Posttranslational modifications in proteins: resources, tools and prediction methods

SSE-Net: A novel network based on sequence spatial equation for Camellia sinensis lysine acetylation identification

Lysine acetylation (Kace) is one of the most important post-translational modifications. It is key to identify Kace sites for understanding regulation mechanisms in Camellia sinensis. In this study, we defined a mathematical formula, named sequence spatial equation (SSE), which could give each amino acid coordinate in 3-D space by rotating and translating. Based on SSE, an optional network SSE-Net was constructed for representing spatial structure information. Centrality metrics of SSE-Net were used to design structure feature vectors for reflecting the importance of sites. The optimal features were fed into classifier to construct model SSE-ET. The results showed that SSE-ET outperformed the other classifiers. Meanwhile, all MCC results were higher than 0.7 for different machine learning, which indicated that SSE-Net was effective for representing Kace sites in Camellia sinensis. Moreover, we implemented the other models on our dataset. The results of comparison showed that SSE-ET was much more powerful than the others. Specifically, the result of SN was nearly 20 % higher than the other models. These results showed that the proposed SSE was a valuable mathematics concept for reflecting 3-D space Kace site information in Camellia sinensis, and SSE-Net may be an essential complementary for biology and bioinformatics research.

Molecular dissection of the role of ACE2 in glucose homeostasis

Angiotensin-converting enzyme 2 (ACE2) was discovered 25 years ago as a negative regulator of the renin-angiotensin system, opposing the effects of angiotensin II. Beyond its well-demonstrated roles in cardiovascular regulation and COVID-19 pathology, ACE2 is involved in a plethora of physiopathological processes. In this review, we summarize the latest discoveries on the role of ACE2 in glucose homeostasis and regulation of metabolism. In the endocrine pancreas, ACE2 is expressed at low levels in β-cells, but loss of its expression inhibits glucose-stimulated insulin secretion and impairs glucose tolerance. Conversely, overexpression of ACE2 improved glycemia, suggesting that recombinant ACE2 might be a future therapy for diabetes. In the skeletal muscle of ACE2-deficient mice a progressive triglyceride accumulation was observed, whereas in diabetic kidney the initial increase in ACE2 is followed by a chronic reduction of expression in kidney tubules and impairment of glucose metabolism. At the intestinal level dysregulation of the enzyme alters the amino acid absorption and intestinal microbiome, whereas at the hepatic level ACE2 protects against diabetic fatty liver disease. Not least, ACE2 is upregulated in adipocytes in response to nutritional stimuli, and administration of recombinant ACE2 decreased body weight and increased thermogenesis. In addition to tissue-specific regulation of ACE2 function, the enzyme undergoes complex cellular posttranslational modifications that are changed during diabetes evolution, with at least proteolytic cleavage and ubiquitination leading to modifications in ACE2 activity. Detailed characterization of ACE2 in a cellular and tissue-specific manner holds promise for improving therapeutic outcomes in diabetes and metabolic disorders.

Human Mn-superoxide dismutase acetylation protects from enzyme nitration and inactivation

Manganese superoxide dismutase (MnSOD) is a critical enzyme responsible for detoxifying superoxide radicals in mitochondria, thereby ensuring oxidative balance within cells. Post-translational modifications (PTMs), such as acetylation and nitration, significantly influence MnSOD's catalytic efficiency. Site-specific nitration of MnSOD at tyrosine 34 by peroxynitrite leads to an irreversible inactivation, which has been widely observed in diverse pathologies. On the other hand, acetylation of MnSOD is a reversible modification that modulates the activity of the enzyme and it is finely regulated by the action of the protein Sirt3, responsible for the deacetylation of a wide variety of mitochondrial enzymes. This study focuses on Lys29 acetylation and its impact on the enzyme's activity and its interplay with peroxynitrite-mediated nitration of Tyr34. Through molecular dynamics (MD) simulations, we observed that acetylation of Lys29 partially obstructs the access channel to the active site, reducing superoxide accessibility. Electrostatic potential calculations further revealed that Lys29 acetylation diminishes the positive charge around the active site, contributing to decreased affinity for superoxide radicals. Brownian dynamics (BD) simulations confirmed a 50 % reduction in the enzyme's association rate constant (kon) for superoxide upon Lys29 acetylation. In contrast, Lys98 acetylation had a minor effect on kon. In vitro studies also supported our findings and showed that acetylation could play a role in the irreversible inactivation of MnSOD by peroxynitrite, likely by sterically hindering Tyr34 nitration. These findings highlight the role of acetylation as a reversible protective mechanism that can regulate superoxide and peroxynitrite accessibility to MnSOD under stress conditions.

'Intelligent' proteins

We present an idea of protein molecules that challenges the traditional view of proteins as simple molecular machines and suggests instead that they exhibit a basic form of "intelligence". The idea stems from suggestions coming from Integrated Information Theory (IIT), network theory, and allostery to explore how proteins process information, adapt to their environment, and even show memory-like behaviors. We define protein intelligence using IIT and focus on how proteins integrate information (in terms of the parameter Φ coming from IIT) and balance their core (stable, ordered regions) and periphery (flexible, disordered regions). This balance allows proteins to remain stable while adapting to changes and operating in a critical state where order and disorder coexist. We summarize recent findings on conformational memory, allosteric regulation, protein intrinsic disorder, liquid-liquid phase separation, and critical transitions, and compare protein behavior to other complex systems like ecosystems and neural networks. While our perspective offers a unified framework to understand proteins, it also raises questions about applying intelligence concepts to molecular systems. We discuss how this understanding could advance protein engineering, drug design, and synthetic biology, while at the same time acknowledging the challenges of creating adaptive, "intelligent" proteins. This concept bridges the gap between mechanistic and systems-level views of proteins and offers a comprehensive understanding of their dynamic and adaptive nature. We have tried to redefine the traditionally metaphorical concept of "intelligence" in biochemistry as a measurable property while simultaneously establishing the material foundation of protein intelligence through the identification of fundamental elements such as memory and learning in molecular systems.

Aging and diet alter the protein ubiquitylation landscape in the mouse brain

Post-translational modifications (PTMs) regulate protein homeostasis, but how aging impacts PTMs remains unclear. Here, we used mass spectrometry to reveal changes in hundreds of protein ubiquitylation, acetylation, and phosphorylation sites in the mouse aging brain. We show that aging has a major impact on protein ubiquitylation. 29% of the quantified ubiquitylation sites were affected independently of protein abundance, indicating altered PTM stoichiometry. Using iPSC-derived neurons, we estimated that 35% of ubiquitylation changes observed in the aged brain can be attributed to reduced proteasome activity. Finally, we tested whether protein ubiquitylation in the brain can be influenced by dietary intervention. We found that one cycle of dietary restriction and re-feeding modifies the brain ubiquitylome, rescuing some but exacerbating other ubiquitylation changes observed in old brains. Our findings reveal an age-dependent ubiquitylation signature modifiable by dietary intervention, providing insights into mechanisms of protein homeostasis impairment and highlighting potential biomarkers of brain aging.

