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Prephenate dehydratase (PDT), chorismate mutase (CM) and 3-deoxy-D-arabino-7-heptulosonate 7-phosphate (DAHP) synthase are key regulatory enzymes in aromatic amino acid biosynthesis in the actinomycete Amycolatopsis methanolica. Deregulated, feedback-control-resistant mutants were isolated by incubation of A. methanolica on glucose mineral agar containing the toxic analogue p-fluoro-DL-phenylalanine (pFPhe). Several of these mutants had completely lost PDT sensitivity to Phe inhibition and Tyr activation. Mutant characterization yielded new information about PDT amino acid residues involved in Phe and Tyr effector binding sites. A. methanolica wild-type cells grown on glucose mineral medium normally possess a bifunctional CM/DAHP synthase protein complex (with DS1, a plant-type DAHP synthase). The CM activity of this protein complex is feedback-inhibited by Tyr and Phe, while DS1 activity is mainly inhibited by Trp. Isolation of pFPhe-resistant mutants yielded two feedback-inhibition-resistant CM mutants. These were characterized as regulatory mutants, derepressed in (a) synthesis of CM, now occurring as an abundant, feedback-inhibition-resistant, separate protein, and (b) synthesis of an alternative DAHP synthase (DS2, an E. coli-type DAHP synthase), only inhibited by Tyr and Trp. DS1 and DS2 thus are well integrated in A. methanolica primary metabolism: DS1 and CM form a protein complex, which stimulates CM activity and renders it sensitive to feedback inhibition by Phe and Tyr. Synthesis of CM and DS2 proteins appears to be controlled co-ordinately, sensitive to Phe-mediated feedback repression.

Hip fractures are associated with high morbidity and mortality. Sarcopenia is a significant factor contributing to poor prognosis; however, the clinical diagnosis of sarcopenia remains difficult in surgical patients. This systematic review aims to identify the biomarkers of sarcopenia as diagnostic and predictive tools in patients admitted for hip fracture surgery. A systematic search was conducted in the MEDLINE, EMBASE, and Google Scholar databases according to the PRISMA guidelines. Biomarker study quality was assessed using the BIOCROSS score. A total of 7 studies met the inclusion criteria and 515 patients were included, of whom 402 (78%) were female and 113 (22%) were male. The mean age of the participants was 83.1 years (SD: 5.9). Skeletal muscle biopsies were used for biomarker assessment in 14% (1/7) of studies and venous blood samples were used in the remaining 86% (6/7). The highlighted sarcopenia biomarkers included the low expression of insulin-like growth factor (IGF-I) and tumor necrosis factor-α (TNF-α), along with high serum myostatin and low serum vitamin D levels. Overall, the BIOCROSS score was satisfactory, with all studies obtaining at least a score of 13/20. The orthopedic literature is limited; however, the highlighted biomarkers in this review could be used as adjuncts in the diagnosis of sarcopenia in surgical patients. [ABSTRACT FROM AUTHOR]

Discusses a plasmid from the methylotrophic actinomycete Amycolatopsis methanolica capable of site-specific integration. Presence of plasmid both in the free state and integrated at a genomic location; Revelation of the putative attP site and two open reading frames; Similarity of xis and int to genes encoding excisionases and integrases, respectively.

Reports on the construction of a gene library of Amycolatopsis methanolica total DNA in Escherichia coli with a pMEA300-derived shuttle vector. Characterization of the pdt gene; Cloning of the pdt gene.

Reports on the identification and functional analysis of the transfer region of plasmid pMEA300 of the methylotrophic actinomycete Amycolaptosis methanolica. Identification of the DNA region involved in plasmid pock formation; Characteristics of ORFs in the plasmid transfer pock formation.

Background: Sarcopenia is characterized by the progressive loss of skeletal muscle mass, strength, and function, significantly impacting overall health and quality of life in older adults. This narrative review explores emerging targets and potential treatments for sarcopenia, aiming to provide a comprehensive overview of current and prospective interventions. Methods: The review synthesizes current literature on sarcopenia treatment, focusing on recent advancements in muscle regeneration, mitochondrial function, nutritional strategies, and the muscle–microbiome axis. Additionally, pharmacological and lifestyle interventions targeting anabolic resistance and neuromuscular junction integrity are discussed. Results: Resistance training and adequate protein intake remain the cornerstone of sarcopenia management. Emerging strategies include targeting muscle regeneration through myosatellite cell activation, signaling pathways, and chronic inflammation control. Gene editing, stem cell therapy, and microRNA modulation show promise in enhancing muscle repair. Addressing mitochondrial dysfunction through interventions aimed at improving biogenesis, ATP production, and reducing oxidative stress is also highlighted. Nutritional strategies such as leucine supplementation and anti-inflammatory nutrients, along with dietary modifications and probiotics targeting the muscle–microbiome interplay, are discussed as potential treatment options. Hydration and muscle–water balance are emphasized as critical in maintaining muscle health in older adults. Conclusions: A combination of resistance training, nutrition, and emerging therapeutic interventions holds potential to significantly improve muscle function and overall health in the aging population. This review provides a detailed exploration of both established and novel approaches for the prevention and management of sarcopenia, highlighting the need for further research to optimize these strategies. [ABSTRACT FROM AUTHOR]

