scholarly journals The asgardarchaeal-unique contribution to protein families of the eukaryotic common ancestor was 0.3%

2021 ◽  
Author(s):  
Michael Knopp ◽  
Simon Stockhorst ◽  
Mark van der Giezen ◽  
Sriram G. Garg ◽  
Sven B. Gould
Keyword(s):  
Cell Biology ◽  
Common Ancestor ◽  
Unique Contribution ◽  
Clustering Methods ◽  
Protein Families ◽  
Archaeal Lineage ◽  
Specific Proteins ◽  
The Difference ◽  
Coding Capacity ◽  
Eukaryotic Genomes

Significance StatementEver since the first report of a new archaeal lineage, the asgardarchaea, their metagenome analyses have encouraged continued speculations on a type of cell biology ranging between that of prokaryotes and eukaryotes. While it appears a tempting notion, recent microscopic images of an asgardarchaeon suggest otherwise. We inspected the origin of eukaryotic protein families with respect to their distribution across bacteria and archaea. This reveals that the protein families shared exclusively between asgardarchaea and eukaryotes amounts to only 0.3% of the protein families conserved across all eukaryotes. Asgardarchaeal diversity is likely unrivaled across archaea, but their cell biology remains prokaryotic in nature and lends support for the importance of endosymbiosis in evolving eukaryotic traits.SummaryThe difference between pro- and eukaryotic biology is evident in their genomes, cell biology, and evolution of complex and macroscopic body plans. The lack of intermediates between the two types of cells places the endosymbiotic acquisition of the mitochondrion through an archaeal host at the event horizon of eukaryote origin. The identification of eukaryote specific proteins in a new archaeal phylum, the asgardarchaea, has fueled speculations about their cellular complexity, suggesting they could be eukaryote-like. Here we analyzed the coding capacity of 150 eukaryotes, 1000 bacteria, and 226 archaea, including the only cultured member of the asgardarchaea, Candidatus Prometheoarchaeon syntrophicum MK-D1. Established clustering methods that recover endosymbiotic contributions to eukaryotic genomes, recover an asgardarchaeal-unique contribution of a mere 0.3% to protein families present in the last eukaryotic common ancestor, while simultaneously suggesting that asgardarchaeal diversity rivals that of all other archaea combined. Furthermore, we show that the number of homologs shared exclusively between asgardarchaea and eukaryotes is only 27 on average. Genomic and in particular cellular complexity remains a eukaryote-specific feature and, we conclude, is best understood as the archaeal host’s solution to housing an endosymbiont and not as a preparation for obtaining one.

scholarly journals Reconstructing and Analysing The Genome of The Last Eukaryote Common Ancestor to Better Understand the Transition from FECA to LECA

2019 ◽  
Author(s):  
David Newman ◽  
Fiona J. Whelan ◽  
Matthew Moore ◽  
Martin Rusilowicz ◽  
James O. McInerney
Keyword(s):  
Cell Biology ◽  
Common Ancestor ◽  
Transition Period ◽  
Gene Families ◽  
Post Translational Modification ◽  
Kegg Database ◽  
Cellular Processes ◽  
Eukaryote Evolution ◽  
Genetic Information Processing ◽  
Eukaryotic Genomes

AbstractIt is still a matter of debate whether the First Eukaryote Common Ancestor (FECA) arose from the merger of an archaeal host with an alphaproteobacterium, or was a proto-eukaryote with significant eukaryotic characteristics way before endosymbiosis occurred. The Last Eukaryote Common Ancestor (LECA) as its descendant is thought to be an entity that possessed functional and cellular complexity comparable to modern organisms. The precise nature and physiology of both of these organisms has been a long-standing, unanswered question in evolutionary and cell biology. Recently, a much broader diversity of eukaryotic genomes has become available and this means we can reconstruct early eukaryote evolution with a greater deal of precision. Here, we reconstruct a hypothetical genome for LECA from modern eukaryote genomes. The constituent genes were mapped onto 454 pathways from the KEGG database covering cellular, genetic, and metabolic processes across six model species to provide functional insights into it’s capabilities. We reconstruct a LECA that was a facultatively anaerobic, single-celled organism, similar to a modern Protist possessing complex predatory and sexual behaviour. We go on to examine how much of these capabilities arose along the FECA-to-LECA transition period. We see a at least 1,554 genes gained by FECA during this evolutionary period with extensive remodelling of pathways relating to lipid metabolism, cellular processes, genetic information processing, protein processing, and signalling. We extracted the BRITE classifications for the genes from the KEGG database, which arose during the transition from FECA-to-LECA and examine the types of genes that saw the most gains and what novel classifications were introduced. Two-thirds of our reconstructed LECA genome appears to be prokaryote in origin and the remaining third consists of genes with functional classifications that originate from prokaryote homologs in our LECA genome. Signal transduction and Post Translational Modification elements stand out as the primary novel classes of genes developed during this period. These results suggest that largely the eukaryote common ancestors achieved the defining characteristics of modern eukaryotes by primarily expanding on prokaryote biology and gene families.

