Diversity and evolution of viroids and viroid-like agents with circular RNA genomes revealed by metatranscriptome mining DOI Creative Commons
Eugene V. Koonin, Benjamin D. Lee

Nucleic Acids Research, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 27, 2024

Abstract Viroids, the agents of several plant diseases, are smallest and simplest known replicators that consist covalently closed circular (ccc) RNA molecules between 200 400 nucleotides in size. Viroids encode no proteins rely on host polymerases for replication, but some contain ribozymes involved replication intermediate processing. Although other viroid-like with cccRNAs genomes, such as satellite RNAs, ribozyviruses retrozymes, have been discovered, until recently, spread these biosphere appeared narrow, their actual diversity evolution remained poorly understood. Extensive, targeted metatranscriptome mining dramatically expanded genomes. These searches identified numerous, diverse cccRNAs, many found environments devoid animal material, suggesting unicellular eukaryotic and/or prokaryotic hosts. Several by CRISPR systems, supporting association bacteria. In addition to small viroid size range, a broad variety novel viruses genomes reaching nearly 5 kilobases, were discovered. Thus, shows is far greater than previously suspected, prompting reassessment relevance understanding primordial world.

Language: Английский

Using artificial intelligence to document the hidden RNA virosphere DOI Creative Commons
Xin Hou, Yong He,

Pan Fang

et al.

Cell, Journal Year: 2024, Volume and Issue: 187(24), P. 6929 - 6942.e16

Published: Oct. 9, 2024

Highlights•AI-based metagenomic mining greatly expands the diversity of global RNA virosphere•Developed a deep learning model that integrates sequence and structural information•161,979 putative virus species 180 supergroups were identified•RNA viruses are ubiquitous even found in most extreme environmentsSummaryCurrent tools can fail to identify highly divergent viruses. We developed algorithm, termed LucaProt, discover RNA-dependent polymerase (RdRP) sequences 10,487 metatranscriptomes generated from diverse ecosystems. LucaProt both predicted information, enabling accurate detection RdRP sequences. Using this approach, we identified 161,979 potential supergroups, including many previously poorly studied groups, as well genomes exceptional length (up 47,250 nucleotides) genomic complexity. A subset these novel was confirmed by RT-PCR RNA/DNA sequencing. Newly discovered present environments, air, hot springs, hydrothermal vents, with abundance varying substantially among This study advances discovery, highlights scale virosphere, provides computational better document virome.Graphical abstract

Language: Английский

Citations

29
Viroid Replication, Movement, and the Host Factors Involved DOI Creative Commons

Yuhong Zhang,

Yuxin Nie,

Luyou Wang

et al.

Microorganisms, Journal Year: 2024, Volume and Issue: 12(3), P. 565 - 565

Published: March 12, 2024

Viroids represent distinctive infectious agents composed solely of short, single-stranded, circular RNA molecules. In contrast to viruses, viroids do not encode for proteins and lack a protective coat protein. Despite their apparent simplicity, have the capacity induce diseases in plants. Currently, extensive research is being conducted on replication cycle within both Pospiviroidae Avsunviroidae families, shedding light intricacies associated host factors. Utilizing potato spindle tuber viroid as model, investigations into structural motifs involved trafficking between different cell types been thorough. Nevertheless, our understanding factors responsible intra- inter-cellular movement remains highly incomplete. This review consolidates current knowledge emphasizing basis required identified involved. Additionally, we explore potential that may mediate viroids, addressing gaps understanding. Moreover, application emergence novel viroid-like cellular parasites are also discussed.

Language: Английский

Citations

4
Recent advances in viroid research DOI

Yuhong Zhang,

David M. Bisaro, Jian Wu

et al.

Virology, Journal Year: 2025, Volume and Issue: unknown, P. 110424 - 110424

Published: Jan. 1, 2025

Language: Английский

Citations

0
Synechism 2.0: Contours of a New Theory of Continuity in Bioengineering DOI Creative Commons
Ahti‐Veikko Pietarinen, Vera Shumilina

Biosystems, Journal Year: 2025, Volume and Issue: unknown, P. 105410 - 105410

Published: Feb. 1, 2025

Language: Английский

Citations

0
Five things to consider before proposing that a circular RNA is a viroid DOI Creative Commons
Jian Wu, David M. Bisaro

PLoS Pathogens, Journal Year: 2025, Volume and Issue: 21(3), P. e1012958 - e1012958

Published: March 7, 2025

Language: Английский

Citations

0
Advancing RNA phage biology through meta-omics DOI Creative Commons
Jens Hör

Nucleic Acids Research, Journal Year: 2025, Volume and Issue: 53(8)

Published: April 22, 2025

Abstract Bacteriophages with RNA genomes are among the simplest biological entities on Earth. Since their discovery in 1960s, they have been used as important models to understand principal processes of life, including translation and genetic code. While phages were generally thought rare oddities nature, meta-omics methods rapidly changing this simplistic view by studying diverse biomes unprecedented resolution. Metatranscriptomics dramatically expanded number known from tens thousands, revealed widespread abundance, discovered several new families potential largely unknown hosts, biology, environmental impact. At same time, (meta)genomic analyses bacterial hosts discovering an arsenal defense systems bacteria employ protect themselves predation, whose functions immunity against we only beginning understand. Here, I review how approaches advancing field phage biology a focus might fight them.

