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1
Burki, Fabien, Kamran Shalchian-Tabrizi, and Jan Pawlowski. "Phylogenomics reveals a new ‘megagroup’ including most photosynthetic eukaryotes." Biology Letters 4, no. 4 (2008): 366–69. http://dx.doi.org/10.1098/rsbl.2008.0224.
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Advances in molecular phylogeny of eukaryotes have suggested a tree composed of a small number of supergroups. Phylogenomics recently established the relationships between some of these large assemblages, yet the deepest nodes are still unresolved. Here, we investigate early evolution among the major eukaryotic supergroups using the broadest multigene dataset to date (65 species, 135 genes). Our analyses provide strong support for the clustering of plants, chromalveolates, rhizarians, haptophytes and cryptomonads, thus linking nearly all photosynthetic lineages and raising the question of a possible unique origin of plastids. At its deepest level, the tree of eukaryotes now receives strong support for two monophyletic megagroups comprising most of the eukaryotic diversity.
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Tian, Miao, Christiane Agreiter, and Josef Loidl. "Spatial constraints on chromosomes are instrumental to meiotic pairing." Journal of Cell Science 133, no. 22 (2020): jcs253724. http://dx.doi.org/10.1242/jcs.253724.
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ABSTRACTIn most eukaryotes, the meiotic chromosomal bouquet (comprising clustered chromosome ends) provides an ordered chromosome arrangement that facilitates pairing and recombination between homologous chromosomes. In the protist Tetrahymena thermophila, the meiotic prophase nucleus stretches enormously, and chromosomes assume a bouquet-like arrangement in which telomeres and centromeres are attached to opposite poles of the nucleus. We have identified and characterized three meiosis-specific genes [meiotic nuclear elongation 1-3 (MELG1-3)] that control nuclear elongation, and centromere and telomere clustering. The Melg proteins interact with cytoskeletal and telomere-associated proteins, and probably repurpose them for reorganizing the meiotic prophase nucleus. A lack of sequence similarity between the Tetrahymena proteins responsible for telomere clustering and bouquet proteins of other organisms suggests that the Tetrahymena bouquet is analogous, rather than homologous, to the conserved eukaryotic bouquet. We also report that centromere clustering is more important than telomere clustering for homologous pairing. Therefore, we speculate that centromere clustering may have been the primordial mechanism for chromosome pairing in early eukaryotes.
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Nützmann, Hans-Wilhelm, Daniel Doerr, América Ramírez-Colmenero, et al. "Active and repressed biosynthetic gene clusters have spatially distinct chromosome states." Proceedings of the National Academy of Sciences 117, no. 24 (2020): 13800–13809. http://dx.doi.org/10.1073/pnas.1920474117.
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While colocalization within a bacterial operon enables coexpression of the constituent genes, the mechanistic logic of clustering of nonhomologous monocistronic genes in eukaryotes is not immediately obvious. Biosynthetic gene clusters that encode pathways for specialized metabolites are an exception to the classical eukaryote rule of random gene location and provide paradigmatic exemplars with which to understand eukaryotic cluster dynamics and regulation. Here, using 3C, Hi-C, and Capture Hi-C (CHi-C) organ-specific chromosome conformation capture techniques along with high-resolution microscopy, we investigate how chromosome topology relates to transcriptional activity of clustered biosynthetic pathway genes inArabidopsis thaliana. Our analyses reveal that biosynthetic gene clusters are embedded in local hot spots of 3D contacts that segregate cluster regions from the surrounding chromosome environment. The spatial conformation of these cluster-associated domains differs between transcriptionally active and silenced clusters. We further show that silenced clusters associate with heterochromatic chromosomal domains toward the periphery of the nucleus, while transcriptionally active clusters relocate away from the nuclear periphery. Examination of chromosome structure at unrelated clusters in maize, rice, and tomato indicates that integration of clustered pathway genes into distinct topological domains is a common feature in plant genomes. Our results shed light on the potential mechanisms that constrain coexpression within clusters of nonhomologous eukaryotic genes and suggest that gene clustering in the one-dimensional chromosome is accompanied by compartmentalization of the 3D chromosome.
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de Koning, Bart, Fabian Blombach, Hao Wu, Stan J. J. Brouns, and John van der Oost. "Role of multiprotein bridging factor 1 in archaea: bridging the domains?" Biochemical Society Transactions 37, no. 1 (2009): 52–57. http://dx.doi.org/10.1042/bst0370052.
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MBF1 (multiprotein bridging factor 1) is a highly conserved protein in archaea and eukaryotes. It was originally identified as a mediator of the eukaryotic transcription regulator BmFTZ-F1 (Bombyx mori regulator of fushi tarazu). MBF1 was demonstrated to enhance transcription by forming a bridge between distinct regulatory DNA-binding proteins and the TATA-box-binding protein. MBF1 consists of two parts: a C-terminal part that contains a highly conserved helix–turn–helix, and an N-terminal part that shows a clear divergence: in eukaryotes, it is a weakly conserved flexible domain, whereas, in archaea, it is a conserved zinc-ribbon domain. Although its function in archaea remains elusive, its function as a transcriptional co-activator has been deduced from thorough studies of several eukaryotic proteins, often indicating a role in stress response. In addition, MBF1 was found to influence translation fidelity in yeast. Genome context analysis of mbf1 in archaea revealed conserved clustering in the crenarchaeal branch together with genes generally involved in gene expression. It points to a role of MBF1 in transcription and/or translation. Experimental data are required to allow comparison of the archaeal MBF1 with its eukaryotic counterpart.
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Ramírez-Fernández, Lia, Mónica Saldarriaga-Córdoba, Andrea X. Silva, Constanza Napolitano, and Annia Rodríguez-San Pedro. "Eukaryotic gut community of the bat Myotis arescens in anthropized landscapes in Chile." PeerJ 13 (June 30, 2025): e19563. https://doi.org/10.7717/peerj.19563.
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Background Human-driven environmental changes can disrupt wildlife habitats, forcing animals to adapt to fragmented or degraded ecosystems. In some cases, this leads to increased proximity between wildlife and human populations, heightening the risk of pathogen spillover. Bats, as key ecological players, are particularly sensitive to such disturbances. While some species decline in heavily altered environments, others adapt and thrive near human settlements, increasing the likelihood of encounters. Given that bats can host a wide range of zoonotic pathogens, this adaptive behavior raises important public health concerns. Despite their ecological significance and their role in zoonotic disease dynamics, the gut eukaryotes communities associated with bats remain less studied. Methods This study focused on the Valparaíso Myotis (Myotis arescens), an insectivorous bat species endemic to central Chile that is significantly impacted by anthropogenic deforestation and habitat fragmentation. We characterized the gut eukaryotic communities of M. arescens through fecal sample analysis. Targeted microbial groups included fungi, metazoan parasites, and protists. High-throughput sequencing was employed to assess gut eukaryotes diversity, and beta diversity analysis was conducted to explore clustering patterns in relation to environmental variables, such as vegetation cover and land use types. Results Our analyses revealed that the gut eukaryotic community of M. arescens consistently included taxa from the Apicomplexa, Ascomycota, and Basidiomycota phyla, with Apicomplexa being the most abundant. Beta diversity analysis showed distinct clustering by sampling location, with the percentage of native vegetation identified as the primary factor shaping gut eukaryotic community structure. Other influential variables included the presence of annual crops, orchards, water bodies, and urban areas. Notably, a high abundance of Apicomplexa—particularly amplicon sequence variants (ASVs) related to the genus Eimeria—was detected in bat feces across sites with varying degrees of anthropogenic disturbance. Conclusions This study highlights the significant role of native vegetation in shaping the eukaryotic gut community of M. arescens, suggesting that gut eukaryotic composition can serve as a bioindicator of bat health and habitat quality. Among the dominant taxa, members of the genus Eimeria were frequently detected across sites with varying degrees of anthropogenic disturbance. Although Eimeria is generally considered host-specific and not zoonotic, its high prevalence in bat gut communities points to the need for further research into its ecological role and potential implications for wildlife health. Overall, these findings underscore the importance of conserving native habitats to maintain ecosystem integrity and support healthy bat populations.
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Tice, Alexander K., David Žihala, Tomáš Pánek, et al. "PhyloFisher: A phylogenomic package for resolving eukaryotic relationships." PLOS Biology 19, no. 8 (2021): e3001365. http://dx.doi.org/10.1371/journal.pbio.3001365.