Epigenetic and post-translational modifications in ferroptosis regulation and hepatocellular carcinoma: New frontiers in therapeutic targeting

Hepatocellular carcinoma (HCC), the predominant kind of liver cancer, continues to be a significant contributor to cancer-related deaths globally, influenced by intricate molecular processes and strong resistance to existing chemotherapy. Iron-dependent lipid peroxidation induces ferroptosis, a controlled form of cell death that plays a crucial role in inhibiting tumor growth and treatment resistance in HCC. Recent research has shown that epigenetic modifications, such as DNA methylation, histone modifications, regulation by non-coding RNAs (ncRNAs), and post-translational modification (PTM) like ubiquitination, phosphorylation, acetylation, and methylation, play a crucial role in fine-tuning ferroptosis. These alterations alter the structure of chromatin, gene expression, and protein function, thereby affecting cancer cells' fate. This review emphasizes the complex functions of epigenetic and post-translational alterations in controlling ferroptosis, providing valuable insights into their potential as therapeutic targets in HCC. The unraveling of these pathways offers a significant opportunity for novel therapies targeted at surmounting drug resistance and enhancing patient outcomes in liver cancer.

Inhibition of HCN channels decreases motivation for alcohol and deprivation-induced drinking in alcohol preferring rats

Globally, around 400 million people live with an alcohol use disorder (AUD), yet current treatments available are suboptimal at a population level. Hyperpolarization-activated cyclic nucleotide-gated cation (HCN) channels are implicated in the modulation of complex motivated behaviours, including reward seeking. Here, we investigated the potential involvement of HCN channels in alcohol reinforcing effects, contributing to alcohol intake and relapse-like drinking following abstinence in iP rats. The functional role of HCN channels in the motivation to acquire alcohol and relapse-like behaviour was tested in vivo through intracerebroventricular (ICV) infusion of a HCN channel inhibitor, ZD7288 prior to operant progressive ratio responding or the alcohol deprivation effect. Acute ICV infusion of ZD7288 (3 μg/5 μL) significantly reduced motivation to acquire alcohol and attenuated the alcohol deprivation effect after 14 days of abstinence, without affecting spontaneous locomotor activity. HCN channels are densely expressed in cholinergic neurons of the medial habenula (mHb), which have been implicated in stress, aversion, and drug/alcohol intake-associated behaviours. To investigate the impact of alcohol on the expression of HCN channels, cholinergic markers and acetylcholine receptors, we performed qPCR on mHb tissue in alcohol-preferring (iP) rats following chronic voluntary alcohol intake or abstinence. qPCR results showed an upregulation of mRNA encoding key ion channels in the mHb following abstinence from chronic voluntary alcohol use. Collectively, these findings suggest that HCN channels contribute to motivation to consume alcohol and relapse-like behaviour during abstinence in iP rats.

Lactylation-regulated biomolecular condensates: metabolic control of phase separation in physiology and disease

Lactate has long been viewed as a "waste product" of anaerobic glycolysis, with its role in health and disease often overlooked. However, recent discoveries of lactylation-a novel post-translational modification involving lactate-have sparked a renewed understanding of lactate's functions. Lactylation alters the molecular structure of proteins with different cellular localizations, enabling the regulation of their functions and aggregation in specific spatiotemporal contexts, with its impact on biomolecular phase separation being one of its primary effects. However, it remains unknown how lactylation dynamically regulates the spatiotemporal specificity of phase separation and its role in diseases. This article provides an overview of the regulatory mechanisms of biomolecular phase separation driven by lactylation, aiming to offer fresh insights into the role of lactylation in normal and disease-related biological processes while deepening our understanding of its research value and biological significance.

Synthetic Biology for Designing Allostery and Its Potential Biomedical Applications

Allosteric regulation of protein function, where a perturbation at one site induces a conformational shift or alters dynamics at a distal functional site, plays a key role in numerous biological processes. The ability to introduce allostery using synthetic biology principles holds significant potential both for biomedical and biotechnological applications, and for advancing our understanding of natural allostery. By customizing target proteins for sensing specific chemical or physical signals, including ligand binding and environmental cues, we aim to allosterically modulate the function of a target protein depending on the selected triggers. This approach, unlike active-site targeting, offers greater specificity and selectivity and can allosterically couple diverse physiological processes. Synthetic biology strategies have been developed recently for designed allosteric protein regulation, including the design of allosteric modulators such as domain insertion, generation of de novo allosteric protein switches, and application of engineered allosteric mechanisms to control cellular functions. We examine the application of artificial intelligence (AI)-based generative protein design and other important milestones, challenges and opportunities in this field, highlighting how these approaches could be applied for the development of new therapeutic strategies.

Identification of a resistance-exercise-specific signalling pathway that drives skeletal muscle growth

Endurance and resistance exercise lead to distinct functional adaptations: the former increases aerobic capacity and the latter increases muscle mass. However, the signalling pathways that drive these adaptations are not well understood. Here we identify phosphorylation events that are differentially regulated by endurance and resistance exercise. Using a model of unilateral exercise in male participants and deep phosphoproteomic analyses, we find that a prolonged activation of a signalling pathway involving MKK3b/6, p38, MK2 and mTORC1 occurs specifically in response to resistance exercise. Follow-up studies in both male and female participants reveal that the resistance-exercise-induced activation of MKK3b is highly correlated with the induction of protein synthesis (R = 0.87). Additionally, we show that in mice, genetic activation of MKK3b is sufficient to induce signalling through p38, MK2 and mTORC1, along with an increase in protein synthesis and muscle fibre size. Overall, we identify core components of a signalling pathway that drives the growth-promoting effects of resistance exercise.

Glymphatics and meningeal lymphatics unlock the brain-immune code

The central nervous system (CNS) was once perceived as entirely shielded from the immune system, protected behind the blood-brain barrier and thought to lack lymphatic drainage. However, recent evidence has challenged many dogmas in neuroimmunology. Indeed, by means of glymphatics, brain-derived "waste" from deep within the CNS mobilizes toward immunologically active brain borders, where meningeal lymphatic vessels are appropriately positioned to drain antigens from the brain to the periphery. Accordingly, the presentation of brain-derived self-peptides emerges at the brain's borders and drives T cell responses with suppressive properties, critical in allowing active immunosurveillance while limiting aberrant immune reactivity. Taking into consideration these concepts, we further discuss how inflammation, aging, and neurodegenerative diseases potentially reshape the repertoire of self-antigens and immune cells, disrupting the healthy dialogue between the CNS and immune system. Collectively, this evolving perspective unveils new therapeutic avenues for CNS pathologies.

Palmitoylation prevents B7-H4 lysosomal degradation sustaining tumor immune evasion

B7-H4 functions as an immune checkpoint in the tumor microenvironment (TME). However, the post-translational modification (PTM) of B7-H4 and its translational potential in cancer remains incompletely understood. We find that ZDHHC3, a zinc finger DHHC-type palmitoyltransferase, palmitoylates B7-H4 at Cys130 in breast cancer cells, preventing its lysosomal degradation and sustaining B7-H4-mediated immunosuppression. Knockdown of ZDHHC3 in tumors results in robust anti-tumor immunity and reduces tumor progression in murine models. Moreover, abemaciclib, a CDK4/6 inhibitor, primes lysosome activation and promotes lysosomal degradation of B7-H4 independently of the tumor cell cycle. Treatment with abemaciclib results in T cell activation and mitigates B7-H4-mediated immune suppression via inducing B7-H4 degradation in preclinical tumor models. Thus, B7-H4 palmitoylation is an important PTM controlling B7-H4 protein stability and abemaciclib may be repurposed to promote B7-H4 degradation, thereby treating patients with B7-H4 expressing tumors.

