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Article: β

Vedula, Pavan / Fina, Marie E / Bell, Brent A / Nikonov, Sergei S / Kashina, Anna / Dong, Dawei W

bioRxiv : the preprint server for biology

2023

Abstract: Lack of non- ... ...

Abstract	Lack of non-muscle
Language	English
Publishing date	2023-03-27
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.03.27.534392
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Protein Posttranslational Signatures Identified in COVID-19 Patient Plasma.

Vedula, Pavan / Tang, Hsin-Yao / Speicher, David W / Kashina, Anna

Frontiers in cell and developmental biology

2022 Volume 10, Page(s) 807149

Abstract: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a highly contagious virus of the coronavirus family that causes coronavirus disease-19 (COVID-19) in humans and a number of animal species. COVID-19 has rapidly propagated in the world in ... ...

Abstract	Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a highly contagious virus of the coronavirus family that causes coronavirus disease-19 (COVID-19) in humans and a number of animal species. COVID-19 has rapidly propagated in the world in the past 2 years, causing a global pandemic. Here, we performed proteomic analysis of plasma samples from COVID-19 patients compared to healthy control donors in an exploratory study to gain insights into protein-level changes in the patients caused by SARS-CoV-2 infection and to identify potential proteomic and posttranslational signatures of this disease. Our results suggest a global change in protein processing and regulation that occurs in response to SARS-CoV-2, and the existence of a posttranslational COVID-19 signature that includes an elevation in threonine phosphorylation, a change in glycosylation, and a decrease in arginylation, an emerging posttranslational modification not previously implicated in infectious disease. This study provides a resource for COVID-19 researchers and, longer term, and will inform our understanding of this disease and its treatment.
Language	English
Publishing date	2022-02-11
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2737824-X
ISSN	2296-634X
ISSN	2296-634X
DOI	10.3389/fcell.2022.807149
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Arginylation Regulates G-protein Signaling in the Retina.

Fina, Marie E / Wang, Junling / Vedula, Pavan / Tang, Hsin-Yao / Kashina, Anna / Dong, Dawei W

Frontiers in cell and developmental biology

2022 Volume 9, Page(s) 807345

Abstract: Arginylation is a post-translational modification mediated by the arginyltransferase (Ate1). We recently showed that conditional deletion of Ate1 in the nervous system leads to increased light-evoked response sensitivities of ON-bipolar cells in the ... ...

Abstract	Arginylation is a post-translational modification mediated by the arginyltransferase (Ate1). We recently showed that conditional deletion of Ate1 in the nervous system leads to increased light-evoked response sensitivities of ON-bipolar cells in the retina, indicating that arginylation regulates the G-protein signaling complexes of those neurons and/or photoreceptors. However, none of the key players in the signaling pathway were previously shown to be arginylated. Here we show that G
Language	English
Publishing date	2022-01-21
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2737824-X
ISSN	2296-634X
ISSN	2296-634X
DOI	10.3389/fcell.2021.807345
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Differential N-terminal processing of beta and gamma actin.

Chen, Li / Vedula, Pavan / Tang, Hsin Yao / Dong, Dawei W / Kashina, Anna S

iScience

2022 Volume 25, Issue 10, Page(s) 105186

Abstract: Cytoplasmic beta- and gamma-actin are ubiquitously expressed in every eukaryotic cell. They are encoded by different genes, but their amino acid sequences differ only by four conservative substitutions at the N-termini, making it difficult to dissect ... ...

Abstract	Cytoplasmic beta- and gamma-actin are ubiquitously expressed in every eukaryotic cell. They are encoded by different genes, but their amino acid sequences differ only by four conservative substitutions at the N-termini, making it difficult to dissect their individual regulation. Here, we analyzed actin from cultured cells and tissues by mass spectrometry and found that beta, unlike gamma actin, undergoes sequential removal of N-terminal Asp residues, leading to truncated actin species found in both F- and G-actin preparations. This processing affects up to ∼3% of beta actin in different cell types. We used CRISPR/Cas-9 in cultured cells to delete two candidate enzymes capable of mediating this type of processing. This deletion abolishes most of the beta actin N-terminal processing and results in changes in F-actin levels, cell spreading, filopodia formation, and cell migration. Our results demonstrate previously unknown isoform-specific actin regulation that can potentially affect actin functions in cells.
Language	English
Publishing date	2022-09-23
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2022.105186
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The makings of the 'actin code': regulation of actin's biological function at the amino acid and nucleotide level.

Vedula, Pavan / Kashina, Anna

Journal of cell science

2018 Volume 131, Issue 9

Abstract: The actin cytoskeleton plays key roles in every eukaryotic cell and is essential for cell adhesion, migration, mechanosensing, and contractility in muscle and non-muscle tissues. In higher vertebrates, from birds through to mammals, actin is represented ... ...