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Phylogenomic analyses of hundreds of protein-coding genes aimed at resolving phylogenetic relationships is now a common practice. However, no software currently exists that includes tools for dataset construction and subsequent analysis with diverse validation strategies to assess robustness. Furthermore, there are no publicly available high-quality curated databases designed to assess deep (>100 million years) relationships in the tree of eukaryotes. To address these issues, we developed an easy-to-use software package, PhyloFisher (https://github.com/TheBrownLab/PhyloFisher), written in Python 3. PhyloFisher includes a manually curated database of 240 protein-coding genes from 304 eukaryotic taxa covering known eukaryotic diversity, a novel tool for ortholog selection, and utilities that will perform diverse analyses required by state-of-the-art phylogenomic investigations. Through phylogenetic reconstructions of the tree of eukaryotes and of the Saccharomycetaceae clade of budding yeasts, we demonstrate the utility of the PhyloFisher workflow and the provided starting database to address phylogenetic questions across a large range of evolutionary time points for diverse groups of organisms. We also demonstrate that undetected paralogy can remain in phylogenomic “single-copy orthogroup” datasets constructed using widely accepted methods such as all vs. all BLAST searches followed by Markov Cluster Algorithm (MCL) clustering and application of automated tree pruning algorithms. Finally, we show how the PhyloFisher workflow helps detect inadvertent paralog inclusions, allowing the user to make more informed decisions regarding orthology assignments, leading to a more accurate final dataset.
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Woo, Y. H., and W. H. Li. "Gene clustering pattern, promoter architecture, and gene expression stability in eukaryotic genomes." Proceedings of the National Academy of Sciences 108, no. 8 (2011): 3306–11. http://dx.doi.org/10.1073/pnas.1100210108.
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Arnold, Matthew Grant, Pratikshya Adhikari, Baobin Kang, and Hao Xu (徐昊). "Munc18a clusters SNARE-bearing liposomes prior to trans-SNARE zippering." Biochemical Journal 474, no. 19 (2017): 3339–54. http://dx.doi.org/10.1042/bcj20170494.
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Sec1–Munc18 (SM) proteins co-operate with SNAREs {SNAP [soluble NSF (N-ethylmaleimide-sensitive factor) attachment protein] receptors} to mediate membrane fusion in eukaryotic cells. Studies of Munc18a/Munc18-1/Stxbp1 in neurotransmission suggest that SM proteins accelerate fusion kinetics primarily by activating the partially zippered trans-SNARE complex. However, accumulating evidence has argued for additional roles for SM proteins in earlier steps in the fusion cascade. Here, we investigate the function of Munc18a in reconstituted exocytic reactions mediated by neuronal and non-neuronal SNAREs. We show that Munc18a plays a direct role in promoting proteoliposome clustering, underlying vesicle docking during exocytosis. In the three different fusion reactions examined, Munc18a-dependent clustering requires an intact N-terminal peptide (N-peptide) motif in syntaxin that mediates the binary interaction between syntaxin and Munc18a. Importantly, clustering is preserved under inhibitory conditions that abolish both trans-SNARE complex formation and lipid mixing, indicating that Munc18a promotes membrane clustering in a step that is independent of trans-SNARE zippering and activation.
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Richmond, Daniel, Raed Rizkallah, Fengshan Liang, Myra M. Hurt, and Yanchang Wang. "Slk19 clusters kinetochores and facilitates chromosome bipolar attachment." Molecular Biology of the Cell 24, no. 5 (2013): 566–77. http://dx.doi.org/10.1091/mbc.e12-07-0552.
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In all eukaryotic cells, DNA is packaged into multiple chromosomes that are linked to microtubules through a large protein complex called a kinetochore. Previous data show that the kinetochores are clustered together during most of the cell cycle, but the mechanism and the biological significance of kinetochore clustering are unknown. As a kinetochore protein in budding yeast, the role of Slk19 in the stability of the anaphase spindle has been well studied, but its function in chromosome segregation has remained elusive. Here we show that Slk19 is required for kinetochore clustering when yeast cells are treated with the microtubule-depolymerizing agent nocodazole. We further find that slk19Δ mutant cells exhibit delayed kinetochore capture and chromosome bipolar attachment after the disruption of the kinetochore–microtubule interaction by nocodazole, which is likely attributed to defective kinetochore clustering. In addition, we show that Slk19 interacts with itself, suggesting that the dimerization of Slk19 may mediate the interaction between kinetochores for clustering. Therefore Slk19 likely acts as kinetochore glue that clusters kinetochores to facilitate efficient and faithful chromosome segregation.
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Milanesi, L., M. Muselli, and P. Arrigo. "Hamming-Clustering method for signals prediction in 5′ and 3′ regions of eukaryotic genes." Bioinformatics 12, no. 5 (1996): 399–404. http://dx.doi.org/10.1093/bioinformatics/12.5.399.
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Guillou, Laure, Dipankar Bachar, Stéphane Audic, et al. "The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy." Nucleic Acids Research 41, no. 2013 (2012): 597–604. https://doi.org/10.1093/nar/gks1160.
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The interrogation of genetic markers in environmental meta-barcoding studies is currently seriously hindered by the lack of taxonomically curated reference data sets for the targeted genes. The Protist Ribosomal Reference database (PR2, http://ssurrna. org/) provides a unique access to eukaryotic small sub-unit (SSU) ribosomal RNA and DNA sequences, with curated taxonomy. The database mainly consists of nuclear-encoded protistan sequences. However, metazoans, land plants, macrosporic fungi and eukaryotic organelles (mitochondrion, plastid and others) are also included because they are useful for the analysis of hightroughput sequencing data sets. Introns and putative chimeric sequences have been also carefully checked. Taxonomic assignation of sequences consists of eight unique taxonomic fields. In total,136 866 sequences are nuclear encoded, 45 708 (36 501 mitochondrial and 9657 chloroplastic) are from organelles, the remaining being putative chimeric sequences. The website allows the users to download sequences from the entire and partial databases (including representative sequences after clustering at a given level of similarity). Different web tools also allow searches by sequence similarity. The presence of both rRNA and rDNA sequences, taking into account introns (crucial for eukaryotic sequences), a normalized eight terms ranked-taxonomy and updates of new GenBank releases were made possible by a long-term collaboration between experts in taxonomy and computer scientists.
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Brandt, Miriam I., Blandine Trouche, Laure Quintric, et al. "Bioinformatic pipelines combining denoising and clustering tools allow for more comprehensive prokaryotic and eukaryotic metabarcoding." Molecular Ecology Resources 21, no. 6 (2021): 1904–21. http://dx.doi.org/10.1111/1755-0998.13398.
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Anderson, Marybeth, Julian Haase, Elaine Yeh, and Kerry Bloom. "Function and Assembly of DNA Looping, Clustering, and Microtubule Attachment Complexes within a Eukaryotic Kinetochore." Molecular Biology of the Cell 20, no. 19 (2009): 4131–39. http://dx.doi.org/10.1091/mbc.e09-05-0359.
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The kinetochore is a complex protein–DNA assembly that provides the mechanical linkage between microtubules and the centromere DNA of each chromosome. Centromere DNA in all eukaryotes is wrapped around a unique nucleosome that contains the histone H3 variant CENP-A (Cse4p in Saccharomyces cerevisiae). Here, we report that the inner kinetochore complex (CBF3) is required for pericentric DNA looping at the Cse4p-containing nucleosome. DNA within the pericentric loop occupies a spatially confined area that is radially displaced from the interpolar central spindle. Microtubule-binding kinetochore complexes are not involved in pericentric DNA looping but are required for the geometric organization of DNA loops around the spindle microtubules in metaphase. Thus, the mitotic segregation apparatus is a composite structure composed of kinetochore and interpolar microtubules, the kinetochore, and organized pericentric DNA loops. The linkage of microtubule-binding to centromere DNA-looping complexes positions the pericentric chromatin loops and stabilizes the dynamic properties of individual kinetochore complexes in mitosis.
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Xu, Haiqing, Jing-Jing Liu, Zhen Liu, Ying Li, Yong-Su Jin, and Jianzhi Zhang. "Synchronization of stochastic expressions drives the clustering of functionally related genes." Science Advances 5, no. 10 (2019): eaax6525. http://dx.doi.org/10.1126/sciadv.aax6525.
