Genes Coding Research Articles

ConvNeXt-MHC: improving MHC-peptide affinity prediction by structure-derived degenerate coding and the ConvNeXt model.

Peptide binding to major histocompatibility complex (MHC) proteins plays a critical role in T-cell recognition and the specificity of the immune response. Experimental validation such peptides is extremely resource-intensive. As a result, accurate computational prediction of binding peptides is highly important, particularly in the context of cancer immunotherapy applications, such as the identification of neoantigens. In recent years, there is a significant need to continually improve the existing prediction methods to meet the demands of this field. We developed ConvNeXt-MHC, a method for predicting MHC-I-peptide binding affinity. It introduces a degenerate encoding approach to enhance well-established panspecific methods and integrates transfer learning and semi-supervised learning methods into the cutting-edge deep learning framework ConvNeXt. Comprehensive benchmark results demonstrate that ConvNeXt-MHC outperforms state-of-the-art methods in terms of accuracy. We expect that ConvNeXt-MHC will help us foster new discoveries in the field of immunoinformatics in the distant future. We constructed a user-friendly website at http://www.combio-lezhang.online/predict/, where users can access our data and application.

Measuring the performance of CO2 injection into field-cured concrete in the Arabian Gulf climate: an experimental study

ABSTRACT Concrete has experienced significant improvements in recent decades, resulting in lower Portland cement consumption as well as a lower carbon footprint through CO2 injection while keeping comparable fresh, mechanical, and durability performance. The use of CO2 injection in concrete (CarbonCure) in the United States and Canada has enabled advances such as green concrete under normal and severe conditions. While incorporating novel developments, this study focuses on CarbonCure concrete modification in the extreme weather of the Arabian Gulf region. This is a relatively new option that has entered the field in the Middle East. The materials, process, and fresh and hardened properties of the CarbonCure concrete made and field cured in the Arabian Gulf region will be considered here and evaluated in detail. Along with adding CO2 to the mix, the cementitious material was lowered without impacting the quality or performance of the structural concrete. The developed green mix included up to 0.2% CO2 by mass of cementitious material. Because of the benefit of early carbonation, which strengthened the concrete product even with less cementitious material, this green concrete mix retained a 28% increase in slump compared to the standard concrete mix without CO2, a 28-day compressive strength of 48 MPa, low water absorption of 1.3%, and resistance to aggressive chemicals, all within the limits defined by the standard codes. Due to these benefits, and because this green concrete was tested against the severe coastal climate, it would be ideal for maritime applications.

Image-to-ASCII Conversion and Preservation

ASCII (American Standard Code for Information Interchange) art is a fascinating and durable kind of visual expression in the everchanging digital realm. This study delves deeply into the complex craftsmanship associated with converting photos to ASCII characters art, making use of Python's versatility and strength as a programming language. We explore a wide range of methods, libraries, complex algorithms, and many applications related to this fascinating process as we go into a comprehensive investigation. Our main goal is to provide a comprehensive understanding of the image-to-ASCII art conversion by developing a GUI and reveal its deep relevance in modern digital culture. In addition, we analyse the instruments that are at our disposal with great care, meeting the needs of both the creative community and the practical use of this novel medium. We hope to shed light on the subtle nuances and draw attention to the artistic possibilities and useful applications that are there in the field of image-to-ASCII conversion by offering a thorough examination.

Abstract 5120: Direct targeting of the COMPASS complex inhibits neuroblastoma growth by inhibiting cancer stem cells

