Microbial pigments: an untapped resource for teachers, artists and researchers

The journal PLoS Biology has launched a new series of articles on education "to present innovative approaches to teaching critical concepts, developments, and methods in biology." The title of the first article in the series is In Living Color: Bacterial Pigments as an Untapped Resource in the Classroom and Beyond.

From the article:

"Soil bacteria from the Streptomyces genus represent a source of interesting natural products that have been largely overlooked by artists, researchers, and teachers. This article is intended to encourage amateurs and professionals alike to explore this overflowing source of biopigments. Not only does this endeavor have the potential to lead us toward a fertile nexus between art and science, it may also lead to a more sustainable and environmentally friendly way to color the world around us in the future. The relevance of biopigments to many facets of science, technology, and society, makes this material an outstanding tool to engage students of varying academic interests across multiple age groups. Therefore, we encourage teachers of all levels to consider using biopigments as a vehicle to introduce the scientific method to their students. To facilitate the implementation of biopigments into science and art curricula, we have provided a list of useful online resources and information about procuring materials [...] as well as recommend ways to evaluate the effectiveness of the lesson [...]."

Original article (and image source):
Charkoudian LK, Fitzgerald JT, Khosla C, Champlin A (2010) In Living Color: Bacterial Pigments as an Untapped Resource in the Classroom and Beyond. PLoS Biol 8(10): e1000510. doi:10.1371/journal.pbio.1000510
Image: “Elvis Lives!” painted on agar media plates using the bacterium Streptomyces coelicolor.



Related links:
- Microbial Art, a collection of unique artworks created using living bacteria, fungi, and protists.
- Painting With Penicillin: Alexander Fleming's Germ Art. The scientist created works of art using microbes, but did his artwork help lead him to his greatest discovery? By Rob Dunn. Smithsonian.com, July 12, 2010.
- Streptomyces: they're twisted! Twisted Bacteria, Aug 10, 2007.

Read the rest of the article >>>

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:

Click To Play

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

Click To Play

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).

Read the rest of the article >>>

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.

Read the rest of the article >>>

Merck halts natural products research

Bad news: Merck has decided to close down its natural product research facilities. This means the end of CIBE (Centro de Investigación Básica de España) — or Spanish Center for Biological Research — located in Madrid, Spain. Since its creation in 1954, this center has been dedicated to the discovery of new compounds of therapeutical potential produced by microbes. These efforts led to the development of several useful medicines, including antibiotics (fosfomycin, cefoxitin, thienamycin), cholesterol-lowering drugs (lovastatin), and antifungal agents (caspofungin). In May 2006, Merck researchers hit the news with the discovery of platensimycin, a natural product belonging to a new class of antibiotics.

According to Chemical & Engineering News, the high costs are behind the decision to eliminate natural products research. Merck spokesman Ian R. McConnell explains to C&EN:

"The investment involved in finding these chemicals in the environment is significant. The products that came out of our effort have been significant as well, but that was over a 50-year period"

Sad, but true. Many thousands of natural samples need to be screened in order to detect a bunch of potentially useful compounds, most of which will never become a marketed drug. Turning a promising natural product into a useful medicine takes much effort and time (over 10 years) and, hence, money. So, perhaps it is understandable that most pharmaceutical companies dedicate only a very small fraction of their resources, if any, to natural product drug discovery.

However, even with that little dedication, many medicines in the market have a natural origin, being based in substances originally isolated from plants, microbes, etc. Can we imagine the possible results of investing in natural product research as many resources as those dedicated to chemical synthesis?

Natural compounds often have bizarre, complicated chemical structures and exert their biological effects through unexpected mechanisms. They are the result of an on-going combinatorial chemistry performed by organisms since the origin of life.

Are chemists that good?



Related links

A) About job cuts at Merck:

• Merck cuts sales jobs and halts natural products research. Chemical & Engineering News (May 7, 2008).
• Merck bails on natural products. In the Pipeline (May 8, 2008).
• At Merck, some layoffs are made by PowerPoint. Pharmalot (May 8, 2008).
• Layoffs by PowerPoint? BioJobBlog (May 8, 2008).