An atlas of bacterial serine-threonine kinases reveals functional diversity and key distinctions from eukaryotic kinases

Bacterial serine-threonine kinases (STKs) regulate diverse cellular processes associated with cell growth, virulence, and pathogenicity and are evolutionarily related to the druggable eukaryotic STKs. A deeper understanding of how bacterial STKs differ from their eukaryotic counterparts and how they have evolved to regulate diverse bacterial signaling functions is crucial for advancing the discovery and development of new antibiotic therapies. Here, we classified more than 300,000 bacterial STK sequences from the NCBI RefSeq nonredundant and UniProt protein databases into 35 canonical and seven pseudokinase families on the basis of the patterns of evolutionary constraints in the conserved catalytic domain and flanking regulatory domains. Through statistical comparisons, we identified features distinguishing bacterial STKs from eukaryotic STKs, including an arginine residue in a regulatory helix (C helix) that dynamically couples the ATP- and substrate-binding lobes of the kinase domain. Biochemical and peptide library screens demonstrated that evolutionarily constrained residues contributed to substrate specificity and kinase activation in the Mycobacterium tuberculosis kinase PknB. Together, these findings open previously unidentified avenues for investigating bacterial STK functions in cellular signaling and for developing selective bacterial STK inhibitors.

Epigenetics of nonobstructive azoospermia

ABSTRACT

Nonobstructive azoospermia (NOA) is a severe and heterogeneous form of male factor infertility caused by dysfunction of spermatogenesis. Although various factors are well defined in the disruption of spermatogenesis, not all aspects due to the heterogeneity of the disorder have been determined yet. In this review, we focus on the recent findings and summarize the current data on epigenetic mechanisms such as DNA methylation and different metabolites produced during methylation and demethylation and various types of small noncoding RNAs involved in the pathogenesis of different groups of NOA.

PTM-Mamba: a PTM-aware protein language model with bidirectional gated Mamba blocks

Current protein language models (LMs) accurately encode protein properties but have yet to represent post-translational modifications (PTMs), which are crucial for proteomic diversity and influence protein structure, function and interactions. To address this gap, we develop PTM-Mamba, a PTM-aware protein LM that integrates PTM tokens using bidirectional Mamba blocks fused with ESM-2 protein LM embeddings via a newly developed gating mechanism. PTM-Mamba uniquely models both wild-type and PTM sequences, enabling downstream tasks such as disease association and druggability prediction, PTM effect prediction on protein-protein interactions and zero-shot PTM discovery. In total, our work establishes PTM-Mamba as a foundational tool for PTM-aware protein modeling and design.

UFMylation: Exploring a lesser known post translational modification

Ubiquitination is a highly conserved post-translational modification (PTM) in which ubiquitin (Ub) is covalently attached to substrate proteins resulting in the alteration of protein structure, function, and stability. Another class of PTM mediated by ubiquitin-like proteins (UBLs) has gained significant attention among researchers in recent years. This article focuses on one such UBL-mediated PTM i.e. UFMylation. The enzymatic mechanism of UFMylation is similar to ubiquitination, involving three steps regulated by three different enzymes. In plants, reports suggest that UFMylation is predominantly involved in maintaining ER homeostasis including ER-phagy. However, studies related to this PTM are limited and future studies might reveal other molecular pathways regulated by UFMylation.

Lactylation and Ischemic Stroke: Research Progress and Potential Relationship

Ischemic stroke is caused by interrupted cerebral blood flow and is a leading cause of mortality and disability worldwide. Significant advancements have been achieved in comprehending the pathophysiology of stroke and the fundamental mechanisms responsible for ischemic damage. Lactylation, as a newly discovered post-translational modification, has been reported to participate in several physiological and pathological processes. However, research on lactylation and ischemic stroke is scarce. This review summarized the current function of protein lactylation in other diseases or normal physiological processes and explored their potential link with the pathophysiological process and the reparative mechanism of ischemic stroke. We proposed that neuroinflammation, regulation of metabolism, regulation of messenger RNA translation, angiogenesis, and neurogenesis might be the bridge linking lactylation and ischemic stroke. Our study provided a novel perspective for comprehending the role of protein lactylation in the pathophysiological processes underlying ischemic stroke. Lactylation might be a promising target in drug development of ischemic stroke.

Lactate metabolism and lactylation in breast cancer: mechanisms and implications

As the end-product of glycolysis, lactate serves as a regulator of protein lactylation in addition to being an energy substrate, metabolite, and signaling molecule in cancer. The reprogramming of glucose metabolism and the Warburg effect in breast cancer results in extensive lactate production and accumulation, making it likely that lactylation in tumor tissue is also abnormal. This review summarizes evidence on lactylation derived from studies of lactate metabolism and disease, highlighting the role of lactate in the tumor microenvironment of breast cancer and detailing the levels of lactylation and cancer-promoting mechanisms across various tumors. The roles of lactate and lactylation, along with potential intervention mechanisms, are presented and discussed, offering valuable insights for future research on the role of lactylation in tumors.

Comprehensive analysis of the NAC transcription factor gene family in Sophora tonkinensis Gagnep

BACKGROUND

Sophora tonkinensis Gagnep. has long been utilized in the treatment of anti-inflammatory and pain-relieving, with its principal active compounds being alkaloids and flavonoids. NAC transcription factors, a large family of plant-specific regulators, play pivotal roles in growth, development, stress responses, and secondary metabolism. However, comprehensive genome-wide characterization of S. tonkinensis NAC gene family (StNAC) remains unexplored.

RESULTS

This study identified 85 NAC proteins from the S. tonkinensis genome database. Phylogenetic analysis revealed that StNAC proteins were categorized into 15 subgroups based on their homology with Arabidopsis thaliana NAC proteins. Gene structure analysis demonstrated a variation in intron numbers ranging from 1 to 7, with a majority of StNAC genes containing 2-3 introns. Chromosomal distribution analysis indicated an uneven spread of StNAC genes across 9 chromosomes, with the highest number of StNAC genes on Chr3. Detection of 4 tandem duplicates and 32 segmental duplicates revealed that segmental duplication primarily drive StNAC genes amplification. Prediction of cis-regulatory elements suggested the involvement of StNAC genes in growth, stress responses, and hormone regulation. Gene expression analysis showed substantial variability expression of StNAC genes across different tissues. Notably, eight StNAC genes were identified as significantly associated alkaloid and flavonoid levels. qRT-PCR validation indicated that five genes were highly expressed in tissues, corroborating transcriptome data.

CONCLUSION

These findings offer valuable insights for further functional characterization of NAC genes and their potential roles in alkaloid and flavonoid biosynthesis in S. tonkinensis.

