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1.
Gene ; 764: 145094, 2021 Jan 05.
Artigo em Inglês | MEDLINE | ID: mdl-32860898

RESUMO

Long chain acyl-CoA synthetases (ACSLs), which drive the conversion of long chain fatty acid into acyl-CoA, an ingredient of lipid synthesis, have been well-acknowledged to exert an indispensable role in many metabolic processes in mammals, especially lipid metabolism. However, in chicken, the evolutionary characteristics, expression profiles and regulatory mechanisms of ACSL gene family are rarely understood. Here, we analyzed the genomic synteny, gene structure, evolutionary event and functional domains of the ACSL gene family members using bioinformatics methods. The spatiotemporal expression profiles of ACSL gene family, and their regulatory mechanism were investigated via bioinformatics analysis incorporated with in vivo and in vitro estrogen-treated experiments. Our results indicated that ACSL2 gene was indeed evolutionarily lost in the genome of chicken. Chicken ACSLs shared an AMP-binding functional domain, as well as highly conversed ATP/AMP and FACS signature motifs, and were clustered into two clades, ACSL1/5/6 and ACSL3/4, based on high sequence similarity, similar gene features and conversed motifs. Chicken ACSLs showed differential tissue expression distributions, wherein the significantly decreased expression level of ACSL1 and the significantly increased expression level of ACSL5 were found, respectively, the expression levels of the other ACSL members remained unchanged in the liver of peak-laying hens versus pre-laying hens. Moreover, the transcription activity of ACSL1, ACSL3 and ACSL4 was silenced and ACSL6 was activated by estrogen, but no response to ACSL5. In conclusion, though having highly conversed functional domains, chicken ACSL gene family is organized into two separate groups, ACSL1/5/6 and ACSL3/4, and exhibits varying expression profiles and estrogen effects. These results not only pave the way for better understanding the specific functions of ACSL genes in avian lipid metabolism, but also provide a valuable evidence for gene family characteristics.


Assuntos
Galinhas/genética , Coenzima A Ligases/genética , Evolução Molecular , Metabolismo dos Lipídeos/genética , Família Multigênica/genética , Acil Coenzima A/metabolismo , Animais , Células Cultivadas , Embrião de Galinha , Galinhas/crescimento & desenvolvimento , Galinhas/metabolismo , Coenzima A Ligases/metabolismo , Biologia Computacional , Estrogênios/metabolismo , Ácidos Graxos/metabolismo , Feminino , Perfilação da Expressão Gênica , Regulação da Expressão Gênica no Desenvolvimento , Hepatócitos , Cultura Primária de Células , Domínios Proteicos/genética , Análise Espaço-Temporal , Sintenia
2.
Gene ; 766: 145156, 2021 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-32949696

RESUMO

Plant Glycogen Synthase Kinase 3 (GSK3)/SHAGGY-like kinase (GSK) proteins play important roles in modulating growth, development, and stress responses in several plant species. However, little is known about the members of the potato GSK (StGSK) family. Here, nine StGSK genes were identified and phylogenetically grouped into four clades. Gene duplication analysis revealed that segmental duplication contributed to the expansion of the StGSK family. Gene structure and motif pattern analyses indicated that similar exon/intron and motif organizations were found in StGSKs from the same clade. Conserved motif and kinase activity analyses indicated that the StGSKs encode active protein kinases, and they were shown to be distributed throughout whole cells. Cis-acting regulatory element analysis revealed the presence of many growth-, hormone-, and stress-responsive elements within the promoter regions of the StGSKs, which is consistent with their expression in different organs, and their altered expression in response to hormone and stress treatments. Association network analysis indicated that various proteins, including two confirmed BES1 family transcription factors, potentially interact with StGSKs. Overexpression of StSK21 provides enhanced sensitivity to salt stress in Arabidopsis thaliana plants. Overall, these results reveal that StGSK proteins are active protein kinases with purported functions in regulating growth, development, and stress responses.


