbon source utilization. Or, in more laymen’s terms: cells have food preferences.

Cells have food preferences.

Weird, isn’t it? But Escherichia coli’s sweet tooth is one of the cornerstone experiments in the field of microbiology dating back to 1957 (Cohen & Monod). Also there is a link between preferring one type of food and changing cellular metabolism to suit the preference. For example, E. coli loves glucose (a type of sugar). When glucose passes through the outer membrane of the cell, it activates a number of other processes which all help the cell to preferentially eat the glucose.


You can see this in the image on the right: the blue line indicates E. coli cell growth in an environment where both glucose and acetate is available. The total amount of glucose is indicated by the dotted line, which decreases as the cells consume it to grow. Once all the glucose is consumed, the cells are forced to switch to acetate, indicated by the drawn-through line (Image modified from Kotte et al., 2010).

How to sense acetate?

So far, so good.  Yet as always in biology, the picture becomes more complicated as soon as you zoom in on the details.

For glucose, there is an elegant link between transport and regulation. But even though cellular behaviour to acetate is well-documented, it is unknown how cells detect acetate. Generally, there are two main detection systems: membrane-based sensing as with glucose, or transcription-factor based sensing where the molecule is recognised by a specific sensing modules. Neither system has been found for acetate, despite decades of interest.

Here’s the cool bit about Bacterial adaptation through distributed sensing of metabolic fluxes.  The researchers show that the preference of glucose to acetate can be explained by elements of the cell that we already know about. There isn’t some undiscovered acetate sensing system, but rather the elements of the cell can behave in more ways than we thought!

The details? Well, you will just have to wait for our next post…..



Kotte, Oliver, Judith B. Zaugg, and Matthias Heinemann. “Bacterial adaptation through distributed sensing of metabolic fluxes.” Molecular systems biology 6.1 (2010): 355.



SERIES INTRODUCTION: The ups and downs of metabolism

New year, new series on the metaRNA blog!

For the upcoming posts on “Metabolic oscillations”, Josi Buerger introduces us to the publications that inspired the creation of this ITN network. The series will focus on the underlying concepts, explain the four main publications stretching from 2010 to 2016, and lay out how the Fellows’ efforts will push this work forward into 2017.


Life isn’t static. It can’t be – in biological systems, stagnation means death.

Even though cells are rules by homeostasis, this continuous fine-tuning of cellular processes is anything but static.

Homeostasis: Self-regulation to maintain internal equilibrium.

For example, the human body strives to maintain 37 °C as its internal temperature via heat-loss (sweating) or heat retention (goose-bumps).

But remember, the cell itself cannot think or make decision like our human minds. Individual cells don’t have a brain that acts as the central decision maker. Some argue that cellular fate is encoded in its DNA and this should be seen as a “brain” of sorts. However, the cell must still be able to respond to external events or internal catastrophes above and beyond the determination of the DNA code.

So how is this possible? What kind of situation requires immediate and total cellular responses? And what does this response look like?

The following four papers have been chosen as the features of our new series to answer these questions:

  1. Bacterial adaptation through distributed sensing of metabolic fluxes
  2. Functioning of a metabolic flux sensor in Escherichia coli
  3. Phenotypic bistability in Escherichia coli’s central carbon metabolism
  4. Autonomous metabolic oscillations robustly gate the early and late cell cycle

Join in as we explore cellular decision-making!

Functional mining of transporters using synthetic selections

After our successful Meet the Fellows series, we are starting a new project: The metaRNA Fellows will introduce papers new and old that they find interesting or inspiring. Today, Josi Buerger starts  with a recent publication on riboswitches.

On this blog, we have talked at length about aptamers and biosensors. There has been a post on aptamers in general, the specific SPINACH aptamer, and an application on how biosensors can be targeted to specific cells.

Today I want to introduce a biosensor for the vitamin thiamine. This biosensor detects a phosphorylated version of the thiamine molecule and this detection is sensitive enough to sense the very low thiamine concentrations inside the cell. A recent publication describes how this biosensor can explore bacterial biodiversity and how this has ramifications for the discovery of new drug targets.


