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Results for “functional divergence”

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At least 433 records · Page 24Linked to original sources
PubMed2005

Determination of structural and functional overlap/divergence of five proto-type galectins by analysis of the growth-regulatory interaction with ganglioside GM1 in silico and in vitro on human neuroblastoma cells.

The growth-regulatory interplay between ganglioside GM1 on human SK-N-MC neuroblastoma cells and an endogenous lectin provides a telling example for glycan (polysaccharide) functionality. Galectin-1 is the essential link between the sugar signal and the intracellular response. The emerging intrafamily complexity of galectins raises the question on defining extent of their structural and functional overlap/divergence. We address this problem for proto-type galectins in this system: ganglioside GM1 as ligand, neuroblastoma cells as target. Using the way human galectin-1 interacts with this complex natural ligand as template, we first defined equivalent positioning for distinct substitutions in the other tested proto-type galectins, e.g., Lys63 vs. Leu60/Gln72 in galectins-2 and -5. As predicted from our in silico work, the tested proto-type galectins have affinity for the pentasaccharide of ganglioside GM1. In contrast to solid-phase assays, cell surface presentation of the ganglioside did not support binding of galectin-5, revealing the first level of regulation. Next, a monomeric proto-type galectin (CG-14) can impair galectin-1-dependent negative growth control by competitively blocking access to the shared ligand without acting as effector. Thus, the quaternary structure of proto-type galectins is an efficient means to give rise to functional divergence. The identification of this second level of regulation is relevant for diagnostic monitoring. It might be exploited therapeutically by producing galectin variants tailored to interfere with galectin activities associated with the malignant phenotype. Moreover, the given strategy for comparative computational analysis of extended binding sites has implications for the rational design of galectin-type-specific ligands.

Amino Acid Sequence↗
PubMed1990

Characterization of a new model of human prostatic cancer: the multicellular tumor spheroid.

Multicellular tumor spheroids (MTS) provide a closer in vitro correlate to in vivo malignancy than do conventional monolayer cultures; while simulating many parameters of in vivo growth, MTS systems provide those perquisites (i.e., experimental control, economy, expediency) associated with in vitro evaluation of preclinical therapeutic strategies. For these reasons, we exploited the proclivity of the highly metastatic human prostatic carcinoma subline I-LN-PC3-IA to spontaneously assume a spheroid morphology under routine culture conditions. I-LN spheroids demonstrate salient features described in other spheroid systems and exhibit histologic characteristics of human prostate carcinoma. Cells encompassed in the I-LN spheroid format demonstrated functional divergence from their monolayer counterparts with respect to immunoreactivity for prostatic acid phosphatase, positional dependence of prostate-restricted p40 antigen expression, and chemotherapeutic drug response. This new in vitro-in vivo transition model of human prostatic carcinoma should provide a valuable in vitro context to expediently evaluate in vivo correlates of oncolytic protocols on a malignancy that remains refractive to therapy.

Antineoplastic Agents↗
PubMed2004

Emerging roles for bone morphogenetic proteins in central nervous system glial biology.

Bone morphogenetic proteins, members of the TGFbeta superfamily have been implicated in a variety of roles in the developing and mature nervous system. These divergent functions are a reflection of the closely defined spatial and temporal expression of BMPs in the CNS, and the potential interactions of the BMP signaling pathway with the STAT and MAP kinase pathways. In this review we discuss the roles of BMPs in early patterning of the CNS, determination of neural cell fate, and regulation of oligodendrocyte maturation during CNS development. Additional functions for members of the TGFbeta superfamily in CNS injury responses are emerging suggesting these molecules represent useful targets for manipulating neural responses to CNS insults.

Animals↗
PubMed2003

Proteomic analysis of the reactive phenotype of astrocytes following endothelin-1 exposure.

Reactive gliosis is an invariant feature of the pathology of central nervous system (CNS) injury and a major determinant of neuronal survival and regeneration. To begin to understand the alterations in astrocyte protein expression that drive glial changes that occur following injury, we used an established model system (endothelin-1 stimulation of hypertrophy) and proteomic analysis to define a discrete set of differentially expressed proteins and post-translational modifications that occur as the astrocytes change from a quiescent to a reactive state. This orchestrated set of changes included proteins involved in cytoskeletal reorganization (caldesmon, calponin, alpha B-crystallin, stathmin, collapsing response mediator protein-2), cell adhesion (vinculin, galectin-1), signal transduction (RACK-1) and astrocyte differentiation (glutamine synthetase). Using proteomic analysis to understand what drives astrocyte expression of these functionally divergent molecules may offer insight into the mechanisms by which astrocytes can exhibit both pro-regenerative and anti-regenerative activities following CNS injury.

