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1.
Astrobiology ; 23(12): 1348-1367, 2023 12.
Artigo em Inglês | MEDLINE | ID: mdl-38079228

RESUMO

Democratizing genomic data science, including bioinformatics, can diversify the STEM workforce and may, in turn, bring new perspectives into the space sciences. In this respect, the development of education and research programs that bridge genome science with "place" and world-views specific to a given region are valuable for Indigenous students and educators. Through a multi-institutional collaboration, we developed an ongoing education program and model that includes Illumina and Oxford Nanopore sequencing, free bioinformatic platforms, and teacher training workshops to address our research and education goals through a place-based science education lens. High school students and researchers cultivated, sequenced, assembled, and annotated the genomes of 13 bacteria from Mars analog sites with cultural relevance, 10 of which were novel species. Students, teachers, and community members assisted with the discovery of new, potentially chemolithotrophic bacteria relevant to astrobiology. This joint education-research program also led to the discovery of species from Mars analog sites capable of producing N-acyl homoserine lactones, which are quorum-sensing molecules used in bacterial communication. Whole genome sequencing was completed in high school classrooms, and connected students to funded space research, increased research output, and provided culturally relevant, place-based science education, with participants naming three novel species described here. Students at St. Andrew's School (Honolulu, Hawai'i) proposed the name Bradyrhizobium prioritasuperba for the type strain, BL16AT, of the new species (DSM 112479T = NCTC 14602T). The nonprofit organization Kauluakalana proposed the name Brenneria ulupoensis for the type strain, K61T, of the new species (DSM 116657T = LMG = 33184T), and Hawai'i Baptist Academy students proposed the name Paraflavitalea speifideiaquila for the type strain, BL16ET, of the new species (DSM 112478T = NCTC 14603T).


Assuntos
Exobiologia , Instituições Acadêmicas , Humanos , Havaí , Genômica , Bactérias
3.
Commun Biol ; 4(1): 1232, 2021 10 28.
Artigo em Inglês | MEDLINE | ID: mdl-34711923

RESUMO

Some organisms can withstand complete body water loss (losing up to 99% of body water) and stay in ametabolic state for decades until rehydration, which is known as anhydrobiosis. Few multicellular eukaryotes on their adult stage can withstand life without water. We still have an incomplete understanding of the mechanism for metazoan survival of anhydrobiosis. Here we report the 255-Mb genome of Aphelenchus avenae, which can endure relative zero humidity for years. Gene duplications arose genome-wide and contributed to the expansion and diversification of 763 kinases, which represents the second largest metazoan kinome to date. Transcriptome analyses of ametabolic state of A. avenae indicate the elevation of ATP level for global recycling of macromolecules and enhancement of autophagy in the early stage of anhydrobiosis. We catalogue 74 species-specific intrinsically disordered proteins, which may facilitate A. avenae to survive through desiccation stress. Our findings refine a molecular basis evolving for survival in extreme water loss and open the way for discovering new anti-desiccation strategies.


Assuntos
Adaptação Biológica/fisiologia , Dessecação , Proteínas de Helminto/genética , Fosfotransferases/genética , Tylenchida/genética , Água/metabolismo , Animais , Evolução Biológica , Duplicação Gênica/fisiologia , Perfilação da Expressão Gênica , Proteínas de Helminto/metabolismo , Umidade , Fosfotransferases/metabolismo , Tylenchida/enzimologia
4.
PLoS One ; 12(8): e0182782, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-28792538

RESUMO

Globin-coupled diguanylate cyclases contain globin, middle, and diguanylate cyclase domains that sense O2 to synthesize c-di-GMP and regulate bacterial motility, biofilm formation, and virulence. However, relatively few studies have extensively examined the roles of individual residues and domains of globin-coupled diguanylate cyclases, which can shed light on their signaling mechanisms and provide drug targets. Here, we report the critical residues of two globin-coupled diguanylate cyclases, EcGReg from Escherichia coli and BpeGReg from Bordetella pertussis, and show that their diguanylate cyclase activity requires an intact globin domain. In the distal heme pocket of the globin domain, residues Phe42, Tyr43, Ala68 (EcGReg)/Ser68 (BpeGReg), and Met69 are required to maintain full diguanylate cyclase activity. The highly conserved amino acids His223/His225 and Lys224/Lys226 in the middle domain of EcGReg/BpeGReg are essential to diguanylate cyclase activity. We also identified sixteen important residues (Leu300, Arg306, Asp333, Phe337, Lys338, Asn341, Asp342, Asp350, Leu353, Asp368, Arg372, Gly374, Gly375, Asp376, Glu377, and Phe378) in the active site and inhibitory site of the diguanylate cyclase domain of EcGReg. Moreover, BpeGReg266 (residues 1-266) and BpeGReg296 (residues 1-296), which only contain the globin and middle domains, can inhibit bacterial motility. Our findings suggest that the distal residues of the globin domain affect diguanylate cyclase activity and that BpeGReg may interact with other c-di-GMP-metabolizing proteins to form mixed signaling teams.