Assuntos
Regulação da Expressão Gênica de Plantas/genética , Genes de Plantas/genética , Família Multigênica/genética , Proteínas de Plantas/genética , Estresse Salino/genética , Solanum tuberosum/genética , Estresse Fisiológico/genética , Arabidopsis/genética , Cromossomos de Plantas/genética , Duplicação Gênica/genética , Perfilação da Expressão Gênica/métodos , Estudo de Associação Genômica Ampla/métodos , Filogenia , Reguladores de Crescimento de Planta/genética , Fatores de Transcrição/genética
3.
DNA Cell Biol ; 39(11): 1976-1989, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-33001712

RESUMO

The Dof transcription factor is a plant-specific transcriptional regulator that plays important roles in plant development and acts as a mediator in plant external stress responses. However, Dofs have previously been identified in several plants but not in alfalfa (Medicago sativa L.), one of the most widely cultivated forage legumes. In the present study, a total of 40 MsDof genes were identified, and the phylogenetic reconstruction, classification, conserved motifs, and expression patterns under abscisic acid (ABA), cold, heat, drought and salt stresses of these Dof genes were comprehensively analyzed. The Dof genes family in alfalfa could be classified into eight classes. Gene ontology (GO) and tissue-specific analysis indicated that most MsDof genes may be involved in biological functions during plant growth. Moreover, the expression profiles and quantitative real-time PCR analysis indicated that eight candidate abiotic tolerance genes were induced in response to four abiotic stresses. This study identified the possibility of abiotic tolerance candidate genes playing various roles in stress resistance at the whole genome level, which would provide new information on the Dof family in alfalfa.


Assuntos
Medicago sativa/genética , Filogenia , Estresse Fisiológico/genética , Fatores de Transcrição/genética , Ácido Abscísico/efeitos adversos , Temperatura Baixa/efeitos adversos , Secas , Regulação da Expressão Gênica de Plantas/genética , Genoma de Planta/genética , Resposta ao Choque Térmico/genética , Medicago sativa/crescimento & desenvolvimento , Família Multigênica/genética , Sais/efeitos adversos , Fatores de Transcrição/classificação
4.
Med Sci (Paris) ; 36 Hors série n° 1: 61-66, 2020 Oct.
Artigo em Francês | MEDLINE | ID: mdl-33052097

RESUMO

Most prevalent cancers are of epithelial origin and their morbidity often results from secondary tumors. Cancer aggressiveness relates to intratumoral heterogeneity, including rare tumor initiating cells that share many features with adult stem cells. Both normal and cancer stem cells are characterized by their plasticity between epithelial and mesenchymal phenotypes, progressing through a series of reversible intermediates. While a core of regulators (Snail, Zeb1-2,...) is renowned to promote epithelial to mesenchyme transition (EMT), OvoL/Shavenbaby factors now emerge as a family of key epithelial stabilizers. Therefore, pro-EMT and OvoL/Shavenbaby transcription factors could provide a molecular rheostat to control stemness and epithelial-mesenchyme plasticity. We address this question in flies, in which the unique OvoL/Shavenbaby factor offers a powerful in vivo paradigm for functional analyses. Our results show that Shavenbaby is critical for adult stem cell homeostasis, and directly interacts with the Hippo pathway to protect stem cells from death.


Assuntos
Células-Tronco Adultas/fisiologia , Proteínas de Ligação a DNA/fisiologia , Transição Epitelial-Mesenquimal/genética , Células-Tronco Neoplásicas/fisiologia , Fatores de Transcrição/fisiologia , Células-Tronco Adultas/metabolismo , Animais , Plasticidade Celular/genética , Proteínas de Ligação a DNA/genética , Drosophila/genética , Proteínas de Drosophila/genética , Proteínas de Drosophila/fisiologia , Humanos , Família Multigênica/genética , Neoplasias/genética , Neoplasias/patologia , Células-Tronco Neoplásicas/metabolismo , Fatores de Transcrição/genética
5.
PLoS Biol ; 18(9): e3000783, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32925907

RESUMO

Plant nucleotide-binding (NB) leucine-rich repeat (LRR) receptor (NLR) proteins function as intracellular immune receptors that perceive the presence of pathogen-derived virulence proteins (effectors) to induce immune responses. The 2 major types of plant NLRs that "sense" pathogen effectors differ in their N-terminal domains: these are Toll/interleukin-1 receptor resistance (TIR) domain-containing NLRs (TNLs) and coiled-coil (CC) domain-containing NLRs (CNLs). In many angiosperms, the RESISTANCE TO POWDERY MILDEW 8 (RPW8)-CC domain containing NLR (RNL) subclass of CNLs is encoded by 2 gene families, ACTIVATED DISEASE RESISTANCE 1 (ADR1) and N REQUIREMENT GENE 1 (NRG1), that act as "helper" NLRs during multiple sensor NLR-mediated immune responses. Despite their important role in sensor NLR-mediated immunity, knowledge of the specific, redundant, and synergistic functions of helper RNLs is limited. We demonstrate that the ADR1 and NRG1 families act in an unequally redundant manner in basal resistance, effector-triggered immunity (ETI) and regulation of defense gene expression. We define RNL redundancy in ETI conferred by some TNLs and in basal resistance against virulent pathogens. We demonstrate that, in Arabidopsis thaliana, the 2 RNL families contribute specific functions in ETI initiated by specific CNLs and TNLs. Time-resolved whole genome expression profiling revealed that RNLs and "classical" CNLs trigger similar transcriptome changes, suggesting that RNLs act like other CNLs to mediate ETI downstream of sensor NLR activation. Together, our genetic data confirm that RNLs contribute to basal resistance, are fully required for TNL signaling, and can also support defense activation during CNL-mediated ETI.


