Molecular and Genomic Analysis of Genes Encoding Surface-Anchored Proteins from Clostridium difficile

ABSTRACT The gene slpA, encoding the S-layer precursor protein in the virulent Clostridium difficile strains C253 and 79–685, was identified. The precursor protein carries a C-terminal highly conserved anchoring domain, similar to the one found in the Cwp66 adhesin (previously characterized in strain 79–685), an SLH domain, and a variable N-terminal domain mediating cell adherence. The genes encoding the S-layer precursor proteins and the Cwp66 adhesin are present in a genetic locus carrying 17 open reading frames, 11 of which encode a similar two-domain architecture, likely to include surface-anchored proteins.

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Characterization and Genome Analysis of Staphylococcus aureus Podovirus CSA13 and Its Anti-Biofilm Capacity

Viruses ◽

10.3390/v11010054 ◽

2019 ◽

Vol 11 (1) ◽

pp. 54 ◽

Cited By ~ 9

Author(s):

Yoyeon Cha ◽

Jihwan Chun ◽

Bokyung Son ◽

Sangryeol Ryu

Keyword(s):

Staphylococcus Aureus ◽

Biocontrol Agent ◽

Genomic Analysis ◽

Open Reading Frames ◽

Experimental Setting ◽

Human Pathogens ◽

Bacteriophage Therapy ◽

Chromosomal Structure ◽

Inhibition Effect ◽

Reading Frames

Staphylococcus aureus is one of the notable human pathogens that can be easily encountered in both dietary and clinical surroundings. Among various countermeasures, bacteriophage therapy is recognized as an alternative method for resolving the issue of antibiotic resistance. In the current study, bacteriophage CSA13 was isolated from a chicken, and subsequently, its morphology, physiology, and genomics were characterized. This Podoviridae phage displayed an extended host inhibition effect of up to 23 hours of persistence. Its broad host spectrum included methicillin susceptible S. aureus (MSSA), methicillin resistant S. aureus (MRSA), local S. aureus isolates, as well as non-aureus staphylococci strains. Moreover, phage CSA13 could successfully remove over 78% and 93% of MSSA and MRSA biofilms in an experimental setting, respectively. Genomic analysis revealed a 17,034 bp chromosome containing 18 predicted open reading frames (ORFs) without tRNAs, representing a typical chromosomal structure of the staphylococcal Podoviridae family. The results presented here suggest that phage CSA13 can be applicable as an effective biocontrol agent against S. aureus.

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Genetic Investigation of the Catabolic Pathway for Degradation of Abietane Diterpenoids by Pseudomonas abietaniphilaBKME-9

Journal of Bacteriology ◽

10.1128/jb.182.13.3784-3793.2000 ◽

2000 ◽

Vol 182 (13) ◽

pp. 3784-3793 ◽

Cited By ~ 39

Author(s):

Vincent J. J. Martin ◽

William W. Mohn

Keyword(s):

Gene Cluster ◽

Sequence Similarity ◽

Open Reading Frames ◽

Ring Cleavage ◽

Catabolic Pathway ◽

Transcriptional Fusion ◽

Abietane Diterpenoids ◽

Genes Encoding ◽

Dna Fragment ◽

Reading Frames

ABSTRACT We have cloned and sequenced the dit gene cluster encoding enzymes of the catabolic pathway for abietane diterpenoid degradation by Pseudomonas abietaniphila BKME-9. Thedit gene cluster is located on a 16.7-kb DNA fragment containing 13 complete open reading frames (ORFs) and 1 partial ORF. The genes ditA1A2A3 encode the α and β subunits and the ferredoxin of the dioxygenase which hydroxylates 7-oxodehydroabietic acid to 7-oxo-11,12-dihydroxy-8,13-abietadien acid. The dioxygenase mutant strain BKME-941 (ditA1::Tn5) did not grow on nonaromatic abietanes, and transformed palustric and abietic acids to 7-oxodehydroabietic acid in cell suspension assays. Thus, nonaromatic abietanes are aromatized prior to further degradation. Catechol 2,3-dioxygenase activity of xylEtranscriptional fusion strains showed induction of ditA1and ditA3 by abietic, dehydroabietic, and 7-oxodehydroabietic acids, which support the growth of strain BKME-9, as well as by isopimaric and 12,14-dichlorodehydroabietic acids, which are diterpenoids that do not support the growth of strain BKME-9. In addition to the aromatic-ring-hydroxylating dioxygenase genes, thedit cluster includes ditC, encoding an extradiol ring cleavage dioxygenase, and ditR, encoding an IclR-type transcriptional regulator. Although ditR is not strictly required for the growth of strain BKME-9 on abietanes, aditR::Kmr mutation in aditA3::xylE reporter strain demonstrated that it encodes an inducer-dependent transcriptional activator of ditA3. An ORF with sequence similarity to genes encoding permeases (ditE) is linked with genes involved in abietane degradation.

