Dynamic interactions of type I cohesin modules fine-tune the structure of the cellulosome of Clostridium thermocellum

Lignocellulose degradation in bacteria and fungi: cellulosomes and industrial relevance

Lignocellulose biomass is one of the most abundant resources for sustainable biofuels. However, scaling up the biomass-to-biofuels conversion process for widespread usage is still pending. One of the main bottlenecks is the high cost of enzymes used in key process of biomass degradation. Current research efforts are therefore targeted at creative solutions to improve the feasibility of lignocellulosic-degrading enzymes. One way is to engineer multi-enzyme complexes that mimic the bacterial cellulosomal system, known to increase degradation efficiency up to 50-fold when compared to freely-secreted enzymes. However, these designer cellulosomes are instable and less efficient than wild type cellulosomes. In this review, we aim to extensively analyze the current knowledge on the lignocellulosic-degrading enzymes through three aspects. We start by reviewing and comparing sets of enzymes in bacterial and fungal lignocellulose degradation. Next, we focus on the characteristics of cellulosomes in both systems and their feasibility to be engineered. Finally, we highlight three key strategies to enhance enzymatic lignocellulose degradation efficiency: discovering novel lignocellulolytic species and enzymes, bioengineering enzymes for improved thermostability, and structurally optimizing designer cellulosomes. We anticipate these insights to act as resources for the biomass community looking to elevate the usage of lignocellulose as biofuel.

FRET-FCS: Advancing comprehensive insights into complex biological systems

Förster resonance energy transfer (FRET) is a short-range distance-dependent photophysical phenomenon that allows the measurement of intra- and intermolecular distances through fluorescence detection. FRET measurements are sensitive to the movements of fluorescently labeled molecules as they produce fluorescence fluctuations. Fluorescence correlation spectroscopy (FCS) analyzes these fluctuations at faster and broader timescales (from picoseconds to seconds) compared with other techniques, unraveling the thermodynamic and kinetic properties of the system under study. Therefore, the combination of FRET and FCS (FRET-FCS) facilitates the analysis of molecular dynamics. Since its introduction, FRET-FCS has evolved into studying more sophisticated systems, requiring improvements in data acquisition and analysis. In this review, we discuss applications in the field of FRET-FCS that propose novel alternatives to overcome the inherent limitations of experimental setups. This work aims to promote using and enhancing FRET-FCS techniques to develop a comprehensive understanding of biological systems.

Engineering Compositionally Uniform Yeast Whole-Cell Biocatalysts with Maximized Surface Enzyme Density for Cellulosic Biofuel Production

In recent decades, whole-cell biocatalysis has played an increasingly important role in the food, pharmaceutical, and energy sector. One promising application is the use of ethanologenic yeast displaying minicellulosomes on the cell surface to combine cellulose hydrolysis and fermentation into a single step for consolidated bioprocessing. However, cellulosic ethanol production using existing yeast whole-cell biocatalysts (yWCBs) has not reached industrial feasibility due to their inefficient cellulose hydrolysis. As prior studies have demonstrated enzyme density on the yWCB surface to be one of the most important parameters for enhancing cellulose hydrolysis, we sought to maximize this parameter at both the population and single-cell levels in yWCBs displaying tetrafunctional minicellulosomes. At the population level, enzyme density is limited by the presence of a nondisplay population constituting 25-50% of all cells. In this study, we identified the cause to be plasmid loss and successfully eliminated the nondisplay population to generate compositionally uniform yWCBs. At the single-cell level, we demonstrate that enzyme density is limited by molecular crowding, which hinders minicellulosome assembly. By adjusting the integrated gene copy number, we obtained yWCBs of tunable enzyme display levels. This tunability allowed us to avoid the crowding-limited regime and achieve a maximum enzyme density per cell. As a result, the best strain showed a cellulose-to-ethanol yield of 4.92 g/g, corresponding to 96% of the theoretical maximum and near-complete conversion (∼96%) of the starting cellulose (1% PASC). Our holistic engineering strategy that combines a population and single-cell level approach is broadly applicable to enhance the WCB performance in other biocatalytic cascade schemes.