B) About CIBE:

• Centro de Investigación Básica de España (CIBE). Merck Sharp & Dohme de España [in Spanish].
• Ten years of CIBE symposia, 1989-1998 (by Sagrario Mochales, CIBE) [pdf]. Int. Microbiol. (1998) 1, 251-254.
• Forty years of screening programmes for antibiotics (by S. Mochales). Microbiología (1994) 10, 331-342.
• Declaraciones de Fernando Peláez, director del CIBE, durante la presentación del BIO-Europe Spring (Marzo 2008) [video, in Spanish].
• Este pueblo puede salvar a España del colesterol (incluye una entrevista a Sagrario Mochales, "la científica olvidada"). ElMundo.es (16 Dic. 2007) [in Spanish].
• El tesoro de la selva tropical llega a Madrid. ElPaís.com (14 Jun. 1995) [in Spanish].

C) About natural products in drug discovery:

• Natural products to drugs: natural product-derived compounds in clinical trials. Nat. Prod. Rep. (2008) 25, 475-516.
• Natural products: chemical instruments to apprehend biological symphony. Org. Biomol. Chem. (2008) 6, 424-432.
• Natural products as sources of new drugs over the last 25 years. J. Nat. Prod. (2007) 70, 461-477.
• New aspects of natural products in drug discovery. Trends Microbiol. (2007) 15, 279-289.
• The value of natural products to future pharmaceutical discovery. Nat. Prod. Rep. (2007) 24, 1225-1244.
• Natural product drug discovery: the times have never been better. Chem. Biol. (2007) 14, 1098-1104.
• The historical delivery of antibiotics from microbial natural products--can history repeat? (By Fernando Peláez, CIBE). Biochem. Pharmacol. (2006) 71, 981-990.
• Drug discovery from natural sources. AAPS Journal (2006) 8, E239-E253.
• Antibacterial natural products in medicinal chemistry--exodus or revival? Angew. Chem. Int. Ed. Engl. (2006) 45, 5072-5129.
• The renaissance of natural products as drug candidates. Science (2005) 310, 451-453.
• The evolving role of natural products in drug discovery. Nat. Rev. Drug Discov. (2005) 4, 206-220.
• Rediscovering natural products. Chemical & Engineering News (Oct. 13, 2003).

Image credits:
Digital Atlas of Actinomycetes. Copyright: Society for Actinomycetes Japan. Contributor: S. Mochales. This strain produces β-lactam antibiotics, thienamycins. It has the color of cattleya orchids.

Read the rest of the article >>>

Women scientists, sixty years ago

New York City, 1949. During the last three years, Elizabeth Hazen had been isolating hundreds of microbes from dirt samples taken at different locations. Many microbiologists at the time were following a path open by Alexander Fleming, Selman Waksman and others, who discovered that some soil microbes produced certain substances—antibiotics—with powerful activities against bacteria. However, rather than looking for a new agent against prokaryotic microbes, Elizabeth searched for a medicine to fight fungal infections. For this purpose, she grew the soil microbes and tested the cultures against disease-causing fungi (Cryptococcus neoformans, Candida albicans [see image]). Whenever a culture showed an interesting activity, she put it in a glass Mason jar and mailed it to Albany, 250-km away. Here, Rachel Brown—a chemist—used the culture for purification and characterization of the active compound. Then, Rachel mailed the fruit of her efforts back to New York, where the microbiologist tested the sample again for fungicidal potency. Through this collaboration, the two scientists isolated several antifungal compounds that, unfortunately, were too toxic when tested in laboratory animals.

