General Information/IS and Gene Expression

Another important aspect of IS impact on their bacterial hosts is their ability to modulate gene expression. In addition to acting as vectors for gene transmission from one replicon to another in the form composite transposons (two IS flanking any gene; Fig.2.3) and tIS (Fig.8.1) and their ability to interrupt genes, it has been known for some time that IS can also activate gene expression. This capacity has recently received much attention due to the increase in resistance to various antibacterials, a worrying public health threat.

They can accomplish this in two ways: either by providing internal promoters whose transcripts escape into neighboring DNA or by hybrid promoter formation. Many IS carry -35 promoter components oriented towards the flanking DNA (Fig.18.1). In a number of cases this plays an important part in their transposition since a significant number of IS transposes using an excised transposon circle (Fig.18.1) with abutted left and right ends. For these IS, the other end carries a -10 element oriented inwards towards the Tpase gene. Together with the -35, this generates a strong promoter on formation of the circle junction to drive Tpase expression required for catalysis of integration (Fig.18.2) . Thus if integration occurs next to a resident -10 sequence, the IS -35 sequence can contribute to a hybrid promoter to drive expression of neighboring genes [see ]. At present this phenomenon had been reported to occur with over 30 different IS in more than 17 bacterial species (Table IS and Gene Expression below). Indeed, specific vector plasmids have been designed to identify activating insertions (e.g. ).

IS activity can affect efflux mechanisms resulting in increased resistance: IS1 or IS10 insertion can up-regulate the AcrAB-TolC pump in Salmonella enterica; IS1 or IS2 insertion upstream of AcrEF and IS186 insertional inactivation of the AcrAB repressor, AcrR, in Escherichia coli , all lead to increased resistance to fluoroquinolones. Insertional inactivation of specific porins can also play a significant role.

Fig.18.1. Copy out paste in (DDE).Left column. Illustrates the copy out paste in the transposition mechanism. The transposon is represented as a yellow line. Flanking sequences in the donor molecule are blue. Flanking sequences in the target molecule are green. Red circles indicate 3′OH moieties generated by Tpase-catalyzed hydrolysis at the transposon end(s). Red boxes indicate target DNA flanks that are duplicated on insertion. Top to bottom: Tpase catalyzed cleavage at the 3′ transposon ends using H2O as the nucleophile. Liberated 3′OH attack the opposite end to create a bridged molecule which then undergoes replication (dotted line) to generate a circular transponso copy and regenerate the donor molecule. The circle intermediate undergoes cleavage to generate two 3'OH ends which attack the target DNA in a staggered way resulting in integration. Repair at each end then generates the direct target repeat characteristic of many transposons. Right column. Formation of hybrid promoters by copy out -paste in transposition. The left and right terminal inverted repeats of the IS, IRL ,and IRR, are shown as a square and pointed box respectively. The component –10 and –35 promoter elements of pjunc within these ends are also shown together with the weak pIRL promoter and the direction of transcription of the transposase. In a first step, single-strand cleavage and transfer from one IR to the other is catalyzed by OrfAB produced from the weak pIRL promoter. This is indicated at the top of the figure by the curved arrow. In this case, the right end (IRR) is shown attacking the left end (IRL). The resulting figure-eight form is drawn below and shows the free 3’OH group generated on the flanking donor DNA sequence. In a second step, second-strand circularization occurs by an as yet undetermined mechanism involving host functions but independently of transposon proteins [Turlan et al., 2000 ]. The resulting IRR-IRL junction carries suitably placed -35 and –10 hexamers, separated by a canonical 17 bp spacer and form a strong pjunc (bold arrow) promoter able to promote high levels of production of IS911 proteins. Integration of the circle results in disassembly of the promoter restoring low levels of expression from pIRL. Insertion upstream of a resident -10 promoter element can bring the IR-associated -35 element at the correct distance to form a promoter and activate a downstream gene.

Fig.18.2. Promoter Activities of junction fragments from different IS circles.Results of measurements of activities of 9 IS circle junctions when placed upstream of a beta-galactosidase gene.

