Current Genetics最新文献

Description of Ballistura fitchioides (Collembola; Isotomidae) from the Wayanad, Kerala, India with its mitogenome. 弹珠属植物描述；印度喀拉拉邦瓦亚纳德的异tomidae及其有丝分裂基因组。

IF 1.8 4区生物学

Current Genetics Pub Date : 2025-06-05 DOI: 10.1007/s00294-025-01316-x

Jose Anjooriya, Javier Ignacio Arbea, Senthilkumar Narmatha, Guru Pada Mandal, Raveendranathanpillai Sanil

引用次数: 0

First characterization of the resistome, virulome and genomic diversity of Salmonella enterica serovar Inganda: a rare, clinically-related and drug susceptible serovar. 首次鉴定了印度肠沙门氏菌血清型的抵抗组、病毒组和基因组多样性：一种罕见的、临床相关的和药物敏感的血清型。

IF 1.8 4区生物学

Current Genetics Pub Date : 2025-05-31 DOI: 10.1007/s00294-025-01317-w

Felipe Pinheiro Vilela, Dália Dos Prazeres Rodrigues, Marc William Allard, Juliana Pfrimer Falcão

{"title":"First characterization of the resistome, virulome and genomic diversity of Salmonella enterica serovar Inganda: a rare, clinically-related and drug susceptible serovar.","authors":"Felipe Pinheiro Vilela, Dália Dos Prazeres Rodrigues, Marc William Allard, Juliana Pfrimer Falcão","doi":"10.1007/s00294-025-01317-w","DOIUrl":"https://doi.org/10.1007/s00294-025-01317-w","url":null,"abstract":"Non-typhoid Salmonella are among the main causes of foodborne diseases worldwide. However, information on rare serovars is scarce, limiting the understanding of their prevalence, distribution and pathogenesis. Salmonella enterica serovar Inganda (S. Inganda) is a rare non-typhoid serovar. Considering the few existing reports, and the current use of genomics, this study characterized for the first time the antimicrobial resistance, pathogenic potential and diversity of S. Inganda genomes worldwide. A S. Inganda strain from human feces in 2018 in Brazil (SI264) had its resistance determined against 18 antimicrobials by disk-diffusion and had its genome sequenced. S. Inganda publicly available genomes (n = 12) were analyzed for genotypic resistance, stress and virulence genes, plasmids, pathogenicity islands, prophages, Multi-Locus Sequence Typing (MLST), core-genome MLST (cgMLST), and single-nucleotide polymorphisms (SNPs). SI264 showed no phenotypic resistance. All 12 S. Inganda genomes harbored genes or mutations for aminoglycoside (aac(6')-Iaa), quinolone (parC Thr57→Ser), and acid (asr) resistance, multi-drug efflux systems (mdsAB), and gold tolerance (golST). One genome from US harbored pKPC-CAV1321 plasmid. Nine pathogenicity islands, 174 Salmonella virulence genes, and 17 prophages were found in different frequencies. Although a great genomic diversity was noticed, S. Inganda genomes from US and UK were closely related. In conclusion, genomic analyses were able to characterize the current available genomes of S. Inganda strains mostly as genetically diverse, susceptible to antimicrobials, and potentially acid and heavy metal resistant. The presence of numerous virulence features also suggested their pathogenic potential, especially among clinical strains, and reinforced the importance to better characterize rare non-typhoid serovars.","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":"71 1","pages":"13"},"PeriodicalIF":1.8,"publicationDate":"2025-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144191611","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Whole genome sequence analysis of multidrug-resistant Salmonella enterica Typhimurium ms203 provides insights into virulence and antibiotic resistance. 多药耐药肠炎鼠伤寒沙门氏菌ms203的全基因组序列分析提供了毒力和抗生素耐药性的见解。

