Sunday, July 09, 2017

The Vital Question, by Nick Lane

“In the end, respiration and burning are equivalent; the slight delay in the middle is what we know as life.”
This quote, from Nick Lane’s book The Vital Question (2015), is both poetic and true, which is the mark of great popular science writing. What Lane’s book attempts to do (and in my opinion succeeds in doing) is to radically change our perspective on life by showing us the crucial role played by energy. 

Lane is a biochemist at University College London and already the author of three books. I think there’s something to be said about popular science written by scientists, as opposed to science journalists, in the sense that they can sometimes achieve much more than educating. For example, they can fundamentally change our understanding of some topics (that certainly happened to me on some occasions). Actually, reading The Vital Question reminded me of reading Richard Dawkins’ The Selfish Gene many years ago, and Lane’s book did for me with biochemistry what Dawkins did with genetics and evolutionary theory: it opened a window into a fascinating new landscape. 

The universal proton-motive force
The Vital Question offers new glimpses into two of the most fundamental questions about life: why do all life forms use ion gradients to produce energy, and why eukaryotic cells are the way they are [1]. Now this is quite a programme! And Lane does a terrific job at presenting us with some of the best past and present ideas that were put forward in the field (including some of his own).
Regarding the first question, Lane writes (p. 65):  
“Life could have been driven by thermal or mechanical energy, or radioactivity, or electrical discharges, or UV radiation, the imagination is the limit; but no, all life is driven by redox chemistry, via remarkably similar respiratory chains.”
Peter Mitchell. Source:
In discussing the vital and universal role of the proton-motive force in living organisms, which generates ATP (the energy ‘currency’ in the cell)  thanks to a gradient of protons across membranes (see representation of ATP synthase below [2]), Lane pays tribute to Peter Mitchell, the Nobel laureate who first proposed the concept in the early 1960s, which he then called the ‘chemiosmotic hypothesis’.  I was very interested to learn about Mitchell, since as a biology student I was only introduced to the concept of proton-motive force, not to its history or its discoverer. And as Lane notes (p. 68), it was once called ‘the most counterintuitive idea in biology since Darwin’ by the biochemist Leslie Orgel.

Lane continues (p. 83):
“The evolution of chemiosmotic coupling is a mystery. The fact that all life is chemiosmotic implies that chemiosmotic coupling arose very early indeed in evolution.”
The ATP synthase. Image David Goodsell
In that context, I  was amazed to learn that fermentation, which I thought was some kind of ‘primitive’ way of obtaining energy, is most probably a more recent invention than the proton-motive force! (p. 168)

The origin of life
Lane delves into hypotheses on the origin of life with great detail in the second part of the book. It starts with the old ‘primordial soup’ theory that was first proposed by J. B. S. Haldane in 1929 and received support from the famous Miller experiment (published in 1953, the same year as Watson and Crick’s paper on DNA). Miller showed that organic molecules such as amino acids can be formed by the action of lightning on simpler gases like methane, ammonia and hydrogen. Life, the theory posits, would have evolved from those early organic bricks, after they were concentrated by evaporation of tidal pools or by adsorption to inorganic surfaces. As Lane notes, this theory is probably not true, and he explains that the favored explanations now involve deep-sea hydrothermal vents as primordial life incubators. This theory was prominently developed by Bill Martin and Mike Russell in the late eighties and in the nineties, and summed up in papers in 2003 and 2008

In particular, Martin and Russell have pointed at alkaline deep-sea vents as a possible original cradle for life. In such vents, they argue, exist unique geochemical conditions that could have been the biochemical template for the metabolism of the first living cells. For example, in these vents CO2 is abiotically reduced by H2 into methane (CH4), which is also the reaction that powers autotrophic prokaryotes known as methanogens. In addition, alkaline vents harbor strong pH gradients (i.e., proton gradients) between the alkaline interior and the more neutral seawater, as well as porous structures. And this brings us back to chemiosmotic coupling. Martin et al. note (2008): 
"Accordingly, it has been suggested that the ability to harness a continuous and naturally existing proton gradient at an alkaline hydrothermal vent is older than the ability to generate a proton gradient with a chemistry that is specified by genes. [...] Regarding the question of which came first, there are two simple possibilities: either energy-consuming pumping or energy-conserving chemiosmotic harnessing came first."
Martin and Russell favor the latter scenario. The reason why chemiosmotic coupling is universal in living organisms could thus be that early life evolved to use those preexisting proton gradients from deep-sea vents! This, however, is not necessarily how life came to be... But it is an exciting idea that deserves our full attention. As far as I'm concerned, it is still the best hypothesis for the origin of life that I have read.

In a follow-up post, I will write about the last part of the book that discusses the origin of complex (eukaryotic) life.

[1] Incidently,  it reminds me of that curious saying: ‘Science does not answer why questions, only how questions’. This is clearly untrue. Science often deals with ‘why’ questions, in particular questions pertaining to evolution. I’m not sure why this misleading saying persists, including among scientists…
 [2] Almost all cells use protons, but apparently some anerobic prokaryotic species use sodium ions instead.

