Crystal structure and inhibition mechanism of AcrIIA11

Anti-CRISPR (Acr) proteins are naturally evolved inhibitors that precisely target and suppress CRISPR-Cas systems, representing a sophisticated molecular arms race between bacteriophages and their bacterial hosts. While Class 1 systems dominate among sequenced prokaryotic genomes, Class 2 systems remain primary sources of editing tools. Here, we report the structural and mechanistic characterization of AcrIIA11, an anti-CRISPR protein that simultaneously inhibits Streptococcus pyogenes (SpyCas9) and Staphylococcus aureus Cas9 (SauCas9). The 3.2 Å crystal structure reveals a compact α/β fold with distinct electropositive clefts implicated in DNA binding. While DALI analysis identified structural homology to transcriptional regulators and the RecA inhibitor PsiB (RMSD 3.3 Å), functional studies established that AcrIIA11 forms stable ternary complexes with both Cas9 orthologs and sgRNA. Biochemical assays demonstrated stronger inhibition of SauCas9 compared to SpyCas9, with EMSA revealing a critical dichotomy: AcrIIA11 maintains SauCas9-sgRNA binding to specific target DNA while completely blocking cleavage activity. Computational docking localizes AcrIIA11 at the HNH-RuvC interface without obstructing DNA-binding channels in SauCas9, suggesting allosteric inhibition through HNH domain displacement. This work establishes AcrIIA11 as a dual-purpose Cas9 inhibitor that preserves target recognition while inactivating nuclease function-a mechanism with potential applications in precision CRISPR control.

3-D substructure search by transitive closure in AlphaFold database

Identifying structural relationships between proteins is crucial for understanding their functions and evolutionary histories. We present ISS_ProtSci, a Python package designed for structural similarity searches within the AlphaFold Database v2 (AFDB2). ISS_ProtSci incorporates DaliLite to identify geometrically similar structures and uses a transitive closure algorithm to iteratively explore neighboring shells of proteins. The precomputed all-against-all comparisons generated by Foldseek, chosen for its speed, are validated by DaliLite for precision. Search results are annotated with metadata from UniProtKB and Pfam protein family classifications, using hmmsearch to identify protein domains. Outputs, including Dali pairwise alignment data, are provided in TSV format for easy filtering and analysis. Our method offers a significant improvement in recall over existing tools like Foldseek, especially in detecting more distantly related proteins. This is particularly valuable in structurally diverse protein families where traditional sequence-based or fast structural methods struggle. ISS_ProtSci delivers practical runtimes and flexibility, allowing users to input a PDB file, define the minimum size of the common core, and evaluate results using Pfam clans. In evaluating our method across 12 test cases based on Pfam clans, we achieved over 99% recall of relevant proteins, even in challenging cases where Foldseek's recall dropped below 50%. ISS_ProtSci not only identifies closely related proteins but also uncovers previously unrecognized structural relationships, contributing to more accurate protein family classifications. The software can be downloaded from http://ekhidna2.biocenter.helsinki.fi/ISS_ProtSci/.

Enzyme miniaturization: Revolutionizing future biocatalysts

Enzyme miniaturization offers a transformative approach to overcome limitations posed by the large size of conventional enzymes in industrial, therapeutic, and diagnostic applications. However, the evolutionary optimization of enzymes for activity has not inherently favored compact structures, creating challenges for modern applications requiring smaller catalysts. In this review, we surveyed the advantages of miniature enzymes, including enhanced expressivity, folding efficiency, thermostability, and resistance to proteolysis. We described the applications of miniature enzymes as industrial catalysts, therapeutic agents, and diagnostic elements. We highlighted strategies such as genome mining, rational design, random deletion, and de novo design for achieving enzyme miniaturization, integrating both computational and experimental techniques. By investigating these approaches, we aim to provide a framework for advancing enzyme engineering, emphasizing the unique potential of miniature enzymes to revolutionize biocatalysis, gene therapy, and biosensing technologies.

Web-based GTalign: bridging speed and accuracy in protein structure analysis

Accurate protein structure alignment is essential for understanding structural and functional relationships. Here, we introduce GTalign-web, a web-based implementation of GTalign, a spatial index-driven protein structure alignment tool, designed for accessibility and high-performance structural searches. Benchmarked against the DALI and Foldseek servers, GTalign-web demonstrates superior accuracy while maintaining rapid search times. Its utility is further highlighted in annotating uncharacterized proteins through searches against UniRef30. GTalign-web provides a useful resource for protein structure analysis and functional annotation and is available at https://bioinformatics.lt/comer/gtalign. This website is free and open to all users, and there is no login requirement.

Cytochrome P450 Mediated Cyclohexane Ring Formation in Forazoline Biosynthesis

Forazoline A, produced by the marine actinomycete Actinomadura sp. WMMB-499, is a unique PK/NRP hybrid macrolactone with promising antifungal in vivo efficacy through a previously unreported mechanism. Although a PKS/NRPS gene cluster was identified as a candidate for forazoline production, the precise biosynthetic pathway and the functions of the tailoring enzymes remain unclear. In this work, the functions of three cytochrome P450 mono-oxygenases (FrazP1P2P3) were characterized. Notably, FrazP2 was found to mediate cyclohexane ring formation from an 1,3,6-triene precursor during forazoline A biosynthesis, as confirmed by genetic and biochemical analysis. To gain structural and mechanistic insight into the activity of FrazP2, the crystal structure of a FrazP2-substrate complex has been solved at 2.3 Å resolution. The molecular dynamics simulations and DFT calculations revealed an unprecedented enzyme-catalyzed oxidative cyclization reaction by FrazP2. These findings expand our understanding of the catalytic diversity of cytochrome P450s, contributing to the diversification of natural products and enabling the creation of unnatural derivatives with increased antifungal potency.

Similar but Distinct-Biochemical Characterization of the Staphylococcus aureus Serine Hydrolases FphH and FphI

Staphylococcus aureus is a major cause of infections like bacteremia, pneumonia, and endocarditis. These infections are often linked to the ability of S. aureus to form biofilms. Several S. aureus serine hydrolases have previously been identified to be active during biofilm-forming conditions. Here, we present the biochemical characterization of two of these enzymes-fluorophosphonate binding hydrolase H and I (FphH, FphI). Cryogenic and room-temperature X-ray crystallography, enzymatic substrate profiling, small-angle X-ray scattering analysis, and molecular dynamics simulations provide new insights into similarities and differences between these two hydrolase_4 domain family members. We discover that these enzymes share an overall fold, including a flexible lid or cap region above the active site, which can be seen to be mobile in solution. Differences in the active site pocket and lid residues differentiate them and explain speed differences in their carboxyesterase substrate profile toward small unbranched carbon chain ester molecules. The first analysis of FphI is also compared to our previous knowledge of FphH and its association to stress conditions. These results enable the future precise targeting of Fph serine hydrolase family members with a long-term goal to significantly improve the health and wellbeing of individuals and populations worldwide.

