Relation between mRNA expression and sequence information in Desulfovibrio vulgaris: combinatorial contributions of upstream regulatory motifs and coding sequence features to variations in mRNA abundance.

Abstract:

:The context-dependent expression of genes is the core for biological activities, and significant attention has been given to identification of various factors contributing to gene expression at genomic scale. However, so far this type of analysis has been focused either on relation between mRNA expression and non-coding sequence features such as upstream regulatory motifs or on correlation between mRNA abundance and non-random features in coding sequences (e.g., codon usage and amino acid usage). In this study multiple regression analyses of the mRNA abundance and all sequence information in Desulfovibrio vulgaris were performed, with the goal to investigate how much coding and non-coding sequence features contribute to the variations in mRNA expression, and in what manner they act together. Using the AlignACE program, 442 over-represented motifs were identified from the upstream 100bp region of 293 genes located in the known regulons. Regression of mRNA expression data against the measures of coding and non-coding sequence features indicated that 54.1% of the variations in mRNA abundance can be explained by the presence of upstream motifs, while coding sequences alone contribute to 29.7% of the variations in mRNA abundance. Interestingly, most of contribution from coding sequences is overlapping with that from upstream motifs; thereby a total of 60.3% of the variations in mRNA abundance can be explained when coding and non-coding information was included. This result demonstrates that upstream regulatory motifs and coding sequence information contribute to the overall mRNA expression in a combinatorial rather than an additive manner.

authors

Wu G,Nie L,Zhang W

doi

10.1016/j.bbrc.2006.03.124

subject

Has Abstract

pub_date

2006-05-26 00:00:00

pages

114-21

issue

1

eissn

0006-291X

issn

1090-2104

pii

S0006-291X(06)00677-2

journal_volume

344

pub_type

杂志文章
  • Beta-35 is a transferrin-derived inhibitor of angiogenesis and tumor growth.

    abstract::An angiogenesis inhibitor named Beta-35 has been identified and purified from the conditioned medium of mouse pancreatic β cells tumor cells. Beta-35 has a molecular weight of 35 kDa and inhibits DNA synthesis of bovine capillary endothelial cells at a half-maximal concentration of approximately 5 nM. It shows anti-an...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1016/j.bbrc.2011.05.045

    authors: Liang G,Butterfield C,Liang J,Birsner A,Folkman J,Shing Y

    更新日期:2011-06-10 00:00:00

  • Deduction of upstream sequences of Xanthomonas campestris flagellar genes responding to transcription activation by FleQ.

    abstract::Xanthomonas campestris pv. campestris (Xcc), a close relative to Pseudomonas aeruginosa, is the pathogen causing black rot in cruciferous plants. In P. aeruginosa, FleQ serves as a cognate activator of sigma54 in transcription from several sigma54-dependent promoters of flagellar genes. These P. aeruginosa promoters h...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1016/j.bbrc.2005.07.171

    authors: Hu RM,Yang TC,Yang SH,Tseng YH

    更新日期:2005-10-07 00:00:00

  • Probing the catalytic mechanism of bovine pancreatic deoxyribonuclease I by chemical rescue.

    abstract::Previous structural and mutational studies of bovine pancreatic deoxyribonuclease I (bpDNase I) have demonstrated that the active site His134 and His252 played critical roles in catalysis. In our present study, mutations of these two His residues to Gln, Ala or Gly reduced the DNase activity by a factor of four to fiv...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1016/j.bbrc.2006.11.078

    authors: Chen WJ,Lai PJ,Lai YS,Huang PT,Lin CC,Liao TH

    更新日期:2007-01-19 00:00:00

  • Kinetics of fluid-phase pinocytosis in Dictyostelium discoideum amoebae.

