Expression Of Resistance Genes Research Articles

Exploring the molecular mechanisms of rice blast resistance and advances in breeding for disease tolerance.

Rice blast, caused by the fungus Magnaporthe oryzae (syn. Pyricularia oryzae), is a major problem in rice cultivation and ranks among the most severe fungal diseases. Cloning and identifying resistance genes in rice, coupled with a comprehensive examination of the interaction between M. oryzae and rice, may provide insights into the mechanisms of rice disease resistance and facilitate the creation of new rice varieties with improved germplasm. These efforts are essential for protecting food security. This review examines the discovery of genes that confer resistance or susceptiblity to M. oryzae in rice over the last decade. It also discusses how knowledge of molecular mechanisms has been used in rice breeding and outlines key strategies for creating rice varieties resistant to this disease. The strategies discussed include gene pyramiding, molecular design breeding, editing susceptibility genes, and increasing expression of resistance genes through pathogen challenge. We address the prospects and challenges in breeding for rice blast resistance, emphasizing the need to fully exploit germplasm resources, employ cutting-edge methods to identify new resistance genes, and develop innovative breeding cultivars. Additionally, we underscore the importance of understanding the molecular basis of rice blast resistance and developing novel cultivars with broad-spectrum disease resistance.

Application of a metatranscriptomics technology, CSI-Dx, for the detection of pathogens associated with prosthetic joint infections

Preoperative identification of causal organism(s) is crucial for effective prosthetic joint infection treatment. Herein, we explore the clinical application of a novel metatranscriptomic (MT) workflow, CSI-Dx, to detect pathogens associated with prosthetic joint infection. MT provides insight into transcriptionally active microbes, overcoming limitations of culture-based and available molecular methods. This study included 340 human synovial fluid specimens subjected to CSI-Dx and traditional culture-based methods. Exploratory analyses were conducted to determine sensitivity and specificity of CSI-Dx for detecting clinically-relevant taxa. Our findings provide insights into the active microbial community composition of synovial fluid from arthroplasty patients and demonstrate the potential clinical utility of CSI-Dx for aiding prosthetic joint infection diagnosis. This approach offers potential for improved sensitivity and acceptable specificity compared to synovial fluid culture, enabling detection of culturable and non-culturable microorganisms. Furthermore, CSI-Dx provides valuable information on antimicrobial resistance gene expression. While further optimization is needed, integrating metatranscriptomic technologies like CSI-Dx into routine clinical practice can revolutionize prosthetic joint infection diagnosis by offering a comprehensive and active snapshot of associated pathogens.

The impact of antibiotic induction on virulence and antibiotic resistance in Klebsiella pneumoniae: a comparative study of CSKP and CRKP strains

BackgroundKlebsiella pneumoniae is an opportunistic pathogen causing nosocomial infections, classified into carbapenem-sensitive and carbapenem-resistant strains. Understanding the virulence factors and antibiotic resistance of these strains is essential for effective clinical management.ObjectiveThis study compared the virulence genes and antibiotic resistance profiles of 50 CSKP and 50 CRKP strains, examining their expression under antibiotic pressure and the mechanisms contributing to their pathogenicity.MethodsVirulence genes (rmpA, rmpA2, iucA, iutA, Peg-344, ybts, iroB) were detected in both strains using polymerase chain reaction (PCR). Antibiotic susceptibility testing established minimum inhibitory concentrations (MICs) for key antibiotics. Gene expression analysis was performed with quantitative reverse transcription PCR (qRT-PCR) after 10 days of antibiotic exposure.ResultsCSKP strains exhibited significantly higher positivity rates for virulence genes compared to CRKP strains. CRKP strains predominantly expressed resistance genes KPC, SHV, and CTX-M3, whereas no resistance genes were found in CSKP. Antibiotic susceptibility tests showed increased MICs, particularly for ciprofloxacin and imipenem, following antibiotic induction. CSKP demonstrated elevated expression of rmpA and rmpA2, while CRKP showed increased expression of SHV, and KPC after antibiotic exposure.ConclusionThis study highlights the intricate relationship between virulence and resistance in Klebsiella pneumoniae. CSKP strains show strong virulence factor expression, while CRKP strains adapt to antibiotic pressure through altered gene expression patterns. These findings underscore the urgent need for continuous surveillance and innovative therapeutic strategies to combat multidrug-resistant Klebsiella pneumoniae infections.

