scholarly journals Biochemical and genetic analyses of the oomycetePythium insidiosumprovide new insights into clinical identification and urease-based evolution of metabolism-related traits

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4821 ◽  
Author(s):  
Theerapong Krajaejun ◽  
Thidarat Rujirawat ◽  
Teerat Kanpanleuk ◽  
Pitak Santanirand ◽  
Tassanee Lohnoo ◽  
...  
Keyword(s):  
Initial Assessment ◽  
Surgical Removal ◽  
Accessory Protein ◽  
Pythium Insidiosum ◽  
Biochemical Characteristics ◽  
Biochemical Assays ◽  
Protein Encoding ◽  
Encoding Genes ◽  
Hydrolysis Of ◽  
Urease Accessory Protein

The oomycete microorganism,Pythium insidiosum, causes the life-threatening infectious condition, pythiosis, in humans and animals worldwide. Affected individuals typically endure surgical removal of the infected organ(s). Detection ofP. insidiosumby the established microbiological, immunological, or molecular methods is not feasible in non-reference laboratories, resulting in delayed diagnosis. Biochemical assays have been used to characterizeP. insidiosum, some of which could aid in the clinical identification of this organism. Although hydrolysis of maltose and sucrose has been proposed as the key biochemical feature useful in discriminatingP. insidiosumfrom other oomycetes and fungi, this technique requires a more rigorous evaluation involving a wider selection ofP. insidiosumstrains. Here, we evaluated 10 routinely available biochemical assays for characterization of 26P. insidiosumstrains, isolated from different hosts and geographic origins. Initial assessment revealed diverse biochemical characteristics across theP. insidiosumstrains tested. Failure to hydrolyze sugars is observed, especially in slow-growing strains. Because hydrolysis of maltose and sucrose varied among different strains, use of the biochemical assays for identification ofP. insidiosumshould be cautioned. The ability ofP. insidiosumto hydrolyze urea is our focus, because this metabolic process relies on the enzyme urease, an important virulence factor of other pathogens. The ability to hydrolyze urea varied amongP. insidiosumstrains and was not associated with growth rates. Genome analyses demonstrated that urease- and urease accessory protein-encoding genes are present in both urea-hydrolyzing and non-urea-hydrolyzing strains ofP. insidiosum. Urease genes are phylogenetically conserved inP. insidiosumand related oomycetes, while the presence of urease accessory protein-encoding genes is markedly diverse in these organisms. In summary, we dissected biochemical characteristics and drew new insights into clinical identification and urease-related evolution ofP. insidiosum.

scholarly journals What’s all the phos about? Insights into the phosphorylation state of the RNA polymerase II C-terminal domain via mass spectrometry

2021 ◽  
Author(s):  
Blase Matthew LeBlanc ◽  
Rosamaria Yvette Moreno ◽  
Edwin Escobar ◽  
Mukesh Kumar Venkat Ramani ◽  
Jennifer S Brodbelt ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Phosphorylation State ◽  
Terminal Domain ◽  
Carboxy Terminal Domain ◽  
Protein Encoding ◽  
Small Nuclear Rnas ◽  
Rnap Ii ◽  
Carboxy Terminal ◽  
Encoding Genes

RNA polymerase II (RNAP II) is one of the primary enzymes responsible for expressing protein-encoding genes and some small nuclear RNAs. The enigmatic carboxy-terminal domain (CTD) of RNAP II and...

scholarly journals Autotransporter Protein-Encoding Genes of Diarrheagenic Escherichia coli Are Found in both Typical and Atypical Enteropathogenic E. coli Strains

2012 ◽  
Vol 79 (1) ◽  
pp. 411-414 ◽  
Author(s):  
Afonso G. Abreu ◽  
Vanessa Bueris ◽  
Tatiane M. Porangaba ◽  
Marcelo P. Sircili ◽  
Fernando Navarro-Garcia ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Content Type ◽  
E Coli ◽  
Diarrheagenic Escherichia Coli ◽  
Virulence Markers ◽  
Protein Encoding ◽  
Encoding Genes ◽  
Specific Virulence

ABSTRACTAutotransporter (AT) protein-encoding genes of diarrheagenicEscherichia coli(DEC) pathotypes (cah,eatA,ehaABCDJ,espC,espI,espP,pet,pic,sat, andtibA) were detected in typical and atypical enteropathogenicE. coli(EPEC) in frequencies between 0.8% and 39.3%. Although these ATs have been described in particular DEC pathotypes, their presence in EPEC indicates that they should not be considered specific virulence markers.

scholarly journals Draft Genome Sequence of the Axenic Strain Phormidesmispriestleyi ULC007, a Cyanobacterium Isolated from Lake Bruehwiler (Larsemann Hills, Antarctica)

2017 ◽  
Vol 5 (7) ◽  
Author(s):  
Yannick Lara ◽  
Benoit Durieu ◽  
Luc Cornet ◽  
Olivier Verlaine ◽  
Rosmarie Rippka ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Axenic Strain ◽  
Larsemann Hills ◽  
Freshwater Cyanobacterium ◽  
Protein Encoding ◽  
Encoding Genes

ABSTRACT Phormidesmis priestleyi ULC007 is an Antarctic freshwater cyanobacterium. Its draft genome is 5,684,389 bp long. It contains a total of 5,604 protein-encoding genes, of which 22.2% have no clear homologues in known genomes. To date, this draft genome is the first one ever determined for an axenic cyanobacterium from Antarctica.

