Genetic analysis of gliadin-encoding genes reveals gene clusters as well as single remote genes

DNA encodes all sorts of information that makes us human, but, aside from encoding genes, could DNA also encode for a mapping of musical rhythms in a very abstract way? This project sought to generate rhythms out of DNA and compose a musical piece out of a gene's rhythmic sequence. Computational rules inspired by geometric analyses of rhythms guided the mapping of DNA's molecular structure into rhythmic timelines and melodic scales; these basic structures were then used to compose a song according to the sickle cell gene DNA sequence. The rhythms generated by this ‘genetic analysis’ alternate pleasantly between even and odd time signatures.

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The Ether-Cleaving Methyltransferase System of the Strict Anaerobe Acetobacterium dehalogenans: Analysis and Expression of the Encoding Genes

Journal of Bacteriology ◽

10.1128/jb.01104-08 ◽

2008 ◽

Vol 191 (2) ◽

pp. 588-599 ◽

Cited By ~ 27

Author(s):

Anke Schilhabel ◽

Sandra Studenik ◽

Martin Vödisch ◽

Sandra Kreher ◽

Bernhard Schlott ◽

...

Keyword(s):

Amino Acid Sequence Identity ◽

Protein Complexes ◽

Gene Clusters ◽

Single Copy ◽

Anaerobic Microorganisms ◽

Sequence Identity ◽

Copy Gene ◽

Genes Encoding ◽

Encoding Genes ◽

Genetic Context

ABSTRACT Anaerobic O-demethylases are inducible multicomponent enzymes which mediate the cleavage of the ether bond of phenyl methyl ethers and the transfer of the methyl group to tetrahydrofolate. The genes of all components (methyltransferases I and II, CP, and activating enzyme [AE]) of the vanillate- and veratrol-O-demethylases of Acetobacterium dehalogenans were sequenced and analyzed. In A. dehalogenans, the genes for methyltransferase I, CP, and methyltransferase II of both O-demethylases are clustered. The single-copy gene for AE is not included in the O-demethylase gene clusters. It was found that AE grouped with COG3894 proteins, the function of which was unknown so far. Genes encoding COG3894 proteins with 20 to 41% amino acid sequence identity with AE are present in numerous genomes of anaerobic microorganisms. Inspection of the domain structure and genetic context of these orthologs predicts that these are also reductive activases for corrinoid enzymes (RACEs), such as carbon monoxide dehydrogenase/acetyl coenzyme A synthases or anaerobic methyltransferases. The genes encoding the O-demethylase components were heterologously expressed with a C-terminal Strep-tag in Escherichia coli, and the recombinant proteins methyltransferase I, CP, and AE were characterized. Gel shift experiments showed that the AE comigrated with the CP. The formation of other protein complexes with the O-demethylase components was not observed under the conditions used. The results point to a strong interaction of the AE with the CP. This is the first report on the functional heterologous expression of acetogenic phenyl methyl ether-cleaving O-demethylases.

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Genetic Analysis Reveals a Hierarchy of Interactions between Polycystin-Encoding Genes and Genes Controlling Cilia Function during Left-Right Determination

PLoS Genetics ◽

10.1371/journal.pgen.1006070 ◽

2016 ◽

Vol 12 (6) ◽

pp. e1006070 ◽

Cited By ~ 28

Author(s):

Daniel T. Grimes ◽

Jennifer L. Keynton ◽

Maria T. Buenavista ◽

Xingjian Jin ◽

Saloni H. Patel ◽

...

Keyword(s):

Genetic Analysis ◽

Encoding Genes

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Genetic analysis of capsular polysaccharide synthesis gene clusters in 79 capsular types of Klebsiella spp

Scientific Reports ◽

10.1038/srep15573 ◽

2015 ◽

Vol 5 (1) ◽

Cited By ~ 81

Author(s):

Yi-Jiun Pan ◽

Tzu-Lung Lin ◽

Chun-Tang Chen ◽

Yi-Yin Chen ◽

Pei-Fang Hsieh ◽

...

Keyword(s):

Genetic Analysis ◽

Capsular Polysaccharide ◽

Gene Clusters ◽

Polysaccharide Synthesis ◽

Klebsiella Spp

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Genetic analysis of the O-antigen gene clusters of Yersinia pseudotuberculosis O:6 and O:7

Glycobiology ◽

10.1093/glycob/cwr010 ◽

2011 ◽

Vol 21 (9) ◽

pp. 1140-1146 ◽

Cited By ~ 10

Author(s):

M. M. Cunneen ◽

E. Pacinelli ◽

W. C. Song ◽

P. R. Reeves

Keyword(s):

Genetic Analysis ◽

Yersinia Pseudotuberculosis ◽

Gene Clusters ◽

Antigen Gene ◽

O Antigen

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Genuine genetic redundancy in maleylacetate-reductase-encoding genes involved in degradation of haloaromatic compounds by Cupriavidus necator JMP134

