scholarly journals Gene 33/Mig6/ERRFI1, an Adapter Protein with Complex Functions in Cell Biology and Human Diseases

Cells ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1574
Author(s):  
Dazhong Xu ◽  
Cen Li
Keyword(s):  
Cell Biology ◽  
Research Progress ◽  
Cellular Functions ◽  
Protein Protein Interaction ◽  
Calculated Molecular Weight ◽  
New Findings ◽  
Complex Functions ◽  
Associated Functions ◽  
Multiple Cell ◽  
Multiple Domains

Gene 33 (also named Mig6, RALT, and ERRFI1) is an adapter/scaffold protein with a calculated molecular weight of about 50 kD. It contains multiple domains known to mediate protein–protein interaction, suggesting that it has the potential to interact with many cellular partners and have multiple cellular functions. The research over the last two decades has confirmed that it indeed regulates multiple cell signaling pathways and is involved in many pathophysiological processes. Gene 33 has long been viewed as an exclusively cytosolic protein. However, recent evidence suggests that it also has nuclear and chromatin-associated functions. These new findings highlight a significantly broader functional spectrum of this protein. In this review, we will discuss the function and regulation of Gene 33, as well as its association with human pathophysiological conditions in light of the recent research progress on this protein.

Illuminating Cellular Physiology: Recent Developments

2007 ◽  
Vol 90 (2-3) ◽  
pp. 129-160 ◽  
Author(s):  
Lubov Y. Brovko ◽  
Mansel W. Griffiths
Keyword(s):  
Protein Trafficking ◽  
Cell Biology ◽  
Translational Regulation ◽  
Cellular Functions ◽  
Protein Protein Interaction ◽  
Target Drug ◽  
Signal Transduction Protein ◽  
Recent Developments

Bioluminescent methods are gaining more and more attention among scientists due to their sensitivity, selectivity and simplicity; coupled with the fact that the bioluminescence can be monitored both in vitro and in vivo. Since the discovery of bioluminescence in the 19th century, enzymes involved in the bioluminescent process have been isolated and cloned. The bioluminescent reactions in several different organisms have also been fully characterized and used as reporters in a wide variety of biochemical assays. From the 1990s it became clear that bioluminescence can be detected and quantified directly from inside a living cell. This gave rise to numerous possibilities for the in vivo monitoring of intracellular processes non-invasively using bioluminescent molecules as reporters. This review describes recent developments in the area of bioluminescent imaging for cell biology. Newly developed imaging methods allow transcriptional/translational regulation, signal transduction, protein–protein interaction, oncogenic transformation, cell and protein trafficking, and target drug action to be monitored in vivo in real-time with high temporal and spatial resolution; thus providing researchers with priceless information on cellular functions. Advantages and limitations of these novel bioluminescent methods are discussed and possible future developments identified.

Analysis of Protein-Protein Interaction Networks through Computational Approaches

2020 ◽  
Vol 27 (4) ◽  
pp. 265-278 ◽  
Author(s):  
Ying Han ◽  
Liang Cheng ◽  
Weiju Sun
Keyword(s):  
Protein Interaction ◽  
Biological Networks ◽  
Interaction Networks ◽  
Computational Techniques ◽  
Cellular Functions ◽  
Protein Protein Interaction ◽  
Comprehensive Information ◽  
Protein Interaction Prediction ◽  
Or Gene ◽  
Experimental Findings

The interactions among proteins and genes are extremely important for cellular functions. Molecular interactions at protein or gene levels can be used to construct interaction networks in which the interacting species are categorized based on direct interactions or functional similarities. Compared with the limited experimental techniques, various computational tools make it possible to analyze, filter, and combine the interaction data to get comprehensive information about the biological pathways. By the efficient way of integrating experimental findings in discovering PPIs and computational techniques for prediction, the researchers have been able to gain many valuable data on PPIs, including some advanced databases. Moreover, many useful tools and visualization programs enable the researchers to establish, annotate, and analyze biological networks. We here review and list the computational methods, databases, and tools for protein−protein interaction prediction.

