scholarly journals Patterns of Sequence Conservation in the S-Layer Proteins and Related Sequences in Clostridium difficile

2002 ◽  
Vol 184 (14) ◽  
pp. 3886-3897 ◽  
Author(s):  
Emanuela Calabi ◽  
Neil Fairweather
Keyword(s):  
Clostridium Difficile ◽  
Open Reading Frames ◽  
C Terminus ◽  
Antibiotic Associated Diarrhea ◽  
Processing Site ◽  
Different Strains ◽  
Related Proteins ◽  
High Degree ◽  
Insight Into ◽  
Reading Frames

ABSTRACT Clostridium difficile is the etiological agent of antibiotic-associated diarrhea. Among the factors that may play a role in infection are S-layer proteins (SLPs). Previous work has shown these to consist mainly of two components, resulting from the cleavage of a precursor encoded by the slpA gene. The high-molecular-weight (MW) subunit is related both to amidases from B. subtilis and to at least another 28 gene products in C. difficile strain 630. To gain insight into the functions of the SLPs and related proteins, we have further investigated the pattern of variability both at the slpA locus and at six nearby paralogs. Sequencing of the slpA gene from an S-layer group II strain and a variant S-layer group strain confirms a high degree of divergence in the low-MW SLP, which may result from diversifying selection. A highly conserved motif, however, is found at the C terminus in all low-MW subunits and may be essential for SlpA precursor cleavage. In strain 167, a variant cleavage product is present, suggesting a secondary processing site. Southern blotting analysis shows slpA-like open reading frames (ORFs) 2 to 7 to be conserved in all nine strains tested, with one exception: ORF2, which encodes a 66-kDa polypeptide coextracted at low pH with the main SLPs in strain 630, may be partially deleted in strain 167. Polymorphism within the slpA-ORF7 cluster may be more pronounced in the region proximal to the slpA gene. Unexpectedly, a high-MW subunit probe cross hybridizes to sequences outside the slpA locus, which appear to vary in number in different strains.

scholarly journals Genome Data of Four Pythium insidiosum Strains from the Phylogenetically-Distinct Clades I, II, and III

2021 ◽  
Author(s):  
Theerapong Krajaejun ◽  
Weerayuth Kittichotirat ◽  
Preecha Patumcharoenpol ◽  
Thidarat Rujirawat ◽  
Tassanee Lohnoo ◽  
...  
Keyword(s):  
The United States ◽  
Open Reading Frames ◽  
Genome Database ◽  
Pythium Insidiosum ◽  
Data Description ◽  
Genome Data ◽  
Serious Infection ◽  
Gdna Sample ◽  
Different Strains ◽  
Reading Frames

Abstract Objectives: We employed the Illumina NGS platform to sequence genomes of 4 different strains of Pythium insidiosum, an oomycete that causes a serious infection, called pythiosis, in humans and animals. These strains were isolated from humans in Thailand (n=3) and the United States (n=1), and phylogenetically classified into clade-I, -II, and -III. Our study augmented the completeness of the P. insidiosum genome database for exploration of the biology, evolution, and pathogenesis of the pathogen. Data description: Each gDNA sample from the P. insidiosum strains ATCC20026 (clade-I), Pi19 (clade-II), MCC18 (clade-II), and SIMI4763 (clade-III) was processed to prepare one paired-end library (180-bp insert) for whole-genome sequencing by Illumina HiSeq2000/HiSeq2500 NGS platform. A range of 28.4-59.4 million raw reads, accounted for 3.0-7.3 Gb, were obtained and assembled into the genome sizes of 47.1 Mb (15,153 contigs; 85% completeness; 19,329 open reading frames [ORFs]) for strain ATCC20026, 35.4 Mb (14,576 contigs; 83% completeness; 13,895 ORFs) for strain Pi19, 34.5 Mb (11,084 contigs; 84% completeness; 13,249 ORFs) for strain MCC18, and 47.1 Mb (15,162 contigs; 85% completeness; 19,340 ORFs) for strain SIMI4763. The genome data can be downloaded from the NCBI/DDBJ databases under the accessions BCFN00000000.1 (ATCC20026), BCFS00000000.1 (Pi19), BCFT00000000.1 (MCC18), and BCFU00000000.1 (SIMI4763).

scholarly journals Sequence of the Genome of the Temperate, Serotype-Converting,Pseudomonas aeruginosa Bacteriophage D3

2000 ◽  
Vol 182 (21) ◽  
pp. 6066-6074 ◽  
Author(s):  
Andrew M. Kropinski
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Sequence Similarity ◽  
Complete Sequence ◽  
Open Reading Frames ◽  
Gene Encoding ◽  
Virus Family ◽  
Double Stranded Dna ◽  
High Degree ◽  
Phage Proteins ◽  
Reading Frames

