Multidrug-Resistant Transport Proteins in Yeast: Complete Inventory and Phylogenetic Characterization of Yeast Open Reading Frames within the Major Facilitator Superfamily

Enterobacter cloacae is an opportunistic pathogen that causes hospital-acquired infections in immunocompromised patients. Here, we describe vB_EclM_CIP9, a novel Enterobacter phage that infects a multidrug-resistant isolate of E. cloacae. Phage vB_EclM_CIP9 is a myovirus that has a 174,924-bp genome, with 296 predicted open reading frames.

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Characterization of a Novel Phage ΦAb1656-2 and Its Endolysin with Higher Antimicrobial Activity against Multidrug-Resistant Acinetobacter baumannii

Viruses ◽

10.3390/v13091848 ◽

2021 ◽

Vol 13 (9) ◽

pp. 1848

Author(s):

Kyeongmin Kim ◽

Md Maidul Islam ◽

Dooyoung Kim ◽

Sung Ho Yun ◽

Jungmin Kim ◽

...

Keyword(s):

Acinetobacter Baumannii ◽

Therapeutic Agent ◽

Catalytic Domain ◽

Hydrolytic Enzymes ◽

Multidrug Resistant ◽

Open Reading Frames ◽

Nosocomial Pathogen ◽

Prophage Induction ◽

Reading Frames

Acinetobacter baumannii is a nosocomial pathogen, which is a problem worldwide due to the emergence of a difficult-to-treat multidrug-resistant A. baumannii (MDRAB). Endolysins are hydrolytic enzymes produced by a bacteriophage that can be used as a potential therapeutic agent for multidrug-resistant bacterial infection in replacing antibiotics. Here, we isolated a novel bacteriophage through prophage induction using mitomycin C from clinical A. baumannii 1656-2. Morphologically, ΦAb1656-2 was identified as a Siphoviridae family bacteriophage, which can infect MDRAB. The whole genome of ΦAb1656-2 was sequenced, and it showed that it is 50.9 kb with a G + C content of 38.6% and 68 putative open reading frames (ORFs). A novel endolysin named AbEndolysin with an N-acetylmuramidase-containing catalytic domain was identified, expressed, and purified from ΦAb1656-2. Recombinant AbEndolysin showed significant antibacterial activity against MDRAB clinical strains without any outer membrane permeabilizer. These results suggest that AbEndolysin could represent a potential antimicrobial agent for treating MDRAB clinical isolates.

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Isolation and Characterization of a Novel Haloacid Permease from Burkholderia cepacia MBA4

Applied and Environmental Microbiology ◽

10.1128/aem.00576-07 ◽

2007 ◽

Vol 73 (15) ◽

pp. 4874-4880 ◽

Cited By ~ 16

Author(s):

Manda Yu ◽

Yun-Wing Faan ◽

Wilson Y. K. Chung ◽

Jimmy S. H. Tsang

Keyword(s):

Burkholderia Cepacia ◽

Sugar Transport ◽

Transport Proteins ◽

Major Facilitator Superfamily ◽

Integral Membrane Proteins ◽

Reading Frame ◽

Isolation And Characterization ◽

Major Facilitator ◽

Dehalogenase Gene

ABSTRACT Burkholderia cepacia MBA4 is a bacterium that can utilize 2-haloacids as carbon and energy sources for growth. It has been proposed that dehalogenase-associated permease mediates the uptake of haloacid. In this paper, we report the first cloning and characterization of such a haloacid permease. The structural gene, designated deh4p, was found 353 bases downstream of the dehalogenase gene deh4a. Quantitative analysis of the expression of deh4p showed that it was induced by monochloroacetate (MCA), to a level similar to the MCA-induced level of deh4a. The nucleotide sequence of deh4p was determined, and an open reading frame of 1,656 bp encoding a putative peptide of 552 amino acids was identified. Deh4p has a putative molecular weight of 59,414 and an isoelectric point of 9.88. Deh4p has the signatures of sugar transport proteins and integral membrane proteins of the major facilitator superfamily. Uptake of [14C]MCA into the cell was Deh4p dependent. Deh4p has apparent Km s of 5.5 and 8.9 μM and V maxs of 9.1 and 23.1 nmol mg−1 min−1 for acetate and MCA, respectively. A mutant with a transposon-inactivated haloacid operon failed to grow on MCA even when deh4a was provided in trans.

