The roles of CymA in support of the respiratory flexibility of Shewanella oneidensis MR-1

Identification of factors limiting the efficiency of transplanting extracellular electron transfer chains in Escherichia coli

Research in electro-microbiology provides unique opportunities to study and exploit microbial physiology. Several efforts have been made to transplant the extracellular electron transport chain from the native exoelectrogenic model organism Shewanella oneidensis into Escherichia coli. However, systematic comparisons between donor and recipient strain configurations are largely missing. Hence, the proposed minimal protein set, consisting of the c-type cytochromes cytoplasmic membrane protein A (CymA), small tetraheme cytochrome (STC), MtrA, and MtrC, as well as the β-barrel protein MtrB, was heterologously expressed in E. coli in different expansion stages. These stages were compared to corresponding S. oneidensis strains in terms of anthraquinone-2,6-disulfonate (AQDS) and ferric citrate reduction rates. This revealed that transplantation of heterologous extracellular electron transfer (EET) chains is associated with a tremendous decrease in electron transfer rates. As the acquired electron transfer rates were not competitive to S. oneidensis, it was hypothesized that protein localization and maturation might be affected by heterologous expression. Hence, the type II secretion system from S. oneidensis was also transplanted into an E. coli strain. The latter allowed the secretion of the terminal reductase MtrC onto the cell surface of E. coli for the first time. This was correlated with significantly increased but still insufficient extracellular electron transfer rates. Further experiments suggest that the correct folding of MtrB might be a further bottleneck.IMPORTANCEResearch on transplanting extracellular electron transfer (EET) chains into non-native exoelectrogens is vital for advancing bioenergy and bioremediation technologies. Enabling these organisms to transfer electrons to external surfaces like anodes can enhance microbial fuel cell efficiency and electricity generation from organic waste. This approach can broaden the range of substrates and products for biotechnological applications, offering innovative solutions for sustainable production. Our work shows that transplanting the EET chain of Shewanella oneidensis into Escherichia coli is more complex than previously suggested. The heterologous expression of only c-type cytochromes and the β-barrel protein MtrB is insufficient for competitive reduction rates. Predominantly, MtrC and MtrB require specific proteins for transport and folding, necessitating co-expression and maturation. We could identify the type II secretion system of S. oneidensis as crucial for MtrC secretion in E. coli. Thereby, this work highlights the substrate specificity of bacterial type II secretion systems, suggesting methods to optimize protein production and secretion in bioelectrochemical applications.

Decoding in-cell respiratory enzyme dynamics by label-free in situ electrochemistry

Deciphering metabolic enzyme catalysis in living cells remains a formidable challenge due to the limitations of in vivo assays, which focus on enzymes isolated from respiration. This study introduces an innovative whole-cell electrochemical assay to reveal the Michaelis-Menten landscape of respiratory enzymes amid complex molecular interactions. We controlled the microbial current generation's rate-limiting step, extracting in vivo kinetic parameters (Km, Ki, and kcat) for the periplasmic nitrite (NrfA) and fumarate (FccA) reductases. Notably, while NrfA kinetics mirrored those of its purified form, FccA exhibited unique kinetic behavior. Further exploration using a mutant strain lacking CymA, a periplasmic hub protein, revealed its crucial role in modulating FccA's kinetics, challenging the prevailing view that molecular crowding is the main cause of discrepancies between in vivo and in vitro enzyme kinetics. This platform offers a groundbreaking approach to studying cellular respiratory enzymatic kinetics, paving the way for future research in bioenergetics and medicine.

Mineralizing Biofilm towards Sustainable Conversion of Plastic Wastes to Hydrogen

The integration of inorganic materials with biological machinery to convert plastics into fuels offers a promising strategy to alleviate environmental pollution and energy crisis. Herein, we develop a type of hybrid living material via biomineralization of CdS onto Shewanella oneidensis-based biofilm, which is capable of sustainable hydrogen production from poly(lactic acid) (PLA) wastes under daylight. We reveal that the formed biofilm microstructure provides an independent anaerobic microenvironment that simultaneously supports cellular viability, maintains hydrogenase activity, and preserves the functional stability of CdS, giving rise to the efficient plastic-to-hydrogen conversion efficiency as high as 3751 μmol H2 g-1 PLA. Besides, by genetically engineering transmembrane pili conduit and incorporating conductive nanomaterials to strengthen the electron transfer across cellular interface and biofilm matrices, we show that the conversion efficiency is further enhanced to 5862 μmol H2 g-1 PLA. Significantly, we exhibit that a long-term sustainable plastic-to-hydrogen conversion of 63 d could be achieved by periodically replenishing PLA wastes. Overall, by the synergistic integration of biotic-abiotic characteristics the developed biofilm-based biomineralized hybrid living material is anticipated to provide a new platform toward the efficient conversion of plastic wastes into valuable fuels, and bridge the gap between environmental contamination and green energy production.

Shewanella oneidensis: Biotechnological Application of Metal-Reducing Bacteria

What is an unconventional organism in biotechnology? The γ-proteobacterium Shewanella oneidensis might fall into this category as it was initially established as a laboratory model organism for a process that was not seen as potentially interesting for biotechnology. The reduction of solid-state extracellular electron acceptors such as iron and manganese oxides is highly relevant for many biogeochemical cycles, although it turned out in recent years to be quite relevant for many potential biotechnological applications as well. Applications started with the production of nanoparticles and dramatically increased after understanding that electrodes in bioelectrochemical systems can also be used by these organisms. From the potential production of current and hydrogen in these systems and the development of biosensors, the field expanded to anode-assisted fermentations enabling fermentation reactions that were - so far - dependent on oxygen as an electron acceptor. Now the field expands further to cathode-dependent production routines. As a side product to all these application endeavors, S. oneidensis was understood more and more, and our understanding and genetic repertoire is at eye level to E. coli. Corresponding to this line of thought, this chapter will first summarize the available arsenal of tools in molecular biology that was established for working with the organism and thereafter describe so far established directions of application. Last but not least, we will highlight potential future directions of work with the unconventional model organism S. oneidensis.