The formation of atroposelective biaryl compounds in plants and fungi is well understood; however, polyketide aglycone synthesis and dimerization in bacteria remain unclear. Thus, the biosynthetic gene cluster (BGC) responsible for antibacterial setomimycin production from Streptomyces nojiriensis JCM3382 was examined in comparison with the BGCs of spectomycin, julichromes, lincolnenins, and huanglongmycin. The setomimycin BGC includes post-polyketide synthase (PKS) assembly/cycling enzymes StmD (C-9 ketoreductase), StmE (aromatase), and StmF (thioesterase) as key components. The heterodimeric TcmI-like cyclases StmH and StmK are proposed to aid in forming the setomimycin monomer. In addition, StmI (P-450) is predicted to catalyze the biaryl coupling of two monomeric setomimycin units, with StmM (ferredoxin) specific to the setomimycin BGC. The roles of StmL and StmN, part of the nuclear transport factor 2 (NTF-2)-like protein family and unique to setomimycin BGCs, could particularly interest biochemists and combinatorial biologists. α-Glucosidase, a key enzyme in type 2 diabetes, hydrolyzes carbohydrates into glucose, thereby elevating blood glucose levels. This study aimed to assess the α-glucosidase inhibitory activity of EtOAc extracts of JCM 3382 and setomimycin. The JCM 3382 EtOAc extract and setomimycin exhibited greater potency than the standard inhibitor, acarbose, with IC50 values of 285.14 ± 2.04 μg/mL and 231.26 ± 0.41 μM, respectively. Molecular docking demonstrated two hydrogen bonds with maltase-glucoamylase chain A residues Thr205 and Lys480 (binding energy = −6.8 kcal·mol−1), two π–π interactions with Trp406 and Phe450, and one π–cation interaction with Asp542. Residue-energy analysis highlighted Trp406 and Phe450 as key in setomimycin's binding to maltase-glucoamylase. These findings suggest that setomimycin is a promising candidate for further enzymological research and potential antidiabetic therapy. [ABSTRACT FROM AUTHOR]

During gliotoxin biosynthesis in fungi, the cytochrome P450 GliF enzyme catalyzes an unusual C–N ring-closure step while also an aromatic ring is hydroxylated in the same reaction cycle, which may have relevance to drug synthesis reactions in biotechnology. However, as the details of the reaction mechanism are still controversial, no applications have been developed yet. To resolve the mechanism of gliotoxin biosynthesis and gain insight into the steps leading to ring-closure, we ran a combination of molecular dynamics and density functional theory calculations on the structure and reactivity of P450 GliF and tested a range of possible reaction mechanisms, pathways and models. The calculations show that, rather than hydrogen atom transfer from the substrate to Compound I, an initial proton transfer transition state is followed by a fast electron transfer en route to the radical intermediate, and hence a non-synchronous hydrogen atom abstraction takes place. The radical intermediate then reacts by OH rebound to the aromatic ring to form a biradical in the substrate that, through ring-closure between the radical centers, gives gliotoxin products. Interestingly, the structure and energetics of the reaction mechanisms appear little affected by the addition of polar groups to the model and hence we predict that the reaction can be catalyzed by other P450 isozymes that also bind the same substrate. Alternative pathways, such as a pathway starting with an electrophilic attack on the arene to form an epoxide, are high in energy and are ruled out. [ABSTRACT FROM AUTHOR]

The problem of antimicrobial resistance is becoming a daunting challenge for human society and healthcare systems around the world. Hence, there is a constant need to develop new antibiotics to fight resistant bacteria, among other important social and economic measures. In this regard, murepavadin is a cyclic antibacterial peptide in development. The synthesis of murepavadin was undertaken in order to optimize the preparative protocol and scale-up, in particular, the use of new activation reagents. In our hands, classical approaches using carbodiimide/hydroxybenzotriazole rendered low yields. The use of novel carbodiimide and reagents based on OxymaPure® and Oxy-B is discussed together with the proper use of chromatographic conditions for the adequate characterization of peptide crudes. Higher yields and purities were obtained. Finally, the antimicrobial activity of different synthetic batches was tested in three Pseudomonas aeruginosa strains, including highly resistant ones. All murepavadin batches yielded the same highly active MIC values and proved that the chiral integrity of the molecule was preserved throughout the whole synthetic procedure. [ABSTRACT FROM AUTHOR]

Avermectins (AVEs), a family of macrocyclic polyketides produced by Streptomyces avermitilis, have eight components, among which B1a is noted for its strong insecticidal activity. Biosynthesis of AVE "a" components requires 2‐methylbutyryl‐CoA (MBCoA) as starter unit, and malonyl‐CoA (MalCoA) and methylmalonyl‐CoA (MMCoA) as extender units. We describe here a novel strategy for increasing B1a production by enhancing acyl‐CoA precursor supply. First, we engineered meilingmycin (MEI) polyketide synthase (PKS) for increasing MBCoA precursor supply. The loading module (using acetyl‐CoA as substrate), extension module 7 (using MMCoA as substrate) and TE domain of MEI PKS were assembled to produce 2‐methylbutyrate, providing the starter unit for B1a production. Heterologous expression of the newly designed PKS (termed Mei‐PKS) in S. avermitilis wild‐type (WT) strain increased MBCoA level, leading to B1a titer 262.2 μg/mL – 4.36‐fold higher than WT value (48.9 μg/mL). Next, we separately inhibited three key nodes in essential pathways using CRISPRi to increase MalCoA and MMCoA levels in WT. The resulting strains all showed increased B1a titer. Combined inhibition of these key nodes in Mei‐PKS expression strain increased B1a titer to 341.9 μg/mL. Overexpression of fatty acid β‐oxidation pathway genes in the strain further increased B1a titer to 452.8 μg/mL – 8.25‐fold higher than WT value. Finally, we applied our precursor supply strategies to high‐yield industrial strain A229. The strategies, in combination, led to B1a titer 8836.4 μg/mL – 37.8% higher than parental A229 value. These findings provide an effective combination strategy for increasing AVE B1a production in WT and industrial S. avermitilis strains, and our precursor supply strategies can be readily adapted for overproduction of other polyketides. [ABSTRACT FROM AUTHOR]

