The heparanome--the enigma of encoding and decoding heparan sulfate sulfation.

Abstract:

:Heparan sulfate (HS) is a cell surface carbohydrate polymer modified with sulfate moieties whose highly ordered composition is central to directing specific cell signaling events. The ability of the cell to generate these information rich glycans with such specificity has opened up a new field of "heparanomics" which seeks to understand the systems involved in generating these cell type and developmental stage specific HS sulfation patterns. Unlike other instances where biological information is encrypted as linear sequences in molecules such as DNA, HS sulfation patterns are generated through a non-template driven process. Thus, deciphering the sulfation code and the dynamic nature of its generation has posed a new challenge to system biologists. The recent discovery of two sulfatases, Sulf1 and Sulf2, with the unique ability to edit sulfation patterns at the cell surface, has opened up a new dimension as to how we understand the regulation of HS sulfation patterning and pattern-dependent cell signaling events. This review will focus on the functional relationship between HS sulfation patterning and biological processes. Special attention will be given to Sulf1 and Sulf2 and how these key editing enzymes might act in concert with the HS biosynthetic enzymes to generate and regulate specific HS sulfation patterns in vivo. We will further explore the use of knock out mice as biological models for understanding the dynamic systems involved in generating HS sulfation patterns and their biological relevance. A brief overview of new technologies and innovations summarizes advances in the systems biology field for understanding non-template molecular networks and their influence on the "heparanome".

journal_name

J Biotechnol

journal_title

Journal of biotechnology

authors

Lamanna WC,Kalus I,Padva M,Baldwin RJ,Merry CL,Dierks T

doi

10.1016/j.jbiotec.2007.01.022

subject

Has Abstract

pub_date

2007-04-30 00:00:00

pages

290-307

issue

2

eissn

0168-1656

issn

1873-4863

pii

S0168-1656(07)00114-9

journal_volume

129

pub_type

杂志文章,评审
  • The effect of thermodynamic properties of solvent mixtures explains the difference between methanol and ethanol in C.antarctica lipase B catalyzed alcoholysis.

    abstract::Kinetic modelling, molecular modelling, and experimental determination of the initial reaction velocity of lipase-catalyzed alcoholysis were combined to study the effect of the alcohol substrate to catalytic activity. The model system consisted of methanol or ethanol at varying concentrations, vinyl acetate as ester s...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2015.08.023

    authors: Sasso F,Kulschewski T,Secundo F,Lotti M,Pleiss J

    更新日期:2015-11-20 00:00:00

  • Fractionation of sulphite spent liquor for biochemical processing using ion exchange resins.

    abstract::Sulphite spent liquor (SSL) is a side product from acidic sulphite pulping of wood, which organic counterpart is composed mainly by lignosulphonates (LS) and sugars. The last are a prominent substrate for the bioprocessing although a previous purification step is necessary to eliminate microbial inhibitors. In this st...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2012.03.013

    authors: Fernandes DL,Silva CM,Xavier AM,Evtuguin DV

    更新日期:2012-12-31 00:00:00

  • Heterologous production of different styrene oxide isomerases for the highly efficient synthesis of phenylacetaldehyde.

    abstract::The styrene oxide isomerase (SOI, StyC) represents a key enzyme of the styrene-degrading pathway and has been discussed as promising biocatalyst during recent studies. The enzyme enables the synthesis of pure phenylacetaldehyde from styrene oxide. In this study the native as well as the corresponding codon-optimized g...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2017.04.038

    authors: Oelschlägel M,Richter L,Stuhr A,Hofmann S,Schlömann M

    更新日期:2017-06-20 00:00:00

  • Transcript stabilization by mRNA sequences from hrpA of Pseudomonas syringae.

    abstract::Production of heterologous proteins in bacteria is one of the main applications of biotechnology. Although several high-efficiency expression systems have been developed, different steps in protein production may become rate-limiting depending on the production system and the protein being produced. One bottle neck ca...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2006.10.010

    authors: Hienonen E,Romantschuk M,Fenel F,Taira S

    更新日期:2007-02-01 00:00:00

  • Development of grapevine somatic embryogenesis using an air-lift bioreactor as an efficient tool in the generation of transgenic plants.

    abstract::The grapevine genetic transformation programs have relayed on the use of solid media-based somatic embryogenesis. To reach a high throughput of candidate gene evaluation in 'Thompson Seedless', a semi-automatic system allowing viable transformation of explants was designed. An intermediate procedure using liquid media...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2008.09.009

    authors: Tapia E,Sequeida A,Castro A,Montes C,Zamora P,López R,Acevedo F,Prieto H

    更新日期:2009-01-01 00:00:00

  • Molecular cloning and expression in yeast of caprine prochymosin.

