Current Microbiology最新文献_第9页

Harnessing the Power of Donkey's Milk and Homemade Pickles: Unveiling Oxalate-Degrading Probiotics and Their Heat-Killed Cells as Antiadipogenic Agents in 3T3-L1 Adipocytes.

IF 2.3 3区生物学

Current Microbiology Pub Date : 2025-02-26 DOI: 10.1007/s00284-025-04146-9

Shridhar Hiremath, Pragasam Viswanathan

{"title":"Harnessing the Power of Donkey's Milk and Homemade Pickles: Unveiling Oxalate-Degrading Probiotics and Their Heat-Killed Cells as Antiadipogenic Agents in 3T3-L1 Adipocytes.","authors":"Shridhar Hiremath, Pragasam Viswanathan","doi":"10.1007/s00284-025-04146-9","DOIUrl":"10.1007/s00284-025-04146-9","url":null,"abstract":"Gut microbial dysbiosis is associated with the development of critical clinical conditions of metabolic syndrome (obesity, type II diabetes), and calcium oxalate kidney stones. The human gut microbial eubiosis with functional probiotics and their heat-killed cells of lactic acid bacteria (LAB) is considered the current therapy for metabolic syndrome (MS). In accordance with this, our study aimed to isolate oxalate-degrading, cholesterol-lowering, and anti-adipogenic bacterial strains from raw donkey's milk and homemade fermented pickles. Nine LAB strains with potential in vitro oxalate degrading, α-glucosidase inhibiting, and cholesterol-lowering activities were pre-screened from fourteen isolates. Further, the heat-killed cells of selected strains were evaluated for anti-adipogenic activity in murine 3T3-L1 adipocytes. This activity was examined by studying the lipid storage, gene, and protein expression of adipogenic and lipogenic transcription factors. Subsequently, four potential isolates demonstrated a significant reduction in lipid storage by limiting adipogenesis (reducing C/EBPα, PPARγ expression), lipid transportation (downregulating aP2 expression), and lipogenesis (reducing PLIN-1 expression). These effective isolates were characterized using 16S rRNA molecular sequencing, and were identified as closest relatives to the Enterococcus (RRLA5, RRLA1, and RRLD6) and Lactobacillus (RRLM2) genera. Further, they displayed good survivability under in vitro gastric conditions and non-haemolytic activity. Taken together, the live cells of effective isolates depicted significant in vitro oxalate degradation, and their heat-killed cells demonstrated anti-adipogenic activity through downregulating the adipogenesis and lipogenesis. Moreover, future preclinical animal model studies on the synergistic role of probiotics and their heat-killed cells in disease prevention through gut microbial modulation could provide evidence as a biotherapeutic agent.","PeriodicalId":11360,"journal":{"name":"Current Microbiology","volume":"82 4","pages":"155"},"PeriodicalIF":2.3,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143499735","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Deciphering Probiotic Effects of Sulfitobacter pontiacus Strain BL28 on the Host Sea Cucumber Apostichopus japonicus.

IF 2.3 3区生物学

Current Microbiology Pub Date : 2025-02-26 DOI: 10.1007/s00284-025-04138-9

Tomoo Sawabe, Rika Kudo, Juanwen Yu, Thach Nguyen, Andrea Rossi, Yuichi Sakai, Sayaka Mino

