Bioinformatic analysis of promoter, motifs and CpG islands of genes encoding potassium transporters in crop plants

Abstract Dietary flavonoids play an important role in human nutrition and health. Flavonoid biosynthesis genes have recently been identified in lettuce (Lactuca sativa); however, few mutants have been characterized. We now report the causative mutations in Green Super Lettuce (GSL), a natural light green mutant derived from red cultivar NAR; and GSL-Dark Green (GSL-DG), an olive-green natural derivative of GSL. GSL harbors CACTA 1 (LsC1), a 3.9-kb active nonautonomous CACTA superfamily transposon inserted in the 5′ untranslated region of anthocyanidin synthase (ANS), a gene coding for a key enzyme in anthocyanin biosynthesis. Both terminal inverted repeats (TIRs) of this transposon were intact, enabling somatic excision of the mobile element, which led to the restoration of ANS expression and the accumulation of red anthocyanins in sectors on otherwise green leaves. GSL-DG harbors CACTA 2 (LsC2), a 1.1-kb truncated copy of LsC1 that lacks one of the TIRs, rendering the transposon inactive. RNA-sequencing and reverse transcription quantitative PCR of NAR, GSL, and GSL-DG indicated the relative expression level of ANS was strongly influenced by the transposon insertions. Analysis of flavonoid content indicated leaf cyanidin levels correlated positively with ANS expression. Bioinformatic analysis of the cv Salinas lettuce reference genome led to the discovery and characterization of an LsC1 transposon family with a putative transposon copy number greater than 1,700. Homologs of tnpA and tnpD, the genes encoding two proteins necessary for activation of transposition of CACTA elements, were also identified in the lettuce genome.

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Gene Expression Profiles Associated with Radio-Responsiveness in Locally Advanced Rectal Cancer

Biology ◽

10.3390/biology10060500 ◽

2021 ◽

Vol 10 (6) ◽

pp. 500

Author(s):

Jeeyong Lee ◽

Junhye Kwon ◽

DaYeon Kim ◽

Misun Park ◽

KwangSeok Kim ◽

...

Keyword(s):

Candidate Genes ◽

Expression Profiles ◽

Cell Cycle Control ◽

Methylation Status ◽

Locally Advanced ◽

Gene Expression Profiles ◽

Advanced Rectal Cancer ◽

Bioinformatic Analysis ◽

Locally Advanced Rectal Cancer ◽

Genes Encoding

LARC patients were sorted according to their radio-responsiveness and patient-derived organoids were established from the respective cancer tissues. Expression profiles for each group were obtained using RNA-seq. Biological and bioinformatic analysis approaches were used in deciphering genes and pathways that participate in the radio-resistance of LARC. Thirty candidate genes encoding proteins involved in radio-responsiveness–related pathways, including the immune system, DNA repair and cell-cycle control, were identified. Interestingly, one of the candidate genes, cathepsin E (CTSE), exhibited differential methylation at the promoter region that was inversely correlated with the radio-resistance of patient-derived organoids, suggesting that methylation status could contribute to radio-responsiveness. On the basis of these results, we plan to pursue development of a gene chip for diagnosing the radio-responsiveness of LARC patients, with the hope that our efforts will ultimately improve the prognosis of LARC patients.

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Landscape Of HOXA Genes Methylation in Colorectal Cancer

Progress In Microbes & Molecular Biology ◽

10.36877/pmmb.a0000085 ◽

2020 ◽

Vol 3 (1) ◽

Author(s):

Muhiddin Ishak ◽

Rashidah Baharudin ◽

Loh Teng-Hern Tan ◽

Learn-Han Lee ◽

Nurul-Syakima Ab Mutalib

Keyword(s):