3'UTR of tobacco vein mottling virus regulates downstream GFP expression and changes in host gene expression.

Tobacco vein mottling virus (TVMV) is a member of the family Potyviridae. The 3' untranslated region (3'UTR) of viral genomic RNA has been reported to significantly impact viral infection. Nevertheless, the role of the TVMV 3'UTR during viral infection remains unknown. Here, a 3'UTR-GFP expression vector was transiently expressed in Nicotiana benthamiana, in which the 3'UTR of TVMV was introduced upstream of the green fluorescent protein (GFP) gene. Transcriptome sequencing was performed to analyze the genes associated with plant resistance. The effect of the TVMV 3'UTR on GFP expression was studied using an Agrobacterium-mediated transient expression assay, revealing that the TVMV 3'UTR significantly inhibited GFP expression. Transcriptome analysis of differentially expressed genes in 3'UTR-GFP in N. benthamiana was performed to elucidate the why the TVMV 3'UTR inhibited GFP expression. Eighty genes related to plant disease resistance were differentially expressed, including 29 upregulated and 51 downregulated genes. Significantly upregulated genes included those encoding the calcium-binding protein CML24, leucine-rich repeat receptor-like tyrosine-protein kinase, and respiratory burst oxidase homolog protein E. The significantly downregulated genes included calcium-binding protein 7, ethylene-responsive transcription factor 10, endoglucanase 5, and receptor-like protein kinase. These findings indicate that the 3'UTR of TVMV may inhibit the expression of GFP gene by inducing the expression of plant resistance genes. This study provides a theoretical basis for further research on the function and mechanism of the TVMV 3'UTR.

SiO2 nanoparticles can enhance nitrogen retention and reduce copper resistance genes during aerobic composting of swine manure

SiO2 nanoparticles (SiO2 NPs) are low-cost, environmentally friendly materials with significant potential to remove pollutants from complex environments. In this study, SiO2 NPs were used for the first time as an additive in aerobic composting to enhance nitrogen retention and reduce the expression of copper resistance genes. The addition of 0.5 g kg−1 SiO2 NPs effectively reduced nitrogen loss by 72.33 % by decreasing denitrification genes (nosZ, nirK, and napA) and increasing nitrogen fixation gene (nifH). The dominant factors affecting nitrification and denitrification genes were Firmicutes and C/N ratio. Additionally, SiO2 NPs decreased copper resistance genes by 28.96 % − 37.52 % in compost products. Copper resistance genes decreased most in the treatment with 0.5 g kg−1 SiO2 NPs. In summary, 0.5 g kg−1 SiO2 NPs have the potential to reduce copper resistance genes and enhance nitrogen retention during aerobic composting, which may be used to improve compost quality.

Integrated induction of silver resistance determinants and production of extracellular polymeric substances in Cupriavidus metallidurans BS1 in response to silver ions and silver nanoparticles

