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Article ; Online: Natural Competence in the Filamentous, Heterocystous Cyanobacterium

Nies, Fabian / Springstein, Benjamin L / Hanke, Dustin M / Dagan, Tal

mSphere

2022 Volume 7, Issue 4, Page(s) e0099721

Abstract: Lateral gene transfer plays an important role in the evolution of genetic diversity in prokaryotes. DNA transfer via natural transformation depends on the ability of recipient cells to actively transport DNA from the environment into the cytoplasm, ... ...

Abstract	Lateral gene transfer plays an important role in the evolution of genetic diversity in prokaryotes. DNA transfer via natural transformation depends on the ability of recipient cells to actively transport DNA from the environment into the cytoplasm, termed natural competence, which relies on the presence of type IV pili and other competence proteins. Natural competence has been described in cyanobacteria for several organisms, including unicellular and filamentous species. However, natural competence in cyanobacteria that differentiate specialized cells for N
MeSH term(s)	Cyanobacteria/genetics ; Cyanobacteria/metabolism ; Gene Transfer, Horizontal ; Photosynthesis
Language	English
Publishing date	2022-07-14
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2379-5042
ISSN (online)	2379-5042
DOI	10.1128/msphere.00997-21
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Systematic analysis of nonprogrammed frameshift suppression in

Springstein, Benjamin L / Paulo, Joao A / Park, Hankum / Henry, Kemardo / Fleming, Eleanor / Feder, Zoë / Harper, J Wade / Hochschild, Ann

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

2024 Volume 121, Issue 6, Page(s) e2317453121

Abstract: The synthesis of proteins as encoded in the genome depends critically on translational fidelity. Nevertheless, errors inevitably occur, and those that result in reading frame shifts are particularly consequential because the resulting polypeptides are ... ...

Abstract	The synthesis of proteins as encoded in the genome depends critically on translational fidelity. Nevertheless, errors inevitably occur, and those that result in reading frame shifts are particularly consequential because the resulting polypeptides are typically nonfunctional. Despite the generally maladaptive impact of such errors, the proper decoding of certain mRNAs, including many viral mRNAs, depends on a process known as programmed ribosomal frameshifting. The fact that these programmed events, commonly involving a shift to the -1 frame, occur at specific evolutionarily optimized "slippery" sites has facilitated mechanistic investigation. By contrast, less is known about the scope and nature of error (i.e., nonprogrammed) frameshifting. Here, we examine error frameshifting by monitoring spontaneous frameshift events that suppress the effects of single base pair deletions affecting two unrelated test proteins. To map the precise sites of frameshifting, we developed a targeted mass spectrometry-based method called "translational tiling proteomics" for interrogating the full set of possible -1 slippage events that could produce the observed frameshift suppression. Surprisingly, such events occur at many sites along the transcripts, involving up to one half of the available codons. Only a subset of these resembled canonical "slippery" sites, implicating alternative mechanisms potentially involving noncognate mispairing events. Additionally, the aggregate frequency of these events (ranging from 1 to 10% in our test cases) was higher than we might have anticipated. Our findings point to an unexpected degree of mechanistic diversity among ribosomal frameshifting events and suggest that frameshifted products may contribute more significantly to the proteome than generally assumed.
MeSH term(s)	Escherichia coli/genetics ; Escherichia coli/metabolism ; Proteomics ; Frameshift Mutation/genetics ; Frameshifting, Ribosomal/genetics ; Codon/metabolism
Chemical Substances	Codon
Language	English
Publishing date	2024-01-30
Publishing country	United States
Document type	Journal Article
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2317453121
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Article ; Online: A Bacterial Cell-Based Assay To Study SARS-CoV-2 Protein-Protein Interactions.

Springstein, Benjamin L / Deighan, Padraig / Grabe, Grzegorz J / Hochschild, Ann

mBio

2021 Volume 12, Issue 6, Page(s) e0293621

Abstract: Methods for detecting and dissecting the interactions of virally encoded proteins are essential for probing basic viral biology and providing a foundation for therapeutic advances. The dearth of targeted therapeutics for the treatment of coronavirus ... ...

