Genetics of microbes

[kitkat]

How is science ever going to build an accurate database on microbes if they are constantly changing due to HGT? Don't they obtain a new identity with new genes added to them or genes they give away?

 

These critters are mind boggling and they are a continuous source of frustration because they are involved in everything from life to non life in chemical reactions. We cannot solve the mysteries surrounding our DNA until we understand their DNA that is a big part of our beings.

[Mr Skeptic]

Horizontal gene transfer doesn't create new genetic information, it mostly just shuffles it around. But yes, with microbes we have to abandon the idea of a species and focus on "strains" instead.

[kitkat]

Horizontal gene transfer doesn't create new genetic information, it mostly just shuffles it around. But yes, with microbes we have to abandon the idea of a species and focus on "strains" instead.

 

So then is HGT just a reaction that causes genes to be shuffled around. Moved genes allows different reactions that otherwise was not an option prior to HGT. Is HGT done deliberately by the microbe for a reason or because they were in close enough contact with each that HGT is unavoidable?

 

If this is the case, wouldn't HGT interfere with the replicating ability of the microbe?

[CharonY]

HGT allows shuffling of genes between species. This is indeed a problem for taxonomic approaches. This is why most focus on conserved genes as e.g. the 16srRNA gene. Traditionally a new species was assumed when DNA hybridization between strain was less than around 70-75% similar (forgot the actual value). Phylogenetic trees with 16srRNA genes tend to correlate well with that. I disagree that we have to abandon the notion of species in bacteria completely, for most purposes it is quite useful. But it makes it indeed harder.

One particular challenge is thus to distinguish the phylogenetically "old" backbone from more recent HGT events. There are groups that have specialized in looking into that.

[Mr Skeptic]

Is HGT done deliberately by the microbe for a reason or because they were in close enough contact with each that HGT is unavoidable?

 

Yes and yes. Bacterial conjugation is "purposeful" exchange, transduction due to genes transferred by bacteriophages (viruses), and transformation from DNA acquired from the environment (from broken bacterial cells for example).

[CharonY]

It is not really an active process initiated by the cell (purposefully, whatever it may mean) in all cases. Some are (e.g. natural transformation, conjugation) but the above example of bacteriophage is an example of mobile genetic elements hijacking the cell. An example of egoistic genes, if you want. And they can combine. E.g. a plasmid may be acquired by conjugation but carries a transposon and the latter then jumps into the chromosome. In fact, one could also argue that conjugation is not done deliberately as the plasmids carry the function necessary for that. As such one could argue even plasmids, similar to viruses utilize cells to proliferate.

[kitkat]

It is not really an active process initiated by the cell (purposefully, whatever it may mean) in all cases. Some are (e.g. natural transformation, conjugation) but the above example of bacteriophage is an example of mobile genetic elements hijacking the cell. An example of egoistic genes, if you want. And they can combine. E.g. a plasmid may be acquired by conjugation but carries a transposon and the latter then jumps into the chromosome. In fact, one could also argue that conjugation is not done deliberately as the plasmids carry the function necessary for that. As such one could argue even plasmids, similar to viruses utilize cells to proliferate.

 

So are plasmids the initiator for bacteria to acquire new methods of adapting to a changing environment?

All of the literature regarding HGT and the language that is used to describe it is that this is how bacteria swap genes with each other. Shuffling them does not mean transfer. The literature also suggests that HGT is done deliberately for increasing their ability to survive with this new gene.

[CharonY]

Yes, the respective function are usually encoded in the plasmid, in some strains they get incorporated into the chromosome, though.

 

The literature also suggests that HGT is done deliberately for increasing their ability to survive with this new gene.

This then is either poor literature or cited out of context. Plasmids can encode additional functions that increase fitness, but it costs the cell to replicate. Of course, to survive the genetic elements cannot harm the cell too much and often only those genetic elements survive that actually are eventually of benefit, However, it is not that bacteria actively utilize every scrap of DNA there is. Quite the contrary, they have an elaborate restriction system that destroys much of foreign DNA that gets into the cell.

 

In short, HGT does not automatically result in a fitness increase. Shuffling is an appropriate term if you go away from a species-defined gene pool, to a gene pool accessible to the respective mobile genetic elements. As they may pick up bits and pieces from their hosts they reshuffle the genetic content within their host range. The individual species may acquire traits that they did not have before. For HGT it is necessary to go away from species-centric viewpoint towards a gene focused one. Again the egoistic gene is a very simple model for starters.

[Blahah]

HGT allows shuffling of genes between species. This is indeed a problem for taxonomic approaches. This is why most focus on conserved genes as e.g. the 16srRNA gene. Traditionally a new species was assumed when DNA hybridization between strain was less than around 70-75% similar (forgot the actual value). Phylogenetic trees with 16srRNA genes tend to correlate well with that. I disagree that we have to abandon the notion of species in bacteria completely, for most purposes it is quite useful. But it makes it indeed harder.

One particular challenge is thus to distinguish the phylogenetically "old" backbone from more recent HGT events. There are groups that have specialized in looking into that.

 

I believe the American Type Culture Collection defines species delimitation at 97% similarity. SGM uses the same definition. It's just a working definition though, in practice the species concept is false for prokaryotes. It is useful, which is why it's kept around, but I think it would be better to have (and expect a move towards) a new taxonomic nomenclature for prokaryotes, more similar to that used for viruses which actually accounts for the unique properties of the systematics of the clade.

[SMF]

I learned from reading Lynn Margules that horizontal gene transfer is bacterial sex without procreation. SM

[CharonY]

I believe the American Type Culture Collection defines species delimitation at 97% similarity.

Are you sure that they refer to genome hybridization and not e.g. 16S similarity?

[Blahah]

Are you sure that they refer to genome hybridization and not e.g. 16S similarity?

I can't actually find the ATCC definition, I just remember it from lectures. However, you are right, it's almost certainly 16SrRNA. I wasn't even aware of DDH until I read your reply (before my time!).

 

It seems the traditional DDH threshold was 70%:

 

The evaluation showed that the resulting averages reflected the degree of evolutionary distance between the compared genomes, and a value of 94% identity could represent the DDH boundary of 70% (Richter & Rosselló-Móra, 2009).

Richter, Michael, and Ramon Rosselló-Móra. 2009. Shifting the genomic gold standard for the prokaryotic species definition. Proceedings of the National Academy of Sciences.doi:10.1073/pnas.0906412106.

 

confusingly, whilst trying to learn about DDH, I came across this paper which doesn't seem to distinguish between hybridisation and 16S:

 

Genetic divergence can be measured by 16S RNA sequencing or DNA–DNA hybridization. A divergence of ≈5% is required for two bacteria to be considered of different species (de la Cruz & Davies, 2000).

de la Cruz, Fernando, and Julian Davies. 2000. Horizontal gene transfer and the origin of species: lessons from bacteria. Trends in Microbiology 8, no. 3 (March 1): 128-133. doi:10.1016/S0966-842X(00)01703-0.

Edited February 13, 2011 by Blahah

[ewmon]

I learned from reading Lynn Margules that horizontal gene transfer is bacterial sex without procreation. SM

Yes. I see "sexual reproduction" as "sexual" (ie, new genetic combinations) together with "reproduction" (ie, new individuals). So, HGT is "sexual" without being "reproduction", cloning (natural or otherwise) is "reproduction" without being "sexual", and "sexual reproduction" is both.

[CharonY]

confusingly, whilst trying to learn about DDH, I came across this paper which doesn't seem to distinguish between hybridisation and 16S:

 

I agree, the language was a bit inaccurate in that sentence.