  • Lane, N. (2015) The Vital Question. Profile Books, London. Paperback edition (2016), 360 p.
  • Martin, W., Baross, J., Kelley, D. and M. J. Russell. (2008) Hydrothermal vents and the origin of life. Nature Reviews Microbiology 6: 805-814.

Friday, March 17, 2017

Cooperation shapes the spatial patterns of bacterial organization

Cooperative bacterial strains colonizing a surface
Bacteria colonize surfaces in all environments. That could be the surfaces of soil aggregates, of rocks in a stream bed, of plant leaves, of animal skin, or that could be the surface of your showerhead... On such surfaces microbes establish complex communities ('biofilms') that can contain many different interacting species. These various species are usually not randomly distributed in the biofilm, but rather organized depending on their environmental preferences (for example some like well-aerated areas, others not so much...) and on the type of interactions that they have with each other. This can result in complex patterns of organization that manifest at the microscopic scale and up to the millimeter scale. Such patterns are not trivial, as they can sustain microbial activity and functions that would not be possible in a well-mixed environment, which has importance for biotechnology applications as well.

In a new study published this month, we examined the role of cooperation in shaping spatial patterns of bacterial organization on wet surfaces. The paper is available online and is entitled 'Cooperation in carbon source degradation shapes spatial self-organization of microbial consortia on hydrated surfaces'. Our idea was that a feeding dependency between two partners would directly control their distribution in space, hence imposing a specific pattern. We used a simple model system made of two bacterial strains that could grow using the chemical compound toluene (a hydrocarbon), but only when they were working together as a 'team' (a bacterial consortium in the jargon).

Tuesday, September 06, 2016

Symplasmata: a curious case of multicellularity in bacteria

Cells in a symplasmatum and surrounded by a capsule,
seen with transmission electron microscopy.

'Curiouser and curiouser’, famously said Lewis Carrol’s Alice, as she was experiencing some very peculiar events in Wonderland. I have sometimes felt like Alice when I was studying the curious behavior of the bacterium Pantoea agglomerans [1], during my time in the Lab Leveau at UC Davis.

At first sight, Pantoea agglomerans looks quite ordinary. It grows as rods a few micrometers long, it can swim with flagella and it feeds on all sorts of sugars. It belongs to the family Enterobacteriaceae, and thus it is a distant cousin of E. coli. You can find P. agglomerans in all sorts of environments, but it is particularly good at colonizing the surface of plants, and in certain cases it competes with pathogens and thus keeps its plant host healthy (that is, it can serve as a biocontrol agent). Because it is a very good leaf colonizer, we have used it in many studies of bacterial life in the ‘phyllosphere’ (the aerial surfaces of plants), such as the one described in this previous post

Now here’s what special, and actually seemingly unique, about Pantoea bacteria. Under certain conditions, instead of dividing and spreading as individual cells, the bacteria stay close together and form an aggregate containing up to hundreds of tightly packed cells. Aggregation is not uncommon in bacteria but, in the case of Pantoea, cells are constrained by a fibrillar layer, and surrounded by a thick capsule made of polysaccharides, which indicates some level of cooperation and resources sharing (see image on top of the post). The resulting sausage-shaped structures are called symplasmata [2]. Interestingly, the species name 'agglomerans' (forming into a ball), which was coined by the great Dutch microbiologist and botanist Martinus Beijerinck in a paper dating from 1888, probably refers to the species' ability to form symplasmata [3]. Although symplasmata have been known for a very long time, their importance and function in the environment is still a mystery. We have observed symplasmata on bean leaf surfaces, and others have described them attached to the roots of rice plants (Achouak et al., 1994). What is their ecological role? Does it benefit the plant as well? We do not know yet. 

Sunday, April 19, 2015

Principles of Microbial Diversity, by James Brown

Published by ASM Press
A new textbook on microbial diversity has just been published by ASM Press. Principles of Microbial Diversity is a relatively thin textbook (392 pages) that is intended for undergraduate students who need to follow a course on microbial diversity, hence filling a gap in the available teaching material. His author is James W. Brown, a professor at North Carolina State University.

The book is pleasant to read and richly illustrated by hundreds of micrographs. But what is quite original, and to me very justified, is the author's perspective, which is, in James Brown's own words in the preface, "phylogenetic and organismal, from the Carl Woese school".  I applaud that! Woese, as I discussed in a previous post, revolutionized biology by showing that we had until then totally ignored a whole distinct domain of life, the Archaea. This discovery was made through the careful analysis of the sequence of 16S rRNA gene (not an easy feat in the days of Woese's work). Because of this pedagogical and scientifical choice, Brown's book dedicates lots of pages to introduce phylogenetic concepts. Notably, he gives a didactic and useful explanation of how to construct a phylogenetic tree (Chapter 3). Brown explains his focus as follows (p. 351):
"In this book, the vantage point from which all of microbial diversity is viewed is the phylogenetic perspective. Other perspectives are possible and are very useful. Medical microbiology views the microbial world from the perspective of its influence on microbe-human interactions and human health. Environmental microbiology views the microbial world from the perspective of biogeochemical processes and ecosystems. […] However, the organizing principle of biology is evolutionary theory. The phylogenetic perspective is the view of biological diversity as the outcome of evolutionary history. This perspective is not exclusive of any other perspective on microbiology, but instead enriches these other perspectives."
Brown's textbook contribution is very welcome, and should find a place in each university's library.