Colorectal Cancer ◽

Cancer Susceptibility ◽

Cpg Islands ◽

Methylation Pattern ◽

Gene Promoters ◽

Normal Tissues ◽

Genes Encoding ◽

Hoxa Genes ◽

A Minor ◽

Hoxa Gene

Colorectal cancer (CRC) is among the most common cancers worldwide and the second leading cause of cancer-related death in Malaysia. The HOXA gene cluster is a family of Homeobox A genes encoding transcriptional regulators that play vital roles in cancer susceptibility and progression. Dysregulated HOXA expression influences various aspects of carcinogenesis processes. Therefore, this study aims to elucidate the methylation landscape of HOXA genes in CRC. Twelve pairs of CRC — adjacent normal tissues were subjected to Infinium DNA MethyEPIC array. Differentially methylatedregions were identified using the ChAMP Bioconductor and methylation levels of HOXA genes were manually curated. We identified 100 significantly differentially methylated probes annotated to HOXA genes. HOXA3 has the highest number of differentially methylated probes (n=27), followed by HOXA2 (n=20) and HOXA4 (n=14). The majority (43%) of the probes were located at the transcription start site (TSS) 200, which is one of the gene promoters. In respect to CpG islands (CGI), the probes were equally located in the island and shore regions (47% each) while a minor percentage was in the shelf (6%). Our work gave a comprehensive assessment of the DNA methylation pattern of HOXA genes and provide the first evidence of HOXA2, HOXA3 and HOXA4 differential methylation in Malaysian CRC. The new knowledge from this study can be utilized to further increase our understanding of CRC methylomics, particularly on the homeobox A genes. The prognostic and diagnostic roles of the differentially methylated HOXA genes warrant future investigations.

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Draft Genome Sequence of Shewanella sp. Strain ISO12, a Candidate Probiotic Isolated from the Intestine of Fundulus heteroclitus

Microbiology Resource Announcements ◽

10.1128/mra.00399-20 ◽

2020 ◽

Vol 9 (22) ◽

Author(s):

Harold J. Schreier

Keyword(s):

Genome Sequence ◽

Fundulus Heteroclitus ◽

Draft Genome ◽

Bioinformatic Analysis ◽

Draft Genome Sequence ◽

Genes Encoding ◽

Probiotic Activity

ABSTRACT The genome of Shewanella sp. strain ISO12, which was isolated from the intestine of wild-caught Fundulus heteroclitus, was sequenced and is reported here. Bioinformatic analysis revealed genes encoding the bacteriocin marinocine and those potentially associated with probiotic activity. The genome sequence will assist in further identifying probiotic and other antibacterial processes.

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Small-Molecule Inhibition of Choline Catabolism in Pseudomonas aeruginosa and Other Aerobic Choline-Catabolizing Bacteria

Applied and Environmental Microbiology ◽

10.1128/aem.00504-11 ◽

2011 ◽

Vol 77 (13) ◽

pp. 4383-4389 ◽

Cited By ~ 12

Author(s):

Liam F. Fitzsimmons ◽

Stevenson Flemer ◽

A. Sandy Wurthmann ◽

P. Bruce Deker ◽

Indra Neil Sarkar ◽

...

Keyword(s):

Pseudomonas Aeruginosa ◽

Burkholderia Cepacia ◽

Sinorhizobium Meliloti ◽

Growth Inhibitor ◽

Bioinformatic Analysis ◽

Content Type ◽

Genes Encoding ◽

Dependent Growth

ABSTRACTCholine is abundant in association with eukaryotes and plays roles in osmoprotection, thermoprotection, and membrane biosynthesis in many bacteria. Aerobic catabolism of choline is widespread among soil proteobacteria, particularly those associated with eukaryotes. Catabolism of choline as a carbon, nitrogen, and/or energy source may play important roles in association with eukaryotes, including pathogenesis, symbioses, and nutrient cycling. We sought to generate choline analogues to study bacterial choline catabolismin vitroandin situ. Here we report the characterization of a choline analogue, propargylcholine, which inhibits choline catabolism at the level of Dgc enzyme-catalyzed dimethylglycine demethylation inPseudomonas aeruginosa. We used genetic analyses and13C nuclear magnetic resonance to demonstrate that propargylcholine is catabolized to its inhibitory form, propargylmethylglycine. Chemically synthesized propargylmethylglycine was also an inhibitor of growth on choline. Bioinformatic analysis suggests that there are genes encoding DgcA homologues in a variety of proteobacteria. We examined the broader utility of propargylcholine and propargylmethylglycine by assessing growth of other members of the proteobacteria that are known to grow on choline and possess putative DgcA homologues. Propargylcholine showed utility as a growth inhibitor inP. aeruginosabut did not inhibit growth in other proteobacteria tested. In contrast, propargylmethylglycine was able to inhibit choline-dependent growth in all tested proteobacteria, includingPseudomonas mendocina,Pseudomonas fluorescens,Pseudomonas putida,Burkholderia cepacia,Burkholderia ambifaria, andSinorhizobium meliloti. We predict that chemical inhibitors of choline catabolism will be useful for studying this pathway in clinical and environmental isolates and could be a useful tool to study proteobacterial choline catabolismin situ.

