Protein N-termini, as the beginning of translation, has a major impact on protein's biological functions. Its sequence and various post-translational modifications often affect protein activation, stability and cellular-localization, regulate the signal transduction, and even determine protein's final destiny. The systematic study of protein N-termini can clarify the vital function of the N-terminus, and provide in-depth knowledge of the multifunctional roles that protein has played in diverse biological processes. In addition, N-terminal research may help us to achieve high-coverage proteomics and re-annotate genomics. Combined with our own research, this review highlights recent progress of N-terminomics, especially some important enrichment strategies and technologies based on mass spectrometry.
Mass Spectrometry ; Protein Processing, Post-Translational ; Proteins ; chemistry ; Proteomics

Proteins, which exist mainly in linear form in vivo, are easily affected by the change of ambient temperature and pH. The application of proteins (enzymes) in the fields of industrial catalyzing, food manufacturing and medicine are restricted due to their properties. The cyclic structure of natural cyclic peptides confers high thermal stability on itself; such mechanism can be referred to in further enhancement of the thermal stability and transformation of the structure of enzymes. This article reviewed the latest progress in the domestic and international studies on protein cyclization and summarized the traditional methods (such as protein trans-splicing, expressed protein ligation and sortase-catalyzed transpeptidation) in protein cyclization. A novel method based on SpyTag/SpyCather-mediated enzyme cyclization was discussed in more detail.
Cyclization ; Peptides, Cyclic ; chemistry ; Protein Processing, Post-Translational ; Proteins ; chemistry

C-termini of proteins often play an important role in various biological processes, such as the transcription and translation from DNA to protein and also participating in various biological regulations. The determination of protein C-terminus is so crucial because it provides not only distinct functional annotation, but also a way to monitor the proteolysis-modified proteins. Based on the biological mass spectrometry, a series of novel methods and technologies were developed both for qualitative and quantitative analyses of protein C-terminus. These methods or technologies can be applied to accurate and effective protein C-terminus profiling, including the sequences and quantitative information of C-termini, which reveals the biological function of C-termini in life's activities and provides a better understanding of the degradation of mature proteins. Combined with our research, this review highlights the improvements in C-terminal proteomics study in the past decades, including the methodologies for recognition and identification of C-terminus, as well as the enrichment strategies for protein C-terminus.
Mass Spectrometry ; Protein Processing, Post-Translational ; Proteins ; chemistry ; Proteolysis ; Proteomics

Ubiquitination is a post-translational modification of proteins in eukaryotes, which mediates the specific degradation and signal transduction of proteins to regulate a variety of life processes and thus affects functions of the body. The disorder and imbalance of ubiquitination network is a major cause of serious human diseases. Ubiquitin molecules can form eight homogeneous ubiquitin chains with different topological structures, which vary greatly in abundance and function. At present, the classical ubiquitin chains K48 and K63 with high abundance and rich substrates have been intensively studied, while other atypical ubiquitin chains with low content remain to be studied. However, it has been proved that atypical ubiquitin chains play a key role in intracellular regulation. K6 is an important atypical ubiquitin chain, which is similar to K48 chain and has a tight spatial structure. It plays a role in DNA damage repair, mitochondrial quality control, the occurrence and development of tumor, and the pathogenesis of Parkinson's disease. Due to the lack of specific antibodies and effective enrichment methods for K6, little is known about its substrate and regulatory mechanism. This paper systematically reviews the structural characteristics, regulatory mechanism, biological functions, and relevant diseases of atypical K6 linkages, aiming to provide reference for the functional study of K6.
Humans ; Protein Processing, Post-Translational ; Signal Transduction ; Ubiquitin/chemistry* ; Ubiquitination

Cardiovascular Diseases ; Extracellular Vesicles/metabolism* ; Humans ; Protein Processing, Post-Translational

Proteolytic cleavage is one of the post-translational modifications and plays important roles in many biological processes, such as apoptosis and tumor cell metastasis. The identification of the cleavage events can improve our understanding of their biological functions in these processes. Although proteomic approaches using N-terminal labeling have resulted in the discovery of many proteolytic cleavages, this strategy has its own inherent drawbacks. Labeling of protein C-termini is an alternative approach. Here, we optimized the labeling procedure in the profiling protein C-termini by enzymatic labeling (ProC-TEL) and improved the labeling efficiency for the positive isolation of protein C-terminal peptides and mass spectrometric identification. We applied this approach to a complex protein mixture from Escherichia coli and identified many C-terminal peptides and internal cleaved peptides from more than 120 proteins. From the identified cleavages, we found several previously known internal proteolytic cleavage sites and many novel ones which may play roles in regulating normal biological processes. This work provides a potential new way, complementary to the N-terminomics, for the identification of proteolytic cleavages in complex biological systems.
Cathepsin A ; chemistry ; Protein C ; chemistry ; Protein Processing, Post-Translational ; Proteolysis ; Proteomics