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Characterization of Marek's disease virus insertion and deletion mutants that lack US1 (ICP22 homolog), US10, and/or US2 and neighboring short-component open reading frames.

Journal of Virology ◽

10.1128/jvi.68.12.8239-8253.1994 ◽

1994 ◽

Vol 68 (12) ◽

pp. 8239-8253 ◽

Cited By ~ 37

Author(s):

M S Parcells ◽

A S Anderson ◽

J L Cantello ◽

R W Morgan

Keyword(s):

Disease Virus ◽

Marek's Disease Virus ◽

Open Reading Frames ◽

Marek's Disease ◽

Deletion Mutants ◽

Marek’S Disease Virus ◽

Insertion And Deletion ◽

Short Component ◽

Reading Frames

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Isolation and Characterization of Salmonella Jumbo-Phage pSal-SNUABM-04

Viruses ◽

10.3390/v13010027 ◽

2020 ◽

Vol 13 (1) ◽

pp. 27

Author(s):

Jun Kwon ◽

Sang Guen Kim ◽

Hyoun Joong Kim ◽

Sib Sankar Giri ◽

Sang Wha Kim ◽

...

Keyword(s):

Morphological Traits ◽

Open Reading Frames ◽

Genome Comparison ◽

The Novel ◽

Promising Alternative ◽

Isolation And Characterization ◽

Global Issue ◽

Reading Frames ◽

Predicted Function

The increasing emergence of antimicrobial resistance has become a global issue. Therefore, many researchers have attempted to develop alternative antibiotics. One promising alternative is bacteriophage. In this study, we focused on a jumbo-phage infecting Salmonella isolated from exotic pet markets. Using a Salmonella strain isolated from reptiles as a host, we isolated and characterized the novel jumbo-bacteriophage pSal-SNUABM-04. This phage was investigated in terms of its morphology, host infectivity, growth and lysis kinetics, and genome. The phage was classified as Myoviridae based on its morphological traits and showed a comparatively wide host range. The lysis efficacy test showed that the phage can inhibit bacterial growth in the planktonic state. Genetic analysis revealed that the phage possesses a 239,626-base pair genome with 280 putative open reading frames, 76 of which have a predicted function and 195 of which have none. By genome comparison with other jumbo phages, the phage was designated as a novel member of Machinavirus composed of Erwnina phages.

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Pan-cancer analysis of transcripts encoding novel open-reading frames (nORFs) and their potential biological functions

npj Genomic Medicine ◽

10.1038/s41525-020-00167-4 ◽

2021 ◽

Vol 6 (1) ◽

Cited By ~ 2

Author(s):

Chaitanya Erady ◽

Adam Boxall ◽

Shraddha Puntambekar ◽

N. Suhas Jagannathan ◽

Ruchi Chauhan ◽

...

Keyword(s):

Transcript Level ◽

Open Reading Frames ◽

The Cancer Genome Atlas ◽

Small Subset ◽

Cancer Tissue ◽

Post Translational Modifications ◽

Cancer Genome Atlas ◽

Systematic Identification ◽

Reading Frames

AbstractUncharacterized and unannotated open-reading frames, which we refer to as novel open reading frames (nORFs), may sometimes encode peptides that remain unexplored for novel therapeutic opportunities. To our knowledge, no systematic identification and characterization of transcripts encoding nORFs or their translation products in cancer, or in any other physiological process has been performed. We use our curated nORFs database (nORFs.org), together with RNA-Seq data from The Cancer Genome Atlas (TCGA) and Genotype-Expression (GTEx) consortiums, to identify transcripts containing nORFs that are expressed frequently in cancer or matched normal tissue across 22 cancer types. We show nORFs are subject to extensive dysregulation at the transcript level in cancer tissue and that a small subset of nORFs are associated with overall patient survival, suggesting that nORFs may have prognostic value. We also show that nORF products can form protein-like structures with post-translational modifications. Finally, we perform in silico screening for inhibitors against nORF-encoded proteins that are disrupted in stomach and esophageal cancer, showing that they can potentially be targeted by inhibitors. We hope this work will guide and motivate future studies that perform in-depth characterization of nORF functions in cancer and other diseases.