scholarly journals Proteomic Analysis of Capacitated and Non-Capacitated Spermatozoa of Yanbian Yellow Cattle

2020 ◽  
Author(s):  
Xuan Chen ◽  
Zuochen Li ◽  
Yanqiu Lv ◽  
Yichao Xu ◽  
Mimi Cheng ◽  
...  
Keyword(s):  
Protein Transport ◽  
Expression Level ◽  
Molecular Processes ◽  
Proteomics Data ◽  
Pathway Enrichment ◽  
Protein Protein Interaction ◽  
Go Enrichment ◽  
Yellow Cattle ◽  
Specific Proteins ◽  
The Difference

Abstract Background: Sperm capacitation is a process which occurs prior to fertilization, and is essential for producing high-quality living embryos. The main purpose of this study was to explore the difference of proteomics between capacitated and non-capacitated sperm of Yanbian yellow cattle. Bioinformatic analyses of LC-MS/MS data included GO enrichment, KEGG pathway enrichment, and protein-protein interaction (PPI) analysis. Results: The results revealed 23 specific proteins in the capacitated group and 345 in the non-capacitated group. Compared with non-capacitated sperm, capacitated sperm exhibited 89 upregulated proteins and 509 downregulated proteins. Western blotting was used to confirm our proteomics data. The expression level of PSMD1 in the capacitated sperm group was significantly lower than that in the non-capacitated sperm group, and the expression level of HSPA5 was significantly higher than in the non-capacitated sperm group. Conclusions: Our results revealed that many proteins were differentially expressed between capacitated and non-capacitated sperm, particularly those involved in the proteasome signaling and protein transport signaling pathways. This work enhances our understanding of molecular processes involved in sperm viability in Yanbian yellow cattle, and provides a framework for future studies.

scholarly journals Early acquisition of conserved, lineage-specific proteins currently lacking functional predictions were central to the rise and diversification of archaea

2020 ◽  
Author(s):  
Raphaël Méheust ◽  
Cindy J. Castelle ◽  
Alexander L. Jaffe ◽  
Jillian F. Banfield
Keyword(s):  
Phylogenetic Tree ◽  
Ammonia Oxidation ◽  
Hypothetical Proteins ◽  
Protein Families ◽  
Eukaryotic Evolution ◽  
Community Resource ◽  
Archaeal Protein ◽  
Genomic Analyses ◽  
Specific Proteins ◽  
Early Acquisition

AbstractRecent genomic analyses of Archaea have profoundly reshaped our understanding of their distribution, functionalities and roles in eukaryotic evolution. Within the domain, major supergroups are Euryarchaeota, which includes many methanogens, the TACK, which includes Thaumarchaeaota that impact ammonia oxidation in soils and the ocean, the Asgard, which includes lineages inferred to be ancestral to eukaryotes, and the DPANN, a group of mostly symbiotic small-celled archaea. Here, we investigated the extent to which clustering based on protein family content recapitulates archaeal phylogeny and identified the proteins that distinguish the major subdivisions. We also defined 10,866 archaeal protein families that will serve as a community resource. Clustering based on these families broadly recovers the archaeal phylogenetic tree. Interestingly, all major groups are distinguished primarily by the presence of families of conserved hypothetical proteins that are either novel or so highly diverged that their functions are obscured. Given that these hypothetical proteins are near ubiquitous within phyla, we conclude that they were important in the origin of most of the major archaeal lineages.

