Horizontal gene transfer

Understanding the personalities of bacteria

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Bacteria are as individual as people, according to new research by Professor Peter Young and his team in the Department of Biology at the University of York. Bacteria are essential to health, agriculture and the environment, and new research tools are starting to shed more light on them.

The York team dug up a square metre of roadside verge on the University campus in search of a bacterium called Rhizobium leguminosarum. The name means “root dweller of the legumes”, and these bacteria are natural fertilizer factories that extract nitrogen from the air and make it available to peas, beans, clover and their wild relatives.

In the laboratory, the team extracted the bacteria from the plant roots and established 72 separate strains. They determined the DNA sequence of the genome of each strain. Their research, published today in Open Biology, shows that each of those 72 strains is unique – each has different and is capable of growing on different food sources.

People are unique because each of us inherits half our genes from our mother and half from our father, but bacteria reproduce by binary fission, making two identical daughters. What are good at, though, is passing packages of genes from one cell to another. It is this process of horizontal gene transfer that made every rhizobium unique.

“We can think of the as having two parts,” says Professor Young. “The core genome does the basic housekeeping and is much the same in all members of the species, while the accessory genome has packages of genes that are not essential to the operation of the cell, but can be very useful in coping with aspects of the real world.

“Bacteria are like smartphones. Each phone comes out of the factory with standard hardware and operating system (core genome), but gains a unique combination of capabilities through apps (accessory genes) downloaded through the internet (by ).”

We increasingly recognise the vital roles played by bacterial communities, such as those in our gut or on the roots of plants. Many researchers have used variation in a standard core gene to draw up lists of the species in a community, but the new research shows that a list of names is not sufficient.

“There may be 300 people called Baker in your city, but you can’t assume that there are 300 people baking bread,” explains Professor Young.

It is possible, with more sequencing effort, to look at all the genes in a bacterial community – an approach called “metagenomics” – but to understand how they are functioning we also need to know which genes occur together in the same bacterium. This new study helps us to understand the way in which bacterial genomes are assembled.

Read more at: http://phys.org/news/2015-01-personalities-bacteria.html#jCp

Bacterial Gene Transfer Gets Sexier.

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Mycobacterium smegmatis can donate larger portions of its genome to other bacteria than previously thought, approaching the level of gene shuffling seen in sexual reproduction.

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n what appears to be a novel form of bacterial gene transfer, or conjugation, the microbeMycobacterium smegmatis can share multiple segments of DNA at once to fellow members of its species, according to a study published today (July 9) in PLOS Biology. The result: the generation of genetic diversity at a pace once believed to be reserved for sexual organisms.

“It is a very nice study providing clear evidence that, in Mycobacterium smegmatis at least, conjugation underlies much of species diversity,” said Richard Meyer, who studies conjugation at The University of Texas at Austin, in an email toThe Scientist.

Traditionally, transfer of genetic material through conjugation has been considered an incremental process. Plasmids mediate the transfer of short segments of DNA, one at a time, between pairs of touching bacterial cells, often conferring such traits as antibiotic resistance.

But M. smegmatis, a harmless bacterium related to the pathogen M. tuberculosis, appears to use a more extensive method of gene shuffling, endowing each recipient cell with a different combination of new genes. The researchers dubbed this form of conjugation “distributive conjugal transfer.” “We can generate a million [hybrid bacteria] overnight, and each of those million will be different than each other,” said coauthor Todd Gray, a geneticist at the New York State Department of Health’s Wadsworth Center.

Coauthor Keith Derbyshire, also a geneticist at the Wadsworth Center, and colleagues had previously published data indicating that M. smegmatis used a novel form of conjugation, but the new study confirms and expands on their suspicions using genetic data. The researchers compared the whole genome sequences of donor and recipient bacteria before and after the massive gene transfers.

The researchers found that, after the transfers, up to a quarter of the recipient bacteria’s genomes were made up of donated DNA, scattered through the chromosomes in segments of varying lengths.

According to the authors, the diversity resulting from distributive conjugal transfer approaches that achieved by meiosis, the process of cell division that underlies sexual reproduction. “The progeny were like meiotic blends,” said Derbyshire. “The genomes are totally mosaic.”

The genes and machinery behind distributive conjugal transfer remain largely unknown, but Gray, Derbyshire, and colleagues have zeroed in on a region of the genome that may determine whether a bacterium becomes a DNA donor or recipient. The region encodes the ESX-1 family of proteins, which are also involved in secreting molecules from M. tuberculosis that give the bacterium its pathogenicity.

The researchers suspect distributive conjugal transfer is important in multiple species of Mycobacteria. Earlier this year, Roland Brosch, a tuberculosis researcher at the Pasteur Institute in France, and colleagues sequenced various strains of the pathogenic M. canettii, which is closely related to M. tuberculosis, and found they were genetically variable—possible evidence of distributive conjugal transfer, according to Gray and Derbyshire. Brosch said he had not yet been able to demonstrate distributive conjugal transfer in M. canettii, however, and he noted that such large-scale gene transfer is unlikely to be occurring in M. tuberculosis, which is a highly genetically homogenous species that shows little sign of recent horizontal gene transfer.

Brosch agreed with Derbyshire and Gray that distributive conjugal transfer could have been important in the evolutionary history of the Mycobacteria genus as a whole, however.  Gray pointed out that understanding the prevalence of distributive conjugal transfer could change views on the time scale of mycobacterial evolution. “I think it’s really going to open some eyes about how quickly things can change,” he said.

Asked whether distributive conjugal transfer could be happening in bacteria outside of theMycobacterium genus, Derbyshire said it remained a mystery, but added: “It’s likely to be more prevalent than currently is known.”

T.A. Gray, “Distributive conjugal transfer in Mycobacteria generates progeny with meiotic-like genome-wide mosaicism, allowing mapping of a mating identity locus,” PLOS Biology, 11: e1001602, 2013.

Source: the-scientist.com

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sexual reproduction , mycobacteria, DNA sequencing, diversity, conjugation, bacterial evolution andbacteria