ABSTRACT Temperate bacteriophage D3, a member of the virus familySiphoviridae, is responsible for serotype conversion in its host, Pseudomonas aeruginosa. The complete sequence of the double-stranded DNA genome has been determined. The 56,426 bp contains 90 putative open reading frames (ORFs) and four genes specifying tRNAs. The latter are specific for methionine (AUG), glycine (GGA), asparagine (AAC), and threonine (ACA). The tRNAs may function in the translation of certain highly expressed proteins from this relatively AT-rich genome. D3 proteins which exhibited a high degree of sequence similarity to previously characterized phage proteins included the portal, major head, tail, and tail tape measure proteins, endolysin, integrase, helicase, and NinG. The layout of genes was reminiscent of lambdoid phages, with the exception of the placement of the endolysin gene, which parenthetically also lacked a cognate holin. The greatest sequence similarity was found in the morphogenesis genes to coliphages HK022 and HK97. Among the ORFs was discovered the gene encoding the fucosamine O-acetylase, which is in part responsible for the serotype conversion events.

scholarly journals Sequence and Organization of pXO1, the Large Bacillus anthracis Plasmid Harboring the Anthrax Toxin Genes

1999 ◽  
Vol 181 (20) ◽  
pp. 6509-6515 ◽  
Author(s):  
R. T. Okinaka ◽  
K. Cloud ◽  
O. Hampton ◽  
A. R. Hoffmaster ◽  
K. K. Hill ◽  
...  
Keyword(s):  
Bacillus Anthracis ◽  
Regulatory Elements ◽  
Open Reading Frames ◽  
Significant Similarity ◽  
Toxin Genes ◽  
Theta Replication ◽  
Large Plasmids ◽  
High Degree ◽  
Degree Of Similarity ◽  
Reading Frames

ABSTRACT The Bacillus anthracis Sterne plasmid pXO1 was sequenced by random, “shotgun” cloning. A circular sequence of 181,654 bp was generated. One hundred forty-three open reading frames (ORFs) were predicted using GeneMark and GeneMark.hmm, comprising only 61% (110,817 bp) of the pXO1 DNA sequence. The overall guanine-plus-cytosine content of the plasmid is 32.5%. The most recognizable feature of the plasmid is a “pathogenicity island,” defined by a 44.8-kb region that is bordered by inverted IS1627 elements at each end. This region contains the three toxin genes (cya, lef, and pagA), regulatory elements controlling the toxin genes, three germination response genes, and 19 additional ORFs. Nearly 70% of the ORFs on pXO1 do not have significant similarity to sequences available in open databases. Absent from the pXO1 sequence are homologs to genes that are typically required to drive theta replication and to maintain stability of large plasmids in Bacillus spp. Among the ORFs with a high degree of similarity to known sequences are a collection of putative transposases, resolvases, and integrases, suggesting an evolution involving lateral movement of DNA among species. Among the remaining ORFs, there are three sequences that may encode enzymes responsible for the synthesis of a polysaccharide capsule usually associated with serotype-specific virulent streptococci.

scholarly journals Microarray Identification of Clostridium difficile Core Components and Divergent Regions Associated with Host Origin

2009 ◽  
Vol 191 (12) ◽  
pp. 3881-3891 ◽  
Author(s):  
Tavan Janvilisri ◽  
Joy Scaria ◽  
Angela D. Thompson ◽  
Ainsley Nicholson ◽  
Brandi M. Limbago ◽  
...  
Keyword(s):  
Clostridium Difficile ◽  
Gene List ◽  
Core Gene ◽  
Comparative Genomic ◽  
Functional Categories ◽  
Genomic Changes ◽  
Core Components ◽  
Host Origin ◽  
High Degree ◽  
Insight Into

ABSTRACT Clostridium difficile is a gram-positive, spore-forming enteric anaerobe which can infect humans and a wide variety of animal species. Recently, the incidence and severity of human C. difficile infection has markedly increased. In this study, we evaluated the genomic content of 73 C. difficile strains isolated from humans, horses, cattle, and pigs by comparative genomic hybridization with microarrays containing coding sequences from C. difficile strains 630 and QCD-32g58. The sequenced genome of C. difficile strain 630 was used as a reference to define a candidate core genome of C. difficile and to explore correlations between host origins and genetic diversity. Approximately 16% of the genes in strain 630 were highly conserved among all strains, representing the core complement of functional genes defining C. difficile. Absent or divergent genes in the tested strains were distributed across the entire C. difficile 630 genome and across all the predicted functional categories. Interestingly, certain genes were conserved among strains from a specific host species, but divergent in isolates with other host origins. This information provides insight into the genomic changes which might contribute to host adaptation. Due to a high degree of divergence among C. difficile strains, a core gene list from this study offers the first step toward the construction of diagnostic arrays for C. difficile.

