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Chemical Society Reviews Jan 2014The nitrate anion is a simple, abundant and relatively stable species, yet plays a significant role in global cycling of nitrogen, global climate change, and human... (Review)
Review
The nitrate anion is a simple, abundant and relatively stable species, yet plays a significant role in global cycling of nitrogen, global climate change, and human health. Although it has been known for quite some time that nitrate is an important species environmentally, recent studies have identified potential medical applications. In this respect the nitrate anion remains an enigmatic species that promises to offer exciting science in years to come. Many bacteria readily reduce nitrate to nitrite via nitrate reductases. Classified into three distinct types--periplasmic nitrate reductase (Nap), respiratory nitrate reductase (Nar) and assimilatory nitrate reductase (Nas), they are defined by their cellular location, operon organization and active site structure. Of these, Nap proteins are the focus of this review. Despite similarities in the catalytic and spectroscopic properties Nap from different Proteobacteria are phylogenetically distinct. This review has two major sections: in the first section, nitrate in the nitrogen cycle and human health, taxonomy of nitrate reductases, assimilatory and dissimilatory nitrate reduction, cellular locations of nitrate reductases, structural and redox chemistry are discussed. The second section focuses on the features of periplasmic nitrate reductase where the catalytic subunit of the Nap and its kinetic properties, auxiliary Nap proteins, operon structure and phylogenetic relationships are discussed.
Topics: Bacterial Proteins; Catalytic Domain; Gene Expression Regulation, Bacterial; Gram-Negative Bacteria; Gram-Positive Bacteria; Humans; Models, Molecular; Nitrate Reductases; Nitrates; Nitrogen Cycle; Operon; Oxidation-Reduction; Periplasm; Phylogeny; Proteobacteria
PubMed: 24141308
DOI: 10.1039/c3cs60249d -
Protein Science : a Publication of the... Dec 2015Nitrate reductases (NR) belong to the DMSO reductase family of Mo-containing enzymes and perform key roles in the metabolism of the nitrogen cycle, reducing nitrate to... (Review)
Review
Nitrate reductases (NR) belong to the DMSO reductase family of Mo-containing enzymes and perform key roles in the metabolism of the nitrogen cycle, reducing nitrate to nitrite. Due to variable cell location, structure and function, they have been divided into periplasmic (Nap), cytoplasmic, and membrane-bound (Nar) nitrate reductases. The first crystal structure obtained for a NR was that of the monomeric NapA from Desulfovibrio desulfuricans in 1999. Since then several new crystal structures were solved providing novel insights that led to the revision of the commonly accepted reaction mechanism for periplasmic nitrate reductases. The two crystal structures available for the NarGHI protein are from the same organism (Escherichia coli) and the combination with electrochemical and spectroscopic studies also lead to the proposal of a reaction mechanism for this group of enzymes. Here we present an overview on the current advances in structural and functional aspects of bacterial nitrate reductases, focusing on the mechanistic implications drawn from the crystallographic data.
Topics: Bacteria; Bacterial Proteins; Catalytic Domain; Cell Membrane; Crystallography, X-Ray; Cytoplasm; Models, Molecular; Nitrate Reductase; Periplasm
PubMed: 26362109
DOI: 10.1002/pro.2801 -
Journal of Bacteriology Dec 2022Reduction of extracellular acceptors requires electron transfer across the periplasm. In Geobacter sulfurreducens, three separate cytoplasmic membrane cytochromes are...
