# | Rank | Similarity | Title + Abs. | Year | PMID |
|---|---|---|---|---|---|
| 0 | 1 | 2 | 3 | 4 | 5 |
| 8259 | 0 | 0.9900 | Secondary Metabolite Transcriptomic Pipeline (SeMa-Trap), an expression-based exploration tool for increased secondary metabolite production in bacteria. For decades, natural products have been used as a primary resource in drug discovery pipelines to find new antibiotics, which are mainly produced as secondary metabolites by bacteria. The biosynthesis of these compounds is encoded in co-localized genes termed biosynthetic gene clusters (BGCs). However, BGCs are often not expressed under laboratory conditions. Several genetic manipulation strategies have been developed in order to activate or overexpress silent BGCs. Significant increases in production levels of secondary metabolites were indeed achieved by modifying the expression of genes encoding regulators and transporters, as well as genes involved in resistance or precursor biosynthesis. However, the abundance of genes encoding such functions within bacterial genomes requires prioritization of the most promising ones for genetic manipulation strategies. Here, we introduce the 'Secondary Metabolite Transcriptomic Pipeline' (SeMa-Trap), a user-friendly web-server, available at https://sema-trap.ziemertlab.com. SeMa-Trap facilitates RNA-Seq based transcriptome analyses, finds co-expression patterns between certain genes and BGCs of interest, and helps optimize the design of comparative transcriptomic analyses. Finally, SeMa-Trap provides interactive result pages for each BGC, allowing the easy exploration and comparison of expression patterns. In summary, SeMa-Trap allows a straightforward prioritization of genes that could be targeted via genetic engineering approaches to (over)express BGCs of interest. | 2022 | 35580059 |
| 8633 | 1 | 0.9896 | Bacterial interactions with arsenic: Metabolic pathways, resistance mechanisms, and bioremediation approaches. Arsenic contamination in natural waters is one of the biggest threats to human health, mainly due to its carcinogenic potential. Given its toxicity, nearly all organisms have evolved to develop an arsenic resistance mechanism. Conventional techniques of arsenic remediation suffer from various limitations of their applicability, cost and/or chemical intensive nature. In past few decades, bioremediation has emerged as a potential alternative to the conventional techniques. Microbial bioremediation, bacteria in particular, offers an eco-friendly and sustainable alternative, owing to its inherent metabolic capabilities to transform, immobilize or volatilize arsenic. Diverse biochemical pathways involving oxidation of As(III) to As(V), reduction of As(V) under anaerobic respiration or detoxification, methylation and demethylation, bioleaching and biomineralization into insoluble forms are essential mechanisms for arsenic remediation. These transformations, detoxification and resistance are regulated by specific genetic systems, including the ars operon, aio, arr and arsM, accessory genes such as arsR, arsB, acr3, arsC and arsP. The metabolic regulation of arsenic detoxification involves complex cofactor-dependent enzyme systems and environmental signal-responsive transcriptional control. Integrated approaches such as immobilization of bacteria on biochar or their encapsulation have also been known to enhance stability, reusability and stress tolerance. However, bioremediation is a very complex process due to the interrelationship of various influences such as, presence of specific microorganisms, nutrients and environmental factors. Therefore, it is of utmost importance to understand the bacterial interactions with arsenic for the development of bioremediation technologies. This review article tries to discuss the current status of arsenic bioremediation using bacteria, its field applications, challenges and future perspectives. It also includes the strengths, weaknesses, opportunities, threats (SWOT) analysis to assess the merits and demerits of using bacteria for bioremediation of arsenic. | 2025 | 41043264 |
| 664 | 2 | 0.9893 | Ferric Uptake Regulator Provides a New Strategy for Acidophile Adaptation to Acidic Ecosystems. Acidophiles play a dominant role in driving elemental cycling in natural acid mine drainage (AMD) habitats and exhibit important application value in bioleaching and bioremediation. Acidity is an inevitable environmental stress and a key factor that affects the survival of acidophiles in their acidified natural habitats; however, the regulatory strategies applied by acidophilic bacteria to withstand low pH are unclear. We identified the significance of the ferric uptake regulator (Fur) in acidophiles adapting to acidic environments and discovered that Fur is ubiquitous as well as highly conserved in acidophilic bacteria. Mutagenesis of the fur