Abstract:
BACKGROUND:Phenylalanine ammonia-lyase (PAL; E.C.4.3.1.5) is a key enzyme of the phenylpropanoid pathway in plant development, and it catalyses the deamination of phenylalanine to trans-cinnamic acid, leading to the production of secondary metabolites. This enzyme has been identified in many organisms, ranging from prokaryotes to higher plants. Because Nelumbo nucifera is a basal dicot rich in many secondary metabolites, it is a suitable candidate for research on the phenylpropanoid pathway. RESULTS:Three PAL members, NnPAL1, NnPAL2 and NnPAL3, have been identified in N. nucifera using genome-wide analysis. NnPAL1 contains two introns; however, both NnPAL2 and NnPAL3 have only one intron. Molecular and evolutionary analysis of NnPAL1 confirms that it is an ancient PAL member of the angiosperms and may have a different origin. However, PAL clusters, except NnPAL1, are monophyletic after the split between dicots and monocots. These observations suggest that duplication events remain an important occurrence in the evolution of the PAL gene family. Molecular assays demonstrate that the mRNA of the NnPAL1 gene is 2343 bp in size and encodes a 717 amino acid polypeptide. The optimal pH and temperature of the recombinant NnPAL1 protein are 9.0 and 55°C, respectively. The NnPAL1 protein retains both PAL and weak TAL catalytic activities with Km values of 1.07 mM for L-phenylalanine and 3.43 mM for L-tyrosine, respectively. Cis-elements response to environmental stress are identified and confirmed using real-time PCR for treatments with abscisic acid (ABA), indoleacetic acid (IAA), ultraviolet light, Neurospora crassa (fungi) and drought. CONCLUSIONS:We conclude that the angiosperm PAL genes are not derived from a single gene in an ancestral angiosperm genome; therefore, there may be another ancestral duplication and vertical inheritance from the gymnosperms. The different evolutionary histories for PAL genes in angiosperms suggest different mechanisms of functional regulation. The expression patterns of NnPAL1 in response to stress may be necessary for the survival of N. nucifera since the Cretaceous Period. The discovery and characterisation of the ancient NnPAL1 help to elucidate PAL evolution in angiosperms.
journal_name
BMC Evol Bioljournal_title
BMC evolutionary biologyauthors
Wu Z,Gui S,Wang S,Ding Ydoi
10.1186/1471-2148-14-100subject
Has Abstractpub_date
2014-05-09 00:00:00pages
100issn
1471-2148pii
1471-2148-14-100journal_volume
14pub_type
杂志文章abstract:BACKGROUND:The mitochondria of contemporary organisms contain fewer genes than the ancestral bacteria are predicted to have contained. Because most of the mitochondrial proteins are encoded in the nucleus, the genes would have been transferred from the mitochondrion to the nucleus at some stage of evolution and they mu...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-8-314
更新日期:2008-11-14 00:00:00
abstract:BACKGROUND:Dispersal is often associated with a suite of phenotypic traits that might reduce dispersal costs, but can be energetically costly themselves outside dispersal. Hence, dispersing and philopatric individuals might differ throughout their life cycle in their management of energy production. Because higher ener...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-016-0697-x
更新日期:2016-06-14 00:00:00
abstract:BACKGROUND:The spread of agriculture greatly modified the selective pressures exerted by plants on phytophagous insects, by providing these insects with a high-level resource, structured in time and space. The life history, behavioural and physiological traits of some insect species may have evolved in response to thes...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-6-75
更新日期:2006-10-02 00:00:00
abstract:BACKGROUND:Chordate evolution is a history of innovations that is marked by physical and behavioral specializations, which led to the development of a variety of forms from a single ancestral group. Among other important characteristics, vertebrates obtained a well developed brain, anterior sensory structures, a closed...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-11-234
更新日期:2011-08-09 00:00:00
abstract:BACKGROUND:Hemerythrins, are the non-heme, diiron binding respiratory proteins of brachiopods, priapulids and sipunculans; they are also found in annelids and bacteria, where their functions have not been fully elucidated. RESULTS:A search for putative Hrs in the genomes of 43 archaea, 444 bacteria and 135 eukaryotes,...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-8-244
更新日期:2008-09-02 00:00:00
abstract:BACKGROUND:The rate of nucleotide substitutions is not constant across the Tree of Life, and departures from a molecular clock have been commonly reported. Within parmelioid lichens, the largest group of macrolichens, large discrepancies in branch lengths between clades were found in previous studies. Using an extended...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-8-257
更新日期:2008-09-22 00:00:00