Abstract Epigenetic regulator COMPASS Complex, a histone H3K4 methyltransferase has recently been shown to be involved in multiple cancers and attaining focus as a novel therapeutic target. High-risk neuroblastoma (NB) is a heterogeneous pediatric cancer with high mortality and relapse rates. The relapse of refractory cancer is shown to be driven by cancer stem cells (CSCs), which are maintained by epigenetic malfunctions. In the present study, we determined the effects of inhibiting the COMPASS complex on NB CSCs and overall NB growth. A high-throughput shRNA screening of methyltransferases and demethylases reveals the role of COMPASS complex partners MLL1 and Menin in NB proliferation. We found that both MLL1 and Menin are overexpressed in our previously identified CD114+ NB CSCs. Further, MEN1 (gene coding Menin) expression showed an inverse correlation with overall NB patient survival and cancer progression in a comprehensive analysis of 1235 primary NB patient data. Our ChIP results show that the CSF3R gene which codes for CD114 and maintains CD114+ NB CSCs, is regulated by the presence of high H3K4me3 activating marks. Further, we used MI-503 to inhibit MLL1-Menin interaction and also developed MEN1 stable knockdown and found that both strategies significantly inhibit H3K4me3 activity in NB, particularly at the CSF3R gene promoter. This led to decreased CSF3R expression and NB CSC levels. MI-503 significantly inhibits proliferation in different NB cell lines and primary patient-derived xenograft (PDX) lines, with minimal effect on non-cancerous fibroblasts. MI-503 significantly inhibits NB cell cycle progression at the S phase, induces apoptosis, and inhibits NB 3D spheroid growth and development. Interestingly, we overserved differential selectivity of MI-503 in inducing apoptosis and in blocking the cell cycle in NB CSCs in contrast to non-CSCs. MEN1 knockdown also inhibits NB proliferation and 3D spheroid growth. Furthermore, MI-503 in a dose-dependent manner synergistically sensitizes NB to chemotherapy doxorubicin and significantly inhibits NB proliferation and spheroid growth compared to either agent alone. Further, by using the NB xenograft in vivo tumor model, we established that MI-503 significantly inhibits NB tumor growth and tumor metastasis by directly inhibiting tumor NB CSCs, without any observed toxicities. Similar results of significantly reduced tumor growth, metastasis, and NB CSCs were shown by the MEN1 knockdown in vivo. Overall, our data show that the MLL1-Menin of the COMPASS complex directly activates the CSF3R gene to maintain NB CSCs and drive NB pathogenesis. Our data show that MI-503 or MEN1 knockdown leads to significant inhibition of NB growth by directly inhibiting NB CSCs in both in vitro and in vivo tumor models. Further developing these epigenetic-based therapeutic strategies and combining them with current therapies will pave the way for effectively managing NB. Citation Format: Rameswari Chilamakuri, Saurabh Agarwal. Direct targeting of the COMPASS complex inhibits neuroblastoma growth by inhibiting cancer stem cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5120.

Non‐Canonical Amino Acids for Engineering Peptides and Proteins with new Functions

AbstractThe universal genetic code, which specifies the 20 standard amino acids (AAs), forms the basis for all natural proteins. Researchers have developed efficient and robust in vivo and in vitro strategies to overcome the constraints of the genetic code to expand the repertoire of AA building blocks that can be ribosomally incorporated into proteins. This review summarizes the development of these in vivo and in vitro systems and their subsequent use for engineering of peptides and proteins with new functions. In vivo genetic code expansion employing engineered othogonal tRNA/aaRS pairs has led to the development of proteins that selectively bind small molecules, cleave nucleic acids and catalyze non‐natural chemical transformations. In vitro genetic code reprogramming using Flexizymes coupled with mRNA display has resulted in potent macrocyclic peptides that selectively bind to therapeutically important proteins. Through these examples, we hope to illustrate how genetic code expansion and reprogramming, especially when coupled with directed evolution or in vitro selection techniques, have emerged as powerful tools for expanding the functional capabilities of peptides and proteins.

Implementasi Quick Response Code Indonesian Standard (QRIS) Untuk Pelaku Usaha Di Pasar Tradisional

In the development of financial technology, many payment system innovations have emerged, one of which is the Indonesian Standard Quick Response Code (QRIS). This research aims to determine the implementation of QRIS for business actors in the Kupang City Traditional Market. This research uses a qualitative approach, with data collection methods conducting interviews, observation, documentation. The results of this research show that the Quick Response Code Indonesian Standard (QRIS) is an electronic payment tool to make it easier for people to carry out transactions. Through QRIS, people can feel the ease of making transactions anytime and anywhere, even outside bank operational hours. However, in its implementation there are several obstacles, namely a weak internet connection so that the transaction process carried out by traders is hampered, the cellphones owned by traders are not yet sophisticated so they cannot make transactions, lack of knowledge and a 0.3% deduction from the transaction value.

Socio-Digital Challenges for Social Work in the Metaverse

Abstract The metaverse will have a direct impact on the way we relate to each other as. The interest of the young population explains the extent to which this new developing technological paradigm is already present in our society, generating environments where people will feel part of them and where interactions will be more authentic, immersive, and it remains to be seen whether these relationships will also be more inclusive. The article identifies these challenges through a literature review, making a categorical comparison with the professional competences of social work drawn from the professional codes of standards and competences. A qualitative analysis has been carried out to identify those competences that may be affected by one or more social challenges arising from the popularisation of the metaverse. It presents important challenges for social work, such as changes in community, governance and individual behaviour, as well as implications for ethics, privacy and the way we understand social intervention that require an epistemological, methodological and practical debate in the profession, as yet unpublished, to adapt to this new socio-virtual dimension in which millions of people have already settled. Finally, v-social work is proposed as a new professional field with specific competences.

