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1.
Electron. j. biotechnol ; 51: 40-49, May. 2021. tab, ilus, graf
Article in English | LILACS | ID: biblio-1343322

ABSTRACT

BACKGROUND: Scavenger receptor class B (SRB) is a multifunctional protein in animals that participates in physiological processes, including recognition of a wide range of ligands. Astaxanthin is a major carotenoid found in shrimp. However, the molecular mechanism of astaxanthin and SRB protein binding has not been reported. RESULTS: In the present study, a member of the SRB subfamily, named PmSRB, was identified from the transcriptome of black tiger shrimp (Penaeus monodon). The open reading frame of PmSRB was 1557 bp in length and encoded 518 amino acids. The structure of PmSRB included a putative transmembrane structure at the N-terminal region and a CD36 domain. Multiple sequence alignment indicated that the CD36 domain were conserved. Phylogenetic analysis showed four separate branches (SRA, SRB, SRC, and croquemort) in the phylogenetic tree and that PmSRB was clustered with SRB of Eriocheir sinensis. Quantitative real-time polymerase chain reaction showed that the PmSRB gene was widely expressed in all tissues tested, with the highest expression level observed in the lymphoid organ and brain. Subcellular localization analysis revealed that PmSRB-GFP (green fluorescent protein) fusion proteins were predominantly localized in the cell membrane. The recombinant proteins of PmSRB showed binding activities against astaxanthin in vitro. CONCLUSIONS: PmSRB was identified and characterized in this study. It is firstly reported that PmSRB may take as an important mediator of astaxanthin uptake in shrimp.


Subject(s)
Animals , Penaeidae , Receptors, Scavenger/metabolism , In Vitro Techniques , Blotting, Western , Chromatography, High Pressure Liquid , Sequence Alignment , Xanthophylls , Receptors, Scavenger/isolation & purification , Receptors, Scavenger/genetics , Real-Time Polymerase Chain Reaction/methods , Transcriptome
2.
Article in Chinese | WPRIM | ID: wpr-921672

ABSTRACT

Dirigent(DIR) proteins are involved in the biosynthesis of lignin, lignans, and gossypol in plants and respond to biotic and abiotic stresses. Based on the full-length transcriptome of Schisandra chinensis, bioinformatics methods were used to preliminarily identify the DIR gene family and analyze the physico-chemical properties, subcellular localization, conserved motifs, phylogeny, and expression patterns of the proteins. The results showed that a total of 34 DIR genes were screened and the encoded proteins were 156-387 aa. The physico-chemical properties of the proteins were different and the secondary structure was mainly random coil. Half of the DIR proteins were located in chloroplast, while the others in extracellular region, endoplasmic reticulum, cytoplasm, etc. Phylogenetic analysis of DIR proteins from S. chinensis and the other 8 species such as Arabidopsis thaliana, Oryza sativa, and Glycine max demonstrated that all DIR proteins were clustered into 5 subfamilies and that DIR proteins from S. chinensis were in 4 subfamilies. DIR-a subfamily has the unique structure of 8 β-sheets, as verified by multiple sequence alignment. Finally, through the analysis of the transcriptome of S. chinensis fruit at different development stages, the expression pattern of DIR was clarified. Combined with the accumulation of lignans in fruits at different stages, DIR might be related to the synthesis of lignans in S. chinensis. This study lays a theoretical basis for exploring the biological functions of DIR genes and elucidating the biosynthesis pathway of lignans in S. chinensis.


Subject(s)
Fruit/genetics , Lignans/analysis , Phylogeny , Schisandra , Sequence Alignment
3.
Chinese Journal of Biotechnology ; (12): 4187-4200, 2021.
Article in Chinese | WPRIM | ID: wpr-921498

ABSTRACT

The amino acid sequence of ancestral enzymes from extinct organisms can be deduced through in silico approach termed ancestral sequence reconstruction (ASR). ASR usually has six steps, which are the collection of nucleic acid/amino acid sequences of modern enzymes, multiple sequence alignment, phylogenetic tree construction, computational deduction of ancestral enzyme sequence, gene cloning, and characterization of enzyme properties. This method is widely used to study the adaptation and evolution mechanism of molecules to the changing environmental conditions on planetary time scale. As enzymes play key roles in biocatalysis, this method has become a powerful method for studying the relationship among the sequence, structure, and function of enzymes. Notably, most of the ancestral enzymes show better temperature stability and mutation stability, making them ideal protein scaffolds for further directed evolution. This article summarizes the computer algorithms, applications, and commonly used computer software of ASR, and discusses the potential application in directed evolution of enzymes.


Subject(s)
Amino Acid Sequence , Evolution, Molecular , Phylogeny , Proteins/genetics , Sequence Alignment
4.
Chinese Journal of Biotechnology ; (12): 3242-3252, 2021.
Article in Chinese | WPRIM | ID: wpr-921421

ABSTRACT

L-asparaginase hydrolyzes L-asparagine to produce L-aspartic acid and ammonia. It is widely distributed in microorganisms, plants and serum of some rodents, and has important applications in the pharmaceutical and food industries. However, the poor thermal stability, low catalytic efficiency and low yield hampered the further application of L-asparaginase. In this paper, rational design and 5' untranslated region (5'UTR) design strategies were used to increase the specific enzyme activity and protein expression of L-asparaginase derived from Rhizomucor miehei (RmAsnase). The results showed that among the six mutants constructed through homology modeling combined with sequence alignment, the specific enzyme activity of the mutant A344E was 1.5 times higher than the wild type. Subsequently, a food-safe strain Bacillus subtilis 168/pMA5-A344E was constructed, and the UTR strategy was used for the construction of recombinant strain B. subtilis 168/pMA5 UTR-A344E. The enzyme activity of B. subtilis 168/pMA5 UTR-A344E was 7.2 times higher than that of B. subtilis 168/pMA5-A344E. The recombinant strain B. subtilis 168/pMA5 UTR-A344E was scaled up in 5 L fermenter, and the final yield of L-asparaginase was 489.1 U/mL, showing great potential for industrial application.


