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1.
Trends Plant Sci ; 25(4): 317-319, 2020 04.
Artículo en Inglés | MEDLINE | ID: mdl-32191866

RESUMEN

Although it is known that novel genes facilitated plant colonization of land, the evolutionary origin of these genes remains largely unclear. A recent study by Cheng et al. suggests that some key genes related to plant development and stress responses were acquired from soil bacteria during the early evolution of land plants.


Asunto(s)
Embryophyta , Plantas , Bacterias , Evolución Biológica , Evolución Molecular , Filogenia
2.
Photochem Photobiol Sci ; 19(2): 274-280, 2020 Feb 19.
Artículo en Inglés | MEDLINE | ID: mdl-32002529

RESUMEN

In the present study, we aimed to purify and characterize LuxG obtained from Photobacterium leiognathi YL and examine its improvement for NADH detection. To this end, we cloned and expressed the putative luxG gene of P. leiognathi YL in the Escherichia coli BL21 strain. The product of luxG is a flavin reductase that consists of 206 amino acids, corresponding to a subunit molecular mass of ∼26 kDa. Phylogenetic analysis demonstrated that P. leiognathi YL LuxG has a rather distant evolutionary relationship with Frase I of Aliivibrio fischeri and Frp of Vibrio harveyi, but a close evolutionary relationship with Fre from Escherichia coli, which are all enzymes related to oxido-reductase. Further comparison shows that the changes in the functionally conserved sites may contribute to the functional divergence of LuxG and Fre. LuxG could supply reduced flavin mononucleotide (FMN) for bacterial luminescence by catalyzing the oxidation of nicotinamide adenine dinucleotide hydrogen (NADH). Based on this, a coupled pure enzyme bioluminescent system was established and used for NADH detection. The NADH samples with concentrations of 0.1-1 nM were used to validate the linear relationship, and it was found that the logarithmic deviations were less than 3%, which showed more sensitive and stable results than the NADH detection by recombinant E. coli including the exogenously expressed luciferase and intrinsic Fre. Investigation of P. leiognathi YL LuxG would provide a basic understanding of its evolution, and structural and functional properties, which might contribute to the development of a NADH detection kit in the future.


Asunto(s)
Proteínas Bacterianas/metabolismo , Mediciones Luminiscentes , NAD/análisis , Oxidorreductasas/metabolismo , Photobacterium/enzimología , Secuencia de Aminoácidos , Proteínas Bacterianas/clasificación , Proteínas Bacterianas/genética , Clonación Molecular , Escherichia coli/metabolismo , Evolución Molecular , Oxidorreductasas/clasificación , Oxidorreductasas/genética , Filogenia , Estructura Secundaria de Proteína , Proteínas Recombinantes/biosíntesis , Proteínas Recombinantes/química , Proteínas Recombinantes/aislamiento & purificación , Alineación de Secuencia
3.
Medicine (Baltimore) ; 99(7): e18777, 2020 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-32049783

RESUMEN

This study sought to determine the dominant circulating human immunodeficiency virus type 1 (HIV-1) subtype and associated drug resistance mutations in Ghana.This cross-sectional study was conducted with archived samples collected from patients who received care at 2 hospitals in Ghana from 2014 to 2016. Blood samples were earlier processed into plasma and peripheral blood mononuclear cells and stored at -80 °C. Ribonucleic acid (RNA) was extracted from the archived plasma. Two HIV-1 genes; protease and reverse transcriptase, were amplified, sequenced using gene-specific primers and analyzed for subtype and drug resistance mutations using the Stanford HIV Database.Of 16 patient samples successfully sequenced, we identified the predominance of HIV-1 subtype CRF02_AG (11/16, 68%). Subtypes G (2/16, 13%), dual CRF02_AG/G (2/16, 13%), and CRF01_AE (1/16, 6%) were also observed. Major nucleoside reverse transcriptase inhibitor (NRTI) resistance mutations, M184I/V, D67N, T215F, and K70R/E were found. Non-nucleoside reverse transcriptase inhibitor (NNRTI) resistance mutations, K103N, Y181C, V90I, F227L, and V106A were also prevalent. Additionally, and at a lower level, protease inhibitor (PI)-resistance mutations, M46I, I54 V, V82A, L90 M, and I471 V, were also present in the sequences from antiretroviral therapy (ART)-experienced individuals. Two NRTI-associated drug resistance mutations (DRMs) (D67N and T69N) were present in sequences from 1 ART-naive individual.HIV-1 subtype CRF02_AG was most frequently detected in this study thus confirming earlier reports of dominance of this subtype in the West-African sub-region and Ghana in particular. The detection of these drug resistance mutations in individuals on first-line regimen composed of NRTI and NNRTI is an indication of prolonged drug exposure without viral load monitoring. Routine viral load monitoring is necessary for early detection of virologic failure and drug resistance testing will inform appropriate choice of regimens for such patients.