Assuntos
Arabidopsis/imunologia , Proteínas NLR/fisiologia , Imunidade Vegetal/genética , Receptores Imunológicos/fisiologia , Arabidopsis/genética , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/fisiologia , Resistência à Doença/genética , Resistência à Doença/imunologia , Regulação da Expressão Gênica de Plantas , Peptídeos e Proteínas de Sinalização Intracelular/genética , Peptídeos e Proteínas de Sinalização Intracelular/fisiologia , Família Multigênica/genética , Família Multigênica/fisiologia , Proteínas NLR/genética , Doenças das Plantas/genética , Doenças das Plantas/imunologia , Plantas Geneticamente Modificadas , Receptores Imunológicos/genética , Transdução de Sinais/genética , Transdução de Sinais/imunologia , Transcriptoma
6.
PLoS One ; 15(9): e0239054, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32925967

RESUMO

The type I polyketide SF2487/A80577 (herein referred to as tetromadurin) is a polyether tetronate ionophore antibiotic produced by the terrestrial Gram-positive bacterium Actinomadura verrucosospora. Tetromadurin is closely related to the polyether tetronates tetronasin (M139603) and tetronomycin, all of which are characterised by containing a tetronate, cyclohexane, tetrahydropyran, and at least one tetrahydrofuran ring. We have sequenced the genome of Actinomadura verrucosospora to identify the biosynthetic gene cluster responsible for tetromadurin biosynthesis (the mad gene cluster). Based on bioinformatic analysis of the 32 genes present within the cluster a plausible biosynthetic pathway for tetromadurin biosynthesis is proposed. Functional confirmation of the mad gene cluster is obtained by performing in-frame deletions in each of the genes mad10 and mad31, which encode putative cyclase enzymes responsible for cyclohexane and tetrahydropyran formation, respectively. Furthermore, the A. verrucosospora Δmad10 mutant produces a novel tetromadurin metabolite that according to mass spectrometry analysis is analogous to the recently characterised partially cyclised tetronasin intermediate lacking its cyclohexane and tetrahydropyran rings. Our results therefore elucidate the biosynthetic machinery of tetromadurin biosynthesis and lend support for a conserved mechanism of cyclohexane and tetrahydropyran biosynthesis across polyether tetronates.


Assuntos
Macrolídeos/química , Policetídeo Sintases/genética , Policetídeos/metabolismo , Actinobacteria/enzimologia , Actinobacteria/metabolismo , Sequência de Aminoácidos/genética , Antibacterianos/química , Sequência de Bases/genética , Vias Biossintéticas , Clonagem Molecular , Éteres/metabolismo , Furanos/metabolismo , Família Multigênica/genética , Alinhamento de Sequência
7.
Nucleic Acids Res ; 48(18): 10297-10312, 2020 10 09.
Artigo em Inglês | MEDLINE | ID: mdl-32941623

RESUMO

Beyond their key role in translation, cytosolic transfer RNAs (tRNAs) are involved in a wide range of other biological processes. Nuclear tRNA genes (tDNAs) are transcribed by the RNA polymerase III (RNAP III) and cis-elements, trans-factors as well as genomic features are known to influence their expression. In Arabidopsis, besides a predominant population of dispersed tDNAs spread along the 5 chromosomes, some clustered tDNAs have been identified. Here, we demonstrate that these tDNA clusters are transcriptionally silent and that pathways involved in the maintenance of DNA methylation play a predominant role in their repression. Moreover, we show that clustered tDNAs exhibit repressive chromatin features whilst their dispersed counterparts contain permissive euchromatic marks. This work demonstrates that both genomic and epigenomic contexts are key players in the regulation of tDNAs transcription. The conservation of most of these regulatory processes suggests that this pioneering work in Arabidopsis can provide new insights into the regulation of RNA Pol III transcription in other organisms, including vertebrates.


