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1.
Vladimir Kanazin Tom Blake Randy C. Shoemaker 《Molecular & general genetics : MGG》1996,250(2):137-147
Several variants of the replacement histone H3 genes from soybean, barley and wheat have been cloned and sequenced. Analysis of segregating populations in barley and soybean, as well as analysis of clones isolated from a soybean genomic library, suggested that these genes are dispersed throughout the genome. Several genes contain introns located in similar positions, but of different lengths and sequence. Comparison of mRNA levels in different tissues revealed that the intron-containing and intronless genes have different expression patterns. The distribution of the introns in the histone H3 genes across several plant species suggests that some of the introns might have been lost during the evolution of the gene family. Sequence divergence among introns and gene-flanking sequences in cloned gene variants allowed us to use them as specific probes for localizing individual gene copies and analyzing the genomic distribution of these variants across a range of genotypes.Journal paper No. J-16127 of the Iowa Agriculture and Home Economics Experiment Station, Ames, IowaMention of a trademark or proprietary product does not constitute a guarantee or warranty of the product by the United States Department of Agriculture and does not imply its approval to the exclusion of other products that may be suitable 相似文献
2.
Histones of the H1 group (linker histones) are abundant components of chromatin in eukaryotes, occurring on average at one
molecule per nucleosome. The recent reports on the lack of a clear phenotypic effect of knock-out mutations as well as overexpression
of histone H1 genes in different organisms have seriously undermined the long-held view that linker histones are essential
for the basic functions of eukaryotic cells. In an attempt to resolve the paradox of an abundant conserved protein without
a clear function, we re-examined the molecular and phylogenetic data on linker histones to see if they could reveal any correlation
between the features of H1 and the functional or morphological characteristics of cells or organisms. Because of an earlier
demonstration that in sea urchin the chromatin-type histone H1 is also found in the flagellar microtubules (Multigner et al.
1992), we focused on the correlation between the features of H1 and those of microtubular structures. A phylogenetic tree
based on multiple alignment of over 100 available H1 sequences suggests that the first divergence of the globular domain of
H1 (GH1) resulted in branching into separate types characteristic for plants/Dictyostelium and for animals/ascomycetes, respectively. The GH1s of these two types differ by a short region (usually 5 amino acids) placed
at a specific location within the C-terminal wing subdomain of GH1. Evolutionary analysis of the diversification of H1 mRNA
into cell-cycle-dependent (polyA−) and independent (polyA+) forms showed a mosaic occurrence of these two forms in plants and animals, despite the fact that the H1 proteins of plants
and animals belong to two well-distinguished groups. However, among organisms from both animal and plant kingdom, only those
with H1 mRNA of a polyA− type have flagellated gametes. This correlation as well as the demonstration that in Volvox carteri the accumulation of polyA− mRNA of H1 occurs concurrently with the production of new flagella (Lindauer et al. 1993), suggests a direct link between
polyA− phenotype of histone H1 mRNA and flagellogenesis.
Received: 25 May 2000 / Accepted: 5 February 2001 相似文献
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4.
Ferritin, a protein widespread in nature, concentrates iron ∼1011–1012-fold above the solubility within a spherical shell of 24 subunits; it derives in plants and animals from a common ancestor
(based on sequence) but displays a cytoplasmic location in animals compared to the plastid in contemporary plants. Ferritin
gene regulation in plants and animals is altered by development, hormones, and excess iron; iron signals target DNA in plants
but mRNA in animals. Evolution has thus conserved the two end points of ferritin gene expression, the physiological signals
and the protein structure, while allowing some divergence of the genetic mechanisms. Comparison of ferritin gene organization
in plants and animals, made possible by the cloning of a dicot (soybean) ferritin gene presented here and the recent cloning
of two monocot (maize) ferritin genes, shows evolutionary divergence in ferritin gene organization between plants and animals
but conservation among plants or among animals; divergence in the genetic mechanism for iron regulation is reflected by the
absence in all three plant genes of the IRE, a highly conserved, noncoding sequence in vertebrate animal ferritin mRNA. In
plant ferritin genes, the number of introns (n= 7) is higher than in animals (n= 3). Second, no intron positions are conserved when ferritin genes of plants and animals are compared, although all ferritin
gene introns are in the coding region; within kingdoms, the intron positions in ferritin genes are conserved. Finally, secondary
protein structure has no apparent relationship to intron/exon boundaries in plant ferritin genes, whereas in animal ferritin
genes the correspondence is high. The structural differences in introns/exons among phylogenetically related ferritin coding
sequences and the high conservation of the gene structure within plant or animal kingdoms suggest that kingdom-specific functional
constraints may exist to maintain a particular intron/exon pattern within ferritin genes. In the case of plants, where ferritin
gene intron placement is unrelated to triplet codons or protein structure, and where ferritin is targeted to the plastid,
the selection pressure on gene organization may relate to RNA function and plastid/nuclear signaling.