Animals↗
PubMed2006

Comparative analysis of regulatory transcription factors in Schizosaccharomyces pombe and budding yeasts.

Regulatory transcription factors (rTFs), which bind specific DNA sequences in the regulatory regions of genes and subsequently activate or repress transcription, play a central role in programming genomic expression. The number of rTFs in a species might therefore reflect its functional complexity. For simple organisms like yeast, a relatively small number of rTFs might be expected that is fairly constant between yeast species. We show that the budding yeast, Saccharomyces cerevisiae, contains 201 rTfs, which is one of the largest rTF numbers found in yeast species for which genome sequences are available. This is a much higher number than the 129 rTFs found in the fission yeast, Schizosaccharomyces pombe, which is currently the yeast with the lowest number of rTFs. Comparative analysis of several different budding yeast species shows that most of the 'extra' rTFs found in S. cerevisiae were probably acquired as a result of a whole genome duplication (WGD) event that occurred in an ancestor of a subset of budding yeast species. However, we also show that budding yeast species that have not been affected by the WGD contain a greater number of rTFs than S. pombe (mean = 145). Thus, two or more mechanisms have led to the 60% increase in rTFs in S. cerevisiae compared to S. pombe. This difference may correlate with a more extensive functional divergence in budding yeasts compared to fission yeasts. The relatively small number of rTFs in S. pombe make this organism an attractive model for global studies of mechanisms that programme gene expression.

Evolution, Molecular↗
PubMed1995

Microfilament assembly is required for anti-IgM dependent MAPK and p90rsk activation in human B lymphocytes.

Mitogen-activated protein kinases (MAPK) are important mediators of signal transduction from the cell surface to the nucleus. These MAPK pathways serve different receptor-mediated signaling pathways leading to dual phosphorylation on serine/threonine and tyrosine residues. The mechanisms linking cytoplasmic MAPK activation to later events is still unclear. In this study we demonstrate that the microfilament system has an active role in MAPK activation. Cross-linking of surface IgM or direct activation of PKC with PMA resulted in time and concentration-dependent increases in F-actin content, MAPK (p42erk-2) activation, and phosphorylation of p90rsk. Pretreatment of the B cells with cytochalasin D or botulinum C2 toxin, microfilament-disrupting agents, prevented the increases in F-actin content as well as MAPK and p90rsk activation. These data indicate a role for the microfilament system in the complex and divergent functions of MAPK.

Actin Cytoskeleton↗
PubMed1999

Colinear and segmental expression of amphioxus Hox genes.

The cephalochordate amphioxus has a single Hox gene cluster. Here we describe the genomic organization of four adjacent amphioxus genes, AmphiHox-1 to AmphiHox-4, together with analysis of their spatiotemporal expression patterns. We demonstrate that these genes obey temporal colinearity and that three of the genes also obey spatial colinearity in the developing neural tube. AmphiHox-1, AmphiHox-3, and AmphiHox-4 show segmental modulation of their expression levels, a two-segment phasing of spatial colinearity, and, at least for AmphiHox-4, asymmetrical expression. AmphiHox-2 is unlike other amphioxus Hox genes: it does not obey spatial colinearity and it has no positional expression in the neural tube. AmphiHox-2 is expressed in the preoral pit of larvae, from which the homologue of the anterior pituitary develops. We suggest that the ancestral role of chordate Hox genes was primarily in the neural tube and that chordate Hox genes can functionally diverge in a manner analogous to that of Drosophila ftz or zen.

Amino Acid Sequence↗
PubMed2001

The secreted glycoprotein Noelin-1 promotes neurogenesis in Xenopus.

