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1.
Ann Lab Med ; 42(2): 196-202, 2022 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-34635613

RESUMO

Background: Identifying the causal pathogen of encephalitis remains a clinical challenge. A 50-year-old man without a history of neurological disease was referred to our department for the evaluation of an intracranial lesion observed on brain magnetic resonance imaging (MRI) scans, and the pathology results suggested protozoal infection. We identified the species responsible for encephalitis using thymine-adenine (TA) cloning, suitable for routine clinical practice. Methods: We extracted DNA from a paraffin-embedded brain biopsy sample and performed TA cloning using two universal eukaryotic primers targeting the V4-5 and V9 regions of the 18S rRNA gene. The recombinant plasmids were extracted, and the inserted amplicons were identified by Sanger sequencing and a homology search of sequences in the National Center for Biotechnology Information Basic Local Alignment Search Tool. Results: The infection was confirmed to be caused by the free-living amoeba Balamuthia mandrillaris. Two of 41 colonies recombinant with 18S V4-5 primers and 35 of 63 colonies recombinant with the 18S V9 primer contained B. mandrillaris genes; all other colonies contained human genes. Pathogen-specific PCR ruled out Entamoeba histolytica, Naegleria fowleri, Acanthamoeba spp., and Toxoplasma gondii infections. Conclusions: This is the first report of B. mandrillaris-induced encephalitis in Korea based on molecular identification. TA cloning with the 18S rRNA gene is a feasible and affordable diagnostic tool for the detection of infectious agents of unknown etiology.


Assuntos
Balamuthia mandrillaris , Encefalite , Adenina , Balamuthia mandrillaris/genética , Clonagem Molecular , Encefalite/diagnóstico , Eucariotos , Humanos , Masculino , Pessoa de Meia-Idade , Timina
2.
BMC Genomics ; 22(1): 644, 2021 Sep 06.
Artigo em Inglês | MEDLINE | ID: mdl-34488632

RESUMO

BACKGROUND: Inversion Symmetry is a generalization of the second Chargaff rule, stating that the count of a string of k nucleotides on a single chromosomal strand equals the count of its inverse (reverse-complement) k-mer. It holds for many species, both eukaryotes and prokaryotes, for ranges of k which may vary from 7 to 10 as chromosomal lengths vary from 2Mbp to 200 Mbp. Building on this formalism we introduce the concept of k-mer distances between chromosomes. We formulate two k-mer distance measures, D1 and D2, which depend on k. D1 takes into account all k-mers (for a single k) appearing on single strands of the two compared chromosomes, whereas D2 takes into account both strands of each chromosome. Both measures reflect dissimilarities in global chromosomal structures. RESULTS: After defining the various distance measures and summarizing their properties, we also define proximities that rely on the existence of synteny blocks between chromosomes of different bacterial strains. Comparing pairs of strains of bacteria, we find negative correlations between synteny proximities and k-mer distances, thus establishing the meaning of the latter as measures of evolutionary distances among bacterial strains. The synteny measures we use are appropriate for closely related bacterial strains, where considerable sections of chromosomes demonstrate high direct or reversed equality. These measures are not appropriate for comparing different bacteria or eukaryotes. K-mer structural distances can be defined for all species. Because of the arbitrariness of strand choices, we employ only the D2 measure when comparing chromosomes of different species. The results for comparisons of various eukaryotes display interesting behavior which is partially consistent with conventional understanding of evolutionary genomics. In particular, we define ratios of minimal k-mer distances (KDR) between unmasked and masked chromosomes of two species, which correlate with both short and long evolutionary scales. CONCLUSIONS: k-mer distances reflect dissimilarities among global chromosomal structures. They carry information which aggregates all mutations. As such they can complement traditional evolution studies , which mainly concentrate on coding regions.