Abstract	Methods for detecting and dissecting the interactions of virally encoded proteins are essential for probing basic viral biology and providing a foundation for therapeutic advances. The dearth of targeted therapeutics for the treatment of coronavirus disease 2019 (COVID-19), an ongoing global health crisis, underscores the importance of gaining a deeper understanding of the interactions of proteins encoded by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here, we describe the use of a convenient bacterial cell-based two-hybrid (B2H) system to analyze the SARS-CoV-2 proteome. We identified 16 distinct intraviral protein-protein interactions (PPIs), involving 16 proteins. We found that many of the identified proteins interact with more than one partner. Further, our system facilitates the genetic dissection of these interactions, enabling the identification of selectively disruptive mutations. We also describe a modified B2H system that permits the detection of disulfide bond-dependent PPIs in the normally reducing Escherichia coli cytoplasm, and we used this system to detect the interaction of the SARS-CoV-2 spike protein receptor-binding domain (RBD) with its cognate cell surface receptor ACE2. We then examined how the RBD-ACE2 interaction is perturbed by several RBD amino acid substitutions found in currently circulating SARS-CoV-2 variants. Our findings illustrate the utility of a genetically tractable bacterial system for probing the interactions of viral proteins and investigating the effects of emerging mutations. In principle, the system could also facilitate the identification of potential therapeutics that disrupt specific interactions of virally encoded proteins. More generally, our findings establish the feasibility of using a B2H system to detect and dissect disulfide bond-dependent interactions of eukaryotic proteins.
MeSH term(s)	Angiotensin-Converting Enzyme 2/genetics ; Angiotensin-Converting Enzyme 2/metabolism ; Binding Sites ; Biological Assay/methods ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Humans ; Mutation ; Protein Binding ; Protein Interaction Domains and Motifs ; Proteome ; SARS-CoV-2/chemistry ; SARS-CoV-2/genetics ; Spike Glycoprotein, Coronavirus/metabolism ; Viral Proteins/genetics ; Viral Proteins/metabolism
Chemical Substances	Proteome ; Spike Glycoprotein, Coronavirus ; Viral Proteins ; spike protein, SARS-CoV-2 ; ACE2 protein, human (EC 3.4.17.23) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
Language	English
Publishing date	2021-11-16
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2557172-2
ISSN	2150-7511 ; 2161-2129
ISSN (online)	2150-7511
ISSN	2161-2129
DOI	10.1128/mBio.02936-21
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Article ; Online: Role of natural transformation in the evolution of small cryptic plasmids in Synechocystis sp. PCC 6803.

Nies, Fabian / Wein, Tanita / Hanke, Dustin M / Springstein, Benjamin L / Alcorta, Jaime / Taubenheim, Claudia / Dagan, Tal

Environmental microbiology reports

2023 Volume 15, Issue 6, Page(s) 656–668

Abstract: Small cryptic plasmids have no clear effect on the host fitness and their functional repertoire remains obscure. The naturally competent cyanobacterium Synechocystis sp. PCC 6803 harbours several small cryptic plasmids; whether their evolution with this ... ...

Abstract	Small cryptic plasmids have no clear effect on the host fitness and their functional repertoire remains obscure. The naturally competent cyanobacterium Synechocystis sp. PCC 6803 harbours several small cryptic plasmids; whether their evolution with this species is supported by horizontal transfer remains understudied. Here, we show that the small cryptic plasmid DNA is transferred in the population exclusively by natural transformation, where the transfer frequency of plasmid-encoded genes is similar to that of chromosome-encoded genes. Establishing a system to follow gene transfer, we compared the transfer frequency of genes encoded in cryptic plasmids pCA2.4 (2378 bp) and pCB2.4 (2345 bp) within and between populations of two Synechocystis sp. PCC 6803 labtypes (termed Kiel and Sevilla). Our results reveal that plasmid gene transfer frequency depends on the recipient labtype. Furthermore, gene transfer via whole plasmid uptake in the Sevilla labtype ranged among the lowest detected transfer rates in our experiments. Our study indicates that horizontal DNA transfer via natural transformation is frequent in the evolution of small cryptic plasmids that reside in naturally competent organisms. Furthermore, we suggest that the contribution of natural transformation to cryptic plasmid persistence in Synechocystis is limited.
MeSH term(s)	Synechocystis/genetics ; Plasmids/genetics ; DNA
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2023-10-04
Publishing country	United States
Document type	Journal Article
ISSN	1758-2229
ISSN (online)	1758-2229
DOI	10.1111/1758-2229.13203
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: SepT, a novel protein specific to multicellular cyanobacteria, influences peptidoglycan growth and septal nanopore formation in

