Dissection of hydrogen bond interaction network around an iron-sulfur cluster by site-specific isotope labeling of hyperthermophilic archaeal Rieske-type ferredoxin

Optogenetic Control of Bacterial Cell-Cell Adhesion Dynamics: Unraveling the Influence on Biofilm Architecture and Functionality

The transition of bacteria from an individualistic to a biofilm lifestyle profoundly alters their biology. During biofilm development, the bacterial cell-cell adhesions are a major determinant of initial microcolonies, which serve as kernels for the subsequent microscopic and mesoscopic structure of the biofilm, and determine the resulting functionality. In this study, the significance of bacterial cell-cell adhesion dynamics on bacterial aggregation and biofilm maturation is elucidated. Using photoswitchable adhesins between bacteria, modifying the dynamics of bacterial cell-cell adhesions with periodic dark-light cycles is systematic. Dynamic cell-cell adhesions with liquid-like behavior improve bacterial aggregation and produce more compact microcolonies than static adhesions with solid-like behavior in both experiments and individual-based simulations. Consequently, dynamic cell-cell adhesions give rise to earlier quorum sensing activation, better intermixing of different bacterial populations, improved biofilm maturation, changes in the growth of cocultures, and higher yields in fermentation. The here presented approach of tuning bacterial cell-cell adhesion dynamics opens the door for regulating the structure and function of biofilms and cocultures with potential biotechnological applications.

Origin of the multi-phasic quenching dynamics in the BLUF domains across the species

Blue light using flavin (BLUF) photoreceptors respond to light via one of nature's smallest photo-switching domains. Upon photo-activation, the flavin cofactor in the BLUF domain exhibits multi-phasic dynamics, quenched by a proton-coupled electron transfer reaction involving the conserved Tyr and Gln. The dynamic behavior varies drastically across different species, the origin of which remains controversial. Here, we incorporate site-specific fluorinated Trp into three BLUF proteins, i.e., AppA, OaPAC and SyPixD, and characterize the percentages for the Wout, WinNHin and WinNHout conformations using 19F nuclear magnetic resonance spectroscopy. Using femtosecond spectroscopy, we identify that one key WinNHin conformation can introduce a branching one-step proton transfer in AppA and a two-step proton transfer in OaPAC and SyPixD. Correlating the flavin quenching dynamics with the active-site structural heterogeneity, we conclude that the quenching rate is determined by the percentage of WinNHin, which encodes a Tyr-Gln configuration that is not conducive to proton transfer.

Impact of weak radiofrequency and static magnetic fields on key signaling molecules, intracellular pH, membrane potential, and cell growth in HT-1080 fibrosarcoma cells

There are substantial concerns that extended exposures to weak radiofrequency (RF) fields can lead to adverse health effects. In this study, HT-1080 fibrosarcoma cells were simultaneously exposed to a static magnetic flux density between 10 [Formula: see text] and 300 [Formula: see text] and RF magnetic fields with amplitudes ranging from 1 nT to 1.5 μT in the frequency range from 1.8 to 7.2 MHz for four days. Cell growth rates, intracellular pH, hydrogen peroxide, peroxynitrite, membrane potential and mitochondrial calcium were measured. Results were dependent on carrier frequency and the magnitude of the RF magnetic field, modulation frequencies and the background static magnetic field (SMF). Iron sulphur (Fe-S) clusters are essential for the generation of reactive oxygen species and reactive nitrogen species (ROS and RNS). We believe the observed changes are associated with hyperfine couplings between the chemically active electrons and nuclear spins. Controlling external magnetic fields may have important clinical implications on aging, cancer, arthritis, and Alzheimer's.

Escherichia coli amino acid auxotrophic expression host strains for investigating protein structure-function relationships

A set of C43(DE3) and BL21(DE3) Escherichia coli host strains that are auxotrophic for various amino acids is briefly reviewed. These strains require the addition of a defined set of one or more amino acids in the growth medium, and have been specifically designed for overproduction of membrane or water-soluble proteins selectively labelled with stable isotopes, such as 2H, 13C and 15N. The strains described here are available for use and have been deposited into public strain banks. Although they cannot fully eliminate the possibility of isotope dilution and mixing, metabolic scrambling of the different amino acid types can be minimized through a careful consideration of the bacterial metabolic pathways. The use of a suitable auxotrophic expression host strain with an appropriately isotopically labelled growth medium ensures high levels of isotope labelling efficiency as well as selectivity for providing deeper insight into protein structure-function relationships.

Blue-Light-Switchable Bacterial Cell-Cell Adhesions Enable the Control of Multicellular Bacterial Communities

Although the fundamental importance and biotechnological potential of multibacterial communities, also called biofilms, are well-known, our ability to control them is limited. We present a new way of dynamically controlling bacteria-bacteria adhesions by using blue light and how these photoswitchable adhesions can be used to regulate multicellularity and associated bacterial behavior. To achieve this, the photoswitchable proteins nMagHigh and pMagHigh were expressed on bacterial surfaces as adhesins to allow multicellular clusters to assemble under blue light and reversibly disassemble in the dark. Regulation of the bacterial cell-cell adhesions with visible light provides unique advantages including high spatiotemporal control, tunability, and noninvasive remote regulation. Moreover, these photoswitchable adhesions make it possible to regulate collective bacterial functions including aggregation, quorum sensing, biofilm formation, and metabolic cross-feeding between auxotrophic bacteria with light. Overall, the photoregulation of bacteria-bacteria adhesions provides a new way of studying bacterial cell biology and will enable the design of biofilms for biotechnological applications.