Neurogenesis in Xenopus neural ectoderm involves multiple gene families, including basic helix-loop-helix transcription factors, which initiate and control primary neurogenesis. Equally important, though less well understood, are the downstream effectors of the activity of these transcription factors. We have investigated the role of a candidate downstream effector, Noelin-1, during Xenopus development. Noelin-1 is a secreted glycoprotein that likely forms large multiunit complexes. In avians, overexpression of Noelin-1 causes prolonged and excessive neural crest migration. Our studies in Xenopus reveal that this gene, while highly conserved in sequence, has a divergent function in primary neurogenesis. Xenopus Noelin-1 is expressed mainly by postmitotic neurogenic tissues in the developing central and peripheral nervous systems, first appearing after neural tube closure. Its expression is upregulated in ectopic locations upon overexpression of the neurogenic genes X-ngnr-1 and XNeuroD. Noelin-1 expression in animal caps induces expression of neural markers XBrn-3d and XNeuroD, and co-expression of secreted Noelin-1 with noggin amplifies noggin-induced expression of XBrn-3d and XNeuroD. Furthermore, in animal caps neuralized by expression of noggin, co-expression of Noelin-1 causes expression of neuronal differentiation markers several stages before neurogenesis normally occurs in this tissue. Finally, only secreted forms of the protein can activate sensory marker expression, while all forms of the protein can induce early neurogenesis. This suggests that the cellular localization of Noelin-1 may be important to its function. Thus, Noelin-1 represents a novel secreted factor involved in neurogenesis.

Amino Acid Sequence↗
PubMed1998

A second mammalian antizyme: conservation of programmed ribosomal frameshifting.

A second mammalian ornithine decarboxylase antizyme was discovered. The deduced protein sequence of the human antizyme2 is 54% identical and 67% similar to human antizyme1 but 99.5% identical to mouse antizyme2. Polyamine-regulated programmed ribosomal frameshifting is used in decoding antizyme2 mRNA as it is for antizyme1 mRNA. The mRNA signals for the programmed frameshifting are similar in the mRNAs for the two antizymes. However, in the stimulatory pseudoknot 3' of the shift site, while the sequences of the stems are highly conserved, the sequences of the loops are divergent. Functional distinctions between antizymes seem likely, but no distinction in the tissue distribution of human antizyme1 and 2 mRNAs was distinguished, though antizyme2 mRNA is 16-fold less abundant than its antizyme1 counterpart. In addition to the previously characterized human antizyme1 mRNA, a second antizyme1 mRNA with an additional 160 nucleotides at its 3' end was identified, and it has a tissue distribution different from that of the shorter antizyme1 mRNA.

Amino Acid Sequence↗
PubMed1999

Divergent allosteric patterns verify the regulatory paradigm for aspartate transcarbamylase.

The native Escherichia coli aspartate transcarbamoylase (ATCase, E.C. 2.1.3.2) provides a classic allosteric model for the feedback inhibition of a biosynthetic pathway by its end products. Both E. coli and Erwinia herbicola possess ATCase holoenzymes which are dodecameric (2(c3):3(r2)) with 311 amino acid residues per catalytic monomer and 153 and 154 amino acid residues per regulatory (r) monomer, respectively. While the quaternary structures of the two enzymes are identical, the primary amino acid sequences have diverged by 14 % in the catalytic polypeptide and 20 % in the regulatory polypeptide. The amino acids proposed to be directly involved in the active site and nucleotide binding site are strictly conserved between the two enzymes; nonetheless, the two enzymes differ in their catalytic and regulatory characteristics. The E. coli enzyme has sigmoidal substrate binding with activation by ATP, and inhibition by CTP, while the E. herbicola enzyme has apparent first order kinetics at low substrate concentrations in the absence of allosteric ligands, no ATP activation and only slight CTP inhibition. In an apparently important and highly conserved characteristic, CTP and UTP impose strong synergistic inhibition on both enzymes. The co-operative binding of aspartate in the E. coli enzyme is correlated with a T-to-R conformational transition which appears to be greatly reduced in the E. herbicola enzyme, although the addition of inhibitory heterotropic ligands (CTP or CTP+UTP) re-establishes co-operative saturation kinetics. Hybrid holoenzymes assembled in vivo with catalytic subunits from E. herbicola and regulatory subunits from E. coli mimick the allosteric response of the native E. coli holoenzyme and exhibit ATP activation. The reverse hybrid, regulatory subunits from E. herbicola and catalytic subunits from E. coli, exhibited no response to ATP. The conserved structure and diverged functional characteristics of the E. herbicola enzyme provides an opportunity for a new evaluation of the common paradigm involving allosteric control of ATCase.

Allosteric Regulation↗
PubMed1998

Bacterial helicases.

