Another highly radiation-resistant bacterial species

Perhaps you recall that just about a year ago research identified some of the mechanism by which what was long thought to be unique species of bacterium – Deinococcus radiodurans – managed to survive extremes of exposure to radiation and dessication.

Now it turns out that the species isn't so unique, and a distant relative also has exceptional durability, despite significant genetic differences:

Second Extremely Resistant Bacteria Sequenced Is Surprisingly Different From First

Researchers have completed the whole-genome sequence of Deinococcus geothermalis, which is only the second extremely radiation- and desiccation-resistant bacterium to be sequenced.

The first was for the Guinness World Records-holder Deinococcus radiodurans, which for 50 years has been the subject of extensive investigations aimed at solving the mystery of how this microbe and its close relatives survive immense doses of x-rays and gamma-rays.

Most surprisingly, many of the unique D. radiodurans genes that were strongly implicated in resistance over the last decade have turned out to be unrelated to its survival, and are not present in D. geothermalis.

However, now that complete genome sequences are available, it turns out that the genes they have in common to account for their durability are surprisingly few:

Using computer-based systems to compare the D. geothermalis genome sequence with the sequence of D. radiodurans, a minimal set of genes which encode extreme resistance was defined. Far fewer genes than initially believed appear to be responsible for the extreme resistance trait.

Among other things, this finding apparently rules out one possible source of the durability:

The phenomenal resistance of Deinococcus bacteria has given rise to numerous descriptions of their origin, including that they evolved on Mars under harsh cosmic radiation. The present analysis firmly places the origin of Deinococcus bacteria on Earth, where the evolutionary steps that led to their survival mechanisms clearly occurred in their terrestrial ancestors - most likely in a desert near you.

Tags: microbiology, extremeophiles

Researchers Find Smallest Cellular Genome

Here's another thing to remember in case you're at a party and running our of conversational ideas. The living creature (other than viruses) with the smallest number of genes is the bacterium Carsonella ruddii – just 182 genes and 159,662 base-pairs of DNA.

Researchers Find Smallest Cellular Genome

The bacteria Carsonella ruddii has the fewest genes of any cell. The bacteria's newly sequenced genome, the complete set of DNA for the organism, is only one-third the size of the previously reported "smallest" cellular genome.

"It's the smallest genome -- not by a bit but by a long way," said co-author Nancy A. Moran, UA Regents' Professor of ecology and evolutionary biology and a member of the National Academy of Sciences. "It's very surprising. It's unbelievable, really. We would not have predicted such a small size. It's believed that more genes are required for a cell to work."

Carsonella ruddii has only 159,662 base-pairs of DNA, which translates to only 182 protein-coding genes, reports a team of scientists from The University of Arizona in Tucson and from Japan.

Of course, C. ruddii is cheating a little. It lives only in certain specialized cells of a sap-eating insect (Pachypsylla venusta). The bacterium has no genes needed for certain enzymes (required for replication) and nutrients such as folic acid, so it must rely on its host for these. Consequently, C. ruddii is not a good guide for identifying a minumum set of genes needed for a free-living organism.

If you want to sound really well-informed about this, here are some other things to read:

Bacteria boast the 'tiniest genomes' to date – New Scientist

Tiny Genome May Reflect Organelle in the Making – Scientific American

Smallest Genome of Living Creature Discovered – LiveScience

The 160-Kilobase Genome of the Bacterial Endosymbiont Carsonella and The Bacterial World Gets Smaller – Science [subscription rqd. for full access]

Tags: conversational ideas

Self-resurrecting bacteria

Who said resurrection is impossible? One species of bacterium, Deinococcus radiodurans, can do it — but it's the only case known.

