scholarly journals The Mycobacterium avium Complex gtfTB Gene Encodes a Glucosyltransferase Required for the Biosynthesis of Serovar 8-Specific Glycopeptidolipid

2008 ◽  
Vol 190 (24) ◽  
pp. 7918-7924 ◽  
Author(s):  
Yuji Miyamoto ◽  
Tetsu Mukai ◽  
Yumi Maeda ◽  
Masanori Kai ◽  
Takashi Naka ◽  
...  
Keyword(s):  
Mycobacterium Avium ◽  
Mycobacterium Smegmatis ◽  
Cell Envelope ◽  
Gene Clusters ◽  
Genomic Region ◽  
Open Reading Frames ◽  
Opportunistic Pathogens ◽  
Glucose Residue ◽  
Functional Analyses ◽  
Reading Frames

ABSTRACT Mycobacterium avium complex (MAC) is one of the most common opportunistic pathogens widely distributed in the natural environment. The 28 serovars of MAC are defined by variable oligosaccharide portions of glycopeptidolipids (GPLs) that are abundant on the surface of the cell envelope. These GPLs are also known to contribute to the virulence of MAC. Serovar 8 is one of the dominant serovars isolated from AIDS patients, but the biosynthesis of serovar 8-specific GPL remains unknown. To clarify this, we compared gene clusters involved in the biosynthesis of several serovar-specific GPLs and identified the genomic region predicted to be responsible for GPL biosynthesis in a serovar 8 strain. Sequencing of this region revealed the presence of four open reading frames, three unnamed genes and gtfTB, the function of which has not been elucidated. The simultaneous expression of gtfTB and two downstream genes in a recombinant Mycobacterium smegmatis strain genetically modified to produce serovar 1-specific GPL resulted in the appearance of 4,6-O-(1-carboxyethylidene)-3-O-methyl-glucose, which is unique to serovar 8-specific GPL, suggesting that these three genes participate in its biosynthesis. Furthermore, functional analyses of gtfTB indicated that it encodes a glucosyltransferase that transfers a glucose residue via 1→3 linkage to a rhamnose residue of serovar 1-specific GPL, which is critical to the formation of the oligosaccharide portion of serovar 8-specific GPL. Our findings might provide a clue to understanding the biosynthetic regulation that modulates the biological functions of GPLs in MAC.

scholarly journals Genome Sequence of Cluster W Mycobacteriophage Taptic

2017 ◽  
Vol 5 (11) ◽  
Author(s):  
Catherine M. Mageeney ◽  
Emily R. Seier ◽  
Elise C. Esposito ◽  
Lee H. Graham ◽  
Emily L. Heckman ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Mycobacterium Smegmatis ◽  
Open Reading Frames ◽  
Content Type ◽  
Reading Frames

ABSTRACT The Taptic genome is the first to be annotated from the W cluster of mycobacteriophages infecting Mycobacterium smegmatis mc2155. All 92 predicted open reading frames (ORFs) and a single tRNA specifying glycine (tRNA-gly) are transcribed rightward. Many functionally uncharacterized ORFs appear to be W cluster specific, as nucleotide similarity is shared only with other W cluster genomes.

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

2001 ◽  
Vol 183 (12) ◽  
pp. 3663-3679 ◽  
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.

scholarly journals Lactococcal 949 Group Phages Recognize a Carbohydrate Receptor on the Host Cell Surface

2015 ◽  
Vol 81 (10) ◽  
pp. 3299-3305 ◽  
Author(s):  
Jennifer Mahony ◽  
Walter Randazzo ◽  
Horst Neve ◽  
Luca Settanni ◽  
Douwe van Sinderen
Keyword(s):  
Cheese Whey ◽  
Phage Genome ◽  
Bioinformatic Analysis ◽  
Genomic Region ◽  
Open Reading Frames ◽  
Host Recognition ◽  
Phage Group ◽  
Host Cell Surface ◽  
Reading Frames ◽  
Dairy Fermentation