MAST Kinases' Function and Regulation: Insights from Structural Modeling and Disease Mutations

Background/Objectives: The MAST kinases are ancient AGC kinases associated with many human diseases, such as cancer, diabetes, and neurodevelopmental disorders. We set out to describe the origins and diversification of MAST kinases from a structural and bioinformatic perspective to inform future research directions. Methods: We investigated MAST-lineage kinases using database and sequence analysis. We also estimate the functional consequences of disease point mutations on protein stability by integrating predictive algorithms and AlphaFold. Results: Higher-order organisms often have multiple MASTs and a single MASTL kinase. MAST proteins conserve an AGC kinase domain, a domain of unknown function 1908 (DUF), and a PDZ binding domain. D. discoideum contains MAST kinase-like proteins that exhibit a characteristic insertion within the T-loop but do not conserve DUF or PDZ domains. While the DUF domain is conserved in plants, the PDZ domain is not. The four mammalian MASTs demonstrate tissue expression heterogeneity by mRNA and protein. MAST1-4 are likely regulated by 14-3-3 proteins based on interactome data and in silico predictions. Comparative ΔΔG estimation identified that MAST1-L232P and G522E mutations are likely destabilizing. Conclusions: We conclude that MAST and MASTL kinases diverged from the primordial MAST, which likely operated in both biological niches. The number of MAST paralogs then expanded to the heterogeneous subfamily seen in mammals that are all likely regulated by 14-3-3 protein interaction. The reported pathogenic mutations in MASTs primarily represent alterations to post-translational modification topology in the DUF and kinase domains. Our report outlines a computational basis for future work in MAST kinase regulation and drug discovery.

Leaving the mark: FMOs as an emerging class of cytokinetic regulators

Posttranslational modification of proteins plays a fundamental role in cell biology. It provides cells a means to regulate the signaling, enzymatic or structural properties of proteins without continuous cycles of synthesis and degradation, offering multiple distinct functions to individual proteins in a rapid and reversible manner. Modifications can include phosphorylation, ubiquitination or methylation, which are widespread and simple to detect using current approaches. More challenging to identify, one modification of growing significance is the direct oxidation of cysteine and methionine side chains. Protein oxidation has long been known to occur spontaneously upon the accumulation of cellular reactive oxygen species (ROS), but new data are providing insight into the targeted oxidation of proteins by flavin-containing monooxygenases (FMOs). Here, we review how oxidation of cellular proteins can modulate their activity and consider potential roles for FMOs in the targeted modification of proteins shaping cell division, with a particular focus on two families of FMOs: MICAL and OSGIN.

Nanopore sensing of protein and peptide conformation for point-of-care applications

The global population's aging and growth will likely result in an increase in chronic aging-related diseases. Early diagnosis could improve the medical care and quality of life. Many diseases are linked to misfolding or conformational changes in biomarker peptides and proteins, which affect their function and binding properties. Current clinical methods struggle to detect and quantify these changes. Therefore, there is a need for sensitive conformational sensors that can detect low-concentration analytes in biofluids. Nanopore electrical detection has shown potential in sensing subtle protein and peptide conformation changes. This technique can detect single molecules label-free while distinguishing shape or physicochemical property changes. Its proven sensitivity makes nanopore sensing technology promising for ultra-sensitive, personalized point-of-care devices. We focus on the capability of nanopore sensing for detecting and quantifying conformational modifications and enantiomers in biomarker proteins and peptides and discuss this technology as a solution to future societal health challenges.

SpecPeptidOMS Directly and Rapidly Aligns Mass Spectra on Whole Proteomes and Identifies Peptides That Are Not Necessarily Tryptic: Implications for Peptidomics

SpecPeptidOMS directly aligns peptide fragmentation spectra to whole and undigested protein sequences. The algorithm was specifically and initially designed for peptidomics, where the aim is to identify peptides that do not result from the hydrolysis of a known protein and therefore, whose termini cannot be predicted. Thus, SpecPeptidOMS can perform alignments starting and ending anywhere in the protein sequence. The underlying computational method of SpecPeptidOMS, which is based on a dynamic programming approach, was drastically optimized. As a result, SpecPeptidOMS can process around 12,000 spectra per hour on an ordinary laptop, with alignment performed against the entire human proteome. The performance of SpecPeptidOMS was first evaluated on a publicly available data set of (nontryptic) synthetic mass spectra. Accuracy was estimated by considering the results obtained by MaxQuant on the same data set as the "ground truth". A second series of tests on a larger, well-known proteomics data set (HEK293) highlighted SpecPeptidOMS' additional ability to search for open modifications, a feature of interest in peptidomics but also more broadly in conventional proteomics. SpecPeptidOMS is open-source, cross-platform (written in Java), and freely available.

Post-translational modifications of epigenetic modifier TIP60: their role in cellular functions and cancer

TIP60 is a crucial lysine acetyltransferase protein that catalyzes the acetylation of histone and non-histone proteins. This enzyme plays a crucial role in maintaining genomic integrity, by participating in DNA damage repair, ensuring accurate chromosomal segregation, and regulating a myriad of cellular processes such as apoptosis, autophagy, and wound-induced cell migration. One of the primary mechanisms through which TIP60 executes these diverse cellular functions is via post-translational modifications (PTMs). Over the years, extensive studies have demonstrated the importance of PTMs in controlling protein functions. This review aims to summarize the findings on PTMs occurring on the TIP60 protein and their functional implications. We also discuss previously uncharacterized PTM sites identified on TIP60 and examine their relationship with cancer-associated mutations, with a particular focus on residues potentially modified by various PTMs, to understand the cause of deregulation of TIP60 in various cancers.

The Complexities of Interspecies Somatic Cell Nuclear Transfer: From Biological and Molecular Insights to Future Perspectives

For nearly three decades, interspecies somatic cell nuclear transfer (iSCNT) has been explored as a potential tool for cloning, regenerative medicine, and wildlife conservation. However, developmental inefficiencies remain a major challenge, largely due to persistent barriers in nucleocytoplasmic transport, mitonuclear communication, and epigenome crosstalk. This review synthesized peer-reviewed English articles from PubMed, Web of Science, and Scopus, spanning nearly three decades, using relevant keywords to explore the molecular mechanisms underlying iSCNT inefficiencies and potential improvement strategies. We highlight recent findings deepening the understanding of interspecies barriers in iSCNT, emphasizing their interconnected complexities, including the following: (1) nucleocytoplasmic incompatibility may disrupt nuclear pore complex (NPC) assembly and maturation, impairing the nuclear transport of essential transcription factors (TFs), embryonic genome activation (EGA), and nuclear reprogramming; (2) mitonuclear incompatibility could lead to nuclear and mitochondrial DNA (nDNA-mtDNA) mismatches, affecting electron transport chain (ETC) assembly, oxidative phosphorylation, and energy metabolism; (3) these interrelated incompatibilities can further influence epigenetic regulation, potentially leading to incomplete epigenetic reprogramming in iSCNT embryos. Addressing these challenges requires a multifaceted, species-specific approach that balances multiple incompatibilities rather than isolating a single factor. Gaining insight into the molecular interactions between the donor nucleus and recipient cytoplast, coupled with optimizing strategies tailored to specific pairings, could significantly enhance iSCNT efficiency, ultimately transforming experimental breakthroughs into real-world applications in reproductive biotechnology, regenerative medicine, and species conservation.

Potential of lactylation as a therapeutic target in cancer treatment (Review)

Post‑translational modifications (PTMs) of proteins influence their functionality by altering the structure of precursor proteins. These modifications are closely linked to tumor progression through the regulation of processes such as cell proliferation, apoptosis, angiogenesis and invasion. Tumors produce large amounts of lactic acid through aerobic glycolysis. Lactic acid not only serves an important role in cell metabolism, but also serves an important role in cell communication. Lactylation, a PTM involving lactate and lysine residues as substrates, serves as an epigenetic regulator that modulates intracellular signaling, gene expression and protein function, thereby serving a crucial role in tumorigenesis and progression. The identification of lactylation provides a key breakthrough in elucidating the interaction between tumor metabolic reprogramming and epigenetic modification. The present review primarily summarizes the occurrence of lactylation, its effect on tumor progression, drug resistance, the tumor microenvironment and gut microbiota, and its potential as a therapeutic target for cancer. The aim of the present review was to provide novel strategies for potential cancer therapies.

