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At least 613 records · Page 34Linked to original sources
PubMed2004

Pattern of phylogenetic diversification of the Cychrini ground beetles in the world as deduced mainly from sequence comparisons of the mitochondrial genes.

The phylogenetic position of the tribe Cychrini within the subfamily Carabinae (the family Carabidae) was estimated by comparing the nucleotide sequences of the mitochondrial NADH dehydrogenase subunit 5 (ND5) gene and the nuclear 28S ribosomal DNA (rDNA). The phylogenetic trees suggest that the Cychrini would most probably be the oldest line within the Carabinae. Phylogenetic trees were constructed by comparing the mitochondrial cytochrome C oxidase subunit I (COI) gene sequences from 33 species of the Cychrini from various localities that include the whole distribution ranges of the representative species within all the known genera in the world. The trees suggest that the Cychrini members radiated into a number of phylogenetic lineages within a short period, starting about 44 million years ago (MYA). Most of the phylogenetic lineages or sublineages are geographically linked, each consisting of a single or only a few species without scarce morphological differentiation in spite of their long evolutionary histories (silent or near-silent evolution [see Adv. Biophys. 36 (1999) 65; J. Mol. Evol. 53 (2001) 517]). The fact suggests that the geographic isolation per se did not bring about conspicuous morphological differentiation. The phylogenetic lineages of the Cychrini well correspond to the taxonomically defined genera and the subgenera.

Animals↗
PubMed2004

Phylogeny and regulation of four lipocalin genes clustered in the chicken genome: evidence of a functional diversification after gene duplication.

A novel lipocalin gene is here reported that represents the fourth member of a cluster we have identified in the chicken genome. This cluster also includes Chondrogenesis-Associated Lipocalins beta and gamma (CAL beta, CAL gamma) and Extracellular Fatty Acid Binding Protein (Ex-FABP). The new gene codes for a 22-kDa secreted protein with three cysteine residues and a series of sequence features well conserved in the lipocalin family. All the genes in the cluster are structurally similar presenting comparable exon/intron boundary positions and exon sizes. A phylogenetic analysis indicates the monophyletic grouping of these genes, and their relationship with the lipocalins alpha-1-microglobulin (A1mg), complement factor 8 gamma chain (C8GC), prostaglandin D synthase (PGDS), and neutrophil-gelatinase-associated lipocalin (NGAL). The new cluster gene appears to be the ortholog of the mammalian C8GC and was thus named Ggal-C8GC. This orthology also suggests that this lipocalin was present in the ancestor common to reptiles and mammals. In addition to other expressing tissues, Ex-FABP, CAL beta and CAL gamma genes are highly transcribed in chondrocytes at late stages of chondrogenesis during endochondral bone formation and/or upon inflammatory stimulation. Here, we show that they are also transcriptionally induced when chondrocytes are subjected to various biological events as cell quiescence, cell shape transition, and hormonal stimulation. By contrast, Ggal-C8GC transcripts are only barely detectable in chondrocytes, but are more abundant in liver, kidney, brain, heart, skeletal muscle and particularly in skin. Moreover, no expression induction was observed neither during chondrocyte differentiation, nor upon any of the stimulations mentioned above. This indicates that the Ggal-C8GC gene was co-opted for a novel function after the duplication events that gave rise to the cluster. The peculiar coordinated regulation of Ex-FABP, CAL beta and CAL gamma, and the apparent divergent role of Ggal-C8GC suggest that these gene duplications may have been maintained during evolution by a sub-functionalization mechanism where some common function(s) are shared by several members of the cluster and some other specialized function(s) are unique to other members.

Amino Acid Sequence↗
PubMed2004

Construction and diversification of yeast cell surface displayed libraries by yeast mating: application to the affinity maturation of Fab antibody fragments.