Assuntos
Epigênese Genética/genética , RNA Polimerase III/genética , RNA de Transferência/genética , Transcrição Genética , Arabidopsis/genética , Núcleo Celular/genética , Cromatina/genética , Inativação Gênica , Família Multigênica/genética
8.
Nat Commun ; 11(1): 4022, 2020 08 11.
Artigo em Inglês | MEDLINE | ID: mdl-32782248

RESUMO

One major bottleneck in natural product drug development is derivatization, which is pivotal for fine tuning lead compounds. A promising solution is modifying the biosynthetic machineries of middle molecules such as macrolides. Although intense studies have established various methodologies for protein engineering of type I modular polyketide synthase(s) (PKSs), the accurate targeting of desired regions in the PKS gene is still challenging due to the high sequence similarity between its modules. Here, we report an innovative technique that adapts in vitro Cas9 reaction and Gibson assembly to edit a target region of the type I modular PKS gene. Proof-of-concept experiments using rapamycin PKS as a template show that heterologous expression of edited biosynthetic gene clusters produced almost all the desired derivatives. Our results are consistent with the promiscuity of modular PKS and thus, our technique will provide a platform to generate rationally designed natural product derivatives for future drug development.


Assuntos
Sistemas CRISPR-Cas , Edição de Genes/métodos , Policetídeo Sintases/genética , Produtos Biológicos/química , Produtos Biológicos/metabolismo , Estrutura Molecular , Família Multigênica/genética , Policetídeo Sintases/metabolismo , Sirolimo/química , Sirolimo/metabolismo , Estereoisomerismo , Streptomyces/enzimologia , Streptomyces/genética , Streptomyces/metabolismo
9.
Proc Natl Acad Sci U S A ; 117(34): 20836-20847, 2020 08 25.
Artigo em Inglês | MEDLINE | ID: mdl-32769205

RESUMO

The type VII protein secretion system (T7SS) is conserved across Staphylococcus aureus strains and plays important roles in virulence and interbacterial competition. To date, only one T7SS substrate protein, encoded in a subset of S. aureus genomes, has been functionally characterized. Here, using an unbiased proteomic approach, we identify TspA as a further T7SS substrate. TspA is encoded distantly from the T7SS gene cluster and is found across all S. aureus strains as well as in Listeria and Enterococci. Heterologous expression of TspA from S. aureus strain RN6390 indicates its C-terminal domain is toxic when targeted to the Escherichia coli periplasm and that it depolarizes the cytoplasmic membrane. The membrane-depolarizing activity is alleviated by coproduction of the membrane-bound TsaI immunity protein, which is encoded adjacent to tspA on the S. aureus chromosome. Using a zebrafish hindbrain ventricle infection model, we demonstrate that the T7SS of strain RN6390 promotes bacterial replication in vivo, and deletion of tspA leads to increased bacterial clearance. The toxin domain of TspA is highly polymorphic and S. aureus strains encode multiple tsaI homologs at the tspA locus, suggestive of additional roles in intraspecies competition. In agreement, we demonstrate TspA-dependent growth inhibition of RN6390 by strain COL in the zebrafish infection model that is alleviated by the presence of TsaI homologs.


Assuntos
Staphylococcus aureus/metabolismo , Sistemas de Secreção Tipo VII/metabolismo , Animais , Antígenos de Bactérias/metabolismo , Proteínas de Bactérias/metabolismo , Membrana Celular/metabolismo , Regulação Bacteriana da Expressão Gênica/genética , Proteínas de Membrana/metabolismo , Família Multigênica/genética , Transporte Proteico/genética , Proteômica , Infecções Estafilocócicas/microbiologia , Toxinas Biológicas/metabolismo , Sistemas de Secreção Tipo VII/fisiologia , Virulência/genética , Peixe-Zebra/microbiologia
10.
Arch Microbiol ; 202(10): 2711-2726, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-32728830

RESUMO

In recent years, bioremediation is considered as an efficient method to remove the pollutants from the industrial wastewater. In this study, quantitative gene expressions (Real-time RT-PCR) of mtr gene cluster (mtrA, mtrB, mtrC, mtrD, mtrE, mtrF and omcA) in five different uranium concentrations (0.1, 0.25, 0.5, 1 and 2 mM) were performed with ICP and microscopic live cell counting analysis under anaerobic condition, by Shewanella RCRI7 as a native bacterium. The results indicated that the amount of uranium removal and live-cell counting were decreased in the higher uranium concentrations (1 and 2 mM), due to the uranium toxicity, suggesting 0.5 mM as the optimum uranium concentration for Shewanella RCRI7 resistance. The expression of mtrCED and omcA genes presented increasing trend in the lower uranium concentrations (0.1, 0.25 and 0.5 mM) and a decreasing trend in 1 and 2 mM, while mtrABF, presented an inverse pattern, proving the alternative role of mtrF for mtrC and omcA, as the substantial multiheme cytochromes in Extracellular Electron Transfer (EET) pathway. These data are a proof of these gene vital roles in the EET pathway, proposing them for genetic engineering toward EET optimization, as the certain pathway in heavy metal bioremediation process.


