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1.
Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen.
Liu, JK, Lloyd, C, Al-Bassam, MM, Ebrahim, A, Kim, JN, Olson, C, Aksenov, A, Dorrestein, P, Zengler, K
PLoS computational biology. 2019;(3):e1006848
Abstract
The unique capability of acetogens to ferment a broad range of substrates renders them ideal candidates for the biotechnological production of commodity chemicals. In particular the ability to grow with H2:CO2 or syngas (a mixture of H2/CO/CO2) makes these microorganisms ideal chassis for sustainable bioproduction. However, advanced design strategies for acetogens are currently hampered by incomplete knowledge about their physiology and our inability to accurately predict phenotypes. Here we describe the reconstruction of a novel genome-scale model of metabolism and macromolecular synthesis (ME-model) to gain new insights into the biology of the model acetogen Clostridium ljungdahlii. The model represents the first ME-model of a Gram-positive bacterium and captures all major central metabolic, amino acid, nucleotide, lipid, major cofactors, and vitamin synthesis pathways as well as pathways to synthesis RNA and protein molecules necessary to catalyze these reactions, thus significantly broadens the scope and predictability. Use of the model revealed how protein allocation and media composition influence metabolic pathways and energy conservation in acetogens and accurately predicted secretion of multiple fermentation products. Predicting overflow metabolism is of particular interest since it enables new design strategies, e.g. the formation of glycerol, a novel product for C. ljungdahlii, thus broadening the metabolic capability for this model microbe. Furthermore, prediction and experimental validation of changing secretion rates based on different metal availability opens the window into fermentation optimization and provides new knowledge about the proteome utilization and carbon flux in acetogens.
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2.
Metal-Mediated Functionalization of Natural Peptides and Proteins: Panning for Bioconjugation Gold.
Ohata, J, Martin, SC, Ball, ZT
Angewandte Chemie (International ed. in English). 2019;(19):6176-6199
Abstract
Selective modification of natural proteins is a daunting methodological challenge and a stringent test of selectivity and reaction scope. There is a continued need for new reactivity and new selectivity concepts. Transition metals exhibit a wealth of unique reactivity that is orthogonal to biological reactions and processes. As such, metal-based methods play an increasingly important role in bioconjugation. This Review examines metal-based methods as well as their reactivity and selectivity for the functionalization of natural proteins and peptides.
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3.
Additive manufacturing of biodegradable metals: Current research status and future perspectives.
Qin, Y, Wen, P, Guo, H, Xia, D, Zheng, Y, Jauer, L, Poprawe, R, Voshage, M, Schleifenbaum, JH
Acta biomaterialia. 2019;:3-22
Abstract
The combination of biodegradable metals and additive manufacturing (AM) leads to a revolutionary change of metal implants in many aspects including materials, design, manufacturing, and clinical applications. The AM of nondegradable metals such as titanium and CoCr alloys has proven to be a tremendous success in clinical applications. The AM of biodegradable metals including magnesium (Mg), iron (Fe), and zinc (Zn) is still in its infancy, although much progress has been made in the research field. Element loss and porosity are common processing problems for AM of biodegradable metals like Zn and Mg, which are mainly caused by evaporation during melting under a high-energy beam. The resulting formation quality and properties are closely related to material, design, and processing, making AM of biodegradable metals a typical interdisciplinary subject involving biomaterials, mechanical engineering, and medicine. This work reviews the state of research and future perspective on AM of biodegradable metals from extensive viewpoints such as material, processing, formation quality, design, microstructure, and properties. Effects of powder properties and processing parameters on formation quality are characterized in detail. The microstructure and metallurgical defects encountered in the AM parts are described. Mechanical and biodegradable properties of AM samples are introduced. Design principles and potential applications of biodegradable metal implants produced by AM are discussed. Finally, current research status is summarized together with some proposed future perspectives for advancing knowledge about AM of biodegradable metals. STATEMENT OF SIGNIFICANCE Rapid development of research and applications on biodegradable metals and additive manufacturing (AM) has been made in recent years. Customized geometric shapes of medical metals with porous structure can be realized accurately and efficiently by laser powder bed fusion (L-PBF), which is beneficial to achieve reliable stress conduction and balanced properties. This review introduces the development history and current status of AM of biodegradable metals and then critically surveys L-PBF of Mg-, Fe-, and Zn-based metals from multiple viewpoints including materials, processing, formation quality, structural design, microstructure, and mechanical and biological properties. The present findings are summarized together with some proposed future challenges for advancing AM of biodegradable metals into real clinical applications.
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4.
