Maddalena V Coppi's research while affiliated with University of Massachusetts Amherst and other places
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Publications (34)
Clostridium phytofermentans was isolated from forest soil and is distinguished by its capacity to directly ferment plant cell wall polysaccharides into ethanol as the primary product, suggesting that it possesses unusual catabolic pathways. The objective of the present study was to understand the molecular mechanisms of biomass conversion to ethano...
Primer names, sequences and conditions used for qPCR analysis.
(DOC)
Clostridium phytofermentans, an anaerobic soil bacterium, can directly convert plant biomass into biofuels. The genome of C. phytofermentans contains three loci with genes encoding shell proteins of bacterial microcompartments (BMC), organelles composed entirely of proteins.
One of the BMC loci has homology to a BMC-encoding locus implicated in the...
Whole-genome microarray analysis of Geobacter sulfurreducens grown on insoluble Fe(III) oxide or Mn(IV) oxide versus soluble Fe(III) citrate revealed significantly different expression patterns. The most up-regulated genes, omcS and omcT, encode cell surface c-type cytochromes, OmcS being required for Fe(III) and Mn(IV) oxide reduction. Other elect...
Geobacter sulfurreducens is one of the few microorganisms available in pure culture known to directly accept electrons from a negatively poised electrode. Microarray analysis was used to compare gene transcript abundance in biofilms of G. sulfurreducens using a graphite electrode as the sole electron donor for fumarate reduction compared with trans...
Geobacter sulfurreducens is capable of coupling the complete oxidation of organic compounds to iron reduction. The metabolic response of G. sulfurreducens towards variations in electron donors (acetate, hydrogen) and acceptors (Fe(III), fumarate) was investigated via (13)C-based metabolic flux analysis. We examined the (13)C-labeling patterns of pr...
GC/MS mass isotopomer distributions. Carbon mass isotopomer distributions of different amino acid fragments computed from GC/MS measurements of TBDMS-amino acid derivatives are listed.
Anabolic precursor demand. Precursor stoichiometry given for the anabolic demand of G. sulfurreducens are listed.
Mass spectrometric (MS) isotopomer analysis has become a standard tool for investigating biological systems using stable isotopes. In particular, metabolic flux analysis uses mass isotopomers of metabolic products typically formed from (13)C-labeled substrates to quantitate intracellular pathway fluxes. In the current work, we describe a model-driv...
Limitations on the availability of Fe(III) as an electron acceptor are thought to play an important role in restricting the growth and activity of Geobacter species during bioremediation of contaminated subsurface environments, but the possibility that these organisms might also be limited in the subsurface by the availability of iron for assimilat...
The central metabolic model for Geobacter sulfurreducens included a single pathway for the biosynthesis of isoleucine that was analogous to that of Escherichia coli, in which the isoleucine precursor 2-oxobutanoate is generated from threonine. 13C labeling studies performed in G. sulfurreducens indicated that this pathway accounted for a minor frac...
Geobacteraceae are a family of metal reducing bacteria with important applications in bioremediation and electricity generation. G. sulfurreducens is a representative of Geobacteraceae that has been extensively studied with the goal of extending the understanding of this family of organisms for optimizing their practical applications. Here, we have...
A soluble ferric reductase, SfrAB, which catalysed the NADPH-dependent reduction of chelated Fe(III), was previously purified from the dissimilatory Fe(III)-reducing micro-organism Geobacter sulfurreducens, suggesting that reduction of chelated forms of Fe(III) might be cytoplasmic. However, metabolically active spheroplast suspensions could not ca...
In order to study the mechanism of U(VI) reduction, the effect of deleting c-type cytochrome genes on the capacity of Geobacter sulfurreducens to reduce U(VI) with acetate serving as the electron donor was investigated.
The ability of several c-type cytochrome deficient mutants to reduce U(VI) was lower than that of the wild type strain. Eliminatio...
Deletion of two homologous Geobacter sulfurreducens c-type cytochrome genes, omcG and omcH, decreased the rate of Fe(III) reduction and decreased the level of an outer membrane cytochrome critical for Fe(III) reduction,
OmcB, without affecting its transcription. Expression of either gene restored Fe(III) reduction and OmcB expression, suggesting
fu...
Geobacter sulfurreducens is a well-studied representative of the Geobacteraceae, which play a critical role in organic matter oxidation coupled to Fe(III) reduction, bioremediation of groundwater contaminated with organics or metals, and electricity production from waste organic matter. In order to investigate G. sulfurreducens central metabolism a...
The potential role of outer membrane proteins in electron transfer to insoluble Fe(III) oxides by Geobacter sulfurreducens was investigated because this organism is closely related to the Fe(III) oxide-reducing organisms that are predominant in many Fe(III)-reducing environments. Two of the most abundant proteins that were easily sheared from the o...
