Phytochrome Signaling Networks

2021 ◽  
Vol 72 (1) ◽  
Author(s):  
Mei-Chun Cheng ◽  
Praveen Kumar Kathare ◽  
Inyup Paik ◽  
Enamul Huq
Keyword(s):  
Protein Interactions ◽  
Translational Regulation ◽  
Regulatory Networks ◽  
Annual Review ◽  
Publication Date ◽  
Protein Protein Interactions ◽  
Conformational Switching ◽  
E3 Ligases ◽  
Almost All

The perception of light signals by the phytochrome family of photoreceptors has a crucial influence on almost all aspects of growth and development throughout a plant's life cycle. The holistic regulatory networks orchestrated by phytochromes, including conformational switching, subcellular localization, direct protein-protein interactions, transcriptional and posttranscriptional regulations, and translational and posttranslational controls to promote photomorphogenesis, are highly coordinated and regulated at multiple levels. During the past decade, advances using innovative approaches have substantially broadened our understanding of the sophisticated mechanisms underlying the phytochrome-mediated light signaling pathways. This review discusses and summarizes these discoveries of the role of the modular structure of phytochromes, phytochrome-interacting proteins, and their functions; the reciprocal modulation of both positive and negative regulators in phytochrome signaling; the regulatory roles of phytochromes in transcriptional activities, alternative splicing, and translational regulation; and the kinases and E3 ligases that modulate PHYTOCHROME INTERACTING FACTORs to optimize photomorphogenesis. Expected final online publication date for the Annual Review of Plant Biology, Volume 72 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Small-Molecule Approaches to Targeted Protein Degradation

2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Tyler B. Faust ◽  
Katherine A. Donovan ◽  
Hong Yue ◽  
Philip P. Chamberlain ◽  
Eric S. Fischer
Keyword(s):  
Protein Degradation ◽  
Protein Interactions ◽  
Cancer Biology ◽  
Ubiquitin Ligases ◽  
Ubiquitin Proteasome System ◽  
Annual Review ◽  
Publication Date ◽  
Protein Protein Interactions ◽  
Rate Limiting Step ◽  
Ubiquitin Proteasome

Many essential biological processes are regulated through proximity, from membrane receptor signaling to transcriptional activity. The ubiquitin-proteasome system controls protein degradation, with ubiquitin ligases as the rate-limiting step. Ubiquitin ligases are commonly controlled at the level of substrate recruitment and, therefore, by proximity. There are natural and synthetic small molecules that also operate through induced proximity. For example, thalidomide is effective in treating multiple myeloma and functions as a molecular glue that stabilizes novel protein-protein interactions between a ubiquitin ligase and proteins not otherwise targeted by the ligase, leading to neo-substrate degradation. Emerging data on new degrader molecules have uncovered diverse mechanisms distinct from molecular glues, which often mirror the regulatory mechanisms that control substrate-ligase proximity in nature. In this review, we summarize our current understanding of biological and synthetic regulation of protein degradation and share our view on how these diverse mechanisms have inspired novel therapeutic directions. Expected final online publication date for the Annual Review of Cancer Biology, Volume 5 is March 4, 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Quantitative Temporal Viromics

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Alice Fletcher-Etherington ◽  
Michael P. Weekes
Keyword(s):  
Mass Spectrometry ◽  
Virus Infection ◽  
Protein Interactions ◽  
Time Course ◽  
Annual Review ◽  
Publication Date ◽  
Tandem Mass ◽  
Protein Protein Interactions ◽  
Comprehensive Understanding ◽  
Tandem Mass Tags

The abundance, localization, modifications, and protein-protein interactions of many host cell and virus proteins can change dynamically throughout the course of any viral infection. Studying these changes is critical for a comprehensive understanding of how viruses replicate and cause disease, as well as for the development of antiviral therapeutics and vaccines. Previously, we developed a mass spectrometry–based technique called quantitative temporal viromics (QTV), which employs isobaric tandem mass tags (TMTs) to allow precise comparative quantification of host and virus proteomes through a whole time course of infection. In this review, we discuss the utility and applications of QTV, exemplified by numerous studies that have since used proteomics with a variety of quantitative techniques to study virus infection through time. Expected final online publication date for the Annual Review of Virology, Volume 8 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Algorithmic and Stochastic Representations of Gene Regulatory Networks and Protein-Protein Interactions

2019 ◽  
Vol 19 (6) ◽  
pp. 413-425 ◽  
Author(s):  
Athanasios Alexiou ◽  
Stylianos Chatzichronis ◽  
Asma Perveen ◽  
Abdul Hafeez ◽  
Ghulam Md. Ashraf
Keyword(s):  
Protein Interactions ◽  
Biological Networks ◽  
Regulatory Networks ◽  
Review Paper ◽  
Boolean Networks ◽  
Diagnostic Tools ◽  
Complex Nature ◽  
Cellular Interactions ◽  
Protein Protein Interactions ◽  
Deterministic Models