Abstract	The actin cytoskeleton plays key roles in every eukaryotic cell and is essential for cell adhesion, migration, mechanosensing, and contractility in muscle and non-muscle tissues. In higher vertebrates, from birds through to mammals, actin is represented by a family of six conserved genes. Although these genes have evolved independently for more than 100 million years, they encode proteins with ≥94% sequence identity, which are differentially expressed in different tissues, and tightly regulated throughout embryogenesis and adulthood. It has been previously suggested that the existence of such similar actin genes is a fail-safe mechanism to preserve the essential function of actin through redundancy. However, knockout studies in mice and other organisms demonstrate that the different actins have distinct biological roles. The mechanisms maintaining this distinction have been debated in the literature for decades. This Review summarizes data on the functional regulation of different actin isoforms, and the mechanisms that lead to their different biological roles
MeSH term(s)	Actins/metabolism ; Amino Acid Sequence ; Amino Acids/metabolism ; Animals ; Humans ; Mice ; Nucleotides/metabolism
Chemical Substances	Actins ; Amino Acids ; Nucleotides
Language	English
Publishing date	2018-05-08
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	2993-2
ISSN	1477-9137 ; 0021-9533
ISSN (online)	1477-9137
ISSN	0021-9533
DOI	10.1242/jcs.215509
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Arginylation Regulates G-protein Signaling in the Retina

Marie E. Fina / Junling Wang / Pavan Vedula / Hsin-Yao Tang / Anna Kashina / Dawei W. Dong

Frontiers in Cell and Developmental Biology, Vol

2022 Volume 9

Abstract	Arginylation is a post-translational modification mediated by the arginyltransferase (Ate1). We recently showed that conditional deletion of Ate1 in the nervous system leads to increased light-evoked response sensitivities of ON-bipolar cells in the retina, indicating that arginylation regulates the G-protein signaling complexes of those neurons and/or photoreceptors. However, none of the key players in the signaling pathway were previously shown to be arginylated. Here we show that Gαt1, Gβ1, RGS6, and RGS7 are arginylated in the retina and RGS6 and RGS7 protein levels are elevated in Ate1 knockout, suggesting that arginylation plays a direct role in regulating their protein level and the G-protein-mediated responses in the retina.
Keywords	arginylation ; G-protein signaling ; RGS ; retina ; mass spectrometry ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Protein Posttranslational Signatures Identified in COVID-19 Patient Plasma

Pavan Vedula / Hsin-Yao Tang / David W. Speicher / Anna Kashina / The UPenn COVID Processing Unit

Frontiers in Cell and Developmental Biology, Vol

2022 Volume 10

Abstract	Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a highly contagious virus of the coronavirus family that causes coronavirus disease-19 (COVID-19) in humans and a number of animal species. COVID-19 has rapidly propagated in the world in the past 2 years, causing a global pandemic. Here, we performed proteomic analysis of plasma samples from COVID-19 patients compared to healthy control donors in an exploratory study to gain insights into protein-level changes in the patients caused by SARS-CoV-2 infection and to identify potential proteomic and posttranslational signatures of this disease. Our results suggest a global change in protein processing and regulation that occurs in response to SARS-CoV-2, and the existence of a posttranslational COVID-19 signature that includes an elevation in threonine phosphorylation, a change in glycosylation, and a decrease in arginylation, an emerging posttranslational modification not previously implicated in infectious disease. This study provides a resource for COVID-19 researchers and, longer term, and will inform our understanding of this disease and its treatment.
Keywords	COVID-19 ; proteomics ; peptidomics ; posttranslational modifications ; arginylation ; Biology (General) ; QH301-705.5
Subject code	610
Language	English
Publishing date	2022-02-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Different translation dynamics of β- and γ-actin regulates cell migration.

Vedula, Pavan / Kurosaka, Satoshi / MacTaggart, Brittany / Ni, Qin / Papoian, Garegin / Jiang, Yi / Dong, Dawei W / Kashina, Anna

eLife

2021 Volume 10

Abstract: β- and γ-cytoplasmic actins are ubiquitously expressed in every cell type and are nearly identical at the amino acid level but play vastly different roles in vivo. Their essential roles in embryogenesis and mesenchymal cell migration critically depend on ...

