General Information/What Is an IS?

Classical IS

The original definition of an IS (Fig.3.1) was: a short, generally phenotypically cryptic, DNA segment encoding only the enzymes necessary for its transposition and capable of repeated insertion into many different sites within a genome using mechanisms independent of large regions of DNA homology between the IS and target . Classical IS are between 0.7 and 2.5 kb in length, genetically compact with one or two open reading frames (orfs) which occupy the entire length of the IS and terminate in flanking imperfect terminal repeat sequences (IR) (Table 1). The orfs include the Tpase that catalyzes the DNA cleavages and strand transfers leading to IS movement and, in some cases, regulatory proteins. Their highly compact nature is illustrated by the fact that some IS have developed “recoding” strategies such as Programmed Ribosomal Frameshifting (involving ribosome slippage) and Programmed Transcriptional Realignment (involving RNA polymerase slippage) .

These permit assembly of different functional protein domains effectively encoding two proteins of different functions in one DNA segment. IS also often generates a short flanking directly repeated duplication (DR) of the target DNA on insertion. These characteristics are not limited to prokaryotic IS but are also shared with most eukaryotic DNA transposons. Classical IS generally transpose using a double-strand DNA intermediate. However, for prokaryotic IS, this strict definition has been broadened over the years with the discovery of an increasing number of non-canonical derivatives and variants, some of which are described in the following sections. Moreover, as we learn more about diversity from sequenced genomes, classification is becoming more problematic because the large degree of MGE diversity is obscuring the borders between certain types of TE (Fuzzy Borders) . Despite their abundance and diversity, the number of different chemical mechanisms used in TE movement is surprisingly limited and many quite divergent TE share a similar mechanism.

Fig.3.1. What is an Insertion Sequence? Terminal inverted repeats (IRL and IRR) are shown as two-colored boxes (a and b) with functions for transposase binding (a) and recognition for cleavage and strand transfer (a). A single (left) or double (right) open reading frame is shown underneath the IS (blue arrow). The transposase of the IS on the right is produced by programmed -1 translational frameshifting. The reading frames are indicated within the IS. The product of the upstream frame generally acts as a regulatory protein. The indigenous Tpase promoter is shown located (by convention) in IRL. XXX and YYYY represent the short direct target repeat sequence which is generally duplicated during the insertion event.

