Wednesday, February 22, 2006

Survey of Recent studies on Mutator like elements (Mules) , mobile DNA that moves and different species and scrambles and mutates the genome.

Mutator mobile genes (Mules) that move around between species such as maize, millet, rice diverse angiosperms, yeast Yarrowia lipolytica, Petunia, flatworm Caenorhabditis, sugarcane, fungus Fusarium oxysporum, fruitfly Drosophila, and grasses, which scramble and delete genes, are genetically unstable, and which are common in nature - and completely NATURAL:

Diao X, Freeling M, Lisch D.
Horizontal Transfer of a Plant Transposon.
PLoS Biol. 2005 Dec 20;4(1):e5 [Epub ahead of print]

McCarty DR, Settles AM, Suzuki M, Tan BC, Latshaw S, Porch T, Robin K, Baier
J, Avigne W, Lai J, Messing J, Koch KE, Hannah LC.
Steady-state transposon mutagenesis in inbred maize.
Plant J. 2005 Oct;44(1):52-61.

Cowan RK, Hoen DR, Schoen DJ, Bureau TE.
MUSTANG is a novel family of domesticated transposase genes found in diverse
Mol Biol Evol. 2005 Oct;22(10):2084-9. Epub 2005 Jun 29.
6: Mol Biol Evol. 2005 Oct;22(10):2084-9. Epub 2005 Jun 29.

While transposons have traditionally been viewed as genomic parasites or "junk DNA," the discovery of transposon-derived host genes has fueled an ongoing debate over the evolutionary role of transposons. In particular, while mobility-related open reading frames have been known to acquire host functions, the contribution of these types of events to the evolution of genes is not well understood. Here we report that genome-wide searches for Mutator transposase-derived host genes in Arabidopsis thaliana (Columbia-0) and Oryza
sativa ssp. japonica (cv. Nipponbare) (domesticated rice) identified 121 sequences, including the taxonomically conserved MUSTANG1. Syntenic MUSTANG1 orthologs in such varied plant species as rice, poplar, Arabidopsis, and Medicago truncatula appear to be under purifying selection. However, despite the evidence of this pathway of gene evolution, MUSTANG1 belongs to one of only two Mutator-like gene families with members in both monocotyledonous and
dicotyledonous plants, suggesting that Mutator-like elements seldom evolve into taxonomically widespread host genes.

Neuveglise C, Chalvet F, Wincker P, Gaillardin C, Casaregola S.
Mutator-like element in the yeast Yarrowia lipolytica displays multiple
alternative splicings.
Eukaryot Cell. 2005 Mar;4(3):615-24.

Stuurman J, Kuhlemeier C.
Stable two-element control of dTph1 transposition in mutator strains of Petunia
by an inactive ACT1 introgression from a wild species.
Plant J. 2005 Mar;41(6):945-55.

Brownlie JC, Johnson NM, Whyard S.
The Caenorhabditis briggsae genome contains active CbmaT1 and Tcb1 transposons.
Mol Genet Genomics. 2005 Mar;273(1):92-101. Epub 2005 Feb 9.

Rossi M, Araujo PG, de Jesus EM, Varani AM, Van Sluys MA.
Comparative analysis of Mutator -like transposases in sugarcane.
Mol Genet Genomics. 2004 Sep;272(2):194-203. Epub 2004 Aug 24.

The maize Mutator ( Mu) system has been described as the most active and mutagenic plant transposon so far discovered. Mu -like elements (MULEs) are widespread among plants, and many and diverse variants can coexist in a particular genome. The autonomous regulatory element MuDR contains two genes:
mudrA encodes the transposase, while the function of the mudrB gene product remains unknown. Although mudrA -like sequences are ubiquitous in plants, mudrB seems to be restricted to the genus Zea. In the SUCEST (the Brazilian Sugarcane EST Sequencing Project) database, several mudrA -like cDNAs have been identified, suggesting the presence of a transcriptionally active Mu system in sugarcane. Phylogenetic studies have revealed the presence in plants of four classes of mudrA -like sequences, which arose prior to the monocot/eudicot split. At least three of the four classes are also found in the progenitors of
the sugarcane hybrid (Saccharum spp.), Saccharum officinarum and S. spontaneum.
The frequency of putatively functional transposase ORFs varies among the classes, as revealed at both cDNA and genomic levels. The predicted products of some sugarcane mudrA -like transcripts contain both a DNA-binding domain and a transposase catalytic-site motif, supporting the idea that an active Mu system exists in this hybrid genome.