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Characterization of Chlamydia trachomatis Plasmid-Encoded Open Reading Frames

Journal of Bacteriology ◽

10.1128/jb.00511-13 ◽

2013 ◽

Vol 195 (17) ◽

pp. 3819-3826 ◽

Cited By ~ 58

Author(s):

S. Gong ◽

Z. Yang ◽

L. Lei ◽

L. Shen ◽

G. Zhong

Keyword(s):

Chlamydia Trachomatis ◽

Open Reading Frames ◽

Reading Frames

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Molecular characterization of a novel mycovirus isolated from Rhizoctonia solani AG-1 IA 9-11

10.21203/rs.3.rs-520549/v1 ◽

2021 ◽

Author(s):

Yang Sun ◽

Yan qiong Li ◽

Wen han Dong ◽

Ai li Sun ◽

Ning wei Chen ◽

...

Keyword(s):

Rhizoctonia Solani ◽

Rna Virus ◽

Dsrna Virus ◽

Open Reading Frames ◽

The Family ◽

Significant Amino Acid Sequence ◽

Overlapping Open Reading Frames ◽

Significant Amino Acid ◽

Reading Frames

Abstract The complete genome of the dsRNA virus isolated from Rhizoctonia solani AG-1 IA 9–11 (designated as Rhizoctonia solani dsRNA virus 11, RsRV11 ) were determined. The RsRV11 genome was 9,555 bp in length, contained three conserved domains, SMC, PRK and RT-like super family, and encoded two non-overlapping open reading frames (ORFs). ORF1 potentially coded for a 204.12 kDa predicted protein, which shared low but significant amino acid sequence identities with the putative protein encoded by Rhizoctonia solani RNA virus HN008 (RsRV-HN008) ORF1. ORF2 potentially coded for a 132.41 kDa protein which contained the conserved motifs of the RNA-dependent RNA polymerase (RdRp). Phylogenetic analysis indicated that RsRV11 was clustered with RsRV-HN008 in a separate clade independent of other virus families. It implies that RsRV11, along with RsRV-HN008 possibly a new fungal virus taxa closed to the family Megabirnaviridae, and RsRV11 is a new member of mycoviruses.

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Characterization of Two Virulent Phages of Lactobacillus plantarum

Applied and Environmental Microbiology ◽

10.1128/aem.02565-12 ◽

2012 ◽

Vol 78 (24) ◽

pp. 8719-8734 ◽

Cited By ~ 27

Author(s):

Mariángeles Briggiler Marcó ◽

Josiane E. Garneau ◽

Denise Tremblay ◽

Andrea Quiberoni ◽

Sylvain Moineau

Keyword(s):

Lactobacillus Plantarum ◽

Corn Silage ◽

Open Reading Frames ◽

High Identity ◽

Content Type ◽

Defense Systems ◽

Double Stranded Dna ◽

Type Phage ◽

Reading Frames

ABSTRACTWe characterized twoLactobacillus plantarumvirulent siphophages, ATCC 8014-B1 (B1) and ATCC 8014-B2 (B2), previously isolated from corn silage and anaerobic sewage sludge, respectively. Phage B2 infected two of the eightL. plantarumstrains tested, while phage B1 infected three. Phage adsorption was highly variable depending on the strain used. Phage defense systems were found in at least twoL. plantarumstrains, LMG9211 and WCSF1. The linear double-stranded DNA genome of thepac-type phage B1 had 38,002 bp, a G+C content of 47.6%, and 60 open reading frames (ORFs). Surprisingly, the phage B1 genome has 97% identity with that ofPediococcus damnosusphage clP1 and 77% identity with that ofL. plantarumphage JL-1; these phages were isolated from sewage and cucumber fermentation, respectively. The double-stranded DNA (dsDNA) genome of thecos-type phage B2 had 80,618 bp, a G+C content of 36.9%, and 127 ORFs with similarities to those ofBacillusandLactobacillusstrains as well as phages. Some phage B2 genes were similar to ORFs fromL. plantarumphage LP65 of theMyoviridaefamily. Additionally, 6 tRNAs were found in the phage B2 genome. Protein analysis revealed 13 (phage B1) and 9 (phage B2) structural proteins. To our knowledge, this is the first report describing such high identity between phage genomes infecting different genera of lactic acid bacteria.

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