{"title":"Deciphering Probiotic Effects of Sulfitobacter pontiacus Strain BL28 on the Host Sea Cucumber Apostichopus japonicus.","authors":"Tomoo Sawabe, Rika Kudo, Juanwen Yu, Thach Nguyen, Andrea Rossi, Yuichi Sakai, Sayaka Mino","doi":"10.1007/s00284-025-04138-9","DOIUrl":"10.1007/s00284-025-04138-9","url":null,"abstract":"Recently, sea cucumber has been an increasingly important marine invertebrate in the fields of EcoDevo and fisheries studies. After the discovery of Sulfitobacter pontiacus strain BL28, which is a growth-promoting probiotic bacteria isolated from blastula of Apostichopus japonicus, host-microbes interaction has become a major new focus of study to be unveiled. Previous genome assessments of the strain BL28 hypothesized involvements of cobalamin/B12 biosynthesis, type IV secretion system, polyhydroxybutyrate production, and sulfate metabolism for host growth promotions. Here, we performed A. japonicus host transcriptome after five weeks of supplementation with S. pontiacus BL28. Unexpectedly, the host transcriptome revealed significant gene regulations of the BL28 supplementation on the host lipid and chondroitin metabolisms and transcriptionally \"rest\" status of heat shock protein genes un-expressed. Physiological and environmental crossover by the S. pontiacus BL28 supplementation may trigger stress-free growth promotion in the host sea cucumber. These symbiotics-type probiotics could help herald the future eco-friendly aquaculture of sea cucumber.","PeriodicalId":11360,"journal":{"name":"Current Microbiology","volume":"82 4","pages":"156"},"PeriodicalIF":2.3,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143499731","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Impact of Species and Developmental Stage on the Bacterial Communities of Aphaenogaster Ants.

IF 2.3 3区生物学

Current Microbiology Pub Date : 2025-02-26 DOI: 10.1007/s00284-025-04128-x

Lily A Kelleher, Manuela O Ramalho

{"title":"Impact of Species and Developmental Stage on the Bacterial Communities of Aphaenogaster Ants.","authors":"Lily A Kelleher, Manuela O Ramalho","doi":"10.1007/s00284-025-04128-x","DOIUrl":"10.1007/s00284-025-04128-x","url":null,"abstract":"Ants are distributed across the globe and there are currently over 14,000 described species. Due to the high diversity between species, ants are considered vital keystone species to many ecosystems. They provide basic ecosystem services such as: seed dispersal, soil bioturbation, decomposition, and pest control. Within these ecosystems ants form complex symbiotic relationships with plants, fungi, and bacteria. Studying the interaction between ants and their bacteria is important because of the crucial role that microbes play in the overall health of ants. Aphaenogaster Mayr, 1853, which is a globally distributed ant genus, remains understudied in terms of their bacterial community. This study aims to determine the taxonomic composition and abundance of the Aphaenogaster bacterial community and to determine if development stage and species impact the bacterial community composition. For this study, ants from several colonies were collected from the Gordon Natural Area in West Chester, Pennsylvania, USA. DNA was then extracted from the ants in all stages of development and the 16S rRNA gene was amplified and sequencing following the NGS amplicon approach. The findings from this study reveal that species and development stage have a significant impact upon the bacterial community composition and abundance of Aphaenogaster ants, and Wolbachia is highly associated with these ants.","PeriodicalId":11360,"journal":{"name":"Current Microbiology","volume":"82 4","pages":"157"},"PeriodicalIF":2.3,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143499757","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Archaeal and Bacterial Communities Within the Wetland Alkaline Har Lake of the Qinghai-Xizang Plateau.