Xu Z, Yan X, Maurais S, Fu H, O'Brien DG, Mottinger J, Dooner HK.
Jittery, a Mutator distant relative with a paradoxical mobile behavior:
excision without reinsertion.
Plant Cell. 2004 May;16(5):1105-14. Epub 2004 Apr 9.

The unstable mutation bz-m039 arose in a maize (Zea mays) stock that originated from a plant infected with barley stripe mosaic virus. The instability of the mutation is caused by a 3.9-kb mobile element that has been named Jittery (Jit).
Jit has terminal inverted repeats (TIRs) of 181 bp, causes a 9-bp direct duplication of the target site, and appears to excise autonomously. It is predicted to encode a single 709-amino acid protein, JITA, which is distantly related to the MURA transposase protein of the Mutator system but is more closely related to the MURA protein of Mutator-like elements (MULEs) from Arabidopsis thaliana and rice (Oryza sativa). Like MULEs, Jit resembles Mutator in the length of the element's TIRs, the size of the target site duplication, and in the makeup of its transposase but differs from the autonomous element Mutator-Don Robertson in that it encodes a single protein. Jit also differs from Mutator elements in the high frequency with which it excises to produce germinal revertants and in its copy number in the maize genome: Jit-like TIRs are present at low copy number in all maize lines and teosinte accessions examined, and JITA sequences occur in only a few maize inbreds. However, Jit cannot be considered a bona fide transposon in its present host line because it does not leave footprints upon excision and does not reinsert in the genome. These unusual mobile element properties are discussed in light of the structure and gene organization of Jit and related elements.

Sijen T, Plasterk RH.
Transposon silencing in the Caenorhabditis elegans germ line by natural RNAi.
Nature. 2003 Nov 20;426(6964):310-4.

Slotkin RK, Freeling M, Lisch D.
Mu killer causes the heritable inactivation of the Mutator family of
transposable elements in Zea mays.
Genetics. 2003 Oct;165(2):781-97.

May BP, Liu H, Vollbrecht E, Senior L, Rabinowicz PD, Roh D, Pan X, Stein
L, Freeling M, Alexander D, Martienssen R.
Maize-targeted mutagenesis: A knockout resource for maize.
Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11541-6. Epub 2003 Sep 3.

Vastenhouw NL, Fischer SE, Robert VJ, Thijssen KL, Fraser AG, Kamath RS,
Ahringer J, Plasterk RH.
A genome-wide screen identifies 27 genes involved in transposon silencing in C.
Curr Biol. 2003 Aug 5;13(15):1311-6.

Chalvet F, Grimaldi C, Kaper F, Langin T, Daboussi MJ.
Hop, an active Mutator-like element in the genome of the fungus Fusarium
Mol Biol Evol. 2003 Aug;20(8):1362-75. Epub 2003 May 30.

Pooma W, Gersos C, Grotewold E.
Transposon insertions in the promoter of the Zea mays a1 gene differentially
affect transcription by the Myb factors P and C1.
Genetics. 2002 Jun;161(2):793-801.

Bessereau JL, Wright A, Williams DC, Schuske K, Davis MW, Jorgensen EM.
Mobilization of a Drosophila transposon in the Caenorhabditis elegans germ
Nature. 2001 Sep 6;413(6851):70-4.

Lisch DR, Freeling M, Langham RJ, Choy MY.
Mutator transposase is widespread in the grasses.
Plant Physiol. 2001 Mar;125(3):1293-303.

Singer T, Yordan C, Martienssen RA.
Robertson's Mutator transposons in A. thaliana are regulated by the
chromatin-remodeling gene Decrease in DNA Methylation (DDM1).
Genes Dev. 2001 Mar 1;15(5):591-602.

Fedoroff NV.
The suppressor-mutator element and the evolutionary riddle of transposons.
Genes Cells. 1999 Jan;4(1):11-9. Review.

Kloeckener-Gruissem B, Freeling M.
Transposon-induced promoter scrambling: a mechanism for the evolution of new
Proc Natl Acad Sci U S A. 1995 Mar 14;92(6):1836-40.

Eisen JA, Benito MI, Walbot V.
Sequence similarity of putative transposases links the maize Mutator autonomous
element and a group of bacterial insertion sequences.
Nucleic Acids Res. 1994 Jul 11;22(13):2634-6.

Pan and Peterson (1988) note that it would appear that the corn genome is highly volatile. That is, these transposons are now known to be quiescent in the genome. They appear also to be spontaneously activated. This is evident in almost any line one looks at with appropriate reporter alleles as indicated in the paper by Pan and Peterson (1988), where sectors were pervasive in these lines. It would appear, therefore, that the corn genome has a built-in system of activation and redeployment of genome segments and in a final result, leads to a great deal of variability.

