Viral histones: pickpocket’s prize or primordial progenitor?

Epigenetics & Chromatin, Journal Year: 2022, Volume and Issue: 15(1)

Published: May 28, 2022

Abstract The common histones H2A, H2B, H3, and H4 are the characteristic components of eukaryotic nucleosomes, which function to wrap DNA compact genome as well regulate access for transcription replication in all eukaryotes. In past two decades, have also been found be encoded some viruses, where their functions properties largely unknown, though recently from related viruses shown form nucleosome-like structures vitro. Viral can highly similar primary sequence, suggesting they picked up hosts, or radically divergent sequence may occur conjoined histone doublets, triplets, quadruplets, ancient origins prior divergence modern Here, we review what is known viral discuss possible functions. We consider how life cycle affect histories, reflect on roles origin nucleus cells.

Language: Английский

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Archaea and the Tree of Life

Published: Jan. 24, 2025

The rapid development of research on archaea by biochemists in the 1980s led to a completely unexpected discovery. Alongside characteristics unique them, such as structure their lipids, exhibited numerous traits that brought them closer eukaryotes. In 1990s, Karl Stetter redesigned Carl Woese's universal tree life, highlighting lines leading organisms whose optimal growth temperatures exceed 80 degree Celsius. Starting 2000s, genome sequencing across three domains life enabled construction phylogenetic trees based universally conserved proteins. context 2D hypothesis, eukaryotic proteins distribution is limited certain groups are called ESPs (eukaryotic signature proteins) because they suggest an evolutionary proximity between these and hypothesis Asgard our ancestors has gained popularity it motivated teams search within for evidence could support this hypothesis.

Language: Английский

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Ribosome and Transfer RNA Biogenesis

Published: April 25, 2025

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A Comparative Perspective on Ribosome Biogenesis: Unity and Diversity Across the Tree of Life

Methods in molecular biology, Journal Year: 2022, Volume and Issue: unknown, P. 3 - 22

Published: Jan. 1, 2022

Abstract Ribosomes are universally conserved ribonucleoprotein complexes involved in the decoding of genetic information contained messenger RNAs into proteins. Accordingly, ribosome biogenesis is a fundamental cellular process required for functional homeostasis and to preserve satisfactory gene expression capability. Although conserved, its shows an intriguing degree variability across tree life. These differences also raise yet unresolved questions. Among them (a) what are, if existing, remaining ancestral common principles biogenesis; (b) molecular impacts evolution history how did they contribute (re)shape pathway life; (c) extent divergence and/or convergence (functional mimicry), latter case (if existing) basis; (d) considering universal conservation, capability plasticity adaptation pathway? In this review, we provide brief overview life try illustrate some potential emerging answers these

Language: Английский

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On the origin of the nucleus: a hypothesis

Microbiology and Molecular Biology Reviews, Journal Year: 2023, Volume and Issue: 87(4)

Published: Nov. 29, 2023

SUMMARY In this hypothesis article, we explore the origin of eukaryotic nucleus. doing so, first look afresh at nature defining feature cell and its core functions—emphasizing utility seeing nucleoplasm cytoplasm as distinct regions a common compartment. We then discuss recent progress in understanding evolution from archaeal bacterial ancestors, focusing on phylogenetic experimental data which have revealed that many machines with nuclear activities counterparts. addition, review literature describing biology representatives TACK Asgardarchaeaota - closest known living relatives eukaryotes. Finally, bringing these strands together, propose model for nucleus explains much current data, including predictions can be used to put test.

Language: Английский

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Methanomethylophilus alvi gen. nov., sp. nov., a Novel Hydrogenotrophic Methyl-Reducing Methanogenic Archaea of the Order Methanomassiliicoccales Isolated from the Human Gut and Proposal of the Novel Family Methanomethylophilaceae fam. nov.