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Functionally related genes tend to be chromosomally clustered in eukaryotic genomes even after the exclusion of tandem duplicates, but the biological significance of this widespread phenomenon is unclear. We propose that stochastic expression fluctuations of neighboring genes resulting from chromatin dynamics are more or less synchronized such that their expression ratio is more stable than that for unlinked genes. Consequently, chromosomal clustering could be advantageous when the expression ratio of the clustered genes needs to stay constant, for example, because of the accumulation of toxic compounds when this ratio is altered. Evidence from manipulative experiments on the yeast GAL cluster, comprising three chromosomally adjacent genes encoding enzymes catalyzing consecutive reactions in galactose catabolism, unequivocally supports this hypothesis and elucidates how disorder in one biological phenomenon—gene expression noise—could prompt the emergence of order in another—genome organization.
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Cisse, Ibrahim I., Ignacio Izeddin, Sebastien Z. Causse, et al. "Real-Time Dynamics of RNA Polymerase II Clustering in Live Human Cells." Science 341, no. 6146 (2013): 664–67. http://dx.doi.org/10.1126/science.1239053.
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Transcription is reported to be spatially compartmentalized in nuclear transcription factories with clusters of RNA polymerase II (Pol II). However, little is known about when these foci assemble or their relative stability. We developed a quantitative single-cell approach to characterize protein spatiotemporal organization, with single-molecule sensitivity in live eukaryotic cells. We observed that Pol II clusters form transiently, with an average lifetime of 5.1 (± 0.4) seconds, which refutes the notion that they are statically assembled substructures. Stimuli affecting transcription yielded orders-of-magnitude changes in the dynamics of Pol II clusters, which implies that clustering is regulated and plays a role in the cell’s ability to effect rapid response to external signals. Our results suggest that transient crowding of enzymes may aid in rate-limiting steps of gene regulation.
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Schrank, Benjamin, and Jean Gautier. "Assembling nuclear domains: Lessons from DNA repair." Journal of Cell Biology 218, no. 8 (2019): 2444–55. http://dx.doi.org/10.1083/jcb.201904202.
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Eukaryotic nuclei are organized into nuclear domains that unite loci sharing a common function. These domains are essential for diverse processes including (1) the formation of topologically associated domains (TADs) that coordinate replication and transcription, (2) the formation of specialized transcription and splicing factories, and (3) the clustering of DNA double-strand breaks (DSBs), which concentrates damaged DNA for repair. The generation of nuclear domains requires forces that are beginning to be identified. In the case of DNA DSBs, DNA movement and clustering are driven by actin filament nucleators. Furthermore, RNAs and low-complexity protein domains such as RNA-binding proteins also accumulate around sites of transcription and repair. The link between liquid–liquid phase separation and actin nucleation in the formation of nuclear domains is still unknown. This review discusses DSB repair domain formation as a model for functional nuclear domains in other genomic contexts.
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Asfare, Sarah, Reem Eldabagh, Khizar Siddiqui, et al. "Systematic Analysis of Functionally Related Gene Clusters in the Opportunistic Pathogen, Candida albicans." Microorganisms 9, no. 2 (2021): 276. http://dx.doi.org/10.3390/microorganisms9020276.
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The proper balance of gene expression is essential for cellular health, organismal development, and maintaining homeostasis. In response to complex internal and external signals, the cell needs to modulate gene expression to maintain proteostasis and establish cellular identity within its niche. On a genome level, single-celled prokaryotic microbes display clustering of co-expressed genes that are regulated as a polycistronic RNA. This phenomenon is largely absent from eukaryotic microbes, although there is extensive clustering of co-expressed genes as functional pairs spread throughout the genome in Saccharomyces cerevisiae. While initial analysis demonstrated conservation of clustering in divergent fungal lineages, a comprehensive analysis has yet to be performed. Here we report on the prevalence, conservation, and significance of the functional clustering of co-regulated genes within the opportunistic human pathogen, Candida albicans. Our analysis reveals that there is extensive clustering within this organism—although the identity of the gene pairs is unique compared with those found in S. cerevisiae—indicating that this genomic arrangement evolved after these microbes diverged evolutionarily, rather than being the result of an ancestral arrangement. We report a clustered arrangement in gene families that participate in diverse molecular functions and are not the result of a divergent orientation with a shared promoter. This arrangement coordinates the transcription of the clustered genes to their neighboring genes, with the clusters congregating to genomic loci that are conducive to transcriptional regulation at a distance.
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Lee, Y. "The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes." Nucleic Acids Research 33, Database issue (2004): D71—D74. http://dx.doi.org/10.1093/nar/gki064.
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Song, Hokyung, Ian Crawford, Jonathan Lloyd, et al. "Airborne Bacterial and Eukaryotic Community Structure across the United Kingdom Revealed by High-Throughput Sequencing." Atmosphere 11, no. 8 (2020): 802. http://dx.doi.org/10.3390/atmos11080802.
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Primary biological aerosols often include allergenic and pathogenic microorganisms posing potential risks to human health. Moreover, there are airborne plant and animal pathogens that may have ecological and economic impact. In this study, we used high-throughput sequencing techniques (Illumina, MiSeq) targeting the 16S rRNA genes of bacteria and the 18S rRNA genes of eukaryotes, to characterize airborne primary biological aerosols. We used a filtration system on the UK Facility for Airborne Atmospheric Measurements (FAAM) research aircraft to sample a range of primary biological aerosols across southern England overflying surface measurement sites from Chilbolton to Weybourne. We identified 30 to 60 bacterial operational taxonomic units (OTUs) and 108 to 224 eukaryotic OTUs per sample. Moreover, 16S rRNA gene sequencing identified significant numbers of genera that have not been found in atmospheric samples previously or only been described in limited number of atmospheric field studies, which are rather old or published in local journals. This includes the genera Gordonia, Lautropia, and Psychroglaciecola. Some of the bacterial genera found in this study include potential human pathogens, for example, Gordonia, Sphingomonas, Chryseobacterium, Morganella, Fusobacterium, and Streptococcus. 18S rRNA gene sequencing showed Cladosporium to be the major genus in all of the samples, which is a well-known allergen and often found in the atmosphere. There were also genetic signatures of potentially allergenic taxa; for example, Pleosporales, Phoma, and Brassicales. Although there was no significant clustering of bacterial and eukaryotic communities depending on the sampling location, we found meteorological factors explaining significant variations in the community composition. The findings in this study support the application of DNA-based sequencing technologies for atmospheric science studies in combination with complementary spectroscopic and microscopic techniques for improved identification of primary biological aerosols.
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Jannuzzi, Ayse Tarbin, Gulce Sari, Ayse Mine Yilmaz, Betul Karademir, and Buket Alpertunga. "Proteasomal Inhibition with Bortezomib Causes Selective Autophagy Upregulation and Perinuclear Clustering of Mitochondria in Human Neuronal Cells." Proceedings 2, no. 25 (2018): 1583. http://dx.doi.org/10.3390/proceedings2251583.
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The ubiquitin proteasomal system and autophagic pathway are two main protein degradation systems in eukaryotic cells. Inhibition of the proteasomal system with proteasome inhibitors for cancer treatment can cause neurotoxic side effects. In this study, we investigated neurotoxic side effects of bortezomib (BTZ) and carfilzomib (CFZ) in a human neuronal cell model. Inhibition of proteasome with BTZ upregulated autophagy receptor protein p62 level. BTZ caused reduced mitochondrial mass per cell in a greater extent than CFZ. BTZ caused more clustering of mitochondria than CFZ. In conclusion, mitochondrial toxicity and autophagic upregulation with BTZ may be the reason for more severe neurotoxic profile than CFZ.
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Jin, Ye, Satoru Uzawa, and W. Z. Cande. "Fission Yeast Mutants Affecting Telomere Clustering and Meiosis-Specific Spindle Pole Body Integrity." Genetics 160, no. 3 (2002): 861–76. http://dx.doi.org/10.1093/genetics/160.3.861.
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Abstract In meiotic prophase of many eukaryotic organisms, telomeres attach to the nuclear envelope and form a polarized configuration called the bouquet. Bouquet formation is hypothesized to facilitate homologous chromosome pairing. In fission yeast, bouquet formation and telomere clustering occurs in karyogamy and persists throughout the horsetail stage. Here we report the isolation and characterization of six mutants from our screen for meiotic mutants. These mutants show defective telomere clustering as demonstrated by mislocalization of Swi6::GFP, a heterochromatin-binding protein, and Taz1p::GFP, a telomere-specific protein. These mutants define four complementation groups and are named dot1 to dot4—defective organization of telomeres. dot3 and dot4 are allelic to mat1-Mm and mei4, respectively. Immunolocalization of Sad1, a protein associated with the spindle pole body (SPB), in dot mutants showed an elevated frequency of multiple Sad1-nuclei signals relative to wild type. Many of these Sad1 foci were colocalized with Taz1::GFP. Impaired SPB structure and function were further demonstrated by failure of spore wall formation in dot1, by multiple Pcp1::GFP signals (an SPB component) in dot2, and by abnormal microtubule organizations during meiosis in dot mutants. The coincidence of impaired SPB functions with defective telomere clustering suggests a link between the SPB and the telomere cluster.
