Characterization of the 16S-23S internal transcribed spacer among 34 higher plants: Suitability for interspecific plastid transformation

Plant Cell Reports

Volumn 26, Issue 1, 2007, Pages 47-60

  McNutt, Patrick M ^a   Dehart, Mary J ^a   Matej, Louis A ^a  

^a MADIGAN ARMY MEDICAL CENTER   (United States)

Author keywords

Homologous recombination; Internal transcribed spacer; Interspecific transformation; Minimal essential processing segment; Phylogenetic analysis; Plastid transformation

Indexed keywords

DNA; GENETIC ENGINEERING; STATISTICAL METHODS;

HOMOLOGOUS RECOMBINATION; INTERNAL-TRANSCRIBED SPACER; INTERSPECIFIC TRANSFORMATION; MINIMAL ESSENTIAL PROCESSING SEGMENT; PHYLOGENETIC ANALYSIS; PLASTID TRANSFORMATION;

PLANTS (BOTANY);

CHLOROPLAST DNA; RIBOSOMAL SPACER DNA; RNA 16S; RNA 23S;

ARTICLE; CHEMISTRY; CLASSIFICATION; CONFORMATION; DNA SEQUENCE; GENETICS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANT; PLASTID; POLYMERASE CHAIN REACTION; SEQUENCE ALIGNMENT;

BASE SEQUENCE; DNA, CHLOROPLAST; DNA, RIBOSOMAL SPACER; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PHYLOGENY; PLANTS; PLASTIDS; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; RNA, RIBOSOMAL, 23S; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

GENETIC ENGINEERING; NUCLEIC ACIDS; PLANTS; PLASTIDS; STATISTICAL ANALYSIS;

EMBRYOPHYTA; MAGNOLIOPHYTA;

EID: 33845671348     PISSN: 07217714     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00299-006-0203-9     Document Type: Article

References (49)