Assuntos
Cromossomos , Genômica , Inversão Cromossômica , Cromossomos/genética , Eucariotos , Evolução Molecular , Humanos , Sintenia
3.
Methods Enzymol ; 658: 407-418, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34517956

RESUMO

The 7-methylguanosine (m7G) cap structure, an essential epitranscriptomic mark at the 5' terminus of eukaryotic mRNAs, plays critical roles in mRNA stability, export, and translation. Following the cap structure, the first and second nucleotides at the 5' ends of mRNAs are frequently methylated to give more diverse modifications, especially in vertebrates. To understand the biological roles of the cap structures, precise analyses of the 5' terminal modifications are necessary. Here, we describe a detailed protocol for mass spectrometric analysis of 5' terminal fragments of mRNAs.


Assuntos
Eucariotos , Estabilidade de RNA , Animais , Eucariotos/metabolismo , Espectrometria de Massas , Biossíntese de Proteínas , RNA Mensageiro/genética , RNA Mensageiro/metabolismo
4.
Water Res ; 204: 117617, 2021 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-34555587

RESUMO

Large water diversion projects are important constructions for reallocation of human-essential water resources. Deciphering microbiota dynamics and assembly mechanisms underlying canal water ecosystem services especially during long-distance diversion is a prerequisite for water quality monitoring, biohazard warning and sustainable management. Using a 1432-km canal of the South-to-North Water Diversion Projects as a model system, we answer three central questions: how bacterial and micro-eukaryotic communities spatio-temporally develop, how much ecological stochasticity contributes to microbiota assembly, and which immigrating populations better survive and navigate across the canal. We applied quantitative ribosomal RNA gene sequence analyses to investigate canal water microbial communities sampled over a year, as well as null model- and neutral model-based approaches to disentangle the microbiota assembly processes. Our results showed clear microbiota dynamics in community composition driven by seasonality more than geographic location, and seasonally dependent influence of environmental parameters. Overall, bacterial community was largely shaped by deterministic processes, whereas stochasticity dominated micro-eukaryotic community assembly. We defined a local growth factor (LGF) and demonstrated its innovative use to quantitatively infer microbial proliferation, unraveling taxonomically dependent population response to local environmental selection across canal sections. Using LGF as a quantitative indicator of immigrating capacities, we also found that most micro-eukaryotic populations (82%) from the source water sustained growth in the canal and better acclimated to the hydrodynamical water environment than bacteria (67%). Taxa inferred to largely propagate include Limnohabitans sp. and Cryptophyceae, potentially contributing to water auto-purification. Combined, our work poses first and unique insights into the microbiota assembly patterns and dynamics in the world's largest water diversion canal, providing important ecological knowledge for long-term sustainable water quality maintenance in such a giant engineered system.


Assuntos
Microbiota , Água , Eucariotos , Humanos , Qualidade da Água , Recursos Hídricos
5.
Biochemistry (Mosc) ; 86(9): 1053-1059, 2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-34565311

RESUMO

"Would it be possible to analyze molecular mechanisms and structural organisation of polyribosome assemblies using cryo electron tomography?" - we asked through a longstanding collaboration between my research group and that of Alexander S. Spirin. Indeed, it was: we found that double-row polyribosomes can have both circular and linear arrangements of their mRNA [Afonina, Z. A., et al. (2013) Biochemistry (Moscow)], we figured out how eukaryotic ribosomes assemble on an mRNA to form supramolecular left-handed helices [Myasnikov, A. G., et al. (2014) Nat. Commun.], that the circularization of polyribosomes is poly-A and cap-independent [Afonina, Z. A., et al. (2014) Nucleic Acids Res.], and that intermediary polyribosomes with open structures exist after a transition from a juvenile phase to strongly translating polysomes of medium size [Afonina, Z. A., et al. (2015) Nucleic Acids Res.] until they form densely packed helical structures with reduced activity. Our joint fruitful exchanges, hence, led to major advances in the field, which are reviewed here from a personal and historical perspective in memory of Alexander S. Spirin.


