scholarly journals Leveraging peptide substrate libraries to design inhibitors of bacterial Lon protease

2019 ◽  
Author(s):  
Brett M. Babin ◽  
Paulina Kasperkiewicz ◽  
Tomasz Janiszewski ◽  
Euna Yoo ◽  
Marcin Drąg ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Sequence Specificity ◽  
Cellular Functions ◽  
Peptide Substrates ◽  
Acid Inhibitor ◽  
Functional Studies ◽  
Fluoroquinolone Antibiotics ◽  
Positional Scanning ◽  
Domains Of Life ◽  
Amino Acid Binding

AbstractLon is a widely-conserved housekeeping protease found in all domains of life. Bacterial Lon is involved in the recovery from various types of stress, including tolerance to fluoroquinolone antibiotics, and is linked to pathogenesis in a number of organisms. However, detailed functional studies of Lon have been limited by the lack of selective, cell-permeable inhibitors. Here we describe the use of positional scanning libraries of hybrid peptide substrates to profile the primary sequence specificity of bacterial Lon. In addition to identifying optimal natural amino acid binding preferences, we identified several non-natural residues that were leveraged to develop optimal peptide substrates as well as a potent peptidic boronic acid inhibitor of Lon. Treatment ofE. coliwith this inhibitor promotes UV-induced filamentation and reduces tolerance to ciprofloxacin, phenocopying establishedlon-deletion phenotypes. It is also non-toxic to mammalian cells due to its increased selectivity for Lon over the proteasome. Our results provide new insight into the primary substrate specificity of Lon and identify substrates and an inhibitor that will serve as useful tools for dissecting the diverse cellular functions of Lon.

scholarly journals Model-guided design of mammalian genetic programs

2021 ◽  
Vol 7 (8) ◽  
pp. eabe9375
Author(s):  
J. J. Muldoon ◽  
V. Kandula ◽  
M. Hong ◽  
P. S. Donahue ◽  
J. D. Boucher ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Computational Models ◽  
Biological Complexity ◽  
Genetic Circuits ◽  
Cellular Functions ◽  
High Performing ◽  
Design Objective ◽  
Complex Functions ◽  
Mammalian Genetic ◽  
Analog Processing

Genetically engineering cells to perform customizable functions is an emerging frontier with numerous technological and translational applications. However, it remains challenging to systematically engineer mammalian cells to execute complex functions. To address this need, we developed a method enabling accurate genetic program design using high-performing genetic parts and predictive computational models. We built multifunctional proteins integrating both transcriptional and posttranslational control, validated models for describing these mechanisms, implemented digital and analog processing, and effectively linked genetic circuits with sensors for multi-input evaluations. The functional modularity and compositional versatility of these parts enable one to satisfy a given design objective via multiple synonymous programs. Our approach empowers bioengineers to predictively design mammalian cellular functions that perform as expected even at high levels of biological complexity.

Sterol and lipid trafficking in mammalian cells

2006 ◽  
Vol 34 (3) ◽  
pp. 335-339 ◽  
Author(s):  
F.R. Maxfield ◽  
M. Mondal
Keyword(s):  
Membrane Trafficking ◽  
Mammalian Cells ◽  
Intracellular Transport ◽  
Vesicular Transport ◽  
Cholesterol Content ◽  
Cellular Functions ◽  
Lipid Trafficking ◽  
Sterol Transport ◽  
A Cell ◽  
Asymmetrically Distributed

The pathways involved in the intracellular transport and distribution of lipids in general, and sterols in particular, are poorly understood. Cholesterol plays a major role in modulating membrane bilayer structure and important cellular functions, including signal transduction and membrane trafficking. Both the overall cholesterol content of a cell, as well as its distribution in specific organellar membranes are stringently regulated. Several diseases, many of which are incurable at present, have been characterized as results of impaired cholesterol transport and/or storage in the cells. Despite their importance, many fundamental aspects of intracellular sterol transport and distribution are not well understood. For instance, the relative roles of vesicular and non-vesicular transport of cholesterol have not yet been fully determined, nor are the non-vesicular transport mechanisms well characterized. Similarly, whether cholesterol is asymmetrically distributed between the two leaflets of biological membranes, and if so, how this asymmetry is maintained, is poorly understood. In this review, we present a summary of the current understanding of these aspects of intracellular trafficking and distribution of lipids, and more specifically, of sterols.

scholarly journals Remote control of neural function by X-ray-induced scintillation

2019 ◽  
Author(s):  
Takanori Matsubara ◽  
Takayuki Yanagida ◽  
Noriaki Kawaguchi ◽  
Takashi Nakano ◽  
Junichiro Yoshimoto ◽  
...  
Keyword(s):  
Dopamine Neurons ◽  
Neural Function ◽  
X Rays ◽  
Cellular Functions ◽  
X Ray ◽  
Functional Studies ◽  
Clinical Dose ◽  
Visible Luminescence ◽  
Midbrain Dopamine ◽  
The Brain