Comparative analysis of the influence of BpfA and BpfG on biofilm development and current density in Shewanella oneidensis under oxic, fumarate- and anode-respiring conditions

Biofilm formation by Shewanella oneidensis has been extensively studied under oxic conditions; however, relatively little is known about biofilm formation under anoxic conditions and how biofilm architecture and composition can positively influence current generation in bioelectrochemical systems. In this study, we utilized a recently developed microfluidic biofilm analysis setup with automated 3D imaging to investigate the effects of extracellular electron acceptors and synthetic modifications to the extracellular polymeric matrix on biofilm formation. Our results with the wild type strain demonstrate robust biofilm formation even under anoxic conditions when fumarate is used as the electron acceptor. However, this pattern shifts when a graphite electrode is employed as the electron acceptor, resulting in biofilm formation falling below the detection limit of the optical coherence tomography imaging system. To manipulate biofilm formation, we aimed to express BpfG with a single amino acid substitution in the catalytic center (C116S) and to overexpress bpfA. Our analyses indicate that, under oxic conditions, overarching mechanisms predominantly influence biofilm development, rather than the specific mutations we investigated. Under anoxic conditions, the bpfG mutation led to a quantitative increase in biofilm formation, but both strains exhibited significant qualitative changes in biofilm architecture compared to the controls. When an anode was used as the sole electron acceptor, both the bpfA and bpfG mutations positively impacted mean current density, yielding a 1.8-fold increase for each mutation.

Engineering artificial photosynthesis based on rhodopsin for CO2 fixation

Microbial rhodopsin, a significant contributor to sustaining life through light harvesting, holds untapped potential for carbon fixation. Here, we construct an artificial photosynthesis system which combines the proton-pumping ability of rhodopsin with an extracellular electron uptake mechanism, establishing a pathway to drive photoelectrosynthetic CO2 fixation by Ralstonia eutropha (also known as Cupriavidus necator) H16, a facultatively chemolithoautotrophic soil bacterium. R. eutropha is engineered to heterologously express an extracellular electron transfer pathway of Shewanella oneidensis MR-1 and Gloeobacter rhodopsin (GR). Employing GR and the outer-membrane conduit MtrCAB from S. oneidensis, extracellular electrons and GR-driven proton motive force are integrated into R. eutropha's native electron transport chain (ETC). Inspired by natural photosynthesis, the photoelectrochemical system splits water to supply electrons to R. eutropha via the Mtr outer-membrane route. The light-activated proton pump - GR, supported by canthaxanthin as an antenna, powers ATP synthesis and reverses the ETC to regenerate NADH/NADPH, facilitating R. eutropha's biomass synthesis from CO2. Overexpression of a carbonic anhydrase further enhances CO2 fixation. This artificial photosynthesis system has the potential to advance the development of efficient photosynthesis, redefining our understanding of the ecological role of microbial rhodopsins in nature.

Microbial population properties in the hierarchically structured aerobic granular sludge: Phenotype and genotype

Aerobic granular sludge (AGS) is a layered microbial aggregate formed by the ordered self-assembly of different microbial populations. In this study, the outer layer (OL), middle layer (ML), and the inner layer (IL) of matured AGS were obtained by circular cutting. The adhesion of microorganisms in IL was significantly higher than that in OL and ML during the famine period, while the adhesion of microorganisms in ML and OL was significantly higher than that in IL during the feast period, confirming that the formation of AGS started in the famine period, and the feast period promoted the increase of particle size. Microorganisms in the three-layer structure were highly diverse and rich in genes for cytochrome c oxidase synthesis with oxygen as the electron acceptor. G_Pseudoxanthomonas was the dominant bacterium in OL. Its spatial distribution increased gradually from the inside to the outside. G_Rhodanobacter was the dominant bacterium in IL. Its spatial distribution gradually decreased from the inside to the outside. The microorganisms in IL contained abundant pili genes. During the self-assembly process of particle formation, G_ Rhodanobaker adhered stronger than G_ Pseudoxanthomonas. The interface between aerobic and anoxic was about 0.6 mm away from the granule surface. Combined with the electron mediator properties of the extracellular polymeric substance (EPS) in granules, it was speculated that the degradation of organic substrates located in the anoxic layer relied on EPS as a mediator for long-range electron transfer, and finally transferred electrons to O₂. This study provides a new viewpoint on the formation mechanism of AGS from the perspective of the ordered self-assembly of microorganisms, offering a theoretical basis for the optimal selection of culture conditions and the application of AGS technology.

Extracellular pollutant degradation feedback regulates intracellular electron transfer process of exoelectrogens: Strategy and mechanism

Exoelectrogens possess extraordinary degradation ability to various pollutants through extracellular electron transfer (EET). Compared with extracellular electron release process, intracellular electron transfer network is not yet fully recognized. Especially, controversy remains regarding the role of CymA, an essential electron-transfer hub of Shewanella oneidensis MR-1, in EET process. In this study, we thoroughly surveyed the intracellular transfer strategies during EET through dye decolorization. Loss of CymA severely impaired the reduction ability of S. oneidensis MR-1 to methyl orange (MO), but hardly affected the decolorization of aniline blue (AB). Complement of cymA fully restored the MO decolorization ability of ΔcymA mutant. The contribution of CymA to extracellular decolorization was subjected to MO concentrations. The defect in the decolorization ability of ΔcymA mutant was not evident at low MO concentration, but severe at high MO concentration. Further investigation revealed that EET rate determined the significance of CymA in the extracellular bioremediation by S. oneidensis MR-1. Coupled with MO concentrations increasing from 15 to 120 mg/L, the initial electron transfer rates of S. oneidensis MR-1 increased accordingly from 2.69 × 10⁴ to 11.21 × 10⁴ electrons CFU^-1 s^-1, which led to a gradual increase of the dependency_CymA. Thus, we first revealed that extracellular degradation performance could feedback regulate the intracellular electron transfer process of S. oneidensis MR-1. This work is helpful to fully understand the complex EET process of exoelectrogens and facilitates the application of exoelectrogens in bioremediation of environmental pollutants.