gene of Acidithiobacillus caldus, a prototypical acidophilic sulfur-oxidizing bacterium found in AMD, revealed that Fur is required for the acid resistance of this acidophilic bacterium. Phenotypic characterization, transcriptome sequencing (RNA-seq), mutagenesis, and biochemical assays indicated that the Acidithiobacillus caldus ferric uptake regulator (AcFur) is involved in extreme acid resistance by regulating the expression of several key genes of certain cellular activities, such as iron transport, biofilm formation, sulfur metabolism, chemotaxis, and flagellar biosynthesis. Finally, a Fur-dependent acid resistance regulatory strategy in A. caldus was proposed to illustrate the ecological behavior of acidophilic bacteria under low pH. This study provides new insights into the adaptation strategies of acidophiles to AMD ecosystems and will promote the design and development of engineered biological systems for the environmental adaptation of acidophiles.IMPORTANCE This study advances our understanding of the acid tolerance mechanism of A. caldus, identifies the key fur gene responsible for acid resistance, and elucidates the correlation between fur and acid resistance, thus contributing to an understanding of the ecological behavior of acidophilic bacteria. These findings provide new insights into the acid resistance process in Acidithiobacillus species, thereby promoting the study of the environmental adaptation of acidophilic bacteria and the design of engineered biological systems. | 2020 | 32245756 |
| 8647 | 3 | 0.9892 | Eco-evolutionary strategies for relieving carbon limitation under salt stress differ across microbial clades. With the continuous expansion of saline soils under climate change, understanding the eco-evolutionary tradeoff between the microbial mitigation of carbon limitation and the maintenance of functional traits in saline soils represents a significant knowledge gap in predicting future soil health and ecological function. Through shotgun metagenomic sequencing of coastal soils along a salinity gradient, we show contrasting eco-evolutionary directions of soil bacteria and archaea that manifest in changes to genome size and the functional potential of the soil microbiome. In salt environments with high carbon requirements, bacteria exhibit reduced genome sizes associated with a depletion of metabolic genes, while archaea display larger genomes and enrichment of salt-resistance, metabolic, and carbon-acquisition genes. This suggests that bacteria conserve energy through genome streamlining when facing salt stress, while archaea invest in carbon-acquisition pathways to broaden their resource usage. These findings suggest divergent directions in eco-evolutionary adaptations to soil saline stress amongst microbial clades and serve as a foundation for understanding the response of soil microbiomes to escalating climate change. | 2024 | 39019914 |
| 8360 | 4 | 0.9892 | Genome mining of Streptomyces scabrisporus NF3 reveals symbiotic features including genes related to plant interactions. Endophytic bacteria are wide-spread and associated with plant physiological benefits, yet their genomes and secondary metabolites remain largely unidentified. In this study, we explored the genome of the endophyte Streptomyces scabrisporus NF3 for discovery of potential novel molecules as well as genes and metabolites involved in host interactions. The complete genomes of seven Streptomyces and three other more distantly related bacteria were used to define the functional landscape of this unique microbe. The S. scabrisporus NF3 genome is larger than the average Streptomyces genome and not structured for an obligate endosymbiotic lifestyle; this and the fact that can grow in R2YE media implies that it could include a soil-living stage. The genome displays an enrichment of genes associated with amino acid production, protein secretion, secondary metabolite and antioxidants production and xenobiotic degradation, indicating that S. scabrisporus NF3 could contribute to the metabolic enrichment of soil microbial communities and of its hosts. Importantly, besides its metabolic advantages, the genome showed evidence for differential functional specificity and diversification of plant interaction molecules, including genes for the production of plant hormones, stress resistance molecules, chitinases, antibiotics and siderophores. Given the diversity of S. scabrisporus mechanisms for host upkeep, we propose that these strategies were necessary for its adaptation to plant hosts and to face changes in environmental conditions. | 2018 | 29447216 |