Asunto(s)
Farmacorresistencia Viral , Infecciones por VIH/virología , VIH-1/clasificación , Mutación , Adulto , Fármacos Anti-VIH/uso terapéutico , Estudios Transversales , Evolución Molecular , Femenino , Ghana , Infecciones por VIH/tratamiento farmacológico , Proteasa del VIH/genética , Transcriptasa Inversa del VIH/genética , VIH-1/genética , VIH-1/fisiología , Humanos , Masculino , Persona de Mediana Edad , Inhibidores de la Transcriptasa Inversa/uso terapéutico , Carga Viral
4.
Syst Appl Microbiol ; 43(2): 126065, 2020 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-32057584

RESUMEN

To date, the phylum Bacteroidetes comprises more than 1,500 described species with diverse ecological roles. However, there is little understanding of archetypal Bacteroidetes traits at a genomic level. In this study, a representative set of 89 Bacteroidetes genomes was compiled, and pairwise reciprocal best-match gene comparisons and gene syntenies were used to identify common traits that allowed Bacteroidetes evolution and adaptive radiation to be traced. The type IX secretion system (T9SS) was highly conserved among all studied Bacteroidetes. Class-level comparisons furthermore suggested that the ACIII-caa3COX super-complex evolved in the ancestral aerobic bacteroidetal lineage, and was secondarily lost in extant anaerobic Bacteroidetes. Another Bacteroidetes-specific respiratory chain adaptation was the sodium-pumping Nqr complex I that replaced the ancestral proton-pumping complex I in marine species. T9SS plays a role in gliding motility and the acquisition of complex macro-molecular organic compounds, and the ACIII-caa3COX super-complex allows effective control of electron flux during respiration. This combination likely provided ancestral Bacteroidetes with a decisive competitive advantage to effectively scavenge, uptake and degrade complex organic molecules, and therefore has played a pivotal role in the successful adaptive radiation of the phylum.


Asunto(s)
Adaptación Fisiológica/genética , Bacteroidetes/genética , Evolución Molecular , Genoma Bacteriano/genética , Proteínas Bacterianas/genética , Sistemas de Secreción Bacterianos/genética , Bacteroidetes/clasificación , Bacteroidetes/fisiología , Transporte de Electrón/genética , Locomoción/genética , Filogenia
5.
Cell Host Microbe ; 27(3): 428-440.e9, 2020 03 11.
Artículo en Inglés | MEDLINE | ID: mdl-32075743

RESUMEN

Alphaviruses are emerging, mosquito-transmitted RNA viruses with poorly understood cellular tropism and species selectivity. Mxra8 is a receptor for multiple alphaviruses including chikungunya virus (CHIKV). We discovered that while expression of mouse, rat, chimpanzee, dog, horse, goat, sheep, and human Mxra8 enables alphavirus infection in cell culture, cattle Mxra8 does not. Cattle Mxra8 encodes a 15-amino acid insertion in its ectodomain that prevents Mxra8 binding to CHIKV. Identical insertions are present in zebu, yak, and the extinct auroch. As other Bovinae lineages contain related Mxra8 sequences, this insertion likely occurred at least 5 million years ago. Removing the Mxra8 insertion in Bovinae enhances alphavirus binding and infection, while introducing the insertion into mouse Mxra8 blocks CHIKV binding, prevents infection by multiple alphaviruses in cells, and mitigates CHIKV-induced pathogenesis in mice. Our studies on how this insertion provides resistance to CHIKV infection could facilitate countermeasures that disrupt Mxra8 interactions with alphaviruses.


Asunto(s)
Fiebre Chikungunya/genética , Virus Chikungunya , Proteínas de la Membrana/genética , Receptores Virales/genética , Secuencia de Aminoácidos , Animales , Sitios de Unión , Bovinos/genética , Resistencia a la Enfermedad , Evolución Molecular , Femenino , Técnicas de Sustitución del Gen , Células HEK293 , Humanos , Inmunoglobulinas/genética , Proteínas de la Membrana/química , Ratones , Ratones Endogámicos C57BL , Simulación del Acoplamiento Molecular , Células 3T3 NIH , Dominios Proteicos , Receptores Virales/química , Células Vero
6.
Biol Lett ; 16(1): 20190702, 2020 01.
Artículo en Inglés | MEDLINE | ID: mdl-31910734