Assuntos
Polirribossomos/química , Microscopia Crioeletrônica , Eucariotos/química , Eucariotos/genética , Eucariotos/metabolismo , Conformação de Ácido Nucleico , Poli A/química , Poli A/metabolismo , Polirribossomos/metabolismo , Capuzes de RNA/química , Capuzes de RNA/metabolismo , RNA Mensageiro/química , RNA Mensageiro/metabolismo , Subunidades Ribossômicas/química , Subunidades Ribossômicas/metabolismo
6.
Biochemistry (Mosc) ; 86(9): 1095-1106, 2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-34565313

RESUMO

Ribosome profiling (riboseq) has opened the possibilities for the genome-wide studies of translation in all living organisms. This method is based on deep sequencing of mRNA fragments protected by the ribosomes from hydrolysis by ribonucleases, the so-called ribosomal footprints (RFPs). Ribosomal profiling together with RNA sequencing allows not only to identify with a reasonable accuracy translated reading frames in the transcriptome, but also to track changes in gene expression in response to various stimuli. Notably, ribosomal profiling in its classical version has certain limitations. The size of the selected mRNA fragments is 25-35 nts, while RFPs of other sizes are usually omitted from analysis. Also, ribosomal profiling "averages" the data from all ribosomes and does not allow to study specific ribosomal complexes associated with particular translation factors. However, recently developed modifications of ribosomal profiling provide answers to a number of questions. Thus, it has become possible to analyze not only elongating, but also scanning and reinitiating ribosomes, to study events associated with the collision of ribosomes during mRNA translation, to discover new ways of cotranslational assembly of multisubunit protein complexes during translation, and to selectively isolate ribosomal complexes associated with certain protein factors. New data obtained using these modified approaches provide a better understanding of the mechanisms of translation regulation and the functional roles of translational apparatus components.


Assuntos
RNA Mensageiro/metabolismo , Ribossomos/metabolismo , Eucariotos/genética , Eucariotos/metabolismo , Fatores de Iniciação de Peptídeos/metabolismo , Biossíntese de Proteínas , Subunidades Proteicas/genética , Subunidades Proteicas/metabolismo
7.
J Enzyme Inhib Med Chem ; 36(1): 1988-1995, 2021 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-34482770

RESUMO

Carbonic anhydrases (CAs, EC 4.2.1.1) have been studied for decades and have been classified as a superfamily of enzymes which includes, up to date, eight gene families or classes indicated with the Greek letters α, ß, γ, δ, ζ, η, θ, ι. This versatile enzyme superfamily is involved in multiple physiological processes, catalysing a fundamental reaction for all living organisms, the reversible hydration of carbon dioxide to bicarbonate and a proton. Recently, the ι-CA (LCIP63) from the diatom Thalassiosira pseudonana and a bacterial ι-CA (BteCAι) identified in the genome of Burkholderia territorii were characterised. The recombinant BteCAι was observed to act as an excellent catalyst for the physiologic reaction. Very recently, the discovery of a novel ι-CAs (COG4337) in the eukaryotic microalga Bigelowiella natans and the cyanobacterium Anabaena sp. PCC7120 has brought to light an unexpected feature for this ancient superfamily: this ι-CAs was catalytically active without a metal ion cofactor, unlike the previous reported ι-CAs as well as all known CAs investigated so far. This review reports recent investigations on ι-CAs obtained in these last three years, highlighting their peculiar features, and hypothesising that possibly this new CA family shows catalytic activity without the need of metal ions.


Assuntos
Burkholderia/enzimologia , Anidrases Carbônicas/metabolismo , Cianobactérias/enzimologia , Eucariotos/enzimologia , Biocatálise , Anidrases Carbônicas/genética
8.
BMC Res Notes ; 14(1): 306, 2021 Aug 09.
Artigo em Inglês | MEDLINE | ID: mdl-34372933

RESUMO

OBJECTIVES: Complex algae are photosynthetic organisms resulting from eukaryote-to-eukaryote endosymbiotic-like interactions. Yet the specific lineages and mechanisms are still under debate. That is why large scale phylogenomic studies are needed. Whereas available proteomes provide a limited diversity of complex algae, MMETSP (Marine Microbial Eukaryote Transcriptome Sequencing Project) transcriptomes represent a valuable resource for phylogenomic analyses, owing to their broad and rich taxonomic sampling, especially of photosynthetic species. Unfortunately, this sampling is unbalanced and sometimes highly redundant. Moreover, we observed contaminated sequences in some samples. In such a context, tree inference and readability are impaired. Consequently, the aim of the data processing reported here is to release a unique set of clean and non-redundant transcriptomes produced through an original protocol featuring decontamination, pooling and dereplication steps. DATA DESCRIPTION: We submitted 678 MMETSP re-assembly samples to our parallel consolidation pipeline. Hence, we combined 423 samples into 110 consolidated transcriptomes, after the systematic removal of the most contaminated samples (186). This approach resulted in a total of 224 high-quality transcriptomes, easy to use and suitable to compute less contaminated, less redundant and more balanced phylogenies.


