scholarly journals Anomalous phylogenetic behavior of ribosomal proteins in metagenome assembled asgard archaea

2020 ◽  
Author(s):  
Sriram G Garg ◽  
Nils Kapust ◽  
Weili Lin ◽  
Michael Knopp ◽  
Fernando D K Tria ◽  
...  
Keyword(s):  
Data Quality ◽  
Microbial Diversity ◽  
Pure Culture ◽  
Ribosomal Proteins ◽  
Eukaryotic Cell ◽  
Genomic Sequences ◽  
Morphological Evidence ◽  
Genome Sequences ◽  
Simple Cells ◽  
Phylogenomic Analyses

Abstract Metagenomic studies permit the exploration of microbial diversity in a defined habitat and binning procedures enable phylogenomic analyses, taxon description and even phenotypic characterizations in the absence of morphological evidence. Such lineages include asgard archaea, which were initially reported to represent archaea with eukaryotic cell complexity, although the first images of such an archaeon show simple cells with prokaryotic characteristics. However, these metagenome-assembled genomes (MAGs) might suffer from data quality problems not encountered in sequences from cultured organisms due to two common analytical procedures of bioinformatics: assembly of metagenomic sequences and binning of assembled sequences on the basis of innate sequence properties and abundance across samples. Consequently, genomic sequences of distantly related taxa, or domains, can in principle be assigned to the same MAG and result in chimeric sequences. The impacts of low-quality or chimeric MAGs on phylogenomic and metabolic prediction remain unknown. Debates that asgard archaeal data are contaminated with eukaryotic sequences are overshadowed by the lack of evidence indicating that individual asgard MAGs stem from the same chromosome. Here we show that universal proteins including ribosomal proteins of asgard archaeal MAGs fail to meet the basic phylogenetic criterion fulfilled by genome sequences of cultured archaea investigated to date: these proteins do not share common evolutionary histories to the same extent as pure culture genomes (PCGs) do, pointing to a chimeric nature of asgard archaeal MAGs. Our analysis suggests that some asgard archaeal MAGs represent unnatural constructs, genome-like patchworks of genes resulting from assembly and/or the binning process.

scholarly journals Anomalous phylogenetic behavior of ribosomal proteins in metagenome assembled genomes

2019 ◽  
Author(s):  
Sriram G. Garg ◽  
Nils Kapust ◽  
Weili Lin ◽  
Fernando D. K. Tria ◽  
Shijulal Nelson-Sathi ◽  
...  
Keyword(s):  
Ribosomal Proteins ◽  
Gc Content ◽  
Eukaryotic Cell ◽  
Gene Content ◽  
Metagenomic Data ◽  
Genome Sequences ◽  
Taxonomic Assignment ◽  
Candidate Phyla Radiation ◽  
Domain Level

SummaryMetagenomic studies have claimed the existence of novel lineages with unprecedented properties never before observed in prokaryotes. Such lineages include Asgard archaea1–3, which are purported to represent archaea with eukaryotic cell complexity, and the Candidate Phyla Radiation (CPR), a novel domain level taxon erected solely on the basis of metagenomic data4. However, it has escaped the attention of most biologists that these metagenomic sequences are not assembled into genomes by sequence overlap, as for cultured archaea and bacteria. Instead, short contigs are sorted into computer files by a process called binning in which they receive taxonomic assignment on the basis of sequence properties like GC content, dinucleotide frequencies, and stoichiometric co-occurrence across samples. Consequently, they are not genome sequences as we know them, reflecting the gene content of real organisms. Rather they are metagenome assembled genomes (MAGs). Debates that Asgard data are contaminated with individual eukaryotic sequences5–7 are overshadowed by the more pressing issue that no evidence exists to indicate that any sequences in binned Asgard MAGs actually stem from the same chromosome, as opposed to simply stemming from the same environment. Here we show that Asgard and CPR MAGs fail spectacularly to meet the most basic phylogenetic criterion8 fulfilled by genome sequences of all cultured prokaryotes investigated to date: the ribosomal proteins of Asgard and CPR MAGs do not share common evolutionary histories. Their phylogenetic behavior is anomalous to a degree never observed with genomes of real organisms. CPR and Asgard MAGs are binning artefacts, assembled from environments where up to 90% of the DNA is from dead cells9–12. Asgard and CPR MAGs are unnatural constructs, genome-like patchworks of genes that have been stitched together into computer files by binning.