For decades, the comparison of experimental data with theoretical results in studying the biochemistry of vitamin B12 has been very confusing. While the methylcobalamin cofactor-dependent Methionine Synthase process can undergo unlimited turnovers, and some of the adenosylcobalamin-dependent processes run with close-to-unity equilibrium constants (e.g., with close-to-zero energy barriers), the DFT and QM/MM based on density functional theory, the most used and appreciated methods for calculating the electronic structure of molecules, have been showing a much shorter than experimental-determined Co-N distances in the vitamin B12 cofactors of Co+2 and the inadequate large energetic barriers of their enzymology bioprocesses. The confusion was even larger since some in vitro experimental data showed large barriers to the vitamin B12 cofactor reactions (which in fact play a destructive role in the Methionine Synthase process and which barriers were caused mostly by the influence of the solvents in which the reaction took place). It reached the point where solid contributions to the study of the biochemical processes of vitamin B12 were almost officially questioning the correctness of the experimental determination of the Co-N chemical bond distances in the cobalt(II) cofactors of vitamin B12. Unexpectedly, all the theoretical biochemistry of the vitamin B12 cofactors began to agree with all in vivo experimental data only when they were treated with the MCSCF method, the method that considers the orbital mixing, or in other words, the Pseudo-Jahn–Teller Effect. MCSCF data establish unknown mechanistic details of the methyl radical and hydrogen transfers, the origin of the electronic transfers between bioreagents, and the nature and the relationship between the bioreactions. The Pseudo-Jahn–Teller Effect, e.g., orbital mixing, governs vitamin B12 chemistry in general and provides insight into particular details of vitamin B12-dependent reactions in the human body. It turns out that the DFT or QM/MM based on DFT method theoretical data are incongruent with the experimental data due to their limitations, e.g., the unaccounted-for effects of orbital mixing. [ABSTRACT FROM AUTHOR]

Sarcopenia, a geriatric syndrome characterized by progressive skeletal muscle mass and function decline, poses a significant health risk among the elderly, contributing to frailty, falls, hospitalization, loss of independence and mortality. The prevalence of sarcopenia varies significantly based on various factors, such as living status, demographics, measurement techniques and diagnostic criteria. Although the overall prevalence is reported at 10% in individuals aged 60 and above, disparities exist across settings, with higher rates in nursing homes and hospitals. Additionally, the differences in prevalence between Asian and non-Asian countries highlight the impact of cultural and ethnic factors, and variations in diagnostic criteria, cut-off values and assessment methods contribute to the observed heterogeneity in reported rates. This review outlines diverse diagnostic criteria and several measurement techniques supporting decision making in clinical practice. Moreover, it facilitates the selection of appropriate tools to assess sarcopenia, emphasizing its multifactorial nature. Various scientific groups, including the European Working Group of Sarcopenia in Older People (EWGSOP), the International Working Group on Sarcopenia (IWGS), the Asian Working Group on Sarcopenia (AWGS), the American Foundation for the National Institutes of Health (FNIH) and the Sarcopenia Definition and Outcomes Consortium (SDOC), have published consensus papers outlining diverse definitions of sarcopenia. The choice of diagnostic criteria should be aligned with the specific objectives of the study or clinical practice, considering the characteristics of the study population and available resources. [ABSTRACT FROM AUTHOR]

Menopause causes a reduction in estradiol (E2) and may be associated with neuromuscular degeneration. Compared to pre-menopausal (PRE-M) women, this study sought to determine dietary protein intake and whether lower levels of circulating E2 in post-menopausal women (POST-M) were occurring alongside increased levels of biomarkers of axonal and neuromuscular junction degeneration (NMJ), inflammation, muscle protein degradation, and reduced indices of muscle quality and performance. Employing a cross-sectional design, PRE-M (n = 6) and POST-M (n = 6) dietary analysis data were collected and participants then donated a blood and urine sample followed by assessments for body composition, motor unit activation, and muscle performance. Independent group t-tests were performed to determine differences between groups (p ≤ 0.05). In POST-M women, E2, motor unit activity, muscle quality, and muscle performance were significantly less than those for PRE-M women; however, the levels of c-terminal fragment of agrin, tumor necrosis factor-α, and urinary titin were significantly greater (p < 0.05). POST-M women were also shown to be ingesting fewer total calories and less protein than PRE-M (p < 0.05). Reduced E2 and dietary protein intake in POST-M women occurs in conjunction with increased levels of biomarkers of NMJ degradation, inflammation, and muscle proteolysis, which may be associated with reduced motor unit activation and muscle quality. [ABSTRACT FROM AUTHOR]

Would another origin of life resemble Earth's biochemical use of amino acids? Here, we review current knowledge at three levels: (1) Could other classes of chemical structure serve as building blocks for biopolymer structure and catalysis? Amino acids now seem both readily available to, and a plausible chemical attractor for, life as we do not know it. Amino acids thus remain important and tractable targets for astrobiological research. (2) If amino acids are used, would we expect the same L-alpha-structural subclass used by life? Despite numerous ideas, it is not clear why life favors L-enantiomers. It seems clearer, however, why life on Earth uses the shortest possible (alpha-) amino acid backbone, and why each carries only one side chain. However, assertions that other backbones are physicochemically impossible have relaxed into arguments that they are disadvantageous. (3) Would we expect a similar set of side chains to those within the genetic code? Many plausible alternatives exist. Furthermore, evidence exists for both evolutionary advantage and physicochemical constraint as explanatory factors for those encoded by life. Overall, as focus shifts from amino acids as a chemical class to specific side chains used by post-LUCA biology, the probable role of physicochemical constraint diminishes relative to that of biological evolution. Exciting opportunities now present themselves for laboratory work and computing to explore how changing the amino acid alphabet alters the universe of protein folds. Near-term milestones include: (a) expanding evidence about amino acids as attractors within chemical evolution; (b) extending characterization of other backbones relative to biological proteins; and (c) merging computing and laboratory explorations of structures and functions unlocked by xeno peptides. [ABSTRACT FROM AUTHOR]

