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Article ; Online: Luminidependens (LD) is an Arabidopsis protein with prion behavior.

Chakrabortee, Sohini / Kayatekin, Can / Newby, Greg A / Mendillo, Marc L / Lancaster, Alex / Lindquist, Susan

Proceedings of the National Academy of Sciences of the United States of America

2016 Volume 113, Issue 21, Page(s) 6065–6070

Abstract: Prion proteins provide a unique mode of biochemical memory through self-perpetuating changes in protein conformation and function. They have been studied in fungi and mammals, but not yet identified in plants. Using a computational model, we identified ... ...

Abstract	Prion proteins provide a unique mode of biochemical memory through self-perpetuating changes in protein conformation and function. They have been studied in fungi and mammals, but not yet identified in plants. Using a computational model, we identified candidate prion domains (PrDs) in nearly 500 plant proteins. Plant flowering is of particular interest with respect to biological memory, because its regulation involves remembering and integrating previously experienced environmental conditions. We investigated the prion-forming capacity of three prion candidates involved in flowering using a yeast model, where prion attributes are well defined and readily tested. In yeast, prions heritably change protein functions by templating monomers into higher-order assemblies. For most yeast prions, the capacity to convert into a prion resides in a distinct prion domain. Thus, new prion-forming domains can be identified by functional complementation of a known prion domain. The prion-like domains (PrDs) of all three of the tested proteins formed higher-order oligomers. Uniquely, the Luminidependens PrD (LDPrD) fully replaced the prion-domain functions of a well-characterized yeast prion, Sup35. Our results suggest that prion-like conformational switches are evolutionarily conserved and might function in a wide variety of normal biological processes.
MeSH term(s)	Arabidopsis/chemistry ; Arabidopsis Proteins/chemistry ; Models, Molecular ; Peptide Termination Factors/chemistry ; Prion Proteins/chemistry ; Protein Domains ; Saccharomyces cerevisiae Proteins/chemistry
Chemical Substances	Arabidopsis Proteins ; LD protein, Arabidopsis ; Peptide Termination Factors ; Prion Proteins ; SUP35 protein, S cerevisiae ; Saccharomyces cerevisiae Proteins
Language	English
Publishing date	2016-05-24
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.1604478113
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Article ; Online: Complexity of the heat-soluble LEA proteome in Artemia species.

Warner, Alden H / Chakrabortee, Sohini / Tunnacliffe, Alan / Clegg, James S

Comparative biochemistry and physiology. Part D, Genomics & proteomics

2012 Volume 7, Issue 3, Page(s) 260–267

Abstract: The brine shrimp Artemia is a well known stress tolerant invertebrate found on most continents. Under certain conditions females produce cysts (encysted gastrulae) that enter diapause, a state of obligate dormancy. During developmental formation of ... ...

Abstract	The brine shrimp Artemia is a well known stress tolerant invertebrate found on most continents. Under certain conditions females produce cysts (encysted gastrulae) that enter diapause, a state of obligate dormancy. During developmental formation of diapause embryos several different types of stress proteins accumulate in large amounts, including the late embryogenesis abundant (LEA) proteins. In this study we used a combination of heterologous group 3 LEA antibodies to demonstrate that the heat-soluble proteome of the cysts contains up to 12 distinct putative group 3 LEA proteins that complement the group 1 LEA proteins found previously. Most antibody-positive, heat-soluble proteins were larger than 50 kDa although antibody positive proteins of 20-38 kDa were also detected. Both nuclei and mitochondria had distinct complements of the putative group 3 LEA proteins. A few small group 3 LEA proteins were induced by cycles of hydration-dehydration along with one protein of about 62 kDa. The expression of group 3 LEA proteins, unlike members of group 1, was not restricted to encysted diapause embryos. Three to five putative group 3 LEA proteins were expressed in gravid females and in larvae. Cysts of different species from various geographic locations had distinct complements of group 3 LEA proteins suggesting rapid evolution of the LEA proteins or differences in the type of group 3 Lea genes expressed. Our results demonstrate the potential importance of group 3 LEA proteins in embryos and other life cycle stages of this animal extremophile.
MeSH term(s)	Animals ; Artemia/embryology ; Artemia/genetics ; Artemia/metabolism ; Blotting, Western ; Desiccation ; Electrophoresis, Polyacrylamide Gel ; Embryo, Nonmammalian/metabolism ; Embryonic Development/genetics ; Female ; Gene Expression Regulation, Developmental ; Geography ; Hot Temperature ; Organelles/metabolism ; Proteome/genetics ; Proteome/metabolism ; Solubility ; Species Specificity ; Subcellular Fractions/metabolism
Chemical Substances	Proteome
Language	English
Publishing date	2012-09
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2212119-5
ISSN	1878-0407 ; 1744-117X
ISSN (online)	1878-0407
ISSN	1744-117X
DOI	10.1016/j.cbd.2012.04.002
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Article ; Online: Both plant and animal LEA proteins act as kinetic stabilisers of polyglutamine-dependent protein aggregation.