Origin and Early Evolution of the Eukaryotic Cell

2021 ◽  
Vol 75 (1) ◽  
Author(s):  
Toni Gabaldón
Keyword(s):  
Current Knowledge ◽  
Eukaryotic Cell ◽  
Early Evolution ◽  
Annual Review ◽  
Publication Date ◽  
Eukaryotic Evolution ◽  
Life Itself ◽  
Metabolic Interactions ◽  
Phylogenomic Analyses ◽  
Origin Of Eukaryotes

The origin of eukaryotes has been defined as the major evolutionary transition since the origin of life itself. Most hallmark traits of eukaryotes, such as their intricate intracellular organization, can be traced back to a putative common ancestor that predated the broad diversity of extant eukaryotes. However, little is known about the nature and relative order of events that occurred in the path from preexisting prokaryotes to this already sophisticated ancestor. The origin of mitochondria from the endosymbiosis of an alphaproteobacterium is one of the few robustly established events to which most hypotheses on the origin of eukaryotes are anchored, but the debate is still open regarding the time of this acquisition, the nature of the host, and the ecological and metabolic interactions between the symbiotic partners. After the acquisition of mitochondria, eukaryotes underwent a fast radiation into several major clades whose phylogenetic relationships have been largely elusive. Recent progress in the comparative analyses of a growing number of genomes is shedding light on the early events of eukaryotic evolution as well as on the root and branching patterns of the tree of eukaryotes. Here I discuss current knowledge and debates on the origin and early evolution of eukaryotes. I focus particularly on how phylogenomic analyses have challenged some of the early assumptions about eukaryotic evolution, including the widespread idea that mitochondrial symbiosis in an archaeal host was the earliest event in eukaryogenesis. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Complete Genome Sequences of Two Hydrangea Ringspot Virus Isolates from Japan

2016 ◽  
Vol 4 (2) ◽  
Author(s):  
Akira Yusa ◽  
Nozomu Iwabuchi ◽  
Hiroaki Koinuma ◽  
Takuya Keima ◽  
Yutaro Neriya ◽  
...  
Keyword(s):  
Complete Genome ◽  
Rna Virus ◽  
Nucleotide Sequences ◽  
Ringspot Virus ◽  
Genomic Sequences ◽  
Genome Sequences ◽  
Hydrangea Macrophylla ◽  
Hydrangea Ringspot Virus ◽  
Virus Isolates

Hydrangea ringspot virus (HdRSV) is a plant RNA virus, naturally infecting Hydrangea macrophylla . Here, we report the first genomic sequences of two HdRSV isolates from hydrangea plants in Japan. The overall nucleotide sequences of these Japanese isolates were 96.0 to 96.3% identical to those of known European isolates.

scholarly journals Complete Genome Sequences of Chikungunya Viruses Isolated from Plasma Specimens Collected from Haitians in 2014

2017 ◽  
Vol 5 (15) ◽  
Author(s):  
Sarah K. White ◽  
J. Glenn Morris ◽  
Maha A. Elbadry ◽  
Valery Madsen Beau De Rochars ◽  
Bernard A. Okech ◽  
...  
Keyword(s):  
Human Plasma ◽  
Complete Genome ◽  
Chikungunya Virus ◽  
Phylogenetic Analyses ◽  
Genomic Sequences ◽  
Genome Sequences ◽  
Chikungunya Fever ◽  
Asian Lineage ◽  
Virus Isolates

ABSTRACT Ten chikungunya virus isolates from human plasma collected in Haiti from May to August 2014, in the midst of a chikungunya fever outbreak, were fully sequenced. The resulting genomic sequences are nearly identical, and phylogenetic analyses indicate they belong to the Asian lineage of the virus.

scholarly journals Central Role of the Cell in Microbial Ecology

2009 ◽  
Vol 73 (4) ◽  
pp. 712-729 ◽  
Author(s):  
Karsten Zengler
Keyword(s):  
Microbial Diversity ◽  
Microbial Ecology ◽  
Single Cell ◽  
Community Composition ◽  
Pure Culture ◽  
Current Knowledge ◽  
Community Level ◽  
Central Unit ◽  
Genome Heterogeneity

