Comparison Of Structures Research Articles

Cryo-EM structure of cadmium-bound human ABCB6

ATP-binding cassette transporter B6 (ABCB6), a protein essential for heme biosynthesis in mitochondria, also functions as a heavy metal efflux pump. Here, we present cryo-electron microscopy structures of human ABCB6 bound to a cadmium Cd(II) ion in the presence of antioxidant thiol peptides glutathione (GSH) and phytochelatin 2 (PC2) at resolutions of 3.2 and 3.1 Å, respectively. The overall folding of the two structures resembles the inward-facing apo state but with less separation between the two halves of the transporter. Two GSH molecules are symmetrically bound to the Cd(II) ion in a bent conformation, with the central cysteine protruding towards the metal. The N-terminal glutamate and C-terminal glycine of GSH do not directly interact with Cd(II) but contribute to neutralizing positive charges of the binding cavity by forming hydrogen bonds and van der Waals interactions with nearby residues. In the presence of PC2, Cd(II) binding to ABCB6 is similar to that observed with GSH, except that two cysteine residues of each PC2 molecule participate in Cd(II) coordination to form a tetrathiolate. Structural comparison of human ABCB6 and its homologous Atm-type transporters indicate that their distinct substrate specificity might be attributed to variations in the capping residues situated at the top of the substrate-binding cavity.

Electrochemical study and structural comparison of Ni electrodepositions on W/Si and Cr/C multilayered structure films

The Ni electrodeposition combined with multilayered structure film is a promising strategy in modern optical manufacturing, while less effort has been devoted to comprehending the electrochemical reaction process, which is essential for their practical applications. In view of this, the initial reduction dynamics and nucleation mechanisms of Ni electrodepositions on multilayer W/Si and Cr/C films were analyzed in this work, and the morphological, crystal, and mechanical characteristics of produced Ni electrodeposits were further determined and compared. The results show that the considerably irregular crystals accompanied by high tensile stress of 119.5 MPa were formed for the Ni electrodeposit on W/Si film, which were mainly attributed to the progressive nucleation process with more severe side reaction of hydrogen evolution. By contrast, the instantaneous nucleation mode with lower reduction resistance were revealed for the Ni electrodeposition on Cr/C film, which presented a comparatively fine–grained texture, less roughness, and smaller stress structure. To summarize, the more stable electrochemical reaction process and improved structure uniformity are obtained for the Ni electrodeposition on metal/C–based film, which offers a theoretical guidance for optimized fabrication of multilayer optical devices in extreme ultraviolet, x-ray, and neutron focusing fields.

Structural basis for pegRNA-guided reverse transcription by a prime editor

The prime editor system composed of Streptococcus pyogenes Cas9 nickase (nSpCas9) and engineered Moloney murine leukaemia virus reverse transcriptase (M-MLV RT) collaborates with a prime editing guide RNA (pegRNA) to facilitate a wide variety of precise genome edits in living cells1. However, owing to a lack of structural information, the molecular mechanism of pegRNA-guided reverse transcription by the prime editor remains poorly understood. Here we present cryo-electron microscopy structures of the SpCas9–M-MLV RTΔRNaseH–pegRNA–target DNA complex in multiple states. The termination structure, along with our functional analysis, reveals that M-MLV RT extends reverse transcription beyond the expected site, resulting in scaffold-derived incorporations that cause undesired edits at the target loci. Furthermore, structural comparisons among the pre-initiation, initiation and elongation states show that M-MLV RT remains in a consistent position relative to SpCas9 during reverse transcription, whereas the pegRNA–synthesized DNA heteroduplex builds up along the surface of SpCas9. On the basis of our structural insights, we rationally engineered pegRNA variants and prime-editor variants in which M-MLV RT is fused within SpCas9. Collectively, our findings provide structural insights into the stepwise mechanism of prime editing, and will pave the way for the development of a versatile prime editing toolbox.