abstract:BACKGROUND:The self-fertile hermaphrodite worm C. elegans is an important model organism for biology, yet little is known about the origin and persistence of the self-fertilizing mode of reproduction in this lineage. Recent work has demonstrated an extraordinary degree of selfing combined with a high deleterious mutati...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-8-125
更新日期:2008-04-30 00:00:00
abstract:BACKGROUND:Widely used substitution models for proteins, such as the Jones-Taylor-Thornton (JTT) or Whelan and Goldman (WAG) models, are based on empirical amino acid interchange matrices estimated from databases of protein alignments that incorporate the average amino acid frequencies of the data set under examination...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-8-331
更新日期:2008-12-16 00:00:00
abstract:BACKGROUND:The right sampling of homologous sequences for phylogenetic or molecular evolution analyses is a crucial step, the quality of which can have a significant impact on the final interpretation of the study. There is no single way for constructing datasets suitable for phylogenetic analysis, because this task in...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-10-8
更新日期:2010-01-12 00:00:00
abstract:BACKGROUND:The mechanism by which duplicate genes originate - whether by duplication of a whole genome or of a genomic segment - influences their genetic fates. To study events that trigger duplicate gene persistence after whole genome duplication in vertebrates, we have analyzed molecular evolution and expression of h...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-8-43
更新日期:2008-02-08 00:00:00
abstract:BACKGROUND:Prions are transmissible, propagating alternative states of proteins, and are usually made from the fibrillar, beta-sheet-rich assemblies termed amyloid. Prions in the budding yeast Saccharomyces cerevisiae propagate heritable phenotypes, uncover hidden genetic variation, function in large-scale gene regulat...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-016-0594-3
更新日期:2016-01-25 00:00:00
abstract:BACKGROUND:The coincidence of long distance dispersal (LDD) and biome shift is assumed to be the result of a multifaceted interplay between geographical distance and ecological suitability of source and sink areas. Here, we test the influence of these factors on the dispersal history of the flowering plant genus Erica ...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-019-1545-6
更新日期:2019-12-05 00:00:00
abstract:BACKGROUND:RNA editing is a post-transcriptional process that, in seed plants, involves a cytosine to uracil change in messenger RNA, causing the translated protein to differ from that predicted by the DNA sequence. RNA editing occurs extensively in plant mitochondria, but large differences in editing frequencies are f...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-10-349
更新日期:2010-11-11 00:00:00
abstract:BACKGROUND:Despite the common assumption that multiple mating should in general be favored in males, but not in females, to date there is no consensus on the general impact of multiple mating on female fitness. Notably, very little is known about the genetic and physiological features underlying the female response to ...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-014-0239-3
更新日期:2014-11-19 00:00:00
abstract:BACKGROUND:Teleost radiation in the oceans required specific physiological adaptations in eggs and early embryos to survive in the hyper-osmotic seawater. Investigating the evolution of aquaporins (AQPs) in these vertebrates should help to elucidate how mechanisms for water homeostasis evolved. The marine teleost gilth...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-8-259
更新日期:2008-09-23 00:00:00
abstract:BACKGROUND:Comparative mapping of 5S and 45S rDNA by fluorescent in situ hybridization (FISH) technique is an excellent tool to determine cytogenetic relationships among closely related species. RESULTS:In this study, the number and position of 5S and 45S rDNA loci in all Citrullus species and subspecies were determin...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-016-0656-6
更新日期:2016-04-18 00:00:00
abstract:BACKGROUND:: Duplicated genes are common in vertebrate genomes. Their persistence is assumed to be either a consequence of gain of novel function (neofunctionalisation) or partitioning of the function of the ancestral molecule (sub-functionalisation). Surprisingly few studies have evaluated the extent of such modificat...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-7-221
更新日期:2007-11-12 00:00:00
abstract:BACKGROUND:Perception of sugars is an invaluable ability for insects which often derive quickly accessible energy from these molecules. A distinctive subfamily of eight proteins within the gustatory receptor (Gr) family has been identified as sugar receptors (SRs) in Drosophila melanogaster (Gr5a, Gr61a, and Gr64a-f). ...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-9-41
更新日期:2009-02-18 00:00:00
