Molecular handcraft of a well‐folded protein chimera

Molecular handcraft of a well-folded protein chimera

Discovering new proteins through modular assembly, inspired by both nature's evolution and protein engineering, offers exciting possibilities. By leveraging information on subdomain-sized fragments from the database Fuzzle, we seamlessly integrated a flavodoxin-like fragment into a periplasmic binding protein. The resulting chimera exhibits remarkable folding and stable interfaces, showcasing the adaptability of α/β-proteins. Our work pioneers novel avenues in protein engineering and sheds light on the evolutionary origins of periplasmic binding proteins.


Modular assembly is a compelling pathway to create new proteins, a concept supported by protein engineering and millennia of evolution. Natural evolution provided a repository of building blocks, known as domains, which trace back to even shorter segments that underwent numerous ‘copy-paste’ processes culminating in the scaffolds we see today. Utilizing the subdomain-database Fuzzle, we constructed a fold-chimera by integrating a flavodoxin-like fragment into a periplasmic binding protein. This chimera is well-folded and a crystal structure reveals stable interfaces between the fragments. These findings demonstrate the adaptability of α/β-proteins and offer a stepping stone for optimization. By emphasizing the practicality of fragment databases, our work pioneers new pathways in protein engineering. Ultimately, the results substantiate the conjecture that periplasmic binding proteins originated from a flavodoxin-like ancestor.

Global transcriptome analysis reveals Salmonella Typhimurium employs nitrate metabolism to combat bile stress

Global transcriptome analysis reveals Salmonella Typhimurium employs nitrate metabolism to combat bile stress

Our study showed that bile-mediated modulation of bacterial metabolism involves induction of various metabolic processes, e.g., anaerobic respiration dependent on nitrate. We observed that the activation of the nitrate metabolism-related genes fnr and narL is notably higher in the bile-tolerant WT strain compared to the bile-sensitive ΔcspE strain. Consequently, the WT strain displays lower amounts of reactive oxygen species and higher survival compared to the ΔcspE strain during bile stress.


Salmonella Typhimurium is an enteric pathogen that is highly tolerant to bile. Next-generation mRNA sequencing was performed to analyze the adaptive responses to bile in two S. Typhimurium strains: wild type (WT) and a mutant lacking cold shock protein E (ΔcspE). CspE is an RNA chaperone which is crucial for survival of S. Typhimurium during bile stress. This study identifies transcriptional responses in bile-tolerant WT and bile-sensitive ΔcspE. Upregulation of several genes involved in nitrate metabolism was observed, including fnr, a global regulator of nitrate metabolism. Notably, Δfnr was susceptible to bile stress. Also, complementation with fnr lowered reactive oxygen species and enhanced the survival of bile-sensitive ΔcspE. Importantly, intracellular nitrite amounts were highly induced in bile-treated WT compared to ΔcspE. Also, the WT strain pre-treated with nitrate displayed better growth with bile. These results demonstrate that nitrate-dependent metabolism promotes adaptation of S. Typhimurium to bile.

Inflammasomes in epithelial innate immunity: front line warriors

Inflammasomes in epithelial innate immunity: front line warriors

Strategically placed, our epithelium plays an essential role in maintaining and guarding tissue homeostasis. One key set of defense mechanisms is represented by our inflammasomes, which sense and respond to pathogen attack, through the secretion of pro-inflammatory cytokines. This review will focus on how the inflammasomes, our front-line warriors, maintain our skin, respiratory, and gut epithelial barrier immunity.


Our epithelium represents a battle ground against a variety of insults including pathogens and danger signals. It encodes multiple sensors that detect and respond to such insults, playing an essential role in maintaining and defending tissue homeostasis. One key set of defense mechanisms is our inflammasomes which drive innate immune responses including, sensing and responding to pathogen attack, through the secretion of pro-inflammatory cytokines and cell death. Identification of physiologically relevant triggers for inflammasomes has greatly influenced our ability to decipher the mechanisms behind inflammasome activation. Furthermore, identification of patient mutations within inflammasome components implicates their involvement in a range of epithelial diseases. This review will focus on exploring the roles of inflammasomes in epithelial immunity and cover: the diversity and differential expression of inflammasome sensors amongst our epithelial barriers, their ability to sense local infection and damage and the contribution of the inflammasomes to epithelial homeostasis and disease.

