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1.
Genes Dev ; 36(3-4): 225-240, 2022 02 01.
Artigo em Inglês | MEDLINE | ID: mdl-35144965

RESUMO

The BEN domain is a recently recognized DNA binding module that is present in diverse metazoans and certain viruses. Several BEN domain factors are known as transcriptional repressors, but, overall, relatively little is known of how BEN factors identify their targets in humans. In particular, X-ray structures of BEN domain:DNA complexes are only known for Drosophila factors bearing a single BEN domain, which lack direct vertebrate orthologs. Here, we characterize several mammalian BEN domain (BD) factors, including from two NACC family BTB-BEN proteins and from BEND3, which has four BDs. In vitro selection data revealed sequence-specific binding activities of isolated BEN domains from all of these factors. We conducted detailed functional, genomic, and structural studies of BEND3. We show that BD4 is a major determinant for in vivo association and repression of endogenous BEND3 targets. We obtained a high-resolution structure of BEND3-BD4 bound to its preferred binding site, which reveals how BEND3 identifies cognate DNA targets and shows differences with one of its non-DNA-binding BEN domains (BD1). Finally, comparison with our previous invertebrate BEN structures, along with additional structural predictions using AlphaFold2 and RoseTTAFold, reveal distinct strategies for target DNA recognition by different types of BEN domain proteins. Together, these studies expand the DNA recognition activities of BEN factors and provide structural insights into sequence-specific DNA binding by mammalian BEN proteins.


Assuntos
Proteínas Repressoras , Fatores de Transcrição , Animais , Sítios de Ligação , Drosophila/metabolismo , Mamíferos , Ligação Proteica , Domínios Proteicos , Proteínas Repressoras/genética , Fatores de Transcrição/metabolismo
2.
Cell ; 158(6): 1431-1443, 2014 Sep 11.
Artigo em Inglês | MEDLINE | ID: mdl-25215497

RESUMO

Transcription factor (TF) DNA sequence preferences direct their regulatory activity, but are currently known for only ∼1% of eukaryotic TFs. Broadly sampling DNA-binding domain (DBD) types from multiple eukaryotic clades, we determined DNA sequence preferences for >1,000 TFs encompassing 54 different DBD classes from 131 diverse eukaryotes. We find that closely related DBDs almost always have very similar DNA sequence preferences, enabling inference of motifs for ∼34% of the ∼170,000 known or predicted eukaryotic TFs. Sequences matching both measured and inferred motifs are enriched in chromatin immunoprecipitation sequencing (ChIP-seq) peaks and upstream of transcription start sites in diverse eukaryotic lineages. SNPs defining expression quantitative trait loci in Arabidopsis promoters are also enriched for predicted TF binding sites. Importantly, our motif "library" can be used to identify specific TFs whose binding may be altered by human disease risk alleles. These data present a powerful resource for mapping transcriptional networks across eukaryotes.


Assuntos
Arabidopsis/genética , Motivos de Nucleotídeos , Análise de Sequência de DNA , Fatores de Transcrição/metabolismo , Arabidopsis/metabolismo , Imunoprecipitação da Cromatina , Humanos , Polimorfismo de Nucleotídeo Único , Regiões Promotoras Genéticas , Ligação Proteica , Locos de Características Quantitativas
3.
Genome Res ; 2023 Nov 09.
Artigo em Inglês | MEDLINE | ID: mdl-37945377

RESUMO

Mammalian mRNA and lncRNA exons are often small compared to introns. The exon definition model predicts that exons splice autonomously, dependent on proximal exon sequence features, explaining their delineation within large introns. This model has not been examined on a genome-wide scale, however, leaving open the question of how often mRNA and lncRNA exons are autonomous. It is also unknown how frequently such exons can arise by chance. Here, we directly assayed large fragments (500-1000 bp) of the human genome by exon trapping, which detects exons spliced into a heterologous transgene, here designed with a large intron context. We define the trapped exons as "autonomous." We obtained ∼1.25 million trapped exons, including most known mRNA and well-annotated lncRNA internal exons, demonstrating that human exons are predominantly autonomous. mRNA exons are trapped with the highest efficiency. Nearly a million of the trapped exons are unannotated, most located in intergenic regions and antisense to mRNA, with depletion from the forward strand of introns. These exons are not conserved, suggesting they are nonfunctional and arose from random mutations. They are nonetheless highly enriched with known splicing promoting sequence features that delineate known exons. Novel autonomous exons are more numerous than annotated lncRNA exons, and computational models also indicate they will occur with similar frequency in any randomly generated sequence. These results show that most human coding exons splice autonomously, and provide an explanation for the existence of many unconserved lncRNAs, as well as a new annotation and inclusion levels of spliceable loci in the human genome.