Although the antimicrobial mechanisms of nanomaterials have been extensively investigated, bacterial defense mechanisms associated with AgNPs have not been fully elucidated. We here report that dissolved Ag+ (>0.05 μg·mL-1) displayed higher toxicity on cell growth of strain Cupriavidus metallidurans BS1 (GCA_003260185.2) in comparison to 2 and 20 nm AgNPs. The genes necessary for synthesis of distinct abundance and composition of extracellular polymeric substances (EPS) were induced in strain BS1 exposed to Ag stress. This resulted in 20.1% (Ag(I)-EPS) and 24.2% (2 nm AgNPs-EPS) of the C=O band integrated intensities being converted into C-OH/C-O-C group vibrations and the Ag-O bond was formed between EPS and 20 nm AgNPs. Meanwhile, the expression of primary resistance genes of the cus, sil and cup operon encoding HME-RND-driven efflux systems as well as a PIB1-type ATPase (CupA) were significantly induced after exposure to Ag(I), 2 and 20 nm AgNPs, respectively. Furthermore, distinct genes involved in biosynthesis pathways responsible for production of EPS were induced to relieve the toxicity of Ag(I), 2 nm and 20 nm AgNPs. This combined action is one potential reason why strain BS1 displayed distinct resistances in response to Ag(I) compared to 2 and 20 nm AgNPs. This work will help in understanding processes important in bacterial defensive mechanisms to AgNPs.

Metabolic Adaptations in Phosphine-Resistant Tribolium castaneum Driven by Mitochondrial Enzyme Variability and Gene Expression.

Phosphine fumigation is essential for controlling storage pests like Tribolium castaneum, but its frequent application has resulted in resistance, primarily due to mutations in the Dihydrolipoamide dehydrogenase (DLD) gene associated with the rph2 allele. This study demonstrates that the Patiala population exhibits homozygous resistance variations across populations, contrasting with the susceptibility observed in laboratory cultures. Our assessment of mitochondrial DLD and Cytochrome c oxidase (COX) activities showed significantly elevated levels in the Patiala population, with increases of approximately sevenfold for DLD and 6.92-fold for COX, indicating mitochondrial adaptations for enhanced energy production. Kinetic analyses of DLD in the resistant Patiala population showed a higher Vmax (0.005 mmol/min) and a significantly increased Km (16.66 mM), indicating variations in maximal enzyme activity and substrate affinity. Furthermore, resistant T. castaneum populations displayed substantial upregulation of DLD and COX gene expression, with DLD expression increasing by 10.53-fold and COX expression peaking at 102.57-fold in Patiala. Pearson correlation analysis indicated strong positive correlations (r > 0.8) between enzymatic activity and gene expression for both DLD and COX, suggesting a coordinated role in resistance mechanisms. The PCA biplot illustrated distribution patterns of enzymatic activity and gene expression among field-resistant populations, highlighting the association between increased resistance and elevated enzymatic activity and gene expression levels. Therefore, the upregulation of DLD and COX activities in resistant populations underscores their critical roles in counteracting phosphine, reflecting metabolic reprogramming for improved energy production under stress.

Feedstock-dependent antibiotic resistance gene patterns and expression profiles in industrial scale biogas plants revealed by meta-omics technology

This study investigated antimicrobial resistance in the anaerobic digesters of two industrial-scale biogas plants processing agricultural biomass and municipal wastewater sludge. A combination of deep sequencing and genome-centric workflow was implemented for metagenomic and metatranscriptomics data analysis to comprehensively examine potential antimicrobial resistance in microbial communities. Anaerobic microbes were found to harbour numerous antibiotic resistance genes (ARGs), with 58.85% of the metagenome-assembled genomes (MAGs) harbouring antibiotic resistance. A moderately positive correlation was observed between the abundance and expression of ARGs. ARGs were located primarily on bacterial chromosomes. A higher expression of resistance genes was observed on plasmids than on chromosomes. Risk index assessment suggests that most ARGs identified posed a significant risk to human health. However, potentially pathogenic bacteria showed lower ARG expression than non-pathogenic ones, indicating that anaerobic treatment is effective against pathogenic microbes. Resistomes at the gene category level were associated with various antibiotic resistance categories, including multidrug resistance, beta-lactams, glycopeptides, peptides, and macrolide-lincosamide-streptogramin (MLS). Differential expression analysis revealed specific genes associated with potential pathogenicity, emphasizing the importance of active gene expression in assessing the risks associated with ARGs.