| 8254 | 5 | 0.9891 | Transgenic Improvement for Biotic Resistance of Crops. Biotic constraints, including pathogenic fungi, viruses and bacteria, herbivory insects, as well as parasitic nematodes, cause significant yield loss and quality deterioration of crops. The effect of conventional management of these biotic constraints is limited. The advances in transgenic technologies provide a direct and directional approach to improve crops for biotic resistance. More than a hundred transgenic events and hundreds of cultivars resistant to herbivory insects, pathogenic viruses, and fungi have been developed by the heterologous expression of exogenous genes and RNAi, authorized for cultivation and market, and resulted in a significant reduction in yield loss and quality deterioration. However, the exploration of transgenic improvement for resistance to bacteria and nematodes by overexpression of endogenous genes and RNAi remains at the testing stage. Recent advances in RNAi and CRISPR/Cas technologies open up possibilities to improve the resistance of crops to pathogenic bacteria and plant parasitic nematodes, as well as other biotic constraints. | 2022 | 36430848 |
| 8692 | 6 | 0.9891 | Genetic mechanisms of arsenic detoxification and metabolism in bacteria. Arsenic, distributed pervasively in the natural environment, is an extremely toxic substance which can severely impair the normal functions of living cells. Research on the genetic mechanisms of arsenic metabolism is of great importance for remediating arsenic-contaminated environments. Many organisms, including bacteria, have developed various strategies to tolerate arsenic, by either detoxifying this harmful element or utilizing it for energy generation. This review summarizes arsenic detoxification as well as arsenic respiratory metabolic pathways in bacteria and discusses novel arsenic resistance pathways in various bacterial strains. This knowledge provides insights into the mechanisms of arsenic biotransformation in bacteria. Multiple detoxification strategies among bacteria imply possible functional relationships among different arsenic detoxification/metabolism pathways. In addition, this review sheds light on the bioremediation of arsenic-contaminated environments and prevention of antibiotic resistance. | 2019 | 30349994 |
| 8631 | 7 | 0.9891 | Bacterial metal(loid) resistance genes (MRGs) and their variation and application in environment: A review. Toxic metal(loid)s are widespread and permanent in the biosphere, and bacteria have evolved a wide variety of metal(loid) resistance genes (MRGs) to resist the stress of excess metal(loid)s. Via active efflux, permeability barriers, extracellular/intracellular sequestration, enzymatic detoxification and reduction in metal(loid)s sensitivity of cellular targets, the key components of bacterial cells are protected from toxic metal(loid)s to maintain their normal physiological functions. Exploiting bacterial metal(loid) resistance mechanisms, MRGs have been applied in many environmental fields. Based on the specific binding ability of MRGs-encoded regulators to metal(loid)s, MRGs-dependent biosensors for monitoring environmental metal(loid)s are developed. MRGs-related biotechnologies have been applied to environmental remediation of metal(loid)s by using the metal(loid) tolerance, biotransformation, and biopassivation abilities of MRGs-carrying microorganisms. In this work, we review the historical evolution, resistance mechanisms, environmental variation, and environmental applications of bacterial MRGs. The potential hazards, unresolved problems, and future research directions are also discussed. | 2023 | 36758696 |
| 9727 | 8 | 0.9890 | Metal Toxicity and Resistance in Plants and Microorganisms in Terrestrial Ecosystems. Metals are major abiotic stressors of many organisms, but their toxicity in plants is not as studied as in microorganisms and animals. Likewise, research in plant responses to metal contamination is sketchy. Candidate genes associated with metal resistance in plants have been recently discovered and characterized. Some mechanisms of plant adaptation to metal stressors have been now decrypted. New knowledge on microbial reaction to metal contamination and the relationship between bacterial, archaeal, and fungal resistance to metals has broadened our understanding of metal homeostasis in living organisms. Recent reviews on metal toxicity and resistance mechanisms focused only on the role of transcriptomics, proteomics, metabolomics, and ionomics. This review is a critical analysis of key findings on physiological and genetic processes in plants and microorganisms in responses to soil metal contaminations. | 2020 | 30725190 |
