scholarly journals Protein lysine crotonylation: past, present, perspective

2021 ◽  
Vol 12 (7) ◽  
Author(s):  
Gaoyue Jiang ◽  
Chunxia Li ◽  
Meng Lu ◽  
Kefeng Lu ◽  
Huihui Li
Keyword(s):  
Cross Talk ◽  
Tissue Injury ◽  
Regulatory Mechanisms ◽  
Biological Processes ◽  
Histone Proteins ◽  
Physiological Functions ◽  
Neuropsychiatric Disease ◽  
Enzymatic Mechanisms ◽  
Substrate Proteins ◽  
Tools And Methods

AbstractLysine crotonylation has been discovered in histone and non-histone proteins and found to be involved in diverse diseases and biological processes, such as neuropsychiatric disease, carcinogenesis, spermatogenesis, tissue injury, and inflammation. The unique carbon–carbon π-bond structure indicates that lysine crotonylation may use distinct regulatory mechanisms from the widely studied other types of lysine acylation. In this review, we discussed the regulation of lysine crotonylation by enzymatic and non-enzymatic mechanisms, the recognition of substrate proteins, the physiological functions of lysine crotonylation and its cross-talk with other types of modification. The tools and methods for prediction and detection of lysine crotonylation were also described.

scholarly journals Emerging multifaceted roles of BAP1 complexes in biological processes

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Aileen Patricia Szczepanski ◽  
Lu Wang
Keyword(s):  
Transcriptional Repression ◽  
Target Genes ◽  
Regulatory Mechanisms ◽  
Biological Processes ◽  
Multiprotein Complex ◽  
Downstream Target ◽  
Evolutionarily Conserved ◽  
Complex Forms ◽  
Polycomb Repressive Complex 1

AbstractHistone H2AK119 mono-ubiquitination (H2AK119Ub) is a relatively abundant histone modification, mainly catalyzed by the Polycomb Repressive Complex 1 (PRC1) to regulate Polycomb-mediated transcriptional repression of downstream target genes. Consequently, H2AK119Ub can also be dynamically reversed by the BAP1 complex, an evolutionarily conserved multiprotein complex that functions as a general transcriptional activator. In previous studies, it has been reported that the BAP1 complex consists of important biological roles in development, metabolism, and cancer. However, identifying the BAP1 complex’s regulatory mechanisms remains to be elucidated due to its various complex forms and its ability to target non-histone substrates. In this review, we will summarize recent findings that have contributed to the diverse functional role of the BAP1 complex and further discuss the potential in targeting BAP1 for therapeutic use.

scholarly journals MicroRNA biogenesis: Epigenetic modifications as another layer of complexity to the microRNA expression regulation

2017 ◽  
Vol 63 (4) ◽  
Author(s):  
Susheel Sagar Bhat ◽  
Artur Jarmolowski ◽  
Zofia Szweykowska-Kulinska
Keyword(s):  
Epigenetic Modifications ◽  
Expression Regulation ◽  
Microrna Expression ◽  
Regulatory Mechanisms ◽  
Mirna Biogenesis ◽  
Biological Processes ◽  
Critical Importance ◽  
Microrna Biogenesis ◽  
Regulatory Machinery

Since their discovery, microRNAs have led to a huge shift in our understanding of the regulation of key biological processes. The discovery of epigenetic modifications that affect microRNA expression has added another layer of complexity to the already tightly controlled regulatory machinery. The presence of N6-methyl-adenosine (m6A) mark and its critical importance in miRNA biogenesis in animals adds to our understanding of the regulatory mechanisms.

Volume Preservation: Then and Now

Physiology ◽  
1989 ◽  
Vol 4 (5) ◽  
pp. 169-172 ◽  
Author(s):  
SG Schultz
Keyword(s):  
Cell Lysis ◽  
Regulatory Mechanisms ◽  
Physiological Functions ◽  
Volume Preservation

Volume regulatory mechanisms, which evolved in Precambrian life and served to prevent cell lysis when our bacterial and invertebrate ancestors were confronted with hypotonic extracellular milieus, have been preserved in vertebrate cells but with redefined and highly sophisticated physiological functions.

