scholarly journals Bacterial Genes Outnumber Archaeal Genes in Eukaryotic Genomes

2020 ◽  
Vol 12 (4) ◽  
pp. 282-292 ◽  
Author(s):  
Julia Brueckner ◽  
William F Martin
Keyword(s):  
Gene Loss ◽  
Protein Sequences ◽  
Metabolic Processes ◽  
Encephalitozoon Intestinalis ◽  
Human Parasite ◽  
Intracellular Parasites ◽  
Genetic Information Processing ◽  
Bacterial Genes ◽  
Eukaryotic Genomes ◽  
Eukaryote Genome

Abstract Eukaryotes are typically depicted as descendants of archaea, but their genomes are evolutionary chimeras with genes stemming from archaea and bacteria. Which prokaryotic heritage predominates? Here, we have clustered 19,050,992 protein sequences from 5,443 bacteria and 212 archaea with 3,420,731 protein sequences from 150 eukaryotes spanning six eukaryotic supergroups. By downsampling, we obtain estimates for the bacterial and archaeal proportions. Eukaryotic genomes possess a bacterial majority of genes. On average, the majority of bacterial genes is 56% overall, 53% in eukaryotes that never possessed plastids, and 61% in photosynthetic eukaryotic lineages, where the cyanobacterial ancestor of plastids contributed additional genes to the eukaryotic lineage. Intracellular parasites, which undergo reductive evolution in adaptation to the nutrient rich environment of the cells that they infect, relinquish bacterial genes for metabolic processes. Such adaptive gene loss is most pronounced in the human parasite Encephalitozoon intestinalis with 86% archaeal and 14% bacterial derived genes. The most bacterial eukaryote genome sampled is rice, with 67% bacterial and 33% archaeal genes. The functional dichotomy, initially described for yeast, of archaeal genes being involved in genetic information processing and bacterial genes being involved in metabolic processes is conserved across all eukaryotic supergroups.

scholarly journals Bacterial genes outnumber archaeal genes in eukaryotic genomes

2019 ◽  
Author(s):  
Julia Brückner ◽  
William F. Martin
Keyword(s):  
Ribosomal Proteins ◽  
Phylogenetic Trees ◽  
Higher Plants ◽  
Protein Sequences ◽  
Eukaryotic Genome ◽  
Metabolic Processes ◽  
Eukaryotic Genes ◽  
Bacterial Genes ◽  
Origin Of Eukaryotes ◽  
Eukaryotic Genomes

AbstractThe origin of eukaryotes is one of evolution’s most important transitions, yet it is still poorly understood. Evidence for how it occurred should be preserved in eukaryotic genomes. Based on phylogenetic trees from ribosomal RNA and ribosomal proteins, eukaryotes are typically depicted as branching together with or within archaea. This ribosomal affiliation is widely interpreted as evidence for an archaeal origin of eukaryotes. However, the extent to which the archaeal ancestry of genes for the cytosolic ribosomes of eukaryotic cells is representative for the rest of the eukaryotic genome is unknown. Here we have clustered 19,050,992 protein sequences from 5,443 bacteria and 212 archaea with 3,420,731 protein sequences from 150 eukaryotes spanning six eukaryotic supergroups to identify genes that link eukaryotes exclusively to bacteria and archaea respectively. By downsampling the bacterial sample we obtain estimates for the bacterial and archaeal proportions of genes among 150 eukaryotic genomes. Eukaryotic genomes possess a bacterial majority of genes. On average, eukaryotic genes are 56% bacterial in origin. The majority drops to 53% in eukaryotes that never possessed plastids, and increases to 61% in photosynthetic eukaryotic lineages, where the cyanobacterial ancestor of plastids contributed additional genes to the eukaryotic genome, reaching 67% in higher plants. Intracellular parasites, which undergo reductive evolution in adaptation to the nutrient rich environment of the cells that they infect, relinquish bacterial genes for metabolic processes. In the current sample, this process of adaptive gene loss is most pronounced in the human parasite Encephalitozoon intestinalis with 86% archaeal and 14% bacterial derived genes. The most bacterial eukaryote genome sampled is rice, with 67% bacterial and 33% archaeal genes. The functional dichotomy, initially described for yeast, of archaeal genes being involved in genetic information processing and bacterial genes being involved in metabolic processes is conserved across all eukaryotic supergroups.

scholarly journals Progress in quickly finding orthologs as reciprocal best hits: comparing blast, last, diamond and MMseqs2