IF 1.8 4区生物学

Current Genetics Pub Date : 2025-05-31 DOI: 10.1007/s00294-025-01318-9

Saumya Darshana Patra, Soujanya Ghosh, Rakesh Kumar Panda, Bikash Ranjan Sahu, Namrata Misra, Gajraj Singh Kushwaha, Mrutyunjay Suar

{"title":"Whole genome sequence analysis of multidrug-resistant Salmonella enterica Typhimurium ms203 provides insights into virulence and antibiotic resistance.","authors":"Saumya Darshana Patra, Soujanya Ghosh, Rakesh Kumar Panda, Bikash Ranjan Sahu, Namrata Misra, Gajraj Singh Kushwaha, Mrutyunjay Suar","doi":"10.1007/s00294-025-01318-9","DOIUrl":"https://doi.org/10.1007/s00294-025-01318-9","url":null,"abstract":"Salmonella enterica subspecies enterica serovar Typhimurium, is a leading cause of gastroenteritis food-borne illness that leads to hospitalizations worldwide. These infections are further complicated because of the rapid development of antibiotic resistance and the spread of infections by the resistant strains. Thus, the overall aim of this study is to identify a multidrug-resistant strain of Salmonella Typhimurium, whole genome sequencing, and computational analysis of genome sequence. This study presents a comprehensive analysis of Salmonella Typhimurium ms203, isolated from a gastroenteritis patient in Odisha, India. The strain was characterized by microbiological and biochemical assays using a set of standard tests. An antibiotic-susceptibility test of the strain was carried out using VITEK system. Whole genome sequencing facilitated an in-depth examination of genomic architecture, distribution of pathogenic island regions, and antibiotic-resistant sequences. Utilizing diverse computational tools and bioinformatics analysis, including Prokka annotations, protein-protein interaction analysis, genomic island identification, plasmid and phage characterization, antibiotic resistance gene profiling, and average nucleotide identity (AAI) determination, this study elucidates key insights into the genetic makeup and pathogenic potential of S. Typhimurium ms203. These findings may provide valuable contributions to understanding the epidemiology, pathogenesis, and antibiotic resistance mechanisms of this Salmonella strain, with implications for public health interventions and surveillance strategies.","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":"71 1","pages":"12"},"PeriodicalIF":1.8,"publicationDate":"2025-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144191612","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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 DNA damage tolerance factor Rad5 and telomere replication. DNA损伤耐受因子Rad5与端粒复制。

IF 1.8 4区生物学

Current Genetics Pub Date : 2025-05-26 DOI: 10.1007/s00294-025-01315-y

Stefano Mattarocci

{"title":"The DNA damage tolerance factor Rad5 and telomere replication.","authors":"Stefano Mattarocci","doi":"10.1007/s00294-025-01315-y","DOIUrl":"10.1007/s00294-025-01315-y","url":null,"abstract":"The DNA Damage Tolerance pathway (DDT) is one of the major mechanisms for resolving replication fork blocks. A key factor in DDT is the fork-associated clamp PCNA, which can undergo to mono- or polyubiquitination, leading to error-prone or error-free modes of DNA damage bypass, respectively. In the yeast Saccharomyces cerevisiae, Rad5HLTF/SNF2 factor plays important roles in both pathways: (i) promoting the error-free mode through PCNA polyubiquitination and transient template switching and (ii) interacting with specialized DNA polymerases involved in the error-prone pathway. Rad5 also associates with telomeres, the repetitive DNA regions present at the ends of chromosomes. Telomeric DNA, tightly bound by tandem proteins arrays, poses unique challenges to replication fork progression. Here, I review the current understanding of the link between Rad5 and telomeres and provide evidence that Rad5 binds to yeast telomeres, with notable enrichment during telomere replication. This finding highlights a connection between telomeres and an important DDT factor in unperturbed wild-type cells, raising intriguing possibilities regarding the functional interplay between telomere replication and DNA damage tolerance mechanisms.","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":"71 1","pages":"11"},"PeriodicalIF":1.8,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12106482/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144141601","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Adaptive responses of Rhodococcus aetherivorans L13 to oligotrophy: genome and transcriptomic analysis. 嗜热红球菌L13对寡营养的适应性反应：基因组和转录组学分析。