Velázquez-Suárez, Cristina / Springstein, Benjamin L / Nieves-Morión, Mercedes / Helbig, Andreas O / Kieninger, Ann-Katrin / Maldener, Iris / Nürnberg, Dennis J / Stucken, Karina / Luque, Ignacio / Dagan, Tal / Herrero, Antonia

mBio

2023 Volume 14, Issue 5, Page(s) e0098323

Abstract: Importance: Multicellular organization is a requirement for the development of complex organisms, and filamentous cyanobacteria such ... ...

Abstract	Importance: Multicellular organization is a requirement for the development of complex organisms, and filamentous cyanobacteria such as
MeSH term(s)	Peptidoglycan/metabolism ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Nanopores ; Anabaena/genetics ; Anabaena/metabolism ; Cytoskeleton/metabolism ; Gene Expression Regulation, Bacterial
Chemical Substances	Peptidoglycan ; Bacterial Proteins
Language	English
Publishing date	2023-08-31
Publishing country	United States
Document type	Journal Article
ZDB-ID	2557172-2
ISSN	2150-7511 ; 2161-2129
ISSN (online)	2150-7511
ISSN	2161-2129
DOI	10.1128/mbio.00983-23
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Article: The role of the cytoskeletal proteins MreB and FtsZ in multicellular cyanobacteria

Springstein, Benjamin L. / Weissenbach, Julia / Koch, Robin / Stücker, Fenna / Stucken, Karina

FEBS Open Bio. 2020 Dec., v. 10, no. 12

2020

Abstract: Multiseriate and true‐branching cyanobacteria are at the peak of prokaryotic morphological complexity. However, little is known about the mechanisms governing multiplanar cell division and morphogenesis. Here, we study the function of the prokaryotic ... ...

Abstract	Multiseriate and true‐branching cyanobacteria are at the peak of prokaryotic morphological complexity. However, little is known about the mechanisms governing multiplanar cell division and morphogenesis. Here, we study the function of the prokaryotic cytoskeletal proteins, MreB and FtsZ in Fischerella muscicola PCC 7414 and Chlorogloeopsis fritschii PCC 6912. Vancomycin and HADA labeling revealed a mixed apical, septal, and lateral trichome growth mode in F. muscicola, whereas C. fritschii exhibits septal growth. In all morphotypes from both species, MreB forms either linear filaments or filamentous strings and can interact with FtsZ. Furthermore, multiplanar cell division in F. muscicola likely depends on FtsZ dosage. Our results lay the groundwork for future studies on cytoskeletal proteins in morphologically complex cyanobacteria.
Keywords	Chlorogloeopsis fritschii ; Fischerella muscicola ; cell division ; cytoskeleton ; morphogenesis ; morphs ; trichomes ; vancomycin
Language	English
Dates of publication	2020-12
Size	p. 2510-2531.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	2651702-4
ISSN	2211-5463
ISSN	2211-5463
DOI	10.1002/2211-5463.13016
Database	NAL-Catalogue (AGRICOLA)

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Article: Structural Determinants and Their Role in Cyanobacterial Morphogenesis.

Springstein, Benjamin L / Nürnberg, Dennis J / Weiss, Gregor L / Pilhofer, Martin / Stucken, Karina

Life (Basel, Switzerland)

2020 Volume 10, Issue 12

Abstract: Cells have to erect and sustain an organized and dynamically adaptable structure for an efficient mode of operation that allows drastic morphological changes during cell growth and cell division. These manifold tasks are complied by the so-called ... ...