scholarly journals Chytrid rhizoid morphogenesis is adaptive and resembles hyphal development in ‘higher’ fungi

2019 ◽  
Author(s):  
Davis Laundon ◽  
Nathan Chrismas ◽  
Glen Wheeler ◽  
Michael Cunliffe
Keyword(s):  
Cell Biology ◽  
Developmental Plasticity ◽  
Common Ancestor ◽  
Spatial Differentiation ◽  
Morphological Plasticity ◽  
Recent Common Ancestor ◽  
Significant Component ◽  
Most Recent Common Ancestor ◽  
Fungal Evolution ◽  
Dependent Cell

AbstractFungi are major components of the Earth’s biosphere [1], sustaining many critical ecosystem processes [2, 3]. Key to fungal prominence is their characteristic cell biology, our understanding of which has been principally based on ‘higher’ dikaryan hyphal and yeast forms [4–6]. The early-diverging Chytridiomycota (chytrids) are ecologically important [2, 7, 8] and a significant component of fungal diversity [9–11], yet their cell biology remains poorly understood. Unlike dikaryan hyphae, chytrids typically attach to substrates and feed osmotrophically via anucleate rhizoids [12]. The evolution of fungal hyphae appears to have occurred from lineages exhibiting rhizoidal growth [13] and it has been hypothesised that a rhizoid-like structure was the precursor to multicellular hyphae and mycelial feeding in fungi [14]. Here we show in a unicellular chytrid, Rhizoclosmatium globosum, that rhizoid development has equivalent features to dikaryan hyphae and is adaptive to resource availability. Rhizoid morphogenesis exhibits analogous properties with growth in hyphal forms, including tip production, branching and decreasing fractal geometry towards the growing edge, and is controlled by β-glucan-dependent cell wall synthesis and actin polymerisation. Chytrid rhizoids from individual cells also demonstrate adaptive morphological plasticity in response to substrate availability, developing a searching phenotype when carbon starved and exhibiting spatial differentiation when interacting with particulate substrates. Our results show striking similarities between unicellular early-diverging and dikaryan fungi, providing insights into chytrid cell biology, ecological prevalence and fungal evolution. We demonstrate that the sophisticated cell biology and developmental plasticity previously considered characteristic of hyphal fungi are shared more widely across the Kingdom Fungi and therefore could be conserved from their most recent common ancestor.

scholarly journals A hot spring Asgard archaeon sheds light on the origin of eukaryotic endosomal system.

2020 ◽  
Author(s):  
Weili Lin ◽  
Lu Fan ◽  
Jing Xiao ◽  
Sa Fang ◽  
Yanbing Xu ◽  
...  
Keyword(s):  
Carbon Dioxide ◽  
Common Ancestor ◽  
Hot Spring ◽  
Carbon Dioxide Reduction ◽  
Endosomal Sorting ◽  
Metabolic Analysis ◽  
Terminal Domain ◽  
Family Level ◽  
Specific Proteins ◽  
Endosomal System

Abstract Recent metagenomics studies have identified a novel archaeal superphylum namely Asgard, which are characterized by enriched eukaryotic-specific proteins. In this study, we screened unclassified archaeal genomes in public databases and obtained a high-qualified metagenome-assembled genome that can be assigned as a novel family-level Asgard member namely Odinarchaeceae Tengchong. Metabolic analysis indicates an autotrophic lifestyle of this hot spring archaeon with a complete tetrahydromethanopterin Wood-Ljungdahl pathway for carbon dioxide reduction and an arsenic efflux detoxification. Examination of public databases found that thus far Odinarchaeceae Tengchong may be the only prokaryote that encodes a C-terminal domain of Vps28 in the endosomal sorting complex required for transport (ESCRT), a critical connector of multiple ESCRT components. Therefore, the identification of this archaeon provides valuable evidence of the archaeal origin of eukaryotic ESCRT. We posit that all the key components of the eukaryotic endosomal system might have evolved from a common ancestor of Asgard archaea and eukaryotes.

scholarly journals Circular RNA-Centered Regulatory Networks in the Physiopathology of Cardiovascular Diseases

