Anaerobic spp. degrade sulfoquinovose via a bifurcated 6-deoxy-6-sulfofructose transketolase/transaldolase pathway to both C- and C-sulfonate intermediates.

Plant-produced sulfoquinovose (SQ, 6-deoxy-6-sulfoglucose) is one of the most abundant sulfur-containing compounds in nature and its bacterial degradation plays an important role in the biogeochemical sulfur and carbon cycles and in all habitats where SQ is produced and degraded, particularly in gut microbiomes. Here, we report the enrichment and characterization of a strictly anaerobic SQ-degrading bacterial consortium that produces the C-sulfonate isethionate (ISE) as the major product but also the C-sulfonate 2,3-dihydroxypropanesulfonate (DHPS), with concomitant production of acetate and hydrogen (H). In the second step, the ISE was degraded completely to hydrogen sulfide (HS) when an additional electron donor (external H) was supplied to the consortium.

Protein kinase 2 of the giant sarcomeric protein UNC-89 regulates mitochondrial morphology and function.

UNC-89 is a giant sarcomeric M-line protein required for sarcomere organization and optimal muscle function. UNC-89 contains two protein kinase domains, PK1 and PK2, separated by an elastic region. Here we show that PK2 is a canonical kinase expected to be catalytically active.

Metformin hydrolase is a recently evolved nickel-dependent heteromeric ureohydrolase.

The anti-diabetic drug metformin is one of the most widely prescribed medicines in the world. Together with its degradation product guanylurea, it is a major pharmaceutical pollutant in wastewater treatment plants and surface waters. An operon comprising two genes of the ureohydrolase family in Pseudomonas and Aminobacter species has recently been implicated in metformin degradation.

Liver receptor homolog-1 (NR5A2) orchestrates hepatic inflammation and TNF-induced cell death.

The nuclear receptor liver receptor homolog-1 (LRH-1) has been shown to promote apoptosis resistance in various tissues and disease contexts; however, its role in liver cell death remains unexplored. Hepatocyte-specific deletion of LRH-1 causes mild steatosis and inflammation but unexpectedly shields female mice from tumor necrosis factor (TNF)-induced hepatocyte apoptosis and associated hepatitis. LRH-1-deficient hepatocytes show markedly attenuated estrogen receptor alpha and elevated nuclear factor κB (NF-κB) activity, while LRH-1 overexpression inhibits NF-κB activity.

AMP-dependent phosphite dehydrogenase, a phosphorylating enzyme in dissimilatory phosphite oxidation.

Oxidation of phosphite (HPO) to phosphate (HPO) releases electrons at a very low redox potential (E= -690 mV) which renders phosphite an excellent electron donor for microbial energy metabolism. To date, two pure cultures of strictly anaerobic bacteria have been isolated that run their energy metabolism on the basis of phosphite oxidation, the Gram-negative (DSM 13687) and the Gram-positive (DSM 112739). Here, we describe the key enzyme for dissimilatory phosphite oxidation in these bacteria.

Crystal structure of a GCN5-related N-acetyltransferase from Lactobacillus curiae.

Members of the GCN5-related N-acetyltransferase (GNAT) family are found in all domains of life and are involved in processes ranging from protein synthesis and gene expression to detoxification and virulence. Due to the variety of their macromolecular targets, GNATs are a highly diverse family of proteins. Currently, 3D structures of only a small number of GNAT representatives are available and thus the family remains poorly characterized.

Titin UN2A Acts as a Stable, Non-Polymorphic Scaffold in its Binding to CARP.

The N2A segment of titin functions as a pivotal hub for signal transduction and interacts with various proteins involved in structural support, chaperone activities, and transcriptional regulation. Notably, the "unique N2A" (UN2A) subdomain has been shown to interact with the stress-regulated cardiac ankyrin repeat protein (CARP), which contributes to the regulation of sarcomeric stiffness. Previously, the UN2A domain's three-dimensional structure was modelled based on its secondary structure content identified by NMR spectroscopy, considering the domain in isolation.

Molecular insights into titin's A-band.