Assuntos
Eucariotos , Transcriptoma , Descontaminação , Eucariotos/genética , Filogenia , Plantas , Transcriptoma/genética
9.
Water Res ; 203: 117566, 2021 Sep 15.
Artigo em Inglês | MEDLINE | ID: mdl-34438261

RESUMO

Wastewater is treated by concerted actions of the microbial communities within bioreactors. Although protists (unicellular eukaryotes) are good bioindicators and important players influencing denitrification, nitrification, and flocculation, they are the least known organisms in WWTPs. The few recent environmental surveys of the protistan diversity in WWTPs show that the most abundant protistan sequences in WWTPs belong to Thecofilosea (Rhizaria). We re-investigated previously published environmental sequencing data and gathered strains from seven WWTPs to determine which species dominate WWTPs worldwide. We found that all highly abundant thecofilosean sequences represent a single species - Rhogostoma minus. Considering that Thecofilosea are frequent hosts for Legionellales, i.e. bacteria linked to waterborne diseases, we confirm that Rhogostoma minus functions as a host for Legionellales in WWTPs. Whether the highly abundant Rhogostoma minus also serves as a host for known human pathogenic Legionellales requires further attention.


Assuntos
Cercozoários , Rhizaria , Bactérias , Cercozoários/genética , Eucariotos , Humanos , Águas Residuárias
10.
Environ Pollut ; 286: 117439, 2021 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-34438479

RESUMO

This study investigated the biogeography, the presence and diversity of potentially harmful taxa harbored, and potential interactions between and within bacterial and eukaryotic domains of life on plastic debris in the Mediterranean. Using a combination of high-throughput DNA sequencing (HTS), Causal Network Analysis, and Scanning Electron Microscopy (SEM), we show regional differences and gradients in the Mediterranean microbial communities associated with marine litter, positive causal effects between microbes including between and within domains of life, and how these might impact the marine ecosystems surrounding them. Adjacent seas within the Mediterranean region showed a gradient in the microbial communities on plastic with non-overlapping endpoints (Adriatic and Ligurian Seas). The largest predicted inter-domain effects included positive effects of a novel red-algal Plastisphere member on its potential microbiome community. Freshwater and marine samples housed a diversity of fungi including some related to disease-causing microbes. Algal species related to those responsible for Harmful Blooms (HABs) were also observed on plastic pieces including members of genera not previously reported on Plastic Marine Debris (PMD).


Assuntos
Microbiota , Plásticos , Bactérias , Eucariotos , Fungos
11.
Int J Mol Sci ; 22(15)2021 Jul 29.
Artigo em Inglês | MEDLINE | ID: mdl-34360907

RESUMO

The superfamily of P-loop channels includes various potassium channels, voltage-gated sodium and calcium channels, transient receptor potential channels, and ionotropic glutamate receptors. Despite huge structural and functional diversity of the channels, their pore-forming domain has a conserved folding. In the past two decades, scores of atomic-scale structures of P-loop channels with medically important drugs in the inner pore have been published. High structural diversity of these complexes complicates the comparative analysis of these structures. Here we 3D-aligned structures of drug-bound P-loop channels, compared their geometric characteristics, and analyzed the energetics of ligand-channel interactions. In the superimposed structures drugs occupy most of the sterically available space in the inner pore and subunit/repeat interfaces. Cationic groups of some drugs occupy vacant binding sites of permeant ions in the inner pore and selectivity-filter region. Various electroneutral drugs, lipids, and detergent molecules are seen in the interfaces between subunits/repeats. In many structures the drugs strongly interact with lipid and detergent molecules, but physiological relevance of such interactions is unclear. Some eukaryotic sodium and calcium channels have state-dependent or drug-induced π-bulges in the inner helices, which would be difficult to predict. The drug-induced π-bulges may represent a novel mechanism of gating modulation.