RESUMEN

Bacterial endosymbionts evolve under strong host-driven selection. Factors influencing host evolution might affect symbionts in similar ways, potentially leading to correlations between the molecular evolutionary rates of hosts and symbionts. Although there is evidence of rate correlations between mitochondrial and nuclear genes, similar investigations of hosts and symbionts are lacking. Here, we demonstrate a correlation in molecular rates between the genomes of an endosymbiont (Blattabacterium cuenoti) and the mitochondrial genomes of their hosts (cockroaches). We used partial genome data for multiple strains of B. cuenoti to compare phylogenetic relationships and evolutionary rates for 55 cockroach/symbiont pairs. The phylogenies inferred for B. cuenoti and the mitochondrial genomes of their hosts were largely congruent, as expected from their identical maternal and cytoplasmic mode of inheritance. We found a correlation between evolutionary rates of the two genomes, based on comparisons of root-to-tip distances and on comparisons of the branch lengths of phylogenetically independent species pairs. Our results underscore the profound effects that long-term symbiosis can have on the biology of each symbiotic partner.


Asunto(s)
Cucarachas , Genoma Mitocondrial , Animales , Evolución Molecular , Genoma Bacteriano , Filogenia , Simbiosis
7.
Gene ; 735: 144397, 2020 Apr 20.
Artículo en Inglés | MEDLINE | ID: mdl-31991161

RESUMEN

Bacteria and archaea accumulate cytoplasmic polyhydroxyalkanoate (PHA) granules under nutrient-limited conditions with excess carbon. The transcriptional regulatory (TR) proteins found on the surface of PHA granules act as repressors as well as activators for the expression of major surface proteins called phasins. Until now, detailed information on the evolutionary relationships between these transcription regulators has not been available. Here, we conducted homology searches and analyzed information available for the domains and protein families of the TR proteins through phylogenetic studies. A total of 282 TR proteins were identified and further classified into four distinct subfamilies based upon the presence of conserved motifs: PHB_acc, TetR-like, AbrB-like, and PadR-like. Depending upon the particular family, the DNA-binding domains were located at either the N- or C-terminus. Our results indicated that TR proteins containing the PHB_acc domain are highly conserved within the bacteria, while other TR proteins are present only within archaea (AbrB-like), gram positive bacteria (PadR-like), or the Pseudomonas genera (TetR-like). The repression domains are charged, hydrophobic, and rich in leucine or glutamine. In phylogenetic analyses, many groups of TR proteins were clustered together according to identical domain architectures showing the independent origins of the TR proteins in the PHA reserve storage system. Further analyses revealed that the TR proteins have experienced multiple gene duplications across prokaryotes. Thus, this study investigated the evolutionary framework of TR proteins and has provided a comprehensive catalog of TR proteins for ongoing studies to characterize the functions of these proteins within diverse organisms.


Asunto(s)
Proteínas Arqueales/genética , Proteínas Bacterianas/genética , Secuencia Conservada , Evolución Molecular , Lectinas de Plantas/genética , Polihidroxialcanoatos/biosíntesis , Factores de Transcripción/genética , Proteínas Arqueales/química , Proteínas Arqueales/metabolismo , Proteínas Bacterianas/química , Proteínas Bacterianas/metabolismo , Filogenia , Lectinas de Plantas/metabolismo , Polihidroxialcanoatos/genética , Factores de Transcripción/química , Factores de Transcripción/metabolismo
8.
Genome Biol ; 21(1): 5, 2020 01 07.
Artículo en Inglés | MEDLINE | ID: mdl-31910870

RESUMEN

BACKGROUND: CTCF binding contributes to the establishment of a higher-order genome structure by demarcating the boundaries of large-scale topologically associating domains (TADs). However, despite the importance and conservation of TADs, the role of CTCF binding in their evolution and stability remains elusive. RESULTS: We carry out an experimental and computational study that exploits the natural genetic variation across five closely related species to assess how CTCF binding patterns stably fixed by evolution in each species contribute to the establishment and evolutionary dynamics of TAD boundaries. We perform CTCF ChIP-seq in multiple mouse species to create genome-wide binding profiles and associate them with TAD boundaries. Our analyses reveal that CTCF binding is maintained at TAD boundaries by a balance of selective constraints and dynamic evolutionary processes. Regardless of their conservation across species, CTCF binding sites at TAD boundaries are subject to stronger sequence and functional constraints compared to other CTCF sites. TAD boundaries frequently harbor dynamically evolving clusters containing both evolutionarily old and young CTCF sites as a result of the repeated acquisition of new species-specific sites close to conserved ones. The overwhelming majority of clustered CTCF sites colocalize with cohesin and are significantly closer to gene transcription start sites than nonclustered CTCF sites, suggesting that CTCF clusters particularly contribute to cohesin stabilization and transcriptional regulation. CONCLUSIONS: Dynamic conservation of CTCF site clusters is an apparently important feature of CTCF binding evolution that is critical to the functional stability of a higher-order chromatin structure.