Scintillators emit visible luminescence when irradiated with X-rays. Given the unlimited tissue penetration of X-rays, the employment of scintillators could enable remote optogenetic control of neural functions at any depth of the brain. Here we show that a yellow-emitting inorganic scintillator, Ce-doped Gd3(Al,Ga)5O12 (Ce:GAGG), could effectively activate red-shifted excitatory and inhibitory opsins, ChRmine and GtACR1, respectively. Using injectable Ce:GAGG microparticles, we successfully activated and inhibited midbrain dopamine neurons in freely moving mice by X-ray irradiation, producing bidirectional modulation of place preference behavior. Ce:GAGG microparticles were non-cytotoxic and biocompatible, allowing for chronic implantation. Pulsed X-ray irradiation at a clinical dose level was sufficient to elicit behavioral changes without reducing the number of radiosensitive cells in the brain and bone marrow. Thus, scintillator-mediated optogenetics enables less invasive, wireless control of cellular functions at any tissue depth in living animals, expanding X-ray applications to functional studies of biology and medicine.

Metallo-oxidase Enzymes: Design of their Active Sites

2011 ◽  
Vol 64 (3) ◽  
pp. 231 ◽  
Author(s):  
Zhiguang Xiao ◽  
Anthony G. Wedd
Keyword(s):  
Metal Ions ◽  
Active Sites ◽  
Specific Binding ◽  
Large Family ◽  
Outer Sphere ◽  
Transition Metal Ions ◽  
Substrate Oxidation ◽  
Cellular Functions ◽  
Domains Of Life ◽  
Low Valent

Multi-copper oxidases are a large family of enzymes prevalent in all three domains of life. They couple the one-electron oxidation of substrate to the four-electron reduction of dioxygen to water and feature at least four Cu atoms, traditionally divided into three sites: T1, T2, and (binuclear) T3. The T1 site catalyzes substrate oxidation while a trinuclear cluster (comprising combined T2 and T3 centres) catalyzes the reduction of dioxygen. Substrate oxidation at the T1 Cu site occurs via an outer-sphere mechanism and consequently substrate specificities are determined primarily by the nature of a substrate docking/oxidation (SDO) site associated with the T1 Cu centre. Many of these enzymes ‘moonlight’, i.e. display broad specificities towards many different substrates and may have multiple cellular functions. A sub-set are robust catalysts for the oxidation of low-valent transition metal ions such as FeII, CuI, and MnII and are termed ‘metallo-oxidases’. They play essential roles in nutrient metal uptake and homeostasis, with the ferroxidase ceruloplasmin being a prominent member. Their SDO sites are tailored to facilitate specific binding and facile oxidation of these low-valent metal ions and this is the focus of this review.

scholarly journals Oxygen radicals, nitric oxide, and peroxynitrite: Redox pathways in molecular medicine

2018 ◽  
Vol 115 (23) ◽  
pp. 5839-5848 ◽  
Author(s):  
Rafael Radi
Keyword(s):  
Nitric Oxide ◽  
Free Radical ◽  
Mammalian Cells ◽  
Oxygen Radicals ◽  
Biochemical Characterization ◽  
Cell Function ◽  
Molecular Medicine ◽  
Antioxidant Systems ◽  
Cellular Functions ◽  
Cell Degeneration

Oxygen-derived free radicals and related oxidants are ubiquitous and short-lived intermediates formed in aerobic organisms throughout life. These reactive species participate in redox reactions leading to oxidative modifications in biomolecules, among which proteins and lipids are preferential targets. Despite a broad array of enzymatic and nonenzymatic antioxidant systems in mammalian cells and microbes, excess oxidant formation causes accumulation of new products that may compromise cell function and structure leading to cell degeneration and death. Oxidative events are associated with pathological conditions and the process of normal aging. Notably, physiological levels of oxidants also modulate cellular functions via homeostatic redox-sensitive cell signaling cascades. On the other hand, nitric oxide (•NO), a free radical and weak oxidant, represents a master physiological regulator via reversible interactions with heme proteins. The bioavailability and actions of •NO are modulated by its fast reaction with superoxide radical (O2•−), which yields an unusual and reactive peroxide, peroxynitrite, representing the merging of the oxygen radicals and •NO pathways. In this Inaugural Article, I summarize early and remarkable developments in free radical biochemistry and the later evolution of the field toward molecular medicine; this transition includes our contributions disclosing the relationship of •NO with redox intermediates and metabolism. The biochemical characterization, identification, and quantitation of peroxynitrite and its role in disease processes have concentrated much of our attention. Being a mediator of protein oxidation and nitration, lipid peroxidation, mitochondrial dysfunction, and cell death, peroxynitrite represents both a pathophysiologically relevant endogenous cytotoxin and a cytotoxic effector against invading pathogens.