IF 2.3 3区生物学

Current Microbiology Pub Date : 2025-02-25 DOI: 10.1007/s00284-025-04140-1

Yujie Tao, Bohan Shi, Minhaoxue Zou, Lijuan Qiao, Rong Wang, Derui Zhu, Rui Han

{"title":"Archaeal and Bacterial Communities Within the Wetland Alkaline Har Lake of the Qinghai-Xizang Plateau.","authors":"Yujie Tao, Bohan Shi, Minhaoxue Zou, Lijuan Qiao, Rong Wang, Derui Zhu, Rui Han","doi":"10.1007/s00284-025-04140-1","DOIUrl":"10.1007/s00284-025-04140-1","url":null,"abstract":"Har Lake (HL) is in the northeastern basin of the Qinghai-Xizang Plateau (QTP), sits at an altitude of 4379 m, and is classified as a soda lake within a wetland ecosystem. Evaluating the archaeal and bacterial communities in HL could offer valuable insights into the biogeochemical cycling within plateau wetland lakes. Consequently, high-throughput sequencing of 16S rRNA genes was conducted in this study to assess the composition of HL microbial communities and their association with environmental factors. The HL archaeal communities comprised 5 phyla, 5 classes, and 30 genera, while the bacterial communities comprised 28 phyla, 52 classes, and 542 genera. The dominant archaeal phylum was Thaumarchaeota (30.30-93.07% relative abundances), followed by Woesearchaeota (6.79-67.78%), while the most abundant genus was Nitrososphaera (30.30-93.07%). The distribution of Nitrososphaera was significantly correlated with TN, Mg2+, and Ca2+ concentrations. Bacterial communities predominantly comprised the Proteobacteria phylum (59.33-74.70%), followed by Bacteroidetes (13.92-19.19%) and Firmicutes (0.69-9.60%). Dominant bacterial genera included halophilic hydrocarbon-degrading bacteria like Oleibacter (1.90-18.69%), Perlucidibaca (5.19-17.46%), and Thalassolituus (0.80-11.98%). The results suggest Nitrososphaera and Woesearchaeota may be key taxa involved in carbon and nitrogen biogeochemical cycling within HL. Additionally, the high abundances of halophilic hydrocarbon-degrading bacteria suggests that potential contamination of HL may have occurred due to frequent animal and human activities. Overall, this study provides valuable insights into the archaeal and bacterial community structures in high-altitude soda lake wetlands and their interactions with their unique environments.","PeriodicalId":11360,"journal":{"name":"Current Microbiology","volume":"82 4","pages":"153"},"PeriodicalIF":2.3,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143491345","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Association of TOLLIP mRNA Expression and TOLLIP rs5743899A/G, TOLLIP rs3750920C/T, and IL-10 -1082G/A Single-Nucleotide Polymorphisms with Susceptibility to Tuberculosis.

IF 2.3 3区生物学

Current Microbiology Pub Date : 2025-02-25 DOI: 10.1007/s00284-025-04144-x

Togrul Nagiyev, Emel Eker, Ali Uckayabasi, Ismail Hanta, Begum Kayar, Hulya Binokay, Yasar Sertdemir, Fatih Koksal

{"title":"Association of TOLLIP mRNA Expression and TOLLIP rs5743899A/G, TOLLIP rs3750920C/T, and IL-10 -1082G/A Single-Nucleotide Polymorphisms with Susceptibility to Tuberculosis.","authors":"Togrul Nagiyev, Emel Eker, Ali Uckayabasi, Ismail Hanta, Begum Kayar, Hulya Binokay, Yasar Sertdemir, Fatih Koksal","doi":"10.1007/s00284-025-04144-x","DOIUrl":"10.1007/s00284-025-04144-x","url":null,"abstract":"The early innate host immune response is crucial in the susceptibility to tuberculosis (TB). This study aimed to investigate the potential role of Toll-interacting protein (TOLLIP), a negative regulator of the human innate immune response, and interleukin-10 (IL-10), an anti-inflammatory cytokine, in susceptibility to TB. The peripheral blood mononuclear cells of 30 active pulmonary TB patients and 30 healthy volunteers were included. TOLLIP mRNA expression levels, single nucleotide polymorphisms (SNPs) of the TOLLIP gene, such as rs5743899A/G and rs3750920C/T, and IL-10 -1082G/A SNP were detected using real-time PCR, PCR-restriction fragment length polymorphism (PCR-RFLP) and amplification refractory mutation system-PCR (ARMS-PCR), respectively. TOLLIP mRNA expression levels were significantly higher in TB patients than in healthy controls (expression fold difference = 2.72, the delta-delta Ct method, also known as the 2-∆∆Ct method). The heterozygous (GA) genotype of the IL-10 -1080G/A polymorphism was significantly predominant among the patient group (p = 0.02, Hardy-Weinberg equilibrium). However, the Kruskal‒Wallis analysis found no significant relationship between TOLLIP mRNA expression levels and SNPs. TOLLIP mRNA and IL-10 -1082G/A SNP were assessed as potential biomarkers to predict TB susceptibility. For more significant results, they should be examined with other negative regulators of innate immunity and other immune factors associated with susceptibility to TB. Our study is the first to investigate the association of TOLLIP polymorphisms and expression levels with TB susceptibility in Turkey.","PeriodicalId":11360,"journal":{"name":"Current Microbiology","volume":"82 4","pages":"154"},"PeriodicalIF":2.3,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143491347","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The Faecal Microbiome Analysed from Healthy, Free-Roaming Giraffes (Giraffa camelopardalis).

