Genetic Basis for Lipopolysaccharide O-Antigen Biosynthesis in Bordetellae

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.

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Genetic Path of the Emergence of SARS-CoV-2

Gene Cell and Tissue ◽

10.5812/gct.118302 ◽

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.

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

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-01-13-0012-r ◽

2013 ◽

Vol 26 (5) ◽

pp. 554-565 ◽

Cited By ~ 28

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.

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Bias between the Left and Right Inverted Repeats during IS911 Targeted Insertion

Journal of Bacteriology ◽

10.1128/jb.00452-08 ◽

2008 ◽

Vol 190 (18) ◽

pp. 6111-6118 ◽

Cited By ~ 5

Author(s):

P. Rousseau ◽

C. Loot ◽

C. Turlan ◽

S. Nolivos ◽

M. Chandler

Keyword(s):

Insertion Sequence ◽

Regulatory Protein ◽

Open Reading Frames ◽

Inverted Repeats ◽

Functional Differences ◽

Left And Right ◽

Ordered Assembly ◽

Overlapping Open Reading Frames ◽

Reading Frames

ABSTRACT IS911 is a bacterial insertion sequence composed of two consecutive overlapping open reading frames (ORFs [orfA and orfB]) encoding the transposase (OrfAB) as well as a regulatory protein (OrfA). These ORFs are bordered by terminal left and right inverted repeats (IRL and IRR, respectively) with several differences in nucleotide sequence. IS911 transposition is asymmetric: each end is cleaved on one strand to generate a free 3′-OH, which is then used as the nucleophile in attacking the opposite insertion sequence (IS) end to generate a free IS circle. This will be inserted into a new target site. We show here that the ends exhibit functional differences which, in vivo, may favor the use of one compared to the other during transposition. Electromobility shift assays showed that a truncated form of the transposase [OrfAB(1-149)] exhibits higher affinity for IRR than for IRL. While there was no detectable difference in IR activities during the early steps of transposition, IRR was more efficient during the final insertion steps. We show here that the differential activities between the two IRs correlate with the different affinities of OrfAB(1-149) for the IRs during assembly of the nucleoprotein complexes leading to transposition. We conclude that the two inverted repeats are not equivalent during IS911 transposition and that this asymmetry may intervene to determine the ordered assembly of the different protein-DNA complexes involved in the reaction.

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

Journal of Bacteriology ◽

10.1128/jb.01524-07 ◽

2008 ◽

Vol 190 (6) ◽

pp. 2231-2238 ◽

Cited By ~ 16

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.

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Nucleotide Sequence and Genetic Structure of a Novel Carbaryl Hydrolase Gene (cehA) from Rhizobium sp. Strain AC100

Applied and Environmental Microbiology ◽

10.1128/aem.68.3.1220-1227.2002 ◽

2002 ◽

Vol 68 (3) ◽

pp. 1220-1227 ◽

Cited By ~ 50

Author(s):

Masayuki Hashimoto ◽

Mitsuru Fukui ◽

Kouichi Hayano ◽

Masahito Hayatsu

Keyword(s):

Nucleotide Sequence ◽

Insertion Sequence ◽

Amino Acid Sequences ◽

Open Reading Frames ◽

Homology Search ◽

Sequencing Analysis ◽

Terminal Sequence ◽

Homologous Sequences ◽

Naphthyl Acetate ◽

Reading Frames

ABSTRACT Rhizobium sp. strain AC100, which is capable of degrading carbaryl (1-naphthyl-N-methylcarbamate), was isolated from soil treated with carbaryl. This bacterium hydrolyzed carbaryl to 1-naphthol and methylamine. Carbaryl hydrolase from the strain was purified to homogeneity, and its N-terminal sequence, molecular mass (82 kDa), and enzymatic properties were determined. The purified enzyme hydrolyzed 1-naphthyl acetate and 4-nitrophenyl acetate indicating that the enzyme is an esterase. We then cloned the carbaryl hydrolase gene (cehA) from the plasmid DNA of the strain and determined the nucleotide sequence of the 10-kb region containing cehA. No homologous sequences were found by a database homology search using the nucleotide and deduced amino acid sequences of the cehA gene. Six open reading frames including the cehA gene were found in the 10-kb region, and sequencing analysis shows that the cehA gene is flanked by two copies of insertion sequence-like sequence, suggesting that it makes part of a composite transposon.

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Autophagy Intertwines with Different Diseases—Recent Strategies for Therapeutic Approaches

Diseases ◽

10.3390/diseases7010015 ◽

2019 ◽

Vol 7 (1) ◽

pp. 15 ◽

Cited By ~ 6

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.