scholarly journals Functional Studies of MLL-AF4 and a Murinized pSer-variant thereof: MLL-AF4 Impairs the Ribosome Biosynthesis Pathway

2021 ◽  
Author(s):  
Anna Lena Siemund ◽  
Eric Kowarz ◽  
Rolf Marschalek
Keyword(s):  
Transcription Factor ◽  
Fusion Protein ◽  
Mammalian Cells ◽  
Biological Activities ◽  
Intracellular Localization ◽  
Biological Behavior ◽  
Hematopoietic Stem ◽  
Functional Studies ◽  
Pol I ◽  
Transcription Factor Complex

Abstract Background: Recent pathomolecular studies on the MLL-AF4 fusion protein revealed that the murinized version of MLL-AF4, the MLL-Af4 fusion protein, was able to induce leukemia when expressed in murine or human hematopoietic stem/progenitor cells (1). In parallel, a group from Japan demonstrated that the pSer domain of the AF4 protein, as well as the pSer domain of the MLL-AF4 fusion is able to bind the Pol I transcription factor complex SL1 (2).Here, we investigated the human MLL-AF4 and a pSer-murinized version thereof for their functional properties in mammalian cells. Gene expression profiling studies were complemented by intracellular localization studies and functional experiments concerning the biological activities in the nuecleolus.Results: Based on our results, we have to conclude that MLL-AF4 is predominantly localizing in the nucleolus, thereby interfering withPol I transcription, and subsequently,also ribosomebiogenesis. The murinized pSer-variant is more localizing in the nucleus, which may explain their different biological behavior. Of note, AF4-MLL is cooperating at the molecular level with MLL-AF4, but not with the pSer-murinized version of it.Conclusion: This study provides new insights and a molecular explanation for the known differences between hMLL-hAF4 (not leukemogenic) and hMLL-mAf4 (leukemogenic). While the human pSer domain is able to efficiently recruit the SL1 transcription factor complex, the murine counterpart is not. This has several consequences for our understanding of t(4;11) leukemia which is by far the most frequent leukemia in infants, childhood and adults suffering from MLL-r acute leukemia.

scholarly journals Molybdenum Enzymes and How They Support Virulence in Pathogenic Bacteria

2020 ◽  
Vol 11 ◽  
Author(s):  
Qifeng Zhong ◽  
Bostjan Kobe ◽  
Ulrike Kappler
Keyword(s):  
Drug Targets ◽  
Pathogenic Bacteria ◽  
Bacterial Pathogens ◽  
Energy Generation ◽  
Cellular Functions ◽  
Pathogen Fitness ◽  
Future Drug ◽  
Domains Of Life ◽  
Cofactor Biosynthesis ◽  
And Function

Mononuclear molybdoenzymes are highly versatile catalysts that occur in organisms in all domains of life, where they mediate essential cellular functions such as energy generation and detoxification reactions. Molybdoenzymes are particularly abundant in bacteria, where over 50 distinct types of enzymes have been identified to date. In bacterial pathogens, all aspects of molybdoenzyme biology such as molybdate uptake, cofactor biosynthesis, and function of the enzymes themselves, have been shown to affect fitness in the host as well as virulence. Although current studies are mostly focused on a few key pathogens such as Escherichia coli, Salmonella enterica, Campylobacter jejuni, and Mycobacterium tuberculosis, some common themes for the function and adaptation of the molybdoenzymes to pathogen environmental niches are emerging. Firstly, for many of these enzymes, their role is in supporting bacterial energy generation; and the corresponding pathogen fitness and virulence defects appear to arise from a suboptimally poised metabolic network. Secondly, all substrates converted by virulence-relevant bacterial Mo enzymes belong to classes known to be generated in the host either during inflammation or as part of the host signaling network, with some enzyme groups showing adaptation to the increased conversion of such substrates. Lastly, a specific adaptation to bacterial in-host survival is an emerging link between the regulation of molybdoenzyme expression in bacterial pathogens and the presence of immune system-generated reactive oxygen species. The prevalence of molybdoenzymes in key bacterial pathogens including ESKAPE pathogens, paired with the mounting evidence of their central roles in bacterial fitness during infection, suggest that they could be important future drug targets.

scholarly journals New Tetrahymena basal body protein components identify basal body domain structure