IF 2.3 3区生物学

Current Microbiology Pub Date : 2025-02-24 DOI: 10.1007/s00284-025-04127-y

Andri Grobbelaar, Gernot Osthoff, Francois Deacon, Errol D Cason

{"title":"The Faecal Microbiome Analysed from Healthy, Free-Roaming Giraffes (Giraffa camelopardalis).","authors":"Andri Grobbelaar, Gernot Osthoff, Francois Deacon, Errol D Cason","doi":"10.1007/s00284-025-04127-y","DOIUrl":"10.1007/s00284-025-04127-y","url":null,"abstract":"Similar to other herbivores, healthy giraffes (Giraffa camelopardalis) rely on a variety of symbiotic microorganisms in their digestive systems to break down cellulose and hemicellulose. In this study, we investigate the impact that external stimuli might have on the faecal prokaryote composition of healthy, free-roaming giraffes. Faecal samples were collected from six male and seven female giraffe individuals, over a 2-year period, during the wet and dry seasons, from six locations within the Free State Province, South Africa. Giraffe populations were exposed to one of two feeding practices which included provision of supplemental feed or only naturally available vegetation. Seventeen (17) different prokaryotic phyla, consisting of 8370 amplicon sequence variants (ASVs), were identified from the 13 healthy, adult, free-roaming giraffes included in the study. Overall, the bacterial phyla with the largest relative abundance included Fusobacteria (22%), followed by Lentisphaera (17%) and Cyanobacteria (16%), which included 21 dominant prokaryotic ASVs. The relative abundance of Ruminococcaceae UCG 014 and Treponema 2 were found to be significantly (P < 0.05) higher and Escherichia / Shigella, Romboutsia and Ruminococcus 1 significantly lower for giraffes receiving supplemental feed compared to natural available vegetation. This is the first study to investigate the composition of the faecal prokaryotic communities of healthy, free-roaming giraffes. The analysis of faecal prokaryotes contributes to the development of non-invasive methods for assessing the nutritional status and identifying health issues in giraffe populations. Ultimately, such advances are beneficial towards the larger-scale conservation, determining nutritional needs and management of other sensitive wildlife species, as well.","PeriodicalId":11360,"journal":{"name":"Current Microbiology","volume":"82 4","pages":"151"},"PeriodicalIF":2.3,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11850562/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143491349","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Uliginosibacterium silvisoli sp. nov., Isolated from Subtropical Forest Soil in Hunan Province, China.

IF 2.3 3区生物学

Current Microbiology Pub Date : 2025-02-24 DOI: 10.1007/s00284-025-04136-x

Yu Lv, Qi Zhang, Le Liu, Jian He, Shimei Wang, Qirong Shen

{"title":"Uliginosibacterium silvisoli sp. nov., Isolated from Subtropical Forest Soil in Hunan Province, China.","authors":"Yu Lv, Qi Zhang, Le Liu, Jian He, Shimei Wang, Qirong Shen","doi":"10.1007/s00284-025-04136-x","DOIUrl":"10.1007/s00284-025-04136-x","url":null,"abstract":"A Gram negative bacterium, designated H3T, was isolated from a forest soil sample collected in Zhangjiajie National Forest Park, Hunan Province, PR China. Cells of strain H3T were yellow-pigmented, strictly aerobic, motile by means of a single polar flagellum. Growth occurred at 15-37 °C (optimum, 25-30 °C), pH 6.0-8.0 (optimum, 7.0) and 0-1.0% (w/v) NaCl (optimum 0%). Phylogenetic analysis based on 16S rRNA gene sequences and genome showed that strain H3T was affiliated to the genus Uliginosibacterium within the family Rhodocyclaceae of the class Betaproteobacteria and shared the highest sequence similarities with U. sediminicola M1-21 T (96.3%). The DNA G + C content of the genomic DNA was 61.4%. The major fatty acids of strain H3T were C16:0, summed feature 3 (16:1 ω7c/16:1 ω6c) and C12:0. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, two unidentified aminophospholipid, an unidentified aminolipid, three unidentified lipids, an unidentified glycolipid, and two uncharacterized phospholipids. The major respiratory quinone was ubiquinone-8. The dDDH and ANI values between strain H3T and the type strains of the genus Uliginosibacterium were 19.2-20.7% and 71.4-76.0%, respectively. Based on the evidences in this study, strain H3T represents a novel species of the genus Uliginosibacterium, for which the name Uliginosibacterium silvisoli sp. nov. is proposed. The type strain is H3T (= MCCC 1K09133T = KCTC 8564 T = JSACC 33374 T).","PeriodicalId":11360,"journal":{"name":"Current Microbiology","volume":"82 4","pages":"152"},"PeriodicalIF":2.3,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143491351","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Spatial and Temporal Characteristics of Riverine Fungal Communities and Their Responses to Environmental Factors in China's Largest Jiang-Flavor Baijiu-Producing Region.