SUMMARY Over the last few decades, advances in cultivation-independent methods have significantly contributed to our understanding of microbial diversity and community composition in the environment. At the same time, cultivation-dependent methods have thrived, and the growing number of organisms obtained thereby have allowed for detailed studies of their physiology and genetics. Still, most microorganisms are recalcitrant to cultivation. This review not only conveys current knowledge about different isolation and cultivation strategies but also discusses what implications can be drawn from pure culture work for studies in microbial ecology. Specifically, in the light of single-cell individuality and genome heterogeneity, it becomes important to evaluate population-wide measurements carefully. An overview of various approaches in microbial ecology is given, and the cell as a central unit for understanding processes on a community level is discussed.

scholarly journals Draft Genome Sequences of Four Aeromonas salmonicida subsp. achromogenes Strains, 23051, 23053, 23055, and 23056, Isolated from Senegalese Sole (Solea senegalensis)

2019 ◽  
Vol 8 (33) ◽  
Author(s):  
Antony T. Vincent ◽  
Alain Le Breton ◽  
Alex Bernatchez ◽  
Cynthia Gagné-Thivierge ◽  
Valérie E. Paquet ◽  
...  
Keyword(s):  
Bacterial Species ◽  
Draft Genome ◽  
Aeromonas Salmonicida ◽  
Large Majority ◽  
Genomic Sequences ◽  
Solea Senegalensis ◽  
Senegalese Sole ◽  
Genome Sequences ◽  
Content Type ◽  
Genomic Analyses

The bacterial species Aeromonas salmonicida officially has five subspecies. A large majority of the currently available sequences come from Aeromonas salmonicida subsp. salmonicida, which causes furunculosis in salmonids. We present the genomic sequences of four Aeromonas salmonicida subsp. achromogenes strains. This will help increase the robustness of genomic analyses for this subspecies.

scholarly journals Localization and Functional Roles of Components of the Translation Apparatus in the Eukaryotic Cell Nucleus

Cells ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 3239
Author(s):  
Zaur M. Kachaev ◽  
Sergey D. Ivashchenko ◽  
Eugene N. Kozlov ◽  
Lyubov A. Lebedeva ◽  
Yulii V. Shidlovskii
Keyword(s):  
Gene Expression ◽  
Cell Nucleus ◽  
Ribosomal Proteins ◽  
Nuclear Translocation ◽  
Eukaryotic Cell ◽  
Current Data ◽  
Cell Nuclei ◽  
Functional Roles ◽  
Translation Apparatus ◽  
Cell Stress Response

Components of the translation apparatus, including ribosomal proteins, have been found in cell nuclei in various organisms. Components of the translation apparatus are involved in various nuclear processes, particularly those associated with genome integrity control and the nuclear stages of gene expression, such as transcription, mRNA processing, and mRNA export. Components of the translation apparatus control intranuclear trafficking; the nuclear import and export of RNA and proteins; and regulate the activity, stability, and functional recruitment of nuclear proteins. The nuclear translocation of these components is often involved in the cell response to stimulation and stress, in addition to playing critical roles in oncogenesis and viral infection. Many components of the translation apparatus are moonlighting proteins, involved in integral cell stress response and coupling of gene expression subprocesses. Thus, this phenomenon represents a significant interest for both basic and applied molecular biology. Here, we provide an overview of the current data regarding the molecular functions of translation factors and ribosomal proteins in the cell nucleus.

scholarly journals The Correlation Between Cell and Nucleus Size is Explained by an Eukaryotic Cell Growth Model

2021 ◽  
Author(s):  
Yufei Wu ◽  
Paul Janmey ◽  
Sean X. Sun
Keyword(s):  
Growth Rate ◽  
Cell Growth ◽  
Cell Volume ◽  
Ribosomal Proteins ◽  
Ribosome Biogenesis ◽  
Eukaryotic Cell ◽  
Nuclear Volume ◽  
Strongly Correlated ◽  
Cell Growth Rate ◽  
A Cell

