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At least 343 records · Page 19Linked to original sources
PubMed2005

Molecular evolution of the plant virus family Bromoviridae based on RNA3-encoded proteins.

We have carried out an evolutionary study of the two proteins encoded by the RNA 3 from members of the plant virus family Bromoviridae. Using maximum likelihood methods, we have inferred the patterns of amino acid substitution that better explain the diversification of this viral family. The results indicate that the molecular evolution of this family was rather complex, with each protein evolving at different rates and according to different patterns of amino acid substitution. These differences include different amino acid equilibrium frequencies, heterogeneity in substitution rates among sites, and covariation among sites. Despite these differences, the model of protein evolution that better fits both proteins is one specifically proposed for the evolution of globular proteins. We also found evidence for coevolution between domains of these two proteins. Finally, our analyses suggest that the molecular clock hypothesis does not hold, since different lineages evolved at different rates. The implications of these results for the taxonomy of this important family of plant viruses are discussed.

Bromoviridae↗
PubMed2005

Sequence evidence for sporadic intergeneric DNA introgression from wheat into a wild Aegilops species.

Introgressive hybridization has played a crucial role in the evolution of many plant species, especially polyploids. The duplicated genetic material and wide geographical distribution facilitate hybridization and introgression among polyploid species having either homologous or homoeologous genomes. Such introgression may lead to the production of recombinant genomes that are more difficult to form at the diploid level. Crop genes that have introgressed into wild relatives can increase the capability of the wild relatives to adapt to agricultural environments and compete with crops or to compete with other wild species. Although the transfer of genes from crops into their conspecific immediate wild progenitors has been reported, little is known about spontaneous gene movement from crops to more distantly related species. We describe recent spontaneous DNA introgression from domesticated polyploid wheat into distantly related, wild tetraploid Aegilops peregrina (syn. Aegilops variabilis) and the stabilization of this sequence in wild populations despite not having homologous chromosomes. Our results show that DNA can spontaneously introgress between homoeologous genomes of species of the tribe Triticeae and, in the case of crop-wild relatives, possibly enrich the wild population. These results also emphasize the need for fail-safe mechanisms in transgenic crops to prevent gene flow where there may be ecological risks.

Base Sequence↗
PubMed2004

The evolution of host plant manipulation by insects: molecular and ecological evidence from gall-forming aphids on Pistacia.

One of the most striking characteristics of gall-forming insects is the variability in gall position, morphology, and complexity. Our knowledge of the driving forces behind the evolutionary divergence of gall types is limited. Natural enemies, competition, and behavioral constraints might be involved. We present a cladogram, based on sequences of COI and COII (1952bp), of mitochondrial DNA for the evolution of 14 species of gall-forming aphids (Fordinae). These insects induce five gall types with remarkable morphological variation on Pistacia spp. hosts. The parsimony cladogram divides the Fordinae into three lineages, Fordini and Baizongiini, and a third (new) sister group including the previously Fordini member, Smynthurodes betae (West). We then use ecological data to trace and explain the evolution of gall morphology. The aphids seem to have evolved gradually towards better ability to manipulate their host plant, induce stronger sinks, and gain higher reproductive success. We suggest that the ancestral gall type was a simple, open, "pea"-sized gall located on the leaflet midvein. Some Fordini and S. betae evolved a two-gall life cycle, inducing a new gall type on the leaflet margin. The Baizongiini improved the manipulation of their host by inducing larger galls near the midvein, with stronger sinks supporting thousands of aphids. Similar gall types are induced at similar sites on different Pistacia hosts suggesting control of the aphids on gall morphology and frequent host shifts. Thus, even extreme specialization (specific gall and host) is flexible.

Animals↗
PubMed2006

Evolution of filamentous plant pathogens: gene exchange across eukaryotic kingdoms.

Filamentous fungi and oomycetes are eukaryotic microorganisms that grow by producing networks of thread-like hyphae, which secrete enzymes to break down complex nutrients, such as wood and plant material, and recover the resulting simple sugars and amino acids by osmotrophy. These organisms are extremely similar in both appearance and lifestyle and include some of the most economically important plant pathogens . However, the morphological similarity of fungi and oomycetes is misleading because they represent some of the most distantly related eukaryote evolutionary groupings, and their shared osmotrophic growth habit is interpreted as being the result of convergent evolution . The fungi branch with the animals, whereas the oomycetes branch with photosynthetic algae as part of the Chromalveolata . In this report, we provide strong phylogenetic evidence that multiple horizontal gene transfers (HGT) have occurred from filamentous ascomycete fungi to the distantly related oomycetes. We also present evidence that a subset of the associated gene families was initially the product of prokaryote-to-fungi HGT. The predicted functions of the gene products associated with fungi-to-oomycete HGT suggest that this process has played a significant role in the evolution of the osmotrophic, filamentous lifestyle on two separate branches of the eukaryote tree.

