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At least 271 records · Page 15Linked to original sources
PubMed1995

Genomic sequence, structural organization and evolutionary conservation of the 13.2-kDa subunit of rat NADH:ubiquinone oxidoreductase.

The 13.2-kDa subunit of NADH:ubiquinone oxidoreductase has been shown to be an integral part of the bovine iron-sulfur (IP) part of the protein. This subunit has been shown to interact with at least two other protein subunits of the IP fragment. The amino acid (aa) sequence of this subunit, determined from an acid extract of rat heart was used to generate an oligodeoxyribonucleotide probe which allowed isolation of a cDNA coding for the rat homologue of 13.2-kDa IP. The cDNA was used as a probe of a rat genomic DNA library and two clones were isolated, one of which contained the entire coding region for 13.2-kDa IP. Southern analysis indicates that the IP13 sequence exists as a single copy gene. The sequence of the genomic clone contains one intron and promoter elements including a TATAAA region. The 5' flank region has several potential regulatory sites, most notably regions similar to the nuclear respiratory factor 1 (NRF-1) motif, found in other genes which code for mitochondrial proteins [Evans and Scarpulla, Genes Dev. 4 (1990) 1023-1034]. The core domain of the deduced rat aa sequence has a high degree of identity with the mouse and cow homologues of this protein. The high degree of conservation of this protein indicates that the protein is essential for the function of complex I.

Amino Acid Sequence↗
PubMed1995

Regions of evolutionary conservation between the rat and human prohibitin-encoding genes.

We have analyzed and compared the 5' promoter region, the intron structure and the exon-intron flanking sequences in the rat and human prohibitin-encoding genes (PHB). Comparative analysis of a 350-nt region immediately 5' to and including the first exon identifies eight highly conserved regions, four of which correspond to binding sites for known transcriptional control proteins (CCAAT box, 'SV40' site and two Sp1 sites). The promoter lacks a TATA box. Four transcription start points (tsp) clustered within a 35-bp region were identified by rapid amplification of cDNA ends (RACE). The exon-intron boundaries in rat and human are highly conserved, with identical positioning of splice junctions. PCR analysis with conserved exon primers was used to detect length variation between rat and human PHB, and length differences were observed in all of the introns.

Animals↗
PubMed1996

NBP35 encodes an essential and evolutionary conserved protein in Saccharomyces cerevisiae with homology to a superfamily of bacterial ATPases.

We have cloned a novel and essential gene, NBP35, from Saccharomyces cerevisiae that encodes a putative Nucleotide Binding Protein of 35 kDa. Sequence analysis revealed structural homology of Nbp35p with a family of bacterial ATPases involved in cell division processes and chromosome partitioning. A search in databases identified closely related sequences from yeast and higher eukaryotes, suggesting a conserved function for this family of proteins. By indirect immunofluorescence, a tagged version of Nbp35p carrying two immunoglobulin G-binding domains derived from Staphylococcus aureus Protein A was localised to the nucleus. A single amino-acid substitution in the conserved nucleotide-binding motif of Nbp35p renders the protein non-functional. Furthermore, a conserved cluster of four cysteines in the N-terminal end of the protein is also required for an essential role of Nbp35p.

Adenosine Triphosphatases↗
PubMed1996

Nucleotide sequence of ub52 from the cnidarian Acropora millepora reveals high evolutionary conservation.

We report the cDNA sequence encoding Ub52 from the cnidarian Acropora millepora. As in other eukaryotes, the N-terminal region of the deduced amino-acid sequence is a ubiquitin moiety and the C-terminal region CEP52, a protein component of the large ribosomal subunit. A millepora Ub52 is highly homologous (> 95% identical) with the corresponding Drosophila and vertebrate sequences, the cnidarian sequence having higher identity with these 'higher' metazoan homologs than does the corresponding Caenorhabditis elegans protein. However, the cnidarian sequence contains two unique substitutions in the ubiquitin moiety, Ser22 and Thr28. Northern analysis indicates that A. millepora Ub52 is encoded by a small (< 800 nt) mRNA present in eggs and is first expressed after the early gastrula stage in embryonic development.

Amino Acid Sequence↗
PubMed1992

The murine Sm-D autoantigen: multiple genes, genetic polymorphism, evolutionary conservation and lack of intervening sequences in the coding region.