Outer membrane cytochromes are often proposed as likely agents for electron transfer to extracellular electron acceptors,
such as Fe(III). The omcF gene in the dissimilatory Fe(III)-reducing microorganism Geobacter sulfurreducens is predicted to code for a small outer membrane monoheme c-type cytochrome. An OmcF-deficient strain was constructed, an...
The hydrogenase content of the genome of Geobacter sulfurreducens, a member of the family Geobacteraceae within the delta-subdivision of the Proteobacteria, was examined and found to be distinct from that of Desulfovibrio species, another family of delta-Proteobacteria on which extensive research concerning hydrogen metabolism has been conducted. F...
A 36-kDa diheme c-type cytochrome abundant in Fe(III)-respiring Geobacter sulfurreducens, designated MacA, was more highly expressed during growth with Fe(III) as the electron acceptor than with fumarate. Although
MacA has homology to proteins with in vitro peroxidase activity, deletion of macA had no impact on response to oxidative stress. However...
Geobacter sulfurreducens, a representative of the family Geobacteraceae that predominates in Fe(III)-reducing subsurface environments, can grow by coupling the oxidation of hydrogen to the reduction
of a variety of electron acceptors, including Fe(III), fumarate, and quinones. An examination of the G. sulfurreducens genome revealed two operons, hya...
Geobacter sulfurreducens, previously classified as a strict anaerobe, tolerated exposure to atmospheric oxygen for at least 24 h and grew with oxygen
as the sole electron acceptor at concentrations of 10% or less in the headspace. These results help explain how Geobacter species may survive in oxic subsurface environments, being poised to rapidly t...
Technetium is a key radioactive pollutant in subsurface environments contaminated with radioactive waste. However, dissimilatory Fe(III)-reducing bacteria can control its mobility through the enzymatic reduction and precipitation of soluble Tc(VII) to insoluble Tc(IV). We have investigated the mechanism of electron transfer to Tc(VII) in the model...
Microorganisms in the family Geobacteraceae are the predominant Fe(III)-reducing microorganisms in a variety of subsurface environments in which Fe(III) reduction is
an important process, but little is known about the mechanisms for electron transport to Fe(III) in these organisms. The Geobacter sulfurreducens genome was found to contain a 10-kb ch...
A 9.6 kDa periplasmic c -type cytochrome, designated PpcA, was purified from the Fe(III)-reducing bacterium Geobacter sulfurreducens and characterized. The purified protein is basic (pI 9.5), contains three haems and has an N-terminal amino acid sequence closely related to those of the previously described trihaem c (7) cytochromes of Geobacter met...
Members of the genus Geobacter are the dominant metal-reducing microorganisms in a variety of anaerobic subsurface environments and have been shown to be
involved in the bioremediation of both organic and metal contaminants. To facilitate the study of the physiology of these
organisms, a genetic system was developed forGeobacter sulfurreducens. The...
The Na,K-ATPase is specifically inhibited by the cardiac glycoside, ouabain. Via a largely undefined mechanism, the ouabain affinity of the Na,K-ATPase can be manipulated by mutating the residues at the borders of the first extracellular (M1-M2) loop of the alpha subunit [Price, E. M., Rice, D. A., and Lingrel, J. B. (1990) J. Biol. Chem. 265, 6638...
The Na,K-ATPase is an essential plasma membrane transporter of mammalian cells composed of two subunits, alpha and beta, of which there are several isoforms. We investigated the effect of a substitution, S364P, on the subcellular localization and enzymatic activity of the wild-type alpha2 and alpha2L111R,N122D (alpha2RD) subunits. The substitutions...
Isotopically labeled n-hexadecane doped at the percent level in three crude oils is used to determine the intrinsic decomposition kinetics and mechanism of n-alkanes in petroleum. Adjacent 13C labels at the end of the hexadecane and dodecene give a mass fragment sufficiently unique that its disappearance and many of its products can be followed by...
In the rat adipocyte, insulin increases potassium uptake by a preferential activation of the alpha2 isoform of the Na,K-ATPase. The question under consideration here is whether expression of the alpha2 isoform is sufficient to replicate its differential activation by insulin. Accordingly, we compared the effect of insulin on the activity of the oua...
Na,K-ATPase, an essential transporter of mammalian cells, is an oligomeric transmembrane protein composed of two subunits, alpha and beta, of which there are several isoforms. In this study, we demonstrate that the alpha1 and alpha2 isoforms of the Na,K-ATPase alpha subunit are modified by the covalent attachment of ubiquitin polymers in COS-7 cell...
Na,K-ATPase, an essential transporter of mammalian cells, is an oligomeric transmembrane protein composed of two subunits, alpha and beta, of which there are several isoforms. In this study, me demonstrate that the alpha 1 and alpha 2 isoforms of the Na,K-ATPase alpha subunit are modified by the covalent attachment of ubiquitin polymers in COS-7 ce...
