THE NATURE OF NUCLEOTIDE SEQUENCE DIVERGENCE BETWEEN BARLEY AND MAIZE CHLOROPLAST DNA

Genetics ◽  
1984 ◽  
Vol 106 (4) ◽  
pp. 735-749
Author(s):  
Gerard Zurawski ◽  
Michael T Clegg ◽  
Anthony H D Brown
Keyword(s):  
Chloroplast Dna ◽  
Dna Sequences ◽  
Large Subunit ◽  
Leader Region ◽  
Coding Region ◽  
Nucleotide Substitutions ◽  
Bisphosphate Carboxylase ◽  
Noncoding Regions ◽  
The Third ◽  
Maize Chloroplast

ABSTRACT Analysis of a 2175-base pair (bp) SmaI-HindIII fragment of barley chloroplast DNA revealed that rbcL (the gene for the large subunit of ribulose 1,5-bisphosphate carboxylase) and atpB (the gene for the β subunit of ATPase) are transcribed divergently and are separated by an untranscribed region of 155-166 bp. The rbcL mRNA has a 320-residue untranslated leader region, whereas the atpB mRNA has a 296- to 309-residue leader region. The sequence of these regions, together with the initial 113 bp of the atpB-coding region and the initial 1279 bp of the rbcL-coding region, is compared with the analogous maize chloroplast DNA sequences. Two classes of nucleotide differences are present, substitutions and insertions/deletions. Nucleotide substitutions show a 1.9-fold bias toward transitions in the rbcL-coding region and a 1.5-fold bias toward transitions in the noncoding region. The level of nucleotide substitutions between the barley and maize sequences is about 0.065/bp. Seventy-one percent of the substitutions in the rbcL-coding region are at the third codon position, and 95% of these are synonymous changes. Insertion/deletion events, which are confined to the noncoding regions, are not randomly distributed in these regions and are often associated with short repeated sequences. The extent of change for the noncoding regions (about 0.093 events/bp) is less than the extent of change at the third codon positions in the rbcL-coding region (about 0.135 events/bp), including insertion/delection events. Limited sequence analysis of the analogous DNA from a wild line (Hordeum spontaneum) and a primitive Iranian barley (H. vulgare) suggested a low rate of chloroplast DNA evolution. Compared to spinach chloroplast DNA, the barley rbcL-atpB untranslated region is extremely diverged, with only the putative rbcL promoters and ribosome-binding site being extensively conserved.

scholarly journals In vitro synthesis and processing of a maize chloroplast transcript encoded by the ribulose 1,5-bisphosphate carboxylase large subunit gene.

1985 ◽  
Vol 5 (10) ◽  
pp. 2733-2745 ◽  
Author(s):  
L Hanley-Bowdoin ◽  
E M Orozco ◽  
N H Chua
Keyword(s):  
Transcription Initiation ◽  
Large Subunit ◽  
Plastid Dna ◽  
Subunit Gene ◽  
Coding Region ◽  
Protein Coding ◽  
Bisphosphate Carboxylase ◽  
Transcription In Vitro ◽  
Maize Chloroplast

The large subunit gene (rbcL) of ribulose 1,5-bisphosphate carboxylase was transcribed in vitro by using maize and pea chloroplast extracts and a cloned plastid DNA template containing 172 base pairs (bp) of the maize rbcL protein-coding region and 791 bp of upstream sequences. Three major in vitro RNA species were synthesized which correspond to in vivo maize rbcL RNAs with 5' termini positioned 300, 100 to 105, and 63 nucleotides upstream of the protein-coding region. A deletion of 109 bp, including the "-300" 5' end (the 5' end at position -300), depressed all rbcL transcription in vitro. A plasmid DNA containing this 109-bp fragment was sufficient to direct correct transcription initiation in vitro. A cloned template, containing 191 bp of plastid DNA which includes the -105 and -63 rbcL termini, did not support transcription in vitro. Exogenously added -300 RNA could be converted to the -63 transcript by maize chloroplast extract. These results established that the -300 RNA is the primary maize rbcL transcript, the -63 RNA is a processed form of the -300 transcript, and synthesis of the -105 RNA is dependent on the -300 region. The promoter for the maize rbcL gene is located within the 109 bp flanking the -300 site. Mutagenesis of the 109-bp chloroplast sequence 11 bp upstream of the -300 transcription initiation site reduced rbcL promoter activity in vitro.