Subject(s)
Asparaginase/genetics , Bacillus subtilis/genetics , Industrial Microbiology , Protein Engineering , Rhizomucor/enzymology , Sequence Alignment
5.
Mem. Inst. Oswaldo Cruz ; 112(6): 447-451, June 2017. graf
Article in English | LILACS | ID: biblio-1040570

ABSTRACT

The current yellow fever outbreak in Brazil is the most severe one in the country in recent times. It has rapidly spread to areas where YF virus (YFV) activity has not been observed for more than 70 years and vaccine coverage is almost null. Here, we sequenced the whole YFV genome of two naturally infected howler-monkeys (Alouatta clamitans) obtained from the Municipality of Domingos Martins, state of Espírito Santo, Brazil. These two ongoing-outbreak genome sequences are identical. They clustered in the 1E sub-clade (South America genotype I) along with the Brazilian and Venezuelan strains recently characterised from infections in humans and non-human primates that have been described in the last 20 years. However, we detected eight unique amino acid changes in the viral proteins, including the structural capsid protein (one change), and the components of the viral replicase complex, the NS3 (two changes) and NS5 (five changes) proteins, that could impact the capacity of viral infection in vertebrate and/or invertebrate hosts and spreading of the ongoing outbreak.


Subject(s)
Animals , Polymorphism, Genetic/genetics , Yellow Fever/veterinary , Yellow fever virus/genetics , Genome, Viral/genetics , Alouatta/virology , Monkey Diseases/virology , Phylogeny , Yellow Fever/epidemiology , Yellow Fever/virology , Brazil/epidemiology , Disease Outbreaks , Sequence Alignment , Amino Acid Sequence , Genotype , Monkey Diseases/epidemiology
6.
São Paulo; s.n; 2017. 222 p.
Thesis in Portuguese | LILACS | ID: biblio-868171

ABSTRACT

Introdução. A leishmaniose tegumentar americana (LTA) é uma endemia de importância em saúde pública na Amazônia Brasileira, onde possui diferentes perfis de transmissão com a participação de diversas espécies de vetores e de protozoários do gênero Leishmania. O Estado do Acre apresenta altos índices de LTA e, no ano de 2015, apresentou o mais alto coeficiente de detecção de casos (137,7/100.000 hab.) da doença no Brasil. Objetivo. Analisar aspectos epidemiológicos da LTA no município de Xapuri, Estado do Acre, Brasil, envolvendo população humana, cães domésticos, vetores e identificação de Leishmania. Materiais e Métodos. Para a avaliação epidemiológica, foram analisadas fichas de notificação dos casos humanos no período de 2008 a 2014 obtidas do sistema de vigilância epidemiológica do município. Foram analisadas as variáveis: sexo, grupo etário, escolaridade, forma clínica, diagnóstico, tratamento e evolução clínica. Os dados foram submetidos à análise descritiva e teste estatístico do qui-quadrado de Pearson utilizando o pacote estatístico STATA. Também foram obtidas amostras de material de pacientes (escarificação das lesões fixadas em lâminas) atendidos no centro médico do município, durante o período de novembro de 2014 a janeiro de 2016. As amostras foram submetidas à análise molecular para diagnóstico de Leishmania spp. O inquérito canino foi realizado em áreas urbanas e rurais; nestas, predominantemente, em seringais, onde a doença foi reportada em humanos avaliação clínica dos animais para busca de lesões e sinais característicos de leishmanioses, foram coletadas amostras de sangue venoso por punção jugular ou cefálica, e quando havia lesões sugestivas da doença, foram anestesiados e submetidos à biopsia para colheita do fragmento de lesão. Amostras destes fragmentos foram submetidas a técnicas parasitológicas, inoculação em meio de cultura Neal, Novy e Nicolle, exame direto e técnicas moleculares para detecção do parasita. A identificação de Leishmania spp. foi realizada por técnicas moleculares. Os flebotomíneos foram coletados em ambiente domiciliar e florestal de dois seringais (Floresta e Cachoeira) e na área urbana, com armadilhas luminosas tipo CDC, instaladas mensalmente, no período de agosto de 2013 a julho de 2015. Neste período, apenas no seringal Cachoeira, também foram feitas coletas utilizando armadilhas de Shannon nas cores branca e preta, e de janeiro a maio de 2016, coletas em trocos de árvores com aspiradores manuais. Uma amostra de fêmeas coletadas pelas diferentes técnicas foi dissecada viii para investigação da presença de flagelados. Para a análise do comportamento da fauna flebotomínea foram utilizados índices ecológicos como de Shannon, Pielou e Abundância das Espécies Padronizado, média geométrica de Williams e análise dos componentes principais. Para estimar a atratividade dos flebotomíneos pelas cores branca e preta foi utilizado o teste de Mann-Whitney (p<0,05). Análises morfométricas utilizando o teste de Gabriel (teste F, p <0,05) foram feitas para distinguir alguns táxons. Para as análises moleculares dos parasitas foi empregada a técnica de Nested-PCR SSU rRNA utilizando os iniciadores S4/S12 e S17/S18 e sequenciamento. Resultados. No estudo de casos humanos, constatou-se que a doença ocorre predominantemente em populações rurais e isoladas do município, em indivíduos de ambos os sexos, com as incidências mais elevadas em crianças e adolescentes. Em 33 dos 45 pacientes com clínica positiva para LTA foram detectadas a presença de DNA de Leishmania spp. Nos cães domésticos, verificou-se alta taxa de infecção (20,0 por cento ) por Leishmania (Viannia) sp. Nos estudos de flebotomíneos, foram coletados 21.197 espécimes (14.210 fêmeas e 7.107 machos) com armadilhas CDC, e 6.309 (864 machos e 5.445 fêmeas) com armadilhas de Shannon. As frequências, abundâncias e densidades mais elevadas foram dos gêneros Nyssomyia, Psychodopygus e Trichophoromyia, coletados em ambientes silvestres, peri e intradomiciliares. Em ambiente rural foram coletados 99,9 por cento dos espécimes e no urbano apenas 0,1 por cento . Nyssomyia shawi predominou no Seringal Cachoeira, e Trichophoromyia spp. (Th. auraensis/Th. ruifreitasi) no Seringal Floresta. Espécies do gênero Psychodopygus predominaram no período chuvoso, enquanto as de Nyssomyia, no período seco. Infecções por Leishmania spp. foram detectadas em Brumptomyia sp., Nyssomyia antunesi, Ny. shawi, Lutzomyia sherlocki, Psathyromyia aragaoi, Psychodopygus carrerai carrerai, Ps. davisi, Ps. hirsutus hisutus, Ps. llanosmartinsi, Ps. lainsoni, Thrichophoromyia ubiquitalis e Trichophoromyia spp. Por meio de análises morfológicas e morfométricas das fêmeas de Trichophoromyia sugeriu-se a distinção de Th. octavioi de Trichophoromyia spp. (Th. auraensis/Th. ruifreitasi) e descreveu-se, Psathyromyia elizabethdorvalae sp. n. Conclusões. A LTA em Xapuri apresenta um perfil de transmissão silvestre e outro domiciliar. As populações humanas e caninas que frequentam ambientes florestais estão expostas a uma alta diversidade de vetores e de agentes etiológicos, o que aumenta o risco de infecção de LTA. As informações aqui apresentadas podem nortear as medidas de controle, planejamento das ações e definição de prioridades dos órgãos de vigilância epidemiológica do Estado do Acre, visando o diagnóstico precoce e tratamento adequado dos casos de leishmanioses da população humana de Xapuri


