New Insights on Coffea miRNAs: Features and Evolutionary Conservation.

Abstract:

:Small RNAs influence the gene expression at the post-transcriptional level by guiding messenger RNA (mRNA) cleavage, translational repression, and chromatin modifications. In addition to model plants, the microRNAs (miRNAs) have been identified in different crop species. In this work, we developed a specific pipeline to search for coffee miRNA homologs on expressed sequence tags (ESTs) and genome survey sequences (GSS) databases. As a result, 36 microRNAs were identified and a total of 616 and 362 potential targets for Coffea arabica and Coffea canephora, respectively. The evolutionary analyses of these molecules were performed by comparing the primary and secondary structures of precursors and mature miRNAs with their orthologs. Moreover, using a stem-loop RT-PCR assay, we evaluated the accumulation of mature miRNAs in genomes with different ploidy levels, detecting an increase in the miRNAs accumulation according to the ploidy raising. Finally, a 5' RACE (Rapid Amplification of cDNA Ends) assay was performed to verify the regulation of auxin responsive factor 8 (ARF8) by MIR167 in coffee plants. The great variety of target genes indicates the functional plasticity of these molecules and reinforces the importance of understanding the RNAi-dependent regulatory mechanisms. Our results expand the study of miRNAs and their target genes in this crop, providing new challenges to understand the biology of these species.

authors

Chaves SS,Fernandes-Brum CN,Silva GF,Ferrara-Barbosa BC,Paiva LV,Nogueira FT,Cardoso TC,Amaral LR,de Souza Gomes M,Chalfun-Junior A

doi

10.1007/s12010-015-1785-x

subject

Has Abstract

pub_date

2015-10-01 00:00:00

pages

879-908

issue

4

eissn

0273-2289

issn

1559-0291

pii

10.1007/s12010-015-1785-x

journal_volume

177

pub_type

杂志文章
  • Improvement of bioethanol productivity of immobilized Saccharomyces bayanus with using sodium alginate-graft-poly(N-vinyl-2-pyrrolidone) matrix.

    abstract::In this study, immobilization conditions and bioethanol production characteristics of immobilized Saccharomyces bayanus were investigated into sodium alginate-graft-poly(N-vinyl-2-pyrrolidone; NaAlg-g-PVP) matrix. The matrix that crosslinked with calcium clorid was used for immobilization of S. bayanus. Bioethanol pro...

    journal_title:Applied biochemistry and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s12010-012-9770-0

    authors: İnal M,Yiğitoğlu M

    更新日期:2012-09-01 00:00:00

  • Isolation and Characterization of Bacteria That Use Furans as the Sole Carbon Source.

    abstract::Five bacterial strains were isolated from wastewater treatment facilities which were able to use furfural as the sole carbon source. Based on 16S rRNA phylogenetic analysis, these strains were identified as Cupriavidus pinatubonensis (designated ALS1280), Pigmentiphaga sp. (ALS1172), Pseudomonas sp. BWDY (ALS1279), Ps...

    journal_title:Applied biochemistry and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s12010-015-1859-9

    authors: Lee SA,Wrona LJ,Cahoon AB,Crigler J,Eiteman MA,Altman E

    更新日期:2016-01-01 00:00:00

  • Crosslinked penicillin acylase aggregates for synthesis of beta-lactam antibiotics in organic medium.

    abstract::Crosslinked enzyme aggregates (CLEAs) of a partially purified penicillin acylase from a recombinant Escherichia coli strain have been produced as a novel type of biocatalysts well endowed to perform in organic media. Different protein precipitants were studied and glutaraldehyde was used as the crosslinking agent. Pre...

    journal_title:Applied biochemistry and biotechnology

    pub_type: 杂志文章

    doi:10.1385/abab:133:3:189

    authors: Illanes A,Wilson L,Caballero E,Fernández-Lafuente R,Guisán JM

    更新日期:2006-06-01 00:00:00

  • Two-dimensional analysis of proteins specific to the bacterial magnetic particle membrane from Magnetospirillum sp. AMB-1.

    abstract::We report the identification of five proteins expressed specifically on the bacterial magnetic particle (BMP) membrane of Magnetospirillum sp. AMB-1. These proteins are major components of the BMP membrane. The molecular weights were determined to be 12.0, 16.0, 24.8, 35.6, and 66.2 kDa by sodium dodecyl sulfate polya...