Algal Proteins↗
PubMed2006

EST analysis of the scaly green flagellate Mesostigma viride (Streptophyta): implications for the evolution of green plants (Viridiplantae).

BACKGROUND: The Viridiplantae (land plants and green algae) consist of two monophyletic lineages, the Chlorophyta and the Streptophyta. The Streptophyta include all embryophytes and a small but diverse group of freshwater algae traditionally known as the Charophyceae (e.g. Charales, Coleochaete and the Zygnematales). The only flagellate currently included in the Streptophyta is Mesostigma viride Lauterborn. To gain insight into the genome evolution in streptophytes, we have sequenced 10,395 ESTs from Mesostigma representing 3,300 independent contigs and compared the ESTs of Mesostigma with available plant genomes (Arabidopsis, Oryza, Chlamydomonas), with ESTs from the bryophyte Physcomitrella, the genome of the rhodophyte Cyanidioschyzon, the ESTs from the rhodophyte Porphyra, and the genome of the diatom Thalassiosira. RESULTS: The number of expressed genes shared by Mesostigma with the embryophytes (90.3 % of the expressed genes showing similarity to known proteins) is higher than with Chlamydomonas (76.1 %). In general, cytosolic metabolic pathways, and proteins involved in vesicular transport, transcription, regulation, DNA-structure and replication, cell cycle control, and RNA-metabolism are more conserved between Mesostigma and the embryophytes than between Mesostigma and Chlamydomonas. However, plastidic and mitochondrial metabolic pathways, cytoskeletal proteins and proteins involved in protein folding are more conserved between Mesostigma and Chlamydomonas than between Mesostigma and the embryophytes. CONCLUSION: Our EST-analysis of Mesostigma supports the notion that this organism should be a suitable unicellular model for the last flagellate common ancestor of the streptophytes. Mesostigma shares more genes with the embryophytes than with the chlorophyte Chlamydomonas reinhardtii, although both organisms are flagellate unicells. Thus, it seems likely that several major physiological changes (e.g. in the regulation of photosynthesis and photorespiration) took place early during the evolution of streptophytes, i.e. before the transition to land.

Biological Evolution↗
PubMed1989

Variability and evolution of the plant RNA virus pepper mild mottle virus.

The RNA genomes of 26 isolates of pepper mild mottle virus were compared by their RNase T1 fingerprints. Twenty-three isolates came from epidemic outbreaks in greenhouse-grown peppers in Almería (southeastern Spain) from 1983 to 1987; three other isolates, from 1980, came from Sicily (Italy) and Zaragoza (central Spain). The 26 fingerprints can be classified into 10 different types; nucleotide substitution rates show them to be very similar. Cluster and cladistic analyses group types corresponding to the Almería isolates separate from those of 1980. Intraannual and interannual nucleotide differences were estimated. An evolutionary model for pepper mild mottle virus built on these data indicates a highly stable population, maintaining its diversity through time, with a main prevailing haplotype from which closely related variants arise that do not replace it. This high stability could be due to strong functional constraints on variation, as suggested by the high proportion of invariant versus polymorphic sites in fingerprints.

Biological Evolution↗
PubMed2003

Energy and the rate of evolution: inferences from plant rDNA substitution rates in the western Pacific.

In this study, we compare rDNA substitution rates for a group of closely related plant species in the western Pacific that exist in different biomes. The results of this comparison indicate higher rates of substitution for species living in habitats with greater biologically available energy. We interpret that finding as potentially important in understanding evolution because of its implication that substitution rate may be a function of biologically available energy and its correlate, productivity. The relevance of this research is twofold. First, contrasting closely related species across different biomes allows for a comparison between rates of molecular evolution across different energetic/productivity regimes while controlling for phylogenetically influenced variation. Second, the research indicates some of the design parameters for future studies that are required to explore the importance of this relationship among different groups of related organisms. If higher rates of molecular evolution where there is greater available energy are found to be widespread this might bring an additional dimension to the understanding of macroevolutionary pattern and process.