Analysis and Design of Steel Cement Storage Silo

Storage is an important aspect of any business. All businesses must store goods and materials safely, especially warehouses, factories, shops, food, agricultural, and construction businesses. Leaving materials exposed reduces their overall quality; hence, certain structures are used to safely retain the materials for further use. These are called storage structures. A silo is a commonly used storage structure for the storage of bulk materials such as grain and cement. This paper deals with the design of a steel silo for the storage of pozzolana cement. A storage silo is essentially made up of a cylinder-shaped wall and a hopper bottom. Steel Silos are gaining more popularity in terms of cement storage usage. A 150-ton capacity steel silo has been designed for a seismic zone-2 [1] location in Madurai, Tamil Nadu, India (therefore omitting the inclusion of seismic loads). The preliminary design of the silo structure is carried out with the help of Indian Standard code books. Indian Standard code books such as IS 9178-Parts 1,2 & 3 (1979) were used for the basic design. Other necessary code books were used for load calculations. The plan and elevation of the Silo have been drafted by using AutoCAD. The designed Silo is analysed using STAAD Pro. The pile foundation of the Steel Silo has also been designed and analysed using STAAD Foundation.

Systematic and quantitative analysis of stop codon readthrough in Rett syndrome nonsense mutations

Rett syndrome (RTT) is a neurodevelopmental disorder resulting from genetic mutations in the methyl CpG binding protein 2 (MeCP2) gene. Specifically, around 35% of RTT patients harbor premature termination codons (PTCs) within the MeCP2 gene due to nonsense mutations. A promising therapeutic avenue for these individuals involves the use of aminoglycosides, which stimulate translational readthrough (TR) by causing stop codons to be interpreted as sense codons. However, the effectiveness of this treatment depends on several factors, including the type of stop codon and the surrounding nucleotides, collectively referred to as the stop codon context (SCC). Here, we develop a high-content reporter system to precisely measure TR efficiency at different SCCs, assess the recovery of the full-length MeCP2 protein, and evaluate its subcellular localization. We have conducted a comprehensive investigation into the intricate relationship between SCC characteristics and TR induction, examining a total of 14 pathogenic MeCP2 nonsense mutations with the aim to advance the prospects of personalized therapy for individuals with RTT. Our results demonstrate that TR induction can successfully restore full-length MeCP2 protein, albeit to varying degrees, contingent upon the SCC and the specific position of the PTC within the MeCP2 mRNA. TR induction can lead to the re-establishment of nuclear localization of MeCP2, indicating the potential restoration of protein functionality. In summary, our findings underscore the significance of SCC-specific approaches in the development of tailored therapies for RTT. By unraveling the relationship between SCC and TR therapy, we pave the way for personalized, individualized treatment strategies that hold promise for improving the lives of individuals affected by this debilitating neurodevelopmental disorder. Key messagesThe efficiency of readthrough induction at MeCP2 premature termination codons strongly depends on the stop codon context.The position of the premature termination codon on the transcript influences the readthrough inducibility.A new high-content dual reporter assay facilitates the measurement and prediction of readthrough efficiency of specific nucleotide stop contexts.Readthrough induction results in the recovery of full-length MeCP2 and its re-localization to the nucleus.MeCP2 requires only one of its annotated nuclear localization signals.

Particular and General Limitations in Gene Coding and Synonymous Recoding of Genes

Particular and General Limitations in Gene Coding and Synonymous Recoding of Genes

Design study of a 450MW thermal Modified CANDLE fast reactor using helium gas as a coolant