Helicases are proteins that use the energy of ATP hydrolysis to open double-stranded DNA, RNA, or RNA-DNA hybrids into two single strands. Based upon sequence analysis, at least 12 helicases exist in Escherichia coli. We know that these proteins play important roles in DNA replication, recombination, repair, and transcription, as well as in RNA processing. Recent crystallographic studies have revealed a highly conserved catalytic core in the helicases, shared with the RecA protein and the F1-ATPase. However, evidence suggests that the functional divergence may be large.

Bacteria↗
PubMed1979

The half-life of mRNA in Saccharomyces cerevisiae.

The decay kinetics of mRNA was studied in a yeast temperature-sensitive mutant, ts136, which is defective in cytoplasmic RNA production at 37 degree C. The disappearance of the synthetic capacity of mRNA was determined by withdrawing equal volumes of ts136 cell culture and pulse-labelling with [35S]methionine at various time intervals after the shift to 37 degrees C from 23 degrees C. The synthesized proteins were separated on a two-dimensional gel electrophoretic system and then quantitatively analyzed for theri incorporated radioactivities by scintillation counting. Our results show that yeast mRNAs have divergent functional half-lives ranging from 4.5 to 41 min, with an average value of 22 min. Each mRNA exhibits a simple exponential decay with its own characteristic dacay pattern. Of the approximately 500 major polypeptides made by yeast cells, which are detectable on autoradiograms of the gels, 80 were arbitrarily selected and the mRNAs coding for those polypeptides were examined for their decay kinetics.

Electrophoresis↗
PubMed1992

Macrophages in melanocytic naevi.

Whereas the inflammatory infiltrates of malignant melanoma have been widely investigated, little is known about the infiltrates accompanying benign melanocytic naevi. Using monoclonal antibodies directed against HLA-DR antigens, the CD1 antigen, the transferrin receptor and functionally divergent macrophage subpopulations, frozen fresh material of 87 melanocytic naevi (MN), ten primary cutaneous melanomas (PCM) and ten samples of normal skin were studied. Compared with normal skin, abundant HLA-DR+ cells were found in the stroma of MN equivalent to the quantity present in PCM. In MN we found higher numbers of dermal CD1+ dendritic cells compared with PCM and normal skin. There were more macrophages that expressed the transferrin receptor or the antigens 27E10, RM3/1 and 25F9 in MN than in normal skin but fewer than in PCM. No significant differences were found between congenital MN (n = 40), common acquired MN (n = 27) and dysplastic MN (n = 20) macrophage subpopulations. Also, no correlations were evident between macrophage infiltrates and naevus location or patients' age. Our data show that potential melanoma precursors among melanocytic naevi cannot be identified by the pattern of macrophage infiltrates.

Antigens, CD↗
PubMed1977

Origin of alpha-glycerophosphate dehydrogenase isozymes in Drosophila melanogaster and their functional relationship in the alpha-glycerophosphate cycle.

The basis for the differentiation of L-glycerol-3-phosphate dehydrogenase (alpha-GPDH) into larval and adult isozymes in Drosophila melanogaster was investigated by the correlation of a lack of appearance of each isozyme during development within Drosophila bearing alpha-GPDH "null" alleles and by the study of a putative conversion factor. Conversion studies indicate the presence of a heat-labile RNase-resistant conversion factor present in crude larval extracts with the ability to convert GPDH-1 to GPDH-2 and GPDH-3 but not vice versa. In addition, "null" mutations at the Gpdh locus obliterate all isozymatic species of alpha-GPDH in all developmental stages. These observations suggest that all alpha-GPDH isozymes are the product of a single structural gene and that the multiple forms of this enzyme arise during successive developmental stages through an epigenetic modification of the primary Gpdh+ polypeptide. Finally, observations are reported which bear on the functional divergence of the alpha-glycerophosphate cycle in the adult and larval stage of development.

Alleles↗
PubMed1997

Molecular evolution of the photolyase-blue-light photoreceptor family.

The photolyase-blue-light photoreceptor family is composed of cyclobutane pyrimidine dimer (CPD) photolyases, (6-4) photolyases, and blue-light photoreceptors. CPD photolyase and (6-4) photolyase are involved in photoreactivation for CPD and (6-4) photoproducts, respectively. CPD photolyase is classified into two subclasses, class I and II, based on amino acid sequence similarity. Blue-light photoreceptors are essential light detectors for the early development of plants. The amino acid sequence of the receptor is similar to those of the photolyases, although the receptor does not show the activity of photoreactivation. To investigate the functional divergence of the family, the amino acid sequences of the proteins were aligned. The alignment suggested that the recognition mechanisms of the cofactors and the substrate of class I CPD photolyases (class I photolyases) are different from those of class II CPD photolyases (class II photolyases). We reconstructed the phylogenetic trees based on the alignment by the NJ method and the ML method. The phylogenetic analysis suggested that the ancestral gene of the family had encoded CPD photolyase and that the gene duplication of the ancestral proteins had occurred at least eight times before the divergence between eubacteria and eukaryotes.