Abstract	Cells have to erect and sustain an organized and dynamically adaptable structure for an efficient mode of operation that allows drastic morphological changes during cell growth and cell division. These manifold tasks are complied by the so-called cytoskeleton and its associated proteins. In bacteria, FtsZ and MreB, the bacterial homologs to tubulin and actin, respectively, as well as coiled-coil-rich proteins of intermediate filament (IF)-like function to fulfil these tasks. Despite generally being characterized as Gram-negative, cyanobacteria have a remarkably thick peptidoglycan layer and possess Gram-positive-specific cell division proteins such as SepF and DivIVA-like proteins, besides Gram-negative and cyanobacterial-specific cell division proteins like MinE, SepI, ZipN (Ftn2) and ZipS (Ftn6). The diversity of cellular morphologies and cell growth strategies in cyanobacteria could therefore be the result of additional unidentified structural determinants such as cytoskeletal proteins. In this article, we review the current advances in the understanding of the cyanobacterial cell shape, cell division and cell growth.
Language	English
Publishing date	2020-12-17
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2662250-6
ISSN	2075-1729
ISSN	2075-1729
DOI	10.3390/life10120355
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Article ; Online: A bacteria-based assay to study SARS-CoV-2 protein-protein interactions

Hochschild, Ann / Springstein, Benjamin L / Deighan, Padraig / Grabe, Grzegorz

bioRxiv

Abstract	Methods for detecting and dissecting the interactions of virally encoded proteins are essential for probing basic viral biology and providing a foundation for therapeutic advances. The dearth of targeted therapeutics for the treatment of COVID-19, an ongoing global health crisis, underscores the importance of gaining a deeper understanding of the interactions of SARS-CoV-2-encoded proteins. Here we describe the use of a convenient bacteria-based two-hybrid (B2H) system to analyze the SARS-CoV-2 proteome. We identify sixteen distinct intraviral protein-protein interactions (PPIs), involving sixteen proteins. We find that many of the identified proteins interact with more than one partner. We further show how our system facilitates the genetic dissection of these interactions, enabling the identification of selectively disruptive mutations. We also describe a modified B2H system that permits the detection of disulfide bond-dependent PPIs in the normally reducing Escherichia coli cytoplasm and we use this system to detect the interaction of the SARS-CoV-2 spike protein receptor-binding domain (RBD) with its cognate cell surface receptor ACE2. We then examine how the RBD-ACE2 interaction is perturbed by several RBD amino acid substitutions found in currently circulating SARS-CoV-2 variants. Our findings illustrate the utility of a genetically tractable bacterial system for probing the interactions of viral proteins and investigating the effects of emerging mutations. In principle, the system could also facilitate the identification of potential therapeutics that disrupt specific interactions of virally encoded proteins. More generally, our findings establish the feasibility of using a B2H system to detect and dissect disulfide bond-dependent interactions of eukaryotic proteins.
Keywords	covid19
Language	English
Publishing date	2021-10-08
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2021.10.07.463611
Database	COVID19

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Article ; Online: The role of the cytoskeletal proteins MreB and FtsZ in multicellular cyanobacteria.

Springstein, Benjamin L / Weissenbach, Julia / Koch, Robin / Stücker, Fenna / Stucken, Karina

FEBS open bio

2020 Volume 10, Issue 12, Page(s) 2510–2531

Abstract: Multiseriate and true-branching cyanobacteria are at the peak of prokaryotic morphological complexity. However, little is known about the mechanisms governing multiplanar cell division and morphogenesis. Here, we study the function of the prokaryotic ... ...