The Modified CANDLE (MCANDLE) burnup scheme divides the reactor core into several regions in an axial or radial direction with equal volume. It works like the CANDLE burnup scheme except that, in the CANDLE burnup scheme, the reactor core is divided into three main regions in the axial direction. Namely, spent fuel, burning region and fresh fuel region. In this study, the design of a modular modified CANDLE fast reactor using helium gas as a coolant has been performed. One of the important roles of a modified CANDLE fast reactor is that it can utilize natural uranium as fuel without the need for enrichment or reprocessing. This type of reactor can be used, including in developing countries, without the nuclear proliferation problem. Using helium gas as a coolant gives hope for a fast reactor due to its properties, such as its less neutron absorption, less radioactive, and as helium is an inert gas, prevents chemical reactions with other materials. The study was performed on a rector with a thermal power of 450MWth. The active core was divided into ten regions with equal volume in radial directions. The refueling scheme has been optimized every ten years of burnup to obtain a good reactor design. In the beginning, the fuel was put in the first region after ten years of burnup was moved to the second region, after another ten years of burnup was moved to the third region and so on until the tenth region where the fuel gets out. The neutronic calculation has been performed using the SRAC (Standard Reactor Analysis Code system). The collision probability method (PIJ) was employed for cell burnup calculation, and CITATION was used for the reactor core design with JENDL 4.0 as the nuclear data library.

Assessment of mechanical, durability and microstructural performance of sulphate-resisting cement concrete over portland cement in the presence of salinity

The current understanding of the sulphate attack mechanism on ordinary Portland cement (OPC) concrete within the construction sector is not yet well understood. The primary objective of this study is to focus on and discuss how to minimize the sulphate attack on concrete. The main purpose of this research is to better understand and improve the mechanical, durability, and microstructural characteristics of concrete under saline and non-saline/normal environments. This investigation involved the use of artificial seawater in the concrete mixing process and ensuring saline conditions for the concrete specimens in the laboratory. In addition, an approach for assessing the influence of using sulphate-resisting cement (SRC) in concrete to differentiate the performance from OPC concrete is also investigated. Silica fume (SF) is used as a partial cementitious material in SRC concrete by 10% and 20%. The concrete performances were examined by several rheological, mechanical, durability, and microstructural tests and compared the corresponding performances with the SRC-artificial seawater (SRCASW) and OPC-freshwater (OPCFW) concrete. Test results show that the strength of concrete decreased linearly from the OPCFW to SRCASW. Among SRC-artificial seawater concrete mixes, the mix with 10% SF shows the best strength outcomes i.e., 28.84, 36.22, and 37.54 MPa at 7, 28, and 56 days respectively, which is an average of 12.5% higher than the mix with 20% SF. A concrete mix of SRC with 10% SF displays the highest durable behavior, achieving chloride penetration and electrical resistivity at a very low range (936 columbus and 290.7 Ω-m, respectively). In addition, microstructural images of the SRC concrete mixes indicate no visible crack due to sulphate inclusion. An analytical approach has provided a conservative estimate with the experimental results and standard code of practice for predicting mechanical properties. Finally, this study revealed that SRC incorporation in concrete increased the long-term serviceability of the structures against salinity.

Neutronic design of small modular long­life pressurized water reactor using thorium carbide fuel at a power level of 300–500 MWth

This study presents the neutronic design of a small modular long­life Pressurized Water Reactor (PWR) using thorium carbide fuel with 233U fissile material. The target optimization for this study is a reactor designed to operate for 20 years, with excess reacti­vity throughout the reactor operational cycle consistently below 1.00 % dk/k. The analysis involves dividing the reactor core into three fuel regions with 233U enrichment levels ranging from 3 % to 8 %, with a 1 % difference for each fuel region. To achieve optimum conditions, 231Pa was randomly added to the fuel. The fuel volume fraction in this design varied from 30 % to 65 %, with a 5 % incremental variation. Power level variations are also studied within the 300–500 MWth with increments of 50 MWth. Calculations were performed using the Standard Reactor Analysis Code (SRAC) program with the PIJ and CITATION modules for cell and core calculations utilizing JENDL­4.0 nuclide data. Neutronic calculations indicate that the fuel with a 60 % volume fraction achieves optimum conditions at a power level of 300 MWth. The best performance was observed with a fuel volume fraction of 65 %, reaching optimum conditions across power levels ranging from 300 to 500 MWth. For the fuel with the best performance, the power density distributions for low and high power levels follow the same pattern radially and axially. The power peaking factor (PPF) for all fuel configurations approaching the optimum conditions remains below two, a safe limit for the PWR. Other neutronic safety parameters, such as the Doppler coefficient and void fraction coefficient, also stay within the safe limits for the PWR, with both values remaining negative throughout the reactor operational cycle

Code of Ethics and Professional Standards of Conduct for Emergency Management Professionals.

