Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 25
Filtrar
1.
Int J Mol Sci ; 25(15)2024 Jul 23.
Artigo em Inglês | MEDLINE | ID: mdl-39125576

RESUMO

Epitranscriptomics is considered as a new regulatory step in eukaryotes for developmental processes and stress responses. The aim of this study was, for the first time, to identify RNA methyltransferase (writers) and demethylase (erasers) in four investigated species, i.e., the dinoflagellates Alexandrium tamutum and Amphidinium carterae, the diatom Cylindrotheca closterium, and the green alga Tetraselmis suecica. As query sequences for the enzymatic classes of interest, we selected those ones that were previously detected in marine plants, evaluating their expression upon nutrient starvation stress exposure. The hypothesis was that upon stress exposure, the activation/deactivation of specific writers and erasers may occur. In microalgae, we found almost all plant writers and erasers (ALKBH9B, ALKBH10B, MTB, and FIP37), except for three writers (MTA, VIRILIZER, and HAKAI). A sequence similarity search by scanning the corresponding genomes confirmed their presence. Thus, we concluded that the three writer sequences were lacking from the studied transcriptomes probably because they were not expressed in those experimental conditions, rather than a real lack of these genes from their genomes. This study showed that some of them were expressed only in specific culturing conditions. We also investigated their expression in other culturing conditions (i.e., nitrogen depletion, phosphate depletion, and Zinc addition at two different concentrations) in A. carterae, giving new insights into their possible roles in regulating gene expression upon stress.


Assuntos
Microalgas , Transcriptoma , Microalgas/genética , Microalgas/metabolismo , Perfilação da Expressão Gênica/métodos , Dinoflagellida/genética , Dinoflagellida/metabolismo , Estresse Fisiológico/genética , Metiltransferases/metabolismo , Metiltransferases/genética , Diatomáceas/genética , Diatomáceas/metabolismo
2.
BMC Genomics ; 24(1): 106, 2023 Mar 10.
Artigo em Inglês | MEDLINE | ID: mdl-36899305

RESUMO

BACKGROUND: Dormancy is widespread in both multicellular and unicellular organisms. Among diatoms, unicellular microalgae at the base of all aquatic food webs, several species produce dormant cells (spores or resting cells) that can withstand long periods of adverse environmental conditions. RESULTS: We present the first gene expression study during the process of spore formation induced by nitrogen depletion in the marine planktonic diatom Chaetoceros socialis. In this condition, genes related to photosynthesis and nitrate assimilation, including high-affinity nitrate transporters (NTRs), were downregulated. While the former result is a common reaction among diatoms under nitrogen stress, the latter seems to be exclusive of the spore-former C. socialis. The upregulation of catabolic pathways, such as tricarboxylic acid cycle, glyoxylate cycle and fatty acid beta-oxidation, suggests that this diatom could use lipids as a source of energy during the process of spore formation. Furthermore, the upregulation of a lipoxygenase and several aldehyde dehydrogenases (ALDHs) advocates the presence of oxylipin-mediated signaling, while the upregulation of genes involved in dormancy-related pathways conserved in other organisms (e.g. serine/threonine-protein kinases TOR and its inhibitor GATOR) provides interesting avenues for future explorations. CONCLUSIONS: Our results demonstrate that the transition from an active growth phase to a resting one is characterized by marked metabolic changes and provides evidence for the presence of signaling pathways related to intercellular communication.


Assuntos
Diatomáceas , Diatomáceas/genética , Nitrogênio/metabolismo , Plâncton , Esporos , Expressão Gênica
3.
New Phytol ; 233(2): 809-822, 2022 01.
Artigo em Inglês | MEDLINE | ID: mdl-34533849

RESUMO

Because of their importance as chemical mediators, the presence of a rich and varied family of lipoxygenase (LOX) products, collectively named oxylipins, has been investigated thoroughly in diatoms, and the involvement of these products in important processes such as bloom regulation has been postulated. Nevertheless, little information is available on the enzymes and pathways operating in these protists. Exploiting transcriptome data, we identified and characterized a LOX gene, PaLOX, in Pseudo-nitzschia arenysensis, a marine diatom known to produce different species of oxylipins by stereo- and regio-selective oxidation of eicosapentaenoic acid (EPA) at C12 and C15. PaLOX RNA interference correlated with a decrease of the lipid-peroxidizing activity and oxylipin synthesis, as well as with a reduction of growth of P. arenysensis. In addition, sequence analysis and structure models of the C-terminal part of the predicted protein closely fitted with the data for established LOXs from other organisms. The presence in the genome of a single LOX gene, whose downregulation impairs both 12- and 15-oxylipins synthesis, together with the in silico 3D protein modelling suggest that PaLOX encodes for a 12/15S-LOX with a dual specificity, and provides additional support to the correlation between cell growth and oxylipin biosynthesis in diatoms.