Microorganisms, Journal Year: 2023, Volume and Issue: 11(11), P. 2794 - 2794

Published: Nov. 17, 2023

The methanogenic strain Mx-05T was isolated from the human fecal microbiome. A phylogenetic analysis based on 16S rRNA gene and protein marker genes indicated that is affiliated with order Methanomassiliicoccales. It shares 86.9% sequence identity Methanomassiliicoccus luminyensis, only member of this previously isolated. cells were non-motile cocci, a diameter range 0.4-0.7 μm. They grew anaerobically reduced methanol, monomethylamine, dimethylamine, trimethylamine into methane, using H2 as an electron donor. H2/CO2, formate, ethanol, acetate not used energy sources. growth required unknown medium factor(s) provided by Eggerthella lenta present in rumen fluid. between 30 °C 40 (optimum 37 °C), over pH 6.9-8.3 7.5), 0.02 0.34 mol.L-1 NaCl 0.12 NaCl). genome 1.67 Mbp G+C content 55.5 mol%. Genome annotation confirmed absence methyl branch H4MPT Wood-Ljungdahl pathway, described for other Methanomassiliicoccales members. Based average nucleotide analysis, we propose being novel representative Methanomassiliicoccales, within family Methanomethylophilaceae, which name Methanomethylophilus alvi gen. nov, sp. nov. proposed. type (JCM 31474T).

Language: Английский

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Carl Woese: Still ahead of our time