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Julie E. Hernández-Salmerón ◽  
Gabriel Moreno-Hagelsieb
Keyword(s):  
Comparative Genomics ◽  
Protein Sequences ◽  
Fast Algorithms ◽  
Error Rates ◽  
Estimated Error ◽  
Bacterial Proteomes ◽  
Eukaryotic Genomes

Abstract Background Finding orthologs remains an important bottleneck in comparative genomics analyses. While the authors of software for the quick comparison of protein sequences evaluate the speed of their software and compare their results against the most usual software for the task, it is not common for them to evaluate their software for more particular uses, such as finding orthologs as reciprocal best hits (RBH). Here we compared RBH results obtained using software that runs faster than blastp. Namely, lastal, diamond, and MMseqs2. Results We found that lastal required the least time to produce results. However, it yielded fewer results than any other program when comparing the proteins encoded by evolutionarily distant genomes. The program producing the most similar number of RBH to blastp was diamond ran with the “ultra-sensitive” option. However, this option was diamond’s slowest, with the “very-sensitive” option offering the best balance between speed and RBH results. The speeding up of the programs was much more evident when dealing with eukaryotic genomes, which code for more numerous proteins. For example, lastal took a median of approx. 1.5% of the blastp time to run with bacterial proteomes and 0.6% with eukaryotic ones, while diamond with the very-sensitive option took 7.4% and 5.2%, respectively. Though estimated error rates were very similar among the RBH obtained with all programs, RBH obtained with MMseqs2 had the lowest error rates among the programs tested. Conclusions The fast algorithms for pairwise protein comparison produced results very similar to blast in a fraction of the time, with diamond offering the best compromise in speed, sensitivity and quality, as long as a sensitivity option, other than the default, was chosen.

scholarly journals Toll-Like Receptor 2 Recognition of the Microsporidia Encephalitozoon spp. Induces Nuclear Translocation of NF-κB and Subsequent Inflammatory Responses

2008 ◽  
Vol 76 (10) ◽  
pp. 4737-4744 ◽  
Author(s):  
Jeffrey Fischer ◽  
Colby Suire ◽  
Hollie Hale-Donze
Keyword(s):  
Nuclear Translocation ◽  
Inflammatory Responses ◽  
Host Recognition ◽  
Direct Role ◽  
Necrosis Factor Alpha ◽  
Human Macrophages ◽  
Encephalitozoon Intestinalis ◽  
Intracellular Parasites ◽  
Tnf Α ◽  
Interfering Rna

ABSTRACT Microsporidia are obligate intracellular parasites that are ubiquitous in nature and have been recognized as causing an important emerging disease among immunocompromised individuals. Limited knowledge exists about the immune response against these organisms, and virtually nothing is known about the receptors involved in host recognition. Toll-like receptors (TLR) are pattern recognition receptors that bind to specific molecules found on pathogens and signal a variety of inflammatory responses. In this study, we show that both Encephalitozoon cuniculi and Encephalitozoon intestinalis are preferentially recognized by TLR2 and not by TLR4 in primary human macrophages. This is the first demonstration of host receptor recognition of any microsporidian species. TLR2 ligation is known to activate NF-κB, resulting in inflammatory cytokines, such as tumor necrosis factor alpha (TNF-α) and interleukin-8 (IL-8). We found that the infection of primary human macrophages leads to the nuclear translocation of NF-κB in as early as 1 h and the subsequent production of TNF-α and IL-8. To verify the direct role of TLR2 parasite recognition in the production of these cytokines, the receptor was knocked down in primary human macrophages using small interfering RNA. This knockdown resulted in decreases in both the nuclear translocation of NF-κB and the levels of TNF-α and IL-8 after challenge with spores. Taken together, these experiments directly link the initial inflammatory response induced by Encephalitozoon spp. to TLR2 stimulation in human macrophages.

Gene Regulation in and out of Equilibrium

2020 ◽  
Vol 49 (1) ◽  
pp. 199-226 ◽  
Author(s):  
Felix Wong ◽  
Jeremy Gunawardena
Keyword(s):  
Gene Regulation ◽  
Information Processing ◽  
Thermodynamic Equilibrium ◽  
Fundamental Limits ◽  
Linear Framework ◽  
Biophysical Studies ◽  
Genetic Information Processing ◽  
Gene Regulatory ◽  
Regulatory Properties ◽  
Eukaryotic Genomes