4.
J Biol Chem ; 299(6): 104734, 2023 06.
Artigo em Inglês | MEDLINE | ID: mdl-37086783

RESUMO

The BEN domain-containing transcription factors regulate transcription by recruiting chromatin-modifying factors to specific chromatin regions via their DNA-binding BEN domains. The BEN domain of BANP has been shown to bind to a CGCG DNA sequence or an AAA-containing matrix attachment regions DNA sequence. Consistent with these in vivo observations, we identified an optimal DNA-binding sequence of AAATCTCG by protein binding microarray, which was also confirmed by our isothermal titration calorimetry and mutagenesis results. We then determined crystal structures of the BANP BEN domain in apo form and in complex with a CGCG-containing DNA, respectively, which revealed that the BANP BEN domain mainly used the electrostatic interactions to bind DNA with some base-specific interactions with the TC motifs. Our isothermal titration calorimetry results also showed that BANP bound to unmethylated and methylated DNAs with comparable binding affinities. Our complex structure of BANP-mCGCG revealed that the BANP BEN domain bound to the unmethylated and methylated DNAs in a similar mode and cytosine methylation did not get involved in binding, which is also consistent with our observations from the complex structures of the BEND6 BEN domain with the CGCG or CGmCG DNAs. Taken together, our results further elucidate the elements important for DNA recognition and transcriptional regulation by the BANP BEN domain-containing transcription factor.


Assuntos
Proteínas de Ligação a DNA , Regulação da Expressão Gênica , Fatores de Transcrição , Cromatina , DNA/química , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/química , Ligação Proteica , Fatores de Transcrição/genética , Fatores de Transcrição/química , Humanos
5.
BMC Genomics ; 25(1): 710, 2024 Jul 23.
Artigo em Inglês | MEDLINE | ID: mdl-39044130

RESUMO

BACKGROUND: Identifying the DNA-binding specificities of transcription factors (TF) is central to understanding gene networks that regulate growth and development. Such knowledge is lacking in oomycetes, a microbial eukaryotic lineage within the stramenopile group. Oomycetes include many important plant and animal pathogens such as the potato and tomato blight agent Phytophthora infestans, which is a tractable model for studying life-stage differentiation within the group. RESULTS: Mining of the P. infestans genome identified 197 genes encoding proteins belonging to 22 TF families. Their chromosomal distribution was consistent with family expansions through unequal crossing-over, which were likely ancient since each family had similar sizes in most oomycetes. Most TFs exhibited dynamic changes in RNA levels through the P. infestans life cycle. The DNA-binding preferences of 123 proteins were assayed using protein-binding oligonucleotide microarrays, which succeeded with 73 proteins from 14 families. Binding sites predicted for representatives of the families were validated by electrophoretic mobility shift or chromatin immunoprecipitation assays. Consistent with the substantial evolutionary distance of oomycetes from traditional model organisms, only a subset of the DNA-binding preferences resembled those of human or plant orthologs. Phylogenetic analyses of the TF families within P. infestans often discriminated clades with canonical and novel DNA targets. Paralogs with similar binding preferences frequently had distinct patterns of expression suggestive of functional divergence. TFs were predicted to either drive life stage-specific expression or serve as general activators based on the representation of their binding sites within total or developmentally-regulated promoters. This projection was confirmed for one TF using synthetic and mutated promoters fused to reporter genes in vivo. CONCLUSIONS: We established a large dataset of binding specificities for P. infestans TFs, representing the first in the stramenopile group. This resource provides a basis for understanding transcriptional regulation by linking TFs with their targets, which should help delineate the molecular components of processes such as sporulation and host infection. Our work also yielded insight into TF evolution during the eukaryotic radiation, revealing both functional conservation as well as diversification across kingdoms.


Assuntos
Evolução Molecular , Filogenia , Phytophthora infestans , Fatores de Transcrição , Phytophthora infestans/genética , Phytophthora infestans/metabolismo , Fatores de Transcrição/metabolismo , Fatores de Transcrição/genética , Sítios de Ligação , Ligação Proteica
6.
Dev Med Child Neurol ; 66(11): 1496-1501, 2024 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-38773804