ABSTRACTLactococcal bacteriophages represent one of the leading causes of dairy fermentation failure and product inconsistencies. A new member of the lactococcal 949 phage group, named WRP3, was isolated from cheese whey from a Sicilian factory in 2011. The genome sequence of this phage was determined, and it constitutes the largest lactococcal phage genome currently known, at 130,008 bp. Detailed bioinformatic analysis of the genomic region encoding the presumed initiator complex and baseplate of WRP3 has aided in the functional assignment of several open reading frames (ORFs), particularly that for the receptor binding protein required for host recognition. Furthermore, we demonstrate that the 949 phages target cell wall phospho-polysaccharides as their receptors, accounting for the specificity of the interactions of these phages with their lactococcal hosts. Such information may ultimately aid in the identification of strains/strain blends that do not present the necessary saccharidic target for infection by these problematic phages.

scholarly journals Synthesis of a Klebsiella pneumoniae O-Antigen Heteropolysaccharide (O12) Requires an ABC 2 Transporter

2003 ◽  
Vol 185 (5) ◽  
pp. 1634-1641 ◽  
Author(s):  
Luis Izquierdo ◽  
Susana Merino ◽  
Miguel Regué ◽  
Florencia Rodriguez ◽  
Juan M. Tomás
Keyword(s):  
Klebsiella Pneumoniae ◽  
Genomic Library ◽  
Gene Clusters ◽  
Open Reading Frames ◽  
Complete Analysis ◽  
E Coli ◽  
O Antigen ◽  
High Level ◽  
K 12 ◽  
Reading Frames

ABSTRACT A recombinant clone encoding enzymes for Klebsiella pneumoniae O12-antigen lipopolysaccharide (LPS) was found when we screened for serum resistance of a cosmid-based genomic library of K. pneumoniae KT776 (O12:K80) introduced into Escherichia coli DH5α. A total of eight open reading frames (ORFs) (wb O12 gene cluster) were necessary to produce K. pneumoniae O12-antigen LPS in E. coli K-12. A complete analysis of the K. pneumoniae wb O12 cluster revealed an interesting coincidence with the wb O4 cluster of Serratia marcescens from ORF5 to ORF8 (or WbbL to WbbA). This prompted us to generate mutants of K. pneumoniae strain KT776 (O12) and to study complementation between the two enterobacterial wb clusters using mutants of S. marcescens N28b (O4) obtained previously. Both wb gene clusters are examples of ABC 2 transporter-dependent pathways for O-antigen heteropolysaccharides. The wzm-wzt genes and the wbbA or wbbB genes were not interchangeable between the two gene clusters despite their high level of similarity. However, introduction of three cognate genes (wzm-wzt-wbbA or wzm-wzt-wbbB) into mutants unable to produce O antigen allowed production of the specific O antigen. The K. pneumoniae O12 WbbL protein performs the same function as WbbL from S. marcescens O4 in either the S. marcescens O4 or E. coli K-12 genetic background.

scholarly journals Genome Sequence of JangDynasty, a Newly Isolated Mycobacteriophage

2018 ◽  
Vol 6 (21) ◽  
Author(s):  
Casey Jang ◽  
Nancy Kalaj ◽  
Brian Hwang ◽  
Lorelei Hughes ◽  
Connie Yang ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Mycobacterium Smegmatis ◽  
Open Reading Frames ◽  
Genome Length ◽  
Content Type ◽  
A Genome ◽  
Reading Frames

ABSTRACT JangDynasty is a bacteriophage that infects Mycobacterium smegmatis mc2155. It has a genome length of 70,883 bp, with 124 predicted open reading frames (ORFs), 42 of which have known functions. JangDynasty belongs to cluster O, and like other cluster O phages, it is a siphovirus with a prolate capsid.

Phylogeny of Mycobacterium avium strains inferred from glycopeptidolipid biosynthesis pathway genes

Microbiology ◽  
2004 ◽  
Vol 150 (6) ◽  
pp. 1699-1706 ◽  
Author(s):  
Elzbieta Krzywinska ◽  
Jaroslaw Krzywinski ◽  
Jeffrey S. Schorey
Keyword(s):  
Mycobacterium Avium ◽  
Epidemiological Studies ◽  
Genomic Region ◽  
Opportunistic Pathogens ◽  
Apparent Lack ◽  
Alternative Placement ◽  
Multiple Origins ◽  
Serotype 1 ◽  
History Of ◽  
Genomic Regions