Metal-responsive RNA polymerase extracytoplasmic function (ECF) sigma factors.
Moraleda-Muñoz, A, Marcos-Torres, FJ, Pérez, J, Muñoz-Dorado, J
Molecular microbiology. 2019;(2):385-398
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Abstract
In order to survive, bacteria must adapt to multiple fluctuations in their environment, including coping with changes in metal concentrations. Many metals are essential for viability, since they act as cofactors of indispensable enzymes. But on the other hand, they are potentially toxic because they generate reactive oxygen species or displace other metals from proteins, turning them inactive. This dual effect of metals forces cells to maintain homeostasis using a variety of systems to import and export them. These systems are usually inducible, and their expression is regulated by metal sensors and signal-transduction mechanisms, one of which is mediated by extracytoplasmic function (ECF) sigma factors. In this review, we have focused on the metal-responsive ECF sigma factors, several of which are activated by iron depletion (FecI, FpvI and PvdS), while others are activated by excess of metals such as nickel and cobalt (CnrH), copper (CarQ and CorE) or cadmium and zinc (CorE2). We focus particularly on their physiological roles, mechanisms of action and signal transduction pathways.
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Metallacarboranes as a tool for enhancing the activity of therapeutic peptides.
Fink, K, Boratyński, J, Paprocka, M, Goszczyński, TM
Annals of the New York Academy of Sciences. 2019;(1):128-141
Abstract
Metallacarboranes are anionic boron clusters with high affinity to serum albumin, ability to cross biological membranes, and no apparent toxicity in vitro and in vivo. Thus, conjugation with cobalt bis(1,2-dicarbollide), [COSAN]- , ([3,3'-Co(1,2-C2 B9 H11 )2 ]- ) may improve the properties of therapeutic peptides or proteins at both molecular and systemic levels. Here, we conjugated [COSAN]- with the therapeutic peptide thymosin β4 (Tβ4), which has a pleiotropic activity that results in enhanced healing and regeneration of injured tissues. Using fluorescence quenching of human serum albumin and surface plasmon resonance techniques, we showed that the conjugates have a high affinity to human serum albumin. Using an in vitro wound closure assay, we showed that conjugation with [COSAN]- enhances the activity of Tβ4 toward fibroblasts (MSU1.1 cell line). These results indicate an application of metallacarboranes in the development of analogs of various therapeutic peptides/proteins with superior pharmacological properties.
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Metal ligands in micronutrient acquisition and homeostasis.
Clemens, S
Plant, cell & environment. 2019;(10):2902-2912
Abstract
Acquisition and homeostasis of micronutrients such as iron (Fe) and zinc (Zn) pose specific challenges. Poor solubility and high reactivity require controlled synthesis and supply of ligands to complex these metals extracellularly and intracellularly. Cytosolic labile pools represent only a minute fraction of the total cellular content. Several low-molecular-weight ligands are known in plants, including sulfur ligands (cysteine and peptides), nitrogen/oxygen ligands (S-adenosyl-l-methionine-derived molecules and histidine), and oxygen ligands (phenolics and organic acids). Some ligands are secreted into the extracellular space and influence the phytoavailability of metal ions. A second principal function is the intracellular buffering of micronutrients as well as the facilitation of long-distance transport in xylem and phloem. Furthermore, low-molecular-weight ligands are involved in the storage of metals, predominantly in vacuoles. A detailed molecular understanding is hampered by technical limitations, in particular the difficulty to detect and quantify cellular metal-ligand complexes. More, but still too little, is known about ligand synthesis and the transport across membranes, either with or without a complexed metal. Metal ligands have an immediate impact on human well-being. Engineering metal ligand synthesis and distribution in crops has tremendous potential to improve the nutritional quality of food and to tackle major human health risks.
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Transition metal transporters in rhizobia: tuning the inorganic micronutrient requirements to different living styles.
Abreu, I, Mihelj, P, Raimunda, D
Metallomics : integrated biometal science. 2019;(4):735-755
Abstract
A group of bacteria known as rhizobia are key players in symbiotic nitrogen fixation (SNF) in partnership with legumes. After a molecular exchange, the bacteria end surrounded by a plant membrane forming symbiosomes, organelle-like structures, where they differentiate to bacteroids and fix nitrogen. This symbiotic process is highly dependent on dynamic nutrient exchanges between the partners. Among these are transition metals (TM) participating as inorganic and organic cofactors of fundamental enzymes. While the understanding of how plant transporters facilitate TMs to the very near environment of the bacteroid is expanding, our knowledge on how bacteroid transporters integrate to TM homeostasis mechanisms in the plant host is still limited. This is significantly relevant considering the low solubility and scarcity of TMs in soils, and the in crescendo gradient of TM bioavailability rhizobia faces during the infection and bacteroid differentiation processes. In the present work, we review the main metal transporter families found in rhizobia, their role in free-living conditions and, when known, in symbiosis. We focus on discussing those transporters which could play a significant role in TM-dependent biochemical and physiological processes in the bacteroid, thus paving the way towards an optimized SNF.