Assuntos
Diatomáceas , Diatomáceas/metabolismo , Lipoxigenase/genética , Lipoxigenase/metabolismo , Oxilipinas/metabolismo , Transcriptoma
4.
Crit Rev Biotechnol ; 41(2): 155-171, 2021 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-33530761

RESUMO

Phenolic compounds (PCs) are a family of secondary metabolites with recognized biological activities making them attractive for the biomedical "red" biotechnology. The development of the eco-sustainable production of natural bioactive metabolites requires using easy cultivable organisms, such as microalgae, which represents one of the most promising sources for biotechnological applications. Microalgae are photosynthetic organisms inhabiting aquatic systems, displaying high levels of biological and functional diversities, and are well-known producers of fatty acids and carotenoids. They are also rich in other families of bioactive molecules e.g. phenolic compounds. Microalgal PCs however are less investigated than other molecular components. This study aims to provide a state-of-art picture of the actual knowledge on microalgal phenolic compounds, reviewing information on the PC content variety and chemodiversity in microalgae, their environmental modulation, and we aim to report discuss data on PC biosynthetic pathways. We report the challenges of promoting microalgae as a relevant source of natural PCs, further enhancing the interests of microalgal "biofactories" for biotechnological applications (i.e. nutraceutical, pharmacological, or cosmeceutical products).


Assuntos
Microalgas , Vias Biossintéticas , Biotecnologia , Carotenoides/metabolismo , Suplementos Nutricionais , Microalgas/metabolismo
5.
Dev Biol ; 448(2): 101-110, 2019 04 15.
Artigo em Inglês | MEDLINE | ID: mdl-30579696

RESUMO

Non-coding regions with dozens to several hundred base pairs of extreme conservation have been found in all metazoan genomes. The distribution of these conserved non-coding elements (CNE) within and across genomes has suggested that many of them may have roles as transcriptional regulatory elements. A combination of bioinformatics and experimental approaches can be used to identify CNEs with regulatory activity in phylogenetically distant species. Nevertheless, the high divergent rate of genomic sequences of several organisms, such as tunicates, complicates the characterization of these conserved elements and very few examples really may prove their functional activity. We used a comparative approach to facilitate the identification of CNEs among distantly related or highly divergent species and experimentally demonstrated the functional significance of these novel CNEs. We first experimentally tested, in C. robusta and D. rerio transgenic embryos, the regulatory activity of conserved elements associated to genes involved in developmental control among different chordates (Homo sapiens and Danio rerio for vertebrates, Ciona robusta and Ciona savignyi for tunicates and Branchiostoma floridae for cephalochordates). Once demonstrated the cross-species functional conservation of these CNEs, the same gene loci were used as references to locate homologous regions and possible CNEs in available tunicate genomes. Comparison of tunicate-specific and chordate-specific CNEs revealed absence of conservation of the regulatory elements in spite of conservation of regulatory patterns, likely due to evolutionary specification of the respective developmental networks. This result highlights the importance of an integrative in-silico/in-vivo approach to CNEs investigation, encompassing both bioinformatics, essential for putative CNEs identification, and laboratory experiments, pivotal for the understanding of CNEs functionality.


Assuntos
Cordados/genética , Sequência Conservada/genética , DNA Intergênico/genética , Urocordados/genética , Animais , Animais Geneticamente Modificados , Sequência de Bases , Embrião não Mamífero/metabolismo , Regulação da Expressão Gênica no Desenvolvimento , Proteínas de Homeodomínio/genética , Proteínas de Homeodomínio/metabolismo , Especificidade da Espécie
6.
Int J Mol Sci ; 21(20)2020 Oct 12.
Artigo em Inglês | MEDLINE | ID: mdl-33053767

RESUMO

Circadian regulations are essential for enabling organisms to synchronize physiology with environmental light-dark cycles. Post-transcriptional RNA modifications still represent an understudied level of gene expression regulation in plants, although they could play crucial roles in environmental adaptation. N6-methyl-adenosine (m6A) is the most prevalent mRNA modification, established by "writer" and "eraser" proteins. It influences the clockwork in several taxa, but only few studies have been conducted in plants and none in marine plants. Here, we provided a first inventory of m6A-related genes in seagrasses and investigated daily changes in the global RNA methylation and transcript levels of writers and erasers in Cymodocea nodosa and Zostera marina. Both species showed methylation peaks during the dark period under the same photoperiod, despite exhibiting asynchronous changes in the m6A profile and related gene expression during a 24-h cycle. At contrasting latitudes, Z. marina populations displayed overlapping daily patterns of the m6A level and related gene expression. The observed rhythms are characteristic for each species and similar in populations of the same species with different photoperiods, suggesting the existence of an endogenous circadian control. Globally, our results indicate that m6A RNA methylation could widely contribute to circadian regulation in seagrasses, potentially affecting the photo-biological behaviour of these plants.