Assessing Structural Classification Using AlphaFold2 Models Through ECOD-Based Comparative Analysis

Identifying homologous proteins is a fundamental task in structural bioinformatics. While AlphaFold2 has revolutionized protein structure prediction, the extent to which structure comparison of its models can reliably detect homologs remains unclear. In this study, we evaluate the feasibility of homology detection using AlphaFold2-predicted structures through structural comparisons. We considered the classification of the ECOD database for experimental structures as the correct standard and obtained their corresponding predicted models from AlphaFoldDB. To ensure blind assessment, we divided the structures into test and train sets according to their release date. Predicted and experimental 3D structures in the test and train sets were compared using 3D structure comparisons (MATRAS, Dali, and Foldseek) and sequence comparisons (BLAST and HHsearch). The results were evaluated based on the homology annotations in the ECOD database. For top-1 accuracy, the performance of structural comparisons was comparable to that of HHsearch. However, when considering metrics that included all structural pairs, including more remote homology, structural comparisons outperformed HHsearch. No significant differences were observed between comparisons of experimental versus experimental, predicted versus experimental, and predicted versus predicted structures with pLDDT (prediction confidence) values greater than 60. We also demonstrate that predicted protein structures, determined by NMR, had lower pLDDT values and contained fewer coils than their experimental counterparts. These findings highlight the potential of AlphaFold2 models in structural classification and suggest that 3D structural searches should be conducted not only against the PDB but also against AlphaFoldDB to identify more potential homologs.

An acyl-homoserine lactone acylase found in Stenotrophomonas maltophilia exhibits both quorum quenching activity and the ability to degrade penicillin antibiotics

Stenotrophomonas maltophilia are opportunistic, multi-drug-resistant Gram-negative pathogens increasingly prevalent in clinical settings. Quorum sensing (QS) systems play a crucial role in their pathogenesis, coordinating bacterial populations and enabling interactions within polymicrobial communities. While not the primary QS mechanism in S. maltophilia, these bacteria can respond to acyl-homoserine lactone (AHL)-type autoinducers. Some isolates exhibit AHL-quorum quenching activity, though the responsible components remain unidentified. Homology searches in S. maltophilia K279a revealed a protein with the locus tag SMLT_RS07305 (old locus tag Smlt1522), annotated as a putative penicillin acylase 2 precursor. Sequence and structural analyses classify this protein within the bacterial AHL-acylase group B, characterized by a heterodimeric structure consisting of α- and β-subunits connected by a spacer polypeptide. We experimentally confirmed the dual activity of Smlt1522 as an AHL-acylase and a penicillin acylase. This protein degrades AHLs with varying acyl chains and hydrolyses penicillin antibiotics in vitro, in vivo, and as an heterologously expressed product. Its physiological role includes the modulation of beta-lactam resistance, biofilm formation and bacterial fitness under specific conditions. Evolutionary analysis suggests structural and functional conservation, pointing to its potential role in the adaptation of S. maltophilia to diverse and competitive environments.

Discovery of mono-ADP ribosylating toxins with high structural homology to Pseudomonas exotoxin A

Mono-ADP-ribosyl transferase (mART) proteins are secreted virulence factors produced by several human pathogens, the founding member being diphtheria toxin (DT). Pseudomonas aeruginosa can also secrete a mART toxin, known as exotoxin A (PE), but with an organization of its three functional domains (receptor, translocation, and enzymatic elements) that is opposite to DT. Two additional PE-like toxins (PLTs) have been identified from Vibrio cholerae and Aeromonas hydrophila, suggesting more PLT family members may exist. Database mining discovered six additional putative homologues, considerably extending this group of PLTs across a wide range of bacterial species. Here, we examine sequence and structural information for these new family members with respect to previously identified PLTs. The X-ray crystal structures of four new homologues show the conservation of critical features responsible for structure and function. This study shows the potential of these newly described toxins for the development of novel drug delivery platforms. Additionally, genomic analysis suggests horizontal gene transfer to account for the wide distribution of PLTs across a range of eubacteria species, highlighting the need to monitor emerging pathogens and their virulence factors.

Multi-scale structural similarity embedding search across entire proteomes

The rapid expansion of three-dimensional (3D) biomolecular structure information, driven by breakthroughs in artificial intelligence/deep learning (AI/DL)-based structure predictions, has created an urgent need for scalable and efficient structure similarity search methods. Traditional alignment-based approaches, such as structural superposition tools, are computationally expensive and challenging to scale with the vast number of available macromolecular structures. Herein, we present a scalable structure similarity search strategy designed to navigate extensive repositories of experimentally determined structures and computed structure models predicted using AI/DL methods. Our approach leverages protein language models and a deep neural network architecture to transform 3D structures into fixed-length vectors, enabling efficient large-scale comparisons. Although trained to predict TM-scores between single-domain structures, our model generalizes beyond the domain level, accurately identifying 3D similarity for full-length polypeptide chains and multimeric assemblies. By integrating vector databases, our method facilitates efficient large-scale structure retrieval, addressing the growing challenges posed by the expanding volume of 3D biostructure information.

Refinement and curation of homologous groups facilitated by structure prediction

Domain classification of protein predictions released in the AlphaFold Database (AFDB) has been a recent focus of the Evolutionary Classification of protein Domains (ECOD). Although a primary focus of our recent work has been the partition and assignment of domains from these predictions, we here show how these diverse predictions can be used to examine the reference domain set more closely. Using results from DPAM, our AlphaFold-specific domain parsing algorithm, we examine hierarchical groupings that share significant levels of homologous links, both between groups that were not previously assessed to be definitively homologous and between groups that were not previously observed to share significant homologous links. Combined with manual analysis, these large datasets of structural and sequence similarities allow us to merge homologous groups in multiple cases which we detail within. These domains tend to be families of domains from families that are either small, previously had few experimental representatives, or had unknown function. The exception to this is the chromodomains, a large homologous group which were increased from "possibly homologous" to "definitely homologous" to increase the consistency of ECOD based their strong homologous links to the SH3 domains.

The Lipocone Superfamily: A Unifying Theme In Metabolism Of Lipids, Peptidoglycan And Exopolysaccharides, Inter-Organismal Conflicts And Immunity

Wnt proteins are critical signaling molecules in developmental processes across animals. Despite intense study, their evolutionary roots have remained enigmatic. Using sensitive sequence analysis and structure modeling, we establish that the Wnts are part of a vast assemblage of domains, the Lipocone superfamily, defined here for the first time. It includes previously studied enzymatic domains like the phosphatidylserine synthases (PTDSS1/2) and the TelC toxin domain from Streptococcus intermedius , the enigmatic VanZ proteins, the animal Serum Amyloid A (SAA) and a further host of uncharacterized proteins in a total of 30 families. Though the metazoan Wnts are catalytically inactive, we present evidence for a conserved active site across this superfamily, versions of which are consistently predicted to operate on head groups of either phospholipids or polyisoprenoid lipids, catalyzing transesterification and phosphate-containing head group severance reactions. We argue that this superfamily originated as membrane proteins, with one branch (including Wnt and SAA) evolving into soluble versions. By comprehensively analyzing contextual information networks derived from comparative genomics, we establish that they act in varied functional contexts, including regulation of membrane lipid composition, extracellular polysaccharide biosynthesis, and biogenesis of bacterial outer-membrane components, like lipopolysaccharides. On multiple occasions, members of this superfamily, including the bacterial progenitors of Wnt and SAA, have been recruited as effectors in biological conflicts spanning inter-organismal interactions and anti-viral immunity in both prokaryotes and eukaryotes. These findings establish a unifying theme in lipid biochemistry, explain the origins of Wnt signaling and provide new leads regarding immunity across the tree of life.