In vitro synthesis and processing of a maize chloroplast transcript encoded by the ribulose 1,5-bisphosphate carboxylase large subunit gene

1985 ◽  
Vol 5 (10) ◽  
pp. 2733-2745
Author(s):  
L Hanley-Bowdoin ◽  
E M Orozco ◽  
N H Chua
Keyword(s):  
Transcription Initiation ◽  
Large Subunit ◽  
Plastid Dna ◽  
Subunit Gene ◽  
Coding Region ◽  
Protein Coding ◽  
Bisphosphate Carboxylase ◽  
Transcription In Vitro ◽  
Maize Chloroplast

The large subunit gene (rbcL) of ribulose 1,5-bisphosphate carboxylase was transcribed in vitro by using maize and pea chloroplast extracts and a cloned plastid DNA template containing 172 base pairs (bp) of the maize rbcL protein-coding region and 791 bp of upstream sequences. Three major in vitro RNA species were synthesized which correspond to in vivo maize rbcL RNAs with 5' termini positioned 300, 100 to 105, and 63 nucleotides upstream of the protein-coding region. A deletion of 109 bp, including the "-300" 5' end (the 5' end at position -300), depressed all rbcL transcription in vitro. A plasmid DNA containing this 109-bp fragment was sufficient to direct correct transcription initiation in vitro. A cloned template, containing 191 bp of plastid DNA which includes the -105 and -63 rbcL termini, did not support transcription in vitro. Exogenously added -300 RNA could be converted to the -63 transcript by maize chloroplast extract. These results established that the -300 RNA is the primary maize rbcL transcript, the -63 RNA is a processed form of the -300 transcript, and synthesis of the -105 RNA is dependent on the -300 region. The promoter for the maize rbcL gene is located within the 109 bp flanking the -300 site. Mutagenesis of the 109-bp chloroplast sequence 11 bp upstream of the -300 transcription initiation site reduced rbcL promoter activity in vitro.

scholarly journals Molecular analysis of the hot spot region related to length mutations in wheat chloroplast DNAs. I. Nucleotide divergence of genes and intergenic spacer regions located in the hot spot region.

Genetics ◽  
1991 ◽  
Vol 129 (3) ◽  
pp. 873-884 ◽  
Author(s):  
Y Ogihara ◽  
T Terachi ◽  
T Sasakuma
Keyword(s):  
Dna Sequences ◽  
Gene Evolution ◽  
Hot Spot ◽  
Intergenic Spacer ◽  
Open Reading Frames ◽  
Coding Region ◽  
Nucleotide Substitutions ◽  
Plant Groups ◽  
Nucleotide Divergence ◽  
Chloroplast Dnas

Abstract The nucleotide divergence of chloroplast DNAs around the hot spot region related to length mutation in Triticum (wheat) and Aegilops was analyzed. DNA sequences (ca. 4.5 kbp) of three chloroplast genome types of wheat complex were compared with one another and with the corresponding region of other grasses. The sequences region contained rbcL and psaI, two open reading frames, and a pseudogene, rpl23' (pseudogene for ribosomal protein L23) disrupted by AT-rich intergic spacer regions. The evolution of these genes in the closely related wheat complex is characterized by nonbiased nucleotide substitutions in terms of being synonymous/nonsynonymous, having A-T pressure transitions over transversions, and frequent changes at the third codon position, in contrast with the gene evolution among more distant plant groups where biased nucleotide substitutions have frequently occurred. The sequences of these genes had diverged almost in proportion to taxonomic distance. The sequence of the pseudogene rpl23' changed approximately two times faster than that of the coding region. Sequence comparison between the pseudogene and its protein-coding counterpart revealed different degrees of nucleotide homology in wheat, rice and maize, suggesting that the transposition timing of the pseudogene differed and/or that different rates of gene conversion operated on the pseudogene in the cpDNA of the three plant groups in Gramineae. The intergenic spacer regions diverged approximately ten times faster than the genes. The divergence of wheat from barley, and that from rice are estimated based on the nucleotide similarity to be 1.5, 10 and 40 million years, respectively.

A reassessment of tribal affinities of the enigmatic genera Printzia and Isoetopsis (Asteraceae), based on three chloroplast sequences

2002 ◽  
Vol 50 (6) ◽  
pp. 677 ◽  
Author(s):  
Randall J. Bayer ◽  
Edward W. Cross
Keyword(s):  
Phylogenetic Analysis ◽  
Chloroplast Dna ◽  
Dna Sequences ◽  
Trnl Intron ◽  
Coding Region ◽  
Strong Affinity ◽  
Taxonomic History ◽  
Chloroplast Dna Sequences ◽  
Chemical Characters