2020 ◽  
Vol 21 (2) ◽  
pp. 456 ◽  
Author(s):  
André F. Gabriel ◽  
Marina C. Costa ◽  
Francisco J. Enguita
Keyword(s):  
Cardiovascular Diseases ◽  
Cell Biology ◽  
Regulatory Networks ◽  
Current Knowledge ◽  
Circular Rna ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
Regulatory Rnas ◽  
Eukaryotic Genomes

Non-coding regulatory RNAs are generated as a core output of the eukaryotic genomes, being essential players in cell biology. At the organism level, they are key functional actors in those tissues and organs with limited proliferation capabilities such as the heart. The role of regulatory networks mediated by non-coding RNAs in the pathophysiology of cardiovascular conditions is starting to be unveiled. However, a deeper knowledge of the functional interactions among the diverse non-coding RNA families and their phenotypic consequences is required. This review presents the current knowledge about the functional crosstalk between circRNAs and other biomolecules in the framework of the cardiovascular diseases.

scholarly journals VIPER is a genetically encoded peptide tag for fluorescence and electron microscopy

2018 ◽  
Vol 115 (51) ◽  
pp. 12961-12966 ◽  
Author(s):  
Julia K. Doh ◽  
Jonathan D. White ◽  
Hannah K. Zane ◽  
Young Hwan Chang ◽  
Claudia S. López ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Cell Biology ◽  
Iron Uptake ◽  
Fluorescent Proteins ◽  
Coiled Coil ◽  
Protein Targets ◽  
Cellular Environment ◽  
Fluorescence And Electron Microscopy ◽  
Specific Proteins ◽  
Peptide Tag

Many discoveries in cell biology rely on making specific proteins visible within their native cellular environment. There are various genetically encoded tags, such as fluorescent proteins, developed for fluorescence microscopy (FM). However, there are almost no genetically encoded tags that enable cellular proteins to be observed by both FM and electron microscopy (EM). Herein, we describe a technology for labeling proteins with diverse chemical reporters, including bright organic fluorophores for FM and electron-dense nanoparticles for EM. Our technology uses versatile interacting peptide (VIP) tags, a class of genetically encoded tag. We present VIPER, which consists of a coiled-coil heterodimer formed between the genetic tag, CoilE, and a probe-labeled peptide, CoilR. Using confocal FM, we demonstrate that VIPER can be used to highlight subcellular structures or to image receptor-mediated iron uptake. Additionally, we used VIPER to image the iron uptake machinery by correlative light and EM (CLEM). VIPER compared favorably with immunolabeling for imaging proteins by CLEM, and is an enabling technology for protein targets that cannot be immunolabeled. VIPER is a versatile peptide tag that can be used to label and track proteins with diverse chemical reporters observable by both FM and EM instrumentation.

A cytogenetic survey of 25 species of lower termites from Australia

Genome ◽  
1990 ◽  
Vol 33 (1) ◽  
pp. 80-88 ◽  
Author(s):  
Peter Luykx
Keyword(s):  
Sex Determination ◽  
Sex Chromosomes ◽  
Common Ancestor ◽  
Systematic Position ◽  
Necessary Condition ◽  
X Chromosomes ◽  
Y Chromosomes ◽  
Cytogenetic Survey ◽  
The Difference ◽  
High Degree

A survey of 25 species of lower termites (families Mastotermitidae, Termopsidae, and Kalotermitidae) in Australia revealed that centric fusions are a common theme in karyotype evolution in these insects. All but one of the species studied have a basic XX/XY mechanism of sex determination, secondarily complicated in about a third of a species by centric fusions between autosomes and sex chromosomes. There is no obvious relationship between systematic position and presence or absence of these fusions. Fusions between Y chromosomes and autosomes were more common than fusions between X chromosomes and autosomes, in accord with the prediction of the hypothesis that differential selection between the two sexes is the basis for the spread of sex-linked fusions. The absence of these fusions in many species does not favor the idea that a high degree of sex linkage is a necessary condition for the establishment or maintenance of eusocial behavior in termites. The difference in the mechanism of sex determination from that of cockroaches (XX/XO) argues against the evolutionary derivation of termites from ancestral cockroaches; derivation of both groups from some common ancestor with XX/XY sex determination is more likely.Key words: termites, karotype, evolution, sex chromosomes, Australia.