Assuntos
Domínio AAA , Canais de Cálcio/metabolismo , Microscopia Crioeletrônica/métodos , Preparações Farmacêuticas/metabolismo , Canais de Potássio/metabolismo , Receptores Ionotrópicos de Glutamato/metabolismo , Canais de Potencial de Receptor Transitório/metabolismo , Canais de Sódio Disparados por Voltagem/metabolismo , Sequência de Aminoácidos , Sítios de Ligação , Canais de Cálcio/química , Biologia Computacional/métodos , Eucariotos/metabolismo , Ligantes , Modelos Moleculares , Canais de Potássio/química , Conformação Proteica em alfa-Hélice , Receptores Ionotrópicos de Glutamato/química , Alinhamento de Sequência , Canais de Potencial de Receptor Transitório/química , Canais de Sódio Disparados por Voltagem/química
12.
Nat Commun ; 12(1): 4948, 2021 08 16.
Artigo em Inglês | MEDLINE | ID: mdl-34400630

RESUMO

Since the middle of the past century, the Western Antarctic Peninsula has warmed rapidly with a significant loss of sea ice but the impacts on plankton biodiversity and carbon cycling remain an open question. Here, using a 5-year dataset of eukaryotic plankton DNA metabarcoding, we assess changes in biodiversity and net community production in this region. Our results show that sea-ice extent is a dominant factor influencing eukaryotic plankton community composition, biodiversity, and net community production. Species richness and evenness decline with an increase in sea surface temperature (SST). In regions with low SST and shallow mixed layers, the community was dominated by a diverse assemblage of diatoms and dinoflagellates. Conversely, less diverse plankton assemblages were observed in waters with higher SST and/or deep mixed layers when sea ice extent was lower. A genetic programming machine-learning model explained up to 80% of the net community production variability at the Western Antarctic Peninsula. Among the biological explanatory variables, the sea-ice environment associated plankton assemblage is the best predictor of net community production. We conclude that eukaryotic plankton diversity and carbon cycling at the Western Antarctic Peninsula are strongly linked to sea-ice conditions.


Assuntos
Biodiversidade , Ciclo do Carbono , Camada de Gelo , Plâncton/fisiologia , Regiões Antárticas , Carbono/metabolismo , Diatomáceas , Ecossistema , Eucariotos , Microbiota , Plâncton/genética , Temperatura
13.
J Gen Virol ; 102(8)2021 08.
Artigo em Inglês | MEDLINE | ID: mdl-34356002

RESUMO

The family Marnaviridae comprises small non-enveloped viruses with positive-sense RNA genomes of 8.6-9.6 kb. Isolates infect marine single-celled eukaryotes (protists) that come from diverse lineages. Some members are known from metagenomic studies of ocean virioplankton, with additional unclassified viruses described from metagenomic datasets derived from marine and freshwater environments. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Marnaviridae, which is available at ictv.global/report/marnaviridae.


Assuntos
Genoma Viral , Filogenia , Vírus de RNA/classificação , Vírus de RNA/genética , Animais , Proteínas do Capsídeo , Eucariotos , Especificidade de Hospedeiro , Hidrobiologia , Metagenômica , Infecções por Vírus de RNA/virologia , Vírus de RNA/ultraestrutura , RNA Viral , Vírion/classificação , Vírion/genética , Vírion/ultraestrutura , Replicação Viral
14.
Development ; 148(15)2021 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-34338279