IS and Gene Expression

Table. IS and gene expression.
IS family	IS name	Mechanism	Gene(s) affected	Organism	Reference	Clinical/Experimental
IS1	IS1	Cointegrate	EmR	Escherichia coli		C?
		Copy-paste circles	blaTEM-1			E
		—	acrEF pump	Salmonella enterica		E
IS3	IS2	Copy-paste circles	gal	Escherichia coli		E
			gal			E
			argE			E
			EmR			C?
			blaampC			E
			acrEF pump			E
	IS3	Copy-paste circles	argE	Escherichia coli		E
			argE			E
			citT			E
	IS981	Copy-paste circles	ldhB	Lactococcus lactis		E
	IS6110	Copy-paste circles	Rv2280 and PE-PGRS gene, Rv1468c	Mycobacterium tuberculosis		E
	ISKpn8	Copy-paste circles	blaKCP-2	Escherichia coli, Citrobacter freundii, Enterobacter cloacae, Enterobacter aerogenes, and Klebsiella oxytoca		C
IS4	IS10	Cut-paste (hairpin)	his	Salmonella typhimurium		E
		Cut-paste	—	Escherichia coli		E
		Cut-paste	acrEF pump	Salmonella enterica		E
	IS50	Cut-paste (hairpin)	aph3’II	Escherichia coli		E
	IS1999	—	blaVEB-1	Pseudomonas aeruginosa		C
			blaVEB-1/blaOXA-48	Escherichia coli		C
	ISPa12	—	blaPER-1	Salmonella enterica, Pseudomonas aeruginosa, Providencia stuartii, Acinetobacter baumannii		C
	ISAba1	—	blaampC	Acinetobacter baumannii		C
			blaOXA-51/blaOXA-23			C
IS5	IS5	—	EmR	Escherichia coli		C?
	ISFtu2		general	Francisella tularensis		Natural isolate
	ISVa1		(iron uptake)	Vibrio anguilarum		Natural isolate
	IS1168		nimA, nimB	Bacteroides sp.		C
	IS1186		cfiA	Bacteroides fragilis		C
	IS402		bla	Pseudomonas cepacia		E
IS6	IS257	Cointegrate	dfrA	Staphylococcus aureus		C
	IS257	Cointegrate	tet	Staphylococcus aureus
	IS1008	—	blaOXA-58	Acinetobacter baumannii
	IS26	—	aphA7, blaS2A	Klebsiella pneumoniae
			blaSHV-2a	Pseudomonas aeruginosa
	IS140	—	aac(3)-III and -IV	—
IS21	ISBf1	Copy-paste circle	cepA	Bacteroides fragilis		C
	ISKpn7		blaKPC	Klebsiellea pneumonia
IS30	IS30	Copy-paste circle	galK	Escherichia coli		E
	IS18		aac(6’)-Ij	Acinetobacter sp.		C
			blaOXA257
	IS4351		ermF	Bacteroides fragilis		C
			cfiA
	IS1086		cnrCBAT (ZnR)	Cupriavidus metallidurans		E
IS256	IS256	Copy-paste circles	mecA	Staphylococcus sciuri		—
			llm	Staphylococcus aureus
	IS1490		—	Burkholderia cepacia		—
	IS406		—	Burkholderia cepacia		E
IS481	IS481	Copy-paste circles	katA	Bordetella pertussis		—
	ISRme5		cnrCBAT (Zn R)	Cupriavidus metallidurans		E
IS630	ISFtu1	Tc-like	general	Francisella tularensis		Natural isolate
IS982	IS1187	—	cfiA	Bacteroides fragilis		E+C
						C
	IS982		citQRP	Lactococcus lactis		—
IS1380	ISBf12	—	cfiA	Bacteroides fragilis		C
	IS612
	IS613
	IS614
	IS1188
	IS942
	ISEcp1		blaCTX-M-15	Enterobacteriaceae
			blaCTX-M-17	Klebsiella pneumoniae
			blaCTX-M-19	Klebsiella pneumoniae
			blaCTX-M	Kluyvera ascorbata
			rmtC	Escherichia coli
	IS1187		cfiA	Bacteroides fragilis
ISL3	ISSg1	Copy-paste circles	sspB (surface antigen)	Streptococcus gordonii		—
	IS1411		pheBA	Pseudomonas putida
ISAs1	IS1548	—	lmb (lamelin binding)	Streptococcus agalactiae		—
	nd		—	Acinetobacter baumannii		C
ISNYC	IS403	—	bla	Burkholderia cepacia		E
	IS404
	IS405