Antibodies to the Sm nuclear antigen are diagnostic of systemic lupus erythematosus (SLE). MRL/Mp-lpr/lpr mice develop a similar illness, and a proportion also develop anti-Sm. To understand better anti-Sm reactivity in this murine model, we have cloned the murine Sm-D autoantigen. One cDNA clone was 517 bp long with an open reading frame of 357 nucleotides, encoding a 13.3 kDa protein of 119 amino acids. At the nucleotide level, the murine Sm-D cDNA was 89.8% homologous with human Sm-D (94% in the coding region), yet there was identity at the protein level, including a Gly-Arg nine-fold repeated C-terminus motif. Southern blot analysis of PstI-digested genomic DNA from seven mouse strains demonstrated a 7.8 kb band in every strain; in addition, a 2.8 kb band was seen in AKR/J, LG/J and MRL/Mp-lpr/lpr. PCR amplification of genomic DNA showed a single Sm-D gene product of 360 bp, which indicated a lack of intervening sequences. The Sm-D protein is thus highly conserved in evolution, probably owing to its essential role in the physiology of the cell.

Alleles↗
PubMed1992

Evolutionary conservation of the active site of soluble inorganic pyrophosphatase.

Soluble inorganic pyrophosphatases (PPases) are essential enzymes that are important for controlling the cellular levels of inorganic pyrophosphate (PPi). Although prokaryotic and eukaryotic PPases differ substantially in amino acid sequence, recent evidence now demonstrates clearly that PPases throughout evolution show a remarkable level of conservation of both an extended active site structure, which has the character of a mini-mineral, and a catalytic mechanism. PPases require several (three or four) Mg2+ ions at the active site for activity and many of the 15-17 fully conserved active site residues are directly involved in the binding of metal ions. Each of the eight microscopic rate constants that has been evaluated for the PPases from both Escherichia coli and Saccharomyces cerevisiae is quite similar in magnitude for the two enzymes, supporting the notion of a conserved mechanism.

Amino Acid Sequence↗
PubMed2005

Evolutionary conserved N-terminal domain of Nrf2 is essential for the Keap1-mediated degradation of the protein by proteasome.

Under homeostatic conditions, Nrf2 activity is constitutively repressed. This process is dependent on Keap1, to which Nrf2 binds through the Neh2 domain. Since the N-terminal subdomain of Neh2 (Neh2-NT) contains evolutionarily conserved motifs, we examined the roles they play in the degradation of Nrf2. In Neh2-NT, we defined a novel motif that is distinct from the previously characterized DIDLID motif and designated it DLG motif. Deletion of Neh2-NT or mutation of the DLG motif largely abolished the Keap1-mediated degradation of Nrf2. These mutations were found to enfeeble the binding affinity of Nrf2 to Keap1. The Neh2-NT subdomain directed DLG-dependent, Keap1-independent, degradation of a reporter protein in the nucleus. By contrast, mutation of DLG did not affect the half-life of native Nrf2 protein in the nucleus under oxidative stress conditions. These results thus demonstrate that DLG motif plays essential roles in the Keap1-mediated proteasomal degradation of Nrf2 in the cytoplasm.

Adaptor Proteins, Signal Transducing↗
PubMed2004

The COP9 signalosome (CSN): an evolutionary conserved proteolysis regulator in eukaryotic development.

The COP9 signalosome (CSN) is a multiprotein complex of the ubiquitin-proteasome pathway. CSN is typically composed of eight subunits, each of which is related to one of the eight subunits that form the lid of the 26S proteasome regulatory particle. CSN was first identified in Arabidopsis where it is required for the repression of photomorphogenic seedling development in the dark. CSN or CSN-related complexes have by now been reported from most eukaryotic model organisms and CSN has been implicated in a vast array of biological processes. It is widely accepted that CSN directly interacts with cullin-containing E3 ubiquitin ligases, and that CSN is required for their proper function. The requirement of CSN for proper E3 function may at least in part be explained by the observation that CSN subunit 5 (CSN5) is the isopeptidase that deconjugates the essential ubiquitin-like Nedd8 modification from the E3 cullin subunit. In addition to its interaction with E3s, CSN may also regulate proteolysis by its association with protein kinases and deubiquitylating enzymes. This review provides a summary of the role of CSN in regulating protein degradation and in eukaryotic development.

Animals↗
PubMed2005

Evolutionary conservation of nuclear and nucleolar targeting sequences in yeast ribosomal protein S6A.

