{"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":"https://doi.org/10.1007/s00294-025-01308-x","url":null,"abstract":"<p><p>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.</p>","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}
{"title":"Metagenomic profiling of plaque microbiota in Indian subjects: identified hidden ecological tapestry.","authors":"Sangram Sandhu, Sachin Kumar, Paurabhi Singh, Balendra Pratap Singh, Sunit Kumar Jurel, Nand Lal, Mohit, Varun Sharma, Niraj Rai, Pooran Chand","doi":"10.1007/s00294-024-01306-5","DOIUrl":"https://doi.org/10.1007/s00294-024-01306-5","url":null,"abstract":"<p><p>Dental plaque biofilms are the primary etiologic factor for various chronic oral infectious diseases. In recent years, dental plaque shows enormous potential to know about an individual microbiota. Various microbiome studies of oral cavity from different geographical locations reveals abundance of microbial species. Although, the representation of Indian population in this respect is limited, which make us curious to undergo this study. This study investigates the dental plaque microbiota of North Indian individuals based on their age, gender, and dietary patterns; specifically, food preference and availability of water source using 16 S rRNA metagenomics analysis. The findings from this study revealed that Streptococcus levels are high across genders, age groups, and water source, highlighting its role as a predominant dental caries associated species like Streptococcus mutans, Streptococcus pyogenes, Streptococcus sobrinus and Streptococcus oralis in the studied population groups. Additionally, the abundance of Actinomyces is observed higher in young individuals and females whereas Fusobacterium and Leptotrichia were high in elderly individuals. Moreover, non-vegetarians have higher abundance of Streptococcus and Fusobacterium, whereas vegetarians show higher abundance of Prevotella and Leptotrichia. The study also highlights the influence of water type on bacterial composition of dental plaque in the studied population i.e., individuals consuming underground water has high abundance of Streptococcus, whereas individuals consuming RO water exhibit elevated Prevotella and Leptotrichia. Insights emerged from the analysis illuminates the complex dynamics of microbiota in dental plaque among North Indians. This study also highlight that this variation of microbiome is influenced by age, gender, and dietary habits (vegetarian or non-vegetarian lifestyle). These results will fill a significant knowledge gap regarding the Indian dental plaque microbiome but also offer a foundation to conduct metagenome studies and potential therapeutic implications for future personalized oral health interventions.</p>","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":"71 1","pages":"3"},"PeriodicalIF":1.8,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143028155","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}
Current GeneticsPub Date : 2025-01-24DOI: 10.1007/s00294-024-01307-4
Kiran Fatima, Syed Zeeshan Haider Naqvi, Hazrat Ali, Noor Hassan, Farheen Ansari, Sidrah Saleem, Shah Jahan, Mushtaq Ahmad, Aniqa Nawaz, Anam Saqib
{"title":"Whole-genome evaluation and prophages characterization associated with genome of carbapenem-resistant Acinetobacter baumannii UOL-KIMZ-24-2.","authors":"Kiran Fatima, Syed Zeeshan Haider Naqvi, Hazrat Ali, Noor Hassan, Farheen Ansari, Sidrah Saleem, Shah Jahan, Mushtaq Ahmad, Aniqa Nawaz, Anam Saqib","doi":"10.1007/s00294-024-01307-4","DOIUrl":"https://doi.org/10.1007/s00294-024-01307-4","url":null,"abstract":"<p><p>Carbapenem-resistant Acinetobacter baumannii (CRAB) is an emerging threat to healthcare settings in many countries, principally in South Asia. The current study was aimed to identify, evaluate whole-genome and characterize the prophages in genome of CRAB strain, recovered from patients of Lahore General Hospital, Lahore. More than 200 samples were collected and identified by morphological and biochemical tests. These strains were also subjected to a comprehensive antimicrobial susceptibility evaluation using Kirby-Bauer method and further confirmed as CRAB strains by exploring bla<sub>OXA-51</sub>. In