The thiamine biosensor consists of a riboswitch which is placed in front of a gene that makes a bacterial cell resistant to antibiotics. When thiamine is present, the riboswitch is turned ON and the bacteria cell can survive the antibiotic. However, if there is no thiamine present in the cell, the resistance gene can not be utilised and the cell is killed by the antibiotic. This has the distinct advantage that those cells that do not have  thiamine are killed by the riboswitch-modulated system.

Riboswitch: An RNA molecules that switches conformation upon binding of a particular target molecules. Riboswitches are often used to control gene expression.

This riboswitch was used to look at how bacterial cells transport thiamine from their environments through the cell wall into the cell. The image on the right is a nice representation of this – transporters are a hole in the cell membrane that can allotransporterw particular molecules to enter or exit the cell. There are particular strains of E. coli that do not have a naturally occurring importer for thiamine and instead synthesise whatever they need. The trick for the selection system here is that the strain is engineered to lose its biosynthetic capability, so that it is dependent on external thiamine – but it can’t take up the external thiamine!

In order to survive, the cell is exposed to a “metagenomic library” which is a pool of many fragments of DNA from many different microorganisms. Then, the cell randomly takes up bits of this external DNA. If it manages to take up a gene that encodes a transporter, voila! It can survive.

So where does the riboswitch come in? There are countless types of transporters in the metagenomic gene pool and some of them are non-specific. But as this study wanted to find highly specific and efficient thiamine transporters, it needed to increase the amount of thiamine required for survival. Therefore, coupling the presence of thiamine to the ability to survive high levels of antibiotics can do just that. The image below shows how the cells survive only if they manage to find a transporter from the metagenomic library. Furthermore, this transporter has to be functional.


From Genee et al., 2016

So what are the results of the riboswitch selection? The researchers found a type of thiamine transporters that was previously undiscovered. In particular, this type of thiamine transporter, called PnuT, is prevalent in bacteria of the human gut. Moreover, some known human pathogens have only the new transporter type for their thiamine uptake and therefore, their survival depends on it. This means that the Pnu transporters constitutes an interesting new drug target for human health.

The publication is a nice example of how synthetic biology, cell metabolism, and metagenomic DNA can all come together and point to a new direction for drug targets.


Genee, Hans J., et al. “Functional mining of transporters using synthetic selections.” Nature Chemical Biology 12.12 (2016): 1015-1022.

Facebook, mySpace, Twitter, and RNA-based metabolic sensors: Remnants of ancient control machinery or ever-present control mechanism?

Social media and riboswitches? They might be more related than you think…. Today, Ruben talks about the ancient origins of riboswitches and poses interesting questions about their future.

If you were a teenager in the early 2000s, you probably used mySpace as your first social media. You might have even posted Emo-inspired pictures and used glittery GIFs. However, unfortunately for mySpace, Facebook was created in 2004 and soon after it started to rapidly overtake mySpace´s users, until 2008 when Facebook became the most used social platform worldwide. Other social media such as Twitter also remain active because it is specialized in a different type of social interaction: less about personal social connections and more about staying informed by following topics, conversations and people. These differences allowed Twitter to conserve their niche on an ever-growing sea of social media options.

This analogy came to my mind while reading about different sensing molecules. In order to survive and reproduce, organism have evolved mechanisms to sense and translate environmental signals as efficiently as possible. It is generally recognized that many of these mechanisms are protein-based molecules, which regulate gene expression in response to a chemical signal (e.g. transcription factors).

Although these protein-based sensing mechanisms explained the regulation of certain biological processes, they are not the only mechanism in action.This is often seen in the lack of correlation between transcriptome and proteome data. Insights into unknown interactions of RNA with metabolites led to the discovery of RNA sensing molecules able to control their own activity, so called: Riboswitches (Templeton et al., 2004).

Continue reading Facebook, mySpace, Twitter, and RNA-based metabolic sensors: Remnants of ancient control machinery or ever-present control mechanism?


It’s appearing all over the place : CRISPR/Cas9. The method has boomed since its 2012 breakthrough moment. Adam Mol walks us through this technology.