Clinical Proteomics, Quo Vadis?

The field of clinical proteomics has seen enormous growth in the past 20 years, with over 40,000 scientific manuscripts published to date. At the same time, actual clinical application of the reported findings is obviously scarce. In this viewpoint article, we discuss the key issues that may be responsible for this apparent lack of success. We conclude that success must not be assessed based on the number of publications, but via the impact on patient management and treatment. We proceed with specific suggestions for potential solutions, which include keeping a strict focus on potential patient benefit. We hope this article can help shape the field, so it can in fact deliver on its realistic promise to bring significant improvement in management and care to patients.

The emerging role of protein L-lactylation in metabolic regulation and cell signalling

L-Lactate has emerged as a crucial metabolic intermediate, moving beyond its traditional view as a mere waste product. The recent discovery of L-lactate-driven protein lactylation as a post-translational modification has unveiled a pathway that highlights the role of lactate in cellular signalling. In this Perspective, we explore the enzymatic and metabolic mechanisms underlying protein lactylation and its impacts on both histone and non-histone proteins in the contexts of physiology and diseases. We discuss growing evidence suggesting that this modification regulates a wide range of cellular functions and is involved in various physiological and pathological processes, such as cell-fate determination, development, cardiovascular diseases, cancer and autoimmune disorders. We propose that protein lactylation acts as a pivotal mechanism, integrating metabolic and signalling pathways to enable cellular adaptation, and highlight its potential as a therapeutic target in various diseases.

Monitoring Functional Posttranslational Modifications Using a Data-Driven Proteome Informatic Pipeline

Posttranslational modifications (PTMs) are of significant interest in molecular biomedicine due to their crucial role in signal transduction across various cellular and organismal processes. Characterizing PTMs, distinguishing between functional and inert modifications, quantifying their occupancies, and understanding PTM crosstalk are challenging tasks in any biosystem. Studying each PTM often requires a specific, labor-intensive experimental design. Here, we present a PTM-centric proteome informatic pipeline for predicting relevant PTMs in mass spectrometry-based proteomics data without prior information. Once predicted, these in silico identified PTMs can be incorporated into a refined database search and compared to measured data. As a practical application, we demonstrate how this pipeline can be used to study glycoproteomics in oral squamous cell carcinoma based on the proteome profile of primary tumors. Subsequently, we experimentally identified cellular proteins that are differentially expressed in cells treated with multikinase inhibitors dasatinib and staurosporine using mass spectrometry-based proteomics. Computational enrichment analysis was then employed to determine the potential PTMs of differentially expressed proteins induced by both drugs. Finally, we conducted an additional round of database search with the predicted PTMs. Our pipeline successfully analyzed the enriched PTMs, and detected proteins not identified in the initial search. Our findings support the effectiveness of PTM-centric searching of MS data in proteomics based on computational enrichment analysis, and we propose integrating this approach into future proteomics search engines.

Insights into structural and proteomic alterations related to pH-induced changes and protein deamidation in hair

OBJECTIVES

The hair shaft is often exposed to shampoo and haircare products that have unknown or varying pH levels. These products contain a combination of surfactants and other active ingredients to treat the hair or the scalp. As amphoteric proteins, hair keratins have limited buffering capacity, so variations in pH can have multifaceted impacts on them. However, there is limited knowledge about how pH affects keratins and keratin-associated proteins (KAPs). Therefore, this study aims to examine the effects of varying pH levels (pH 3-pH 12) on hair structure and analyse consequent alterations in the hair proteome using mass spectrometry-based proteomics.

METHODS

A scanning electron microscope was used to examine changes in hair-shaft morphology due to exposure to various pH levels, while mass spectrometry was employed to analyse protein alterations.

RESULTS

We found that exposing the hair shaft to varying pH levels led to specific effects on the cuticle, including cuticle lifting at certain pH levels, while proteomics analysis identified alterations in the hair proteome along with significant deamidation of keratins types I and II and KAPs. More pronounced effects were observed at extreme acidic conditions (pH 3) and alkaline conditions (above pH 8) on both hair morphology and hair proteins. pH levels between pH 5 and pH 7 had minimal impact on hair structure and proteins, suggesting that haircare products with pH in this range are ideal for hair-shaft health. In contrast, alkaline pH levels were found to negatively affect hair.

CONCLUSIONS

The structure evaluation and proteomics data emphasize the critical role of pH in hair health. The extreme acidic or alkaline pH impacts the hair structure and hair proteins. The study highlights the optimal pH range for maintaining healthy hair.

Recombinant protein expression in Acanthamoeba castellanii

The ongoing quest to improve protein production efficiency, quality, and versatility fuels the exploration of novel expression systems. In this research, we explored the potential of the axenically culturable Acanthamoeba as an alternative for producing recombinant eukaryotic proteins. We constructed plasmid vectors utilizing the TBP promoter to facilitate recombinant protein expression within this protozoan system. Our primary objectives were to develop an efficient transfection method and assess the capacity of Acanthamoeba castellanii for glycoprotein expression. Our initial efforts yielded successful expression of the firefly luciferase reporter gene, allowing us to optimize the transfection protocol. Subsequently, we compared the expression of the Chikungunya virus E2 protein across three systems: E. coli, Acanthamoeba, and mammalian cells. Interestingly, the E2 protein expressed in Acanthamoeba exhibited a molecular weight higher than bacterial cells but lower than mammalian cells, suggesting the possibility of glycosylation occurring in the protozoan system. These findings collectively suggest that protozoa, like A. castellanii, represent a promising avenue for developing low-cost and efficient eukaryotic expression systems.

Nanopore toward Genuine Single-Molecule Sensing: Molecular Ping-Pong Technology

Nanopore sensing is a so-called label-free, single-molecule technology; however, multiple events of different molecules are recorded to obtain statistically robust data, which can limit both efficiency and sample use. To overcome these challenges, nanopore molecular ping-pong technology enables precise single-molecule manipulation, reducing systematic and stochastic errors by repeatedly measuring the same molecule. This review introduces the fundamentals and advancements of ping-pong technology, highlighting a recent breakthrough achieving over 10,000 recaptures of a single dsDNA molecule within minutes. This innovation not only minimizes sample requirements, which is critical for nonamplifiable samples, but also significantly enhances experimental precision. While current applications focus on dsDNA, extending this technology to protein and glycan analysis could transform nanopore research. Just as nanopore technology revolutionized DNA sequencing, it holds the potential to drive the development of nanopore-based protein and glycan sequencers, paving the way for groundbreaking advancements in molecular biology and biomedicine.