Received: 25 July 1995 / Accepted: 3 October 1995 相似文献
5.
Whereas the genomes of many organisms contain several nonallelic types of linker histone genes, one single histone H1 type
is known in Drosophila melanogaster that occurs in about 100 copies per genome. Amplification of H1 gene sequences from genomic DNA of wild type strains of D. melanogaster from Oregon, Australia, and central Africa yielded numerous clones that all exhibited restriction patterns identical to each
other and to those of the known H1 gene sequence. Nucleotide sequences encoding the evolutionarily variable domains of H1
were determined in two gene copies of strain Niamey from central Africa and were found to be identical to the known H1 sequence.
Most likely therefore, the translated sequences of D. melanogaster H1 genes do not exhibit intragenomic or intergenomic variations.
In contrast, three different histone H1 genes were isolated from D. virilis and found to encode proteins that differ remarkably from each other and from the H1 of D. melanogaster and D. hydei. About 40 copies of H1 genes are organized in the D. virilis genome with copies of core histone genes in gene quintets that were found to be located in band 25F of chromosome 2. Another
type of histone gene cluster is present in about 15 copies per genome and contains a variable intergenic sequence instead
of an H1 gene. The H1 heterogeneity in D. virilis may have arisen from higher recombination rates than occur near the H1 locus in D. melanogaster and might provide a basis for formation of different chromatin subtypes.
Received: 2 March 2000 / Accepted: 1 June 2000 相似文献
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8.
Birgit Drabent Jae-Sun Kim Werner Albig Eva Prats Luis Cornudella Detlef Doenecke 《Journal of molecular evolution》1999,49(5):645-655
We isolated five different phage clones containing histone gene clusters with up to five H1 genes per phage clone from a
Mytilus edulis genomic library. Among these H1 genes, nine gene types coding for five different H1 proteins have been identified. All H1
histone genes were located on repetitive restriction fragments with only slightly different sizes. The H1 coding regions show
highly related sequences, suggesting that the multitude of H1 genes has evolved by gene duplication events. Core histone genes
could not be found on these five Mytilus edulis genome fragments.
Received: 28 July 1998 / Accepted: 17 May 1999 相似文献
9.
The histones H4 are known as highly conserved proteins. However, in ciliates a high degree of variation was found compared
both to other eukaryotes and between the ciliate species. To date, only H4 histones of species belonging to two distantly
related classes have been investigated. In order to obtain more detailed information on histone H4 variation in ciliates we
undertook a comprehensive sequence analysis of PCR-amplified internal H4 fragments from 12 species belonging to seven out
of the nine currently recognized ciliate classes. In addition, we used PCR primers to amplify longer fragments of H3 and H4
genes including the intergenic region.
The encoded amino acid sequences reveal a high number of differences when compared with those of other eukaryotes and the
ciliate species investigated. Furthermore, in some species H4 gene variants were detected, which result in amino acid differences.
The greatest number of substitutions and insertions found was in the amino terminal region of the H4 histones. However, all
sequences possess a conserved region corresponding to those of all other eukaryotic H4 histones.
The histone gene variations were used to reconstruct phylogenetic relationships. The tree from our data matches perfectly
with the ribosomal RNA data: The heterotrichs, which were considered as a late branching lineage, diverge at the base of the
ciliate tree and groups formerly thought to represent ancestral lineages now appear as highly derived ciliates.