Language: Английский

Citations

0
A parasite odyssey: An RNA virus concealed in Toxoplasma gondii DOI Creative Commons
P. P. Gupta, A. Hiller, Jawad Chowdhury

et al.

Virus Evolution, Journal Year: 2024, Volume and Issue: 10(1)

Published: Jan. 1, 2024

We are entering a 'Platinum Age of Virus Discovery', an era marked by exponential growth in the discovery virus biodiversity, and driven advances metagenomics computational analysis. In ecosystem human (or any animal) there more species viruses than simply those directly infecting animal cells. Viruses can infect all organisms constituting microbiome, including bacteria, fungi, unicellular parasites. Thus complexity possible interactions between host, microbe, is unfathomable. To understand this interaction network we must employ computationally assisted virology as means analyzing interpreting millions available samples to make inferences about ways which may intersect health. From viral screen neuronal datasets, identified novel narnavirus Apocryptovirus odysseus (Ao) likely infects neurotropic parasite Toxoplasma gondii. Previously, several parasitic protozoan (PPVs) have been mechanistically established triggers host innate responses, here present silico evidence that Ao plausible pro-inflammatory factor mouse cells infected T. gondii billions people worldwide, yet prognosis toxoplasmosis disease highly variable, PPVs like could function hitherto undescribed hypervirulence factor. broader over 7.6 million samples, explored phylogenetically proximal discovered nineteen species, found libraries annotated vertebrate transcriptome or metatranscriptomes. While containing genus narnaviruses derived from sheep, goat, bat, rabbit, chicken, pigeon presence strongly predictive Apicomplexa nucleic acid co-occurrence, supporting fact parasite-infecting viruses. This proof-of-concept study rapidly analyze datasets distilled mechanistically, ecologically, refined hypothesis. predict diverged RNA biologically infection, Ao, other it, will modulate afflicts worldwide.

Language: Английский

Citations

3
Translation of circular RNAs DOI Creative Commons
Giorgi Margvelani, Karol Andrea Arizaca Maquera, Justin R. Welden

et al.

Nucleic Acids Research, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 8, 2024

Circular RNAs (circRNAs) are covalently closed that present in all eukaryotes tested. Recent RNA sequencing (RNA-seq) analyses indicate although generally less abundant than messenger (mRNAs), over 1.8 million circRNA isoforms exist humans, much more the number of currently known mRNA isoforms. Most circRNAs generated through backsplicing depends on pre-mRNA structures, which influenced by intronic elements, for example, primate-specific Alu leading to species-specific circRNAs. CircRNAs mostly cytosolic, stable and some were shown influence cells sequestering miRNAs RNA-binding proteins. We review increasing evidence translated into proteins using several cap-independent translational mechanisms, include internal ribosomal entry sites, N6-methyladenosine modification, adenosine inosine editing interaction with eIF4A3 component exon junction complex. under conditions favor translation, notably cancer generate shorter mRNA-encoded proteins, can acquire new functions relevant diseases.

Language: Английский

Citations

2
The potential of including the microbiome as biomarker in population-based health studies: methods and benefits DOI Creative Commons
Florence E. Buytaers, Nicolas Berger, Johan Van der Heyden

et al.

Frontiers in Public Health, Journal Year: 2024, Volume and Issue: 12

Published: Oct. 23, 2024

The key role of our microbiome in influencing health status, and its relationship with environment lifestyle or behaviors, have been shown the last decades. Therefore, human has potential to act as a biomarker indicator exposure risks general population, if information on can be collected population-based surveys cohorts. It could then associated epidemiological participant data such demographic, clinical profiles. However, knowledge, sampling not yet included biological evidence large studies representative population. In this mini-review, we first highlight some practical considerations for analysis that need considered context population study. We present examples topics where benefit public health, how developed future. doing so, aim benefits having available at level combined from surveys, hence microbiological used future assess health. also stress challenges remain overcome allow use order improve proactive policies.

Language: Английский

Citations

1
Adaptive immunity of type VI CRISPR-Cas systems associated with reverse transcriptase–Cas1 fusion proteins DOI Creative Commons
María Dolores Molina-Sánchez, Francisco Martínez‐Abarca, Vicenta Millán

et al.

Nucleic Acids Research, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 30, 2024

Abstract Cas13-containing type VI CRISPR-Cas systems specifically target RNA; however, the mechanism of spacer acquisition remains unclear. We have previously reported association reverse transcriptase–Cas1 (RT–Cas1) fusion proteins with certain types VI-A systems. Here, we show that RT–Cas1 are also recruited by VI-B in bacteria from gut microbiomes, constituting a VI-B1 variant system includes CorA-encoding locus addition to CRISPR array and RT–Cas1/Cas2 adaptation module. found RT-CRISPR were functional for acquisition, processing interference activity, demonstrating adaptive immunity mediated these can function independently other trans provide evidence RT associated enables RNA molecules. CorA encoded RT-associated transport divalent metal ions downregulate Cas13b-mediated interference. These findings highlight importance RTs RNA-targeting systems, potentially enabling integration RNA-derived spacers into arrays as against RNA-based invaders specific environments.

Language: Английский

Citations

1