Characteristics of insertion sequence families

Table 1. Abbreviations: DR, duplication repeat; IS, insertion sequence; ORF, open reading frame.
Families	Sub-Groups	Typical size-range	DR (bp)	Ends	IRs	No ORFs	Frameshift	Catalytic residues	Mechanism
IS1	—	740–1180	8–9	GGnnnTG	Y	2	ORFAB	DDE	copy-and-paste and cointegrate
	single ORF	800–1200	0–9		N	1	—
	ISMhu11	900–4600	0–10		Y	2	ORFAB
IS1595	ISPna2	1000–1150	8	GGCnnTG	Y	1	—	DDNK	copy-and-paste?
	ISPna2+pass	1500–2600	8	—				—
	ISH4	1000	8	CGCTCTT				DDNK
	IS1016	700–745	7–9	GGGgctg				DDEK
	IS1595	900–1100	8	CcTGATT				DDNK+ER4R7
	ISSod11	1000–1100	8	nnnGcnTATC				DDHK+ER4R7
	ISNwi1	1080–1200	8	ggnnatTAT				DDEK+ER4
	ISNwi1+pass	1750–4750	8	—				—
	ISNha5	3450–7900	8	CGGnnTT				DDER/K
IS3	IS150	1200–1600	3–4	TG	Y	2	ORFAB	DDE	copy-and-paste
	IS407	1100–1400	4	TG
	IS51	1000–1400	3–4	TG
	IS3	1150–1750	3–4	TGa/g
	IS2	1300–1400	5	TG
IS481	950–1300	4–15	TGT	Y	1	—	DDE	copy-paste?
ISNCY	IS1202	1400–1700	5	TGT	Y	1	—	DDEQ	—
IS4	IS10	1200–1350	9	CT	Y	1	DDE	hairpin intermediate	cut-and-paste
	IS50	1350–1550	8–9	C				hairpin intermediate
	ISPepr1	1500–1600	7–8	-T-AA				?
	IS4	1400–1600	10–13	-AAT				?
	IS4Sa	1150–1750	8–10	CA				?
	ISH8	1400–1800	10	?
	IS231	1450–5400	10–12	CAT		1 or + *		*passenger genes
IS701	—	1400–1550	4	—	Y	1	—	DDE	—
	ISAba11	—	—
ISH3	—	1225–1500	4–5	C-GT	Y	1	—	DDE	—
IS1634	—	1500–2000	5–6	C	Y	1	—	DDE	—
IS5	IS903	950–1150	9	GG	Y	1	—	DDE	—
	ISL2	850–1200	2–3	—
	ISH1	900–1150	8	-GC
	IS5	1000–1500	4	Ga/g
	IS1031	850–1050	3	GAa/g
	IS427	800–1000	2–4	Ga/g		2	ORFAB
IS1182	—	1330–1950	0–60	—	Y	1	—	DDE	—
ISNCY	ISDol1	1600–1900	6–7	—	Y	1	—	DDE	—
IS6	—	700–900	8	GG	Y	1	—	DDE	co-integrate
IS21	—	1750–2600	4–8	TG	Y	2 *	—	DDE	—
IS30	—	1000–1700	2–3	—	Y	1	—	DDE	copy-and-paste
IS66	—	2000–3000	8–9	GTAA	Y	3*	—	DDE*	—
	ISBst12	1350–1900				1		DDE
IS256	—	1200–1500	8–9	Ga/g	Y	1	—	DDE	copy-and-paste
	IS1249	1300	0–10	GG
	ISC1250	1250	0–9	GG
ISH6	—	1450	8	GGT	Y	1	—	DDE	—
ISLre2	—	1500–2000	9	—	Y	1	—	DDE	—
ISKra4	ISAzba1	1400–2900	0	—	Y	1 or + *	—	DDE	—
	ISMich2	1250–1400	8	GGG		1 or 2	ORFAB
	ISKra4	1400–3700	9	GGG		1 or + *	—
IS630	—	1000–1400	2*	—	Y	1 or 2	ORFAB	DDE	cut-and-paste
IS982	—	1000	3–9	AC	Y	1	—	DDE	—
IS1380	—	1550–2000	4–5	CC	Y	1	—	DDE	—
ISAs1	—	1200–1500	8–10	CAGGG	Y	1	—	—	—
ISL3	—	1300–2300	8	GG	Y	1	—	—	—
Tn3	—	>3000	0	GGGG	Y	>1	—	DDE	co-integrate
ISAzo13	—	1250–2200	0–4	Ga/g	Y	1	—	—	—
IS110	—	1200–1550	0	—	N	1	—	DEDD	—
	IS1111	—	—	—	Y*	—	—	—	—
IS91	—	1500–2000	0	—	N	1	—	HUH/Y2	rolling circle
IS200/IS605	IS200	600–750	0	—	0	1*	—	HUH/Y1	peel-and-paste
	IS605	1300–2000	—	—	—	2*	—	HUH/Y1**
IS607	—	1700–2500	0	—	N	2*	—	Serine**	—
ISNCY	IS892	1600	0–8	CTAG	Y	2	ORFAB	—	—
	ISLbi1	1400–1500	5	—	Y	1
	ISMae2	1400–2400	9	CAG	Y	1
	ISPlu15	800–1000	0	—	N	1
	ISA1214	1000–1200	8–12	—	Y	2
	ISC1217	1200	6–8	TAG	Y	1
	ISM1	1300–1600	8–9	—	Y	1

New types of IS

One example of this expanding diversity is the identification of another entire class of IS . Members of this class use an entirely different mechanism of transposition involving single-strand circular DNA intermediates which appear to target stalled replication forks (Fig.3.2). They possess small transposases (~150 aa) which are completely different to the classical IS in the type of chemistry they catalyze (Groups with HUH Enzymes). Another example are the casposons which are related to CRISPRs but whose transposition has yet to be fully characterized .

Fig.3.2. Organization of the IS200/IS605 family insertion sequences that transpose using single-strand DNA intermediates. The top of the figure shows the genetic organization. The generic IS is shown as a box. The element-specific tetra- (IS608) or penta- (ISDra2) nucleotide target site is shown boxed in red on the left. Left (LE) and right (RE) ends carrying subterminal hairpins are presented as red boxes. The transposase reading frame, tnpA, is shown within the IS as a red line and the accessory frame tnpB as a blue line. The direction of transcription is indicated by the arrowhead. The bottom of the figure shows the subterminal secondary structures at the left (red) end LE and the right (blue) end RE. The left and right cleavage sites are presented as black The blue arrows indicate the interaction between the cleavage sites and the "guide" sequences at the foot of the secondary structures necessary for the cleavage reactions.