Bioorthogonal Elastin-like Polypeptide Scaffolds for Immunoassay Enhancement

Artificial multiprotein complexes are sought after reagents for biomolecular engineering. A current limiting factor is the paucity of molecular scaffolds which allow for site-specific multicomponent assembly. Here, we address this limitation by synthesizing bioorthogonal elastin-like polypeptide (ELP) scaffolds containing periodic noncanonical l-azidohomoalanine amino acids in the guest residue position. The nine azide ELP guest residues served as conjugation sites for site-specific modification with dibenzocyclooctyne (DBCO)-functionalized single-domain antibodies (SdAbs) through strain-promoted alkyne-azide cycloaddition (SPAAC). Sortase A and ybbR tags at the C- and N-termini of the ELP scaffold provided two additional sites for derivatization with small molecules and peptides by Sortase A and 4'-phosphopantetheinyl transferase (Sfp), respectively. These functional groups are chemically bioorthogonal, mutually compatible, and highly efficient, thereby enabling synthesis of multi-antibody ELP complexes in a one-pot reaction. We demonstrate application of this material for enhancing the performance of sandwich immunoassays of the recombinant protein mCherry. In undiluted human plasma, surfaces modified with multi-antibody ELP complexes showed between 2.3- and 14.3-fold improvement in sensitivity and ∼30-40% lower limits of detection as compared with nonspecifically adsorbed antibodies. Dual-labeled multi-antibody ELP complexes were further used for cytometric labeling and analysis of live eukaryotic cells. These results demonstrate how multiple antibodies complexed onto bioorthogonal protein-based polymers can be used to enhance immunospecific binding interactions through multivalency effects.

g-Tensor Directions in the Protein Structural Frame of Hyperthermophilic Archaeal Reduced Rieske-Type Ferredoxin Explored by 13C Pulsed Electron Paramagnetic Resonance

Interpretation of magnetic resonance data in the context of structural and chemical biology requires prior knowledge of the g-tensor directions for paramagnetic metallo-cofactors with respect to the protein structural frame. Access to this information is often limited by the strict requirement of suitable protein crystals for single-crystal electron paramagnetic resonance (EPR) measurements or the reliance on protons (with ambiguous locations in crystal structures) near the paramagnetic metal site. Here we develop a novel pulsed EPR approach with selective ¹³C_β-cysteine labeling of model [2Fe-2S] proteins to help bypass these problems. Analysis of the ¹³C_β-cysteine hyperfine tensors reproduces the g-tensor of the Pseudomonas putida ISC-like [2Fe-2S] ferredoxin (FdxB). Its application to the hyperthermophilic archaeal Rieske-type [2Fe-2S] ferredoxin (ARF) from Sulfolobus solfataricus, for which the single-crystal EPR approach was not feasible, supports the best-fit g _x-, g _z-, and g _y-tensor directions of the reduced cluster as nearly along Fe-Fe, S-S, and the cluster plane normal, respectively. These approximate principal directions of the reduced ARF g-tensor, explored by ¹³C pulsed EPR, are less skewed from the cluster molecular axes and are largely consistent with those previously determined by single-crystal EPR for the cytochrome bc₁-associated, reduced Rieske [2Fe-2S] center. This suggests the approximate g-tensor directions are conserved across the phylogenetically and functionally divergent Rieske-type [2Fe-2S] proteins.

Mechanistic elucidation of the mycofactocin-biosynthetic radical S-adenosylmethionine protein, MftC

Ribosomally synthesized and posttranslationally modified peptide (RiPP) pathways produce a diverse array of natural products. A subset of these pathways depends on radical S-adenosylmethionine proteins to modify the RiPP-produced peptide. Mycofactocin biosynthesis is one example of an S-adenosylmethionine protein-dependent RiPP pathway. Recently, it has been shown that MftC catalyzes the oxidative decarboxylation of the C-terminal tyrosine (Tyr-30) on the mycofactocin precursor peptide MftA; however, this product has not been verified by techniques other than MS. Herein, we provide a more detailed study of MftC catalysis and report a revised mechanism for MftC chemistry. We show that MftC catalyzes the formation of two isomeric products. Using a combination of MS, isotope labeling, and ¹H and ¹³C NMR techniques, we established that the major product, MftA*, is a tyramine-valine-cross-linked peptide formed by MftC through two S-adenosylmethionine-dependent turnovers. In addition, we show that the hydroxyl group on MftA Tyr-30 is required for MftC catalysis. Furthermore, we show that a substitution in the penultimate MftA Val-29 position causes the accumulation of an MftA** minor product. The ¹H NMR spectrum indicates that this minor product contains an αβ-unsaturated bond that likely arises from an aborted intermediate of MftA* synthesis. The finding that MftA* is the major product formed during MftC catalysis could have implications for the further elucidation of mycofactocin biosynthesis.