IF 1.8 4区生物学

Current Genetics Pub Date : 2025-04-12 DOI: 10.1007/s00294-025-01314-z

Andrea L Gallegos, María E Nashmias, Juan Pablo Zubimendi, Martín A Hernández, Verónica Acosta, Gonzalo A Torres Tejerizo, Juan I Quelas, Roxana A Silva, Héctor M Alvarez

{"title":"Adaptive responses of Rhodococcus aetherivorans L13 to oligotrophy: genome and transcriptomic analysis.","authors":"Andrea L Gallegos, María E Nashmias, Juan Pablo Zubimendi, Martín A Hernández, Verónica Acosta, Gonzalo A Torres Tejerizo, Juan I Quelas, Roxana A Silva, Héctor M Alvarez","doi":"10.1007/s00294-025-01314-z","DOIUrl":"https://doi.org/10.1007/s00294-025-01314-z","url":null,"abstract":"The wide ecological distribution of actinobacteria suggests that they have developed efficient mechanisms to adapt to extremely nutritionally deficient (oligotrophic) conditions. The impact of nutrient limitation typically observed in oligotrophic areas on bacteria remains to be assessed for many species. The non-model Rhodococcus aetherivorans L13can grow under oligotrophic conditions, even without an added carbon source. Oligotrophic cells of L13 undergo physiological and morphological changes compared to glucose-grown cells, including forming short-fragmenting cells, producing an extracellular polymeric substance, and a 26-fold decrease in respiratory activity. We conducted genome sequencing of L13 and assembled the entire genome, subsequently comparing the abundance of gene transcripts in oligotrophic cells to those of glucose-grown cells, to explore the oligotrophy-responsive mechanisms at the genetic level. The genome comprises 6,543,485 base pairs, distributed across a single chromosome and six extrachromosomal plasmids (one linear and five circular). RNA-Seq analysis revealed the significant dysregulation of 2,665 genes (44% of the total genes detected). Results suggested a profound reorganization of its carbon and energy metabolism, including the activation of (i) mechanisms for utilizing air components; (ii) various dehydrogenases involved in aldehyde and alcohol metabolism, (iii) several enzymes involved in C2 metabolism, glyoxylate shunt, and TCA bypass routes, and downregulation of several genes that encode CO2 releasing-decarboxylase enzymes. Our results suggested that the adaptation strategy of L13 to oligotrophic conditions is supported by a combination of metabolic events, including low metabolic activity, the activation of C2 and ketoacids metabolism, and the display of a carbon conservative metabolic program.","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":"71 1","pages":"10"},"PeriodicalIF":1.8,"publicationDate":"2025-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143978702","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Interactions between insecticidal cry toxins and their receptors. 杀虫哭泣毒素与其受体之间的相互作用。

IF 1.8 4区生物学

Current Genetics Pub Date : 2025-03-29 DOI: 10.1007/s00294-025-01312-1

Pravukalyan Mohanty, G Rajadurai, S Mohankumar, N Balakrishnan, R Raghu, V Balasubramani, U Sivakumar

引用次数: 0

Total propagation of yeast prion conformers in ssz1∆ upf1∆ Hsp104^T160M triple mutants. 酵母朊病毒构象在ssz1∆upf1∆Hsp104T160M三突变体中的总增殖量。

