Maize haplotype with a helitron-amplified cytidine deaminase gene copy

被引:34
作者
Xu, Jian-Hong [1 ]
Messing, Joachim [1 ]
机构
[1] Rutgers State Univ, Waksman Inst Microbiol, Piscataway, NJ 08854 USA
关键词
D O I
10.1186/1471-2156-7-52
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
Background: Genetic maps are based on recombination of orthologous gene sequences between different strains of the same species. Therefore, it was unexpected to find extensive noncollinearity of genes between different inbred strains of maize. Interestingly, disruption of gene collinearity can be caused among others by a rolling circle-type copy and paste mechanism facilitated by Helitrons. However, understanding the role of this type of gene amplification has been hampered by the lack of finding intact gene sequences within Helitrons. Results: By aligning two haplotypes of the zICI locus of maize we found a Helitron that contains two genes, one encoding a putative cytidine deaminase and one a hypothetical protein with part of a 40S ribosomal protein. The cytidine deaminase gene, called ZmCDA3, has been copied from the ZmCDA1 gene on maize chromosome 7 about 4.5 million years ago (mya) after maize was formed by whole-genome duplication from two progenitors. Inbred lines contain gene copies of both progenitors, the ZmCDA1 and ZmCDA2 genes. Both genes diverged when the progenitors of maize split and are derived from the same progenitor as the rice OsCDA1 gene. The ZmCDA1 and ZmCDA2 genes are both transcribed in leaf and seed tissue, but transcripts of the paralogous ZmCDA3 gene have not been found yet. Based on their protein structure the maize CDA genes encode a nucleoside deaminase that is found in bacterial systems and is distinct from the mammalian RNA and/or DNA modifying enzymes. Conclusion: The conservation of a paralogous gene sequence encoding a cytidine deaminase gene over 4.5 million years suggests that Helitrons could add functional gene sequences to new chromosomal positions and thereby create new haplotypes. However, the function of such paralogous gene copies cannot be essential because they are not present in all maize strains. However, it is interesting to note that maize hybrids can outperform their inbred parents. Therefore, certain haplotypes may function only in combination with other haplotypes or under specialized environmental conditions.
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页数:13
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共 47 条
[1]   Gapped BLAST and PSI-BLAST: a new generation of protein database search programs [J].
Altschul, SF ;
Madden, TL ;
Schaffer, AA ;
Zhang, JH ;
Zhang, Z ;
Miller, W ;
Lipman, DJ .
NUCLEIC ACIDS RESEARCH, 1997, 25 (17) :3389-3402
[2]   INTRODUCTION OF A HETEROLOGOUS EDITING SITE INTO THE TOBACCO PLASTID GENOME - THE LACK OF RNA EDITING LEADS TO A MUTANT PHENOTYPE [J].
BOCK, R ;
KOSSEL, H ;
MALIGA, P .
EMBO JOURNAL, 1994, 13 (19) :4623-4628
[3]   Uneven chromosome contraction and expansion in the maize genome [J].
Bruggmann, Remy ;
Bharti, Arvind K. ;
Gundlach, Heidrun ;
Lai, Jinsheng ;
Young, Sarah ;
Pontaroli, Ana C. ;
Wei, Fusheng ;
Haberer, Georg ;
Fuks, Galina ;
Du, Chunguang ;
Raymond, Christina ;
Estep, Matt C. ;
Liu, Renyi ;
Bennetzen, Jeffrey L. ;
Chan, Agnes P. ;
Rabinowicz, Pablo D. ;
Quackenbush, John ;
Barbazuk, W. Brad ;
Wing, Rod A. ;
Birren, Bruce ;
Nusbaum, Chad ;
Rounsley, Steve ;
Mayer, Klaus F. X. ;
Messing, Joachim .
GENOME RESEARCH, 2006, 16 (10) :1241-1251
[4]   Evolution of DNA sequence nonhomologies among maize inbreds [J].
Brunner, S ;
Fengler, K ;
Morgante, M ;
Tingey, S ;
Rafalski, A .
PLANT CELL, 2005, 17 (02) :343-360
[5]   Duplicated fie genes in maize:: Expression pattern and imprinting suggest distinct functions [J].
Danilevskaya, ON ;
Hermon, P ;
Hantke, S ;
Muszynski, MG ;
Kollipara, K ;
Ananiev, EV .
PLANT CELL, 2003, 15 (02) :425-438
[6]   De novo protein synthesis is required for the activation-induced cytidine deaminase function in class-switch recombination [J].
Doi, T ;
Kinoshita, K ;
Ikegawa, M ;
Muramatsu, M ;
Honjo, T .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2003, 100 (05) :2634-2638
[7]   Recombination occurs uniformly within the bronze gene, a meiotic recombination hotspot in the maize genome [J].
Dooner, HK ;
MartinezFerez, IM .
PLANT CELL, 1997, 9 (09) :1633-1646
[8]   Retrotranspositions in orthologous regions of closely related grass species [J].
Du, Chunguang ;
Swigonova, Zuzana ;
Messing, Joachim .
BMC EVOLUTIONARY BIOLOGY, 2006, 6 (1)
[9]   A prokaryotic-type cytidine deaminase from Arabidopsis thaliana -: Gene expression and functional characterization [J].
Faivre-Nitschke, SE ;
Grienenberger, JM ;
Gualberto, JM .
EUROPEAN JOURNAL OF BIOCHEMISTRY, 1999, 263 (03) :896-903
[10]  
Freytag SO, 2002, CANCER RES, V62, P4968