Protein charge and mass contribute to the spatio-temporal dynamics of protein-protein interactions in a minimal proteome

Yu Xu; Hong Wang; Ruth Nussinov; Buyong Ma

doi:10.1002/pmic.201100540

Novel biochemical, structural and systems insights into inflammatory signaling revealed by contextual interaction proteomics

10.1101/2021.09.18.460902 ◽

2021 ◽

Author(s):

Rodolfo Ciuffa ◽

Federico Uliana ◽

Martin Mehnert ◽

Cathy Marulli ◽

Ari Satanowski ◽

...

Keyword(s):

Protein Interactions ◽

Large Scale ◽

Functional Organization ◽

Temporal Organization ◽

Protein Protein Interactions ◽

Main Mode ◽

Signaling Complex ◽

Ppi Networks ◽

Level Information ◽

Spatio Temporal

Protein-protein interactions (PPI) represent the main mode of the proteome organization in the cell. In the last decade, several large-scale representations of PPI networks have captured generic aspects of the functional organization of network components, but mostly lack the context of cellular states. However, the generation of contextual representations of PPI networks is essential for structural and systems-level modeling of biological processes and remains an unsolved challenge. In this study we describe an integrated experimental/computational strategy to achieve a contextualized modeling of PPI. This strategy defines the composition, stoichiometry, spatio-temporal organization and cellular requirements for the formation of target assemblies. We used this approach to generate an integrated model of the formation principles and architecture of a large signalosome, the TNF-receptor signaling complex (TNF-RSC). Overall, we show that the integration of systems- and structure-level information provides a generic, largely unexplored link between the modular proteome and cellular function.

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Shugoshin promotes efficient activation of spindle assembly checkpoint and timely spindle disassembly

10.1101/2020.09.04.282871 ◽

2020 ◽

Author(s):

Aakanksha Sane ◽

Shreyas Sridhar ◽

Kaustuv Sanyal ◽

Santanu K Ghosh

Keyword(s):

Protein Interactions ◽

Spindle Assembly Checkpoint ◽

Spindle Assembly ◽

Protein Protein Interactions ◽

Cellular Functions ◽

Spindle Disassembly ◽

Spatio Temporal ◽

Species Specific ◽

Chromosome Passenger Complex

AbstractShugoshin proteins are evolutionary conserved across eukaryotes with some species-specific cellular functions ensuring the fidelity of chromosome segregation. Shugoshin being present at various subcellular locales, acts as an adaptor to mediate various protein-protein interactions in a spatio-temporal manner. Here, we characterize shugoshin (Sgo1) in the human fungal pathogen, Candida albicans. Interestingly, we discover a novel in vivo localization of Sgo1 along the length of the mitotic spindle. Further, Sgo1 performs a hitherto unknown function of facilitating timely disassembly of spindle in this organism. We observe that Sgo1 retains its centromeric localization and performs its conserved functions that include regulating the centromeric condensin localization, chromosome passenger complex (CPC) maintenance and sister chromatid biorientation. We identify novel roles of Sgo1 as a spindle assembly checkpoint (SAC) component with functions in maintaining the SAC proteins, Mad2 and Bub1, at the kinetochores, in response to faulty kinetochore-microtubule attachments. These findings provide an excellent evidence of the functional rewiring of shugoshin in maintaining genomic stability.

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Dissection of the Spindle Assembly Checkpoint by Proximity Proteomics

10.1101/2020.06.04.133710 ◽

2020 ◽

Author(s):

Yenni A. Garcia ◽

Erick F. Velasquez ◽

Lucy W. Gao ◽

Keith Cheung ◽

Kevin M. Clutario ◽

...

Keyword(s):

Protein Interactions ◽

Posttranslational Modifications ◽

Spindle Assembly Checkpoint ◽

Protein Complexes ◽

Spindle Assembly ◽

Protein Protein Interactions ◽

Proteomic Approach ◽

Multiple Protein ◽

Spatio Temporal ◽

Insight Into

SUMMARYThe spindle assembly checkpoint (SAC) is critical for sensing defective microtubule-kinetochore attachments and tension across the kinetochore and functions to arrest cells in prometaphase to allow time to repair any errors prior to proceeding into anaphase. The SAC has a central role in ensuring the fidelity of chromosome segregation and its dysregulation has been linked to the development of human diseases like cancer. The establishment and maintenance of the SAC relies on multiple protein complexes that are intricately regulated in a spatial and temporal manner through posttranslational modifications like phosphorylation. Over the past few decades the SAC has been highly investigated and much has been learned about its protein constituents and the pathways and factors that regulate its activity. However, the spatio-temporal proximity associations of the core SAC components have not been explored in a systematic manner. Here, we have taken a BioID2 proximity-labeling proteomic approach to define the proximity protein environment for each of the five core SAC proteins BUB1, BUB3, BUBR1, MAD1L1, and MAD2L1 under conditions where the SAC is active in prometaphase. These five protein association maps were integrated to generate the SAC proximity protein network that contains multiple layers of information related to core SAC protein complexes, protein-protein interactions, and proximity associations. Our analysis validated many of the known SAC complexes and protein-protein interactions. Additionally, it uncovered new protein associations that lend insight into the functioning of the SAC and highlighted future areas that should be investigated to generate a comprehensive understanding of the SAC.