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8.
Finding High-Quality Metal Ion-Centric Regions Across the Worldwide Protein Data Bank.
Yao, S, Moseley, HNB
Molecules (Basel, Switzerland). 2019;(17)
Abstract
As the number of macromolecular structures in the worldwide Protein Data Bank (wwPDB) continues to grow rapidly, more attention is being paid to the quality of its data, especially for use in aggregated structural and dynamics analyses. In this study, we systematically analyzed 3.5 Å regions around all metal ions across all PDB entries with supporting electron density maps available from the PDB in Europe. All resulting metal ion-centric regions were evaluated with respect to four quality-control criteria involving electron density resolution, atom occupancy, symmetry atom exclusion, and regional electron density discrepancy. The resulting list of metal binding sites passing all four criteria possess high regional structural quality and should be beneficial to a wide variety of downstream analyses. This study demonstrates an approach for the pan-PDB evaluation of metal binding site structural quality with respect to underlying X-ray crystallographic experimental data represented in the available electron density maps of proteins. For non-crystallographers in particular, we hope to change the focus and discussion of structural quality from a global evaluation to a regional evaluation, since all structural entries in the wwPDB appear to have both regions of high and low structural quality.
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A Review of Biomarkers Used for Assessing Human Exposure to Metals from E-Waste.
Arain, AL, Neitzel, RL
International journal of environmental research and public health. 2019;(10)
Abstract
Electronic waste recycling presents workers and communities with a potential for exposures to dangerous chemicals, including metals. This review examines studies that report on blood, hair, and urine biomarkers of communities and workers exposed to metals from e-waste. Our results from the evaluation of 19 publications found that there are consistently elevated levels of lead found in occupationally and non-occupationally exposed populations, in both the formal and the informal e-waste recycling sectors. Various other metals were found to be elevated in different exposure groups assessed using various types of biomarkers, but with less consistency than found in lead. Antimony and cadmium generally showed higher concentrations in exposed groups compared to reference group(s). Mercury and arsenic did not show a trend among exposure groups due to the dietary and environmental considerations. Observed variations in trends amongst exposure groups within studies using multiple biomarkers highlights the need to carefully select appropriate biomarkers. Our study concludes that there is a need for more rigorous research that moves past cross-sectional study designs, involves more thoughtful and methodical selection of biomarkers, and a systematic reporting standard for exposure studies to ensure that results can be compared across studies.
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10.
Switching on Endogenous Metal Binding Proteins in Parkinson's Disease.
McLeary, FA, Rcom-H'cheo-Gauthier, AN, Goulding, M, Radford, RAW, Okita, Y, Faller, P, Chung, RS, Pountney, DL
Cells. 2019;(2)
Abstract
The formation of cytotoxic intracellular protein aggregates is a pathological signature of multiple neurodegenerative diseases. The principle aggregating protein in Parkinson's disease (PD) and atypical Parkinson's diseases is α-synuclein (α-syn), which occurs in neural cytoplasmic inclusions. Several factors have been found to trigger α-syn aggregation, including raised calcium, iron, and copper. Transcriptional inducers have been explored to upregulate expression of endogenous metal-binding proteins as a potential neuroprotective strategy. The vitamin-D analogue, calcipotriol, induced increased expression of the neuronal vitamin D-dependent calcium-binding protein, calbindin-D28k, and this significantly decreased the occurrence of α-syn aggregates in cells with transiently raised intracellular free Ca, thereby increasing viability. More recently, the induction of endogenous expression of the Zn and Cu binding protein, metallothionein, by the glucocorticoid analogue, dexamethasone, gave a specific reduction in Cu-dependent α-syn aggregates. Fe accumulation has long been associated with PD. Intracellularly, Fe is regulated by interactions between the Fe storage protein ferritin and Fe transporters, such as poly(C)-binding protein 1. Analysis of the transcriptional regulation of Fe binding proteins may reveal potential inducers that could modulate Fe homoeostasis in disease. The current review highlights recent studies that suggest that transcriptional inducers may have potential as novel mechanism-based drugs against metal overload in PD.