Identification and characterization of homeobox gene clusters in harpacticoid and calanoid copepods

2021 ◽  
Author(s):  
Duck‐Hyun Kim ◽  
Haksoo Jeong ◽  
Min‐Sub Kim ◽  
Sanghee Kim ◽  
Sami Souissi ◽  
...  
Keyword(s):  
Homeobox Gene ◽  
Gene Clusters ◽  
Calanoid Copepods ◽  
Identification And Characterization

scholarly journals Identification and Characterization of Inorganic Pyrophosphatase and PAP Phosphatase from Thermococcus onnurineus NA1

2009 ◽  
Vol 191 (10) ◽  
pp. 3415-3419 ◽  
Author(s):  
Hyun Sook Lee ◽  
Yun Jae Kim ◽  
Jung-Hyun Lee ◽  
Sung Gyun Kang
Keyword(s):  
Gene Clusters ◽  
Inorganic Pyrophosphatase ◽  
Thermococcus Onnurineus Na1 ◽  
First Report ◽  
Activation System ◽  
Sulfate Activation ◽  
Pyrococcus Abyssi ◽  
Identification And Characterization ◽  
Hypothetical Genes

ABSTRACT Two hypothetical genes were functionally verified to be a pyrophosphatase and a PAP phosphatase in Thermococcus onnurineus NA1. This is the first report of the pyrophosphatases and the PAP phosphatases being organized in the gene clusters of the sulfate activation system only in T. onnurineus NA1 and “Pyrococcus abyssi.”

scholarly journals Identification and Characterization of the Asperthecin Gene Cluster of Aspergillus nidulans

2008 ◽  
Vol 74 (24) ◽  
pp. 7607-7612 ◽  
Author(s):  
Edyta Szewczyk ◽  
Yi-Ming Chiang ◽  
C. Elizabeth Oakley ◽  
Ashley D. Davidson ◽  
Clay C. C. Wang ◽  
...  
Keyword(s):  
Secondary Metabolite ◽  
Polyketide Synthase ◽  
Gene Clusters ◽  
Laboratory Culture ◽  
Culture Conditions ◽  
Type I ◽  
Genes Encoding ◽  
Identification And Characterization ◽  
Normal Laboratory

ABSTRACT The sequencing of Aspergillus genomes has revealed that the products of a large number of secondary metabolism pathways have not yet been identified. This is probably because many secondary metabolite gene clusters are not expressed under normal laboratory culture conditions. It is, therefore, important to discover conditions or regulatory factors that can induce the expression of these genes. We report that the deletion of sumO, the gene that encodes the small ubiquitin-like protein SUMO in A. nidulans, caused a dramatic increase in the production of the secondary metabolite asperthecin and a decrease in the synthesis of austinol/dehydroaustinol and sterigmatocystin. The overproduction of asperthecin in the sumO deletion mutant has allowed us, through a series of targeted deletions, to identify the genes required for asperthecin synthesis. The asperthecin biosynthesis genes are clustered and include genes encoding an iterative type I polyketide synthase, a hydrolase, and a monooxygenase. The identification of these genes allows us to propose a biosynthetic pathway for asperthecin.

scholarly journals Activation and Identification of a Griseusin Cluster in Streptomyces sp. CA-256286 by Employing Transcriptional Regulators and Multi-Omics Methods

Molecules ◽  
2021 ◽  
Vol 26 (21) ◽  
pp. 6580
Author(s):  
Charlotte Beck ◽  
Tetiana Gren ◽  
Francisco Javier Ortiz-López ◽  
Tue Sparholt Jørgensen ◽  
Daniel Carretero-Molina ◽  
...  
Keyword(s):  
Biosynthetic Pathway ◽  
Genome Mining ◽  
Gene Clusters ◽  
Transcriptional Regulators ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Heterologous Host ◽  
Streptomyces Sp ◽  
Identification And Characterization

Streptomyces are well-known producers of a range of different secondary metabolites, including antibiotics and other bioactive compounds. Recently, it has been demonstrated that “silent” biosynthetic gene clusters (BGCs) can be activated by heterologously expressing transcriptional regulators from other BGCs. Here, we have activated a silent BGC in Streptomyces sp. CA-256286 by overexpression of a set of SARP family transcriptional regulators. The structure of the produced compound was elucidated by NMR and found to be an N-acetyl cysteine adduct of the pyranonaphtoquinone polyketide 3′-O-α-d-forosaminyl-(+)-griseusin A. Employing a combination of multi-omics and metabolic engineering techniques, we identified the responsible BGC. These methods include genome mining, proteomics and transcriptomics analyses, in combination with CRISPR induced gene inactivations and expression of the BGC in a heterologous host strain. This work demonstrates an easy-to-implement workflow of how silent BGCs can be activated, followed by the identification and characterization of the produced compound, the responsible BGC, and hints of its biosynthetic pathway.