Australasia↗
PubMed2000

Mechanisms of plant embryo development.

1. Evolution in plants has favored both a simpler body plan with fewer cell types and the epigenetic flexibility to regenerate, via growth, dedifferentiation, and redifferentiation, to recover from environmental insults. It has become increasingly apparent that a plant cell uses external signals to differentiate and to maintain or to change the differentiated state. A cell-cell signaling and positional information strategy seems to be the predominant mechanism employed in plant development. 2. An axis can be initiated by physical/chemical forces such as light and ion current, requiring no new gene action. Random chemical fluctuations and physicochemical forces could explain the initiation of differences among cells of equal developmental potential. Amplification of chemical polarizing events may lead to biochemical differences, new gene expression, and finally shoot/root axis establishment. 3. Radial and axial patterning may be governed by a mechanism involving polar auxin transport. 4. Because the meristems and the three fundamental tissues formed during embryogenesis are renewed and extended throughout the life of the plant, with some exceptions, most genes expressed in the embryo are also expressed during postgermination development. 5. Embryogenic competence is acquired during reproductive development. While the zygote is determined for embryogenesis, the developing embryo and often the seedling remain embryogenic. Embryogenic potential declines during vegetative development. The embryogenic strength of a tissue is correlated with its developmental distance from the zygote.

Embryonic Induction↗
PubMed2005

Chloroplasts as source and target of cellular redox regulation: a discussion on chloroplast redox signals in the context of plant physiology.

During the evolution of plants, chloroplasts have lost the exclusive genetic control over redox regulation and antioxidant gene expression. Together with many other genes, all genes encoding antioxidant enzymes and enzymes involved in the biosynthesis of low molecular weight antioxidants were transferred to the nucleus. On the other hand, photosynthesis bears a high risk for photo-oxidative damage. Concomitantly, an intricate network for mutual regulation by anthero- and retrograde signals has emerged to co-ordinate the activities of the different genetic and metabolic compartments. A major focus of recent research in chloroplast regulation addressed the mechanisms of redox sensing and signal transmission, the identification of regulatory targets, and the understanding of adaptation mechanisms. In addition to redox signals communicated through signalling cascades also used in pathogen and wounding responses, specific chloroplast signals control nuclear gene expression. Signalling pathways are triggered by the redox state of the plastoquinone pool, the thioredoxin system, and the acceptor availability at photosystem I, in addition to control by oxolipins, tetrapyrroles, carbohydrates, and abscisic acid. The signalling function is discussed in the context of regulatory circuitries that control the expression of antioxidant enzymes and redox modulators, demonstrating the principal role of chloroplasts as the source and target of redox regulation.

Cell Nucleus↗
PubMed1990

Contrasting modes and tempos of genome evolution in land plant organelles.

Despite inhabiting the same cell lineage for roughly a billion years and being dependent on the same nucleus for most of their gene products and genetic control, the two organelle genomes of land plants exhibit remarkably different tempos and patterns of evolutionary change. With a few notable exceptions, chloroplast genomes are highly conserved in size and gene arrangement, whereas mitochondrial genomes vary enormously in size and organization. Conversely, nucleotide substitution rates are on average several times higher in chloroplast DNA than in mitochondrial DNA. Mechanistic and selective forces underlying these differences are only poorly understood.

Biological Evolution↗
PubMed2025

NGATHA carpel development genes evolved in the common ancestor of seed plants.

The evolution of the carpel, the defining feature of angiosperms, remains a fundamental question in plant biology. Understanding how this organ originated is crucial because it underpins the reproductive success and diversity of flowering plants. Here, we investigated the functional conservation between gymnosperms and angiosperms of key transcription factors involved in carpel development. We found that Ginkgo biloba homologs can functionally substitute for their angiosperm counterparts in stigma development. We discovered that GbRAV5 is related to angiosperm NGA genes, challenging previous notions that these are exclusive to angiosperms, and we found a parallel loss of the AP2 domain in gymnosperms providing a rare snapshot of how protein families evolve. Conserved protein interactions and overlapping expression patterns of GbRAV5 and GbHEC in Ginkgo ovules suggest that the molecular toolkit for carpel development was largely present in the last common ancestor of seed plants, offering new insights into the evolution of reproductive structures.

Plant Proteins↗
PubMed1989

Roles of Ca2+ in O2 evolution in higher plant photosystem II: effects of replacement of Ca2+ site by other cations.

