Gene transfer in bacterial arm races

The following videos are two short documentaries made by students in the MIT Graduate Program in Science Writing. Both films refer to a recent discovery of new antibiotics by scientists at the Massachusetts Institute of Technology and the University of Florida. But, please, don't say: "bah, another antibiotic discovering, so boring". What makes this an interesting story is not the particular antibiotics themselves (we'll see if they ever become useful), but the way they were discovered. Or should we say "created"?

It's been known for some time that the genomes of many microbes contain genes putatively coding for the production of many small molecules. Some of these molecules may have antibiotic, anticancer or other potentially useful activities. By looking at the genomic DNA sequence, scientists can often predict that such a microbe has the potential to produce specific metabolites, belonging to defined structural classes (polyketides, non-ribosomal peptides, glycosides, etc.). However, very often, the predicted metabolites are not detected when the microbe is cultured under standard laboratory conditions. Why is this? The usual explanation is that these molecules are only produced under specific circumstances that the microorganism faces in its natural environment.

With this idea in mind, the above mentioned researchers tried to find antibiotics in the cultures of a bacterium called Rhodococcus fascians (let's call it "Rhodo"). Rhodo belongs to a group of bacteria known as actinomycetes, which are well-known antibiotic producers and whose genomes are rich in information coding for the synthesis of potentially useful metabolites. The scientists cultured the microorganism under a variety of conditions: they tried both standard and unusual ones (starvation, sub-optimal temperatures or culture media, etc.). However, no antibiotic activity was ever detected.

So, they tried to "stress" Rhodo by adding another microbe in the same flasks: the name of the second partner was Streptomyces padanus ("Strepto", for short). Strepto produces a potent antibiotic (actinomycin) that kills bacteria such as Rhodo. So, what was the point? Rhodo died in all flasks, didn't it? Well, not in all of them. In one particular flask (out of hundreds), Rhodo not only survived but actually exterminated Strepto! The "Super-Rhodo" did this by producing a new antibiotic substance, never seen before. Moreover, Super-Rhodo was able to do this thanks to a piece of DNA that Rhodo stole from Strepto!

Both documentaries refer to the same story, but they use remarkably different styles. Please watch both of them, and post a comment if you want to share your thoughts (about them or about the story).

The first video is War in a Petri Dish, by Grace Chua, Allyson Collins, and Lissa Harris:

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The second video is Shot in the Dark, by Andrew Moseman, Rachel VanCott, Megan Rulison, and Ashley Yeager:

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There are some scientific aspects that may need some clarification. The initial idea was that Rhodo contained the genetic potential to make antibiotics, and the genes responsible for this were only "switched on" under certain unknown circumstances. This might be correct, but the mentioned results don't clearly validate it. When Rhodo faced a Strepto attack, it simply died. The only survivor (and now a killer itself), Super-Rhodo, had acquired genetic material from its enemy. This extra piece of DNA was essential for production of the new compounds. Although full details have yet to be published, it is not clear if the transferred DNA contained all, or some, of the genes coding for biosynthetic enzymes for antibiotic production. The new antibiotics are not related to actinomycin; however, it is possible that Strepto is able to produce them, in addition to actinomycin (again, under certain unknown circumstances...). Alternatively, the real effect of the extra DNA might be just regulatory, coding for some factor that induced the "switching on" of Rhodo's own genes. We'll wait for the answers to these doubts.

Scholar article:
K. Kurosawa, I. Ghiviriga, T.G. Sambandan, P.A. Lessard, J.E. Barbara, C. Rha, A.J. Sinskey (2008). Rhodostreptomycins, Antibiotics Biosynthesized Following Horizontal Gene Transfer from Streptomyces padanus to Rhodococcus fascians Journal of the American Chemical Society, 130 (4), 1126-1127 DOI: 10.1021/ja077821p

Related link:
Deadly mycelia: predatory streptomycetes. Twisted Bacteria (Jan. 15, 2008).

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A new way to make polyketides

Polyketides are a class of natural products isolated from microbes, plants and invertebrates which includes an impressive number of clinically effective drugs with diverse activities. To name a few examples: erythromycin (antibiotic), rapamycin (immunosuppressive), amphotericin (antifungal), avermectin (antiparasitic), and doxorubicin (anticancer). As other natural products do, polyketides may play disparate roles in the producing organisms, from defensive weapons (inhibiting growth of competitors, or acting against predators) to signaling molecules (working as messengers between social organisms). In Mycobacterium tuberculosis, some polyketides are key intermediates in the synthesis of complex lipids. These lipids are important components of the unusually thick cell envelope, and help the microbe to be a successful pathogen. Therefore, the study of polyketide synthesis in this bacterium may lead to the design of specific inhibitors as new anti-mycobacterial drugs.

Polyketides are produced through a stepwise condensation of simple carboxylic acid precursors, resembling fatty acid biosythesis. This task is performed by enzymes known as polyketide synthases (PKSs). There are several types of PKSs, from relatively simple proteins to large multienzymatic complexes possessing tens of catalytic sites. They use any of two general mechanisms: (1) modular — in which each set of catalytic sites is used only once during the biosynthetic process, and (2) iterative — in which the same set of active sites is used repeatedly. This week in PLoS Biology, Rajesh Gokhale and colleagues present their research involving a peculiar PKS from M. tuberculosis. The PKS12 protein is encoded by the largest gene in the microbe's genome, and participates in the synthesis of an antigenic phosphoglycolipid. Most remarkably, this PKS appears to use a new hybrid "modularly iterative" mechanism for polyketide synthesis. Several molecules of the PKS12 protein join together to form a supramolecular assembly, which performs repetitive cycles of iterations. The protein assembly is formed by specific intermolecular interactions between N- and C-terminus linkers. This study provides another example of the catalytic and mechanistic versatility of PKSs — natural product biosynthesis is an inexhaustible source for new biochemistry!

Citation (open access):
Chopra T, Banerjee S, Gupta S, Yadav G, Anand S, Surolia A, Roy RP, Mohanty D, Gokhale RS (2008). Novel intermolecular iterative mechanism for biosynthesis of mycoketide catalyzed by a bimodular polyketide synthase. PLoS Biology 6(7), e163. DOI: 10.1371/journal.pbio.0060163

Image: model of the PKS12 protein, modified from Figure 5 of the cited article.


Related links:

• Cracking the Polyketide Code. PLoS Biology (2004) 2(2): e35.
• Polyketide Biosynthesis: The Erythromycin Example (video of an excellent talk by Chaitan Khosla, May 2007). iBioSeminars, American Society for Cell Biology. The first part of the talk (Polyketides and Polyketide Biosynthesis) is also available at Google Video, and is embedded below.

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