Liu, Yun / Chakrabortee, Sohini / Li, Ranhui / Zheng, Yizhi / Tunnacliffe, Alan

FEBS letters

2011 Volume 585, Issue 4, Page(s) 630–634

Abstract: LEA (late embryogenesis abundant) proteins are intrinsically disordered proteins that contribute to stress tolerance in plants and invertebrates. Here we show that, when both plant and animal LEA proteins are co-expressed in mammalian cells with self- ... ...

Abstract	LEA (late embryogenesis abundant) proteins are intrinsically disordered proteins that contribute to stress tolerance in plants and invertebrates. Here we show that, when both plant and animal LEA proteins are co-expressed in mammalian cells with self-aggregating polyglutamine (polyQ) proteins, they reduce aggregation in a time-dependent fashion, showing more protection at early time points. A similar effect was also observed in vitro, where recombinant LEA proteins were able to slow the rate of polyQ aggregation, but not abolish it altogether. Thus, LEA proteins act as kinetic stabilisers of aggregating proteins, a novel function in protein homeostasis consistent with a proposed role as molecular shields.
MeSH term(s)	Amino Acid Motifs ; Animals ; Benzothiazoles ; Cell Line ; Fluorescent Dyes ; Helminth Proteins/genetics ; Helminth Proteins/metabolism ; Homeostasis ; Humans ; Kinetics ; Microscopy, Confocal ; Microscopy, Fluorescence ; Molecular Chaperones/genetics ; Molecular Chaperones/metabolism ; Peptides/metabolism ; Plant Proteins/genetics ; Plant Proteins/metabolism ; Protein Folding ; Recombinant Fusion Proteins/metabolism ; Thiazoles/metabolism ; Triticum/metabolism ; Tylenchida/metabolism
Chemical Substances	Benzothiazoles ; Em protein, Triticum aestivum ; Fluorescent Dyes ; Helminth Proteins ; Molecular Chaperones ; Peptides ; Plant Proteins ; Recombinant Fusion Proteins ; Thiazoles ; late embryogenesis abundant protein, plant ; thioflavin T (2390-54-7) ; polyglutamine (26700-71-0)
Language	English
Publishing date	2011-01-18
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	212746-5
ISSN	1873-3468 ; 0014-5793
ISSN (online)	1873-3468
ISSN	0014-5793
DOI	10.1016/j.febslet.2011.01.020
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Article: Complexity of the heat-soluble LEA proteome in Artemia species

Warner, Alden H / Chakrabortee, Sohini / Tunnacliffe, Alan / Clegg, James S

Comparative biochemistry and physiology. 2012 Sept., v. 7, no. 3

2012

Abstract	The brine shrimp Artemia is a well known stress tolerant invertebrate found on most continents. Under certain conditions females produce cysts (encysted gastrulae) that enter diapause, a state of obligate dormancy. During developmental formation of diapause embryos several different types of stress proteins accumulate in large amounts, including the late embryogenesis abundant (LEA) proteins. In this study we used a combination of heterologous group 3 LEA antibodies to demonstrate that the heat-soluble proteome of the cysts contains up to 12 distinct putative group 3 LEA proteins that complement the group 1 LEA proteins found previously. Most antibody-positive, heat-soluble proteins were larger than 50kDa although antibody positive proteins of 20–38kDa were also detected. Both nuclei and mitochondria had distinct complements of the putative group 3 LEA proteins. A few small group 3 LEA proteins were induced by cycles of hydration–dehydration along with one protein of about 62kDa. The expression of group 3 LEA proteins, unlike members of group 1, was not restricted to encysted diapause embryos. Three to five putative group 3 LEA proteins were expressed in gravid females and in larvae. Cysts of different species from various geographic locations had distinct complements of group 3 LEA proteins suggesting rapid evolution of the LEA proteins or differences in the type of group 3 Lea genes expressed. Our results demonstrate the potential importance of group 3 LEA proteins in embryos and other life cycle stages of this animal extremophile.
Keywords	Artemia ; Geographical Locations ; antibodies ; diapause ; dormancy ; embryogenesis ; evolution ; extremophiles ; gene expression ; gravid females ; invertebrates ; larvae ; mitochondria ; protein synthesis ; proteins ; proteome
Language	English
Dates of publication	2012-09
Size	p. 260-267.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	2212119-5
ISSN	1878-0407 ; 1744-117X
ISSN (online)	1878-0407
ISSN	1744-117X
DOI	10.1016/j.cbd.2012.04.002
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Article: Intrinsically Disordered Proteins Drive Emergence and Inheritance of Biological Traits