Mycolicibacterium gadium IBE100 and Mycobacterium paragordonae IBE200 are aerobic, chemoorganoheterotrophic bacteria isolated from activated sludge from a wastewater treatment plant. They use 2‐methylpropene (isobutene, 2‐MP) as the sole source of carbon and energy. Here, we postulate a degradation pathway of 2‐methylpropene derived from whole genome sequencing, differential expression analysis and peptide‐mass fingerprinting. Key genes identified are coding for a 4‐component soluble diiron monooxygenase with epoxidase activity, an epoxide hydrolase, and a 2‐hydroxyisobutyryl‐CoA mutase. In both strains, involved genes are arranged in clusters of 61.0 and 58.5 kbp, respectively, which also contain the genes coding for parts of the aerobic pathway of adenosylcobalamin synthesis. This vitamin is essential for the carbon rearrangement reaction catalysed by the mutase. These findings provide data for the identification of potential 2‐methylpropene degraders. [ABSTRACT FROM AUTHOR]

Epidemiological studies of older adults have suggested a differential sex-specific prevalence of sarcopenia, which is a condition characterized by a progressive loss of skeletal muscle mass and function. Recently, we collected serum samples from 80 fully evaluated older adults and identified CXCL12α as a sex-independent serum marker of sarcopenia. Here, we used this serum collection to find potential sex-specific serum markers via the simultaneous quantification of 34 inflammatory cytokines/chemokines. The appendicular skeletal muscle index (ASMI) was used as a decisive criterion for diagnosing sarcopenia. A Pearson correlation analysis revealed a negative correlation between ASMI and serum IL-16 in females only (p = 0.021). Moreover, women with sarcopenia exhibited significantly higher IL-16 (p = 0.025) serum levels than women in a control group. In contrast, males with sarcopenia had lower IL-16 (p = 0.013) levels than males in a control group. The further use of Fisher's exact test identified obesity (p = 0.027) and high serum levels of IL-16 (p = 0.029) as significant risk factors for sarcopenia in females. In male older adults, however, malnutrition (p = 0.028) and low serum levels of IL-16 (p = 0.031) were the most significant risk factors for sarcopenia. The differential sex-specific associations of IL-16 in older adults may contribute to the development of more precise regression models for future research and elucidate the role of IL-16 in the progression of sarcopenic obesity. [ABSTRACT FROM AUTHOR]

Protegrin-1 (PG-1) is a cationic β-hairpin pore-forming antimicrobial peptide having a membranolytic mechanism of action. It possesses in vitro a potent antimicrobial activity against a panel of clinically relevant MDR ESKAPE pathogens. However, its extremely high hemolytic activity and cytotoxicity toward mammalian cells prevent the further development of the protegrin-based antibiotic for systemic administration. In this study, we rationally modulated the PG-1 charge and hydrophobicity by substituting selected residues in the central β-sheet region of PG-1 to design its analogs, which retain a high antimicrobial activity but have a reduced toxicity toward mammalian cells. In this work, eight PG-1 analogs with single amino acid substitutions and five analogs with double substitutions were obtained. These analogs were produced as thioredoxin fusions in Escherichia coli. It was shown that a significant reduction in hemolytic activity without any loss of antimicrobial activity could be achieved by a single amino acid substitution, V16R in the C-terminal β-strand, which is responsible for the PG-1 oligomerization. As the result, a selective analog with a ≥30-fold improved therapeutic index was obtained. FTIR spectroscopy analysis of analog, [V16R], revealed that the peptide is unable to form oligomeric structures in a membrane-mimicking environment, in contrast to wild-type PG-1. Analog [V16R] showed a reasonable efficacy in septicemia infection mice model as a systemic antibiotic and could be considered as a promising lead for further drug design. [ABSTRACT FROM AUTHOR]

Cyclic peptides are molecules that are already used as drugs in therapies approved for various pharmacological activities, for example, as antibiotics, antifungals, anticancer, and immunosuppressants. Interest in these molecules has been growing due to the improved pharmacokinetic and pharmacodynamic properties of the cyclic structure over linear peptides and by the evolution of chemical synthesis, computational, and in vitro methods. To date, 53 cyclic peptides have been approved by different regulatory authorities, and many others are in clinical trials for a wide diversity of conditions. In this review, the potential of cyclic peptides is presented, and general aspects of their synthesis and development are discussed. Furthermore, an overview of already approved cyclic peptides is also given, and the cyclic peptides in clinical trials are summarized. [ABSTRACT FROM AUTHOR]

Sarcopenia refers to the loss of muscle strength and mass in older individuals and is a major determinant of fall risk and impaired ability to perform activities of daily living, often leading to disability, loss of independence, and death. Owing to its impact on morbidity, mortality, and healthcare expenditure, sarcopenia in the elderly has become a major focus of research and public policy debates worldwide. Despite its clinical importance, sarcopenia remains under-recognized and poorly managed in routine clinical practice, partly owing to the lack of available diagnostic testing and uniform diagnostic criteria. Since the World Health Organization and the United States assigned a disease code for sarcopenia in 2016, countries worldwide have assigned their own disease codes for sarcopenia. However, there are currently no approved pharmacological agents for the treatment of sarcopenia; therefore, interventions for sarcopenia primarily focus on physical therapy for muscle strengthening and gait training as well as adequate protein intake. In this review, we aimed to examine the latest information on the epidemiology, molecular mechanisms, interventions, and possible treatments with new drugs for sarcopenia. [ABSTRACT FROM AUTHOR]

Declines in physical performance and cognition are commonly observed in older adults. The geroscience paradigm posits that a set of processes and pathways shared among age-associated conditions may also serve as a molecular explanation for the complex pathophysiology of physical frailty, sarcopenia, and cognitive decline. Mitochondrial dysfunction, inflammation, metabolic alterations, declines in cellular stemness, and altered intracellular signaling have been observed in muscle aging. Neurological factors have also been included among the determinants of sarcopenia. Neuromuscular junctions (NMJs) are synapses bridging nervous and skeletal muscle systems with a relevant role in age-related musculoskeletal derangement. Patterns of circulating metabolic and neurotrophic factors have been associated with physical frailty and sarcopenia. These factors are mostly related to disarrangements in protein-to-energy conversion as well as reduced calorie and protein intake to sustain muscle mass. A link between sarcopenia and cognitive decline in older adults has also been described with a possible role for muscle-derived mediators (i.e., myokines) in mediating muscle–brain crosstalk. Herein, we discuss the main molecular mechanisms and factors involved in the muscle–brain axis and their possible implication in cognitive decline in older adults. An overview of current behavioral strategies that allegedly act on the muscle–brain axis is also provided. [ABSTRACT FROM AUTHOR]