Introduction. American cutaneous leishmaniasis (ACL) is an endemic disease that deserves the attention of public health in the Brazilian Amazon, where it has various transmission profiles with the participation of several species of vectors and protozoa of the genus Leishmania. The state of Acre registers high rates of ACL, having in 2015 the highest coefficient of detection of cases (137.7 / 100,000 inhab.) in Brazil. Objective. To analyze the epidemiological aspects of LTA in the municipality of Xapuri, State of Acre, Brazil, involving the human population, domestic dogs, vectors and the identification of Leishmania ssp. Materials and Methods. For the epidemiological evaluation, records of the human cases notified between 2008 and 2014 obtained from the epidemiological surveillance system of the municipality, were analyzed. The following variables were selected for analysis: sex, age group, schooling, clinical form, diagnosis, treatment and clinical evolution. The data were submitted to descriptive analysis and the Pearson chi-squared statistical test using the statistical package STATA. Samples of patient material (scarification of lesions fixed on slides) were also obtained from the medical center of the city during the period from November 2014 to January 2016. These samples were submitted to molecular analysis for the diagnosis of Leishmania spp. The canine survey was carried out in both urban and rural areas, in the latter rubber plantations where the disease had been reported in humans predominated. After a clinical evaluation to search for lesions and characteristic signs of leishmaniasis, samples of venous blood were collected by jugular or cephalic puncture, and when the animals presented lesions suggestive of cutaneous leishmaniasis, they were anesthetized and submitted to biopsy to harvest the lesion fragment. Samples of these fragments were submitted to parasitological techniques, inoculation in Neal, Novy and Nicolle culture medium, direct examination and molecular techniques to detect Leishmania spp. The samples were submitted to molecular analysis for the diagnosis of Leishmania spp. The phlebotomine survey was carried out in forest and the domiciliary environment of the city and in two rubber plantation areas (Seringal Cachoeira and Seringal Floresta), monthly using CDC light traps, from August 2013 to July 2015. In this period, only in the Seringal Cachoeira were collections also made using black and white Shannon traps. Collections in tree trunks and among tree roots with manual aspirators were also undertaken from January to May 2016. xi Samples of females collected by different techniques were dissected to investigate the presence of flagellates. For the analysis of the behavior of the phlebotomine fauna, ecological indexes such as Shannon, Pielou, and Standardized Species Abundance, Williams geometric mean and main component analysis were used. The Mann-Whitney test (p <0.05) was used to estimate the attractiveness of the black and white colors to sandflies. Morphometric analyses using the Gabriel test (test F, p <0.05) were made to distinguish between some taxa. For the molecular analyses of the parasites the Nested-PCR SSU rRNA technique was used using primers S4 / S12 and S17 / S18 and sequencing. Results. In the study of human cases, it was found that the disease occurs in rural and isolated populations and in individuals of both sexes, especially in children and adolescents. In 33 of the 45 patients with positive ACL, the presence of Leishmania spp DNA was detected. The domestic dogs have shown a high infection rate (20.0 per cent ) attributed to Leishmania (Viannia) sp. In the sandfly studies, 21,197 specimens (14,210 females and 7,107 males) were collected in CDC traps, and 6,309 (864 males and 5,445 females) were collected in Shannon traps. The highest frequencies, abundances and densities were of the genera Nyssomyia, Psychodopygus and Trichophoromyia collected in wild, peri and intradomiciliary environments. Nyssomyia shawi predominated in the Seringal Cachoeira, and the Trichophoromyia spp. (Th. auraensis/Th. ruifreitasi) in the Seringal Floresta. Species of the genus Psychodopygus predominated in the rainy season while those of Nyssomyia in the dry period. Natural infections by Leishmania spp were detected in Brumptomyia sp., Nyssomyia antunesi, Ny. shawi, Lutzomyia sherlocki, Psathyromyia aragaoi, Psychodopygus carrerai carrerai, Ps. davisi, Ps. hirsutus hirsutus, Ps. llanosmartinsi, Ps. lainsoni, Trichophoromyia ubiquitalis and Trichophoromyia sp. Morphological and morphometric analyses of Trichophoromyia females were suggested to distinguish Th. octavioi from Trichophoromyia spp (Th. auraensis/Th. ruifreitasi), Pa. elizabethdorvalae being described for the first time. Conclusions. ACL in Xapuri presents one profile of wild transmission and another of domiciliar transmission. Both populations, human and canine, because they live in forest environments are exposed to a high diversity of vectors and etiological agents, which increases the risk of ACL infection. The information presented here may guide the measures of control, planning of actions and definition of priorities taken by the organs of surveillance and epidemiology of the State of Acre, aiming at the early diagnosis and appropriate treatment of the human cases in Xapuri