Chakrabortee, Sohini / James S. Byers / Sandra Jones / David M. Garcia / Bhupinder Bhullar / Amelia Chang / Richard She / Laura Lee / Brayon Fremin / Susan Lindquist / Daniel F. Jarosz

Cell. 2016 Oct. 06, v. 167

2016

Abstract: Prions are a paradigm-shifting mechanism of inheritance in which phenotypes are encoded by self-templating protein conformations rather than nucleic acids. Here, we examine the breadth of protein-based inheritance across the yeast proteome by assessing ... ...

Abstract	Prions are a paradigm-shifting mechanism of inheritance in which phenotypes are encoded by self-templating protein conformations rather than nucleic acids. Here, we examine the breadth of protein-based inheritance across the yeast proteome by assessing the ability of nearly every open reading frame (ORF; â¼5,300 ORFs) to induce heritable traits. Transient overexpression of nearly 50 proteins created traits that remained heritable long after their expression returned to normal. These traits were beneficial, had prion-like patterns of inheritance, were common in wild yeasts, and could be transmitted to naive cells with protein alone. Most inducing proteins were not known prions and did not form amyloid. Instead, they are highly enriched in nucleic acid binding proteins with large intrinsically disordered domains that have been widely conserved across evolution. Thus, our data establish a common type of protein-based inheritance through which intrinsically disordered proteins can drive the emergence of new traits and adaptive opportunities.
Keywords	amyloid ; binding proteins ; evolution ; gene overexpression ; genetic traits ; inheritance (genetics) ; nucleic acids ; open reading frames ; phenotype ; prions ; proteome ; yeasts
Language	English
Dates of publication	2016-1006
Size	p. 369-381.e12.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2016.09.017
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Article: Both plant and animal LEA proteins act as kinetic stabilisers of polyglutamine-dependent protein aggregation

Liu, Yun / Chakrabortee, Sohini / Li, Ranhui / Zheng, Yizhi / Tunnacliffe, Alan

FEBS letters. 2011 Feb. 18, v. 585, no. 4

2011

Abstract	LEA (late embryogenesis abundant) proteins are intrinsically disordered proteins that contribute to stress tolerance in plants and invertebrates. Here we show that, when both plant and animal LEA proteins are co-expressed in mammalian cells with self-aggregating polyglutamine (polyQ) proteins, they reduce aggregation in a time-dependent fashion, showing more protection at early time points. A similar effect was also observed in vitro, where recombinant LEA proteins were able to slow the rate of polyQ aggregation, but not abolish it altogether. Thus, LEA proteins act as kinetic stabilisers of aggregating proteins, a novel function in protein homeostasis consistent with a proposed role as molecular shields.
Keywords	embryogenesis ; homeostasis ; invertebrates ; mammals ; proteins ; stress tolerance
Language	English
Dates of publication	2011-0218
Size	p. 630-634.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	212746-5
ISSN	1873-3468 ; 0014-5793
ISSN (online)	1873-3468
ISSN	0014-5793
DOI	10.1016/j.febslet.2011.01.020
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: A Genetic Tool to Track Protein Aggregates and Control Prion Inheritance.

Newby, Gregory A / Kiriakov, Szilvia / Hallacli, Erinc / Kayatekin, Can / Tsvetkov, Peter / Mancuso, Christopher P / Bonner, J Maeve / Hesse, William R / Chakrabortee, Sohini / Manogaran, Anita L / Liebman, Susan W / Lindquist, Susan / Khalil, Ahmad S

Cell

2017 Volume 171, Issue 4, Page(s) 966–979.e18

Abstract: Protein aggregation is a hallmark of many diseases but also underlies a wide range of positive cellular functions. This phenomenon has been difficult to study because of a lack of quantitative and high-throughput cellular tools. Here, we develop a ... ...