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Razin, Sergey V., Elena S. Ioudinkova, Omar L. Kantidze, and Olga V. Iarovaia. "Co-Regulated Genes and Gene Clusters." Genes 12, no. 6 (2021): 907. http://dx.doi.org/10.3390/genes12060907.
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There are many co-regulated genes in eukaryotic cells. The coordinated activation or repression of such genes occurs at specific stages of differentiation, or under the influence of external stimuli. As a rule, co-regulated genes are dispersed in the genome. However, there are also gene clusters, which contain paralogous genes that encode proteins with similar functions. In this aspect, they differ significantly from bacterial operons containing functionally linked genes that are not paralogs. In this review, we discuss the reasons for the existence of gene clusters in vertebrate cells and propose that clustering is necessary to ensure the possibility of selective activation of one of several similar genes.
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Burke, Evan J., Samuel S. Rodda, Sean R. Lund, et al. "Phage-encoded ten-eleven translocation dioxygenase (TET) is active in C5-cytosine hypermodification in DNA." Proceedings of the National Academy of Sciences 118, no. 26 (2021): e2026742118. http://dx.doi.org/10.1073/pnas.2026742118.
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TET/JBP (ten-eleven translocation/base J binding protein) enzymes are iron(II)- and 2-oxo-glutarate–dependent dioxygenases that are found in all kingdoms of life and oxidize 5-methylpyrimidines on the polynucleotide level. Despite their prevalence, few examples have been biochemically characterized. Among those studied are the metazoan TET enzymes that oxidize 5-methylcytosine in DNA to hydroxy, formyl, and carboxy forms and the euglenozoa JBP dioxygenases that oxidize thymine in the first step of base J biosynthesis. Both enzymes have roles in epigenetic regulation. It has been hypothesized that all TET/JBPs have their ancestral origins in bacteriophages, but only eukaryotic orthologs have been described. Here we demonstrate the 5mC-dioxygenase activity of several phage TETs encoded within viral metagenomes. The clustering of these TETs in a phylogenetic tree correlates with the sequence specificity of their genomically cooccurring cytosine C5-methyltransferases, which install the methyl groups upon which TETs operate. The phage TETs favor Gp5mC dinucleotides over the 5mCpG sites targeted by the eukaryotic TETs and are found within gene clusters specifying complex cytosine modifications that may be important for DNA packaging and evasion of host restriction.
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Lang, Yanhe, Yuan Sun, Miao Yu, Yubin Ji, Lei Wang, and Zhizhou Zhang. "Differential Colonization Dynamics of Marine Biofilm-Forming Eukaryotic Microbes on Different Protective Coating Materials." Polymers 11, no. 1 (2019): 161. http://dx.doi.org/10.3390/polym11010161.
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In this study, the actual anti-biofouling (AF) efficacy of three protective coatings, including a chlorinated rubber-based coating (C0) and two polydimethylsiloxane (PDMS)-based coatings (P0 and PF), were estimated via the static field exposure assays. The surface properties of these protective coatings, including surface wettability and morphology features, were characterized using the static water contact angle (WCA) and scanning electron microscope (SEM). The colonization and succession dynamics of the early-adherent biofilm-forming eukaryotic microbial communities occupied on these protective coatings were explored using the Single-stranded Conformation Polymorphism (SSCP) technique. The field data clearly revealed that coating P0 and PF performed better in the long-term static submergence, as compared with the C0 surface, while coating PF showed excellent AF efficacy in the field. Fingerprinting analysis suggested that the diversity, abundance, the clustering patterns, and colonization dynamics of the early-colonized eukaryotic microbes were significantly perturbed by these protective coatings, particularly by the PF surfaces. These differential AF efficacy and perturbation effects would be largely ascribed to the differences in the wettability and surface nanostructures between the C0, P0 and PF surfaces, as evidenced by WCA and SEM analysis.
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Moreno-Hagelsieb, Gabriel, Bennett Vitug, Arturo Medrano-Soto, and Milton H. Saier Jr. "The Membrane Attack Complex/Perforin Superfamily." Journal of Molecular Microbiology and Biotechnology 27, no. 4 (2017): 252–67. http://dx.doi.org/10.1159/000481286.
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The membrane attack complex/perforin (MACPF) superfamily consists of a diverse group of proteins involved in bacterial pathogenesis and sporulation as well as eukaryotic immunity, embryonic development, neural migration and fruiting body formation. The present work shows that the evolutionary relationships between the members of the superfamily, previously suggested by comparison of their tertiary structures, can also be supported by analyses of their primary structures. The superfamily includes the MACPF family (TC 1.C.39), the cholesterol-dependent cytolysin (CDC) family (TC 1.C.12.1 and 1.C.12.2) and the pleurotolysin pore-forming (pleurotolysin B) family (TC 1.C.97.1), as revealed by expansion of each family by comparison against a large protein database, and by the comparisons of their hidden Markov models. Clustering analyses demonstrated grouping of the CDC homologues separately from the 12 MACPF subfamilies, which also grouped separately from the pleurotolysin B family. Members of the MACPF superfamily revealed a remarkably diverse range of proteins spanning eukaryotic, bacterial, and archaeal taxonomic domains, with notable variations in protein domain architectures. Our strategy should also be helpful in putting together other highly divergent protein families.
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Kuitche, Esaie, Manuel Lafond, and Aïda Ouangraoua. "Reconstructing protein and gene phylogenies using reconciliation and soft-clustering." Journal of Bioinformatics and Computational Biology 15, no. 06 (2017): 1740007. http://dx.doi.org/10.1142/s0219720017400078.
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The architecture of eukaryotic coding genes allows the production of several different protein isoforms by genes. Current gene phylogeny reconstruction methods make use of a single protein product per gene, ignoring information on alternative protein isoforms. These methods often lead to inaccurate gene tree reconstructions that require to be corrected before phylogenetic analyses. Here, we propose a new approach for the reconstruction of gene trees and protein trees accounting for alternative protein isoforms. We extend the concept of reconciliation to protein trees, and we define a new reconciliation problem called MinDRGT that consists in finding a gene tree that minimizes a double reconciliation cost with a given protein tree and a given species tree. We define a second problem called MinDRPGT that consists in finding a protein supertree and a gene tree minimizing a double reconciliation cost, given a species tree and a set of protein subtrees. We propose a shift from the traditional view of protein ortholog groups as hard-clusters to soft-clusters and we study the MinDRPGT problem under this assumption. We provide algorithmic exact and heuristic solutions for versions of the problems, and we present the results of applications on protein and gene trees from the Ensembl database. The implementations of the methods are available at https://github.com/UdeS-CoBIUS/Protein2GeneTree and https://github.com/UdeS-CoBIUS/SuperProteinTree .
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Kittelmann, Sandra, Michelle R. Kirk, Arjan Jonker, Alan McCulloch, and Peter H. Janssen. "Buccal Swabbing as a Noninvasive Method To Determine Bacterial, Archaeal, and Eukaryotic Microbial Community Structures in the Rumen." Applied and Environmental Microbiology 81, no. 21 (2015): 7470–83. http://dx.doi.org/10.1128/aem.02385-15.
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ABSTRACTAnalysis of rumen microbial community structure based on small-subunit rRNA marker genes in metagenomic DNA samples provides important insights into the dominant taxa present in the rumen and allows assessment of community differences between individuals or in response to treatments applied to ruminants. However, natural animal-to-animal variation in rumen microbial community composition can limit the power of a study considerably, especially when only subtle differences are expected between treatment groups. Thus, trials with large numbers of animals may be necessary to overcome this variation. Because ruminants pass large amounts of rumen material to their oral cavities when they chew their cud, oral samples may contain good representations of the rumen microbiota and be useful in lieu of rumen samples to study rumen microbial communities. We compared bacterial, archaeal, and eukaryotic community structures in DNAs extracted from buccal swabs to those in DNAs from samples collected directly from the rumen by use of a stomach tube for sheep on four different diets. After bioinformatic depletion of potential oral taxa from libraries of samples collected via buccal swabs, bacterial communities showed significant clustering by diet (R= 0.37; analysis of similarity [ANOSIM]) rather than by sampling method (R= 0.07). Archaeal, ciliate protozoal, and anaerobic fungal communities also showed significant clustering by diet rather than by sampling method, even without adjustment for potentially orally associated microorganisms. These findings indicate that buccal swabs may in future allow quick and noninvasive sampling for analysis of rumen microbial communities in large numbers of ruminants.