scholarly journals Model-guided design of mammalian genetic programs

2021 ◽  
Vol 7 (8) ◽  
pp. eabe9375
Author(s):  
J. J. Muldoon ◽  
V. Kandula ◽  
M. Hong ◽  
P. S. Donahue ◽  
J. D. Boucher ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Computational Models ◽  
Biological Complexity ◽  
Genetic Circuits ◽  
Cellular Functions ◽  
High Performing ◽  
Design Objective ◽  
Complex Functions ◽  
Mammalian Genetic ◽  
Analog Processing

Genetically engineering cells to perform customizable functions is an emerging frontier with numerous technological and translational applications. However, it remains challenging to systematically engineer mammalian cells to execute complex functions. To address this need, we developed a method enabling accurate genetic program design using high-performing genetic parts and predictive computational models. We built multifunctional proteins integrating both transcriptional and posttranslational control, validated models for describing these mechanisms, implemented digital and analog processing, and effectively linked genetic circuits with sensors for multi-input evaluations. The functional modularity and compositional versatility of these parts enable one to satisfy a given design objective via multiple synonymous programs. Our approach empowers bioengineers to predictively design mammalian cellular functions that perform as expected even at high levels of biological complexity.

scholarly journals Update on Giardia: Highlights from the seventh International Giardia and Cryptosporidium Conference

Parasite ◽  
2020 ◽  
Vol 27 ◽  
pp. 49 ◽  
Author(s):  
André G. Buret ◽  
Simone M. Cacciò ◽  
Loïc Favennec ◽  
Staffan Svärd
Keyword(s):  
Cell Biology ◽  
Health Management ◽  
Giardia Duodenalis ◽  
Basic Research ◽  
Basic Knowledge ◽  
Future Research ◽  
World Knowledge ◽  
Main Research ◽  
Research Perspectives ◽  
New Findings

Although Giardia duodenalis is recognized as one of the leading causes of parasitic human diarrhea in the world, knowledge of the mechanisms of infection is limited, as the pathophysiological consequences of infection remain incompletely elucidated. Similarly, the reason for and consequences of the very specific genome-organization in this parasite with 2 active nuclei is only partially known. Consistent with its tradition, the 7th International Giardia and Cryptosporidium Conference (IGCC 2019) was held from June 23 to 26, 2019, at the Faculty of Medicine and Pharmacy of the University of Rouen-Normandie, France, to discuss current research perspectives in the field. This renowned event brought together an international delegation of researchers to present and debate recent advances and identify the main research themes and knowledge gaps. The program for this interdisciplinary conference included all aspects of host-parasite relationships, from basic research to applications in human and veterinary medicine, as well as the environmental issues raised by water-borne parasites and their epidemiological consequences. With regard to Giardia and giardiasis, the main areas of research for which new findings and the most impressive communications were presented and discussed included: parasite ecology and epidemiology of giardiasis, Giardia-host interactions, and cell biology of Giardia, genomes and genomic evolution. The high-quality presentations discussed at the Conference noted breakthroughs and identified new opportunities that will inspire researchers and funding agencies to stimulate future research in a “one health” approach to improve basic knowledge and clinical and public health management of zoonotic giardiasis.

scholarly journals A journey from reductionist to systemic cell biology aboard the schooner Tara

2012 ◽  
Vol 23 (13) ◽  
pp. 2403-2406 ◽  
Author(s):  
Eric Karsenti
Keyword(s):  
Complex Systems ◽  
Molecular Interactions ◽  
Cell Biology ◽  
Statistical Physics ◽  
Interaction Networks ◽  
Cellular Functions ◽  
Personal Journey ◽  
New Approaches ◽  
The World ◽  
The Way

In this essay I describe my personal journey from reductionist to systems cell biology and describe how this in turn led to a 3-year sea voyage to explore complex ocean communities. In describing this journey, I hope to convey some important principles that I gleaned along the way. I realized that cellular functions emerge from multiple molecular interactions and that new approaches borrowed from statistical physics are required to understand the emergence of such complex systems. Then I wondered how such interaction networks developed during evolution. Because life first evolved in the oceans, it became a natural thing to start looking at the small organisms that compose the plankton in the world's oceans, of which 98% are … individual cells—hence the Tara Oceans voyage, which finished on 31 March 2012 in Lorient, France, after a 60,000-mile around-the-world journey that collected more than 30,000 samples from 153 sampling stations.