The tribal affinities of two dubiously placed genera of the Asteraceae, Printzia and Isoetopsis, were assessed by using three chloroplast DNA sequences, the trnL/F spacer, the trnL intron and the matK coding region. The outgroup was represented by two species of the tribe Barnadesieae, whereas one to six genera (43 species including Printzia and Isoetopsis) of the tribes of the Asteroideae [Anthemideae (six genera), Astereae (five) Calenduleae (two), Gnaphalieae (six), Heliantheae s.l. (five), Inuleae s.str. (three), Plucheeae (two), Senecioneae (four)] and Cichorioideae [Arctotideae (one), Cardueae (two), Lactuceae (two), Liabeae (one), Mutisieae (one), Vernonieae (one)] were chosen as the ingroup. Phylogenetic analysis indicates that both Printzia and Isoetopsis have a strong affinity with members of the tribe Astereae. At some point in their taxonomic history, both genera had been placed in this tribe and there are good morphological and chemical characters that justify this placement.

scholarly journals Evolution of Cyanobacteria by Exchange of Genetic Material among Phyletically Related Strains

1998 ◽  
Vol 180 (13) ◽  
pp. 3453-3461 ◽  
Author(s):  
Knut Rudi ◽  
Olav M. Skulberg ◽  
Kjetill S. Jakobsen
Keyword(s):  
16S Rdna ◽  
Molecular Mechanisms ◽  
Large Subunit ◽  
Genetic Material ◽  
The Other ◽  
Small Subunit Rrna ◽  
Nucleotide Substitutions ◽  
Bisphosphate Carboxylase ◽  
Other Hand ◽  
Conserved Gene

ABSTRACT The cyanobacterial radiation consists of several lineages of phyletically (morphologically and genetically) related organisms. Several of these organisms show a striking resemblance to fossil counterparts. To investigate the molecular mechanisms responsible for stabilizing or homogenizing cyanobacterial characters, we compared the evolutionary rates and phylogenetic origins of the small-subunit rRNA-encoding DNA (16S rDNA), the conserved gene rbcL(encoding d-ribulose 1,5-bisphosphate carboxylase-oxygenase large subunit), and the less conserved gene rbcX. This survey includes four categories of phyletically related organisms: 16 strains of Microcystis, 6 strains of Tychonema, 10 strains of Planktothrix, and 12 strains ofNostoc. Both rbcL and rbcX can be regarded as neutrally evolving genes, with 95 to 100% and 50 to 80% synonymous nucleotide substitutions, respectively. There is generally low sequence divergence within the Microcystis,Tychonema, and Planktothrix categories both forrbcLX and 16S rDNA. The Nostoc category, on the other hand, consists of three genetically clustered lineages for these loci. The 16S rDNA and rbcLX phylogenies are not congruent for strains within the clustered groups. Furthermore, analysis of the phyletic structure for rbcLX indicates recombinational events between the informative sites within this locus. Thus, our results are best explained by a model involving both intergenic and intragenic recombinations. This evolutionary model explains the DNA sequence clustering for the modern species as a result of sequence homogenization (concerted evolution) caused by exchange of genetic material for neutrally evolving genes. The morphological clustering, on the other hand, is explained by structural and functional stability of these characters. We also suggest that exchange of genetic material for neutrally evolving genes may explain the apparent stability of cyanobacterial morphological characters, perhaps over billions of years.

Isolation and characterization of calmodulin genes from Xenopus laevis

1984 ◽  
Vol 4 (3) ◽  
pp. 507-513
Author(s):  
Y H Chien ◽  
I B Dawid
Keyword(s):  
Xenopus Laevis ◽  
Dna Sequences ◽  
Complete Analysis ◽  
Cdna Clones ◽  
Coding Region ◽  
Nucleotide Substitutions ◽  
Protein Coding ◽  
Isolation And Characterization ◽  
Electric Eel ◽  
Complete Protein

Two cDNAs derived from Xenopus laevis calmodulin mRNA have been cloned. Both cDNAs contain the complete protein-coding region and various lengths of untranslated segments. The two cDNAs encode an identical protein but differ from each other by 5% nucleotide substitutions. The 5' and 3' untranslated regions, to the extent available, are highly homologous between the two cDNAs. The predicted sequence of X. laevis calmodulin is identical to that of vertebrate calmodulins from mammals and chickens and shows one substitution compared with electric eel calmodulin. Genomic DNA sequences homologous to each of the two cDNA clones have been isolated and were shown to account for the major calmodulin-coding DNA sequences in X. laevis. These data suggest that X. laevis carries two active, nonallelic calmodulin genes. Although no complete analysis has been carried out, it appears that the X. laevis calmodulin genes are interrupted by at least four introns. The relative concentrations of calmodulin mRNA have been estimated in different embryonic stages and adult tissues and found to vary by up to a factor of 10. The highest levels of calmodulin mRNA were found in ovaries, testes, and brains. In these three tissues, the two calmodulin genes appear to be expressed at approximately equal levels.

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