Genetic Organization of the Escherichia coli K10 Capsule Gene Cluster: Identification and Characterization of Two Conserved Regions in Group III Capsule Gene Clusters Encoding Polysaccharide Transport Functions

1999 ◽  
Vol 181 (7) ◽  
pp. 2279-2285 ◽  
Author(s):  
Bradley R. Clarke ◽  
Rowan Pearce ◽  
Ian S. Roberts
Keyword(s):  
Escherichia Coli ◽  
Gene Cluster ◽  
Gene Clusters ◽  
Group Iii ◽  
Genetic Organization ◽  
Conserved Regions ◽  
Cluster Identification ◽  
Capsule Production ◽  
Identification And Characterization

ABSTRACT Analysis of the Escherichia coli K10 capsule gene cluster identified two regions, regions 1 and 3, conserved between different group III capsule gene clusters. Region 1 encodes homologues of KpsD, KpsM, KpsT, and KpsE proteins, and region 3 encodes homologues of the KpsC and KpsS proteins. An rfaH mutation abolished K10 capsule production, suggesting that expression of the K10 capsule was regulated by RfaH in a manner analogous to group II capsule gene clusters. An IS3 element and a φR73-like prophage, both of which may have played a role in the acquisition of group III capsule gene clusters, were detected flanking the K10 capsule genes.

scholarly journals Identification and Characterization of Genes Involved in the Downstream Degradation Pathway of γ-Hexachlorocyclohexane in Sphingomonas paucimobilis UT26

2005 ◽  
Vol 187 (3) ◽  
pp. 847-853 ◽  
Author(s):  
Ryo Endo ◽  
Mayuko Kamakura ◽  
Keisuke Miyauchi ◽  
Masao Fukuda ◽  
Yoshiyuki Ohtsubo ◽  
...  
Keyword(s):  
Aromatic Compounds ◽  
Gene Clusters ◽  
Sole Source ◽  
Degradation Pathway ◽  
Ring Cleavage ◽  
Sphingomonas Paucimobilis ◽  
Reductase Gene ◽  
Chlorinated Aromatic Compounds ◽  
Identification And Characterization

ABSTRACT Sphingomonas paucimobilis UT26 utilizes γ-hexachlorocyclohexane (γ-HCH) as a sole source of carbon and energy. In our previous study, we cloned and characterized genes that are involved in the conversion of γ-HCH to maleylacetate (MA) via chlorohydroquinone (CHQ) in UT26. In this study, we identified and characterized an MA reductase gene, designated linF, that is essential for the utilization of γ-HCH in UT26. A gene named linEb, whose deduced product showed significant identity to LinE (53%), was located close to linF. LinE is a novel type of ring cleavage dioxygenase that catalyzes the conversion of CHQ to MA. LinEb expressed in Escherichia coli transformed CHQ and 2,6-dichlorohydroquinone to MA and 2-chloromaleylacetate, respectively. Our previous and present results indicate that UT26 (i) has two gene clusters for degradation of chlorinated aromatic compounds via hydroquinone-type intermediates and (ii) uses at least parts of both clusters for γ-HCH utilization.

scholarly journals Identification and characterization of Rhox13, a novel X-linked mouse homeobox gene

Gene ◽  
2008 ◽  
Vol 423 (2) ◽  
pp. 194-200 ◽  
Author(s):  
Christopher B. Geyer ◽  
Edward M. Eddy
Keyword(s):  
Homeobox Gene ◽  
Identification And Characterization

scholarly journals The Architecture of Metabolism Maximizes Biosynthetic Diversity in the Largest Class of Fungi