The thick filament-associated A-band region of titin is a highly repetitive component of the titin chain with important scaffolding properties that support thick filament assembly. It also has a demonstrated link to human disease. Despite its functional significance, it remains a largely uncharacterized part of the titin protein.

PK1 from obscurin is an inactive pseudokinase with scaffolding properties.

Obscurins are large filamentous proteins with crucial roles in the assembly, stability and regulation of muscle. Characteristic of these proteins is a tandem of two C-terminal kinase domains, PK1 and PK2, that are separated by a long intrinsically disordered sequence. The significance of this conserved domain arrangement is unknown.

Immunological and Structural Characterization of Titin Main Immunogenic Region; I110 Domain Is the Target of Titin Antibodies in Myasthenia Gravis.

Myasthenia gravis (MG) is an autoimmune disease caused by antibodies targeting the neuromuscular junction (NJ) of skeletal muscles. The major MG autoantigen is nicotinic acetylcholine receptor. Other autoantigens at the NJ include MuSK, LRP4 and agrin.

Guanidino acid hydrolysis by the human enzyme annotated as agmatinase.

Guanidino acids such as taurocyamine, guanidinobutyrate, guanidinopropionate, and guanidinoacetate have been detected in humans. However, except for guanidionacetate, which is a precursor of creatine, their metabolism and potential functions remain poorly understood. Agmatine has received considerable attention as a potential neurotransmitter and the human enzyme so far annotated as agmatinase (AGMAT) has been proposed as an important modulator of agmatine levels.

Pairwise sequence similarity mapping with PaSiMap: Reclassification of immunoglobulin domains from titin as case study.

Sequence comparison is critical for the functional assignment of newly identified protein genes. As uncharacterized protein sequences accumulate, there is an increasing need for sensitive tools for their classification. Here, we present a novel multidimensional scaling pipeline, PaSiMap, which creates a map of pairwise sequence similarities.

Production and analysis of titin kinase: Exploiting active/inactive kinase homologs in pseudokinase validation.

Protein pseudokinases are key regulators of the eukaryotic cell. Understanding their unconventional molecular mechanisms relies on deciphering their putative potential to perform phosphotransfer, their scaffolding properties and the nature of their regulation. Titin pseudokinase (TK) is the defining member of a family of poorly characterized muscle-specific kinases thought to act as sensors and transducers of mechanical signals in the sarcomere.

Discovery of a Ni-dependent guanidine hydrolase in bacteria.

Nitrogen availability is a growth-limiting factor in many habitats, and the global nitrogen cycle involves prokaryotes and eukaryotes competing for this precious resource. Only some bacteria and archaea can fix elementary nitrogen; all other organisms depend on the assimilation of mineral or organic nitrogen. The nitrogen-rich compound guanidine occurs widely in nature, but its utilization is impeded by pronounced resonance stabilization, and enzymes catalysing hydrolysis of free guanidine have not been identified.

Conformational changes in twitchin kinase in vivo revealed by FRET imaging of freely moving .

The force-induced unfolding and refolding of proteins is speculated to be a key mechanism in the sensing and transduction of mechanical signals in the living cell. Yet, little evidence has been gathered for its existence in vivo. Prominently, stretch-induced unfolding is postulated to be the activation mechanism of the twitchin/titin family of autoinhibited sarcomeric kinases linked to the mechanical stress response of muscle.

Titin kinase ubiquitination aligns autophagy receptors with mechanical signals in the sarcomere.

Striated muscle undergoes remodelling in response to mechanical and physiological stress, but little is known about the integration of such varied signals in the myofibril. The interaction of the elastic kinase region from sarcomeric titin (A168-M1) with the autophagy receptors Nbr1/p62 and MuRF E3 ubiquitin ligases is well suited to link mechanosensing with the trophic response of the myofibril. To investigate the mechanisms of signal cross-talk at this titin node, we elucidated its 3D structure, analysed its response to stretch using steered molecular dynamics simulations and explored its functional relation to MuRF1 and Nbr1/p62 using cellular assays.