The Roles of DmsEFAB and MtrCAB in Extracellular Reduction of Iodate by Shewanella oneidensis MR-1 with Lactate as the Sole Electron Donor

To investigate their roles in extracellular reduction of iodate (IO₃ ^- ) with lactate as an electron donor, the gene clusters of dmsEFAB, mtrCAB, mtrDEF, and so4360-4357 in Shewanella oneidensis MR-1were systematically deleted. Deletions of dmsEFAB and/or mtrCAB gene clusters diminished the bacterial ability to reduce IO₃ ^- . Furthermore, DmsEFAB and MtrCAB worked collaboratively to reduce IO₃ ^- of which DmsEFAB played a more dominant role than MtrCAB. MtrCAB was involved in detoxifying the reaction intermediate hydrogen peroxide (H₂ O₂ ). The reaction intermediate hypoiodous acid (HIO) was also found to inhibit microbial IO₃ ^- reduction. SO4360-4357 and MtrDEF, however, were not involved in IO₃ ^- reduction. Collectively, these results suggest a novel mechanism of extracellular reduction of IO₃ ^- at molecular level, in which DmsEFAB reduces IO₃ ^- to HIO and H₂ O₂ . The latter is further reduced to H₂ O by MtrCAB to facilitate the DmsEFAB-mediated IO₃ ^- reduction. The extracellular electron transfer pathway of S. oneidensis MR-1is believed to mediate electron transfer from bacterial cytoplasmic membrane, across the cell envelope to the DmsEFAB and MtrCAB on the bacterial outer membrane.

The Proposed Molecular Mechanisms Used by Archaea for Fe(III) Reduction and Fe(II) Oxidation

Iron (Fe) is the fourth most abundant element in the Earth's crust where ferrous Fe [Fe(II)] and ferric Fe [Fe(III)] can be used by archaea for energy conservation. In these archaea-Fe interactions, Fe(III) serves as terminal electron acceptor for anaerobic respiration by a variety of archaea, while Fe(II) serves as electron donor and/or energy sources for archaeal growth. As no Fe is incorporated into the archaeal cells, these redox reactions are referred to as dissimilatory Fe(III) reduction and Fe(II) oxidation, respectively. Dissimilatory Fe(III)-reducing archaea (FeRA) and Fe(II)-oxidizing archaea (FeOA) are widespread on Earth where they play crucial roles in biogeochemical cycling of not only Fe, but also carbon and sulfur. To reduce extracellular Fe(III) (oxyhydr)oxides, some FeRA transfer electrons directly to the Fe(III) (oxyhydr)oxides most likely via multiheme c-type cytochromes (c-Cyts). These multiheme c-Cyts may form the pathways similar to those found in bacteria for transferring electrons from the quinone/quinol pool in the cytoplasmic membrane to the Fe(III) (oxyhydr)oxides external to the archaeal cells. Use of multiheme c-Cyts for extracellular Fe(III) reduction by both Domains of Archaea and Bacteria emphasizes an ancient mechanism of extracellular electron transfer, which is well conserved. Other FeRA, however, reduce Fe(III) (oxyhydr)oxides indirectly via electron shuttles. Similarly, it is proposed that FeOA use pathways to oxidize Fe(II) on the surface of the cytoplasmic membrane and then to transfer the released electrons across the cytoplasmic membrane inward to the O2 and NAD+ in the cytoplasm. In this review, we focus on the latest understandings of the molecular mechanisms used by FeRA and FeOA for Fe(III) reduction and Fe(II) oxidation, respectively.

Peripheral Membrane Proteins: Promising Therapeutic Targets across Domains of Life

Membrane proteins can be classified into two main categories-integral and peripheral membrane proteins-depending on the nature of their membrane interaction. Peripheral membrane proteins are highly unique amphipathic proteins that interact with the membrane indirectly, using electrostatic or hydrophobic interactions, or directly, using hydrophobic tails or GPI-anchors. The nature of this interaction not only influences the location of the protein in the cell, but also the function. In addition to their unique relationship with the cell membrane, peripheral membrane proteins often play a key role in the development of human diseases such as African sleeping sickness, cancer, and atherosclerosis. This review will discuss the membrane interaction and role of periplasmic nitrate reductase, CymA, cytochrome c, alkaline phosphatase, ecto-5'-nucleotidase, acetylcholinesterase, alternative oxidase, type-II NADH dehydrogenase, and dihydroorotate dehydrogenase in certain diseases. The study of these proteins will give new insights into their function and structure, and may ultimately lead to ground-breaking advances in the treatment of severe diseases.

Pyruvate accelerates palladium reduction by regulating catabolism and electron transfer pathway in Shewanella oneidensis

Shewanella oneidensis is a model strain of the electrochemical active bacteria (EAB) because of its strong capability of extracellular electron transfer (EET) and genetic tractability. In this study, we investigated the effect of carbon sources on EET in S. oneidensis by using reduction of palladium ions (Pd(II)) as a model and found that pyruvate greatly accelerated the Pd(II) reduction compared with lactate by resting cells. Both Mtr pathway and hydrogenases played a role in Pd(II) reduction when pyruvate was used as a carbon source. Furthermore, in comparison with lactate-feeding S. oneidensis, the transcriptional levels of formate dehydrogenases involving in pyruvate catabolism, Mtr pathway, and hydrogenases in pyruvate-feeding S. oneidensis were up-regulated. Mechanistically, the enhancement of electron generation from pyruvate catabolism and electron transfer to Pd(II) explains the pyruvate effect on Pd(II) reduction. Interestingly, a 2-h time window is required for pyruvate to regulate transcription of these genes and profoundly improve Pd(II) reduction capability, suggesting a hierarchical regulation for pyruvate sensing and response in S. oneidensis IMPORTANCE The unique respiration of EET is crucial for the biogeochemical cycling of metal elements and diverse applications of EAB. Although a carbon source is a determinant factor of bacterial metabolism, the research into the regulation of carbon source on EET is rare. In this work, we reported the pyruvate-specific regulation and improvement of EET in S. oneidensis and revealed the underlying mechanism, which suggests potential targets to engineer and improve the EET efficiency of this bacterium. This study sheds light on the regulatory role of carbon sources in anaerobic respiration in EAB, providing a way to regulate EET for diverse applications from a novel perspective.