    abstract::We cloned and characterized a preprochymosin cDNA from the abomasum of milk-fed kid goats. This cDNA contained an open reading frame that predicts a polypeptide of 381 amino acid residues, with a signal peptide and a proenzyme region of 16 and 42 amino acids, respectively. Comparison of the caprine preprochymosin sequ...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2004.06.002

    authors: Vega-Hernández MC,Gómez-Coello A,Villar J,Claverie-Martín F

    更新日期:2004-10-19 00:00:00

  • Expression enhancement of bubaline somatotropin in E. coli through gene modifications in the 5'-end coding region.

    abstract::This study addresses the problem of poor expression of somatotropin (ST) gene in E. coli and describes expression enhancement through silent and non-silent gene modifications. A series of constructs with codon optimization, substitution, deletion or addition in the 5'-region of the sequence encoding bubaline ST (BbST)...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2008.03.010

    authors: Sadaf S,Khan MA,Akhtar MW

    更新日期:2008-06-01 00:00:00

  • The effect of the partition locus on plasmid stability and expression of a prolonged chemostat culture.

    abstract::The stability, copy number, and gene expression of the pBR322 plasmid containing the par-locus under prolonged cultivation were studied. In the initial stage of the experiment it was observed that the par-locus had a stabilization effect on plasmid maintenance. This observation was consistent with previously reported ...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/0168-1656(91)90242-n

    authors: Weber AE,Yu P,San KY

    更新日期:1991-04-01 00:00:00

  • A simple analysis system for the estimation of recombination efficiency using fluorescence-activated cell sorting.

    abstract::A simple and accurate analysis system for the estimation of recombination efficiency in vivo using fluorescence-activated cell sorting (FACS) was designed and was subsequently used to compare the efficiency of recombination related to different spacer mutants. F(3) and F(5) mutant sequences were used for Flpe-mediated...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2006.07.027

    authors: Kim MS,Kim WH,Lee GM

    更新日期:2007-01-10 00:00:00

  • Polyhydroxyalkanoate (PHA) synthase genes and PHA-associated gene clusters in Pseudomonas spp. and Janthinobacterium spp. isolated from Antarctica.

    abstract::The polyhydroxyalkanoate (PHA) producing capability of four bacterial strains isolated from Antarctica was reported in a previous study. This study analyzed the PHA synthase genes and the PHA-associated gene clusters from the two antarctic Pseudomonas isolates (UMAB-08 and UMAB-40) and the two antarctic Janthinobacter...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2020.03.006

    authors: Tan IKP,Foong CP,Tan HT,Lim H,Zain NA,Tan YC,Hoh CC,Sudesh K

    更新日期:2020-04-10 00:00:00

  • High-level expression of porcine muscle adenylate kinase in Escherichia coli: effects of the copy number of the gene and the translational initiation signals.

    abstract::Porcine muscle adenylate kinase (ADK) was overproduced in Escherichia coli using the expression plasmid with double A-T-G codon at the translational starting site and the Shine-Dalgarno (SD) sequence 10 bp apart from the first A-T-G. We used the expression vectors pKK223-3 and pMK2. pMK2 is about 10-20 times larger in...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/0168-1656(94)90176-7

    authors: Hibino T,Misawa S,Wakiyama M,Maeda S,Yazaki K,Kumagai I,Ooi T,Miura K

    更新日期:1994-02-14 00:00:00

  • Efficient production and recovery of diterpenoid tanshinones in Salvia miltiorrhiza hairy root cultures with in situ adsorption, elicitation and semi-continuous operation.

    abstract::In Salvia miltiorrhiza hairy root cultures, the desired secondary metabolites diterpenoid tanshinones are normally produced at low yields and stored within the roots. To enhance tanshinone production and the secondary product recovery, we employed three means, elicitation with a yeast elicitor (YE), in situ adsorption...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2005.04.020

    authors: Yan Q,Hu Z,Tan RX,Wu J

    更新日期:2005-10-10 00:00:00

  • Isolation and characterization of a metagenome-derived and cold-active lipase with high stereospecificity for (R)-ibuprofen esters.

    abstract::We report on the isolation and biochemical characterization of a novel, cold-active and metagenome-derived lipase with a high stereo-selectivity for pharmaceutically important substrates. The respective gene was isolated from a cosmid library derived from oil contaminated soil and designated lipCE. The deduced aa sequ...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2007.05.015

    authors: Elend C,Schmeisser C,Hoebenreich H,Steele HL,Streit WR

    更新日期:2007-07-15 00:00:00

  • High-yield production of D-1,2,4-butanetriol from lignocellulose-derived xylose by using a synthetic enzyme cascade in a cell-free system.