Subject(s)
Humans , Dogs , Biodiversity , Disease Transmission, Infectious , Disease Vectors , Leishmaniasis, Cutaneous/epidemiology , Psychodidae , Animals, Wild , Chi-Square Distribution , Hevea , Leishmania , Sequence Alignment
7.
Protein & Cell ; (12): 590-600, 2017.
Article in English | WPRIM | ID: wpr-756983

ABSTRACT

Entero virus 71 (EV71) causes hand, foot, and mouth disease (HFMD) and occasionally leads to severe neurological complications and even death. Scavenger receptor class B member 2 (SCARB2) is a functional receptor for EV71, that mediates viral attachment, internalization, and uncoating. However, the exact binding site of EV71 on SCARB2 is unknown. In this study, we generated a monoclonal antibody (mAb) that binds to human but not mouse SCARB2. It is named JL2, and it can effectively inhibit EV71 infection of target cells. Using a set of chimeras of human and mouse SCARB2, we identified that the region containing residues 77-113 of human SCARB2 contributes significantly to JL2 binding. The structure of the SCARB2-JL2 complex revealed that JL2 binds to the apical region of SCARB2 involving α-helices 2, 5, and 14. Our results provide new insights into the potential binding sites for EV71 on SCARB2 and the molecular mechanism of EV71 entry.


Subject(s)
Amino Acid Sequence , Animals , Antibodies, Monoclonal , Chemistry , Genetics , Metabolism , Binding Sites , Cell Line , Crystallography, X-Ray , Enterovirus A, Human , Genetics , Allergy and Immunology , Fibroblasts , Virology , Gene Expression , HEK293 Cells , Humans , Immunoglobulin Fab Fragments , Chemistry , Genetics , Metabolism , Lysosome-Associated Membrane Glycoproteins , Chemistry , Genetics , Allergy and Immunology , Mice , Models, Molecular , Protein Binding , Protein Conformation, alpha-Helical , Protein Conformation, beta-Strand , Protein Interaction Domains and Motifs , Receptors, Scavenger , Chemistry , Genetics , Allergy and Immunology , Receptors, Virus , Chemistry , Genetics , Allergy and Immunology , Recombinant Fusion Proteins , Chemistry , Genetics , Allergy and Immunology , Sequence Alignment , Sequence Homology, Amino Acid , Sf9 Cells , Spodoptera , Thermodynamics
8.
Article in English | WPRIM | ID: wpr-812040

ABSTRACT

Salvia miltiorrhiza is a medicinal plant widely used in the treatment of cardiovascular and cerebrovascular diseases. Hydrophilic phenolic acids, including rosmarinic acid (RA) and lithospermic acid B (LAB), are its primary medicinal ingredients. However, the biosynthetic pathway of RA and LAB in S. miltiorrhiza is still poorly understood. In the present study, we accomplished the isolation and characterization of a novel S. miltiorrhiza Hydroxyphenylpyruvate reductase (HPPR) gene, SmHPPR, which plays an important role in the biosynthesis of RA. SmHPPR contained a putative catalytic domain and a NAD(P)H-binding motif. The recombinant SmHPPR enzyme exhibited high HPPR activity, converting 4-hydroxyphenylpyruvic acid (pHPP) to 4-hydroxyphenyllactic acid (pHPL), and exhibited the highest affinity for substrate 4-hydroxyphenylpyruvate. SmHPPR expression could be induced by various treatments, including SA, GA, MeJA and Ag, and the changes in SmHPPR activity were correlated well with hydrophilic phenolic acid accumulation. SmHPPR was localized in cytoplasm, most likely close to the cytosolic NADPH-dependent hydroxypyruvate reductase active in photorespiration. In addition, the transgenic S. miltiorrhiza hairy roots overexpressing SmHPPR exhibited up to 10-fold increases in the products of hydrophilic phenolic acid pathway. In conclusion, our findings provide a new insight into the synthesis of active pharmaceutical compounds at molecular level.