A brief survey of the "cytochromome"

Multihaem cytochromes c are widespread in nature where they perform numerous roles in diverse anaerobic metabolic pathways. This is achieved in two ways: multihaem cytochromes c display a remarkable diversity of ways to organize multiple hemes within the protein frame; and the hemes possess an intrinsic reactive versatility derived from diverse spin, redox and coordination states. Here we provide a brief survey of multihaem cytochromes c that have been characterized in the context of their metabolic role. The contribution of multihaem cytochromes c to dissimilatory pathways handling metallic minerals, nitrogen compounds, sulfur compounds, organic compounds and phototrophism are described. This aims to set the stage for the further exploration of the vast unknown "cytochromome" that can be anticipated from genomic databases.

Genomic Analyses of the Quinol Oxidases and/or Quinone Reductases Involved in Bacterial Extracellular Electron Transfer

To exchange electrons with extracellular substrates, some microorganisms employ extracellular electron transfer (EET) pathways that physically connect extracellular redox reactions to intracellular metabolic activity. These pathways are made of redox and structural proteins that work cooperatively to transfer electrons between extracellular substrates and the cytoplasmic membrane. Crucial to the bacterial and archaeal EET pathways are the quinol oxidases and/or quinone reductases in the cytoplasmic membrane where they recycle the quinone/quinol pool in the cytoplasmic membrane during EET reaction. Up to date, three different families of quinol oxidases and/or quinone reductases involved in bacterial EET have been discovered. They are the CymA, CbcL/MtrH/MtoC, and ImcH families of quinol oxidases and/or quinone reductases that are all multiheme c-type cytochromes (c-Cyts). To investigate to what extent they are distributed among microorganisms, we search the bacterial as well as archaeal genomes for the homologs of these c-Cyts. Search results reveal that the homologs of these c-Cyts are only found in the Domain Bacteria. Moreover, the CymA homologs are only found in the phylum of Proteobacteria and most of them are in the Shewanella genus. In addition to Shewanella sp., CymA homologs are also found in other Fe(III)-reducing bacteria, such as of Vibrio parahaemolyticus. In contrast to CymA, CbcL/MtrH/MtoC, and ImcH homologs are much more widespread. CbcL/MtrH/MtoC homologs are found in 15 phyla, while ImcH homologs are found in 12 phyla. Furthermore, the heme-binding motifs of CbcL/MtrH/MtoC and ImcH homologs vary greatly, ranging from 3 to 23 and 6 to 10 heme-binding motifs for CbcL/MtrH/MtoC and ImcH homologs, respectively. Moreover, CymA and CbcL/MtrH/MtoC homologs are found in both Fe(III)-reducing and Fe(II)-oxidizing bacteria, suggesting that these families of c-Cyts catalyze both quinol-oxidizing and quinone-reducing reactions. ImcH homologs are only found in the Fe(III)-reducing bacteria, implying that they are only the quinol oxidases. Finally, some bacteria have the homologs of two different families of c-Cyts, which may improve the bacterial capability to exchange electrons with extracellular substrates.

Electrochemical Study on the Extracellular Electron Transfer Pathway from Shewanella Strain Hac319 to Electrodes

Shewanella can transfer electrons to various extracellular electron acceptors. We electrochemically investigated the pathway of extracellular electron transfer from Shewanella strain Hac319 to electrodes. A resting cell suspension of Shewanella strain Hac319 containing lactate produced a steady-state sigmoidal wave in the presence of flavin mononucleotide (FMN) in cyclic voltammetry, but not in the absence of FMN. A harvested cell suspension without cell-washing also produced a similar catalytic wave without any external addition of free FMN. The midpoint potentials of the two sigmoidal waves were identical to the redox potential of free FMN. The data indicate that FMN secreted from the Shewanella strain Hac319 works as an electron-transfer mediator from the cell to electrodes. An addition of cyanide to a resting cell suspension of Shewanella strain Hac319 increased the rate of the FMN reduction in the presence of lactate, while it decreased the respiration rate. By considering the fact that cyanide is coordinated to the heme moiety of hemoproteins and shifts the redox potential to the negative potential side, the data indicate that the electron derived from lactate is predominantly transferred in a down-hill mode from an electron donor with a redox potential more negative than that of FMN without going through outer membrane cytochromes c molecules.

Structural modeling of an outer membrane electron conduit from a metal-reducing bacterium suggests electron transfer via periplasmic redox partners

Many subsurface microorganisms couple their metabolism to the reduction or oxidation of extracellular substrates. For example, anaerobic mineral-respiring bacteria can use external metal oxides as terminal electron acceptors during respiration. Porin-cytochrome complexes facilitate the movement of electrons generated through intracellular catabolic processes across the bacterial outer membrane to these terminal electron acceptors. In the mineral-reducing model bacterium Shewanella oneidensis MR-1, this complex is composed of two decaheme cytochromes (MtrA and MtrC) and an outer-membrane β-barrel (MtrB). However, the structures and mechanisms by which porin-cytochrome complexes transfer electrons are unknown. Here, we used small-angle neutron scattering (SANS) to study the molecular structure of the transmembrane complexes MtrAB and MtrCAB. Ab initio modeling of the scattering data yielded a molecular envelope with dimensions of ∼105 × 60 × 35 Å for MtrAB and ∼170 × 60 × 45 Å for MtrCAB. The shapes of these molecular envelopes suggested that MtrC interacts with the surface of MtrAB, extending ∼70 Å from the membrane surface and allowing the terminal hemes to interact with both MtrAB and an extracellular acceptor. The data also reveal that MtrA fully extends through the length of MtrB, with ∼30 Å being exposed into the periplasm. Proteoliposome models containing membrane-associated MtrCAB and internalized small tetraheme cytochrome (STC) indicate that MtrCAB could reduce Fe(III) citrate with STC as an electron donor, disclosing a direct interaction between MtrCAB and STC. Taken together, both structural and proteoliposome experiments support porin-cytochrome-mediated electron transfer via periplasmic cytochromes such as STC.