Transcriptomic insights into the epigenetic modulation of turnip mosaic virus evolution in Arabidopsis thaliana

BackgroundPlant-virus interaction models propose that a virus’s ability to infect a host genotype depends on the compatibility between virulence and resistance genes. Recently, we conducted an evolution experiment in which lineages of turnip mosaic virus (TuMV) were passaged in Arabidopsis thaliana genotypes carrying mutations in components of the DNA methylation and the histone demethylation epigenetic pathways. All evolved lineages increased infectivity, virulence and viral load in a host genotype-dependent manner.ResultsTo better understand the underlying reasons for these evolved relationships, we delved into the transcriptomic responses of mutant and WT plant genotypes in mock conditions and infected with either the ancestral or evolved viruses. Such a comparison allowed us to classify every gene into nine basic expression profiles. Regarding the targets of viral adaptation, our analyses allowed the identification of common viral targets as well as host genotype-specific genes and categories of biological processes. As expected, immune response-related genes were found to be altered upon infection. However, we also noticed the pervasive over-representation of other functional groups, suggesting that viral adaptation was not solely driven by the level of expression of plant resistance genes. In addition, a significant association between the presence of transposable elements within or upstream the differentially expressed genes was observed. Finally, integration of transcriptomic data into a virus-host protein-protein interaction network highlighted the most impactful interactions.ConclusionsThese findings shed extra light on the complex dynamics between plants and viruses, indicating that viral infectivity depends on various factors beyond just the plant’s resistance genes.

Targeting Hypoxia-Inducible Factor-1α in Pancreatic Cancer: siRNA Delivery Using Hyaluronic Acid-Displaying Nanoparticles

Background/Objectives: Conventional anticancer therapies often lack specificity, targeting both cancerous and normal cells, which reduces efficacy and leads to undesired off-target effects. An additional challenge is the presence of hypoxic regions in tumors, where the Hypoxia Inducible Factor (HIF) transcriptional system drives the expression of pro-survival and drug resistance genes, leading to radio- and chemo-resistance. This study aims to explore the efficacy of targeted nanoparticle (NP)-based small interfering RNA (siRNA) therapies in downregulating these genes to enhance treatment outcomes in pancreatic cancer, a tumor type characterized by high CD44 expression and hypoxia. Methods: We utilized hyaluronic acid (HA)-displaying nanoparticles composed of positively charged chitosan (CS) complexed with siRNA to target and knock down HIF-1α in pancreatic cancer cells. Two NP formulations were prepared using either low molecular weight (LMW) or high molecular weight (HMW) CS. These formulations were evaluated for their internalization by cells and their effectiveness in gene silencing, both in vitro and in vivo. Results: The study found that the molecular weight (MW) of CS influenced the interaction between HA and CD44, as well as the release of siRNA upon internalization. The LMW CS formulation shows faster uptake kinetics, while HMW CS is more effective in gene knockdown across different cell lines in vitro. In vivo, both were able to significantly knockdown HIF-1α and some of its downstream genes. Conclusions: The results suggest that HMW and LMW CS-based NPs exhibit distinct characteristics, showing that both MWs have potential for targeted pancreatic cancer therapy by influencing different aspects of delivery and gene silencing, particularly in the hypoxic tumor microenvironment.

Research Progress in the Joint Remediation of Plants–Microbes–Soil for Heavy Metal-Contaminated Soil in Mining Areas: A Review