Posttranslational Regulation of Mammalian Sulfur Amino Acid Metabolism

Metabolism of the mammalian proteinogenic sulfur amino acids methionine and cysteine includes the methionine cycle and reverse transsulfuration pathway, establishing many connections with other important metabolic routes. The main source of these amino acids is the diet, which also provides B vitamins required as cofactors for several enzymes of the metabolism of these amino acids. While methionine is considered an essential amino acid, cysteine can be produced from methionine in a series of reactions that also generate homocysteine, a non-proteinogenic amino acid linking reverse transsulfuration with the methionine and folate cycles. These pathways produce key metabolites that participate in synthesizing a large variety of compounds and important regulatory processes (e.g., epigenetic methylations). The impairment of sulfur amino acid metabolism manifests in many pathological processes, mostly correlated with oxidative stress and alterations in glutathione levels that also depend on this part of the cellular metabolism. This review analyzes the current knowledge on the posttranslational regulation of mammalian sulfur amino acid metabolism, highlighting the large number of modification sites reported through high-throughput studies and the surprisingly limited knowledge of their functional impact.

Proteo-Transcriptomic Analysis of the Venom Gland of the Cone Snail Cylinder canonicus Reveals the Origin of the Predatory-Evoked Venom

Cone snails are carnivorous marine predators that prey on mollusks, worms, or fish. They purposefully inject a highly diversified and peptide-rich venom, which can vary according to the predatory or defensive intended use. Previous studies have shown some correlations between the predation- and defense-evoked venoms and specific sections of the venom gland. In this study, we focus on the characterization of the venom of Cylinder canonicus, a molluscivorous species collected from Mayotte Island. Integrated proteomics and transcriptomics studies allowed for the identification of 108 conotoxin sequences from 24 gene superfamilies, with the most represented sequences belonging to the O1, O2, M, and conkunitzin superfamilies. A comparison of the predatory injected venom and the distal, central, and proximal sections of the venom duct suggests mostly distal origin. Identified conotoxins will contribute to a better understanding of venom-ecology relationships in cone snails and provide a novel resource for potential drug discovery.

Regulation of respiratory syncytial virus nucleoprotein oligomerization by phosphorylation

The negative-sense RNA genome of respiratory syncytial virus (RSV) is encapsidated by the viral nucleoprotein N, forming a left-handed helical nucleocapsid which serves as template for the viral polymerase. Specific oligomerization of N along the viral genome necessitates a switch of conformation of N, from the neosynthesized monomeric and RNA-free N protein, named N0, to N-RNA oligomers. Although the binding of the N-terminal part of RSV phosphoprotein P plays the role of chaperone to impair RNA binding to N, N0-P interaction alone is not sufficient to prevent N oligomerization. Here, we explored the potential role of post translational modifications that could participate in the stability of N0. Among the post translational modifications specifically identified on recombinant monomeric N, we validated the presence of a phosphorylation site on residue Y88 of N which modulates N oligomerization. Our results suggest that RSV N oligomerization depends on the regulation by post translational modifications.

Mass Spectrometry-Based Proteomics in Clinical Diagnosis of Amyloidosis and Multiple Myeloma: A Review (2012-2024)

Proteomics is nowadays increasingly becoming part of the routine clinical practice of diagnostic laboratories, especially due to the advent of advanced mass spectrometry techniques. This review focuses on the application of proteomic analysis in the identification of pathological conditions in a hospital setting, with a particular focus on the analysis of protein biomarkers. In particular, the main purpose of the review is to highlight the challenges associated with the identification of specific disease-causing proteins, given their complex nature and the variety of posttranslational modifications (PTMs) they can undergo. PTMs, such as phosphorylation and glycosylation, play critical roles in protein function but can also lead to diseases if dysregulated. Proteomics plays an important role especially in various medical fields ranging from cardiology, internal medicine to hemato-oncology emphasizing the interdisciplinary nature of this field. Traditional methods such as electrophoretic or immunochemical methods have been mainstay in protein detection; however, these techniques are limited in terms of specificity and sensitivity. Examples include the diagnosis of multiple myeloma and the detection of its specific protein or amyloidosis, which relies heavily on these conventional methods, which sometimes lead to false positives or inadequate disease monitoring. Mass spectrometry in this respect emerges as a superior alternative, providing high sensitivity and specificity in the detection and quantification of specific protein sequences. This technique is particularly beneficial for monitoring minimal residual disease (MRD) in the diagnosis of multiple myeloma where traditional methods fall short. Furthermore mass spectrometry can provide precise typing of amyloid proteins, which is crucial for the appropriate treatment of amyloidosis. This review summarizes the opportunities for proteomic determination using mass spectrometry between 2012 and 2024, highlighting the transformative potential of mass spectrometry in clinical proteomics and encouraging its wider use in diagnostic laboratories.

The main sources of molecular organization in the cell. Atlas of self-organized and self-regulated dynamic biostructures

One of the most important goals of contemporary biology is to understand the principles of the molecular order underlying the complex dynamic architecture of cells. Here, we present an overview of the main driving forces involved in the cellular molecular complexity and in the emergent functional dynamic structures, spanning from the most basic molecular organization levels to the complex emergent integrative systemic behaviors. First, we address the molecular information processing which is essential in many complex fundamental mechanisms such as the epigenetic memory, alternative splicing, regulation of transcriptional system, and the adequate self-regulatory adaptation to the extracellular environment. Next, we approach the biochemical self-organization, which is central to understand the emergency of metabolic rhythms, circadian oscillations, and spatial traveling waves. Such a complex behavior is also fundamental to understand the temporal compartmentalization of the cellular metabolism and the dynamic regulation of many physiological activities. Numerous examples of biochemical self-organization are considered here, which show that practically all the main physiological processes in the cell exhibit this type of dynamic molecular organization. Finally, we focus on the biochemical self-assembly which, at a primary level of organization, is a basic but important mechanism for the order in the cell allowing biomolecules in a disorganized state to form complex aggregates necessary for a plethora of essential structures and physiological functions. In total, more than 500 references have been compiled in this review. Due to these main sources of order, systemic functional structures emerge in the cell, driving the metabolic functionality towards the biological complexity.

Integrating CNN and Bi-LSTM for protein succinylation sites prediction based on Natural Language Processing technique

Protein succinylation, a post-translational modification wherein a succinyl group (-CO-CH₂-CH₂-CO-) attaches to lysine residues, plays a critical regulatory role in cellular processes. Dysregulated succinylation has been implicated in the onset and progression of various diseases, including liver, cardiac, pulmonary, and neurological disorders. However, identifying succinylation sites through experimental methods is often labor-intensive, costly, and technically challenging. To address this, we introduce an approach called CbiLSuccSite, that integrates Convolutional Neural Networks (CNN) with Bidirectional Long Short-Term Memory (Bi-LSTM) networks for the accurate prediction of protein succinylation sites. Our approach employs a word embedding layer to encode protein sequences, enabling the automatic learning of intricate patterns and dependencies without manual feature extraction. In 10-fold cross-validation, CBiLSuccSite achieved superior predictive performance, with an Area Under the Curve (AUC) of 0.826 and a Matthews Correlation Coefficient (MCC) of 0.502. Independent testing further validated its robustness, yielding an AUC of 0.818 and an MCC of 0.53. The integration of CNN and Bi-LSTM leverages the strengths of both architectures, establishing CBiLSuccSite as an effective tool for protein language processing and succinylation site prediction. Our model and code are publicly accessible at: https://github.com/nuinvtnu/CBiLSuccSite.