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Narayanasamy, Sasirekha, Hwei Ling Ong, and Indu S. Ambudkar. "A Deep Dive into the N-Terminus of STIM Proteins: Structure–Function Analysis and Evolutionary Significance of the Functional Domains." Biomolecules 14, no. 10 (2024): 1200. http://dx.doi.org/10.3390/biom14101200.
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Calcium is an important second messenger that is involved in almost all cellular processes. Disruptions in the regulation of intracellular Ca2+ levels ([Ca2+]i) adversely impact normal physiological function and can contribute to various diseased conditions. STIM and Orai proteins play important roles in maintaining [Ca2+]i through store-operated Ca2+ entry (SOCE), with STIM being the primary regulatory protein that governs the function of Orai channels. STIM1 and STIM2 are single-pass ER-transmembrane proteins with their N- and C-termini located in the ER lumen and cytoplasm, respectively. The N-terminal EF-SAM domain of STIMs senses [Ca2+]ER changes, while the C-terminus mediates clustering in ER-PM junctions and gating of Orai1. ER-Ca2+ store depletion triggers activation of the STIM proteins, which involves their multimerization and clustering in ER-PM junctions, where they recruit and activate Orai1 channels. In this review, we will discuss the structure, organization, and function of EF-hand motifs and the SAM domain of STIM proteins in relation to those of other eukaryotic proteins.
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Bunnik, Evelien M., Aarthi Venkat, Jianlin Shao, et al. "Comparative 3D genome organization in apicomplexan parasites." Proceedings of the National Academy of Sciences 116, no. 8 (2019): 3183–92. http://dx.doi.org/10.1073/pnas.1810815116.
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The positioning of chromosomes in the nucleus of a eukaryotic cell is highly organized and has a complex and dynamic relationship with gene expression. In the human malaria parasite Plasmodium falciparum, the clustering of a family of virulence genes correlates with their coordinated silencing and has a strong influence on the overall organization of the genome. To identify conserved and species-specific principles of genome organization, we performed Hi-C experiments and generated 3D genome models for five Plasmodium species and two related apicomplexan parasites. Plasmodium species mainly showed clustering of centromeres, telomeres, and virulence genes. In P. falciparum, the heterochromatic virulence gene cluster had a strong repressive effect on the surrounding nuclear space, while this was less pronounced in Plasmodium vivax and Plasmodium berghei, and absent in Plasmodium yoelii. In Plasmodium knowlesi, telomeres and virulence genes were more dispersed throughout the nucleus, but its 3D genome showed a strong correlation with gene expression. The Babesia microti genome showed a classical Rabl organization with colocalization of subtelomeric virulence genes, while the Toxoplasma gondii genome was dominated by clustering of the centromeres and lacked virulence gene clustering. Collectively, our results demonstrate that spatial genome organization in most Plasmodium species is constrained by the colocalization of virulence genes. P. falciparum and P. knowlesi, the only two Plasmodium species with gene families involved in antigenic variation, are unique in the effect of these genes on chromosome folding, indicating a potential link between genome organization and gene expression in more virulent pathogens.
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Fahmi, Muhamad, Hiromu Kitagawa, Gen Yasui, Yukihiko Kubota, and Masahiro Ito. "The Functional Classification of ORF8 in SARS-CoV-2 Replication, Immune Evasion, and Viral Pathogenesis Inferred through Phylogenetic Profiling." Evolutionary Bioinformatics 17 (January 2021): 117693432110030. http://dx.doi.org/10.1177/11769343211003079.
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ORF8 is a highly variable genomic region of SARS-CoV-2. Although non-essential and the precise functions are unknown, it has been suggested that this protein assists in SARS-CoV-2 replication in the early secretory pathway and in immune evasion. We utilized the binding partners of SARS-CoV-2 proteins in human HEK293T cells and performed genome-wide phylogenetic profiling and clustering analyses in 446 eukaryotic species to predict and discover ORF8 binding partners that share associated functional mechanisms based on co-evolution. Results classified 47 ORF8 binding partner proteins into 3 clusters (groups 1-3), which were conserved in vertebrates (group 1), metazoan (group 2), and eukaryotes (group 3). Gene ontology analysis indicated that group 1 had no significant associated biological processes, while groups 2 and 3 were associated with glycoprotein biosynthesis process and ubiquitin-dependent endoplasmic reticulum-associated degradation pathways, respectively. Collectively, our results classified potential genes that might be associated with SARS-CoV-2 viral pathogenesis, specifically related to acute respiratory distress syndrome, and the secretory pathway. Here, we discuss the possible role of ORF8 in viral pathogenesis and in assisting viral replication and immune evasion via secretory pathway, as well as the possible factors associated with the rapid evolution of ORF8.
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Moreno-Gallego, Jaime Leonardo, and Alejandro Reyes. "Informative Regions In Viral Genomes." Viruses 13, no. 6 (2021): 1164. http://dx.doi.org/10.3390/v13061164.
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Viruses, far from being just parasites affecting hosts’ fitness, are major players in any microbial ecosystem. In spite of their broad abundance, viruses, in particular bacteriophages, remain largely unknown since only about 20% of sequences obtained from viral community DNA surveys could be annotated by comparison with public databases. In order to shed some light into this genetic dark matter we expanded the search of orthologous groups as potential markers to viral taxonomy from bacteriophages and included eukaryotic viruses, establishing a set of 31,150 ViPhOGs (Eukaryotic Viruses and Phages Orthologous Groups). To do this, we examine the non-redundant viral diversity stored in public databases, predict proteins in genomes lacking such information, and used all annotated and predicted proteins to identify potential protein domains. The clustering of domains and unannotated regions into orthologous groups was done using cogSoft. Finally, we employed a random forest implementation to classify genomes into their taxonomy and found that the presence or absence of ViPhOGs is significantly associated with their taxonomy. Furthermore, we established a set of 1457 ViPhOGs that given their importance for the classification could be considered as markers or signatures for the different taxonomic groups defined by the ICTV at the order, family, and genus levels.
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Munshi, Rahul. "How Transcription Factor Clusters Shape the Transcriptional Landscape." Biomolecules 14, no. 7 (2024): 875. http://dx.doi.org/10.3390/biom14070875.
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In eukaryotic cells, gene transcription typically occurs in discrete periods of promoter activity, interspersed with intervals of inactivity. This pattern deviates from simple stochastic events and warrants a closer examination of the molecular interactions that activate the promoter. Recent studies have identified transcription factor (TF) clusters as key precursors to transcriptional bursting. Often, these TF clusters form at chromatin segments that are physically distant from the promoter, making changes in chromatin conformation crucial for promoter–TF cluster interactions. In this review, I explore the formation and constituents of TF clusters, examining how the dynamic interplay between chromatin architecture and TF clustering influences transcriptional bursting. Additionally, I discuss techniques for visualizing TF clusters and provide an outlook on understanding the remaining gaps in this field.
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Mo, Shushan, Xiaoya Li, Yuanhang Li, et al. "Mimicking the process from secretory vesicles to organelles in eukaryotic cell evolution by clustering enzyme-liposomes in artificial cells." Journal of Colloid and Interface Science 696 (October 2025): 137863. https://doi.org/10.1016/j.jcis.2025.137863.
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Wohlschlegel, James A., Erica S. Johnson, Steven I. Reed, and John R. Yates. "Global Analysis of Protein Sumoylation inSaccharomyces cerevisiae." Journal of Biological Chemistry 279, no. 44 (2004): 45662–68. http://dx.doi.org/10.1074/jbc.m409203200.
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Although the modification of cellular factors by SUMO is an essential process inSaccharomyces cerevisiae, the identities of the substrates remain largely unknown. Using a mass spectrometry-based approach, we have identified 271 new SUMO targets. These substrates play roles in a diverse set of biological processes and greatly expand the scope of SUMO regulation in eukaryotic cells. Transcription appears to be the most prevalent process associated with sumoylation with novel SUMO substrates found in basal transcription machinery for RNA polymerases I, II, and III, pol II transcriptional elongation complexes, and a variety of chromatin remodeling, chromatin modifying, and chromatin silencing complexes. Additionally, our global analysis has revealed a number of interesting biological patterns in the list of SUMO targets including a clustering of sumoylation targets within macromolecular complexes.