Yeast display is a powerful technology for the affinity maturation of human antibody fragments. However, the technology thus far has been limited by the size of antibody libraries that can be generated, as using current transformation protocols libraries of only between 10(6) and 10(7) are typically possible. We have recently shown that Fab antibodies can be displayed on the cell surface of Saccharomyces cerevisiae [van den Beucken, T., Pieters, H., Steukers, M., van der Vaart, M., Ladner, R.C., Hoogenboom, H.R., Hufton, S.E., 2003. Affinity maturation of Fab antibody fragments by fluorescent-activated cell sorting of yeast-displayed libraries. FEBS Lett. 546, 288-294]. This discovery and the knowledge that Fab antibodies are heterodimeric suggest that independent repertoires of heavy chain (HC) and light chain (LC) can be constructed in haploid yeast strains of opposite mating type. These separate repertoires can then be combined by highly efficient yeast mating. Using this approach, we have rapidly generated a naive human Fab yeast display library of over 10(9) clones. In addition, utilizing error-prone polymerase chain reaction, we have diversified Fab sequences and generated combinatorial and hierarchical chain shuffled libraries with complexities of up to 5 x 10(9) clones. These libraries have been selected for higher affinity using a repeating process of mating-driven chain shuffling and flow cytometric sorting.

Antibody Affinity↗
PubMed2005

Origin and diversification of minisatellites derived from human Alu sequences.

We analyze minisatellites derived from Alu fragments corresponding approximately to the first 44 bases of human Alu consensus sequences from different subfamilies. The origin of Alu-derived minisatellites appears to have been mediated by short flanking repeats, as first proposed by Haber and Louis [Haber, J.E., Louis, E.J., 1998. Minisatellite origins in yeast and humans. Genomics 48, 132-135.]. We also present evidence for base substitutions and deletions introduced to minisatellites by gene conversion with partially similar but unrelated flanking regions. Segments flanked by short direct repeats are relatively common in different regions of Alu and other repetitive sequences. Our analysis shows that they can be effectively used in comparative studies of the overall sequence context which may contribute to instability of DNA segments flanked by short direct repeats.

Alu Elements↗
PubMed2006

Quorum sensing in vibrios: complexity for diversification.

N-acylhomoserine lactone-dependent quorum sensing was first discovered in two luminescent marine bacteria, Vibrio fischeri and Vibrio harveyi. The LuxI/R system of V. fischeri is the paradigm of Gram-negative quorum-sensing systems; however, it is not found in all vibrios. A more complex quorum-sensing regulation is found in V. harveyi. Three parallel systems transmit signals via phosphorelays that converge onto one regulatory protein LuxO. Components of the three systems are found only in vibrios. Of the five Vibrio strains analysed, the number and types of signal circuits found in each strain are diverse. The signalling systems have different regulatory responses depending on the type of association the Vibrio strains have with an animal host, which may reflect the diverse roles the vibrios have in structuring and maintaining microniches within the aquatic milieu. Further studies are likely to show that the diversity and complexity of the Vibrio quorum-sensing systems coordinate intraspecies behaviour, niche occupation, and possibly evolution.

Aliivibrio fischeri↗
PubMed2005

Diversification of catalytic activities and ligand interactions in the protein fold shared by the sugar isomerases, eIF2B, DeoR transcription factors, acyl-CoA transferases and methenyltetrahydrofolate synthetase.

Evolution of diverse catalytic and ligand-binding activities in a given protein fold is a widely observed phenomenon in the protein-domain universe. However, the details of this evolutionary process, general principles, if any, and implications for origins of particular catalytic mechanisms are poorly understood in many common protein folds. Taking advantage of the wealth of currently available protein structure and sequence data, we explore these issues in the context of a large assemblage of biochemically diverse protein domains sharing a common origin, namely the sugar isomerases, translation factor eIF2B, ligand-binding domains of the DeoR-family transcription factors, acetyl-CoA transferases and methenyltetrahydrofolate synthetase. We show that in at least three independent instances, including the sugar-binding domains of the DeoR family transcription factors, this domain has been used as small molecule sensor coupled to helix-turn-helix DNA-binding domains. In at least two of these instances the domain functions as a non-catalytic sensor of ligands. We provide evidence that the ancestral version of this fold was a distinct version of the Rosmann-like folds, which probably possessed two distinct ligand-binding areas that were differentially utilized in different descendents. Analyzing the sequences and structures of proteins in this fold we show that there are two principal factors related to the origin of catalytic diversity in this fold. Firstly, specific inserts and extension added to the core domain on multiple occasions in evolution have affected the access to the active site regions, and thereby allowed for different substrates and allosteric regulators. The second major factor appears to be the emergence of considerable diversity of family-specific residues with important biochemical roles. Interestingly, proteins of this fold, which catalyze similar reactions on similar substrates, might possess very distinctive sets of active residues required for substrate binding catalysis. In particular, different sugar isomerases or acyl transferases in this fold might show distinct constellations of active site residues. These findings suggest that whereas ligand-binding, and even generic catalytic ability emerged early in the evolution of the fold, the specific catalytic mechanisms appear to have independently emerged on multiple occasions in the generic precursors of this fold.