    abstract::Kinetics of pinocytosis in Dictyostelium discoideum were investigated over an extended period of time (up to 6 hours) using fluorescein isothiocyanate (FITC)-dextran as a fluid-phase marker. FITC-dextran added to the medium accumulated rapidly inside the cells with a rate of influx equivalent to 9 microns3 of fluid/ce...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1016/s0006-291x(86)80402-8

    authors: Klein G,Satre M

    更新日期:1986-08-14 00:00:00

  • Cloning of a cDNA for heat-shock protein hsp40, a human homologue of bacterial DnaJ.

    abstract::We here isolated and characterized a cDNA clone encoding 40-kDa heat-shock protein hsp40 from cDNA expression library of human placenta by immunoscreening with anti-hsp40 antibody. N-terminal amino acid sequence (48 residues) deduced from the base sequence was completely identical to that of hsp40 purified from HeLa c...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1006/bbrc.1993.2466

    authors: Ohtsuka K

    更新日期:1993-11-30 00:00:00

  • Induction of benzo(a)pyrene hydroxylase in Aspergillus ochraceus TS: evidences of multiple forms of cytochrome P-450.

    abstract::The filamentous fungus Aspergillus ochraceus TS produces an inducible microsomal cytochrome P-450 linked monooxygenase which is capable of hydroxylating benzo(a)pyrene in presence of O2 and NADPH. The addition of Benzo(a)pyrene, 3-Methyl cholanthrene, beta-Naphthoflavone and other aryl hydrocarbons during the inductio...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1016/s0006-291x(83)80200-9

    authors: Dutta D,Ghosh DK,Mishra AK,Samanta TB

    更新日期:1983-09-15 00:00:00

  • Nitric oxide stimulates tyrosine phosphorylation of p125(FAK) and paxillin in rat pancreatic acini.

    abstract::Some of the effects of several oncogenes, integrins, growth factors, and neuropeptides are mediated by tyrosine phosphorylation of the non-receptor tyrosine kinase p125(FAK) and the cytoskeletal protein paxillin. We have demonstrated that different stimuli cause tyrosine phosphorylation of p125(FAK) and paxillin in ra...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1006/bbrc.2000.3192

    authors: García-Benito M,San Román JI,López MA,García-Marín LJ,Calvo JJ

    更新日期:2000-08-11 00:00:00

  • The main protease and RNA-dependent RNA polymerase are two prime targets for SARS-CoV-2.

    abstract::The coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), poses an unprecedented global health crisis. It is particularly urgent to develop clinically effective therapies to contain the pandemic. The main protease (Mpro) and the RNA-dependent RNA poly...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1016/j.bbrc.2020.10.091

    authors: Jin Z,Wang H,Duan Y,Yang H

    更新日期:2020-11-21 00:00:00

  • Caveolin-1 up-regulates ST6Gal-I to promote the adhesive capability of mouse hepatocarcinoma cells to fibronectin via FAK-mediated adhesion signaling.

    abstract::Caveolin-1 is a major structural protein of caveolae and plays important functions in tumorigenesis and development. Hca-F and Hepa1-6 are mouse hepatocarcinoma cell lines with high and low malignant potential, respectively. Our previous studies revealed that caveolin-1 promoted cell invasion by up-regulating the glyc...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1016/j.bbrc.2012.09.086

    authors: Yu S,Zhang L,Li N,Fan J,Liu L,Zhang J,Wang S

    更新日期:2012-10-26 00:00:00

  • Activation of plasminogen by Streptococcus mutans.

    abstract::Streptococcus mutans, a member of the viridans streptococci, is the etiologic agent of dental caries and is also a causative agent of subacute infective endocarditis. The generation of proteolytic molecules, such as plasmin, may be important in the pathogenesis of endocarditis caused by S. mutans. In this study, we de...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1016/j.bbrc.2004.07.077

    authors: Jones MN,Holt RG

    更新日期:2004-09-10 00:00:00

  • Mast cell activation induces P-selectin-dependent leukocyte rolling and adhesion in postcapillary venules in vivo.