PI(4,5)P2 Clustering and Its Impact on Biological Functions

2021 ◽  
Vol 90 (1) ◽  
Author(s):  
Yi Wen ◽  
Volker M. Vogt ◽  
Gerald W. Feigenson
Keyword(s):  
Plasma Membrane ◽  
Cell Biology ◽  
Cellular Proteins ◽  
Annual Review ◽  
Publication Date ◽  
Biological Functions ◽  
Cellular Functions ◽  
Dynamic Distribution ◽  
Multivalent Cation ◽  
Lipid Environment

Located at the inner leaflet of the plasma membrane, phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] comprises only 1–2 mol% of total PM lipids. With its synthesis and turnover both spatially and temporally regulated, PI(4,5)P2 recruits and interacts with hundreds of cellular proteins to support a broad spectrum of cellular functions. Several factors contribute to the versatile and dynamic distribution of PI(4,5)P2 in membranes. Physiological multivalent cations such as Ca2+ and Mg2+ can bridge between PI(4,5)P2 headgroups, forming nanoscopic PI(4,5)P2–cation clusters. The distinct lipid environment surrounding PI(4,5)P2 affects the degree of PI(4,5)P2 clustering. In addition, diverse cellular proteins interacting with PI(4,5)P2 can further regulate PI(4,5)P2 lateral distribution and accessibility. This review summarizes the current understanding of PI(4,5)P2 behavior in both cells and model membranes, with emphasis on both multivalent cation– and protein-induced PI(4,5)P2 clustering. Understanding the nature of spatially separated pools of PI(4,5)P2 is fundamental to cell biology. Expected final online publication date for the Annual Review of Biochemistry, Volume 90 is June 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Allosteric changes in HDM2 by the ATM phosphomimetic S395D mutation: implications on HDM2 function

2019 ◽  
Vol 476 (21) ◽  
pp. 3401-3411 ◽  
Author(s):  
Lukas Uhrik ◽  
Lixiao Wang ◽  
Lucia Haronikova ◽  
Ixaura Medina-Medina ◽  
Yolanda Rebolloso-Gomez ◽  
...  
Keyword(s):  
Ataxia Telangiectasia ◽  
P53 Protein ◽  
Intrinsic Disorder ◽  
26S Proteasome ◽  
Ataxia Telangiectasia Mutated ◽  
Cellular Functions ◽  
Post Translational Modifications ◽  
Protein Protein Interaction ◽  
Positive Regulator ◽  
P53 Mrna

Allosteric changes imposed by post-translational modifications regulate and differentiate the functions of proteins with intrinsic disorder regions. HDM2 is a hub protein with a large interactome and with different cellular functions. It is best known for its regulation of the p53 tumour suppressor. Under normal cellular conditions, HDM2 ubiquitinates and degrades p53 by the 26S proteasome but after DNA damage, HDM2 switches from a negative to a positive regulator of p53 by binding to p53 mRNA to promote translation of the p53 mRNA. This change in activity is governed by the ataxia telangiectasia mutated kinase via phosphorylation on serine 395 and is mimicked by the S395D phosphomimetic mutant. Here we have used different approaches to show that this event is accompanied by a specific change in the HDM2 structure that affects the HDM2 interactome, such as the N-termini HDM2–p53 protein–protein interaction. These data will give a better understanding of how HDM2 switches from a negative to a positive regulator of p53 and gain new insights into the control of the HDM2 structure and its interactome under different cellular conditions and help identify interphases as potential targets for new drug developments.

scholarly journals Publication Trends on Mitophagy in the World and China: A 16-Year Bibliometric Analysis

