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1.
Ignacio Marín 《PloS one》2010,5(7)
Background
RBR ubiquitin ligases are components of the ubiquitin-proteasome system present in all eukaryotes. They are characterized by having the RBR (RING – IBR – RING) supradomain. In this study, the patterns of emergence of RBR genes in plants are described.Methodology/Principal Findings
Phylogenetic and structural data confirm that just four RBR subfamilies (Ariadne, ARA54, Plant I/Helicase and Plant II) exist in viridiplantae. All of them originated before the split that separated green algae from the rest of plants. Multiple genes of two of these subfamilies (Ariadne and Plant II) appeared in early plant evolution. It is deduced that the common ancestor of all plants contained at least five RBR genes and the available data suggest that this number has been increasing slowly along streptophyta evolution, although losses, especially of Helicase RBR genes, have also occurred in several lineages. Some higher plants (e. g. Arabidopsis thaliana, Oryza sativa) contain a very large number of RBR genes and many of them were recently generated by tandem duplications. Microarray data indicate that most of these new genes have low-level and sometimes specific expression patterns. On the contrary, and as occurs in animals, a small set of older genes are broadly expressed at higher levels.Conclusions/Significance
The available data suggests that the dynamics of appearance and conservation of RBR genes is quite different in plants from what has been described in animals. In animals, an abrupt emergence of many structurally diverse RBR subfamilies in early animal history, followed by losses of multiple genes in particular lineages, occurred. These patterns are not observed in plants. It is also shown that while both plants and animals contain a small, similar set of essential RBR genes, the rest evolves differently. The functional implications of these results are discussed. 相似文献2.
Ignacio Marín 《PloS one》2013,8(7)
HECT ubiquitin ligases are key components of the ubiquitin-proteasome system, which is present in all eukaryotes. In this study, the patterns of emergence of HECT genes in plants are described. Phylogenetic and structural data indicate that viridiplantae have six main HECT subfamilies, which arose before the split that separated green algae from the rest of plants. It is estimated that the common ancestor of all plants contained seven HECT genes. Contrary to what happened in animals, the number of HECT genes has been kept quite constant in all lineages, both in chlorophyta and streptophyta, although evolutionary recent duplications are found in some species. Several of the genes found in plants may have originated very early in eukaryotic evolution, given that they have clear similarities, both in sequence and structure, to animal genes. Finally, in Arabidopsis thaliana, we found significant correlations in the expression patterns of HECT genes and some ancient, broadly expressed genes that belong to a different ubiquitin ligase family, called RBR. These results are discussed in the context of the evolution of the gene families required for ubiquitination in plants. 相似文献
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Siddique M Gernhard S von Koskull-Döring P Vierling E Scharf KD 《Cell stress & chaperones》2008,13(2):183-197
The small heat shock proteins (sHsps), which are ubiquitous stress proteins proposed to act as chaperones, are encoded by
an unusually complex gene family in plants. Plant sHsps are classified into different subfamilies according to amino acid
sequence similarity and localization to distinct subcellular compartments. In the whole Arabidopsis thaliana genome, 19 genes were annotated to encode sHsps, of which 14 belong to previously defined plant sHsp families. In this paper,
we report studies of the five additional sHsp genes in A. thaliana, which can now be shown to represent evolutionarily distinct sHsp subfamilies also found in other plant species. While two
of these five sHsps show expression patterns typical of the other 14 genes, three have unusual tissue specific and developmental
profiles and do not respond to heat induction. Analysis of intracellular targeting indicates that one sHsp represents a new
class of mitochondrion-targeted sHsps, while the others are cytosolic/nuclear, some of which may cooperate with other sHsps
in formation of heat stress granules. Three of the five new proteins were purified and tested for chaperone activity in vitro.
Altogether, these studies complete our basic understanding of the sHsp chaperone family in plants.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
5.