addition, the whole-genome evaluation of a Acinetobacter baumannii UOL-KIMZ-24-2 was carried out using various Bioinformatics tools. A total of 150 strains of A. baumannii were recovered and identified in the current study. Among them, 49% strains were found resistant to carbapenem. The bla<sub>OXA-51</sub> was found prevalent in the genome of A. baumannii recovered from medical ICU (38%). In addition, the UOL-KIMZ-24-2 genome analysis based on multilocus sequence typing (MLST) highlighted that UOL-KIMZ-24-2 belonged to ST2 (Pasteur scheme) sequence type. A total of 29 antimicrobial resistance (AMR) genes were present, importantly, bla<sub>OXA-66</sub>, bla<sub>OXA-23</sub> and bla<sub>OXA-25</sub>. The mobile genetic elements (MGEs) were identified as transposases and belonged to four classes e.g. IS15d1, ISAba24, ISEc29, and ISEc35. A total of 14 virulence factors encoded by 58 different genes were detected in UOL-KIMZ-24-2. In addition, the phage sequences were identified in genome of UOL-KIMZ-24-2, divided into 3 regions. In conclusion, UOL-KIMZ-24-2 contained a mixture of AMR genes, MGEs. prophages sequences and virulence genes.</p>","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":"71 1","pages":"4"},"PeriodicalIF":1.8,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143028174","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}
Current GeneticsPub Date : 2025-01-16DOI: 10.1007/s00294-025-01309-w
Eva-Carina Wendegatz, Julia Lettow, Wiktoria Wierzbicka, Hans-Joachim Schüller
{"title":"Transcriptional activation and coactivator binding by yeast Ino2 and human proto-oncoprotein c-Myc.","authors":"Eva-Carina Wendegatz, Julia Lettow, Wiktoria Wierzbicka, Hans-Joachim Schüller","doi":"10.1007/s00294-025-01309-w","DOIUrl":"https://doi.org/10.1007/s00294-025-01309-w","url":null,"abstract":"<p><p>Basic helix-loop-helix domains in yeast regulatory proteins Ino2 and Ino4 mediate formation of a heterodimer which binds to and activates expression of phospholipid biosynthetic genes. The human proto-oncoprotein c-Myc (Myc) and its binding partner Max activate genes important for cellular proliferation and contain functional domains structure and position of which strongly resembles Ino2 and Ino4. Since Ino2-Myc and Ino4-Max may be considered as orthologs we performed functional comparisons in yeast. We demonstrate that Myc and Max could be stably synthesized in S. cerevisiae and together significantly activated a target gene of Ino2/Ino4 but nevertheless were unable to functionally complement an ino2 ino4 double mutant. We also map two efficient transcriptional activation domains in the N-terminus of Myc (TAD1: aa 1-41 and TAD2: aa 91-140), corresponding to TAD positions in Ino2. We finally show that coactivators such as TFIID subunits Taf1, Taf4, Taf6, Taf10 and Taf12 as well as ATPase subunits of chromatin remodelling complexes Swi2, Sth1 and Ino80 previously shown to interact with TADs of Ino2 were also able to bind TADs of Myc, supporting the view that heterodimers Ino2/Ino4 and Myc/Max are evolutionary related but have undergone transcriptional rewiring of target genes.</p>","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":"71 1","pages":"2"},"PeriodicalIF":1.8,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11739200/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143055755","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}
Current GeneticsPub Date : 2024-12-26DOI: 10.1007/s00294-024-01305-6
Umama Shahid, Suet Li Hooi, Shu Yong Lim, Alijah Mohd Aris, Bee Chin Khor, Qasim Ayub, Hock Siew Tan