Folding pathway of a discontinuous two-domain protein

It is estimated that two-thirds of all proteins in higher organisms are composed of multiple domains, many of them containing discontinuous folds. However, to date, most in vitro protein folding studies have focused on small, single-domain proteins. As a model system for a two-domain discontinuous protein, we study the unfolding/refolding of a slow-folding double mutant of the maltose binding protein (DM-MBP) using single-molecule two- and three-color Förster Resonance Energy Transfer experiments. We observe a dynamic folding intermediate population in the N-terminal domain (NTD), C-terminal domain (CTD), and at the domain interface. The dynamic intermediate fluctuates rapidly between unfolded states and compact states, which have a similar FRET efficiency to the folded conformation. Our data reveals that the delayed folding of the NTD in DM-MBP is imposed by an entropic barrier with subsequent folding of the highly dynamic CTD. Notably, accelerated DM-MBP folding is routed through the same dynamic intermediate within the cavity of the GroEL/ES chaperone system, suggesting that the chaperonin limits the conformational space to overcome the entropic folding barrier. Our study highlights the subtle tuning and co-dependency in the folding of a discontinuous multi-domain protein.

Probing the conformational dynamics of thiol-isomerases using non-canonical amino acids and single-molecule FRET

Disulfide bonds drive protein correct folding, prevent protein aggregation, and stabilize three-dimensional structures of proteins and their assemblies. Dysregulation of this activity leads to several disorders, including cancer, neurodegeneration, and thrombosis. A family of 20+ enzymes, called thiol-isomerases (TIs), oversee this process in the endoplasmic reticulum of human cells to ensure efficacy and accuracy. While the biophysical and biochemical properties of cysteine residues are well-defined, our structural knowledge of how TIs select, interact and process their substrates remains poorly understood. How TIs structurally and functionally respond to changes in redox environment and other post-translational modifications remain unclear, too. We recently developed a workflow for site-specific incorporation of non-canonical amino acids into protein disulfide isomerase (PDI), the prototypical member of TIs. Combined with click chemistry, this strategy enabled us to perform single-molecule biophysical studies of PDI under various solution conditions. This paper details protocols and discusses challenges in performing these experiments. We expect this approach, combined with other emerging technologies in single-molecule biophysics and structural biology, to facilitate the exploration of the mechanisms by which TIs carry out their fascinating but poorly understood roles in humans, especially in the context of thrombosis.

Coupling of binding and differential subdomain folding of the intrinsically disordered transcription factor CREB

The cyclic AMP response element binding protein (CREB) contains a basic leucine zipper motif (bZIP) that forms a coiled coil structure upon dimerization and specific DNA binding. Although this state is well characterized, key features of CREB bZIP binding and folding are not well understood. We used single-molecule Förster resonance energy transfer (smFRET) to probe conformations of CREB bZIP subdomains. We found differential folding of the basic region and leucine zipper in response to different binding partners; a strong and previously unreported DNA-independent dimerization affinity; folding upon binding to nonspecific DNA; and evidence of long-range interdomain interactions in full-length CREB that modulate DNA binding. These studies provide new insights into DNA binding and dimerization and have implications for CREB function.

Shrinking gate fluorescence correlation spectroscopy yields equilibrium constants and separates photophysics from structural dynamics

Fluorescence correlation spectroscopy is a versatile tool for studying fast conformational changes of biomolecules especially when combined with Förster resonance energy transfer (FRET). Despite the many methods available for identifying structural dynamics in FRET experiments, the determination of the forward and backward transition rate constants and thereby also the equilibrium constant is difficult when two intensity levels are involved. Here, we combine intensity correlation analysis with fluorescence lifetime information by including only a subset of photons in the autocorrelation analysis based on their arrival time with respect to the excitation pulse (microtime). By fitting the correlation amplitude as a function of microtime gate, the transition rate constants from two fluorescence-intensity level systems and the corresponding equilibrium constants are obtained. This shrinking-gate fluorescence correlation spectroscopy (sg-FCS) approach is demonstrated using simulations and with a DNA origami-based model system in experiments on immobilized and freely diffusing molecules. We further show that sg-FCS can distinguish photophysics from dynamic intensity changes even if a dark quencher, in this case graphene, is involved. Finally, we unravel the mechanism of a FRET-based membrane charge sensor indicating the broad potential of the method. With sg-FCS, we present an algorithm that does not require prior knowledge and is therefore easily implemented when an autocorrelation analysis is carried out on time-correlated single-photon data.

Structural dynamics of DNA strand break sensing by PARP-1 at a single-molecule level

Single-stranded breaks (SSBs) are the most frequent DNA lesions threatening genomic integrity. A highly kinked DNA structure in complex with human PARP-1 domains led to the proposal that SSB sensing in Eukaryotes relies on dynamics of both the broken DNA double helix and PARP-1's multi-domain organization. Here, we directly probe this process at the single-molecule level. Quantitative smFRET and structural ensemble calculations reveal how PARP-1's N-terminal zinc fingers convert DNA SSBs from a largely unperturbed conformation, via an intermediate state into the highly kinked DNA conformation. Our data suggest an induced fit mechanism via a multi-domain assembly cascade that drives SSB sensing and stimulates an interplay with the scaffold protein XRCC1 orchestrating subsequent DNA repair events. Interestingly, a clinically used PARP-1 inhibitor Niraparib shifts the equilibrium towards the unkinked DNA conformation, whereas the inhibitor EB47 stabilizes the kinked state.