Sarcopenia refers to a decline in muscle mass and strength with age, causing significant impairment in the ability to carry out normal daily functions and increased risk of falls and fractures, eventually leading to loss of independence. Maintaining protein homeostasis is an important factor in preventing muscle loss, and the decrease in muscle mass is caused by an imbalance between anabolism and catabolism of muscle proteins. Although β-sitosterol has various effects such as anti-inflammatory, protective effect against nonalcoholic fatty liver disease (NAFLD), antioxidant, and antidiabetic activity, the mechanism of β-sitosterol effect on the catabolic pathway was not well known. β-sitosterol was assessed in vitro and in vivo using a dexamethasone-induced muscle atrophy mice model and C2C12 myoblasts. β-sitosterol protected mice from dexamethasone-induced muscle mass loss. The thickness of gastrocnemius muscle myofibers was increased in dexamethasone with the β-sitosterol treatment group (DS). Grip strength and creatine kinase (CK) activity were also recovered when β-sitosterol was treated. The muscle loss inhibitory efficacy of β-sitosterol in dexamethasone-induced muscle atrophy in C2C12 myotube was also verified in C2C12 myoblast. β-sitosterol also recovered the width of myotubes. The protein expression of muscle atrophy F-box (MAFbx) was increased in dexamethasone-treated animal models and C2C12 myoblast, but it was reduced when β-sitosterol was treated. MuRF1 also showed similar results to MAFbx in the mRNA level of C2C12 myotubes. In addition, in the gastrocnemius and tibialis anterior muscles of mouse models, Forkhead Box O1 (FoxO1) protein was increased in the dexamethasone-treated group (Dexa) compared with the control group and reduced in the DS group. Therefore, β-sitosterol would be a potential treatment agent for aging sarcopenia. [ABSTRACT FROM AUTHOR]

Background: Polycystic kidney disease (PKD) is an inherited disorder characterized by renal cysts that may mask lean body loss. This study quantified and compared muscle mass by using computed tomography (CT) and magnetic resonance imaging (MRI) images between the PKD and control groups and correlated muscle mass with total kidney volume (TKV). Methods: We retrospectively enrolled patients who had a new diagnosis of PKD from May 2015 to May 2016. The CT and MRI images at the third lumbar level were processed to measure the total abdominal muscle (TAM) area for the diagnosis of sarcopenia, and TKV was estimated using the ellipsoid formula. Results: We included 37 women and 25 men (mean age: 50.40 years) in the PKD group. There was no difference in body mass index and albumin levels, but significant differences in creatinine level (p < 0.001), TAM area (p = 0.047), and TKV (p < 0.001), were noted between the two groups. A significantly negative correlation was observed between TKV and TAM area after adjustment for body height (r = −0.217, p = 0.003). Conclusions: CT and MRI images can accurately diagnose sarcopenia, which may be masked by cysts in patients with PKD. [ABSTRACT FROM AUTHOR]

3-Ketosteroid-Δ1-dehydrogenases (KstDs [EC 1.3.99.4]) catalyze the Δ1-dehydrogenation of steroids and are a class of important enzymes for steroid biotransformations. In this study, nine putative kstD genes from different origins were selected and overexpressed in Escherichia coli BL21(DE3). These recombinant enzymes catalyzed the Δ1-desaturation of a variety of steroidal compounds. Among them, the KstD from Propionibacterium sp. (PrKstD) displayed the highest specific activity and broad substrate spectrum. The detailed catalytic characterization of PrKstD showed that it can convert a wide range of 3-ketosteroid compounds with diverse substituents, ranging from substituents at the C9, C10, C11 and C17 position through substrates without C4-C5 double bond, to previously inactive C6-substituted ones such as 11β,17-dihydroxy-6α-methyl-pregn-4-ene-3,20-dione. Reaction conditions were optimized for the biotransformation of hydrocortisone in terms of pH, temperature, co-solvent and electron acceptor. By using 50 g/L wet resting E. coli cells harboring PrKstD enzyme, the conversion of hydrocortisone was about 92.5% within 6 h at the substrate concentration of 80 g/L, much higher than the previously reported results, demonstrating the application potential of this new KstD. [ABSTRACT FROM AUTHOR]

Summary: Degradation of acetone by the sulfate‐reducing bacterium Desulfococcus biacutus involves an acetone‐activation reaction different from that used by aerobic or nitrate‐reducing bacteria, because the small energy budget of sulfate‐reducing bacteria does not allow for major expenditures into ATP‐consuming carboxylation reactions. In the present study, an inducible coenzyme B12‐dependent conversion of 2‐hydroxyisobutyryl‐CoA to 3‐hydroxybutyryl‐CoA was demonstrated in cell‐free extracts of acetone‐grown D. biacutus cells, together with a NAD+‐dependent oxidation of 3‐hydroxybutyryl‐CoA to acetoacetyl‐CoA. Genes encoding two mutase subunits and a dehydrogenase, which were found previously to be strongly induced during growth with acetone, were heterologously expressed in E. coli. The activities of the purified recombinant proteins matched with the inducible activities observed in cell‐free extracts of acetone‐grown D. biacutus: proteins (IMG locus tags) DebiaDRAFT_04573 and 04574 constituted a B12‐dependent 2‐hydroxyisobutyryl‐CoA/3‐hydroxybutyryl‐CoA mutase, and DebiaDRAFT_04571 was a 3‐hydroxybutyryl‐CoA dehydrogenase. Hence, these enzymes play key roles in the degradation of acetone and define an involvement of CoA esters in the pathway. Further, the involvement of 2‐hydroxyisobutyryl‐CoA strongly indicates that the carbonyl‐C2 of acetone is added, most likely, to formyl‐CoA through a TDP‐dependent enzyme that is co‐induced in acetone‐grown cells and is encoded in the same gene cluster as the identified mutase and dehydrogenase. [ABSTRACT FROM AUTHOR]