Proteins of the ring between ring fingers (RBR)-domain family are characterized by three groups of specifically clustered (typically eight) cysteine and histidine residues. Whereas the amino-terminal ring domain (N-RING) binds two zinc ions and folds into a classical cross-brace ring finger, the carboxy-terminal ring domain (C-RING) involves only one zinc ion. The three-dimensional structure of the central ring domain, the IBR domain, is still unsolved. About 400 genes coding for RBR proteins have been identified in the genomes of uni- and multicellular eukaryotes and some of their viruses, but the family has not been found in archaea or bacteria. The RBR proteins are classified into 15 major subfamilies (besides some orphan cases) by the phylogenetic relationships of the RBR segments and the conservation of their sequence architecture. The RBR domain mediates protein-protein interactions and a subset of RBR proteins has been shown to function as E3 ubiquitin ligases. RBR proteins have attracted interest because of their involvement in diseases such as parkinsonism, dementia with Lewy bodies, and Alzheimer's disease, and in susceptibility to some intracellular bacterial pathogens. Here, we present an overview of the RBR-domain containing proteins and their subcellular localization, additional domains, function, specificity, and regulation. 相似文献
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In mammals, AMP-activated protein kinase (AMPK) is involved in the regulation of cellular energy homeostasis and, on the whole
animal level, in regulating energy balance and food intake. In this paper, the relative synonymous codon use frequency of
40 AMPK family genes from seven mammal species (Bos taurus, Homo sapiens, Macaca mulatta, Mus musculus, Pan troglodytes, Rattus norvegicus, Sus scrofa) were analyzed using correspondence analysis and hierarchical cluster method. The result suggests that gene function is the
dominant factor that determines codon usage bias in AMPK family genes, while species is a minor factor that determines further
difference in codon usage bias for genes with similar functions.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
8.
In this study we compare patterns of mandibular integration between mice and baboons using both phenotypic and quantitative
genetic data. Specifically, we test how well each species fits with the mosaic model of mandibular integration suggested by
Atchley and Hall (Biol Rev Camb Philos Soc 66:101–157, 1991) based on developmental modules. We hypothesize that patterns
of integration will be similar for mice and baboons and that both species will show strong integration within developmental
modules and weaker integration between modules. Corresponding landmark data were collected from the hemi-mandibles of an advanced
intercross mouse sample (N = 1239) and mandibles from a baboon sample of known pedigree from the Southwest Foundation for Biomedical Research (N = 430). We used four methods of analysis to quantify and compare the degree of mandibular integration between species including
two methods based on a priori assumptions, and two a posteriori analyses. We found that patterns of integration are broadly
similar for baboon and mouse mandibles, with both species displaying a modular pattern of integration. While there is a general
trend of similarity in integration patterns between species, there were some marked differences. Mice are strongly correlated
among distances within the coronoid process and the incisive alveolar region, whereas baboons are strongly integrated within
the condylar process. We discuss the potential evolutionary implications of the similar patterns of integration between these
species with an emphasis on the role of modularity.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
9.
The small heat shock proteins (sHSPs) are a diverse family of molecular chaperones. It is well established that these proteins
are crucial components of the plant heat shock response. They also have important roles in other stress responses and in normal
development. We have conducted a comparative sequence analysis of the sHSPs in three complete angiosperms genomes: Arabidopsis thaliana, Populus trichocarpa, and Oryza sativa. Our phylogenetic analysis has identified four additional plant sHSP subfamilies and thus has increased the number of plant
sHSP subfamilies from 7 to 11. We have also identified a number of novel sHSP genes in each genome that lack close homologs
in other genomes. Using publicly available gene expression data and predicted secondary structures, we have determined that
the sHSPs in plants are far more diverse in sequence, expression profile, and in structure than had been previously known.
Some of the newly identified subfamilies are not stress regulated, may not posses the highly conserved large oligomer structure,
and may not even function as molecular chaperones. We found no consistent evolutionary patterns across the three species studied.