From Nanozymes to Multi-Purpose Nanomaterials: The Potential of Metal-Organic Frameworks for Proteomics Applications

Metal-organic frameworks (MOFs) have the potential to revolutionize the biotechnological and medical landscapes due to their easily tunable crystalline porous structure. Herein, the study presents MOFs' potential impact on proteomics, unveiling the diverse roles MOFs can play to boost it. Although MOFs are excellent catalysts in other scientific disciplines, their role as catalysts in proteomics applications remains largely underexplored, despite protein cleavage being of crucial importance in proteomics protocols. Additionally, the study discusses evolving MOF materials that are tailored for proteomics, showcasing their structural diversity and functional advantages compared to other types of materials used for similar applications. MOFs can be developed to seamlessly integrate into proteomics workflows due to their tunable features, contributing to protein separation, peptide enrichment, and ionization for mass spectrometry. This review is meant as a guide to help bridge the gap between material scientists, engineers, and MOF chemists and on the other side researchers in biology or bioinformatics working in proteomics.

Dynamic proteome and phosphoproteome profiling reveals regulatory mechanisms in LPS-stimulated macrophage inflammatory responses

Macrophage-mediated acute inflammation is crucial for pathogen clearance and tissue repair, yet the underlying molecular mechanisms remain inadequately understood. The present study focused on the dynamic profiles of the proteome and phosphoproteome of macrophages exposed to lipopolysaccharide within 1 h. Gene Set Enrichment Analysis (GSEA) identified significantly enriched pathways in fatty acid metabolism and translation during the early inflammatory phase. Further trend analysis of the differentially expressed proteins revealed patterns associated with translation regulation such as translation initiation. Importantly, the nascent chain experiment demonstrated no significant changes in overall gene translation levels during this phase. These data indicate that macrophages maintain intracellular protein homeostasis through translational regulation, with post-translational modifications (PTMs) playing a crucial role in the rapid cellular response to pathogen invasion. Phosphorylation is a key PTM that regulates protein functions in almost all cellular processes. Time-resolved phosphoproteome analysis identified 367 differentially expressed phosphopeptides involved in immune-related pathways that resist infection. Additionally, weighted gene co-expression network analysis (WGCNA) discovered core modules that regulate translation-related processes such as RNA export from nucleus. Moreover, conjoint analysis of the proteome and phosphoproteome identified the hub protein EF1B that exhibited the largest fold change and is also involved in translation. Our data not only provide a more comprehensive understanding of the dynamic molecular networks of acute macrophage inflammation but also provide a systematic proteomic resource for further studies.

A Narrative Review of the Role of S-Glutathionylation in Bacteria

Protein glutathionylation is defined as a reversible, ubiquitous post-translational modification, resulting in the formation of mixed disulfides between glutathione and proteins' cysteine residues. Glutathionylation has been implicated in several cellular mechanisms ranging from protection from oxidative stress to the control of cellular homeostasis and the cell cycle. A significant body of research has examined the multifaceted effects of this post-translational modification under physiological conditions in eukaryotes, with a particular focus on its impact on the development of various diseases in humans. In contrast, the role of glutathionylation in prokaryotic organisms remains to be extensively investigated. However, there has been a recent increase in the number of studies investigating this issue, providing details about the role of glutathione and other related thiols as post-translational modifiers of selected bacterial proteins. It can be concluded that in addition to the classical role of such thiols in protecting against cysteine oxidation and consequent protein inactivation, many more specialized roles of glutathionylation in bacterial pathogenicity, virulence, interspecies competition and survival, and control of gene expression are emerging, and new ones may emerge in the future. In this short review, we aim to summarize the current state-of-the-art in this field of research.

Optogenetics with Atomic Precision─A Comprehensive Review of Optical Control of Protein Function through Genetic Code Expansion

Conditional control of protein activity is important in order to elucidate the particular functions and interactions of proteins, their regulators, and their substrates, as well as their impact on the behavior of a cell or organism. Optical control provides a perhaps optimal means of introducing spatiotemporal control over protein function as it allows for tunable, rapid, and noninvasive activation of protein activity in its native environment. One method of introducing optical control over protein activity is through the introduction of photocaged and photoswitchable noncanonical amino acids (ncAAs) through genetic code expansion in cells and animals. Genetic incorporation of photoactive ncAAs at key residues in a protein provides a tool for optical activation, or sometimes deactivation, of protein activity. Importantly, the incorporation site can typically be rationally selected based on structural, mechanistic, or computational information. In this review, we comprehensively summarize the applications of photocaged lysine, tyrosine, cysteine, serine, histidine, glutamate, and aspartate derivatives, as well as photoswitchable phenylalanine analogues. The extensive and diverse list of proteins that have been placed under optical control demonstrates the broad applicability of this methodology.

NanoAbLLaMA: construction of nanobody libraries with protein large language models

Introduction

Traditional methods for constructing synthetic nanobody libraries are labor-intensive and time-consuming. This study introduces a novel approach leveraging protein large language models (LLMs) to generate germline-specific nanobody sequences, enabling efficient library construction through statistical analysis.

Methods

We developed NanoAbLLaMA, a protein LLM based on LLaMA2, fine-tuned using low-rank adaptation (LoRA) on 120,000 curated nanobody sequences. The model generates sequences conditioned on germlines (IGHV3-301 and IGHV3S5301). Training involved dataset preparation from SAbDab and experimental data, alignment with IMGT germline references, and structural validation using ImmuneBuilder and Foldseek.

Results

NanoAbLLaMA achieved near-perfect germline generation accuracy (100% for IGHV3-301, 95.5% for IGHV3S5301). Structural evaluations demonstrated superior predicted Local Distance Difference Test (pLDDT) scores (90.32 ± 10.13) compared to IgLM (87.36 ± 11.17), with comparable TM-scores. Generated sequences exhibited fewer high-risk post-translational modification sites than IgLM. Statistical analysis of CDR regions confirmed diversity, particularly in CDR3, enabling the creation of synthetic libraries with high humanization (>99.9%) and low risk.

Discussion

This work establishes a paradigm shift in nanobody library construction by integrating LLMs, significantly reducing time and resource demands. While NanoAbLLaMA excels in germline-specific generation, limitations include restricted germline coverage and framework flexibility. Future efforts should expand germline diversity and incorporate druggability metrics for clinical relevance. The model's code, data, and resources are publicly available to facilitate broader adoption.

Expression profile and characterization of respiratory burst oxidase homolog genes in rice under MeJA, SA and Xoo treatments

Respiratory burst oxidase homologs (Rboh) genes is essential for synthesizing reactive oxygen species, which play a crucial role in environmental stress response. The Rboh gene family has been studied in model plants such as Arabidopsis. Nevertheless, Rboh remained largely unexplored in Rice (Oryza sativa L.). Here, we performed characterization of the Rboh genes family in rice (OsRboh) under Xanthomonas oryzae pv. oryzae (Xoo), salicylic acid (SA), and methyl jasmonate (MeJA) treatments. Nine OsRboh genes were retrieved distributed across six chromosomes (1, 5, 8, 9, 11, 12).These genes vary in amino acid sequence length (728-1034), isoelectric point (9.05-9.84), and molecular weight (8.341-115.014 kDa). Analysis of gene structure, motifs and conserved domains showed that OsRboh genes have similar protein sequences and functions. The promoter region of OsRboh genes was found to contain mainly cis-acting elements associated with light, jasmonic acid (JA), abscisic acid (ABA), and SA responsiveness. Predictions of functional protein-protein interaction showed that OsRboh genes were associated with MAPK signaling, plant-pathogen interaction, and other mRNA surveillance pathways. Prediction of miRNA targets and post-translational modification sites indicated that OsRboh genes may be regulated by miRNA and protein phosphorylation. Phylogenetic analysis showed that OsRboh genes were distributed into 7 clusters. Furthermore, 9 OsRboh genes were differentially expressed in different tissues (roots, stems, and leaves). OsRbohA, OsRbohB, and OsRbohD are significant genes in rice defense responses, showing unique and increased expression profiles under (Xoo-PXO99), (MeJA), and (SA) treatments. These genes important function in triggering defense mechanisms is further stressed by the high (> 20-fold) changes in expression they exhibit under these treatments. These findings enhance our understanding of rice OsRboh genes functions and contribute to stress tolerance improvement strategies.