    journal_title:Applied biochemistry and biotechnology

    pub_type: 杂志文章

    doi:10.1385/abab:84-86:1-9:441

    authors: Okamura Y,Takeyama H,Matsunaga T

    更新日期:2000-04-01 00:00:00

  • Lactase production by solid-state cultivation of Kluyveromyces marxianus CDBBL 278 on an inert support: effect of inoculum, buffer, and nitrogen source.

    abstract::A study was carried out to select the conditions for cultivation of Kluyveromyces marxianus CDBBL 278 in solid-state culture (SSC) using polyurethane foam (PUF) as an inert support. PUF was impregnated with culture media containing lactose (50 g/L) as the carbon and energy source. Evaluation of culture parameters duri...

    journal_title:Applied biochemistry and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s12010-008-8268-2

    authors: Tovar-Castro L,García-Garibay M,Saucedo-Castañeda G

    更新日期:2008-12-01 00:00:00

  • Apoptosis induced by aqueous extracts of crocodile bile in human heptacarcinoma SMMC-7721.

    abstract::In the present study, effects of aqueous extracts from Crocodylus siamensis bile (AE-CB) on SMMC-7721 cell growth, cell cycle, and apoptosis were investigated by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide assay, inverted microscopy, fluorescence microscopy, propidium iodide (PI) single- and fluoresc...

    journal_title:Applied biochemistry and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s12010-013-0120-7

    authors: Song W,Li SS,Qiu PP,Shen DY,Tian L,Zhang QY,Liao LX,Chen QX

    更新日期:2013-05-01 00:00:00

  • Comparative analysis and modeling of superoxide dismutases (SODs) in Brachypodium distachyon L.

    abstract::Superoxide dismutase (SOD, EC 1.15.1.1) is an enzyme catalyzing the dismutation of superoxide radical to hydrogen peroxide and dioxygen. To date, four types of SODs--Cu/ZnSOD, MnSOD, FeSOD, and NiSOD--have been identified. In this study, SOD proteins of Brachypodium distachyon (L.) Beauv. were screened by utilization ...

    journal_title:Applied biochemistry and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s12010-014-0922-2

    authors: Filiz E,Koc I,Ozyigit II

    更新日期:2014-07-01 00:00:00

  • Enhanced formation of extracellular laccase activity by the white-rot fungus Trametes multicolor.

    abstract::The white-rot fungus Trametes multicolor MB 49 has been identified as an excellent producer of the industrially important enzyme laccase. The formation of extracellular laccase could be considerably stimulated by the addition of Cu(II) to a simple, glycerol-based culture medium. In this study, optimal concentrations o...

    journal_title:Applied biochemistry and biotechnology

    pub_type: 杂志文章

    doi:10.1385/abab:98-100:1-9:229

    authors: Hess J,Leitner C,Galhaup C,Kulbe KD,Hinterstoisser B,Steinwender M,Haltrich D

    更新日期:2002-04-01 00:00:00

  • An Innovator Support Material for Tyrosinase Immobilization: Antimony-Doped Tin Oxide Thin Films (ATO-TF).

    abstract::Tyrosinase (T3824, Sigma) enzymes were immobilized onto SnO2: Sb thin films (ATO-TF) which were synthesized in laboratory conditions by spray pyrolysis technique. Immobilization of tyrosinase onto SnO2: Sb thin film (ATO-TF) was confirmed by scanning electron microscopy (SEM) and Fourier transformed infrared spectrosc...

    journal_title:Applied biochemistry and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s12010-020-03337-3

    authors: Türkhan A,Kaya ED,Koçyiğit A

    更新日期:2020-10-01 00:00:00

  • Influence of blocking of 2,3-butanediol pathway on glycerol metabolism for 1,3-propanediol production by Klebsiella oxytoca.

    abstract::Glycerol metabolism is a typical biological oxidoreductive reaction. 1,3-Propanediol (1,3-PD) is the final product of the reductive branch, while acetate, succinate, lactate, 2,3-butanediol (2,3-BD), and ethanol were produced in the oxidative branch. 2,3-BD, which has similar properties of high boiling point and water...

    journal_title:Applied biochemistry and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s12010-011-9363-3

    authors: Zhang G,Yang G,Wang X,Guo Q,Li Y,Li J

    更新日期:2012-09-01 00:00:00

  • Isolation of xylose reductase gene of Pichia stipitis and its expression in Saccharomyces cerevisiae.