mLife, Journal Year: 2022, Volume and Issue: 1(4), P. 359 - 367

Published: Dec. 1, 2022

The work of Carl Woese and his colleagues the Urbana University has been one most important breakthroughs in biology last century (for historical sketches, see Refs.1, 2). pioneered use macromolecule sequences to decipher relationships between all organisms, fulfilling Darwin's dream get a "fairly true genealogical trees each great kingdom nature"3. He went even beyond this objective since he was finally able identify connect nature (which called domains) into single tree. apex discovery 1977 an entire new domain life, hidden before our eyes, Archaea4. 16S ribosomal RNA (rRNA) as molecular chronometer later probe for PCR not only revealed third life but also paved way detection identification microorganisms that were yet amenable cultivation5. I deeply affected when passed away 10 years ago because my three scientific heroes: together with James Watson, DNA double-helix, Wang, topoisomerases (the Ws). surprised still shocked despite monumental achievements, death completely ignored French media, suspect it same countries worldwide. Notably, died day famous horse, Ourasi, had won several competitions such "le grand prix de l'arc Triumphe." horse made headlines media day, including prime-time TV news. could resist sending short piece entitled "the scientist horse" Journal Liberation which emphasize difference treatment (and like horses) greatest scientists century. It published online version journal link now removed, you can read at end fourth chapter book, Microbes from Hell1. ardent activist promoting vision living world by discoveries. criticized misleading prokaryotic/eukaryotic paradigm, classification organisms is based on phenotypic features, sequel anthropic lower higher ones, humans top classifications6. paradigm establish 15 Archaea7. Therefore, George Fox their seminar paper Proc Natl Acad Sci USA 1977, already firmly established. prokaryote/eukaryote easy explain (with or without nucleus) quickly became pillar cellular organisms8. dichotomy welcomed cytologists biologists alike modern classification, be opposed five-kingdom favored zoologists botanists9. This probably explains why so many biologists, strongly time Woese's proposal though data2, 10, 11 (see Ref.12 answer Ernst Mayer). Why should we change winning team? Here, will briefly describe various encounters Woese, focusing agreements disagreements concerning universal tree Last Universal Common Ancestor (LUCA), which, according definitely less recognized major question today"13. discuss how legacy challenged occasions reactions. Unfortunately, no longer among us defend legacy. All aware existence Archaea recognize merit revealing deep divide "prokaryotic world," too (in opinion) believe view fundamentally wrong favor pre-Woesian evolutionary model. dominant one, paralleled virus/phage virosphere, layman politicians journalists ignore (still confused Bacteria). More troublesome fact (except those working Archaea) are unaware vastly underestimate importance. seems remind generations importance history science fight ideas think they forefront science. discovered reading 1981 review Scientific American described "Archaebacteria" possibility studying "primary kingdom" determine common ancestor domains, progenote14. turning point career immediately stop replication Bacteria (Escherichia coli) started Archaea, polymerases. Thanks inspiration help few pioneers field, especially Wolfram Zillig15, rapidly accumulate significant results study Halobacterium halobium Sulfolobus acidocaldarius16, 17. first publications topic, invited Zillig participate second meeting organized Martinsried Institute, near Munich 1985. gave me opportunity time. vividly remember memorable sparring Lake took place meeting. Based electron microscopic pictures ribosomes, just two papers Science18, 19 proposed replacing "urkingdoms" (Figure 1A) four 1B). In unrooted tree, ribosome structure, Archaebacteria split "Archaebacteria proper," limited halophiles methanogens, urkingdom, Eocytes, grouping other thermophilic archaea, Thermococcus Thermoplasma18. Lake, who spoke first, violently attacked explained him different values versus genotypic data. came back shivering much argument opinion people present explanation. structural signatures Jim used define Eocyte indeed observed mesophilic methanogen, Methanococcus vanielli29. paper, although Science, cited today, whereas Lake's 1984 proponents two-domains (2D) hypothesis below) supporting favorite hypothesis30, 31. discouraged failure held Victoria Canadian east coast fresh arguments. meantime, learned phylogenetic techniques designed method own, parsimony32, produced rRNA Thermoplasma removed Eocytes33. If root localized bacteria obtains 2D trees, 1988 (Ref.33) clearly (instead 1984) description 1D). After talk meeting, stage conclude speaker brought arguments theory. striking contrast mute Canada, leaving coworker Gary Olsen against Lake34. seemed bit ongoing debate. How realize scenario good one? wondering mathematician here settle dispute. realized myself problem primarily mathematical (today, speaking about choose best model) more data sets22. fed up meetings eager person opponents. Besides conflict rejection theory evolutionists, Mayer Lynn Margulis, continue support paradigm2. My encounter thus delayed until 1994, very beginning genomic era. Despite reluctance attend meetings, joined friendship Zillig, influential bringing gospel Europe15. We waiting genome sequenced (most likely bacterial one), Roger Garret Aarhus Denmark35 small roundtable five colleagues, one) archaeal selected mammoth task. Each participant name archaeon floor expected (hoping would one). "We sequence least five," declared stupefaction incredulity. fact, right genomes available century, Craig Venter's team done collaboration 1996 (Methanocaldococcus vannielii)36. example lifetime. being heroes, did hesitate disagree him. strong proponent rooting groups 1980s37, 38. obtained combining analysis paralogous proteins originated gene duplication LUCA. For time, Hervé Philippe, these reliable attraction long branch separated corresponding respective outgroup39, 40. suspected preferred Bacteria. Indeed, rooted justify changing Archaea20 hoped topology simply extreme environments 1C). while, disagreed Eukaryotes domains. liked idea some eukaryotic spliceosome, possibly Of course, rejected have old division. When Philippe defended reporting presence bacterial-like genes than eukaryotic-like genomes39, ridiculed