Assuntos
Biodegradação Ambiental , Proteínas de Membrana Transportadoras/genética , Shewanella/genética , Shewanella/metabolismo , Urânio/análise , Poluentes Químicos da Água/análise , Proteínas da Membrana Bacteriana Externa/genética , Grupo dos Citocromos c/genética , Transporte de Elétrons/genética , Família Multigênica/genética , Oxirredução , Águas Residuárias/química , Poluição da Água/análise
11.
Arch Microbiol ; 202(10): 2841-2847, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-32681430

RESUMO

Planococcus halotolerans, recently described as a novel species with SCU63T as the type strain, is capable of thriving in up to 15% NaCl and temperatures as low as 0 °C. To better understand its adaptation strategies at the genomic level, strain SCU63T was subjected to whole-genome sequencing and data mining. The high-quality assembly yielded 17 scaffolds with a genome size of 3,622,698 bp. Its genome harbors 3683 protein-coding sequences and 127 RNA genes, as well as three biosynthetic gene clusters and 25 genomic islands. The phylogenomic tree provided compelling insights into the evolutionary relationships of Planococcus. Comparative genomic analysis revealed key similarities and differences in the functional gene categories among Planococcus species. Strain SCU63T was shown to have diverse stress response systems for high salt and cold habitats. Further comparison with three related species showed the presence of numerous unique gene clusters in the SCU63T genome. The strain might serve as a good model for using extremozymes in various biotechnological processes.


Assuntos
Aclimatação/genética , Planococáceas/genética , Planococcus (Bactéria)/genética , Tolerância ao Sal/genética , Temperatura Baixa , Genômica , Família Multigênica/genética , Filogenia , Planococáceas/metabolismo , Planococcus (Bactéria)/metabolismo , Tolerância ao Sal/fisiologia , Análise de Sequência de DNA , Sequenciamento Completo do Genoma
12.
PLoS One ; 15(7): e0236454, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32702710

RESUMO

Flax (Linum usitatissimum) is a member of family linaceae with annual growth habit. It is included among those crops which were domesticated very early and has been used in development related studies as a model plant. In plants, Calmodulin-binding transcription activators (CAMTAs) comprise a unique set of Calmodulin-binding proteins. To elucidate the transport mechanism of secondary metabolites in flax, a genome-based study on these transporters was performed. The current investigation identified nine CAMTAs proteins, classified into three categories during phylogenetic analysis. Each group had significant evolutionary role as illustrated by the conservation of gene structures, protein domains and motif organizations over the distinctive phylogenetic classes. GO annotation suggested a link to sequence-specific DNA and protein binding, response to low temperature and transcription regulation by RNA polymerase II. The existence of different hormonal and stress responsive cis-regulatory elements in promotor region may directly correlate with the variation of their transcripts. MicroRNA target analysis revealed that various groups of miRNA families targeted the LuCAMTAs genes. Identification of CAMTA genes, miRNA studies and phylogenetic analysis may open avenues to uncover the underlying functional mechanism of this important family of genes in flax.


Assuntos
Proteínas de Ligação a Calmodulina/genética , Evolução Molecular , Linho/genética , Família Multigênica/genética , Proteínas de Ligação a Calmodulina/classificação , Genoma de Planta/genética , Filogenia , Ligação Proteica
13.
PLoS Genet ; 16(7): e1008964, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32716939

RESUMO

Chromatin regulation of eukaryotic genomes depends on the formation of nucleosome complexes between histone proteins and DNA. Histone variants, which are diversified by sequence or expression pattern, can profoundly alter chromatin properties. While variants in histone H2A and H3 families are well characterized, the extent of diversification of histone H2B proteins is less understood. Here, we report a systematic analysis of the histone H2B family in plants, which have undergone substantial divergence during the evolution of each major group in the plant kingdom. By characterising Arabidopsis H2Bs, we substantiate this diversification and reveal potential functional specialization that parallels the phylogenetic structure of emergent clades in eudicots. In addition, we identify a new class of highly divergent H2B variants, H2B.S, that specifically accumulate during chromatin compaction of dry seed embryos in multiple species of flowering plants. Our findings thus identify unsuspected diverse properties among histone H2B proteins in plants that has manifested into potentially novel groups of histone variants.