Reduction of protein disulfide isomerase results in open conformations and stimulates dynamic exchange between structural ensembles

Human protein disulfide isomerase (PDI) is an essential redox-regulated enzyme required for oxidative protein folding. It comprises four thioredoxin domains, two catalytically active (a, a’) and two inactive (b, b’), organized to form a flexible abb’a’ U-shape. Snapshots of unbound oxidized and reduced PDI have been obtained by X-ray crystallography. Yet, how PDI’s structure changes in response to the redox environment and inhibitor binding remains controversial. Here, we used multiparameter confocal single-molecule FRET to track the movements of the two catalytic domains with high temporal resolution. We found that at equilibrium, PDI visits three structurally distinct conformational ensembles, two “open” (O₁ and O₂) and one “closed” (C). We show that the redox environment dictates the time spent in each ensemble and the rate at which they exchange. While oxidized PDI samples O₁, O₂, and C more evenly and in a slower fashion, reduced PDI predominantly populates O₁ and O₂ and exchanges between them more rapidly, on the submillisecond timescale. These findings were not expected based on crystallographic data. Using mutational analyses, we further demonstrate that the R300-W396 cation-π interaction and active site cysteines dictate, in unexpected ways, how the catalytic domains relocate. Finally, we show that irreversible inhibitors targeting the active sites of reduced PDI did not abolish these protein dynamics but rather shifted the equilibrium toward the closed ensemble. This work introduces a new structural framework that challenges current views of PDI dynamics, helps rationalize its multifaceted role in biology, and should be considered when designing PDI-targeted therapeutics.

Unraveling multi-state molecular dynamics in single-molecule FRET experiments. I. Theory of FRET-lines

Conformational dynamics of biomolecules are of fundamental importance for their function. Single-molecule studies of Förster Resonance Energy Transfer (smFRET) between a tethered donor and acceptor dye pair are a powerful tool to investigate the structure and dynamics of labeled molecules. However, capturing and quantifying conformational dynamics in intensity-based smFRET experiments remains challenging when the dynamics occur on the sub-millisecond timescale. The method of multiparameter fluorescence detection addresses this challenge by simultaneously registering fluorescence intensities and lifetimes of the donor and acceptor. Together, two FRET observables, the donor fluorescence lifetime τD and the intensity-based FRET efficiency E, inform on the width of the FRET efficiency distribution as a characteristic fingerprint for conformational dynamics. We present a general framework for analyzing dynamics that relates average fluorescence lifetimes and intensities in two-dimensional burst frequency histograms. We present parametric relations of these observables for interpreting the location of FRET populations in E-τD diagrams, called FRET-lines. To facilitate the analysis of complex exchange equilibria, FRET-lines serve as reference curves for a graphical interpretation of experimental data to (i) identify conformational states, (ii) resolve their dynamic connectivity, (iii) compare different kinetic models, and (iv) infer polymer properties of unfolded or intrinsically disordered proteins. For a simplified graphical analysis of complex kinetic networks, we derive a moment-based representation of the experimental data that decouples the motion of the fluorescence labels from the conformational dynamics of the biomolecule. Importantly, FRET-lines facilitate exploring complex dynamic models via easily computed experimental observables. We provide extensive computational tools to facilitate applying FRET-lines.

Decoding the roles of extremophilic microbes in the anaerobic environments: Past, Present, and Future

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The inaccessible extreme environments harbor a large majority of anaerobic microbes which remain unknown.

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Anaerobic microbes are used in a variety of industrial applications.

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In the future, metagenomic-assisted techniques can be used to identify novel anaerobic microbes from the unexplored extreme environments.

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Genetic engineering can be used to enhance the efficiency of anaerobic microbes for various processes.

The genome of an organism is directly or indirectly correlated with its environment. Consequently, different microbes have evolved to survive and sustain themselves in a variety of environments, including unusual anaerobic environments. It is believed that their genetic material could have played an important role in the early evolution of their existence in the past. Presently, out of the uncountable number of microbes found in different ecosystems we have been able to discover only one percent of the total communities. A large majority of the microbial populations exists in the most unusual and extreme environments. For instance, many anaerobic bacteria are found in the gastrointestinal tract of humans, soil, and hydrothermal vents. The recent advancements in Metagenomics and Next Generation Sequencing technologies have improved the understanding of their roles in these environments. Presently, anaerobic bacteria are used in various industries associated with biofuels, fermentation, production of enzymes, vaccines, vitamins, and dairy products. This broad applicability brings focus to the significant contribution of their genomes in these functions. Although the anaerobic microbes have become an irreplaceable component of our lives, a major and important section of such anaerobic microbes still remain unexplored. Therefore, it can be said that unlocking the role of the microbial genomes of the anaerobes can be a noteworthy discovery not just for mankind but for the entire biosystem as well.