quantitative qualitative, quality hallmark translation apparatus studies41. soon right, allowing parsimonious distribution domains life27 1E). However, cannot solved analyses reasonable guess comparative (Box 1). LUCA smaller 33–34 ribosomes contain around 60–80 proteins27. mechanism biosynthesis simpler, protein involved process42. initiation transcription specific, factor set elongation Finn Werner)43. RNA, explaining replication, replicase, primase, helicase, homologous Arkarya Bacteria44 (Arkarya clade Eukarya)27. (processivity factor) might introduced independently lineages viruses. ATPase synthase ATP fermentation subunit essential synthesis Arkarya45. These reasoning sophistication fundamental mechanisms takes lineages. Alternative hypotheses (complex LUCA) involve replacement Arkaryal features ones vice versa ones. There obvious selection pressure suggested replacement, except simplification branch40. Although simpler progenote, sensu Fox21, 46, sophisticated membrane pumps capable faithful synthesis27. seminal "The concept evolution"46, unfaithful apparatus. Again, gap exists hand Eukarya evolution always parsimonious, remain open possible alternatives47. partly agree LUCA, do stricto sensu, translate mRNA message rather faithfully. conclusion contained transfer (tRNA) modifications crucial translation. A provided Kae1 Sua5 t6A biosynthesis, tRNA modification ANN codons. need additional factors perform task sufficient synthesize mitochondria, suggesting mitochondria recapitulates LUCA27. adopted promoted so-called "bacterial branch," never considered finding Eukarya. departure cladistic rules due fear weakening three-domain promoted. if follows rules, usually assumed, two-domain Bacteria, naming Arkarya27. Probably bypassing case 2002, Darwinian threshold transition period ancestors Archaeal Ancestor, LACA; Bacterial LBCA; Eukaryotic LECA), hereafter referred ancestors21. moment transmission genetic information moves predominantly horizontal mode lateral (LGT) vertical mode. assumed LGTs allow organisms. Accordingly, argue applicable threshold, separation leading Killing birds once, tempo dramatically decreased emergence ancestors. dramatic reduction observations early looking shape tree13. rate within extrapolated ancestors, born formation Earth! LGT prevalence correct rarely LGT48, 49. 2006, replicated repaired faithfully RNA50. viruses triggers independent RNA-to-DNA transitions, domain. To delight, reject agreed refer USA. respond critics challenge life. prevalent once thought, sometimes far apart led buzz forgetting trumpeting "Darwin wrong" discussion Ref.51). profoundly views, authors jokingly percent"52 networks53. save upper part (those context. chance meet another 2003 personal discussions evolution. little afraid knowledge previous disagreement negative impact encounter. case; friendly, real lover something give happy figure 1982, someone remembered review14. Lund Sweden honor awarded Crafoord prize Royal Swedish Academy Sciences. received King Sweden, Gustav XVI, descendant Marshal Napoleon Bernadotte, unexpected turn history. occasion humor mimicked official dinner ritual master ceremony Chap. 4 Ref.1). prize, 3 Nobel (both terms money ceremony!), exception complete absence press coverage. pity Prize. speak archaea. deserved medicine, considering markers microorganism medicine. recent Svante Pääbo sequencing Neanderthal confirms advances fields prize. wonder opposition adversaries evolutionists played role final distinction. met 2007 Illinois Urbana-Champaign celebrate 30th anniversary Archaea. "hidden your eyes" resembling visible, decades cousins under microscope. visit laboratory opening box containing film two-dimensional gel chromatography collection oligonucleotides after digestion Methanobacterium thermoautotrophicum RNase T1 1 Ref.15). honored own university surrounded friends introduce countries, Karl Stetter Germany, Yoshizumi Ishino Japan, David Prangishvili former USSR. 2012, reawakening Asgard archaea24, 25. am really reacted twist biology. imagine disturbed, view. decade, paraphyletic, considers belong 1F). make things worse, often depicted fusions (one mitochondria) archaeon, Margulis highly despised (figure Ref14). Archaebacteria, hence illustrated contrasting eukaryotes emerged fusion prokaryotes (only time)14. much. going past becoming one. classical during decade fast-evolving species sets, combined difficulty recovering testifying monophyly reviews results, Ref.54). does mean archaea breakthrough provide exciting understand Phylogenetic odd Signature Proteins (ESPs) extensive proto-eukaryotes54. Studying reconstruct proto-eukaryotic lineage. proto-eukaryotes suggests thriving LECA environments, indicating shed light type environment inhabited cultivated Candidatus Prometheoarchaem synthrophicum, turned out dependent growth its physical association methanogenic archaeon55. tour force concluded publication genomics "most them, all, symbiotic interactions." tempting suggest facilitated interactions Asgard54. One live ectosymbionts today. search associations biotopes adventure young (or young) microbial ecologists54. assault three-domains concept, deny prokaryotic At 2020, heralded putting nail coffin. From 10,575 genomes, 381 markers, "1.16 trillions non amino-acids," separates shorter previously thought56. branches separating altogether. correct, there reason separate reunified domain, pre-Woese area. Looking cursorily claim, flaws conclusion. included 6 34 shared proteins. They is, instance, gyrase, recruited (Ref. 50 references therein). subsequently refuted Moody identified both paralogy Zhu colleagues49. noticed 14 include priori unbelievable aim measure distance 68 others 25% sampled Strikingly, (a prerequisite kind analysis) recovered 22 trees49. indicated that, transferred other. review, Refs.23, 57) confirmed recently using data, non-ribosomal proteins22, 48, Long lengths criterion determining besides widespread domains48, 58. Failure consider Weiss colleagues59. reported 355 supposed starting "6.1 million protein-coding genes" "286,514 clusters." showed metabolism similar Clostridia genome, "prokaryote" progenote. thrived high temperatures reverse enzymes found mesophiles hyperthermophiles, gyrases formed monophyletic analysis, them short, gyrase intermixed, domains58. reanalysis colleagues' Berkemer McGlynn 82% all), LUCA48. again underrepresented low diversity. looked arrived Using criteria represented distantly related phylums, 15–20 "LUCA" (unpublished observations). proteome table. scenarios origin

