Genetic Path of the Emergence of SARS-CoV-2

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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Genetic Basis for Lipopolysaccharide O-Antigen Biosynthesis in Bordetellae

Infection and Immunity ◽

10.1128/iai.67.8.3763-3767.1999 ◽

1999 ◽

Vol 67 (8) ◽

pp. 3763-3767 ◽

Cited By ~ 64

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.

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

Oncogene ◽

10.1038/sj.onc.1202949 ◽

1999 ◽

Vol 18 (41) ◽

pp. 5631-5637 ◽

Cited By ~ 59

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

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A plasmid-encoded papB paralogue modulates autoaggregation of Escherichia coli transconjugants

10.21203/rs.3.rs-36006/v2 ◽

2020 ◽

Author(s):

Ruben Monarrez ◽

Iruka Okeke

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Genetic Basis ◽

Mobile Element ◽

Enteric Bacteria ◽

Selective Advantage ◽

Open Reading Frames ◽

Bacterial Strains ◽

Element Bearing ◽

Reading Frames

Abstract Objective: Plasmids are key to antimicrobial resistance transmission among enteric bacteria. It is becoming increasingly clear that resistance genes alone do not account for the selective advantage of plasmids and bacterial strains that harbor them. Deletion of a 32 Kb fitness-conferring region of pMB2, a conjugative resistance plasmid, produced a hyper-autoaggregation phenotype in laboratory Escherichia coli. This study sought to determine the genetic basis for hyper-autoaggregation conferred by the pMB2-derived mini-plasmid. Results: The 32 Kb fragment deleted from pMB2 included previously characterized nutrient acquisition genes as well as putative transposase and integrase genes, a 272 bp papB/ pefB-like gene, and several open-reading frames of unknown function. We cloned the papB/ pefB paralogue and found it sufficient to temper the hyper-autoaggregation phenotype. Hyper-autoaggregation conferred by the mini-plasmid did not occur in a fim-negative background. This study has identified and characterized a gene capable of down-regulating host adhesins and has shown that trans-acting papB/pefB paralogues can occur outside the context of an adhesin cluster. This plasmid-mediated modification of a bacterial host’s colonization program may optimize horizontal transfer of the mobile element bearing the genes.

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Phage composition of a fermented milk and colostrum product assessed by microbiome array; putative role of open reading frames in reference to cell signaling and neurological development

10.1101/714154 ◽

2019 ◽

Author(s):

Stefania Pacini ◽

Marco Ruggiero

Keyword(s):

Dna Sequences ◽

Bovine Milk ◽

Fermented Milk ◽

Open Reading Frames ◽

Neurological Development ◽

Putative Role ◽

Biological Entities ◽

Reading Frames

AbstractBacteriophages (phages), Earth’s most numerous biological entities, are natural constituents of alimentary matrices; in this study we describe the characterization of phage populations in a product obtained by fermentation of bovine milk and colostrum. Such characterizations were achieved using a microarray consisting of a chip covered in short DNA sequences that are specific to certain target organisms for a total of approximately 12,000 species. The only viruses evidenced by the array belonged to Siphoviridae, the largest phage family that targets bacteria and archea. The array yielded 27 iterations corresponding to a unique target. We discuss the putative role of some open reading frames of these phages in conferring health-supporting properties with particular reference to cells signaling and neurological development. We also describe the in vitro interaction of this fermented product with alpha-N-acetylgalactosaminidase, an enzyme whose activity in serum is elevated in neurodevelopmental disorders.

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Emerging role of long noncoding RNA-encoded micropeptides in cancer

Cancer Cell International ◽

10.1186/s12935-020-01589-x ◽

2020 ◽

Vol 20 (1) ◽

Cited By ~ 1

Author(s):

Mujie Ye ◽

Jingjing Zhang ◽

Meng Wei ◽

Baihui Liu ◽

Kuiran Dong

Keyword(s):

Noncoding Rna ◽

Cancer Metabolism ◽

Chain Complex ◽

Ribosome Profiling ◽

Open Reading Frames ◽

Clinical Value ◽

Anti Cancer ◽

Nascent Chain ◽

Reading Frames

Abstract Increasing evidence has indicated that long noncoding RNAs (lncRNAs) play various important roles in the development of cancers. The widespread applications of ribosome profiling and ribosome nascent chain complex sequencing revealed that some short open reading frames of lncRNAs have micropeptide-coding potential. The resulting micropeptides have been shown to participate in N6-methyladenosine modification, tumor angiogenesis, cancer metabolism, and signal transduction. This review summarizes current information regarding the reported roles of lncRNA-encoded micropeptides in cancer, and explores the potential clinical value of these micropeptides in the development of anti-cancer drugs and prognostic tumor biomarkers.