But, finally, Elizabeth and Rachel found a useful fungicidal agent with a lower toxicity. It was produced by a soil bacterium isolated from a sample that Elizabeth had collected, while on holiday, in Warranton, Virginia. She had taken a bit of soil at the edge of a cow pasture, near a dairy barn, at the farm of a certain Walter B. Nourse. Because the microbe appeared to be a new species of streptomycetes, it received the name Streptomyces noursei, in honor of Mr. Nourse. The fungicidal agent was initially named fungicidin, but it was soon renamed nystatin, as both Elizabeth and Rachel worked for the New York State Department of Health (although in different locations). Since then, nystatin has been widely used to treat candidiasis and other fungal infections.


Related links:

• Elizabeht Hazen, seeker. Arts of Innovation.
• Elizabeth Hazen and Rachel Fuller Brown, Pharmaceutical Achievers. Antibiotics in Action.
• News of Science: Scientists in the News (on E. Hazen). Science (1955) 122, 914.
• Women in Microbiology, Microbes and Society: A Closer Look.
• Elizabeth Hazen Biography. World of Microbiology and Immunology.
• Elizabeth Lee Hazen and Rachel Fuller Brown. Inventor of the Week, Lemelson-MIT Program.

This post modestly celebrates March 8th, International Women's Day. The discovery of nystatin seems a good example of an important contribution of women scientists to microbiology, natural product chemistry, and medicine. A related story is that of Alma Whiffen, who discovered cycloheximide—also known as actidione—around the same time (1947). She isolated the compound from cultures of a soil microbe, Streptomyces griseus. Cycloheximide has antifungal activity, and was employed to treat fungal infections in plants; however, it is not useful for human treatment. The compound is better known as a general inhibitor of protein synthesis in eukaryotes, and it is widely used for research purposes. Read more here:

• Antibiotic for Plants. Time (Nov. 22, 1948).
• Alma Whiffen Barksdale Records. The New York Botanical Garden.

More related links:

• Microbiology pioneer dies (Esther Lederberg, discoverer of the lambda phage). Aetiology (Nov. 30, 2006).
• Committee on the Status of Women in Microbiology, American Society for Microbiology.
  
• Women in Science, the blog.
• Iraq's women scientists. BBC News, Middle East (Sept. 22, 2004). The dark side of microbiology...

Image credits: Wikipedia.

Read the rest of the article >>>

Phytochemistry Letters

The Phytochemical Society of Europe and Elsevier have given birth to a new journal, Phytochemistry Letters, which will cover all aspects related to natural products. Submissions from any field of natural product research are encouraged, including: structural elucidation of natural products, clinical efficacy, safety and pharmacovigilance of herbal medicines, natural product biosynthesis and chemical synthesis, chemical ecology, biotechnology, pharmacology, metabolomics, ethnobotany and traditional usage, natural product metabolism, genetics of natural products...
Despite the "phyto-" (= plant) in its name, the journal will not deal only with natural products from plants, but also with those from microorganisms (one of the editors is specifically associated to the subject of "microbial natural products").

Read the rest of the article >>>

Microbial Astronauts

Do you want to increase your productivity? Buy a ticket for the next spaceflight!

It may work... if you are a microbe with the ability to produce an interesting metabolite, such as an antifungal agent. The treatment involves some kind of unknown mutation, but that's OK as long as you become a better producer with a stable behavior.

Scientists from Zhejiang University and Shandong Lukang Pharmaceutical Co. (China), recently published the following article (open access):

Jingle, L., Jianping, L., Zhinan, X., Wei, S., Peilin, C. (2007). Space-flight mutation of Streptomyces gilvosporeus for enhancing natamycin production. Chinese Journal of Chemical Engineering, 15(5), 720-724. Link to publication.

Streptomyces gilvosporeus is a bacterium that produces natamycin (also known as pimaricin), which is an antifungal agent used as a treatment for fungal keratitis and also as a food preservative. Tubes containing spores of this microbe were placed in a sample module of a returnable satellite, which was launched from the Jiuquan Satellite Launching Center in Gansu Province, China. After orbiting the earth for 18 days, the bacterial taikonauts landed safely in a returning module. Then, ground-based scientists grew these spores and studied their colony morphology, survival rate, and natamycin production. As compared to similar spores that had never left the Earth, some of the space travelers behaved differently. This was expected, and most likely due to mutations produced by the spaceflight conditions (including cosmic radiation, microgravity, and vacuum). After selecting for the best natamycin producers, a stable overproducer strain was isolated.