Over 1 billion years ago, the animal kingdom diverged from the fungi. Nevertheless, a high sequence homology of 62% exists between human ribosomal protein S6 and S6A of Saccharomyces cerevisiae. To investigate whether this similarity in primary structure is mirrored in corresponding functional protein domains, the nuclear and nucleolar targeting signals were delineated in yeast S6A and compared to the known human S6 signals. The complete sequence of S6A and cDNA fragments was fused to the 5'-end of the LacZ gene, the constructs were transiently expressed in COS cells, and the subcellular localization of the fusion proteins was detected by indirect immunofluorescence. One bipartite and two monopartite nuclear localization signals as well as two nucleolar binding domains were identified in yeast S6A, which are located at homologous regions in human S6 protein. Remarkably, the number, nature, and position of these targeting signals have been conserved, albeit their amino acid sequences have presumably undergone a process of co-evolution with their corresponding rRNAs.

Cell Nucleolus↗
PubMed2006

Evolutionary conservation and murine embryonic expression of the gene encoding the SERTA domain-containing protein CDCA4 (HEPP).

Cdca4 (Hepp) was originally identified as a gene expressed specifically in hematopoietic progenitor cells as opposed to hematopoietic stem cells. More recently, it has been shown to stimulate p53 activity and also lead to p53-independent growth inhibition when overexpressed. We independently isolated the murine Cdca4 gene in a genomic expression-based screen for genes involved in mammalian craniofacial development, and show that Cdca4 is expressed in a spatio-temporally restricted pattern during mouse embryogenesis. In addition to expression in the facial primordia including the pharyngeal arches, Cdca4 is expressed in the developing limb buds, brain, spinal cord, dorsal root ganglia, teeth, eye and hair follicles. Along with a small number of proteins from a range of species, the predicted CDCA4 protein contains a novel SERTA motif in addition to cyclin A-binding and PHD bromodomain-binding regions of homology. While the function of the SERTA domain is unknown, proteins containing this domain have previously been linked to cell cycle progression and chromatin remodelling. Using in silico database mining we have extended the number of evolutionarily conserved orthologues of known SERTA domain proteins and identified an uncharacterised member of the SERTA domain family, SERTAD4, with orthologues to date in human, mouse, rat, dog, cow, Tetraodon and chicken. Immunolocalisation of transiently and stably transfected epitope-tagged CDCA4 protein in mammalian cells suggests that it resides predominantly in the nucleus throughout all stages of the cell cycle.

Amino Acid Sequence↗
PubMed2005

Intramolecular cross-linking in a bacterial homolog of mammalian SLC6 neurotransmitter transporters suggests an evolutionary conserved role of transmembrane segments 7 and 8.

The extracellular concentration of the neurotransmitters dopamine, serotonin, norepinephrine, GABA and glycine is tightly controlled by plasma membrane transporters belonging to the SLC6 gene family. A very large number of putative transport proteins with a remarkable homology to the SLC6 transporters has recently been identified in prokaryotes. Here we have probed structural relationships in a 'microdoman' corresponding to the extracellular ends of transmembrane segments (TM) 7 and 8 in one of these homologs, the tryptophan transporter TnaT from Symbiobacterium thermophilum. We found that simultaneous - but not individual - substitution of Ala286 at the top of TM7 and Met311 at the top of TM8 with cysteines conferred sensitivity to submicromolar concentrations of Hg(2+) as assessed in a [(3)H]tryptophan uptake assay. Because Hg(2+) can cross-link pairs of cysteines, this suggests close proximity between TM 7 and 8 in the tertiary structure of TnaT as previously suggested for the mammalian counterparts. Furthermore, the inhibition of uptake upon cross-linking the two cysteines provides indirect support for a conserved conformational role of these transmembrane domains in the transport process. It was not possible, however, to transfer to TnaT binding sites for another metal ion, Zn(2+), that we previously engineered in the dopamine (DAT) and GABA (GAT-1) transporters between TM 7 and 8. This suggests that the structure of the TM7/8 microdomain is not identical with that of DAT and GAT-1. Hence, our data also emphasize possible structural differences that should be taken into account when interpreting future data on bacterial homologs of the SLC6 transporters.

Animals↗
PubMed2005

Evolutionary conservation of the structural, pharmacological, and genomic characteristics of the melanocortin receptor subtypes.