Summary: In this work, we have characterized the C‐19+ gene cluster (MSMEG_2851 to MSMEG_2901) of Mycobacterium smegmatis. By in silico analysis, we have identified the genes encoding enzymes involved in the modification of the A/B steroid rings during the catabolism of C‐19 steroids in certain M. smegmatis mutants mapped in the PadR‐like regulator (MSMEG_2868), that constitutively express the C‐19+ gene cluster. By using gene complementation assays, resting‐cell biotransformations and deletion mutants, we have characterized the most critical genes of the cluster, that is, kstD2, kstD3, kshA2, kshB2, hsaA2, hsaC2 and hsaD2. These results have allowed us to propose a new catabolic route named C‐19+ pathway for the mineralization of C‐19 steroids in M. smegmatis. Our data suggest that the deletion of the C‐19+ gene cluster may be useful to engineer more robust and efficient M. smegmatis strains to produce C‐19 steroids from sterols. Moreover, the new KshA2, KshB2, KstD2 and KstD3 isoenzymes may be useful to design new microbial cell factories for the 9α‐hydroxylation and/or Δ1‐dehydrogenation of 3‐ketosteroids. [ABSTRACT FROM AUTHOR]

The C-19 steroids 4-androstene-3,17-dione (AD), 1,4-androstadiene-3,17-dione (ADD) or 9α-hydroxy-4-androstene-3,17-dione (9OH-AD), which have been postulated as intermediates of the cholesterol catabolic pathway in Mycobacterium smegmatis, cannot be used as sole carbon and energy sources by this bacterium. Only the ΔkstR mutant which constitutively expresses the genes repressed by the KstR regulator can metabolize AD and ADD with severe difficulties but still cannot metabolize 9OH-AD, suggesting that these compounds are not true intermediates but side products of the cholesterol pathway. However, we have found that some M. smegmatis spontaneous mutants mapped in the PadR-like regulator ( MSMEG_2868) can efficiently metabolize all C-19 steroids. We have demonstrated that the PadR mutants allow the expression of a gene cluster named C-19+ ( MSMEG_2851 to MSMEG_2901) encoding steroid degrading enzymes, that are not expressed under standard culture conditions. The C-19+ cluster has apparently evolved independently from the upper cholesterol kstR-regulon, but both clusters converge on the lower cholesterol kstR2-regulon responsible for the metabolism of C and D steroid rings. Homologous C-19+ clusters have been found only in other actinobacteria that metabolize steroids, but remarkably it is absent in Mycobacterium tuberculosis. [ABSTRACT FROM AUTHOR]

The regulatory mechanisms involved in lipogenesis and triacylglycerol (TAG) accumulation are largely unknown in oleaginous rhodococci. In this study a regulatory protein (here called NlpR: Nitrogen li pid Regulator), which contributes to the modulation of nitrogen metabolism, lipogenesis and triacylglycerol accumulation in oleaginous rhodococci was identified. Under nitrogen deprivation conditions, in which TAG accumulation is stimulated, the nlpR gene was significantly upregulated, whereas a significant decrease of its expression and TAG accumulation occurred when cerulenin was added. The nlpR disruption negatively affected the nitrate/nitrite reduction as well as lipid biosynthesis under nitrogen-limiting conditions. In contrast, its overexpression increased TAG production during cultivation of cells in nitrogen-rich media. A putative 'NlpR-binding motif' upstream of several genes related to nitrogen and lipid metabolisms was found. The nlpR disruption in RHA1 strain led to a reduced transcription of genes involved in nitrate/nitrite assimilation, as well as in fatty acid and TAG biosynthesis. Purified NlpR was able to bind to narK, nirD, fasI, plsC and atf3 promoter regions. It was suggested that NlpR acts as a pleiotropic transcriptional regulator by activating of nitrate/nitrite assimilation genes and others genes involved in fatty acid and TAG biosynthesis, in response to nitrogen deprivation. [ABSTRACT FROM AUTHOR]

Aims To evaluate the antibacterial efficacy of novel antimicrobial peptides (AMPs) against multidrug-resistant (MDR) Salmonella enterica serovar Choleraesuis ( Salm. Choleraesuis) and to delineate the AMP-responsive mechanisms of wild-type (WT) and MDR strains. Methods and Results Proteomic approaches were performed based on two-dimensional gel electrophoresis and liquid chromatography-electrospray ionization-quadrupole- time-of-flight tandem mass spectrometry to analyse the protein profiles of these two strains upon exposure to AMP GW-Q6. Quantitative real-time PCR was conducted to determine the mRNA expression level of the target genes. Furthermore, lipopolysaccharide (LPS) competition analysis was used to verify whether LPS may serve as the potential binding target when AMP approach and adhere to the bacterial surface. Conclusions The minimal inhibitory concentration assay revealed that our AMPs were even more effective against the MDR strains (4-32 μg ml−1), compared with those for the WT (8-64 μg ml−1). LPS dose-dependently suppressed the GW-Q6 antimicrobial activity. Clusters of orthologous groups analysis showed that the majority of the AMP-responsive proteins were involved in cell envelope biogenesis and outer membrane, translation and chaperones. Significance and Impact of the Study These results indicated that the novel AMP GW-Q6 serves as a potential candidate for antimicrobial drug development against MDR strains. These findings will also be helpful for expanding our knowledge on the molecular mechanisms of AMP-microbe interaction and the pathogenicity of salmonellosis caused by MDR strains of Salm. Choleraesuis. [ABSTRACT FROM AUTHOR]