Shewanella putrefaciens CN32 outer membrane cytochromes MtrC and UndA reduce electron shuttles to produce electricity in microbial fuel cells

The extracellular electron transfer (EET) process of Shewanella species is believed to be indispensable for their anaerobic respiration with an electrode. However, the function of outer membrane c-type cytochromes (OM c-Cyts, the primary components of the EET pathway) is still controversial. In this study, we investigated the effect of two OM c-Cyts (MtrC and UndA) of Shewanella putrefaciens CN32 with respect to electricity production and anodic EET efficiency. Deletion of the mtrC gene severely prolonged the microbial fuel cell (MFC) start-up time and decreased electricity production due to depressed flavin-mediated electron transfer, whereas deletion of the undA gene did not have a significant impact. Strikingly, the depression of EET by the deletion of mtrC could be partially relieved by acclimation, which might be due to an increase in the transmembrane transport of electron shuttles and/or the activation of other redox proteins. These results suggested that MtrC may be the primary reductase of flavins to ensure fast indirect EET, which plays a crucial role in MFC electricity generation.

Tracking Electron Uptake from a Cathode into Shewanella Cells: Implications for Energy Acquisition from Solid-Substrate Electron Donors

While typically investigated as a microorganism capable of extracellular electron transfer to minerals or anodes, Shewanella oneidensis MR-1 can also facilitate electron flow from a cathode to terminal electron acceptors, such as fumarate or oxygen, thereby providing a model system for a process that has significant environmental and technological implications. This work demonstrates that cathodic electrons enter the electron transport chain of S. oneidensis when oxygen is used as the terminal electron acceptor. The effect of electron transport chain inhibitors suggested that a proton gradient is generated during cathode oxidation, consistent with the higher cellular ATP levels measured in cathode-respiring cells than in controls. Cathode oxidation also correlated with an increase in the cellular redox (NADH/FMNH₂) pool determined with a bioluminescence assay, a proton uncoupler, and a mutant of proton-pumping NADH oxidase complex I. This work suggested that the generation of NADH/FMNH₂ under cathodic conditions was linked to reverse electron flow mediated by complex I. A decrease in cathodic electron uptake was observed in various mutant strains, including those lacking the extracellular electron transfer components necessary for anodic-current generation. While no cell growth was observed under these conditions, here we show that cathode oxidation is linked to cellular energy acquisition, resulting in a quantifiable reduction in the cellular decay rate. This work highlights a potential mechanism for cell survival and/or persistence on cathodes, which might extend to environments where growth and division are severely limited.

The majority of our knowledge of the physiology of extracellular electron transfer derives from studies of electrons moving to the exterior of the cell. The physiological mechanisms and/or consequences of the reverse processes are largely uncharacterized. This report demonstrates that when coupled to oxygen reduction, electrode oxidation can result in cellular energy acquisition. This respiratory process has potentially important implications for how microorganisms persist in energy-limited environments, such as reduced sediments under changing redox conditions. From an applied perspective, this work has important implications for microbially catalyzed processes on electrodes, particularly with regard to understanding models of cellular conversion of electrons from cathodes to microbially synthesized products.

Geobacter sulfurreducens Extracellular Multiheme Cytochrome PgcA Facilitates Respiration to Fe(III) Oxides But Not Electrodes

Extracellular cytochromes are hypothesized to facilitate the final steps of electron transfer between the outer membrane of the metal-reducing bacterium Geobacter sulfurreducens and solid-phase electron acceptors such as metal oxides and electrode surfaces during the course of respiration. The triheme c-type cytochrome PgcA exists in the extracellular space of G. sulfurreducens, and is one of many multiheme c-type cytochromes known to be loosely bound to the bacterial outer surface. Deletion of pgcA using a markerless method resulted in mutants unable to transfer electrons to Fe(III) and Mn(IV) oxides; yet the same mutants maintained the ability to respire to electrode surfaces and soluble Fe(III) citrate. When expressed and purified from Shewanella oneidensis, PgcA demonstrated a primarily alpha helical structure, three bound hemes, and was processed into a shorter 41 kDa form lacking the lipodomain. Purified PgcA bound Fe(III) oxides, but not magnetite, and when PgcA was added to cell suspensions of G. sulfurreducens, PgcA accelerated Fe(III) reduction similar to addition of FMN. Addition of soluble PgcA to ΔpgcA mutants also restored Fe(III) reduction. This report highlights a distinction between proteins involved in extracellular electron transfer to metal oxides and poised electrodes, and suggests a specific role for PgcA in facilitating electron transfer at mineral surfaces.

Physiological and transcriptional approaches reveal connection between nitrogen and manganese cycles in Shewanella algae C6G3

To explain anaerobic nitrite/nitrate production at the expense of ammonium mediated by manganese oxide (Mn(IV)) in sediment, nitrate and manganese respirations were investigated in a strain (Shewanella algae C6G3) presenting these features. In contrast to S. oneidensis MR-1, a biotic transitory nitrite accumulation at the expense of ammonium was observed in S. algae during anaerobic growth with Mn(IV) under condition of limiting electron acceptor, concomitantly, with a higher electron donor stoichiometry than expected. This low and reproducible transitory accumulation is the result of production and consumption since the strain is able to dissimilative reduce nitrate into ammonium. Nitrite production in Mn(IV) condition is strengthened by comparative expression of the nitrate/nitrite reductase genes (napA, nrfA, nrfA-2), and rates of the nitrate/nitrite reductase activities under Mn(IV), nitrate or fumarate conditions. Compared with S. oneidensis MR-1, S. algae contains additional genes that encode nitrate and nitrite reductases (napA-α and nrfA-2) and an Outer Membrane Cytochrome (OMC)(mtrH). Different patterns of expression of the OMC genes (omcA, mtrF, mtrH and mtrC) were observed depending on the electron acceptor and growth phase. Only gene mtrF-2 (SO1659 homolog) was specifically expressed under the Mn(IV) condition. Nitrate and Mn(IV) respirations seem connected at the physiological and transcriptional levels.