IF 1.8 4区生物学

Current Genetics Pub Date : 2025-03-29 DOI: 10.1007/s00294-025-01313-0

Chih-Yen King

{"title":"Total propagation of yeast prion conformers in ssz1∆ upf1∆ Hsp104T160M triple mutants.","authors":"Chih-Yen King","doi":"10.1007/s00294-025-01313-0","DOIUrl":"10.1007/s00294-025-01313-0","url":null,"abstract":"It was reported that yeast proteins Ssz1 and Upf1 can cure certain [PSI+] variants in wild-type cells and there is a special class of variants whose propagation requires the triple mutation of ssz1∆ upf1∆ Hsp104T160M. Attempts to isolate variants with the exact properties from the 74-D694 strain (and tested there) are not yet successful. The effort nevertheless leads to an alternative analysis about how ssz1∆ and upf1∆ mutations can help prion propagation. The cellular propagation of the yeast prion [PSI+] requires appropriate activities of the Hsp104 disaggregase. Many [PSI+] variants isolated in wild-type strains cannot propagate in cells expressing Hsp104T160M, which has weaker activities. Yet another group of [PSI+] variants shows the opposite, propagating well with Hsp104T160M but is eliminated by the wild-type protein. Deletion of SSZ1 and UPF1 genes in Hsp104T160M cells generates a just-right environment that supports the propagation of both types of [PSI+] variants. The pro-prion effect is not due to the removal of active curing by Ssz1 or Upf1-such curing activity is not observed for the variants. Rather, the double deletion causes a cellular response, which enables more efficient fragmentation of prion fibers, thus remedying the weak activity of Hsp104T160M. The \"Goldilocks\" conditioning seems also applicable to other yeast prions. Two [PIN+] variants that propagate well with wild-type Hsp104 but poorly with Hsp104∆N, lacking residues (2-147), can however thrive with the latter if Ssz1 and Upf1 are also deleted from the cell. In this case, the double deletion results in higher Hsp104∆N expression, leading to improved generation of prion seeds for robust propagation.","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":"71 1","pages":"8"},"PeriodicalIF":1.8,"publicationDate":"2025-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11954717/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143742457","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Internalization of affinity tags enables the purification of secreted Chlamydomonas proteins. 亲和标签的内在化使分泌衣藻蛋白的纯化成为可能。

IF 1.8 4区生物学

Current Genetics Pub Date : 2025-03-19 DOI: 10.1007/s00294-025-01311-2

Anna Probst, Doreen Knochenhauer, Justus Niemeyer, Laura Fischer, Michael Schroda

{"title":"Internalization of affinity tags enables the purification of secreted Chlamydomonas proteins.","authors":"Anna Probst, Doreen Knochenhauer, Justus Niemeyer, Laura Fischer, Michael Schroda","doi":"10.1007/s00294-025-01311-2","DOIUrl":"10.1007/s00294-025-01311-2","url":null,"abstract":"There is great interest in establishing microalgae as new platforms for the sustainable production of high-value products such as recombinant proteins. Many human therapeutic proteins must be glycosylated, which requires their passage through the secretory pathway into the culture medium. While the low complexity of proteins in the culture medium should facilitate affinity purification of secreted recombinant proteins, this has proven challenging for proteins secreted by the unicellular green alga Chlamydomonas reinhardtii. In Leishmania tarentulae, we observed that C-terminally exposed affinity tags are frequently truncated, presumably due to proteolytic activity. We wondered whether this might also occur in Chlamydomonas and contribute to the difficulties in affinity purification of secreted proteins in this alga. Using the methionine-rich 2S albumin from Bertholletia excelsa and the ectodomain of the SARS-CoV-2 spike protein produced and secreted in Chlamydomonas, we demonstrate that they can be efficiently affinity-purified from the culture medium by Ni-NTA chromatography when the 8xHis affinity tag is internalized. This finding represents an important step towards further development of Chlamydomonas as a host for the sustainable production of high-value recombinant proteins.","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":"71 1","pages":"7"},"PeriodicalIF":1.8,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11923035/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143662813","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Complete genome sequence of Pseudomonas sp. HT11 isolated from broad bean (Vicia faba L.). 蚕豆假单胞菌HT11的全基因组序列分析。