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Daugherty, Matthew, Veronika Vonstein, Ross Overbeek, and Andrei Osterman. "Archaeal Shikimate Kinase, a New Member of the GHMP-Kinase Family." Journal of Bacteriology 183, no. 1 (2001): 292–300. http://dx.doi.org/10.1128/jb.183.1.292-300.2001.
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ABSTRACT Shikimate kinase (EC 2.7.1.71 ) is a committed enzyme in the seven-step biosynthesis of chorismate, a major precursor of aromatic amino acids and many other aromatic compounds. Genes for all enzymes of the chorismate pathway except shikimate kinase are found in archaeal genomes by sequence homology to their bacterial counterparts. In this study, a conserved archaeal gene (gi‖1500322 in Methanococcus jannaschii) was identified as the best candidate for the missing shikimate kinase gene by the analysis of chromosomal clustering of chorismate biosynthetic genes. The encoded hypothetical protein, with no sequence similarity to bacterial and eukaryotic shikimate kinases, is distantly related to homoserine kinases (EC 2.7.1.39 ) of the GHMP-kinase superfamily. The latter functionality in M. jannaschii is assigned to another gene (gi‖1591748), in agreement with sequence similarity and chromosomal clustering analysis. Both archaeal proteins, overexpressed in Escherichia coliand purified to homogeneity, displayed activity of the predicted type, with steady-state kinetic parameters similar to those of the corresponding bacterial kinases:K m,shikimate = 414 ± 33 μM,K m,ATP = 48 ± 4 μM, andk cat = 57 ± 2 s−1 for the predicted shikimate kinase andK m,homoserine = 188 ± 37 μM,K m,ATP = 101 ± 7 μM, andk cat = 28 ± 1 s−1 for the homoserine kinase. No overlapping activity could be detected between shikimate kinase and homoserine kinase, both revealing a >1,000-fold preference for their own specific substrates. The case of archaeal shikimate kinase illustrates the efficacy of techniques based on reconstruction of metabolism from genomic data and analysis of gene clustering on chromosomes in finding missing genes.
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Shopland, Lindsay S., Carol V. Johnson, Meg Byron, John McNeil, and Jeanne B. Lawrence. "Clustering of multiple specific genes and gene-rich R-bands around SC-35 domains." Journal of Cell Biology 162, no. 6 (2003): 981–90. http://dx.doi.org/10.1083/jcb.200303131.
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Typically, eukaryotic nuclei contain 10–30 prominent domains (referred to here as SC-35 domains) that are concentrated in mRNA metabolic factors. Here, we show that multiple specific genes cluster around a common SC-35 domain, which contains multiple mRNAs. Nonsyntenic genes are capable of associating with a common domain, but domain “choice” appears random, even for two coordinately expressed genes. Active genes widely separated on different chromosome arms associate with the same domain frequently, assorting randomly into the 3–4 subregions of the chromosome periphery that contact a domain. Most importantly, visualization of six individual chromosome bands showed that large genomic segments (∼5 Mb) have striking differences in organization relative to domains. Certain bands showed extensive contact, often aligning with or encircling an SC-35 domain, whereas others did not. All three gene-rich reverse bands showed this more than the gene-poor Giemsa dark bands, and morphometric analyses demonstrated statistically significant differences. Similarly, late-replicating DNA generally avoids SC-35 domains. These findings suggest a functional rationale for gene clustering in chromosomal bands, which relates to nuclear clustering of genes with SC-35 domains. Rather than random reservoirs of splicing factors, or factors accumulated on an individual highly active gene, we propose a model of SC-35 domains as functional centers for a multitude of clustered genes, forming local euchromatic “neighborhoods.”
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Wangensteen, Owen S., Creu Palacín, Magdalena Guardiola, and Xavier Turon. "DNA metabarcoding of littoral hard-bottom communities: high diversity and database gaps revealed by two molecular markers." PeerJ 6 (May 4, 2018): e4705. http://dx.doi.org/10.7717/peerj.4705.
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Biodiversity assessment of marine hard-bottom communities is hindered by the high diversity and size-ranges of the organisms present. We developed a DNA metabarcoding protocol for biodiversity characterization of structurally complex natural marine hard-bottom communities. We used two molecular markers: the “Leray fragment” of mitochondrialcytochrome c oxidase(COI), for which a novel primer set was developed, and the V7 region of the nuclear small subunit ribosomal RNA (18S). Eight different shallow marine littoral communities from two National Parks in Spain (one in the Atlantic Ocean and another in the Mediterranean Sea) were studied. Samples were sieved into three size fractions from where DNA was extracted separately. Bayesian clustering was used for delimiting molecular operational taxonomic units (MOTUs) and custom reference databases were constructed for taxonomic assignment. Despite applying stringent filters, we found high values for MOTU richness (2,510 and 9,679 MOTUs with 18S and COI, respectively), suggesting that these communities host a large amount of yet undescribed eukaryotic biodiversity. Significant gaps are still found in sequence reference databases, which currently prevent the complete taxonomic assignment of the detected sequences. In our dataset, 85% of 18S MOTUs and 64% of COI MOTUs could be identified to phylum or lower taxonomic level. Nevertheless, those unassigned were mostly rare MOTUs with low numbers of reads, and assigned MOTUs comprised over 90% of the total sequence reads. The identification rate might be significantly improved in the future, as reference databases are further completed. Our results show that marine metabarcoding, currently applied mostly to plankton or sediments, can be adapted to structurally complex hard bottom samples. Thus, eukaryotic metabarcoding emerges as a robust, fast, objective and affordable method to comprehensively characterize the diversity of marine benthic communities dominated by macroscopic seaweeds and colonial or modular sessile metazoans. The 18S marker lacks species-level resolution and thus cannot be recommended to assess the detailed taxonomic composition of these communities. Our new universal primers for COI can potentially be used for biodiversity assessment with high taxonomic resolution in a wide array of marine, terrestrial or freshwater eukaryotic communities.
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Blanc, Guillaume, Lucie Gallot-Lavallée, and Florian Maumus. "Provirophages in the Bigelowiella genome bear testimony to past encounters with giant viruses." Proceedings of the National Academy of Sciences 112, no. 38 (2015): E5318—E5326. http://dx.doi.org/10.1073/pnas.1506469112.
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Virophages are recently discovered double-stranded DNA virus satellites that prey on giant viruses (nucleocytoplasmic large DNA viruses; NCLDVs), which are themselves parasites of unicellular eukaryotes. This coupled parasitism can result in the indirect control of eukaryotic cell mortality by virophages. However, the details of such tripartite relationships remain largely unexplored. We have discovered ∼300 predicted genes of putative virophage origin in the nuclear genome of the unicellular alga Bigelowiella natans. Physical clustering of these genes indicates that virophage genomes are integrated into the B. natans genome. Virophage inserts show high levels of similarity and synteny between each other, indicating that they are closely related. Virophage genes are transcribed not only in the sequenced B. natans strain but also in other Bigelowiella isolates, suggesting that transcriptionally active virophage inserts are widespread in Bigelowiella populations. Evidence that B. natans is also a host to NCLDV members is provided by the identification of NCLDV inserts in its genome. These putative large DNA viruses may be infected by B. natans virophages. We also identify four repeated elements sharing structural and genetic similarities with transpovirons—a class of mobile elements first discovered in giant viruses—that were probably independently inserted in the B. natans genome. We argue that endogenized provirophages may be beneficial to both the virophage and B. natans by (i) increasing the chances for the virophage to coinfect the host cell with an NCLDV prey and (ii) defending the host cell against fatal NCLDV infections.
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Deep, Aman, Dana Bludau, Marius Welzel, et al. "Natrix2 – Improved amplicon workflow with novel Oxford Nanopore Technologies support and enhancements in clustering, classification and taxonomic databases." Metabarcoding and Metagenomics 7 (October 24, 2023): e109389. https://doi.org/10.3897/mbmg.7.109389.
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Sequencing of amplified DNA is the first step towards the generation of Amplicon Sequence Variants (ASVs) or Operational Taxonomic Units (OTUs) for biodiversity assessment and comparative analyses of environmental communities and microbiomes. Notably, the rapid advancements in sequencing technologies have paved the way for the growing utilization of third-generation long-read approaches in recent years. These sequence data imply increasing read lengths, higher error rates, and altered sequencing chemistry. Likewise, methods for amplicon classification and reference databases have progressed, leading to the expansion of taxonomic application areas and higher classification accuracy. With Natrix, a user-friendly and reducible workflow solution, processing of prokaryotic and eukaryotic environmental Illumina sequences using 16S or 18S is possible. Here, we present an updated version of the pipeline, Natrix2, which incorporates VSEARCH as an alternative clustering method with better performance for 16S metabarcoding approaches and mothur for taxonomic classification on further databases, including PR2, UNITE and SILVA. Additionally, Natrix2 includes the handling of Nanopore reads, which entails initial error correction and refinement of reads using Medaka and Racon to subsequently determine their taxonomic classification.