Abstract	Multiseriate and true-branching cyanobacteria are at the peak of prokaryotic morphological complexity. However, little is known about the mechanisms governing multiplanar cell division and morphogenesis. Here, we study the function of the prokaryotic cytoskeletal proteins, MreB and FtsZ in Fischerella muscicola PCC 7414 and Chlorogloeopsis fritschii PCC 6912. Vancomycin and HADA labeling revealed a mixed apical, septal, and lateral trichome growth mode in F. muscicola, whereas C. fritschii exhibits septal growth. In all morphotypes from both species, MreB forms either linear filaments or filamentous strings and can interact with FtsZ. Furthermore, multiplanar cell division in F. muscicola likely depends on FtsZ dosage. Our results lay the groundwork for future studies on cytoskeletal proteins in morphologically complex cyanobacteria.
MeSH term(s)	Bacterial Proteins/chemistry ; Bacterial Proteins/metabolism ; Cyanobacteria/chemistry ; Cytoskeletal Proteins/chemistry ; Cytoskeletal Proteins/metabolism
Chemical Substances	Bacterial Proteins ; Cytoskeletal Proteins ; FtsZ protein, Bacteria
Language	English
Publishing date	2020-11-13
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2651702-4
ISSN	2211-5463 ; 2211-5463
ISSN (online)	2211-5463
ISSN	2211-5463
DOI	10.1002/2211-5463.13016
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Identification and characterization of novel filament-forming proteins in cyanobacteria.

Springstein, Benjamin L / Woehle, Christian / Weissenbach, Julia / Helbig, Andreas O / Dagan, Tal / Stucken, Karina

Scientific reports

2020 Volume 10, Issue 1, Page(s) 1894

Abstract: Filament-forming proteins in bacteria function in stabilization and localization of proteinaceous complexes and replicons; hence they are instrumental for myriad cellular processes such as cell division and growth. Here we present two novel filament- ... ...

Abstract	Filament-forming proteins in bacteria function in stabilization and localization of proteinaceous complexes and replicons; hence they are instrumental for myriad cellular processes such as cell division and growth. Here we present two novel filament-forming proteins in cyanobacteria. Surveying cyanobacterial genomes for coiled-coil-rich proteins (CCRPs) that are predicted as putative filament-forming proteins, we observed a higher proportion of CCRPs in filamentous cyanobacteria in comparison to unicellular cyanobacteria. Using our predictions, we identified nine protein families with putative intermediate filament (IF) properties. Polymerization assays revealed four proteins that formed polymers in vitro and three proteins that formed polymers in vivo. Fm7001 from Fischerella muscicola PCC 7414 polymerized in vitro and formed filaments in vivo in several organisms. Additionally, we identified a tetratricopeptide repeat protein - All4981 - in Anabaena sp. PCC 7120 that polymerized into filaments in vitro and in vivo. All4981 interacts with known cytoskeletal proteins and is indispensable for Anabaena viability. Although it did not form filaments in vitro, Syc2039 from Synechococcus elongatus PCC 7942 assembled into filaments in vivo and a Δsyc2039 mutant was characterized by an impaired cytokinesis. Our results expand the repertoire of known prokaryotic filament-forming CCRPs and demonstrate that cyanobacterial CCRPs are involved in cell morphology, motility, cytokinesis and colony integrity.
MeSH term(s)	Amino Acid Motifs/genetics ; Anabaena/cytology ; Anabaena/genetics ; Anabaena/metabolism ; Bacterial Proteins/genetics ; Bacterial Proteins/isolation & purification ; Bacterial Proteins/metabolism ; Cyanobacteria/cytology ; Cyanobacteria/genetics ; Cyanobacteria/metabolism ; Cytoskeletal Proteins/genetics ; Cytoskeletal Proteins/isolation & purification ; Cytoskeletal Proteins/metabolism ; Cytoskeleton/metabolism ; Genes, Bacterial/genetics ; Mutation ; Protein Conformation, alpha-Helical/genetics ; Protein Multimerization ; Recombinant Proteins/genetics ; Recombinant Proteins/isolation & purification ; Recombinant Proteins/metabolism ; Synechococcus/cytology ; Synechococcus/genetics ; Synechococcus/metabolism
Chemical Substances	Bacterial Proteins ; Cytoskeletal Proteins ; Recombinant Proteins
Language	English
Publishing date	2020-02-05
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-020-58726-9
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