RESUMO

AIM: To examine patients with cerebral palsy (CP) undergoing open reduction and internal fixation (ORIF) for ankle fractures. METHOD: This was a retrospective study of adult patients undergoing ankle fracture ORIF for closed, isolated ankle fractures identified in between 2010 and 2021 in the Q1 PearlDiver M151 database. Patients with CP were identified with International Classification of Diseases (ICD)-9 and ICD-10 codes, and were matched to those without 1:10 on age, sex, and Elixhauser comorbidity index (ECI). Ninety-day adverse events were assessed with multivariable logistic regression. RESULTS: A total of 148 993 patients with isolated ankle fracture ORIF were identified, of whom 407 (0.27%) had CP. After matching, 3863 without CP were compared to 389 with CP. Patients with CP were at increased odds of: 90-day urinary tract infection (odds ratios [OR] 6.26), pneumonia (OR 3.50), minor adverse events (OR 3.46), sepsis (OR 3.30), any adverse events (OR 3.04), emergency department visits (OR 2.28), serious adverse events (OR 1.77), and prolonged length of stay more than 4 days (OR 22.44) (p < 0.001 for all). INTERPRETATION: Patients with CP undergoing ORIF for isolated, closed ankle fractures are at increased odds of several 90-day adverse events and prolonged length of stay compared to matched patients without CP. WHAT THIS PAPER ADDS: Patients with cerebral palsy (CP) undergoing ankle fracture open reduction and internal fixation (ORIF) were at increased odds of 90-day adverse events. Many of the 90-day adverse events related to previously described comorbidities associated with CP. Patients with CP undergoing ankle fracture ORIF experienced increased rates of prolonged length of stay.


Assuntos
Fraturas do Tornozelo , Paralisia Cerebral , Fixação Interna de Fraturas , Redução Aberta , Humanos , Paralisia Cerebral/cirurgia , Paralisia Cerebral/complicações , Feminino , Masculino , Estudos Retrospectivos , Fraturas do Tornozelo/cirurgia , Fixação Interna de Fraturas/efeitos adversos , Adulto , Pessoa de Meia-Idade , Complicações Pós-Operatórias/epidemiologia , Adulto Jovem
7.
J Pediatr Orthop ; 44(9): e852-e857, 2024 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-38938106

RESUMO

INTRODUCTION: The Greulich & Pyle (G&P) Radiographic Atlas of Skeletal Development uses hand x-rays obtained between 1926 and 1942 on children of Caucasian ancestry. Our study uses modern Caucasian, Black, Hispanic, and Asian children to investigate patterns of development as a function of percent final height (PFH). METHODS: A retrospective review, at a single institution, was conducted using children who received a hand x-ray, a height measurement taken within 60 days of that x-ray, and a final height. BA and CA were compared between races. PFH was calculated by dividing height at the time of the x-ray by their final height. To further evaluate differences between races in CA or BA, PFH was then modeled as a function of CA or BA using a fifth-degree polynomial regression, and mean ages at the 85th PFH were compared. Patients were then divided into Sanders stages 1, 2-4, and 5-8 and the mean PFH, CA, and BA of the Asian, Black, and Hispanic children were compared with the White children using Student t test. P values less than 0.05 were considered significant. RESULTS: We studied 498 patients, including 53 Asian, 83 Black, 190 Hispanic, and 172 White patients. Mean BA was significantly greater than CA in Black males (1.27 y) and females (1.36 y), Hispanic males (1.12 y) and females (1.29 y), and White females (0.74 y). Hispanic and Black patients were significantly more advanced in BA than White patients ( P <0.001). At the 85th PFH, White and Hispanic males were older than Black males by at least 7 months ( P <0.001), and White females were significantly older than Hispanic females by 6.4 months ( P <0.001). At 85th PFH for males, Hispanic and Black males had greater BA than White males by at least 5 months ( P <0.001), and Asian females had a greater BA than Black females by at least 5 months ( P <0.001). Compared with White children, Hispanic children were significantly younger at Sanders 2-4 than White children, and Black children were skeletally older at Sanders 5-8. CONCLUSIONS: BA was greater than CA by ≥1 year in Black and Hispanic children, and that these children had a significantly greater BA than their White counterparts. Black males and Hispanic females reached their 85th PFH at younger ages, and Hispanic males and Asian females were the most skeletally mature at their 85th PFH. Our results suggest that BA and CA may vary as a function of race, and further studies evaluating growth via the 85th PFH may be necessary. LEVEL OF EVIDENCE: Therapeutic Study - Level IV.


