The most common marker so far has been a gene that confers resistance to Kanamycin, an antibiotic that belongs to a group of valuable antibiotics. Even if it is itself not used much today, it is closely related to valuable antibiotics. And there is a tendenency for cross resistance. That is resistance to Kanamycin may also confer resistance to its relatives. It is suspected that the antibiotic gene markers might lead to an increase of the numbers of bacteria that are resistant to the antibiotic.
Promoter genes are natural parts of chromosomes.
Their function is to enhance the activity of a certain gene. Normally these are under the control of regulator genes that turn them on and off. But in genetic engineering the corresponding regulators are normally not present as the promoter comes from an other species. This means that the promoter will exert a strong and persistent stimulating influence on the Trait Gene. This is basically unnatural as normally the activities of all genes are regulated in response to the conditions in the cell.