The Sucrose Non-Fermenting 1-Related Protein Kinase 2 (SnRK2) Genes Are Multifaceted Players in Plant Growth, Development and Response to Environmental Stimuli

2019 ◽  
Vol 61 (2) ◽  
pp. 225-242 ◽  
Author(s):  
Xinguo Mao ◽  
Yuying Li ◽  
Shoaib Ur Rehman ◽  
Lili Miao ◽  
Yanfei Zhang ◽  
...  
Keyword(s):  
Protein Kinase ◽  
Protein Kinases ◽  
Specific Protein ◽  
Regulatory Mechanisms ◽  
Biological Processes ◽  
Related Protein ◽  
Biological Functions ◽  
Reversible Protein Phosphorylation ◽  
Growth Development ◽  
Regulatory Event

Abstract Reversible protein phosphorylation orchestrated by protein kinases and phosphatases is a major regulatory event in plants and animals. The SnRK2 subfamily consists of plant-specific protein kinases in the Ser/Thr protein kinase superfamily. Early observations indicated that SnRK2s are mainly involved in response to abiotic stress. Recent evidence shows that SnRK2s are multifarious players in a variety of biological processes. Here, we summarize the considerable knowledge of SnRK2s, including evolution, classification, biological functions and regulatory mechanisms at the epigenetic, post-transcriptional and post-translation levels.

scholarly journals Identification, Characterization, and Regulatory Mechanisms of a Novel EGR1 Splicing Isoform

2019 ◽  
Vol 20 (7) ◽  
pp. 1548 ◽  
Author(s):  
Vincenza Aliperti ◽  
Giulia Sgueglia ◽  
Francesco Aniello ◽  
Emilia Vitale ◽  
Laura Fucci ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Cell Types ◽  
Regulatory Mechanisms ◽  
Brain Diseases ◽  
Regulation Of Transcription ◽  
Biological Processes ◽  
Activation Domain ◽  
Post Translational Modifications ◽  
Pathological Conditions ◽  
Proliferation And Apoptosis

EGR1 is a transcription factor expressed in many cell types that regulates genes involved in different biological processes including growth, proliferation, and apoptosis. Dysregulation of EGR1 expression has been associated with many pathological conditions such as tumors and brain diseases. Known molecular mechanisms underlying the control of EGR1 function include regulation of transcription, mRNA and protein stability, and post-translational modifications. Here we describe the identification of a splicing isoform for the human EGR1 gene. The newly identified splicing transcript encodes a shorter protein compared to the canonical EGR1. This isoform lacks a region belonging to the N-terminal activation domain and although it is capable of entering the nucleus, it is unable to activate transcription fully relative to the canonical isoform.

A physiological perspective on targets of nitration in NO-based signaling networks in plants

2019 ◽  
Vol 70 (17) ◽  
pp. 4379-4389 ◽  
Author(s):  
Magdalena Arasimowicz-Jelonek ◽  
Jolanta Floryszak-Wieczorek
Keyword(s):  
Fatty Acids ◽  
Cellular Responses ◽  
Regulatory Mechanisms ◽  
Signaling Networks ◽  
Tyrosine Nitration ◽  
Biological Processes ◽  
Modeling Tools ◽  
Intracellular Traffic ◽  
Dna And Rna ◽  
Fine Tune

Abstract Although peroxynitrite (ONOO−) has been well documented as a nitrating cognate of nitric oxide (NO) in plant cells, modifications of proteins, fatty acids, and nucleotides by nitration are relatively under-explored topics in plant NO research. As a result, they are seen mainly as hallmarks of redox processes or as markers of nitro-oxidative stress under unfavorable conditions, similar to those observed in human and other animal systems. Protein tyrosine nitration is the best-known nitrative modification in the plant system and can be promoted by the action of both ONOO− and related NO-derived oxidants within the cell environment. Recent progress in ‘omics’ and modeling tools have provided novel biochemical insights into the physiological and pathophysiological fate of nitrated proteins. The nitration process can be specifically involved in various cell regulatory mechanisms that control redox signaling via nitrated cGMP or nitrated fatty acids. In addition, there is evidence to suggest that nitrative modifications of nucleotides embedded in DNA and RNA can be considered as smart switches of gene expression that fine-tune adaptive cellular responses to stress. This review highlights recent advances in our understanding of the potential implications of biotargets in the regulation of intracellular traffic and plant biological processes.