Structural and functional comparisons in cognitive impairments in patients with multiple sclerosis

Background. Multiple sclerosis (MS) is an inflammatory demyelinating and neurodegenerative disease characterized by a variety of neurological symptoms. Cognitive impairment is an important clinical aspect of MS and require careful interviewing and neuropsychological testing to detect it. Contrast-enhanced magnetic resonance imaging (MRI) is the primary diagnostic method in MS, which helps confirm the presence and assess the extent of structural damage to the brain and spinal cord. The purpose of the study was to determine the frequency and severity of cognitive impairment in patients with relapsing-remitting multiple sclerosis, taking into account the localization of brain lesions according to MRI. Materials and methods. Seventy-two patients with a diagnosis of relapsing-remitting MS according to the McDonald criteria (2017) were examined. All of them underwent a thorough neurolo-gical, neuropsychological, and instrumental examination. The average duration of the disease was 8.2 ± 0.8 years. The average score on the Expanded Disability Status Scale was 3.38 ± 0.18 points. Symbol Digit Modalities Test (SDMT), Paced Auditory Serial Addition Test 3 (PASAT-3), and Montreal Cognitive Assessment (MoСA) were used to assess the neuropsychological status of patients. All participants underwent a 1.5T MRI of the brain with dotavist contrast enhancement. Results. A thorough survey of examined patients with MS revealed the presence of complaints of cognitive decline in 91.67 % of cases (66 patients). The average score on the SDMT was 32.6 ± 1.6 (controls 57.1 ± 0.9), on the PASAT-3 — 30.3 ± 1.8 (controls 56.8 ± 0.5), the evaluation score on the MoСA was 22.4 ± ± 0.5 points compared to the control group (28.4 ± 0.2 points). The conducted correlation analysis revealed statistically significant negative correlations in the corpus callosum (MoCA: r = –0.255; SDMT: r = –0.263; PASAT-3: r = –0.171; p < 0.05) and in the brainstem (MoCA: r = –0.191; SDMT: r = –0.209; PASAT-3: r = –0.214; p < 0.05). The results of the analysis of variance confirmed the correlations described above between the localization of brain lesions and the results of neuropsychological testing and revealed statistically significant differences in the scores on the MoCA and SDMT depending on the localization of lesions (MoCA: F(14, 57) = 5.052, p < 0.001; SDMT: F(14, 57) = 2.609, p < 0.05). Conclusions. Patients with relapsing-remitting multiple sclerosis quite often have cognitive impairment, which is confirmed by the results of neuropsychological testing. Correlation analysis revealed a significant negative relationship between the localization of foci in the corpus callosum and the brainstem and cognitive decline according to the results of tests (MoCA, SDMT, PASAT-3). The results of our study confirm the presence of structural and functional connections between the localization of focal brain lesions and the development of cognitive disorders, which has important diagnostic and prognostic value.

Study and Analysis of Steel, RCC, and Composite Structure Comparison

In India, plain concrete is a common building material, especially for medium- and low-rise buildings. Even while steel is still widely used in high-rise structures and composite construction is less frequent, it's possible that composite construction could prove more beneficial in these projects. Reinforced concrete is often used in construction projects. Steel beams are put into concrete to make reinforced concrete, an efficient composite material. The distinguishing feature of composite construction is the secure joining and bending of two load-bearing structural elements into a single piece. When compared to RCC most steel frames, composite constructions are considered to be some of the least expensive and transient building materials. The main component of a composite construction is an I-section column embedded or encased in building materials, or a tube of steel filled with steel and concrete. Composed of cold steel plates plus mortar, Part I consists of a beam plus a plate for the deck. The beams are connected to the top slab using fire-resistant and robust shear connections. Keywords— Steel Concrete Composite Building, RCC building, Seismic Analysis etc.