    abstract::A NADPH/NADH-dependent xylose reductase gene was isolated from the xylose-assimilating yeast, Pichia stipitis. DNA sequence analysis showed that the gene consists of 951 bp. The gene introduced in Saccharomyces cerevisiae was transcribed to mRNA, and a considerable amount of enzyme activity was observed constitutively...

    journal_title:Applied biochemistry and biotechnology

    pub_type: 杂志文章

    doi:10.1007/BF02922612

    authors: Takuma S,Nakashima N,Tantirungkij M,Kinoshita S,Okada H,Seki T,Yoshida T

    更新日期:1991-04-01 00:00:00

  • Improving stability and activity of cross-linked enzyme aggregates based on polyethylenimine in hydrolysis of fish oil for enrichment of polyunsaturated fatty acids.

    abstract::Cross-linking of enzyme aggregates from recombinant Geotrichum sp. lipase based on polyethylenimine (PEI) was applied to hydrolyze fish oil for enrichment of polyunsaturated fatty acids successfully. Through acetone precipitation and cross-linking of physical aggregates using glutaraldehyde in the presence of PEI, fir...

    journal_title:Applied biochemistry and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s12010-011-9480-z

    authors: Yan J,Gui X,Wang G,Yan Y

    更新日期:2012-02-01 00:00:00

  • Potential Application and Bactericidal Mechanism of Lactic Acid-Hydrogen Peroxide Consortium.

    abstract::It has been found that lactic acid and hydrogen peroxide (H2O2) displayed co-operatively enhanced killing activity to pathogens. The synergistic effect was investigated with using several microbe species, suggesting that low concentration of lactic acid and H2O2 could kill both Gram-negative and Gram-positive bacteria...

    journal_title:Applied biochemistry and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s12010-019-03031-z

    authors: Zhang C,Zhang S,Liu W,Guo T,Gu R,Kong J

    更新日期:2019-11-01 00:00:00

  • Comparison of catalytic properties of free and immobilized cellobiase novozym 188.

    abstract::The enzyme cellobiase from Novo was immobilized in controlled pore silica particles by covalent binding with the silane-glutaraldehyde method with protein and activity yields of 67 and 13.7%, respectively. The activity of the free enzyme (FE) and immobilized enzyme (IE) was determined with 2 g/L of cellobiose, from 40...

    journal_title:Applied biochemistry and biotechnology

    pub_type: 杂志文章

    doi:10.1385/abab:91-93:1-9:615

    authors: Calsavara LP,De Moraes FF,Zanin GM

    更新日期:2001-04-01 00:00:00

  • Observation of geometric structure of collagen molecules by atomic force microscopy.

    abstract::Atomic force microscopy was used to study the geometric structure of collagen fibrils and molecules of rat calcanean tendon tissues. The authors found that the diameter of the fibrils ranged from 124 to 170 nm, and their geometric form suggested a helical winding with spectral period from 59.4 to 61.7 nm, close to the...

    journal_title:Applied biochemistry and biotechnology

    pub_type: 杂志文章

    doi:10.1007/BF02919391

    authors: Baranauskas V,Vidal BC,Parizotto NA

    更新日期:1998-02-01 00:00:00

  • Use of different adsorbents for sorption and Bacillus polymyxa protease immobilization.

    abstract::Proteases constitute one of the most important groups of industrial enzymes, accounting for at least 25% of the total enzyme sales, with two-thirds of the proteases produced commercially being of microbial origin. Immobilized enzymes are currently the subject of considerable interest because of their advantages over s...

    journal_title:Applied biochemistry and biotechnology

    pub_type: 杂志文章

    doi:

    authors: Kirkkopru I,Alpaslan C,Omay D,Güvenilir Y

    更新日期:2006-04-01 00:00:00

  • Profiling of phosphatidylinositol 3-kinase (PI3K) proteins in insulin signaling pathway.

    abstract::Phosphoinositide 3-kinase (PI3K) enzyme plays a vital role in the insulin signaling pathway as well as in other pathways that are involved in the growth, migration, and survival of cells. In the insulin signaling pathway, PI3K proteins that include p50α, p85α, p85β, p55γ, p110α, p110β, and p110γ are associated with th...