    abstract::As studied by intravital microscopy, local challenge with the mast cell secretagogue compound 48/80 was found to increase the leukocyte rolling fraction, decrease rolling velocity and induce firm leukocyte adhesion in postcapillary venules of the rat mesentery. These effects of compound 48/80 were inhibited by a monoc...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1006/bbrc.1994.2287

    authors: Thorlacius H,Raud J,Rosengren-Beezley S,Forrest MJ,Hedqvist P,Lindbom L

    更新日期:1994-09-15 00:00:00

  • Therapeutic effect of IL-12/23 and their signaling pathway blockade on brain ischemia model.

    abstract::Recently, T cell cytokines such as IL-17 and IFN-γ have been shown to play important roles in the progression of brain injury induced by ischemia. We have shown that IL-23 from infiltrated macrophages activates γδT cells, thereby inducing IL-17 from these cells. However, deletion of the IL-23 gene in mice showed a mor...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1016/j.bbrc.2010.10.058

    authors: Konoeda F,Shichita T,Yoshida H,Sugiyama Y,Muto G,Hasegawa E,Morita R,Suzuki N,Yoshimura A

    更新日期:2010-11-19 00:00:00

  • Measurement of nitric oxide release in the isolated perfused rat lung.

    abstract::In this study we have continuously measured real-time production of nitric oxide (NO) in the isolated, perfused rat lung by using an NO monitor (model NO-501, Inter Medical Co., Nagoya, Japan) with an NO-selective resin microsensor. A stable NO response was obtained when the sensor was placed in the pulmonary artery o...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1006/bbrc.1995.1435

    authors: Wang D,Hsu K,Hwang CP,Chen HI

    更新日期:1995-03-28 00:00:00

  • Biochemical characterization of recombinant phosphoglucose isomerase of Mycobacterium tuberculosis.

    abstract::Phosphoglucose isomerase (PGI) is a well-characterized ubiquitous enzyme involved in the glycolytic pathway. It catalyzes the reversible isomerization of D-glucopyranose-6-phosphate and D-fructofuranose-6-phosphate and is present in all living cells. However, there is interspecies variation at the level of the primary...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1016/j.bbrc.2005.09.092

    authors: Mathur D,Ahsan Z,Tiwari M,Garg LC

    更新日期:2005-11-18 00:00:00

  • Growth retardation, testicular stimulation, and increased melatonin synthesis by weak magnetic fields (50 Hz) in Djungarian hamsters, Phodopus sungorus.

    abstract::Male Djungarian hamsters (Phodopus sungorus; 45 animals per group) were either sham-exposed or exposed to a sinusoidal magnetic field for 56 days (Experiment 1: 50 Hz, 450 microTesla peak; max. dB/dt = 140 mTesla s(-1); 24 hrs day(-1)). Except for day 7, no effects were observed with respect to body weights during exp...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1006/bbrc.1997.6561

    authors: Niehaus M,Brüggemeyer H,Behre HM,Lerchl A

    更新日期:1997-05-29 00:00:00

  • Galanin inhibits glucose-stimulated insulin release by a mechanism involving hyperpolarization and lowering of cytoplasmic free Ca2+ concentration.

    abstract::The intrapancreatic neuropeptide galanin has been demonstrated to lower plasma insulin levels in vivo. The effects of this peptide on insulin secretion, cytoplasmic free Ca2+ concentration and membrane potential have now been studied in vitro. Glucose-stimulated insulin secretion was inhibited by galanin under these c...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1016/0006-291x(86)90742-4

    authors: Ahrén B,Arkhammar P,Berggren PO,Nilsson T

    更新日期:1986-11-14 00:00:00

  • Hexose transport in plasma membrane vesicles prepared from L6 rat myoblasts.