RESUMO

The conserved exocyst complex regulates plasma membrane-directed vesicle fusion in eukaryotes. However, its role in stem cell proliferation has not been reported. Germline stem cell (GSC) proliferation in the nematode Caenorhabditis elegans is regulated by conserved Notch signaling. Here, we reveal that the exocyst complex regulates C. elegans GSC proliferation by modulating Notch signaling cell autonomously. Notch membrane density is asymmetrically maintained on GSCs. Knockdown of exocyst complex subunits or of the exocyst-interacting GTPases Rab5 and Rab11 leads to Notch redistribution from the GSC-niche interface to the cytoplasm, suggesting defects in plasma membrane Notch deposition. The anterior polarity (aPar) protein Par6 is required for GSC proliferation, and for maintaining niche-facing membrane levels of Notch and the exocyst complex. The exocyst complex biochemically interacts with the aPar regulator Par5 (14-3-3ζ) and Notch in C. elegans and human cells. Exocyst components are required for Notch plasma membrane localization and signaling in mammalian cells. Our study uncovers a possibly conserved requirement of the exocyst complex in regulating GSC proliferation and in maintaining optimal membrane Notch levels.


Assuntos
Caenorhabditis elegans/metabolismo , Caenorhabditis elegans/fisiologia , Membrana Celular/metabolismo , Proliferação de Células/fisiologia , Células Germinativas/metabolismo , Células Germinativas/fisiologia , Nicho de Células-Tronco/fisiologia , Proteínas 14-3-3/metabolismo , Animais , Proteínas de Caenorhabditis elegans/metabolismo , Comunicação Celular/fisiologia , Membrana Celular/fisiologia , Citoplasma/metabolismo , Citoplasma/fisiologia , Eucariotos/metabolismo , Eucariotos/fisiologia , Fusão de Membrana/fisiologia , Morfogênese/fisiologia , Transdução de Sinais/fisiologia
16.
FEMS Microbiol Ecol ; 97(9)2021 08 17.
Artigo em Inglês | MEDLINE | ID: mdl-34338764

RESUMO

East African Great Lakes are old and unique natural resources heavily utilized by their bordering countries. In those lakes, ecosystem functioning is dominated by pelagic processes, where microorganisms are key components; however, protistan diversity is barely known. We investigated the community composition of small eukaryotes (<10 µm) in surface waters of four African Lakes (Kivu, Edward, Albert and Victoria) by sequencing the 18S rRNA gene. Moreover, in the meromictic Lake Kivu, two stations were vertically studied. We found high protistan diversity distributed in 779 operational taxonomic units (OTUs), spanning in 11 high-rank lineages, being Alveolata (31%), Opisthokonta (20%) and Stramenopiles (17%) the most represented supergroups. Surface protistan assemblages were associated with conductivity and productivity gradients, whereas depth had a strong effect on protistan community in Kivu, with higher contribution of heterotrophic organisms. Approximately 40% of OTUs had low similarity (<90%) with reported sequences in public databases; these were mostly coming from deep anoxic waters of Kivu, suggesting a high extent of novel diversity. We also detected several taxa so far considered exclusive of marine ecosystems. Our results unveiled a complex and largely undescribed protistan community, in which several lineages have adapted to different niches after crossing the salinity boundary.


Assuntos
Eucariotos , Estramenópilas , Biodiversidade , Ecossistema , Eucariotos/genética , Lagos , Filogenia , RNA Ribossômico 18S/genética , Estramenópilas/genética
17.
FEMS Microbiol Ecol ; 97(9)2021 09 06.
Artigo em Inglês | MEDLINE | ID: mdl-34427631

RESUMO

In the last decades, rewetting of drained peatlands is on the rise worldwide, to restore their significant carbon sink function. Despite the increasing understanding of peat microbiomes, little is known about the seasonal dynamics and network interactions of the microbial communities in these ecosystems, especially in rewetted fens (groundwater-fed peatlands). Here, we investigated the seasonal dynamics in both prokaryotic and eukaryotic microbiomes in three common fen types in Northern Germany. The eukaryotic microbiomes, including fungi, protists and microbial metazoa, showed significant changes in their community structures across the seasons in contrast to largely unaffected prokaryotic microbiomes. Furthermore, our results proved that the dynamics in eukaryotic microbiomes in the rewetted sites differed between fen types, specifically in terms of saprotrophs, arbuscular mycorrhiza and grazers of bacteria. The co-occurrence networks also exhibited strong seasonal dynamics that differed between rewetted and drained sites, and the correlations involving protists and prokaryotes were the major contributors to these dynamics. Our study provides the insight that microbial eukaryotes mainly define the seasonal dynamics of microbiomes in rewetted fen peatlands. Accordingly, future research should unravel the importance of eukaryotes for biogeochemical processes, especially the under-characterized protists and metazoa, in these poorly understood ecosystems.