Determining whether and how a gene is transcribed are two of the central processes of life. The conceptual basis for understanding such gene regulation arose from pioneering biophysical studies in eubacteria. However, eukaryotic genomes exhibit vastly greater complexity, which raises questions not addressed by this bacterial paradigm. First, how is information integrated from many widely separated binding sites to determine how a gene is transcribed? Second, does the presence of multiple energy-expending mechanisms, which are absent from eubacterial genomes, indicate that eukaryotes are capable of improved forms of genetic information processing? An updated biophysical foundation is needed to answer such questions. We describe the linear framework, a graph-based approach to Markov processes, and show that it can accommodate many previous studies in the field. Under the assumption of thermodynamic equilibrium, we introduce a language of higher-order cooperativities and show how it can rigorously quantify gene regulatory properties suggested by experiment. We point out that fundamental limits to information processing arise at thermodynamic equilibrium and can only be bypassed through energy expenditure. Finally, we outline some of the mathematical challenges that must be overcome to construct an improved biophysical understanding of gene regulation.

scholarly journals Multilayered horizontal operon transfers from bacteria reconstruct a thiamine salvage pathway in yeasts

2019 ◽  
Vol 116 (44) ◽  
pp. 22219-22228 ◽  
Author(s):  
Carla Gonçalves ◽  
Paula Gonçalves
Keyword(s):  
Vitamin B1 ◽  
Salvage Pathway ◽  
Gene Relocation ◽  
Coordinated Expression ◽  
Intergenic Regions ◽  
Eukaryotic Microbes ◽  
Bacterial Genes ◽  
Direct Genetic Evidence ◽  
Horizontal Acquisition ◽  
Eukaryotic Genomes

Horizontal acquisition of bacterial genes is presently recognized as an important contribution to the adaptation and evolution of eukaryotic genomes. However, the mechanisms underlying expression and consequent selection and fixation of the prokaryotic genes in the new eukaryotic setting are largely unknown. Here we show that genes composing the pathway for the synthesis of the essential vitamin B1 (thiamine) were lost in an ancestor of a yeast lineage, the Wickerhamiella/Starmerella (W/S) clade, known to harbor an unusually large number of genes of alien origin. The thiamine pathway was subsequently reassembled, at least twice, by multiple HGT events from different bacterial donors involving both single genes and entire operons. In the W/S-clade species Starmerella bombicola we obtained direct genetic evidence that all bacterial genes of the thiamine pathway are functional. The reconstructed pathway is composed by yeast and bacterial genes operating coordinately to scavenge thiamine derivatives from the environment. The adaptation of the newly acquired operons to the eukaryotic setting involved a repertoire of mechanisms until now only sparsely documented, namely longer intergenic regions, post-horizontal gene transfer (HGT) gene fusions fostering coordinated expression, gene relocation, and possibly recombination generating mosaic genes. The results provide additional evidence that HGT occurred recurrently in this yeast lineage and was crucial for the reestablishment of lost functions and that similar mechanisms are used across a broad range of eukaryotic microbes to promote adaptation of prokaryotic genes to their new environment.

scholarly journals Multiple origins of interdependent endosymbiotic complexes in a genus of cicadas

2017 ◽  
Vol 115 (2) ◽  
pp. E226-E235 ◽  
Author(s):  
Piotr Łukasik ◽  
Katherine Nazario ◽  
James T. Van Leuven ◽  
Matthew A. Campbell ◽  
Mariah Meyer ◽  
...  
Keyword(s):  
Gene Loss ◽  
Gene Content ◽  
Gene Products ◽  
Multiple Origins ◽  
Genetic Information Processing ◽  
Small Set ◽  
Bacterial Endosymbionts ◽  
High Level ◽  
Representative Samples ◽  
Core Genes

Bacterial endosymbionts that provide nutrients to hosts often have genomes that are extremely stable in structure and gene content. In contrast, the genome of the endosymbiont Hodgkinia cicadicola has fractured into multiple distinct lineages in some species of the cicada genus Tettigades. To better understand the frequency, timing, and outcomes of Hodgkinia lineage splitting throughout this cicada genus, we sampled cicadas over three field seasons in Chile and performed genomics and microscopy on representative samples. We found that a single ancestral Hodgkinia lineage has split at least six independent times in Tettigades over the last 4 million years, resulting in complexes of between two and six distinct Hodgkinia lineages per host. Individual genomes in these symbiotic complexes differ dramatically in relative abundance, genome size, organization, and gene content. Each Hodgkinia lineage retains a small set of core genes involved in genetic information processing, but the high level of gene loss experienced by all genomes suggests that extensive sharing of gene products among symbiont cells must occur. In total, Hodgkinia complexes that consist of multiple lineages encode nearly complete sets of genes present on the ancestral single lineage and presumably perform the same functions as symbionts that have not undergone splitting. However, differences in the timing of the splits, along with dissimilar gene loss patterns on the resulting genomes, have led to very different outcomes of lineage splitting in extant cicadas.