Cheating DNA Death: How an Extremophile Repairs Shattered Chromosomes

Fifty years ago, scientists uncovered a microbe capable of withstanding radiation in canned meat that had been bombarded with gamma rays. Named Deinococcus radiodurans — or "strange berry that withstands radiation" — the microorganism can survive doses of radiation up to 500 times that which would kill a human. These doses shatter D. radiodurans's DNA — just as they would in a human — but the microbe can repair its broken DNA and spring back to life within hours, depending on the dose. Researchers in France have finally determined how the most durable of extremophiles manages this trick. "We have discovered the mechanism by which a clinically dead cell resurrects back to life," explains Miroslav Radman of INSERM, France's public biomedical research institution. "This extreme radiation resistance is but a by-product of its selection for resistance to desiccation."

It's taken microbiologists 50 years, but the details of how D. radiodurans accomplishes the feat of resurrection have finally been figured out. Well, almost all the details.

When any type of cell is exposed to enough toxic chemicals, oxidative damage, high levels of ionizing radiation, or dehydration, what kills the cell is the fragmentation of its DNA. Without intact DNA, a cell can't manufacture proteins required to sustain its life. What D. radiodurans seems uniquely capable of doing is putting all of its fragmented DNA back together, and in just the right order. Something that all the king's horses and all the king's men could not do for Humpty Dumpty.

It turns out there are two stages to this process. In the first stage, the short fragments of (single-stranded) DNA are gradually reassembled into longer and longer pieces, until they are complete again. This is possible at all only because of the unique structure of DNA — DNA segments will stick together only when they have precisely matching base sequences in common. The process is facilitated in bacterial DNA by an enzyme called DNA polymerase I. The enzyme is encoded by a gene known as polA, which is present in all prokaryotes. However, the DNA polymerase I found in D. radiodurans apparently performs its job much more efficiently than its analogue in other bacteria. This natural process is similar to the laboratory process known as polymerase chain reaction (PCR), which also uses a polymerase enzyme.

But it's the second stage that is really special in D. radiodurans, and which has just been elucidated in the latest research:

... single long strands of DNA do little to resurrect the microorganism until the second stage of the newly discovered process kicks in: the simple pairing discovered by Watson and Crick decades ago — adenine (A) bonds with thymine (T), and cytosine (C) bonds with guanine (G). By inserting a special version of the nucleotide thymine that only binds to single strands of DNA — known as 5-bromodeoxyuridine — the researchers could observe as the single strands bonded with complementary strands to form complete chromosomes. "Once the chromosome is functional, the synthesis of all cellular components starts, and the cellular life is back," Radman says.

Interesting questions remain unanswered. An obvious one is how this unique capability of D. radiodurans evolved. Of course, it's obvious that the capability is highly advantageous to the survival of any microbe that inhabits an extreme environment. But there are few, if any, environments on Earth that have the level of ionizing radiation in which D. radiodurans can survive. So there must have been some other extreme feature of the environment, like toxic chemicals or frequent dessication. But then, why don't many other kinds of bacteria have the same abilities as D. radiodurans? Perhaps something even stranger happened, and D. radiodurans evolved in an environment outside Earth, with much more radiation — like Mars — and later migrated to Earth on a meteorite.

Another important question is: what makes the form of DNA polymerase in D. radiodurans so special and efficient? Knowing this could be very useful, for instance if we wanted to endow other bacteria with the same kind of survivability in extreme environments. We might want to do that to create bacteria that could detoxify toxic wastes.

Eukaryotic cells (found in "higher" animals than bacteria) use a different type of DNA polymerase than what prokaryotes use, and they are much more complex in general than bacteria. But yet another interesting question is whether it is possible to endow eukaryotic cells with a more effective DNA repair capability.

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Further information:

Microbe probe -- announcement of earlier (2001) research on D. radiodurans

Radiation-resistant organism reveals its defense strategies -- announcement of earlier (2003) research on D. radiodurans

Deinococcus radiodurans -- History and summary of research on D. radiodurans

D. radiodurans -- links to more information on D. radiodurans

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Tags: biology, microbiology, extremeophiles