For example, gene conversion was found among the sHSPs in O. sativa but not in A. thaliana or P. trichocarpa. Among the three species, P. trichocarpa had the most sHSPs. This was due to an expansion of the cytosolic I sHSPs that was not seen in the other two species. Our
analysis indicates that the sHSPs are a dynamic protein family in angiosperms with unexpected levels of diversity.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
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Compared with the X chromosome, the mammalian Y chromosome is considerably diminished in size and has lost most of its ancestral
genes during evolution. Interestingly, for the X-degenerate region on the Y chromosome, human has retained all 16 genes, while
chimpanzee has lost 4 of the 16 genes since the divergence of the two species. To uncover the evolutionary forces governing
ape Y chromosome degeneration, we determined the complete sequences of the coding exons and splice sites for 16 gorilla Y
chromosome genes of the X-degenerate region. We discovered that all studied reading frames and splice sites were intact, and
thus, this genomic region experienced no gene loss in the gorilla lineage. Higher nucleotide divergence was observed in the
chimpanzee than the human lineage, particularly for genes with disruptive mutations, suggesting a lack of functional constraints
for these genes in chimpanzee. Surprisingly, our results indicate that the human and gorilla orthologues of the genes disrupted
in chimpanzee evolve under relaxed functional constraints and might not be essential. Taking mating patterns and effective
population sizes of ape species into account, we conclude that genetic hitchhiking associated with positive selection due
to sperm competition might explain the rapid decline in the Y chromosome gene number in chimpanzee. As we found no evidence
of positive selection acting on the X-degenerate genes, such selection likely targets other genes on the chimpanzee Y chromosome.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
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Chunzhao Zhao Cees Waalwijk Pierre JGM de Wit Dingzhong Tang Theo van der Lee 《BMC genomics》2014,15(1)
Background
Genome comparisons between closely related species often show non-conserved regions across chromosomes. Some of them are located in specific regions of chromosomes and some are even confined to one or more entire chromosomes. The origin and biological relevance of these non-conserved regions are still largely unknown. Here we used the genome of Fusarium graminearum to elucidate the significance of non-conserved regions.Results
The genome of F. graminearum harbours thirteen non-conserved regions dispersed over all of the four chromosomes. Using RNA-Seq data from the mycelium of F. graminearum, we found weakly expressed regions on all of the four chromosomes that exactly matched with non-conserved regions. Comparison of gene expression between two different developmental stages (conidia and mycelium) showed that the expression of genes in conserved regions is stable, while gene expression in non-conserved regions is much more influenced by developmental stage. In addition, genes involved in the production of secondary metabolites and secreted proteins are enriched in non-conserved regions, suggesting that these regions could also be important for adaptations to new environments, including adaptation to new hosts. Finally, we found evidence that non-conserved regions are generated by sequestration of genes from multiple locations. Gene relocations may lead to clustering of genes with similar expression patterns or similar biological functions, which was clearly exemplified by the PKS2 gene cluster.Conclusions
Our results showed that chromosomes can be functionally divided into conserved and non-conserved regions, and both could have specific and distinct roles in genome evolution and regulation of gene expression.Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-191) contains supplementary material, which is available to authorized users. 相似文献16.
Carr M 《Genetica》2008,132(2):113-122
The Diopsid stalk-eyed flies are an increasingly well-studied group. Presented here is evidence of the first known transposable
elements discovered in these flies. The vertumnana mariner subfamily was identified in the Diopsini tribe, but could not be amplified in species of the Sphyracephalini tribe. PCR screening
with degenerate primers revealed that multiple mariner subfamilies are present within the Diopsidae. Most of the sequenced elements appear to be pseudogenes; however two subfamilies
are shown to be evolving under purifying selection, raising the possibility that mariner is active in some Diopsid species. Evidence is presented of a possible horizontal transfer event involving an unknown Teleopsis species and the Tephritid fly Bactrocera neohumeralis.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
17.