scholarly journals The Ordospora colligata Genome: Evolution of Extreme Reduction in Microsporidia and Host-To-Parasite Horizontal Gene Transfer

mBio ◽  
2015 ◽  
Vol 6 (1) ◽  
Author(s):  
Jean-François Pombert ◽  
Karen Luisa Haag ◽  
Shadi Beidas ◽  
Dieter Ebert ◽  
Patrick J. Keeling
Keyword(s):  
Horizontal Transfer ◽  
Water Flea ◽  
Content Type ◽  
Invasion Mechanism ◽  
Obligate Intracellular ◽  
Evolutionary Forces ◽  
Intracellular Parasites ◽  
Order Of Magnitude ◽  
Vertebrate Hosts ◽  
Eukaryotic Genomes

ABSTRACT  Microsporidia are a group of obligate intracellular parasites that are best known for their unique infection mechanism and their unparalleled levels of genomic reduction and compaction. We sequenced the genome of Ordospora colligata, a gut parasite of the microcrustacean Daphnia sp. and the closest known relative to the microsporidia characterized by the most extreme genomic reduction, the model genus Encephalitozoon. We found that the O. colligata genome is as compact as those of Encephalitozoon spp., featuring few introns and a similar complement of about 2,000 genes, altogether showing that the extreme reduction took place before the origin of Encephalitozoon spp. and their adaptation to vertebrate hosts. We also found that the O. colligata genome has acquired by horizontal transfer from its animal host a septin that is structurally analogous to septin 7, a protein that plays a major role in the endocytosis-based invasion mechanism of the fungal pathogen Candida albicans. Microsporidian invasion is most often characterized by injection through a projectile tube, but microsporidia are also known to invade cells by inducing endocytosis. Given the function of septins in other systems, we hypothesize that the acquired septin could help O. colligata induce its uptake by mimicking host receptors. IMPORTANCE The smallest known eukaryotic genomes are found in members of the Encephalitozoon genus of microsporidian parasites. Their extreme compaction, however, is not characteristic of the group, whose genomes can differ by an order of magnitude. The processes and evolutionary forces that led the Encephalitozoon genomes to shed so much of their ancestral baggage are unclear. We sequenced the genome of Ordospora colligata, a parasite of the water flea Daphnia sp. and the closest known relative of Encephalitozoon species, and show that this extreme reduction predated the split between the two lineages. We also found that O. colligata has acquired a septin gene by host-to-parasite horizontal transfer and predicted that the encoded protein folds like a septin 7, which plays a major role in endocytosis. We hypothesize that this acquisition could help O. colligata parasitize its hosts by facilitating endocytic infection, a mechanism that occurs in microsporidia but that is not yet well understood.

scholarly journals Human microsporidian pathogen Encephalitozoon intestinalis impinges on enterocyte membrane trafficking and signaling

2021 ◽  
pp. jcs.253757
Author(s):  
Juan Flores ◽  
Peter M. Takvorian ◽  
Louis M. Weiss ◽  
Ann Cali ◽  
Nan Gao
Keyword(s):  
Membrane Trafficking ◽  
Transcriptional Profiling ◽  
Host Cell Signaling ◽  
Encephalitozoon Intestinalis ◽  
Transmission Electron ◽  
Intracellular Parasites ◽  
Infected Cells ◽  
Resolution Imaging ◽  
Spread Of Infection ◽  
The Impact

Microsporidia are a large phylum of obligate intracellular parasites. Approximately a dozen species of microsporidia infect humans where they are responsible for a variety of diseases and occasionally death, especially in immunocompromised individuals. To better understand the impact of microsporidia on human cells, we infected human colonic Caco2 cells with Encephalitozoon intestinalis, and showed that these enterocyte cultures can be used to recapitulate the parasites’ life cycle, including the spread of infection with infective spores. Using transmission electron microscopy, we describe this lifecycle and demonstrate nuclear, mitochondrial, and microvillar alterations by this pathogen. We also analyzed the transcriptome of infected cells to reveal host cell signaling alterations upon infection. These high-resolution imaging and transcriptional profiling analysis shed light on the impact of the microsporidial infection on its primary human target cell type.

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.

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