Background:Latest studies reveal the importance of Protein-Protein interactions on physiologic functions and biological structures. Several stochastic and algorithmic methods have been published until now, for the modeling of the complex nature of the biological systems.Objective:Biological Networks computational modeling is still a challenging task. The formulation of the complex cellular interactions is a research field of great interest. In this review paper, several computational methods for the modeling of GRN and PPI are presented analytically.Methods:Several well-known GRN and PPI models are presented and discussed in this review study such as: Graphs representation, Boolean Networks, Generalized Logical Networks, Bayesian Networks, Relevance Networks, Graphical Gaussian models, Weight Matrices, Reverse Engineering Approach, Evolutionary Algorithms, Forward Modeling Approach, Deterministic models, Static models, Hybrid models, Stochastic models, Petri Nets, BioAmbients calculus and Differential Equations.Results:GRN and PPI methods have been already applied in various clinical processes with potential positive results, establishing promising diagnostic tools.Conclusion:In literature many stochastic algorithms are focused in the simulation, analysis and visualization of the various biological networks and their dynamics interactions, which are referred and described in depth in this review paper.

scholarly journals Interactome Analysis of KIN (Kin17) Shows New Functions of This Protein

2021 ◽  
Vol 43 (2) ◽  
pp. 767-781
Author(s):  
Vanessa Pinatto Gaspar ◽  
Anelise Cardoso Ramos ◽  
Philippe Cloutier ◽  
José Renato Pattaro Junior ◽  
Francisco Ferreira Duarte Junior ◽  
...  
Keyword(s):  
Dna Replication ◽  
Protein Interactions ◽  
Ribosome Biogenesis ◽  
Cell Metabolism ◽  
Cell Types ◽  
Protein Protein Interactions ◽  
Cellular Mechanisms ◽  
Cancerous Cell ◽  
First Time

KIN (Kin17) protein is overexpressed in a number of cancerous cell lines, and is therefore considered a possible cancer biomarker. It is a well-conserved protein across eukaryotes and is ubiquitously expressed in all cell types studied, suggesting an important role in the maintenance of basic cellular function which is yet to be well determined. Early studies on KIN suggested that this nuclear protein plays a role in cellular mechanisms such as DNA replication and/or repair; however, its association with chromatin depends on its methylation state. In order to provide a better understanding of the cellular role of this protein, we investigated its interactome by proximity-dependent biotin identification coupled to mass spectrometry (BioID-MS), used for identification of protein–protein interactions. Our analyses detected interaction with a novel set of proteins and reinforced previous observations linking KIN to factors involved in RNA processing, notably pre-mRNA splicing and ribosome biogenesis. However, little evidence supports that this protein is directly coupled to DNA replication and/or repair processes, as previously suggested. Furthermore, a novel interaction was observed with PRMT7 (protein arginine methyltransferase 7) and we demonstrated that KIN is modified by this enzyme. This interactome analysis indicates that KIN is associated with several cell metabolism functions, and shows for the first time an association with ribosome biogenesis, suggesting that KIN is likely a moonlight protein.

Structure, Function, Involvement in Diseases and Targeting of 14-3-3 Proteins: An Update

2018 ◽  
Vol 25 (1) ◽  
pp. 5-21 ◽  
Author(s):  
Ylenia Cau ◽  
Daniela Valensin ◽  
Mattia Mori ◽  
Sara Draghi ◽  
Maurizio Botta
Keyword(s):  
Protein Interactions ◽  
Molecular Mechanisms ◽  
Physiological Role ◽  
Specific Protein ◽  
Protein Protein Interactions ◽  
Cellular Processes ◽  
Protein Partners ◽  
High Sequence Homology ◽  
Small Molecule Modulators

14-3-3 is a class of proteins able to interact with a multitude of targets by establishing protein-protein interactions (PPIs). They are usually found in all eukaryotes with a conserved secondary structure and high sequence homology among species. 14-3-3 proteins are involved in many physiological and pathological cellular processes either by triggering or interfering with the activity of specific protein partners. In the last years, the scientific community has collected many evidences on the role played by seven human 14-3-3 isoforms in cancer or neurodegenerative diseases. Indeed, these proteins regulate the molecular mechanisms associated to these diseases by interacting with (i) oncogenic and (ii) pro-apoptotic proteins and (iii) with proteins involved in Parkinson and Alzheimer diseases. The discovery of small molecule modulators of 14-3-3 PPIs could facilitate complete understanding of the physiological role of these proteins, and might offer valuable therapeutic approaches for these critical pathological states.

scholarly journals Investigating the Role of Large-Scale Domain Dynamics in Protein-Protein Interactions

2016 ◽  
Vol 3 ◽  
Author(s):  
Elise Delaforge ◽  
Sigrid Milles ◽  
Jie-rong Huang ◽  
Denis Bouvier ◽  
Malene Ringkjøbing Jensen ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Large Scale ◽  
Protein Protein Interactions ◽  
Domain Dynamics