Asunto(s)
Factor de Unión a CCCTC/genética , Factor de Unión a CCCTC/metabolismo , Cromatina/metabolismo , Evolución Molecular , Ratones/genética , Animales , Genoma
9.
Gene ; 732: 144355, 2020 Mar 30.
Artículo en Inglés | MEDLINE | ID: mdl-31935501

RESUMEN

Curcuma is an important member of Zingiberaceae. Many species of this genus are widely used in traditional medicine and have important cultural value in East Asia. Among them, C. longa is considered to be the main source of curcumin and has a very wide range of uses. The rapid development of molecular phylogeny has deepened our understanding of taxonomy and evolution of Curcuma. However, little is known about the chloroplast genome phylogeny and the genetic bases of adaptative evolution. In this work, we sequenced the complete chloroplast genome of 4 Curcuma species. Curcuma chloroplast genomes showed highly conserved structures and the length ranged from 159,423 bp to 152,723 bp. A total of 133 genes were observed. Multiple repeats and simple sequence repeats (SSRs) were detected. By comparing with related species, 7 highly variable regions were identified as potential specific DNA barcodes for species identification. Phylogenetic analysis of complete plastome sequences and specific data sets revealed discordance with expected genus boundary. Chloroplast phylogenetic relationships were better predicted by geography than by morphological and nuclear DNA, indicating a substantial existence of introgression. 9 genes were proved to have high posteriori probability in positive selection analysis, and 4 of them (psbA, psbD, PetA and rbcL) closely related to photosynthesis, implying that chloroplast genes may had undergone positive selection pressure in evolution. These results are of great significance for us to understand the genetic basis, phylogeny and adaptive evolution of Curcuma chloroplast.


Asunto(s)
Curcuma/clasificación , Genoma del Cloroplasto , Secuenciación Completa del Genoma/métodos , Cloroplastos/genética , Curcuma/citología , Curcuma/genética , Evolución Molecular , Tamaño del Genoma , Repeticiones de Microsatélite , Filogenia
10.
Gene ; 732: 144350, 2020 Mar 30.
Artículo en Inglés | MEDLINE | ID: mdl-31935505

RESUMEN

THO complex is a multisubunit family with a function in transcription and mRNA export. In the present study, transcripts of THO complex (thoc) were identified in developing ovary of common carp and their role during ovarian development and growth has been characterized for the first time in a teleost using expression profiling and transient siRNA silencing. Thoc expression revealed a spatiotemporal pattern in the gonads with high levels at 120 days post-hatch, with moderately high levels thereafter. In situ hybridization and immunohistochemical localization revealed the presence of thoc3 in follicular layer of stage-III/IV oocytes. High levels of thoc3, thoc5, and thoc7 genes in the follicular layer suggest a possible role in ovarian growth. Reduced levels of serum estradiol-17ß and 17α, 20ß-dihydroxypregn-4-en-3-one after thoc3 transient silencing indicated differential action on steroidogenic enzyme, transcription factor, and growth factor genes. Furthermore, transient silencing of thoc3, in vivo and in vitro, downregulated ad4bp/sf1, amh, cyp19a1a, foxl2, hsd3b, hsd11b1, hsd20b, hsd17b1, rspo1, and vtg. Incidentally, gdf9 and igf1 were upregulated, while no change was seen in esr1/2, nanos, and vasa. These observations imply that thoc3 seems to regulate ovarian function including steroidogenesis, either directly or indirectly.


Asunto(s)
Carpas/genética , Perfilación de la Expresión Génica/veterinaria , Proteínas Nucleares/genética , Proteínas Nucleares/metabolismo , Ovario/crecimiento & desarrollo , Animales , Núcleo Celular/genética , Estradiol/metabolismo , Evolución Molecular , Femenino , Proteínas de Peces/genética , Proteínas de Peces/metabolismo , Regulación del Desarrollo de la Expresión Génica , Folículo Ovárico , Ovario/química , ARN Interferente Pequeño/farmacología , Diferenciación Sexual
11.
World J Microbiol Biotechnol ; 36(1): 12, 2020 Jan 02.
Artículo en Inglés | MEDLINE | ID: mdl-31897767