Assuntos
Eucariotos , Microbiota , Sequestro de Carbono , Estações do Ano , Solo
18.
Nat Commun ; 12(1): 4109, 2021 07 05.
Artigo em Inglês | MEDLINE | ID: mdl-34226549

RESUMO

Expanding the genetic toolbox for prokaryotic synthetic biology is a promising strategy for enhancing the dynamic range of gene expression and enabling new engineered applications for research and biomedicine. Here, we reverse the current trend of moving genetic parts from prokaryotes to eukaryotes and demonstrate that the activating eukaryotic transcription factor QF and its corresponding DNA-binding sequence can be moved to E. coli to introduce transcriptional activation, in addition to tight off states. We further demonstrate that the QF transcription factor can be used in genetic devices that respond to low input levels with robust and sustained output signals. Collectively, we show that eukaryotic gene regulator elements are functional in prokaryotes and establish a versatile and broadly applicable approach for constructing genetic circuits with complex functions. These genetic tools hold the potential to improve biotechnology applications for medical science and research.


Assuntos
Eucariotos/genética , Regulação da Expressão Gênica , Expressão Gênica , Células Procarióticas , Fatores de Transcrição/genética , Proteínas de Ligação a DNA , Escherichia coli , Células Eucarióticas , Redes Reguladoras de Genes , Técnicas Genéticas , Regiões Promotoras Genéticas , Biologia Sintética , Transcrição Genética , Ativação Transcricional
19.
Artigo em Inglês | MEDLINE | ID: mdl-34196605

RESUMO

A new family, genus and species of centrohelid heliozoans, Clypifer cribrifer gen. nov., sp. nov. (Clypiferidae fam. nov.), from the Gulf of Aqaba (Israel) was studied with light and electron microscopy and SSU rRNA gene sequencing. Clypifer cribrifer has only one type of scales, partially running up the sides of the axopodia. Plate scales [0.8-2.3 (av. 1.5)×0.6-1.8 (av. 1.2) µm] are flat, elliptical or circular, fenestrated with holes of irregular shape and have a marginal rim and a very short axial rib. The cell diameter is 3.9-9.6 (av. 6.0) µm. Molecular phylogenetic analysis robustly places C. cribrifer in the C4 clade for which the new family Clypiferidae is proposed here. This position is confirmed with the short sequences in the panacanthocystid increased regions. The morphology of the new genus has similarities to the genus Raphidocystis. The probability that another Clypifer species was described under a different name in the centrohelid literature is discussed. Clypiferidae represent the second lineage of Pterocystida, which are characterized by the presence of only tangentially oriented plate scales of one type. Possible ways of evolution of the centrohelid siliceous coverings are also discussed.


Assuntos
Eucariotos/classificação , Eucariotos/citologia , Israel , RNA Ribossômico/genética , Análise de Sequência de DNA
20.
J Cell Sci ; 134(13)2021 07 01.
Artigo em Inglês | MEDLINE | ID: mdl-34228793

RESUMO

Autophagy is a degradative pathway for cytoplasmic constituents, and is conserved across eukaryotes. Autophagy-related (ATG) genes have undergone extensive multiplications and losses in different eukaryotic lineages, resulting in functional diversification and specialization. Notably, even though bacteria and archaea do not possess an autophagy pathway, they do harbor some remote homologs of Atg proteins, suggesting that preexisting proteins were recruited when the autophagy pathway developed during eukaryogenesis. In this Review, we summarize our current knowledge on the distribution of Atg proteins within eukaryotes and outline the major multiplication and loss events within the eukaryotic tree. We also discuss the potential prokaryotic homologs of Atg proteins identified to date, emphasizing the evolutionary relationships and functional differences between prokaryotic and eukaryotic proteins.


Assuntos
Eucariotos , Células Procarióticas , Archaea/genética , Autofagia/genética , Eucariotos/genética , Células Eucarióticas , Evolução Molecular , Filogenia
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