Why do bacteria insert their genes into a host?

[mark!]

"Acute myeloid leukaemia cells were particularly rife with bacterial sequences. A third of the microbial genes came from a genus called Acinetobacter, and had been inserted into the mitochondrial genome.

"Stomach cancer cells also contained lots of bacterial DNA, especially from Pseudomonas. Most of this DNA had been inserted into five genes, four of which were already known to be proto-oncogenes that can give rise to cancer, emphasizing a possible link between LGT and cancerous growth".

“We know already that a significant proportion of cancers are due to insertion of genetic material from viruses,” said Etienne Danchin from the French National Institute for Agricultural Research. “But this is the first time, as far as I know, that horizontal gene transfer from bacteria could be suspected as a cause of cancer.”

Source: https://www.the-scientist.com/news-opinion/bacterial-dna-in-human-genomes-391471) Does anybody know why bacteria show this (retro)virus-like behaviour?

2) Which bacterial species (don't) do this?

3) What type of genes are inserted?

4) How does this process go about, by using (selfish/parasitic) transposons in their plasmids (i.e. replicative transposition)?

 

[BillTre]

It might be more fruitful to ask about the cells receiving the inserted DNA.

Cancer cells are the cells cells receiving the inserted DNA in your post, not normal cells. They cancer cells often are unusual in how they take care of themselves (such as their DNA repair mechanisms) and might be more susceptible to picking up DNA from their environment.

I would guess the bacteria they are getting the DNA from are those in the environment of the body which they reside. They might be getting the DNA from dead bacteria just laying around in the area.

From the little you posted, it looks like it is more significant where the bacterial DNA went in the cancer cells (in to oncogenes, genes that when mutated can be involved in causing cancer) than what the inserted genes code for. Almost any sequence inserted into a functioning gene will disrupt its normal function, which in cancer genes (oncogenes) could result in cancer.

Cells made cancerous by a mutation will be positively selected with in its organism's body (because it is reproducing more rapidly, as cancer cells typically do). This will result in ore cells inheriting these mutations when surveyed at a later time (after the cancer cells have had time to proliferate).

These kinds of insertions will not usually be inherited from parents (they would have to get into gametes (eggs or sperm) and the organism would have to reproduce for them to be passed onto offspring), but will be formed in a single life time.

 

[mark!]

I have done a bit of research, and found some new information to better determine the answer the the question regarding the origin of giant viruses: it involves transpovirons.

Transpovirons are linear plasmids in a girus. Based on the phylogenetic analysis of the helicase domain the discoverers of PLVs (Polinton Like Viruses) concluded that transpovirons evolved from PLV via the loss of several genes including those encoding the morphogenetic module proteins. https://en.wikipedia.org/wiki/Transpoviron.
Polintons were the first group of eukaryotic double-stranded DNA viruses to evolve from bacteriophages and that they gave rise to most large DNA viruses of eukaryotes and various other selfish genetic elements. https://www.nature.com/articles/nrmicro3389 .
The Mavirus shows by far the closest affinity with the Polintons among the currently known viruses, and accordingly, it has been proposed that the Polintons evolved from the virophages. https://virologyj.biomedcentral.com/track/pdf/10.1186/1743-422X-10-158. (Virophages, such as Sputnik, are even smaller viruses that use the machinery of giant viruses to replicate).

Also, the origin of viral replicative modules seems likely to hark all the way back to the precellular era. At that stage, some of these primordial replicators coalesced and gave rise to the first cellular genomes, whereas others became genetic parasites. Conceivably, however, such parasites gave rise to true viruses only after the emergence of cells.https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5373398/

This leads me to ask a few other questions:

1) From virus to host genome, or vice versa?
Why scientists argue whether transposons in our genome came from viruses, but not the other way around?
https://link.springer.com/article/10.3103/S0891416818040067
Same with polydnavirus of wasps, two proposals have been advanced for how the wasp/virus association developed. The first suggests that the virus is derived from wasp genes.
https://en.wikipedia.org/wiki/Polydnavirus

2) Girus machinery
The transposon 'Alu' is a SINE (Short Interspersed Nuclear Element).
Most SINEs do not encode any functional molecules and depend on the machinery of active L1 elements (L1 = LINE, or Long Interspersed Nuclear Element) to be transposed; that is, copied and pasted in new locations. https://www.biology-pages.info/T/Transposons.html
The virophages do not have the necessary enzymes to replicate on their own. Virophages use the giant viral replication machinery to replicate their own genomes and continue their existence. https://en.wikipedia.org/wiki/Virophage
What exactly is this girus machinery?

3) Transposase clean-up
What happens to transposase after a transposon has been inserted? How is it cleaned or get rid of?
And 'composite transposons' have two Transposase genes on each side. Which one is used for replication?

4) Transduction
Does 'transduction' always involve a plasmid moving through a pilus? Or does genetic material also flow from one bacterium to the other (through budding off?) without using a pilus, but simply a plasmid flowing through the empty space between two bacteria (just like the autoinducers in quorum sensing)?
And does a transposon on a plasmid of a donor bacterium go to the plasmid of the recipient, and then from that second plasmid to the recipient bacterium, or does that initial plasmid go directly to the bacterial genome?

5) Heterochromatin
Many noncoding genetic material (such as transposons) are located on the heterochromatin region of a chromosome (although not all of it, such as MITEs, which are located in the euchromatin region). But I'm a bit confused, is heterochromatin a part of a chromosome, or a location in the nucleus? Images on the web show that heterochromatin is the (outer) location inside nucleus, but also the centromeric (inner) region on a chromosome https://geneticeducation.co.in/role-of-transposons-in-evolution/. So if the centromere (and telomeres) part of the chromosome lie closer to the center of the nucleus (euchromatin), closer to the nucleolus, and the midpoint of all 4 arms lie more to the center of the nucleus that its outer parts, does this mean then that chromosomes don’t have their recognizable X-shape?

If anyone knows the answer to any of these 5 questions, thanks in advance for answering them!