abstract:BACKGROUND:Recent models suggest that escalating reciprocal selection among antagonistically interacting species is predicted to occur in areas of higher resource productivity. In a putatively coevolved interaction between a freshwater snail (Mexipyrgus churinceanus) and a molluscivorous cichlid (Herichthys minckleyi),...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-7-50
更新日期:2007-03-30 00:00:00
abstract:BACKGROUND:The existence of "ancient asexuals", taxa that have persisted for long periods of evolutionary history without sexual recombination, is both controversial and important for our understanding of the evolution and maintenance of sexual reproduction. A lack of sex has consequences not only for the ecology of th...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-8-194
更新日期:2008-07-07 00:00:00
abstract:BACKGROUND:Effects of polyploidisation on gene flow between natural populations are little known. Central European diploid and tetraploid populations of Arabidopsis arenosa and A. lyrata are here used to study interspecific and interploidal gene flow, using a combination of nuclear and plastid markers. RESULTS:Ploidal...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-11-346
更新日期:2011-11-29 00:00:00
abstract:BACKGROUND:Synonymous codon usage is typically biased towards translationally superior codons in many organisms. In Drosophila, genomic data indicates that translationally optimal codons and splice optimal codons are mostly mutually exclusive, and adaptation to translational efficiency is reduced in the intron-exon bou...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-9-214
更新日期:2009-08-27 00:00:00
abstract:BACKGROUND:The flat periwinkles, Littorina fabalis and L. obtusata, are two sister species widely distributed throughout the Northern Atlantic shores with high potential to inform us about the process of ecological speciation in the intertidal. However, whether gene flow has occurred during their divergence is still a ...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-019-1561-6
更新日期:2020-02-10 00:00:00
abstract:BACKGROUND:The Carpathians and the Alps are the largest mountain ranges of the European Alpine System and important centres of endemism. Among the distinctive endemic species of this area is Saxifraga wahlenbergii, a Western Carpathians member of the speciose genus Saxifraga. It was frequently considered a taxonomicall...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-019-1355-x
更新日期:2019-01-11 00:00:00
abstract:BACKGROUND:Histone modification is an epigenetic mechanism that influences gene regulation in eukaryotes. In particular, histone modifications in CpG islands (CGIs) are associated with different chromatin states and with transcription activity. Changes in gene expression play a crucial role in adaptation and evolution....
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-13-145
更新日期:2013-07-10 00:00:00
abstract:BACKGROUND:Orb-web weaving spiders and their relatives use multiple types of task-specific silks. The majority of spider silk studies have focused on the ultra-tough dragline silk synthesized in major ampullate glands, but other silk types have impressive material properties. For instance, minor ampullate silks of orb-...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-017-0927-x
更新日期:2017-03-14 00:00:00
abstract:BACKGROUND:Recent approaches for context-dependent evolutionary modelling assume that the evolution of a given site depends upon its ancestor and that ancestor's immediate flanking sites. Because such dependency pattern cannot be imposed on the root sequence, we consider the use of different orders of Markov chains to ...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-10-244
更新日期:2010-08-10 00:00:00
abstract:BACKGROUND:Modern flamingos (Phoenicopteridae) occupy a highly specialized ecology unique among birds and represent a potentially powerful model system for informing the mechanisms by which a lineage of birds adapts and radiates. However, despite a rich fossil record and well-studied feeding morphology, molecular inves...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-14-36
更新日期:2014-03-01 00:00:00
abstract:BACKGROUND:The scavenger receptor cysteine rich (SRCR) domain is an ancient and conserved protein domain. CD163 and WC1 molecules are classed together as group B SRCR superfamily members, along with Spalpha, CD5 and CD6, all of which are expressed by immune system cells. There are three known types of CD163 molecules i...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-10-181
更新日期:2010-06-15 00:00:00
abstract:BACKGROUND:The secretin family is a pleotropic group of brain-gut peptides with affinity for class 2 G-protein coupled receptors (secretin family GPCRs) proposed to have emerged early in the metazoan radiation via gene or genome duplications. In human, 10 members exist and sequence and functional homologues and ligand-...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-10-135
更新日期:2010-05-06 00:00:00