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.

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.

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

Genetics ◽

10.1093/genetics/106.4.735 ◽

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.

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Isolation and characterization of calmodulin genes from Xenopus laevis

Molecular and Cellular Biology ◽

10.1128/mcb.4.3.507-513.1984 ◽

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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Limited and Localized Outbreak of Newly Emergent Type 2 Vaccine-Derived Poliovirus in Sichuan, China

Clinical and Vaccine Immunology ◽

10.1128/cvi.00196-14 ◽

2014 ◽

Vol 21 (7) ◽

pp. 1012-1018 ◽

Cited By ~ 10

Author(s):

Dongmei Yan ◽

Yong Zhang ◽

Shuangli Zhu ◽

Na Chen ◽

Xiaolei Li ◽

...

Keyword(s):

Temperature Sensitivity ◽

Close Contact ◽

Oral Poliovirus Vaccine ◽

Nucleotide Sequencing ◽

Coding Region ◽

Nucleotide Substitutions ◽

Inactivated Polio Vaccine ◽

Polio Vaccine ◽

Nucleotide Divergence

ABSTRACTFrom August 2011 to February 2012, an outbreak caused by type 2 circulating vaccine-derived poliovirus (cVDPV) occurred in Aba County, Sichuan, China. During the outbreak, four type 2 VDPVs (≥0.6% nucleotide divergence in theVP1region relative to the Sabin 2 strain) were isolated from 3 patients with acute flaccid paralysis (AFP) and one close contact. In addition, a type 2 pre-VDPV (0.3% to 0.5% divergence from Sabin 2) that was genetically related to these type 2 VDPVs was isolated from another AFP patient. These 4 patients were all unimmunized children 0.7 to 1.1 years old. Nucleotide sequencing revealed that the 4 VDPV isolates differed from Sabin 2 by 0.7% to 1.2% in nucleotides in theVP1region and shared 5 nucleotide substitutions with the pre-VDPV. All 5 isolates were closely related, and all were S2/S3/S2/S3 recombinants sharing common recombination crossover sites. Although the two major determinants of attenuation and temperature sensitivity phenotype of Sabin 2 (A481in the 5′ untranslated region and Ile143in theVP1protein) had reverted in all 5 isolates, one VDPV (strain CHN16017) still retained the temperature sensitivity phenotype. Phylogenetic analysis of the third coding position of the completeP1coding region suggested that the cVDPVs circulated locally for about 7 months following the initiating oral poliovirus vaccine (OPV) dose. Our findings reinforce the point that cVDPVs can emerge and spread in isolated communities with immunity gaps and highlight the emergence risks of type 2 cVDPVs accompanying the trivalent OPV used. To solve this issue, it is recommended that type 2 OPV be removed from the trivalent OPV or that inactivated polio vaccine (IPV) be used instead.

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Sequence changes in six variants of rice tungro bacilliform virus and their phylogenetic relationships

Journal of General Virology ◽

10.1099/0022-1317-80-8-2229 ◽

1999 ◽

Vol 80 (8) ◽

pp. 2229-2237 ◽

Cited By ~ 13

Author(s):

Pepito Q. Cabauatan ◽

Ulrich Melcher ◽

Koichi Ishikawa ◽

Toshihiro Omura ◽

Hiroyuki Hibino ◽

...

Keyword(s):

Dna Sequences ◽

Phylogenetic Relationships ◽

Open Reading Frames ◽

Rice Tungro Bacilliform Virus ◽

Likelihood Methods ◽

Nucleotide Substitutions ◽

Rich Region ◽

Evolutionary Forces ◽

Maximum Likelihood Methods ◽

Tree Topologies

The DNA of three biological variants, G1, Ic and G2, which originated from the same greenhouse isolate of rice tungro bacilliform virus (RTBV) at the International Rice Research Institute (IRRI), was cloned and sequenced. Comparison of the sequences revealed small differences in genome sizes. The variants were between 95 and 99% identical at the nucleotide and amino acid levels. Alignment of the three genome sequences with those of three published RTBV sequences (Phi-1, Phi-2 and Phi-3) revealed numerous nucleotide substitutions and some insertions and deletions. The published RTBV sequences originated from the same greenhouse isolate at IRRI 20, 11 and 9 years ago. All open reading frames (ORFs) and known functional domains were conserved across the six variants. The cysteine-rich region of ORF3 showed the greatest variation. When the six DNA sequences from IRRI were compared with that of an isolate from Malaysia (Serdang), similar changes were observed in the cysteine-rich region in addition to other nucleotide substitutions and deletions across the genome. The aligned nucleotide sequences of the IRRI variants and Serdang were used to analyse phylogenetic relationships by the bootstrapped parsimony, distance and maximum-likelihood methods. The isolates clustered in three groups: Serdang alone; Ic and G1; and Phi-1, Phi-2, Phi-3 and G2. The distribution of phylogenetically informative residues in the IRRI sequences shared with the Serdang sequence and the differing tree topologies for segments of the genome suggested that recombination, as well as substitutions and insertions or deletions, has played a role in the evolution of RTBV variants. The significance and implications of these evolutionary forces are discussed in comparison with badnaviruses and caulimoviruses.