Currently, more and more discussions are appearing about CRISPR/Cas9. This technology can be used to edit the genome of almost any organism and the most controversial seems to be editing the genes of human embryos. How does this system works? CRISPR (Clustered Regularly Interspaced Short Palindromic Repeat) sequences and CRISPR-associated (Cas) genes were found in a wide variety of bacteria and archaea. The enzyme Cas9 is a DNA endonucleas
e found in many bacteria, where it functions as part of a defense system against invading DNA molecules, e.g. from viruses. The CRISPR/Cas9 system allows for specific genome disruption and replacement in a flexible and simple system, resulting in high specificity and low cell toxicity (Harrison et al., 2014; Peng et al., 2015).


Fig. 1 CRISPR/Cas9 in action (from Pennisi, 2013; modified)

The CRISPR/Cas9 genome editing system requires the co-expression of a Cas9 protein with a guide RNA. The crRNA and tracrRNA can be fused together to create a chimeric, single-guide RNA (sgRNA). Cas9 has two active sites that each cleave one strand of a double-stranded DNA molecule. The enzyme is guided to the target DNA by an sgRNA that contains a sequence that matches the sequence to be cleaved, which is demarcated by PAM (protospacer-adjacent motif) sequence. (There also exists a RNA-targeting CRISPR/Cas9 complex, called RCas9, that can edit RNA! by J. Doudna; O’Connell et al., 2014).


Fig. 2 Schematic of the RNA-guided Cas9 nuclease (from Ran et al., 2013)

Continue reading CRISPS/CAS9

Defining Life

What is Life? Why should we care about defining it? As biologists, our research tends to focus on the details, not the bigger picture. Today, Josi Buerger steps back and looks at how the basic concept of “Life” affects topics from conservation to astrobiology.


The Life Sciences, though young in comparison to other disciplines, have made incredible progress in explaining the tangible world around us. Yet even at the most fundamental level, biological processes remain a mystery. Basic questions remain unanswered: Why did living systems evolve on this planet? Could it have taken radically different forms? Why do organisms display such complexity and diversity?

The fact that we can ask and discuss these questions surely indicates that defining life is unnecessary – we all know what it means and know it when we see it. Our efforts should be aimed at understanding biological processes, not quibbling over a definition…

There are two main concerns why scientists should care about definitions: Firstly, even if we do not fully understand biological processes, there are scenarios where we need to be able to identify and label them. Space exploration comes to mind, or the deep ocean. Secondly, arguing about definitions may not be traditional examples of the “Scientific Method”, but there are concrete examples where definitions affects experimental design: in early evolutionary biology, dentifying life forms from interacting organic material is vital. Or consider the construction of “minimal genomes”: does a self-replicating plasmid suffice as a minimal organism, or does it require a more complex cellular set-up?

Continue reading Defining Life

Meet the Fellow: SERDAR ÖZSEZEN

It’s the end of our Meet the Fellows post, wrapping up with today’s interview with Serdar Özsezen. He is based in Groningen in Prof. Matthias Heinemann’s lab.

What is your background in science (and otherwise)? Why are you mo
tivated to work on this topic? What do you hope to accomplish during your PhD?

I have a background in chemical engineering (both bachelor and master). I wrote my master thesis on a subject that is related to computational structural biology. That was when my interest for biology started to grow. I really like computer programming and mathematical modelling.

Thus, biology is full of problems that you can tackle with computational methods and it is a lot of fun!profilepic_serdar.png

My ambition is to develop genuine approaches to solve some biological problems and meanwhile develop my computational skills.

What led you to decide to do a PhD?

Actually my masters led me to do a PhD because I realized that it was a really satisfying work. You have the opportunity to discover something new and acquire transferable skills meanwhile. On the other hand, you get a chance to teach the young people which could be a lot of fun as well.

It hasn’t been that long since we were interviewing for PhDs; what are some pointers you would give to students looking for a PhD to do during their undergraduate or Master’s?