Assuntos
Arabidopsis/genética , Cromatina/genética , Evolução Molecular , Histonas/genética , Arabidopsis/classificação , Eucariotos , Genoma de Planta/genética , Histonas/classificação , Família Multigênica/genética
14.
Sheng Wu Gong Cheng Xue Bao ; 36(6): 1138-1149, 2020 Jun 25.
Artigo em Chinês | MEDLINE | ID: mdl-32597063

RESUMO

Pyrroloquinoline quinone (PQQ), an important redox enzyme cofactor, has many physiological and biochemical functions, and is widely used in food, medicine, health and agriculture industry. In this study, PQQ production by recombinant Gluconobacter oxydans was investigated. First, to reduce the by-product of acetic acid, the recombinant strain G. oxydans T1 was constructed, in which the pyruvate decarboxylase (GOX1081) was knocked out. Then the pqqABCDE gene cluster and tldD gene were fused under the control of endogenous constitutive promoter P0169, to generate the recombinant strain G. oxydans T2. Finally, the medium composition and fermentation conditions were optimized. The biomass of G. oxydans T1 and G. oxydans T2 were increased by 43.02% and 38.76% respectively, and the PQQ production was 4.82 and 20.5 times higher than that of the wild strain, respectively. Furthermore, the carbon sources and culture conditions of G. oxydans T2 were optimized, resulting in a final PQQ yield of (51.32±0.899 7 mg/L), 345.6 times higher than that of the wild strain. In all, the biomass of G. oxydans and the yield of PQQ can be effectively increased by genetic engineering.


Assuntos
Gluconobacter oxydans , Microbiologia Industrial , Cofator PQQ , Fermentação , Técnicas de Inativação de Genes , Gluconobacter oxydans/genética , Gluconobacter oxydans/metabolismo , Microbiologia Industrial/métodos , Família Multigênica/genética , Organismos Geneticamente Modificados , Cofator PQQ/biossíntese , Cofator PQQ/genética , Regiões Promotoras Genéticas/genética
15.
Immunogenetics ; 72(5): 325-332, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32488290

RESUMO

Described here is a new, more efficient method for defining major histocompatibility complex-Y (MHC-Y) genotypes in chickens. The MHC-Y region is genetically independent from the classical MHC (MHC-B) region. MHC-Y is highly polymorphic and potentially important in the genetics of disease resistance. MHC-Y haplotypes contain variable numbers of specialized MHC class I-like genes, along with members of four additional gene families. Previously, MHC-Y haplotypes were defined by patterns of restriction fragments (RF) generated in labor-intensive procedures that were difficult to use to define MHC-Y genotypes for large numbers of samples. The method reported here is much simpler. MHC-Y genotypes are distinguished via patterns of PCR products generated from heritable short tandem repeat (STR) regions found immediately upstream of the MHC class I-like genes located throughout MHC-Y haplotypes. To validate the method, fully pedigreed families were analyzed for STR-defined haplotypes in light of haplotypes defined previously by RF patterns. STR-defined MHC-Y patterns segregate in fully pedigreed families as expected and correspond with haplotypes assigned by RF patterns. The patterns provided in STR chromatograms generated by capillary electrophoresis are distinct for different haplotypes and can be scored easily. Investigations into the influence of MHC-Y genetics on immune responses can now realistically be conducted with large sample sets.


Assuntos
Galinhas/genética , Complexo Principal de Histocompatibilidade/genética , Repetições de Microssatélites/genética , Animais , Genótipo , Haplótipos , Família Multigênica/genética , Reação em Cadeia da Polimerase/veterinária , Reprodutibilidade dos Testes , Fatores de Tempo
16.
Nat Commun ; 11(1): 2322, 2020 05 08.
Artigo em Inglês | MEDLINE | ID: mdl-32385269

RESUMO

The evolutionary history of horseshoe crabs, spanning approximately 500 million years, is characterized by remarkable morphological stasis and a low species diversity with only four extant species. Here we report a chromosome-level genome assembly for the mangrove horseshoe crab (Carcinoscorpius rotundicauda) using PacBio reads and Hi-C data. The assembly spans 1.67 Gb with contig N50 of 7.8 Mb and 98% of the genome assigned to 16 chromosomes. The genome contains five Hox clusters with 34 Hox genes, the highest number reported in any invertebrate. Detailed analysis of the genome provides evidence that suggests three rounds of whole-genome duplication (WGD), raising questions about the relationship between WGD and species radiation. Several gene families, particularly those involved in innate immunity, have undergone extensive tandem duplication. These expanded gene families may be important components of the innate immune system of horseshoe crabs, whose amebocyte lysate is a sensitive agent for detecting endotoxin contamination.