Plants growing in heavy metal (HM)-contaminated soil have evolved a special detoxification mechanism. The rhizosphere gathers many living substances and their secretions at the center of plant roots, which has a unique ecological remediation effect. It is of great significance to thoroughly understand the ecological process of rhizosphere pollution under heavy metals (HMs) stress and develop biotechnology for joint remediation using plants and their coexisting microbial systems according to the mechanism of rhizosphere stress. Microbes can weaken the toxicity of HM pollutants by transforming the existing forms or reducing the bioavailability in the rhizosphere. Microbes survive in the HM-polluted soils through the production of stress-resistant substances, the participation of proteins, and the expression of heavy metal resistance genes, which strengthens the resistance of plants. Moreover, microbes can improve the nutritional status of plants to improve plant resistance to HMs. Plants, in turn, provide a habitat for microbes to survive and reproduce, which greatly accelerates the process of bioremediation. Briefly, the combined remediation of soil HMs pollution by plants and microbes is a promising, green, and sustainable strategy. Here, we mainly elucidate the joint remediation mechanism of plant–microbe symbiosis and introduce the coping characteristics of plants, microbes, and their symbiotic system, hoping to provide a scientific basis for the remediation of HM-contaminated soil in mining areas and the sustainable development of the ecological environment.

Antimicrobial resistance profiling of bacteria isolated from wastewater and samples of pharmaceutical industries in South India

The study was aimed to determine the phenotypic and genotypic antimicrobial resistance in the isolated bacteria from the influent (25), effluent (15), surface and ground water samples (15) surrounding the pharmaceutical industries located in south India. From 55 samples, 48 isolates of 10 different bacteria were obtained. The identified bacterial isolates were viz. Klebsiella pneumoniae, Pseudomonas aeruginosa, Enterobacter aerogenes, Corynebacterium sp., Acinetobacter sp., Aeromonas punctata, Ralstonia picketti, Staphylococcus aureus, Stenotrophomonas maltophillia, and Citrobacter freundii. The phenotypic profile of resistance through antibiotic susceptibility test was carried out against sixteen different antibiotics. Standard PCR technique was used for the detection of 12 resistance genes encoding carbapenems, quinoline, aminoglycoside, β-lactam belonging blaOXA-58,blaOXA-22,qnrA, qnrB, aac(6)-Ib-cr, aac (3)-XI, mec A, qepA, aadB, blaVIM, blaOXA-48 and blaNDM. Pseudomonas aeruginosa (1: TN/I/2020) showed presence of 3 resistance genes. qnrB (489 bp) gene was present in maximum of 7 isolates while blaVIM (196 bp) gene was present in 6 isolates. The resistance genes blaNDM (621 bp) was present in three different isolates; aac (X):6)-lb-cr (482 bp), qepA (495 bp), aadB (500 bp), blaOXA-58 (843 bp) resistant genes were present in two different isolates each among the bacterial isolates obtained in this study. In phenotypic resistance profiling by AST method, out of 16 antibiotics tested, 14 showed resistance. Similarly, in genotypic resistance profiling, among 12 resistance genes tested, a maximum of three resistance genes were noticed in Pseudomonas aeruginosa. There were positive and negative correlations observed between phenotypic and genotypic resistance among different antibiotics and their resistance genes indicating the variations in the resistance gene expression.

Unravelling the impact of epigenetic mechanisms on offspring growth, production, reproduction and disease susceptibility.

Epigenetic mechanisms, such as DNA methylation, histone modifications and non-coding RNA molecules, play a critical role in gene expression and regulation in livestock species, influencing development, reproduction and disease resistance. DNA methylation patterns silence gene expression by blocking transcription factor binding, while histone modifications alter chromatin structure and affect DNA accessibility. Livestock-specific histone modifications contribute to gene expression and genome stability. Non-coding RNAs, including miRNAs, piRNAs, siRNAs, snoRNAs, lncRNAs and circRNAs, regulate gene expression post-transcriptionally. Transgenerational epigenetic inheritance occurs in livestock, with environmental factors impacting epigenetic modifications and phenotypic traits across generations. Epigenetic regulation revealed significant effect on gene expression profiling that can be exploited for various targeted traits like muscle hypertrophy, puberty onset, growth, metabolism, disease resistance and milk production in livestock and poultry breeds. Epigenetic regulation of imprinted genes affects cattle growth and metabolism while epigenetic modifications play a role in disease resistance and mastitis in dairy cattle, as well as milk protein gene regulation during lactation. Nutri-epigenomics research also reveals the influence of maternal nutrition on offspring's epigenetic regulation of metabolic homeostasis in cattle, sheep, goat and poultry. Integrating cyto-genomics approaches enhances understanding of epigenetic mechanisms in livestock breeding, providing insights into chromosomal structure, rearrangements and their impact on gene regulation and phenotypic traits. This review presents potential research areas to enhance production potential and deepen our understanding of epigenetic changes in livestock, offering opportunities for genetic improvement, reproductive management, disease control and milk production in diverse livestock species.