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Trgovec-Greif, Lovro, Hans-Jörg Hellinger, Jean Mainguy, et al. "VOGDB—Database of Virus Orthologous Groups." Viruses 16, no. 8 (2024): 1191. http://dx.doi.org/10.3390/v16081191.
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Computational models of homologous protein groups are essential in sequence bioinformatics. Due to the diversity and rapid evolution of viruses, the grouping of protein sequences from virus genomes is particularly challenging. The low sequence similarities of homologous genes in viruses require specific approaches for sequence- and structure-based clustering. Furthermore, the annotation of virus genomes in public databases is not as consistent and up to date as for many cellular genomes. To tackle these problems, we have developed VOGDB, which is a database of virus orthologous groups. VOGDB is a multi-layer database that progressively groups viral genes into groups connected by increasingly remote similarity. The first layer is based on pair-wise sequence similarities, the second layer is based on the sequence profile alignments, and the third layer uses predicted protein structures to find the most remote similarity. VOGDB groups allow for more sensitive homology searches of novel genes and increase the chance of predicting annotations or inferring phylogeny. VOGD B uses all virus genomes from RefSeq and partially reannotates them. VOGDB is updated with every RefSeq release. The unique feature of VOGDB is the inclusion of both prokaryotic and eukaryotic viruses in the same clustering process, which makes it possible to explore old evolutionary relationships of the two groups. VOGDB is freely available at vogdb.org under the CC BY 4.0 license.
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Keikhosravi, Adib, Krishnendu Guin, Gianluca Pegoraro, and Tom Misteli. "Simulation and Quantitative Analysis of Spatial Centromere Distribution Patterns." Cells 14, no. 7 (2025): 491. https://doi.org/10.3390/cells14070491.
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A prominent feature of eukaryotic chromosomes are centromeres, which are specialized regions of repetitive DNA required for faithful chromosome segregation during cell division. In interphase cells, centromeres are non-randomly positioned in the three-dimensional space of the nucleus in a cell type-specific manner. The functional relevance and the cellular mechanisms underlying this localization are unknown, and quantitative methods to measure distribution patterns of centromeres in 3D space are needed. Here, we developed an analytical framework that combines sensitive clustering metrics and advanced modeling techniques for the quantitative analysis of centromere distributions at the single-cell level. To identify a robust quantitative measure for centromere clustering, we benchmarked six metrics for their ability to sensitively detect changes in centromere distribution patterns from high-throughput imaging data of human cells, both under normal conditions and upon experimental perturbation of centromere distribution. We found that Ripley’s K function has the highest accuracy with minimal sensitivity to variations in the number of centromeres, making it the most suitable metric for measuring centromere distributions. As a complementary approach, we also developed and validated spatial models to replicate centromere distribution patterns, and we show that a radially shifted Gaussian distribution best represents the centromere patterns seen in human cells. Our approach creates tools for the quantitative characterization of spatial centromere distributions with applications in both targeted studies of centromere organization and unbiased screening approaches.
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Sun, Gordon, Christine Hwang, Tony Jung, Jian Liu, and Rong Li. "Biased placement of Mitochondria fission facilitates asymmetric inheritance of protein aggregates during yeast cell division." PLOS Computational Biology 19, no. 11 (2023): e1011588. http://dx.doi.org/10.1371/journal.pcbi.1011588.
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Mitochondria are essential and dynamic eukaryotic organelles that must be inherited during cell division. In yeast, mitochondria are inherited asymmetrically based on quality, which is thought to be vital for maintaining a rejuvenated cell population; however, the mechanisms underlying mitochondrial remodeling and segregation during this process are not understood. We used high spatiotemporal imaging to quantify the key aspects of mitochondrial dynamics, including motility, fission, and fusion characteristics, upon aggregation of misfolded proteins in the mitochondrial matrix. Using these measured parameters, we developed an agent-based stochastic model of dynamics of mitochondrial inheritance. Our model predicts that biased mitochondrial fission near the protein aggregates facilitates the clustering of protein aggregates in the mitochondrial matrix, and this process underlies asymmetric mitochondria inheritance. These predictions are supported by live-cell imaging experiments where mitochondrial fission was perturbed. Our findings therefore uncover an unexpected role of mitochondrial dynamics in asymmetric mitochondrial inheritance.
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Trikha, Saurabh, and Aleksandar M. Jeremic. "Clustering and Internalization of Toxic Amylin Oligomers in Pancreatic Cells Require Plasma Membrane Cholesterol." Journal of Biological Chemistry 286, no. 41 (2011): 36086–97. http://dx.doi.org/10.1074/jbc.m111.240762.
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Self-assembly of the human pancreatic hormone amylin into toxic oligomers and aggregates is linked to dysfunction of islet β-cells and pathogenesis of type 2 diabetes mellitus. Recent evidence suggests that cholesterol, an essential component of eukaryotic cells membranes, controls amylin aggregation on model membranes. However, the pathophysiological consequence of cholesterol-regulated amylin polymerization on membranes and biochemical mechanisms that protect β-cells from amylin toxicity are poorly understood. Here, we report that plasma membrane (PM) cholesterol plays a key role in molecular recognition, sorting, and internalization of toxic amylin oligomers but not monomers in pancreatic rat insulinoma and human islet cells. Depletion of PM cholesterol or the disruption of the cytoskeleton network inhibits internalization of amylin oligomers, which in turn enhances extracellular oligomer accumulation and potentiates amylin toxicity. Confocal microscopy reveals an increased nucleation of amylin oligomers across the plasma membrane in cholesterol-depleted cells, with a 2-fold increase in cell surface coverage and a 3-fold increase in their number on the PM. Biochemical studies confirm accumulation of amylin oligomers in the medium after depletion of PM cholesterol. Replenishment of PM cholesterol from intracellular cholesterol stores or by the addition of water-soluble cholesterol restores amylin oligomer clustering at the PM and internalization, which consequently diminishes cell surface coverage and toxicity of amylin oligomers. In contrast to oligomers, amylin monomers followed clathrin-dependent endocytosis, which is not sensitive to cholesterol depletion. Our studies identify an actin-mediated and cholesterol-dependent mechanism for selective uptake and clearance of amylin oligomers, impairment of which greatly potentiates amylin toxicity.
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Yang, Xueqin, Xiuli Chen, Chengzhang Liu, et al. "Dynamic Alternative Polyadenylation during Litopenaeus Vannamei Metamorphosis Development." Genes 15, no. 7 (2024): 837. http://dx.doi.org/10.3390/genes15070837.
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As an important mechanism in the post-transcriptional regulation of eukaryotic gene expression, alternative polyadenylation (APA) plays a key role in biological processes such as cell proliferation and differentiation. However, the role and dynamic pattern of APA during Litopenaeus vannamei metamorphosis are poorly understood. Here, RNA-seq data covering from the embryo to the maturation (16 time points) of L. vannamei were utilized. We identified 247 differentially expressed APA events between early and adult stages, and through fuzzy mean clustering analysis, we discovered five dynamic APA patterns. Among them, the gradual elongation of the 3′UTR is the major APA pattern that changes over time, and its genes are enriched in the pathways of protein and energy metabolism. Finally, we constructed mRNA-miRNA and PPI networks and detected several central miRNAs that may regulate L. vannamei development. Our results revealed the complex APA mechanisms in L. vannamei metamorphosis, shedding new light on post-transcriptional regulation of crustacean metamorphosis.
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CARAT, SOLENNE, RÉMI HOULGATTE, and JÉRÉMIE BOURDON. "A PARALLEL SCHEME FOR COMPARING TRANSCRIPTION FACTOR BINDING SITES MATRICES." Journal of Bioinformatics and Computational Biology 08, no. 03 (2010): 485–502. http://dx.doi.org/10.1142/s0219720010004689.