Microbiology ◽

10.1099/mic.0.032086-0 ◽

2009 ◽

Vol 155 (11) ◽

pp. 3641-3651 ◽

Cited By ~ 14

Author(s):

Danilo Pérez-Pantoja ◽

Raúl A. Donoso ◽

Miguel A. Sánchez ◽

Bernardo González

Keyword(s):

Aromatic Compounds ◽

Gene Clusters ◽

Cupriavidus Necator ◽

Gene Products ◽

Genetic Redundancy ◽

Rt Pcr ◽

Cell Extracts ◽

Maleylacetate Reductase ◽

Encoding Genes

Maleylacetate reductases (MAR) are required for biodegradation of several substituted aromatic compounds. To date, the functionality of two MAR-encoding genes (tfdF I and tfdF II) has been reported in Cupriavidus necator JMP134(pJP4), a known degrader of aromatic compounds. These two genes are located in tfd gene clusters involved in the turnover of 2,4-dichlorophenoxyacetate (2,4-D) and 3-chlorobenzoate (3-CB). The C. necator JMP134 genome comprises at least three other genes that putatively encode MAR (tcpD, hqoD and hxqD), but confirmation of their functionality and their role in the catabolism of haloaromatic compounds has not been assessed. RT-PCR expression analyses of C. necator JMP134 cells exposed to 2,4-D, 3-CB, 2,4,6-trichlorophenol (2,4,6-TCP) or 4-fluorobenzoate (4-FB) showed that tfdF I and tfdF II are induced by haloaromatics channelled to halocatechols as intermediates. In contrast, 2,4,6-TCP only induces tcpD, and any haloaromatic compounds tested did not induce hxqD and hqoD. However, the tcpD, hxqD and hqoD gene products showed MAR activity in cell extracts and provided the MAR function for 2,4-D catabolism when heterologously expressed in MAR-lacking strains. Growth tests for mutants of the five MAR-encoding genes in strain JMP134 showed that none of these genes is essential for degradation of the tested compounds. However, the role of tfdF I/tfdF II and tcpD genes in the expression of MAR activity during catabolism of 2,4-D and 2,4,6-TCP, respectively, was confirmed by enzyme activity tests in mutants. These results reveal a striking example of genetic redundancy in the degradation of aromatic compounds.

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Genetic analysis of complex gene clusters inEscherichia coli: the genetic analysis of F72 fimbrial genes

Antonie van Leeuwenhoek ◽

10.1007/bf02386228 ◽

1984 ◽

Vol 50 (5-6) ◽

pp. 585-596

Author(s):

W. P. M. Hoekstra ◽

I. M. Van Die ◽

J. E. N. Bergmans

Keyword(s):

Genetic Analysis ◽

Gene Clusters ◽

Inescherichia Coli

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Transcriptome Comparison of Secondary Metabolite Biosynthesis Genes Expressed in Cultured and Lichenized Conditions of Cladonia rangiferina

Diversity ◽

10.3390/d13110529 ◽

2021 ◽

Vol 13 (11) ◽

pp. 529

Author(s):

Natalia Sveshnikova ◽

Michele D. Piercey-Normore

Keyword(s):

Secondary Metabolite ◽

Environmental Changes ◽

Gene Clusters ◽

Biosynthetic Gene Clusters ◽

Secondary Metabolite Biosynthesis ◽

Metabolite Synthesis ◽

Transcriptome Comparison ◽

Encoding Genes ◽

Cladonia Rangiferina ◽

Active Genes

Lichen secondary metabolites are natural products of high medicinal and industrial value, which are produced by the fungal symbiont (mycobiont) of lichens in response to environmental changes. It has been shown that the cultured mycobiont is capable of secondary metabolite production, specifically polyketides, and polyketide production is affected by the presence or absence of the algal or cyanobacterial symbiont (photobiont). Identification of polyketide synthases encoding genes is, in turn, key for understanding the regulation of secondary metabolite synthesis. Using a previously established method of resynthesis for Cladonia rangiferina as well as the sequenced and assembled genome of that species, we compared transcriptomes of C. rangiferina cultured alone and resynthesized with the photobiont (Asterochloris glomerata) to reveal transcriptionally active genes in secondary metabolic gene clusters, as well some of the neighbouring genes, induced by the presence of the photobiont and events of lichenization. The results identify potential candidates for PKS genes in C. rangiferina, identify potential neighbouring genes in the PKS cluster, and offer insights into further research. The study provides preliminary insights into the activity of several identified biosynthetic gene clusters (BGC) as well as interactions of genes within those clusters.