Quinolone antibiotics stimulate bacterial mercury methylation by Geobacter metallireducens GS-15

Bacterial mercury (Hg) methylation is critical for bioremediating Hg pollution, but the impact of emerging antibiotics on this process has rarely been reported. This study innovatively investigated the interactions between Hg-methylating bacteria of Geobacter metallireducens GS-15 and two quinolone antibiotics: lomefloxacin (LOM) and ciprofloxacin (CIP) at 5 μg/L. Short-term LOM exposure increased methylmercury (MeHg) yield by 36 % compared to antibiotic-free conditions, caused by hormesis to alter bioactivities of single GS-15 cells. Long-term CIP exposure led to more antibiotic resistance and mercury tolerance in GS-15 cells, doubling MeHg productivity and significantly increasing expression of Hg methylation (hgcA by 95 folds) and antibiotic resistance (gyrA by 54 folds) genes, while mercury resistance gene merA only increased by 2.5 folds than without selective pressure. These results suggest quinolone antibiotics at environmentally contaminated concentrations stimulate bacterial Hg methylation to form highly toxic MeHg, raising considerable concern for the Hg-antibiotic complex in contaminated environments.

Csn-miR171b-3p_2 targets CsSCL6-4 to participate in the defense against drought stress in tea plant

Drought stress is a serious natural challenge for tea plants that significantly affects tea yield and quality. miR171s play critical roles in plant stress responses, however, their role in drought stress tolerance in tea plants (Camellia sinensis) is poorly understood. This study experimentally verified the expression patterns of csn-miR171b-3p_2 and its target, scarecrow-like (SCL). We found that csn-miR171b-3p_2 could target and regulate CsSCL6-4 to play an important role in the defense against drought stress in tea plants. CsSCL6-4 is located in the nucleus and is self-activated in vivo. In addition, we obtained 819 putative binding regions of CsSCL6-4 using DNA affinity purification sequencing analysis, which were assigned to 786 different genes, four of which were drought-resistant genes (CsPrx, CsSDR, CsFAD7, and CsCER1). Yeast one-hybrid and dual-luciferase reporter assays revealed that CsSCL6-4 directly promoted the expression of these four drought resistance genes by binding motifs 1/2/3 in their promoter regions. Both overexpression and suppression of CsSCL6-4 proved that CsSCL6-4 participated in the defense against drought stress in tea plants by regulating the expression of CsPrx, CsSDR, CsFAD7, and CsCER1. In addition, suppression of csn-miR171b-3p_2 expression significantly increased the expression of CsSCL6-4 and activated CsSCL6-4-bound gene transcription under drought stress. Therefore, the csn-miR171b-3p_2-CsSCL6-4 module participates in tea plant resistance to drought stress by promoting the expression of drought resistance genes. Our results revealed the function of csn-miR171b-3p_2 in tea plants and provided new insights into the mechanism of tea plant resistance to drought stress.

Effects of acetic acid fermentation product and its components on defense signaling in rice.