High-resolution in situ structures of mammalian respiratory supercomplexes

Mitochondria play a pivotal part in ATP energy production through oxidative phosphorylation, which occurs within the inner membrane through a series of respiratory complexes1–4. Despite extensive in vitro structural studies, determining the atomic details of their molecular mechanisms in physiological states remains a major challenge, primarily because of loss of the native environment during purification. Here we directly image porcine mitochondria using an in situ cryo-electron microscopy approach. This enables us to determine the structures of various high-order assemblies of respiratory supercomplexes in their native states. We identify four main supercomplex organizations: I1III2IV1, I1III2IV2, I2III2IV2 and I2III4IV2, which potentially expand into higher-order arrays on the inner membranes. These diverse supercomplexes are largely formed by ‘protein–lipids–protein’ interactions, which in turn have a substantial impact on the local geometry of the surrounding membranes. Our in situ structures also capture numerous reactive intermediates within these respiratory supercomplexes, shedding light on the dynamic processes of the ubiquinone/ubiquinol exchange mechanism in complex I and the Q-cycle in complex III. Structural comparison of supercomplexes from mitochondria treated under different conditions indicates a possible correlation between conformational states of complexes I and III, probably in response to environmental changes. By preserving the native membrane environment, our approach enables structural studies of mitochondrial respiratory supercomplexes in reaction at high resolution across multiple scales, from atomic-level details to the broader subcellular context.

Discovery, Structure, and Engineering of a cis‐Geranylfarnesyl Diphosphate Synthase

Abstractcis‐Prenyltransferases (cis‐PTs) catalyze the sequential head‐to‐tail condensation of isopentenyl diphosphate (IPP) to allylic diphosphates, producing mixed E–Z prenyl diphosphates of varying lengths; however, the specific enzymes synthesizing cis‐C25 prenyl diphosphates have not been identified. Herein, we present the discovery and characterization of a cis‐geranylfarnesyl diphosphate synthase (ScGFPPS) from Streptomyces clavuligerus. This enzyme demonstrates high catalytic proficiency in generating six distinct cis‐polyisoprenoids, including three C25 and three C20 variants. We determined the crystal structure of ScGFPPS. Additionally, we unveil the crystal structure of nerylneryl diphosphate synthase (NNPS), known for synthesizing an all‐cis‐C20 polyisoprenoid. Comparative structural analysis of ScGFPPS and NNPS has identified key differences that influence product specificity. Through site‐directed mutagenesis, we have identified eight single mutations that significantly refine the selectivity of ScGFPPS for cis‐polyisoprenoids. Our findings not only expand the functional spectrum of cis‐PTs but also provide a structural comparison strategy in cis‐PTs engineering.

Discovery, Structure, and Engineering of a cis-Geranylfarnesyl Diphosphate Synthase.

cis-Prenyltransferases (cis-PTs) catalyze the sequential head-to-tail condensation of isopentenyl diphosphate (IPP) to allylic diphosphates, producing mixed E-Z prenyl diphosphates of varying lengths; however, the specific enzymes synthesizing cis-C25 prenyl diphosphates have not been identified. Herein, we present the discovery and characterization of a cis-geranylfarnesyl diphosphate synthase (ScGFPPS) from Streptomyces clavuligerus. This enzyme demonstrates high catalytic proficiency in generating six distinct cis-polyisoprenoids, including three C25 and three C20 variants. We determined the crystal structure of ScGFPPS. Additionally, we unveil the crystal structure of nerylneryl diphosphate synthase (NNPS), known for synthesizing an all-cis-C20 polyisoprenoid. Comparative structural analysis of ScGFPPS and NNPS has identified key differences that influence product specificity. Through site-directed mutagenesis, we have identified eight single mutations that significantly refine the selectivity of ScGFPPS for cis-polyisoprenoids. Our findings not only expand the functional spectrum of cis-PTs but also provide a structural comparison strategy in cis-PTs engineering.