Reduction of extracellular acceptors requires electron transfer across the periplasm. In Geobacter sulfurreducens, three separate cytoplasmic membrane cytochromes are utilized depending on redox potential, and at least five cytochrome conduits span the outer membrane. Because G. sulfurreducens produces 5 structurally similar triheme periplasmic cytochromes (PpcABCDE) that differ in expression level, midpoint potential, and heme biochemistry, many hypotheses propose distinct periplasmic carriers could be used for specific redox potentials, terminal acceptors, or growth conditions. Using a panel of marker-free single, quadruple, and quintuple mutants, little support for these models could be found. Three quadruple mutants containing only one paralog (PpcA, PpcB, and PpcD) reduced Fe(III) citrate and Fe(III) oxide at the same rate and extent, even though PpcB and PpcD were at much lower periplasmic levels than PpcA. Mutants containing only PpcC and PpcE showed defects, but these cytochromes were nearly undetectable in the periplasm. When expressed sufficiently, PpcC and PpcE supported wild-type Fe(III) reduction. PpcA and PpcE from similarly restored metal respiration in G. sulfurreducens. PgcA, an unrelated extracellular triheme -type cytochrome, also participated in periplasmic electron transfer. While triheme cytochromes were important for metal reduction, sextuple Δ Δ mutants grew near wild-type rates with normal cyclic voltammetry profiles when using anodes as electron acceptors. These results reveal broad promiscuity in the periplasmic electron transfer network of metal-reducing and suggest that an as-yet-undiscovered periplasmic mechanism supports electron transfer to electrodes. Many inner and outer membrane cytochromes used by for electron transfer to extracellular acceptors have specific functions. How these are connected by periplasmic carriers remains poorly understood. G. sulfurreducens contains multiple triheme periplasmic cytochromes with unique biochemical properties and expression profiles. It is hypothesized that each could be involved in a different respiratory pathway, depending on redox potential or energy needs. Here, we show that periplasmic cytochromes instead show evidence of being highly promiscuous. Any of 6 triheme cytochromes supported similar growth with soluble or insoluble metals, but none were required when cells utilized electrodes. These findings fail to support many models of electron transfer, and question why these organisms produce such an array of periplasmic cytochromes.
Topics: Geobacter; Periplasm; Ferric Compounds; Electrons; Electron Transport; Cytochromes; Oxidation-Reduction
PubMed: 36383007
DOI: 10.1128/jb.00322-22 -
Trends in Biochemical Sciences Nov 2016Biochemical processes take place in heterogeneous and highly volume-occupied or crowded environments that can considerably influence the reactivity and distribution of... (Review)
Review
Biochemical processes take place in heterogeneous and highly volume-occupied or crowded environments that can considerably influence the reactivity and distribution of participating macromolecules. We summarize here the thermodynamic consequences of excluded-volume and long-range nonspecific intermolecular interactions for macromolecular reactions in volume-occupied media. In addition, we summarize and compare the information content of studies of crowding in vitro and in vivo. We emphasize the importance of characterizing the behavior not only of labeled tracer macromolecules but also the composition and behavior of unlabeled macromolecules in the immediate vicinity of the tracer. Finally, we propose strategies for extending quantitative analyses of crowding in simple model systems to increasingly complex media up to and including intact cells.
Topics: Bacterial Proteins; Cell Compartmentation; Cell Membrane; DNA, Bacterial; Escherichia coli; Kinetics; Organelles; Periplasm; RNA, Bacterial; Thermodynamics
PubMed: 27669651
DOI: 10.1016/j.tibs.2016.08.013 -
Journal of Biotechnology Mar 2021Soluble expression of recombinant proteins in E. coli is often done by translocation of the product across the inner membrane (IM) into the periplasm, where it is... (Review)
Review
Soluble expression of recombinant proteins in E. coli is often done by translocation of the product across the inner membrane (IM) into the periplasm, where it is retained by the outer membrane (OM). While the integrity of the IM is strongly coupled to viability and impurity release, a decrease in OM integrity (corresponding to increased "leakiness") leads to accumulation of product in the extracellular space, strongly impacting the downstream process. Whether leakiness is desired or not, differential monitoring and control of IM and OM integrity are necessary for an efficient E. coli bioprocess in compliance with the guidelines of Quality by Design and Process Analytical Technology. In this review, we give an overview of relevant monitoring tools, summarize the research on factors affecting E. coli membrane integrity and provide a brief discussion on how the available monitoring technology can be implemented in real-time control of E. coli cultivations.