Acetic acid fermentation product made from isomalto-oligosaccharide as the main raw material is composed of isomalto-oligosaccharide and acetic acid. In this paper, we have shown that the fermentation product enhanced the expression of disease resistance genes in rice, and that its main functional component was acetic acid. It has been reported so far that acetic acid enhances the jasmonic acid signaling pathway, while the role of isomalto-oligosaccharide in plant defense signaling remains unclear. In this study, we demonstrated the possibility that isomalto-oligosaccharide shifted part of the jasmonic acid signaling pathway, which is enhanced by acetic acid, to the salicylic acid signaling pathway, which is the other major defense pathway. Furthermore, glucose, a constituent monosaccharide of isomalto-oligosaccharide, and a disaccharide maltose had little effect on the signaling pathway, but a trisaccharide maltotriose tended to have a similar effect to isomalto-oligosaccharide on the defense signaling pathway.

The effect of novel β-lactam derivatives synthesized from substituted phenethylamines on resistance genes of MRSA isolates.

This study focuses on the activity of previously reported imine and β-lactam derivatives against methicillin-resistant Staphylococcus aureus (MRSA) isolates. The presence of mecA and blaZ genes in the isolates was determined, and the minimum inhibitory concentration (MIC) values were determined based on the antibacterial activity against these isolates. Active compounds were selected and their ability to act against resistant isolates in vitro was determined. Concurrently, biochemical (nitrocefin) and molecular (qRT-PCR) tests were used to investigate the ability of the compounds to induce resistance genes in MRSA isolates. The cytotoxicity of the compounds on human dermal fibroblasts (HDF) was investigated. The MIC values of compounds (10) and (12) against MSSA and MRSA isolates were 7.81 and 15.62 μg ml-1, respectively. The most active compounds were identified as (10) and (12), and it was observed that the isolates did not develop resistance to these compounds in vitro. These compounds were found to inhibit β-lactamase, reduce the expression of resistance genes, and exhibit reduced HDF cell toxicity in a dose-dependent manner. According to the findings of the study, it can be concluded that these compounds show promise as hits with an interesting mechanism of action for further chemical modifications to develop new MRSA inhibitors.

Synonymous codon substitutions modulate transcription and translation of a divergent upstream gene by modulating antisense RNA production

Synonymous codons were originally viewed as interchangeable, with no phenotypic consequences. However, substantial evidence has now demonstrated that synonymous substitutions can perturb a variety of gene expression and protein homeostasis mechanisms, including translational efficiency, translational fidelity, and cotranslational folding of the encoded protein. To date, most studies of synonymous codon-derived perturbations have focused on effects within a single gene. Here, we show that synonymous codon substitutions made far within the coding sequence of Escherichia coli plasmid-encoded chloramphenicol acetyltransferase (cat) can significantly increase expression of the divergent upstream tetracycline resistance gene, tetR. In four out of nine synonymously recoded cat sequences tested, expression of the upstream tetR gene was significantly elevated due to transcription of a long antisense RNA (asRNA) originating from a transcription start site within cat. Surprisingly, transcription of this asRNA readily bypassed the native tet transcriptional repression mechanism. Even more surprisingly, accumulation of the TetR protein correlated with the level of asRNA, rather than total tetR RNA. These effects of synonymous codon substitutions on transcription and translation of a neighboring gene suggest that synonymous codon usage in bacteria may be under selection to both preserve the amino acid sequence of the encoded gene and avoid DNA sequence elements that can significantly perturb expression of neighboring genes. Avoiding such sequences may be especially important in plasmids and prokaryotic genomes, where genes and regulatory elements are often densely packed. Similar considerations may apply to the design of genetic circuits for synthetic biology applications.

Genome-Wide Identification and Expression Analyses of the Thaumatin-Like Protein Gene Family in Tetragonia tetragonoides (Pall.) Kuntze Reveal Their Functions in Abiotic Stress Responses.