scholarly journals Roles of NAD+, PARP-1, and Sirtuins in Cell Death, Ischemic Brain Injury, and Synchrotron Radiation X-Ray-Induced Tissue Injury

Scientifica ◽  
2013 ◽  
Vol 2013 ◽  
pp. 1-11 ◽  
Author(s):  
Weihai Ying
Keyword(s):  
Cell Death ◽  
Brain Injury ◽  
Synchrotron Radiation ◽  
Brain Damage ◽  
Tissue Injury ◽  
Ischemic Brain Injury ◽  
Biological Processes ◽  
Ischemic Brain ◽  
X Ray ◽  
Parp 1

NAD+plays crucial roles in a variety of biological processes including energy metabolism, aging, and calcium homeostasis. Multiple studies have also shown that NAD+administration can profoundly decrease oxidative cell death and ischemic brain injury. A number of recent studies have further indicated that NAD+administration can decrease ischemic brain damage, traumatic brain damage and synchrotron radiation X-ray-induced tissue injury by such mechanisms as inhibiting inflammation, decreasing autophagy, and reducing DNA damage. Our latest study that applies nano-particles as a NAD+carrier has also provided first direct evidence demonstrating a key role of NAD+depletion in oxidative stress-induced ATP depletion. Poly(ADP-ribose) polymerase-1 (PARP-1) and sirtuins are key NAD+-consuming enzymes that mediate multiple biological processes. Recent studies have provided new information regarding PARP-1 and sirtuins in cell death, ischemic brain damage and synchrotron radiation X-ray-induced tissue damage. These findings have collectively supported the hypothesis that NAD+metabolism, PARP-1 and sirtuins play fundamental roles in oxidative stress-induced cell death, ischemic brain injury, and radiation injury. The findings have also supported “the Central Regulatory Network Hypothesis”, which proposes that a fundamental network that consists of ATP, NAD+and Ca2+as its key components is the essential network regulating various biological processes.

scholarly journals Diverse Physiological Functions and Regulatory Mechanisms for Signal-Transducing Small GTPases

2020 ◽  
Vol 21 (19) ◽  
pp. 7291
Author(s):  
Takaya Satoh
Keyword(s):  
Cell Types ◽  
Small Gtpases ◽  
Regulatory Mechanisms ◽  
Physiological Functions

Diverse GTPases act as signal transducing enzymes in a variety of organisms and cell types [...]

scholarly journals A framework for exhaustive modelling of genetic interaction patterns using Petri nets

2019 ◽  
Vol 36 (7) ◽  
pp. 2142-2149
Author(s):  
Annika Jacobsen ◽  
Olga Ivanova ◽  
Saman Amini ◽  
Jaap Heringa ◽  
Patrick Kemmeren ◽  
...  
Keyword(s):  
Petri Nets ◽  
Drug Response ◽  
Genetic Interaction ◽  
Regulatory Mechanisms ◽  
Supplementary Information ◽  
Biological Processes ◽  
Interaction Patterns ◽  
Supplementary Data ◽  
Gene Pairs ◽  
Computational Analyses

Abstract Motivation Genetic interaction (GI) patterns are characterized by the phenotypes of interacting single and double mutated gene pairs. Uncovering the regulatory mechanisms of GIs would provide a better understanding of their role in biological processes, diseases and drug response. Computational analyses can provide insights into the underpinning mechanisms of GIs. Results In this study, we present a framework for exhaustive modelling of GI patterns using Petri nets (PN). Four-node models were defined and generated on three levels with restrictions, to enable an exhaustive approach. Simulations suggest ∼5 million models of GIs. Generalizing these we propose putative mechanisms for the GI patterns, inversion and suppression. We demonstrate that exhaustive PN modelling enables reasoning about mechanisms of GIs when only the phenotypes of gene pairs are known. The framework can be applied to other GI or genetic regulatory datasets. Availability and implementation The framework is available at http://www.ibi.vu.nl/programs/ExhMod. Supplementary information Supplementary data are available at Bioinformatics online.

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