Aldose-Ketose Isomerases↗
PubMed2004

The generation and diversification of spinal motor neurons: signals and responses.

Motor neurons are probably the best characterised neuronal class in the vertebrate central nervous system and have become a paradigm for understanding the mechanisms that control the development of vertebrate neurons. For many investigators working on this problem the chick embryo is the model system of choice and from these studies a picture of the steps involved in motor neuron generation has begun to emerge. These findings suggest that motor neuron generation is shaped by extracellular signals that regulate intrinsic, cell-autonomous determinants at sequential steps during development. The chick embryo has played a prominent role in identifying the sources of these signals, defining their molecular identities and determining the cell intrinsic programs they regulate.

Animals↗
PubMed2005

Characterization of a novel cDNA encoding a short venom peptide derived from venom gland of scorpion Buthus martensii Karsch: trans-splicing may play an important role in the diversification of scorpion venom peptides.

A novel cDNA clone (named BmKT-u) which is a hybrid molecule of the 5'-terminal region of BmKT' cDNA and the 3'-terminal region of an undocumented cDNA (named BmKu), was isolated from a cDNA library made from the venom gland of scorpion Buthus martensii Karsch. BmKT-u codes for a 30 amino acid residue precursor peptide composed of a 20-residue signal sequence, and a putative 10-residue novel mature peptide. Northern blot hybridization showed BmKT-u cDNA is generated from a transcript. RT-PCR experiments excluded the possibility that BmKT-u cDNA is an artifact generated during reverse transcription. Genomic amplifications performed with three pairs of BmKT-u gene-specific primers showed the BmKT-u gene does not exist in the genome of the scorpion as a single transcriptional unit. Genomic cloning for BmKT' showed that the BmKT' gene contains an intron of 509 bp inserted into the region encoding the C-terminal region of the signal peptide. A sequence alignment comparison of the cDNA of BmKT-u with genomic BmKT' revealed that the junction site of the hybrid molecule is located at the 5'-splicing site of the intron. The data suggest that the BmKT-u transcript is a naturally occurring mature mRNA that is generated by trans-splicing. Trans-splicing may contribute to the diversity of venom peptides from venomous animals.

Amino Acid Sequence↗
PubMed2005

Geographic and evolutionary diversification of glucosinolates among near relatives of Arabidopsis thaliana (Brassicaceae).

Glucosinolates are biologically active secondary metabolites that display both intra- and interspecific variation in the order Brassicales. Glucosinolate profiles have not been interpreted within a phylogenic framework and little is known regarding the processes that influence the evolution of glucosinolate diversity at a macroevolutionary scale. We have analyzed leaf glucosinolate profiles from members of the Brassicaceae that have diverged from Arabidopsis thaliana within the last 15 million years and interpreted our findings relative to the phylogeny of this group. We identified several interspecific polymorphisms in glucosinolate composition. A majority of these polymorphisms are lineage-specific secondary losses of glucosinolate characters, but a gain-of-character polymorphism was also detected. The genetic basis of most observed polymorphisms appears to be regulatory. In the case of A. lyrata, geographic distribution is also shown to contribute to glucosinolate metabolic diversity. Further, we observed evidence of gene-flow between sympatric species, parallel evolution, and the existence of genetic constraints on the evolution of glucosinolates within the Brassicaceae.

Brassicaceae↗
PubMed2006

Nep1-like proteins from plant pathogens: recruitment and diversification of the NPP1 domain across taxa.