DPAM-AI: a domain parser for AlphaFold models powered by artificial intelligence

MOTIVATION

Due to the breakthrough in protein structure prediction by AlphaFold, the scientific community has access to 200 million predicted protein structures with near-atomic accuracy from the AlphaFold protein structure DataBase (AFDB), covering nearly the entire protein universe. Segmenting these models into domains and classifying them into an evolutionary hierarchy hold tremendous potential for unraveling essential insights into protein function.

RESULTS

We introduce DPAM-AI, a Domain Parser for AlphaFold Models based on Artificial Intelligence. DPAM-AI utilizes a convolutional neural network trained with previously classified domains in the Evolutionary Classification Of protein Domains (ECOD) database. DPAM-AI integrates inter-residue distances, predicted aligned errors, and sequence and structural alignments to previously classified domains detected via sequence (HHsuite) and structural (Dali) similarity searches. DPAM-AI has demonstrated its power through rigorous tests, excelling in several benchmark sets compared to its predecessor, DPAM, and other recently published domain parsers, Merizo and Chainsaw. We applied DPAM-AI to representative AFDB models for proteins classified in Pfam. We obtained representative 3D structures for 18 487 (89%) of the 20 795 Pfam families. The remaining families either (i) belong to viral proteins that were excluded from AFDB or (ii) do not adopt globular 3D structures. Our structure-aware domain delineation uncovered a considerable fraction (15%) of Pfam domains containing multiple structural and evolutionary units and refined the boundaries for over half.

AVAILABILITY AND IMPLEMENTATION

Pfam and corresponding DPAM-AI domains are at http://prodata.swmed.edu/DPAM-pfam/. Our code is deposited at https://github.com/Jsauce5p/DPAM/tree/dpam_ai, and updates will be released through https://github.com/CongLabCode/DPAM.

Discovery and biochemical characterization of thermostable glycerol oxidases

Alditol oxidases are promising tools for the biocatalytic oxidation of glycerol to more valuable chemicals. By integrating in silico bioprospecting with cell-free protein synthesis and activity screening, an effective pipeline was developed to rapidly identify enzymes that are active on glycerol. Three thermostable alditol oxidases from Actinobacteria Bacterium, Streptomyces thermoviolaceus, and Thermostaphylospora chromogena active on glycerol were discovered. The characterization of these three flavoenzymes demonstrated their glycerol oxidation activities, preference for alkaline conditions, and excellent thermostabilities with melting temperatures higher than 75 °C. Structural elucidation of the alditol oxidase from Actinobacteria Bacterium highlighted a constellation of side chains that engage the substrate through several hydrogen bonds, a histidine residue covalently bound to the FAD prosthetic group, and a tunnel leading to the active site. Upon computational simulations of substrate binding, a double mutant targeting a residue pair at the tunnel entrance was created and found to display an improved thermal stability and catalytic efficiency for glycerol oxidation. The hereby described alditol oxidases form a valuable panel of oxidative biocatalysts that can perform regioselective oxidation of glycerol and other polyols. KEY POINTS: • Rapid pipeline designed to identify putative oxidases • Biochemical and structural characterization of alditol oxidases • Glycerol oxidation to more valuable derivatives.

Structural Classification Insights Into the Plant Defensive Peptides

This study presents a structural phylogenetic analysis of plant defensive peptides, revealing their evolutionary relationships, structural diversification, and functional adaptations. Utilizing a robust dataset comprising both experimental and predicted structures sourced from the RCSB Protein Data Bank and AlphaFold DB, we constructed a detailed phylogenetic tree to elucidate the distinct evolutionary paths of plant defensive peptide families. Our findings showcase the evolutionary intricacies of defensive peptides, highlighting their diversity and the conservation of key structural motifs critical to their antimicrobial or defensive functions. The results also underscore the adaptive significance of defensive peptides in plant evolution, highlighting their roles in responding to ecological pressures and pathogen interactions.

Protein structure alignment by Reseek improves sensitivity to remote homologs

MOTIVATION

Recent breakthroughs in protein fold prediction from amino acid sequences have unleashed a deluge of new structures, presenting new opportunities and challenges to bioinformatics.

RESULTS

Reseek is a novel protein structure alignment algorithm based on sequence alignment where each residue in the protein backbone is represented by a letter in a "mega-alphabet" of 85 899 345 920 (∼1011) distinct states. Reseek achieves substantially improved sensitivity to remote homologs compared to state-of-the-art methods including DALI, TMalign, and Foldseek, with comparable speed to Foldseek, the fastest previous method. Scaling to large databases of AI-predicted folds is analyzed. Foldseek E-values are shown to be under-estimated by several orders of magnitude, while Reseek E-values are in good agreement with measured error rates.

AVAILABILITY AND IMPLEMENTATION

https://github.com/rcedgar/reseek.

GTalign: spatial index-driven protein structure alignment, superposition, and search

With protein databases growing rapidly due to advances in structural and computational biology, the ability to accurately align and rapidly search protein structures has become essential for biological research. In response to the challenge posed by vast protein structure repositories, GTalign offers an innovative solution to protein structure alignment and search-an algorithm that achieves optimal superposition at high speeds. Through the design and implementation of spatial structure indexing, GTalign parallelizes all stages of superposition search across residues and protein structure pairs, yielding rapid identification of optimal superpositions. Rigorous evaluation across diverse datasets reveals GTalign as the most accurate among structure aligners while presenting orders of magnitude in speedup at state-of-the-art accuracy. GTalign's high speed and accuracy make it useful for numerous applications, including functional inference, evolutionary analyses, protein design, and drug discovery, contributing to advancing understanding of protein structure and function.

Structure-guided discovery of ancestral CRISPR-Cas13 ribonucleases

The RNA-guided ribonuclease CRISPR-Cas13 enables adaptive immunity in bacteria and programmable RNA manipulation in heterologous systems. Cas13s share limited sequence similarity, hindering discovery of related or ancestral systems. To address this, we developed an automated structural-search pipeline to identify an ancestral clade of Cas13 (Cas13an) and further trace Cas13 origins to defense-associated ribonucleases. Despite being one-third the size of other Cas13s, Cas13an mediates robust programmable RNA depletion and defense against diverse bacteriophages. However, unlike its larger counterparts, Cas13an uses a single active site for both CRISPR RNA processing and RNA-guided cleavage, revealing that the ancestral nuclease domain has two modes of activity. Discovery of Cas13an deepens our understanding of CRISPR-Cas evolution and expands opportunities for precision RNA editing, showcasing the promise of structure-guided genome mining.

The ABC toxin complex from Yersinia entomophaga can package three different cytotoxic components expressed from distinct genetic loci in an unfolded state: the structures of both shell and cargo

Bacterial ABC toxin complexes (Tcs) comprise three core proteins: TcA, TcB and TcC. The TcA protein forms a pentameric assembly that attaches to the surface of target cells and penetrates the cell membrane. The TcB and TcC proteins assemble as a heterodimeric TcB-TcC subcomplex that makes a hollow shell. This TcB-TcC subcomplex self-cleaves and encapsulates within the shell a cytotoxic `cargo' encoded by the C-terminal region of the TcC protein. Here, we describe the structure of a previously uncharacterized TcC protein from Yersinia entomophaga, encoded by a gene at a distant genomic location from the genes encoding the rest of the toxin complex, in complex with the TcB protein. When encapsulated within the TcB-TcC shell, the C-terminal toxin adopts an unfolded and disordered state, with limited areas of local order stabilized by the chaperone-like inner surface of the shell. We also determined the structure of the toxin cargo alone and show that when not encapsulated within the shell, it adopts an ADP-ribosyltransferase fold most similar to the catalytic domain of the SpvB toxin from Salmonella typhimurium. Our structural analysis points to a likely mechanism whereby the toxin acts directly on actin, modifying it in a way that prevents normal polymerization.