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

2001 ◽  
Vol 69 (5) ◽  
pp. 3442-3446 ◽  
Author(s):  
Tuomo Karjalainen ◽  
Anne-Judith Waligora-Dupriet ◽  
Marina Cerquetti ◽  
Patrizia Spigaglia ◽  
Andrea Maggioni ◽  
...  
Keyword(s):  
Clostridium Difficile ◽  
Genetic Locus ◽  
Domain Architecture ◽  
Genomic Analysis ◽  
Open Reading Frames ◽  
Precursor Protein ◽  
Precursor Proteins ◽  
Genes Encoding ◽  
The One ◽  
Reading Frames

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.

scholarly journals Distribution of cp32 Prophages among Lyme Disease-Causing Spirochetes and Natural Diversity of Their Lipoprotein-EncodingerpLoci

2013 ◽  
Vol 79 (13) ◽  
pp. 4115-4128 ◽  
Author(s):  
Dustin Brisson ◽  
Wei Zhou ◽  
Brandon L. Jutras ◽  
Sherwood Casjens ◽  
Brian Stevenson
Keyword(s):  
Lyme Disease ◽  
Surface Proteins ◽  
Open Reading Frames ◽  
Protein Coding ◽  
Content Type ◽  
Coding Regions ◽  
Natural Diversity ◽  
Different Strains ◽  
Main Chromosome ◽  
Reading Frames

ABSTRACTLyme disease spirochetes possess complex genomes, consisting of a main chromosome and 20 or more smaller replicons. Among those small DNAs are the cp32 elements, a family of prophages that replicate as circular episomes. All complete cp32s contain anerplocus, which encodes surface-exposed proteins. Sequences were compared for all 193erpalleles carried by 22 different strains of Lyme disease-causing spirochete to investigate their natural diversity and evolutionary histories. These included multiple isolates from a focus where Lyme disease is endemic in the northeastern United States and isolates from across North America and Europe. Bacteria were derived from diseased humans and from vector ticks and included members of 5 differentBorreliagenospecies. Allerpoperon 5′-noncoding regions were found to be highly conserved, as were the initial 70 to 80 bp of allerpopen reading frames, traits indicative of a common evolutionary origin. However, the majority of the protein-coding regions are highly diverse, due to numerous intra- and intergenic recombination events. Mosterpalleles are chimeras derived from sequences of closely related and distantly relatederpsequences and from unknown origins. Since known functions of Erp surface proteins involve interactions with various host tissue components, this diversity may reflect both their multiple functions and the abilities of Lyme disease-causing spirochetes to successfully infect a wide variety of vertebrate host species.

scholarly journals Identification of Methyl Halide-Utilizing Genes in the Methyl Bromide-Utilizing Bacterial Strain IMB-1 Suggests a High Degree of Conservation of Methyl Halide-Specific Genes in Gram-Negative Bacteria

2001 ◽  
Vol 67 (4) ◽  
pp. 1959-1963 ◽  
Author(s):  
Claire A. Woodall ◽  
Karen L. Warner ◽  
Ronald S. Oremland ◽  
J. Colin Murrell ◽  
Ian R. McDonald
Keyword(s):  
Energy Source ◽  
Methyl Bromide ◽  
Open Reading Frames ◽  
Binding Motif ◽  
Gram Negative Bacteria ◽  
Gram Negative ◽  
High Sequence Homology ◽  
Methyl Halide ◽  
High Degree ◽  
Reading Frames

ABSTRACT Strain IMB-1, an aerobic methylotrophic member of the alpha subgroup of the Proteobacteria, can grow with methyl bromide as a sole carbon and energy source. A single cmugene cluster was identified in IMB-1 that contained six open reading frames: cmuC, cmuA, orf146, paaE, hutI, and partialmetF. CmuA from IMB-1 has high sequence homology to the methyltransferase CmuA from Methylobacterium chloromethanicum and Hyphomicrobium chloromethanicum and contains a C-terminal corrinoid-binding motif and an N-terminal methyltransferase motif. However,cmuB, identified in M. chloromethanicumand H. chloromethanicum, was not detected in IMB-1.

scholarly journals Genome data of four Pythium insidiosum strains from the phylogenetically-distinct clades I, II, and III

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Theerapong Krajaejun ◽  
Weerayuth Kittichotirat ◽  
Preecha Patumcharoenpol ◽  
Thidarat Rujirawat ◽  
Tassanee Lohnoo ◽  
...  
Keyword(s):  
The United States ◽  
Open Reading Frames ◽  
Whole Genome ◽  
Genome Database ◽  
Pythium Insidiosum ◽  
Data Description ◽  
Genome Data ◽  
Gdna Sample ◽  
Different Strains ◽  
Reading Frames