Assuntos
Organismos Aquáticos , Regulação da Expressão Gênica de Plantas , Plantas/genética , RNA de Plantas/genética , Relógios Circadianos , Biologia Computacional , Perfilação da Expressão Gênica , Ontologia Genética , Metilação , Metiltransferases/genética , Metiltransferases/metabolismo , Filogenia , Fenômenos Fisiológicos Vegetais , Plantas/classificação , Plantas/metabolismo
7.
Mar Drugs ; 17(10)2019 Oct 11.
Artigo em Inglês | MEDLINE | ID: mdl-31614509

RESUMO

The sea represents a major source of biodiversity. It exhibits many different ecosystems in a huge variety of environmental conditions where marine organisms have evolved with extensive diversification of structures and functions, making the marine environment a treasure trove of molecules with potential for biotechnological applications and innovation in many different areas. Rapid progress of the omics sciences has revealed novel opportunities to advance the knowledge of biological systems, paving the way for an unprecedented revolution in the field and expanding marine research from model organisms to an increasing number of marine species. Multi-level approaches based on molecular investigations at genomic, metagenomic, transcriptomic, metatranscriptomic, proteomic, and metabolomic levels are essential to discover marine resources and further explore key molecular processes involved in their production and action. As a consequence, omics approaches, accompanied by the associated bioinformatic resources and computational tools for molecular analyses and modeling, are boosting the rapid advancement of biotechnologies. In this review, we provide an overview of the most relevant bioinformatic resources and major approaches, highlighting perspectives and bottlenecks for an appropriate exploitation of these opportunities for biotechnology applications from marine resources.


Assuntos
Organismos Aquáticos/genética , Organismos Aquáticos/metabolismo , Biologia Computacional/métodos , Animais , Biodiversidade , Biotecnologia/métodos , Ecossistema , Humanos
8.
BMC Bioinformatics ; 19(Suppl 15): 435, 2018 Nov 30.
Artigo em Inglês | MEDLINE | ID: mdl-30497367

RESUMO

BACKGROUND: "Omics" approaches may provide useful information for a deeper understanding of speciation events, diversification and function innovation. This can be achieved by investigating the molecular similarities at sequence level between species, allowing the definition of ortholog and paralog genes. However, the spreading of sequenced genome, often endowed with still preliminary annotations, requires suitable bioinformatics to be appropriately exploited in this framework. RESULTS: We presented here a multilevel comparative approach to investigate on genome evolutionary relationships and peculiarities of two fleshy fruit species of relevant agronomic interest, Solanum lycopersicum (tomato) and Vitis vinifera (grapevine). We defined 17,823 orthology relationships between tomato and grapevine reference gene annotations. The resulting orthologs are associated with the detected paralogs in each species, permitting the definition of gene networks, useful to investigate the different relationships. The reconciliation of the compared collections in terms of an updating of the functional descriptions was also exploited. All the results were made accessible in ComParaLogs, a dedicated bioinformatics platform available at http://biosrv.cab.unina.it/comparalogs/gene/search . CONCLUSIONS: The aim of the work was to suggest a reliable approach to detect all similarities of gene loci between two species based on the integration of results from different levels of information, such as the gene, the transcript and the protein sequences, overcoming possible limits due to exclusive protein versus protein comparisons. This to define reliable ortholog and paralog genes, as well as species specific gene loci in the two species, overcoming limits due to the possible draft nature of preliminary gene annotations. Moreover, reconciled functional descriptions, as well as common or peculiar enzymatic classes and protein domains from tomato and grapevine, together with the definition of species-specific gene sets after the pairwise comparisons, contributed a comprehensive set of information useful to comparatively exploit the two species gene annotations and investigate on differences between species with climacteric and non-climacteric fruits. In addition, the definition of networks of ortholog genes and of associated paralogs, and the organization of web-based interfaces for the exploration of the results, defined a friendly computational bench-work in support of comparative analyses between two species.


