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Regulation of actin isoforms in cellular and developmental processes

SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY 2020年 102卷 113-121页

作者： Kashina, Anna S. Univ Penn Philadelphia PA 19104 USA

Actin is one of the most abundant and essential intracellular proteins that mediates nearly every form of cellular movement and underlies such key processes as embryogenesis, tissue integrity, cell division and contractility of all types of muscle and non-muscle cells. In mammals, actin is represented by six isoforms, which are encoded by different genes but produce proteins that are 95-99 % identical to each other. The six actin genes have vastly different functions in vivo, and the small amino acid differences between the proteins they encode are rigorously maintained through evolution, but the underlying differences behind this distinction, as well as the importance of specific amino acid sequences for each actin isoform, are not well understood. This review summarizes different levels of actin isoform-specific regulation in cellular and developmental processes, starting with the nuclear actin's role in transcription, and covering the gene-level, mRNA-level, and protein-level regulation, with a special focus on mammalian actins in non-muscle cells.

关键词： Actin Regulation of cytoskeleton coding sequence Translation rate Posttranslational modifications

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Nitric oxide mediates cold- and dehydration-induced expression of a novel MfHyPRP that confers tolerance to abiotic stress

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PHYSIOLOGIA PLANTARUM 2013年第3期149卷 310-320页

作者： Tan, Jiali Zhuo, Chunliu Guo, Zhenfei South China Agr Univ State Key Lab Conservat & Utilizat Subtrop Agrobi Guangzhou 510642 Guangdong Peoples R China South China Agr Univ Guangdong Key Lab Innovat Dev & Utilizat Forest P Guangzhou 510642 Guangdong Peoples R China

Hybrid proline-rich proteins (HyPRPs) are cell wall-localized proteins, and are frequently responsive to environmental stresses. The coding sequence of a HyPRPcDNA was isolated from Medicago falcata, a forage crop that shows cold and drought tolerance. The predicted MfHyPRP contains a proline-rich domain at N-terminus after the signal peptide and a conserved eight-cysteine motif at the C-terminus. Higher level of MfHyPRP transcript was observed in leaves than in stems and roots under control conditions, while more MfHyPRP transcript was induced in leaves and stems than in roots after cold treatment. Levels of MfHyPRP transcript and MfHyPRP protein in leaves were induced by cold, dehydration, abscisic acid (ABA), hydrogen peroxide (H2O2) and nitric oxide (NO), but not responsive to salt stress. The cold- or dehydration-induced expression of MfHyPRP was blocked by scavenger of NO, but not affected by inhibitor of ABA biosynthesis or scavenger of H2O2. The results indicated that NO, but not ABA and H2O2, was essential in the cold- and dehydration-induced expression of MfHyPRP. Overexpression of MfHyPRP in tobacco led to increased tolerance to freezing, chilling and osmotic stress as well as methyl viologen-induced oxidative stress. The increased cold and osmotic stress tolerance was proposed to be associated with improved protection against oxidative damages. It is suggested that NO mediates cold- and dehydration-induced expression of MfHyPRP that confers tolerance to abiotic stress.

关键词： Medicago falcata Nitric Oxide Common Cold hydrogen peroxide Osmotic Stress stress tolerance Proline-Rich Domain COLD Signal Peptides TOLERANCE INCREASED transcript coding sequence NOBELIUM abiotic stress Abscisic Acid

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PREDICTION OF GENE STRUCTURE

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JOURNAL OF MOLECULAR BIOLOGY 1992年第1期226卷 141-157页

作者： GUIGO, R KNUDSEN, S DRAKE, N SMITH, T HARVARD UNIV SCH MEDDANA FARBER CANC INSTMOLEC BIOL COMP RES RESOURCEBOSTONMA 02115 HARVARD UNIV SCH PUBL HLTHBOSTONMA 02115

We have developed a hierarchical rule base system for identifying genes in DNA sequences. Atomic sites (such as initiation codons, stop codons, acceptor sites and donor sites) are identified by a number of different methods and evaluated by a set of filters and rules chosen to maximize sensitivity; these are combined into higher-order gene elements (such as exons), evaluated, filtered and combined as equivalence classes into probable genes, which are evaluated and ranked. The system has been tested on an extensive collection of vertebrate genes smaller than 15,000 bases. Results obtained show that, on average, 88% of the predicted coding region for a transcription unit is actually coding, and 80% of the actual coding is correctly predicted. This will, in most applications, be sufficient for a search against protein sequence databases for the identification of probable gene function. In addition, the system provides a general test platform for both gene atomic site identification and the rules for their evaluation and assembly.