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Isolation and characterization of calmodulin genes from Xenopus laevis.

Molecular and Cellular Biology ◽

10.1128/mcb.4.3.507 ◽

1984 ◽

Vol 4 (3) ◽

pp. 507-513 ◽

Cited By ~ 105

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

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Mutation Spectrum in Patients with Wiskott-Aldrich Syndrome and X-linked Thrombocytopenia: Identification of Twelve Different Mutations in the WASP Gene

Thrombosis and Haemostasis ◽

10.1055/s-0038-1650318 ◽

1996 ◽

Vol 75 (04) ◽

pp. 546-550 ◽

Cited By ~ 21

Author(s):

Marianne Schwartz ◽

Albert Békássy ◽

Mikael Donnér ◽

Thomas Hertel ◽

Stefan Hreidarson ◽

...

Keyword(s):

Base Pair ◽

Hot Spot ◽

Missense Mutations ◽

Nucleotide Substitutions ◽

Exon 2 ◽

Wiskott Aldrich Syndrome ◽

Base Pair Deletion ◽

Reliable Diagnosis ◽

Wasp Gene ◽

Detection Of Mutations

SummaryTwelve different mutations in the WASP gene were found in twelve unrelated families with Wiskott-Aldrich syndrome (WAS) or X-linked thrombocytopenia (XLT). Four frameshift, one splice, one nonsense mutation, and one 18-base-pair deletion were detected in seven patients with WAS. Only missense mutations were found in five patients diagnosed as having XLT. One of the nucleotide substitutions in exon 2 (codon 86) results in an Arg to Cys replacement. Two other nucleotide substitutions in this codon, R86L and R86H, have been reported previously, both giving rise to typical WAS symptoms, indicating a mutational hot spot in this codon. The finding of mutations in the WASP gene in both WAS and XLT gives further evidence of these syndromes being allelic. The relatively small size of the WASP gene facilitates the detection of mutations and a reliable diagnosis of both carriers and affected fetuses in families with WAS or XLT.

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Woot, an Active Gypsy-Class Retrotransposon in the Flour Beetle, Tribolium castaneum, is Associated With a Recent Mutation

Genetics ◽

10.1093/genetics/143.1.417 ◽

1996 ◽

Vol 143 (1) ◽

pp. 417-426

Author(s):

Richard W Beeman ◽

M Scott Thomson ◽

John M Clark ◽

Marco A DeCamillis ◽

Susan J Brown ◽

...

Keyword(s):

Sequence Analysis ◽

Tribolium Castaneum ◽

Frameshift Mutation ◽

Open Reading Frames ◽

Red Flour Beetle ◽

Intron Sequence ◽

Coding Region ◽

Long Terminal Repeats ◽

Flour Beetle ◽

Reading Frames

Abstract A recently isolated, lethal mutation of the homeotic Abdominal gene of the red flour beetle Tribolium castaneum is associated with an insertion of a novel retrotransposon into an intron. Sequence analysis indicates that this retrotransposon, named Woot, is a member of the gypsy family of mobile elements. Most strains of T. castaneum appear to harbor ~25-35 copies of Woot per genome. Woot is composed of long terminal repeats of unprecedented length (3.6 kb each), flanking an internal coding region 5.0 kb in length. For most copies of Woot, the internal region includes two open reading frames (ORFs) that correspond to the gag and pol genes of previously described retrotransposons and retroviruses. The copy of Woot inserted into Abdominal bears an apparent single frameshift mutation that separates the normal second ORF into two. Woot does not appear to generate infectious virions by the criterion that no envelop gene is discernible. The association of Woot with a recent mutation suggests that this retroelement is currently transpositionally active in at least some strains.