The Mla system and its role in maintaining outer membrane barrier function in Stenotrophomonas maltophilia

Stenotrophomonas maltophilia are ubiquitous Gram-negative bacteria found in both natural and clinical environments. It is a remarkably adaptable species capable of thriving in various environments, thanks to the plasticity of its genome and a diverse array of genes that encode a wide range of functions. Among these functions, one notable trait is its remarkable ability to resist various antimicrobial agents, primarily through mechanisms that regulate the diffusion across cell membranes. We have investigated the Mla ABC transport system of S. maltophilia, which in other Gram-negative bacteria is known to transport phospholipids across the periplasm and is involved in maintaining outer membrane homeostasis. First, we structurally and functionally characterized the periplasmic substrate-binding protein MlaC, which determines the specificity of this system. The predicted structure of the S. maltophilia MlaC protein revealed a hydrophobic cavity of sufficient size to accommodate the phospholipids commonly found in this species. Moreover, recombinant MlaC produced heterologously demonstrated the ability to bind phospholipids. Gene knockout experiments in S. maltophilia K279a revealed that the Mla system is involved in baseline resistance to antimicrobial and antibiofilm agents, especially those with divalent-cation chelating activity. Co-culture experiments with Pseudomonas aeruginosa also showed a significant contribution of this system to the cooperation between both species in the formation of polymicrobial biofilms. As suggested for other Gram-negative pathogenic microorganisms, this system emerges as an appealing target for potential combined antimicrobial therapies.

TM-search: An Efficient and Effective Tool for Protein Structure Database Search

The quickly increasing size of the Protein Data Bank is challenging biologists to develop a more scalable protein structure alignment tool for fast structure database search. Although many protein structure search algorithms and programs have been designed and implemented for this purpose, most require a large amount of computational time. We propose a novel protein structure search approach, TM-search, which is based on the pairwise structure alignment program TM-align and a new iterative clustering algorithm. Benchmark tests demonstrate that TM-search is 27 times faster than a TM-align full database search while still being able to identify ∼90% of all high TM-score hits, which is 2-10 times more than other existing programs such as Foldseek, Dali, and PSI-BLAST.

Insights into virulence: structure classification of the Vibrio parahaemolyticus RIMD mobilome

IMPORTANCE

The pandemic Vpar strain RIMD causes seafood-borne illness worldwide. Previous comparative genomic studies have revealed pathogenicity islands in RIMD that contribute to the success of the strain in infection. However, not all virulence determinants have been identified, and many of the proteins encoded in known pathogenicity islands are of unknown function. Based on the EOCD database, we used evolution-based classification of structure models for the RIMD proteome to improve our functional understanding of virulence determinants acquired by the pandemic strain. We further identify and classify previously unknown mobile protein domains as well as fast evolving residue positions in structure models that contribute to virulence and adaptation with respect to a pre-pandemic strain. Our work highlights key contributions of phage in mediating seafood born illness, suggesting this strain balances its avoidance of phage predators with its successful colonization of human hosts.

A Mechanistic Understanding of the Distinct Regio- and Chemoselectivity of Multifunctional P450s by Structural Comparison of IkaD and CftA Complexed with Common Substrates

Regio- and chemoselective C-H activation at multi-positions of a single molecule is fascinating but chemically challenging. The homologous cytochrome P450 enzymes IkaD and CftA catalyze multiple C-H oxidations on the same polycyclic tetramate macrolactam (PoTeM) ikarugamycin, with distinct regio- and chemoselectivity. Herein we provide mechanistic understanding of their functional differences by solving crystal structures of IkaD and CftA in complex with ikarugamycin and unnatural substrates. Distinct conformations of the F/G region in IkaD and CftA are found to differentiate the orientation of PoTeM substrates, by causing different binding patterns with polar moieties to determine site selection, oxidation order, and chemoselectivity. Fine-tuning the polar subpocket altered the regioselectivity of IkaD, indicating that substrate re-orientation by mutating residues distal to the oxidation site could serve as an important method in future engineering of P450 enzymes.

Ribosomal stalk-captured CARF-RelE ribonuclease inhibits translation following CRISPR signaling

Prokaryotic type III CRISPR-Cas antiviral systems employ cyclic oligoadenylate (cAn) signaling to activate a diverse range of auxiliary proteins that reinforce the CRISPR-Cas defense. Here we characterize a class of cAn-dependent effector proteins named CRISPR-Cas-associated messenger RNA (mRNA) interferase 1 (Cami1) consisting of a CRISPR-associated Rossmann fold sensor domain fused to winged helix-turn-helix and a RelE-family mRNA interferase domain. Upon activation by cyclic tetra-adenylate (cA4), Cami1 cleaves mRNA exposed at the ribosomal A-site thereby depleting mRNA and leading to cell growth arrest. The structures of apo-Cami1 and the ribosome-bound Cami1-cA4 complex delineate the conformational changes that lead to Cami1 activation and the mechanism of Cami1 binding to a bacterial ribosome, revealing unexpected parallels with eukaryotic ribosome-inactivating proteins.

Biochemical and Cellular Characterization of the Function of Fluorophosphonate-Binding Hydrolase H (FphH) in Staphylococcus aureus Support a Role in Bacterial Stress Response

The development of new treatment options for bacterial infections requires access to new targets for antibiotics and antivirulence strategies. Chemoproteomic approaches are powerful tools for profiling and identifying novel druggable target candidates, but their functions often remain uncharacterized. Previously, we used activity-based protein profiling in the opportunistic pathogen Staphylococcus aureus to identify active serine hydrolases termed fluorophosphonate-binding hydrolases (Fph). Here, we provide the first characterization of S. aureus FphH, a conserved, putative carboxylesterase (referred to as yvaK in Bacillus subtilis) at the molecular and cellular level. First, phenotypic characterization of fphH-deficient transposon mutants revealed phenotypes during growth under nutrient deprivation, biofilm formation, and intracellular survival. Biochemical and structural investigations revealed that FphH acts as an esterase and lipase based on a fold well suited to act on a small to long hydrophobic unbranched lipid group within its substrate and can be inhibited by active site-targeting oxadiazoles. Prompted by a previous observation that fphH expression was upregulated in response to fusidic acid, we found that FphH can deacetylate this ribosome-targeting antibiotic, but the lack of FphH function did not infer major changes in antibiotic susceptibility. In conclusion, our results indicate a functional role of this hydrolase in S. aureus stress responses, and hypothetical functions connecting FphH with components of the ribosome rescue system that are conserved in the same gene cluster across Bacillales are discussed. Our atomic characterization of FphH will facilitate the development of specific FphH inhibitors and probes to elucidate its physiological role and validity as a drug target.