The N2A region of titin has a unique structural configuration.

The N2A segment of titin is a main signaling hub in the sarcomeric I-band that recruits various signaling factors and processing enzymes. It has also been proposed to play a role in force production through its Ca2+-regulated association with actin. However, the molecular basis by which N2A performs these functions selectively within the repetitive and extensive titin chain remains poorly understood.

Molecular Characterisation of Titin N2A and Its Binding of CARP Reveals a Titin/Actin Cross-linking Mechanism.

Striated muscle responds to mechanical overload by rapidly up-regulating the expression of the cardiac ankyrin repeat protein, CARP, which then targets the sarcomere by binding to titin N2A in the I-band region. To date, the role of this interaction in the stress response of muscle remains poorly understood. Here, we characterise the molecular structure of the CARP-receptor site in titin (UN2A) and its binding of CARP.

Histone mRNA is subject to 3' uridylation and re-adenylation in Aspergillus nidulans.

The role of post-transcriptional RNA modification is of growing interest. One example is the addition of non-templated uridine residues to the 3' end of transcripts. In mammalian systems, uridylation is integral to cell cycle control of histone mRNA levels.

Structural annotation of the conserved carbohydrate esterase vb_24B_21 from Shiga toxin-encoding bacteriophage Φ24.

Shiga toxin-encoding bacteriophages transfer Shiga toxin genes to Escherichia coli and are responsible for the emergence of pathogenic bacterial strains that cause severe foodborne human diseases. Gene vb_24B_21 is the most highly conserved gene across sequenced Shiga bacteriophages. Protein vb_24B_21 (also termed 933Wp42 and NanS-p) is a carbohydrate esterase with homology to the E.

Strategy to replace animal-derived ECM by a modular and highly defined matrix.

Many extracellular matrices (ECM) used for modern cell culture are derived from animals. An alternative approach is the recombinant production of individual matrix protein components. A further development of this strategy uses a constant core protein polymer that is modifiable with functional domains of various ECM proteins.

The importance of chain context in assessing small nucleotide variants in titin: case study of the I10-I11 tandem and its arrhythmic right ventricular cardiomyopathy linked position T2580.

Non-synonymous small nucleotide variations (nsSNVs) in the giant muscle protein, titin, have key roles in the development of several myopathologies. Although there is considerable motive to screen at-risk individuals for nsSNVs, to identify patients in early disease stages while therapeutic intervention is still possible, the clinical significance of most titin variations remains unclear. Therefore, there is a growing need to establish methods to classify nsSNVs in a simple, economic and rapid manner.

Single-Molecule Force Spectroscopy on the N2A Element of Titin: Effects of Phosphorylation and CARP.

Titin is a large filamentous protein that forms a sarcomeric myofilament with a molecular spring region that develops force in stretched sarcomeres. The molecular spring has a complex make-up that includes the N2A element. This element largely consists of a 104-residue unique sequence (N2A-Us) flanked by immunoglobulin domains (I80 and I81).

What does fluorine do to a protein? Thermodynamic, and highly-resolved structural insights into fluorine-labelled variants of the cold shock protein.

Fluorine labelling represents one promising approach to study proteins in their native environment due to efficient suppressing of background signals. Here, we systematically probe inherent thermodynamic and structural characteristics of the Cold shock protein B from Bacillus subtilis (BsCspB) upon fluorine labelling. A sophisticated combination of fluorescence and NMR experiments has been applied to elucidate potential perturbations due to insertion of fluorine into the protein.

The ZT Biopolymer: A Self-Assembling Protein Scaffold for Stem Cell Applications.

The development of cell culture systems for the naturalistic propagation, self-renewal and differentiation of cells ex vivo is a high goal of molecular engineering. Despite significant success in recent years, the high cost of up-scaling cultures, the need for xeno-free culture conditions, and the degree of mimicry of the natural extracellular matrix attainable in vitro using designer substrates continue to pose obstacles to the translation of cell-based technologies. In this regard, the ZT biopolymer is a protein-based, stable, scalable, and economical cell substrate of high promise.