Received: 4 April 1997 / Accepted: 1 August 1997 相似文献
10.
Ronald W. DeBry 《Journal of molecular evolution》1998,46(3):355-360
Sequences were obtained from five species of rodents that are orthologous to an H2a histone pseudogene from Mus musculus. The pseudogene is part of the cluster of replication-dependent histone genes found on Mus musculus chromosome 13. Comparative analysis of these five sequences together with the previously published sequence from M. musculus shows that this gene has likely been a pseudogene throughout the evolution of the genus Mus, while the gene from Rattus norvegicus is likely functional. Three large (>20 bp) deletions were found among the Mus pseudogenes, a feature that is very unusual compared to surveys of processed pseudogenes. In addition, there are two single-base
deletions and one 4-bp insertion among the Mus pseudogenes. The species distributions of one of the large deletions and the 4-bp insertion require either independent insertions
of an identical sequence, independent deletions with identical boundaries, or a deletion followed by precise reintegration
of the original sequence. The evidence favors the hypothesis of multiple deletions with identical boundaries. The ``coding'
regions of the Mus pseudogenes show a much reduced level of among-species variability in the 3′ half of the pseudogene, compared both to the
5′ half and to flanking sequences. This supports a hypothesis that the 3′ end of the pseudogene is the target of frequent
gene conversion by functional H2a genes.
Received: 1 April 1997 / Accepted: 12 June 1997 相似文献
11.
The uni linkage group (ULG) of Chlamydomonas reinhardtii contains many genes involved in the basal body-flagellar system. Recent evidence suggests that the corresponding uni chromosome is located in close proximity to the basal body complex. In the course of studies into its molecular organization, we have found a cluster of four histone genes on the ULG. The genes are arranged as divergently-transcribed pairs: H3-H4 and H2B-H2A. Genomic sequencing reveals that these genes lack introns and contain characteristic 3' palindromes similar to those of animals. The predicted amino acid sequences are highly conserved across species, with greatest similarities to the histone genes of Volvox. Southern analysis shows that each histone gene is present in 15-20 copies in Chlamydomonas and suggests a dispersed genomic organization. Northern analysis of mitotically-synchronized cells shows that, like the replication-dependent histones of higher eukaryotes, Chlamydomonas histone genes are expressed during S-phase. Using a gene-specific probe on Northern blots, we provide evidence that the ULG H4 gene is regulated in the same manner as other Chlamydomonas histone genes. Finally, micrococcal nuclease protection experiments show that the uni chromosome itself associates with histone proteins and displays a conventional nucleosomal banding pattern. 相似文献
12.
Ustilago maydis is a haploid basidiomycete with single genes for two distinct histone H3 variants. The solitary U1 gene codes for H3.1, predicted to be a replication-independent replacement histone. The U2 gene is paired with histone H4 and produces a putative replication-coupled H3.2 variant. These predictions were evaluated experimentally. U2 was confirmed to be highly expressed in the S phase and had reduced expression in hydroxyurea, and H3.2 protein was not incorporated into transcribed chromatin of stationary phase cells. Constitutive expression of U1 during growth produced ~25% of H3 as H3.1 protein, more highly acetylated than H3.2. The level of H3.1 increased when cell proliferation slowed, a hallmark of replacement histones. Half of new H3.1 incorporated into highly acetylated chromatin was lost with a half-life of 2.5 h, the fastest rate of replacement H3 turnover reported to date. This response reflects the characteristic incorporation of replacement H3 into transcribed chromatin, subject to continued nucleosome displacement and a loss of H3 as in animals and plants. Although the two H3 variants are functionally distinct, neither appears to be essential for vegetative growth. KO gene disruption transformants of the U1 and U2 loci produced viable cell lines. The structural and functional similarities of the Ustilago replication-coupled and replication-independent H3 variants with those in animals, in plants, and in ciliates are remarkable because these distinct histone H3 pairs of variants arose independently in each of these clades and in basidiomycetes. 相似文献
13.