Locally acting dermatology drug products: Pharmaco-analytic considerations for bioequivalence

Bioequivalence determinations for locally acting dermatology drug products rely on assessing product sameness thru physicochemical composition and structure comparison, comparing the concentration of the active ingredient at the putative site of action, or comparing the clinical performance of the test (would-be generic) and reference products. Topical product action on cutaneous disease may be confounded by the action of excipients and are also subject to the inherent variability of how product may interact with the skin, including thermodynamic factors such as evaporation, spreadability, and interaction with the local environment such as heat and light and skin moisture.

Integration of Semantic and Topological Structural Similarity Comparison for Entity Alignment without Pre-Training

Entity alignment (EA) is a critical task in integrating diverse knowledge graph (KG) data and plays a central role in data-driven AI applications. Traditional EA approaches rely on entity embeddings, but their effectiveness is limited by scarce KG input data and representation learning techniques. Large language models have shown promise, but face challenges such as high hardware requirements, large model sizes and computational inefficiency, which limit their applicability. To overcome these limitations, we propose an entity-alignment model that compares the similarity between entities by capturing both semantic and topological information to enable the alignment of entities with high similarity. First, we analyze descriptive information to quantify semantic similarity, including individual features such as types and attributes. Then, for topological analysis, we introduce four conditions based on graph connectivity and structural patterns to determine subgraph similarity within three hops of the entity’s neighborhood, thereby improving accuracy. Finally, we integrate semantic and topological similarity using a weighted approach that considers dataset features. Our model requires no pre-training and is designed to be compact and generalizable to different datasets. Experimental results on four standard EA datasets validate the effectiveness of our proposed model.

The complete catalog of antimicrobial resistance secondary active transporters in Clostridioides difficile: evolution and drug resistance perspective

Secondary active transporters shuttle substrates across eukaryotic and prokaryotic membranes, utilizing different electrochemical gradients. They are recognized as one of the antimicrobial efflux pumps among pathogens. While primary active transporters within the genome of C. difficile 630 have been completely cataloged, the systematical study of secondary active transporters remains incomplete. Here, we not only identify secondary active transporters but also disclose their evolution and role in drug resistance in C. difficile 630. Our analysis reveals that C. difficile 630 carries 147 secondary active transporters belonging to 27 (super)families. Notably, 50 (34%) of them potentially contribute to antimicrobial resistance (AMR). AMR-secondary active transporters are structurally classified into five (super)families: the p-aminobenzoyl-glutamate transporter (AbgT), drug/metabolite transporter (DMT) superfamily, major facilitator (MFS) superfamily, multidrug and toxic compound extrusion (MATE) family, and resistance-nodulation-division (RND) family. Surprisingly, complete RND genes found in C. difficile 630 are likely an evolutionary leftover from the common ancestor with the diderm. Through protein structure comparisons, we have potentially identified six novel AMR-secondary active transporters from DMT, MATE, and MFS (super)families. Pangenome analysis revealed that half of the AMR-secondary transporters are accessory genes, which indicates an important role in adaptive AMR function rather than innate physiological homeostasis. Gene expression profile firmly supports their ability to respond to a wide spectrum of antibiotics. Our findings highlight the evolution of AMR-secondary active transporters and their integral role in antibiotic responses. This marks AMR-secondary active transporters as interesting therapeutic targets to synergize with other antibiotic activity.

Non-prime- and prime-side profiling of Pro-Pro endopeptidase specificity using synthetic combinatorial peptide libraries and mass spectrometry.