Abstract	Protein aggregation is a hallmark of many diseases but also underlies a wide range of positive cellular functions. This phenomenon has been difficult to study because of a lack of quantitative and high-throughput cellular tools. Here, we develop a synthetic genetic tool to sense and control protein aggregation. We apply the technology to yeast prions, developing sensors to track their aggregation states and employing prion fusions to encode synthetic memories in yeast cells. Utilizing high-throughput screens, we identify prion-curing mutants and engineer "anti-prion drives" that reverse the non-Mendelian inheritance pattern of prions and eliminate them from yeast populations. We extend our technology to yeast RNA-binding proteins (RBPs) by tracking their propensity to aggregate, searching for co-occurring aggregates, and uncovering a group of coalescing RBPs through screens enabled by our platform. Our work establishes a quantitative, high-throughput, and generalizable technology to study and control diverse protein aggregation processes in cells.
MeSH term(s)	Genetic Engineering ; Genetic Techniques/economics ; Prions/genetics ; RNA-Binding Proteins/metabolism ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Synthetic Biology/methods ; mRNA Cleavage and Polyadenylation Factors/metabolism
Chemical Substances	HRP1 protein, S cerevisiae ; Prions ; RNA-Binding Proteins ; Saccharomyces cerevisiae Proteins ; mRNA Cleavage and Polyadenylation Factors
Language	English
Publishing date	2017-10-19
Publishing country	United States
Document type	Evaluation Studies ; Journal Article
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2017.09.041
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Article ; Online: Prion-like proteins sequester and suppress the toxicity of huntingtin exon 1

Kayatekin, Can / Matlack, Kent E. S. / Hesse, William R. / Guan, Yinghua / Chakrabortee, Sohini / Russ, Jennifer M. / Wanker, Erich E. / Shah, Jagesh V. / Lindquist, Susan

Proceedings of the National Academy of Sciences of the United States of America. 2014 Aug. 19, v. 111, no. 33 p.12085-12090

2014

Abstract: Expansions of preexisting polyglutamine (polyQ) tracts in at least nine different proteins cause devastating neurodegenerative diseases. There are many unique features to these pathologies, but there must also be unifying mechanisms underlying polyQ ... ...

Abstract	Expansions of preexisting polyglutamine (polyQ) tracts in at least nine different proteins cause devastating neurodegenerative diseases. There are many unique features to these pathologies, but there must also be unifying mechanisms underlying polyQ toxicity. Using a polyQ-expanded fragment of huntingtin exon-1 (Htt103Q), the causal protein in Huntington disease, we and others have created tractable models for investigating polyQ toxicity in yeast cells. These models recapitulate key pathological features of human diseases and provide access to an unrivalled genetic toolbox. To identify toxicity modifiers, we performed an unbiased overexpression screen of virtually every protein encoded by the yeast genome. Surprisingly, there was no overlap between our modifiers and those from a conceptually identical screen reported recently, a discrepancy we attribute to an artifact of their overexpression plasmid. The suppressors of Htt103Q toxicity recovered in our screen were strongly enriched for glutamine- and asparagine-rich prion-like proteins. Separated from the rest of the protein, the prion-like sequences of these proteins were themselves potent suppressors of polyQ-expanded huntingtin exon-1 toxicity, in both yeast and human cells. Replacing the glutamines in these sequences with asparagines abolished suppression and converted them to enhancers of toxicity. Replacing asparagines with glutamines created stronger suppressors. The suppressors (but not the enhancers) coaggregated with Htt103Q, forming large foci at the insoluble protein deposit in which proteins were highly immobile. Cells possessing foci had fewer (if any) small diffusible oligomers of Htt103Q. Until such foci were lost, cells were protected from death. We discuss the therapeutic implications of these findings.
Keywords	human diseases ; proteins ; humans ; gene overexpression ; yeasts ; models ; plasmids ; toxicity ; neurodegenerative diseases ; exons ; protein misfolding ; genome ; prions
Language	English
Dates of publication	2014-0819
Size	p. 12085-12090.
Publishing place	National Academy of Sciences
Document type	Article ; Online
Note	2019-12-04 ; Resource is Open Access
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.1412504111
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Article ; Online: Intrinsically Disordered Proteins Drive Emergence and Inheritance of Biological Traits.