RESUMEN

Superoxide dismutases (SODs) have been shown to exhibit high levels of conservation and exist in almost all aerobic organisms and even many strict anaerobes. There are four SODs in Bacillus cereus 0-9, and this coexistence of multiple homologous enzymes is of great significance in the evolution of bacteria. We hypothesized that the four sod genes in B. cereus 0-9 constituted non-redundant protection against oxidative damage in vivo and played unique roles in the pathogenicity of B. cereus 0-9 during different phases or growth environments. To test this hypothesis, we constructed four single-knockout mutants (∆sodA1, ∆sodA2, ∆sodS, and ∆sodC) and a mutant lacking all four sod genes (∆sod-4) of B. cereus 0-9 and assessed their various phenotypes. Our results indicated that sodA1 plays a major role in tolerance to intracellular oxidative stress and spore formation. The ∆sodA1 and ∆sod-4 mutants were very sensitive to oxidants. The spore formation of the ∆sodA1 mutant was dramatically delayed, and the ∆sod-4 mutant did not form any spores under our experimental conditions. The sodA2 gene may play an important role in negative regulation of swarming motility, pathogenicity, and phospholipase and haemolytic activity of B. cereus but also a role in positive regulation of biofilm formation under our experimental conditions. The other two genes, sodS and sodC, were key to the pathogenicity of B. cereus. The lethal rates of Helicoverpa armigera infected by the ∆sodS and ∆sodC mutants were only 26.67%, while wild-type B. cereus 0-9 caused lethality in up to 86.67% of the insects at 24 h after injection. Moreover, the ∆sod-4 mutant caused a reduced death rate of H. armigera of 46.70%, which was slightly higher than that caused by the ∆sodS and ∆sodC strains. Thus, these four sod genes were non-redundant for oxidative stress and may play different additional roles in B. cereus 0-9. These results can help us to further understand the biocontrol characteristics of B. cereus 0-9 and lay a theoretical foundation for further research.


Asunto(s)
Bacillus cereus/crecimiento & desarrollo , Lepidópteros/microbiología , Superóxido Dismutasa/genética , Animales , Bacillus cereus/enzimología , Bacillus cereus/genética , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Evolución Molecular , Técnicas de Inactivación de Genes , Familia de Multigenes , Estrés Oxidativo , Fenotipo , Superóxido Dismutasa/metabolismo
12.
Genes Dev ; 34(1-2): 7-23, 2020 01 01.
Artículo en Inglés | MEDLINE | ID: mdl-31896689

RESUMEN

53BP1 is an enigmatic DNA damage response factor that gained prominence because it determines the efficacy of PARP1 inhibitory drugs (PARPi) in BRCA1-deficient cancers. Recent studies have elevated 53BP1 from its modest status of (yet another) DNA damage factor to master regulator of double-strand break (DSB) repair pathway choice. Our review of the literature suggests an alternative view. We propose that 53BP1 has evolved to avoid mutagenic repair outcomes and does so by controlling the processing of DNA ends and the dynamics of DSBs. The consequences of 53BP1 deficiency, such as diminished PARPi efficacy in BRCA1-deficient cells and altered repair of damaged telomeres, can be explained from this viewpoint. We further propose that some of the fidelity functions of 53BP1 coevolved with class switch recombination (CSR) in the immune system. We speculate that, rather than being deterministic in DSB repair pathway choice, 53BP1 functions as a DSB escort that guards against illegitimate and potentially tumorigenic recombination.


Asunto(s)
Roturas del ADN de Doble Cadena , Reparación del ADN/genética , Proteína 1 de Unión al Supresor Tumoral P53/metabolismo , Evolución Molecular , Humanos , Cambio de Clase de Inmunoglobulina/genética , Telómero/genética , Proteína 1 de Unión al Supresor Tumoral P53/deficiencia , Proteína 1 de Unión al Supresor Tumoral P53/genética
13.
Plant Mol Biol ; 102(6): 659-676, 2020 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-31997112

RESUMEN

KEY MESSAGE: Seven divergence hotspots as plastid markers for DNA barcoding was selected, and the phylogeny of 13 Lagerstroemia species based on the cp genome data was reconstructed within Myrtales. The Lagerstroemia species used in this study originated in China and have high economic and ecological value. The shared interspecific morphological characteristics and intraspecific morphological variation resulting from hybridization among Lagerstroemia taxa have made resolving their classification problems and phylogenetic relationships difficult. Systematic comparative genomic analysis has been shown to resolve phylogenetic relationships. We sequenced and annotated 6 Lagerstroemia cp genomes (Lagerstroemia excelsa, Lagerstroemia limii, Lagerstroemia siamica, Lagerstroemia tomentosa, Lagerstroemia venusta, and Lagerstroemia calyculata) for the first time and combined them with previously published genomes for Lagerstroemia species. Bioinformatics was used to analyse the 13 cp genomes in terms of gene structure and organization, codon usage, contraction and expansion of inverted repeat regions, repeat structure, divergence hotspots, species pairwise Ka/Ks ratios and phylogenetic relationships. The length varied between 152,049 bp in Lagerstroemia subcostata and 152,521 bp in L. venusta. We selected seven divergence hotspots in the cp genomes that had the potential to act as plastid markers to distinguish Lagerstroemia species. The phylogenetic relationships within Myrtales inferred from the cp genomes of 13 Lagerstroemia species and 27 other Myrtales species were highly supported, which illustrated several novel relationships within Myrtales. Taken together, our results provide comprehensive chloroplast genomic resources, which can be used further for species identification and molecular breeding of Lagerstroemia species.