Molecular evolution of calmodulin-like domain protein kinases (CDPKs) in plants and protists 总被引:1,自引:0,他引:1
Many genes for calmodulin-like domain protein kinases (CDPKs) have been identified in plants and Alveolate protists. To study
the molecular evolution of the CDPK gene family, we performed a phylogenetic analysis of CDPK genomic sequences. Analysis
of introns supports the phylogenetic analysis; CDPK genes with similar intron/exon structure are grouped together on the phylogenetic
tree. Conserved introns support a monophyletic origin for plant CDPKs, CDPK-related kinases, and phosphoenolpyruvate carboxylase
kinases. Plant CDPKs divide into two major branches. Plant CDPK genes on one branch share common intron positions with protist
CDPK genes. The introns shared between protist and plant CDPKs presumably originated before the divergence of plants from
Alveolates. Additionally, the calmodulin-like domains of protist CDPKs have intron positions in common with animal and fungal
calmodulin genes. These results, together with the presence of a highly conserved phase zero intron located precisely at the
beginning of the calmodulin-like domain, suggest that the ancestral CDPK gene could have originated from the fusion of protein
kinase and calmodulin genes facilitated by recombination of ancient introns.
Received: 11 July 2000 / Accepted: 18 April 2001 相似文献
14.
Kelemen Z Mai A Kapros T Fehér A Györgyey J Waterborg JH Dudits D 《Transgenic research》2002,11(1):69-72
This study explored the possibility of using non-viral, plant-based gene sequences to create strong and constitutive expression vectors. Replacement histone H3 genes are highly and constitutively expressed in all plants. Sequences of the cloned alfalfa histone H3.2 gene MsH3g1 were tested. Constructs of the -glucuronidase (GUS) reporter gene were produced with H3.2 gene promoter and intron sequences. Their efficiency was compared with that of the commonly used strong 35S cauliflower mosaic virus promoter in transgenic tobacco plants. Combination of the H3.2 promoter and intron produced significantly higher GUS expression than the strong viral 35S promoter. Histochemical GUS analysis revealed a constitutive pattern of expression. Thus, alfalfa replacement H3 gene sequences can be used instead of viral promoters to drive heterologous gene expression in plants, avoiding perceived risks of viral sequences. 相似文献
15.
To study the evolution of human X-linked red and green opsin genes, genomic sequences in large regions of the two genes were
compared. The divergences in introns 3, 4, and 5 and the 3′ flanking sequence of the two genes are significantly lower than
those in exons 4 and 5. The homogenization mechanism of introns and the 3′ flanking sequence of human red and green opsin
genes is probably gene conversion, which also occurred in exons 1 and 6. At least one gene conversion event occurred in each
of three regions (1, 3, and 5) in the sequences compared. In conclusion, gene conversion has occurred frequently between human
red and green opsin genes, but exons 2, 3, 4, and 5 have been maintained distinct between the two genes by natural selection.
Received: 29 September 1997 / Accepted: 29 September 1997 相似文献
16.
D Brush J B Dodgson O R Choi P W Stevens J D Engel 《Molecular and cellular biology》1985,5(6):1307-1317
17.
Vinogradov AE 《Journal of molecular evolution》2001,52(1):2-5
The correlation was shown between the length of introns and the codon usage of the coding sequences of the corresponding
genes, which in some cases can be related to the level of gene expression. The link is positive in the unicellular organisms,
i.e., genes with the longer introns show the higher bias of codon usage. It is most pronounced in baker's yeast, where it
is definitely related to the level of gene expression—genes with the higher level of expression have the longer introns. The
correlation is inverted in multicellular organisms as compared to unicellular ones. Some organisms, however, do not show the
link. The presence or absence of the link does not seem to be related to the GC percent of the coding sequences.
Received: 7 December 1999 / Accepted: 10 May 2000 相似文献
18.
Gerhard Schenk Roy Layfield Judith M. Candy Ronald G. Duggleby Peter F. Nixon 《Journal of molecular evolution》1997,44(5):552-572
Members of the transketolase group of thiamine-diphosphate-dependent enzymes from 17 different organisms including mammals,
yeast, bacteria, and plants have been used for phylogenetic reconstruction. Alignment of the amino acid and DNA sequences
for 21 transketolase enzymes and one putative transketolase reveals a number of highly conserved regions and invariant residues
that are of predicted importance for enzyme activity, based on the crystal structure of yeast transketolase. One particular
sequence of 36 residues has some similarities to the nucleotide-binding motif and we designate it as the transketolase motif.