The Mycobacterium avium complex (MAC) encompasses two species, M. avium and Mycobacterium intracellulare, which are opportunistic pathogens of humans and animals. The standard method of MAC strain differentiation is serotyping based on a variation in the antigenic glycopeptidolipid (GPL) composition. To elucidate the relationships among M. avium serotypes a phylogenetic analysis of 13 reference and clinical M. avium strains from 8 serotypes was performed using as markers two genomic regions (890 bp of the gtfB gene and 2150 bp spanning the rtfA–mtfC genes) which are associated with the strains' serological properties. Strains belonging to three other known M. avium serotypes were not included in the phylogeny inference due to apparent lack of the marker sequences in their genomes, as revealed by PCR and Southern blot analysis. These studies suggest that serotypes prevalent in AIDS patients have multiple origins. In trees inferred from both markers, serotype 1 strains, known to have the simplest and shortest GPLs among all other serotypes, were polyphyletic. Likewise, comparisons of the inferred phylogenies with the molecular typing results imply that the existing tools used in epidemiological studies may be poor estimators of M. avium strain relatedness. Additionally, trees inferred from each marker had significantly incongruent topologies due to a well supported alternative placement of strain 2151, suggesting a complex evolutionary history of this genomic region.

scholarly journals Acid-Adaptive Genes of Helicobacter pylori

2003 ◽  
Vol 71 (10) ◽  
pp. 5921-5939 ◽  
Author(s):  
Yi Wen ◽  
Elizabeth A. Marcus ◽  
Uday Matrubutham ◽  
Martin A. Gleeson ◽  
David R. Scott ◽  
...  
Keyword(s):  
Gene Expression ◽  
Helicobacter Pylori ◽  
Cell Envelope ◽  
Open Reading Frames ◽  
Ph Optimum ◽  
Transcriptional Regulatory ◽  
Adaptive Mechanisms ◽  
H Pylori ◽  
Reading Frames ◽  
External Ph

ABSTRACT Helicobacter pylori is the only neutralophile that has been able to colonize the human stomach by using a variety of acid-adaptive mechanisms. One of the adaptive mechanisms is increased buffering due to expression of an acid-activated inner membrane urea channel, UreI, and a neutral pH-optimum intrabacterial urease. To delineate other possible adaptive mechanisms, changes in gene expression in response to acid exposure were examined using genomic microarrays of H. pylori exposed to different levels of external pH (7.4, 6.2, 5.5, and 4.5) for 30 min in the absence and presence of 5 mM urea. Gene expression was correlated with intrabacterial pH measured using 2′,7′-bis-(2-carboxyethyl)-5-carboxyfluorescein and compared to that observed with exposure to 42°C for 30 min. Microarrays containing the 1,534 open reading frames of H. pylori strain 26695 were hybridized with cDNAs from control (pH 7.4; labeled with Cy3) and acidic (labeled with Cy5) conditions. The intrabacterial pH was 8.1 at pH 7.4, fell to 5.3 at pH 4.5, and rose to 6.2 with urea. About 200 genes were up-regulated and ∼100 genes were down-regulated at pH 4.5 in the absence of urea, and about half that number changed in the presence of urea. These genes included pH-homeostatic, transcriptional regulatory, motility, cell envelope, and pathogenicity genes. The up-regulation of some pH-homeostatic genes was confirmed by real-time PCR. There was little overlap with the genes induced by temperature stress. These results suggest that H. pylori has evolved multifaceted acid-adaptive mechanisms enabling it to colonize the stomach that may be novel targets for eliminating infection.

scholarly journals Genome Sequence of Serratia marcescens subsp. sakuensis Strain K27, a Marine Bacterium Isolated from Sponge (Haliclona amboinensis)

2018 ◽  
Vol 6 (6) ◽  
pp. e00022-18 ◽  
Author(s):  
Tzi Him Cheng ◽  
Jasnizat Saidin ◽  
Muhd Danish-Daniel ◽  
Han Ming Gan ◽  
Mohd Noor Mat Isa ◽  
...  
Keyword(s):  
Serratia Marcescens ◽  
Genome Sequence ◽  
Marine Bacterium ◽  
Gene Clusters ◽  
Open Reading Frames ◽  
Nonribosomal Peptides ◽  
Reading Frames