Asunto(s)
Cloroplastos/genética , Genoma del Cloroplasto/genética , Lagerstroemia/clasificación , Lagerstroemia/genética , Filogenia , Secuencia de Bases , Bases de Datos de Ácidos Nucleicos , Evolución Molecular , Anotación de Secuencia Molecular , Proteínas de Plantas/genética , Plastidios , Análisis de Secuencia de ADN
14.
Viruses ; 12(2)2020 Jan 24.
Artículo en Inglés | MEDLINE | ID: mdl-31991671

RESUMEN

Widespread vaccination programmes led to the global eradication of smallpox, which was certified by the World Health Organisation (WHO), and, since 1978, there has been no case of smallpox anywhere in the world. However, the viable variola virus (VARV), the causative agent of smallpox, is still kept in two maximum security laboratories in Russia and the USA. Despite the eradication of the disease smallpox, clandestine stocks of VARV may exist. In a rapidly changing world, the impact of an intentional VARV release in the human population would nowadays result in a public health emergency of global concern: vaccination programmes were abolished, the percentage of immunosuppressed individuals in the human population is higher, and an increased intercontinental air travel allows for the rapid viral spread of diseases around the world. The WHO has authorised the temporary retention of VARV to enable essential research for public health benefit to take place. This work aims to develop diagnostic tests, antiviral drugs, and safer vaccines. Advances in synthetic biology have made it possible to produce infectious poxvirus particles from chemicals in vitro so that it is now possible to reconstruct VARV. The status of smallpox in the post-eradication era is reviewed.


Asunto(s)
Erradicación de la Enfermedad , Vacuna contra Viruela , Viruela/prevención & control , Antivirales/uso terapéutico , Derrame de Material Biológico , Evolución Molecular , Genoma Viral , Humanos , Programas de Inmunización , Riesgo , Viruela/diagnóstico , Viruela/tratamiento farmacológico , Viruela/virología , Vacuna contra Viruela/efectos adversos , Vacuna contra Viruela/inmunología , Vacuna contra Viruela/provisión & distribución , Biología Sintética , Virus de la Viruela/genética , Organización Mundial de la Salud
15.
J Med Virol ; 92(4): 433-440, 2020 04.
Artículo en Inglés | MEDLINE | ID: mdl-31967321

RESUMEN

The current outbreak of viral pneumonia in the city of Wuhan, China, was caused by a novel coronavirus designated 2019-nCoV by the World Health Organization, as determined by sequencing the viral RNA genome. Many initial patients were exposed to wildlife animals at the Huanan seafood wholesale market, where poultry, snake, bats, and other farm animals were also sold. To investigate possible virus reservoir, we have carried out comprehensive sequence analysis and comparison in conjunction with relative synonymous codon usage (RSCU) bias among different animal species based on the 2019-nCoV sequence. Results obtained from our analyses suggest that the 2019-nCoV may appear to be a recombinant virus between the bat coronavirus and an origin-unknown coronavirus. The recombination may occurred within the viral spike glycoprotein, which recognizes a cell surface receptor. Additionally, our findings suggest that 2019-nCoV has most similar genetic information with bat coronovirus and most similar codon usage bias with snake. Taken together, our results suggest that homologous recombination may occur and contribute to the 2019-nCoV cross-species transmission.


Asunto(s)
Betacoronavirus/genética , Quirópteros/virología , Infecciones por Coronavirus/transmisión , Infecciones por Coronavirus/virología , Reservorios de Enfermedades , Neumonía Viral/transmisión , Neumonía Viral/virología , Serpientes/virología , Glicoproteína de la Espiga del Coronavirus/genética , Animales , Betacoronavirus/clasificación , Betacoronavirus/fisiología , Bungarus/genética , Bungarus/virología , Quirópteros/genética , Infecciones por Coronavirus/epidemiología , Brotes de Enfermedades , Evolución Molecular , Genoma Viral , Recombinación Homóloga , Especificidad del Huésped , Humanos , Naja naja/genética , Naja naja/virología , Filogenia , Neumonía Viral/epidemiología , Serpientes/genética , Zoonosis
16.
Nat Commun ; 11(1): 6, 2020 01 03.
Artículo en Inglés | MEDLINE | ID: mdl-31900419