Subject(s)
Amino Acid Sequence , Benzofurans , Biosynthetic Pathways , Genetics , Cinnamates , Depsides , Gene Expression Regulation, Plant , Genetics , Oxidoreductases , Genetics , Phenylpropionates , Metabolism , Phenylpyruvic Acids , Metabolism , Phylogeny , Plant Proteins , Genetics , Metabolism , Plant Roots , Chemistry , Genetics , Metabolism , Plants, Genetically Modified , Recombinant Proteins , Salvia miltiorrhiza , Chemistry , Genetics , Metabolism , Sequence Alignment
9.
Braz. j. microbiol ; 47(2): 468-479, Apr.-June 2016. tab, graf
Article in English | LILACS | ID: lil-780832

ABSTRACT

Abstract Metabolites of mycoparasitic fungal species such as Trichoderma harzianum 88 have important biological roles. In this study, two new ketoacyl synthase (KS) fragments were isolated from cultured Trichoderma harzianum 88 mycelia using degenerate primers and analysed using a phylogenetic tree. The gene fragments were determined to be present as single copies in Trichoderma harzianum 88 through southern blot analysis using digoxigenin-labelled KS gene fragments as probes. The complete sequence analysis in formation of pksT-1 (5669 bp) and pksT-2 (7901 bp) suggests that pksT-1 exhibited features of a non-reducing type I fungal PKS, whereas pksT-2 exhibited features of a highly reducing type I fungal PKS. Reverse transcription polymerase chain reaction indicated that the isolated genes are differentially regulated in Trichoderma harzianum 88 during challenge with three fungal plant pathogens, which suggests that they participate in the response of Trichoderma harzianum 88 to fungal plant pathogens. Furthermore, disruption of the pksT-2 encoding ketosynthase–acyltransferase domains through Agrobacterium -mediated gene transformation indicated that pksT-2 is a key factor for conidial pigmentation in Trichoderma harzianum 88.


Subject(s)
Trichoderma/enzymology , Fungal Proteins/metabolism , Polyketide Synthases/metabolism , Plant Diseases/microbiology , Trichoderma/classification , Trichoderma/genetics , Fungal Proteins/genetics , Fungal Proteins/chemistry , Molecular Sequence Data , Gene Expression Regulation, Fungal , Sequence Alignment , Amino Acid Sequence , Mycelium/enzymology , Mycelium/genetics , Polyketide Synthases/genetics , Polyketide Synthases/chemistry
10.
Electron. j. biotechnol ; 19(2): 9-13, Mar. 2016. ilus
Article in English | LILACS | ID: lil-782610

ABSTRACT

Background: Protein structural alignment is one of the most fundamental and crucial areas of research in the domain of computational structural biology. Comparison of a protein structure with known structures helps to classify it as a new or belonging to a known group of proteins. This, in turn, is useful to determine the function of protein, its evolutionary relationship with other protein molecules and grasping principles underlying protein architecture and folding. Results: A large number of protein structure alignment methods are available. Each protein structure alignment tool has its own strengths and weaknesses that need to be highlighted. We compared and presented results ofsix most popular and publically available servers for protein structure comparison. These web-based servers were compared with the respect to functionality (features provided by these servers) and accuracy (how well the structural comparison is performed). The CATH was used as a reference. The results showed that overall CE was top performer. DALI and PhyreStorm showed similar results whereas PDBeFold showed the lowest performance. In case of few secondary structural elements, CE, DALI and PhyreStorm gave 100% success rate. Conclusion: Overall none of the structural alignment servers showed 100% success rate. Studies of overall performance, effect of mainly alpha and effect of mainly beta showed consistent performance. CE, DALI, FatCat and PhyreStorm showed more than 90% success rate.


Subject(s)
Protein Conformation , Software , Sequence Alignment/methods
11.
Braz. j. biol ; 76(1): 55-58, Feb. 2016. graf
Article in English | LILACS | ID: lil-774512

ABSTRACT

Abstract Paca (Cuniculus paca Linnaeus, 1766) is the second largest rodent found in Brazil. The quality of the meat and a long tradition of hunting have contributed to the decline of the natural populations of this species. Hunting of paca is strictly prohibited in Brazil, but in spite of this restriction, no forensic tools are available for the identification of the meat. We describe an efficient method, based on single nucleotide polymorphisms of the cytochrome b gene, that can be used to differentiate biological material derived from paca from those of domestic species commonly used as sources of meat. The identification of the presence of C. paca in the samples was 100% reliable.


Resumo Paca (Cuniculus paca Linnaeus, 1766) é o segundo maior roedor brasileiro. A qualidade da carne e a forte tradição da caça de subsistência são fatores que contribuem significativamente para o declínio das populações. Apesar da proibição a caça no Brasil, no momento ainda não há ferramentas disponíveis para identificar a carne e seus produtos como prova forense. Neste trabalho propomos um método eficaz de identificação, baseado em polimorfismos de único nucleotídeo no gene Citocromo b, objetivando diferenciar material biológico de paca das espécies domésticas comumente utilizadas como alimento no Brasil. A identificação das amostras de paca foram possíveis em 100% das amostras analisadas.