2021 ◽  
Vol 9 ◽  
Author(s):  
Jingli Chen ◽  
Xin Li ◽  
Yifan Jia ◽  
Zhongyuan Xia ◽  
Jishi Ye
Keyword(s):  
Bibliometric Analysis ◽  
Cell Biology ◽  
Developed Countries ◽  
The United States ◽  
Research Progress ◽  
Publication Trends ◽  
Quality Of Results ◽  
The Past ◽  
The World

In the past 16 years, research on mitophagy has increasingly expanded to a wider range of subjects. Therefore, comprehensively analyzing the relevant progress and development trends on mitophagy research requires specific methods. To assess the hotspots, directions, and quality of results in this field worldwide, we used multiple tools to examine research progress and growing trends in research on the matter during the last 16 years (from 2005 to 2020). We also compared the quantity and quality of the literature records on mitophagy published by research institutions in China and other developed countries, reviewed China’s contribution, and examined the gap between China and these developed countries. According to the results of our bibliometric analysis, the United States and its research institutes published the most papers. We identified cell biology as the most commonly researched subject on mitophagy and AUTOPHAGY as the most popular journal for research on mitophagy. We also listed the most cited documents from around the world and China. With gradually increased funding, China is progressively becoming prominent in the field of mitophagy; nevertheless, the gap between her and major countries in the world must be closed.

scholarly journals Cytochemical methods for the localization of adenylate cyclase. A review and evaluation of the efficacy of the procedures.

1983 ◽  
Vol 31 (1) ◽  
pp. 85-93 ◽  
Author(s):  
L S Cutler
Keyword(s):  
Adenylate Cyclase ◽  
Cyclic Nucleotides ◽  
Cell Biology ◽  
Enzyme System ◽  
Cyclic Adenosine Monophosphate ◽  
Adenosine Monophosphate ◽  
Cellular Functions ◽  
Cytochemical Localization ◽  
Biochemical Evaluation

The cytochemical procedures for localizing adenylate cyclase have been a source of controversy since their introduction. The importance of cyclic adenosine monophosphate (AMP), the product of adenylate cyclase's action on adenosine triphosphate (ATP), in cell biology is clear. Thus, the ability to localize this enzyme system reliably is an important tool in the study of various cellular functions. This report reviews the literature and presents a biochemical evaluation of the methods for localizing adenylate cyclase. The review and data presented serve to clarify many of the controversies surrounding this important cytochemical procedure. It is evident that although there are problems associated with localizing the enzyme, several valid procedures are currently available for the cytochemical localization of adenylate cyclase. In using these procedures, the effects of fixation and the capture agent on adenylate cyclase activity in the particular tissue being studied should be considered. Only repurified adenylyl imidodiphosphate [App(NH)p] should be used in the incubation medium. If care is taken, the use of these techniques can be of great value in the continued study of the role of cyclic nucleotides in cell biology.

scholarly journals Eukaryotic systems broaden the scope of synthetic biology

2009 ◽  
Vol 187 (5) ◽  
pp. 589-596 ◽  
Author(s):  
Karmella A. Haynes ◽  
Pamela A. Silver
Keyword(s):  
Synthetic Biology ◽  
Nucleic Acids ◽  
Cell Biology ◽  
Cell Behavior ◽  
Cellular Functions ◽  
Complex Cells ◽  
Cellular Processes ◽  
Challenges And Opportunities ◽  
Foundational Work ◽  
Biology Research

Synthetic biology aims to engineer novel cellular functions by assembling well-characterized molecular parts (i.e., nucleic acids and proteins) into biological “devices” that exhibit predictable behavior. Recently, efforts in eukaryotic synthetic biology have sprung from foundational work in bacteria. Designing synthetic circuits to operate reliably in the context of differentiating and morphologically complex cells presents unique challenges and opportunities for progress in the field. This review surveys recent advances in eukaryotic synthetic biology and describes how synthetic systems can be linked to natural cellular processes in order to manipulate cell behavior and to foster new discoveries in cell biology research.

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