We report further evidence that the recP protein from Streptococcus pneumoniae might be a transketolase and we list a number of invariant residues which might be involved in substrate binding. Phylogenies
derived from the nucleotide and the amino acid sequences by various methods show a conventional clustering for mammalian,
plant, and gram-negative bacterial transketolases. The branching order of the gram-positive bacteria could not be inferred
reliably. The formaldehyde transketolase (sometimes known as dihydroxyacetone synthase) of the yeast Hansenula polymorpha appears to be orthologous to the mammalian enzymes but paralogous to the other yeast transketolases. The occurrence of more
than one transketolase gene in some organisms is consistent with several gene duplications. The high degree of similarity
in functionally important residues and the fact that the same kinetic mechanism is applicable to all characterized transketolase
enzymes is consistent with the proposition that they are all derived from one common ancestral gene. Transketolase appears
to be an ancient enzyme that has evolved slowly and might serve as a model for a molecular clock, at least within the mammalian
clade.
Received: 13 September 1995 / Accepted: 14 November 1996 相似文献
19.
We have determined the genomic structure of an integrin β-subunit gene from the coral, Acropora millepora. The coding region of the gene contains 26 introns, spaced relatively uniformly, and this is significantly more than have
been found in any integrin β-subunit genes from higher animals. Twenty-five of the 26 coral introns are also found in a β-subunit
gene from at least one other phylum, indicating that the coral introns are ancestral. While there are some suggestions of
intron gain or sliding, the predominant theme seen in the homologues from higher animals is extensive intron loss. The coral
baseline allows one to infer that a number of introns found in only one phylum of higher animals result from frequent intron
loss, as opposed to the seemingly more parsimonious alternative of isolated intron gain. The patterns of intron loss confirm
results from protein sequences that most of the vertebrate genes, with the exception of β4, belong to one of two β subunit
families. The similarity of the patterns within each of the β1,2,7 and β3,5,6,8 groups indicates that these gene structures
have been very stable since early vertebrate evolution. Intron loss has been more extensive in the invertebrate genes, and
obvious patterns have yet to emerge in this more limited data set.
Received: 5 March 2001 / Accepted: 17 May 2001 相似文献
20.
Alexander E. Vinogradov 《Journal of molecular evolution》1999,49(3):376-384
The intron–genome size relationship was studied across a wide evolutionary range (from slime mold and yeast to human and
maize), as well as the relationship between genome size and the ratio of intervening/coding sequence size. The average intron
size is scaled to genome size with a slope of about one-fourth for the log-transformed values; i.e., on the global scale its
increase in evolution is lower than the increase in genome size by four orders of magnitude. There are exceptions to the general
trend. In baker's yeast introns are extraordinarily long for its genome size. Tetrapods also have longer introns than expected
for their genome sizes. In teleost fish the mean intron size does not differ significantly, notwithstanding the differences
in genome size. In contrast to previous reports, avian introns were not found to be significantly shorter than introns of
mammals, although avian genomes are smaller than genomes of mammals on average by about a factor of 2.5. The extra-/intragenic
ratio of noncoding DNA can be higher in fungi than in animals, notwithstanding the smaller fungal genomes. In vertebrates
and invertebrates taken separately, this ratio is increasing as the increase in genome size. Two hypotheses are proposed to
explain the variation in the extra-/intragenic ratio of noncoding DNA in organisms with similar numbers of genes: transition
(dynamic) and equilibrium (static). According to the transition model, this variation arises with the rapid shift of genome
size because the bulk of extragenic DNA can be changed more rapidly than the finely interspersed intron sequences. The equilibrium
model assumes that this variation is a result of selective adjustment of genome size with constraints imposed on the intron
size due to its putative link to chromatin structure (and constraints of the splicing machinery).
Received: 23 October 1997 / Accepted: 14 April 1999 相似文献