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An interaction map of transcription factors controlling gynoecium development in Arabidopsis

10.1101/500736 ◽

2018 ◽

Author(s):

Humberto Herrera-Ubaldo ◽

Sergio E. Campos ◽

Valentin Luna Garcia ◽

Victor M. Zuniga-Mayo ◽

Gerardo Armas-Caballero ◽

...

Keyword(s):

Transcription Factors ◽

Protein Interactions ◽

Specific Interaction ◽

Protein Protein Interactions ◽

Cytokinin Signaling ◽

Reproductive Unit ◽

Reproductive Part ◽

Spatio Temporal ◽

Interaction Map ◽

Gynoecium Development

Flowers are composed of different organs, whose identity is defined at the molecular by the combinatorial activity of transcription factors (TFs). MADS-box TFs interact forming complexes that have been schematized in the quartet model. The gynoecium is the female reproductive part in the flower, crucial for plant reproduction, and fruit and seed production. Once carpel identity is established, a gynoecium containing many tissues arises. Several TFs have been identified as regulators of gynoecium development, and some of these TFs form complexes. However, broad knowledge about the interactions among these TFs is still scarce. In this work, we used a systems biology approach to understand the formation of a complex reproductive unit as the gynoecium by mapping binary interactions between well-characterized TFs. We analyzed over 3500 combinations and detected more than 200 protein-protein interactions (PPIs), resulting in a process specific interaction map. Topological analyses suggest hidden functions and novel roles for many TFs. Furthermore, a relationship between TFs involved in auxin and cytokinin signaling pathways and other TFs was observed. We analyzed the network by combining PPI data, expression and genetic data, allowing us to dissect it into several dynamic spatio-temporal sub-networks related to gynoecium development subprocesses.

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LUCIFERASES FOR THE STUDY OF PROTEIN–PROTEIN INTERACTIONS IN LIVE CELLS AND ANIMALS

Nano LIFE ◽

10.1142/s1793984410000079 ◽

2010 ◽

Vol 01 (01n02) ◽

pp. 79-87 ◽

Cited By ~ 3

Author(s):

A. K. M. KAFI ◽

MITSURU HATTORI ◽

TAKEAKI OZAWA

Keyword(s):

Transcriptional Regulation ◽

Protein Interactions ◽

Protein Modification ◽

Specific Protein ◽

Live Cells ◽

Protein Protein Interactions ◽

Recent Developments ◽

Split Luciferase Complementation ◽

Spatio Temporal ◽

Split Luciferase

Many imaging technologies based on luminescent proteins have proven useful for detecting protein–protein interactions, tracking cells in mice, and monitoring transcriptional regulation of specific genes. Especially, novel bioluminescent proteins have advanced the study of induced protein interactions and protein modification in live cells and animals. This review focuses on recent developments of bioluminescent probes for quantitative evaluation of specific protein–protein interactions and their spatio-temporal imaging by means of split luciferase complementation techniques. From the comparison between fluorescent and bioluminescent proteins, advantages and drawbacks of the bioluminescence techniques are described.

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Tracking transcription factor mobility and interaction in Arabidopsis roots with fluorescence correlation spectroscopy

eLife ◽

10.7554/elife.14770 ◽

2016 ◽

Vol 5 ◽

Cited By ~ 40

Author(s):

Natalie M Clark ◽

Elizabeth Hinde ◽

Cara M Winter ◽

Adam P Fisher ◽

Giuseppe Crosti ◽

...

Keyword(s):

Steady State ◽

Cell Fate ◽

Protein Interactions ◽

Temporal Dynamics ◽

Quantitative Information ◽

Correlation Spectroscopy ◽

Oligomeric State ◽

Downstream Target ◽

Regulatory Processes ◽

Spatio Temporal

To understand complex regulatory processes in multicellular organisms, it is critical to be able to quantitatively analyze protein movement and protein-protein interactions in time and space. During Arabidopsis development, the intercellular movement of SHORTROOT (SHR) and subsequent interaction with its downstream target SCARECROW (SCR) control root patterning and cell fate specification. However, quantitative information about the spatio-temporal dynamics of SHR movement and SHR-SCR interaction is currently unavailable. Here, we quantify parameters including SHR mobility, oligomeric state, and association with SCR using a combination of Fluorescent Correlation Spectroscopy (FCS) techniques. We then incorporate these parameters into a mathematical model of SHR and SCR, which shows that SHR reaches a steady state in minutes, while SCR and the SHR-SCR complex reach a steady-state between 18 and 24 hr. Our model reveals the timing of SHR and SCR dynamics and allows us to understand how protein movement and protein-protein stoichiometry contribute to development.

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