The Code of Ethics and Professional Standards of Conduct for Emergency Management Professionals (2022) was recently created to further delineate the ethical boundaries and conduct expectations for professional emergency management practice. Significantly, the code of ethics provides an essential foundation toward recognition as a profession with hallmarks of monopoly, autonomy, and authority. The code and standards of conduct establish a clear definition of the role emergency management has in overseeing a complex, diverse risk portfolio that protects lives, livelihoods, and quality of life. The document captures the intent, challenges, dimensions, and significance of emergency management practice in a rapidly changing world and brings ethics to the forefront of decisions. This article speaks to the discursive dialogue toward, methodological development of, and future tools for integrating into practice the Code of Ethics and Professional Standards of Conduct for Emergency Management Professionals.

BROM: An extension of beam theory through model order reduction

Beam analysis played a crucial role in the design of structures throughout modern history. Classical beam theories rely on analytical derivations under certain a priori kinematic assumptions (and are accurate with low computational cost), but they are not amenable to, for example, orthotropic materials and arbitrary cross sections. On the other hand, full 3D linear elasticity theory solved via the Finite Element (FE) method provides solutions for a wide range of engineering problems at the expense of a high computational cost. Reduced-order models try to provide a theory as general as 3D linear elasticity but as efficient as classical beam theories by assuming the solution to be represented in a low-dimensional basis. Among the several options available in the literature, the domain decomposition and hyperreduction via Empirical Cubature Method (ECM), which we name ddROM [1], exhibits this compelling feature. However, ddROM applied to beam structures, may provide more Degrees of Freedom (DoF) per node than most standard commercial FE codes which only consider rigid body motion of the cross section. This paper presents a methodology, called beam Reduced Order Model (bROM), to integrate ddROM in standard FE codes by means of a condensation process followed by a regression procedure. Condensation gives the stiffness matrix, required by FE commercial codes, of a super-element of a given length. This is achieved by assembling several elements and finding the relationship between applied displacements and reactions (Lagrange multipliers). The condensation process is then used to create a database of stiffness matrices as a function of the beam length over which a regression is performed. Some numerical examples are first presented to validate the proposed methodology against the classical beam theory for the case of isotropic beams, and finally, two orthotropic beam showing the utility of the method in comparison with FE.

DERNA Enables Pareto Optimal RNA Design.

The design of an RNA sequence that encodes an input target protein sequence is a crucial aspect of messenger RNA (mRNA) vaccine development. There are an exponential number of possible RNA sequences for a single target protein due to codon degeneracy. These potential RNA sequences can assume various secondary structure conformations, each with distinct minimum free energy (MFE), impacting thermodynamic stability and mRNA half-life. Furthermore, the presence of species-specific codon usage bias, quantified by the codon adaptation index (CAI), plays a vital role in translation efficiency. While earlier studies focused on optimizing either MFE or CAI, recent research has underscored the advantages of simultaneously optimizing both objectives. However, optimizing one objective comes at the expense of the other. In this work, we present the Pareto Optimal RNA Design problem, aiming to identify the set of Pareto optimal solutions for which no alternative solutions exist that exhibit better MFE and CAI values. Our algorithm DEsign RNA (DERNA) uses the weighted sum method to enumerate the Pareto front by optimizing convex combinations of both objectives. We use dynamic programming to solve each convex combination in time and space. Compared with a CDSfold, previous approach that only optimizes MFE, we show on a benchmark data set that DERNA obtains solutions with identical MFE but superior CAI. Moreover, we show that DERNA matches the performance in terms of solution quality of LinearDesign, a recent approach that similarly seeks to balance MFE and CAI. We conclude by demonstrating our method's potential for mRNA vaccine design for the SARS-CoV-2 spike protein.

Fatigue load spectrum generation of Indonesian high-speed trains

The high-speed trains designed and constructed in Indonesia will use Aluminum alloy Al 6061-T6 as a structural material. Aluminum alloys are prone to fatigue failure due to the absence of endurance limit of the material, hence fatigue life prediction has to be carried out. Fatigue cracks could initiate at the defects of welded joints. Analyzing the fatigue load spectrum of critical locations in the train structures is crucial to predicting fatigue life. These critical locations are selected from areas with high static stress and stress concentration. The loads are analyzed using the multibody dynamic with rigid body assumptions and track roughness following UIC Standard Code 518. The finite element method is used to calculate the stresses from the loads generated by the multibody dynamic. The load sequence is further analyzed with rainflow counting method, and the load exceedance curve can be constructed. Finally, the Miner Linear Cumulative Damage Model is used to predict fatigue life.