IF 1.8 4区生物学

Current Genetics Pub Date : 2025-02-12 DOI: 10.1007/s00294-025-01310-3

Hui Zhang, Lian-Jie Ma, Dun-Xiu Liao, Rong-Li Tang, Xiao-Ning Hang, Wen-Cai Lu

{"title":"Complete genome sequence of Pseudomonas sp. HT11 isolated from broad bean (Vicia faba L.).","authors":"Hui Zhang, Lian-Jie Ma, Dun-Xiu Liao, Rong-Li Tang, Xiao-Ning Hang, Wen-Cai Lu","doi":"10.1007/s00294-025-01310-3","DOIUrl":"10.1007/s00294-025-01310-3","url":null,"abstract":"The bacterial strain HT11 isolated from broad bean (Vicia faba L.) exhibited strong antifungal activity against Botrytis fabiopsis, the causative agent of red spot disease in broad bean. To gain insights into the secondary metabolites produced by HT11,its entire genome was sequenced and subjected to comprehensive analysis. The genome comprised a single circular chromosome of 6,335,588 base pairs (bp) in length. Comparative analysis of the 16 S rRNA gene and the average nucleotide identity (ANI) confirmed the HT11 strain as a new Pseudomonas strain. The complete genome encoded 5,366 predicted open reading frames (ORFs), 66 tRNA genes and 16 rRNA genes. The total length of the annotated genes accounted for 82.93% (5,254,103/6,335,588 bp) of the complete genome. Functional categorization of the predicted ORFs revealed 24 Clusters of Orthologous Groups of proteins (COG). Fourteen gene clusters were identified with in the genome, associated with the biosynthesis of pyochelin, pyocyanin, viscosin, and tolaasin I/tolaasin F. Additionally, three gene clusters were implicated in the biosynthesis of unknown metabolites. These findings establish a foundational basis for further investigations into the interactions between Pseudomonas sp. HT11 and the pathogenic fungus Botrytis fabiopsis.","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":"71 1","pages":"6"},"PeriodicalIF":1.8,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143398433","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Codon usage analysis in selected virulence genes of Staphylococcal species. 葡萄球菌毒力基因密码子使用分析。

IF 1.8 4区生物学

Current Genetics Pub Date : 2025-01-24 DOI: 10.1007/s00294-025-01308-x

Pinky Arora, Shubham Kumar, Chandra Shekhar Mukhopadhyay, Sandeep Kaur

{"title":"Codon usage analysis in selected virulence genes of Staphylococcal species.","authors":"Pinky Arora, Shubham Kumar, Chandra Shekhar Mukhopadhyay, Sandeep Kaur","doi":"10.1007/s00294-025-01308-x","DOIUrl":"10.1007/s00294-025-01308-x","url":null,"abstract":"The Staphylococcus genus, composed of Gram-positive bacteria, includes several pathogenic species such as Staphylococcus aureus, S. epidermidis, S. haemolyticus, and S. saprophyticus, each implicated in a range of infections. This study investigates the codon usage patterns in key virulence genes, including Autolysin (alt), Elastin Binding protein (EbpS), Lipase, Thermonuclease, Intercellular Adhesion Protein (IcaR), and V8 Protease, across four Staphylococcus species. Using metrics such as the Effective Number of Codons (ENc), Relative Synonymous Codon Usage (RSCU), Codon Adaptation Index (CAI), alongside neutrality and parity plots, we explored the codon preferences and nucleotide composition biases. Our findings revealed a pronounced AT-rich codon preference, with AT-rich genomes likely aiding in energy-efficient translation and bacterial survival in host environments. These insights provide a deeper understanding of the evolutionary adaptations and translational efficiency mechanisms that contribute to the pathogenicity of Staphylococcus species. This knowledge could pave the way for novel therapeutic interventions targeting codon usage to disrupt virulence gene expression.","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":"71 1","pages":"5"},"PeriodicalIF":1.8,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143032429","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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