关键词： GENE IDENTIFICATION EXON STRUCTURE INTRON SPLICING coding sequence ARTIFICIAL INTELLIGENCE

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ORNITHINE DECARBOXYLASE GENE OF NEUROSPORA-CRASSA - ISOLATION, sequence, AND POLYAMINE-MEDIATED REGULATION OF ITS MESSENGER-RNA

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MOLECULAR AND CELLULAR BIOLOGY 1992年第1期12卷 347-359页

作者： WILLIAMS, LJ BARNETT, GR RISTOW, JL PITKIN, J PERRIERE, M DAVIS, RH UNIV CALIF IRVINE DEPT MOLEC BIOL & BIOCHEMIRVINECA 92717

Ornithine decarboxylase (ODC), which initiates the biosynthesis of the polyamines putrescine, spermidine, and spermine, is encoded by the spe-1 gene of the fungus Neurospora crassa. This gene and its cDNA have been cloned and sequenced. The gene has a single 70-nucleotide intron in the coding sequence. The cDNA, comprising the entire coding region, recognizes a single 2.4-kb mRNA in Northern (RNA) blots. The mRNA transcript, defined by S1 mapping, has an extremely long, 535-base leader without strong secondary-structure features or an upstream reading frame. The translational start of the protein is ambiguous: a Met-Val-Met sequence precedes the Pro known to be the N terminus of the ODC polypeptide. The polypeptide encoded by the N. crassa spe-1 gene (484 amino acids) has 46% amino acid identity with that of Saccharomyces cerevisiae (466 amino acids) and 42% with that of mouse (461 amino acids). Alignment of the longer N. crassa sequence with S. cerevisiae and mouse sequences creates gaps in different sites in the S. cerevisiae and mouse sequences, suggesting that N. crassa ODC is closer to an ancestral form of the enzyme than that of either yeast or mouse ODC. N. crassa ODC, which turns over rapidly in vivo in the presence of polyamines, has two PEST sequences, found in most ODCs and other proteins with rapid turnover. In striking contrast to other eucaryotic organisms, the variation in the rate of ODC synthesis in response to polyamines in N. crassa is largely correlated with proportional changes in the abundance of ODC mRNA. Spermidine is the main effector of repression, while putrescine has a weaker effect. However, putrescine accumulation appears to increase the amount of active ODC that is made from a given amount of ODC mRNA, possibly by improving its translatability. Conversely, prolonged starvation for both putrescine and spermidine leads to the differentially impaired translation of ODC mRNA.

关键词： .Putrescine Spermidine decarboxylase crassa blots coding sequence coding region California Irvine Ornithine ODC spe gene Gene of Neurospora Polyamine-Mediated

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REGULATION OF ARGININE METABOLISM IN SACCHAROMYCES-CEREVISIAE - EXPRESSION OF THE 3 ARGR REGULATORY GENES AND CELLULAR-LOCALIZATION OF THEIR PRODUCTS

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GENE 1987年第2-3期55卷 277-285页

作者： BERCY, J DUBOIS, E MESSENGUY, F CTR ENSEIGNMENT & RECH IND ALIMENTAIRES INST RECH 1 AVE EMILE GRYSON B-1070 BRUSSELS BELGIUM UNIV LIBRE BRUXELLES FAC SCI MICROBIOL LAB B-1070 BRUSSELS BELGIUM

Three regulatory proteins are involved in the control arginine metabolism in yeast: ARGRI, ARGRII and ARGRIII. The control region and part of the coding sequence of the ARGR genes were fused to the Escherichia coli lacZ gene. These chimeras were used to study the expression of the regulatory genes as well as the cellular compartmentalization of the regulatory products. Our results show that the three ARGR proteins are localized in the nucleus and that their synthesis is not regulated by arginine nor by any of the other ARGR products. However, some data suggest that the ARGRIII protein could control ARGRI activity.