Assuntos
Estatura , Desenvolvimento Infantil , Adolescente , Criança , Pré-Escolar , Feminino , Humanos , Lactente , Masculino , Negro ou Afro-Americano , Hispânico ou Latino , Grupos Raciais , Radiografia/métodos , Estudos Retrospectivos , Estados Unidos , Brancos , Asiático
8.
Mol Biol Evol ; 38(5): 2070-2075, 2021 05 04.
Artigo em Inglês | MEDLINE | ID: mdl-33561217

RESUMO

The human transcription factor (TF) CGGBP1 (CGG-binding protein) is conserved only in amniotes and is believed to derive from the zf-BED and Hermes transposase DNA-binding domains (DBDs) of a hAT DNA transposon. Here, we show that sequence-specific DNA-binding proteins with this bipartite domain structure have resulted from dozens of independent hAT domestications in different eukaryotic lineages. CGGBPs display a wide range of sequence specificity, usually including preferences for CGG or CGC trinucleotides, whereas some bind AT-rich motifs. The CGGBPs are almost entirely nonsyntenic, and their protein sequences, DNA-binding motifs, and patterns of presence or absence in genomes are uncharacteristic of ancestry via speciation. At least eight CGGBPs in the coelacanth Latimeria chalumnae bind distinct motifs, and the expression of the corresponding genes varies considerably across tissues, suggesting tissue-restricted function.


Assuntos
Elementos de DNA Transponíveis , Proteínas de Ligação a DNA/genética , Peixes/genética , Animais , Proteínas de Ligação a DNA/metabolismo , Peixes/metabolismo , Humanos
9.
J Surg Orthop Adv ; 31(1): 53-55, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35377309

RESUMO

The purpose of this study is to report the operative outcomes in a consecutive series of adolescent patients with symptomatic accessory navicular (AN). A retrospective review was conducted. Patient characteristics, operative techniques, and outcomes were recorded. Radiographs were used to identify the type of AN, skeletal maturity, and presence of concurrent pes planus. Twenty-two patients and 24 feet were studied. All 22 patients had an excision of the AN, and 19 patients had an additional reefing of the tibialis posterior tendon. At final follow up, 22 cases reported no pain, one had minimal pain, and one reported no change in pain. Symptomatic AN is more common in females. Surgery technique was not correlated with postoperative pain. Surgery eliminated pain in 91% of patients and can be safely performed in athletes with high rate of return to their previous athletic performance. (Journal of Surgical Orthopaedic Advances 31(1):053-055, 2022).


Assuntos
Doenças do Pé , Ossos do Tarso , Adolescente , Feminino , Humanos , Dor Pós-Operatória , Ossos do Tarso/diagnóstico por imagem , Ossos do Tarso/cirurgia , Tendões/cirurgia , Resultado do Tratamento
10.
Biochem J ; 477(7): 1345-1362, 2020 04 17.
Artigo em Inglês | MEDLINE | ID: mdl-32207815

RESUMO

We report the identification and characterization of a bacteriophage λ-encoded protein, NinH. Sequence homology suggests similarity between NinH and Fis, a bacterial nucleoid-associated protein (NAP) involved in numerous DNA topology manipulations, including chromosome condensation, transcriptional regulation and phage site-specific recombination. We find that NinH functions as a homodimer and is able to bind and bend double-stranded DNA in vitro. Furthermore, NinH shows a preference for a 15 bp signature sequence related to the degenerate consensus favored by Fis. Structural studies reinforced the proposed similarity to Fis and supported the identification of residues involved in DNA binding which were demonstrated experimentally. Overexpression of NinH proved toxic and this correlated with its capacity to associate with DNA. NinH is the first example of a phage-encoded Fis-like NAP that likely influences phage excision-integration reactions or bacterial gene expression.


Assuntos
Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Bacteriófago lambda/genética , Bacteriófago lambda/metabolismo , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/metabolismo , Proteínas Virais/genética , Proteínas Virais/metabolismo , Proteínas de Bactérias/química , Sequência de Bases , Sítios de Ligação , Simulação por Computador , DNA/metabolismo , DNA Viral/metabolismo , Proteínas de Ligação a DNA/química , Escherichia coli/genética , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/genética , Fator Proteico para Inversão de Estimulação/química , Fator Proteico para Inversão de Estimulação/genética , Expressão Gênica , Proteínas Mutantes/metabolismo , Conformação Proteica em alfa-Hélice , Conformação Proteica em Folha beta , Multimerização Proteica/genética , Proteínas Virais/química
11.
J Biol Chem ; 293(19): 7344-7354, 2018 05 11.
Artigo em Inglês | MEDLINE | ID: mdl-29567833