    journal_title:Applied biochemistry and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s12010-015-1515-4

    authors: Chakraborty C,Doss CG,Bhatia R,Agoramoorthy G

    更新日期:2015-04-01 00:00:00

  • In Silico Structure-Based Identification and Validation of Key Residues of Vip3Aa Involving in Lepidopteran Brush Border Receptor Binding.

    abstract::The vegetative insecticidal proteins (VIPs) of Bacillus thuringiensis (Bt) have a broad-spectrum insecticidal activity against Lepidopteran pests and no cross-resistance with the insecticidal crystal protein Cry protein. So there are great potentials for the control of agricultural pests and the resolution of resistan...

    journal_title:Applied biochemistry and biotechnology

    pub_type: 杂志文章,评审

    doi:10.1007/s12010-018-2880-6

    authors: Chi B,Li H,Zhang J,Wei P,Gao J,Liu R

    更新日期:2019-04-01 00:00:00

  • The study of ascorbate peroxidase, catalase and peroxidase during in vitro regeneration of Argyrolobium roseum.

    abstract::Here, we demonstrate the micropropagation protocol of Argyrolobium roseum (Camb.), an endangered herb exhibiting anti-diabetic and immune-suppressant properties, and antioxidant enzymes pattern is evaluated. Maximum callogenic response (60 %) was observed from leaf explant at 1.0 mg L(-1) 1-nephthalene acetic acid (NA...

    journal_title:Applied biochemistry and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s12010-013-0591-6

    authors: Habib D,Chaudhary MF,Zia M

    更新日期:2014-01-01 00:00:00

  • Molecular cloning and characterization of the light-harvesting chlorophyll a/b gene from the pigeon pea (Cajanus cajan).

    abstract::Light-harvesting chlorophyll a/b-binding proteins (LHCB) have been implicated in the stress response. In this study, a gene encoding LHCB in the pigeon pea was cloned and characterized. Based on the sequence of a previously obtained 327 bp Est, a full-length 793 bp cDNA was cloned using the rapid amplification of cDNA...

    journal_title:Applied biochemistry and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s12010-015-1825-6

    authors: Qiao G,Wen XP,Zhang T

    更新日期:2015-12-01 00:00:00

  • Development and application of a system for analysis of mixed cultures of microorganisms.

    abstract::Development and application of a system for real-time quantitative assessment of individual cell activities in a mixed culture system was investigated. This was based on a concept that the activities of individual cells in a mixed culture can be assessed if the cells are physically separated (in separate compartments)...

    journal_title:Applied biochemistry and biotechnology

    pub_type: 杂志文章

    doi:10.1385/abab:80:1:51

    authors: Tanaka H,Ebata T,Kuwahara I,Matsuo M,Ogbonna JC

    更新日期:1999-04-01 00:00:00

  • An oxidant- and solvent-stable protease produced by Bacillus cereus SV1: application in the deproteinization of shrimp wastes and as a laundry detergent additive.

    abstract::The current increase in amount of shrimp wastes produced by the shrimp industry has led to the need in finding new methods for shrimp wastes disposal. In this study, an extracellular organic solvent- and oxidant-stable metalloprotease was produced by Bacillus cereus SV1. Maximum protease activity (5,900 U/mL) was obta...

    journal_title:Applied biochemistry and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s12010-009-8703-z

    authors: Manni L,Jellouli K,Ghorbel-Bellaaj O,Agrebi R,Haddar A,Sellami-Kamoun A,Nasri M

    更新日期:2010-04-01 00:00:00

  • Metabolic Engineering of Chlamydomonas reinhardtii for Enhanced β-Carotene and Lutein Production.

    abstract::The metabolic engineering of Chlamydomonas reinhardtii, one of the fastest-growing microalgae, is a potential alternative for enhanced carotenoid productivity. CrtYB (phytoene-β-carotene synthase - PBS) gene from red yeast Xanthophyllomyces dendrorhous encodes for a bifunctional enzyme that harbours both phytoene synt...

    journal_title:Applied biochemistry and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s12010-019-03194-9

    authors: Rathod JP,Vira C,Lali AM,Prakash G

    更新日期:2020-04-01 00:00:00

  • Laccase from Coriolus hirsutus as alternate label for enzyme immunoassay. Determination of pesticide 2,4-dichlorophenoxyacetic acid.