Amino Acid Sequence↗
PubMed1996

Metal binding and resultant loss of phototoxicity of alpha-terthienyl: metal detoxification versus alpha-terthienyl inactivation.

The members of the plant family asteraceae are noted for their cosmopolitan distribution and their versatility is attributed to be largely due to their morphological adaptations. Interestingly members of this family are endowed with rich levels of secondary plant metabolites, many of which are photochemically active (Bakker et al. 1979; Kagan et al. 1989). The secondary plant metabolite alpha-terthienyl derived from the plant family asteraceae is among the new class of light activated insecticide. The photobiocidal effects associated with alpha-terthienyl in presence of sunlight and ultraviolet light (300-400 nm), has stimulated a great deal of interest in its toxic mechanism of action against a number of organisms including phytopathogenic fungi, nematodes and mosquito larvae. Trials under tropical conditions indicate a very high level of activity as a larvicide to mosquito. There is no cross resistance to this compound in malathion resistant mosquito larvae (Arnason et al. 1989). Even though many researchers feel that the phototoxicity of secondary plant metabolites has arisen independently many times in evolution as a defense mechanism, the physiological impact of such biologically active compounds in the plant producing them also should be addressed (Arnason et al. 1987). Moreover, the accumulation of secondary plant metabolites in the roots of many asteraceae members as is the case with alpha-terthienyl in marigold (Tagetes sp.) roots, hints towards their functional divergence. In this study, we demonstrate a potent heavy metal quenching activity of alpha-terthienyl.

Animals↗
PubMed2003

Interspecies comparison of a gene pair with partially redundant function: the rst and kirre genes in D. virilis and D. melanogaster.

The D. melanogaster rst and kirre genes encode two highly related immunoglobulin-like cell adhesion molecules that function redundantly during embryonic muscle development. The two genes appear to be derived from a common ancestor by gene duplication. Gene duplications have been proposed to be of major evolutionary significance since duplicated redundant sequences can accumulate mutations without detrimental effects for the organism and leave the duplicated genes free to assume novel functions. To address the issue of conservation of the duplicated sequences and their putative redundancy, as well as to identify putative functional divergence of the paralogs during drosophilid evolution, we performed an interspecies comparison of the rst and kirre genes from D. virilis and D. melanogaster. The D. virilis genome contains orthologues of both rst and kirre and hence the duplication took place before the split of the two lineages and has subsequently been conserved. However, whilst the Rst orthologues show a high degree of sequence similarity, this similarity is lower in Kirre orthologues. Especially the intracellular domains of D. virilis and D. melanogaster Kirre sequences are highly divergent: the D. virilis kirre gene lacks the 3'-most exon present in D. melanogaster, which contains motifs conserved between kirre and rst in D. melanogaster. Hence, while each of the two genes is highly conserved at the level of its exon-intron organization, the selection forces acting on the rst and kirre coding sequences are different. These findings are discussed in the light of general evolutionary mechanisms.

Amino Acid Sequence↗
PubMed2005

Tyrosinase activity and hemocyanin in the hemolymph of the slipper lobster Scyllarides latus.

The respiratory protein hemocyanin is present in molluscans and in some species of arthropods, and its dioxygen binding site strongly resembles that of the monophenol-hydroxylating and catechol-quinonising enzyme tyrosinase. Moreover, some hemocyanins show a certain extent of tyrosinase activity, so a common ancestry between the two proteins has been suggested. However, in the case purified hemocyanin of Scyllarides latus any attempts to evoke tyrosinase activity failed. A distinct tyrosinase has been purified to homogeneity from the hemolymph, and kinetically characterised. The purified tyrosinase showed both monophenolase and diphenolase enzyme activity and therefore it could be well defined as a true tyrosinase. This finding suggests that in the case of the studied crustacean the evolutionary functional divergence between dioxygen transport and oxidation of phenolics has already reached its completeness.

Animals↗