Press Release
2011-10-03
The Nobel Assembly at Karolinska Institutet has today decided that
The Nobel Prize in Physiology or Medicine 2011
shall be divided, with one half jointly to
Bruce A. Beutler and Jules A. Hoffmann
for their discoveries concerning the activation of innate immunity
and the other half to
Ralph M. Steinman
for his discovery of the dendritic cell and its role in adaptive immunity

(Unfortunately, Steinman died between the committee’s decision and the announcement. He still received the Prize, though.)

However, it is not news (and not good)  that we are losing the arms race against bacteria. We are overusing antibiotics in medicine and in agriculture, virtually nurturing today’s and tomorrow’s killers. A report  in Wired earlier this year paints a bleak picture:

Truly new antibiotics are critically needed because bacteria, having no experience of them, cannot immediately mount resistance to them — something that does happen with me-too compounds featuring some slight molecular change. But they’re rare. As this chart from the research group Extending the Cure shows, antibiotic development has slowed dramatically over the past 30 years, and among the few drugs being brought forth, most share the mechanisms of already-existing classes.

To understand the extent of the crisis, we have to remember that antibiotics are the foundation of a huge number of  medical procedures, from cancer treatment to dentistry. Taking away this foundation would cripple modern medicine. Together with vaccines and public hygiene, antibiotics are the reason that many of us live longer — and better — than our grandparents’ generation and before that.

So lacking drug company motivation (more on that in McKenna’s report) and facing a dwindling supply of effective antibiotics, what are we to do?

A good start is to take a second look at nature. For example, here is a Kangaroo being born:

Awww…

The interesting thing about Kangaroos and other marsupials is that their young are being exposed at a very precarious stage to the outside world. Roo is born in a fetal state: underdeveloped, blind, barely moving and has little to no body temperature regulation. All of these problems are taken care of by Kanga’s protecting Roo’s six minute trip to her pouch where things are warm and cozy, and maternal milk flows in abundance. All except one: pathogens. During his trip, Roo can acquire a whole bunch of nasty bugs from Kanga’s fur and the air. Also, the pouch is not exactly a sterile environment and there is a possibility of infection there. So how is little Roo to survive the trip to the pouch and subsequent stay?

Joey in pouch. Photograph by Geoff Shaw (Zoology, University of Melbourne, Australia). From Wikimedia Commons.

The answer is innate immunity, that collection of mechanisms which protect the host in a non-specific manner. While his adaptive immunity is quite undeveloped, Roo does produce some killer all-purpose peptides he can use against microbes. The same class of peptides are produced in Kanga’s milk. Collectively they are known as cathelicidins. Only about 30 amino acids long, these highly charged molecules kill both gram-positive and gram-negative bacteria.

Since the tammar wallaby genome has recently been sequenced,  a group of Australian scientists has decided to hunt for cathelicidins in the tammar’s genome. They also looked for cathelicidins in the genomes of the duck-billed platypus (a monotreme) in the opossum (an American marsupial), in human, mouse, cow & sheep (all placentals).  Here is what they found. Each leaf on the tree represents a cathelicidin gene. The leaf colors and shapes are for different species of origin.

From Wang J, et al. 2011 PLoS ONE 6(8): e24030. doi:10.1371/journal.pone.0024030 Reproduced under CC license.

The marsupials and monotremes have a much higher diversity of cathelicidin genes than the placental mammals. Note that there are many duplicates of the cathelicidin gene in Pig and Cow, but these duplications are very recent as we can tell by the highly similar sequences of the genes. These duplications are probably because herd animals are more susceptible to pathogens.  In any case,  pig and cow have higher copy number of cathelicidin genes, and thus perhaps a large number of proteins, but not many different ones as in marsupials and monotremes. Diverse cathelicidin genes in the genome can offer a wider protective umbrella against many different types of pathogens.

Back to the antibiotic crisis: can we use marsupial cathelicidins as an antibiotic in humans? Do cathelicidins kill human pathogens? Are they toxic to humans? The authors checked the first two. They used cathelicidins from wallaby and platypus to kill human pathogens: P. aeruginosa, K. pneumoniae and A. baumanii, including antibiotic resistant strains. Cathelicidins were much more effective than, well, antibiotics against those bacteria. Also, cathelicidins did not kill human red blood cells, which makes them a potential drug. Of course,  immune reaction against cathelicidins as a foreign  still needs to be checked, among many, many other things, but the whole idea of looking at marsupials is that, as mamals, they may be able to supply us with clues on how to synthesize a cathelicidin to be used as a drug in humans.