关键词： coding sequence lacZ fusion Recombinant DNA regulatory proteins subcellular localization yeast

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TN curve: A novel 3D graphical representation of DNA sequence based on trinucleotides and its applications

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JOURNAL OF THEORETICAL BIOLOGY 2009年第3期261卷 459-468页

作者： Yu, Jia-Feng Sun, Xiao Wang, Ji-Hua Southeast Univ Sch Biol Sci & Med Engn State Key Lab Bioelect Nanjing 210096 Peoples R China Dezhou Univ Dept Phys Key Lab Biophys Shandong Univ Dezhou 253023 Peoples R China

In this paper, a novel 3D graphical representation of DNA sequence based on trinucleotides is proposed. This representation allows direct inspection of composition as well as distribution of trinucleotides in DNA sequence for the first time and avoids loss of information, from which one can obtain more information. Based on this novel model, six numerical descriptors of DNA sequence are deduced without complicated calculations, and the applications in similarities/dissimilarities analysis of coding sequences and conserved genes discrimination illustrate their utilities. In addition, two simple methods for similarities/dissimilarities analysis of coding sequences among different species are exploited by using two vectors composed of 64 and six components, respectively, which can provide convenient sequence alignment tools for both computational scientists and molecular biologists. (C) 2009 Elsevier Ltd. All rights reserved.

关键词： Numerical descriptor Similarity/dissimilarity analysis Projection coding sequence

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An approach of encoding for prediction of splice sites using SVM

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BIOCHIMIE 2006年第7期88卷 923-929页

作者： Huang, J. Li, T. Chen, K. Wu, J. Tongji Univ Dept Chem Shanghai 200092 Peoples R China

In splice sites prediction, the accuracy is lower than 90% though the sequences adjacent to the splice sites have a high conservation. In order to improve the prediction accuracy, much attention has been paid to the improvement of the performance of the algorithms used, and few used for solving the fundamental issues, namely, nucleotide encoding. In this paper, a predictor is constructed to predict the true and false splice sites for higher eukaryotes based on support vector machines (SVM). Four types of encoding, which were mono-nucleotide (MN) encoding, MN with frequency difference between the true sites and false sites (FDTF) encoding, Pair-wise nucleotides (PN) encoding and PN with FDTF encoding, were applied to generate the input for the SVM. The results showed that PN with FDTF encoding as input to SVM led to the most reliable recognition of splice sites and the accuracy for the prediction of true donor sites and false sites were 96.3%, 93.7%, respectively, and the accuracy for predicting of true acceptor sites and false sites were 94.0%, 93.2%, respectively. (c) 2006 Elsevier SAS. All rights reserved.

关键词： splice sites coding sequence support vector machines

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Characterisation of the genomes of four putative vesiculoviruses: tench rhabdovirus, grass carp rhabdovirus, perch rhabdovirus and eel rhabdovirus European X

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ARCHIVES OF VIROLOGY 2013年第11期158卷 2371-2377页

作者： Stone, David M. Kerr, Rose C. Hughes, Margaret Radford, Alan D. Darby, Alistair C. Cefas Weymouth DT4 8UB Dorset England Univ Liverpool Inst Integrat Biol Liverpool L69 7ZB Merseyside England Univ Liverpool Inst Infect & Global Hlth Wirral CH64 7TE Merseyside England

The complete coding sequences were determined for four putative vesiculoviruses isolated from fish. sequence alignment and phylogenetic analysis based on the predicted amino acid sequences of the five main proteins assigned tench rhabdovirus and grass carp rhabdovirus together with spring viraemia of carp and pike fry rhabdovirus to a lineage that was distinct from the mammalian vesiculoviruses. Perch rhabdovirus, eel virus European X, lake trout rhabdovirus 903/87 and sea trout virus were placed in a second lineage that was also distinct from the recognised genera in the family Rhabdoviridae. Establishment of two new rhabdovirus genera, "Perhabdovirus" and "Sprivivirus", is discussed.

关键词： Distinct descent Tinca Genome Rhabdoviridae Spring viremia of carp coding sequence Vesiculovirus

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Generation and Characterization of a Breast Cancer Resistance Protein Humanized Mouse Model

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MOLECULAR PHARMACOLOGY 2016年第5期89卷 492-504页

作者： Dallas, Shannon Salphati, Laurent Gomez-Zepeda, David Wanek, Thomas Chen, Liangfu Chu, Xiaoyan Kunta, Jeevan Mezler, Mario Menet, Marie-Claude Chasseigneaux, Stephanie Decleves, Xavier Langer, Oliver Pierre, Esaie DiLoreto, Karen Hoft, Carolin Laplanche, Loic Pang, Jodie Pereira, Tony Andonian, Clara Simic, Damir Rode, Anja Yabut, Jocelyn Zhang, Xiaolin Scheer, Nico Abbvie Deutschland GmbH & Co KG DMPK & Bioanalyt Res Ludwigshafen Germany Genentech Inc Drug Metab & Pharmacokinet San Francisco CA 94080 USA GlaxoSmithKline Drug Metab & Pharmacokinet King Of Prussia PA USA AIT Austrian Inst Technol GmbH Hlth & Environm Dept Seibersdorf Austria Med Univ Vienna Dept Clin Pharmacol Vienna Austria Janssen Res & Dev LLC Preclin Dev & Safety Spring House PA USA Merck Sharp & Dohme Corp Whitehouse Stn NJ USA Univ Paris 05 UMR S 1144 Paris France Tacon Biosci GmbH Cologne Germany Teva Pharmaceut Res & Dev Discovery & Prod Dev W Chester PA USA