RESUMO

Cytosine methylation is a well-characterized epigenetic mark and occurs at both CG and non-CG sites in DNA. Both methylated CG (mCG)- and mCH (H = A, C, or T)-containing DNAs, especially mCAC-containing DNAs, are recognized by methyl-CpG-binding protein 2 (MeCP2) to regulate gene expression in neuron development. However, the molecular mechanism involved in the binding of methyl-CpG-binding domain (MBD) of MeCP2 to these different DNA motifs is unclear. Here, we systematically characterized the DNA-binding selectivities of the MBD domains in MeCP2 and MBD1-4 with isothermal titration calorimetry-based binding assays, mutagenesis studies, and X-ray crystallography. We found that the MBD domains of MeCP2 and MBD1-4 bind mCG-containing DNAs independently of the sequence identity outside the mCG dinucleotide. Moreover, some MBD domains bound to both methylated and unmethylated CA dinucleotide-containing DNAs, with a preference for the CAC sequence motif. We also found that the MBD domains bind to mCA or nonmethylated CA DNA by recognizing the complementary TG dinucleotide, which is consistent with an overlooked ligand of MeCP2, i.e. the matrix/scaffold attachment regions (MARs/SARs) with a consensus sequence of 5'-GGTGT-3' that was identified in early 1990s. Our results also explain why MeCP2 exhibits similar binding affinity to both mCA- and hmCA-containing dsDNAs. In summary, our results suggest that in addition to mCG sites, unmethylated CA or TG sites also serve as DNA-binding sites for MeCP2 and other MBD-containing proteins. This discovery expands the genome-wide activity of MBD-containing proteins in gene regulation.


Assuntos
Proteínas de Ligação a DNA/química , DNA/metabolismo , Endodesoxirribonucleases/química , Proteína 2 de Ligação a Metil-CpG/química , Fatores de Transcrição/química , Sítios de Ligação , Calorimetria/métodos , Cristalografia por Raios X , Citosina/química , Metilação de DNA , Proteínas de Ligação a DNA/genética , Endodesoxirribonucleases/genética , Regulação da Expressão Gênica , Guanina/química , Humanos , Proteína 2 de Ligação a Metil-CpG/genética , Mutagênese , Nucleotídeos/metabolismo , Domínios Proteicos , Timina/química , Fatores de Transcrição/genética
12.
J Biol Chem ; 293(9): 3218-3233, 2018 03 02.
Artigo em Inglês | MEDLINE | ID: mdl-29217772

RESUMO

Plant nucleotide-binding leucine-rich repeat (NLR) proteins enable the immune system to recognize and respond to pathogen attack. An early consequence of immune activation is transcriptional reprogramming, and some NLRs have been shown to act in the nucleus and interact with transcription factors. The Rx1 NLR protein of potato is further able to bind and distort double-stranded DNA. However, Rx1 host targets that support a role for Rx1 in transcriptional reprogramming at DNA are unknown. Here, we report a functional interaction between Rx1 and NbGlk1, a Golden2-like transcription factor. Rx1 binds to NbGlk1 in vitro and in planta. NbGlk1 binds to known Golden2-like consensus DNA sequences. Rx1 reduces the binding affinity of NbGlk1 for DNA in vitro. NbGlk1 activates cellular responses to potato virus X, whereas Rx1 associates with NbGlk1 and prevents its assembly on DNA in planta unless activated by PVX. This study provides new mechanistic insight into how an NLR can coordinate an immune signaling response at DNA following pathogen perceptions.


Assuntos
DNA/metabolismo , Espaço Intracelular/metabolismo , Proteínas NLR/metabolismo , Proteínas de Plantas/metabolismo , Fatores de Transcrição/metabolismo , Proteínas NLR/química , Proteínas de Plantas/química , Ligação Proteica , Domínios Proteicos , Nicotiana
13.
Nature ; 499(7457): 172-7, 2013 Jul 11.
Artigo em Inglês | MEDLINE | ID: mdl-23846655

RESUMO

RNA-binding proteins are key regulators of gene expression, yet only a small fraction have been functionally characterized. Here we report a systematic analysis of the RNA motifs recognized by RNA-binding proteins, encompassing 205 distinct genes from 24 diverse eukaryotes. The sequence specificities of RNA-binding proteins display deep evolutionary conservation, and the recognition preferences for a large fraction of metazoan RNA-binding proteins can thus be inferred from their RNA-binding domain sequence. The motifs that we identify in vitro correlate well with in vivo RNA-binding data. Moreover, we can associate them with distinct functional roles in diverse types of post-transcriptional regulation, enabling new insights into the functions of RNA-binding proteins both in normal physiology and in human disease. These data provide an unprecedented overview of RNA-binding proteins and their targets, and constitute an invaluable resource for determining post-transcriptional regulatory mechanisms in eukaryotes.