Chakrabortee, Sohini / Byers, James S / Jones, Sandra / Garcia, David M / Bhullar, Bhupinder / Chang, Amelia / She, Richard / Lee, Laura / Fremin, Brayon / Lindquist, Susan / Jarosz, Daniel F

Cell

2016 Volume 167, Issue 2, Page(s) 369–381.e12

Abstract	Prions are a paradigm-shifting mechanism of inheritance in which phenotypes are encoded by self-templating protein conformations rather than nucleic acids. Here, we examine the breadth of protein-based inheritance across the yeast proteome by assessing the ability of nearly every open reading frame (ORF; ∼5,300 ORFs) to induce heritable traits. Transient overexpression of nearly 50 proteins created traits that remained heritable long after their expression returned to normal. These traits were beneficial, had prion-like patterns of inheritance, were common in wild yeasts, and could be transmitted to naive cells with protein alone. Most inducing proteins were not known prions and did not form amyloid. Instead, they are highly enriched in nucleic acid binding proteins with large intrinsically disordered domains that have been widely conserved across evolution. Thus, our data establish a common type of protein-based inheritance through which intrinsically disordered proteins can drive the emergence of new traits and adaptive opportunities.
MeSH term(s)	Amyloid/metabolism ; Evolution, Molecular ; HSP70 Heat-Shock Proteins/genetics ; HSP70 Heat-Shock Proteins/metabolism ; HSP90 Heat-Shock Proteins/genetics ; HSP90 Heat-Shock Proteins/metabolism ; Heat-Shock Proteins/genetics ; Heat-Shock Proteins/metabolism ; Intrinsically Disordered Proteins/chemistry ; Intrinsically Disordered Proteins/genetics ; Intrinsically Disordered Proteins/metabolism ; Open Reading Frames ; Prions/chemistry ; Prions/metabolism ; Proteome ; Quantitative Trait, Heritable ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae Proteins/chemistry ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism
Chemical Substances	Amyloid ; HSP70 Heat-Shock Proteins ; HSP82 protein, S cerevisiae ; HSP90 Heat-Shock Proteins ; Heat-Shock Proteins ; Intrinsically Disordered Proteins ; Prions ; Proteome ; Saccharomyces cerevisiae Proteins ; HsP104 protein, S cerevisiae (143012-44-6)
Language	English
Publishing date	2016-09-29
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2016.09.017
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Article: Hydrophilic protein associated with desiccation tolerance exhibits broad protein stabilization function

Chakrabortee, Sohini / Boschetti, Chiara / Walton, Laura J / Sarkar, Sovan / Rubinsztein, David C / Tunnacliffe, Alan

Proceedings of the National Academy of Sciences of the United States of America. 2007 Nov. 13, v. 104, no. 46

2007

Abstract: The ability of certain plants, invertebrates, and microorganisms to survive almost complete loss of water has long been recognized, but the molecular mechanisms of this phenomenon remain to be defined. One phylogenetically widespread adaptation is the ... ...

Abstract	The ability of certain plants, invertebrates, and microorganisms to survive almost complete loss of water has long been recognized, but the molecular mechanisms of this phenomenon remain to be defined. One phylogenetically widespread adaptation is the presence of abundant, highly hydrophilic proteins in desiccation-tolerant organisms. The best characterized of these polypeptides are the late embryogenesis abundant (LEA) proteins, first described in plant seeds >20 years ago but recently identified in invertebrates and bacteria. The function of these largely unstructured proteins has been unclear, but we now show that a group 3 LEA protein from the desiccation-tolerant nematode Aphelenchus avenae is able to prevent aggregation of a wide range of other proteins both in vitro and in vivo. The presence of water is essential for maintenance of the structure of many proteins, and therefore desiccation stress induces unfolding and aggregation. The nematode LEA protein is able to abrogate desiccation-induced aggregation of the water-soluble proteomes from nematodes and mammalian cells and affords protection during both dehydration and rehydration. Furthermore, when coexpressed in a human cell line, the LEA protein reduces the propensity of polyglutamine and polyalanine expansion proteins associated with neurodegenerative diseases to form aggregates, demonstrating in vivo function of an LEA protein as an antiaggregant. Finally, human cells expressing LEA protein exhibit increased survival of dehydration imposed by osmotic upshift, consistent with a broad protein stabilization function of LEA proteins under conditions of water stress.
Language	English
Dates of publication	2007-1113
Size	p. 18073-18078.
Publishing place	National Academy of Sciences
Document type	Article
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
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