Physicist finds that E. coli replicate close to thermodynamic limits of efficiency

Aug 27, 2013 by Anne Trafton
How quickly can a bacterium grow?

All living things must obey the laws of physics—including the second law of thermodynamics, which states that the universe's disorder, or entropy, can only grow. Highly ordered cells and organisms appear to contradict this principle, but they actually do conform because they generate heat that increases the universe's overall entropy.

Still, questions remain: What is the theoretical threshold for how much heat a living cell must generate to fulfill its thermodynamic constraints? And how closely do cells approach that limit?

In a recent paper in the Journal of Chemical Physics, MIT physicist Jeremy England mathematically modeled the of E. coli bacteria and found that the process is nearly as efficient as possible: E. coli produce at most only about six times more heat than they need to meet the constraints of the second law of thermodynamics.

"Given what the is made of, and given how rapidly it grows, what would be the minimum amount of heat that it would have to exhaust into its surroundings? When you compare that with the amount of heat it's actually exhausting, they're roughly on the same scale," says England, an assistant professor of physics. "It's relatively close to the ."

England's approach to modeling biological systems involves , which calculates the probabilities of different arrangements of atoms or . He focused on the of cell division, through which one cell becomes two. During the 20-minute replication process, a bacterium consumes a great deal of food, rearranges many of its molecules—including DNA and proteins—and then splits into two cells.

To calculate the minimum amount of heat a bacterium needs to generate during this process, England decided to investigate the thermodynamics of the reverse process—that is, two cells becoming one. This is so unlikely that it will probably never happen. However, the likelihood of it happening can be estimated by aggregating the of reversing all of the smaller reactions that take place during replication.

One of the common reactions that occur during replication is formation of new peptide bonds, which form the backbone of proteins. Spontaneously reversing that type of reaction would take about 600 years, England says. The number of peptide bonds in a typical bacterium is about 1.6 billion, and the heat wattage needed to break all of those bonds is about 100 billion natural units.

"I would have to wait a really long time to see all of those bonds fall apart," England says.

By estimating the waiting time needed to observe a spontaneous reversal of replication, England calculated that the minimum amount of heat a bacterium needs to generate as it divides is a little more than one-sixth of the amount an E. coli cell actually produces during replication.

The finding suggests that bacteria could grow dramatically faster than they do now and still obey the . England says that because cell replication is just one of the many tasks E. coli need to perform, it's unlikely they would evolve to their most efficient possible growth rate. However, for synthetic biology applications, it may be useful to create bacteria that can divide faster, which this paper shows is theoretically possible.

The paper may also offer some evidence for why DNA, and not RNA, evolved as the main form of genetic material, England says: DNA is more durable and doesn't spontaneously break its bonds as readily as RNA does. This means that RNA may have an advantage over DNA because it can grow faster and use up available resources. This supports a previously suggested hypothesis that RNA may have evolved first, before life arose on Earth, and DNA showed up later on.

"I think it's a helpful way of trying to get a little bit more of a handle on the different kinds of selection forces that may have been acting on [early] nucleic acids," England says.

He is now using the same theoretical approach to model how self-replicating cells evolve by working out new ways of adapting to environmental fluctuations.

The paper is titled "Statistical physics of self-replication."

Explore further: Bent out of shape: Stressed bacteria accumulate misfolded proteins and stop growing

More information: jcp.aip.org/resource/1/jcpsa6/… 21923_s1?bypassSSO=1

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Benni
1 / 5 (6) Aug 27, 2013

Makes me wonder how well this will fit in with the Asymptotic Pseudo-Tensor theory whereby ENTROPY is an unimportant concept in the manner in which the entire Universe functions.

The "infinite universe" crowd should be showing up shortly with their one star ratings to protest the scientific the concept that ENTROPY cannot be established in anything other than Einstein's spherical "closed universe" for which he plainly stated his case in his General Theory of Relativity. The leader of the Asymptotic Pseudo-Tensors will almost certainly be here to make a fictional statement that Einstein never made such a case in his GR.

OK "Open", get the ball rolling here so the rest of the retirement community can get their one star rating orders.
Benni
1 / 5 (6) Aug 27, 2013
TOOT-aren't you out of bed kind of early? You beat OPEN to the one star click. Maybe it's the difference in that European time zone?
Torbjorn_Larsson_OM
not rated yet Aug 27, 2013
It's awesome that England's paper finally moved from arxiv to peer review! It was uniquely constraining the protocells to RNA for replication until recently.

It has now been shown that RNA can catalyze electron transfer just as proteins under Archean conditions (no oxygen, lots of free iron(II)). Meaning there is also a possible pathway where the original replicators can be DNA directly.

But it is less likely and indeed it didn't happen for us as RNA is the core replication machinery. And one can note that RNA is the key biochemical machinery for either pathway.

@Benni: You mean getting eye balls rolling. Entropy has nothing to do with life, except as a constraint. The above work tests that yet again, btw.
Benni
1 / 5 (7) Aug 27, 2013
@Tor- you only read the bottom half of the article, selective reading on your part. You always start in the middle of anything your reading?
marraco
1 / 5 (1) Aug 27, 2013
Escherichia: On THIS house, we obey the laws of thermodynamics!
johnhew
not rated yet Aug 27, 2013
Been just about a year now since the arxiv release and still trying to make sense of a few points.
Clearly idea of DNA being more stable is an old one.
What is the justification for assuming reverse processes can be used to constrain the forward ones?
If we take just the heat released from ATP hydrolysis, only a percentage of it would seem capable of being harnessed to do chemical-molecular work, and I assume the rest not absorbed in various reactions or configurations shows up at least partially as heat. I think there was even a recent paper, maybe arxiv (author from Asia) who calculated from experiments the distance at which ATP hydrolysis is actually felt in cellular environments. But if the reactions are better, in theory the heat could be in principle very small. I think the interesting question is rather what % of the sum total of molecular motion leads to successful reactions, as a measure of how efficient cells are. Also http://arxiv.org/...3778.pdf
johnhew
1 / 5 (1) Aug 28, 2013
I might guess that a cocooned, and insulated, morphing caterpillar operates at a lower metabolic rate than a crawling one. However note that in the case of a potentially double-yoked (Schrodinger egg we could call it) egg, we probably couldn't tell if it contains 2 developing chicks or one, from the entropy of a heat bath in which it sits.
mrlewish
not rated yet Aug 28, 2013
Do does this suggest that given similar environments and the use of DNA as a basis for life that alien life ecosystems might have "E. coli" so similar that they would be indistinguishable from terrestrial life?