Assuntos
Regulação da Expressão Gênica/genética , Motivos de Nucleotídeos/genética , Proteínas de Ligação a RNA/metabolismo , Transtorno Autístico/genética , Sequência de Bases , Sítios de Ligação/genética , Sequência Conservada/genética , Células Eucarióticas/metabolismo , Humanos , Dados de Sequência Molecular , Estrutura Terciária de Proteína/genética , Fatores de Processamento de RNA , Estabilidade de RNA/genética , Proteínas de Ligação a RNA/química , Proteínas de Ligação a RNA/genética
14.
PLoS Genet ; 12(11): e1006401, 2016 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-27855160

RESUMO

Proteins secreted by pathogens during host colonization largely determine the outcome of pathogen-host interactions and are commonly called 'effectors'. In fungal plant pathogens, coordinated transcriptional up-regulation of effector genes is a key feature of pathogenesis and effectors are often encoded in genomic regions with distinct repeat content, histone code and rate of evolution. In the tomato pathogen Fusarium oxysporum f. sp. lycopersici (Fol), effector genes reside on one of four accessory chromosomes, known as the 'pathogenicity' chromosome, which can be exchanged between strains through horizontal transfer. The three other accessory chromosomes in the Fol reference strain may also be important for virulence towards tomato. Expression of effector genes in Fol is highly up-regulated upon infection and requires Sge1, a transcription factor encoded on the core genome. Interestingly, the pathogenicity chromosome itself contains 13 predicted transcription factor genes and for all except one, there is a homolog on the core genome. We determined DNA binding specificity for nine transcription factors using oligonucleotide arrays. The binding sites for homologous transcription factors were highly similar, suggesting that extensive neofunctionalization of DNA binding specificity has not occurred. Several DNA binding sites are enriched on accessory chromosomes, and expression of FTF1, its core homolog FTF2 and SGE1 from a constitutive promoter can induce expression of effector genes. The DNA binding sites of only these three transcription factors are enriched among genes up-regulated during infection. We further show that Ftf1, Ftf2 and Sge1 can activate transcription from their binding sites in yeast. RNAseq analysis revealed that in strains with constitutive expression of FTF1, FTF2 or SGE1, expression of a similar set of plant-responsive genes on the pathogenicity chromosome is induced, including most effector genes. We conclude that the Fol pathogenicity chromosome may be partially transcriptionally autonomous, but there are also extensive transcriptional connections between core and accessory chromosomes.


Assuntos
Proteínas de Ligação a DNA/genética , Fusarium/genética , Doenças das Plantas/genética , Fatores de Transcrição/genética , Cromossomos Fúngicos , Proteínas de Ligação a DNA/metabolismo , Fusarium/crescimento & desenvolvimento , Fusarium/patogenicidade , Regulação Fúngica da Expressão Gênica , Transferência Genética Horizontal/genética , Genoma Fúngico , Sequenciamento de Nucleotídeos em Larga Escala , Interações Hospedeiro-Patógeno/genética , Solanum lycopersicum/crescimento & desenvolvimento , Solanum lycopersicum/microbiologia , Filogenia , Doenças das Plantas/microbiologia , Regiões Promotoras Genéticas , Fatores de Transcrição/metabolismo
15.
PLoS Pathog ; 11(6): e1004967, 2015 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-26068099

RESUMO

Bacterial xenogeneic silencing proteins selectively bind to and silence expression from many AT rich regions of the chromosome. They serve as master regulators of horizontally acquired DNA, including a large number of virulence genes. To date, three distinct families of xenogeneic silencers have been identified: H-NS of Proteobacteria, Lsr2 of the Actinomycetes, and MvaT of Pseudomonas sp. Although H-NS and Lsr2 family proteins are structurally different, they all recognize the AT-rich DNA minor groove through a common AT-hook-like motif, which is absent in the MvaT family. Thus, the DNA binding mechanism of MvaT has not been determined. Here, we report the characteristics of DNA sequences targeted by MvaT with protein binding microarrays, which indicates that MvaT prefers binding flexible DNA sequences with multiple TpA steps. We demonstrate that there are clear differences in sequence preferences between MvaT and the other two xenogeneic silencer families. We also determined the structure of the DNA-binding domain of MvaT in complex with a high affinity DNA dodecamer using solution NMR. This is the first experimental structure of a xenogeneic silencer in complex with DNA, which reveals that MvaT recognizes the AT-rich DNA both through base readout by an "AT-pincer" motif inserted into the minor groove and through shape readout by multiple lysine side chains interacting with the DNA sugar-phosphate backbone. Mutations of key MvaT residues for DNA binding confirm their importance with both in vitro and in vivo assays. This novel DNA binding mode enables MvaT to better tolerate GC-base pair interruptions in the binding site and less prefer A tract DNA when compared to H-NS and Lsr2. Comparison of MvaT with other bacterial xenogeneic silencers provides a clear picture that nature has evolved unique solutions for different bacterial genera to distinguish foreign from self DNA.