RESUMEN

Uncovering whether convergent adaptations share a genetic basis is consequential for understanding the evolution of phenotypic diversity. This information can help us understand the extent to which shared ancestry or independent evolution shape adaptive phenotypes. In this study, we first ask whether the same genes underlie polymorphic mimicry in Papilio swallowtail butterflies. By comparing signatures of genetic variation between polymorphic and monomorphic species, we then investigate how ancestral variation, hybridization, and independent evolution contributed to wing pattern diversity in this group. We report that a single gene, doublesex (dsx), controls mimicry across multiple taxa, but with species-specific patterns of genetic differentiation and linkage disequilibrium. In contrast to widespread examples of phenotypic evolution driven by introgression, our analyses reveal distinct mimicry alleles. We conclude that mimicry evolution in this group was likely facilitated by ancestral polymorphism resulting from early co-option of dsx as a mimicry locus, and that evolutionary turnover of dsx alleles may underlie the wing pattern diversity of extant polymorphic and monomorphic lineages.


Asunto(s)
Mariposas Diurnas/genética , Proteínas de Unión al ADN/genética , Proteínas de Insectos/genética , Animales , Mimetismo Biológico , Mariposas Diurnas/clasificación , Mariposas Diurnas/metabolismo , Proteínas de Unión al ADN/metabolismo , Evolución Molecular , Femenino , Proteínas de Insectos/metabolismo , Masculino , Fenotipo , Filogenia , Especificidad de la Especie
17.
Gene ; 731: 144340, 2020 Mar 20.
Artículo en Inglés | MEDLINE | ID: mdl-31923575

RESUMEN

As a member of the large Brassicaceae family, yellow mustard (Sinapis alba L.) has been used as an important gene pool for the genetic improvement of cash crops in Brassicaceae. Understanding the phylogenetic relationship between Sinapis alba (S. alba) and other Brassicaceae crops can provide guidance on the introgression of its favorable alleles into related species. The chloroplast (cp) genome is an ideal model for assessing genome evolution and the phylogenetic relationships of complex angiosperm families. Herein, we de novo assembled the complete cp genome of S. alba by integrating the PacBio and Illumina sequencing platforms. A 153,760 bp quadripartite cycle without any gap was obtained, including a pair of inverted repeats (IRa and IRb) of 26,221 bp, separated by a large single copy (LSC) region of 83,506 bp and a small single copy (SSC) region of 17,821 bp. A total of 78 protein-coding genes, 30 tRNA genes, and four rRNA genes were identified in this cp genome, as were 89 simple sequence repeat (SSR) loci of 18 types. The codon usage analysis revealed a preferential use of the Leu codon with the A/U ending. The phylogenetic analysis using 82 Brassicaceae species demonstrated that S. alba had a close relationship with important Brassica and Raphanus species; moreover, it likely originated from a separate evolutionary pathway compared with the congeneric Sinapis arvensis. The synonymous (Ks) and non-synonymous (Ks) substitution rate analysis showed that genes encoding "Subunits of cytochrome b/f complex" were under the lowest purifying selection pressure, whereas those associated with "Maturase", "Subunit of acetyl-CoA", and "Subunits of NADH-dehydrogenase" underwent relatively higher purifying selection pressures. Our results provide valuable information for fully utilizing the S. alba cp genome as a potential genetic resource for the genetic improvement of Brassica and Raphanus species.


Asunto(s)
Brassicaceae/clasificación , Brassicaceae/genética , Genoma del Cloroplasto/genética , Planta de la Mostaza/genética , Sinapis/genética , Cloroplastos/genética , Evolución Molecular , Secuenciación de Nucleótidos de Alto Rendimiento , Planta de la Mostaza/clasificación , Planta de la Mostaza/citología , Filogenia , Raphanus/clasificación , Raphanus/citología , Raphanus/genética , Análisis de Secuencia de ADN/métodos , Sinapis/clasificación , Sinapis/citología , Secuenciación Completa del Genoma
18.
Gene ; 733: 144387, 2020 Apr 05.
Artículo en Inglés | MEDLINE | ID: mdl-31972308

RESUMEN

The forkhead box (Fox) gene family is a family of transcription factors that play important roles in a variety of biological processes in vertebrates, including early development and cell proliferation and differentiation. However, at present, studies on the mollusk Fox family are relatively lacking. In the present study, the Fox gene family of the Yesso scallop (Patinopecten yessoensis) was systematically identified. In addition, the expression profiles of the Fox gene family in early development and adult tissues were analyzed. The results showed that there were 26 Fox genes in P. yessoensis. Of the 26 genes, 24 belonged to 20 subfamilies. The Fox genes belonging to the I, Q1, R and S subfamilies were absent in P. yessoensis. The other 2 genes formed 2 independent clades with the Fox genes of other mollusks and protostomes. They might be new members of the Fox family and were named FoxY and FoxZ. P. yessoensis contained a FoxC-FoxL1 gene cluster similar in structure to that of Branchiostoma floridae, suggesting that the cluster might already exist in the ancestors of bilaterally symmetrical animals. The gene expression analysis of Fox showed that most of the genes were continuously expressed in multiple stages of early development, suggesting that Fox genes might be widely involved in the regulation of embryo and larval development of P. yessoensis. Nine Fox genes were specifically expressed in certain tissues, such as the nerve ganglia, foot, ovary, testis, and gills. For the 9 genes that were differentially expressed between the testis and ovary, their expression levels were analyzed during the 4 developmental stages of gonads. The results showed that FoxL2, FoxE and FoxY were highly expressed in the ovary during all developmental stages, while FoxZ was highly expressed in the testis during all developmental stages. The results suggested that these genes might play an important role in sex maintenance or gametogenesis. The present study could provide a reference for evolutionary and functional studies of the Fox family in metazoans.