An emerging group of proteins found in many plant pathogens are related to their ability to cause plant cell death. These proteins may be identified by the presence of a common NPP1 (necrosis-inducing Phytophthora protein) domain, and have collectively been named NLPs (Nep1-like proteins). The NLPs are distinguished by their wide distribution across taxa and their broad spectrum of activity against dicotyledonous plants. The function of NLPs is not known but there is strong evidence that they may act as positive virulence factors, accelerating disease and pathogen growth in plant hosts. Interest in NLPs is gaining momentum as more members of this protein family are discovered in more species of plant pathogens.

Bacteria↗
PubMed2006

Diversification, dioecy and dimorphism in schistosomes.

In addition to causing one of the great neglected diseases of the world, schistosomes have unusual biological features that further command attention, including their habit of living in the blood of their hosts and the presence of separate, dimorphic sexes. Phylogenetic studies including a more complete sampling of pivotal and rare schistosomes and their relatives, provide an improved framework for interpreting schistosome biology. From such studies, it is inferred that schistosomes are exclusively parasites of endotherms. It is argued that a commitment to life in the endothermic hepatic portal system favored a filiform body form for egg deposition and led to the emergence of dioecy. Schistosome sexual dimorphism and mating systems have subsequently been influenced by the duration of opportunities for transmission and by the nature of the vascular habitats in which they live. A comparative perspective provides valuable insights for interpreting the biology of schistosomes, including the species that cause disease in humans.

Animals↗
PubMed2006

Signal integration and diversification through the p62 scaffold protein.

Signal specificity of multifunctional enzymes is achieved through protein-protein interactions involving specific domains on scaffold proteins. p62 (also known as sequestosome 1) is such a scaffold protein that possesses PB1 and UBA domains, and the TRAF6 binding sequence. Proteins recruited to these domains enable p62 to integrate kinase-activated and ubiquitin-mediated signaling pathways. The biological function of p62 has been studied in diverse systems and processes such as osteoclastogenesis, inflammation, differentiation, neurotrophin biology and obesity. The availability of mice in which p62 has been genetically inactivated is providing new insight into the mechanism and function of p62 at a whole-organism level.

Adaptor Proteins, Signal Transducing↗
PubMed2005

Differentiation and diversification of follicular cells in polytrophic ovaries of crane flies (Diptera: Nematocera: Tipulomorpha and Trichoceridae).

To gain insight into the evolution of differentiation pathways that are involved in the follicular cells' morphogenesis in dipteran ovaries we have undertaken the comparative morphological analysis of the follicular cell behavior in crane flies, representatives of more ancestral nematocerous flies. This analysis revealed that initially the organization of the follicular epithelium in the species under study shows significant similarities to that reported in the ovaries of true flies (Brachycera), indicating that the ancestors of dipterans must have evolved a common and specific system of the early patterning of their follicular epithelium. On the other hand, in contrast to Drosophila and other advanced brachycerans, the follicular cells in the studied nematoceran ovaries do not exhibit any migratory activity. Instead, they were found to change their relative position but only within the epithelial layer. These "translocations" appeared to depend merely on cell shape changes. Although the "immobility" of the follicular cells in the ovaries of crane flies results in the lower number of their specialized subgroups when compared with the true flies, the functional homology between particular subsets of follicular cells can be postulated. We suggest that the anterior polar cells and the micropyle forming anterior terminal follicular cells in crane fly ovaries have their counterparts in the brachyceran anterior polar cells and border cells, respectively.

Animals↗
PubMed2005

The contested role of uracil DNA glycosylase in immunoglobulin gene diversification.

Class switch recombination (CSR) and somatic hypermutation (SHM) of immunoglobulin (Ig) genes are initiated by the activation-induced cytosine deaminase AID. The resulting uracils in Ig genes were believed to be removed by the uracil glycosylase (UNG) and the resulting abasic sites treated in an error-prone fashion, creating breaks in the Ig switch regions and mutations in the variable regions. A recent report suggests that UNG does not act as a glycosylase in CSR and SHM but rather has unknown activity subsequent to DNA breaks that were created by other mechanisms.