IF 2.3 3区生物学

Current Microbiology Pub Date : 2025-02-24 DOI: 10.1007/s00284-025-04135-y

Yufeng Xiao, Jianguo Zhou, Fengxue Wu, Fan Yang, Bi Chen, Zhibin Li, Yong Liu, Dengjun Wang, Jingfu Wang

{"title":"Spatial and Temporal Characteristics of Riverine Fungal Communities and Their Responses to Environmental Factors in China's Largest Jiang-Flavor Baijiu-Producing Region.","authors":"Yufeng Xiao, Jianguo Zhou, Fengxue Wu, Fan Yang, Bi Chen, Zhibin Li, Yong Liu, Dengjun Wang, Jingfu Wang","doi":"10.1007/s00284-025-04135-y","DOIUrl":"10.1007/s00284-025-04135-y","url":null,"abstract":"The Chishui River is the prime production area for Jiang-flavor Baijiu in China, with 85% of the country's production capacity. To understand the spatial and temporal characteristics of fungal communities in the water column of the Maotai reach of the Chishui River and the relationship between fungal communities and environmental factors as well as the brewing of Jiang-flavor Baijiu, we analyzed the fungal species richness and diversity, structural changes, community composition, and correlation with environmental factors in different seasons and river reaches of the Chishui River Maotai reach. It was found that species richness and diversity followed the following seasonal pattern: summer > autumn > winter ≈ spring. Fungal species richness and diversity were significantly higher in polluted tributary river water than in main stream. The composition and structure of the fungal community varied in all seasons and in different river reaches. Ascomycota (76.5%), Basidiomycota (13.53%), and Chytridiomycota (9.37%) are the relatively dominant phyla, and a number of genera such as Trichosporon, Aspergillus, and Thermomyces have been reported to be associated with the brewing of Jiang-flavor Baijiu. In addition, total nitrogen (TN), chemical oxygen demand (COD), water temperature (WT), dissolved oxygen (DO), sulfate (SO42-), and manganese (Mn) affected the fungal community structure of the Chishui River water body to different degrees (p < 0.05), and they were significantly correlated with Millerozyma and Candida, the genera related to Jiang-flavor Baijiu brewing, respectively. Our findings provide scientific basis and reference for further understanding the water ecological environment of Chishui River and its relationship with the brewing of Jiang-flavor Baijiu.","PeriodicalId":11360,"journal":{"name":"Current Microbiology","volume":"82 4","pages":"150"},"PeriodicalIF":2.3,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143482524","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Structural and Phylogenetic Analysis on the Proofreading Activity of SARS-CoV-2.