Assuntos
Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Globinas/metabolismo , Heme/metabolismo , Fósforo-Oxigênio Liases/genética , Fósforo-Oxigênio Liases/metabolismo , Sequência de Aminoácidos , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Bordetella pertussis/enzimologia , Bordetella pertussis/genética , Sequência Conservada , Escherichia coli/enzimologia , Escherichia coli/genética , Modelos Moleculares , Mutação , Fenótipo , Domínios Proteicos , Estrutura Secundária de Proteína , Salmonella typhimurium , Homologia de Sequência de Aminoácidos , Natação
5.
Nat Plants ; 3: 16223, 2017 01 30.
Artigo em Inglês | MEDLINE | ID: mdl-28134914

RESUMO

Jute (Corchorus sp.) is one of the most important sources of natural fibre, covering ∼80% of global bast fibre production1. Only Corchorus olitorius and Corchorus capsularis are commercially cultivated, though there are more than 100 Corchorus species2 in the Malvaceae family. Here we describe high-quality draft genomes of these two species and their comparisons at the functional genomics level to support tailor-designed breeding. The assemblies cover 91.6% and 82.2% of the estimated genome sizes for C. olitorius and C. capsularis, respectively. In total, 37,031 C. olitorius and 30,096 C. capsularis genes are identified, and most of the genes are validated by cDNA and RNA-seq data. Analyses of clustered gene families and gene collinearity show that jute underwent shared whole-genome duplication ∼18.66 million years (Myr) ago prior to speciation. RNA expression analysis from isolated fibre cells reveals the key regulatory and structural genes involved in fibre formation. This work expands our understanding of the molecular basis of fibre formation laying the foundation for the genetic improvement of jute.


Assuntos
Corchorus/genética , Genoma de Planta , Corchorus/metabolismo , Genes de Plantas , Genômica , Filogenia , Melhoramento Vegetal , Especificidade da Espécie
6.
Genome Announc ; 4(6)2016 Dec 08.
Artigo em Inglês | MEDLINE | ID: mdl-27932650

RESUMO

Marinobacter sp. strain X15-166BT was cultivated from sediment in Honolulu Harbor, Hawai'i. The X15-166BT draft genome of 3,490,661 bp encodes 3,115 protein-coding open reading frames. We anticipate that the genome will provide insights into the strain's lifestyle and the evolution of Marinobacter.

7.
Genome Announc ; 4(5)2016 Oct 20.
Artigo em Inglês | MEDLINE | ID: mdl-27795280

RESUMO

The genus Terasakiispira hosts only Terasakiispira papahanaumokuakeensis PH27AT, cultivated from an anchialine pond on Pearl and Hermes Atoll, Northwestern Hawaiian Islands. The strain's genome sequence may provide insights into the evolution of free-living Oceanospirillaceae.

8.
Genome Announc ; 3(5)2015 Oct 22.
Artigo em Inglês | MEDLINE | ID: mdl-26494668

RESUMO

Flavobacterium spp. have been cultivated from diverse aquatic and terrestrial habitats. F. akiainvivens IK-1(T) was cultivated from decaying wood of Wikstroemia oahuensis, an endemic Hawaiian shrub. The strain's genome sequence may provide insights into niche adaptation and evolution of the genus in a mid-ocean archipelago.

9.
Stand Genomic Sci ; 10: 76, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-26457128

RESUMO

Thermus sp. strain CCB_US3_UF1 is a thermophilic bacterium of the genus Thermus, a member of the family Thermaceae. Members of the genus Thermus have been widely used as a biological model for structural biology studies and to understand the mechanism of microbial adaptation under thermal environments. Here, we present the complete genome sequence of Thermus sp. CCB_US3_UF1 isolated from a hot spring in Malaysia, which is the fifth member of the genus Thermus with a completely sequenced and publicly available genome (Genbank date of release: December 2, 2011). Thermus sp. CCB_US3_UF1 has the third largest genome within the genus. The complete genome comprises of a chromosome of 2.26 Mb and a plasmid of 19.7 kb. The genome contains 2279 protein-coding and 54 RNA genes. In addition, its genome revealed potential pathways for the synthesis of secondary metabolites (isoprenoid) and pigments (carotenoid).