Abstract　　The promyelocytic leukemia (PML) gene encoded PML protein as a tumor suppressor protein, plays important roles in the occurrence and development of various cancers including acute promyelocytic leukemia. Recent studies have indicated that there are a variety of post-translational modifications of the PML protein, such as SUMOylation, ubiquitination, phosphorylation, and acetylation in cells. These modifications of the PML protein can directly affect the formation of PML nuclear bodies (PML-NBs), repair DNA damage, and modulate cell apoptosis. Furthermore, the abnormal modifications of PML not only result in the occurrence of hematopoietic tumors, but also are closely related to the drug-resistance of cancer. Therefore, investigating the post-translational modifications of PML is significant to uncover the mechanism of formation and functions of PML-NBs, thus contributing to the prevention and treatment of related hematopoietic tumors. In this review, the characteristics of the post-translational modifications of PML protein and the relationship between these modifications and functions of PML-NBs are summarized so as to provide the potential targets for the treatment of related cancers.
Humans ; Intranuclear Inclusion Bodies ; Leukemia, Promyelocytic, Acute ; Nuclear Proteins ; Promyelocytic Leukemia Protein ; Protein Processing, Post-Translational

As a consequence of the Earth's rotation, almost all organisms experience day and night cycles within a 24-hr period. To adapt and synchronize biological rhythms to external daily cycles, organisms have evolved an internal time-keeping system. In mammals, the master circadian pacemaker residing in the suprachiasmatic nucleus (SCN) of the anterior hypothalamus generates circadian rhythmicity and orchestrates numerous subsidiary local clocks in other regions of the brain and peripheral tissues. Regardless of their locations, these circadian clocks are cell-autonomous and self-sustainable, implicating rhythmic oscillations in a variety of biochemical and metabolic processes. A group of core clock genes provides interlocking molecular feedback loops that drive the circadian rhythm even at the single-cell level. In addition to the core transcription/translation feedback loops, post-translational modifications also contribute to the fine regulation of molecular circadian clocks. In this article, we briefly review the molecular mechanisms and post-translational modifications of mammalian circadian clock regulation. We also discuss the organization of and communication between central and peripheral circadian oscillators of the mammalian circadian clock.
Brain ; Circadian Clocks ; Circadian Rhythm ; Hypothalamus, Anterior ; Mammals ; Protein Processing, Post-Translational ; Suprachiasmatic Nucleus

Human physiology and pathology can be affected by different nutritional conditions. At cellular level, the availability of a nutritional component not only mediates metabolic reactions but also transmits signals for diverse biological activities. Epigenetic regulation such as DNA methylation and histone post-translational modifications is considered as one of the nutrient-mediated signaling receivers as almost all of the epigenetic enzyme activities require intermediary metabolites as cofactors. The gut microbiome as “forgotten organ” has been suggested as a metabolite generator as well as a nutrient sensor for its host organism, affecting human health and diseases. Given the metabolite-dependent activities of epigenetic regulators, the gut microbiome has a high potential to influence the epigenetics in human physiology. Here, I review the involvement of gut microbiome in diverse human diseases and the mechanisms of epigenetic regulation by different metabolites. Thereafter, I discuss how the gut microbiome-generated metabolites affect host epigenetics, raising a possibility to develop a therapeutic intervention based on the interaction between the microbiome and epigenetics for human health.
DNA Methylation ; Epigenomics* ; Gastrointestinal Microbiome* ; Histones ; Humans* ; Metabolism ; Microbiota ; Pathology ; Physiology ; Protein Processing, Post-Translational

Heart failure (HF) is a multifactorial disease brought about by numerous, and oftentimes complex, etiological mechanisms. Although well studied, HF continues to affect millions of people worldwide and current treatments can only prevent further progression of HF. Mitochondria undoubtedly play an important role in the progression of HF, and numerous studies have highlighted mitochondrial components that contribute to HF. This review presents an overview of the role of mitochondrial biogenesis, mitochondrial oxidative stress, and mitochondrial permeability transition pore in HF, discusses ongoing studies that attempt to address the disease through mitochondrial targeting, and provides an insight on how these studies can affect future research on HF treatment.
Heart Failure* ; Heart* ; Mitochondria ; Organelle Biogenesis ; Oxidative Stress ; Permeability ; Protein Processing, Post-Translational