Thaumatin-like proteins (TLPs), including osmotins, are multifunctional proteins related to plant biotic and abiotic stress responses. TLPs are often present as large multigene families. Tetragonia tetragonoides (Pall.) Kuntze (Aizoaceae, 2n = 2x = 32), a vegetable used in both food and medicine, is a halophyte that is widely distributed in the coastal areas of the tropics and subtropics. Saline-alkaline soils and drought are two major abiotic stress factors significantly affecting the distribution of tropical coastal plants. The expression of stress resistance genes would help to alleviate the cellular damage caused by abiotic stress factors such as high temperature, salinity-alkalinity, and drought. This study aimed to better understand the functions of TLPs in the natural ecological adaptability of T. tetragonoides to harsh habitats. In the present study, we used bioinformatics approaches to identify 37 TtTLP genes as gene family members in the T. tetragonoides genome, with the purpose of understanding their roles in different developmental processes and the adaptation to harsh growth conditions in tropical coral regions. All of the TtTLPs were irregularly distributed across 32 chromosomes, and these gene family members were examined for conserved motifs of their coding proteins and gene structure. Expression analysis based on RNA sequencing and subsequent qRT-PCR showed that the transcripts of some TtTLPs were decreased or accumulated with tissue specificity, and under environmental stress challenges, multiple TtTLPs exhibited changeable expression patterns at short (2 h), long (48 h), or both stages. The expression pattern changes in TtTLPs provided a more comprehensive overview of this gene family being involved in multiple abiotic stress responses. Furthermore, several TtTLP genes were cloned and functionally identified using the yeast expression system. These findings not only increase our understanding of the role that TLPs play in mediating halophyte adaptation to extreme environments but also improve our knowledge of plant TLP evolution. This study also provides a basis and reference for future research on the roles of plant TLPs in stress tolerance and ecological environment suitability.

How can the microbial community in watershed sediment maintain its resistance in the presence of shifting antibiotic residuals?

The widespread presence of antibiotics in global watershed environments poses a serious threat to public health and ecosystems. It is essential to examine the resistance of microbial communities in watershed environments in response to shifting antibiotic residues. Sediment samples were collected from seven sites across a watershed, encompassing surface sediment (0–10 cm) and bottom sediment (30–40 cm) depths. The aim was to replicate exposure scenarios to different antibiotics (oxytetracycline (OTC) and sulfadiazine (SD)) at varying concentrations (0, 10, and 100 μg/L) in sediment overlying water, within controlled laboratory settings. The study findings revealed significant variations in the microbial community structure of sediments between different treatments, with distinct differences observed in the upper stream and top sediment layers compared to the sediments located downstream and in the bottom layers. After the introduction of antibiotics, a significant decrease in microbial nodes was observed in the genus-level co-occurrence network analysis of the bottom sediment layer, particularly in the OTC treatment groups. In contrast, the downstream region displayed more robust correlations among the top 20 genera than the upstream area. There was no significant variance observed in the expression of Antibiotic resistance genes (ARGs), consisting of tetracycline resistance genes (tetC, tetG, tetM, tetW, and tetX) and sulfonamide resistance genes (sul1, sul2, and sul3), between sediments in the top and bottom layers. Nevertheless, downstream samples exhibited significantly higher levels of ARGs when compared to upstream samples. Network correlation analysis indicated notably lower correlations between ARGs and bacterial genera in sediments from upstream or surface layers compared to those in downstream or deeper layers. Moreover, correlations in the sediments from surface layers and upstream regions showed a decreasing trend with increasing SD exposure concentrations, while those in deeper layers and downstream areas remained relatively stable. The presence of antibiotics notably enhanced the correlation between sediment properties and ARGs, particularly emphasizing associations with total carbon, nitrogen, and sulfur content. However, the introduction of SD and OTC resulted in a decrease in the influence of these sediment factors on microbial community functions related to sulfur and nitrogen metabolism, as indicated by KEGG (Kyoto Encyclopedia of Genes and Genomes) annotation. The research provided empirical evidence on how microbial resistance responds to changes in antibiotics in sediment samples taken from various depths and locations within a watershed. It emphasized the urgent need for heightened awareness of the movement and alteration of antibiotic resistance patterns in watershed ecosystems.