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Network Protein Interaction in Parkinson's Disease and Periodontitis Interplay: A Bioinformatic Analysis

10.20944/preprints202009.0050.v1 ◽

2020 ◽

Author(s):

João Botelho ◽

Paulo Mascarenhas ◽

José João Mendes ◽

Vanessa Machado

Keyword(s):

Protein Interaction ◽

Protein Interactions ◽

Molecular Mechanisms ◽

Interaction Analysis ◽

Bioinformatic Analysis ◽

Comprehensive Analysis ◽

Protein Network ◽

Protein Protein Interactions ◽

Network Interaction ◽

Genes Encoding

Recent studies supported a clinical association between Parkinson’s Disease (PD) and periodontitis. Hence, investigating possible protein interactions between these two conditions is of interest. In this study, we conducted a protein-protein network interaction analysis with recognized genes encoding proteins for PD and periodontitis. Genes of interest were collected via GWAS database. Then, we conducted a protein interaction analysis using STRING database, with a highest confidence cut-off of 0.9. Our protein network casted a comprehensive analysis of potential protein-protein interactions between PD and periodontitis. This analysis may underpin valuable information for new candidate molecular mechanisms between PD and periodontitis and may serve new potential targets for research purposes. These results should be carefully interpreted giving the limitations of this approach.

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RegR Virulence Regulon of Rabbit-Specific Enteropathogenic Escherichia coli Strain E22

Infection and Immunity ◽

10.1128/iai.01325-12 ◽

2013 ◽

Vol 81 (4) ◽

pp. 1078-1089 ◽

Cited By ~ 7

Author(s):

Yogitha N. Srikhanta ◽

Dianna M. Hocking ◽

Judyta Praszkier ◽

Matthew J. Wakefield ◽

Roy M. Robins-Browne ◽

...

Keyword(s):

Escherichia Coli ◽

Regulatory Protein ◽

Bioinformatic Analysis ◽

Coli Strain ◽

Mobility Shift ◽

Gene Encoding ◽

Gene Target ◽

Content Type ◽

E Coli ◽

Genes Encoding

ABSTRACTAraC-like regulators play a key role in the expression of virulence factors in enteric pathogens, such as enteropathogenicEscherichia coli(EPEC), enterotoxigenicE. coli, enteroaggregativeE. coli, andCitrobacter rodentium. Bioinformatic analysis of the genome of rabbit-specific EPEC (REPEC) strain E22 (O103:H2) revealed the presence of a gene encoding an AraC-like regulatory protein, RegR, which shares 71% identity to the global virulence regulator, RegA, ofC. rodentium. Microarray analysis demonstrated that RegR exerts 25- to 400-fold activation on transcription of several genes encoding putative virulence-associated factors, including a fimbrial operon (SEF14), a serine protease, and an autotransporter adhesin. These observations were confirmed by proteomic analysis of secreted and heat-extracted surface-associated proteins. The mechanism of RegR-mediated activation was investigated by using its most highly upregulated gene target,sefA. Transcriptional analyses and electrophoretic mobility shift assays showed that RegR activates the expression ofsefAby binding to a region upstream of thesefApromoter, thereby relieving gene silencing by the global regulatory protein H-NS. Moreover, RegR was found to contribute significantly to virulence in a rabbit infection experiment. Taken together, our findings indicate that RegR controls the expression of a series of accessory adhesins that significantly enhance the virulence of REPEC strain E22.

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Pivotal role of the Francisella tularensis heat-shock sigma factor RpoH

Microbiology ◽

10.1099/mic.0.029058-0 ◽

2009 ◽

Vol 155 (8) ◽

pp. 2560-2572 ◽

Cited By ~ 28

Author(s):

Nathalie Grall ◽

Jonathan Livny ◽

Matthew Waldor ◽

Monique Barel ◽

Alain Charbit ◽

...

Keyword(s):

Heat Shock ◽

Francisella Tularensis ◽

Sigma Factor ◽

Bacterial Species ◽

Bioinformatic Analysis ◽

Alternative Sigma Factor ◽

Heat Stress Response ◽

Alternative Sigma Factors ◽

Genes Encoding

Francisella tularensis is a highly infectious pathogen that infects animals and humans to cause the disease tularemia. The primary targets of this bacterium are macrophages, in which it replicates in the cytoplasm after escaping the initial phagosomal compartment. The ability to replicate within macrophages relies on the tightly regulated expression of a series of genes. One of the most commonly used means of coordinating the regulation of multiple genes in bacteria consists of the association of dedicated alternative sigma factors with the core of the RNA polymerase (RNAP). In silico analysis of the F. tularensis LVS genome led us to identify, in addition to the genes encoding the RNAP core (comprising the α1, α2, β, β′ and ω subunits), one gene (designated rpoD) encoding the major sigma factor σ 70, and a unique gene (FTL_0851) encoding a putative alternative sigma factor homologue of the σ 32 heat-shock family (designated rpoH). Hence, F. tularensis represents one of the minority of bacterial species that possess only one or no alternative sigma factor in addition to the main factor σ 70. In the present work, we show that FTL_0851 encodes a genuine σ 32 factor. Transcriptomic analyses of the F. tularensis LVS heat-stress response allowed the identification of a series of orthologues of known heat-shock genes (including those for Hsp40, GroEL, GroES, DnaK, DnaJ, GrpE, ClpB and ClpP) and a number of genes implicated in Francisella virulence. A bioinformatic analysis was used to identify genes preceded by a putative σ 32-binding site, revealing both similarities to and differences from RpoH-mediated gene expression in Escherichia coli. Our results suggest that RpoH is an essential protein of F. tularensis, and positively regulates a subset of genes involved in the heat-shock response.

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Tartary Buckwheat (Fagopyrum tataricum) NAC Transcription Factors FtNAC16 Negatively Regulates of Pod Cracking and Salinity Tolerant in Arabidopsis

International Journal of Molecular Sciences ◽

10.3390/ijms22063197 ◽

2021 ◽

Vol 22 (6) ◽

pp. 3197

Author(s):

Jing Wang ◽

ZhaoTang Ma ◽

Bo Tang ◽

HaoYu Yu ◽

ZiZhong Tang ◽

...

Keyword(s):

Transcription Factor ◽

Salt Stress ◽

Lignin Content ◽

Bioinformatic Analysis ◽

Soil Salinization ◽

Fagopyrum Tataricum ◽

Nac Transcription Factors ◽

Physiological Indicators ◽

Lignin Synthesis ◽

Genes Encoding

The thick and hard fruit shell of Fagopyrum tataricum (F. tataricum) represents a processing bottleneck. At the same time, soil salinization is one of the main problems faced by modern agricultural production. Bioinformatic analysis indicated that the F. tataricum transcription factor FtNAC16 could regulate the hull cracking of F. tataricum, and the function of this transcription factor was verified by genetic transformation of Arabidopsis thaliana (A. thaliana). Phenotypic observations of the wild-type (WT), OE-FtNAC16, nst1/3 and nst1/3-FtNAC16 plant lines confirmed that FtNAC16 negatively regulated pod cracking by downregulating lignin synthesis. Under salt stress, several physiological indicators (POD, GSH, Pro and MDA) were measured, A. thaliana leaves were stained with NBT (Nitroblue Tetrazolium) and DAB (3,3’-diaminobenzidine), and all genes encoding enzymes in the lignin synthesis pathway were analyzed. These experiments confirmed that FtNAC16 increased plant sensitivity by reducing the lignin content or changing the proportions of the lignin monomer. The results of this study may help to elucidate the possible association between changes in lignin monomer synthesis and salt stress and may also contribute to fully understanding the effects of FtNAC16 on plant growth and development, particularly regarding fruit pod cracking and environmental adaptability. In future studies, it may be useful to obtain suitable cracking varieties and salt-tolerant crops through molecular breeding.

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Bioinformatic analysis of Arabidopsis reverse transcriptases with a zinc-finger domain

Biologia ◽

10.1515/biolog-2016-0145 ◽

2016 ◽

Vol 71 (11) ◽

Author(s):

Santiago Valentín Galván-Gordillo ◽

Angélica Concepción Martínez-Navarro ◽

Beatriz Xoconostle-Cázares ◽

Roberto Ruiz-Medrano

Keyword(s):

Zinc Finger ◽

Structural Characteristics ◽

Bioinformatic Analysis ◽

Plant Evolution ◽

Zinc Finger Domain ◽

Reverse Transcriptase Domain ◽

Reverse Transcriptases ◽

Genes Encoding ◽

Endogenous Genes ◽

Eukaryotic Organisms

AbstractPlants, as most eukaryotic organisms, harbor several genes encoding a reverse transcriptase domain. The majority of them are part of transposable elements (TEs) and/or retroviral genomes that have been inserted into their genomes. However, there are some examples of RT domain-containing genes that have been endogenized during plant evolution; these genes appear to display functions other than “selfish” maintenance and replication of TEs, and subjected to host gene regulation. In the present work we have analyzed a subset of genes in Arabidopsis with an RT domain (RVT) containing a zinc finger motif (Znf), termed RVT-Znf domain, with structural characteristics of endogenous genes i.e., contain potential upstream regions as well as 5’UTR, and 3’UTR, and are not flanked by retroelement features. Phylogenetic analysis of these genes, based on the RVT-Znf domain, indicates that there are three clades, the members of which having additional domains. When compared to additional sequences, RVT-Znf formed a cluster that is more closely related to non-LTR retrotransposons and group II introns. Extant data from microarray databases indicate that several Arabidopsis genes are expressed. These data indicate that these RTs may have been endogenized. Possible roles for these genes are discussed.

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