{"title":"Metagenomic surveillance of microbial community and antibiotic resistant genes associated with Malaysian wastewater during the COVID-19 pandemic.","authors":"Umama Shahid, Suet Li Hooi, Shu Yong Lim, Alijah Mohd Aris, Bee Chin Khor, Qasim Ayub, Hock Siew Tan","doi":"10.1007/s00294-024-01305-6","DOIUrl":"https://doi.org/10.1007/s00294-024-01305-6","url":null,"abstract":"<p><p>Wastewater is a reservoir of pathogens and hotspots for disseminating antibiotic resistance genes across species. The metagenomic surveillance of wastewater provides insight into the native microbial community, antibiotic-resistance genes (ARGs) and mobile genetic elements. t. The COVID-19 pandemic has caused wider dissemination of ARGs and resistant bacteria in wastewater. Although immensely significant, no research has been performed on the Malaysian wastewater microbial community and ARGs or their correlation with COVID-19 infections. This study utilised a 16S metagenomics approach to characterise the microbial community in Malaysian wastewater during high and low-case phases of the pandemic. Bacteria belonging to Bacteriodales, Bacillales, Actinomycetales and opportunistic pathogens-Arcobacters, Flavobacteria, and Campylobacterales, Neisseriales, were enriched during higher COVID-19 pandemic (active cases). Additionally, copy number profiling of ARGs in water samples showed the prevalence of elements conferring resistance to antibiotics like sulphonamides, cephalosporins, and colistin. The high prevalence of intI1 and other ion-based transporters in samples highlights an extensive risk of horizontal gene transfer to previously susceptible species. Our study emphasises the importance of wastewater surveillance in understanding microbial community dynamics and ARG dissemination, particularly during public health crises like the COVID-19 pandemic.</p>","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":"71 1","pages":"1"},"PeriodicalIF":1.8,"publicationDate":"2024-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142892537","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}
Current GeneticsPub Date : 2024-11-12DOI: 10.1007/s00294-024-01303-8
Sahar Salimi, M Foad Abdi, Mostafa Rahnama
{"title":"Characterization and organization of telomeric-linked helicase (tlh) gene families in Fusarium oxysporum.","authors":"Sahar Salimi, M Foad Abdi, Mostafa Rahnama","doi":"10.1007/s00294-024-01303-8","DOIUrl":"10.1007/s00294-024-01303-8","url":null,"abstract":"<p><p>Telomere-linked RecQ helicase (tlh) genes have been reported in several fungi and a choanoflagellate in the regions adjacent to the terminal telomere repeats. In this study, we explored the Telomere-linked RecQ helicase (tlh) genes in four strains of Fusarium oxysporum, offering new insights into their genomic structure, functional motifs, and impact on chromosomal ends. We conducted a comprehensive analysis, comparing the tlh genes of F. oxysporum with those previously identified in other organisms and uncovering significant similarities. Through comparative genomics, we identified conserved protein motifs across these genes, including a TLH domain, C<sub>2</sub>H<sub>2</sub>, and RecQ helicase motifs. Our phylogenetic analysis positions the F. oxysporum tlh genes in a cluster with other known tlhs, suggesting a shared evolutionary origin. Mutation analysis revealed a relatively low level of deleterious mutations in tlh gene paralogs, with a notable proportion of full-size structures maintained across strains. Analysis of subtelomeric sequences indicates that a region with almost identical sequences flanks the majority of chromosome ends, termed tlh-containing region (TLHcr), across these strains. The presence of TLHcrs at chromosome ends, either as single entities or in arrays, underscores their potential role in telomere function and genome stability. Our findings provide a detailed examination of tlh genes in four strains of F. oxysporum, laying the groundwork for future studies on their biological significance and evolutionary history in fungal genomes.</p>","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":"70 1","pages":"19"},"PeriodicalIF":1.8,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142616426","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}
Current GeneticsPub Date : 2024-11-09DOI: 10.1007/s00294-024-01304-7
Roshan Shaikh, Ghosh Kanjaksha, Ajit Gorakshakar