CymA and Exogenous Flavins Improve Extracellular Electron Transfer and Couple It to Cell Growth in Mtr-Expressing Escherichia coli

Introducing extracellular electron transfer pathways into heterologous organisms offers the opportunity to explore fundamental biogeochemical processes and to biologically alter redox states of exogenous metals for various applications. While expression of the MtrCAB electron nanoconduit from Shewanella oneidensis MR-1 permits extracellular electron transfer in Escherichia coli, the low electron flux and absence of growth in these cells limits their practicality for such applications. Here we investigate how the rate of electron transfer to extracellular Fe(III) and cell survival in engineered E. coli are affected by mimicking different features of the S. oneidensis pathway: the number of electron nanoconduits, the link between the quinol pool and MtrA, and the presence of flavin-dependent electron transfer. While increasing the number of pathways does not significantly improve the extracellular electron transfer rate or cell survival, using the native inner membrane component, CymA, significantly improves the reduction rate of extracellular acceptors and increases cell viability. Strikingly, introducing both CymA and riboflavin to Mtr-expressing E. coli also allowed these cells to couple metal reduction to growth, which is the first time an increase in biomass of an engineered E. coli has been observed under Fe2O3 (s) reducing conditions. Overall, this work provides engineered E. coli strains for modulating extracellular metal reduction and elucidates critical factors for engineering extracellular electron transfer in heterologous organisms.

Formate Metabolism in Shewanella oneidensis Generates Proton Motive Force and Prevents Growth without an Electron Acceptor

Shewanella oneidensis strain MR-1 is a facultative anaerobe that thrives in redox-stratified environments due to its ability to utilize a wide array of terminal electron acceptors. Conversely, the electron donors utilized by S. oneidensis are more limited and include products of primary fermentation such as lactate, pyruvate, formate, and hydrogen. Lactate, pyruvate, and hydrogen metabolisms inS. oneidensis have been described previously, but little is known about the role of formate oxidation in the ecophysiology of these bacteria. Formate is produced by S. oneidensis through pyruvate formate lyase during anaerobic growth on carbon sources that enter metabolism at or above the level of pyruvate, and the genome contains three gene clusters predicted to encode three complete formate dehydrogenase complexes. To determine the contribution of each complex to formate metabolism, strains lacking one, two, or all three annotated formate dehydrogenase gene clusters were generated and examined for growth rates and yields on a variety of carbon sources. Here, we report that formate oxidation contributes to both the growth rate and yield of S. oneidensis through the generation of proton motive force. Exogenous formate also greatly accelerated growth on N-acetylglucosamine, a carbon source normally utilized very slowly by S. oneidensis under anaerobic conditions. Surprisingly, deletion of all three formate dehydrogenase gene clusters enabled growth of S. oneidensis using pyruvate in the absence of a terminal electron acceptor, a mode of growth never before observed in these bacteria. Our results demonstrate that formate oxidation is a fundamental strategy under anaerobic conditions for energy conservation inS. oneidensis.

IMPORTANCE

Shewanella species have garnered interest in biotechnology applications for their ability to respire extracellular terminal electron acceptors, such as insoluble iron oxides and electrodes. While much effort has gone into studying the proteins for extracellular electron transport, how electrons generated through the oxidation of organic carbon sources enter this pathway remains understudied. Here, we quantify the role of formate oxidation in the anaerobic physiology of Shewanella oneidensis Formate oxidation contributes to both the growth rate and yield on a variety of carbon sources through the generation of proton motive force. Advances in our understanding of the anaerobic metabolism of S. oneidensis are important for our ability to utilize and engineer this organism for applications in bioenergy, biocatalysis, and bioremediation.

Functional roles of CymA and NapC in reduction of nitrate and nitrite by Shewanella putrefaciens W3-18-1

Shewanella putrefaciens W3-18-1 harbours two periplasmic nitrate reductase (Nap) gene clusters, NapC-associated nap-alpha (napEDABC) and CymA-dependent nap-beta (napDAGHB), for dissimilatory nitrate respiration. CymA is a member of the NapC/NirT quinol dehydrogenase family and acts as a hub to support different respiratory pathways, including those on iron [Fe(III)] and manganese [Mn(III, IV)] (hydr)oxide, nitrate, nitrite, fumarate and arsenate in Shewanella strains. However, in our analysis it was shown that another NapC/NirT family protein, NapC, was only involved in nitrate reduction, although both CymA and NapC can transfer quinol-derived electrons to a periplasmic terminal reductase or an electron acceptor. Furthermore, our results showed that NapC could only interact specifically with the Nap-alpha nitrate reductase while CymA could interact promiscuously with Nap-alpha, Nap-beta and the NrfA nitrite reductase for nitrate and nitrite reduction. To further explore the difference in specificity, site-directed mutagenesis on both CymA and NapC was conducted and the phenotypic changes in nitrate and nitrite reduction were tested. Our analyses demonstrated that the Lys-91 residue played a key role in nitrate reduction for quinol oxidation and the Asp-166 residue might influence the maturation of CymA. The Asp-97 residue might be one of the key factors that influence the interaction of CymA with the cytochromes NapB and NrfA.