The really cool thing about this study is that the authors used phylogenetics to design an ancestral wallaby cathelicidin. They aligned all the wallaby cathelicidin protein sequences, which were conserved in 40 of the 46 amino-acid positions. They used PAML, GASP and Ancescon to reconstruct an ancestral wallaby sequence, estimated to be 59 million years old, marked by an asterisk (*) in the above gene tree.  They then synthesized the ancestral WAM (Wallaby Anti Microbial) peptide and used it to kill bacteria. Guess what: the ancestral WAM was even better than the existing WAMs, as even a lower concentration was needed to kill bacteria. They are still working on red blood cell toxicity (yay for PLoS-enabled comments!)

So maybe the answer to  the increase in bacterial resistance to antibiotics lies in Kanga’s pouch. After all, she was very protective of Roo.

EDIT: clarified that the part about synthesizing and testing ancestral-WAM to kill bacteria.

Wang, J., Wong, E., Whitley, J., Li, J., Stringer, J., Short, K., Renfree, M., Belov, K., & Cocks, B. (2011). Ancient Antimicrobial Peptides Kill Antibiotic-Resistant Pathogens: Australian Mammals Provide New Options PLoS ONE, 6 (8) DOI: 10.1371/journal.pone.0024030

We will never look at life at quite the same way again.

Until now, information flow in biology looked like this:

DNA gets transcribed to RNA, wheich in turn is translated to protein. While reverse transcription does take place with retroviruses using reverse transcriptase, the central dogma of molecular biology held that proteins is an end product, and there is no information flow back from protein to nucleic acids.

This has just changed.

Today, a press release and a paper by a joint group of scientists at Franklin National Lab and NASA reveals a new RNA-Protein complex that can read short protein sequences and reverse-translate them back to RNA.  The reverse-translation complex, which they call the  emosobir  (that’s “ribosme” in reverse) is larger even than the ribosome. This reverse translation activity has been initially observed in isolates of sludge-derived Amoeba lupicus from Lake Erie, but not published yet as the researchers wanted to duplicate the results in controlled lab conditions, which proved to be extremely challenging.  Apparently reverse translation is due to the activity of a new kind of intracellular parasite. The Emosobir Containing Particle (ECP) resembles a giant virus. However, it is devoid of chromosomal DNA or RNA. Rather, it contains the ebosomir itself. Once the amoeba is infected, the capsid dissolves, and the protein is reverse-translated to RNA. From that point on, the amoeba’s cellular machinery is hijacked just like in a virus to translate the ECP mRNA to new ebosomir and ECP capsids. The process of reverse-translation and RNA-dependent RNA replication and translation is considerably slower than a viral infection — it can take 14-30 days for enough ECPs  to accumulate to burst from an amoeba and infect another. The process is also quite inefficient, as it seems that in only 1% of the infected amoebas ongoing reverse translation is successful.

A Lattice of Ebosomirs in the infected Amoeba lupicus

The consequences of this finding are enormous. Although we are familiar with prions as replicating proteins without nucleic acids, and viroids as replicating nucleic acids without proteins, this is the first time that information flow from a protein to nucleic acids has been discovered.

The press conference will be held today at 4:00pm EDT.  More details here: http://www.nasa.gov/

UPDATE: (April 2)  too many people thought this was serious. Please check the date of this post. Then look up if there is even a Franklin National Lab or an A. lupicus. Then chill out.

I wanted to write a blog post about it. I really did. Something original, inspiring, funny, critical and deep. But so many others beat me to it, so no matter what angle I took, it’s already been covered in the last 24 hours. Informative? Yes. Debateable achievement? Yes yes, and yes. Thoughts from bigshots? Yes. Funny? totally. Religiously suspect? Verily. Government weighing in? Naturally. Reddit? Yes, even Reddit! (Thanks Shirley!)

So here’s the interview Science journal conducted with Craig Venter:

Or, if you’d rather, the Scorpions’ comment:

And the paper in Science. I’m done.

JOB POST

We are seeking to hire a creative computational scientist for a
transformative project: COMBREX: A Computational Bridge to Experiments.

The work will involve building a novel resource that combines databases,
science, social networking and machine learning.

The position is available immediately.

For some preliminary information pls. see

www.combrex.org

BS or MS in Computer Science, Informatics, Engineering or related field is required.

Applicants with PhD’s would be considered for a separate Research Associate position.