Discovery of an Insect Neuroactive Helix Ring Peptide from Ant Venom

Ants are among the most abundant terrestrial invertebrate predators on Earth. To overwhelm their prey, they employ several remarkable behavioral, physiological, and biochemical innovations, including an effective paralytic venom. Ant venoms are thus cocktails of toxins finely tuned to disrupt the physiological systems of insect prey. They have received little attention yet hold great promise for the discovery of novel insecticidal molecules. To identify insect-neurotoxins from ant venoms, we screened the paralytic activity on blowflies of nine synthetic peptides previously characterized in the venom of Tetramorium bicarinatum. We selected peptide U11, a 34-amino acid peptide, for further insecticidal, structural, and pharmacological experiments. Insecticidal assays revealed that U11 is one of the most paralytic peptides ever reported from ant venoms against blowflies and is also capable of paralyzing honeybees. An NMR spectroscopy of U11 uncovered a unique scaffold, featuring a compact triangular ring helix structure stabilized by a single disulfide bond. Pharmacological assays using Drosophila S2 cells demonstrated that U11 is not cytotoxic, but suggest that it may modulate potassium conductance, which structural data seem to corroborate and will be confirmed in a future extended pharmacological investigation. The results described in this paper demonstrate that ant venom is a promising reservoir for the discovery of neuroactive insecticidal peptides.

Domain Architecture Based Methods for Comparative Functional Genomics Toward Therapeutic Drug Target Discovery

Genes duplicate, mutate, recombine, fuse or fission to produce new genes, or when genes are formed from de novo, novel functions arise during evolution. Researchers have tried to quantify the causes of these molecular diversification processes to know how these genes increase molecular complexity over a period of time, for instance protein domain organization. In contrast to global sequence similarity, protein domain architectures can capture key structural and functional characteristics, making them better proxies for describing functional equivalence. In Prokaryotes and eukaryotes it has proven that, domain designs are retained over significant evolutionary distances. Protein domain architectures are now being utilized to categorize and distinguish evolutionarily related proteins and find homologs among species that are evolutionarily distant from one another. Additionally, structural information stored in domain structures has accelerated homology identification and sequence search methods. Tools for functional protein annotation have been developed to discover, protein domain content, domain order, domain recurrence, and domain position as all these contribute to the prediction of protein functional accuracy. In this review, an attempt is made to summarise facts and speculations regarding the use of protein domain architecture and modularity to identify possible therapeutic targets among cellular activities based on the understanding their linked biological processes.

Phage SPO1 Protein Gp49 Is a Novel RNA Binding Protein That Is Involved in Host Iron Metabolism

Bacillus subtilis is a model organism for studying Gram-positive bacteria and serves as a cell factory in the industry for enzyme and chemical production. Additionally, it functions as a probiotic in the gastrointestinal tract, modulating the gut microbiota. Its lytic phage SPO1 is also the most studied phage among the genus Okubovrius, including Bacillus phage SPO1 and Camphawk. One of the notable features of SPO1 is the existence of a "host-takeover module", a cluster of 24 genes which occupies most of the terminal redundancy. Some of the gene products from the module have been characterized, revealing their ability to disrupt host metabolism by inhibiting DNA replication, RNA transcription, cell division, and glycolysis. However, many of the gene products which share limited similarity to known proteins remain under researched. In this study, we highlight the involvement of Gp49, a gene product from the module, in host RNA binding and heme metabolism-no observation has been reported in other phages. Gp49 folds into a structure that does not resemble any protein in the database and has a new putative RNA binding motif. The transcriptome study reveals that Gp49 primarily upregulates host heme synthesis which captures cytosolic iron to facilitate phage development.

Biochemical functions and structure of Caenorhabditis elegans ZK177.8 protein: Aicardi-Goutières syndrome SAMHD1 dNTPase ortholog

Mutations in sterile alpha motif domain and histidine-aspartate domain-containing protein 1 (SAMHD1) are found in a neurodevelopmental disorder, Aicardi-Goutières syndrome, and cancers, and SAMHD1, which is a deoxynucleoside triphosphate (dNTP) triphosphorylase, was identified as a myeloid-specific HIV-1 restriction factor. Here, we characterized the enzymology and structure of an SAMHD1 ortholog of Caenorhabditis elegans, ZK177.8, which also reportedly induces developmental defects upon gene knockdown. We found ZK177.8 protein is a dNTPase allosterically regulated by dGTP. The active site of ZK177.8 recognizes both 2' OH and triphosphate moieties of dNTPs but not base moiety. The dGTP activator induces the formation of the enzymatically active ZK177.8 tetramers, and ZK177.8 protein lowers cellular dNTP levels in a human monocytic cell line. Finally, ZK177.8 tetramers display very similar X-ray crystal structure with human and mouse SAMHD1s except that its lack of the canonical sterile alpha motif domain. This striking conservation in structure, function, and allosteric regulatory mechanism for the hydrolysis of the DNA building blocks supports their host developmental roles.

Recent progress in leptin signaling from a structural perspective and its implications for diseases

As a multi-potency cytokine, leptin not only plays a crucial role in controlling weight and energy homeostasis but also participates in the metabolic balance in the human body. Leptin is a small helical protein with a molecular weight of 16 kDa. It can interact with multiple subtypes of its receptors to initiate intracellular signal transduction and exerts physiological effects. Disturbances in leptin signaling may lead to obesity and a variety of metabolic diseases. Leptin was also found to be a critical factor in many diseases of the elderly. In this review, we focus on recent advances in the structural and molecular mechanisms of leptin signaling through its receptors with the aim of a deeper understanding of leptin-related diseases.

Identifying and profiling structural similarities between Spike of SARS-CoV-2 and other viral or host proteins with Machaon

Using protein structure to predict function, interactions, and evolutionary history is still an open challenge, with existing approaches relying extensively on protein homology and families. Here, we present Machaon, a data-driven method combining orientation invariant metrics on phi-psi angles, inter-residue contacts and surface complexity. It can be readily applied on whole structures or segments-such as domains and binding sites. Machaon was applied on SARS-CoV-2 Spike monomers of native, Delta and Omicron variants and identified correlations with a wide range of viral proteins from close to distant taxonomy ranks, as well as host proteins, such as ACE2 receptor. Machaon's meta-analysis of the results highlights structural, chemical and transcriptional similarities between the Spike monomer and human proteins, indicating a multi-level viral mimicry. This extended analysis also revealed relationships of the Spike protein with biological processes such as ubiquitination and angiogenesis and highlighted different patterns in virus attachment among the studied variants. Available at: https://machaonweb.com .

A biosynthetic aspartate N-hydroxylase performs successive oxidations by holding intermediates at a site away from the catalytic center

Nitrosuccinate is a biosynthetic building block in many microbial pathways. The metabolite is produced by dedicated L-aspartate hydroxylases that use NADPH and molecular oxygen as co-substrates. Here, we investigate the mechanism underlying the unusual ability of these enzymes to perform successive rounds of oxidative modifications. The crystal structure of Streptomyces sp. V2 L-aspartate N-hydroxylase outlines a characteristic helical domain wedged between two dinucleotide-binding domains. Together with NADPH and FAD, a cluster of conserved arginine residues forms the catalytic core at the domain interface. Aspartate is found to bind in an entry chamber that is close to but not in direct contact with the flavin. It is recognized by an extensive H-bond network that explains the enzyme's strict substrate-selectivity. A mutant designed to create steric and electrostatic hindrance to substrate binding disables hydroxylation without perturbing the NADPH oxidase side-activity. Critically, the distance between the FAD and the substrate is far too long to afford N-hydroxylation by the C4a-hydroperoxyflavin intermediate whose formation is confirmed by our work. We conclude that the enzyme functions through a catch-and-release mechanism. L-aspartate slides into the catalytic center only when the hydroxylating apparatus is formed. It is then re-captured by the entry chamber where it waits for the next round of hydroxylation. By iterating these steps, the enzyme minimizes the leakage of incompletely oxygenated products and ensures that the reaction carries on until nitrosuccinate is formed. This unstable product can then be engaged by a successive biosynthetic enzyme or undergoes spontaneous decarboxylation to produce 3-nitropropionate, a mycotoxin.