Asunto(s)
Factores de Transcripción Forkhead/genética , Factores de Transcripción Forkhead/metabolismo , Regulación del Desarrollo de la Expresión Génica , Pectinidae/genética , Transcriptoma , Secuencia de Aminoácidos , Animales , Evolución Molecular , Perfilación de la Expresión Génica , Pectinidae/crecimiento & desarrollo , Filogenia , Homología de Secuencia
19.
Gene ; 727: 144231, 2020 Feb 15.
Artículo en Inglés | MEDLINE | ID: mdl-31707000

RESUMEN

Autophagy is the cellular process of removal of misfolded or damaged macromolecules and organelles. Experimental studies have demonstrated autophagy as a major mechanism of lifespan extension in long-lived mammals such as bats and mole rat rodents. Moreover, the role of this biological process has been well documented in protection against age-associated diseases and viral infection. However, studies on the molecular adaptive changes of autophagy factors during evolution are scarce. Here, we conducted a bioinformatics study of the molecular evolution of the Lysosomal Associated Membrane Protein 2 (LAMP2), as a rate-limiting factor in the lysosomal degradation stage of autophagy (the communal step of two of autophagy types: macroautophagy and chaperone-mediated). Analyzing LAMP2 across placental mammals, our phylogenetic-based maximum likelihood analyses indicate that the majority of the coding sites undergo purifying selection. However, around 27% of sites display a relaxation of purifying constraints (average ω = 0.42128), among which, 14 particular sites undergo positive selection (ω > 1). These sites are mostly located in the first luminal domain of LAMP2 (N-domain), with a hotspot region in the 135-144 codons interval. Therefore, the N-domain may account for the functional diversity and regulation of LAMP2. In addition, the identified positive selection sites could act as key regulatory sites in the LAMP2 function. On the other hand, testing the rate of evolution in LAMP2 along different clades of placental mammals revealed a relatively relaxed evolution in LAMP2 along megabats' clade. It is not clear yet whether an expedited evolution of LAMP2 in megabats has contributed to their reported up-regulation of autophagy. Finally, our data indicate positive selection sites along the ancestral branch of the clades of rodents, mouse-related rodents, and mole-rats; and suggest the potentially important regulatory role of these sites in LAMP2. Identifying the residues under positive selection, our findings pave the way for future experimental investigations to define how these selective substitutions have functionally affected autophagy.


Asunto(s)
Euterios/genética , Proteína 2 de la Membrana Asociada a los Lisosomas/genética , Proteína 2 de la Membrana Asociada a los Lisosomas/metabolismo , Adaptación Biológica/genética , Animales , Autofagia/genética , Secuencia Conservada/genética , Euterios/metabolismo , Evolución Molecular , Humanos , Mamíferos/genética , Mamíferos/metabolismo , Tasa de Mutación , Filogenia , Análisis de Secuencia de ADN/métodos
20.
Arch Virol ; 165(1): 185-192, 2020 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-31637514

RESUMEN

Cucumber mosaic virus (CMV) is a geographically widespread plant virus with a very broad host range. The virus has been detected in diverse crops all over Iran. In this study, we estimated the timescale of the evolution of CMV subgroup I and the geographical movement of the virus with a focus on Iranian strains. Analyses using the MP and CP genes and their concatenation revealed that the CMV population within subgroup I had a single ancestor dating back to about 450-550 years ago. The Iranian strains formed three clusters in a maximum-clade-credibility phylogenetic tree. It was found that the most recent common ancestor of the Iranian strains within each cluster dates back to less than 100 years ago. Our results also suggest that both short- and long-distance migration of Iranian CMV strains has occurred in the last 100 years.


Asunto(s)
Cucumovirus/clasificación , Análisis de Secuencia de ARN/métodos , Proteínas de la Cápside/genética , Cucumovirus/genética , Evolución Molecular , Irán , Filogenia , Proteínas Virales/genética
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