| 8636 | 9 | 0.9890 | Insights into the synthesis, engineering, and functions of microbial pigments in Deinococcus bacteria. The ability of Deinococcus bacteria to survive in harsh environments, such as high radiation, extreme temperature, and dryness, is mainly attributed to the generation of unique pigments, especially carotenoids. Although the limited number of natural pigments produced by these bacteria restricts their industrial potential, metabolic engineering and synthetic biology can significantly increase pigment yield and expand their application prospects. In this study, we review the properties, biosynthetic pathways, and functions of key enzymes and genes related to these pigments and explore strategies for improving pigment production through gene editing and optimization of culture conditions. Additionally, studies have highlighted the unique role of these pigments in antioxidant activity and radiation resistance, particularly emphasizing the critical functions of deinoxanthin in D. radiodurans. In the future, Deinococcus bacterial pigments will have broad application prospects in the food industry, drug production, and space exploration, where they can serve as radiation indicators and natural antioxidants to protect astronauts' health during long-term space flights. | 2024 | 39119139 |
| 8634 | 10 | 0.9890 | Synthetic bacteria designed using ars operons: a promising solution for arsenic biosensing and bioremediation. The global concern over arsenic contamination in water due to its natural occurrence and human activities has led to the development of innovative solutions for its detection and remediation. Microbial metabolism and mobilization play crucial roles in the global cycle of arsenic. Many microbial arsenic-resistance systems, especially the ars operons, prevalent in bacterial plasmids and genomes, play vital roles in arsenic resistance and are utilized as templates for designing synthetic bacteria. This review novelty focuses on the use of these tailored bacteria, engineered with ars operons, for arsenic biosensing and bioremediation. We discuss the advantages and disadvantages of using synthetic bacteria in arsenic pollution treatment. We highlight the importance of genetic circuit design, reporter development, and chassis cell optimization to improve biosensors' performance. Bacterial arsenic resistances involving several processes, such as uptake, transformation, and methylation, engineered in customized bacteria have been summarized for arsenic bioaccumulation, detoxification, and biosorption. In this review, we present recent insights on the use of synthetic bacteria designed with ars operons for developing tailored bacteria for controlling arsenic pollution, offering a promising avenue for future research and application in environmental protection. | 2024 | 38709285 |
| 8644 | 11 | 0.9890 | Biotic and abiotic drivers of soil carbon, nitrogen and phosphorus and metal dynamic changes during spontaneous restoration of Pb-Zn mining wastelands. The biotic and abiotic mechanisms that drive important biogeochemical processes (carbon, nitrogen, phosphorus and metals dynamics) in metal mine revegetation remains elusive. Metagenomic sequencing was used to explored vegetation, soil properties, microbial communities, functional genes and their impacts on soil processes during vegetation restoration in a typical Pb-Zn mine. The results showed a clear niche differentiation between bacteria, fungi and archaea. Compared to bacteria and fungi, the archaea richness were more tightly coupled with natural restoration changes. The relative abundances of CAZyme-related, denitrification-related and metal resistance genes reduced, while nitrification, urease, inorganic phosphorus solubilisation, phosphorus transport, and phosphorus regulation -related genes increased. Redundancy analysis, hierarchical partitioning analysis, relative-importance analysis and partial least squares path modelling, indicated that archaea diversity, primarily influenced by available lead, directly impacts carbon dynamics. Functional genes, significantly affected by available cadmium, directly alter nitrogen dynamics. Additionally, pH affects phosphorus dynamics through changes in bacterial diversity, while metal dynamics are directly influenced by vegetation. These insights elucidate natural restoration mechanisms in mine and highlight the importance of archaea in soil processes. | 2025 | 40054196 |
| 8422 | 12 | 0.9890 | Slightly beneficial genes are retained by bacteria evolving DNA uptake despite selfish elements. Horizontal gene transfer (HGT) and gene loss result in rapid changes in the gene content of bacteria. While HGT aids bacteria to adapt to new environments, it also carries risks such as selfish genetic elements (SGEs). Here, we use modelling to study how HGT of slightly beneficial genes impacts growth rates of bacterial populations, and if bacterial collectives can evolve to take up DNA despite selfish elements. We find four classes of slightly beneficial genes: indispensable, enrichable, rescuable, and unrescuable genes. Rescuable genes - genes with small fitness benefits that are lost from the population without HGT - can be collectively retained by a community that engages in costly HGT. While this 'gene-sharing' cannot evolve in well-mixed cultures, it does evolve in a spatial population like a biofilm. Despite enabling infection by harmful SGEs, the uptake of foreign DNA is evolutionarily maintained by the hosts, explaining the coexistence of bacteria and SGEs. | 2020 | 32432548 |