ABSTRACTSerratia marcescens subsp. sakuensis strain K27 was isolated from sponge (Haliclona amboinensis). The genome of this strain consists of 5,325,727 bp, with 5,140 open reading frames (ORFs), 3 rRNAs, and 67 tRNAs. It contains genes for the production of amylases, lipases, and proteases. Gene clusters for the biosynthesis of nonribosomal peptides and thiopeptide were also identified.

scholarly journals Functional Genomic Analysis of Two Staphylococcus aureus Phages Isolated from the Dairy Environment

2009 ◽  
Vol 75 (24) ◽  
pp. 7663-7673 ◽  
Author(s):  
Pilar García ◽  
Beatriz Martínez ◽  
José María Obeso ◽  
Rob Lavigne ◽  
Rudi Lurz ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Dna Recombination ◽  
Point Mutations ◽  
Genomic Analysis ◽  
Open Reading Frames ◽  
Functional Genomic Analysis ◽  
Replication Point ◽  
Terminal Amino ◽  
Functional Analyses ◽  
Reading Frames

ABSTRACT The genomes of the two lytic mutant Staphylococcus aureus bacteriophages, vB_SauS-phiIPLA35 (phiIPLA35) and vB_SauS-phiIPLA88 (phiIPLA88), isolated from milk have been analyzed. Their genomes are 45,344 bp and 42,526 bp long, respectively, and contain 62 and 61 open reading frames (ORFS). Enzymatic analyses and sequencing revealed that the phiIPLA35 DNA molecule has 3′-protruding cohesive ends (cos) 10 bp long, whereas phiIPLA88 DNA is 4.5% terminally redundant and most likely is packaged by a headful mechanism. N-terminal amino acid sequencing, mass spectrometry, bioinformatic analyses, and functional analyses enabled the assignment of putative functions to 58 gene products, including DNA packaging proteins, morphogenetic proteins, lysis components, and proteins necessary for DNA recombination, modification, and replication. Point mutations in their lysogeny control-associated genes explain their strictly lytic behavior. Muralytic activity associated with other structural components has been detected in virions of both phages. Comparative analysis of phiIPLA35 and phiIPLA88 genome structures shows that they resemble those of φ12 and φ11, respectively, both representatives of large genomic groupings within the S. aureus-infecting phages.

scholarly journals Soluble Methane Monooxygenase Gene Clusters from Trichloroethylene-Degrading Methylomonas sp. Strains and Detection of Methanotrophs during In Situ Bioremediation

1999 ◽  
Vol 65 (12) ◽  
pp. 5198-5206 ◽  
Author(s):  
Toru Shigematsu ◽  
Satoshi Hanada ◽  
Masahiro Eguchi ◽  
Yoichi Kamagata ◽  
Takahiro Kanagawa ◽  
...  
Keyword(s):  
Sequence Data ◽  
Gene Clusters ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Soluble Methane Monooxygenase ◽  
Group I ◽  
Monooxygenase Gene ◽  
Group Ii ◽  
Reading Frames

ABSTRACT The soluble MMO (sMMO) gene clusters from group I methanotrophs were characterized. An 8.1-kb KpnI fragment fromMethylomonas sp. strain KSWIII and a 7.5-kbSalI fragment from Methylomonas sp. strain KSPIII which contained the sMMO gene clusters were cloned and sequenced. The sequences of these two fragments were almost identical. The sMMO gene clusters in the fragment consisted of six open reading frames which were 52 to 79% similar to the corresponding genes of previously described sMMO gene clusters of the group II and group X methanotrophs. The phylogenetic analysis of the predicted amino acid sequences of sMMO demonstrated that the sMMOs from these strains were closer to that from M. capsulatus Bath in the group X methanotrophs than to those from Methylosinus trichosporiumOB3b and Methylocystis sp. strain M in the group II methanotrophs. Based on the sequence data of sMMO genes of our strains and other methanotrophs, we designed a new PCR primer to amplify sMMO gene fragments of all the known methanotrophs harboring themmoX gene. The primer set was successfully used for detecting methanotrophs in the groundwater of trichloroethylene-contaminated sites during in situ-biostimulation treatments.

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