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Characterization of the IS200/IS605 Insertion Sequence Family in Halanaerobium Hydrogeniformans

Genes ◽

10.3390/genes11050484 ◽

2020 ◽

Vol 11 (5) ◽

pp. 484

Author(s):

Michael Sadler ◽

Melanie R. Mormile ◽

Ronald L. Frank

Keyword(s):

Insertion Sequence ◽

Open Reading Frames ◽

Insertion Sequences ◽

Genome Plasticity ◽

Mobile Dna ◽

Dna Elements ◽

Left And Right ◽

Evolutionary Role ◽

Reading Frames

Mobile DNA elements play a significant evolutionary role by promoting genome plasticity. Insertion sequences are the smallest prokaryotic transposable elements. They are highly diverse elements, and the ability to accurately identify, annotate, and infer the full genomic impact of insertion sequences is lacking. Halanaerobium hydrogeniformans is a haloalkaliphilic bacterium with an abnormally high number of insertion sequences. One family, IS200/IS605, showed several interesting features distinct from other elements in this genome. Twenty-three loci harbor elements of this family in varying stages of decay, from nearly intact to an ends-only sequence. The loci were characterized with respect to two divergent open reading frames (ORF), tnpA and tnpB, and left and right ends of the elements. The tnpB ORF contains two nearly identical insert sequences that suggest recombination between tnpB ORF is occurring. From these results, insertion sequence activity can be inferred, including transposition capability and element interaction.

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Evolutionary Trends of the Transposase-Encoding Open Reading Frames A and B (orfA and orfB) of the Mycobacterial IS6110 Insertion Sequence

PLoS ONE ◽

10.1371/journal.pone.0130161 ◽

2015 ◽

Vol 10 (6) ◽

pp. e0130161 ◽

Cited By ~ 2

Author(s):

Sara Thabet ◽

Amine Namouchi ◽

Helmi Mardassi

Keyword(s):

Insertion Sequence ◽

Open Reading Frames ◽

Evolutionary Trends ◽

Reading Frames

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Genetic Characterization and Evolutionary Implications of a car Gene Cluster in the Carbazole Degrader Pseudomonas sp. Strain CA10

Journal of Bacteriology ◽

10.1128/jb.183.12.3663-3679.2001 ◽

2001 ◽

Vol 183 (12) ◽

pp. 3663-3679 ◽

Cited By ~ 75

Author(s):

Hideaki Nojiri ◽

Hiroyo Sekiguchi ◽

Kana Maeda ◽

Masaaki Urata ◽

Sei-Ichiro Nakai ◽

...

Keyword(s):

Gene Cluster ◽

Insertion Sequence ◽

Gene Clusters ◽

Open Reading Frames ◽

The Novel ◽

Gene Duplications ◽

Homology Searching ◽

Reading Frames ◽

Strain Ca10 ◽

Recombination Gene

ABSTRACT The nucleotide sequences of the 27,939-bp-long upstream and 9,448-bp-long downstream regions of thecarAaAaBaBbCAc(ORF7)Ad genes of carbazole-degrading Pseudomonas sp. strain CA10 were determined. Thirty-two open reading frames (ORFs) were identified, and the car gene cluster was consequently revealed to consist of 10 genes (carAaAaBaBbCAcAdDFE) encoding the enzymes for the three-step conversion of carbazole to anthranilate and the degradation of 2-hydroxypenta-2,4-dienoate. The high identities (68 to 83%) with the enzymes involved in 3-(3-hydroxyphenyl)propionic acid degradation were observed only for CarFE. This observation, together with the fact that two ORFs are inserted between carDand carFE, makes it quite likely that thecarFE genes were recruited from another locus. In the 21-kb region upstream from carAa, aromatic-ring-hydroxylating dioxygenase genes (ORF26, ORF27, and ORF28) were found. Inductive expression in carbazole-grown cells and the results of homology searching indicate that these genes encode the anthranilate 1,2-dioxygenase involved in carbazole degradation. Therefore, these ORFs were designated antABC. Four homologous insertion sequences, IS5car1 to IS5car4, were identified in the neighboring regions ofcar and ant genes. IS5car2and IS5car3 constituted the putative composite transposon containing antABC. One-ended transposition of IS5car2 together with the 5′ portion ofantA into the region immediately upstream ofcarAa had resulted in the formation of IS5car1 and ORF9. In addition to the insertion sequence-dependent recombination, gene duplications and presumed gene fusion were observed. In conclusion, through the above gene rearrangement, the novel genetic structure of the cargene cluster has been constructed. In addition, it was also revealed that the car and ant gene clusters are located on the megaplasmid pCAR1.

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