Structural and biochemical characterisation of Co2+-binding sites on serum albumins and their interplay with fatty acids

Serum albumin-Co²⁺ interactions are of clinical importance. They play a role in mediating the physiological effects associated with cobalt toxicity and are central to the albumin cobalt binding (ACB) assay for diagnosis of myocardial ischemia. To further understand these processes, a deeper understanding of albumin-Co²⁺ interactions is required. Here, we present the first crystallographic structures of human serum albumin (HSA; three structures) and equine serum albumin (ESA; one structure) in complex with Co²⁺. Amongst a total of sixteen sites bearing a cobalt ion across the structures, two locations were prominent, and they relate to metal-binding sites A and B. Site-directed mutagenesis and isothermal titration calorimetry (ITC) were employed to characterise sites on HSA. The results indicate that His9 and His67 contribute to the primary (putatively corresponding to site B) and secondary Co²⁺-binding sites (site A), respectively. The presence of additional multiple weak-affinity Co²⁺ binding sites on HSA was also supported by ITC studies. Furthermore, addition of 5 molar equivalents of the non-esterified fatty acid palmitate (C16:0) reduced the Co²⁺-binding affinity at both sites A and B. The presence of bound myristate (C14:0) in the HSA crystal structures provided insight into the fatty acid-mediated structural changes that diminish the affinity of the protein toward Co²⁺. Together, these data provide further support for the idea that ischemia-modified albumin corresponds to albumin with excessive fatty-acid loading. Collectively, our findings provide a comprehensive understanding of the molecular underpinnings governing Co²⁺ binding to serum albumin.

Reclassification of family A DNA polymerases reveals novel functional subfamilies and distinctive structural features

Family A DNA polymerases (PolAs) form an important and well-studied class of extant polymerases participating in DNA replication and repair. Nonetheless, despite the characterization of multiple subfamilies in independent, dedicated works, their comprehensive classification thus far is missing. We therefore re-examine all presently available PolA sequences, converting their pairwise similarities into positions in Euclidean space, separating them into 19 major clusters. While 11 of them correspond to known subfamilies, eight had not been characterized before. For every group, we compile their general characteristics, examine their phylogenetic relationships and perform conservation analysis in the essential sequence motifs. While most subfamilies are linked to a particular domain of life (including phages), one subfamily appears in Bacteria, Archaea and Eukaryota. We also show that two new bacterial subfamilies contain functional enzymes. We use AlphaFold2 to generate high-confidence prediction models for all clusters lacking an experimentally determined structure. We identify new, conserved features involving structural alterations, ordered insertions and an apparent structural incorporation of a uracil-DNA glycosylase (UDG) domain. Finally, genetic and structural analyses of a subset of T7-like phages indicate a splitting of the 3'-5' exo and pol domains into two separate genes, observed in PolAs for the first time.

TnpB structure reveals minimal functional core of Cas12 nuclease family

The widespread TnpB proteins of IS200/IS605 transposon family have recently emerged as the smallest RNA-guided nucleases capable of targeted genome editing in eukaryotic cells1,2. Bioinformatic analysis identified TnpB proteins as the likely predecessors of Cas12 nucleases3-5, which along with Cas9 are widely used for targeted genome manipulation. Whereas Cas12 family nucleases are well characterized both biochemically and structurally6, the molecular mechanism of TnpB remains unknown. Here we present the cryogenic-electron microscopy structures of the Deinococcus radiodurans TnpB-reRNA (right-end transposon element-derived RNA) complex in DNA-bound and -free forms. The structures reveal the basic architecture of TnpB nuclease and the molecular mechanism for DNA target recognition and cleavage that is supported by biochemical experiments. Collectively, these results demonstrate that TnpB represents the minimal structural and functional core of the Cas12 protein family and provide a framework for developing TnpB-based genome editing tools.

Ab Initio Modelling of the Structure of ToxA-like and MAX Fungal Effector Proteins

Pathogenic fungal diseases in crops are mediated by the release of effector proteins that facilitate infection. Characterising the structure of these fungal effectors is vital to understanding their virulence mechanisms and interactions with their hosts, which is crucial in the breeding of plant cultivars for disease resistance. Several effectors have been identified and validated experimentally; however, their lack of sequence conservation often impedes the identification and prediction of their structure using sequence similarity approaches. Structural similarity has, nonetheless, been observed within fungal effector protein families, creating interest in validating the use of computational methods to predict their tertiary structure from their sequence. We used Rosetta ab initio modelling to predict the structures of members of the ToxA-like and MAX effector families for which experimental structures are known to validate this method. An optimised approach was then used to predict the structures of phenotypically validated effectors lacking known structures. Rosetta was found to successfully predict the structure of fungal effectors in the ToxA-like and MAX families, as well as phenotypically validated but structurally unconfirmed effector sequences. Interestingly, potential new effector structural families were identified on the basis of comparisons with structural homologues and the identification of associated protein domains.

Molecular Structure of Phosphoserine Aminotransferase from Saccharomyces cerevisiae

Phosphoserine aminotransferase (PSAT) is a pyridoxal 5′-phosphate-dependent enzyme involved in the second step of the phosphorylated pathway of serine biosynthesis. PSAT catalyzes the transamination of 3-phosphohydroxypyruvate to 3-phosphoserine using L-glutamate as the amino donor. Although structural studies of PSAT have been performed from archaea and humans, no structural information is available from fungi. Therefore, to elucidate the structural features of fungal PSAT, we determined the crystal structure of Saccharomyces cerevisiae PSAT (ScPSAT) at a resolution of 2.8 Å. The results demonstrated that the ScPSAT protein was dimeric in its crystal structure. Moreover, the gate-keeping loop of ScPSAT exhibited a conformation similar to that of other species. Several distinct structural features in the halide-binding and active sites of ScPSAT were compared with its homologs. Overall, this study contributes to our current understanding of PSAT by identifying the structural features of fungal PSAT for the first time.

New biochemistry in the Rhodanese-phosphatase superfamily: emerging roles in diverse metabolic processes, nucleic acid modifications, and biological conflicts

The protein-tyrosine/dual-specificity phosphatases and rhodanese domains constitute a sprawling superfamily of Rossmannoid domains that use a conserved active site with a cysteine to catalyze a range of phosphate-transfer, thiotransfer, selenotransfer and redox activities. While these enzymes have been extensively studied in the context of protein/lipid head group dephosphorylation and various thiotransfer reactions, their overall diversity and catalytic potential remain poorly understood. Using comparative genomics and sequence/structure analysis, we comprehensively investigate and develop a natural classification for this superfamily. As a result, we identified several novel clades, both those which retain the catalytic cysteine and those where a distinct active site has emerged in the same location (e.g. diphthine synthase-like methylases and RNA 2' OH ribosyl phosphate transferases). We also present evidence that the superfamily has a wider range of catalytic capabilities than previously known, including a set of parallel activities operating on various sugar/sugar alcohol groups in the context of NAD+-derivatives and RNA termini, and potential phosphate transfer activities involving sugars and nucleotides. We show that such activities are particularly expanded in the RapZ-C-DUF488-DUF4326 clade, defined here for the first time. Some enzymes from this clade are predicted to catalyze novel DNA-end processing activities as part of nucleic-acid-modifying systems that are likely to function in biological conflicts between viruses and their hosts.