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Elucidating the diversity and potential function of nonribosomal peptide and polyketide biosynthetic gene clusters in the root microbiome

10.1101/2020.06.07.138487 ◽

2020 ◽

Author(s):

Barak Dror ◽

Zongqiang Wang ◽

Sean F. Brady ◽

Edouard Jurkevitch ◽

Eddie Cytryn

Keyword(s):

Secondary Metabolite ◽

Gene Clusters ◽

Bulk Soil ◽

Large Set ◽

Biosynthetic Gene ◽

Plant Interactions ◽

Biosynthetic Gene Clusters ◽

Shotgun Metagenomics ◽

Nonribosomal Peptide ◽

Encoding Genes

AbstractPolyketides (PKs) and nonribosomal peptides (NRPs) are two microbial secondary metabolite (SM) families known for their variety of functions, including antimicrobials, siderophores and others. Despite their involvement in bacteria-bacteria and bacteria-plant interactions, root-associated SMs are largely unexplored due to the limited cultivability of bacteria. Here, we analyzed the diversity and expression of SM-encoding biosynthetic gene clusters (BGCs) in root microbiomes by culture-independent amplicon sequencing, shotgun metagenomics and metatranscriptomics. Roots (tomato and lettuce) harbored distinct compositions of nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) relative to the adjacent bulk soil, and specific BGC markers were both enriched and highly expressed in the root microbiomes. While several of the highly abundant and expressed sequences were remotely associated with known BGCs, the low similarity to characterized genes suggests their potential novelty. Low similarity genes were screened against a large set of soil-derived cosmid libraries, from which five whole BGCs of unknown function were retrieved. Three clusters were taxonomically affiliated with Actinobacteria, while the remaining were not associated with known bacteria. One Streptomyces-derived BGC was predicted to encode for a polyene with potential antifungal activity, while the others were too novel to predict chemical structure. Screening against a suite of metagenomic datasets revealed a higher abundance of retrieved clusters in roots and soil samples. In contrast, they were almost completely absent in aquatic and gut environments, supporting the notion that they might play an important role in root ecosystems. Overall, our results indicate that root microbiomes harbor a specific assemblage of undiscovered SMs.ImportanceWe identified distinct secondary metabolite (polyketide and nonribosomal peptide) encoding genes that are enriched (relative to adjacent bulk soil) and expressed in root ecosystems, yet almost completely absent in human gut and aquatic environments. Several of the genes were distantly related to genes encoding for antimicrobials and siderophores, and their high sequence variability relative to known sequences suggests that they may encode for novel metabolites and may have unique ecological functions. This study demonstrates that plant roots harbor a diverse array of unique secondary metabolite encoding genes that are highly enriched and expressed in the root ecosystem. The secondary metabolites encoded by these genes might assist the bacteria that produce them in colonization and persistence in the root environment. To explore this hypothesis, future investigations should assess their potential role in inter-bacterial and bacterial-plant interactions.

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Genome-wide Identification of Disease Resistance Genes (R Genes) in Wheat

10.1101/2020.07.18.210286 ◽

2020 ◽

Author(s):

Ethan J. Andersen ◽

Lauren E. Lindsey ◽

Madhav P. Nepal

Keyword(s):

Resistance Genes ◽

Functional Divergence ◽

Interleukin 1 ◽

Crop Improvement ◽

Aegilops Tauschii ◽

Gene Clusters ◽

R Genes ◽

Genome Wide ◽

Large Expansion ◽

Encoding Genes

ABSTRACTProteins encoded by plant resistance genes (R genes) detect pathogenic effectors and initiate immune responses. Although R genes in many plant genomes are identified, they are yet to be identified in wheat. The major objectives of this project were to conduct genome-wide identification of the NB-ARC-encoding R genes in wheat (Triticum aestivum L.) and assess their genomic architecture and potential functional divergence. Wheat protein sequences were obtained from the Ensembl Genomes database, and genes were identified using interpro program. Chromosomal locations of the R genes were determined and syntenic analyses were performed. Altogether, 2151 wheat NB-ARC-encoding genes were identified, among which 1298 genes formed 547 gene clusters. Many of these gene clusters included highly similar genes likely formed by tandem duplications. Among the NB-ARC-encoding genes, 1552 (∼72%) encode Leucine-Rich Repeats (LRRs), 802 are Coiled-Coil (CC) domain-encoding CC-NBS-LRR (CNL) genes and three are Resistance to Powdery mildew 8 (RPW8) domain-encoding RPW8-NBS-LRR (RNL) genes. Surprisingly, five of the NB-ARC-encoding genes encoded a Toll/Interleukin-1 Receptor (TIR), with no LRR, known as TN genes. CNL clades formed similar nesting patterns with a large expansion of CNL-C group like previously reported findings in wheat relatives. Comparisons of the wheat genome with barley (Hordeum vulgare L.) and Tausch’s goatgrass (Aegilops tauschii Coss.), showed similar locations for homologous NB-ARC-encoding genes. These results showed that R genes in wheat have diversified through duplication to encode receptors that recognize rapidly evolving pathogenic effectors. Identified R genes in this study have implications in plant breeding, as a source of resistance for crop improvement.

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