The authors cite other reports on the use of spaceflight for obtaining improved microbial strains. But, more generally, the relationship between microbes and space is fascinating, involving different aspects such as:

• physiological responses of microbes to spaceflight conditions (affecting growth, pathogenicity, production of interesting metabolites...),
  
• health of astronauts (microgravity weakens the immune system, which might make astronauts prone to infections),
• microbial contamination of spaceships (terrestrial microbes landing on other worlds, and vice versa?),
  
• panspermia theory and the origin of life,
• etc.

Some links:

- NASAexplores: Microbes in Space!
- Microbes May Threaten Lengthy Spaceflights, washintonpost.com.
- NASA Study Will Help Stop Tiny Stowaways To Mars, ScienceDaily.
- Russian rocket carries experiment to be analyzed at MSU, Montana State University.
- Spaceflight shown to alter ability of bacteria to cause disease, Biology news Net.
- Microbial responses to microgravity and other low-shear environments, Microbiol Mol Biol Rev.

Read the rest of the article >>>

Antibiotics and viruses: a natural alliance?

At the right concentration, an antibiotic may be effective enough to kill a microbe, or at least to stop its growth. But lower antibiotic concentrations may have subtler effects on microorganisms. For instance, some bacteria respond in a funny way to very low, sub-lethal amounts of those antibiotics inhibiting cell division (such as penicillins): instead of dividing, cells become longer and longer, forming filaments. In this situation, cells are stressed but alive and still growing. Now, researchers from Université Paul Sabatier-Toulouse, France, have noticed that bacterial viruses (or phages) have also adapted to these circumstances.

When infected by these viruses, filamenting cells produce more offspring phages than the "healthier" cells do. The increased production of phages seems to be the result of faster lysis (due to defects on cell wall caused by the antibiotic) and a higher phage assembly. From the point of view of a phage making its living off bacteria, filamenting cells might be a warning sign: "hey, watch out, something is going wrong, the cells may die soon, so we better sack the place while we can."

The discovery of this phenomenon (where serendipity played a part) may have implications for medicine and biotechnology. For instance, the use of a combination of antibiotics and phages might be a new effective treatment for some bacterial infections. But the findings also bring out a possible, unexpected relationship between antibiotics and phages in the natural environment. It suggests that phages may work as amplifiers of the deadly effects of antibiotics, which are naturally produced by microorganisms such as actinomycetes. Both the phage and the antibiotic producer get some benefit: the former gets an extra burst from its unhealthy, filamenting host; while the latter gets rid of bacterial rivals in the neighborhood. Here, the antibiotic- and phage-sensitive bacteria get the worst part. But it's a cruel world.

Citation:
Comeau, A.M., Tétart, F., Trojet, S.N., Prère, M., Krisch, H.M., Fox, D. (2007). Phage-Antibiotic Synergy (PAS): β-Lactam and Quinolone Antibiotics Stimulate Virulent Phage Growth. PLoS ONE, 2(8), e799. DOI: 10.1371/journal.pone.0000799

Image: The PAS effect of phage ΦMFP on Escherichia coli MFP. Disks containing the β-lactam antibiotics (indicated by “+” symbols) produced large phage plaques in their proximity.