The properties of the S2 states formed in Ca2+-extracted, Sr2+-substituted, and Cd2+-substituted photosystem II (PSII) were comparatively studied by means of thermoluminescence (TL) and low temperature EPR spectroscopy. The following results were obtained: (i) Ca-extracted PSII showed neither EPR multiline nor g = 4.1 signals but showed an abnormal TL band with an upshifted peak temperature, which did not oscillate on excitation with two or more flashes. Addition of Ca2+ to the extracted PSII reversed most of these effects concomitant with marked restoration of O2 evolution, but the EPR g = 4.1 signal remained lost. (ii) Sr2+ substitution largely restored the g = 4.1 signal and partly restored the multiline signal in a modified form having a reduced hyperfine line spacing concomitant with partial restoration of O2 evolution. Sr2+ substitution also reversed the abnormal TL peak temperature to normal, but the oscillation of the restored TL peak was much damped. (iii) Cd2+ substitution restored neither of the two EPR signals nor O2 evolution but reversed the abnormal TL peak temperature to normal. However, the reversed TL peak did not show any oscillatory behavior. Given these results, the function of the weakly bound Ca2+ in S-state turnovers in higher plant PSII is discussed.

Cadmium↗
PubMed2006

Interactive effects of habitat productivity and herbivore pressure on the evolution of anti-herbivore defense in invasive plant populations.

The evolution of increased competitive ability (EICA) hypothesis predicts that plants released from natural enemies should evolve to become more invasive through a shift in resource allocation from defense to growth. Resource availability in the environment is widely regarded as a major determinant of defense investment and invasiveness, and thus should be incorporated into the conceptual framework of EICA. Analysis of a simple model from the optimal defense literature demonstrates that, in contrast to the EICA hypothesis, enemy release is neither sufficient nor necessary for evolution of reduced resistance among introduced plants when habitat productivity co-varies. In particular, if the invasive range is more nutrient-poor than the native range, there could be selection for more plant defenses even with enemy release.

Animals↗
PubMed2002

Characterization of phenylpropene O-methyltransferases from sweet basil: facile change of substrate specificity and convergent evolution within a plant O-methyltransferase family.

Some basil varieties are able to convert the phenylpropenes chavicol and eugenol to methylchavicol and methyleugenol, respectively. Chavicol O-methyltransferase (CVOMT) and eugenol O-methyltransferase (EOMT) cDNAs were isolated from the sweet basil variety EMX-1 using a biochemical genomics approach. These cDNAs encode proteins that are 90% identical to each other and very similar to several isoflavone O-methyltransferases such as IOMT, which catalyzes the 4'-O-methylation of 2,7,4'-trihydroxyisoflavanone. On the other hand, CVOMT1 and EOMT1 are related only distantly to (iso)eugenol OMT from Clarkia breweri, indicating that the eugenol O-methylating enzymes in basil and C. breweri evolved independently. Transcripts for CVOMT1 and EOMT1 were highly expressed in the peltate glandular trichomes on the surface of the young basil leaves. The CVOMT1 and EOMT1 cDNAs were expressed in Escherichia coli, and active proteins were produced. CVOMT1 catalyzed the O-methylation of chavicol, and EOMT1 also catalyzed the O-methylation of chavicol with equal efficiency to that of CVOMT1, but it was much more efficient in O-methylating eugenol. Molecular modeling, based on the crystal structure of IOMT, suggested that a single amino acid difference was responsible for the difference in substrate discrimination between CVOMT1 and EOMT1. This prediction was confirmed by site-directed mutagenesis, in which the appropriate mutants of CVOMT1 (F260S) and EOMT1 (S261F) were produced that exhibited the opposite substrate preference relative to the respective native enzyme.

Allylbenzene Derivatives↗
PubMed2004

The Fusarium oxysporum f. sp. ciceris/Cicer arietinum pathosystem: a case study of the evolution of plant-pathogenic fungi into races and pathotypes.

The use of resistant cultivars is one of the most practical and cost-efficient strategies for managing plant diseases. However, the efficiency of resistant cultivars in disease management is limited by pathogenic variability in pathogen populations. Knowledge of the evolutionary history and potential of the pathogen population may help to optimize the management of disease-resistance genes, irrespective of the breeding strategy used for their development. In this review, we examine the diversity in virulence phenotypes of Fusarium oxysporum f. sp. ciceris, the causal agent of Fusarium wilt of chickpeas, analyze the genetic variability existing within and among those phenotypes, and infer a phylogenetic relationship among the eight known pathogenic races of this fungus. The inferred intraspecific phylogeny shows that each of those races forms a monophyletic lineage. Moreover, virulence of races to resistant chickpea cultivars has been acquired in a simple stepwise pattern, with few parallel gains or losses. Although chickpea cultivars resistant to Fusarium wilt are available, they have not yet been extensively deployed, so that the stepwise acquisition of virulence is still clearly evident.