    abstract::A new label--laccase from the fungus Coriolus hirsutus--was applied for solid-phase enzyme-linked immunosorbent assays of the pesticide 2,4-dichlorophenoxyacetic acid (2,4-D). Two proposed assays are based on (1) competitive binding of antibody-laccase conjugate with immobilized 2,4-D-protein conjugate and 2,4-D in te...

    journal_title:Applied biochemistry and biotechnology

    pub_type: 杂志文章

    doi:10.1385/abab:76:3:203

    authors: Zherdev AV,Bizova NA,Yaropolov AI,Lyubimova NV,Morozova OV,Dzantiev BB

    更新日期:1999-03-01 00:00:00

  • Isolation and Characterization of a Novel myovirus Infecting Shigella dysenteriae from the Aeration Tank Water.

    abstract::The genome sequence, morphology, and genetic features of a novel phage, named SSE1, is reported here. Phage SSE1 that infects Shigella dysenteriae (China General Microbiological Culture Collection Center number: 1.1869) was isolated from the aeration tank water of a sewage treatment plant. SSE1 showed morphological fe...

    journal_title:Applied biochemistry and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s12010-020-03310-0

    authors: Lu H,Liu H,Lu M,Wang J,Liu X,Liu R

    更新日期:2020-09-01 00:00:00

  • Immunoaffinity purification of subcellular particles and organelles.

    abstract::The application of immunoaffinity techniques to subcellular fractionation is reviewed and the basic principles underlying the various methods that have been successfully employed, identified. The requirement for organelle-specific antigens and high-avidity antibodies is discussed, as is the widespread use of indirect ...

    journal_title:Applied biochemistry and biotechnology

    pub_type: 杂志文章

    doi:10.1007/BF02798907

    authors: Richardson PJ,Luzio JP

    更新日期:1986-10-01 00:00:00

  • Enhanced production of artemisinin by hairy root cultivation of Artemisia annua in a modified stirred tank reactor.

    abstract::Artemisinin is an important drug commonly used in the treatment of malaria as a combination therapy. It is primarily produced by a plant Artemisia annua, however, its supply from plant is significantly lower than its huge demand and therefore alternative in vitro production routes are sought. Hairy root cultivation co...

    journal_title:Applied biochemistry and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s12010-014-1176-8

    authors: Patra N,Srivastava AK

    更新日期:2014-11-01 00:00:00

  • Thermal stability and energy of deactivation of free and immobilized amyloglucosidase in the saccharification of liquefied cassava starch.

    abstract::Amyloglucosidase from Novo (Copenhagen, Denmark) was immobilized in controlled pore silica particles with the silane-glutaraldehyde covalent method. Thermal stability of the free and immobilized enzyme (IE) was determined with 30% (w/v) alpha-amylase liquefied cassava starch, pH 4.5, temperatures from 35 to 75 degrees...

    journal_title:Applied biochemistry and biotechnology

    pub_type: 杂志文章

    doi:10.1007/BF02920153

    authors: Zanin GM,De Moraes FF

    更新日期:1998-04-01 00:00:00

  • Isolation of halotolerant Bacillus licheniformis WX-02 and regulatory effects of sodium chloride on yield and molecular sizes of poly-gamma-glutamic acid.

    abstract::A poly-gamma-glutamic acid (gamma-PGA) productive strain, halotolerant bacterium WX-02 was isolated from the saline soil of China (Yingcheng). By physiological, biochemical, and 16S rDNA sequence analysis methods, the strain was identified as Bacillus licheniformis. The effect of NaCl concentration on gamma-PGA produc...

    journal_title:Applied biochemistry and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s12010-009-8681-1

    authors: Wei X,Ji Z,Chen S

    更新日期:2010-03-01 00:00:00

  • Improvement in thermal stability and substrate binding of pig kidney D-amino acid oxidase by chemical modification.

    abstract::Chemical modification was evaluated to stabilize pig kidney D-amino acid oxidase (pkDAAO), which is required for analytical determination of D-amino acids. Optimization of modification conditions was performed to obtain high recovery yield and stability, and chemical modification at 30 degrees C for 12 h with a highly...

    journal_title:Applied biochemistry and biotechnology

    pub_type: 杂志文章

    doi:10.1385/abab:112:3:123

    authors: Bakke M,Kajiyama N

    更新日期:2004-03-01 00:00:00