2007 ◽  
Vol 178 (6) ◽  
pp. 905-912 ◽  
Author(s):  
Chandra L. Kilburn ◽  
Chad G. Pearson ◽  
Edwin P. Romijn ◽  
Janet B. Meehl ◽  
Thomas H. Giddings ◽  
...  
Keyword(s):  
Basal Body ◽  
Ultrastructural Level ◽  
Cellular Functions ◽  
Structural Domains ◽  
Body Protein ◽  
Functional Studies ◽  
Specific Localization ◽  
Body Components ◽  
Protein Components ◽  
Molecular Components

Basal bodies organize the nine doublet microtubules found in cilia. Cilia are required for a variety of cellular functions, including motility and sensing stimuli. Understanding this biochemically complex organelle requires an inventory of the molecular components and the contribution each makes to the overall structure. We define a basal body proteome and determine the specific localization of basal body components in the ciliated protozoan Tetrahymena thermophila. Using a biochemical, bioinformatic, and genetic approach, we identify 97 known and candidate basal body proteins. 24 novel T. thermophila basal body proteins were identified, 19 of which were localized to the ultrastructural level, as seen by immunoelectron microscopy. Importantly, we find proteins from several structural domains within the basal body, allowing us to reveal how each component contributes to the overall organization. Thus, we present a high resolution localization map of basal body structure highlighting important new components for future functional studies.

scholarly journals NAA10 p.(N101K) disrupts N-terminal acetyltransferase complex NatA and is associated with developmental delay and hemihypertrophy

2020 ◽  
Author(s):  
Nina McTiernan ◽  
◽  
Harinder Gill ◽  
Carlos E. Prada ◽  
Harry Pachajoa ◽  
...  
Keyword(s):  
Intellectual Disability ◽  
Developmental Delay ◽  
Genetic Disorders ◽  
Cellular Functions ◽  
Functional Studies ◽  
Phenotypic Spectrum ◽  
Independent Functions ◽  
Evolutionarily Conserved ◽  
Human Proteins ◽  
The Impact

Abstract Nearly half of all human proteins are acetylated at their N-termini by the NatA N-terminal acetyltransferase complex. NAA10 is evolutionarily conserved as the catalytic subunit of NatA in complex with NAA15, but may also have NatA-independent functions. Several NAA10 variants are associated with genetic disorders. The phenotypic spectrum includes developmental delay, intellectual disability, and cardiac abnormalities. Here, we have identified the previously undescribed NAA10 c.303C>A and c.303C>G p.(N101K) variants in two unrelated girls. These girls have developmental delay, but they both also display hemihypertrophy a feature normally not observed or registered among these cases. Functional studies revealed that NAA10 p.(N101K) is completely impaired in its ability to bind NAA15 and to form an enzymatically active NatA complex. In contrast, the integrity of NAA10 p.(N101K) as a monomeric acetyltransferase is intact. Thus, this NAA10 variant may represent the best example of the impact of NatA mediated N-terminal acetylation, isolated from other potential NAA10-mediated cellular functions and may provide important insights into the phenotypes observed in individuals expressing pathogenic NAA10 variants.

scholarly journals Methyltransferase DnmA is responsible for genome-wide N6-methyladenosine modifications at non-palindromic recognition sites in Bacillus subtilis

2020 ◽  
Vol 48 (10) ◽  
pp. 5332-5348
Author(s):  
Taylor M Nye ◽  
Lieke A van Gijtenbeek ◽  
Amanda G Stevens ◽  
Jeremy W Schroeder ◽  
Justin R Randall ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Bacillus Subtilis ◽  
Consensus Sequence ◽  
Dna Uptake ◽  
Cellular Functions ◽  
Promoter Regions ◽  
Gram Positive Bacteria ◽  
Genome Wide ◽  
Domains Of Life ◽  
Reporter Assays

Abstract The genomes of organisms from all three domains of life harbor endogenous base modifications in the form of DNA methylation. In bacterial genomes, methylation occurs on adenosine and cytidine residues to include N6-methyladenine (m6A), 5-methylcytosine (m5C), and N4-methylcytosine (m4C). Bacterial DNA methylation has been well characterized in the context of restriction-modification (RM) systems, where methylation regulates DNA incision by the cognate restriction endonuclease. Relative to RM systems less is known about how m6A contributes to the epigenetic regulation of cellular functions in Gram-positive bacteria. Here, we characterize site-specific m6A modifications in the non-palindromic sequence GACGmAG within the genomes of Bacillus subtilis strains. We demonstrate that the yeeA gene is a methyltransferase responsible for the presence of m6A modifications. We show that methylation from YeeA does not function to limit DNA uptake during natural transformation. Instead, we identify a subset of promoters that contain the methylation consensus sequence and show that loss of methylation within promoter regions causes a decrease in reporter expression. Further, we identify a transcriptional repressor that preferentially binds an unmethylated promoter used in the reporter assays. With these results we suggest that m6A modifications in B. subtilis function to promote gene expression.

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