A group of bacterial proteases, the Pro-Pro endopeptidases (PPEPs), possess the unique ability to hydrolyze proline-proline bonds in proteins. Since a protease's function is largely determined by its substrate specificity, methods that can extensively characterize substrate specificity are valuable tools for protease research. Previously, we achieved an in-depth characterization of PPEP prime-side specificity. However, PPEP specificity is also determined by the non-prime-side residues in the substrate. To gain a more complete insight into the determinants of PPEP specificity, we characterized the non-prime- and prime-side specificity of various PPEPs using a combination of synthetic combinatorial peptide libraries and mass spectrometry. With this approach, we deepened our understanding of the P3-P3' specificities of PPEP-1 and PPEP-2, while identifying the endogenous substrate of PPEP-2 as the most optimal substrate in our library data. Furthermore, by employing the library approach, we investigated the altered specificity of mutants of PPEP-1 and PPEP-2. Additionally, we characterized a novel PPEP from Anoxybacillus tepidamans, which we termed PPEP-4. Based on structural comparisons, we hypothesized that PPEP-4 displays a PPEP-1-like prime-side specificity, which was substantiated by the experimental data. Intriguingly, another putative PPEP from Clostridioides difficile, CD1597, did not display Pro-Pro endoproteolytic activity. Collectively, we characterized PPEP specificity in detail using our robust peptide library method and, together with additional structural information, provide more insight into the intricate mechanisms that govern protease specificity.

Biochemical, Bioinformatic, and Structural Comparisons of Transketolases and Position of Human Transketolase in the Enzyme Evolution.

Transketolases (TKs) are key enzymes of the pentose phosphate pathway, regulating several other critical pathways in cells. Considering their metabolic importance, TKs are expected to be conserved throughout evolution. However, Tittmann et al. (J Biol Chem, 2010, 285(41): 31559-31570) demonstrated that Homo sapiens TK (hsTK) possesses several structural and kinetic differences compared to bacterial TKs. Here, we study 14 TKs from pathogenic bacteria, fungi, and parasites and compare them with hsTK using biochemical, bioinformatic, and structural approaches. For this purpose, six new TK structures are solved by X-ray crystallography, including the TK of Plasmodium falciparum. All of these TKs have the same general fold as bacterial TKs. This comparative study shows that hsTK greatly differs from TKs from pathogens in terms of enzymatic activity, spatial positions of the active site, and monomer-monomer interface residues. An ubiquitous structural pattern is identified in all TKs as a six-residue histidyl crown around the TK cofactor (thiamine pyrophosphate), except for hsTK containing only five residues in the crown. Residue mapping of the monomer-monomer interface and the active site reveals that hsTK contains more unique residues than other TKs. From an evolutionary standpoint, TKs from animals (including H. sapiens) and Schistosoma sp. belong to a distinct structural group from TKs of bacteria, plants, fungi, and parasites, mostly based on a different linker between domains, raising hypotheses regarding evolution and regulation.

The rearrangement features and phylogenetic signals of mitochondrial genomes of gall midge subfamily Cecidomyiinae (Diptera: Cecidomyiidae) with first complete mitogenome of an economically important mango gall midge pest, Procontarina fructiculi from Guangxi, China

ABSTRACT In this study, we obtained the first complete mitochondrial genome of Procontarina fructiculi, an important mango gall midge pest from Guangxi, China. The mitogenome of P. fructiculi was sequenced and annotated for the first time, and compared with all the published and annotated data of Cecidomyiidae species to summarise the gall midge organisation and rearrangement features of mitochondrial genomes with phylogenetic analysis. The comparison of gall midge mitochondrial genome structure shows that the rearrangement of the mitochondrial gene structure is very common, and most rearrangements are embodied in rearrangement in the order of tRNAs. The phylogenetic results based on the maximum likelihood (ML) and Bayesian inference (BI) methods both highly supported the monophyly of Cecidomyiinae. Cecidomyiinae can be divided into two distinct clades (except Cecidomyiidae sp. 3): A: (Mayetiola destructor + Rhopalomyia pomum) and B: (Asphondylia rosetta + ((Procontarinia fructiculi + Orseolia oryzae) + ((Cecidomyiidae sp. 1 + Aphidoletes aphidimyza) + Cecidomyiidae sp. 2))). Based on the above results, some phylogenetic signals in rearrangement have been found in the mitochondrial genome structure of Cecidomyiinae for the first time.