On Sept. 19, I added the following comment at the article site:

In addition to the potential implications for medicine (i.e., antibiotics+phages combination therapy), I like the thought-provoking idea of a possible co-evolution of certain traits in antibiotic-producing microbes and in phages infecting antibiotic-sensitive bacteria. One can imagine (have a look at Figure 1) several concentric, inhibition zones surrounding the cells (or mycelia) of an antibiotic producer. Inner zones, where antibiotic concentration is deadly for different microbes (depending on their respective sensitivities). And outer zones, where the antibiotic concentration is only sub-lethal but stimulate phage production in sensitive phage-microbe couples; we might picture it as a "defensive barrier" consisting of a higher local concentration of phages, ready to attack sensitive newcomers. Given that we really don't know the antibiotic concentrations that are actually produced by microorganisms in natural environments (at least I don't know), the sub-lethal effects of secondary metabolites may be more significant than their "antibiotic" effects. Just let your imagination fly...

Read the rest of the article >>>

Finding a needle in the ocean

The deep ocean may be similar to a rainforest in terms of the range of existing microbes and their genetic diversity. The resulting biochemical diversity might provide us with novel natural drugs and enzymes for cleaner industrial processes. The following clips are available for download from Out of the Blue, a DVD on marine microbes produced by Panache Productions with support from the NERC BlueMicrobe knowledge transfer network. The interviewed researchers are Alan Bull and Jem Stach, from the Universities of Kent and Newcastle (UK), respectively. For bioprospecting, the researchers use a combination of molecular techniques, bioinformatics, novel culturing strategies and screening approaches. In addition to potential pharmaceutical and biotechnological applications, these efforts will broaden our knowledge of microbial ecology and evolution (scarce knowledge, by the way).



*******************************************************
This post is a contribution to Microbial Week, a collection of posts highlighting the many roles of microbes in deep-sea or marine environments. The event is organized by Christina Kellogg and the guys at Deep-Sea News.
*******************************************************

Read the rest of the article >>>

From Aladdin’s Cave to Treasure Island

For a long time, it was thought that the land of actinomycetes was... well, land. I mean, they were supposed to be terrestrial creatures, even although some of them were isolated from samples taken in sea habitats (for instance, read this article from 1958). But these "marine" bacteria, generally found in shallow waters, were quite similar to their counterparts from land. For this reason, it was assumed that any actinomycetes obtained from the sea were just wash-offs from the shore.

Now this view is changing. But how can we say if a microbe isolated from a particular sea location is a true neighbor on the block (as opposed to be just derived from a passing-by or dormant spore, coming from land)? Ideally, it should be recognized by the following criteria: its ability to grow optimally at native conditions (salinity, pressure, temperature, nutrients); demonstration that the organism is really active on location; and the recognition of particular metabolic profiles, not found in terrestrial relatives. Nowadays, the existence of truly marine actinomycetes seems to be supported by solid data.

Similarly to their terrestrial relatives, marine microbes are a rich source of bioactive metabolites (antibiotics, antitumor drugs) and enzymes with different applications. For instance, cultivation of a marine actinomycete known as Salinispora tropica yielded a number of novel metabolites, not found before. One of these compounds, salinosporamide A, has antitumor properties and is currently being tested in humans for the treatment of cancer. Sequencing the genome of Salinispora tropica unveiled a number of genes coding for the synthesis of 17 potential metabolites; most of these compounds had not been detected in previous culturing of the microbe. Then, the researchers used the genetic information to guide a new chemical analysis of Salinispora cultures. The analysis uncovered an additional, novel compound (salinilactam), which had a structure corresponding to that deduced from the DNA sequence.

Let me finish with David Hopwood's words from Therapeutic treasures from the deep:

"In a recent book I likened the plethora of previously unknown genes in a newly sequenced Streptomyces genome to an Aladdin's Cave. Perhaps Treasure Island would be a more apt metaphor in this case [Salinispora]"

Neat.