Macromolecular crowding has opposite effects on two critical sub‐steps of transcription initiation

Macromolecular crowding has opposite effects on two critical sub-steps of transcription initiation

In this work, we study the effect of macromolecular crowding on transcription initiation and report a surprising result: while the first step of promoter opening slows down, the subsequent step of RNA synthesis and promoter escape becomes faster in the presence of crowders. This suggests that the crowded cellular environment significantly impacts gene function, with the effect varying between promoters.


Transcription initiation, the first step in gene expression, has been studied extensively in dilute buffer, a condition which fails to consider the crowded environment in live cells. Recent reports indicate the kinetics of promoter escape is altered in crowded conditions for a consensus bacterial promoter. Here, we use a real-time fluorescence enhancement assay to study the kinetics of unwound bubble formation and promoter escape for three separate promoters. We find that the effect of crowding on transcription initiation is complex, with lower rates of unwound bubble formation, higher rates of promoter escape, and large variations depending on promoter identity. Based on our results, we suggest that altered conditions of crowding inside a live cell can trigger global changes.

Phosphorylation of TG‐interacting factor 1 at carboxyl‐terminal sites in response to insulin regulates adipocyte differentiation

Phosphorylation of TG-interacting factor 1 at carboxyl-terminal sites in response to insulin regulates adipocyte differentiation

TG-interacting factor 1 (TGIF1) contributes to the differentiation of white preadipocytes; however, its regulation is not well elucidated. We highlight that the insulin-induced ERK activation phosphorylates the T235 or T239 residue of TGIF1, which is crucial for the promotion of mitotic clonal expansion and adipocyte differentiation.


TG-interacting factor 1 (TGIF1) contributes to the differentiation of murine white preadipocyte and human adipose tissue-derived stem cells; however, its regulation is not well elucidated. Insulin is a component of the adipogenic cocktail that induces ERK signaling. TGIF1 phosphorylation and sustained stability in response to insulin were reduced through the use of specific MEK inhibitor U0126. Mutagenesis at T235 or T239 residue of TGIF1 in preadipocytes led to dephosphorylation of TGIF1. The reduced TGIF1 stability resulted in an increase in p27 kip1 expression, a decrease in phosphorylated Rb expression and cellular proliferation, and a reduced accumulation of lipids compared to the TGIF1-overexpressed cells. These findings highlight that insulin/ERK-driven phosphorylation of the T235 or T239 residue at TGIF1 is crucial for adipocyte differentiation.

Redox imbalance and metabolic defects in the context of Alzheimer disease

Redox imbalance and metabolic defects in the context of Alzheimer disease

During aging, a progressive failure of energy metabolism occurs resulting in brain hypometabolism. This condition, combined with redox disturbance, contributes to increase neuronal cell vulnerability ultimately leading to neurodegeneration. Down syndrome and Alzheimer disease neuropathologies present several molecular similarities, among which perturbation of redox homeostasis and reduced energy production are major players that accelerate neuronal damage.


Redox reactions play a critical role for intracellular processes, including pathways involved in metabolism and signaling. Reactive oxygen species (ROS) act either as second messengers or generators of protein modifications, fundamental mechanisms for signal transduction. Disturbance of redox homeostasis is associated with many disorders. Among these, Alzheimer's disease is a neurodegenerative pathology that presents hallmarks of oxidative damage such as increased ROS production, decreased activity of antioxidant enzymes, oxidative modifications of macromolecules, and changes in mitochondrial homeostasis. Interestingly, alteration of redox homeostasis is closely associated with defects of energy metabolism, involving both carbohydrates and lipids, the major energy fuels for the cell. As the brain relies exclusively on glucose metabolism, defects of glucose utilization represent a harmful event for the brain. During aging, a progressive perturbation of energy metabolism occurs resulting in brain hypometabolism. This condition contributes to increase neuronal cell vulnerability ultimately resulting in cognitive impairment. The current review discusses the crosstalk between alteration of redox homeostasis and brain energy defects that seems to act in concert in promoting Alzheimer's neurodegeneration.

How enzyme‐centered approaches are advancing research on cyclic oligo‐nucleotides

How enzyme-centered approaches are advancing research on cyclic oligo-nucleotides

Cyclic nucleotides serve as second messengers throughout kingdoms of life and regulate various pathways. Here, we review recent milestones in cyclic nucleotide biology, focusing on different enzyme folds that synthesize these signals, their regulatory mechanisms, and pleiotropic downstream signaling events. Our particular focus is on enzyme-centered approaches specifically targeting nucleotidyltransferases, which have enabled the discovery of novel cyclic nucleotides.