СТРУКТУРНАЯ ОРГАНИЗАЦИЯ МОЛЕКУЛ СОЙМОРФИНОВ

The conformational capabilities of soymorphine-5 (Thr1-Pro2-Phe3-Val4-Val5-NH2), soymorphine-6 (Tyr1-Pro2-Phe3-Val4-Val5-Asn6-NH2) and soymorphine-7 (Tyr1- Pro2-Tyr3-Val4-Val5-Asn6-Ala7-NH2) molecules have been studied by the method of theoretical conformational analysis. The potential function of the system is chosen as the sum of non-valence, electrostatic and torsion interactions and the energy of hydrogen bonds. The low-energy conformations of soymorphine-5, soymorphine-6 and soymorphine-7 molecules were found, the dihedral angles of the main and side chains of amino acid residues that make up the molecule were found, and the energy of intra- and interresidual interactions was estimated. Thus, the spatial structure of soymorphine-5, soymorphine-6 and soymorphine-7 molecules can be represented by eight structural types. It can be assumed that the molecules perform their physiological functions in these structures. Comparison of the low-energy structures of soymorphins shows that in all molecules the first four low-energy conformations are representatives of the structural types efef, efee, efff, effe for soymorphine-5, effff, efeff, efffe, effee for soymorphine-6, efffff, efeffe, efffef, effeee for soymorphine-6. soymorphine-7. On the basis of these structures, it is possible to propose their artificial analogues for synthesis. It was shown that the spatial structure of soymorphine-5, soymorphine-6 and soymorphine-7 molecules is represented by the conformations of eight shapes of the peptide skeleton. The results obtained can be used to elucidate the structural and structural-functional organization of soymorphine molecules.

Mycobacterial biotin synthases require an auxiliary protein to convert dethiobiotin into biotin

Lipid biosynthesis in the pathogen Mycobacterium tuberculosis depends on biotin for posttranslational modification of key enzymes. However, the mycobacterial biotin synthetic pathway is not fully understood. Here, we show that rv1590, a gene of previously unknown function, is required by M. tuberculosis to synthesize biotin. Chemical–generic interaction experiments mapped the function of rv1590 to the conversion of dethiobiotin to biotin, which is catalyzed by biotin synthases (BioB). Biochemical studies confirmed that in contrast to BioB of Escherichia coli, BioB of M. tuberculosis requires Rv1590 (which we named “biotin synthase auxiliary protein” or BsaP), for activity. We found homologs of bsaP associated with bioB in many actinobacterial genomes, and confirmed that BioB of Mycobacteriumsmegmatis also requires BsaP. Structural comparisons of BsaP-associated biotin synthases with BsaP-independent biotin synthases suggest that the need for BsaP is determined by the [2Fe–2S] cluster that inserts sulfur into dethiobiotin. Our findings open new opportunities to seek BioB inhibitors to treat infections with M. tuberculosis and other pathogens.

Insights into the Mechanism of Catalytic Activity of Plasmodium Parasite Malate-Quinone Oxidoreductase.

Plasmodium malate-quinone oxidoreductase (MQO) is a membrane flavoprotein catalyzing the oxidation of malate to oxaloacetate and the reduction of quinone to quinol. Recently, using a yeast expression system, we demonstrated that MQO, expressed in place of mitochondrial malate dehydrogenase (MDH), contributes to the TCA cycle and the electron transport chain in mitochondria, making MQO attractive as a promising drug target in Plasmodium malaria parasites, which lack mitochondrial MDH. However, there is little information on the structure of MQO and its catalytic mechanism, information that will be required to develop novel drugs. Here, we investigated the catalytic site of P. falciparum MQO (PfMQO) using our yeast expression system. We generated a model structure for PfMQO with the AI tool AlphaFold and used protein footprinting by acetylation with acetic anhydride to analyze the surface topology of the model, confirming the computational prediction to be reasonably accurate. Moreover, a putative catalytic site, which includes a possible flavin-binding site, was identified by this combination of protein footprinting and structural prediction model. This active site was analyzed by site-directed mutagenesis. By measuring enzyme activity and protein expression levels in the PfMQO mutants, we showed that several residues at the active site are essential for enzyme function. In addition, a single substitution mutation near the catalytic site resulted in enhanced sensitivity to ferulenol, an inhibitor of PfMQO that competes with malate for binding to the enzyme. This strongly supports the notion that the substrate binds to the proposed catalytic site. Then, the location of the catalytic site was demonstrated by structural comparison with a homologous enzyme. Finally, we used our results to propose a mechanism for the catalytic activity of MQO by reference to the mechanism of action of structurally or functionally homologous enzymes.