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Ferrous Iron- and Sulfur-Induced Genes in Sulfolobus metallicus

Applied and Environmental Microbiology ◽

10.1128/aem.02589-06 ◽

2007 ◽

Vol 73 (8) ◽

pp. 2491-2497 ◽

Cited By ~ 63

Author(s):

Stephan Bathe ◽

Paul R. Norris

Keyword(s):

Reverse Transcription ◽

Ferrous Iron ◽

Subtractive Hybridization ◽

Open Reading Frames ◽

Gene Encoding ◽

Reverse Transcription Pcr ◽

Genes Encoding ◽

Induced Genes ◽

Reading Frames ◽

Sulfur Oxygenase Reductase

ABSTRACT Genes of Sulfolobus metallicus that appeared to be upregulated in relation to growth on either ferrous iron or sulfur were identified using subtractive hybridization of cDNAs. The genes upregulated during growth on ferrous iron were found in a cluster, and most were predicted to encode membrane proteins. Quantitative reverse transcription-PCR of cDNA showed upregulation of most of these genes during growth on ferrous iron and pyrite compared to results during growth on sulfur. The highest expression levels observed included those for genes encoding proteins with similarities to cytochrome c oxidase subunits and a CbsA-like cytochrome. The genes identified here that may be involved in oxidation of ferrous iron by S. metallicus are termed fox genes. Of three available genomes of Sulfolobus species (S. tokodaii, S. acidocaldarius, and S. solfataricus), only that of S. tokodaii has a cluster of highly similar open reading frames, and only S. tokodaii of these three species was also able to oxidize ferrous iron. A gene encoding sulfur oxygenase-reductase was identified as the source of the dominant transcript in sulfur-grown cells of S. metallicus, with the predicted protein showing high identities to the previously described examples from S. tokodaii and species of Acidianus.

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Biochemical and Genetic Analysis of 4-Hydroxypyridine Catabolism in Arthrobacter sp. Strain IN13

Microorganisms ◽

10.3390/microorganisms8060888 ◽

2020 ◽

Vol 8 (6) ◽

pp. 888

Author(s):

Justas Vaitekūnas ◽

Renata Gasparavičiūtė ◽

Jonita Stankevičiūtė ◽

Gintaras Urbelis ◽

Rolandas Meškys

Keyword(s):

Recombinant Expression ◽

Expression Profiles ◽

Peptide Mass Fingerprinting ◽

Sole Source ◽

Open Reading Frames ◽

Expression Of Genes ◽

Peptide Mass ◽

Genes Encoding ◽

Protein Expression Profiles ◽

Reading Frames

N-Heterocyclic compounds are widely spread in the biosphere, being constituents of alkaloids, cofactors, allelochemicals, and artificial substances. However, the fate of such compounds including a catabolism of hydroxylated pyridines is not yet fully understood. Arthrobacter sp. IN13 is capable of using 4-hydroxypyridine as a sole source of carbon and energy. Three substrate-inducible proteins were detected by comparing protein expression profiles, and peptide mass fingerprinting was performed using MS/MS. After partial sequencing of the genome, we were able to locate genes encoding 4-hydroxypyridine-inducible proteins and identify the kpi gene cluster consisting of 16 open reading frames. The recombinant expression of genes from this locus in Escherichia coli and Rhodococcus erytropolis SQ1 allowed an elucidation of the biochemical functions of the proteins. We report that in Arthrobacter sp. IN13, the initial hydroxylation of 4-hydroxypyridine is catalyzed by a flavin-dependent monooxygenase (KpiA). A product of the monooxygenase reaction is identified as 3,4-dihydroxypyridine, and a subsequent oxidative opening of the ring is performed by a hypothetical amidohydrolase (KpiC). The 3-(N-formyl)-formiminopyruvate formed in this reaction is further converted by KpiB hydrolase to 3-formylpyruvate. Thus, the degradation of 4-hydroxypyridine in Arthrobacter sp. IN13 was analyzed at genetic and biochemical levels, elucidating this catabolic pathway.

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

Applied and Environmental Microbiology ◽

10.1128/aem.65.7.2871-2876.1999 ◽

1999 ◽

Vol 65 (7) ◽

pp. 2871-2876 ◽

Cited By ~ 26

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.

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Tn6350, a Novel Transposon Carrying Pyocin S8 Genes Encoding a Bacteriocin with Activity against Carbapenemase-Producing Pseudomonas aeruginosa

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00100-17 ◽

2017 ◽

Vol 61 (5) ◽

Cited By ~ 2

Author(s):

Helena Turano ◽

Fernando Gomes ◽

Gesiele A. Barros-Carvalho ◽

Ralf Lopes ◽

Louise Cerdeira ◽

...

Keyword(s):

Pseudomonas Aeruginosa ◽

Type A ◽

Sequence Type ◽

Open Reading Frames ◽

Hypothetical Proteins ◽

Immunity Protein ◽

Content Type ◽

Commensal Strain ◽

Genes Encoding ◽

Reading Frames

ABSTRACT A novel transposon belonging to the Tn3-like family was identified on the chromosome of a commensal strain of Pseudomonas aeruginosa sequence type 2343 (ET02). Tn6350 is 7,367 bp long and harbors eight open reading frames (ORFs), an ATPase (IS481 family), a transposase (DDE catalytic type), a Tn3 resolvase, three hypothetical proteins, and genes encoding the new pyocin S8 with its immunity protein. We show that pyocin S8 displays activity against carbapenemase-producing P. aeruginosa, including IMP-1, SPM-1, VIM-1, GES-5, and KPC-2 producers.