    abstract::Approaches using metabolic engineering to produce D-1, 2, 4-butanetriol (BT) from renewable biomass in microbial systems have achieved initial success. However, due to the lack of incomplete understanding of the complex branch pathway, the efficient fermentation system for BT production was difficult to develop. Here ...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2019.01.004

    authors: Gao Q,Wang X,Hu S,Xu N,Jiang M,Ma C,Yang J,Xu S,Chen K,Ouyang P

    更新日期:2019-02-20 00:00:00

  • Microbial activities in hydrocarbon-laden wastewaters: Impact on diesel fuel stability and the biocorrosion of carbon steel.

    abstract::Anaerobic hydrocarbon biodegradation not only diminishes fuel quality, but also exacerbates the biocorrosion of the metallic infrastructure. While successional events in marine microbial ecosystems impacted by petroleum are well documented, far less is known about the response of communities chronically exposed to hyd...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2017.02.021

    authors: Liang R,Duncan KE,Le Borgne S,Davidova I,Yakimov MM,Suflita JM

    更新日期:2017-08-20 00:00:00

  • Implication of a mutation in the flavin binding site on the specific activity and substrate specificity of glycine oxidase from Bacillus subtilis produced by directed evolution.

    abstract::Directed evolution was used to expand the substrate specificity and functionality of glycine oxidase by using a high-throughput screening assay based on the 4-aminoantipyrine peroxidase system, with a coefficient of variance below 4%. After screening the library, one mutant with the desired changes was found. The muta...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2007.07.950

    authors: Martínez-Martínez I,Navarro-Fernández J,García-Carmona F,Sánchez-Ferrer A

    更新日期:2008-01-01 00:00:00

  • Production of single chain fragment variable (scFv) antibodies in Escherichia coli using the LEX™ bioreactor.

    abstract::For proteome research, antibodies against a growing number of antigens must be generated and characterized. The high throughput generation of antibody fragments, using in vitro selection, requires bacterial expression of antibody fragments. This created a need to establish an expression method to improve the parallel ...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2012.07.011

    authors: Miethe S,Meyer T,Wöhl-Bruhn S,Frenzel A,Schirrmann T,Dübel S,Hust M

    更新日期:2013-01-20 00:00:00

  • Complete genome sequence of Pedobacter cryoconitis PAMC 27485, a CRISPR-Cas system-containing psychrophile isolated from Antarctica.

    abstract::Pedobacter cryoconitis PAMC 27485, an aerobic, Gram-negative, facultatively psychrophilic bacterium, was isolated from Antarctic soil. Here we report the complete genome of P. cryoconitis PAMC 27485, which contains a type II CRISPR-Cas system and genes encoding useful enzymes (e.g. proteases). The genome sequence of P...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2016.03.035

    authors: Lee J,Jung YJ,Lee HK,Hong SG,Kim OS

    更新日期:2016-05-20 00:00:00

  • Diffusion in Pseudomonas aeruginosa biofilms: a pulsed field gradient NMR study.

    abstract::A Pseudomonas aeruginosa biofilm is studied with pulsed field gradient echo nuclear magnetic resonance. Although not all spectral components are assigned yet, the experimental results show that a biofilm consists of components with very different diffusion coefficients. The various biofilm components that give motiona...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/s0168-1656(99)00213-8

    authors: Vogt M,Flemming HC,Veeman WS

    更新日期:2000-01-28 00:00:00

  • Towards the in vivo production of tocotrienol compounds: engineering of a plasmid-free Escherichia coli strain for the heterologous synthesis of 2-methyl-6-geranylgeranyl-benzoquinol.

    abstract::The vitamin E family consists of 4 tocopherol and 4 tocotrienol compounds. During recent years, tocotrienols have gained increased interest due to their biological activities that are beyond the vitamin E activity. Here we report the engineering of plasmid-free Escherichia coli strains for an efficient synthesis of 2-...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2012.08.010

    authors: Ghanegaonkar S,Conrad J,Beifuss U,Sprenger GA,Albermann C

    更新日期:2012-12-15 00:00:00

  • Characterization of stress and protein turnover from protein overexpression in fed-batch E. coli cultures.

    abstract::A structured kinetic model that accounts for proteolytic degradation due to recombinant protein overexpression is introduced and its performance evaluated by comparison with previously reported fed-batch experimental data. This mathematical model contains an additional pool for a generic key precursor (in our case phe...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/s0168-1656(99)00014-0

    authors: Ramírez DM,Bentley WE

    更新日期:1999-05-28 00:00:00

  • Biosynthesis of glycolate-based polyesters containing medium-chain-length 3-hydroxyalkanoates in recombinant Escherichia coli expressing engineered polyhydroxyalkanoate synthase.