10.
Sci Rep ; 5: 11407, 2015 Jun 22.
Artigo em Inglês | MEDLINE | ID: mdl-26094577

RESUMO

Globins are haem-binding proteins with a conserved fold made up of α-helices and can possess diverse properties. A putative globin-coupled sensor from Methylacidiphilum infernorum, HGbRL, contains an N-terminal globin domain whose open and closed structures reveal an untypical dimeric architecture. Helices E and F fuse into an elongated helix, resulting in a novel site-swapped globin fold made up of helices A-E, hence the distal site, from one subunit and helices F-H, the proximal site, from another. The open structure possesses a large cavity binding an imidazole molecule, while the closed structure forms a unique Lys-His hexacoordinated species, with the first turn of helix E unravelling to allow Lys52(E10) to bind to the haem. Ligand binding induces reorganization of loop CE, which is stabilized in the closed form, and helix E, triggering a large conformational movement in the open form. These provide a mechanical insight into how a signal may be relayed between the globin domain and the C-terminal domain of HGbRL, a Roadblock/LC7 domain. Comparison with HGbI, a closely related globin, further underlines the high degree of structural versatility that the globin fold is capable of, enabling it to perform a diversity of functions.


Assuntos
Globinas/ultraestrutura , Verrucomicrobia/metabolismo , Sítios de Ligação , Cristalografia por Raios X , Globinas/genética , Modelos Moleculares , Ligação Proteica , Dobramento de Proteína , Transdução de Sinais
11.
J Mol Graph Model ; 52: 103-13, 2014 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-25023665

RESUMO

The allosteric pocket of the Dengue virus (DENV2) NS2B/NS3 protease, which is proximal to its catalytic triad, represents a promising drug target (Othman et al., 2008). We have explored this binding site through large-scale virtual screening and molecular dynamics simulations followed by calculations of binding free energy. We propose two mechanisms for enzyme inhibition. A ligand may either destabilize electronic density or create steric effects relating to the catalytic triad residues NS3-HIS51, NS3-ASP75, and NS3-SER135. A ligand may also disrupt movement of the C-terminal of NS2B required for inter-conversion between the "open" and "closed" conformations. We found that chalcone and adenosine derivatives had the top potential for drug discovery hits, acting through both inhibitory mechanisms. Studying the molecular mechanisms of these compounds might be helpful in further investigations of the allosteric pocket and its potential for drug discovery.


Assuntos
Sítio Alostérico , Vírus da Dengue/enzimologia , Avaliação Pré-Clínica de Medicamentos , Simulação de Dinâmica Molecular , Inibidores de Proteases/análise , Serina Endopeptidases/metabolismo , Vírus da Dengue/efeitos dos fármacos , Ligação de Hidrogênio , Ligantes , Inibidores de Proteases/química , Inibidores de Proteases/farmacologia , Homologia Estrutural de Proteína , Termodinâmica
12.
J Biochem ; 156(2): 97-106, 2014 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-24733432

RESUMO

A truncated haemoglobin (tHb) has been identified in an acidophilic and thermophilic methanotroph Methylacidiphilium infernorum. Hell's Gate Globin IV (HGbIV) and its related tHbs differ from all other bacterial tHbs due to their distinctively large sequence and polar distal haem pocket residues. Here we report the crystal structure of HGbIV determined at 1.96 Å resolution. The HGbIV structure has the distinctive 2/2 α-helical structure with extensions at both termini. It has a large distal site cavity in the haem pocket surrounded by four polar residues: His70(B9), His71(B10), Ser97(E11) and Trp137(G8). This cavity can bind bulky ligands such as a phosphate ion. Conformational shifts of His71(B10), Leu90(E4) and Leu93(E7) can also provide more space to accommodate larger ligands than the phosphate ion. The entrance/exit of such bulky ligands might be facilitated by positional flexibility in the CD1 loop, E helix and haem-propionate A. Therefore, the large cavity in HGbIV with polar His70(B9) and His71(B10), in contrast to the distal sites of other bacterial tHbs surrounded by non-polar residues, suggests its distinct physiological functions.