Subject(s)
Animals , Conservation of Natural Resources/methods , Cuniculidae/genetics , Cytochromes b/analysis , Meat/analysis , Amino Acid Sequence , Brazil , Cuniculidae/classification , Meat/classification , Sequence Alignment
12.
Article in English | WPRIM | ID: wpr-28309

ABSTRACT

Boiled silkworm pupa is a traditional food in Asia, and patients with silkworm pupa food allergy are common in these regions. Still now only one allergen from silkworm, arginine kinase, has been identified. The purpose of this study was to identify novel food allergens in silkworm pupa by analyzing a protein extract after heat treatment. Heat treated extracts were examined by proteomic analysis. A 27-kDa glycoprotein was identified, expressed in Escherichia coli, and purified. IgE reactivity of the recombinant protein was investigated by ELISA. High molecular weight proteins (above 100 kDa) elicited increased IgE binding after heat treatment compared to that before heat treatment. The molecular identities of these proteins, however, could not be determined. IgE reactivity toward a 27-kDa glycoprotein was also increased after heating the protein extract. The recombinant protein was recognized by IgE antibodies from allergic subjects (33.3%). Glycation or aggregation of protein by heating may create new IgE binding epitopes. Heat stable allergens are shown to be important in silkworm allergy. Sensitization to the 27-kDa glycoprotein from silkworm may contribute to elevation of IgE to silkworm.


Subject(s)
Adolescent , Adult , Allergens/chemistry , Amino Acid Sequence , Animals , Bombyx/chemistry , Epitopes/immunology , Female , Food Hypersensitivity/etiology , Glycoproteins/chemistry , Hot Temperature , Humans , Immunoglobulin E/immunology , Male , Molecular Sequence Data , Molecular Weight , Proteomics , Pupa/chemistry , Recombinant Proteins/biosynthesis , Sequence Alignment
13.
Article in English | WPRIM | ID: wpr-34240

ABSTRACT

To investigate the function and regulation mechanism of ATP-binding cassette, subfamily G, member 2 (ABCG2) in retinoblastoma cancer stem cells (RCSCs), a long-term culture of RCSCs from WERI-Rb1 cell line was successfully established based on the high expression level of ABCG2 on the surface of RCSCs. To further explore the molecular mechanism of ABCG2 on RCSCs, a microRNA that specifically targets ABCG2 was predicted. Subsequently, miR-3163 was selected and confirmed as the ABCG2-regulating microRNA. Overexpression of miR-3163 led to a significant decrease in ABCG2 expression. Additionally, ABCG2 loss-of-function induced anti-proliferation and apoptosis-promoting functions in RCSCs, and multidrug resistance to cisplatin, carboplatin, vincristine, doxorubicin, and etoposide was greatly improved in these cells. Our data suggest that miR-3163 has a significant impact on ABCG2 expression and can influence proliferation, apoptosis, and drug resistance in RCSCs. This work may provide new therapeutic targets for retinoblastoma.


Subject(s)
3' Untranslated Regions , ATP Binding Cassette Transporter, Subfamily G, Member 2/antagonists & inhibitors , Antagomirs/metabolism , Antineoplastic Agents/toxicity , Apoptosis/drug effects , Base Sequence , Cell Line, Tumor , Cell Proliferation/drug effects , Drug Resistance, Neoplasm/drug effects , Gene Silencing , Humans , MicroRNAs/antagonists & inhibitors , Neoplasm Proteins/antagonists & inhibitors , Neoplastic Stem Cells/metabolism , Retinoblastoma/metabolism , Sequence Alignment , Transfection
14.
Protein & Cell ; (12): 403-416, 2016.
Article in English | WPRIM | ID: wpr-757127

ABSTRACT

YfiBNR is a recently identified bis-(3'-5')-cyclic dimeric GMP (c-di-GMP) signaling system in opportunistic pathogens. It is a key regulator of biofilm formation, which is correlated with prolonged persistence of infection and antibiotic drug resistance. In response to cell stress, YfiB in the outer membrane can sequester the periplasmic protein YfiR, releasing its inhibition of YfiN on the inner membrane and thus provoking the diguanylate cyclase activity of YfiN to induce c-di-GMP production. However, the detailed regulatory mechanism remains elusive. Here, we report the crystal structures of YfiB alone and of an active mutant YfiB(L43P) complexed with YfiR with 2:2 stoichiometry. Structural analyses revealed that in contrast to the compact conformation of the dimeric YfiB alone, YfiB(L43P) adopts a stretched conformation allowing activated YfiB to penetrate the peptidoglycan (PG) layer and access YfiR. YfiB(L43P) shows a more compact PG-binding pocket and much higher PG binding affinity than wild-type YfiB, suggesting a tight correlation between PG binding and YfiB activation. In addition, our crystallographic analyses revealed that YfiR binds Vitamin B6 (VB6) or L-Trp at a YfiB-binding site and that both VB6 and L-Trp are able to reduce YfiB(L43P)-induced biofilm formation. Based on the structural and biochemical data, we propose an updated regulatory model of the YfiBNR system.


