Types Of Gene Clusters Research Articles

A novel multiplex PCR method forClostridium botulinumneurotoxin type A gene cluster typing

A rapid, simple and sensitive multiplex PCR method for boNT/A gene cluster typing was developed by combining the results of BoNT/A subtype (boNT/A1 or /A2) gene detection with ha33 and/or p47 gene detection. Ten isolates associated with infant botulism in Japan were examined and divided into boNT/A gene cluster types 2 and 3 by origin (honey feeding or not) and period (1986-1987 or 1999-2007). It is suggested that this multiplex PCR method will be be useful for epidemiological studies of botulism.

A genome-wide analysis of nonribosomal peptide synthetase gene clusters and their peptides in a Planktothrix rubescens strain

BackgroundCyanobacteria often produce several different oligopeptides, with unknown biological functions, by nonribosomal peptide synthetases (NRPS). Although some cyanobacterial NRPS gene cluster types are well described, the entire NRPS genomic content within a single cyanobacterial strain has never been investigated. Here we have combined a genome-wide analysis using massive parallel pyrosequencing ("454") and mass spectrometry screening of oligopeptides produced in the strain Planktothrix rubescens NIVA CYA 98 in order to identify all putative gene clusters for oligopeptides.ResultsThirteen types of oligopeptides were uncovered by mass spectrometry (MS) analyses. Microcystin, cyanopeptolin and aeruginosin synthetases, highly similar to already characterized NRPS, were present in the genome. Two novel NRPS gene clusters were associated with production of anabaenopeptins and microginins, respectively. Sequence-depth of the genome and real-time PCR data revealed three copies of the microginin gene cluster. Since NRPS gene cluster candidates for microviridin and oscillatorin synthesis could not be found, putative (gene encoded) precursor peptide sequences to microviridin and oscillatorin were found in the genes mdnA and oscA, respectively. The genes flanking the microviridin and oscillatorin precursor genes encode putative modifying enzymes of the precursor oligopeptides. We therefore propose ribosomal pathways involving modifications and cyclisation for microviridin and oscillatorin. The microviridin, anabaenopeptin and cyanopeptolin gene clusters are situated in close proximity to each other, constituting an oligopeptide island.ConclusionAltogether seven nonribosomal peptide synthetase (NRPS) gene clusters and two gene clusters putatively encoding ribosomal oligopeptide biosynthetic pathways were revealed. Our results demonstrate that whole genome shotgun sequencing combined with MS-directed determination of oligopeptides successfully can identify NRPS gene clusters and the corresponding oligopeptides. The analyses suggest independent evolution of all NRPS gene clusters as functional units. Our data indicate that the Planktothrix genome displays evolution of dual pathways (NRPS and ribosomal) for production of oligopeptides in order to maximize the diversity of oligopeptides with similar but functional discrete bioactivities.

Associations between enterotoxin gene cluster types egc1, egc2 and egc3, agr types, enterotoxin and enterotoxin-like gene profiles, and molecular typing characteristics of human nasal carriage and animal isolates of Staphylococcus aureus

Twenty genes encoding enterotoxin and enterotoxin-like proteins have been described in Staphylococcus aureus strains. Five of these occur commonly in the enterotoxin gene cluster (egc: selo, selm, sei, seln and seg). In the sei-seln intergenic region, two pseudogenes, psient1 and psient2, can be present or an additional gene designated selu or a variant selu(v). Whilst frequencies of loci bearing pseudogenes (egc1) or the selu gene (egc2) have been reported, the distinction between selu-bearing and selu(v)-bearing (egc3) loci has rarely been made. A PCR-RFLP procedure involving cleavage of the sei-seln intergenic region by restriction endonuclease BbvI or TseI was developed that allowed differentiation of selu(+) and selu(v)(+) loci. In addition, PCR primers were designed to yield a 203 bp amplimer for sequencing of a selu or selu(v) intragenic region, which encompassed ten signature nucleotide differences. A total of 43 egc(+) human nasal isolates and 53 egc(+) bovine, ovine, caprine, leporine and gallinaceous isolates were egc typed and agr typed. None of the animal isolates was of agr type III. A total of 12 out of 17 egc3(+) human nasal isolates were of agr type III, the other 5 being agr type I. On the basis of representative multilocus sequence typing, agr type III/egc3(+) strains belonged to CC30. Human nasal isolates bearing an egc1 locus were distributed evenly across agr types I, II and III. Only two nasal isolates had an egc2 locus. All 14 agr type IV isolates, only 1 of which was of human origin, possessed an egc2 locus. The agr IV nasal isolate was fusidic acid sensitive and was found to be ST123 (CC121). There were strong associations between bovine, leporine and gallinaceous S. aureus clonal types and egc locus types. The PCR-RFLP procedure was used to screen an additional 45 S. aureus isolates from dogs, cats, rats, pigs and horses for egc locus types. Of these, 33 were egc(-). Six equine isolates were selu(+). One canine and three porcine isolates possessed pseudogenes psient1 and psient2. One porcine and one canine isolate each had the selu(v) gene. Putative relationships between disease-causing propensity and egc type need (re-)evaluation.