Cohesin-dockerin code in cellulosomal dual binding modes and its allosteric regulation by proline isomerization

Cellulose is the most abundant organic molecule on Earth and represents a renewable and practically everlasting feedstock for the production of biofuels and chemicals. Self-assembled owing to the high-affinity cohesin-dockerin interaction, cellulosomes are huge multi-enzyme complexes with unmatched efficiency in the degradation of recalcitrant lignocellulosic substrates. The recruitment of diverse dockerin-borne enzymes into a multicohesin protein scaffold dictates the three-dimensional layout of the complex, and interestingly two alternative binding modes have been proposed. Using single-molecule fluorescence resonance energy transfer and molecular simulations on a range of cohesin-dockerin pairs, we directly detect varying distributions between these binding modes that follow a built-in cohesin-dockerin code. Surprisingly, we uncover a prolyl isomerase-modulated allosteric control mechanism, mediated by the isomerization state of a single proline residue, which regulates the distribution and kinetics of binding modes. Overall, our data provide a novel mechanistic understanding of the structural plasticity and dynamics of cellulosomes.

FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices

Single-molecule FRET (smFRET) has become a mainstream technique for studying biomolecular structural dynamics. The rapid and wide adoption of smFRET experiments by an ever-increasing number of groups has generated significant progress in sample preparation, measurement procedures, data analysis, algorithms and documentation. Several labs that employ smFRET approaches have joined forces to inform the smFRET community about streamlining how to perform experiments and analyze results for obtaining quantitative information on biomolecular structure and dynamics. The recent efforts include blind tests to assess the accuracy and the precision of smFRET experiments among different labs using various procedures. These multi-lab studies have led to the development of smFRET procedures and documentation, which are important when submitting entries into the archiving system for integrative structure models, PDB-Dev. This position paper describes the current 'state of the art' from different perspectives, points to unresolved methodological issues for quantitative structural studies, provides a set of 'soft recommendations' about which an emerging consensus exists, and lists openly available resources for newcomers and seasoned practitioners. To make further progress, we strongly encourage 'open science' practices.

Unraveling protein's structural dynamics: from configurational dynamics to ensemble switching guides functional mesoscale assemblies

Evidence regarding protein structure and function manifest the imperative role that dynamics play in proteins, underlining reconsideration of the unanimated sequence-to-structure-to-function paradigm. Structural dynamics portray a heterogeneous energy landscape described by conformational ensembles where each structural representation can be responsible for unique functions or enable macromolecular assemblies. Using the human p27/Cdk2/Cyclin A ternary complex as an example, we highlight the vital role of intramolecular and intermolecular dynamics for target recognition, binding, and inhibition as a critical modulator of cell division. Rapidly sampling configurations is critical for the population of different conformational ensembles encoding functional roles. To garner this knowledge, we present how the integration of (sub)ensemble and single-molecule fluorescence spectroscopy with molecular dynamic simulations can characterize structural dynamics linking the heterogeneous ensembles to function. The incorporation of dynamics into the sequence-to-structure-to-function paradigm promises to assist in tackling various challenges, including understanding the formation and regulation of mesoscale assemblies inside cells.

Hierarchical dynamics in allostery following ATP hydrolysis monitored by single molecule FRET measurements and MD simulations

We report on a study that combines advanced fluorescence methods with molecular dynamics (MD) simulations to cover timescales from nanoseconds to milliseconds for a large protein. This allows us to delineate how ATP hydrolysis in a protein causes allosteric changes at a distant protein binding site, using the chaperone Hsp90 as test system. The allosteric process occurs via hierarchical dynamics involving timescales from nano- to milliseconds and length scales from Ångstroms to several nanometers. We find that hydrolysis of one ATP is coupled to a conformational change of Arg380, which in turn passes structural information via the large M-domain α-helix to the whole protein. The resulting structural asymmetry in Hsp90 leads to the collapse of a central folding substrate binding site, causing the formation of a novel collapsed state (closed state B) that we characterise structurally. We presume that similar hierarchical mechanisms are fundamental for information transfer induced by ATP hydrolysis through many other proteins.