List of links:
- Article from 1958: Grein A, Meyers SP, Growth characteristics and antibiotic production of actinomycetes isolated from littoral sediments and materials suspended in sea water. J. Bacteriol. 1958, 76, 457-463.
- Marine actinomycetes: Bull AT, Stach JE, Ward AC, Goodfellow M, Marine actinobacteria: perspectives, challenges, future directions. Antonie Van Leeuwenhoek, 2005, 87, 65-79.
- Salinosporamide A: Wikipedia.
- Sequencing the genome of Salinispora tropica: Udwary DW, Zeigler L, Asolkar RN, Singan V, Lapidus A, Fenical W, Jensen PR, Moore BS, Genome sequencing reveals complex secondary metabolome in the marine actinomycete Salinispora tropica. Proc. Natl. Acad. Sci. USA, 2007 , 104, 10376-10381.
- Therapeutic treasures from the deep: Hopwood DA, Nat. Chem. Biol. 2007, 3, 457-458.
- Aladdin's Cave: Aladdin - Wikipedia.
- Treasure Island: Wikipedia.


Images:
Left, Aladdin in the Magic Garden, an illustration by Max Liebert for Ludwig Fulda's Aladin und die Wunderlampe. Source: Wikipedia.
Right, Jim Hawkins and the treasure of Treasure Island, an illustration by Georges Roux for the 1885 edition of Treasure Island by Robert Louis Stevenson. Source: Wikipedia.

*****************************************************
This post is my contribution to Microbial Week, a collection of posts highlighting the many roles of microbes in deep-sea or marine environments. The event is organized by Christina Kellogg and the guys at Deep-Sea News.
*****************************************************

Read the rest of the article >>>

Yondelis: from the seas to the pharmacy

Yondelis (trabectedin, ecteinascidin-743, ET-743) is an anticancer natural product isolated from a marine organism, the tunicate Ecteinascidia turbinata. The compound was initially extracted from the naturally growing and farmed tunicate, but now it's manufactured by semi-synthesis from a structurally-related metabolite produced by the bacterium Pseudomonas fluorescens. It is likely that the actual producer of Yondelis is not the tunicate itself but some unknown, symbiotic bacteria living in close relationship to the tunicate. The drug is being developed by PharmaMar, a Spanish biopharmaceutical company subsidiary of the Zeltia Group. For several years, Yondelis has being studied in clinical trials for treatment of several cancer types.

This morning, finally, good news: the European Medicines Agency has recommended Yondelis be approved by the European Comission, which means that the drug should be available to treat soft tissue sarcomas by the end of the year. I want to cite the words of José María Fernández Sousa (president of Zeltia), taken from the PharmaMar press release:

“This is excellent news. Firstly for the patients and their families, since a new therapeutic option is now available. Also for the PharmaMar and Zeltia employees who have devoted long years of effort and dedication in pursuit of this challenge. It is also excellent news for Spanish science as well as for the investigators from all over the world who have participated in the clinical trials and believed in the therapeutic potential of compounds of marine origin.”

I completely agree with him. Yondelis is the first anticancer drug developed and produced by a Spanish biopharmaceutical company. Hope more are coming.

(Image: left, a cluster of Ecteinascidia turbinata, photo courtesy of PharmaMar; right, structure of Yondelis)

Read the rest of the article >>>

Romans, dried figs and Streptomyces

In the year 79 AD, the Roman towns of Herculaneum and Pompeii were devastated by a terrible eruption of Mount Vesuvius. As a result, the towns were buried under many meters of volcanic ash, which left buildings, food remains and human bodies in a remarkable state of preservation. This allows to study the state of health of ancient Romans and its relationship to nutrition and other environmental conditions. For instance, analysis of human remains from Herculaneum showed lesions typically produced by tuberculosis and, especially, brucellosis. The high frequency of brucellosis has been related to the eating of contaminated cheese: Herculaneum had an important production of goat's milk and cheese. Remarkably, the study of carbonized cheese showed particles of the right size and shape, suggesting that they were bacteria of the Brucella group.

However, the Herculaneum inhabitants appeared to suffer few non-specific infections, which were common in antiquity due to poor sanitary conditions. A recent study suggests that people were protected against these infections due to consumption of dried fruits contaminated by antibiotic-producing Streptomyces!