Can Campylobacter coli induce Guillain-Barré syndrome?

Can Campylobacter coli induce Guillain-Barré syndrome?

Gene expression profiles of two accelerations in a CML patient

0 d ially treated with hydroxyurea (HU) and interferon alpha IFN). Response to treatment was poor and in the 21st month fter diagnosis the disease accelerated. Intensive chemotherpy with the FLAM/FLAG regimen (fludarabine, cytosine rabinoside and mitoxantrone/G-CSF) was started followed ith crossover to imatinib (IM). After initial complete hemaologic response to IM, lasting for 7 weeks, the patient elapsed again and the disease rapidly progressed to blast risis. Gene expression profiling in the course of the disease as performed using 5 DB Biosciencase’s AtlasTM Human ancer cDNA Expression Arrays with a set of 588 genes. aw data obtained with Clontech’s Atlas ImageTM 15 softare were log transformed and hierarchical clustering was genes, Fig. 1B2). The expression patterns of these two accelerations resemble each other; however, one must bear in mind that the analysis of the second acceleration was performed not from chronic phase, but from the early accelerated phase following complete hematological response. Examples of products of genes in these two clusters are members of ECM molecules, collagens and procollagens (COL11A1, 11A2, 4A2, 16A1, 8A1, 3A1, 1A2 and 2A1) and laminins (LAMC1, A4, B1 and B2). Also ECM binding integrins (ITGA1, A3, B1, B4, B5 and B6), with ITGA3 already described to be up-regulated in CML cells [4], belong to this group. Other members of these clusters are vascular endothelial growth factor receptors (VEGFR2 and 3), known to play a role in leukemias including CML [5]. Also cyclin C and cyclin D1 erformed with average linking clustering and Euclidian disance measurement using Genesis software [1]. Disease charcteristics at the time of array analyses are given in Table 1. The results show that three types of gene clusters can e recognized in the two CML accelerations in this patient were up-regulated in both accelerations. The results suggest that the genes from the second group may be typical for the disease acceleration. The third set of genes included groups of genes expressed differently in the first and second acceleration. The express r w e a f a i T b Fig. 1). First, genes with expression remaining up-regulated 22 genes, Fig. 1A1) or down-regulated (9 genes, Fig. 1A2), ompared to the standard, throughout the whole course of the isease. Among up-regulated genes were, e.g., collagens and nsulin-like growth factor 1 (IGF1). IGF1 is known to stimlate AML and ALL blast colony growth [2]. Among downegulated genes were, e.g., extracellular signal-regulated

Surf5:A Gene in the Tightly Clustered Mouse Surfeit Locus Is Highly Conserved and Transcribed Divergently from therpL7A(Surf3) Gene

The four previously characterized genes (Surf1to4) of the mouse Surfeit locus do not share any sequence homology, and the transcription of each gene alternates with respect to its neighbor(s). Adjacent Surfeit genes are separated by very small distances, and two of the genes overlap at their 3′ ends. In this work we have further defined the Surfeit gene cluster by the isolation ofSurf5,a fifth gene of the locus, and determination of its relationship to the other Surfeit genes.Surf5does not share any sequence homology with the four cloned Surfeit genes. The transcription ofSurf5is divergent with respect to its neighbor theSurf3gene, and the 5′ ends ofSurf5andSurf3are separated by only 159 bp, suggesting the presence of a second bidirectional promoter in the locus. The 3′ end ofSurf5maps only 68 bp away from the processed 3′ end of a pseudogene. The human and partial chickenSurf5coding regions show greater than 95% identity, and aCaenorhabditis eleganshomologue shows 38% identity and 56% similarity with the mouseSurf5amino acid sequence. The 3.5-kb transcript ofSurf5encodes a small hydrophilic protein of 140 amino acid residues, which differs from the ribosomal protein L7a encoded by theSurf3gene or the integral membrane protein encoded by theSurf4gene. Subcellular fractionation located theSurf5protein to the soluble fraction of the cytoplasm. The Surfeit locus appears to represent a novel type of gene cluster in which the genes are unrelated by sequence or function; however, their organization may play a role in their gene expression.

The Organization, Function, and Evolution of Gene Clusters in Eucaryotes

Present genetic and biochemical evidence suggests that two basic types of gene clusters occur in eucalypts. The first type encodes an enzyme aggregate (multienzyme complex). In an increasing number of instances, such gene clusters have been shown to be cluster-genes, i.e., single genes encoding multifunctional polypeptide chains, typically associated as homopolymeric aggregates. In several instances, evidence supports a channeling role for such enzyme aggregates, i.e., the aggregate serves to sequester intermediates in a particular biochemical pathway and to prevent competition between two potential competitive pathways. Gene clusters are considered to have evolved by retroevolution involving successive tandem gene duplications followed by functional divergence. Apparently, natural selection has often resulted in the further evolution of such gene clusters into cluster-genes by the process of gene fusion, especially in eucaryotes. The second (and apparently less frequent) type of gene cluster in eucaryote...