New Directions in the Study of Institutional Logics: From Tools to Phenomena

2021 ◽  
Vol 47 (1) ◽  
Author(s):  
Michael Lounsbury ◽  
Christopher W.J. Steele ◽  
Milo Shaoqing Wang ◽  
Madeline Toubiana
Keyword(s):  
Recent Work ◽  
Online Publication ◽  
Institutional Logics ◽  
Annual Review ◽  
Publication Date ◽  
Complex Dynamic ◽  
New Directions ◽  
Analytical Tools ◽  
Dynamic Phenomena

In this article, we take stock of the institutional logics perspective and highlight opportunities for new scholarship. While we celebrate the growth and generativity of the literature on institutional logics, we also note that there has been a troubling tendency in recent work to use logics as analytical tools, feeding disquiet about reification and reductionism. Seeding a broader scholarly agenda that addresses such weaknesses in the literature, we highlight nascent efforts that aim to more systematically understand institutional logics as complex, dynamic phenomena in their own right. In doing so, we argue for more research that probes how logics cohere and endure by unpacking the role of values, the centrality of practice, and the governance dynamics of institutional logics and their orders. Furthermore, we encourage bridging the study of institutional logics with various literatures, including ethnomethodology, phenomenology, professions, elites, world society, and the old institutionalism, to enhance progress in these directions. Expected final online publication date for the Annual Review of Sociology, Volume 47 is July 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

The Role of Citizen Science in Promoting Health Equity

2021 ◽  
Vol 43 (1) ◽  
Author(s):  
Lisa G. Rosas ◽  
Patricia Rodriguez Espinosa ◽  
Felipe Montes Jimenez ◽  
Abby C. King
Keyword(s):  
Public Health ◽  
Citizen Science ◽  
Health Equity ◽  
Healthy Eating ◽  
Mobile Applications ◽  
Health Inequities ◽  
Annual Review ◽  
Publication Date ◽  
Scientific Process

While there are many definitions of citizen science, the term usually refers to the participation of the general public in the scientific process in collaboration with professional scientists. Citizen scientists have been engaged to promote health equity, especially in the areas of environmental contaminant exposures, physical activity, and healthy eating. Citizen scientists commonly come from communities experiencing health inequities and have collected data using a range of strategies and technologies, such as air sensors, water quality kits, and mobile applications. On the basis of our review, and to advance the field of citizen science to address health equity, we recommend ( a) expanding the focus on topics important for health equity, ( b) increasing the diversity of people serving as citizen scientists, ( c) increasing the integration of citizen scientists in additional research phases, ( d) continuing to leverage emerging technologies that enable citizen scientists to collect data relevant for health equity, and ( e) strengthening the rigor of methods to evaluate impacts on health equity. Expected final online publication date for the Annual Review of Public Health, Volume 43 is April 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Recent Research on the Archaeology of War and Violence

2021 ◽  
Vol 50 (1) ◽  
Author(s):  
Andrew K. Scherer
Keyword(s):  
State Formation ◽  
Online Publication ◽  
General Trend ◽  
Annual Review ◽  
Publication Date ◽  
Modern Times ◽  
The Past ◽  
Definition Of ◽  
Consequences Of Violence

The mid-1990s through the first decade of the new millennium marked an increase in publications pertaining to war and violence in the ancient past. This review considers how scholars of the past decade have responded to that work. The emerging consensus is that war and violence were endemic to all societies studied by archaeologists, and yet the frequency, intensity, causes, and consequences of violence were highly variable for reasons that defy simplistic explanation. The general trend has been toward archaeologies of war and violence that focus on understanding the nuances of particular places and historical moments. Nevertheless, archaeologists continue to grapple with grand narratives of war, such as the proposition that violence has decreased from ancient to modern times and the role of war and violence in state formation and collapse. Recent research also draws attention to a more expansive definition of violence. Expected final online publication date for the Annual Review of Anthropology, Volume 50 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

The Role of the Medial Prefrontal Cortex in Moderating Neural Representations of Self and Other in Primates

2021 ◽  
Vol 44 (1) ◽  
Author(s):  
Masaki Isoda
Keyword(s):  
Prefrontal Cortex ◽  
Medial Prefrontal Cortex ◽  
Critical Role ◽  
Autism Spectrum ◽  
Annual Review ◽  
Publication Date ◽  
Self And Other ◽  
Neural Representations ◽  
The Social

As a frontal node in the primate social brain, the medial prefrontal cortex (MPFC) plays a critical role in coordinating one's own behavior with respect to that of others. Current literature demonstrates that single neurons in the MPFC encode behavior-related variables such as intentions, actions, and rewards, specifically for self and other, and that the MPFC comes into play when reflecting upon oneself and others. The social moderator account of MPFC function can explain maladaptive social cognition in people with autism spectrum disorder, which tips the balance in favor of self-centered perspectives rather than taking into consideration the perspective of others. Several strands of evidence suggest a hypothesis that the MPFC represents different other mental models, depending on the context at hand, to better predict others’ emotions and behaviors. This hypothesis also accounts for aberrant MPFC activity in autistic individuals while they are mentalizing others. Expected final online publication date for the Annual Review of Neuroscience, Volume 44 is July 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Sign in / Sign up

Export Citation Format

Share Document