Abstract Objectives We employed the Illumina NGS platform to sequence genomes of 4 different strains of the pathogenic oomycete Pythium insidiosum, the causative agent of pythiosis. These strains were isolated from humans in Thailand (n = 3) and the United States (n = 1), and phylogenetically classified into clade-I, -II, and -III. Our study augmented the completeness of the P. insidiosum genome database for exploration of the biology, evolution, and pathogenesis of the pathogen. Data description One paired-end library (180-bp insert) was prepared from a gDNA sample of P. insidiosum strains ATCC200269 (clade-I), Pi19 (clade-II), MCC18 (clade-II), and SIMI4763 (clade-III) for whole-genome sequencing by Illumina HiSeq2000/HiSeq2500 NGS platform. A range of 28.4–59.4 million raw reads, accounted for 3.0–7.3 Gb, were obtained and assembled into the genome sizes of 47.1 Mb (15,153 contigs; 85% completeness; 19,329 open reading frames [ORFs]) for strain ATCC200269, 35.4 Mb (14,576 contigs; 83% completeness; 13,895 ORFs) for strain Pi19, 34.5 Mb (11,084 contigs; 84% completeness; 13,249 ORFs) for strain MCC18, and 47.1 Mb (15,162 contigs; 85% completeness; 19,340 ORFs) for strain SIMI4763. The genome data can be downloaded from the NCBI/DDBJ databases under the accessions BCFN00000000.1 (ATCC200269), BCFS00000000.1 (Pi19), BCFT00000000.1 (MCC18), and BCFU00000000.1 (SIMI4763).

scholarly journals Biosynthetic Gene Cluster for the Polyenoyltetramic Acid α-Lipomycin

2006 ◽  
Vol 50 (6) ◽  
pp. 2113-2121 ◽  
Author(s):  
C. Bihlmaier ◽  
E. Welle ◽  
C. Hofmann ◽  
K. Welzel ◽  
A. Vente ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Polyketide Synthase ◽  
Biosynthetic Gene Cluster ◽  
Open Reading Frames ◽  
Biosynthetic Gene ◽  
Peptide Synthetases ◽  
Insight Into ◽  
Reading Frames ◽  
Module System

ABSTRACT The gram-positive bacterium Streptomyces aureofaciens Tü117 produces the acyclic polyene antibiotic α-lipomycin. The entire biosynthetic gene cluster (lip gene cluster) was cloned and characterized. DNA sequence analysis of a 74-kb region revealed the presence of 28 complete open reading frames (ORFs), 22 of them belonging to the biosynthetic gene cluster. Central to the cluster is a polyketide synthase locus that encodes an eight-module system comprised of four multifunctional proteins. In addition, one ORF shows homology to those for nonribosomal peptide synthetases, indicating that α-lipomycin belongs to the classification of hybrid peptide-polyketide natural products. Furthermore, the lip cluster includes genes responsible for the formation and attachment of d-digitoxose as well as ORFs that resemble those for putative regulatory and export functions. We generated biosynthetic mutants by insertional gene inactivation. By analysis of culture extracts of these mutants, we could prove that, indeed, the genes involved in the biosynthesis of lipomycin had been cloned, and additionally we gained insight into an unusual biosynthesis pathway.

scholarly journals Phage ϕC2 Mediates Transduction of Tn6215, Encoding Erythromycin Resistance, between Clostridium difficile Strains

mBio ◽  
2013 ◽  
Vol 4 (6) ◽  
Author(s):  
Shan Goh ◽  
Haitham Hussain ◽  
Barbara J. Chang ◽  
Warren Emmett ◽  
Thomas V. Riley ◽  
...  
Keyword(s):  
Clostridium Difficile ◽  
Genetic Manipulation ◽  
Recipient Strain ◽  
Open Reading Frames ◽  
Human Pathogen ◽  
Erythromycin Resistance ◽  
Content Type ◽  
Filter Mating ◽  
First Time ◽  
Reading Frames

ABSTRACTIn this work, we show thatClostridium difficilephage ϕC2 transduceserm(B), which confers erythromycin resistance, from a donor to a recipient strain at a frequency of 10−6per PFU. The transductants were lysogenic for ϕC2 and contained theerm(B) gene in a novel transposon, Tn6215. This element is 13,008 bp in length and contains 17 putative open reading frames (ORFs). It could also be transferred at a lower frequency by filter mating.IMPORTANCEClostridium difficileis a major human pathogen that causes diarrhea that can be persistent and difficult to resolve using antibiotics.C. difficileis potentially zoonotic and has been detected in animals, food, and environmental samples.C. difficilegenomes contain large portions of horizontally acquired genetic elements. The conjugative elements have been reasonably well studied, but transduction has not yet been demonstrated. Here, we show for the first time transduction as a mechanism for the transfer of a novel genetic element inC. difficile. Transduction may also be a useful tool for the genetic manipulation ofC. difficile.

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