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Genetic Analysis of the AdnA Regulon in Pseudomonas fluorescens: Nonessential Role of Flagella in Adhesion to Sand and Biofilm Formation

Journal of Bacteriology ◽

10.1128/jb.185.2.453-460.2003 ◽

2003 ◽

Vol 185 (2) ◽

pp. 453-460 ◽

Cited By ~ 39

Author(s):

Eduardo A. Robleto ◽

Inmaculada López-Hernández ◽

Mark W. Silby ◽

Stuart B. Levy

Keyword(s):

Pseudomonas Aeruginosa ◽

Transcription Factor ◽

Pseudomonas Fluorescens ◽

Biofilm Formation ◽

Deletion Mutant ◽

Open Reading Frames ◽

Cell Processes ◽

Reading Frames ◽

Insertion Mutants

ABSTRACT AdnA is a transcription factor in Pseudomonas fluorescens that affects flagellar synthesis, biofilm formation, and sand adhesion. To identify the AdnA regulon, we used a promoterless Tn5-lacZ element to study the phenotypes of insertion mutants in the presence and absence of AdnA. Of 12,000 insertions, we identified seven different putative open reading frames (ORFs) activated by AdnA (named aba for activated by AdnA). aba120 and aba177 showed homology to flgC and flgI, components of the basal body of the flagella in Pseudomonas aeruginosa. Two other insertions, aba18 and aba51, disrupted genes affecting chemotaxis. The mutant loci aba160 (possibly affecting lipopolysaccharide synthesis) and aba175 (unknown function) led to loss of flagella. The mutant bearing aba203 became motile when complemented with adnA, but the mutated gene showed no similarity to known genes. Curiously, aba18, aba51, aba160, and aba203 mutants formed biofilms even in the absence of AdnA, suppressing the phenotype of the adnA deletion mutant. The combined findings suggest that flagella are nonessential for sand attachment or biofilm formation. Sequence and promoter analyses indicate that AdnA affects at least 23 ORFs either directly or by polar effects. These results support the concept that AdnA regulates cell processes other than those directly related to flagellar synthesis and define a broader cadre of genes in P. fluorescens than that described so far for its homolog, FleQ, in P. aeruginosa.

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Aquaporin AQP11 in the testis: molecular identity and association with the processing of residual cytoplasm of elongated spermatids

Reproduction ◽

10.1530/rep-09-0298 ◽

2010 ◽

Vol 139 (1) ◽

pp. 209-216 ◽

Cited By ~ 39

Author(s):

C H Yeung ◽

T G Cooper

Keyword(s):

Cell Types ◽

Open Reading Frames ◽

Molecular Forms ◽

Reading Frame ◽

Pcr Products ◽

Mrna And Protein Expression ◽

Intracellular Organelles ◽

Residual Bodies ◽

Reading Frames

AQP11 is one of the latest aquaporin (AQP) family members found, which differs from the other AQPs by its intracellular localisation and unusual water pore nucleotides with unclear function. Despite the highest mRNA expression among organs having been reported in the testis, the testicular molecule has not been studied in detail. Immunohistochemistry of rat adult testis localised AQP11 to the elongated spermatids (ES) and no other cell types except residual bodies inside Sertoli cells. It was absent from early ES at least until stage 13, and after a first diffuse appearance in the caudal cytoplasm became concentrated in intracellular organelles by stage 17, was strongest in vesicles in the anterior cytoplasm at the final ES stages and appeared in residual bodies. Staining was detected on the distal quarter of the sperm tail only immediately before spermiation. A similar localisation was found in the mouse and developmental profiles for both the open reading frame mRNA and protein expression in 8–50 dpp testis pinpointed its first appearance coinciding with late stage ES. Sequencing of PCR products of testicular Aqp11 containing the open reading frames confirmed a full match with GenBank databases for rat, mouse and human. Western blotting revealed two or more molecular forms with the 26/27 kDa species dominating in the rat/mouse testis and the 33/34 kDa form selectively allocated to the spermatozoa. In view of intracellular vacuolation leading to polycystic kidney in Aqp11-null mice, a possible role of testicular AQP11 in the recycling of surplus cytoplasmic components of the ES and sustaining Sertoli cell capacity in the support of spermatogenesis was discussed.

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