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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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Genetic Identification of the Bacteriocins Produced by Enterococcus faecium IT62 and Evidence that Bacteriocin 32 Is Identical to Enterocin IT

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00052-09 ◽

2009 ◽

Vol 53 (5) ◽

pp. 1907-1911 ◽

Cited By ~ 3

Author(s):

Esther Izquierdo ◽

Yimin Cai ◽

Eric Marchioni ◽

Saïd Ennahar

Keyword(s):

Amino Acids ◽

Genetic Analysis ◽

Structural Gene ◽

Enterococcus Faecium ◽

Open Reading Frames ◽

Genetic Identification ◽

Leader Peptide ◽

Sequencing Analysis ◽

The One ◽

Reading Frames

ABSTRACT Enterococcus faecium IT62, a strain isolated from ryegrass in Japan, produces three bacteriocins (enterocins L50A, L50B, and IT) that have been previously purified and the primary structures of which have been determined by amino acid sequencing (E. Izquierdo, A. Bednarczyk, C. Schaeffer, Y. Cai, E. Marchioni, A. Van Dorsselaer, and S. Ennahar, Antimicrob. Agents Chemother., 52:1917-1923, 2008). Genetic analysis showed that the bacteriocins of E. faecium IT62 are plasmid encoded, but with the structural genes specifying enterocin L50A and enterocin L50B being carried by a plasmid (pTAB1) that is separate from the one (pTIT1) carrying the structural gene of enterocin IT. Sequencing analysis of a 1,475-bp region from pTAB1 identified two consecutive open reading frames corresponding, with the exception of 2 bp, to the genes entL50A and entL50B, encoding EntL50A and EntL50B, respectively. Both bacteriocins are synthesized without N-terminal leader sequences. Genetic analysis of a sequenced 1,380-bp pTIT1 fragment showed that the genes entIT and entIM, encoding enterocin IT and its immunity protein, respectively, were both found in E. faecium VRE200 for bacteriocin 32. Enterocin IT, a 6,390-Da peptide made up of 54 amino acids, has been previously shown to be identical to the C-terminal part of bacteriocin 32, a 7,998-Da bacteriocin produced by E. faecium VRE200 whose structure was deduced from its structural gene (T. Inoue, H. Tomita, and Y. Ike, Antimicrob. Agents Chemother., 50:1202-1212, 2006). By combining the biochemical and genetic data on enterocin IT, it was concluded that bacteriocin 32 is in fact identical to enterocin IT, both being encoded by the same plasmid-borne gene, and that the N-terminal leader peptide for this bacteriocin is 35 amino acids long and not 19 amino acids long as previously reported.

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Characterization of the Genes for Two Protocatechuate 3,4-Dioxygenases from the 4-Sulfocatechol-Degrading Bacterium Agrobacterium radiobacter Strain S2

Journal of Bacteriology ◽

10.1128/jb.182.21.6123-6129.2000 ◽

2000 ◽

Vol 182 (21) ◽

pp. 6123-6129 ◽

Cited By ~ 21

Author(s):

Matthias Contzen ◽

Andreas Stolz

Keyword(s):

Amino Acid Sequences ◽

Open Reading Frames ◽

Agrobacterium Radiobacter ◽

Sequence Alignments ◽

Degrading Bacterium ◽

Regulator Protein ◽

Putative Operon ◽

Genes Encoding ◽

Reading Frames

ABSTRACT The genes for two different protocatechuate 3,4-dioxygenases (P34Os) were cloned from the 4-sulfocatechol-degrading bacteriumAgrobacterium radiobacter strain S2 (DSMZ 5681). ThepcaH1G1 genes encoded a P34O (P34O-I) which oxidized protocatechuate but not 4-sulfocatechol. These genes were part of a protocatechuate-degradative operon which strongly resembled the isofunctional operon from the protocatechuate-degrading strainAgrobacterium tumefaciens A348 described previously by D. Parke (FEMS Microbiol. Lett. 146:3–12, 1997). The second P34O (P34O-II), encoded by the pcaH2G2 genes, was functionally expressed and shown to convert protocatechuate and 4-sulfocatechol. A comparison of the deduced amino acid sequences of PcaH-I and PcaH-II, and of PcaG-I and PcaG-II, with each other and with the corresponding sequences from the P34Os, from other bacterial genera suggested that the genes for the P34O-II were obtained by strain S2 by lateral gene transfer. The genes encoding the P34O-II were found in a putative operon together with two genes which, according to sequence alignments, encoded transport proteins. Further downstream from this putative operon, two open reading frames which code for a putative regulator protein of the IclR family and a putative 3-carboxymuconate cycloisomerase were identified.

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