Subject(s)
Amino Acid Sequence , Bacterial Proteins , Chemistry , Genetics , Metabolism , Binding Sites , Biofilms , Crystallography, X-Ray , Cyclic GMP , Metabolism , Dimerization , Molecular Dynamics Simulation , Molecular Sequence Data , Mutagenesis , Protein Structure, Quaternary , Pseudomonas aeruginosa , Metabolism , Sequence Alignment , Tryptophan , Chemistry , Metabolism , Vitamin B 6 , Chemistry , Metabolism
15.
Protein & Cell ; (12): 434-444, 2016.
Article in English | WPRIM | ID: wpr-757420

ABSTRACT

Osteosarcoma is the most common primary sarcoma of bone, and it is a leading cause of cancer death among adolescents and young adults. However, the molecular mechanism underlying osteosarcoma carcinogenesis remains poorly understood. Recently, cyclin-dependent kinase 6 (CDK6) was identified as an important oncogene. We found that CDK6 protein level, rather than CDK6 mRNA level, is much higher in osteosarcoma tissues than in normal adjacent tissues, which indicates a post-transcriptional mechanism involved in CDK6 regulation in osteosarcoma. MiRNAs are small non-coding RNAs that repress gene expression at the post-transcriptional level and have widely been shown to play important roles in many human cancers. In this study, we investigated the role of miR-29b as a novel regulator of CDK6 using bioinformatics methods. We demonstrated that CDK6 can be downregulated by miR-29b via binding to the 3'-UTR region in osteosarcoma cells. Furthermore, we identified an inverse correlation between miR-29b and CDK6 protein levels in osteosarcoma tissues. Finally, we examined the function of miR-29b-driven repression of CDK6 expression in osteosarcoma cells. The results revealed that miR-29b acts as a tumor suppressor of osteosarcoma by targeting CDK6 in the proliferation and migration processes. Taken together, our results highlight an important role for miR-29b in the regulation of CDK6 in osteosarcoma and may open new avenues for future osteosarcoma therapies.


Subject(s)
3' Untranslated Regions , Animals , Base Sequence , Bone Neoplasms , Metabolism , Pathology , Cell Line, Tumor , Cell Movement , Cell Proliferation , Cyclin-Dependent Kinase 6 , Genetics , Metabolism , Humans , Mice , MicroRNAs , Metabolism , Osteosarcoma , Metabolism , Pathology , RNA Interference , RNA, Messenger , Metabolism , RNA, Small Interfering , Metabolism , Rats , Sequence Alignment , Up-Regulation
16.
Protein & Cell ; (12): 792-803, 2016.
Article in English | WPRIM | ID: wpr-757369

ABSTRACT

MRG proteins are conserved during evolution in fungi, flies, mammals and plants, and they can exhibit diversified functions. The animal MRGs were found to form various complexes to activate gene expression. Plant MRG1/2 and MRG702 were reported to be involved in the regulation of flowering time via binding to H3K36me3-marked flowering genes. Herein, we determined the crystal structure of MRG701 chromodomain (MRG701). MRG701 forms a novel dimerization fold both in crystal and in solution. Moreover, we found that the dimerization of MRG chromodomains is conserved in green plants. Our findings may provide new insights into the mechanism of MRGs in regulation of gene expression in green plants.


Subject(s)
Amino Acid Sequence , Arabidopsis , Genetics , Metabolism , Arabidopsis Proteins , Chemistry , Genetics , Metabolism , Binding Sites , Chromosomal Proteins, Non-Histone , Chemistry , Genetics , Metabolism , Cloning, Molecular , Crystallography, X-Ray , Escherichia coli , Genetics , Metabolism , Gene Expression , Histones , Chemistry , Genetics , Metabolism , Models, Molecular , Oryza , Genetics , Metabolism , Peptides , Chemistry , Genetics , Metabolism , Protein Binding , Protein Interaction Domains and Motifs , Protein Isoforms , Chemistry , Genetics , Metabolism , Protein Multimerization , Protein Structure, Secondary , Recombinant Proteins , Chemistry , Genetics , Metabolism , Sequence Alignment , Sequence Homology, Amino Acid , Viridiplantae , Genetics , Metabolism
17.
Article in English | WPRIM | ID: wpr-812623

ABSTRACT

Amphibian skin contains rich bioactive peptides. Especially, a large amount of antimicrobial peptides have been identified from amphibian skin secretions. Antimicrobial peptides display potent cytolytic activities against a range of pathogenic bacteria and fungi and play important defense roles. No antimicrobial peptides have been reported from toads belonging to the family of Pelobatidae. In this work, two novel antimicrobial peptides (Megin 1 and Megin 2) were purified and characterized from the skin venoms of spadefoot toad Megophrys minor (Pelobatidae, Anura, Amphibia). Megin 1 had an amino acid sequence of FLKGCWTKWYSLKPKCPF-NH2, which was composed of 18 amino acid residues and contained an intra-molecular disulfide bridge and an amidated C-terminus. Megin 2 had an amino acid sequence of FFVLKFLLKWAGKVGLEHLACKFKNWC, which was composed of 27 amino acid residues and contained an intra-molecular disulfide bridge. Both Megin 1 and Megin 2 showed potential antimicrobial abilities against bacteria and fungi. The MICs of Megin 1 against Escherichia coli, Bacillus dysenteriae, Staphylococcus aureus, Bacillus subtilis, and Candida albicans were 25, 3, 6.25, 3, and 50 μg·mL(-1), respectively. The corresponding MICs for Megin 2 were 6.25, 1.5, 12.5, 1.5, and 12.5 μg·mL(-1), respectively. They also exerted strong hemolytic activity against human and rabbit red cells. The results suggested that megin peptides in the toad skin of M. minor displayed toxic effects on both eukaryotes and prokaryotes. This was the first report of antimicrobial peptides from amphibians belonging to the family of Pelobatidae.