Prion Protein-Encoding Genes

Prion Biology ◽  
2013 ◽  
Author(s):  
Sead Chadi ◽  
Rachel Young ◽  
Sandrine Guillou ◽  
Gaelle Tilly ◽  
Frédérique Bitton ◽  
...  
Keyword(s):  
Prion Protein ◽  
Protein Encoding ◽  
Encoding Genes

scholarly journals The microRNA, miR-133b, functions to slow Duchenne muscular dystrophy pathogenesis

2020 ◽  
Author(s):  
Thomas Taetzsch ◽  
Dillon Shapiro ◽  
Randa Eldosougi ◽  
Tracey Myers ◽  
Robert Settlage ◽  
...  
Keyword(s):  
Duchenne Muscular Dystrophy ◽  
Muscular Dystrophy ◽  
Skeletal Muscles ◽  
Tibialis Anterior Muscle ◽  
Muscle Fibers ◽  
Progressive Degeneration ◽  
Protein Encoding ◽  
Small Muscle ◽  
Encoding Genes

AbstractDuchenne muscular dystrophy (DMD) is characterized by progressive degeneration of skeletal muscles. To date, there are no treatments available to slow or prevent the disease. Hence, it remains essential to identify molecular factors that promote muscle biogenesis since they could serve as therapeutic targets for treating DMD. While the muscle enriched microRNA, miR-133b, has been implicated in the biogenesis of muscle fibers, its role in DMD remains unknown. To assess the role of miR-133b in DMD-affected skeletal muscles, we genetically ablated miR-133b in the mdx mouse model of DMD. In the absence of miR-133b, the tibialis anterior muscle of juvenile and adult mdx mice is populated by small muscle fibers with centralized nuclei, exhibits increased fibrosis, and thickened interstitial space. Additional analysis revealed that loss of miR-133b exacerbates DMD-pathogenesis partly by altering the number of satellite cells and levels of protein-encoding genes, including previously identified miR-133b targets as well as genes involved in cell proliferation and fibrosis. Altogether, our data demonstrate that skeletal muscles utilize miR-133b to mitigate the deleterious effects of DMD.

scholarly journals Transcriptome Analysis Unveils the Effects of Proline on Gene Expression in the Yeast Komagataella phaffii

2021 ◽  
Vol 10 (1) ◽  
pp. 67
Author(s):  
Andrey Rumyantsev ◽  
Anton Sidorin ◽  
Artemii Volkov ◽  
Ousama Al Shanaa ◽  
Elena Sambuk ◽  
...  
Keyword(s):  
Gene Expression ◽  
Recombinant Proteins ◽  
Gene Promoter ◽  
Energy Sources ◽  
Experimental Conditions ◽  
Komagataella Phaffii ◽  
Protein Encoding ◽  
Modern Biotechnology ◽  
Encoding Genes ◽  
Transcriptome Level

Komagataella phaffii yeast is one of the most important biocompounds producing microorganisms in modern biotechnology. Optimization of media recipes and cultivation strategies is key to successful synthesis of recombinant proteins. The complex effects of proline on gene expression in the yeast K. phaffii was analyzed on the transcriptome level in this work. Our analysis revealed drastic changes in gene expression when K. phaffii was grown in proline-containing media in comparison to ammonium sulphate-containing media. Around 18.9% of all protein-encoding genes were differentially expressed in the experimental conditions. Proline is catabolized by K. phaffii even in the presence of other nitrogen, carbon and energy sources. This results in the repression of genes involved in the utilization of other element sources, namely methanol. We also found that the repression of AOX1 gene promoter with proline can be partially reversed by the deletion of the KpPUT4.2 gene.

scholarly journals Complete Genome Sequence of Klebsiella pneumoniae Phage Sweeny

2019 ◽  
Vol 8 (39) ◽  
Author(s):  
Nicholas Martinez ◽  
Eric Williams ◽  
Heather Newkirk ◽  
Mei Liu ◽  
Jason J. Gill ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Complete Genome Sequence ◽  
Protein Level ◽  
Multidrug Resistant ◽  
Content Type ◽  
Hospital Acquired Infections ◽  
Multidrug Resistant Bacterium ◽  
Protein Encoding ◽  
Hospital Acquired ◽  
Encoding Genes

Klebsiella pneumoniae is a multidrug-resistant bacterium causing many severe hospital-acquired infections. Here, we describe siphophage Sweeny that infects K. pneumoniae. Of its 78 predicted protein-encoding genes, a functional assignment was given to 36 of them. Sweeny is most closely related to T1-like phages at the protein level.

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