Expression of terminal oxidases under nutrient-starved conditions in Shewanella oneidensis: detection of the A-type cytochrome c oxidase

Shewanella species are facultative anaerobic bacteria that colonize redox-stratified habitats where O2 and nutrient concentrations fluctuate. The model species Shewanella oneidensis MR-1 possesses genes coding for three terminal oxidases that can perform O2 respiration: a bd-type quinol oxidase and cytochrome c oxidases of the cbb3-type and the A-type. Whereas the bd- and cbb3-type oxidases are routinely detected, evidence for the expression of the A-type enzyme has so far been lacking. Here, we investigated the effect of nutrient starvation on the expression of these terminal oxidases under different O2 tensions. Our results reveal that the bd-type oxidase plays a significant role under nutrient starvation in aerobic conditions. The expression of the cbb3-type oxidase is also modulated by the nutrient composition of the medium and increases especially under iron-deficiency in exponentially growing cells. Most importantly, under conditions of carbon depletion, high O2 and stationary-growth, we report for the first time the expression of the A-type oxidase in S. oneidensis, indicating that this terminal oxidase is not functionally lost. The physiological role of the A-type oxidase in energy conservation and in the adaptation of S. oneidensis to redox-stratified environments is discussed.

Multi-haem cytochromes in Shewanella oneidensis MR-1: structures, functions and opportunities

Multi-haem cytochromes are employed by a range of microorganisms to transport electrons over distances of up to tens of nanometres. Perhaps the most spectacular utilization of these proteins is in the reduction of extracellular solid substrates, including electrodes and insoluble mineral oxides of Fe(III) and Mn(III/IV), by species of Shewanella and Geobacter. However, multi-haem cytochromes are found in numerous and phylogenetically diverse prokaryotes where they participate in electron transfer and redox catalysis that contributes to biogeochemical cycling of N, S and Fe on the global scale. These properties of multi-haem cytochromes have attracted much interest and contributed to advances in bioenergy applications and bioremediation of contaminated soils. Looking forward, there are opportunities to engage multi-haem cytochromes for biological photovoltaic cells, microbial electrosynthesis and developing bespoke molecular devices. As a consequence, it is timely to review our present understanding of these proteins and we do this here with a focus on the multitude of functionally diverse multi-haem cytochromes in Shewanella oneidensis MR-1. We draw on findings from experimental and computational approaches which ideally complement each other in the study of these systems: computational methods can interpret experimentally determined properties in terms of molecular structure to cast light on the relation between structure and function. We show how this synergy has contributed to our understanding of multi-haem cytochromes and can be expected to continue to do so for greater insight into natural processes and their informed exploitation in biotechnologies.

Genomic analyses of bacterial porin-cytochrome gene clusters

The porin-cytochrome (Pcc) protein complex is responsible for trans-outer membrane electron transfer during extracellular reduction of Fe(III) by the dissimilatory metal-reducing bacterium Geobacter sulfurreducens PCA. The identified and characterized Pcc complex of G. sulfurreducens PCA consists of a porin-like outer-membrane protein, a periplasmic 8-heme c-type cytochrome (c-Cyt) and an outer-membrane 12-heme c-Cyt, and the genes encoding the Pcc proteins are clustered in the same regions of genome (i.e., the pcc gene clusters) of G. sulfurreducens PCA. A survey of additionally microbial genomes has identified the pcc gene clusters in all sequenced Geobacter spp. and other bacteria from six different phyla, including Anaeromyxobacter dehalogenans 2CP-1, A. dehalogenans 2CP-C, Anaeromyxobacter sp. K, Candidatus Kuenenia stuttgartiensis, Denitrovibrio acetiphilus DSM 12809, Desulfurispirillum indicum S5, Desulfurivibrio alkaliphilus AHT2, Desulfurobacterium thermolithotrophum DSM 11699, Desulfuromonas acetoxidans DSM 684, Ignavibacterium album JCM 16511, and Thermovibrio ammonificans HB-1. The numbers of genes in the pcc gene clusters vary, ranging from two to nine. Similar to the metal-reducing (Mtr) gene clusters of other Fe(III)-reducing bacteria, such as Shewanella spp., additional genes that encode putative c-Cyts with predicted cellular localizations at the cytoplasmic membrane, periplasm and outer membrane often associate with the pcc gene clusters. This suggests that the Pcc-associated c-Cyts may be part of the pathways for extracellular electron transfer reactions. The presence of pcc gene clusters in the microorganisms that do not reduce solid-phase Fe(III) and Mn(IV) oxides, such as D. alkaliphilus AHT2 and I. album JCM 16511, also suggests that some of the pcc gene clusters may be involved in extracellular electron transfer reactions with the substrates other than Fe(III) and Mn(IV) oxides.

Electrode assemblies composed of redox cascades from microbial respiratory electron transfer chains

Respiratory and photosynthetic electron transfer chains are dependent on vectorial electron transfer through a series of redox proteins. Examples include electron transfer from NapC to NapAB nitrate reductase in Paracoccus denitrificans and from CymA to Fcc3 (flavocytochrome c3) fumarate reductase in Shewanella oneidensis MR-1. In the present article, we demonstrate that graphite electrodes can serve as surfaces for the stepwise adsorption of NapC and NapAB, and the stepwise adsorption of CymA and Fcc3. Aspects of the catalytic properties of these assemblies are different from those of NapAB and Fcc3 adsorbed in isolation. We propose that this is due to the formation of NapC-NapAB and of CymA-Fcc3 complexes that are capable of supporting vectorial electron transfer.

A biochemical approach to study the role of the terminal oxidases in aerobic respiration in Shewanella oneidensis MR-1

The genome of the facultative anaerobic γ-proteobacterium Shewanella oneidensis MR-1 encodes for three terminal oxidases: a bd-type quinol oxidase and two heme-copper oxidases, a A-type cytochrome c oxidase and a cbb₃-type oxidase. In this study, we used a biochemical approach and directly measured oxidase activities coupled to mass-spectrometry analysis to investigate the physiological role of the three terminal oxidases under aerobic and microaerobic conditions. Our data revealed that the cbb₃-type oxidase is the major terminal oxidase under aerobic conditions while both cbb₃-type and bd-type oxidases are involved in respiration at low-O₂ tensions. On the contrary, the low O₂-affinity A-type cytochrome c oxidase was not detected in our experimental conditions even under aerobic conditions and would therefore not be required for aerobic respiration in S. oneidensis MR-1. In addition, the deduced amino acid sequence suggests that the A-type cytochrome c oxidase is a ccaa₃-type oxidase since an uncommon extra-C terminal domain contains two c-type heme binding motifs. The particularity of the aerobic respiratory pathway and the physiological implication of the presence of a ccaa₃-type oxidase in S. oneidensis MR-1 are discussed.