Mechanistic insights into the reductive dehydroxylation pathway for the biosynthesis of isoprenoids promoted by the IspH enzyme

Here, we report an integrated quantum mechanics/molecular mechanics (QM/MM) study of the bio-organometallic reaction pathway of the 2H+/2e- reduction of (E)-4-hydroxy-3-methylbut-2-enyl pyrophosphate (HMBPP) into the so called universal terpenoid precursors isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP), promoted by the IspH enzyme. Our results support the viability of the bio-organometallic pathway through rotation of the OH group of HMBPP away from the [Fe4S4] cluster at the core of the catalytic site, to become engaged in a H-bond with Glu126. This rotation is synchronous with π-coordination of the C2[double bond, length as m-dash]C3 double bond of HMBPP to the apical Fe atom of the [Fe4S4] cluster. Dehydroxylation of HMBPP is triggered by a proton transfer from Glu126 to the OH group of HMBPP. The reaction pathway is completed by competitive proton transfer from the terminal phosphate group to the C2 or C4 atom of HMBPP.

The reduction rates of DEPC-modified mutant Thermus thermophilus Rieske proteins differ when there is a negative charge proximal to the cluster

Rieske and Rieske-type proteins are electron transport proteins involved in key biological processes such as respiration, photosynthesis, and detoxification. They have a [2Fe-2S] cluster ligated by two cysteines and two histidines. A series of mutations, L135E, L135R, L135A, and Y158F, of the Rieske protein from Thermus thermophilus has been produced which probe the effects of the neighboring residues, in the second sphere, on the dynamics of cluster reduction and the reactivity of the ligating histidines. These properties were probed using titrations and modifications with diethyl pyrocarbonate (DEPC) at various pH values monitored using UV-Visible and circular dichroism spectrophotometry. These results, along with results from EPR studies, provide information on ligating histidine modification and rate of reduction of each of the mutant proteins. L135R, L135A, and Y158F react with DEPC similarly to wild type, resulting in modified protein with a reduced [2Fe-2S] cluster in <90 min, whereas L135E requires >15 h under the same conditions. Thus, the negative charge slows down the rate of reduction and provides an explanation as to why negatively charged residues are rarely, if ever, found in the equivalent position of other Rieske and Rieske-type proteins.

Fast proton-coupled electron transfer observed for a high-fidelity structural and functional [2Fe-2S] Rieske model

Rieske cofactors have a [2Fe–2S] cluster with unique {His₂Cys₂} ligation and distinct Fe subsites. The histidine ligands are functionally relevant, since they allow for coupling of electron and proton transfer (PCET) during quinol oxidation in respiratory and photosynthetic ET chains. Here we present the highest fidelity synthetic analogue for the Rieske [2Fe–2S] cluster reported so far. This synthetic analogue 5^x– emulates the heteroleptic {His₂Cys₂} ligation of the [2Fe–2S] core, and it also serves as a functional model that undergoes fast concerted proton and electron transfer (CPET) upon reaction of the mixed-valent (ferrous/ferric) protonated 5H^2– with TEMPO. The thermodynamics of the PCET square scheme for 5^x– have been determined, and three species (diferric 5^2–, protonated diferric 5H^–, and mixed-valent 5^3–) have been characterized by X-ray diffraction. pK_a values for 5H^– and 5H^2– differ by about 4 units, and the reduction potential of 5H^– is shifted anodically by about +230 mV compared to that of 5^2–. While the N–H bond dissociation free energy of 5H^2– (60.2 ± 0.5 kcal mol^–1) and the free energy, ΔG°_CPET, of its reaction with TEMPO (−6.3 kcal mol^–1) are similar to values recently reported for a homoleptic {N₂/N₂}-coordinated [2Fe–2S] cluster, CPET is significantly faster for 5H^2– with biomimetic {N₂/S₂} ligation (k = (9.5 ± 1.2) × 10⁴ M^–1 s^–1, ΔH^‡ = 8.7 ± 1.0 kJ mol^–1, ΔS^‡ = −120 ± 40 J mol^–1 K^–1, and ΔG^‡ = 43.8 ± 0.3 kJ mol^–1 at 293 K). These parameters, and the comparison with homoleptic analogues, provide important information and new perspectives for the mechanistic understanding of the biological Rieske cofactor.

Defining a direction: electron transfer and catalysis in Escherichia coli complex II enzymes

There are two homologous membrane-bound enzymes in Escherichia coli that catalyze reversible conversion between succinate/fumarate and quinone/quinol. Succinate:ubiquinone reductase (SQR) is a component of aerobic respiratory chains, whereas quinol:fumarate reductase (QFR) utilizes menaquinol to reduce fumarate in a final step of anaerobic respiration. Although, both protein complexes are capable of supporting bacterial growth on either minimal succinate or fumarate media, the enzymes are more proficient in their physiological directions. Here we evaluate factors that may underlie this catalytic bias. This article is part of a Special Issue entitled: Respiratory complex II: Role in cellular physiology and disease.