Example of book photo. The eukaryote Arcella. Source: Wikimedia Commons


Tuesday, February 24, 2015

Mining soil for new antibiotics

Methicillin-resistant Staph aureus. Photo NIAID
The beginning of 2015 brought (potentially) good news for medicine: the discovery of a new antibiotic - teixobactin - isolated from soil bacteria. This result was published in Nature on January 22. (Unfortunately the whole text is not visible without payment or subscription.) Many newspapers and news outlets covered the story in early January, for instance the Guardian, and the New York Times. Teixobactin is a small peptide that acts as an inhibitor of cell wall synthesis in Gram-positive bacteria, which means it can kill pathogens like drug-resistant Staphylococcus aureus (often referred to as MRSA, or methicillin-resistant S. aureus).

The issue at stake here is, of course, the increasing prevalence of antibiotic-resistant bacteria worldwide, a situation well summarized in an article at We have thus seen a dramatic increase in resistant strains of, for instance, S. aureus, Escherichia coli and Klebsiella pneumoniae. Who or what is to blame? Most probably the overuse of antibiotics, not only in humans but also in animals. It is frightening to know that some pathogenic strains can survive our entire arsenal of antibiotics, while new potent drugs are extremely hard to find. Some simple solutions have helped mitigate the problem, notably more effective and systematic hand disinfection by hopital personnel, but this will not prevent all cases of infection. New antimicrobials are clearly needed, but where to find them?

Monday, January 26, 2015

The Logic of Life, by François Jacob

The Logic of Life (La logique du vivant) opens with the following quote by the French philosopher and Enlightenment figure Denis Diderot:
"Do you see this egg? It's with it that we overturn all theological schools and all temples on Earth".
[All translations in this post are mine.]
The choice of a 18th century thinker for the epigraph prefigures a lot of this book, which was published by the late Nobel laureate François Jacob in 1970. The booksubtitled "a history of heredity"thus proves to be of great erudition and cites the original work of, among many names, Paré, Montaigne, Paracelse, Descartes, Galilée, Harvey, Réaumur, Buffon, Redi, Leibniz, D'Holbach, La Mettrie, Lamarck, Linné, Geoffroy Saint-Hilaire... and I haven't even mentioned the 20th century references yet! Excusez du peu!

This story of heredity truly is a huge endeavor, spanning about four centuries of philosophical and scientific attempts to understand what kind of stuff we're made of. Articulated in long chapters that correspond to conceptual milestones ("visible structure", "organization", "time", "gene", "molecule", and "integron"), the book follows the chronological development of our biological knowledge (which was part of "natural philosophy") with plenty of referenced sources and with a quality of writing that is hardly matched today.

Sunday, August 31, 2014

The debate over influenza research is still on

H5N1 virion. Photo Cynthia Goldsmith/Jackie Katz

Two years ago, a controversy emerged about the research on influenza virus H5N1, and the potential risk associated with it. This controversy followed the publication of two research articles in Science and Nature, and I wrote about it in January 2012 in this blog post. Briefly, scientists have used so-called “gain-of-functions” experiments, in which strains of influenza viruses are selected for new traits such as higher transmissibility between ferrets (the preferred animal model in these studies). The objections that were raised by some critics of this research were of two kinds: first, the information available in these papers could be used by terrorists in order to produce bioweapons; second, modified influenza viruses could escape the lab by accident and create a pandemic. The first objection led to a very rare decision in scientific publishing, namely the redaction of the articles to remove potentially sensitive data. The important public concern also led the authors of these studies to promulgate a moratorium on this type of work. After this temporary stop, the experiments started again with additional biosafety measures. 

The debate, however, is far from over. The reason for this? Well, the recent publications of several studies dealing with influenza virus, most notably a paper by Y. Kawaoka (the author of the 2012 Nature publication) on avian influenza viruses related to the 1918 “Spanish flu” virus. This research triggered a heated response from several scientists, which was loudly echoed in the mainstream press (see for instance in the Guardian and in the Independent). In that particular case, it seems that the scientific community is truly divided on the matter. An example of this dissent was the publication of a statement of concern by a group of scientists known as the Cambridge Working Group, which in essence asked for a better assessment of the risks of virus research via the organization of a conference that would deal with all present issues. Such a meeting could resemble the famous Asilomar conference of 1975, where the risks associated with recombinant DNA were debated. Other virologists, however, have fought back these reactions of distrust and have created another group, Scientists for Science, which aims at promoting the benefits of this research, and highlight the fact that serious safety regulations are already in place for virus research.