The author of the work arrived to this conclusion through two kinds of experimental evidences:

First, examination of food remains under the microscope (both light and scanning electron) revealed the presence of virus and possible Salmonella on eggshells, and Saccharomyces in wine and bread. More important for us was the observation, under the skin of pomegranate seeds and figs, of a dense net of branching filaments resembling those of Streptomyces. These fruits were originally dried as a mode of preservation: Romans buried them in straw under a weight to achieve dehydration. This technique may explain the proliferation of Streptomyces. And we all know that Streptomycetes are prolific producers of antibiotics, right?

Second, histological study of bone samples from human remains (using a confocal microscope) showed presence of auto-fluorescence with characteristics typical of tetracycline-labeled bone occurring during life. Tetracycline antibiotics mark human bone, as it has been established for both modern and ancient humans. An example of tetracycline-labeled human bones was previously described from a cemetery in Sudanese Nubia dated 350-550 AD; in this case, a possible source of tetracycline was the grain stored in mud containers, which provided a proper environment for proliferation of Streptomyces.

I found that the paper and the whole story (mixing archeology and microbiology together) are fascinating. Of course, I'd certainly appreciate more experimental evidence concerning unequivocal identification of tetracycline in bones (could the fluorescence be due to any other molecule with similar properties but different to tetracycline?). And I wonder how common is tetracycline production among Streptomycetes. It would be very nice if the hypothesized conditions could be replicated, i.e. grow some figs and pomegranates (Roman style = "organically" produced?), and dry them using the Roman technique (ideally in the Herculaneum region). Then, try to detect tetracycline in the fruits. You can even isolate some Streptomycetes from the dried fruits, and screen the isolates for tetracycline production...

Reference:
Capasso, L. (2007). Infectious diseases and eating habits at Herculaneum (1st century AD, southern Italy). International Journal of Osteoarchaeology, 17(4), 350-357. DOI: 10.1002/oa.906

[Sadly, the author uses the word "mould" for Streptomyces, which is a bacterium, not a fungus. This mistake can still be found in medical and other technical literature]

(Image: Mosaic on a wall in the House of Neptune and Amphitrite, in Herculaneum, Italy. Source: Wikipedia)


UPDATE (September 3, 2010):
A scientific article has been published confirming the presence of tetracycline in the Nubian bones! The reference is:
Mass spectroscopic characterization of tetracycline in the skeletal remains of an ancient population from Sudanese Nubia 350–550 CE
Am. J. Phys. Anthropol. (2010) 143, 151-154.
DOI: 10.1002/ajpa.21340
(Found via Biounalm: Los antibióticos se usaban desde hace 2000 años?)


UPDATE (September 10, 2010):
See other blogs (in Spanish): Los nubios ya usaban antibióticos hace 2.000 años (Amazings.es), Una pinta de tetraciclina (Curiosidades de la Microbiología).

Read the rest of the article >>>

Natural products at Nature Chemical Biology

The current issue of Nature Chemical Biology is centered on natural products, with an emphasis on terpenes. I found the following articles most interesting:

• One pathway, many products, by M.A. Fischbach & J. Clardy [Nat. Chem. Biol. (2007) 3, 353-355]. Primary metabolic pathways make single products, while secondary pathways generally make a variety of products, not just one. Why?
  
• The function of terpene natural products in the natural world, by J. Gershenzon & N. Dudareva [Nat. Chem. Biol. (2007) 3, 408-414]. Terpenes are the largest class of natural products, and we are just beginning to understand the biological roles of a few of them.
  
• Mining and engineering natural-product biosynthetic pathways, by B. Wilkinson & J. Micklefield [Nat. Chem. Biol. (2007) 3, 379-386]. With the purpose of developing new therapeutic agents, recent advances in the field come from improved screening technologies, genome mining, expression of entire biosynthetic gene clusters in suitable hosts, gene synthesis, or directed evolution of enzymes.
  