Animals↗
PubMed2005

Seeing double: gene duplication and diversification in plant secondary metabolism.

Gene duplications drive the recruitment of genes for secondary metabolism. Gene copies are gradually modified to create genes with specificities and expression patterns adapted to the needs of the new pathway in which they are involved. Duplicated genes are often in tandem repeats, forming clusters within the plant genome. However, in some cases, clusters of nonhomologous genes have also been identified as forming a functional unit. The selective forces that have caused the establishment of new pathways are far from understood and might have changed repeatedly during evolution owing to the continuously changing environment. Recent data show that the way several classes of secondary compounds are scattered among species is attributable to independent recruitment and the inactivation of biosynthetic enzymes.

Evolution, Molecular↗
PubMed2005

SEPALLATA gene diversification: brave new whorls.

SEPALLATA (SEP) genes form an integral part of models that outline the molecular basis of floral organ determination and are hypothesized to act as co-factors with ABCD floral homeotic genes in specifying different floral whorls. The four SEP genes in Arabidopsis function redundantly, but the extent to which SEP genes in other flowering plants function similarly is unknown. Using a recent 113-gene SEP phylogeny as a framework, we find surprising heterogeneity among SEP gene C-terminal motifs, mRNA expression patterns, protein-protein interactions and inferred function. Although some SEP genes appear to function redundantly, others have novel roles in fruit maturation, floral organ specification and plant architecture, and have played a major role in floral evolution of diverse plants.

Arabidopsis Proteins↗
PubMed2006

RAC/ROP GTPases: 'hubs' for signal integration and diversification in plants.

RAC/ROP GTPases are a family of plant-specific signaling molecules solely representing the Ras and Rho family of Ras-related G proteins in plants. RAC/ROPs potentially interact with cell surface-associated signal perception apparatus for a broad range of extracellular stimuli, including hormones, pathogen elicitors and abiotic stress, and mediate diverse cellular pathways in response to these signals. They are also known to interact with multiple effectors, affecting cellular and biochemical systems that regulate actin dynamics, reactive oxygen species production, proteolysis, and gene expression. RAC/ROPs are, thus, ideally suited as integrators for multiple signals and as coordinators of diverse cellular pathways to control growth, differentiation, development and defense responses. Recent findings that suggest how RAC/ROP signaling activity is regulated and how functional specificity can be achieved are discussed here.

Arabidopsis Proteins↗
PubMed2005

Comparative functional genomics revealed conservation and diversification of three enhancers of the isl1 gene for motor and sensory neuron-specific expression.

Islet-1 (Isl1) is a member of the Isl1 family of LIM-homeodomain transcription factors (LIM-HD) that is expressed in a defined subset of motor and sensory neurons during vertebrate embryogenesis. To investigate how this specific expression of isl1 is regulated, we searched for enhancers of the isl1 gene that are conserved in vertebrate evolution. Initially, two enhancer elements, CREST1 and CREST2, were identified downstream of the isl1 locus in the genomes of fugu, chick, mouse, and human by BLAST searching for highly similar elements to those originally identified as motor and sensory neuron-specific enhancers in the zebrafish genome. The combined action of these elements is sufficient for completely recapitulating the subtype-specific expression of the isl1 gene in motor neurons of the mouse spinal cord. Furthermore, by direct comparison of the upstream flanking regions of the zebrafish and human isl1 genes, we identified another highly conserved noncoding element, CREST3, and subsequently C3R, a similar element to CREST3 with two CDP CR1 recognition motifs, in the upstream regions of all other isl1 family members. In mouse and human, CRESTs are located as far as more than 300 kb away from the isl1 locus, while they are much closer to the isl1 locus in zebrafish. Although all of zebrafish CREST2, CREST3, and C3R activate gene expression in the sensory neurons of zebrafish, CREST2 of mouse and human does not have the sequence necessary for sensory neuron-specific expression. Our results revealed both a remarkable conservation of the regulatory elements regulating subtype-specific gene expression in motor and sensory neurons and the dynamic process of reorganization of these elements whereby each element increases the level of cell-type specificity by losing redundant functions with the other elements during vertebrate evolution.

Animals↗