Assuntos
Proteínas de Bactérias/química , Hemoglobinas/química , Verrucomicrobia , Sequência de Aminoácidos , Sítios de Ligação , Complexos de Coordenação/química , Cristalografia por Raios X , Heme/química , Ligação de Hidrogênio , Concentração de Íons de Hidrogênio , Modelos Moleculares , Dados de Sequência Molecular , Estabilidade Proteica , Estrutura Quaternária de Proteína , Estrutura Secundária de Proteína , Estrutura Terciária de Proteína
13.
Stand Genomic Sci ; 7(3): 483-96, 2013.
Artigo em Inglês | MEDLINE | ID: mdl-24019994

RESUMO

Salmonella enterica subspecies enterica serovar Typhi is a rod-shaped, Gram-negative, facultatively anaerobic bacterium. It belongs to the family Enterobacteriaceae in the class Gammaproteobacteria, and has the capability of residing in the human gallbladder by forming a biofilm and hence causing the person to become a typhoid carrier. Here we present the complete genome of Salmonella enterica subspecies enterica serotype Typhi strain P-stx-12, which was isolated from a chronic carrier in Varanasi, India. The complete genome comprises a 4,768,352 bp chromosome with a total of 98 RNA genes, 4,691 protein-coding genes and a 181,431 bp plasmid. Genome analysis revealed that the organism is closely related to Salmonella enterica serovar Typhi strain Ty2 and Salmonella enterica serovar Typhi strain CT18, although their genome structure is slightly different.

14.
Genome Announc ; 1(3)2013 Jun 20.
Artigo em Inglês | MEDLINE | ID: mdl-23788551

RESUMO

We report here the draft genome sequence of Thermomyces lanuginosus strain SSBP, which was isolated from soil in South Africa. This fungus produces the largest amount of xylanase ever reported in the literature.

15.
Enzyme Microb Technol ; 53(1): 46-54, 2013 Jun 10.
Artigo em Inglês | MEDLINE | ID: mdl-23683704

RESUMO

A truncated form of an α-amylase, GTA, from thermophilic Geobacillus thermoleovorans CCB_US3_UF5 was biochemically and structurally characterized. The recombinant GTA, which lacked both the N- and C-terminal transmembrane regions, functioned optimally at 70°C and pH 6.0. While enzyme activity was not enhanced by the addition of CaCl2, GTA's thermostability was significantly improved in the presence of CaCl2. The structure, in complex with an acarbose-derived pseudo-hexasaccharide, consists of the typical three domains and binds one Ca(2+) ion. This Ca(2+) ion was strongly bound and not chelated by EDTA. A predicted second Ca(2+)-binding site, however, was disordered. With limited subsites, two novel substrate-binding residues, Y147 and Y182, may help increase substrate affinity. No distinct starch-binding domain is present, although two regions rich in aromatic residues have been observed. GTA, with a smaller domain B and several shorter loops compared to other α-amylases, has one of the most compact α-amylase folds that may contribute greatly to its tight Ca(2+) binding and thermostability.


Assuntos
Geobacillus/enzimologia , alfa-Amilases/química , alfa-Amilases/metabolismo , Acarbose/química , Acarbose/metabolismo , Sequência de Aminoácidos , Sítios de Ligação , Cálcio/metabolismo , Cristalização , Cristalografia por Raios X , Estabilidade Enzimática , Geobacillus/classificação , Modelos Moleculares , Dados de Sequência Molecular , Alinhamento de Sequência , Temperatura
16.
BMC Genomics ; 14: 75, 2013 Feb 02.
Artigo em Inglês | MEDLINE | ID: mdl-23375136

RESUMO

BACKGROUND: Hevea brasiliensis, a member of the Euphorbiaceae family, is the major commercial source of natural rubber (NR). NR is a latex polymer with high elasticity, flexibility, and resilience that has played a critical role in the world economy since 1876. RESULTS: Here, we report the draft genome sequence of H. brasiliensis. The assembly spans ~1.1 Gb of the estimated 2.15 Gb haploid genome. Overall, ~78% of the genome was identified as repetitive DNA. Gene prediction shows 68,955 gene models, of which 12.7% are unique to Hevea. Most of the key genes associated with rubber biosynthesis, rubberwood formation, disease resistance, and allergenicity have been identified. CONCLUSIONS: The knowledge gained from this genome sequence will aid in the future development of high-yielding clones to keep up with the ever increasing need for natural rubber.