How fast are the motions of tertiary-structure elements in proteins?

Protein motions occur on multiple time and distance scales. Large-scale motions of protein tertiary-structure elements, i.e., domains, are particularly intriguing as they are essential for the catalytic activity of many enzymes and for the functional cycles of protein machines and motors. Theoretical estimates suggest that domain motions should be very fast, occurring on the nanosecond or microsecond time scales. Indeed, free-energy barriers for domain motions are likely to involve salt bridges, which can break in microseconds. Experimental methods that can directly probe domain motions on fast time scales have appeared only in recent years. This Perspective discusses briefly some of these techniques, including nuclear magnetic resonance and single-molecule fluorescence spectroscopies. We introduce a few recent studies that demonstrate ultrafast domain motions and discuss their potential roles. Particularly surprising is the observation of tertiary-structure element dynamics that are much faster than the functional cycles in some protein machines. These swift motions can be rationalized on a case-by-case basis. For example, fast domain closure in multi-substrate enzymes may be utilized to optimize relative substrate orientation. Whether a large mismatch in time scales of conformational dynamics vs functional cycles is a general design principle in proteins remains to be determined.

A Biological Nanomachine at Work: Watching the Cellulosome Degrade Crystalline Cellulose

The cellulosome is a supramolecular multienzymatic protein complex that functions as a biological nanomachine of cellulosic biomass degradation. How the megadalton-size cellulosome adapts to a solid substrate is central to its mechanism of action and is also key for its efficient use in bioconversion applications. We report time-lapse visualization of crystalline cellulose degradation by individual cellulosomes from Clostridium thermocellum by atomic force microscopy. Upon binding to cellulose, the cellulosomes switch to elongated, even filamentous shapes and morph these dynamically at below 1 min time scale according to requirements of the substrate surface under attack. Compared with noncomplexed cellulases that peel off material while sliding along crystalline cellulose surfaces, the cellulosomes remain bound locally for minutes and remove the material lying underneath. The consequent roughening up of the surface leads to an efficient deconstruction of cellulose nanocrystals both from the ends and through fissions within. Distinct modes of cellulose nanocrystal deconstruction by nature's major cellulase systems are thus revealed.

Engineering of industrially important microorganisms for assimilation of cellulosic biomass: towards consolidated bioprocessing

Conversion of cellulosic biomass (non-edible plant material) to products such as chemical feedstocks and liquid fuels is a major goal of industrial biotechnology and an essential component of plans to move from an economy based on fossil carbon to one based on renewable materials. Many microorganisms can effectively degrade cellulosic biomass, but attempts to engineer this ability into industrially useful strains have met with limited success, suggesting an incomplete understanding of the process. The recent discovery and continuing study of enzymes involved in oxidative depolymerisation, as well as more detailed study of natural cellulose degradation processes, may offer a way forward.

Designed Protein Cages as Scaffolds for Building Multienzyme Materials

The functions of enzymes can be strongly affected by their higher-order spatial arrangements. In this study we combine multiple new technologies-designer protein cages and sortase-based enzymatic attachments between proteins-as a novel platform for organizing multiple enzymes (of one or more types) in specified configurations. As a scaffold we employ a previously characterized 24-subunit designed protein cage whose termini are outwardly exposed for attachment. As a first-use case, we test the attachment of two cellulase enzymes known to act synergistically in cellulose degradation. We show that, after endowing the termini of the cage subunits with a short "sort-tag" sequence (LPXTG) and the opposing termini of the cellulase enzymes with a short polyglycine sequence tag, addition of sortase covalently attaches the enzymes to the cage with good reactivity and high copy number. The doubly modified cages show enhanced activity in a cellulose degradation assay compared to enzymes in solution, and compared to a combination of singly modified cages. These new engineering strategies could be broadly useful in the development of enzymatic material and synthetic biology applications.

Synthetic Protein Scaffolding at Biological Membranes

Protein scaffolding is a natural phenomenon whereby proteins colocalize into macromolecular complexes via specific protein-protein interactions. In the case of metabolic enzymes, protein scaffolding drives metabolic flux through specific pathways by colocalizing enzyme active sites. Synthetic protein scaffolding is increasingly used as a mechanism to improve product specificity and yields in metabolic engineering projects. To date, synthetic scaffolding has focused primarily on soluble enzyme systems, but many metabolic pathways for high-value secondary metabolites depend on membrane-bound enzymes. The compositional diversity of biological membranes and general challenges associated with modifying membrane proteins complicate scaffolding with membrane-requiring enzymes. Several recent studies have introduced new approaches to protein scaffolding at membrane surfaces, with notable success in improving product yields from specific metabolic pathways.