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Mitochondrial Intronic Open Reading Frames in Podospora: Mobility and Consecutive Exonic Sequence Variations

Genetics ◽

10.1093/genetics/143.2.777 ◽

1996 ◽

Vol 143 (2) ◽

pp. 777-788 ◽

Cited By ~ 2

Author(s):

Carole H Sellem ◽

Yves d'Aubenton-Carafa ◽

Michèle Rossignol ◽

Léon Belcour

Keyword(s):

Mitochondrial Genome ◽

Open Reading Frames ◽

Nucleotide Substitutions ◽

Sequence Comparisons ◽

Modular Evolution ◽

Group I ◽

Sequence Variations ◽

Type Strains ◽

Reading Frames ◽

Adjacent Exon

Abstract The mitochondrial genome of 23 wild-type strains belonging to three different species of The mitochondrial genome the filamentous fungus Podospora was examined. Among the 15 optional sequences identified are two intronic reading frames, nad1-i4-orf1 and cox1-i7-orf2. We show that the presence of these sequences was strictly correlated with tightly clustered nucleotide substitutions in the adjacent exon. This correlation applies to the presence or absence of closely related open reading frames (ORFs), found at the same genetic locations, in all the Pyrenomycete genera examined. The recent gain of these optional ORFs in the evolution of the genus Podospora probably account for such sequence differences. In the homoplasmic progeny from heteroplasmons constructed between Podospora strains differing by the presence of these optional ORFs, nad1-i4-orf1 and cox1-i7-orf2 appeared highly invasive. Sequence comparisons in the nad1-i4 intron of various strains of the Pyrenomycete family led us to propose a scenario of its evolution that includes several events of loss and gain of intronic ORFs. These results strongly reinforce the idea that group I intronic ORFs are mobile elements and that their transfer, and comcomitant modification of the adjacent exon, could participate in the modular evolution of mitochondrial genomes.

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Human DNA sequences homologous to a protein coding region conserved between homeotic genes of Drosophila

Cell ◽

10.1016/0092-8674(84)90261-7 ◽

1984 ◽

Vol 38 (3) ◽

pp. 667-673 ◽

Cited By ~ 121

Author(s):

Michael Levine ◽

Gerald M. Rubin ◽

Robert Tjian

Keyword(s):

Dna Sequences ◽

Homeotic Genes ◽

Coding Region ◽

Protein Coding ◽

Human Dna

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Molecular evolution of homologous gene sequences in germline-limited and somatic chromosomes of Acricotopus

Genome ◽

10.1139/g04-026 ◽

2004 ◽

Vol 47 (4) ◽

pp. 732-741 ◽

Cited By ~ 2

Author(s):

Wolfgang Staiber

Keyword(s):

Molecular Evolution ◽

Dna Sequences ◽

Sequence Data ◽

Structural Evolution ◽

5S Rdna ◽

Oligonucleotide Primer ◽

Homologous Gene ◽

Gene Sequences ◽

Nucleotide Substitutions ◽

Degenerate Oligonucleotide

The origin of germline-limited chromosomes (Ks) as descendants of somatic chromosomes (Ss) and their structural evolution was recently elucidated in the chironomid Acricotopus. The Ks consist of large S-homologous sections and of heterochromatic segments containing germline-specific, highly repetitive DNA sequences. Less is known about the molecular evolution and features of the sequences in the S-homologous K sections. More information about this was received by comparing homologous gene sequences of Ks and Ss. Genes for 5.8S, 18S, 28S, and 5S ribosomal RNA were choosen for the comparison and therefore isolated first by PCR from somatic DNA of Acricotopus and sequenced. Specific K DNA was collected by microdissection of monopolar moving K complements from differential gonial mitoses and was then amplified by degenerate oligonucleotide primer (DOP)-PCR. With the sequence data of the somatic rDNAs, the homologous 5.8S and 5S rDNA sequences were isolated by PCR from the DOP-PCR sequence pool of the Ks. In addition, a number of K DOP-PCR sequences were directly cloned and analysed. One K clone contained a section of a putative N-acetyltransferase gene. Compared with its homolog from the Ss, the sequence exhibited few nucleotide substitutions (99.2% sequence identity). The same was true for the 5.8S and 5S sequences from Ss and Ks (97.5%100% identity). This supports the idea that the S-homologous K sequences may be conserved and do not evolve independently from their somatic homologs. Possible mechanisms effecting such conservation of S-derived sequences in the Ks are discussed.Key words: microdissection, DOP-PCR, germline-limited chromosomes, molecular evolution.

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