Abstract: Introduction: Sarcopenia is considered to be an enormous burden for both the individuals affected and for society at large. A multifactorial aetiology of this geriatric syndrome has been discussed. Amongst other pathomechanisms, the degeneration of the neuromuscular junction (NMJ) may be of major relevance. The intact balance between the pro-synaptic agent agrin and the anti-synaptic agent neurotrypsin ensures a structurally and functionally intact NMJ. Excessive cleavage of the native motoneuron-derived agrin by neurotrypsin into a C-terminal Agrin Fragment (CAF) leads to functional disintegration at the NMJ and may consecutively cause sarcopenia. The present study evaluates the hypothesis that CAF serum concentration is a potential marker for the loss of appendicular lean mass in older adults. It also explores how CAF concentration is influenced by vitamin D supplementation and physical exercise. Method: Serum was taken from 69 (47 female) prefrail community-dwelling older adults participating in a training intervention study to measure the CAF concentration using the Western blot technique. All participants were supplemented orally with vitamin D3 before the training intervention period commenced. Appendicular lean mass (aLM) was evaluated by dual energy X-ray absorptiometry. Multiple linear regression models were used to identify factors significantly associated with CAF concentration. Results: Appendicular lean mass, age and sex were identified as significant explanatory factors for CAF concentration. Gait speed and hand grip strength were not associated with CAF concentration. Male participants showed a strong correlation (r=−0.524) between CAF serum concentration and aLM, whereas this was not the case (r=−0.219) in females. Vitamin D supplementation and physical exercise were significantly associated with a reduction in CAF concentration, especially in participants with initially high CAF concentrations. Conclusions: C-terminal Agrin Fragment could be a potential marker for identifying sarcopenia in a subgroup of affected individuals in the future. The decline of muscle mass seems to be a CAF-associated process in males, whereas the situation in females may be more complex and multifactorial. CAF concentration is reduced by vitamin D supplementation and physical exercise and therefore suggests a potentially positive effect on NMJs. Further prospective studies of sarcopenic patients in addition to muscle biopsy and electromyographical investigations are planned to verify the external validity of the CAF concept. [Copyright &y& Elsevier]

Summary The metabolism of cholesterol in Mycobacterium smegmatis mc2155 has been investigated by using a microarray approach. The transcriptome of M. smegmatis growing in cholesterol was compared with that of cells growing in glycerol as the sole carbon and energy sources during the middle exponential phase. Microarray analyses revealed that only 89 genes were upregulated at least threefold during growth on cholesterol compared with growth on glycerol. The upregulated genes are scattered throughout the 7 Mb M. smegmatis genome and likely reflect a general physiological adaptation of the bacterium to grow on this highly hydrophobic polycyclic compound. Nevertheless, 39 of the catabolic genes are organized in three specific clusters. These results not only supported the role of KstR and KstR2 as auto-regulated repressors of cholesterol catabolism, and revealed some metabolic similarities and differences on actinobacteria, but more important, they have facilitated the identification of new catabolic genes, opening a research scenario that might provide important clues on the role of cholesterol in tuberculosis infection. [ABSTRACT FROM AUTHOR]

Biological proteins are known to fold into specific 3D conformations. However, the fundamental question has remained: Do they fold because they are biological, and evolution has selected sequences which fold? Or is folding a common trait, widespread throughout sequence space? To address this question arbitrary, unevolved, random-sequence proteins were examined for structural features found in folded, biological proteins. Libraries of long (71 residue), random-sequence polypeptides, with ensemble amino acid composition near the mean for natural globular proteins, were expressed as cleavable fusions with ubiquitin. The structural properties of both the purified pools and individual isolates were then probed using circular dichroism, fluorescence emission, and fluorescence quenching techniques. Despite this necessarily sparse "sampling" of sequence space, structural properties that define globular biological proteins, namely collapsed conformations, secondary structure, and cooperative unfolding, were found to be prevalent among unevolved sequences. Thus, for polypeptides the size of small proteins, natural selection is not necessary to account for the compact and cooperative folded states observed in nature. [ABSTRACT FROM AUTHOR]

Recently the first community-wide assessments of the prediction of the structures of complexes between proteins and small molecule ligands have been reported in the so-called GPCR Dock 2008 and 2010 assessments. In the current review we discuss the different steps along the protein-ligand modeling workflow by critically analyzing the modeling strategies we used to predict the structures of protein-ligand complexes we submitted to the recent GPCR Dock 2010 challenge. These representative test cases, focusing on the pharmaceutically relevant G Protein-Coupled Receptors, are used to demonstrate the strengths and challenges of the different modeling methods. Our analysis indicates that the proper performance of the sequence alignment, introduction of structural adjustments guided by experimental data, and the usage of experimental data to identify protein-ligand interactions are critical steps in the protein-ligand modeling protocol. [ABSTRACT FROM AUTHOR]

Proteins composed of short polypeptide chains (about 70 amino acid residues) participating in ligand-protein and protein-protein (small size) complex creation were analyzed and classified according to the hydrophobicity deficiency/excess distribution as a measure of structural and functional specificity and similarity. The characterization of this group of proteins is the introductory part to the analysis of the so called `Never Born Proteins' (NBPs) in search of protein compounds of biological activity in pharmacological context. The entropy scale (classification between random and deterministic limits) estimated according to the hydrophobicity irregularity organized in ranking list allows the comparative analysis of proteins under consideration. The comparison of the hydrophobicity deficiency/excess appeared to be useful for similarity recognition, examples of which are shown in the paper. The influence of mutations on structure and hydrophobicity distribution is discussed in detail. [ABSTRACT FROM AUTHOR]