IF 2.3 3区生物学

Current Microbiology Pub Date : 2025-02-24 DOI: 10.1007/s00284-025-04130-3

Soujanya Ghosh, Soumya Biswas, Rupali Mohanty, Namrata Misra, Mrutyunjay Suar, Gajraj Singh Kushwaha

{"title":"Structural and Phylogenetic Analysis on the Proofreading Activity of SARS-CoV-2.","authors":"Soujanya Ghosh, Soumya Biswas, Rupali Mohanty, Namrata Misra, Mrutyunjay Suar, Gajraj Singh Kushwaha","doi":"10.1007/s00284-025-04130-3","DOIUrl":"10.1007/s00284-025-04130-3","url":null,"abstract":"Maintenance of genomic integrity is a fundamental characteristic of viruses, however, RNA-dependent RNA Polymerase (RdRp) lacks exonuclease activity for proofreading. To facilitate genomic proofreading in viruses, an independent exonuclease domain assists RdRp to maintain fidelity during replication. In contrast to high fidelity in DNA viruses, RNA viruses have to evolve into new variants through comparatively delicate mutagenesis activity for genetic diversity. Coronavirideae, a family of single positive-stranded RNA (+ ssRNA) viruses, meticulously sustain a balance between genetic diversity and large-size RNA genome. In coronaviruses, the proofreading activity is accomplished by an exonuclease (ExoN) domain located at the N-terminal of non-structural protein 14 (nsp14). ExoN is responsible for the new variants and antiviral resistance towards nucleotide analogs. Here, we provide an evolutionary characterization of ExoN by using a well-defined phylogenetic pipeline and structural analysis based on host and habitat. We carried out a phylogenetic analysis on ExoN, methyltransferase domain, nsp14, and whole genomes of ExoN-containing viruses. Furthermore, a three-dimensional structural comparison of the ExoN domain from various sources is also carried out to understand structural preservation. Our study has unveiled the evolutionary trajectories and structural conservation of the ExoN domain within the Coronaviridae family, highlighting its distinct evolutionary path independent of other domains. Structural analyses revealed minimal variance in RMSD values, underscoring the conserved nature of ExoN despite diverse ecological settings.","PeriodicalId":11360,"journal":{"name":"Current Microbiology","volume":"82 4","pages":"149"},"PeriodicalIF":2.3,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143482525","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Decoding Codon Usage Patterns in High-Risk Human Papillomavirus Genomes: A Comprehensive Analysis.

IF 2.3 3区生物学

Current Microbiology Pub Date : 2025-02-22 DOI: 10.1007/s00284-025-04131-2

Jiahuan Ren, Qijia Li, Weifeng Shen, Xiaochun Tan

{"title":"Decoding Codon Usage Patterns in High-Risk Human Papillomavirus Genomes: A Comprehensive Analysis.","authors":"Jiahuan Ren, Qijia Li, Weifeng Shen, Xiaochun Tan","doi":"10.1007/s00284-025-04131-2","DOIUrl":"10.1007/s00284-025-04131-2","url":null,"abstract":"Human Papillomavirus (HPV) is a major contributor to various human cancers, particularly cervical cancer. Despite its significant impact, the codon usage bias in high-risk HPV types has not been extensively studied. Understanding this bias, however, could provide valuable insights into the virus itself and inform the optimization of vaccine design. This study explores codon usage bias within the genomes of 17 high-risk HPV types (HPV-16, 18, 26, 31, 33, 35, 39, 45, 51, 52, 53, 56, 58, 59, 66, 68, and 82) through comparative analysis. While overall codon usage preference across these genotypes is not highly significant, a notable trend emerges in the preference for codons ending in A or U, with 24 out of 26 favored codons (Relative Synonymous Codon Usage > 1) ending in A or U. Moreover, no common optimal codons are shared among the 17 genomes. The study also identifies the underrepresentation of CpG and ApA dinucleotides, alongside the overrepresentation of CpA and UpG, which likely contribute to codon usage preferences that may influence viral replication and immune evasion strategies. Integrated analysis further suggests that natural selection is the primary force driving codon usage bias in these high-risk HPV genomes. Additionally, these HPVs exhibit a limited set of favored codons shared with humans, potentially minimizing competition for translation resources. This study offers new insights into codon usage bias in high-risk HPVs and underscores the importance of this understanding for optimizing vaccine design.","PeriodicalId":11360,"journal":{"name":"Current Microbiology","volume":"82 4","pages":"148"},"PeriodicalIF":2.3,"publicationDate":"2025-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143476353","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0