CaO/SiC alkaline fillers for High-Temperature reduction of mercury (II)

The reduction of Hg2+ to Hg0 through high temperature is a crucial technique for mercury monitoring. However, this application encounters two challenges: suboptimal thermal conditions in the reaction zone leading to incomplete decomposition of Hg2+ and the susceptibility of the decomposed Hg0 to re-oxidation by Cl species. This work proposes a novel alkaline filler with alkaline earth metal oxides (AEMOs) as the active component, which enhances the thermal conditions of the reaction while effectively removing Cl species. DFT reveals increased adsorption energies of AEMOs for HCl and Cl with the growing atomic period. Further comparison of the electronic structures and adsorption behaviors between AEMOs and Cl species indicates a similar trend in electron transfer and electron density at the bond critical points. The frontier molecular orbital analysis shows a positive correlation between orbital energy level difference and adsorption energy. Experimental validation of the DFT results, combined with a comparison of costs and de-HCl performance, identifies CaO as the optimal active component. Subsequently, the CaO is loaded onto SiC, and the impact of precursor and loading ratio on the composite performance is investigated through experiments and characterization. The optimal preparation method involves using calcium acetate monohydrate as the precursor with a loading rate of 50 %. Finally, the developed alkaline filler is tested in a Hg-CEMS for industrial application, it shows errors of below 7 % compared to the EPA Method 30B results, validating its industrial feasibility. This work offers a practical solution for Hg2+ high-temperature reduction in industrial settings.

Crashworthiness capability comparison of a 3D Greek cross fractal structure additively manufactured with polyamide and thermoplastic polyurethane

Crashworthiness capability comparison of a 3D Greek cross fractal structure additively manufactured with polyamide and thermoplastic polyurethane

Genomic identification and expression analysis of acid invertase (AINV) gene family in Dendrobium officinale Kimura et Migo

BackgroundDendrobium officinale Kimura et Migo, a renowned traditional Chinese orchid herb esteemed for its significant horticultural and medicinal value, thrives in adverse habitats and contends with various abiotic or biotic stresses. Acid invertases (AINV) are widely considered enzymes involved in regulating sucrose metabolism and have been revealed to participate in plant responses to environmental stress. Although members of AINV gene family have been identified and characterized in multiple plant genomes, detailed information regarding this gene family and its expression patterns remains unknown in D. officinale, despite their significance in polysaccharide biosynthesis.ResultsThis study systematically analyzed the D. officinale genome and identified four DoAINV genes, which were classified into two subfamilies based on subcellular prediction and phylogenetic analysis. Comparison of gene structures and conserved motifs in DoAINV genes indicated a high-level conservation during their evolution history. The conserved amino acids and domains of DoAINV proteins were identified as pivotal for their functional roles. Additionally, cis-elements associated with responses to abiotic and biotic stress were found to be the most prevalent motif in all DoAINV genes, indicating their responsiveness to stress. Furthermore, bioinformatics analysis of transcriptome data, validated by quantitative real-time reverse transcription PCR (qRT-PCR), revealed distinct organ-specific expression patterns of DoAINV genes across various tissues and in response to abiotic stress. Examination of soluble sugar content and interaction networks provided insights into stress release and sucrose metabolism.ConclusionsDoAINV genes are implicated in various activities including growth and development, stress response, and polysaccharide biosynthesis. These findings provide valuable insights into the AINV gene amily of D. officinale and will aid in further elucidating the functions of DoAINV genes.