1. APGII (2003) An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II. Bot J Linn Soc 141:399-436
2. Birky CW Jr, Walsh JB (1992) Biased gene conversion, copy number, and apparent mutation rate differences within chloroplast and bacterial genomes. Genetics 130:677-683
3. Cate JH, Yusupov MM, Yusupova GZ, Earnest TN, Noller HF (1999) X-ray crystal structures of 70S ribosome functional complexes. Science 285:2095-2104
4. Cerutti H, Johnson AM, Boynton JE, Gillham NW (1995) Inhibition of chloroplast DNA recombination and repair by dominant negative mutants of Escherichia coli RecA.Mol Cell Biol 15:3003-3011
5. Cox MM (1998) A broadening view of recombinational DNA repair in bacteria. Genes Cells 3:65-78
6. Curtis SE, Clegg MT (1984) Molecular evolution of chloroplast DNA sequences. Mol Biol Evol 1:291-301
7. Daniell H, Guda C, McPherson DT, Zhang X, Xu J, Urry DW (1997) Hyperexpression of a synthetic protein-based polymer gene. Methods Mol Biol 63:359-371
8. Decker EL, Reski R (2004) The moss bioreactor. Curr Opin Plant Biol 7:166-170
9. del Solar G, Giraldo R, Ruiz-Echevarria MJ, Espinosa M, Diaz-Orejas R (1998) Replication and control of circular bacterial plasmids. Microbiol Mol Biol Rev 62:434-464
10. Firpo MA, Dahlberg AE (1998) The importance of base pairing in the penultimate stem of Escherichia coli 16S rRNA for ribosomal subunit association. Nucleic Acids Res 26:2156-2160
11. Hirose T, Sugiura M (2004) Functional Shine-Dalgarno-like sequences for translational initiation of chloroplast mRNAs. Plant Cell Physiol 45:114-117
12. Hornung S, Fulgosi H, Dorfel P, Herrmann RG (1996) Sequence variation in the putative replication origins of the five genetically distinct basic Euoenothera plastid chromosomes (plastomes). Mol Gen Genet 251:609-612
13. Horvath EM, Peter SO, Joet T, Rumeau D, Cournac L, Horvath GV, Kavanagh TA, Schafer C, Peltier G, Medgyesy P (2000) Targeted inactivation of the plastid ndhB gene in tobacco results in an enhanced sensitivity of photosynthesis to moderate stomatal closure. Plant Physiol 123:1337-1350
14. Kavanagh TA, Thanh ND, Lao NT, McGrath N, Peter SO, Horvath EM, Dix PJ, Medgyesy P (1999) Homeologous plastid DNA transformation in tobacco is mediated by multiple recombination events. Genetics 152:1111-1122
15. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111-120
16. Koch W, Edwards K, Kossel H (1981) Sequencing of the 16S-23S spacer in a ribosomal RNA operon of Zea mays chloroplast DNA reveals two split tRNA genes. Cell 25:203-213
17. Kumar S, Dhingra A, Daniell H (2004) Plastid-expressed betaine aldehyde dehydrogenase gene in carrot cultured cells, roots, and leaves confers enhanced salt tolerance. Plant Physiol 136:2843-2854
18. Kunnimalaiyaan M, Nielsen BL (1997) Fine mapping of replication origins (ori A and ori B) in Nicotiana tabacum chloroplast DNA. Nucleic Acids Res 25:3681-3686
19. Lehmann K, Schmidt U (2003) Group II introns: structure and catalytic versatility of large natural ribozymes. Crit Rev Biochem Mol Biol 38:249-303
20. Lockton S, Gaut BS (2005) Plant conserved non-coding sequences and paralogue evolution. Trends Genet 21:60-65
21. Lugo SK, Kunnimalaiyaan M, Singh NK, Nielsen BL (2004) Required sequence elements for chloroplast DNA replication activity in vitro and in electroporated chloroplasts. Plant Sci 166:151-161
22. Majewski J, Cohan FM (1998) The effect of mismatch repair and heteroduplex formation on sexual isolation in Bacillus. Genetics 148:13-18
23. Maliga P (2004) Plastid transformation in higher plants. Annu Rev Plant Biol 55:289-313
24. Misra VK, Draper DE (1998) On the role of magnesium ions in RNA stability. Biopolymers 48:113-135
25. Modrich P, Lahue R (1996) Mismatch repair in replication fidelity, genetic recombination, and cancer biology. Annu Rev Biochem 65:101-133
26. Muhlbauer SK, Lossl A, Tzekova L, Zou Z, Koop HU (2002) Functional analysis of plastid DNA replication origins in tobacco by targeted inactivation. Plant J 32:175-184
27. Newman SM, Boynton JE, Gillham NW, Randolph-Anderson BL, Johnson AM, Harris EH (1990) Transformation of chloroplast ribosomal RNA genes in Chlamydomonas: molecular and genetic characterization of integration events. Genetics 126:875-888
28. Nobles KN, Yarian CS, Liu G, Guenther RH, Agris PF (2002) Highly conserved modified nucleosides influence Mg2±-dependent tRNA folding. Nucleic Acids Res 30:4751-4760
29. Ogle JM, Brodersen DE, Clemons WM Jr, Tarry MJ, Carter AP, Ramakrishnan V (2001) Recognition of cognate transfer RNA by the 30S ribosomal subunit. Science 292:897-902
30. Oommen A, Li XQ, Gegenheimer P (1992) Cleavage specificity of chloroplast and nuclear tRNA 3′-processing nucleases.Mol Cell Biol 12:865-875
31. Qiu YL, Lee J, Bernasconi-Quadroni F, Soltis DE, Soltis PS, Zanis M, Zimmer EA, Chen Z, Savolainen V, Chase MW (1999) The earliest angiosperms: evidence from mitochondrial, plastid and nuclear genomes. Nature 402:404-407
32. Raue HA, Klootwijk J, Musters W (1988) Evolutionary conservation of structure and function of high molecular weight ribosomal RNA. Prog Biophys Mol Biol 51:77-129
33. Savolainen V, Chase MW, Hoot SB, Morton CM, Soltis DE, Bayer C, Fay MF, de Bruijn AY, Sullivan S, Qiu YL (2000) Phylogenetics of flowering plants based on combined analysis of plastid atpB and rbcL gene sequences. Syst Biol 49:306-362
34. Schmitz-Linneweber C, Regel R, Du TG, Hupfer H, Herrmann RG, Maier RM (2002) The plastid chromosome of Atropa belladonna and its comparison with that of Nicotiana tabacum: the role of RNA editing in generating divergence in the process of plant speciation. Mol Biol Evol 19:1602-1612
35. Shen P, Huang HV (1986) Homologous recombination in Escherichia coli: dependence on substrate length and homology. Genetics 112:441-457
36. Sugiura C, Sugita M (2004) Plastid transformation reveals that moss tRNA(Arg)-CCG is not essential for plastid function. Plant J 40:314-321
37. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680
38. Tracy RB, Kowalczykowski SC (1996) In vitro selection of preferred DNA pairing sequences by the Escherichia coli RecA protein. Genes Dev 10:1890-1903
39. USDA, NRCS (2006) The plants database (http://plants.usda.gov, 31 July 2006). National plant data center, Baton Rouge, LA 70874-4490, USA
40. Vogel J, Borner T (2002) Lariat formation and a hydrolytic pathway in plant chloroplast group II intron splicing. EMBO J 21:3794-3803
41. Vogel J, Hess WR (2001) Complete 5′ and 3′ end maturation of group II intron-containing tRNA precursors. RNA 7:285-292
42. von Ahsen U, Noller HF (1995) Identification of bases in 16S rRNA essential for tRNA binding at the 30S ribosomal P site. Science 267:234-237
43. Vulic M, Dionisio F, Taddei F, Radman M (1997) Molecular keys to speciation: DNA polymorphism and the control of genetic exchange in enterobacteria. Proc Natl Acad Sci USA 94:9763-9767
44. Wang Y, Saitoh Y, Sato T, Hidaka S, Tsutsumi K (2003) Comparison of plastid DNA replication in different cells and tissues of the rice plant. Plant Mol Biol 52:905-913
45. Watson J, Koya V, Leppla SH, Daniell H (2004) Expression of Bacillus anthracis protective antigen in transgenic chloroplasts of tobacco, a non-food/feed crop. Vaccine 22:4374-4384
46. Westmoreland J, Porter G, Radman M, Resnick MA (1997) Highly mismatched molecules resembling recombination intermediates efficiently transformmismatch repair proficient Escherichia coli. Genetics 145:29-38
47. Williamson SE, Doolittle WF (1983) Genes for tRNAIle and tRNAAla in the spacer between the 16S and 23S rRNA genes of a blue-green alga: strong homology to chloroplast tRNA genes and tRNA genes of the E. coli rrnD gene cluster. Nucleic Acids Res 11:225-235
48. Wolfe KH, Li WH, Sharp PM (1987) Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proc Natl Acad Sci USA 84:9054-9058
49. Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31:3406-3415