Assuntos
Proteínas de Bactérias/genética , Regulação Bacteriana da Expressão Gênica/genética , Inativação Gênica/fisiologia , Pseudomonas aeruginosa/genética , Relação Estrutura-Atividade , Transativadores/genética , Proteínas de Bactérias/química , Evolução Biológica , Western Blotting , Ensaio de Desvio de Mobilidade Eletroforética , Transferência Genética Horizontal , Ensaios de Triagem em Larga Escala , Espectroscopia de Ressonância Magnética , Análise Serial de Proteínas , Pseudomonas aeruginosa/química , Transativadores/química
16.
PLoS Genet ; 10(5): e1004336, 2014 May.
Artigo em Inglês | MEDLINE | ID: mdl-24784729

RESUMO

Secondary metabolites are produced by numerous organisms and can either be beneficial, benign, or harmful to humans. Genes involved in the synthesis and transport of these secondary metabolites are frequently found in gene clusters, which are often coordinately regulated, being almost exclusively dependent on transcription factors that are located within the clusters themselves. Gliotoxin, which is produced by a variety of Aspergillus species, Trichoderma species, and Penicillium species, exhibits immunosuppressive properties and has therefore been the subject of research for many laboratories. There have been a few proteins shown to regulate the gliotoxin cluster, most notably GliZ, a Zn2Cys6 binuclear finger transcription factor that lies within the cluster, and LaeA, a putative methyltransferase that globally regulates secondary metabolism clusters within numerous fungal species. Using a high-copy inducer screen in A. fumigatus, our lab has identified a novel C2H2 transcription factor, which plays an important role in regulating the gliotoxin biosynthetic cluster. This transcription factor, named GipA, induces gliotoxin production when present in extra copies. Furthermore, loss of gipA reduces gliotoxin production significantly. Through protein binding microarray and mutagenesis, we have identified a DNA binding site recognized by GipA that is in extremely close proximity to a potential GliZ DNA binding site in the 5' untranslated region of gliA, which encodes an efflux pump within the gliotoxin cluster. Not surprisingly, GliZ and GipA appear to work in an interdependent fashion to positively control gliA expression.


Assuntos
Aspergillus fumigatus/metabolismo , Proteínas Fúngicas/metabolismo , Fatores de Transcrição/fisiologia , Regiões 5' não Traduzidas , Sítios de Ligação , Proteínas Fúngicas/genética , Dosagem de Genes , Regiões Promotoras Genéticas
17.
Mol Cell ; 32(6): 878-87, 2008 Dec 26.
Artigo em Inglês | MEDLINE | ID: mdl-19111667

RESUMO

The sequence specificity of DNA-binding proteins is the primary mechanism by which the cell recognizes genomic features. Here, we describe systematic determination of yeast transcription factor DNA-binding specificities. We obtained binding specificities for 112 DNA-binding proteins representing 19 distinct structural classes. One-third of the binding specificities have not been previously reported. Several binding sequences have striking genomic distributions relative to transcription start sites, supporting their biological relevance and suggesting a role in promoter architecture. Among these are Rsc3 binding sequences, containing the core CGCG, which are found preferentially approximately 100 bp upstream of transcription start sites. Mutation of RSC3 results in a dramatic increase in nucleosome occupancy in hundreds of proximal promoters containing a Rsc3 binding element, but has little impact on promoters lacking Rsc3 binding sequences, indicating that Rsc3 plays a broad role in targeting nucleosome exclusion at yeast promoters.


Assuntos
Proteínas de Ligação a DNA/metabolismo , Nucleossomos/metabolismo , Regiões Promotoras Genéticas , Proteínas de Saccharomyces cerevisiae/metabolismo , Saccharomyces cerevisiae/genética , Fatores de Transcrição/genética , Sequência de Bases , Sítios de Ligação , Genes Fúngicos , Dados de Sequência Molecular , Mutação/genética , Filogenia , Reprodutibilidade dos Testes , Homologia de Sequência de Aminoácidos , Fatores de Transcrição/metabolismo
18.
Proc Natl Acad Sci U S A ; 110(40): 16050-5, 2013 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-24043797