Deep Learning Prediction of Cervical Spine Surgery Revision Outcomes Using Standard Laboratory and Operative Variables

IntroductionCervical spine procedures represent a major proportion of all spine surgery. Mitigating the revision rate following cervical procedures requires careful patient selection. While complication risk has successfully been predicted, revision risk has proven more challenging. This is likely due to the absence of granular variables in claims databases. The objective of this study was to develop a state-of-the-art of revision prediction of cervical spine surgery using laboratory and operative variables. MethodsUsing the Stanford Research Repository, patients undergoing a cervical spine procedure between 2016–2022 were identified (N=3151) and recent laboratory values were collected. Patients were classified into separate cohorts by revision outcome and timeframe. Machine and deep learning models were trained to predict each revision outcome from laboratory and operative variables. ResultsRed blood cell count, Hemoglobin, Hematocrit, Mean Corpuscular Hemoglobin Concentration, Red Blood Cell Distribution Width, Platelet Count, CO2, Anion Gap, and Calcium were all significantly associated with one or more revision cohorts. For the prediction of 3–month revision, the deep neural network achieved AUC of 0.833. The model demonstrated increased performance for anterior than posterior and arthrodesis than decompression procedures. ConclusionsOur deep learning approach successfully predicted 3–month revision outcomes from demographic variables, standard laboratory values, and operative variables, in a cervical spine surgery cohort. This work introduces standard laboratory values and operative codes as meaningful predictive variables for revision outcome prediction. The increased performance on certain procedures evidences the need for careful development and validation of “one-size-fits-all” risk scores for spine procedures.

Comparison of the neutronic properties of the (Th-233U)O2, (Th-233U)C, and (Th-233U)N fuels in small long-life PWR cores with 300, 400, and 500 MWth of power

Abstract The neutronic characteristics of (Th-233U)O2, (Th-233U)C, and (Th-233U)N have been compared in small long-life pressurized water reactors (PWRs). Neutronic calculations were carried out at 300 MWth, 400 MWth, and 500 MWth with two cladding types: zircaloy-4 and ZIRLO (Zr low oxygen). They were performed using the Standard Reactor Analysis Code (SRAC) and JENDL-4.0 nuclide data, dividing the reactor core into three fuel zones with varying 233U enrichment levels, ranging from 3% to 9% and fluctuating by 1%, employing the PIJ module at the fuel cell level and the CITATION module at the reactor core level. In addition, 231Pa was added as burnable poison (BP). The (Th-233U)N fuel demonstrated superior criticality compared to the other fuel types, as it consistently achieves critical conditions throughout the reactor’s operating cycle with excess reactivity <1.00% dk/k for several fuel configurations at the 300 MWth and 400 MWth power levels. Moreover, the (Th-233U)N and (Th-233U)C fuels exhibited similar and flatter power density distribution patterns compared to the (Th-233U)O2 fuel. The power peaking factor (PPF) value was relatively higher for (Th-233U)O2 fuel than the other two fuels. The (Th-233U)N fuel exhibited the most negative Doppler coefficient, followed by (Th-233U)C and (Th-233U)O2 fuels. Analysis of burnup levels revealed that the (Th-233U)O2 fuel achieved significantly higher burnup than the other two fuels.

Identification of HDV-like theta ribozymes involved in tRNA-based recoding of gut bacteriophages

Trillions of microorganisms, collectively known as the microbiome, inhabit our bodies with the gut microbiome being of particular interest in biomedical research. Bacteriophages, the dominant virome constituents, can utilize suppressor tRNAs to switch to alternative genetic codes (e.g., the UAG stop-codon is reassigned to glutamine) while infecting hosts with the standard bacterial code. However, what triggers this switch and how the bacteriophage manipulates its host is poorly understood. Here, we report the discovery of a subgroup of minimal hepatitis delta virus (HDV)-like ribozymes – theta ribozymes – potentially involved in the code switch leading to the expression of recoded lysis and structural phage genes. We demonstrate their HDV-like self-scission behavior in vitro and find them in an unreported context often located with their cleavage site adjacent to tRNAs, indicating a role in viral tRNA maturation and/or regulation. Every fifth associated tRNA is a suppressor tRNA, further strengthening our hypothesis. The vast abundance of tRNA-associated theta ribozymes – we provide 1753 unique examples – highlights the importance of small ribozymes as an alternative to large enzymes that usually process tRNA 3’-ends. Our discovery expands the short list of biological functions of small HDV-like ribozymes and introduces a previously unknown player likely involved in the code switch of certain recoded gut bacteriophages.