| 8635 | 13 | 0.9890 | Techniques for enhancing the tolerance of industrial microbes to abiotic stresses: A review. The diversity of stress responses and survival strategies evolved by microorganism enables them to survive and reproduce in a multitude of harsh environments, whereas the discovery of the underlying resistance genes or mechanisms laid the foundation for the directional enhancement of microbial tolerance to abiotic stresses encountered in industrial applications. Many biological techniques have been developed for improving the stress resistance of industrial microorganisms, which greatly benefited the bacteria on which industrial production is based. This review introduces the main techniques for enhancing the resistance of microorganisms to abiotic stresses, including evolutionary engineering, metabolic engineering, and process engineering, developed in recent years. In addition, we also discuss problems that are still present in this area and offer directions for future research. | 2020 | 31206805 |
| 8658 | 14 | 0.9890 | Microplastic exposure reshapes the virome and virus-bacteria networks with implications for immune regulation in Mytilus coruscus. Microplastic pollution has emerged as a critical environmental concern, yet its impacts on host-associated viral communities and immune balance in marine bivalves remain largely unexplored. In this study, Mytilus coruscus individuals were exposed to microplastics in situ for seven days. Virome sequencing and bioinformatic analyses revealed that microplastic exposure induced divergent responses in DNA and RNA viral communities. DNA viromes exhibited suppressed diversity and downregulation of core viral metabolic pathways, potentially reflecting reduced viral replication capacity under host immune stress. In contrast, RNA viromes displayed metabolic activation and functional shifts, including enriched glycan and nucleotide metabolism, possibly linked to enhanced viral activity or immune evasion. Phage-bacteria interaction networks were also restructured, showing increased associations with opportunistic pathogens such as Vibrio cholerae and Enterobacter, potentially affecting immune surveillance. Furthermore, the expression of antibiotic resistance genes (ARGs) in viral genomes was differentially regulated, suggesting pollutant-induced microbial selection that may challenge host immune resilience. These findings suggest that microplastics not only reshape virome composition and metabolic functions but also influence virus-mediated immune interactions, with important implications for disease susceptibility and immune homeostasis in filter-feeding shellfish. | 2025 | 41056669 |
| 8266 | 15 | 0.9889 | Remarkable Mechanisms in Microbes to Resist Phage Infections. Bacteriophages (phages) specifically infect bacteria and are the most abundant biological entities on Earth. The constant exposure to phage infection imposes a strong selective pressure on bacteria to develop viral resistance strategies that promote prokaryotic survival. Thus, this parasite-host relationship results in an evolutionary arms race of adaptation and counteradaptation between the interacting partners. The evolutionary outcome is a spectrum of remarkable strategies used by the bacteria and phages as they attempt to coexist. These approaches include adsorption inhibition, injection blocking, abortive infection, toxin-antitoxin, and CRISPR-Cas systems. In this review, we highlight the diverse and complementary antiphage systems in bacteria, as well as the evasion mechanisms used by phages to escape these resistance strategies. | 2014 | 26958724 |
| 9180 | 16 | 0.9889 | Novel genes for disease-resistance breeding. Plant disease control is entering an exciting period during which transgenic plants showing improved resistance to pathogenic viruses, bacteria, fungi and insects are being developed. This review summarizes the first successful attempts to engineer fungal resistance in crops, and highlights two promising approaches. Biotechnology provides the promise of new integrated disease management strategies that combine modern fungicides and transgenic crops to provide effective disease control for modern agriculture. | 2000 | 10712959 |