RESUMO

Developmental transcription factors are key players in animal multicellularity, being members of the T-box family that are among the most important. Until recently, T-box transcription factors were thought to be exclusively present in metazoans. Here, we report the presence of T-box genes in several nonmetazoan lineages, including ichthyosporeans, filastereans, and fungi. Our data confirm that Brachyury is the most ancient member of the T-box family and establish that the T-box family diversified at the onset of Metazoa. Moreover, we demonstrate functional conservation of a homolog of Brachyury of the protist Capsaspora owczarzaki in Xenopus laevis. By comparing the molecular phenotype of C. owczarzaki Brachyury with that of homologs of early branching metazoans, we define a clear difference between unicellular holozoan and metazoan Brachyury homologs, suggesting that the specificity of Brachyury emerged at the origin of Metazoa. Experimental determination of the binding preferences of the C. owczarzaki Brachyury results in a similar motif to that of metazoan Brachyury and other T-box classes. This finding suggests that functional specificity between different T-box classes is likely achieved by interaction with alternative cofactors, as opposed to differences in binding specificity.


Assuntos
Evolução Molecular , Proteínas Fetais/genética , Mesomycetozoea/genética , Família Multigênica/genética , Fenótipo , Filogenia , Proteínas com Domínio T/genética , Xenopus/genética , Animais , Histocitoquímica , Análise em Microsséries , Ligação Proteica , Reação em Cadeia da Polimerase em Tempo Real , Especificidade da Espécie
19.
Cureus ; 16(6): e63476, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-39077299

RESUMO

INTRODUCTION: Supracondylar humerus fractures are the most common surgically treated fracture in children. National trends have demonstrated an increase in transfers of supracondylar fractures to pediatric hospitals due to the perception that supracondylar fractures need to be treated by pediatric specialists. The objectives of the study are to compare the outcomes of surgically treated pediatric supracondylar humerus fractures (PSCHF) between a pediatric orthopedic surgeon and a non-pediatric orthopedic surgeon at a single academic medical center; to assess radiographic reduction, the number of pins used, surgical time, Flynn criteria outcomes, and complications associated with PSCHF treatment by both types of surgeons; to determine if there is a significant difference in outcomes between pediatric and non-pediatric orthopedic surgeons in the treatment of PSCHF. METHODS: Forty-seven consecutive pediatric patients, with an average age of 5.5 years old, who had undergone surgical correction for supracondylar humerus fractures during 2019 were included in this study. The intervention performed was closed reduction and percutaneous pinning. The main outcome measured: radiographic reduction on the AP and lateral X-ray view, number of K wires used, use of a medial K wire, time of surgery, the Flynn criteria, and complications. The Human Research Protection Program (HRPP) at Penn State approval was obtained. RESULTS: Radiographic reductions as measured by Bauman's angle and the position of the anterior humeral line were excellent and similar between surgeons. The pediatric orthopedic surgeon used more medial K wires (p=0.0007), fewer K wires (p=0.0065), and the length of surgery was shorter (p=0.019). The Flynn criteria were similar with equal excellent and good results. For both surgeons, no complications such as loss of reduction, infection, iatrogenic nerve injury, compartment syndrome, or cubitus varus occurred. CONCLUSIONS: Outcomes of treatment of displaced PSCHF by the pediatric and non-pediatric orthopedic surgeons were equal. The results of this study reaffirm the assertion that both pediatric and non-pediatric orthopedic surgeons have sufficient training and skill to treat these common fractures, thereby contributing to a more informed decision-making process in clinical practice.

20.
Int J Surg Case Rep ; 124: 110400, 2024 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-39369454

RESUMO

INTRODUCTION: Treatment of diabetic foot ulcer is complex and expensive, and frequently results in amputation. Transverse Tibia Transport is a new strategy for diabetic foot ulcers, which is based on the techniques of distraction histogenesis. PRESENTATION OF CASE: We present a 32-year-old male with longstanding insulin-dependent diabetes mellitus and many medical comorbidities with a non-healing heel ulcer of greater than 1 year. Following diagnosis of his diabetic foot ulcer complicated by osteomyelitis, he underwent a series of vascular and local wound interventions unsuccessfully. Transverse tibia transport was successful in healing the ulcer after 4 months. No complications were observed during follow up. DISCUSSION: Distraction histogenesis mechanically stimulates regeneration of soft tissues such as muscles, tendons, and blood vessels by sustained tension. Inducing vascular regeneration at a targeted site has broad potential value for treating various disorders such as atrophic union and osteomyelitis. CONCLUSION: For patients with refractory diabetic foot ulcers, transverse tibia transport may be considered as a treatment option.

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