Analysis of the Genetic Potential and Gene Expression of Microbial Communities Involved in the In Situ Bioremediation of Uranium and Harvesting Electrical Energy from Organic Matter The primary goal of this research is to develop conceptual and computational models that can describe the functioning of complex microbial communities involved in micro...
Citations
... The overabundance of Cazymes is not necessarily related to high enzymatic activity, as it depends on the genomic context such as the possible presence of a promoter (Williams-Rhaesa et al. 2018), operon (Chakraborty et al. 2021). Indeed, Clostridia phytofermentas, which is a very good lignocellulolytic degrader (Tolonen et al. 2011) and expresses several high lignocellulolytic enzymatic activities (Petit et al. 2015), secreted approximately 80 Cazymes (among the 161 present in its genome) in silico, which confirms that a very high abundance of Cazymes does not necessarily indicate excellent enzymatic activity. ...
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... However, crude oils contain some macromolecules, such as asphaltenes that play the role as kerogen for recycling maturation. Burnham et al. (1997) found that the decomposition rate of n-alkanes is substantially higher in crude oil matrices than pure n-alkanes. In addition to gas formation, oil cracking also results in the formation of pyrobitumen, which acts as kerogen in recycling maturation. ...
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... As well as STAT3, ouabain markedly reduced the abundance of NKAα1 in human myotubes (Figures 1A,E,I). NKAα1 can be modified by ubiquitination (Coppi and Guidotti, 1997) and MG-132 opposes the loss of NKAα1, which is caused by various treatments, including CdCl 2 (Thevenod and Friedmann, 1999) and hypoxia (Comellas et al., 2006). Actions of MG-132 could indicate that NKAα1 is ubiquitinated and at least partially degraded in the proteasome in response to the ouabain treatment. ...
... The essential medium components for bioethanol production from pre-treated from S. wightii biomass (extracted cellulose) were optimized using CCRD-RSM for L. phytofermentans KSM1203. The essential medium components for L. Phytofermentans KSM 1203 were selected from the literature [32]. RSM, was the most widely used statistical method of independent variables optimization for bioethanol production from pretreated S. wightii biomassusing L. phytofermentans KSM 1203. ...
... Frontiers in Microbiology 14 frontiersin.org was detected for the protein DealDRAFT_2539 homologous (24% identity) to OmcN Fe(III)-reducing outer surface cytochrome of G. sulfurreducens (Aklujkar et al., 2013). All these facts emphasize that the reduction of sulfur compounds in D. alkaliphilus is most likely driven by multiheme cytochromes homologous to Fe-cycling proteins. ...
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... These studies addressed the properties and role of G. sulfurreducens pili. However, the majority of research including these two conditions has been performed on planktonic cultures and focused on metabolic features of G. sulfurreducens [35,[51][52][53][54][55][56]. ...
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... Metal-reducing bacteria, such as Geobacter and Shewanella, have been extensively investigated for their diverse electron transfer properties [31]. Studies have demonstrated that Geobacter has the capability to directly acquire electrons from metal surfaces via an extracellular electron transfer process mediated by its nanowires and outer membrane cytochrome C protein [31][32][33][34]. ...
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... Cells, sampled during the cultivation, were analyzed for the 13 C labelling pattern of amino acids from hydrolysed cell protein using GC/MS (GC 7890A, 5975C quadrupole detector, Agilent, Darmstadt, Germany) as described recently (Hoffmann et al., 2018). The measured labelling patterns were corrected for the non-labelled inoculum and for natural isotopes (Yang et al., 2009) and then used to derive the summed fractional labelling for each amino acid (Schwechheimer et al., 2018). The latter value directly reflected the relative amount that was synthetized de novo from Glc and the remaining fraction could be attributed to uptake form the medium, respectively. ...
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... Mitochondrial ROS stimulates phosphorylation of the α1 subunit by protein kinase PKCζ, which triggers endocytosis of the plasma membrane Na + / K + ATPase [35][36][37][38]. Phosphorylation-ubiquitination-recognition-endocytosis-degradation (PURED) is an established pathway for regulating plasma membrane proteins including the Na + /K + ATPase [39][40][41][42]. Phosphorylation of the α1 subunit stimulates ubiquitylation under steady state and hypoxic conditions in alveolar cells and, it inhibits Na + /K + ATPase in neuronal cells [43][44][45]. ...
... Interestingly, however, incubation of muscle cells with ouabain alone induced a modest stimulatory effect on Rb + uptake. This finding is not unprecedented and has been reported previously by others (Bakker-Grunwald et al. 1982;Aiton & Simmons, 1983;Dong et al. 1994;Coppi & Guidotti, 1997). One possible explanation for the stimulatory effect of ouabain upon Rb + uptake is that Na + ,K + -ATPase inhibition leads to increased K + efflux via opening of K + channels, and that the ensuing depletion of cellular K + by this route subsequently promotes increased K + uptake via NKCC. ...