Breast cancer resistance protein (BCRP) is expressed in various tissues, such as the gut, liver, kidney and blood brain barrier (BBB), where it mediates the unidirectional transport of substrates to the apical/luminal side of polarized cells. Thereby BCRP acts as an efflux pump, mediating the elimination or restricting the entry of endogenous compounds or xenobiotics into tissues and it plays important roles in drug disposition, efficacy and safety. Bcrp knockout mice (Bcrp(-/-)) have been used widely to study the role of this transporter in limiting intestinal absorption and brain penetration of substrate compounds. Here we describe the first generation and characterization of a mouse line humanized for BCRP (hBCRP), in which the mouse coding sequence from the start to stop codon was replaced with the corresponding human genomic region, such that the human transporter is expressed under control of the murine Bcrp promoter. We demonstrate robust human and loss of mouse BCRP/Bcrp mRNA and protein expression in the hBCRP mice and the absence of major compensatory changes in the expression of other genes involved in drug metabolism and disposition. Pharmacokinetic and brain distribution studies with several BCRP probe substrates confirmed the functional activity of the human transporter in these mice. Furthermore, we provide practical examples for the use of hBCRP mice to study drug-drug interactions (DDIs). The hBCRP mouse is a promising model to study the in vivo role of human BCRP in limiting absorption and BBB penetration of substrate compounds and to investigate clinically relevant DDIs involving BCRP.

关键词： Gastrointestinal Absorption Blood-Brain Barrier Generations coding sequence

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Evolution of Cold Acclimation and Its Role in Niche Transition in the Temperate Grass Subfamily Pooideae

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PLANT PHYSIOLOGY 2019年第1期180卷 404-419页

作者： Schubert, Marian Gronvold, Lars Sandve, Simen R. Hvidsten, Torgeir R. Fjellheim, Siri Norwegian Univ Life Sci Dept Plant Sci NO-1432 As Norway Norwegian Univ Life Sci Fac Chem Biotechnol & Food Sci NO-1432 As Norway Norwegian Univ Life Sci Dept Anim & Aquacultural Sci Ctr Integrat Genet NO-1432 As Norway Umea Univ Dept Plant Physiol Umea Plant Sci Ctr SE-90187 Umea Sweden

The grass subfamily Pooideae dominates the grass floras in cold temperate regions and has evolved complex physiological adaptations to cope with extreme environmental conditions like frost, winter, and seasonality. One such adaptation is cold acclimation, wherein plants increase their frost tolerance in response to gradually falling temperatures and shorter days in the autumn. However, understanding how complex traits like cold acclimation evolve remains a major challenge in evolutionary biology. Here, we investigated the evolution of cold acclimation in Pooideae and found that a phylogenetically diverse set of Pooideae species displayed cold acclimation capacity. However, comparing differential gene expression after cold treatment in transcriptomes of five phylogenetically diverse species revealed widespread species-specific responses of genes with conserved sequences. Furthermore, we studied the correlation between gene family size and number of cold-responsive genes as well as between selection pressure on coding sequences of genes and their cold responsiveness. We saw evidence of protein-coding and regulatory sequence evolution as well as the origin of novel genes and functions contributing toward evolution of a cold response in Pooideae. Our results reflect that selection pressure resulting from global cooling must have acted on already diverged lineages. Nevertheless, conservation of cold-induced gene expression of certain genes indicates that the Pooideae ancestor may have possessed some molecular machinery to mitigate cold stress. Evolution of adaptations to seasonally cold climates is regarded as particularly difficult. How Pooideae evolved to transition from tropical to temperate biomes sheds light on how complex traits evolve in the light of climate changes.

关键词： Biome Family Size Molecular machinery Transcriptome subfamily selection pressure Cold Climate coding sequence regulatory sequences Global cooling Cold acclimation Genes frost resistance Grasses Cold treatment

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