DPAM: A domain parser for AlphaFold models

The recent breakthroughs in structure prediction, where methods such as AlphaFold demonstrated near-atomic accuracy, herald a paradigm shift in structural biology. The 200 million high-accuracy models released in the AlphaFold Database are expected to guide protein science in the coming decades. Partitioning these AlphaFold models into domains and assigning them to an evolutionary hierarchy provide an efficient way to gain functional insights into proteins. However, classifying such a large number of predicted structures challenges the infrastructure of current structure classifications, including our Evolutionary Classification of protein Domains (ECOD). Better computational tools are urgently needed to parse and classify domains from AlphaFold models automatically. Here we present a Domain Parser for AlphaFold Models (DPAM) that can automatically recognize globular domains from these models based on inter-residue distances in 3D structures, predicted aligned errors, and ECOD domains found by sequence (HHsuite) and structural (Dali) similarity searches. Based on a benchmark of 18,759 AlphaFold models, we demonstrate that DPAM can recognize 98.8% of domains and assign correct boundaries for 87.5%, significantly outperforming structure-based domain parsers and homology-based domain assignment using ECOD domains found by HHsuite or Dali. Application of DPAM to the massive AlphaFold models will enable efficient classification of domains, providing evolutionary contexts and facilitating functional studies.

Canonical or noncanonical? Structural plasticity of serine protease-binding loops in Kunitz-STI protease inhibitors

The Kunitz-Soybean Trypsin Inhibitor (Kunitz-STI) family is a large family of proteins with most of its members being protease inhibitors. The versatility of the inhibitory profile and the structural plasticity of these proteins, make this family a promising scaffold for designing new multifunctional proteins. Historically, Kunitz-STI inhibitors have been classified as canonical serine protease inhibitors, but new inhibitors with novel inhibition mechanisms have been described in recent years. Different inhibition mechanisms could be the result of different evolutionary pathways. In the present work, we performed a structural analysis of all the crystallographic structures available for Kunitz-STI inhibitors to characterize serine protease-binding loop structural features and locations. Our study suggests a relationship between the conformation of serine protease-binding loops and the inhibition mechanism, their location in the β-trefoil fold, and the plant source of the inhibitors. The classical canonical inhibitors of this family are restricted to plants from the Fabales order and bind their targets via the β4-β5 loop, whereas serine protease-binding loops in inhibitors from other plants lie mainly in the β5-β6 and β9-β10 loops. In addition, we found that the β5-β6 loop is used to inhibit two different families of serine proteases through a steric blockade inhibition mechanism. This work will help to change the general perception that all Kunitz-STI inhibitors are canonical inhibitors and proteins with protease-binding loops adopting noncanonical conformations are exceptions. Additionally, our results will help in the identification of protease-binding loops in uncharacterized or newly discovered inhibitors, and in the design of multifunctional proteins.

A comprehensive survey of coronaviral main protease active site diversity in 3D: Identifying and analyzing drug discovery targets in search of broad specificity inhibitors for the next coronavirus pandemic

Although the rapid development of therapeutic responses to combat SARS-CoV-2 represents a great human achievement, it also demonstrates untapped potential for advanced pandemic preparedness. Cross-species efficacy against multiple human coronaviruses by the main protease (MPro) inhibitor nirmatrelvir raises the question of its breadth of inhibition and our preparedness against future coronaviral threats. Herein, we describe sequence and structural analyses of 346 unique MPro enzymes from all coronaviruses represented in the NCBI Virus database. Cognate substrates of these representative proteases were inferred from their polyprotein sequences. We clustered MPro sequences based on sequence identity and AlphaFold2-predicted structures, showing approximate correspondence with known viral subspecies. Predicted structures of five representative MPros bound to their inferred cognate substrates showed high conservation in protease:substrate interaction modes, with some notable differences. Yeast-based proteolysis assays of the five representatives were able to confirm activity of three on inferred cognate substrates, and demonstrated that of the three, only one was effectively inhibited by nirmatrelvir. Our findings suggest that comprehensive preparedness against future potential coronaviral threats will require continued inhibitor development. Our methods may be applied to candidate coronaviral MPro inhibitors to evaluate in advance the breadth of their inhibition and identify target coronaviruses potentially meriting advanced development of alternative countermeasures.

DALI shines a light on remote homologs: One hundred discoveries

Structural comparison reveals remote homology that often fails to be detected by sequence comparison. The DALI web server (http://ekhidna2.biocenter.helsinki.fi/dali) is a platform for structural analysis that provides database searches and interactive visualization, including structural alignments annotated with secondary structure, protein families and sequence logos, and 3D structure superimposition supported by color-coded sequence and structure conservation. Here, we are using DALI to mine the AlphaFold Database version 1, which increased the structural coverage of protein families by 20%. We found 100 remote homologous relationships hitherto unreported in the current reference database for protein domains, Pfam 35.0. In particular, we linked 35 domains of unknown function (DUFs) to the previously characterized families, generating a functional hypothesis that can be explored downstream in structural biology studies. Other findings include gene fusions, tandem duplications, and adjustments to domain boundaries. The evidence for homology can be browsed interactively through live examples on DALI's website.

Bioinformatical Approaches to the Discovery and Classification of Novel Deubiquitinases

Deubiquitinating enzymes (DUBs) are active at multiple levels of the eukaryotic ubiquitin system. DUBs are important for ubiquitin activation and maintaining cellular ubiquitin levels but can also edit or dissolve ubiquitin chains or deconjugate ubiquitin from substrates. Eukaryotic DUBs can be grouped into seven molecular classes, most of which enzymes are cysteine proteases assuming the papain fold. In recent years, an ever-increasing number of pathogen-encoded DUBs have been characterized, which are active inside the host cell and help the pathogens to evade the defense response. At first sight, bacterial and viral DUBs appear to be very different from their eukaryotic counterparts, making them hard to identify by bioinformatic methods. However, apart from very few exceptions, bacterial and viral DUBs are distantly related to eukaryotic DUB classes and possess several hallmarks that can be used to identify high-confidence DUB candidates from pathogen genomes - even in the complete absence of biochemical or functional annotation. This chapter addresses bioinformatical DUB discovery approaches based on a previously published analysis of DUB evolution. The core set of bioinformatical tools required for this endeavor are freely accessible and do not require a particular bioinformatics infrastructure.

Bacterial crystalline cellulose secretion via a supramolecular BcsHD scaffold

Cellulose, the most abundant biopolymer on Earth, is not only the predominant constituent of plants but also a key extracellular polysaccharide in the biofilms of many bacterial species. Depending on the producers, chemical modifications, and three-dimensional assemblies, bacterial cellulose (BC) can present diverse degrees of crystallinity. Highly ordered, or crystalline, cellulose presents great economical relevance due to its ever-growing number of biotechnological applications. Even if some acetic acid bacteria have long been identified as BC superproducers, the molecular mechanisms determining the secretion of crystalline versus amorphous cellulose remain largely unknown. Here, we present structural and mechanistic insights into the role of the accessory subunits BcsH (CcpAx) and BcsD (CesD) that determine crystalline BC secretion in the Gluconacetobacter lineage. We show that oligomeric BcsH drives the assembly of BcsD into a supramolecular cytoskeletal scaffold that likely stabilizes the cellulose-extruding synthase nanoarrays through an unexpected inside-out mechanism for secretion system assembly.