In eukaryotes, the cell volume is observed to be strongly correlated with the nuclear volume. The slope of this correlation depends on the cell type, growth condition, and the physical environment of the cell. We develop a computational model of cell growth and proteome increase, incorporating the kinetics of amino acid import, protein/ribosome synthesis and degradation, and active transport of proteins between the cytoplasm and the nucleoplasm. We also include a simple model of ribosome biogenesis and assembly. Results show that the cell volume is tightly correlated with the nuclear volume, and the cytoplasm-nucleoplasm transport rates strongly influences the cell growth rate as well as the cytoplasm/nucleoplasm ratio. Ribosome assembly and the ratio of ribosomal proteins to mature ribosomes also influence the cell volume and the cell growth rate. We find that in order to regulate the cell growth rate and the cytoplasm/nucleoplasm ratio, the cell must optimally control groups of kinetic parameters together, which could explain the quantitative roles of canonical growth pathways. Finally, using an extension of our model and single cell RNAseq data, it is possible to construct a detailed proteome distribution, provided that a cell division mechanism is known.

scholarly journals The Aquatic Symbiosis Genomics Project: probing the evolution of symbiosis across the tree of life

2021 ◽  
Vol 6 ◽  
pp. 254
Author(s):  
Victoria McKenna ◽  
John M. Archibald ◽  
Roxanne Beinart ◽  
Michael N. Dawson ◽  
Ute Hentschel ◽  
...  
Keyword(s):  
Large Scale ◽  
High Throughput Sequencing ◽  
Eukaryotic Cell ◽  
Genome Sequences ◽  
Wide Range ◽  
Microbial Symbionts ◽  
Symbiotic Organisms ◽  
High Quality Genome ◽  
Reference Genomes ◽  
Environmental Importance

We present the Aquatic Symbiosis Genomics Project, a global collaboration to generate high quality genome sequences for a wide range of eukaryotes and their microbial symbionts. Launched under the Symbiosis in Aquatic Systems Initiative of the Gordon and Betty Moore Foundation, the ASG Project brings together researchers from across the globe who hope to use these reference genomes to augment and extend their analyses of the dynamics, mechanisms and environmental importance of symbiosis. Applying large-scale, high-throughput sequencing and assembly technologies, the ASG collaboration will assemble and annotate the genomes of 500 symbiotic organisms – both the “hosts” and the microbial symbionts with which they associate. These data will be released openly to benefit all who work on symbiosis, from conservation geneticists to those interested in the origin of the eukaryotic cell.

scholarly journals Archaeal Ribosomal Proteins Possess Nuclear Localization Signal-Type Motifs: Implications for the Origin of the Cell Nucleus

2019 ◽  
Vol 37 (1) ◽  
pp. 124-133 ◽  
Author(s):  
Sergey Melnikov ◽  
Hui-Si Kwok ◽  
Kasidet Manakongtreecheep ◽  
Antonia van den Elzen ◽  
Carson C Thoreen ◽  
...  
Keyword(s):  
Nuclear Localization ◽  
Cell Nucleus ◽  
Ribosomal Proteins ◽  
Eukaryotic Cell ◽  
Nuclear Localization Signals ◽  
Sequence Of Events ◽  
Eukaryotic Proteins ◽  
Signal Type ◽  
Localization Signal ◽  
Short Signal

Abstract Eukaryotic cells are divided into the nucleus and the cytosol, and, to enter the nucleus, proteins typically possess short signal sequences, known as nuclear localization signals (NLSs). Although NLSs have long been considered as features unique to eukaryotic proteins, we show here that similar or identical protein segments are present in ribosomal proteins from the Archaea. Specifically, the ribosomal proteins uL3, uL15, uL18, and uS12 possess NLS-type motifs that are conserved across all major branches of the Archaea, including the most ancient groups Microarchaeota and Diapherotrites, pointing to the ancient origin of NLS-type motifs in the Archaea. Furthermore, by using fluorescence microscopy, we show that the archaeal NLS-type motifs can functionally substitute eukaryotic NLSs and direct the transport of ribosomal proteins into the nuclei of human cells. Collectively, these findings illustrate that the origin of NLSs preceded the origin of the cell nucleus, suggesting that the initial function of NLSs was not related to intracellular trafficking, but possibly was to improve recognition of nucleic acids by cellular proteins. Overall, our study reveals rare evolutionary intermediates among archaeal cells that can help elucidate the sequence of events that led to the origin of the eukaryotic cell.

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