Pls send CV and names (emails) of two references to:

Prof. Simon Kasif

kasif@bu.edu

Subject Line: COMBREX POSITION

As part of the process of manufacturing  a new car,  the designers will take the blueprints to the factory floor. There they will set up an experimental assembly line, tinkering with the manufacturing process of the prototype until it is ready for mass-production. Can we do the same with the machinery of life – the assembly of proteins? Can we set up an alternative assembly line for a new protein prototype — and then actually set up a working assembly line for the whole new protein?  A proof-of-concept has been published this week in Nature by Jason Chin’s group at the Medical Research Council Laboratory of Molecular Biology, Cambridge UK.

If there is a single common denominator to all life, it is the genetic code. All life is built around DNA encoding information for proteins  nucleotide triplets or codons. Since there are four types of nucleotides (A,T,G,C)  that are read in words of thee, there are 4³ = 64 possible codons: more than enough to encode for the 22 amino acids that make up proteins. There is nothing more basic and fundamental to life on Earth than the three-letter based genetic code.

Until now.

Chin’s group has created a four-nucleotide codon system.  It is not that the DNA is different: it is the way the cellular machinery decoding  RNA transcripts interprets the nucleotide sequence. Ribosomes –large RNA and protein complexes  which are the platform upon which messenger RNA is read and decoded — are set to serve up messenger RNA three nucleotides at a time. (Messenger RNA or mRNA is a transcript of the DNA which is carried to the ribosome.)  Transfer RNA or tRNA is a short RNA molecule that shuttles the proper amino acid to the ribosome, but will only attach if the proper codon is served up by the ribosome. The whole protein synthesis “assembly line” looks something like this:

Protein synthesis. Credit: Wikimedia Commons.

To change the interpretation of the genetic code from three lettered words  to four, Chin and his colleagues had to make new ribosomes, and new tRNAs.  To create these new ribosomes, they designed orthogonal ribosomes, or o-ribosomes. O-ribosomes are genes inserted to produce extra ribosomes that operate in the cell alongside the regular ribosomes. The cell functions because it has the regular ribosomes to maintain its viability. The ribosomal RNA in the o-ribosomes is free to be mutated to create new unnatural traits: in this case, the ability to serve as a platform read four-letter codons. They selected for Escherichia coli bacterial cells that expressed a o-ribosomes which translated a four-letter codon in a gene, which would otherwise go untranslated by the regular ribosome. The gene gives the bacterial cells resistance to the antibiotic chloramphenicol. So cells that survive a dosage of chloramphenicol are those which have functioning o-ribosomes, as they have the chloramphenicol resistance gene that is being translated by the o-ribosomes.

They also needed to create new tRNAs that have an four-nucleotide anticodon (the part that complementarily binds to the messenger RNA –  see figure above.)  So the surviving E. coli cells have a population of working o-ribosomes, regular ribosomes, modified tRNA (with a  four-letter anticodon) and regular tRNA.

Then they took their work a step further. Each three-letter tRNA carries a specific amino-acid, depending on its anticodon. Thus tRNA_AAG will always have a phenylalanine attached, because CTT (the complement of AAG on the messenger RNA) codes for phenylalanine. If you start messing with that, the translation machinery will produce non-functional proteins, which will probably kill the cells pretty quick. But with the orthogonal 4-letter code machinery, that is not really a problem: the orthogonal machinery operates alongside the normal one. Also, there are no amino acids naturally assigned to any four letter code, because this code does not appear in nature in the first place! So Chin’s lab assigned an unnatural amino acids to a four-letter code. The non-naturally occurring p-azido-l-phenylalanine amino acid was assigned to tRNA_UCCU. They then showed that the whole alternative translational machinery worked by synthesizing a mutant of the protein calmodulin which used this amino-acid in its structure.

Why do it? Well, personally I don’t see the need for justification: just being able to do it is so cool!  But seriously: think of the ability to design proteins from up to 4⁴=256 different amino acids other than the 22 we have now.  The possibilities of tinkering with existing proteins using this orthogonal, four-letter based machinery are huge. The other benefit of this orthogonal synthesis setup is the ability to control this orthogonal translational machinery: because it does not use the three-letter vocabulary, this orthogonal machinery would be much easier to manipulate, tinker with and switch on and off without getting in the way of regular cellular translational machinery. The analogy to a car assembly line breaks here. It is as if two different models are being assembled on the same line just by using different robots. The better analogy is for a program source code to be read by two different compilers, each producing a different program. Awesome.