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Gene regulation implies many mechanisms. Their identification is a crucial task to construct regulatory networks, and is necessary to understand the pathology in many cases. This requires the identification of transcription factors that play a role in regulation. Numerous motif discovery tools are now available. Combining efficiently their results appears useful for comparing and clustering these motifs in order to reduce redundancies and to identify the corresponding transcription factor. We develop a method that produces, compares and clusters a set of motifs and identifies some close motifs in databases like JASPAR and the public version of Transfac. Unlike previous comparison methods, where each matrix column is compared independently, we have developed a global method to compare motifs that also helps to reduce the number of false positives. We also propose an original graph motif model that generalizes the classical position specific pattern matrices. Finally, we present an application of our method to study ChIP-chip data sets in the context of an eukaryotic organism.
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da Silveira dos Santos, Aline Xavier, Isabelle Riezman, Maria-Auxiliadora Aguilera-Romero, et al. "Systematic lipidomic analysis of yeast protein kinase and phosphatase mutants reveals novel insights into regulation of lipid homeostasis." Molecular Biology of the Cell 25, no. 20 (2014): 3234–46. http://dx.doi.org/10.1091/mbc.e14-03-0851.
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The regulatory pathways required to maintain eukaryotic lipid homeostasis are largely unknown. We developed a systematic approach to uncover new players in the regulation of lipid homeostasis. Through an unbiased mass spectrometry–based lipidomic screening, we quantified hundreds of lipid species, including glycerophospholipids, sphingolipids, and sterols, from a collection of 129 mutants in protein kinase and phosphatase genes of Saccharomyces cerevisiae. Our approach successfully identified known kinases involved in lipid homeostasis and uncovered new ones. By clustering analysis, we found connections between nutrient-sensing pathways and regulation of glycerophospholipids. Deletion of members of glucose- and nitrogen-sensing pathways showed reciprocal changes in glycerophospholipid acyl chain lengths. We also found several new candidates for the regulation of sphingolipid homeostasis, including a connection between inositol pyrophosphate metabolism and complex sphingolipid homeostasis through transcriptional regulation of AUR1 and SUR1. This robust, systematic lipidomic approach constitutes a rich, new source of biological information and can be used to identify novel gene associations and function.
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Tria, Fernando D. K., Julia Brueckner, Josip Skejo, et al. "Gene Duplications Trace Mitochondria to the Onset of Eukaryote Complexity." Genome Biology and Evolution 13, no. 5 (2021). http://dx.doi.org/10.1093/gbe/evab055.
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Abstract The last eukaryote common ancestor (LECA) possessed mitochondria and all key traits that make eukaryotic cells more complex than their prokaryotic ancestors, yet the timing of mitochondrial acquisition and the role of mitochondria in the origin of eukaryote complexity remain debated. Here, we report evidence from gene duplications in LECA indicating an early origin of mitochondria. Among 163,545 duplications in 24,571 gene trees spanning 150 sequenced eukaryotic genomes, we identify 713 gene duplication events that occurred in LECA. LECA’s bacterial-derived genes include numerous mitochondrial functions and were duplicated significantly more often than archaeal-derived and eukaryote-specific genes. The surplus of bacterial-derived duplications in LECA most likely reflects the serial copying of genes from the mitochondrial endosymbiont to the archaeal host’s chromosomes. Clustering, phylogenies and likelihood ratio tests for 22.4 million genes from 5,655 prokaryotic and 150 eukaryotic genomes reveal no evidence for lineage-specific gene acquisitions in eukaryotes, except from the plastid in the plant lineage. That finding, and the functions of bacterial genes duplicated in LECA, suggests that the bacterial genes in eukaryotes are acquisitions from the mitochondrion, followed by vertical gene evolution and differential loss across eukaryotic lineages, flanked by concomitant lateral gene transfer among prokaryotes. Overall, the data indicate that recurrent gene transfer via the copying of genes from a resident mitochondrial endosymbiont to archaeal host chromosomes preceded the onset of eukaryotic cellular complexity, favoring mitochondria-early over mitochondria-late hypotheses for eukaryote origin.
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Bazant, Wojtek, Ann S. Blevins, Kathryn Crouch, and Daniel P. Beiting. "Improved eukaryotic detection compatible with large-scale automated analysis of metagenomes." Microbiome 11, no. 1 (2023). http://dx.doi.org/10.1186/s40168-023-01505-1.
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Abstract Background Eukaryotes such as fungi and protists frequently accompany bacteria and archaea in microbial communities. Unfortunately, their presence is difficult to study with “shotgun” metagenomic sequencing since prokaryotic signals dominate in most environments. Recent methods for eukaryotic detection use eukaryote-specific marker genes, but they do not incorporate strategies to handle the presence of eukaryotes that are not represented in the reference marker gene set, and they are not compatible with web-based tools for downstream analysis. Results Here, we present CORRAL (for Clustering Of Related Reference ALignments), a tool for the identification of eukaryotes in shotgun metagenomic data based on alignments to eukaryote-specific marker genes and Markov clustering. Using a combination of simulated datasets, mock community standards, and large publicly available human microbiome studies, we demonstrate that our method is not only sensitive and accurate but is also capable of inferring the presence of eukaryotes not included in the marker gene reference, such as novel strains. Finally, we deploy CORRAL on our MicrobiomeDB.org resource, producing an atlas of eukaryotes present in various environments of the human body and linking their presence to study covariates. Conclusions CORRAL allows eukaryotic detection to be automated and carried out at scale. Implementation of CORRAL in MicrobiomeDB.org creates a running atlas of microbial eukaryotes in metagenomic studies. Since our approach is independent of the reference used, it may be applicable to other contexts where shotgun metagenomic reads are matched against redundant but non-exhaustive databases, such as the identification of bacterial virulence genes or taxonomic classification of viral reads.
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Knopp, Michael, Simon Stockhorst, Mark van der Giezen, Sriram G. Garg, and Sven B. Gould. "The Asgard Archaeal-Unique Contribution to Protein Families of the Eukaryotic Common Ancestor Was 0.3%." Genome Biology and Evolution 13, no. 6 (2021). http://dx.doi.org/10.1093/gbe/evab085.
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Abstract The identification of the asgard archaea has fueled speculations regarding the nature of the archaeal host in eukaryogenesis and its level of complexity prior to endosymbiosis. Here, we analyzed the coding capacity of 150 eukaryotes, 1,000 bacteria, and 226 archaea, including the only cultured member of the asgard archaea. Clustering methods that consistently recover endosymbiotic contributions to eukaryotic genomes recover an asgard archaeal-unique contribution of a mere 0.3% to protein families present in the last eukaryotic common ancestor, while simultaneously suggesting that this group’s diversity rivals that of all other archaea combined. The number of homologs shared exclusively between asgard archaea and eukaryotes is only 27 on average. This tiny asgard archaeal-unique contribution to the root of eukaryotic protein families questions claims that archaea evolved complexity prior to eukaryogenesis. Genomic and cellular complexity remains a eukaryote-specific feature and is best understood as the archaeal host’s solution to housing an endosymbiont.
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Greco, Carla, Dale T. Andersen, Ian Hawes, et al. "Microbial Diversity of Pinnacle and Conical Microbial Mats in the Perennially Ice-Covered Lake Untersee, East Antarctica." Frontiers in Microbiology 11 (December 10, 2020). http://dx.doi.org/10.3389/fmicb.2020.607251.
Full textAbstract:
Antarctic perennially ice-covered lakes provide a stable low-disturbance environment where complex microbially mediated structures can grow. Lake Untersee, an ultra-oligotrophic lake in East Antarctica, has the lake floor covered in benthic microbial mat communities, where laminated organo-sedimentary structures form with three distinct, sympatric morphologies: small, elongated cuspate pinnacles, large complex cones and flat mats. We examined the diversity of prokaryotes and eukaryotes in pinnacles, cones and flat microbial mats using high-throughput sequencing of 16S and 18S rRNA genes and assessed how microbial composition may underpin the formation of these distinct macroscopic mat morphologies under the same environmental conditions. Our analysis identified distinct clustering of microbial communities according to mat morphology. The prokaryotic communities were dominated by Cyanobacteria, Proteobacteria, Verrucomicrobia, Planctomycetes, and Actinobacteria. While filamentous Tychonema cyanobacteria were common in all mat types, Leptolyngbya showed an increased relative abundance in the pinnacle structures only. Our study provides the first report of the eukaryotic community structure of Lake Untersee benthic mats, which was dominated by Ciliophora, Chlorophyta, Fungi, Cercozoa, and Discicristata. The eukaryote richness was lower than for prokaryote assemblages and no distinct clustering was observed between mat morphologies. These findings suggest that cyanobacterial assemblages and potentially other bacteria and eukaryotes may influence structure morphogenesis, allowing distinct structures to form across a small spatial scale.