Rep15 interacts with several Rab GTPases and has a distinct fold for a Rab effector

In their GTP-bound (active) form, Rab proteins interact with effector proteins that control downstream signaling. One such Rab15 effector is Rep15, which is known to have a role in receptor recycling from the endocytic recycling compartment but otherwise remains poorly characterized. Here, we report the characterization of the Rep15:Rab15 interaction and identification of Rab3 paralogs and Rab34 as Rep15 interacting partners from a yeast two-hybrid assay. Biochemical validation of the interactions is presented and crystal structures of the Rep15:Rab3B and Rep15:Rab3C complexes provide additional mechanistic insight. We find that Rep15 adopts a globular structure that is distinct from other reported Rab15, Rab3 and Rab34 effectors. Structure-based mutagenesis experiments explain the Rep15:Rab interaction specificity. Rep15 depletion in U138MG glioblastoma cells impairs cell proliferation, cell migration and receptor recycling, underscoring the need for further clarification of the role of Rep15 in cancer.

A ShK-like Domain from Steinernema carpocapsae with Bioinsecticidal Potential

Entomopathogenic nematodes are used as biological control agents against a broad range of insect pests. We ascribed the pathogenicity of these organisms to the excretory/secretory products (ESP) released by the infective nematode. Our group characterized different virulence factors produced by Steinernema carpocapsae that underlie its success as an insect pathogen. A novel ShK-like peptide (ScK1) from this nematode that presents high sequence similarity with the ShK peptide from a sea anemone was successfully produced recombinantly in Escherichia coli. The secondary structure of ScK1 appeared redox-sensitive, exhibiting a far-UV circular dichroism spectrum consistent with an alpha-helical secondary structure. Thermal denaturation of the ScK1 allowed estimating the melting temperature to 59.2 ± 0.1 °C. The results from toxicity assays using Drosophila melanogaster as a model show that injection of this peptide can kill insects in a dose-dependent manner with an LD₅₀ of 16.9 µM per adult within 24 h. Oral administration of the fusion protein significantly reduced the locomotor activity of insects after 48 h (p < 0.05, Tukey's test). These data show that this nematode expresses insecticidal peptides with potential as next-generation insecticides.

Apprehending the NAD+-ADPr-Dependent Systems in the Virus World

NAD+ and ADP-ribose (ADPr)-containing molecules are at the interface of virus-host conflicts across life encompassing RNA processing, restriction, lysogeny/dormancy and functional hijacking. We objectively defined the central components of the NAD+-ADPr networks involved in these conflicts and systematically surveyed 21,191 completely sequenced viral proteomes representative of all publicly available branches of the viral world to reconstruct a comprehensive picture of the viral NAD+-ADPr systems. These systems have been widely and repeatedly exploited by positive-strand RNA and DNA viruses, especially those with larger genomes and more intricate life-history strategies. We present evidence that ADP-ribosyltransferases (ARTs), ADPr-targeting Macro, NADAR and Nudix proteins are frequently packaged into virions, particularly in phages with contractile tails (Myoviruses), and deployed during infection to modify host macromolecules and counter NAD+-derived signals involved in viral restriction. Genes encoding NAD+-ADPr-utilizing domains were repeatedly exchanged between distantly related viruses, hosts and endo-parasites/symbionts, suggesting selection for them across the virus world. Contextual analysis indicates that the bacteriophage versions of ADPr-targeting domains are more likely to counter soluble ADPr derivatives, while the eukaryotic RNA viral versions might prefer macromolecular ADPr adducts. Finally, we also use comparative genomics to predict host systems involved in countering viral ADP ribosylation of host molecules.

Organism-specific differences in the binding of ketoprofen to serum albumin

Serum albumin is a circulatory transport protein that has a highly conserved sequence and structure across mammalian organisms. Its ligand-binding properties are of importance as albumin regulates the pharmacokinetics of many drugs. Due to the high degree of structural conservation between mammalian albumins, nonhuman albumins such as bovine serum albumin or animal models are often used to understand human albumin-drug interactions. Ketoprofen is a popular nonsteroidal anti-inflammatory drug that is transported by albumin. Here, it is revealed that ketoprofen exhibits different binding-site preferences when interacting with human serum albumin compared with other mammalian albumins, despite the conservation of binding sites across species. The reasons for the observed differences were explored, including identifying ketoprofen binding determinants at specific sites and the influence of fatty acids and other ligands on drug binding. The presented results reveal that the drug-binding properties of albumins cannot easily be predicted based only on a complex of albumin from another organism and the conservation of drug sites between species. This work shows that understanding organism-dependent differences is essential for assessing the suitability of particular albumins for structural or biochemical studies.

Structural and Biochemical Characterization of a Nonbinding SusD-Like Protein Involved in Xylooligosaccharide Utilization by an Uncultured Human Gut Bacteroides Strain

In the human gut microbiota, Bacteroidetes break down dietary and endogenous glycosides through highly specific polysaccharide utilization loci (PULs). PULs encode a variety of sensor regulators, binding proteins, transporters, and carbohydrate-active enzymes (CAZymes). Surface glycan-binding proteins (SGBPs) are essential for the efficient capture of the glycosides present on the cell surface, providing Bacteroidetes with a competitive advantage in colonizing their habitats. Here, we present the functional and structural characterization of a SusD-like protein encoded by a xylooligosaccharide (XOS) PUL from an uncultured human gut Bacteroides strain. This locus is also conserved in Bacteroides vulgatus, thereby providing new mechanistic insights into the role of SGBPs in the metabolism of dietary fiber of importance for gut health. Various in vitro analyses, including saturation transfer difference nuclear magnetic resonance (STD-NMR) spectroscopy, revealed that the SusD-like protein cannot bind to the cognate substrate of the XOS PUL, although its presence is essential for the PUL to function. Analysis of the crystal structure of the SusD-like protein reveals an unfolded binding surface and the absence or inappropriate orientation of several key residues compared with other known SusD-like structures. These results highlight the critical role of the SusD-like protein in the transport of oligosaccharides and provide fundamental knowledge about the structure-function of SusC/D-like transporters, revealing that the binding specificity of SusD-like SGBPs does not necessarily reflect the uptake specificity of the transporter.

IMPORTANCE The metabolization of dietary fiber is a crucial function for many gut bacteria, especially Bacteroidetes, which are particularly well adapted for recognizing, binding, transporting, and degrading glycosides. In this study, we report the functional and structural characterization of a SusD-like protein involved in xylooligosaccharide utilization by an uncultured gut Bacteroides strain. We demonstrate that while this protein is structurally similar to many canonical Bacteroidetes surface glycan-binding proteins, it cannot bind the substrate taken up by the cognate SusC-like transporter. This lack of binding might be explained by the absence of several key residues known to be involved in oligosaccharide binding and/or the possible necessity of the SusC-like protein to be present to create a cooperative binding site. The term “surface glycan-binding proteins” generally used for SusD-like proteins is thus not generic. Overall, this study allowed us to revisit the concept of glycoside utilization by Bacteroidetes, in particular those strains that feed on the short fibers naturally present in some dietary compounds or on the leftovers of other microbes.