    abstract::Hexose transport in plasma membrane vesicles prepared from L6 rat myoblasts was shown to be stereospecific, activated by glucose starvation and occurred by both high and low affinity systems. Transport by the high affinity system was shown to occur by an active transport process. Furthermore, the high affinity system ...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1016/s0006-291x(86)80343-6

    authors: Mesmer O,Cheung MO,D'Amore T,Lo TC

    更新日期:1986-11-26 00:00:00

  • Channel formation in planar lipid bilayers by a neurotoxic fragment of the beta-amyloid peptide.

    abstract::Alzheimer's disease (AD) pathology is characterized by plaques, tangles, and neuronal cell loss. The main constituent of plaques is beta-amyloid peptide (A beta), a 39-42 residue peptide which has been linked to disruption of calcium homeostasis and neurotoxicity in vitro. We demonstrate that a neurotoxic fragment of ...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1006/bbrc.1994.2047

    authors: Mirzabekov T,Lin MC,Yuan WL,Marshall PJ,Carman M,Tomaselli K,Lieberburg I,Kagan BL

    更新日期:1994-07-29 00:00:00

  • Multi-strand binding of nuclear factors to a repressor of mouse mammary tumor virus transcription can be distinguished kinetically.

    abstract::NRE1 is a DNA sequence element in the long terminal repeat of mouse mammary tumor virus that represses viral transcription in mature T cells. In addition to double-stranded binding activity, factors in Jurkat T cell nuclear extracts bind specifically to each of the two single-strands of NRE1. Here we show that binding...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1006/bbrc.1995.1514

    authors: Rodda DJ,Giffin W,Haché RJ

    更新日期:1995-04-06 00:00:00

  • Involvement of the alpha isoenzyme of protein kinase C in the growth inhibition induced by phorbol esters in MH1C1 hepatoma cells.

    abstract::MH1C1 rat hepatoma cells express the alpha isoenzyme as the only phorbol-ester sensitive isoform of protein kinase C (PKC). In this cell line, phorbol 12-myristate 13-acetate (PMA) induced a marked, dose-dependent growth inhibition. The administration of the PKC inhibitor staurosporine was able to mimic the effect of ...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1006/bbrc.1994.2848

    authors: Perletti GP,Smeraldi C,Porro D,Piccinini F

    更新日期:1994-12-30 00:00:00

  • Eukaryotic initiation factor 4B from wheat and Arabidopsis thaliana is a member of a multigene family.

    abstract::Clones of eukaryotic initiation factor (eIF) 4B from wheat and Arabidopsis thaliana were obtained from cDNA and genomic libraries. The exon/intron organization of the genes from wheat and A. thaliana is very similar. The deduced amino acid sequences for the wheat and Arabidopsis eIF4B proteins showed overall similarit...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1006/bbrc.1999.1814

    authors: Metz AM,Wong KC,Malmström SA,Browning KS

    更新日期:1999-12-20 00:00:00

  • Identification of a novel autoantigen UACA in patients with panuveitis.

    abstract::To identify the target autoantigens in Vogt-Koyanagi-Harada disease, we made use of an immunoscreening of a bovine uveal cDNA expression library with serum samples obtained from patients with Vogt-Koyanagi-Harada disease. We identified a novel bovine antigen and homologous human autoantigen and designated it as UACA (...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1006/bbrc.2001.4189

    authors: Yamada K,Senju S,Nakatsura T,Murata Y,Ishihara M,Nakamura S,Ohno S,Negi A,Nishimura Y

    更新日期:2001-02-02 00:00:00

  • H(2)O(2)-induced AP-1 activation and its effect on p21(WAF1/CIP1)-mediated G2/M arrest in a p53-deficient human lung cancer cell.

    abstract::Cellular response to oxidative stress is a complex process that is often connected to cell cycle regulation. The present study examines the effect of H(2)O(2) on cell cycle regulation and involvement of reactive oxygen species (ROS) in these H(2)O(2)-induced responses in a p53-deficient human lung carcinoma cell line,...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1016/S0006-291X(02)00360-1

    authors: Chung YW,Jeong DW,Won JY,Choi EJ,Choi YH,Kim IY

    更新日期:2002-05-17 00:00:00

  • Sck interacts with KDR and Flt-1 via its SH2 domain.