Cyclic nucleotides are the most diversified category of second messengers and are found in all organisms modulating diverse pathways. While cAMP and cGMP have been studied over 50 years, cyclic di-nucleotide signaling in eukaryotes emerged only recently with the anti-viral molecule 2´3´cGAMP. Recent breakthrough discoveries have revealed not only the astonishing chemical diversity of cyclic nucleotides but also surprisingly deep-rooted evolutionary origins of cyclic oligo-nucleotide signaling pathways and structural conservation of the proteins involved in their synthesis and signaling. Here we discuss how enzyme-centered approaches have paved the way for the identification of several cyclic nucleotide signals, focusing on the advantages and challenges associated with deciphering the activation mechanisms of such enzymes.

TERRA and the alternative lengthening of telomeres: a dangerous affair

TERRA and the alternative lengthening of telomeres: a dangerous affair

The long noncoding RNA TERRA controls telomere length homeostasis in human cancers with an activated alternative lengthening of telomeres (ALT) mechanism. Telomeric R-loops formed between TERRA and telomeric DNA (telR-loops) promote telomere elongation through homology-directed repair. However, if not properly regulated, TERRA and telR-loops can lead to rapid cleavage of telomeric DNA and telomere loss.


Eukaryotic telomeres are transcribed into the long noncoding RNA TERRA. A fraction of TERRA remains associated with telomeres by forming RNA:DNA hybrids dubbed telR-loops. TERRA and telR-loops are essential to promote telomere elongation in human cancer cells that maintain telomeres through a homology-directed repair pathway known as alternative lengthening of telomeres or ALT. However, TERRA and telR-loops compromise telomere integrity and cell viability if their levels are not finely tuned. The study of telomere transcription in ALT cells will enormously expand our understanding of the ALT mechanism and of how genome integrity is maintained. Moreover, telomere transcription, TERRA and telR-loops are likely to become exceptionally suited targets for the development of novel anti-cancer therapies.

A life‐time of hematopoietic cell function: ascent, stability, and decline

A life-time of hematopoietic cell function: ascent, stability, and decline

Here we review the aging of the hematopoietic system from its earliest stages in the embryo through fetal and adult life. We focus on the waves of hematopoietic cell generation during embryonic life and how cells of varying lineages, functions and life spans contribute to the normal development of the adult blood system and its progressive gain/loss of function in the aged adult.


Aging is a set of complex processes that occur temporally and continuously. It is generally a unidirectional progression of cellular and molecular changes occurring during the life stages of cells, tissues and ultimately the whole organism. In vertebrate organisms, this begins at conception from the first steps in blastocyst formation, gastrulation, germ layer differentiation, and organogenesis to a continuum of embryonic, fetal, adolescent, adult, and geriatric stages. Tales of the “fountain of youth” and songs of being “forever young” are dominant ideas informing us that growing old is something science should strive to counteract. Here, we discuss the normal life stages of the blood system, particularly the historical recognition of its importance in the early growth stages of vertebrates, and what this means with respect to progressive gain and loss of hematopoietic function in the adult.

How CBX proteins regulate normal and leukemic blood cells

How CBX proteins regulate normal and leukemic blood cells

CBX proteins are epigenetic reader proteins that can recognize histone modifications and thereby dictate cell fate. In this review, we describe how CBX proteins dictate cell fate in normal hematopoiesis and leukemia. In addition, we discuss which CBX proteins can promote leukemic cell growth and whether pharmacological inhibition of CBX proteins can reverse leukemic cell fate.


Hematopoietic stem cell (HSC) fate decisions are dictated by epigenetic landscapes. The Polycomb Repressive Complex 1 (PRC1) represses genes that induce differentiation, thereby maintaining HSC self-renewal. Depending on which chromobox (CBX) protein (CBX2, CBX4, CBX6, CBX7, or CBX8) is part of the PRC1 complex, HSC fate decisions differ. Here, we review how this occurs. We describe how CBX proteins dictate age-related changes in HSCs and stimulate oncogenic HSC fate decisions, either as canonical PRC1 members or by alternative interactions, including non-epigenetic regulation. CBX2, CBX7, and CBX8 enhance leukemia progression. To target, reprogram, and kill leukemic cells, we suggest and describe multiple therapeutic strategies to interfere with the epigenetic functions of oncogenic CBX proteins. Future studies should clarify to what extent the non-epigenetic function of cytoplasmic CBX proteins is important for normal, aged, and leukemic blood cells.