Annual Review of Genetics
Vol. 23: 71-85 (Volume publication date December 1989)
Maize Transposable Elements
A Gierl, ­H Saedler, and ­P A Peterson­

Genetics, Vol 128, 823-830, Copyright © 1991
Spontaneous Germinal Activation of Quiescent Uq Transposable Elements in Zea mays L
Y. B. Pan and P. A. Peterson
Department of Agronomy and Department of Genetics, Iowa State University, Ames, Iowa 50011 Present address: Department of Immunology/Microbiology, Rush-Presbyterian-St. Luke's Medical Center, 1653 West Congress Parkway, Chicago, Illinois 60612-3864.

The spontaneous germinal activation of quiescent Uq transposable elements is reported. Thirty-nine spotted exceptions were observed at a rate of about 2 X 10(-4) from 687 otherwise colorless ears produced from the cross of a-ruq/a-ruq (colorless or occasionally sectored) X an a-ruq tester (colorless). All exceptions had spotting patterns distinct from the pattern of our original standard Uq (Uq1)-a-ruq spotting. From these spotted exceptions five new Uq elements (Uq2, Uq3, Uq4, Uq5 and Uq6) have been isolated. Genetic evidence for the Uq nature of the five germinal isolates is presented. First, each of the five spotted exceptions was homozygous for the a-ruq reporter allele. Second, four new Uq isolates (Uq2, Uq3, Uq4 and Uq5), after being reconstituted into a a{deg} sh2/a{deg} sh2 (no Uq) line, could transactivate the standard a-ruq allele and continue to produce their distinct spotting phenotypes. Third, these five new Uqs are also capable of transactivating the c-ruq65 and c-ruq67 alleles. However, the transactivation of c-ruq is generally weaker than that of a-ruq.

Tagging of a maize gene involved in kernel development by an activated Uq transposable element
Yong-Bao Pan1 and Peter A. Peterson1 Contact Information
(1) Department of Genetics and Department of Agronomy, Iowa State University, 50011 Ames, IA, USA
Received: 12 April 1989
Communicated by H. Saedler

Summary A quiescent Uq transposable element has been activated in a maize plant treated with 5-aza-2prime-deoxycyti-dine. This activated Uq cosegregates with a heritable dominant miniature (Mn) kernel phenotype, indicating its physical association with a maize miniature locus (Mn:: Uq). The Mn:: Uq mutant is dominant in producing a miniature seed phenotype of variable size and in reducing seedling vigor in the early growth stage. Genetic experiments indicate that the Mn:: Uq mutant also affects the activity of the male gametophyte, whereby pollen germination is inhibited, thus lacking pollen tube growth resulting in the male nontransmissibility of this mutant. Proof for the Uq element in this mutant is derived by its ability to transactivate the standard a-ruq reporter allele to yield spotted aleurone tissue. However, the Mn:: Uq mutant does not transactivate a normally Uq-responsive c-ruq allele, suggesting a structural difference between the two ruq receptors at the A1 and C1 loci. It is anticipated that cloning of the Uq transposable element would facilitate the molecular cloning and characterization of the maize miniature gene.

Key words Zea mays - Uq transposable element - miniature gene - Mn:: Uq - Activation
Journal Paper No. J-13425 of the Iowa Agriculture and Home Economics Experiment Station, Ames, Iowa 50011, USA, Project No. 2850

Genetics, Vol 120, 587-596, Copyright © 1988
The Mutator-Related Cy Transposable Element of Zea mays L. Behaves as a Near-Mendelian Factor

P. S. Schnable and P. A. Peterson
Present address: Department of Genetics Iowa State University, Ames, Iowa 50011.

The bz-rcy allele arose in a single gamete of the TEL (transposable-element laden) population, when the rcy receptor element inserted into the Bronze1 locus. This newly arisen receptor allele conditions a stable bronze kernel phenotype in the absence of the independently segregating regulatory element, Cy. In the presence of Cy, bz-rcy conditions fully colored spots on a bronze background. The spots represent clonal sectors arising from mutations of bz-rcy to Bz'. Although Cy exhibits genetic interactions with the Mutator system it differs from Mu-homologous elements in its near-Mendelian behavior which is in contrast to the non-Mendelian inheritance of Mutator and Mu-homologous elements. Evidence is presented which suggests that the timing and mode of Cy transposition differ from those of Mu1.

Further reading at Academics Review

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