scholarly journals Genetic dissection of neuropeptide cell biology at high and low activity in a defined sensory neuron

2018 ◽  
Vol 115 (29) ◽  
pp. E6890-E6899 ◽  
Author(s):  
Patrick Laurent ◽  
QueeLim Ch’ng ◽  
Maëlle Jospin ◽  
Changchun Chen ◽  
Ramiro Lorenzo ◽  
...  
Keyword(s):  
Sensory Neuron ◽  
Neural Activity ◽  
Cell Biology ◽  
De Novo ◽  
Synaptic Activity ◽  
Activity Levels ◽  
Genetic Dissection ◽  
Clustering Methods ◽  
Mutant Phenotypes

Neuropeptides are ubiquitous modulators of behavior and physiology. They are packaged in specialized secretory organelles called dense core vesicles (DCVs) that are released upon neural stimulation. Unlike synaptic vesicles, which can be recycled and refilled close to release sites, DCVs must be replenished by de novo synthesis in the cell body. Here, we dissect DCV cell biology in vivo in a Caenorhabditis elegans sensory neuron whose tonic activity we can control using a natural stimulus. We express fluorescently tagged neuropeptides in the neuron and define parameters that describe their subcellular distribution. We measure these parameters at high and low neural activity in 187 mutants defective in proteins implicated in membrane traffic, neuroendocrine secretion, and neuronal or synaptic activity. Using unsupervised hierarchical clustering methods, we analyze these data and identify 62 groups of genes with similar mutant phenotypes. We explore the function of a subset of these groups. We recapitulate many previous findings, validating our paradigm. We uncover a large battery of proteins involved in recycling DCV membrane proteins, something hitherto poorly explored. We show that the unfolded protein response promotes DCV production, which may contribute to intertissue communication of stress. We also find evidence that different mechanisms of priming and exocytosis may operate at high and low neural activity. Our work provides a defined framework to study DCV biology at different neural activity levels.

scholarly journals Evolution of late steps in exocytosis: conservation, specialization

2019 ◽  
Vol 4 ◽  
pp. 112
Author(s):  
Cordula Boehm ◽  
Mark C. Field
Keyword(s):  
Structure Prediction ◽  
Common Ancestor ◽  
Sequence Data ◽  
Gene Families ◽  
Sequence Evolution ◽  
Endomembrane System ◽  
Last Eukaryotic Common Ancestor ◽  
Exocyst Complex ◽  
Genes Encoding ◽  
Specific Proteins

Background: The eukaryotic endomembrane system likely arose via paralogous expansion of genes encoding proteins specifying organelle identity, coat complexes and government of fusion specificity. While the majority of these gene families were established by the time of the last eukaryotic common ancestor (LECA), subsequent evolutionary events molded these systems, likely reflecting adaptations retained for increased fitness. As well as sequence evolution, these adaptations include loss of otherwise canonical subunits, emergence of lineage-specific proteins and paralog expansion. The exocyst complex is involved in late exocytosis, and possibly additional pathways, and is a member of the complexes associated with tethering containing helical rods (CATCHR) tethering complex family, which includes conserved oligomeric Golgi (COG), homotypic fusion and vacuole protein sorting (HOPS), class C core vacuole/endosome tethering (CORVET) and others. The exocyst is integrated into a complex GTPase signaling network in animals, fungi and other lineages. Prompted by discovery of Exo99, a non-canonical subunit in the excavate protist Trypanosoma brucei, and significantly increased genome sequence data, we examined evolution of the exocyst. Methods: We examined evolution of the exocyst by comparative genomics, phylogenetics and structure prediction. Results: The exocyst is highly conserved, but with substantial losses of subunits in the Apicomplexa and expansions in Streptophyta plants and Metazoa. Significantly, few taxa retain a partial complex, suggesting that, in the main, all subunits are required for functionality. Further, the ninth exocyst subunit Exo99 is specific to the Euglenozoa with a distinct architecture compared to the other subunits and which possibly represents a coat system. Conclusions: These data reveal a remarkable degree of evolutionary flexibility within the exocyst complex, suggesting significant diversity in exocytosis mechanisms.

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