Assuntos
Genoma/genética , Caranguejos Ferradura/genética , Animais , Evolução Molecular , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Família Multigênica/genética , Filogenia
17.
Nat Commun ; 11(1): 2150, 2020 05 01.
Artigo em Inglês | MEDLINE | ID: mdl-32358519

RESUMO

Somatic cell nuclear transfer (SCNT) in mammals is an inefficient process that is frequently associated with abnormal phenotypes, especially in placentas. Recent studies demonstrated that mouse SCNT placentas completely lack histone methylation (H3K27me3)-dependent imprinting, but how it affects placental development remains unclear. Here, we provide evidence that the loss of H3K27me3 imprinting is responsible for abnormal placental enlargement and low birth rates following SCNT, through upregulation of imprinted miRNAs. When we restore the normal paternal expression of H3K27me3-dependent imprinted genes (Sfmbt2, Gab1, and Slc38a4) in SCNT placentas by maternal knockout, the placentas remain enlarged. Intriguingly, correcting the expression of clustered miRNAs within the Sfmbt2 gene ameliorates the placental phenotype. Importantly, their target genes, which are confirmed to cause SCNT-like placental histology, recover their expression level. The birth rates increase about twofold. Thus, we identify loss of H3K27me3 imprinting as an epigenetic error that compromises embryo development following SCNT.


Assuntos
Histonas/metabolismo , MicroRNAs/genética , Placenta/metabolismo , Proteínas Repressoras/genética , Animais , Reprogramação Celular/genética , Reprogramação Celular/fisiologia , Feminino , Impressão Genômica , Camundongos , Família Multigênica/genética , Gravidez , RNA não Traduzido/genética , RNA não Traduzido/metabolismo
18.
PLoS One ; 15(5): e0227396, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32469865

RESUMO

Elsinoë fawcettii, a necrotrophic fungal pathogen, causes citrus scab on numerous citrus varieties around the world. Known pathotypes of E. fawcettii are based on host range; additionally, cryptic pathotypes have been reported and more novel pathotypes are thought to exist. E. fawcettii produces elsinochrome, a non-host selective toxin which contributes to virulence. However, the mechanisms involved in potential pathogen-host interactions occurring prior to the production of elsinochrome are unknown, yet the host-specificity observed among pathotypes suggests a reliance upon such mechanisms. In this study we have generated a whole genome sequencing project for E. fawcettii, producing an annotated draft assembly 26.01 Mb in size, with 10,080 predicted gene models and low (0.37%) coverage of transposable elements. A small proportion of the assembly showed evidence of AT-rich regions, potentially indicating genomic regions with increased plasticity. Using a variety of computational tools, we mined the E. fawcettii genome for potential virulence genes as candidates for future investigation. A total of 1,280 secreted proteins and 276 candidate effectors were predicted and compared to those of other necrotrophic (Botrytis cinerea, Parastagonospora nodorum, Pyrenophora tritici-repentis, Sclerotinia sclerotiorum and Zymoseptoria tritici), hemibiotrophic (Leptosphaeria maculans, Magnaporthe oryzae, Rhynchosporium commune and Verticillium dahliae) and biotrophic (Ustilago maydis) plant pathogens. Genomic and proteomic features of known fungal effectors were analysed and used to guide the prioritisation of 120 candidate effectors of E. fawcettii. Additionally, 378 carbohydrate-active enzymes were predicted and analysed for likely secretion and sequence similarity with known virulence genes. Furthermore, secondary metabolite prediction indicated nine additional genes potentially involved in the elsinochrome biosynthesis gene cluster than previously described. A further 21 secondary metabolite clusters were predicted, some with similarity to known toxin producing gene clusters. The candidate virulence genes predicted in this study provide a comprehensive resource for future experimental investigation into the pathogenesis of E. fawcettii.