We have cloned melanocortin receptors (MCRs) from several species of fish. The MC4R and MC5R subtypes arose early in vertebrate evolution and their primary structure is remarkably conserved. Expression and pharmacological characterization of the MCRs in fish has revealed that they bind and respond to melanocortin peptides with high potency. Detailed characterization of the binding properties of the different subtypes suggests that MCRs in early vertebrates had preference for adrenocorticotropic hormone (ACTH) peptides, while the high sensitivity for the shorter proopiomelanocortin (POMC) products, such as the alpha-, beta-, and gamma-melanocyte-stimulating hormone (MSH), has appeared later, perhaps as the MCR subtypes gained more specialized functions. The MCR repertoire shows in general high similarities in their primary structures, while they are however not similar in terms of functional roles. The MCRs serve therefore as an interesting model family to understand the molecular mechanisms of how functions of the genes can diverge during evolution. In this review, we provide an overview of our recent studies on the cloning, expression, pharmacology, 3D modeling, and genomic studies of the MCRs in non-mammalian species.

Amino Acid Sequence↗
PubMed2006

Functional comparison of two evolutionary conserved insect neurokinin-like receptors.

Tachykinins are multifunctional neuropeptides that have been identified in vertebrates as well as invertebrates. The C-terminal FXGXRa-motif constitutes the consensus active core region of invertebrate tachykinins. In Drosophila, two putative G protein-coupled tachykinin receptors have been cloned: DTKR and NKD. This study focuses on the functional characterization of DTKR, the Drosophila ortholog of the stable fly's tachykinin receptor (STKR). Tachykinins containing an alanine residue instead of the highly conserved glycine (FXAXRa) display partial agonism on STKR-mediated Ca(2+)-responses, but not on cAMP-responses. STKR therefore seems to differentiate between a number of tachykinins. Gly- and Ala-containing tachykinins are both encoded in the Drosophila tachykinin precursor, thus raising the question of whether DTKR can also distinguish between these two tachykinin types. DTKR was activated by all Drosophila tachykinins and inhibited by tachykinin antagonists. Ala-containing analogs did not produce the remarkable activation behavior previously observed with STKR, suggesting different mechanisms of discerning ligands and/or activating effector pathways for STKR and DTKR.

Animals↗
PubMed2004

Evolutionary conserved role of ptf1a in the specification of exocrine pancreatic fates.

We have characterized and mapped the zebrafish ptf1a gene, analyzed its embryonic expression, and studied its role in pancreas development. In situ hybridization experiments show that from the 12-somite stage to 48 hpf, ptf1a is dynamically expressed in the spinal cord, hindbrain, cerebellum, retina, and pancreas of zebrafish embryos. Within the endoderm, ptf1a is initially expressed at 32 hpf in the ventral portion of the pdx1 expression domain; ptf1a is expressed in a subset of cells located on the left side of the embryo posteriorly to the liver primordium and anteriorly to the endocrine islet that arises from the posterodorsal pancreatic anlage. Then the ptf1a expression domain buds giving rise to the anteroventral pancreatic anlage that grows posteriorly to eventually engulf the endocrine islet. By 72 hpf, ptf1a continues to be expressed in the exocrine compartment derived from the anteroventral anlage. Morpholino-induced ptf1a loss of function suppresses the expression of the exocrine markers, while the endocrine markers in the islet are unaffected. In mind bomb (mib) mutants, in which delta-mediated notch signalling is defective [Dev. Cell 4 (2003) 67], ptf1a is normally expressed. In addition, the slow-muscle-omitted (smu) mutants that lack expression of endocrine markers because of a defective hedgehog signalling [Curr. Biol. 11(2001) 1358] exhibit normal levels of ptf1a. This indicates that hedgehog signaling plays a different genetic role in the specification of the anteroventral (mostly exocrine) and posterodorsal (endocrine) pancreatic anlagen.

Animals↗
PubMed2005

An evolutionary conserved role of Wnt signaling in stem cell fate decision.