Topics: Bacterial Outer Membrane Proteins; Cell Membrane; Escherichia coli; Escherichia coli Proteins; Periplasm; Recombinant Proteins
PubMed: 33485861
DOI: 10.1016/j.jbiotec.2021.01.009 -
EcoSal Plus Feb 2019The type II secretion system (T2SS) delivers toxins and a range of hydrolytic enzymes, including proteases, lipases, and carbohydrate-active enzymes, to the cell surface... (Review)
Review
The type II secretion system (T2SS) delivers toxins and a range of hydrolytic enzymes, including proteases, lipases, and carbohydrate-active enzymes, to the cell surface or extracellular space of Gram-negative bacteria. Its contribution to survival of both extracellular and intracellular pathogens as well as environmental species of proteobacteria is evident. This dynamic, multicomponent machinery spans the entire cell envelope and consists of a cytoplasmic ATPase, several inner membrane proteins, a periplasmic pseudopilus, and a secretin pore embedded in the outer membrane. Despite the -envelope configuration of the T2S nanomachine, proteins to be secreted engage with the system first once they enter the periplasmic compartment via the Sec or TAT export system. Thus, the T2SS is specifically dedicated to their outer membrane translocation. The many sequence and structural similarities between the T2SS and type IV pili suggest a common origin and argue for a pilus-mediated mechanism of secretion. This minireview describes the structures, functions, and interactions of the individual T2SS components and the general architecture of the assembled T2SS machinery and briefly summarizes the transport and function of a growing list of T2SS exoproteins. Recent advances in cryo-electron microscopy, which have led to an increased understanding of the structure-function relationship of the secretin channel and the pseudopilus, are emphasized.
Topics: Adenosine Triphosphatases; Bacterial Proteins; Cryoelectron Microscopy; Fimbriae, Bacterial; Gram-Negative Bacteria; Membrane Proteins; Models, Molecular; Periplasm; Protein Binding; Secretin; Type II Secretion Systems
PubMed: 30767847
DOI: 10.1128/ecosalplus.ESP-0034-2018 -
PLoS Biology Jan 2018Gram-negative bacteria are surrounded by two membrane bilayers separated by a space termed the periplasm. The periplasm is a multipurpose compartment separate from the...
Gram-negative bacteria are surrounded by two membrane bilayers separated by a space termed the periplasm. The periplasm is a multipurpose compartment separate from the cytoplasm whose distinct reducing environment allows more efficient and diverse mechanisms of protein oxidation, folding, and quality control. The periplasm also contains structural elements and important environmental sensing modules, and it allows complex nanomachines to span the cell envelope. Recent work indicates that the size or intermembrane distance of the periplasm is controlled by periplasmic lipoproteins that anchor the outer membrane to the periplasmic peptidoglycan polymer. This periplasm intermembrane distance is critical for sensing outer membrane damage and dictates length of the flagellar periplasmic rotor, which controls motility. These exciting results resolve longstanding debates about whether the periplasmic distance has a biological function and raise the possibility that the mechanisms for maintenance of periplasmic size could be exploited for antibiotic development.
Topics: Bacterial Outer Membrane Proteins; Bacterial Proteins; Cell Membrane; Cell Wall; Cytoplasm; Gram-Negative Bacteria; Peptidoglycan; Periplasm; Spatial Analysis
PubMed: 29342145
DOI: 10.1371/journal.pbio.2004935 -
World Journal of Gastroenterology Feb 2014Proteins secreted by Helicobacter pylori (H. pylori), an important human pathogen responsible for severe gastric diseases, are reviewed from the point of view of their... (Review)
Review
Proteins secreted by Helicobacter pylori (H. pylori), an important human pathogen responsible for severe gastric diseases, are reviewed from the point of view of their biochemical characterization, both functional and structural. Despite the vast amount of experimental data available on the proteins secreted by this bacterium, the precise size of the secretome remains unknown. In this review, we consider as secreted both proteins that contain a secretion signal for the periplasm and proteins that have been detected in the external medium in in vitro experiments. In this way, H. pylori's secretome appears to be composed of slightly more than 160 proteins, but this number must be considered very cautiously, not only because the definition of secretome itself is ambiguous but also because the included proteins were observed as secreted in in vitro experiments that were not representative of the environmental situation in vivo. The proteins that appear to be secreted can be grouped into different classes: enzymes (48 proteins), outer membrane proteins (43), components of flagella (11), members of the cytotoxic-associated genes pathogenicity island or other toxins (8 and 5, respectively), binding and transport proteins (9), and others (11). A final group, which includes 28 members, is represented by hypothetical uncharacterized proteins. Despite the large amount of data accumulated on the H. pylori secretome, a considerable amount of work remains to reach a full comprehension of the system at the molecular level.