2020 ◽  
Vol 37 (10) ◽  
pp. 2838-2856
Author(s):  
Emile Gluck-Thaler ◽  
Sajeet Haridas ◽  
Manfred Binder ◽  
Igor V Grigoriev ◽  
Pedro W Crous ◽  
...  
Keyword(s):  
Population Level ◽  
Gene Clusters ◽  
Fungal Species ◽  
Structural Redundancy ◽  
Biosynthetic Gene Clusters ◽  
Taxonomic Class ◽  
Overlapping Sets ◽  
Identification And Characterization ◽  
Insight Into

Abstract Ecological diversity in fungi is largely defined by metabolic traits, including the ability to produce secondary or “specialized” metabolites (SMs) that mediate interactions with other organisms. Fungal SM pathways are frequently encoded in biosynthetic gene clusters (BGCs), which facilitate the identification and characterization of metabolic pathways. Variation in BGC composition reflects the diversity of their SM products. Recent studies have documented surprising diversity of BGC repertoires among isolates of the same fungal species, yet little is known about how this population-level variation is inherited across macroevolutionary timescales. Here, we applied a novel linkage-based algorithm to reveal previously unexplored dimensions of diversity in BGC composition, distribution, and repertoire across 101 species of Dothideomycetes, which are considered the most phylogenetically diverse class of fungi and known to produce many SMs. We predicted both complementary and overlapping sets of clustered genes compared with existing methods and identified novel gene pairs that associate with known secondary metabolite genes. We found that variation among sets of BGCs in individual genomes is due to nonoverlapping BGC combinations and that several BGCs have biased ecological distributions, consistent with niche-specific selection. We observed that total BGC diversity scales linearly with increasing repertoire size, suggesting that secondary metabolites have little structural redundancy in individual fungi. We project that there is substantial unsampled BGC diversity across specific families of Dothideomycetes, which will provide a roadmap for future sampling efforts. Our approach and findings lend new insight into how BGC diversity is generated and maintained across an entire fungal taxonomic class.

Identification and characterization of coding single-nucleotide polymorphisms within human protocadherin-α and -β gene clusters

Gene ◽  
2005 ◽  
Vol 349 ◽  
pp. 1-14 ◽  
Author(s):  
Rie Miki ◽  
Kotaro Hattori ◽  
Yusuke Taguchi ◽  
Motoki N. Tada ◽  
Tomoko Isosaka ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Gene Clusters ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Identification And Characterization

scholarly journals The architecture of metabolism maximizes biosynthetic diversity in the largest class of fungi

2020 ◽  
Author(s):  
Emile Gluck-Thaler ◽  
Sajeet Haridas ◽  
Manfred Binder ◽  
Igor V. Grigoriev ◽  
Pedro W. Crous ◽  
...  
Keyword(s):  
Population Level ◽  
Gene Clusters ◽  
Fungal Species ◽  
Structural Redundancy ◽  
Biosynthetic Gene Clusters ◽  
Taxonomic Class ◽  
Overlapping Sets ◽  
Identification And Characterization ◽  
Insight Into

Abstract:BackgroundEcological diversity in fungi is largely defined by metabolic traits, including the ability to produce secondary or “specialized” metabolites (SMs) that mediate interactions with other organisms. Fungal SM pathways are frequently encoded in biosynthetic gene clusters (BGCs), which facilitate the identification and characterization of metabolic pathways. Variation in BGC composition reflects the diversity of their SM products. Recent studies have documented surprising diversity of BGC repertoires among isolates of the same fungal species, yet little is known about how this population-level variation is inherited across macroevolutionary timescales.ResultsHere, we applied a novel linkage-based algorithm to reveal previously unexplored dimensions of diversity in BGC composition, distribution, and repertoire across 101 species of Dothideomycetes, which are considered to be the most phylogenetically diverse class of fungi and are known to produce many SMs. We predicted both complementary and overlapping sets of clustered genes compared with existing methods and identified novel gene pairs that associate with known secondary metabolite genes. We found that variation in BGC repertoires is due to non-overlapping BGC combinations and that several BGCs have biased ecological distributions, consistent with niche-specific selection. We observed that total BGC diversity scales linearly with increasing repertoire size, suggesting that secondary metabolites have little structural redundancy in individual fungi.ConclusionsWe project that there is substantial unsampled BGC diversity across specific families of Dothideomycetes, which will provide a roadmap for future sampling efforts. Our approach and findings lend new insight into how BGC diversity is generated and maintained across an entire fungal taxonomic class.

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