Assuntos
Genômica , Hevea/genética , Análise de Sequência , Alérgenos/genética , Resistência à Doença/genética , Evolução Molecular , Proteínas F-Box/genética , Genoma de Planta/genética , Haploidia , Hevea/imunologia , Hevea/metabolismo , Látex/metabolismo , Anotação de Sequência Molecular , Filogenia , Reguladores de Crescimento de Plantas/genética , Borracha/metabolismo , Transdução de Sinais/genética , Fatores de Transcrição/genética , Madeira/metabolismo
17.
BMC Genomics ; 13: 493, 2012 Sep 19.
Artigo em Inglês | MEDLINE | ID: mdl-22992219

RESUMO

BACKGROUND: Macrophomina phaseolina is one of the most destructive necrotrophic fungal pathogens that infect more than 500 plant species throughout the world. It can grow rapidly in infected plants and subsequently produces a large amount of sclerotia that plugs the vessels, resulting in wilting of the plant. RESULTS: We sequenced and assembled ~49 Mb into 15 super-scaffolds covering 92.83% of the M. phaseolina genome. We predict 14,249 open reading frames (ORFs) of which 9,934 are validated by the transcriptome. This phytopathogen has an abundance of secreted oxidases, peroxidases, and hydrolytic enzymes for degrading cell wall polysaccharides and lignocelluloses to penetrate into the host tissue. To overcome the host plant defense response, M. phaseolina encodes a significant number of P450s, MFS type membrane transporters, glycosidases, transposases, and secondary metabolites in comparison to all sequenced ascomycete species. A strikingly distinct set of carbohydrate esterases (CE) are present in M. phaseolina, with the CE9 and CE10 families remarkably higher than any other fungi. The phenotypic microarray data indicates that M. phaseolina can adapt to a wide range of osmotic and pH environments. As a broad host range pathogen, M. phaseolina possesses a large number of pathogen-host interaction genes including those for adhesion, signal transduction, cell wall breakdown, purine biosynthesis, and potent mycotoxin patulin. CONCLUSIONS: The M. phaseolina genome provides a framework of the infection process at the cytological and molecular level which uses a diverse arsenal of enzymatic and toxin tools to destroy the host plants. Further understanding of the M. phaseolina genome-based plant-pathogen interactions will be instrumental in designing rational strategies for disease control, essential to ensuring global agricultural crop production and security.


Assuntos
Ascomicetos/genética , Genoma Fúngico/genética , Doenças das Plantas/microbiologia , Fases de Leitura Aberta/genética , Transcriptoma/genética
18.
J Bacteriol ; 194(8): 2115-6, 2012 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-22461552

RESUMO

We report here the complete genome sequence of Salmonella enterica subsp. enterica serovar Typhi P-stx-12, a clinical isolate obtained from a typhoid carrier in India.


Assuntos
Genoma Bacteriano , Salmonella typhi/classificação , Salmonella typhi/genética , Sequência de Bases , Regulação Bacteriana da Expressão Gênica , Dados de Sequência Molecular , Especificidade da Espécie
19.
J Bacteriol ; 194(5): 1239, 2012 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-22328744

RESUMO

Geobacillus thermoleovorans CCB_US3_UF5 is a thermophilic bacterium isolated from a hot spring in Malaysia. Here, we report the complete genome of G. thermoleovorans CCB_US3_UF5, which shows high similarity to the genome of Geobacillus kaustophilus HTA 426 in terms of synteny and orthologous genes.


Assuntos
DNA Bacteriano/química , DNA Bacteriano/genética , Genoma Bacteriano , Geobacillus/genética , Geobacillus/isolamento & purificação , Fontes Termais/microbiologia , Malásia , Dados de Sequência Molecular , Análise de Sequência de DNA
20.
J Bacteriol ; 194(5): 1240, 2012 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-22328745

RESUMO

Thermus sp. strain CCB_US3_UF1, a thermophilic bacterium, has been isolated from a hot spring in Malaysia. Here, we present the complete genome sequence of Thermus sp. CCB_US3_UF1.


Assuntos
DNA Bacteriano/química , DNA Bacteriano/genética , Genoma Bacteriano , Fontes Termais/microbiologia , Thermus/genética , Thermus/isolamento & purificação , Malásia , Dados de Sequência Molecular , Análise de Sequência de DNA
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