Structures of Gas-Phase Hydrated Phosphotyrosine Revealed by Soft X-ray Action Spectroscopy

Gas-phase near-edge X-ray absorption mass spectrometry (NEXAMS) was employed at the carbon and oxygen K-edges to probe the influence of a single water molecule on the protonated phosphotyrosine molecule. The results of the photodissociation experiments revealed that the water molecule forms two bonds, with the phosphate group and another chemical group. By comparing the NEXAMS spectra at the carbon and oxygen K-edges with density functional theory calculations, we attributed the electronic transitions responsible for the observed resonances, especially the transitions due to the presence of the water molecule. We showed that the water molecule leads to a specific spectral feature in the partial ion yield of hydrated fragments at 536.4 eV. Moreover, comparing the NEXAMS spectra with the calculated structures allowed us to identify three possible structures for singly hydrated phosphotyrosine that agree with the observed fragmentation and resonances.

Proteomics- and metabolomics-based analysis of the regulation of germination in Norway maple and sycamore embryonic axes

Norway maple and sycamore belong to the Acer genus and produce desiccation-tolerant and desiccation-sensitive seeds, respectively. We investigated the seed germination process at the imbibed and germinated stages using metabolomic and proteomic approaches to determine why sycamore seeds germinate earlier and are more successful at establishing seedlings than Norway maple seeds under controlled conditions. Embryonic axes and embryonic axes with protruded radicles were analyzed at the imbibed and germinated stages, respectively. Among the 212 identified metabolites, 44 and 67 differentially abundant metabolites were found at the imbibed and germinated stages, respectively, in both Acer species. Higher levels of amines, growth and defense stimulants, including B vitamins, were found in sycamore. We identified 611 and 447 proteins specific to the imbibed and germinated stages, respectively, in addition to groups of proteins expressed at different levels. Functional analysis of significantly regulated proteins revealed that proteins with catalytic and binding activity were enriched during germination, and proteins possibly implicated in nitrogen metabolism and metabolite interconversion enzymes were the predominant classes. Proteins associated with the control of plant growth regulation and seed defense were observed in both species at both germination stages. Sycamore proteins possibly involved in abscisic acid signal transduction pathway, stress tolerance and alleviation, ion binding and oxygenase activities appeared to accompany germination in sycamore. We identified peptides containing methionine (Met) oxidized to methionine sulfoxide (MetO), and functional analyses of proteins with significantly regulated MetO sites revealed that translation, plant growth and development and metabolism of nitrogen compounds were the main processes under Met/MetO redox control. We propose that higher levels of storage proteins and amines, together with higher levels of B vitamins, supported more efficient nitrogen utilization in sycamore, resulting in faster seedling growth. In conclusion, omic signatures identified in sycamore seem to predispose germinated sycamore seeds to better postgerminative growth.

Increased expression of ER stress, inflammasome activation, and mitochondrial biogenesis-related genes in peripheral blood mononuclear cells in major depressive disorder

A subset of major depressive disorder (MDD) is characterized by immune system dysfunction, but the intracellular origin of these immune changes remains unclear. Here we tested the hypothesis that abnormalities in endoplasmic reticulum (ER) stress, inflammasome activity and mitochondrial biogenesis contribute to the development of systemic inflammation in MDD. RT-qPCR was used to measure mRNA expression of key organellar genes from peripheral blood mononuclear cells (PBMCs) isolated from 186 MDD and 67 healthy control (HC) subjects. The comparative CT (2-ΔΔCT) method was applied to quantify mRNA expression using GAPDH as the reference gene. After controlling for age, sex, BMI, and medication status using linear regression models, expression of the inflammasome (NLRC4 and NLRP3) and the ER stress (XBP1u, XBP1s, and ATF4) genes was found to be significantly increased in the MDD versus the HC group. Sensitivity analyses excluding covariates yielded similar results. After excluding outliers, expression of the inflammasome genes was no longer statistically significant but expression of the ER stress genes (XBP1u, XBP1s, and ATF4) remained significant and the mitochondrial biogenesis gene, MFN2, was significantly increased in the MDD group. NLRC4 and MFN2 were positively correlated with serum C-reactive protein concentrations, while ASC trended significant. The altered expression of inflammasome activation, ER stress, and mitochondrial biogenesis pathway components suggest that dysfunction of these organelles may play a role in the pathogenesis of MDD.

DeepPhoPred: Accurate Deep Learning Model to Predict Microbial Phosphorylation

Phosphorylation is a substantial posttranslational modification of proteins that refers to adding a phosphate group to the amino acid side chain after translation process in the ribosome. It is vital to coordinate cellular functions, such as regulating metabolism, proliferation, apoptosis, subcellular trafficking, and other crucial physiological processes. Phosphorylation prediction in a microbial organism can assist in understanding pathogenesis and host-pathogen interaction, drug and antibody design, and antimicrobial agent development. Experimental methods for predicting phosphorylation sites are costly, slow, and tedious. Hence low-cost and high-speed computational approaches are highly desirable. This paper presents a new deep learning tool called DeepPhoPred for predicting microbial phospho-serine (pS), phospho-threonine (pT), and phospho-tyrosine (pY) sites. DeepPhoPred incorporates a two-headed convolutional neural network architecture with the squeeze and excitation blocks followed by fully connected layers that jointly learn significant features from the peptide's structural and evolutionary information to predict phosphorylation sites. Our empirical results demonstrate that DeepPhoPred significantly outperforms the existing microbial phosphorylation site predictors with its highly efficient deep-learning architecture. DeepPhoPred as a standalone predictor, all its source codes, and our employed datasets are publicly available at https://github.com/faisalahm3d/DeepPhoPred.

Generative AI Models for the Protein Scaffold Filling Problem

De novo protein sequencing is an important problem in proteomics, playing a crucial role in understanding protein functions, drug discovery, design and evolutionary studies, etc. Top-down and bottom-up tandem mass spectrometry are popular approaches used in the field of mass spectrometry to analyze and sequence proteins. However, these approaches often produce incomplete protein sequences with gaps, namely scaffolds. The protein scaffold filling problem refers to filling the missing amino acids in the gaps of a scaffold to infer the complete protein sequence. In this article, we tackle the protein scaffold filling problem based on generative AI techniques, such as convolutional denoising autoencoder, transformer, and generative pretrained transformer (GPT) models, to complete the protein sequences and compare our results with recently developed convolutional long short-term memory-based sequence model. We evaluate the model performance both on a real dataset and generated datasets. All proposed models show outstanding prediction accuracy. Notably, the GPT-2 model achieves 100% gap-filling accuracy and 100% full sequence accuracy on the MabCampth protein scaffold, which outperforms the other models.