Language: Английский

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The Importance of Being RNA-est: considering RNA-mediated ribosome plasticity

RNA Biology, Journal Year: 2023, Volume and Issue: 20(1), P. 177 - 185

Published: April 26, 2023

For over 40 years, ribosomes were considered monolithic machines that translate the genetic code indiscriminately. However, past two decades, there have been a growing number of studies suggest to degree compositional and functional adaptability in response tissue type, cell environment stimuli, cycle or development state. In such form, themselves take an active part translation regulation through intrinsic provided by evolution, which furnished with dynamic plasticity confers another layer gene expression regulation. Yet despite identification various sources give rise ribosomal heterogeneity both at protein RNA level, its relevance is still debated, many questions remain. Here, we will review aspects, including evolutionary ones, ribosome emerging nucleic acid aim reframe 'heterogeneity' as adaptive process plasticity.The terms on this article has published allow posting Accepted Manuscript repository author(s) their consent.

Language: Английский

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Studying the Human Microbiota: Advances in Understanding the Fundamentals, Origin, and Evolution of Biological Timekeeping

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(22), P. 16169 - 16169

Published: Nov. 10, 2023

The recently observed circadian oscillations of the intestinal microbiota underscore profound nature human-microbiome relationship and its importance for health. Together with discovery clocks in non-photosynthetic gut bacteria rhythms anucleated cells, these findings have indicated possibility that virtually all microorganisms may possess functional biological clocks. However, they also raised many essential questions concerning fundamentals timekeeping, evolution, origin. This narrative review provides a comprehensive overview recent literature molecular chronobiology, aiming to bring together latest evidence on structure mechanisms driving microbial while pointing potential applications this knowledge medicine. Moreover, it discusses hypotheses regarding evolution timing describes functions peroxiredoxins cells their contribution cellular clockwork. diversity among various human-associated role transcriptional post-translational timekeeping are addressed. Finally, metabolic oscillators host-microbiome communication is presented.

Language: Английский

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Ultra-deep sequencing of 45S rDNA to discern intragenomic diversity in three Chrysodeixis species for molecular identification

Scientific Reports, Journal Year: 2023, Volume and Issue: 13(1)

Published: Aug. 10, 2023

Species identification is necessary to prevent introductions of exotic plant pests through global trade. Many these are understudied and lack publicly available DNA sequence data on which rapid molecular methods can be based. One such lineage the genus Chrysodeixis, includes three species potential concern for United States trade initiatives: C. includens, chalcites, eriosoma. Here we describe a method generate robust 45S rDNA profiles using long read sequencing in order clarify evolutionary relationships develop real-time PCR technique. Such an tool will useful rapidly differentiating between Chrysodeixis quarantine where traditional morphological insufficient. Molecular as this greatly reduce time spent identifying each specimen, allow detection eDNA, vastly increase throughput, probability detection. The presented here generally adaptable any lepidopteran taxa that necessitates diagnostic assay and, with adjustment or testing primers, could applied group development benchtop setting would prove useful.

Language: Английский

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