    abstract::Glycolate(GL)-based polyesters were for the first time produced in the recombinant Escherichia coli fatty acid β-oxidation pathway reinforcing mutant LS5218, using extracellularly added GL as a monomer precursor. Cells expressing a Ser325Thr/Gln481Lys mutant of polyhydroxyalkanoate synthase (PhaC1STQK) from Pseudomona...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2011.07.040

    authors: Matsumoto K,Ishiyama A,Sakai K,Shiba T,Taguchi S

    更新日期:2011-12-10 00:00:00

  • Chemostat studies of bacteriophage M13 infected Escherichia coli JM109 for continuous ssDNA production.

    abstract::Steady state studies in a chemostat enable the control of microbial growth rate at defined reaction conditions. The effects of bacteriophage M13 infection on maximum growth rate of Escherichia coli JM109 were studied in parallel operated chemostats on a milliliter-scale to analyze the steady state kinetics of phage pr...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2017.06.409

    authors: Kick B,Behler KL,Severin TS,Weuster-Botz D

    更新日期:2017-09-20 00:00:00

  • Enzymatic preparation of D-phenyllactic acid at high space-time yield with a novel phenylpyruvate reductase identified from Lactobacillus sp. CGMCC 9967.

    abstract::An NADH-dependent phenylpyruvate reductase (LaPPR) was identified through screening the shotgun library of Lactobacillus sp. CGMCC 9967. It belongs to D-3-phosphoglycerate dehydrogenase (PGDH) subfamily of 2-hydroxy acid dehydrogenase superfamily. LaPPR was stable at pH 6.5 and 30 °C, with a half-life of 152 h. LaPPR ...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2015.12.011

    authors: Xu GC,Zhang LL,Ni Y

    更新日期:2016-03-20 00:00:00

  • Macroporous monolithic gels, cryogels, with immobilized phages from phage-display library as a new platform for fast development of affinity adsorbent capable of target capture from crude feeds.

    abstract::Selected phage clones expressing a peptide with high binding affinity for recombinant human lactoferrin or von Willebrand factor (vWF) were covalently coupled to macroporous poly(dimethylacrylamide) monolithic column. Large pore size (10-100 microm) of macroporous poly(dimethylacrylamide) makes it possible to couple l...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2007.06.021

    authors: Noppe W,Plieva FM,Vanhoorelbeke K,Deckmyn H,Tuncel M,Tuncel A,Galaev IY,Mattiasson B

    更新日期:2007-09-15 00:00:00

  • Engineered Salmonella allows real-time heterologous gene expression monitoring within infected zebrafish embryos.

    abstract::Microbial host-pathogen interactions have been traditionally well studied at genetic and physiological levels, but cell-resolution analyses have been particularly scarce. This has been especially remarkable for intracellular parasites for two major reasons: first, the inherent loss of bacteria traceability once infect...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2011.11.022

    authors: Medina C,Santero E,Gómez-Skarmeta JL,Royo JL

    更新日期:2012-02-10 00:00:00

  • Synthesis and release of the bacterial compatible solute 5-hydroxyectoine in Hansenula polymorpha.

    abstract::Ectoine and 5-hydroxyectoine belong to the family of compatible solutes which are known to mainly contribute to the adaptation of the cell to osmotic stress by mediation of a constant turgor. In addition the cell's essential functions are maintained under stress conditions like high salinity, heat or aridity stress. H...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2013.02.005

    authors: Eilert E,Kranz A,Hollenberg CP,Piontek M,Suckow M

    更新日期:2013-08-20 00:00:00

  • Methods for reducing the ammonia in hybridoma cell cultures.

    abstract::The factors which limit the proliferation of eukaryotic cells in vitro are still not well known. Ammonia is believed to be toxic for mammalian cell proliferation and secretion. We have tried two approaches to reducing the ammonia in the medium. We first limited the ammonia produced by the cells by replacing glutamine ...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/0168-1656(94)00142-y

    authors: Capiaumont J,Legrand C,Carbonell D,Dousset B,Belleville F,Nabet P

    更新日期:1995-02-21 00:00:00

  • Antigen handling in the gastrointestinal lamina propria.

    abstract::Enteric infections associated with bacteria, viruses and parasites are a world health problem accounting for at least one billion episodes of diarrhoea and up to 10 million deaths in the Third World each year. The widely held conclusion that responses which are protective in the gastrointestinal tract are best stimula...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/0168-1656(95)00114-X

    authors: Stokes CR,Bailey M

    更新日期:1996-01-26 00:00:00

  • Large-scale applicable purification and characterization of a membrane-bound PQQ-dependent aldose dehydrogenase.

    abstract::A membrane-bound xylose oxidizing PQQ-dependent dehydrogenase from Gluconobacter oxydans was purified with a simple large-scale applicable purification procedure. The activity recovery from membrane extract was 33% with 130-fold purification. Important characteristic with respect to the application of the dehydrogenas...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/0168-1656(93)90060-z

    authors: Smolander M,Buchert J,Viikari L

    更新日期:1993-06-01 00:00:00