{"title":"Duffy Binding Protein Ligand (PvDBP) gene duplication in Indian P. Vivax Malaria isolates: implication for malaria research.","authors":"Roshan Shaikh, Ghosh Kanjaksha, Ajit Gorakshakar","doi":"10.1007/s00294-024-01304-7","DOIUrl":"10.1007/s00294-024-01304-7","url":null,"abstract":"<p><p>Plasmodium vivax malaria poses a major global health challenge, fueled by the parasite's ability to establish chronic infections via dormant liver hypnozoites that enable immune evasion and show transmission resilience. A key virulence determinant of P. vivax blood-stage infection is the ligand-receptor interaction of infected erythrocytes mediated by the Duffy Binding Protein (PvDBP) ligand. Gene duplication events leading to increased PvDBP copy numbers have been documented in parasite populations in Cambodia, Brazil, and Sudan, but whether such changes exist in Indian isolates is not known. India shoulders a disproportionately high P. vivax burden in the world. DNA extracted from malaria-positive samples from a multisite survey was subjected to diagnostic PCR to evaluate PvDBP duplication. We identified PvDBP duplication at 18.6% frequency across various regions in India via diagnostic PCR. Both 'Cambodian-type' and 'Malagasy-type' duplication patterns were detected. PvDBP copy number variations associated with specific Duffy antigen receptor genotypes were correlated in the patient cohort. While PvDBP duplication was widespread, its geographic distribution varied, occurring most prevalently in northeastern regions of India. The presence of Duffy binding protein gene duplication in nearly one-fifth of P. vivax isolates in India may have significant epidemiological and clinical implications. This genetic variation could potentially impact, parasite fitness and invasion efficiency, possibly leading to higher parasitemia levels and immune evasion capabilities, which may affect the efficacy of natural immunity and vaccine development efforts and / or transmission dynamics if the duplication confers any advantage in mosquito stages. To fully understand these implications, we propose longitudinal studies tracking patients with and without PvDBP duplications, comparing clinical outcomes, parasitemia levels, and transmission rates. Additionally, spatial and temporal analyses of duplication frequency across India could reveal patterns of spread and potential selective pressures driving this genetic change.</p>","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":"70 1","pages":"18"},"PeriodicalIF":1.8,"publicationDate":"2024-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142616427","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}
Current GeneticsPub Date : 2024-09-14DOI: 10.1007/s00294-024-01301-w
Sara Mina, Anaïs Hérivaux, Hajar Yaakoub, Vincent Courdavault, Méline Wéry, Nicolas Papon
{"title":"Structure and distribution of sensor histidine kinases in the fungal kingdom","authors":"Sara Mina, Anaïs Hérivaux, Hajar Yaakoub, Vincent Courdavault, Méline Wéry, Nicolas Papon","doi":"10.1007/s00294-024-01301-w","DOIUrl":"https://doi.org/10.1007/s00294-024-01301-w","url":null,"abstract":"<p>Two-component systems (TCSs) are diverse cell signaling pathways that play a significant role in coping with a wide range of environmental cues in both prokaryotic and eukaryotic organisms. These transduction circuitries are primarily governed by histidine kinases (HKs), which act as sensing proteins of a broad variety of stressors. To date, nineteen HK groups have been previously described in the fungal kingdom. However, the structure and distribution of these prominent sensing proteins were hitherto investigated in a limited number of fungal species. In this study, we took advantage of recent genomic resources in fungi to refine the fungal HK classification by deciphering the structural diversity and phylogenetic distribution of HKs across a large number of fungal clades. To this end, we browsed the genome of 91 species representative of different fungal clades, which yielded 726 predicted HK sequences. A domain organization analysis, coupled with a robust phylogenomic approach, led to an improved categorization of fungal HKs. While most of the compiled sequences were categorized into previously described fungal HK groups, some new groups were also defined. Overall, this study provides an improved overview of the structure, distribution, and evolution of HKs in the fungal kingdom.</p>","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":"31 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142265036","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}