• Plant endophytes as a platform for discovery-based undergraduate science education, by S.A. Strobel & G.A. Strobel [Nat. Chem. Biol. (2007) 3, 356-359]. Imaginative education projects have the potential to yield, as a bonus, direct scientific results. Superb.
  

Read the rest of the article >>>

Combinatorial biosynthesis, but not as we know it

Combinatorial biosynthesis can be understood as a special case of metabolic engineering, where genes responsible for individual metabolic reactions from different organisms are combined to generate hybrid metabolic pathways. An ideal result consists of a genetically-modified organism (or a collection of such microorganisms) that is useful for in vivo production of novel compounds. Nevertheless, there are examples of in vitro combinatorial biosynthesis (*), such as glycorandomization (a biocatalytic technique that uses purified enzymes to activate and attach sugars to natural products).

One step beyond, a recent report in ACS Chemical Biology describes a new in vitro approach for the generation of combinatorial libraries of compounds derived from natural products. As a proof of concept, the authors combined three type-III polyketide synthases (PKSs), 16 different precursors (acyl-CoA esters) and three post-PKS tailoring enzymes. Remarkably, this strategy was adapted to a convenient microarray format (30-nanoliter reactions), to enable high-throughput synthesis. Even better, the same microarray slide was used to screen for bioactivity of the synthesized products, through an assay for inhibition of human protein kinase FynT. This approach is, therefore, potentially useful for the identification of new non-natural compounds displaying biological activities.

Reference: Kwon SJ, Lee My, Ku B, Sherman DH, Dordick JS.
High-throughput, microarray-based synthesis of natural product analogues via in vitro metabolic pathway construction.
ACS Chem. Biol. 2007 May 25 (ASAP Article). PubMed link.

[(*) I understand that some people may prefer to keep the term "combinatorial biosynthesis" only for in vivo approaches. Perhaps they're right, but I view biocatalysis (in vitro utilization of purified enzymes for chemical transformations) as a special type of biosynthesis.]

[Another note: I'm not a Star-Trek fan, but I think that the line "It's life, Jim, but not as we know it" was told by the Doc to the captain on seeing new life on a strange planet. However, I didn't learn the line directly from Star Trek, but from an article titled "Life, Jim, but not as we know it"? Transmissible dementias and the prion protein, Br. J. Psychiatry (1991) 158: 457-4710, authored by PJ Harrison & GW Roberts. I got to know this article while learning about neurodegenerative diseases during my M.S. studies (uf, feels like late Pleistocene). It was such a great title for a story on prions, it just stuck in my mind.]

Read the rest of the article >>>

Actinomycetes, natural drug factories

Actinomycetes are Gram-positive bacteria with a high GC-content in their DNA. Among others, representative genera include Corynebacterium, Micrococcus, Mycobacterium, Nocardia, Propionibacterium, and Streptomyces. Many actinomycetes, such as Streptomyces, grow as branching filaments and live in soil, as fungi do. Because of this resemblance, actinomycetes were originally classified as fungi. This was reflected on their name, where "mycetes" comes from the Greek for "mushroom, fungus".

Some actinomycetes are pathogenic, such as Mycobacterium tuberculosis. However, many others are extremely useful due to their ability to produce compounds with pharmaceutical properties (antibiotic, antifungal, antitumor, immunosuppressive). The genus Streptomyces is well known precisely for this ability.

In this blog, I intend to post mainly about the biology of actinomycetes, especially those aspects related to the biosynthesis of natural products of pharmaceutical interest. However, I may occasionally deviate from the primary theme. There might be some microbiology, some biochemistry, some chemical biology, some genetics...

Oh, about the title: "Twisted Bacteria". No, it's not that they are "perverted" (although some times we researchers in the field may think so...). The title was inspired by the word "Streptomyces", where "strepto" comes from the Greek for "twisted, twined".

(Image: Streptomyces sp. under the microscope. CDC/Dr. David Berd, Public Health Image Library)

Read the rest of the article >>>