Wnt/Frizzled/ss-catenin-based signaling systems play diverse roles in metazoan development, being involved not only in the establishment of body axes in embryogenesis but also in regulating stem cell fate in mammalian post-embryonic development. We have studied the role the canonical Wnt cascade plays in stem cell fate determination in Hydractinia, a member of the ancient metazoan phylum Cnidaria, by analyzing two key molecules in this pathway, frizzled and ss-catenin, and blocking GSK-3. Generally, frizzled was expressed in cells able to divide but absent in post-mitotic, terminally differentiated cells such as nerve cells and nematocytes. Transcripts of frizzled were identified in all embryonic stages beginning with maternal transcripts in the oocyte. Following gastrulation and in the planula larva, frizzled expression concentrated in the central endodermal mass from which the first interstitial stem cells and their derivatives arise. In post-metamorphic development, high levels of frizzled transcripts were detected in interstitial stem cells. Activating downstream events of the Wnt-cascade in the post-metamorphic life phase by blocking GSK-3 with paullones induced recruitment of nematocytes and nerve cells from the pool of interstitial stem cells. Terminal differentiation was preceded by an initial burst of proliferation of frizzled-positive i-cells. In activated i-cells, ss-catenin appeared in the cytoplasm, later in the nucleus. It was subsequently again observed in the cytoplasm and eventually faded out during terminal differentiation. Our results suggest an ancient role of Wnt signaling in stem cell fate determination.

Adenine↗
PubMed2004

Characterisation of an evolutionary conserved protein interacting with the putative guanine nucleotide exchange factor DelGEF and modulating secretion.

A human cDNA library was screened for proteins interacting with the deafness locus putative guanine nucleotide exchange factor (DelGEF) using a yeast two-hybrid system. A protein with a predicted size of 9 kDa was identified as a binding partner, this protein was designated DelGEF interacting protein 1 (DelGIP1). The interaction between DelGEF and DelGIP1 was verified by co-immunoprecipitation of a DelGEF-DelGIP1 complex from cell lysates. Highly conserved homologues of DelGIP1 were identified in higher and lower eukaryotes by database searching. The human DelGIP1 gene is ubiquitously expressed as judged by human multiple tissue Northern blot analysis. DelGEF was recently shown to interact with Sec5, a protein involved in secretion, and to regulate secretion of proteoglycans. Downregulation of endogenous DelGIP1 in HeLa cells induced increased extracellular secretion of proteoglycans indicating a possible role for DelGIP1 in the secretion process.

Amino Acid Sequence↗
PubMed2004

Evolutionary conservation of KLF transcription factors and functional conservation of human gamma-globin gene regulation in chicken.

The Krüppel-like factors (KLFs) are a family of Cys2His2 zinc-finger DNA binding proteins with homology to Drosophila Krüppel. KLFs can bind to CACCC elements, which are important in controlling developmental programs. The CACCC promoter element is critical for the developmental regulation of the human gamma-globin gene. In the present study, chicken homologues of the human KLF2, 3, 4, 5, 9, 11, 12, 13, and 15 genes were identified. Phylogenetic analysis confirms that these genes are more closely related to their human homologues than they are to other chicken KLFs. This work also represents the first systematic study of the expression patterns of KLFs during erythroid development. In addition, transient transfections of human globin constructs into 5-day (primitive) chicken red blood cells show that human gamma-globin expression is regulated via its CACCC promoter element. This indicates that a CACCC-binding factor(s) important for gamma-globin expression functions in 5-day chicken red cells.

Amino Acid Sequence↗
PubMedDate not supplied

Evolutionary conservation of biotinidase: implications for the enzyme's structure and subcellular localization.

Biotinidases from various species ranging from fungi and insects to human have specific amino acids, and regions that are evolutionarily conserved. These specific amino acids and regions are further supported by their homology to a variety of amidases and nitrilases and by the location of missense mutations that cause biotinidase deficiency in humans. Glu-Lys-Cys residues from three of these regions are considered the catalytic triad involved in the catalysis of the amide linkage. The last one-third of the biotinidase sequence is lacking in nitrilases-amidases, which do not bind biocytin or biotin, therefore, it is likely that the biocytin-biotin-binding site of biotinidase is within this portion of the molecule. Although there are many missense mutations at the far C-terminus of the enzyme, the function of this region is still unclear. Biotinidase may have different functions in different cells or in different subcellular compartments. Using computer programs that predict the subcellular localization of proteins based on their N-terminal signal peptides, microsomal localization resulting in secretion was predicted for biotinidase from all species, whereas there is little consistent support for mitochondrial or nuclear localization of the enzymes. Additional immunohistochemical studies of various human tissues at different stages of development are necessary to resolve the ambiguity of subcellular localization of biotinidase.

Amino Acid Sequence↗