Abstract	β- and γ-cytoplasmic actins are ubiquitously expressed in every cell type and are nearly identical at the amino acid level but play vastly different roles in vivo. Their essential roles in embryogenesis and mesenchymal cell migration critically depend on the nucleotide sequences of their genes, rather than their amino acid sequences; however, it is unclear which gene elements underlie this effect. Here we address the specific role of the coding sequence in β- and γ-cytoplasmic actins' intracellular functions, using stable polyclonal populations of immortalized mouse embryonic fibroblasts with exogenously expressed actin isoforms and their 'codon-switched' variants. When targeted to the cell periphery using β-actin 3'UTR; β-actin and γ-actin have differential effects on cell migration. These effects directly depend on the coding sequence. Single-molecule measurements of actin isoform translation, combined with fluorescence recovery after photobleaching, demonstrate a pronounced difference in β- and γ-actins' translation elongation rates in cells, leading to changes in their dynamics at focal adhesions, impairments in actin bundle formation, and reduced cell anchoring to the substrate during migration. Our results demonstrate that coding sequence-mediated differences in actin translation play a key role in cell migration.
MeSH term(s)	Actins/genetics ; Actins/metabolism ; Amino Acid Substitution ; Animals ; Base Sequence ; Cell Movement/physiology ; Focal Adhesions ; Gene Expression Regulation ; Mice ; Protein Biosynthesis/physiology ; Protein Isoforms ; RNA, Messenger/genetics ; RNA, Messenger/metabolism
Chemical Substances	Actins ; Protein Isoforms ; RNA, Messenger
Language	English
Publishing date	2021-06-24
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.68712
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Article ; Online: Protein Posttranslational Signatures Identified in COVID-19 Patient Plasma

Vedula, Pavan / Tang, Hsin-Yao / UPenn COVID Processing Unit / Speicher, David / Kashina, Anna

bioRxiv

Abstract	Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a highly contagious virus of the coronavirus family that causes coronavirus disease-19 (COVID-19) in humans and a number of animal species. COVID-19 has rapidly propagated in the world in the past 2 years, causing a global pandemic. Here, we performed proteomic analysis of plasma samples from COVID-19 patients compared to healthy control donors in an exploratory study to gain insights into protein-level changes in the patients caused by SARS-CoV-2 infection and to identify potential proteomic and posttranslational signatures of this disease. Our results suggest a global change in protein processing and regulation that occurs in response to SARS-CoV-2, and the existence of a posttranslational COVID-19 signature that includes an elevation in threonine phosphorylation, a change in glycosylation, and a decrease in arginylation, an emerging posttranslational modification not previously implicated in infectious disease. This study provides a resource for COVID-19 researchers and, longer term, will inform our understanding of this disease and its treatment.
Keywords	covid19
Language	English
Publishing date	2021-12-16
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2021.12.15.472822
Database	COVID19

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Article ; Online: A new mechanism of fibronectin fibril assembly revealed by live imaging and super-resolution microscopy.

Tomer, Darshika / Arriagada, Cecilia / Munshi, Sudipto / Alexander, Brianna E / French, Brenda / Vedula, Pavan / Caorsi, Valentina / House, Andrew / Guvendiren, Murat / Kashina, Anna / Schwarzbauer, Jean E / Astrof, Sophie

Journal of cell science

2022 Volume 135, Issue 16

Abstract: Fibronectin (Fn1) fibrils have long been viewed as continuous fibers composed of extended, periodically aligned Fn1 molecules. However, our live-imaging and single-molecule localization microscopy data are inconsistent with this traditional view and show ...

Abstract	Fibronectin (Fn1) fibrils have long been viewed as continuous fibers composed of extended, periodically aligned Fn1 molecules. However, our live-imaging and single-molecule localization microscopy data are inconsistent with this traditional view and show that Fn1 fibrils are composed of roughly spherical nanodomains containing six to eleven Fn1 dimers. As they move toward the cell center, Fn1 nanodomains become organized into linear arrays, in which nanodomains are spaced with an average periodicity of 105±17 nm. Periodical Fn1 nanodomain arrays can be visualized between cells in culture and within tissues; they are resistant to deoxycholate treatment and retain nanodomain periodicity in the absence of cells. The nanodomain periodicity in fibrils remained constant when probed with antibodies recognizing distinct Fn1 epitopes or combinations of antibodies recognizing epitopes spanning the length of Fn1. Treatment with FUD, a peptide that binds the Fn1 N-terminus and disrupts Fn1 fibrillogenesis, blocked the organization of Fn1 nanodomains into periodical arrays. These studies establish a new paradigm of Fn1 fibrillogenesis. This article has an associated First Person interview with the first author of the paper.
MeSH term(s)	Epitopes ; Extracellular Matrix/metabolism ; Fibronectins/metabolism ; Microscopy ; Peptides/metabolism
Chemical Substances	Epitopes ; Fibronectins ; Peptides
Language	English
Publishing date	2022-08-25
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2993-2
ISSN	1477-9137 ; 0021-9533
ISSN (online)	1477-9137
ISSN	0021-9533
DOI	10.1242/jcs.260120
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