Biological Evolution↗
PubMed2005

Evolution of plant-like crystalline storage polysaccharide in the protozoan parasite Toxoplasma gondii argues for a red alga ancestry.

Single-celled apicomplexan parasites are known to cause major diseases in humans and animals including malaria, toxoplasmosis, and coccidiosis. The presence of apicoplasts with the remnant of a plastid-like DNA argues that these parasites evolved from photosynthetic ancestors possibly related to the dinoflagellates. Toxoplasma gondii displays amylopectin-like polymers within the cytoplasm of the dormant brain cysts. Here we report a detailed structural and comparative analysis of the Toxoplasma gondii, green alga Chlamydomonas reinhardtii, and dinoflagellate Crypthecodinium cohnii storage polysaccharides. We show Toxoplasma gondii amylopectin to be similar to the semicrystalline floridean starch accumulated by red algae. Unlike green plants or algae, the nuclear DNA sequences as well as biochemical and phylogenetic analysis argue that the Toxoplasma gondii amylopectin pathway has evolved from a totally different UDP-glucose-based metabolism similar to that of the floridean starch accumulating red alga Cyanidioschyzon merolae and, to a lesser extent, to those of glycogen storing animals or fungi. In both red algae and apicomplexan parasites, isoamylase and glucan-water dikinase sequences are proposed to explain the appearance of semicrystalline starch-like polymers. Our results have built a case for the separate evolution of semicrystalline storage polysaccharides upon acquisition of photosynthesis in eukaryotes.

Amino Acid Sequence↗
PubMed1998

Gene silencing in plants: relevance for genome evolution and the acquisition of genomic methylation patterns.

Transgenes often become silenced in plants because of repressive influences exerted by flanking plant DNA and/or because of interactions among multiple copies of closely linked transgenes. Repeated transgenes on different chromosomes can also interact in a way that leads to silencing and methylation, suggesting a previously unrecognized ability of unlinked homologous sequences to cross-talk in complex genomes. Non-Mendelian inheritance is a frequent consequence of these interactions because the silenced genes do not fully reactivate or lose methylation after segregating in progeny. Several examples of gene silencing in plants appear to reflect the action of genome defence system that methylates and inactivates foreign or invasive sequences such as transgenes and transposable elements. Because certain types of transposable elements are embedded in regulatory regions of plant genes and have become greatly amplified in plant genomes, they could contribute substantially to normal gene expression and to the generation of genomic methylation patterns. Polyploidy, which has been a major force in plant and vertebrate evolution, might encourage proliferation of transposable elements because genes in polyploids are duplicated and hence less susceptible to the consequences of insertional mutagenesis. Accordingly, the appearance of genome-wide methylation has often coincided with episodes of polyploidization.

DNA Methylation↗
PubMed2005

Exposure to host resistance mechanisms drives evolution of bacterial virulence in plants.

Bacterial pathogenicity to plants and animals has evolved through an arms race of attack and defense. Key players are bacterial effector proteins, which are delivered through the type III secretion system and suppress basal defenses . In plants, varietal resistance to disease is based on recognition of effectors by the products of resistance (R) genes . When recognized, the effector or in this scenario, avirulence (Avr) protein triggers the hypersensitive resistance reaction (HR), which generates antimicrobial conditions . Unfortunately, such gene-for-gene-based resistance commonly fails because of the emergence of virulent strains of the pathogen that no longer trigger the HR . We have followed the emergence of a new virulent pathotype of the halo-blight pathogen Pseudomonas syringae pv. phaseolicola within leaves of a resistant variety of bean. Exposure to the HR led to the selection of strains lacking the avirulence (effector) gene avrPphB (or hopAR1), which triggers defense in varieties with the matching R3 resistance gene. Loss of avrPphB was through deletion of a 106 kb genomic island (PPHGI-1) that shares features with integrative and conjugative elements (ICElands) and also pathogenicity islands (PAIs) in diverse bacteria . We provide a molecular explanation of how exposure to resistance mechanisms in plants drives the evolution of new virulent forms of pathogens.

Bacterial Proteins↗