BSCI 411

PLANT GENETICS and MOLECULAR BIOLOGY

Department of Cell Biology & Molecular Genetics

Plant Transposons

I. Bacterial transposable elements as model
     A. Insertion (IS) elements- terminal inverted repeat, transposase
		-causes direct repeat (4-12 bp) of target sequence
     B. Transposons- carry additional genes
		-replicative and non-replicative transposition

II. Biological relevance
    A.  Intragenomic parasite	
    B. Associated with flexibility for adaptation- provide variation
		e.g. dissapear with selection for stability of traits
		-recombination can give new genes through fusing others or 
			increasing expression of transposon-proximal gene

III. DNA Transposons (Class II transposons)
    A. Found first in maize- McClintock 
		anthocyanin mutants: saw frequent somatic reversions that 			depended upon separate locus, and that locus would change 			map location.

    B.  Mechanism of movement: conservative (nonreplicative) transposition 

    C. Characteristics of transposons in plants
	1. mutations caused by insertion are unstable
	2. mutation can be caused by two types
		a. autonomous elements- self transposable
		b. nonautonomous elements- transpose only in presence of 
				autonomous element
	3. insertion duplicates target sequence
			-at deletion, leaves footprint of duplicated sequence
			
    D. Families of transposons in plants
	1. Ac-Ds element (maize)
		a. Ac is autonomous- 4565 bp long
		   - 1 mRNA 3.5 kB =92 kDa protein=Ac transposase
		   - 11 bp terminal inverted repeat
		   - subterminal AAACGG repeats
		   - 3 bp duplication of target
		b. Ds is nonautonomous defective Ac element
		   - has both 11 bp TIRs and Subterminal repeats
		   - some associated with chromosome breakage
		c. related elements: Bg, maize; Tam3, snapdragon

	2. En/Spm (maize) 
		a. Parts of element
		    - two functional genes from allternate splicing-
	 	        -tnpA - 2500 nt mRNA=620 aa protein that binds 12bp					consensus next to TIR
	                  -tnpD - 6000 nt mRNA
		    - 13bp TIR
		    - 200 bp 5’ and 300 bp 3’ motifs
		   - 8 bp duplication of target
		b. genetic effects
		   - can induce expression of neighboring genes
		c. similar transposons:
			Tam1, snapdragon; Tgn, soybean; Pis1, pea
	3. Mu
		- 200-500 bp TIR, variable center sequences
		- mutations are leaky- spliced out of exon in mRNA

IV. Retrotransposons in plants
    A. RNA intermediate-  similar to retroviruses
    B. Types of retrotransposons- closely related to retroviruses
	1. LTR containing (Short Interspersed Nuclear Element- SINE) 
	2. non-LTR   (Long Interspersed Nuclear Element- LINE)
    C. Replicative transposition- through RNA polymerase III transcript
    D. Found in all plants, including mosses, ferns, dicots, monocots
	1. often different in sequence between related plants
	2. recent transpositions are rare- but several isolated because of recent 
		insertion into genes
		-cloned tobacco Tto1 works in Arabidopsis and Rice
	 		
V. Controls of transposition
	1. DNA methylation associated with silencing of transposons and 
		retrotransposons
		a. CpG methylation a host-protection mechanism?
			-in certain fungi, duplicated sequences are methylated
			-Arabidopsis- similar diversity of retrotransposons as 
				other plants, but lower copy number
		b. Example- Spm
			-active transposon is demethylated
			-inactivated transposon is partially methylated in 
				promoter and first exon
			-cryptic transposon is fully methylated
			-tnpA can reactivate transposon through demethylation  
	2. Inducers of transposition- 
		a. stress, genome shock (wide cross)- transposons
		b. virus infection, cell culture- retrotransposons

VI. Applications in genetics
    A. Transposon tagging
	1. homologous systems (i.e. Ac in maize)
	2. heterologous systems (i.e. Ac in Arabidopsis)
	3. activation tagging

    B. Knockout mutation in already cloned genes

Links:

Dr. Nina Fedoroff Lab site- good descriptions of transposon tagging
Ac/Ds transposition animation- needs Shockwave plug-in
AC/Ds used in tomato
Transposon tagging in plants-PLSC731 NDSU
Enhancer and gene trapping in Arabidopsis with transposons- tair  summary and protocols
        T-DNA enhancer traps- good pictures
Transposon Tagging in Arabidopsis- Federoff Lab-Transposon lines for insertional mutagenesis
                                                        Arabidopsis Transposon Insertion Service

Arabidopsis Insertaional Tagging gateway-links to different sites
AGR Arabidopsis insert page- search for your sequence in sites with predefined inserts

Readings:

Chin, H.G. ; Choe, M.S. ; Lee, S.H.  et. al Molecular analysis of rice plants harboring an Ac/Ds transposable element-mediated gene trapping system. The Plant journal  vol19, no. 5 (Sept 1999): p. 615-623.

Phillip SanMiguel, Alexander Tikhonov, Young-Kwan Jin, Natasha Motchoulskaia, Dmitrii Zakharov, Admasu Mela 1996. Science Nested Retrotransposons in the Intergenic Regions of the Maize Genome 274: pp. 765-768.  

Nina Fedoroff 2000. Transposons and genome evolution in plants Proc. Natl. Acad. Sci. USA, Vol. 97: 7002-7007

Last revised: April 4, 2001- Straney