Assuntos
Ascomicetos/genética , Citrus/microbiologia , Genoma Fúngico/genética , Anotação de Sequência Molecular , Ascomicetos/patogenicidade , Parede Celular/enzimologia , Mineração de Dados , Família Multigênica/genética , Metabolismo Secundário/genética
19.
Tumour Biol ; 42(5): 1010428320918050, 2020 May.
Artigo em Inglês | MEDLINE | ID: mdl-32456563

RESUMO

Homeobox genes function as master regulatory transcription factors during development, and their expression is often altered in cancer. The HOX gene family was initially studied intensively to understand how the expression of each gene was involved in forming axial patterns and shaping the body plan during embryogenesis. More recent investigations have discovered that HOX genes can also play an important role in cancer. The literature has shown that the expression of HOX genes may be increased or decreased in different tumors and that these alterations may differ depending on the specific HOX gene involved and the type of cancer being investigated. New studies are also emerging, showing the critical role of some members of the HOX gene family in tumor progression and variation in clinical response. However, there has been limited systematic evaluation of the various contributions of each member of the HOX gene family in the pathways that drive the common phenotypic changes (or "hallmarks") and that underlie the transformation of normal cells to cancer cells. In this review, we investigate the context of the engagement of HOX gene targets and their downstream pathways in the acquisition of competence of tumor cells to undergo malignant transformation and tumor progression. We also summarize published findings on the involvement of HOX genes in carcinogenesis and use bioinformatics methods to examine how their downstream targets and pathways are involved in each hallmark of the cancer phenotype.


Assuntos
Biomarcadores Tumorais/genética , Carcinogênese/genética , Genes Homeobox/genética , Neoplasias/genética , Regulação Neoplásica da Expressão Gênica/genética , Humanos , Família Multigênica/genética , Fatores de Transcrição/genética
20.
PLoS One ; 15(4): e0232244, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32353000

RESUMO

BACKGROUND: Microorganisms living in saline environments are forced to regulate turgor via the synthesis of organic osmoprotective compounds. Microbial adaptation to fluctuations in external salinity includes degradation of compatible solutes. Here we have examined the biochemical pathway of degradation of the cyclic imino acid ectoine, the major osmoprotector in halotolerant methane-utilizing bacteria. METHODS: The BLAST search of the genes involved in ectoine degradation in the halotolerant methanotroph Methylotuvimicrobium alcaliphilum 20Z was performed with the reference sequences of Halomonas elongata. The genes for the key enzymes of the pathway were disrupted by insertion mutagenesis and the cellular metabolites in the methanol extracts of mutant cells were analyzed by HPLC. The doeA gene from Mm. alcaliphilum 20Z was heterologously expressed in Escherichia coli to identify the product of ectoine hydrolysis catalyzed by ectoine hydrolase DoeA. RESULTS: We have shown that the halotolerant methanotroph Mm. alcaliphilum 20Z possesses the doeBDAC gene cluster coding for putative ectoine hydrolase (DoeA), Nα-acetyl-L-2,4-diaminobutyrate deacetylase (DoeB), diaminobutyrate transaminase (DoeD) and aspartate-semialdehyde dehydrogenase (DoeC). The deletion of the doeA gene resulted in accumulation of the higher level of ectoine compared to the wild type strain. Nγ-acetyl-L-2,4-diaminobutyrate (Nγ-acetyl-DAB), a substrate for ectoine synthase, was found in the cytoplasm of the wild type strain. Nα-acetyl-L-2,4-diaminobutyrate (Nα-acetyl-DAB), a substrate for the DoeB enzyme, appeared in the cells as a result of exposure of the doeB mutant to low osmotic pressure. The genes for the enzymes involved in ectoine degradation were found in all aerobic methylotrophs capable of ectoine biosynthesis. These results provide the first evidence for the in vivo operation of the ectoine degradation pathway in methanotrophs and thus expand our understanding of the regulation mechanisms of bacterial osmoadaptation. CONCLUSIONS: During adaptation to the changes in external osmolarity, halophilic and halotolerant methylotrophs cleave ectoine, thereby entering the carbon and nitrogen of the compatible solute to the central metabolic pathways. The biochemical route of ectoine degradation in the halotolerant methanotroph Mm. alcaliphilum 20Z is similar to that in heterotrophic halophiles. We have shown that ectoine hydrolase DoeA in this methanotroph hydrolyzes ectoine with the formation of the only isomer: Nα-acetyl-DAB. All aerobic methylotrophs capable of ectoine biosynthesis harbor the genetic determinants for ectoine degradation.


Assuntos
Diamino Aminoácidos/metabolismo , Redes e Vias Metabólicas/fisiologia , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Escherichia coli/genética , Escherichia coli/metabolismo , Regulação Bacteriana da Expressão Gênica/genética , Genes Bacterianos/genética , Halomonas/genética , Halomonas/metabolismo , Redes e Vias Metabólicas/genética , Methylococcaceae/genética , Methylococcaceae/metabolismo , Família Multigênica/genética , Pressão Osmótica/fisiologia , Salinidade
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