{"title":"Adaptative responses of Neurospora crassa by histidine kinases upon the attack of the arthropod Sinella curviseta","authors":"Ting Lu, Xiao-meng Wang, Peng-xu Chen, Juan Xi, Han-bing Yang, Wei-fa Zheng, Yan-xia Zhao","doi":"10.1007/s00294-024-01302-9","DOIUrl":"https://doi.org/10.1007/s00294-024-01302-9","url":null,"abstract":"<p>Histidine kinases (HKs) are important sensor proteins in fungi and play an essential role in environmental adaptation. However, the mechanisms by which fungi sense and respond to fungivores attack via HKs are not fully understood. In this study, we utilized <i>Neurospora crassa</i> to investigate the involvement of HKs in responding to fungivores attack. We found that the 11 HKs in <i>N. crassa</i> not only affected the growth and development, but also led to fluctuations in antioxidant production. Ten mutants in the genes encoding HKs (except ∆<i>phy1</i>) showed increased production of reactive oxygen species (ROS), especially upon <i>Sinella curviseta</i> attack. The ROS burst triggered changes in conidia and perithecial beaks formation, as well as accumulation of β-glucan, ergothioneine, ergosterol, and carotenoids. β-glucan was increased in ∆<i>hk9</i>, ∆<i>os1</i>, ∆<i>hcp1</i>, ∆<i>nik2</i>, ∆<i>sln1</i>, ∆<i>phy1</i> and ∆<i>phy2</i> mutants compared to the wild-type strain. In parallel, ergothioneine accumulation was improved in ∆<i>phy1</i> and ∆<i>hk16</i> mutants and further increased upon attack, except in ∆<i>os1</i> and ∆<i>hk16</i> mutants. Additionally, fungivores attack stimulated ergosterol and dehydroergosterol production in ∆<i>hk9</i> and ∆<i>os1</i> mutants. Furthermore, deletion of these genes altered carotenoid accumulation, with wild-type strain, ∆<i>hk9</i>, ∆<i>os1</i>, ∆<i>hcp1</i>, ∆<i>sln1</i>, ∆<i>phy2</i>, and ∆<i>dcc1</i>mutants showing an increase in carotenoids upon attack. Taken together, HKs are involved in regulating the production of conidia and antioxidants. Thus, HKs may act as sensors of fungivores attack and effectively improve the adaptive capacity of fungi to environmental stimuli.</p>","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":"65 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142265035","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}
{"title":"Transcriptional activation domains interact with ATPase subunits of yeast chromatin remodelling complexes SWI/SNF, RSC and INO80.","authors":"Eva-Carina Wendegatz, Maike Engelhardt, Hans-Joachim Schüller","doi":"10.1007/s00294-024-01300-x","DOIUrl":"10.1007/s00294-024-01300-x","url":null,"abstract":"<p><p>Chromatin remodelling complexes (CRC) are ATP-dependent molecular machines important for the dynamic organization of nucleosomes along eukaryotic DNA. CRCs SWI/SNF, RSC and INO80 can move positioned nucleosomes in promoter DNA, leading to nucleosome-depleted regions which facilitate access of general transcription factors. This function is strongly supported by transcriptional activators being able to interact with subunits of various CRCs. In this work we show that SWI/SNF subunits Swi1, Swi2, Snf5 and Snf6 can bind to activation domains of Ino2 required for expression of phospholipid biosynthetic genes in yeast. We identify an activator binding domain (ABD) of ATPase Swi2 and show that this ABD is functionally dispensable, presumably because ABDs of other SWI/SNF subunits can compensate for the loss. In contrast, mutational characterization of the ABD of the Swi2-related ATPase Sth1 revealed that some conserved basic and hydrophobic amino acids within this domain are essential for the function of Sth1. While ABDs of Swi2 and Sth1 define separate functional protein domains, mapping of an ABD within ATPase Ino80 showed co-localization with its HSA domain also required for binding actin-related proteins. Comparative interaction studies finally demonstrated that several unrelated activators each exhibit a specific binding pattern with ABDs of Swi2, Sth1 and Ino80.</p>","PeriodicalId":10918,"journal":{"name":"Current Genetics","volume":"70 1","pages":"15"},"PeriodicalIF":1.8,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11377671/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142132085","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}