Promotion of iron oxide reduction and extracellular electron transfer in Shewanella oneidensis by DMSO

The dissimilatory metal reducing bacterium Shewanella oneidensis MR-1, known for its capacity of reducing iron and manganese oxides, has great environmental impacts. The iron oxides reducing process is affected by the coexistence of alternative electron acceptors in the environment, while investigation into it is limited so far. In this work, the impact of dimethyl sulphoxide (DMSO), a ubiquitous chemical in marine environment, on the reduction of hydrous ferric oxide (HFO) by S. oneidensis MR-1 was investigated. Results show that DMSO promoted HFO reduction by both wild type and ΔdmsE, but had no effect on the HFO reduction by ΔdmsB, indicating that such a promotion was dependent on the DMSO respiration. With the DMSO dosing, the levels of extracellular flavins and omcA expression were significantly increased in WT and further increased in ΔdmsE. Bioelectrochemical analysis show that DMSO also promoted the extracellular electron transfer of WT and ΔdmsE. These results demonstrate that DMSO could stimulate the HFO reduction through metabolic and genetic regulation in S. oneidensis MR-1, rather than compete for electrons with HFO. This may provide a potential respiratory pathway to enhance the microbial electron flows for environmental and engineering applications.

Changes in translational efficiency is a dominant regulatory mechanism in the environmental response of bacteria

To understand how cell physiological state affects mRNA translation, we used Shewanella oneidensis MR-1 grown under steady state conditions at either 20% or 8.5% O2. Using a combination of quantitative proteomics and RNA-Seq, we generated high-confidence data on >1000 mRNA and protein pairs. By using a steady state model, we found that differences in protein-mRNA ratios were primarily due to differences in the translational efficiency of specific genes. When oxygen levels were lowered, 28% of the proteins showed at least a 2-fold change in expression. Transcription levels were sp. significantly altered for 26% of the protein changes; translational efficiency was significantly altered for 46% and a combination of both was responsible for the remaining 28%. Changes in translational efficiency were significantly correlated with the codon usage pattern of the genes and measurable tRNA pools changed in response to altered O2 levels. Our results suggest that changes in the translational efficiency of proteins, in part due to altered tRNA pools, is a major determinant of regulated alterations in protein expression levels in bacteria.

Protein-protein interaction regulates the direction of catalysis and electron transfer in a redox enzyme complex

Protein–protein interactions are well-known to regulate enzyme activity in cell signaling and metabolism. Here, we show that protein–protein interactions regulate the activity of a respiratory-chain enzyme, CymA, by changing the direction or bias of catalysis. CymA, a member of the widespread NapC/NirT superfamily, is a menaquinol-7 (MQ-7) dehydrogenase that donates electrons to several distinct terminal reductases in the versatile respiratory network of Shewanella oneidensis. We report the incorporation of CymA within solid-supported membranes that mimic the inner membrane architecture of S. oneidensis. Quartz-crystal microbalance with dissipation (QCM-D) resolved the formation of a stable complex between CymA and one of its native redox partners, flavocytochrome c₃ (Fcc₃) fumarate reductase. Cyclic voltammetry revealed that CymA alone could only reduce MQ-7, while the CymA-Fcc₃ complex catalyzed the reaction required to support anaerobic respiration, the oxidation of MQ-7. We propose that MQ-7 oxidation in CymA is limited by electron transfer to the hemes and that complex formation with Fcc₃ facilitates the electron-transfer rate along the heme redox chain. These results reveal a yet unexplored mechanism by which bacteria can regulate multibranched respiratory networks through protein–protein interactions.

Electron transport at the microbe-mineral interface: a synthesis of current research challenges

Many bacterial and archaeal species can couple growth to the respiratory reduction or oxidation of insoluble mineral oxides of transition metals. These solid substrates are abundant electron sinks and sources for life on Earth, but, since they are insoluble in water, they cannot enter the bacterial cells. So, to exploit these electron sinks and sources, specific respiratory electron-transfer mechanisms must overcome the physical limitations associated with electron transfer between a microbe and extracellular metal oxides. Recent microbiological, geochemical, biochemical, spectroscopic and structural work is beginning to shed light on the molecular mechanism and impacts of electron transfer at the microbe-mineral interface from a nanometre to kilometre scale. The research field is attracting attention in applied quarters from those with interests in nanowires, microbial fuel cells, bioremediation and microbial cell factories.

Combined effect of loss of the caa3 oxidase and Crp regulation drives Shewanella to thrive in redox-stratified environments

Shewanella species are a group of facultative Gram-negative microorganisms with remarkable respiration abilities that allow the use of a diverse array of terminal electron acceptors (EA). Like most bacteria, S. oneidensis possesses multiple terminal oxidases, including two heme-copper oxidases (caa3- and cbb3-type) and a bd-type quinol oxidase. As aerobic respiration is energetically favored, mechanisms underlying the fact that these microorganisms thrive in redox-stratified environments remain vastly unexplored. In this work, we discovered that the cbb3-type oxidase is the predominant system for respiration of oxygen (O2), especially when O2 is abundant. Under microaerobic conditions, the bd-type quinol oxidase has a significant role in addition to the cbb3-type oxidase. In contrast, multiple lines of evidence suggest that under test conditions the caa3-type oxidase, an analog to the mitochondrial enzyme, has no physiological significance, likely because of its extremely low expression. In addition, expression of both cbb3- and bd-type oxidases is under direct control of Crp (cAMP receptor protein) but not the well-established redox regulator Fnr (fumarate nitrate regulator) of canonical systems typified in Escherichia coli. These data, collectively, suggest that adaptation of S. oneidensis to redox-stratified environments is likely due to functional loss of the caa3-type oxidase and switch of the regulatory system for respiration.