Assuntos
Evolução Biológica , Biologia Computacional/métodos , Anotação de Sequência Molecular , Análise Multinível , Solanum lycopersicum/genética , Vitis/genética , Regulação da Expressão Gênica de Plantas , Redes Reguladoras de Genes , Genoma de Planta , Filogenia , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Fatores de Transcrição/metabolismo
9.
Curr Issues Mol Biol ; 27: 71-88, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-28885175

RESUMO

The sudden exponential increase of biological data concerning genome structure and functionalities, also fostered by the advent of Next Generation Sequencing (NGS) technologies, while expanding the opportunity to highlight still uncovered molecular aspects, challenges bioinformatics in several repects. Data management, processing, updating, dissemination and integration are the major areas of concern. The rapid increase in various omics technologies causes two major issues, which may even appear contrasting: the dissemination of poorly curated datasets, still in the form of raw collections or preliminary draft results, and the fast updating of information that, as a consequence, affects the establishment of stable reliable resources. These issues are mainly caused by the lower rate of bioinformatics in extracting added value information from the large amount of data, when compared to the faster technologies involved in data production. This review describes main bioinformatics resources for plants genomics to underline the heterogeneity of the available collections, coherent with the multifaceted complexity of plant sciences. It aims to provide an in-depth report highlighting bottlenecks that may significantly affect a fluent progress in the field and attempts to suggest possible solutions to the various issues.


Assuntos
Arabidopsis/genética , Biologia Computacional/métodos , Produtos Agrícolas/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Biologia Computacional/instrumentação , Conjuntos de Dados como Assunto , Processamento Eletrônico de Dados/métodos , Sequenciamento de Nucleotídeos em Larga Escala/instrumentação , Disseminação de Informação/métodos
10.
BMC Biochem ; 17: 1, 2016 Jan 19.
Artigo em Inglês | MEDLINE | ID: mdl-26782782

RESUMO

BACKGROUND: The use of metagenomics in enzyme discovery constitutes a powerful approach to access to genomes of unculturable community of microorganisms and isolate novel valuable biocatalysts for use in a wide range of biotechnological and pharmaceutical fields. RESULTS: Here we present a novel esterase gene (lip3) identified by functional screening of three fosmid metagenomic libraries, constructed from three marine sediment samples. The sequenced positive fosmid revealed an enzyme of 281 amino acids with similarity to class 3 lipases. The 3D modeling of Lip3 was generated by homology modeling on the basis of four lipases templates [PDB ID: 3O0D, 3NGM, 3G7N, 2QUB] to unravel structural features of this novel enzyme. The catalytic triad of Lip3 was predicted to be Asp207, His267 and the catalytic nucleophile Ser150 in a conserved pentapeptide (GXSXG). The 3D model highlighted the presence of a one-helix lid able to regulate the access of the substrate to the active site when the enzyme binds a hydrophobic interface. Moreover an analysis of the external surface of Lip3 model showed that the majority of the surface regions were hydrophobic (59.6 %) compared with homologous lipases (around 35 %) used as templates. The recombinant Lip3 esterase, expressed and purified from Escherichia coli, preferentially hydrolyzed short and medium length p-nitrophenyl esters with the best substrate being p-nitrophenyl acetate. Further characterization revealed a temperature optimum of 35 °C and a pH optimum of 8.0. Lip3 exhibits a broad temperature stability range and tolerates the presence of DTT, EDTA, PMSF, ß-mercaptoethanol and high concentrations of salt. The enzyme was also highly activated by NaCl. CONCLUSIONS: The biochemical characterization and homology model reveals a novel esterase originating from the marine Arctic metagenomics libraries with features of a cold-active, relatively thermostable and highly halotolerant enzyme. Taken together, these results suggest that this esterase could be a highly valuable candidate for biotechnological applications such as organic synthesis reactions and cheese ripening processes.


Assuntos
Temperatura Baixa , Esterases/metabolismo , Metagenômica , Sequência de Aminoácidos , Regiões Árticas , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Clonagem Molecular , DNA Bacteriano/genética , DNA Bacteriano/isolamento & purificação , DNA Bacteriano/metabolismo , Escherichia coli/metabolismo , Esterases/química , Esterases/genética , Biblioteca Gênica , Sedimentos Geológicos/microbiologia , Concentração de Íons de Hidrogênio , Dados de Sequência Molecular , Estabilidade Proteica , Estrutura Terciária de Proteína , Proteínas Recombinantes/biossíntese , Proteínas Recombinantes/química , Proteínas Recombinantes/isolamento & purificação , Alinhamento de Sequência , Cloreto de Sódio/química , Especificidade por Substrato
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA