scholarly journals The dar Genes of Pseudomonas chlororaphis PCL1606 Are Crucial for Biocontrol Activity via Production of the Antifungal Compound 2-Hexyl, 5-Propyl Resorcinol

2013 ◽  
Vol 26 (5) ◽  
pp. 554-565 ◽  
Author(s):  
Claudia E. Calderón ◽  
Alejandro Pérez-García ◽  
Antonio de Vicente ◽  
Francisco M. Cazorla
Keyword(s):  
Genomic Dna ◽  
Genetic Basis ◽  
Genomic Library ◽  
Open Reading Frames ◽  
Antifungal Compound ◽  
Pseudomonas Chlororaphis ◽  
Phylogenetic Studies ◽  
Biocontrol Activity ◽  
Reading Frames

To determine the genetic basis by which 2-hexyl, 5-propyl resorcinol (HPR) is produced by the biocontrol rhizobacterium Pseudomonas chlororaphis (formerly known as P. fluorescens) PCL1606, the presence and role of dar genes were investigated. To accomplish this aim, the pCGNOV-1 plasmid was isolated from a PCL1606 genomic library and was shown to hybridize to various dar probes by Southern blot. An analysis of the pCGNOV-1 genomic DNA revealed the presence of five open reading frames that were homologous to dar genes and had an organization that resembled the arrangement of previously described P. chlororaphis strains. Phylogenetic studies resulted in the clustering of PCL1606 with the P. chlororaphis subgroup, which supported the renaming of this strain from P. fluorescens to P. chlororaphis PCL1606. The construction of insertional mutants for each homologous dar gene in P. chlororaphis PCL1606 along with their corresponding complemented derivative strains restored HPR production and confirmed the key role of the dar A and darB genes in HPR production and in the antagonistic phenotype. Finally, biocontrol assays were performed on avocado–Rosellinia and tomato–Fusarium test systems using the HPR-defective and -complemented derivative strains generated here and demonstrated the crucial role of the biosynthetic dar genes in the biocontrol phenotype of P. chlororaphis PCL1606. This biocontrol phenotype is dependent on the dar genes via their production of the HPR antibiotic. Some of the dar genes not directly involved in the biosynthesis of HPR, such as darS or darR, might contribute to regulatory features of HPR production.

scholarly journals Genetic Basis for Lipopolysaccharide O-Antigen Biosynthesis in Bordetellae

1999 ◽  
Vol 67 (8) ◽  
pp. 3763-3767 ◽  
Author(s):  
Andrew Preston ◽  
Andrew G. Allen ◽  
Joanna Cadisch ◽  
Richard Thomas ◽  
Kim Stevens ◽  
...  
Keyword(s):  
Insertion Sequence ◽  
Genetic Basis ◽  
Genetic Locus ◽  
Bordetella Bronchiseptica ◽  
Open Reading Frames ◽  
Bordetella Parapertussis ◽  
O Antigen ◽  
Surface Polysaccharide ◽  
Reading Frames

ABSTRACT Bordetella bronchiseptica and Bordetella parapertussis express a surface polysaccharide, attached to a lipopolysaccharide, which has been called O antigen. This structure is absent from Bordetella pertussis. We report the identification of a large genetic locus in B. bronchiseptica and B. parapertussis that is required for O-antigen biosynthesis. The locus is replaced by an insertion sequence in B. pertussis, explaining the lack of O-antigen biosynthesis in this species. The DNA sequence of the B. bronchiseptica locus has been determined and the presence of 21 open reading frames has been revealed. We have ascribed putative functions to many of these open reading frames based on database searches. Mutations in the locus in B. bronchiseptica andB. parapertussis prevent O-antigen biosynthesis and provide tools for the study of the role of O antigen in infections caused by these bacteria.

scholarly journals Genetic Path of the Emergence of SARS-CoV-2

2021 ◽  
Vol In Press (In Press) ◽  
Author(s):  
Taslima Nasrin ◽  
Safdar Ali
Keyword(s):  
Genetic Basis ◽  
Proteome Analysis ◽  
Open Reading Frames ◽  
Host Cells ◽  
Present Review ◽  
Intermediate Hosts ◽  
Crown Shape ◽  
Reservoir Hosts ◽  
Reading Frames

Context: SARS-CoV-2 is the seventh coronavirus that has humans as the host. Because of its highly infectious nature, toward the end of January 2020, the WHO declared it a public health emergency of international concern. The present review is about understanding the journey of SARS-CoV-2 to its present form with an attempt to assess the genetic basis of its pandemic-causing abilities. Evidence Acquisition: The data for the present review were accessed through different publications and preprint repositories. Results: SARS-CoV-2 is a beta-coronavirus, and is approximately 60 - 140 nm in size. The appearance of its structure as a crown shape under an electron microscope led to the coining of its name ‘Coronavirus’. Comparative genome and proteome analysis exhibits similarities and differences with reference to SARS-CoV. The Open Reading Frames (ORFs) found on the SARS-CoV-2 genome, and their corresponding proteins have been discussed. Bats may act as reservoir hosts but not exclusively. The possibility of snakes as the host, as well as other intermediate hosts, before reaching humans seems plausible. This has been supported by ACE2 receptor diversity and conservation across different tissues and organisms. The role of spike glycoprotein and its interaction with the receptor through specific residues for invading host cells makes a perfect therapeutic target, but the variations therein and the resulting impact on interactions pose challenges for the same. Conclusions: Though the differences between the MERS, SARS-CoV, and SARS-CoV-2 genomes indicate amino acid changes, leading to the present pandemic situation, the fact that new variants are still emerging signifies that the journey is an ongoing one, which requires monitoring.

scholarly journals Identification of Campylobacter jejuni ATCC 43431-Specific Genes by Whole Microbial Genome Comparisons

2004 ◽  
Vol 186 (14) ◽  
pp. 4781-4795 ◽  
Author(s):  
Frédéric Poly ◽  
Deborah Threadgill ◽  
Alain Stintzi
Keyword(s):  
Dna Sequences ◽  
Genomic Dna ◽  
Genomic Library ◽  
Open Reading Frames ◽  
Dna Fragments ◽  
Helicobacter Hepaticus ◽  
Type Iv ◽  
Novel Approach ◽  
The Mean ◽  
Reading Frames

ABSTRACT This study describes a novel approach to identify unique genomic DNA sequences from the unsequenced strain C. jejuni ATCC 43431 by comparison with the sequenced strain C. jejuni NCTC 11168. A shotgun DNA microarray was constructed by arraying 9,600 individual DNA fragments from a C. jejuni ATCC 43431 genomic library onto a glass slide. DNA fragments unique to C. jejuni ATCC 43431 were identified by competitive hybridization to the array with genomic DNA of C. jejuni NCTC 11168. The plasmids containing unique DNA fragments were sequenced, allowing the identification of up to 130 complete and incomplete genes. Potential biological roles were assigned to 66% of the unique open reading frames. The mean G+C content of these unique genes (26%) differs significantly from the G+C content of the entire C. jejuni genome (30.6%). This suggests that they may have been acquired through horizontal gene transfer from an organism with a G+C content lower than that of C. jejuni. Because the two C. jejuni strains differ by Penner serotype, a large proportion of the unique ATCC 43431 genes encode proteins involved in lipooligosaccharide and capsular biosynthesis, as expected. Several unique open reading frames encode enzymes which may contribute to genetic variability, i.e., restriction-modification systems and integrases. Interestingly, many of the unique C. jejuni ATCC 43431 genes show identity with a possible pathogenicity island from Helicobacter hepaticus and components of a potential type IV secretion system. In conclusion, this study provides a valuable resource to further investigate Campylobacter diversity and pathogenesis.

scholarly journals DNA Microarray Analysis of Central Carbohydrate Metabolism: Glycolytic/Gluconeogenic Carbon Switch in the Hyperthermophilic Crenarchaeum Thermoproteus tenax

2008 ◽  
Vol 190 (6) ◽  
pp. 2231-2238 ◽  
Author(s):  
Melanie Zaparty ◽  
Alexander Zaigler ◽  
Claudia Stamme ◽  
Jörg Soppa ◽  
Reinhard Hensel ◽  
...  
Keyword(s):  
Carbohydrate Metabolism ◽  
Dna Microarray ◽  
Transcript Level ◽  
Open Reading Frames ◽  
Transcriptional Analysis ◽  
Heterotrophic Growth ◽  
Thermoproteus Tenax ◽  
Central Carbohydrate Metabolism ◽  
Reading Frames

ABSTRACT In order to unravel the role of regulation on transcript level in central carbohydrate metabolism (CCM) of Thermoproteus tenax, a focused DNA microarray was constructed by using 85 open reading frames involved in CCM. A transcriptional analysis comparing heterotrophic growth on glucose versus autotrophic growth on CO2-H2 was performed.

scholarly journals Identification and Sequencing of β-Myrcene Catabolism Genes from Pseudomonas sp. Strain M1

1999 ◽  
Vol 65 (7) ◽  
pp. 2871-2876 ◽  
Author(s):  
Sandra Iurescia ◽  
Andrea M. Marconi ◽  
Daniela Tofani ◽  
Augusto Gambacorta ◽  
Annalisa Paternò ◽  
...  
Keyword(s):  
Genomic Library ◽  
Enrichment Culture ◽  
Open Reading Frames ◽  
Gas Chromatography Mass Spectrometry ◽  
Complete Agreement ◽  
Wild Type ◽  
Genomic Insert ◽  
The One ◽  
Acyl Coenzyme A ◽  
Reading Frames

ABSTRACT The M1 strain, able to grow on β-myrcene as the sole carbon and energy source, was isolated by an enrichment culture and identified as a Pseudomonas sp. One β-myrcene-negative mutant, called N22, obtained by transposon mutagenesis, accumulated (E)-2-methyl-6-methylen-2,7-octadien-1-ol (or myrcen-8-ol) as a unique β-myrcene biotransformation product. This compound was identified by gas chromatography-mass spectrometry. We cloned and sequenced the DNA regions flanking the transposon and used these fragments to identify the M1 genomic library clones containing the wild-type copy of the interrupted gene. One of the selected cosmids, containing a 22-kb genomic insert, was able to complement the N22 mutant for growth on β-myrcene. A 5,370-bp-long sequence spanning the region interrupted by the transposon in the mutant was determined. We identified four open reading frames, named myrA,myrB, myrC, and myrD, which can potentially code for an aldehyde dehydrogenase, an alcohol dehydrogenase, an acyl-coenzyme A (CoA) synthetase, and an enoyl-CoA hydratase, respectively. myrA, myrB, andmyrC are likely organized in an operon, since they are separated by only 19 and 36 nucleotides (nt), respectively, and no promoter-like sequences have been found in these regions. ThemyrD gene starts 224 nt upstream of myrA and is divergently transcribed. The myrB sequence was found to be completely identical to the one flanking the transposon in the mutant. Therefore, we could ascertain that the transposon had been inserted inside the myrB gene, in complete agreement with the accumulation of (E)-2-methyl-6-methylen-2,7-octadien-1-ol by the mutant. Based on sequence and biotransformation data, we propose a pathway for β-myrcene catabolism in Pseudomonas sp. strain M1.

scholarly journals Autophagy Intertwines with Different Diseases—Recent Strategies for Therapeutic Approaches

Diseases ◽  
2019 ◽  
Vol 7 (1) ◽  
pp. 15 ◽  
Author(s):  
Janani Ramesh ◽  
Larance Ronsard ◽  
Anthony Gao ◽  
Bhuvarahamurthy Venugopal
Keyword(s):  
Inflammatory Diseases ◽  
Therapeutic Strategies ◽  
Open Reading Frames ◽  
Signaling Cascades ◽  
Progression Rate ◽  
Therapeutic Approaches ◽  
Genes Encoding ◽  
Novel Therapeutic Strategies ◽  
Reading Frames

Autophagy is a regular and substantial “clear-out process” that occurs within the cell and that gets rid of debris that accumulates in membrane-enclosed vacuoles by using enzyme-rich lysosomes, which are filled with acids that degrade the contents of the vacuoles. This machinery is well-connected with many prevalent diseases, including cancer, HIV, and Parkinson’s disease. Considering that autophagy is well-known for its significant connections with a number of well-known fatal diseases, a thorough knowledge of the current findings in the field is essential in developing therapies to control the progression rate of diseases. Thus, this review summarizes the critical events comprising autophagy in the cellular system and the significance of its key molecules in manifesting this pathway in various diseases for down- or upregulation. We collectively reviewed the role of autophagy in various diseases, mainly neurodegenerative diseases, cancer, inflammatory diseases, and renal disorders. Here, some collective reports on autophagy showed that this process might serve as a dual performer: either protector or contributor to certain diseases. The aim of this review is to help researchers to understand the role of autophagy-regulating genes encoding functional open reading frames (ORFs) and its connection with diseases, which will eventually drive better understanding of both the progression and suppression of different diseases at various stages. This review also focuses on certain novel therapeutic strategies which have been published in the recent years based on targeting autophagy key proteins and its interconnecting signaling cascades.

scholarly journals Filtering "genic" open reading frames from genomic DNA samples for advanced annotation

BMC Genomics ◽  
2011 ◽  
Vol 12 (Suppl 1) ◽  
pp. S5 ◽  
Author(s):  
Sara D'Angelo ◽  
Nileena Velappan ◽  
Flavio Mignone ◽  
Claudio Santoro ◽  
Daniele Sblattero ◽  
...  
Keyword(s):  
Genomic Dna ◽  
Open Reading Frames ◽  
Reading Frames

scholarly journals Role of two upstream open reading frames in the translational control of oncogene mdm2

Oncogene ◽  
1999 ◽  
Vol 18 (41) ◽  
pp. 5631-5637 ◽  
Author(s):  
Cheryl Y Brown ◽  
Gregory J Mize ◽  
Mario Pineda ◽  
Donna L George ◽  
David R Morris
Keyword(s):  
Translational Control ◽  
Open Reading Frames ◽  
Upstream Open Reading Frames ◽  
Reading Frames

Protection against bacteriocin 28b in Serratia matcescens is apparently not related to the expression of an immunity gene

1995 ◽  
Vol 41 (3) ◽  
pp. 217-226 ◽  
Author(s):  
Margarita Beatriz Viejo ◽  
Josefina Enfedaque ◽  
Joan Francesc Guasch ◽  
Santiago Ferrer ◽  
Miguel Regué
Keyword(s):  
Nucleotide Sequence ◽  
Serratia Marcescens ◽  
Structural Gene ◽  
Genomic Library ◽  
Open Reading Frames ◽  
Genetic Determinants ◽  
Gene Encoding ◽  
Immunity Gene ◽  
Release Analysis ◽  
Reading Frames

The gene encoding bacteriocin 28b from Serratia marcescens N28b (bss gene) has been cloned in Escherichia coli and its nucleotide sequence has been determined. The genetic determinants coding for other well-characterized bacteriocins from enterobacteria (colicins) are located in plasmids and they have always been shown to contain a gene responsible for immunity located downstream from the bacteriocin structural gene. In some cases there is another gene located downstream from the immunity gene, which is responsible for bacteriocin release. Analysis of bacteriocin 28b release and the sensitivity to this bacteriocin of E. coli strains harbouring recombinant plasmids containing the bss gene showed that bacteriocin 28b is not released from the cell in these strains and that their phenotypic insensitivity is not associated with any region close to the structural gene. The nucleotide sequence of the region downstream from the bss gene contains two putative open reading frames transcribed in the opposite direction to the bss gene. These open reading frames apparently encode proteins that seem not to be involved in bacteriocin immunity or release. Moreover, a S. marcescens N28b genomic library was screened and no immunity gene was found. Therefore, bacteriocin 28b differs greatly from the bacteriocins from other enterobacteria, and in the following senses it is unique: firstly, the gene encoding bacteriocin 28b seems to be located on the chromosome, and secondly, insensitivity to this bacteriocin in S. marcescens N28b is not associated with the expression of an immunity gene.Key words: bacteriocin, pore-forming colicins, immunity, Serratia marcescens.

scholarly journals Comparative Genomic Analysis of Pseudomonas chlororaphis PCL1606 Reveals New Insight into Antifungal Compounds Involved in Biocontrol

2015 ◽  
Vol 28 (3) ◽  
pp. 249-260 ◽  
Author(s):  
Claudia E. Calderón ◽  
Cayo Ramos ◽  
Antonio de Vicente ◽  
Francisco M. Cazorla
Keyword(s):  
Genome Sequence ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Whole Genome Sequence ◽  
Comparative Genomic ◽  
Antifungal Compound ◽  
Antifungal Compounds ◽  
Pseudomonas Chlororaphis ◽  
Biosynthetic Genes ◽  
Biocontrol Activity

Pseudomonas chlororaphis PCL1606 is a rhizobacterium that has biocontrol activity against many soilborne phytopathogenic fungi. The whole genome sequence of this strain was obtained using the Illumina Hiseq 2000 sequencing platform and was assembled using SOAP denovo software. The resulting 6.66-Mb complete sequence of the PCL1606 genome was further analyzed. A comparative genomic analysis using 10 plant-associated strains within the fluorescent Pseudomonas group, including the complete genome of P. chlororaphis PCL1606, revealed a diverse spectrum of traits involved in multitrophic interactions with plants and microbes as well as biological control. Phylogenetic analysis of these strains using eight housekeeping genes clearly placed strain PCL1606 into the P. chlororaphis group. The genome sequence of P. chlororaphis PCL1606 revealed the presence of sequences that were homologous to biosynthetic genes for the antifungal compounds 2-hexyl, 5-propyl resorcinol (HPR), hydrogen cyanide, and pyrrolnitrin; this is the first report of pyrrolnitrin encoding genes in this P. chlororaphis strain. Single-, double-, and triple-insertional mutants in the biosynthetic genes of each antifungal compound were used to test their roles in the production of these antifungal compounds and in antagonism and biocontrol of two fungal pathogens. The results confirmed the function of HPR in the antagonistic phenotype and in the biocontrol activity of P. chlororaphis PCL1606.

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