They should choose a topic that they like to work on. Secondly, they should choose an advisor who  they can communicate well with. These are two very important points in my experience. When you have these both, then you are a happy grad student.

What are your short-term and long-term career goals (aka, what do you want to be “when you grow up” )?

Short-term goals: Acquire enough knowledge in field of microbiology to be able to tackle my research problem.

Long-term goals: I would like to have my own open source software project (ideally related to computational biology). Also, eventually I would like to get experience in industry.

What do you like to do for fun (outside of science, of course)?

Computer music production, digital visual arts, building electronic circuits with Arduino

What is your favorite food?




Aptamers 2016 – Oxford, UK

Adam Mol  was in Oxford at the beginning of the month for the Aptamers Conference. To find out more about this conference, check out @LPMHealthcare,  @AptamerSociety or #AptaOx16 on twitter.

Gladly, I would like to announce that on 04-05 April, I participated in Aptamers 2016: 3rd Oxford symposium on Aptamers. The meeting took place at St Hilda’s College, Oxford, UK. This year the symposium chair was Professor Beatrix Suess from Technical University of Darmstadt, Germany.

aptamer conf 1

Aptamers 2016 was an excellent symposium! It brought together academic and industrial aptamer researchers. During the meeting, therapeutic, diagnostic, analytical as well as basic research applications of aptamers were addressed. The symposium was divided into five sessions:

  1. SELEX – New technological developments
  2. Small molecule binding aptamers – Characterization and their application for gene control
  3. Aptamers as diagnostic tools
  4. Therapeutic aptamers
  5. Further Technologies

aptamer conf 2

Continue reading Aptamers 2016 – Oxford, UK

Meet the Fellow: JOSI BUERGER

Our Meet the Fellow series is almost coming to a close, as we have now met 14 out of 15 Fellows. Today we hear from Josi Buerger based at Biosyntia. Find her on twitter at @josi_bee.

What does your lab do? What is a brief description of the project you work on? What is your background in science (and otherwise)? Why are you motivated to work on this topic? What do you hope to accomplish during your PhD?josi 1

To be perfectly honest, the only reason I enrolled for Molecular Biosciences at my university was because I had good marks in Biology at school… In hindsight, this wasn’t due to any inherent talent on my side, but because I had a fantastic teacher.

This was problematic once I started my undergraduate studies. I had trouble engaging with topics outside of their practical context. In fact, in my second year, I switched to a joint Philosophy and Biology degree and was convinced that research was not for me. Not until honours classes did I re-discover my interest in science, as teaching at that level was centered on critical thinking that encouraged discussion.

I focused on taking courses on applied biotechnology, as I realised I enjoyed engineering and problem solving. I also learnt that I appreciate lab work, despite all its frustrations. I focused my Masters on metabolic engineering and feel incredibly lucky to have my PhD based in a dynamic start-up that builds biosustainable solutions.

Continue reading Meet the Fellow: JOSI BUERGER

The EUSynBio Symposium 2016

Josi Buerger attended the EUSynBio Symposium in London last weekend. Here is a personal account of the conference and why you should go next year…

The first Symposium of the European Association of Students and Post-docs in Synthetic Biology (EUSynBioS) advertised itself as an “open, funky, and slightly unconventional synbio event”.  I’ve been involved with parts of the EUSynBioS community before so I decided to attend the 1.5 day conference.

The symposium was held at Imperial College last Saturday, the 9th of April and included a visit to the London Hackspace the next day. The morning session was kicked off with an inspiring talk by Dr Tom Knight on the future of synthetic biology and the importaeusynbio symponce of in silico approaches. This was followed by students and early-stage researchers presenting their research. SynBio is of course about building tools for any application, so the presentation topics ranged from rhodopsin engineering in E. coli  to changing the lifestyle of Pseudomonas. Overall the atmosphere was very pleasant – never one to hold back in the question section myself, some great discussions took place.

Coffee breaks allowed for networking with other attendees. For example, I learned about the Cambridge Hackathon happening early this summer and even talked with industrial designers who were interested in this new field of engineering.

Continue reading The EUSynBio Symposium 2016