| 9583 | 17 | 0.9889 | Bacteriophages presence in nature and their role in the natural selection of bacterial populations. Phages are the obligate parasite of bacteria and have complex interactions with their hosts. Phages can live in, modify, and shape bacterial communities by bringing about changes in their abundance, diversity, physiology, and virulence. In addition, phages mediate lateral gene transfer, modify host metabolism and reallocate bacterially-derived biochemical compounds through cell lysis, thus playing an important role in ecosystem. Phages coexist and coevolve with bacteria and have developed several antidefense mechanisms in response to bacterial defense strategies against them. Phages owe their existence to their bacterial hosts, therefore they bring about alterations in their host genomes by transferring resistance genes and genes encoding toxins in order to improve the fitness of the hosts. Application of phages in biotechnology, environment, agriculture and medicines demands a deep insight into the myriad of phage-bacteria interactions. However, to understand their complex interactions, we need to know how unique phages are to their bacterial hosts and how they exert a selective pressure on the microbial communities in nature. Consequently, the present review focuses on phage biology with respect to natural selection of bacterial populations. | 2020 | 33170167 |
| 8632 | 18 | 0.9889 | Microbial interactions in the arsenic cycle: adoptive strategies and applications in environmental management. Arsenic (As) is a nonessential element that is often present in plants and in other organisms. However, it is one of the most hazardous of toxic elements globally. In many parts of the world, arsenic contamination in groundwater is a serious and continuing threat to human health. Microbes play an important role in regulating the environmental fate of arsenic. Different microbial processes influence the biogeochemical cycling of arsenic in ways that affect the accumulation of different arsenic species in various ecosystem compartments. For example, in soil, there are bacteria that methylate arsenite to trimethylarsine gas, thereby releasing arsenic to the atmosphere.In marine ecosystems, microbes exist that can convert inorganic arsenicals to organic arsenicals (e.g., di- and tri-methylated arsenic derivatives, arsenocholine,arsenobetaine, arsenosugars, arsenolipids). The organo arsenicals are further metabolized to complete the arsenic cycle.Microbes have developed various strategies that enable them to tolerate arsenic and to survive in arsenic-rich environments. Such strategies include As exclusion from cells by establishing permeability barrier, intra- and extracellular sequestration,active efflux pumps, enzymatic reduction, and reduction in the sensitivity of cellular targets. These strategies are used either singly or in combination. In bacteria,the genes for arsenic resistance/detoxification are encoded by the arsenic resistance operons (ars operon).In this review, we have addressed and emphasized the impact of different microbial processes (e.g., arsenite oxidation, cytoplasmic arsenate reduction, respiratory arsenate reduction, arsenite methylation) on the arsenic cycle. Microbes are the only life forms reported to exist in heavy arsenic-contaminated environments. Therefore,an understanding of the strategies adopted by microbes to cope with arsenic stress is important in managing such arsenic-contaminated sites. Further future insights into the different microbial genes/proteins that are involved in arsenic resistance may also be useful for developing arsenic resistant crop plants. | 2013 | 23232917 |
| 9179 | 19 | 0.9889 | A detailed landscape of CRISPR-Cas-mediated plant disease and pest management. Genome editing technology has rapidly evolved to knock-out genes, create targeted genetic variation, install precise insertion/deletion and single nucleotide changes, and perform large-scale alteration. The flexible and multipurpose editing technologies have started playing a substantial role in the field of plant disease management. CRISPR-Cas has reduced many limitations of earlier technologies and emerged as a versatile toolbox for genome manipulation. This review summarizes the phenomenal progress of the use of the CRISPR toolkit in the field of plant pathology. CRISPR-Cas toolbox aids in the basic studies on host-pathogen interaction, in identifying virulence genes in pathogens, deciphering resistance and susceptibility factors in host plants, and engineering host genome for developing resistance. We extensively reviewed the successful genome editing applications for host plant resistance against a wide range of biotic factors, including viruses, fungi, oomycetes, bacteria, nematodes, insect pests, and parasitic plants. Recent use of CRISPR-Cas gene drive to suppress the population of pathogens and pests has also been discussed. Furthermore, we highlight exciting new uses of the CRISPR-Cas system as diagnostic tools, which rapidly detect pathogenic microorganism. This comprehensive yet concise review discusses innumerable strategies to reduce the burden of crop protection. | 2022 | 35835393 |