Topics: Bacterial Outer Membrane Proteins; Bacterial Proteins; Biological Transport; Flagella; Genes, Bacterial; Genomic Islands; Helicobacter Infections; Helicobacter pylori; Humans; Oxidation-Reduction; Periplasm; Protein Binding; Protein Conformation; Proteome; Stomach
PubMed: 24587618
DOI: 10.3748/wjg.v20.i6.1402 -
Philosophical Transactions of the Royal... Apr 2012Gram-negative bacteria frequently expel toxic chemicals through tripartite efflux pumps that span both the inner and outer membranes. The three parts are the inner... (Review)
Review
Gram-negative bacteria frequently expel toxic chemicals through tripartite efflux pumps that span both the inner and outer membranes. The three parts are the inner membrane, substrate-binding transporter (or pump); a periplasmic membrane fusion protein (MFP, or adaptor); and an outer membrane-anchored channel. The fusion protein connects the transporter to the channel within the periplasmic space. One such efflux system CusCBA is responsible for extruding biocidal Cu(I) and Ag(I) ions. We previously described the crystal structures of both the inner membrane transporter CusA and the MFP CusB of Escherichia coli. We also determined the co-crystal structure of the CusBA adaptor-transporter efflux complex, showing that the transporter CusA, which is present as a trimer, interacts with six CusB protomers and that the periplasmic domain of CusA is involved in these interactions. Here, we summarize the structural information of these efflux proteins, and present the accumulated evidence that this efflux system uses methionine residues to bind and export Cu(I) and Ag(I). Genetic and structural analyses suggest that the CusA pump is capable of picking up the metal ions from both the periplasm and the cytoplasm. We propose a stepwise shuttle mechanism for this pump to export metal ions from the cell.
Topics: Binding Sites; Cell Membrane; Copper; Crystallography, X-Ray; Cytoplasm; Escherichia coli; Escherichia coli Proteins; Membrane Proteins; Membrane Transport Proteins; Methionine; Periplasm; Protein Binding; Protein Conformation; Protein Structure, Tertiary; Silver; Structure-Activity Relationship
PubMed: 22411977
DOI: 10.1098/rstb.2011.0203 -
BMB Reports Dec 2009Periplasmic glucans (PGs) are general constituents in the periplasmic space of Proteobacteria. PGs from bacterial strains are found in larger amounts during growth on... (Review)
Review
Periplasmic glucans (PGs) are general constituents in the periplasmic space of Proteobacteria. PGs from bacterial strains are found in larger amounts during growth on medium with low osmolarity and thus are often been specified as osmoregulated periplasmic glucans (OPGs). Furthermore, they appear to play crucial roles in pathogenesis and symbiosis. PGs have been classified into four families based on the structural features of their backbones, and they can be modified by a variety of non-sugar substituents. It has also recently been confirmed that novel PGs with various degrees of polymerization (DPs) and/or different substituents are produced under different growth conditions among Proteobacteria. In addition to their biological functions as regulators of low osmolarity, PGs have a variety of physico-chemical properties due to their inherent three-dimensional structures, hydrogen-bonding and complex-forming abilities. Thus, much attention has recently been focused on their physico-chemical applications. In this review, we provide an updated classification of PGs, as well as a description of the occurrences of novel PGs with substituents under various bacterial growth environments, the genes involved in PG biosynthesis and the various physico-chemical properties of PGs.
Topics: Periplasm; Polysaccharides, Bacterial; Proteobacteria
PubMed: 20044947
DOI: 10.5483/bmbrep.2009.42.12.769