Subject(s)
Amino Acid Sequence , Amphibian Venoms , Chemistry , Allergy and Immunology , Animals , Anura , Allergy and Immunology , Bacillus , Candida albicans , Erythrocytes , Physiology , Escherichia coli , Female , Hemolysis , Humans , Male , Peptides , Chemistry , Allergy and Immunology , Rabbits , Sequence Alignment , Skin , Chemistry , Allergy and Immunology , Staphylococcus aureus
18.
Article in English | WPRIM | ID: wpr-812572

ABSTRACT

Phenolic compounds, metabolites of the phenylpropanoid pathway, play an important role in the growth and environmental adaptation of many plants. Phenylalanine ammonia-lyase (PAL) is the first key enzyme of the phenylpropanoid pathway. The present study was designed to investigate whether there is a multi-gene family in I. Indigotic and, if so, to characterize their properties. We conducted a comprehensive survey on the transcription profiling database by using tBLASTn analysis. Several bioinformatics methods were employed to perform the prediction of composition and physicochemical characters. The expression levels of IiPAL genes in various tissues of I. indigotica with stress treatment were examined by quantitative real-time PCR. Protoplast transient transformation was used to observe the locations of IiPALs. IiPALs were functionally characterized by expression with pET-32a vector in Escherichia colis strain BL21 (DE3). Integration of transcripts and metabolite accumulations was used to reveal the relation between IiPALs and target compounds. An new gene (IiPAL2) was identified and both IiPALs had the conserved enzymatic active site Ala-Ser-Gly and were classified as members of dicotyledon. IiPAL1 and IiPAL2 were expressed in roots, stems, leaves, and flowers, with the highest expression levels of IiPAL1 and IiPAL2 being observed in stems and roots, respectively. The two genes responded to the exogenous elicitor in different manners. Subcellular localization experiment showed that both IiPALs were localized in the cytosol. The recombinant proteins were shown to catalyze the conversion of L-Phe to trans-cinnamic acid. Correlation analysis indicated that IiPAL1 was more close to the biosynthesis of secondary metabolites than IiPAL2. In conclusion, the present study provides a basis for the elucidation of the role of IiPALs genes in the biosynthesis of phenolic compounds, which will help further metabolic engineering to improve the accumulation of bioactive components in I. indigotica.


Subject(s)
Amino Acid Sequence , Base Sequence , Cloning, Molecular , Gene Expression Regulation, Plant , Isatis , Genetics , Molecular Sequence Data , Multigene Family , Phenylalanine Ammonia-Lyase , Chemistry , Genetics , Metabolism , Phylogeny , Plant Proteins , Chemistry , Genetics , Metabolism , Sequence Alignment
19.
Article in English | WPRIM | ID: wpr-258815

ABSTRACT

<p><b>OBJECTIVE</b>To explore the viral etiology of human breast cancer to determine whether there are novel molecular targets for gene therapy of breast cancer and provide evidence for the research of gene therapy and vaccine development for breast cancer.</p><p><b>METHODS</b>PCR was used to screen HPV16 and HPV18 oncogenes E6 and E7 in the SKBR3 cell line and in 76 paraffin embedded breast cancer tissue samples. RNA interference was used to knock down the expression of HPV18 E6 and E7 in SKBR3 cells, then the changes in the expression of cell-cycle related proteins, cell viability, colony formation, metastasis, and cell cycle progression were determined.</p><p><b>RESULTS</b>HPV18 oncogenes E6 and E7 were amplified and sequenced from the SKBR3 cells. Of the patient samples, 6.58% and 23.68% were tested to be positive for HPV18 E6 and HPV18 E7. In the cell culture models, the knockdown of HPV18 E6 and E7 inhibited the proliferation, metastasis, and cell cycle progression of SKBR3 cell. The knockdown also clearly affected the expression levels of cell cycle related proteins.</p><p><b>CONCLUSION</b>HPV was a contributor to virus caused human breast cancer, suggesting that the oncogenes in HPV were potential targets for gene therapy of breast cancer.</p>


Subject(s)
Adult , Aged , Aged, 80 and over , Base Sequence , Breast Neoplasms , Genetics , Therapeutics , Female , Genetic Therapy , Methods , Humans , Middle Aged , Oncogene Proteins, Viral , Genetics , Metabolism , Papillomaviridae , Physiology , Papillomavirus Infections , Genetics , Therapeutics , Sequence Alignment
20.
Article in Chinese | WPRIM | ID: wpr-279881

ABSTRACT

The clinical data of one patient with autoimmune polyendocrinopathy syndrome type I were collected. PCR-DNA direct bidirectional sequencing was applied for mutation screening of 14 exons in autoimmune regulator (AIRE) gene in the patient and her parents. A total of 50 unrelated healthy controls were selected and tested. The bioinformatic methods were used to predict the possible impact of the mutations on the structure and function of the AIRE protein. The results of sequencing showed that heterozygous mutation c.622G>T (p.G208W) in exon 5 of the AIRE gene was detected in the patient and was a novel mutation, which had not been reported in the HGMD database and latest articles. This mutation was not detected in the 50 unrelated normal controls. The novel mutation of c.622G>T (p.G208W) in AIRE gene might play an important role in the pathogenesis of this case of autoimmune polyendocrinopathy syndrome type I.


Subject(s)
Adolescent , Adult , Amino Acid Sequence , Base Sequence , Exons , Female , Humans , Male , Middle Aged , Molecular Sequence Data , Mutation , Pedigree , Polyendocrinopathies, Autoimmune , Genetics , Sequence Alignment , Transcription Factors , Chemistry , Genetics , Young Adult
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