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 Post subject: fourth domain of life
PostPosted: Wed Aug 03, 2016 10:15 am 
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DAILY NEWS 18 March 2011
Biology’s ‘dark matter’ hints at fourth domain of life

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Step far enough back from the tree of life and it begins to look quite simple. At its heart are just three stout branches, representing the three domains of life: bacteria, archaea and eukaryotes. But that’s too simple, according to a band of biologists who believe we may be on the verge of discovering the fourth domain of life.

The bold statement is the result of an analysis of water samples collected from the world’s seas. Jonathan Eisen at the University of California, Davis, Genome Center has identified gene sequences hidden within these samples that are so unusual they seem to have come from organisms that are only distantly related to cellular life as we know it. So distantly related, in fact, that they may belong to an organism that sits in an entirely new domain.

Most species on the planet look like tiny single cells, and to work out where they fit on the tree of life biologists need to be able to grow them in the lab. Colonies like this give them enough DNA to run their genetic analyses. The problem is, the vast majority of these species – 99 per cent of them is a reasonable bet – refuse to be cultured in this way. “They really are the dark matter of the biological universe,” says Eisen.

Life’s dark matter
To probe life’s dark matter, Eisen, Craig Venter of the J. Craig Venter Institute in Rockville, Maryland, and their colleagues have resorted to a relatively new technique called metagenomics. This can “sequence the crap out of any DNA samples”, whether they are collected from the environment or come from lab cultures, says Eisen.

When Eisen and Venter used the technique on samples collected from the Global Ocean Sampling Expedition, they found that some sequences belonging to two superfamilies of genes – recA and rpoB – were unlike any seen before.

“The question is, what are they from?” says Eisen. Because the team has no idea what organism the genes belong to, the question remains unanswered. There are two possibilities, he says. “They could represent an unusual virus, which is interesting enough. More interestingly still, they could represent a totally new branch in the tree of life.”

The exciting but controversial idea has met with mixed reactions. “It’s a very good piece of careful work,” says Eugene Koonin at the National Center for Biotechnology Information in Bethesda, Maryland.

Younger than they look?
But Koonin and others think any talk of a fourth domain of cellular life is premature. Radhey Gupta at McMaster University in Hamilton, Ontario, Canada, calls the finding “very exciting”, but cautions that there are other explanations.

For instance, the sequences could be from cellular organisms living in unique habitats that caused their genes to undergo rapid evolution. That would give the false impression that the “new” life forms diverged from all others a very long time ago.

“There is still debate [over] how to clearly distinguish the three proposed domains of life, and how they are interrelated,” Gupta says. “The suggestion [of] a fourth domain will only add to the confusion.”

Eric Bapteste at Pierre and Marie Curie University in Paris, France, is far more receptive. “The facts are that there is lots of genetic diversity, and unquestionably most of it is unknown to us,” he says. “It’s legitimate to consider that there’s genuinely new stuff out there.”

Further analysis of the samples could determine whether the two gene families studied have evolved unusually rapidly or are from a cellular organism with a universally bizarre genome, he says.

Parent organism
Looking at the actual samples could also help pin down exactly which organism the strange genetic sequences belong to, says Eisen.

If Eisen’s gene sequences did turn out to belong to a new domain of life, it wouldn’t be the first time the tree of life has had to be redrawn. Until the 1990s, it had just two branches: one for eukaryotes – animals, plants, fungi and some other strange forms, including the slime moulds – and one for everything else. Then, gene analysis revealed that the “everything else” branch could be divided into two domains: bacteria and archaea.

Not only that, some believe that mimivirus, the largest known virus, may also represent a new domain of life: despite being recognised as a virus, it contains many genes found only in cellular organisms. “People have suggested they might be a fourth branch themselves,” says Eisen. “If you think of those mimiviruses as a fourth branch, maybe our sequences represent a fifth branch – we just don’t know yet.”

Journal reference: PLoS One, DOI: 10.1371/journal.pone.0018011

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PostPosted: Wed Aug 03, 2016 10:19 am 
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DAILY NEWS 23 June 2016
New life form discovered in saliva is linked to human disease

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By Andy Coghlan

Parasitic bacteria that are entirely dependent on the other bacteria they infect have been discovered for the first time, in human spit. The tiny cells have gone undetected for decades, but appear to be linked to gum disease, cystic fibrosis and antimicrobial resistance.

We only know of one other strain of bacteria that can infect other bacteria, but this type, called Bdellovibrio, is a free-living cell that hunts down its prey. The newly discovered organism has very few genes and is dependent entirely on its host.

The parasite, which appears to make its host more harmful to humans, evaded our detection until now because it is difficult to grow and study in the laboratory.

“They’re ultra-small bacteria, and live on the surface of other bacteria,” Jeff McLean of the University of Washington School of Dentistry in Seattle told the annual meeting of the American Society for Microbiology in Boston, Massachusetts, last week.

Unlike any known species
McLean and his colleagues discovered the organisms by searching for bacterial strains in human saliva samples. Analysing the DNA of all the species they managed to grow from these samples, they came across a mystery fragment of genetic material. This piece of RNA had been discovered by other researchers before, but no one could tell what organism it came from.

McLean’s team has now shown that this RNA belongs to a bacterium that lives on another species, Actinomyces odontolyticus. When the researchers viewed this species under the microscope, they found that the cells were covered with much smaller bacteria – the first species ever discovered to parasitise another bacterium.

At first, Actinomyces is able to tolerate the parasites, which attach themselves to its outer membrane, drawing nutrients out of their host.

“Later, they start attacking and killing the host,” said McLean. Towards the end of the infection process, holes seem to form in the membrane of the Actinomyces cell and its contents gush out. “We’re trying to decipher what’s going on,” he said.

The parasitic bacterium is unlike any previously known species. It has just 700 genes and is the first bacterial strain identified that cannot make its own amino acids – the building blocks for the proteins essential to life – but depends instead on a supply from its host. By comparison, A. odontolyticus has 2200 genes.

Tip of the iceberg
This discovery explains why the species has never been seen before: it can only be grown in the laboratory alongside a host. McLean suspects A. odontolyticus is not this parasite’s only host, and that many other types of tiny parasitic bacteria may exist.

“This microbe is clearly the tip of the iceberg,” suggests Roland Hatzenpichler of the California Institute of Technology in Pasadena.

“It’s incredibly exciting to see such a major advancement in the study of major lineages of life that until now have been impossible to cultivate,” says Brian Hedlund of the University of Nevada, Las Vegas. “Gene data from other as-yet uncultivated organisms suggests that host-parasite relationships between microbes are common in nature, so this type of study is a great template for others to follow.”

Disease and antibiotic resistance
We might find that these species have an important role in human diseases. McClean says he has found high concentrations of the new bacterium’s DNA in people who have gum disease or cystic fibrosis.

Actinomyces bacteria are known to contribute to gum disease, but are usually kept under control by white blood cells called macrophages, which engulf and destroy them. McLean says he has evidence that when these bacteria are infected with the parasite, they can evade these macrophages and make gum disease worse.

In previous work, the team had identified a type of bacterium that infects some members of the archaea – a different type of single-celled life that is genetically distinct from bacteria, but similar in its lack of a true cell nucleus and other complex cell machinery.

The two parasitic bacteria also both somehow make their host cells become resistant to the antibiotic streptomycin – another finding that may prove important in the midst of our present antimicrobial-resistance crisis.

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