Libraries of de novo proteins provide an opportunity to explore the structural and functional potential of biological molecules that have not been biased by billions of years of evolutionary selection. Given the enormity of sequence space, a rational approach to library design is likely to yield a higher fraction of folded and functional proteins than a stochastic sampling of random sequences. We previously investigated the potential of library design by binary patterning of hydrophobic and hydrophilic amino acids. The structure of the most stable protein from a binary patterned library of de novo 4-helix bundles was solved previously and shown to be consistent with the design. One structure, however, cannot fully assess the potential of the design strategy, nor can it account for differences in the stabilities of individual proteins. To more fully probe the quality of the library, we now report the NMR structure of a second protein, S-836. Protein S-836 proved to be a 4-helix bundle, consistent with design. The similarity between the two solved structures reinforces previous evidence that binary patterning can encode stable, 4-helix bundles. Despite their global similarities, the two proteins have cores that are packed at different degrees of tightness. The relationship between packing and dynamics was probed using the Modelfree approach, which showed that regions containing a high frequency of chemical exchange coincide with less well-packed side chains. These studies show (1) that binary patterning can drive folding into a particular topology without the explicit design of residue-by-residue packing, and (2) that within a superfamily of binary patterned proteins, the structures and dynamics of individual proteins are modulated by the identity and packing of residues in the hydrophobic core. [ABSTRACT FROM AUTHOR]

Aims: To improve KSDH enzyme activity and the transformation level for androst-4-ene-3,17-dione. Methods and Results: 3-ketosteroid-Δ1-dehydrogenase gene from Arthrobacter simplex was expressed in Bacillus subtilis under the control of P43 promoter. The molecular weight of expressed enzyme was about 55 kDa by SDS–PAGE analysis. The activities of intracellular and extracellular soluble enzymes examined by spectrophotometrical method were 110 ± 0·5 mU mg−1 and 15 ± 0·6 mU mg−1 of protein, respectively. The transformation rate of androst-4-ene-3,17-dione was 45·3% in the B. subtilis recombinant cells. Conclusions: The enzyme activity of KSDH expressed in B. subtilis was improved about 30-fold compared with that of Arthrobacter simplex, and the transformation level of androst-4-ene-3,17-dione by the B. subtilis recombinant cells was improved about 10-fold. Significance and Impact of the Study: The recombinant B. subtilis cells used for biotransformation of steroids provide a new method for production of steroid medicine. The time required for transformation of B. subtilis is much shorter than that of other bacteria, which means it will have wider usage in biopharmaceutical industry. [ABSTRACT FROM AUTHOR]

Development of pharmaceutical industry is currently aimed at introducing biotechnological processes on a large-scale and thereby replacing multiple-stage chemical syntheses. Actinobacteria are efficient biocatalysts of many processes involving steroid bioconversion, which hold considerable importance for the synthesis of hormonal drugs. The potential to catalyze the conversion of a broad spectrum of steroid substrates makes it possible to expect efficient utilization of these microorganisms in development of new technologies of manufacturing steroid pharmaceutical substances. The review is a first attempt to systematize data on the potential of actinobacteria to catalyze diverse reactions of steroid transformation (such as hydroxylation, introduction and reduction of double bonds, oxidation of steroid alcohols, reduction of ketones, side chain de-esterification and degradation, etc.), with emphasis on processes of practical biotechnological importance and progress in steroid bioconversion over the last ten years. [ABSTRACT FROM AUTHOR]

Small molecule antagonists of protein–protein interactions represent a particular challenge for pharmaceutical discovery. One approach to finding molecules that can disrupt these interactions is to seek mimics of common protein structure motifs. We present an analysis of how molecules based on the 1,4-benzodiazepine-2,5-dione scaffold serve to mimic the side-chains presented by the hydrophobic face of two turns of an α-helix derived from the tumor suppressor protein p53, and thus antagonize the HDM2-p53 protein–protein binding interaction. [ABSTRACT FROM AUTHOR]

Nocardia farcinica is a Gram positive, filamentous bacterium, and is considered an opportunistic pathogen. In this study, the highly expressed genes in N. farcinica were predicted using the codon adaptation index (CAI) as a numerical estimator of gene expressivity. Using ribosomal protein (RP) genes as references, the top ∼∼10% of the genes were predicted to be the predicted highly expressed (PHX) genes in N. farcinica using a CAI cutoff of greater than 0.73. Consistent with earlier analysis of Streptomyces genomes, most of the PHX genes in N. farcinica were involved in various ‘house-keeping’ functions important for cell growth. However, 15 genes putatively involved in nocardial virulence were predicted as PHX genes in N. farcinica, which included genes encoding four Mce proteins, cyclopropane fatty acid synthase which is involved in the modification of cell wall which may be important for nocardia virulence, polyketide synthase PKS13 for mycolic acid synthesis and a non-ribosomal peptide synthetase involved in biosynthesis of a mycobactin-related siderophore. In addition, multiple genes involved in defense against reactive oxygen species (ROS) produced by the phagocyte were predicted with high expressivity, which included alkylhydroperoxide reductase (ahpC), catalase (katG), superoxide dismutase (sodF), thioredoxin, thioredoxin reductase, glutathione peroxidase, and peptide methionine sulfoxide reductase, suggesting that combating against ROS is essential for survival of N. farcinica in host cells. The study also showed that the distribution of PHX genes in the N. farcinica circular chromosome was uneven, with more PHX genes located in the regions close to replication initiation site. The results provided the first estimates of global gene expression patterns in N.␣farcinica, which will be useful in guiding experimental design for further investigations. [ABSTRACT FROM AUTHOR]

The growth of Micromonospora echinospora was studied in high and low C/N ratio medium using both batch and continuous culture. Asparagine was consumed rapidly in batch cultures where it served as both a nitrogen and carbon source. Glucose consumption was low suggesting that asparagine functions as the major carbon source under these conditions. The effect of nutrient limitation on the accumulation of storage carbohydrate in batch culture revealed an intimate association between nitrogen limitation and the accumulation of carbonaceous reserves. This study revealed that glycogen constituted the major carbohydrate reserve associated with the onset of sporulation. Intracellular trehalose levels were found to be relatively low and may have been affected by the availability of carbon. Continuous culture studies revealed a correlation between glycogen accumulation and increasing growth rate. It was also found that elevated cellular ATP levels correlated with the increase in glycogen, and reduced glycolytic activity. At the higher growth rates cellular ATP levels were elevated and coincided with reduced activity of the key glycolytic enzyme, phosphofructokinase, suggesting that glycogen can act as a convenient energy reservoir when excess carbon flux dictates. [ABSTRACT FROM AUTHOR]