    abstract::Vascular endothelial growth factor (VEGF) is one of the major angiogenesis regulators. It binds to its tyrosine kinase receptors, KDR and Flt-1. However, little is known about their downstream signal transduction properties. We screened human brain cDNA library using the yeast two-hybrid system with the KDR cytoplasmi...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1006/bbrc.1998.9442

    authors: Igarashi K,Shigeta K,Isohara T,Yamano T,Uno I

    更新日期:1998-10-09 00:00:00

  • Crystal structure of the death effector domains of caspase-8.

    abstract::Caspase-8 is a key mediator in various biological processes such as apoptosis, necroptosis, inflammation, T/B cells activation, and cell motility. Caspase-8 is characterized by the N-terminal tandem death effector domains (DEDs) and the C-terminal catalytic protease domain. The DEDs mediate diverse functions of caspas...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1016/j.bbrc.2015.05.054

    authors: Shen C,Yue H,Pei J,Guo X,Wang T,Quan JM

    更新日期:2015-07-31 00:00:00

  • Calcium-dependent proteinase activity in root cultures of Arabidopsis.

    abstract::The presence of calcium-dependent proteinase in plants was investigated using soluble proteins from Arabidopsis root cultures. Calcium increased the proteolytic activity by two to three fold. Calcium-stimulated proteolytic activity was inhibited by different protease inhibitors. The highest inhibition (79%) of calcium...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1006/bbrc.1994.1342

    authors: Reddy AS,Safadi F,Beyette JR,Mykles DL

    更新日期:1994-03-30 00:00:00

  • A receptor-electromigration-based model for cellular electrotactic sensing and migration.

    abstract::Directed cell migration in tissues mediates various physiological processes and is guided by complex cellular factors such as chemoattractant gradients and electric fields. Direct current (DC) electric fields can be generated in physiological settings and the electric field guided migration of various cell types (i.e....

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1016/j.bbrc.2011.07.004

    authors: Wu D,Lin F

    更新日期:2011-08-12 00:00:00

  • Constitutive secretion of an endogenous insulin-like peptide binding protein with high affinity for insulin in Spodoptera frugiperda (Sf9) cell cultures.

    abstract::Serum-free medium from batch cultures of Sf9 insect cells was examined for the occurrence of proteins related to the insulin-like growth factor family. We found that the Sf9 cell line constitutively produced and secreted a soluble protein with a MW of 27 kDa that exerted specific binding to human insulin-like growth f...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1006/bbrc.1999.1745

    authors: Doverskog M,Tally M,Häggström L

    更新日期:1999-11-30 00:00:00

  • Identification of a D-amino acid decapeptide HIV-1 entry inhibitor.

    abstract::Entry of human immunodeficiency virus type 1 (HIV-1) virion into host cells involves three major steps, each being a potential target for the development of entry inhibitors: gp120 binding to CD4, gp120-CD4 complex interacting with a coreceptor, and gp41 refolding to form a six-helix bundle. Using a D-amino acid decap...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1016/j.bbrc.2006.06.150

    authors: Boggiano C,Jiang S,Lu H,Zhao Q,Liu S,Binley J,Blondelle SE

    更新日期:2006-09-08 00:00:00

  • Alternative pathway linked by hydrogen bonds connects heme-Fe of cytochrome c with subunit II-CuA of cytochrome a.

    abstract::The bridging element for electron transfer in proteins is the hydrogen bond according to the new experimental perspective in preference to carbon-carbon σ-bond presently used. The purpose of this study is to identify an alternative pathway linked by hydrogen bonds suitable for electron transfer from heme-Fe of cytochr...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1016/j.bbrc.2018.09.141

    authors: Ramasarma T,Vaigundan D

    更新日期:2018-10-28 00:00:00