Phylogenomic Analysis of the PEBP Gene Family in Cereals 总被引:1,自引:0,他引:1
The TFL1 and FT genes, which are key genes in the control of flowering time in Arabidopsis thaliana, belong to a small multigene family characterized by a specific phosphatidylethanolamine-binding protein domain, termed the
PEBP gene family. Several PEBP genes are found in dicots and monocots, and act on the control of flowering time. We investigated
the evolution of the PEBP gene family in cereals. First, taking advantage of the complete rice genome sequence and EST databases,
we found 19 PEBP genes in this species, 6 of which were not previously described. Ten genes correspond to five pairs of paralogs
mapped on known duplicated regions of the rice genome. Phylogenetic analysis of Arabidopsis and rice genes indicates that the PEBP gene family consists of three main homology classes (the so-called TFL1-LIKE, MFT-LIKE,
and FT-LIKE subfamilies), in which gene duplication and/or loss occurred independently in Arabidopsis and rice. Second, phylogenetic analyses of genomic and EST sequences from five cereal species indicate that the three subfamilies
of PEBP genes have been conserved in cereals. The tree structure suggests that the ancestral grass genome had at least two
MFT-like genes, two TFL1-like genes, and eight FT-like genes. A phylogenomic approach leads to some hypotheses about conservation of gene function within the subfamilies.
[Reviewing Editor: Dr. Yves Van de Peer] 相似文献
18.
RBR (RING1-IBR-RING2) proteins play an important role in protein ubiquitination and are involved in many cellular processes. Recent studies showed plant RBR genes were induced by abiotic and biotic stresses. However, detailed studies on RBR genes in the important oil crop, soybean (Glycine max (L.) Merr.), is still lacking. Here we performed a genome-wide search and identified 24 RBR domain-containing genes from the soybean genome sequence and cloned 11 of them. Most soybean RBR proteins contain a highly conserved RBR supra-domain. Phylogenetic analyses indicated all 24 soybean RBR proteins are most related to the RBR proteins from Phaseolus vulgaris, and could be classified into seven groups including Ariadne A, Ariadne B, ARA54, Plant IIA, Plant IIB, Plant IIC, and Helicase. Tandem duplication and block duplication were found among the Ariadne B and Plant IIC group of soybean RBR genes. Despite the conserved RBR supra-domain, there are extensive variations in the additional protein motifs and exon-intron structures between different groups, which indicate they might have diverse functions. Most soybean RBR proteins are predicted to localize in nucleus, and four of them were experimentally confirmed by GFP fusion proteins. Soybean RBR genes are broadly expressed in many tissue types with a little more abundant in the roots and flowers than leaves, stems, and seeds. The expression of GmRTRTP3 (Plant IIB) and GmRTRTP5 (Plant IIC) are induced by NaCl treatment, which suggests these RBR genes might be involved in soybean response to abiotic stresses. 相似文献
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Xiaoqian Xu Shuhui Song Qun Wang Fen Qin Kan Liu Xiaowei Zhang Songnian Hu Yunlong Zhao 《Molecular genetics and genomics : MGG》2009,282(2):197-203
The water flea Daphnia carinata (D. carinata) reproduces both sexually and parthenogenetically, yet little is known about the genes involved in these processes. To further
clarify the reproductive biology of Daphnia and elucidate their unique mechanism of reproductive transformation, we have generated and characterized an expressed sequence
tag (EST) data set from D. carinata. A set of 1,495 clusters were generated from sequencing 3,072 randomly chosen clones from a parthenogenetic, juvenile water
flea cDNA library. The nucleic acid and deduced amino acid sequences were compared with known GenBank sequences. Functional
annotation found that 959 clusters showed significant homology with known genes involved in a broad range of activities, including
metabolism, translation, development and reproduction, as well as genes involved in sensing environmental factors. We speculate
that genes involved in development and reproduction, along with genes that allow the organism to sense changes in the environment,
play important roles in the process of parthenogenetic reproduction and could be markers of the early steps of sexual differentiation.
Additionally, 86% of the D. Carinata unique sequences could be stringently mapped to the D. pulex genome, of which 125 mapped to intergenic and intronic regions on the current assembly. Our results provide practical insight
into crustacean reproductive biology, in addition to establishing a new animal model for reproductive and developmental biology.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.
Xiaoqian Xu and Shuhui Song contributed equally to this work.
Nucleotide sequence data reported are available in the GenBank databases under the accession numbers: GD269049−GD272045. 相似文献