Identification and in silico characterization of two novel genes encoding peptidases S8 found by functional screening in a metagenomic library of Yucatán underground water

Apolinar-Hernández, Max M.; Peña-Ramírez, Yuri J.; Pérez‐Rueda, Ernesto; Canto-Canché, Blondy; Santos-Briones, César De los; O’Connor-Sánchez, Aileen

doi:10.1016/j.gene.2016.08.009

Cited by 19 publications

(8 citation statements)

References 30 publications

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“…There are two kinds of functional screening. One is to screen the expression of active products of exogenous genes in host cells according to special characterization (such as color and plaque) on various selective media to obtain target clones (Apolinar-Hernández et al, 2016;Popovic et al, 2017). The other is to screen the host strain and its mutants based on their complementary growth characteristics under selective conditions (Cheng et al, 2017).…”

Section: Screening Of Metagenome Librarymentioning

confidence: 99%

“…The function-driven screening method is fast, simple, and does not rely on any known sequence information. Most biocatalysts, such as protease (Apolinar-Hernández et al, 2016), esterase (Popovic et al, 2017), are obtained by this method. The biggest disadvantage is that it depends on the expression of functional genes in foreign hosts, so the success rate of screening is very low.…”

Section: Screening Of Metagenome Librarymentioning

confidence: 99%

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Advances in Metagenomics and Its Application in Environmental Microorganisms

et al. 2021

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Metagenomics is a new approach to study microorganisms obtained from a specific environment by functional gene screening or sequencing analysis. Metagenomics studies focus on microbial diversity, community constitute, genetic and evolutionary relationships, functional activities, and interactions and relationships with the environment. Sequencing technologies have evolved from shotgun sequencing to high-throughput, next-generation sequencing (NGS), and third-generation sequencing (TGS). NGS and TGS have shown the advantage of rapid detection of pathogenic microorganisms. With the help of new algorithms, we can better perform the taxonomic profiling and gene prediction of microbial species. Functional metagenomics is helpful to screen new bioactive substances and new functional genes from microorganisms and microbial metabolites. In this article, basic steps, classification, and applications of metagenomics are reviewed.

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Section: Screening Of Metagenome Librarymentioning

confidence: 99%

Section: Screening Of Metagenome Librarymentioning

confidence: 99%

Advances in Metagenomics and Its Application in Environmental Microorganisms

et al. 2021

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“…The catabolism of proteins is catalyzed by proteases via cleaving the peptide bonds that link amino acids within proteins [64], [65], [66]. Screening of protease activity involves incubating 1% skim-milk on LB agar plates and a positive signal for protease activity is shown as halos due to the degradation of milk proteins [13], [14], [65].…”

Section: Agar Plate Screeningmentioning

confidence: 99%

“…Screening of protease activity involves incubating 1% skim-milk on LB agar plates and a positive signal for protease activity is shown as halos due to the degradation of milk proteins [13], [14], [65]. A lot of proteases with desirable properties have been identified using this simple technique [64], [65], [66], [67]. For instance, a metagenomic library containing DNA from bacteria dwelling on goat skin was functionally screened for protease activity, which leads to the discovery of a serine protease enzyme with a high alkalinity tolerance [13].…”

Section: Agar Plate Screeningmentioning

confidence: 99%

Recent Advances in Function-Based Metagenomic Screening

Ngara

Zhang

2018

Genomics, Proteomics &Amp; Bioinformatics

123

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Metagenomes from uncultured microorganisms are rich resources for novel enzyme genes. The methods used to screen the metagenomic libraries fall into two categories, which are based on sequence or function of the enzymes. The sequence-based approaches rely on the known sequences of the target gene families. In contrast, the function-based approaches do not involve the incorporation of metagenomic sequencing data and, therefore, may lead to the discovery of novel gene sequences with desired functions. In this review, we discuss the function-based screening strategies that have been used in the identification of enzymes from metagenomes. Because of its simplicity, agar plate screening is most commonly used in the identification of novel enzymes with diverse functions. Other screening methods with higher sensitivity are also employed, such as microtiter plate screening. Furthermore, several ultra-high-throughput methods were developed to deal with large metagenomic libraries. Among these are the FACS-based screening, droplet-based screening, and the in vivo reporter-based screening methods. The application of these novel screening strategies has increased the chance for the discovery of novel enzyme genes.

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“…El estudio enfocado al intestino de las vacas permitió conocer los microorganismos presentes en este ambiente y como estos influyen en la producción de leche (Pitta et al, 2016). Un análisis metagenómico de las aguas subterráneas de Yucatán permitió el descubrimiento de dos nuevos genes que codifican para proteasas (Apolinar-Hernández et al, 2016). El proyecto metagenómico realizado a la producción del vino permitió elucidar el consorcio de microorganismos asociados con la fermentación maloláctica (Berbegal et al, 2019).…”

Section: Introductionunclassified

Aportes Y Dificultades De La Metagenómica De Suelos Y Su Impacto en La Agricultura.

Rivera-Urbalejo

Vázquez

et al. 2021

Acta biol. Colomb.

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Los microorganismos son de gran interés porque colonizan todo tipo de ambiente, sin embargo, uno de los problemas al que nos enfrentamos para conocer su diversidad biológica es que no todos los microorganismos son cultivables. El desarrollo de nuevas tecnologías como la generación de vectores de clonación aunado al desarrollo de técnicas de secuenciación de alto rendimiento ha favorecido el surgimiento de una nueva herramienta llamada metagenómica, la cual nos permite estudiar genomas de comunidades enteras de microorganismos. Debido a que ningún ambiente es idéntico a otro, es importante mencionar que dependiendo del tipo de muestra a analizar será el tipo de reto al cual nos enfrentaremos al trabajar con metagenómica, en el caso específico del suelo existen diversas variantes como la contaminación del suelo con metales pesados o diversos compuestos químicos que podrían limitar los estudios. Sin embargo, pese a las limitaciones que el mismo ambiente presenta, la metagenómica ha permitido tanto el descubrimiento de nuevos genes como la caracterización de las comunidades microbianas que influyen positivamente en el desarrollo de plantas, lo cual en un futuro podría generar un gran impacto en la agricultura. En este artículo se realizó una revisión de diversas investigaciones que han empleado metagenómica, reportadas en las bases de datos de PudMed y Google Schoolar, con el objetivo de examinar los beneficios y limitaciones de las diversas metodologías empleadas en el tratamiento del ADN metagenómico de suelo y el impacto de la metagenómica en la agricultura.

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Identification and in silico characterization of two novel genes encoding peptidases S8 found by functional screening in a metagenomic library of Yucatán underground water

Cited by 19 publications

References 30 publications

Advances in Metagenomics and Its Application in Environmental Microorganisms

Advances in Metagenomics and Its Application in Environmental Microorganisms

Recent Advances in Function-Based Metagenomic Screening

Aportes Y Dificultades De La Metagenómica De Suelos Y Su Impacto en La Agricultura.

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